ORCID Profile
0000-0002-4528-9333
Current Organisation
University of Tasmania
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Microbiology | Microbial Ecology | Microbiology Not Elsewhere Classified | Food Packaging, Preservation and Safety | Analytical Chemistry | Separation Science | Geochemistry | Ecological Applications | Ecological Applications not elsewhere classified | Fisheries Sciences | Horticultural Production not elsewhere classified | Plant Biochemistry And Physiology | Bio-Remediation | Food Sciences | Immunology | Pests, Health And Diseases | Aquaculture | Groundwater Hydrology | Environmental Biotechnology | Gene Expression | Bacteriology | Environmental Impact Assessment | Aquaculture | Other Food Sciences | Microbial Systematics, Taxonomy And Phylogeny | Geochemistry Not Elsewhere Classified |
ANZSRC Socio-Economic Objective (SEO)
Rehabilitation of degraded mining lands | Biological sciences | Beverages (e.g. alcohol, wines, soft drinks, excl. fruit juices) | Aquaculture Fin Fish (excl. Tuna) | Barley | Land and water management | Processed food products and beverages not elsewhere classified | Chemical sciences | Fisheries - Aquaculture not elsewhere classified | Environmentally Sustainable Animal Production not elsewhere classified | Aquaculture | Fish | Food safety | Fisheries—commercial | Food Safety
Related Links
Publications
Identification of pH-specific protein expression responses by Campylobacter jejuni strain NCTC 11168
Publisher: Elsevier BV
Date: 06-2023
International committee on systematics of prokaryotes: Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria
Publisher: Microbiology Society
Date: 07-2013
The family Methylococcaceae
Publisher: Springer Berlin Heidelberg
Date: 2014
The family Colwelliaceae
Publisher: Springer Berlin Heidelberg
Date: 2014
Expressing Arabidopsis thaliana V-ATPase subunit C in barley (Hordeum vulgare) improves plant performance under saline condition by enabling better osmotic adjustment
Publisher: CSIRO Publishing
Date: 2017
DOI: 10.1071/FP17133
Abstract: Salinity is a global problem affecting agriculture that results in an estimated US$27 billion loss in revenue per year. Overexpression of vacuolar ATPase subunits has been shown to be beneficial in improving plant performance under saline conditions. Most studies, however, have not shown whether overexpression of genes encoding ATPase subunits results in improvements in grain yield, and have not investigated the physiological mechanisms behind the improvement in plant growth. In this study, we constitutively expressed Arabidopsis Vacuolar ATPase subunit C (AtVHA-C) in barley. Transgenic plants were assessed for agronomical and physiological characteristics, such as fresh and dry biomass, leaf pigment content, stomatal conductance, grain yield, and leaf Na+ and K+ concentration, when grown in either 0 or 300 mM NaCl. When compared with non-transformed barley, AtVHA-C expressing barley lines had a smaller reduction in both biomass and grain yield under salinity stress. The transgenic lines accumulated Na+ and K+ in leaves for osmotic adjustment. This in turn saves energy consumed in the synthesis of organic osmolytes that otherwise would be needed for osmotic adjustment.
Novel members of the family Flavobacteriaceae from Antarctic maritime habitats including Subsaximicrobium wynnwilliamsii gen. nov., sp. nov., Subsaximicrobium saxinquilinus sp. nov., Subsaxibacter broadyi gen. nov., sp. nov., Lacinutrix copepodicola gen. nov., sp. nov., and novel species of the genera Bizionia, Gelidibacter and Gillisia
Publisher: Microbiology Society
Date: 07-2005
Abstract: Several orange- and yellow-pigmented, halophilic, strictly aerobic, chemoheterotrophic, Gram-negative strains were isolated during investigations of maritime Antarctic habitats, including coastal fast sea-ice brine and algae, crustaceans and quartz stone sublithic cyanobacterial biofilms. Isolates investigated in this study belonged to the marine clade of the family Flavobacteriaceae and represented lineages that were either distinct from species with validly published names or appeared to be distinct species within existing genera. A polyphasic taxonomic analysis demonstrated the novelty of these strains, and several new taxa are proposed. Strains from quartz stone sublithic communities were grouped into two new genera designated Subsaximicrobium gen. nov. and Subsaxibacter gen. nov. The genus Subsaximicrobium included the species Subsaximicrobium wynnwilliamsii sp. nov. (type species type strain G#7 T =ACAM 1070 T =CIP 108525 T ) and Subsaximicrobium saxinquilinus sp. nov. (type strain Y4-5 T =ACAM 1063 T =CIP 108526 T ). The genus Subsaxibacter contained a single species designated Subsaxibacter broadyi sp. nov. (type strain P7 T =ACAM 1064 T =CIP 108527 T ). A novel bacterial strain isolated from the lake-dwelling, calanoid copepod Paralabidocera antarctica was given the name Lacinutrix copepodicola gen. nov., sp. nov. (type strain DJ3 T =ACAM 1055 T =CIP 108538 T ). Four novel species of the genus Bizionia were discovered, Bizionia algoritergicola sp. nov. (type strain APA-1 T =ACAM 1056 T =CIP 108533 T ) and Bizionia myxarmorum sp. nov. (type strain ADA-4 T =ACAM 1058 T =CIP 108535 T ), which were isolated from the carapace surfaces of sea-ice algae-feeding hipods, and Bizionia gelidisalsuginis sp. nov. (type strain IC164 T =ACAM 1057 T =CIP 108536 T ) and Bizionia saleffrena sp. nov. (type strain HFD T =ACAM 1059 T =CIP 108534 T ), which were isolated from sea-ice brines. Several other novel species were also isolated from sea-ice s les, including two novel species of the genus Gelidibacter , Gelidibacter gilvus sp. nov. (type strain IC158 T =ACAM 1054 T =CIP 108531 T ) and Gelidibacter salicanalis sp. nov. (type strain IC162 T =ACAM 1053 T =CIP 108532 T ), as well as three novel species of the genus Gillisia , Gillisia illustrilutea sp. nov. (type strain IC157 T =ACAM 1062 T =CIP 108530 T ), Gillisia sandarakina sp. nov. (type strain IC148 T =ACAM 1060 T =CIP 108529 T ) and Gillisia hiemivivida sp. nov. (type strain IC154 T =ACAM 1061 T =CIP 108528 T ).
Culturable microbiota of ranched southern bluefin tuna (Thunnus maccoyii Castelnau)
Publisher: Oxford University Press (OUP)
Date: 19-07-2013
DOI: 10.1111/JAM.12286
Abstract: The Australian tuna industry is based on the ranching of wild southern bluefin tuna (SBT, Thunnus maccoyii). Within this industry, only opportunistic pathogens have been reported infecting external wounds of fish. This study aimed to identify different culturable bacteria present in three cohorts of SBT and to determine normal bacteria and potential pathogens in isolates from harvest fish and moribund/dead fish. Post-mortem changes in the microbiota were also studied. Moribund/dead showed a greater proportion of members from the family Vibrionaceae than harvested fish the latter presented mainly non-Vibrio species. In harvested fish spleens, Vibrio splendidus I complex was the most commonly identified group among Vibrio isolates, while most groups from the family Vibrionaceae were isolated from gills. For moribund/dead, Vibrio chagasii and Photobacterium damselae subsp. damselae were common in gill, spleen and kidney s les. Non-Vibrio isolates from gills were characterized using 16S rRNA sequencing as Flavobacteriaceae and classes Gammaproteobacteria and Alphaproteobacteria, mainly from the genera Winogradskyella and Tenacibaculum. Post-mortem changes showed dynamic shifts in bacterial dominance in gills, with Vibrionaceae and non-Vibrio spp. found in similar proportions initially and types related to Pseudoalteromonas ruthenica prevailing after 27 h. Spleen s les showed little bacterial growth until 5 h post-mortem, while various Vibrio-associated species were isolated 27 h post-mortem. Bacterial isolates found include a range of potentially pathogenic bacteria that should be monitored though most of them have yet to be associated with disease in tuna. This study forms a foundation for future research into the bacterial population dynamics under different culture conditions of SBT. An understanding of the bacterial compositions in SBT is necessary to evaluate the effects of some bacterial species on their health.
Application of chlorine dioxide and peroxyacetic acid during spray chilling as a potential antimicrobial intervention for beef carcasses
Publisher: Elsevier BV
Date: 05-2020
Abstract: Enteric pathogens such as Shiga-toxin producing Escherichia coli (STEC) and Salmonella spp. continue to be a major food safety concern for the beef industry. Currently, no single method is completely effective in controlling these pathogens during carcass processing. Previous research, however, suggested that STEC might become more susceptible to oxidative damage when exposed to carcass chilling (King et al., 2016). We aimed to test that hypothesis by evaluating the antimicrobial effects of an oxidant (chlorine dioxide, ClO
The maximum growth rate of life on Earth
Publisher: Cambridge University Press (CUP)
Date: 06-02-2017
DOI: 10.1017/S1473550416000501
Abstract: Life on Earth spans a range of temperatures and exhibits biological growth rates that are temperature dependent. While the observation that growth rates are temperature dependent is well known, we have recently shown that the statistical distribution of specific growth rates for life on Earth is a function of temperature (Corkrey et al ., 2016). The maximum rates of growth of all life have a distinct limit, even when grown under optimal conditions, and which vary predictably with temperature. We term this distribution of growth rates the biokinetic spectrum for temperature (BKST). The BKST possibly arises from a trade-off between catalytic activity and stability of enzymes involved in a rate-limiting Master Reaction System (MRS) within the cell. We develop a method to extrapolate quantile curves for the BKST to obtain the posterior probability of the maximum rate of growth of any form of life on Earth. The maximum rate curve conforms to the observed data except below 0°C and above 100°C where the predicted value may be positively biased. The deviation below 0°C may arise from the bulk properties of water, while the degradation of biomolecules may be important above 100°C. The BKST has potential application in astrobiology by providing an estimate of the maximum possible growth rate attainable by terrestrial life and perhaps life elsewhere. We suggest that the area under the maximum growth rate curve and the peak rate may be useful characteristics in considerations of habitability. The BKST can serve as a diagnostic for unusual life, such as second biogenesis or non-terrestrial life. Since the MRS must have been heavily conserved the BKST may contain evolutionary relics. The BKST can serve as a signature summarizing the nature of life in environments beyond Earth, or to characterize species arising from a second biogenesis on Earth.
Genomics of psychrophilic bacteria and archaea
Publisher: Springer International Publishing
Date: 2017
Nesiotobacter exalbescens gen. nov., sp. nov., a moderately thermophilic alphaproteobacterium from an Hawaiian hypersaline lake
Publisher: Microbiology Society
Date: 03-2006
Abstract: A Gram-negative bacterium, designated LA33B T , was isolated from water collected from a hypersaline lake on uninhabited Laysan Atoll in the Northwestern Hawaiian Islands. Cells of strain LA33B T are motile, straight rods that grow between 4 and 45 °C and in media containing 1–17·5 % (w/v) NaCl. The strain oxidizes carbohydrates, nucleosides, amino acids and organic acids presented as sole carbon sources and constitutive lipolytic and proteolytic enzymes are expressed. Over 75 % of the fatty acid pool is cis -11-octadecenoic acid (18 : 1 ω 7 c ). Comparative sequence analysis of the 16S rRNA gene indicates that the strain forms a new lineage in the α -2 subclass of the Proteobacteria , with the closest recognized strains being Stappia aggregata NCIMB 2208 T and Roseibium denhamense JCM 10543 T , with which it shares 94–95 % sequence similarity. Strain LA33B T differs phenotypically from extant Stappia and Roseibium species, however, in that it is a moderate thermophile, it requires NaCl and tolerates higher NaCl concentrations and it does not express β -galactosidase or oxidize glycerol. On the basis of genotypic data and phenotypic characteristics, we propose that strain LA33B T does not belong to the genera Stappia or Roseibium and that it represents the type species of a new genus, Nesiotobacter . Strain LA33B T (=ATCC BAA-994 T =CIP 108449 T ) is proposed as the type strain of the type species of this genus, with the name Nesiotobacter exalbescens gen. nov., sp. nov.
The effect of fishmeal inclusion and prebiotic supplementation on the hindgut faecal microbiota of farmed Tasmanian Atlantic salmon (Salmo salarL.)
Publisher: Oxford University Press (OUP)
Date: 24-07-2018
DOI: 10.1111/JAM.13930
Abstract: Factors such as seasonal temperature and diet components, for ex le, fishmeal (FM) inclusion, can influence the composition of the gut microbiota of fish. In this study, we examined changes in the gut bacterial populations, in particular lactic acid bacteria (LAB), of farmed Tasmanian Atlantic salmon in response to different diets, during periods of higher water temperature. Between December 2011 and March 2012 hindgut faecal s les were collected from Atlantic salmon from a commercial fish farm in south of Hobart, Tasmania, fed with one of four trial diets containing either high or low FM inclusion levels with or without prebiotics. Overall there was little difference in the cultivatable bacterial populations in response to varying levels of FM and prebiotic supplementation, with LAB counts decreasing in response to increased water temperatures. However, it was observed that the high FM diet supported the presence of LAB in January, when these were not detected in the low FM diets. Our study indicates that the inclusion of higher amounts of FM rather than the addition of prebiotics has a greater effect on LAB colonization of the gut in Atlantic salmon. This study highlights the importance of the new fish feeds for promoting salmon health in aquaculture industry.
Physiological aspects of Listeria monocytogenes during inactivation accelerated by mild temperatures and otherwise non-growth permissive acidic and hyperosmotic conditions
Publisher: Elsevier BV
Date: 07-2010
DOI: 10.1016/J.IJFOODMICRO.2010.05.015
Abstract: Application of simultaneous low pH (pH 3.5) and low water activity (a(w)=0.9 2.5M NaCl) conditions to Listeria monocytogenes strains ScottA and FW03/0035, and growth permissive temperatures from 25 degrees C up to 45 degrees C result in increasingly accelerated inactivation rates. This phenomenon was related to i) increased cell permeability as suggested by ethidium homodimer-1 uptake and ii) de-energization as indicated by rapidly reduced ATP basal levels. Enrichment-based recovery experiments indicated that the stress conditions eventually lead to complete loss of reproductive capacity, possibly corresponding to an irreversible collapse of pH homeostasis. Transcriptomic analyses were used to obtain further insights into the physiology of the inactivation process occurring at 25 degrees C where inactivation times were more prolonged. QPCR, mRNA decay and microarray experiments revealed transcripts of tufA and other genes become substantially more stable during inactivation resulting from exposure to combined low pH/a(w) and from non-growth permissive temperature exposure. Genes that appear to be important for initial survival of combined low pH/a(w) were delineated by K-means clustering of expression data and included an overrepresentation of SigB-activated genes, the overall response of which fades with increasing time of inactivation exposure.
Algoriphagus ratkowskyi gen. nov., sp. nov., Brumimicrobium glaciale gen. nov., sp. nov., Cryomorpha ignava gen. nov., sp. nov. and Crocinitomix catalasitica gen. nov., sp. nov., novel flavobacteria isolated from various polar habitats
Publisher: Microbiology Society
Date: 09-2003
Abstract: Several cold-adapted strains isolated from a variety of algal-rich Antarctic and Southern Ocean s les formed three distinct groups within the class Flavobacteria, phylogenetically distant from other cultivated species. The first taxon, designated Algoriphagus ratkowskyi gen. nov., sp. nov., was isolated from sea ice and from saline lake cyanobacterial mats and includes non-motile, strictly aerobic, saccharolytic rod-like or serpentine strains that were most closely related to the genus Cyclobacterium according to 16S rDNA sequence analysis (sequence similarity 0.85). The second taxon, designated Brumimicrobium glaciale gen. nov., sp. nov., isolated from sea ice and from continental shelf sediment, formed gliding, rod-like cells that were facultatively anaerobic with a fermentative metabolism. The third taxon, designated Cryomorpha ignava gen. nov., sp. nov., isolated from Southern Ocean particulates and from quartz stone subliths, included strictly aerobic, pleomorphic rod-like cells. Brumimicrobium glaciale and Cryomorpha ignava were most closely allied with 'Microscilla aggregans var. catalatica', which, on the basis of its distinctive taxonomic traits, is also proposed as a new genus and species, Crocinitomix catalasitica gen. nov., sp. nov. It is proposed that the three genera Brumimicrobium, Cryomorpha and Crocinitomix belong to a new family, Cryomorphaceae fam. nov. (type genus Cryomorpha), as they possess generally similar morphological and ecophysiological characteristics and form a common and distinct clade within class FLAVOBACTERIA:
Effect of abattoir and cut on variations in microbial communities of vacuum-packaged beef
Publisher: Elsevier BV
Date: 09-2017
DOI: 10.1016/J.MEATSCI.2017.04.021
Abstract: This report builds on the earlier studies of the shelf-life of chilled Australian vacuum packaged (VP) beef primals (striploin and cube roll), products distinguished in the global marketplace for unusually long shelf-life. Notable findings in those studies were a shelf-life of at least 26weeks at -0.5°C, low microbial counts, and relatively high sensory scores. However, growth rates for total viable counts (TVC) and lactic acid bacteria (LAB) varied among the different abattoirs. The present study adds to these findings, by providing greater definition about temporal changes in bacterial communities using terminal restriction fragment length polymorphism (TRFLP) and clone library analyses of 16S ribosomal RNA (16S rRNA) gene, and measuring statistical associations among abattoir, beef cut, storage time and sensory attributes. Bacterial communities changed over time, with Carnobacterium spp. typically predominating (29-97%) at the end of storage. Variation in TRFLP profiles showed that different Carnobacterium strains predominated in different abattoirs, and that additional variation was due to the presence of other taxa typical of VP meat microbiomes. TRFLP-based community structure correlated significantly (P≤0.01) with sensorial characteristics, such as vacuum integrity, confinement odour, and intact pack appearance of beef. This study shows that Carnobacterium spp. predominate on extended shelf-life VP beef primals, while other taxa may produce subtle effects on shelf-life duration.
Combined high pressure and heat treatment effectively disintegrates spore membranes and inactivates Alicyclobacillus acidoterrestris spores in acidic fruit juice beverage
Publisher: Elsevier BV
Date: 12-2020
Characterization of Ferroplasma Isolates and Ferroplasma acidarmanus sp. nov., Extreme Acidophiles from Acid Mine Drainage and Industrial
Publisher: American Society for Microbiology
Date: 04-2004
DOI: 10.1128/AEM.70.4.2079-2088.2004
Abstract: Three recently isolated extremely acidophilic archaeal strains have been shown to be phylogenetically similar to Ferroplasma acidiphilum Y T by 16S rRNA gene sequencing. All four Ferroplasma isolates were capable of growing chemoorganotrophically on yeast extract or a range of sugars and chemomixotrophically on ferrous iron and yeast extract or sugars, and isolate “ Ferroplasma acidarmanus ” Fer1 T required much higher levels of organic carbon. All four isolates were facultative anaerobes, coupling chemoorganotrophic growth on yeast extract to the reduction of ferric iron. The temperature optima for the four isolates were between 35 and 42°C and the pH optima were 1.0 to 1.7, and “ F. acidarmanus ” Fer1 T was capable of growing at pH 0. The optimum yeast extract concentration for “ F. acidarmanus ” Fer1 T was higher than that for the other three isolates. Phenotypic results suggested that isolate “ F. acidarmanus ” Fer1 T is of a different species than the other three strains, and 16S rRNA sequence data, DNA-DNA similarity values, and two-dimensional polyacrylamide gel electrophoresis protein profiles clearly showed that strains DR1, MT17, and Y T group as a single species. “ F. acidarmanus ” Fer1 T groups separately, and we propose the new species “ F. acidarmanus ” Fer1 T sp. nov.
Assessment of bacterial community composition, methanotrophic and nitrogen-cycling bacteria in three soils with different biochar application rates
Publisher: Springer Science and Business Media LLC
Date: 23-05-2017
Review article: Food safety culture from the perspective of the Australian horticulture industry
Publisher: Elsevier BV
Date: 10-2021
Evolutionary conservation of angiosperm flower development at the molecular and genetic levels
Publisher: Springer Science and Business Media LLC
Date: 09-1997
DOI: 10.1007/BF02703197
Population Dynamics of Vibrio and Pseudomonas Species Isolated from Farmed Tasmanian Atlantic Salmon (Salmo salar L.): A Seasonal Study
Publisher: Springer Science and Business Media LLC
Date: 16-07-2014
DOI: 10.1007/S00248-014-0462-X
Abstract: Vibrio and Pseudomonas species have been shown to be part of the normal microbiota of Atlantic salmon (Salmo salar L.), with some strains causing disease in fish. The factors affecting their prevalence and persistence in the salmon gut, however, have not been well studied. In this study, we collected 340 Vibrio and 150 Pseudomonas isolates from the hindgut of farmed Tasmanian Atlantic salmon, fed with two commercially available diets. S les were collected every 6-8 weeks between July 2011 and May 2012. Isolates from selective agar were initially identified using biochemical tests and confirmed using genus-specific primers and 16S ribosomal RNA (16S rRNA) sequencing. Random lified polymorphic DNA (RAPD) PCR was used to type both Pseudomonas and Vibrio the latter was further typed using a biochemical fingerprinting method (PhP-RV plates). We observed low species ersity with strains comprising Vibrio ichthyoenteri/Vibrio scophthalmi, Vibrio crassostreae/Vibrio splendidus, Aliivibrio finisterrensis, Photobacterium phosphoreum and Pseudomonas fragi. Out of 340 Vibrio isolates, 238 (70 %) belonged to 21 clonal types and were found predominantly during summer when water temperatures reached 15 to 21 °C. Of these, the four major clonal types were found in multiple s les (70 %). P. fragi, on the other hand, was only found during the colder water temperatures and belonged to 18 clonal types. The presence of both groups of bacteria and their clonal types were independent of the fish diets used, suggesting that the water temperature was the main factor of the prevalence and persistence of these bacteria in the gut of Atlantic salmon.
Diversity and community structure within anoxic sediment from marine salinity meromictic lakes and a coastal meromictic marine basin, Vestfold Hills, Eastern Antarctica
Publisher: Wiley
Date: 04-2000
DOI: 10.1046/J.1462-2920.2000.00097.X
Abstract: 16S rDNA clone library analysis was used to examine the bio ersity and community structure within anoxic sediments of several marine-type salinity meromictic lakes and a coastal marine basin located in the Vestfolds Hills area of Eastern Antarctica. From 69 to 130 (555 total) 16S rDNA clones were analysed from each sediment s le, and restriction fragment length polymorphism (RFLP) and sequence analysis grouped the clones into 202 distinct phylotypes (a clone group with sequence similarity of >0.98). A number of phylotypes and phylotype groups predominated in all libraries, with a group of 10 phylotypes (31% of clones) forming a novel deep branch within the low G+C Gram-positive ision. Other abundant phylotypes detected in several different clone libraries grouped with Prochlorococcus cyanobacteria, diatom chloroplasts, delta proteobacteria (Desulfosarcina group, Syntrophus and Geobacterl Pelobacter/Desulphuromonas group), order Chlamydiales (Parachlamydiaceae) and Spirochaetales (wall-less Antarctic spirochaetes). Most archaeal clones detected (3.1% of clones) belonged to a highly erged group of Euryarchaeota clustering with clones previously detected in rice soil, aquifer sediments and hydrothermal vent material. Little similarity existed between the phylotypes detected in this study and other clone libraries based on marine sediment, suggesting that an enormous prokaryotic ersity occurs within marine and marine-derived sediments.
Bacterial exopolysaccharides from extreme marine environments with special consideration of the Southern Ocean, sea ice, and deep-sea hydrothermal vents: A review
Publisher: Springer Science and Business Media LLC
Date: 21-07-2005
DOI: 10.1007/S10126-004-5118-2
Abstract: Exopolysaccharides (EPSs) are high molecular weight carbohydrate polymers that make up a substantial component of the extracellular polymers surrounding most microbial cells in the marine environment. EPSs constitute a large fraction of the reduced carbon reservoir in the ocean and enhance the survival of marine bacteria by influencing the physicochemical environment around the bacterial cell. Microbial EPSs are abundant in the Antarctic marine environment, for ex le, in sea ice and ocean particles, where they may assist microbial communities to endure extremes of temperature, salinity, and nutrient availability. The microbial bio ersity of Antarctic ecosystems is relatively unexplored. Deep-sea hydrothermal vent environments are characterized by high pressure, extreme temperature, and heavy metals. The commercial value of microbial EPSs from these habitats has been established recently. Extreme environments offer novel microbial bio ersity that produces varied and promising EPSs. The biotechnological potential of these biopolymers from hydrothermal vent environments as well as from Antarctic marine ecosystems remains largely untapped.
Salegentibacter flavus sp. nov.
Publisher: Microbiology Society
Date: 03-2006
Abstract: A yellow-pigmented, non-motile, Gram-negative bacterium, designated Fg 69 T , was isolated from a sediment s le collected in Chazhma Bay (Sea of Japan). The novel organism grew at 10–35 °C, was neutrophilic and required 3–10 % NaCl for optimal growth. Strain Fg 69 T was able to degrade starch and to hydrolyse gelatin and Tween 80 weakly but not casein or agar. Predominant cellular fatty acids comprised n-C 15 and n-C 16 branched-chain and straight-chain saturated and unsaturated fatty acids, including iso-C 15 : 0 (5 %), anteiso-C 15 : 0 (11 %), C 15 : 0 (9 %), iso-C 15 : 1 (5 %), iso-C 16 : 0 (8 %), C 16 : 0 (5 %) and C 16 : 1 ω 7 (5 %) and iso- and anteiso-branched 2-OH and 3-OH C 15 : 0 to C 17 : 0 fatty acids (26 % in total). The G+C content of the DNA was 40·4 mol%. 16S rRNA gene sequence data indicated that strain Fg 69 T belonged to the genus Salegentibacter but was distinct from recognized Salegentibacter species (94–95 % sequence similarity). Based on these results, a novel species, Salegentibacter flavus sp. nov., is proposed. The type strain is Fg 69 T (=KMM 6000 T =CIP 107843 T ).
Effect of abattoir, livestock species and storage temperature on bacterial community dynamics and sensory properties of vacuum packaged red meat
Publisher: Elsevier BV
Date: 04-2021
Production of exopolysaccharides by Antarctic marine bacterial isolates
Publisher: Oxford University Press (OUP)
Date: 05-2004
Aequorivita gen. nov., a member of the family Flavobacteriaceae isolated from terrestrial and marine Antarctic habitats
Publisher: Microbiology Society
Date: 09-2002
Colonization and community dynamics of class Flavobacteria on diatom detritus in experimental mesocosms based on Southern Ocean seawater
Publisher: Oxford University Press (OUP)
Date: 08-2005
DOI: 10.1016/J.FEMSEC.2005.01.008
Abstract: In order to better understand the ecology of microorganisms responsible for secondary production in the Southern Ocean the activity of Flavobacteria communities on diatom detritus in seawater mesocosms was investigated. Seawater was collected from different parts of the Southern Ocean including the Polar Front Zone (PFZ), ice-edge area of the Antarctic Zone (AZ), and a site in the AZ ice pack. Detritus from the cosmopolitan marine diatom Nitzschia closterium Ehrenberg was resuspended in mesocosms containing seawater filtered to remove particulate organic matter, including particle-associated bacteria and most eukaryotes, but retaining native planktonic bacterial assemblages. Mesocosms were incubated at 2 degrees C and s les analysed for changes in community composition using denaturing gradient gel electrophoresis (DGGE), real-time PCR and fluorescent in-situ hybridization (FISH). DGGE banding patterns and FISH images demonstrated rapid bacterial colonization of the detritus, dominated by members of class gamma-Proteobacteria, alpha-Proteobacteria and Flavobacteria. Real-time PCR data indicated members of class Flavobacteria were involved in initial colonization of detrital aggregate, however relative abundance stayed at similar levels found for the original native particle-associated populations. 16S rRNA gene DGGE banding patterns and sequence analysis demonstrated significant variation in Flavobacteria community structure occurred in the first 20 days of the experiment before community stabilization occurred. The community structures between the three mesocosms also markedly differed and major colonizers were primarily derived from detectable members of the initial particle-associated Flavobacteria community, however the abundant uncultured Flavobacteria agg58 clone-related and DE cluster 2 clades, previously identified in Southern Ocean seawater were not observed to colonize the detritus.
Variability in biofilm production by Listeria monocytogenes correlated to strain origin and growth conditions
Publisher: Elsevier BV
Date: 10-2011
DOI: 10.1016/J.IJFOODMICRO.2011.07.012
Abstract: This study aimed to identify factors that influence the development of biofilm by Listeria monocytogenes strains and to determine the extent to which biofilm production protects against quaternary ammonium compound (QAC) disinfectant challenge. A total of 95 L. monocytogenes strains were studied and biofilm production was assessed as a function of incubation temperature, media pH, strain origin, serotype, and environmental persistence status. Attachment and biofilm development (inferred by the level of attached biomass) were measured in vitro using a colourimetric 96-well microtitre plate method in nutritive media (Brain-Heart Infusion). Increased biofilm production correlated with increasing temperature and the most acidic, or most alkaline, growth conditions tested. Clinical and environmental (food factory) strains were observed to increase biofilm production at higher and lower incubation temperatures respectively, independent of their rate of planktonic growth. Serotype 1/2a strains produced significantly more biofilm. Biofilm maturity, rather than strain, was correlated with resistance to QAC. Carbohydrate containing exopolymeric material could not be detected in the biofilm of representative strains, and no correlation between strains recovered as persistent food factory contaminants and biofilm production was identified. Although limited to in vitro inference based on the assay system used, our results suggest that environmental conditions determine the level of biofilm production by L. monocytogenes strains, independent of the rate of planktonic growth, and that this may manifest from selection pressures to which a given strain grows optimally.
Protein-based analysis and other new and emerging non-nucleic acid based methods for tracing and investigating foodborne pathogens
Publisher: Elsevier
Date: 2010
Human infection with halomonas venusta following fish bite
Publisher: American Society for Microbiology
Date: 08-2000
DOI: 10.1128/JCM.38.8.3123-3124.2000
Abstract: Halomonas venusta , a moderately halophilic, nonfermentative gram-negative rod, is reported for the first time as a human pathogen in a wound that originated from a fish bite.
Leeuwenhoekiella blandensis sp. nov., a genome-sequenced marine member of the family Flavobacteriaceae
Publisher: Microbiology Society
Date: 07-2006
Abstract: Bacteria in the family Flavobacteriaceae are increasingly recognized to play important roles in the degradation of organic matter during and following algal blooms. A novel heterotrophic, rod-shaped, aerobic, yellow-pigmented and gliding bacterium was isolated from a seawater s le collected in the Bay of Blanes in the north-western Mediterranean Sea. Analysis of its 16S rRNA gene sequence, retrieved from the whole-genome sequence, showed that the bacterium was closely related to members of the genus Leeuwenhoekiella within the family Flavobacteriaceae , phylum Bacteroidetes . Phenotypic, genotypic, chemotaxonomic and phylogenetic analyses supported the creation of a novel species to accommodate this bacterium, for which the name Leeuwenhoekiella blandensis sp. nov. is proposed. The type strain is MED 217 T (=CECT 7118 T =CCUG 51940 T ).
The effect of diet and environmental temperature on the faecal microbiota of farmed Tasmanian Atlantic Salmon (Salmo salarL.)
Publisher: Hindawi Limited
Date: 28-07-2014
DOI: 10.1111/ARE.12522
The phylogenetic position of the family Methylococcaceae (International Journal of Systematic Bacteriology (1995) 1 (184))
Publisher: Microbiology Society
Date: 07-1995
Colwellia demingiae sp. nov., Colwellia hornerae sp. nov., Colwellia rossensis sp. nov. and Colwellia psychrotropica sp. nov.: psychrophilic Antarctic species with the ability to synthesize docosahexaenoic acid (22 : 6 omega 3)
Publisher: Microbiology Society
Date: 10-1998
Psychroflexus tropicus sp. nov., an obligately halophilic Cytophaga-Flavobacterium-Bacteroides group bacterium from an Hawaiian hypersaline lake
Publisher: Microbiology Society
Date: 05-2004
Abstract: A Gram-negative bacterium designated LA1 T was isolated from water collected in hypersaline Lake Laysan on Laysan Island in the Northwestern Hawaiian Islands. Cells occurred singly as fine rods to short filaments. Growth in 50 % strength marine broth occurred optimally when the medium contained 7·5–10 % (w/v) NaCl. The major fatty acids in LA1 T grown at 15 and 30 °C were 12-methyl tetradecanoic acid and 13-methyl tetradecanoic acid, respectively. The nucleotide sequence of the 16S rRNA gene showed that LA1 T belonged in the Cytophaga–Flavobacterium–Bacteroides (CFB) group in the domain Bacteria . The closest described neighbour in terms of 16S rRNA gene sequence identity was Psychroflexus torquis ACAM 623 T (94·4 % over 1423 bases), an obligate psychrophile from Antarctic sea-ice. The G+C content of 35·0 mol% was consistent with this affiliation. Phenotypic and genotypic analyses, including DNA hybridization, indicated that LA1 T could be assigned to the genus Psychroflexus but, based on significant differences, including growth at 43 °C, it constitutes a novel species, Psychroflexus tropicus sp. nov., for which LA1 T (=ATCC BAA-734 T =DSM 15496 T ) is the type strain.
Evaluating contribution of ionic, osmotic and oxidative stress components towards salinity tolerance in barley
Publisher: Springer Science and Business Media LLC
Date: 28-04-2014
OCCURRENCE AND SIGNIFICANCE OF LONG-CHAIN (OMEGA-1)-HYDROXY FATTY-ACIDS IN METHANE-UTILIZING BACTERIA
Publisher: Elsevier BV
Date: 03-1992
Extensive Gene Acquisition in the Extremely Psychrophilic Bacterial Species Psychroflexus torquis and the Link to Sea-Ice Ecosystem Specialism
Publisher: Oxford University Press (OUP)
Date: 2014
DOI: 10.1093/GBE/EVT209
The future of predictive microbiology: Strategic research, innovative applications and great expectations
Publisher: Elsevier BV
Date: 11-2008
DOI: 10.1016/J.IJFOODMICRO.2008.06.026
Abstract: This paper considers the future of predictive microbiology by exploring the balance that exists between science, applications and expectations. Attention is drawn to the development of predictive microbiology as a sub-discipline of food microbiology and of technologies that are required for its applications, including a recently developed biological indicator. As we move into the era of systems biology, in which physiological and molecular information will be increasingly available for incorporation into models, predictive microbiologists will be faced with new experimental and data handling challenges. Overcoming these hurdles may be assisted by interacting with microbiologists and mathematicians developing models to describe the microbial role in ecosystems other than food. Coupled with a commitment to maintain strategic research, as well as to develop innovative technologies, the future of predictive microbiology looks set to fulfil "great expectations".
Methanobrevibacter millerae sp. nov. and Methanobrevibacter olleyae sp. nov., methanogens from the ovine and bovine rumen that can utilize formate for growth
Publisher: Microbiology Society
Date: 03-2007
Abstract: Four formate-utilizing methanogens were isolated from ovine (strain KM1H5-1P T ) and bovine (strains AK-87, OCP and ZA-10 T ) rumen contents. Based on 16S rRNA gene sequence analysis, the methanogen strains were found to belong to the order Methanobacteriales in the genus Methanobrevibacter . Strains ZA-10 T and KM1H5-1P T gained energy for growth by the reduction of CO 2 to CH 4 using H 2 or formate exclusively as electron donors. Increasing formate concentrations to 220 mM in batch cultures increased the growth of strain KM1H5-1P T but did not affect the growth of strain ZA-10 T . Substrate specificity and resistance to cell-wall lysis supported the affiliation of the strains to the genus Methanobrevibacter . Strains ZA-10 T and KM1H5-1P T showed 16S rRNA gene sequence similarity of 98.0 and 98.6 % to their closest recognized relatives, Methanobrevibacter thaueri CW T and Methanobrevibacter ruminantium M1 T , respectively. DNA–DNA hybridization experiments indicated that the strains were not affiliated at the species level to their closest recognized relatives, with DNA reassociation values of only 28 % between strains ZA-10 T and Methanobrevibacter thaueri CW T and % between strains KM1H5-1P T and Methanobrevibacter ruminantium M1 T . Based on the data presented, the new strains are considered to represent two novel species of the genus Methanobrevibacter , for which the names Methanobrevibacter millerae sp. nov. (type strain ZA-10 T =DSM 16643 T =OCM 820 T ) and Methanobrevibacter olleyae sp. nov. (type strain KM1H5-1P T =DSM 16632 T =OCM 841 T ) are proposed.
Genomic analysis of psychrophilic prokaryotes
Publisher: Springer Berlin Heidelberg
Date: 2008
Molecular genetics of gynoecium development in Arabidopsis.
Publisher: Elsevier
Date: 1999
DOI: 10.1016/S0070-2153(08)60316-6
Abstract: Carpels are the ovule-bearing structural units in angiosperms. In Arabidopsis, the specification of carpel identity is achieved by at least two separate pathways: a pathway mediated by the C class gene AG and an AG-independent pathway. Both pathways are negatively regulated by A class genes. Two genes, SPT and CRC, can promote differentiation of carpel tissue independently of AG and are thus components of the AG-independent pathway. CRC and SPT appear to act in a redundant manner to promote the differentiation of subsets of carpel tissues. The carpel primordium is sub ided into regional domains, both medial versus lateral and abaxial versus adaxial. Based on morphological and gene expression analyses, it appears likely that these domains define developmental compartments. The medial domain appears fated to differentiate into the marginal tissue types of the carpel (septum with transmitting tract and placenta with ovules), whereas the lateral domain gives rise to the ovary walls. The expression of ETT defines the abaxial domain, and this gene is involved in the abaxial-adaxial and, possibly, the apical-basal patterning of tissues in the carpel. Once regional domains have been established, the differentiation of tissue and cell types occurs. The MADS-box gene FUL and AGLI/5 are involved in the differentiation of specific tissue types in the valves and valve margins. Thus, the genes identified can be arranged in a functional hierarchy: specification of carpel identity, patterning of the carpel primordium and directing the differentiation of the specialized tissues of the carpel.
Protein Thermodynamics Can Be Predicted Directly from Biological Growth Rates
Publisher: Public Library of Science (PLoS)
Date: 05-2014
Atlantic Salmon (Salmo salar L.) Gastrointestinal Microbial Community Dynamics in Relation to Digesta Properties and Diet
Publisher: Springer Science and Business Media LLC
Date: 16-01-2016
DOI: 10.1007/S00248-015-0728-Y
Abstract: To better understand salmon GI tract microbial community dynamics in relation to diet, a feeding trial was performed utilising diets with different proportions of fish meal, protein, lipid and energy levels. Salmon gut dysfunction has been associated with the occurrence of casts, or an empty hind gut. A categorical scoring system describing expressed digesta consistency was evaluated in relation to GI tract community structure. Faster growing fish generally had lower faecal scores while the diet cohorts showed minor differences in faecal score though the overall lowest scores were observed with a low protein, low energy diet. The GI tract bacterial communities were highly dynamic over time with the low protein, low energy diet associated with the most ergent community structure. This included transiently increased abundance of anaerobic (Bacteroidia and Clostridia) during January and February, and facultatively anaerobic (lactic acid bacteria) taxa from February onwards. The digesta had enriched populations of these groups in relation to faecal cast s les. The majority of s les (60-86 %) across all diet cohorts were eventually dominated by the genus Aliivibrio. The results suggest that an interaction between time of s ling and diet is most strongly related to community structure. Digesta categorization revealed microbes involved with metabolism of diet components change progressively over time and could be a useful system to assess feeding responses.
Erythrobacter vulgaris sp. nov., a novel organism isolated from the marine invertebrates
Publisher: Elsevier BV
Date: 03-2005
DOI: 10.1016/J.SYAPM.2004.11.001
Abstract: Four yellow-pigmented, gram-negative, chemoorganotrophic aerobic bacteria were isolated from starfish Stellaster equestris (strains 022-2-10T, 022-2-9, and 022-2-12) and soft coral (unidentified species) (strain 022-4-7) collected in the South China Sea. 16S rRNA gene sequence-based analyses of the new organisms revealed that Erythrobacter spp. were the closest relatives and shared the highest similarity of 98.7% to E. citreus, 98.5% to E. flavus, 97.9% to E. litoralis and 97.6% to E. longus. The novel organisms were tolerant to 3-6% NaCl, grew between 10 degrees C and 40 degrees C, and were not able to degrade gelatin, casein, and agar, while degraded Tween 80. Two strains (022-2-9 and 022-2-12) could weakly degrade starch. All strains produced a large pool of carotenoids and did not have Bacteriochlorophyll a. Phosphatidylethanolamine (30-36%), phosphatidylglycerol (39-46%), and phosphatidylcholine (21-27%) were the predominant phospholipids. Sphingoglycolipid was not detected. The major fatty acids were 16:0 (6-11%), 16:1omega7 (12-15%), and 18:1omega7 (46-49%). The two-hydroxy fatty acids, 13:0-2OH, 14:0-2OH, 15:0-2OH, 16:0-2OH were also present. The G + C content of the DNAs ranged from 61 to 62 mol%. The level of DNA similarity among four strains was conspecific and ranged from 94% to 98%. Even though new strains and other species of the genus had rather high level of 16S rRNA gene sequence similarities, DNA-DNA hybridization experiments showed only 33-39% of binding with the DNA of the type strains. On the basis of these results and the significant differences demonstrated in the phenotypic and chemotaxonomic characteristics, it is suggested that the new organisms be classified as a novel species the name Erythrobacter vulgaris sp. nov. is proposed. The type strain is 022-2-10T (= KMM 3465T = CIP 107841T).
Benchmarking DNA Extraction Methods for Phylogenomic Analysis of Sub-Antarctic Rhodococcus and Williamsia Species
Publisher: MDPI AG
Date: 09-06-2021
DOI: 10.3390/MICROORGANISMS9061253
Abstract: Bacteria containing mycolic acids in their cell envelope are often recalcitrant to cell lysis, so extracting DNA of sufficient quality for third-generation sequencing and high-fidelity genome assembly requires optimization, even when using commercial kits with protocols for hard-to-lyse bacteria. We benchmarked three spin-column-based kits against a classical DNA extraction method employing lysozyme, proteinase K and SDS for six lysozyme-resistant, sub-Antarctic strains of Corynebaceriales. Prior cultivation in broths containing glycine at highly growth-inhibitory concentrations (4.0–4.5%) improved cell lysis using both classical and kit methods. The classical method produced DNA with average fragment sizes of 27–59 Kbp and tight fragment size ranges, meeting quality standards for genome sequencing, assembly and phylogenomic analyses. By 16S rRNA gene sequencing, we classified two strains as Williamsia and four strains as Rhodococcus species. Pairwise comparison of average nucleotide identity (ANI) and alignment fraction (AF), plus genome clustering analysis, confirmed Rhodococcus sp. 1163 and 1168 and Williamsia sp. 1135 and 1138 as novel species. Phylogenetic, lipidomic and biochemical analyses classified psychrotrophic strains 1139 and 1159 as R. qingshengii and R. erythropolis, respectively, using ANI similarity of % and AF % for species delineation. On this basis, some members of the R. erythropolis genome cluster groups, including strains currently named as R. enclensis, R. baikonurensis, R. opacus and R. rhodochrous, would be reclassified either as R. erythropolis or R. qingshengii.
Expressing AtNHX1 in barley (Hordium vulgare L.) does not improve plant performance under saline conditions
Publisher: Springer Science and Business Media LLC
Date: 09-04-2015
The Biokinetic Spectrum for Temperature
Publisher: Public Library of Science (PLoS)
Date: 18-04-2016
High-throughput screening of biofilm formation of listeria monocytogenes on stainless steel coupons using a 96-well plate format
Publisher: Springer US
Date: 26-09-2021
Bacterial diversity in organically-enriched fish farm sediments
Publisher: Oxford University Press (OUP)
Date: 2006
DOI: 10.1111/J.1574-6941.2005.00012.X
Abstract: The bacterial ersity and community structure within both organically enriched and adjacent, unimpacted, near-shore marine sediments at two fish farms in southern Tasmania, Australia, was examined using 16S rRNA gene clone library construction and analysis. Sediments at both caged and reference sites at both farms showed a very high level of microbial ersity. Over 900 clones were analysed and grouped into 631 unique phylotypes. Reference sites were dominated by Delta- and Gammaproteobacteria and the Cytophaga-Flavobacteria-Bacteroides group. Cage site sediments were also dominated by these phylotypes, as well as members of the Alpha- and Epsilonproteobacteria. Diversity and coverage indices indicated that the actual ersity of the sediments was much greater than that detected, despite a large s ling effort. All libraries were shown to be statistically different from one another (P < 0.05). Many phylotypes did not group with cultured bacteria, but grouped with other environmental clones from a wide array of marine benthic environments. Diversity and evenness indices suggested that although both parameters changed after farming, erse communities were present in all sediments. The response of the microbial community to organic load suggested that random, rather than predictable, succession events determine community composition and ersity, and that sediment type may influence bacterial community and sediment response to organic perturbation.
Erratum: Revised taxonomy of the methanotrophs: Description of Methylobacter gen. nov., emendation of Methylococcus, validation of Methylosinus and Methylocystis species, and a proposal that the family Methylococcaceae includes only the group I methanotrophs (International Journal of Systematic Bacteriology 43:4 (750))
Publisher: Microbiology Society
Date: 04-1994
Shewanella olleyana sp nov., a marine species isolated from a temperate estuary which produces high levels of polyunsaturated fatty acids
Publisher: Microbiology Society
Date: 11-2002
Effect of peracetic acid on Campylobacter in food matrices mimicking commercial poultry processing
Publisher: Elsevier BV
Date: 07-2020
Salmonella enterica in Mexico 2000-2017: Epidemiology, Antimicrobial Resistance, and Prevalence in Food
Publisher: Mary Ann Liebert Inc
Date: 02-2020
Abstract: In Mexico, information of
Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment
Publisher: American Society for Microbiology
Date: 05-2003
DOI: 10.1128/AEM.69.5.2463-2483.2003
Abstract: 16S ribosomal DNA (rDNA) clone library analysis was conducted to assess prokaryotic ersity and community structural changes within a surficial sediment core obtained from an Antarctic continental shelf area (depth, 761 m) within the Mertz Glacier Polynya (MGP) region. Libraries were created from three separate horizons of the core (0- to 0.4-cm, 1.5- to 2.5-cm, and 20- to 21-cm depth positions). The results indicated that at the oxic sediment surface (depth, 0 to 0.4 cm) the microbial community appeared to be dominated by a small subset of potentially r -strategist (fast-growing, opportunistic) species, resulting in a lower-than-expected species richness of 442 operational taxonomic units (OTUs). At a depth of 1.5 to 2.5 cm, the species richness (1,128 OTUs) was much higher, with the community dominated by numerous gamma and delta proteobacterial phylotypes. At a depth of 20 to 21 cm, a clear decline in species richness (541 OTUs) occurred, accompanied by a larger number of more phylogenetically ergent phylotypes and a decline in the predominance of Proteobacteria . Based on rRNA and clonal abundance as well as sequence comparisons, syntrophic cycling of oxidized and reduced sulfur compounds appeared to be the dominant process in surficial MGP sediment, as phylotype groups putatively linked to these processes made up a large proportion of clones throughout the core. Between 18 and 65% of 16S rDNA phylotypes detected in a wide range of coastal and open ocean sediments possessed high levels of sequence similarity ( %) with the MGP sediment phylotypes, indicating that many sediment prokaryote phylotype groups defined in this study are ubiquitous in marine sediment.
Cooling challenges of modern truck diesel engines
Publisher: ASMEDC
Date: 2005
Abstract: Efficient cooling system designs are required for the modern diesel truck engine to meet new standards of increased efficiency and reduced emissions. Often, emissions reduction requires substantial cooled exhaust gas recirculation (EGR) to decrease peak combustion temperatures. This extra heat rejection imposes additional costs on the cooling system, and may not comply with application space constraints. Space and cost constraints require minimization of EGR cooler size and the risks from coolant boiling and exhaust condensation, while restraining growth in radiator frontal area, pumping power, and fan power. These objectives are usually contradictory, and a careful optimization is needed. This paper examines the effect of a coolant flow rate and peak temperature on these objectives, in parallel-flow and counter-flow arrangements of EGR cooler systems. It is concluded that these systems are likely to be inadequate, and alternative configurations may be necessary.
The taxonomy of Antarctic Flavobacterium species: description of Flavobacterium gillisiae sp. nov., Flavobacterium tegetincola sp. nov. and Flavobacterium xanthum nom. rev., sp. nov. and reclassification of [Flavobacterium] salegens as Salegentibacter salegens gen. nov., comb. nov
Publisher: Microbiology Society
Date: 05-2000
DOI: 10.1099/00207713-50-3-1055
Abstract: 16S rRNA phylogenetic analysis of a number of yellow- and orange-pigmented strains isolated from a variety of Antarctic habitats including sea ice, lakewater and cyanobacterial mats indicated a close relationship to the genus Flavobacterium but distinct from known Flavobacterium species. Phenotypic properties, DNA G+C content and whole-cell fatty acid profiles of the Antarctic strains were consistent with those of the genus Flavobacterium. DNA-DNA hybridization analysis indicated the presence of two distinct and novel genospecies each isolated from a different Antarctic habitat. From polyphasic taxonomic data it is proposed that the two groups represent new species with the following proposed names: Flavobacterium gillisiae (ACAM 601T) and Flavobacterium tegetincola (ACAM 602T). In addition polyphasic analysis of the species '[Cytophaga] xantha' (Inoue and Komagata 1976), isolated from Antarctic mud, indicated it was a distinct member of the genus Flavobacterium and was thus revived as Flavobacterium xanthum. Phylogenetic and fatty acid analyses also indicate that the species [Flavobacterium] salegens (Dobson et al. 1993), from Organic Lake, Antarctica, is misclassified at the genus level. It is proposed that this species belongs to a new genus, Salegentibacter salegens gen. nov., comb. nov.
TRFLP analysis reveals that fungi rather than bacteria are associated with premature yeast flocculation in brewing
Publisher: Oxford University Press (OUP)
Date: 12-2012
DOI: 10.1007/S10295-012-1188-8
Abstract: Premature yeast flocculation (PYF) is a sporadic fermentation problem in the brewing industry that results in incomplete yeast utilization of fermentable sugars in wort. Culture-independent, PCR-based fingerprinting techniques were applied in this study to identify the associations between the occurrence of the PYF problem during brewery fermentation with barley malt-associated microbial communities (both bacteria and fungi). Striking differences in the microbial DNA fingerprint patterns for fungi between PYF positive (PYF +ve) and negative (PYF −ve) barley malts were observed using the terminal restriction fragment length polymorphism (TRFLP) technique. The presence of terminal restriction fragments (TRFs) of 360–460 bp size range, for fungal HaeIII restriction enzyme-derived TRFLP profiles appeared to vary substantially between PYF +ve and PYF −ve s les. The source of the barley malt did not influence the fungal taxa implicated in PYF. TRFLP analysis indicates bacterial taxa are unlikely to be important in causing PYF. Virtual digestion of fungal sequences tentatively linked HaeIII TRFs in the 360–460 bp size range to a erse range of yeast/yeast-like species. Findings from this study suggest that direct monitoring of barley malt s les using molecular methods could potentially be an efficient and viable alternative for monitoring PYF during brewery fermentations.
Evolutionary changes in floral structure within Lepidium L. (Brassicaceae)
Publisher: University of Chicago Press
Date: 09-1999
DOI: 10.1086/314194
Abstract: The basic floral ground plan is remarkably constant across Brassicaceae. However, within Lepidium (ca. 175 species), deviations from this ground plan are common, with over half of Lepidium species having only two stamens rather than the usual six and a further eighth of the species having only four stamens. Furthermore, petals are reduced in size in a majority of Lepidium species. In order to determine the frequency and direction of changes in floral structure within Lepidium, we have inferred the phylogeny within the genus from sequences of the internal transcribed spacers of the nuclear ribosomal DNA. On the basis of this inferred phylogeny, we conclude that floral structure within Lepidium is relatively fluid. In order to account for the phylogenetic distributions of the different floral ground plans, at least two independent reductions to the two-stamen condition and at least one reversal to flowers with increased organ numbers are likely to have occurred. To account for the frequency of morphological evolution observed within the genus, we propose that some clades within Lepidium may be predisposed to changes in floral structure. In addition, several transoceanic dispersals are needed to explain the geographic distributions of the clades inferred from the phylogeny.
Light-stimulated growth of proteorhodopsin-bearing sea-ice psychrophile Psychroflexus torquis is salinity dependent
Publisher: Springer Science and Business Media LLC
Date: 20-06-2013
Impact of lactose starvation on the physiology of Lactobacillus casei GCRL163 in the presence or absence of Tween 80
Publisher: American Chemical Society (ACS)
Date: 23-10-2013
DOI: 10.1021/PR400661G
Abstract: The global proteomic response of the nonstarter lactic acid bacteria Lactobacillus casei strain GCRL163 under carbohydrate depletion was investigated to understand aspects of its survival following cessation of fermentation. The proteome of L. casei GCRL163 was analyzed quantitatively after growth in modified MRS (with and without Tween 80) with different levels of lactose (0% lactose, starvation 0.2% lactose, growth limiting 1% lactose, non-growth-limited control) using gel-free proteomics. Results revealed that carbohydrate starvation lead to suppression of lactose and galactose catabolic pathways as well as pathways for nucleotide and protein synthesis. Enzymes of the glycolysis/gluconeogenesis pathway, amino acid synthesis, and pyruvate and citrate metabolism become more abundant as well as other carbohydrate catabolic pathways, suggesting increased optimization of intermediary metabolism and scavenging. Tween 80 did not affect growth yield however, proteins related to fatty acid biosynthesis were repressed in the presence of Tween 80. The data suggest that L. casei adeptly switches to a scavenging mode, using both citrate and Tween 80, and efficiently adjusts energetic requirements when carbohydrate starved and thus can sustain survival for weeks to months. Explaining the adaptation of L. casei during lactose starvation will assist efforts to maintain viability of L. casei and extend its utility as a beneficial dietary adjunct and fermentation processing aid.
Stromatolites on the rise in peat-bound karstic wetlands
Publisher: Springer Science and Business Media LLC
Date: 13-11-2017
DOI: 10.1038/S41598-017-15507-1
Abstract: Stromatolites are the oldest evidence for life on Earth, but modern living ex les are rare and predominantly occur in shallow marine or (hyper-) saline lacustrine environments, subject to exotic physico-chemical conditions. Here we report the discovery of living freshwater stromatolites in cool-temperate karstic wetlands in the Giblin River catchment of the UNESCO-listed Tasmanian Wilderness World Heritage Area, Australia. These stromatolites colonize the slopes of karstic spring mounds which create mildly alkaline (pH of 7.0-7.9) enclaves within an otherwise uniformly acidic organosol terrain. The freshwater emerging from the springs is Ca-HCO 3 dominated and water temperatures show no evidence of geothermal heating. Using 16 S rRNA gene clone library analysis we revealed that the bacterial community is dominated by Cyanobacteria, Alphaproteobacteria and an unusually high proportion of Chloroflexi, followed by Armatimonadetes and Planctomycetes, and is therefore unique compared to other living ex les. Macroinvertebrates are sparse and snails in particular are disadvantaged by the development of debilitating accumulations of carbonate on their shells, corroborating evidence that stromatolites flourish under conditions where predation by metazoans is suppressed. Our findings constitute a novel habitat for stromatolites because cool-temperate freshwater wetlands are not a conventional stromatolite niche, suggesting that stromatolites may be more common than previously thought.
PHOSPHOLIPID FATTY-ACID AND LIPOPOLYSACCHARIDE FATTY-ACID SIGNATURE LIPIDS IN METHANE-UTILIZING BACTERIA
Publisher: Oxford University Press (OUP)
Date: 02-1991
Shewanella pacifica sp. nov., a polyunsaturated fatty acid-producing bacterium isolated from sea water
Publisher: Microbiology Society
Date: 07-2004
Abstract: Six marine bacterial strains, KMM 3597 T , KMM 3775, KMM 3590, KMM 3772, KMM 3605 and KMM 3601, that produce polyunsaturated fatty acids were isolated from sea water s les collected from different locations and depths in Chazhma Bay (Sea of Japan, Pacific Ocean) and characterized to clarify their taxonomic position. The DNA G+C contents of these strains were 39·5–40·3 mol%. The level of DNA hybridization between these strains was conspecific (83–96 %), indicating that they represent a single genospecies. 16S rRNA gene sequence-based phylogenetic analysis of the novel strains revealed that Shewanella japonica KMM 3299 T was the closest relative (99 % similarity). However, DNA–DNA hybridization experiments demonstrated only 45–50 % binding with DNA of S. japonica . The novel organisms grew between 4 and 33 °C, were neutrophilic and haemolytic, and were able to degrade starch, gelatin, agar and Tween 80. The predominant fatty acids were (%± sd ): i13 : 0 (9·3±1·1) i15 : 0 (33·9±1·5) 16 : 0 (8·9±1·6) and 16 : 1 ω 7 (14·8±1·1). The fatty acid 20 : 5 ω 3, formed at 28 °C, was present at up to 5·3 % total fatty acids. The major isoprenoid quinones were Q7 (21–41 %) and Q8 (50–59 %). The phylogenetic, genetic and physiological properties of the six strains placed them within a novel species, Shewanella pacifica sp. nov., the type strain of which is R10SW1 T (=KMM 3597 T =CIP 107849 T ).
Predictive Models for the Effect of Storage Temperature on Vibrio parahaemolyticus Viability and Counts of Total Viable Bacteria in Pacific Oysters (Crassostrea gigas)
Publisher: American Society for Microbiology
Date: 15-12-2011
DOI: 10.1128/AEM.05568-11
Abstract: Vibrio parahaemolyticus is an indigenous bacterium of marine environments. It accumulates in oysters and may reach levels that cause human illness when postharvest temperatures are not properly controlled and oysters are consumed raw or undercooked. Predictive models were produced by injecting Pacific oysters ( Crassostrea gigas ) with a cocktail of V. parahaemolyticus strains, measuring viability rates at storage temperatures from 3.6 to 30.4°C, and fitting the data to a model to obtain parameter estimates. The models were evaluated with Pacific and Sydney Rock oysters ( Saccostrea glomerata ) containing natural populations of V. parahaemolyticus. V. parahaemolyticus viability was measured by direct plating s les on thiosulfate-citrate-bile salts-sucrose (TCBS) agar for injected oysters and by most probable number (MPN)-PCR for oysters containing natural populations. In parallel, total viable bacterial counts (TVC) were measured by direct plating on marine agar. Growth/inactivation rates for V. parahaemolyticus were −0.006, −0.004, −0.005, −0.003, 0.030, 0.075, 0.095, and 0.282 log 10 CFU/h at 3.6, 6.2, 9.6, 12.6, 18.4, 20.0, 25.7, and 30.4°C, respectively. The growth rates for TVC were 0.015, 0.023, 0.016, 0.048, 0.055, 0.071, 0.133, and 0.135 log 10 CFU/h at 3.6, 6.2, 9.3, 14.9, 18.4, 20.0, 25.7, and 30.4°C, respectively. Square root and Arrhenius-type secondary models were generated for V. parahaemolyticus growth and inactivation kinetic data, respectively. A square root model was produced for TVC growth. Evaluation studies showed that predictive growth for V. parahaemolyticus and TVC were “fail safe.” The models can assist oyster companies and regulators in implementing management strategies to minimize V. parahaemolyticus risk and enhancing product quality in supply chains.
Effects of finfish farms on pelagic protist communities in a semi-closed stratified embayment
Publisher: Cold Spring Harbor Laboratory
Date: 08-08-2022
DOI: 10.1101/2022.08.08.503163
Abstract: Coastal aquaculture operations for feed additive species results in the release of waste into the surrounding environment, with the potential for adverse environmental change. Ubiquitous pelagic protists are sensitive to environmental changes making them potential sentinels for detecting and monitoring impacts. This study used 18S rRNA high-throughput licon sequencing as a molecular tool to study the pelagic protist community, with the aim of evaluating their potential as bioindicators of aquaculture activity in a low-oxygen, highly stratified marine embayment. S ling occurred at three different depths along a distance gradient from two leases and at three control sites. Our results showed that the ersity and composition of both phytoplankton and other protist communities were more strongly influenced by depth stratification than the aquaculture activity. Nonetheless, differential abundance and machine learning analyses revealed a suite of potential bioindicators for aquaculture activity this included the phytoplankton taxa Chrysophyceae , Gymnodiniphycidae ( Gyrodinium ), Cryptomonadales and Ciliophora ( Philasterides armatalis, Plagiopylida, and Strombidium). Among the other protists, ciliates were also more abundant in closer proximity to the leases in both surface and bottom s les. Overall, our findings indicated that the use of 18S rRNA sequencing of protist communities is a promising tool for identifying environmental changes from aquaculture in the water column.
Sphingomonas alaskensis Strain AFO1, an Abundant Oligotrophic Ultramicrobacterium from the North Pacific
Publisher: American Society for Microbiology
Date: 11-2001
DOI: 10.1128/AEM.67.11.4945-4954.2001
Abstract: Numerous studies have established the importance of picoplankton (microorganisms of ≤2 μm in length) in energy flow and nutrient cycling in marine oligotrophic environments, and significant effort has been directed at identifying and isolating heterotrophic picoplankton from the world's oceans. Using a method of diluting natural seawater to extinction followed by monthly subculturing for 12 months, a bacterium was isolated that was able to form colonies on solid medium. The strain was isolated from a 10 5 dilution of seawater where the standing bacterial count was 3.1 × 10 5 cells ml −1 . This indicated that the isolate was representative of the most abundant bacteria at the s ling site, 1.5 km from Cape Muroto, Japan. The bacterium was characterized and found to be ultramicrosized (less than 0.1 μm 3 ), and the size varied to only a small degree when the cells were starved or grown in rich media. A detailed molecular (16S rRNA sequence, DNA-DNA hybridization, G+C mol%, genome size), chemotaxonomic (lipid analysis, morphology), and physiological (resistance to hydrogen peroxide, heat, and ethanol) characterization of the bacterium revealed that it was a strain of Sphingomonas alaskensis . The type strain, RB2256, was previously isolated from Resurrection Bay, Alaska, and similar isolates have been obtained from the North Sea. The isolation of this species over an extended period, its high abundance at the time of s ling, and its geographical distribution indicate that it has the capacity to proliferate in ocean waters and is therefore likely to be an important contributor in terms of biomass and nutrient cycling in marine environments.
Necrotic disease in bivalve larval cultures
Publisher: CSIRO Publishing
Date: 2017
DOI: 10.1071/MA17048
Abstract: The health of marine bivalve larvae is greatly affected by bacteria in the environment particularly when reared in marine hatcheries. This is generally because high stocking densities resulting in high organic loads of both food and faeces, can support increased bacterial growth and biomass levels. Increased bacterial load can lead to larval disease referred to as bacillary necrosis (BN) leading in turn to rapid larval mortality and loss of production. Despite more than 50 years since the first detailed description of BN, we still do not fully understand its causes and mechanisms. Through the manipulation of a model larval culture of the Australian blue mussels (Mytilus galloprovincialis), we determined that BN is linked with rapid and systematic changes in the bacterial community.
Distinct mechanisms promote polarity establishment in carpels of Arabidopsis
Publisher: Elsevier BV
Date: 10-1999
DOI: 10.1016/S0092-8674(00)81651-7
Abstract: Lateral organs of plants display asymmetry with abaxial identity being specified by members of the Arabidopsis YABBY gene family. Mutations in CRABS CLAW, the founding family member, display ectopic formation of adaxial carpel tissues only when the functions of other genes, such as GYMNOS or KANADI, are also compromised. Mutations in these genes alone do not result in loss of polar differentiation, and therefore, they act redundantly with CRABS CLAW to establish polarity. As GYMNOS encodes a uniformly expressed homolog of the chromatin-remodeling protein, Mi2, we argue that the unique genetic interactions do not reflect a molecular redundancy. Rather, CRABS CLAW regulates transcription spatially, whereas GYMNOS regulates downstream targets temporally to ensure proper differentiation of the carpels.
Molecular analysis of the bacterial communities in the live Pacific oyster (Crassostrea gigas) and the influence of postharvest temperature on its structure
Publisher: Oxford University Press (OUP)
Date: 11-04-2012
DOI: 10.1111/J.1365-2672.2012.05287.X
Abstract: To evaluate the effect of postharvest temperature on bacterial communities in live Pacific oysters (Crassostrea gigas) using nonculture-based methods. Live oysters were compared before and after storage at 4, 6, 15, 20 and 30°C using terminal restriction fragment length polymorphism (T-RFLP). Bacterial communities in freshly harvested (control) vs stored oysters were significantly different. Changes in bacterial communities at 4, 15 and 30°C observed by T-RFLP were further investigated by clone library analysis. Members of the Proteobacteria predominated (43·0-57·0% of clones) in control oysters, while storage altered the bacterial profile. At 4°C, Psychrilyobacter spp. (phylum Fusobacteria) predominated (43·8% of clones), while at 15 and 30°C, members of the phylum Bacteroidetes represented 63·0 and 60·2% of clones, respectively. High microbial ersity in oysters was observed, with at least 73 different genera-related clones among all s les. Changes in the overall bacterial community of Pacific oysters were influenced by storage temperature and would likely not be detected by standard culture-based methods currently used to assess oyster quality. Certain dominant genera, such as Psychrilyobacter, Polynucleobacter and a bacterial group related to Alkaliflexus, should be further studied as possible indicators for postharvest temperature control. This work is the first report describing the effect of different storage temperatures on bacterial ersity in postharvest live Pacific oysters using molecular-based methods.
Microbial community variation in pristine and polluted nearshore Antarctic sediments
Publisher: Oxford University Press (OUP)
Date: 07-2003
Use of gene probes to assess the impact and effectiveness of aerobic in situ bioremediation of TCE
Publisher: Springer Science and Business Media LLC
Date: 26-11-2008
DOI: 10.1007/S00203-008-0445-8
Abstract: Gene probe hybridization was used to determine distribution and expression of co-metabolic genes at a contaminated site as it underwent in situ methanotrophic bioremediation of trichloroethylene (TCE). The bioremediation strategies tested included a series of air, air:methane, and air:methane:nutrient pulses of the test plot using horizontal injection wells. During the test period, the levels of TCE reduced drastically in almost all test s les. Sediment core s les (n=367) taken from 0 m (surface)-43 m depth were probed for gene coding for methanotrophic soluble methane monooxygenase (sMMO) and heterotrophic toluene dioxygenase (TOD), which are known to co-metabolize TCE. The same sediment s les were also probed for genes coding for methanol dehydrogenase (MDH) (catalyzing the oxidation of methanol to formaldehyde) to assess specifically changes in methylotrophic bacterial populations in the site. Gene hybridization results showed that the frequency of detection of sMMO genes were stimulated approximately 250% following 1% methane:air (v/v) injection. Subsequent injection of 4% methane:air (v/v) resulted in an 85% decline probably due to nutrient limitations, since addition of nutrients (gaseous nitrogen and phosphorus) thereafter caused an increase in the frequency of detection of sMMO genes. Detection of TOD genes declined during the process, and eventually they were non-detectable by the final treatment, suggesting that methanotrophs displaced the TOD gene containing heterotrophs. Active transcription of sMMO and TOD was evidenced by hybridization to mRNA. These analyses combined with results showing the concomitant decline in TCE concentrations, increases in chloride concentration and increases in methanotroph viable counts, provide multiple lines of evidence that TCE remediation was caused specifically by methanotrophs. Our results suggest that sMMO genes are responsible for most, if not all, of the observed biodegradation of TCE. This study demonstrates that the use of nucleic acid analytical methods provided a gene specific assessment of the effects of in situ treatment technologies.
The microbiome of Chinook salmon (Oncorhynchus tshawytscha) in a recirculation aquaculture system
Publisher: Elsevier BV
Date: 03-2021
Algicidal bacteria associated with blooms of a toxic dinoflagellate in a temperate Australian estuary
Publisher: Inter-Research Science Center
Date: 2002
DOI: 10.3354/MEPS244001
The family Cryomorphaceae
Publisher: Springer Berlin Heidelberg
Date: 2014
Heat resistance and genomics of spoilage Alicyclobacillus spp. Isolated from fruit juice and fruit-based beverages
Publisher: Elsevier BV
Date: 04-2021
Out From the Shadows – Resolution of the Taxonomy of the Family Cryomorphaceae
Publisher: Frontiers Media SA
Date: 05-05-2020
Global Genome Response of Escherichia coli O157∶H7 Sakai during Dynamic Changes in Growth Kinetics Induced by an Abrupt Temperature Downshift
Publisher: Public Library of Science (PLoS)
Date: 13-06-2014
Olleya marilimosa gen. nov., sp. nov., an exopolysaccharide-producing marine bacterium from the family Flavobacteriaceae, isolated from the Southern Ocean
Publisher: Microbiology Society
Date: 07-2005
Abstract: A Gram-negative, aerobic, gliding, orange–yellow marine bacterium was isolated from particulate material s led from the Southern Ocean. This strain produced an exopolysaccharide in liquid culture. 16S rRNA gene sequence analysis showed that this isolate was a member of the family Flavobacteriaceae , but represented a separate lineage. Major whole-cell fatty acids included i15 : 1 ω 10 c , i15 : 0, β -OH i15 : 0, a15 : 1 ω 10 c , 15 : 0 and α -OH i15 : 0. The G+C content of the DNA was 49 mol%. Based on phylogenetic, phenotypic, chemotaxonomic and genotypic analyses, this bacterium was placed in a novel taxon as Olleya marilimosa gen. nov., sp. nov. with type strain CAM030 T (=ACAM 1065 T =CIP 108537 T ).
Culture-dependent and culture-independent assessment of spoilage community growth on VP lamb meat from packaging to past end of shelf-life
Publisher: Elsevier BV
Date: 12-2017
Abstract: Packaging and storage temperature are important factors that influence the shelf-life of vacuum packed (VP) meat. In this study the shelf-life of VP bone-in lamb hind shanks stored at 8 °C and -1.2 °C was determined in parallel to analyses of starting and eventual spoilage bacterial communities via Illumina MiSeq based 16S rRNA licon sequencing. The mean total viable counts (TVC) and lactic acid bacterial viable counts (LAB) were observed to increase to log 7.5 CFU/cm
Using Real-Time PCR to Assess Changes in the Hydrocarbon-Degrading Microbial Community in Antarctic Soil During Bioremediation
Publisher: Springer Science and Business Media LLC
Date: 31-08-2006
DOI: 10.1007/S00248-006-9131-Z
Abstract: A real-time polymerase chain reaction (PCR) method to quantify the proportion of microorganisms containing alkane monooxygenase was developed and used to follow changes in the microbial community in hydrocarbon-contaminated Antarctic soil during a bioremediation field trial. Assays for the alkB and rpoB genes were validated and found to be both sensitive and reproducible (less than 2% intrarun variation and 25-38% interrun variation). Results from the real-time PCR analysis were compared to analysis of the microbial population by a culture-based technique [most probable number (MPN) counts]. Both types of analysis indicated that fertilizer addition to hydrocarbon-contaminated soil stimulated the indigenous bacterial population within 1 year. The proportion of alkB containing microorganisms was positively correlated to the concentration of n-alkanes in the soil. After the concentration of n-alkanes in the soil decreased, the proportion of alkane-degrading microorganisms decreased, but the proportion of total hydrocarbon-degrading microorganisms increased, indicating another shift in the microbial community structure and ongoing biodegradation.
Salinity and fish age affect the gut microbiota of farmed Chinook salmon (Oncorhynchus tshawytscha)
Publisher: Elsevier BV
Date: 11-2020
Pyrosequencing-based characterization of gastrointestinal bacteria of Atlantic salmon (Salmo salar L.) within a commercial mariculture system
Publisher: Oxford University Press (OUP)
Date: 05-05-2014
DOI: 10.1111/JAM.12514
Abstract: The relationship of Atlantic salmon gastrointestinal (GI) tract bacteria to environmental factors, in particular water temperature within a commercial mariculture system, was investigated. Salmon GI tract bacterial communities commercially farmed in south-eastern Tasmania were analysed, over a 13-month period across a standard commercial production farm cycle, using 454 16S rRNA-based pyrosequencing. Faecal bacterial communities were highly dynamic but largely similar between randomly selected fish. In postsmolt, the faecal bacteria population was dominated by Gram-positive fermentative bacteria however, by midsummer, members of the family Vibrionaceae predominated. As fish progressed towards harvest, a range of different bacterial genera became more prominent corresponding to a decline in Vibrionaceae. The s led fish were fed two different commercial diet series with slightly different protein, lipid and digestible energy level however, the effect of these differences was minimal. The overall data demonstrated dynamic hind gut communities in salmon that were related to season and fish growth phases but were less influenced by differences in commercial diets used routinely within the farm system studied. This study provides understanding of farmed salmon GI bacterial communities and describes the relative impact of diet, environmental and farm factors.
Molecular site assessment and process monitoring in bioremediation and natural attenuation
Publisher: Springer Science and Business Media LLC
Date: 07-1995
DOI: 10.1007/BF02787926
Desulfosporosinus meridiei sp nov., a spore-forming sulfate-reducing bacterium isolated from gasolene-contaminated groundwater
Publisher: Microbiology Society
Date: 2001
DOI: 10.1099/00207713-51-1-133
Abstract: Eight strains of spore-forming, sulfate-reducing bacteria, isolated from groundwater contaminated with motor fuel [mostly benzene, toluene ethylbenzene and xylene (BTEX) compounds] in sandy soil near Perth, Australia, were closely related to Desulfosporosinus (previously Desulfotomaculum) orientis DSM 765T (95.3-97.3% 16S rDNA sequence similarity). Whole-cell fatty acids were dominated by even-carbon, straight-chain saturated and mono-unsaturated fatty acids, in particular 16:0, 16:1cis9, 14:0 and 18:1cis11. The strains grew at temperatures between 4 and 42 degrees C and in medium containing up to 4% NaCl. The eight strains clustered into two main groups based on phylogeny, randomly lified polymorphic DNA (RAPD)-PCR patterns and nutritional characteristics. Representatives of the two groups, strain S5 (group A) and strain S10T (group B) had 81% DNA-DNA homology with each other and therefore should be accommodated in the same species. Strain S10T had less than 38% homology with Desulfosporosinus orientis DSM 765T, the most closely phylogenetically related type strain available. The new strains were distinguished from Desulfosporosinus orientis DSM 765T by different banding patterns in a RAPD-PCR, and phenotypically by their inability to utilize fumarate as a carbon and energy source with sulfate as the electron acceptor and by their lower tolerance to NaCl. The DNA G+C contents were 46.8 and 46.9 mol% for strains S5 and S10T, respectively (Desulfosporosinus orientis DSM 765T 45.9 mol%). It is proposed that these new strains be placed in a new species of the genus Desulfosporosinus. The name Desulfosporosinus meridiei is proposed, with strain S10T as the type strain (= DSM 13257T = NCIMB 13706T).
Molecular evidence for bicontinental hybridogenous genomic constitution in Lepidium sensu stricto (Brassicaceae) species from Australia and New Zealand
Publisher: Wiley
Date: 02-2004
DOI: 10.3732/AJB.91.2.254
Abstract: Lepidium sensu stricto (s.s.) (Brassicaceae) (ca. 150 species) is distributed worldwide with endemic species on every continent. It is represented in Australia and New Zealand by 19 and seven native species, respectively. In the present study we used a nuclear ribosomal internal transcribed spacer (ITS) phylogeny in comparison with a cpDNA phylogeny to unravel the origin of Australian/New Zealand species. Although phylogenetic relationships within Lepidium s.s. were not fully resolved, the cpDNA data were in agreement with a Californian origin of Lepidium species from Australia/New Zealand. Strongly conflicting signals between the cp- and nuclear DNA phylogenetic analysis clearly indicated hybridogenous genomic constitution of Australian Lepidium s.s. species: All 18 studied Australian/New Zealand Lepidium s.s. species examined shared a Californian cpDNA type. While eleven Australian/New Zealand species appeared to harbor a Californian ITS type, a group of seven species shared a South African ITS type. This pattern is most likely explained by two trans-oceanic dispersals of Lepidium from California and Africa to Australia/New Zealand and subsequent hybridization followed by homogenization of the ribosomal DNA either to the Californian or South African ITS type in the two different lineages. Calibration of our molecular trees indicates a Pliocene/Pleistocene origin of Lepidium in Australia/New Zealand. Low levels of cpDNA and ITS sequence ergence and unresolved topologies within Australian/New Zealand species suggest a rapid and recent radiation of Lepidium after the hybridization event. This coincides with dramatic climatic changes in that geological epoch shaping the composition of the vegetation.
Optimisation of one-tube PCR-ELISA to detect femtogram amounts of genomic DNA
Publisher: Elsevier BV
Date: 10-2002
DOI: 10.1016/S0167-7012(02)00055-6
Abstract: A simple, high-throughput, low-cost polymerase chain reaction-enzyme linked immunosorbent assay (PCR-ELISA) protocol that detects the presence of 4 fg of DNA from four bacterial fish pathogens Yersinia ruckeri, Tenacibaculum maritimum (formerly Flexibacter maritimus), Lactococcus garvieae and Aeromonas salmonicida was developed. DNA lification was undertaken in a biphasic system with free and bound PCR that are achieved in the one NucleoLink tube. Solid-phase licons were detected using biotin labelled hybridization probes and visualised colourimetrically with streptavidin-alkaline phosphatase and p-nitrophenylphosphate as substrate. PCR and hybridization took less than 8 h to perform with maximum signal output for femtogram amounts of template DNA achieved within 24 h. Implementation and optimization of the protocol is discussed.
Investigation and optimization of a passively operated compost-based system for remediation of acidic, highly iron- and sulfate-rich industrial waste water
Publisher: Elsevier BV
Date: 05-2009
DOI: 10.1016/J.WATRES.2009.02.030
Abstract: A passively operated multi-stage bioremediation system utilizing composted agricultural waste products and an artificial wetland system was found to be effective for purification of acidic, iron- and sulfate-rich waste water derived from titanium mineral processing. The main microbial players involved in the remediation system processes and the dynamics were investigated mineral processing waste water-filled sludge dams possessed stable microbial communities that included Acidithiobacillus, Desulfurella, and acidophilic, anaerobic fermenters of the order Bacteroidales. These groups were enriched in a subsequent potato waste-based iron mobilization pre-treatment stage. Within downstream reduction treatment stages ("reduction cells"), compost/straw decomposition and associated sulfur/sulfate and iron reduction were carried out by a complex mix of aerobic and anaerobic bacteria. The efficaciousness of the system without replacement of the compost was found to steadily decline following 2 years of operation and corresponded with the reduction cell communities becoming simultaneously more erse and homogenous. Microcosm-based experiments demonstrated that operational declines were due to unsustained supply of suitable labile carbon sources combined with spatial heterogeneity within the layered design of the reduction stage of the system resulting in inadequate redox conditions. Temperature was not found to be a critical performance factor in the range of 10-25 degrees C. Application of a combined emulsified oil/molasses amendment was found to be highly effective in promoting a microbial community capable of remediating waste water with high iron and sulfate levels. Acidophilic members of the order Bacteroidales were found to be critical in the investigated remediation system, providing organic donors for subsequent metal and sulfur transformations and could have a broader ecological significance than previously suspected.
Proteomic Insight into Functional Changes of Proteorhodopsin-Containing Bacterial Species Psychroflexus torquis under Different Illumination and Salinity Levels
Publisher: American Chemical Society (ACS)
Date: 30-07-2015
DOI: 10.1021/ACS.JPROTEOME.5B00241
Abstract: The extremely psychrophilic proteorhodopsin-containing bacterial species Psychroflexus torquis is considered to be a model sea-ice microorganism, which has adapted to an epiphytic lifestyle. So far, not much is known about proteorhodopsin-based phototrophy and associated life strategies of sea ice bacteria, although it has been previously shown that P. torquis can gain growth advantage from light using a proteorhodopsin proton pump, the activity of which is influenced by environmental salinity. The comprehensive quantitative proteomic study performed here indicated that P. torquis responds to changing salinity and illumination conditions. Proteins in the electron-transfer chain were down-regulated at a suboptimal salinity level, TonB-dependent transporters increased in abundance under supra-optimal salinity and decreased under suboptimal salinity. In addition, several anaplerotic CO2 fixation proteins and three putative light sensing proteins that contain PAS and GAF domains became more abundant under illumination. Furthermore, central metabolic pathways (TCA and glycolysis) were also induced by both salinity stress and illumination. The data suggest that P. torquis responded to changes in both light energy and salinity to modulate membrane and central metabolic proteins that are involved in energy production as well as nutrient uptake and gliding motility processes that would be especially advantageous during the polar summer ice algal bloom.
Changes of the bacterial community diversity on chicken carcasses through an Australian poultry processing line
Publisher: Elsevier BV
Date: 04-2019
Abstract: Understanding the bacterial community profile through poultry processing could help the industry to produce better poultry products. In this study, 10 chicken carcasses were randomly s led from before and after scalding, before and after immersion chilling, and after air chilling each through a modern commercial processing line, along with the contents of 10 caeca. The s led processing line effectively reduced the bacterial counts by > 4.6 Log
Alteromonas addita sp. nov.
Publisher: Microbiology Society
Date: 05-2005
Abstract: On the basis of phenotypic, genotypic characteristics and analysis of 16S rRNA gene sequences, a novel species belonging to the genus Alteromonas is described. A non-pigmented, motile, Gram-negative bacterium designated R10SW13 T was isolated from sea water s les collected in Chazhma Bay (Sea of Japan, Pacific Ocean). The novel organism mainly grew between 4 °C and 37 °C, was neutrophilic and slightly halophilic, tolerating up to 10 % NaCl. Strain R10SW13 T was haemolytic and was able to degrade starch and Tween 80 and to degrade gelatin and agar weakly, but did not degrade casein. Phosphatidylethanolamine (44·3±0·9 %) and phosphatidylglycerol (55·7±0·9 %) were the predominant phospholipids. The major fatty acids formed were typical for the genus Alteromonas , including 16 : 0, 16 : 1 ω -7 and 18 : 1 ω -7. The G+C content of the DNA was 43·4 mol%. DNA–DNA hybridization experiments showed 38–53 % binding with the DNAs of type strains of phylogenetically related species of the genus Alteromonas , namely: Alteromonas macleodii , Alteromonas marina , Alteromonas stellipolaris , Alteromonas litorea , ‘ Alteromonas macleodii subsp. fijiensis ’ and ‘ Alteromonas infernus ’. Based on these results, a novel species, Alteromonas addita sp. nov., is proposed, with strain R10SW13 T (=KMM 3600 T =KCTC 12195 T =LMG 22532 T ) as the type strain.
Effects of incubation temperature on growth and production of exopolysaccharides by an antarctic sea ice bacterium grown in batch culture
Publisher: American Society for Microbiology
Date: 07-2005
DOI: 10.1128/AEM.71.7.3519-3523.2005
Abstract: The sea ice microbial community plays a key role in the productivity of the Southern Ocean. Exopolysaccharide (EPS) is a major component of the exopolymer secreted by many marine bacteria to enhance survival and is abundant in sea ice brine channels, but little is known about its function there. This study investigated the effects of temperature on EPS production in batch culture by CAM025, a marine bacterium isolated from sea ice s led from the Southern Ocean. Previous studies have shown that CAM025 is a member of the genus Pseudoalteromonas and therefore belongs to a group found to be abundant in sea ice by culture-dependent and -independent techniques. Batch cultures were grown at −2°C, 10°C, and 20°C, and cell number, optical density, pH, glucose concentration, and viscosity were monitored. The yield of EPS at −2°C and 10°C was 30 times higher than at 20°C, which is the optimum growth temperature for many psychrotolerant strains. EPS may have a cryoprotective role in brine channels of sea ice, where extremes of high salinity and low temperature impose pressures on microbial growth and survival. The EPS produced at −2°C and 10°C had a higher uronic acid content than that produced at 20°C. The availability of iron as a trace metal is of critical importance in the Southern Ocean, where it is known to limit primary production. EPS from strain CAM025 is polyanionic and may bind dissolved cations such at trace metals, and therefore the presence of bacterial EPS in the Antarctic marine environment may have important ecological implications.
Control of microbes on barley grains using peroxyacetic acid and electrolysed water as antimicrobial agents
Publisher: Elsevier BV
Date: 12-2018
Abstract: The extent and type of microbial growth on barley grain is a key determinant of malt quality for beer production, as problematic microbial products can persist into the brewing process and impact beer quality. Microbial composition on malting barley grain are influenced by field growth, storage and malting conditions. The present study investigated the efficacy of electrolysed water (EW) with free chlorine concentrations of 5, 50, 100 and 500 ppm, as well as peroxyacetic acid (PAA) at 100 and 500 ppm, as pre-steep treatments to control microbes on grains during the malting process. The research determined the reduction in the load of Pseudomonas spp., heterotrophic bacteria, yeasts and filamentous fungi on weathered and on non-weathered grains. Pseudomonas spp., heterotrophic bacteria and yeasts were significantly reduced up to 4 logs when treated with 500 ppm PAA. PAA reduced filamentous fungi but 500 ppm free chlorine EW showed greater reductions. None of the treatments had detrimental effect on grain germination. The variation in antimicrobial efficacy among treatments can be attributed to variations in microbial susceptibility as well as differences in anti-microbial mechanisms specific to each antimicrobial agent.
Microbial ecology of Atlantic salmon, Salmo salar, hatcheries: impacts of the built environment on fish mucosal microbiota
Publisher: Cold Spring Harbor Laboratory
Date: 02-11-2019
DOI: 10.1101/828749
Abstract: Successful rearing of fish in hatcheries is critical for conservation, recreational fishing, and commercial fishing through wild stock enhancements, and aquaculture production. Flow through (FT) hatcheries require more water than Recirculating-Aquaculture-Systems (RAS) which enable up to 99% of water to be recycled thus significantly reducing environmental impacts. Here, we evaluated the biological and physical microbiome interactions of the built environment of a hatchery from three Atl salmon hatcheries (RAS n=2, FT n=1). Six juvenile fish were s led from tanks in each of the hatcheries for a total of 60 fish across 10 tanks. Water and tank side biofilm s les were collected from each of the tanks along with three salmon body sites (gill, skin, and digesta) to assess mucosal microbiota using 16S rRNA sequencing. The water and tank biofilm had more microbial richness than fish mucus while skin and digesta from RAS fish had 2× the richness of FT fish. Body sites each had unique microbial communities (P .001) and were influenced by the various hatchery systems (P .001) with RAS systems more similar. Water and especially tank biofilm richness was positively correlated with skin and digesta richness. Strikingly, the gill, skin and digesta communities were more similar to the origin tank biofilm vs. all other experimental tanks suggesting that the tank biofilm has a direct influence on fish-associated microbial communities. The results from this study provide evidence for a link between the tank microbiome and the fish microbiome with the skin microbiome as an important intermediate. Atlantic salmon, Salmo salar , is the most farmed marine fish worldwide with an annual production of 2,248 million metric tonnes in 2016. Salmon hatcheries are increasingly changing from flow through towards RAS design to accommodate more control over production along with improved environmental sustainability due to lower impacts on water consumption. To date, microbiome studies on hatcheries have focused either on the fish mucosal microbiota or the built environment microbiota, but have not combined the two to understand interactions. Our study evaluates how water and tank biofilm microbiota influences fish microbiota across three mucosal environments (gill, skin, and digesta). Results from this study highlight how the built environment is a unique source of microbes to colonize fish mucus and furthermore how this can influence the fish health. Further studies can use this knowledge to engineer built environments to modulate fish microbiota for a beneficial phenotype.
Pseudomonas mixta sp. nov., a Bacterium from Soil with Degradative Activity on a Variety of Complex Polysaccharides
Publisher: Elsevier BV
Date: 11-1988
Colonisation dynamics of Listeria monocytogenes strains isolated from food production environments
Publisher: Springer Science and Business Media LLC
Date: 09-06-2021
DOI: 10.1038/S41598-021-91503-W
Abstract: Listeria monocytogenes is a ubiquitous bacterium capable of colonising and persisting within food production environments (FPEs) for many years, even decades. This ability to colonise, survive and persist within the FPEs can result in food product cross-contamination, including vulnerable products such as ready to eat food items. Various environmental and genetic elements are purported to be involved, with the ability to form biofilms being an important factor. In this study we examined various mechanisms which can influence colonisation in FPEs. The ability of isolates (n = 52) to attach and grow in biofilm was assessed, distinguishing slower biofilm formers from isolates forming biofilm more rapidly. These isolates were further assessed to determine if growth rate, exopolymeric substance production and/or the agr signalling propeptide influenced these dynamics and could promote persistence in conditions reflective of FPE. Despite no strong association with the above factors to a rapid colonisation phenotype, the global transcriptome suggested transport, energy production and metabolism genes were widely upregulated during the initial colonisation stages under nutrient limited conditions. However, the upregulation of the metabolism systems varied between isolates supporting the idea that L. monocytogenes ability to colonise the FPEs is strain-specific.
In vitro characteristics of an Atlantic salmon (Salmo salar L.) hind gut microbial community in relation to different dietary treatments
Publisher: Elsevier BV
Date: 10-2017
DOI: 10.1016/J.RESMIC.2017.07.003
Abstract: In this study, microbial community dynamics were assessed within a simple in vitro model system in order to understand those changes influenced by diet. The abundance and ersity of bacteria were monitored within different treatment slurries inoculated with salmon faecal s les in order to mimic the effects of dietary variables. A total of five complete diets and two ingredients (plant meal) were tested. The total viable counts (TVCs) and sequencing data revealed that there was very clear separation between the complete diets and the plant meal treatments, suggesting a dynamic response by the allochthonous bacteria to the treatments. Automated ribosomal intergenic spacer analysis (ARISA) results showed that different diet formulations produced different patterns of fragments, with no separation between the complete diets. However, plant-based protein ingredients were clearly separated from the other treatments. 16S rRNA Illumina-based sequencing analysis showed that members of the genera Aliivibrio, Vibrio and Photobacterium became predominant for all complete diets treatments. The plant-based protein ingredient treatments only sustained weak growth of the genus Sphingomonas. In vitro based testing of diets could be a useful strategy to determine the potential impact of either complete feeds or ingredients on major fish gastrointestinal tract microbiome members.
Methanotrophic TCE Biodegradation in a Multi-Stage Bioreactor
Publisher: American Chemical Society (ACS)
Date: 08-1995
DOI: 10.1021/ES00008A029
The effect of biochar loading rates on soil fertility, soil biomass, potential nitrification, and soil community metabolic profiles in three different soils
Publisher: Springer Science and Business Media LLC
Date: 04-2016
Impact of Poultry Processing Operating Parameters on Bacterial Transmission and Persistence on Chicken Carcasses and Their Shelf Life
Publisher: American Society for Microbiology
Date: 02-06-2020
DOI: 10.1128/AEM.00594-20
Abstract: Culture-based and culture-independent approaches were utilized to reveal bacterial community changes on chicken carcasses at different processing steps and potential routes from the local processing environment. Current commercial processing effectively reduced bacterial loads on carcasses. Poultry processes have similar processes across facilities, but various processing arrangements and operating parameters could impact the bacterial transmission and persistence on carcasses differently. This study showed the use of a single tunnel incorporating scalding, defeathering and plucking may undesirably distribute the thermoduric bacteria, e.g., C ylobacter and Anoxybacillus , between the local environment and carcasses, whereas this does not occur when these steps are separated. The length of immersion and air chilling also impacted bacterial ersity on carcasses. Air chilling can transfer Pseudomonas from wall surfaces onto carcasses this may subsequently influence chicken product shelf life. This study helps poultry processors understand the impact of current commercial processing and improve the chicken product quality and safety.
Draft Genome Sequences of Three Sub-Antarctic Rhodococcus spp., Including Two Novel Psychrophilic Genomospecies
Publisher: American Society for Microbiology
Date: 07-09-2017
Abstract: The draft genome sequences of three sub-Antarctic Rhodococcus sp. strains—1159, 1163, and 1168—are reported here. The estimated genome sizes were 7.09 Mb with a 62.3% GC content for strain 1159, 4.45 Mb with a 62.3% GC content for strain 1163, and 5.06 Mb with a 62.10% GC content for strain 1168.
Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of Massilia La Scola et al. 2000 into Telluria Bowman et al. 1993, Mokoshia gen. nov. and Zemynaea gen. nov.
Publisher: Microbiology Society
Date: 17-08-2023
Abstract: Based on genome-wide data, Massilia species belonging to the clade including Telluria mixta LMG 11547 T should be entirely transferred to the genus Telluria owing to the nomenclatural priority of the type species Telluria mixta . This results in the transfer of 35 Massilia species to the genus Telluria . The presented data also supports the creation of two new genera since peripherally branching Massilia species are distinct from Telluria and other related genera. It is proposed that 13 Massilia species are transferred to Mokoshia gen. nov. with the type species designated Mokoshia eurypsychrophila comb. nov. The species Massilia arenosa is proposed to belong to the genus Zemynaea gen. nov. as the type species Zemynaea arenosa comb. nov. The genome-wide analysis was well supported by canonical ordination analysis of Enzyme Commission (EC) codes annotated from genomes via pannzer 2. This new approach was performed to assess the conclusions of the genome-based data and reduce possible ambiguity in the taxonomic decision making. Cross-validation of EC code data compared within canonical plots validated the reclassifications and correctly visualized the expected genus-level taxonomic relationships. The approach is complementary to genome-wide methodology and could be used for testing sequence alignment based data across genetically related genera. In addition to the proposed broader reclassifications, invalidly described species ‘ Massilia antibiotica ’, ‘ Massilia aromaticivorans ’, ‘ Massilia cellulosiltytica ’ and ‘ Massilia humi ’ are described as Telluria antibiotica sp. nov., Telluria aromaticivorans sp. nov., Telluria cellulosilytica sp. nov. and Pseudoduganella humi sp. nov., respectively. In addition, Telluria chitinolytica is reclassified as Pseudoduganella chitinolytica comb. nov. The use of combined genome-wide and annotation descriptors compared using canonical ordination clarifies the taxonomy of Telluria and its sibling genera and provides another way to evaluate complex taxonomic data.
Loktanella agnita sp. nov. and Loktanella rosea sp. nov., from the north-west Pacific Ocean
Publisher: Microbiology Society
Date: 09-2005
Abstract: One whitish and four pinkish strains of Gram-negative, non-motile, aerobic bacteria were isolated from sea-water and sediment s les collected in Chazhma Bay (Sea of Japan, Pacific Ocean). Analysis of 16S rRNA gene sequences revealed that these strains belonged to the ‘ Alphaproteobacteria ’, having highest sequence similarity of about 94–97 % with species of the genus Loktanella . None of the strains degraded gelatin, casein, chitin, agar, DNA or starch and they had limited ability to utilize carbon sources. The four pinkish strains, Fg36 T , Fg1, Fg116 and Fg117, degraded Tween 80. Sea-water strain R10SW5 T grew at 3–6 % NaCl and a temperature range of 8–35 °C, whilst strains Fg36 T , Fg1, Fg116 and Fg117 grew at NaCl concentrations of 1–12 % and a temperature range of 4–35 °C. Phosphatidylglycerol (58/79 %), diphosphatidylglycerol (11/6 %) and phosphatidylcholine (28/22 %) were the major phospholipids. The predominant fatty acids were 16 : 0 (12·2/8·6 %) and 18 : 1 ω 7 (76·6/68·4 %). The DNA G+C content of strain R10SW5 T was 59·1 mol% and those of the four pinkish strains ranged from 60·5 to 61·8 mol%. Based on the results of phenotypic, genotypic, chemotaxonomic and phylogenetic investigation, two novel species, Loktanella agnita sp. nov. and Loktanella rosea sp. nov., are proposed. The type strains are R10SW5 T (=KMM 3788 T =CIP 107883 T ) and Fg36 T (=KMM 6003 T =CIP 107851 T =LMG 22534 T ), respectively.
Investigation of the Listeria monocytogenes Scott A Acid Tolerance Response and Associated Physiological and Phenotypic Features via Whole Proteome Analysis
Publisher: American Chemical Society (ACS)
Date: 15-03-2012
DOI: 10.1021/PR201137C
Abstract: The global proteomic responses of the foodborne pathogen Listeria monocytogenes strain Scott A, during active growth and transition to the stationary growth phase under progressively more acidic conditions, created by addition of lactic acid and HCl, were investigated using label-free liquid chromatography/tandem mass spectrometry. Approximately 56% of the Scott A proteome was quantitatively assessable, and the data provides insight into its acquired acid tolerance response (ATR) as well as the relation of the ATR to the growth phase transition. Alterations in protein abundance due to acid stress were focused in proteins belonging to the L. monocytogenes common genome, with few strain-dependent proteins involved. However, one of the two complete prophage genomes appeared to enter lysogeny. During progressive acidification, the growth rate and yield were reduced 55% and 98%, respectively, in comparison to nonacidified control cultures. The maintenance of the growth rate was determined to be connected to activation of cytoplasmic pH homeostatic mechanisms while cellular reproductive-related and cell component turnover proteins were markedly more abundant in acid stressed cultures. Cell biomass accumulation was impeded predominantly due to repression of phosphodonor-linked enzymes involved with sugar phosphotransfer, glycolysis, and cell wall polymer biosynthesis. Acidification caused a shift from heterofermentation to an oxidatively stressed state in which ATP appears to be generated mainly through the pyruvate dehydrogenase yruvate oxidase hosphotransacetylase/acetate kinase and branched chain acid dehydrogenase pathways. Analysis of regulons indicated energy conservation occurs due to repression by the GTP/isoleucine sensor CodY and also the RelA mediated stringent response. Whole proteome analysis proved to be an effective way to highlight proteins involved with the acquisition of the ATR.
Modelling viability of Listeria monocytogenes in paneer
Publisher: Elsevier BV
Date: 08-2021
Degradation of nonane by bacteria from Antarctic marine sediment
Publisher: Springer Science and Business Media LLC
Date: 18-06-2004
Approaches for the characterization and description of novel methanotrophic bacteria
Publisher: Elsevier
Date: 2011
Methylomonas fodinarum sp. nov. and Methylomonas aurantiaca sp.nov.: Two Closely Related Type I Obligate Methanotrophs
Publisher: Elsevier BV
Date: 08-1990
qPCR quantification of Carnobacterium maltaromaticum, Brochothrix thermosphacta, and Serratia liquefaciens growth kinetics in mixed culture
Publisher: Elsevier BV
Date: 08-2020
Flavobacterial response to organic pollution
Publisher: Inter-Research Science Center
Date: 24-04-2008
DOI: 10.3354/AME01174
Evaluation of thermal inactivation of Escherichia coli using microelectrode ion flux measurements with osmotic stress
Publisher: Oxford University Press (OUP)
Date: 06-01-2012
Detection, quantification, and characterization of Salmonella enterica in mango, tomato, and raw chicken purchased in the central region of Mexico
Publisher: Wiley
Date: 26-12-2021
Abstract: To estimate human exposure to Salmonella enterica , it is essential to understand the pathogen distribution and characteristics. Prevalence and concentration of S. enterica were determined in mango, tomato, and raw chicken s les purchased in three states (Aguascalientes, Querétaro, and Guadalajara) located in the central region of Mexico during two seasons. In addition, S. enterica isolates were characterized by absence resence of 13 virulence genes (chromosomal, prophage, and plasmid) and resistance to 14 antibiotics. A total of 300 s les of mango, 272 of tomato, and 354 of raw chicken were analyzed. The mean of the prevalence (24.9%) and concentration (−0.61 Log MPN/g) of S. enterica in chicken was higher than in mango (1.3%, −1.7 Log MPN/g) and tomato (1.1%, −1.7 Log MPN). Among S. enterica isolates (284), there were 7 different virulotypes, belonging 68.7% of isolates to V2 there was high variability in the presence of mobile genetic elements. The occurrence of specific mobile elements ranged from 81.4% to 11.3% among isolates. Among the isolates, 91.5% were resistant to at least one antibiotic with icillin being the most frequent 54.9% of isolates were multidrug resistant. Data from this study can be used for quantitative microbial risk assessment of S. enterica related to mango, tomato, and raw chicken consumption in the central region of Mexico. Data on the prevalence and concentration of Salmonella enterica obtained in this study can be used to estimate the exposure assessment for the consumption of mango, tomato, and chicken in the central region of Mexico. In addition, the characteristics of the S. enterica isolates could be used to select representative strains for future studies to evaluate the intraspecies variability.
Draft Genome Sequences of Two Lactobacillus casei Strains Isolated from Cheddar Cheese and a Fermented Milk Drink
Publisher: American Society for Microbiology
Date: 02-11-2017
Abstract: MiSeq Illumina shotgun sequencing technology was used to sequence two Lactobacillus casei strains, designated strains GCRL 163 and MJA 12. The estimated genome sizes for GCRL 163 and MJA 12 were 2.9 Mb and 3.1 Mb, with 46.35% and 46.31% GC contents, respectively.
Shewanella affinis sp. nov., isolated from marine invertebrates
Publisher: Microbiology Society
Date: 07-2004
Abstract: Four marine bacterial strains, designated KMM 3587 T , KMM 3586, KMM 3821 and KMM 3822, were isolated from the sipuncula Phascolosoma japonicum , a common inhabitant of Troitza Bay in the Gulf of Peter the Great (Sea of Japan region), and from an unidentified hydrocoral species collected in Makarov Bay (Iturup Islands), Kuril Islands, North-West Pacific Ocean. The strains were characterized to clarify their taxonomic position. 16S rRNA gene sequences of KMM 3587 T and KMM 3586 indicated 99 % similarity to Shewanella colwelliana . Despite such a high level of 16S rRNA gene sequence similarity, DNA–DNA hybridization experiments demonstrated only 45–52 % binding with DNA of S. colwelliana ATCC 39565 T . The DNA G+C contents of the novel strains were 45 mol% and the shared level of DNA hybridization was conspecific (81–97 %), indicating that they represent a single genospecies. The novel strains were mesophilic (able to grow at 10–34 °C), neutrophilic and haemolytic, and able to degrade gelatin, casein and Tween 20, 40 and 80, but not starch, agar, elastin, alginate or chitin. The major fatty acids were i13 : 0, i15 : 0, 16 : 0, 16 : 1 ω 7 and 17 : 1 ω 8 (68·9 % of total). The major isoprenoid quinones were Q7 (47–62 %) and Q8 (26–47 %). Eicosapentaenoic acid was produced in minor amounts. Based on these data, the strains are assigned to a novel species, Shewanella affinis sp. nov. (type strain KMM 3587 T =CIP 107703 T =ATCC BAA-642 T ).
Diversity and guaiacol production of Alicyclobacillus spp. from fruit juice and fruit-based beverages
Publisher: Elsevier BV
Date: 12-2019
DOI: 10.1016/J.IJFOODMICRO.2019.108314
Abstract: Alicyclobacillus acidoterrestris is an acido-thermophilic, spore-forming bacterial species that can spoil acidic fruit juice and fruit-based beverages. The metabolism of taint compounds by this bacterial species has led to its status as a targeted microorganism in the fruit juice industry. This study aims to assess the genetic ersity of Alicyclobacillus spp. including A. acidoterrestris and its correlation to spoilage taint metabolism. Alicyclobacillus cultures, which were previously isolated from a wide range of domestic and international products including fruit juice, fruit drinks and fruit juice concentrates, were subjected to DNA fingerprint analysis by using randomly lified polymorphic DNA (RAPD) - polymerase chain reaction. Isolates were classified on the basis of their RAPD profile and the results were used to select representative strains to undergo taint production assessment. The taint guaiacol produced by Alicyclobacillus spp. was measured by headspace gas chromatography and mass spectrometry. From produced RAPD profiles, two genotypic groups and two sub-groups were identified. The groups were independent of product types and geographical origins. A significant number of isolates were clustered in genotypic group I, including A. acidoterrestris ATCC 49025. These isolates produced significant levels of guaiacol, 8.7 mg/L on average. A smaller number of isolates was found in genotypic group II including A. acidocaldarius and they produced no guaiacol. Primer F-64 was useful to identify Alicyclobacillus at the species level, and permitted rapid identification of strains producing fruit juice taint compounds such as guaiacol.
Characterisation of Listeria monocytogenes food-associated isolates to assess environmental fitness and virulence potential
Publisher: Elsevier BV
Date: 07-2021
Effects of biochar and compost amendments on soil physico-chemical properties and the total community within a temperate agricultural soil
Publisher: Elsevier BV
Date: 02-2016
Physiological Response of Escherichia coli O157:H7 Sakai to Dynamic Changes in Temperature and Water Activity as Experienced during Carcass Chilling
Publisher: Elsevier BV
Date: 11-2016
Integrated Transcriptomic and Proteomic Analysis of the Physiological Response of Escherichia coli O157:H7 Sakai to Steady-state Conditions of Cold and Water Activity Stress
Publisher: Elsevier BV
Date: 2012
The fungal community structure of barley malts from diverse geographical regions correlates with malt quality parameters
Publisher: Elsevier BV
Date: 12-2015
DOI: 10.1016/J.IJFOODMICRO.2015.08.019
Abstract: Malt is a preferred base for fermentations that produce beer or whisky. Barley for malt is grown under erse environments in different geographical locations. Malt provides an ecological niche for a varied range of microorganisms with both positive and negative effects on its quality for brewing. Little information exists in the literature on the microbial community structure of Australian malt as well as broader global geographical differences in the associated fungal and bacterial communities. The aims of the present study were to compare the bacterial and fungal community structures of Australian commercial malt with its international counterparts originating from different geographical regions using terminal restriction fragment length polymorphism (TRFLP) fingerprinting and clone library analyses of ribosomal RNA genes. Further, the relationship between malt associated microbial communities and conventional malt quality parameters was also compared. Results showed that differences in fungal communities of malts from different geographical location were more pronounced than bacterial communities. TRFLP analysis discriminated high quality commercial malts with low fungal loads from malts deliberately infected with fungal inocula (Fusarium/Penicillium). Malt moisture, beta-amylase, α-amylase and limit dextrinase contents showed significant correlations with fungal community structure. This investigation concluded that fungal community structure was more important to subsequent malt quality outcomes than bacteria.
Short-term impact of biochar amendments on eukaryotic communities in three different soils
Publisher: Springer Science and Business Media LLC
Date: 24-10-2018
DOI: 10.1007/S10482-018-1191-9
Abstract: This study determined the loading impacts of wood-based biochar on the eukaryotic community in three different soils (brown sandy loam-BSL, red loam-RL and a black clay loam-BCL) using a pot trial conducted over 10 months. Soil analysis and 18S rRNA gene sequencing performed using the Illumina MiSeq platform was carried out to evaluate the changes in eukaryotic community composition in relation to different added amounts of biochar. It was found that biochar addition had a negligible effect on ersity parameters in the brown sandy loam Kurosol (BSL) and red loam Dermosol (RL) soils. There were, however, significant changes in eukaryotic community composition of these biochar amended soils. These changes were most discernible in the lighter (low clay content) BSL soil for the fungal communities (F = 3.0106, p = 0.0003) present and also when total eukaryotes were considered (F = 2.3907, p = 0.0002). In this respect Glomeromycota seem to be slightly promoted in the lighter BSL soils, which might be due to increased soil porosity and soil chemical fertility. Clay rich BCL soil community structure correlated to a greater degree with soil chemistry influenced by biochar addition. The results showed that soil microeukaryotes were affected by short term carbon amendment, though to a limited extent. The limited effect of biochar loading rates on the soil microbiology could be due to the short incubation period, the lack of added fertiliser nutrients, and also the inherent stability of the soil eukaryotic community. The data suggested the impacts that were observed however included important plant symbiotic organisms. The results also imply biochar applications at different loading levels have differential effects on soil microeurokaryotes in relation to soil properties in particular clay content.
Development of a fully suspended, multi stage bioreactor system for trichloroethylene degradation based on soluble monooxygenase cometabolism
Publisher: Informa UK Limited
Date: 1996
The efficacy of preharvest application of electrolyzed water and chemical sanitizers against foodborne pathogen surrogates on leafy green vegetables
Publisher: Wiley
Date: 20-03-2023
DOI: 10.1111/JFS.13051
Abstract: Preharvest control strategies, to reduce or eliminate pathogenic bacteria in leafy vegetables that may be consumed raw, may provide additional food safety protection and shelf life quality extension beyond what is possible to achieve with postharvest sanitation alone. The aim of this study was to characterize the efficacy and effect of contact time of electrolyzed water (e‐water), 1‐bromo‐3‐chloro‐5‐dimethylhydantoin (BCDMH), and peracetic acid (PAA) at 80 and 150 ppm against pathogen surrogates Escherichia coli M23 ( E. coli M23)and Listeria innocua ATCC 33090 ( L. innocua ), and a representative spoilage microorganism Pseudomonas fluorescens ( P. fluorescens ) on leafy green vegetables (LGV) mizuna, rocket (arugula), and red chard. Each of the leafy vegetables has a distinctly different leaf architectures that could alter the effectiveness of preharvest sanitation treatments. e‐Water, BCDMH and PAA were equally effective in inactivating plant total viable count, E. coli M23, L. innocua and P. fluorescens (reduction compared to water control—0.5–4.0 log CFU/g). On average an additional 0.8 (0.4–1.1) log CFU/g inactivation was obtained by increasing sanitizer contact time from 30 min to 2 h, whereas increasing sanitizer concentrations produced, at maximum, an extra 0.5 log CFU/g inactivation. These findings suggest that e‐water, BCDMH, and PAA are all useful for in‐field preharvest application on a wide range of plants and increasing contact time rather than concentration improves sanitation efficacy.
Effect of Environmental Factors on Intra-Specific Inhibitory Activity of Carnobacterium maltaromaticum
Publisher: MDPI AG
Date: 14-09-2017
A comparison of the short term effects of diesel fuel and lubricant oils on Antarctic benthic microbial communities
Publisher: Elsevier BV
Date: 08-2005
MudPIT analysis of alkaline tolerance by Listeria monocytogenes strains recovered as persistent food factory contaminants
Publisher: Elsevier BV
Date: 05-2012
Abstract: Alkaline solutions are used to clean food production environments but the role of alkaline resistance in persistent food factory contamination by Listeria monocytogenes is unknown. We used shotgun proteomics to characterise alkaline adapted L. monocytogenes recovered as persistent and transient food factory contaminants. Three unrelated strains were studied including two persistent and a transient food factory contaminant determined using multilocus sequence typing (MLST). The strains were adapted to growth at pH 8.5 and harvested in exponential phase. Protein extracts were analysed using multidimensional protein identification technology (MudPIT) and protein abundance compared by spectra counting. The strains elicited core responses to alkaline growth including modulation of intracellular pH, stabilisation of cellular processes and reduced cell- ision, independent to lineage, MLST or whether the strains were transient or persistent contaminants. Alkaline adaptation by all strains corresponded to that expected in stringent-response induced cells, with protein expression supporting metabolic shifts concordant with elevated alarmone production and indicating that the alkaline-stringent response results from energy rather than nutrient limitation. We believe this is the first report describing induction of a stringent response in different L. monocytogenes strains by alkaline pH under non-limiting growth conditions. The work emphasises the need for early intervention to avoid persistent food factory contamination by L. monocytogenes.
Global Genome Response of Escherichia coli O157∶H7 Sakai during Dynamic Changes in Growth Kinetics Induced by an Abrupt Downshift in Water Activity
Publisher: Public Library of Science (PLoS)
Date: 03-03-2014
Proteomic analysis of Lactobacillus casei GCRL163 cell-free extracts reveals a SecB homolog and other biomarkers of prolonged heat stress
Publisher: Public Library of Science (PLoS)
Date: 25-10-2018
Marinobacter algicola sp. nov., isolated from laboratory cultures of paralytic shellfish toxin-producing dinoflagellates
Publisher: Microbiology Society
Date: 03-2006
Abstract: Phylogenetic and phenotypic analysis of cultivable marine bacteria isolated from laboratory cultures of two paralytic shellfish toxin-producing dinoflagellates, Gymnodinium catenatum and Alexandrium tamarense , showed the presence of a novel group of Gram-negative, aerobic, moderately halophilic and hydrocarbon-degrading bacteria, related to the genus Marinobacter . The strains, designated DG893 T , DG1136 and ATAM407-13, grew optimally in media with 3–6 % NaCl and at 25–30 °C, and all could utilize n-hexadecane and n-tetradecane as the sole carbon source. The strains had a 16S rRNA gene sequence similarity of 94·2–94·3 % to Marinobacter hydrocarbonoclasticus ATCC 27132, and a similarity of 97·5–97·8 % to the closest phylogenetically related type strain, Marinobacter flavimaris DSM 16070 T . DNA–DNA hybridization levels to M. flavimaris and other Marinobacter type strains were ⩽42 %, while DNA–DNA reassociation values among DG893 T , DG1136 and ATAM407-13 were ⩾83 %. The DNA G+C content was 54–55 mol% and the major isoprenoid quinone was ubiquinone-9. On the basis of phenotypic, chemotaxonomic, DNA–DNA hybridization and phylogenetic analysis, it is proposed that these three strains represent a novel species, Marinobacter algicola sp. nov. The type strain is DG893 T (=DSM 16394 T =NCIMB 14009 T ).
International committee on systematics of prokaryotes subcommittee on the taxonomy of aerobic bacteroidetes (Formerly flavobacterium and cytophaga-like bacteria). minutes of the meeting, 30 july 2014, Montréal, Canada
Publisher: Microbiology Society
Date: 02-2017
Improving the cost efficiency of quality assurance screening for mycotoxins in malting barley
Publisher: Informa UK Limited
Date: 04-2009
Listeria monocytogenes: illuminating adaptation with proteomics
Publisher: CSIRO Publishing
Date: 2013
DOI: 10.1071/MA13026
Early flower development in Arabidopsis
Publisher: Oxford University Press (OUP)
Date: 08-1990
DOI: 10.1105/TPC.2.8.755
Salmonid gill bacteria and their relationship to amoebic gill disease
Publisher: Wiley
Date: 08-2004
Effects of diesel and lubricant oils on Antarctic benthic microbial communities over five years
Publisher: Inter-Research Science Center
Date: 10-2010
DOI: 10.3354/AME01441
The importance of soil characteristics to the structure of alkane-degrading bacterial communities on sub-Antarctic Macquarie Island
Publisher: Elsevier BV
Date: 11-2010
Shewanella olleyana sp nov., a marine species isolated from a temperate estuary which produces high levels of polyunsaturated fatty acids
Publisher: Microbiology Society
Date: 11-2002
Algicidal bacteria associated with blooms of a toxic dinoflagellate in a temperate Australian estuary
Publisher: Inter-Research Science Center
Date: 2002
DOI: 10.3354/MEPS244001
The effects of glucose on microbial spoilage of vacuum-packed lamb
Publisher: Elsevier BV
Date: 06-2022
DOI: 10.1016/J.MEATSCI.2022.108781
Abstract: Vacuum-packed lamb produced in Australia has a shelf-life of 80-90 days under export conditions (-1 to 0 °C). However, access to some markets could involve >90 days transit time. Studies to understand the potential mechanisms of microbial spoilage of vacuum-packed lamb are, therefore, important to assist the development of shelf-life extension methods. Here, we investigated the effects of glucose on the shelf-life of vacuum-packed lamb. This was done by adding glucose (up to 4.64 mmol/kg) to the surface of meat and conducting a series of shelf-life trials, in which the sensorial qualities, bacterial growth, pH, and residual glucose and lactic acid were measured over time. Based on sensory analysis glucose extended the shelf-life, ranging from 8% to >76% increase relative to the control. Glucose reduced meat pH, potentially affecting the microbial community composition and the accumulation of spoilage metabolites. These results indicate that glucose plays an important role in microbial spoilage of vacuum-packed lamb possibly by pH reduction.
Arcobacter halophilus sp. nov., the first obligate halophile in the genus Arcobacter
Publisher: Microbiology Society
Date: 05-2005
Abstract: A Gram-negative bacterium, designated LA31B T , was isolated from water collected from a hypersaline lagoon on Laysan Atoll in the north-western Hawaiian Islands. Single cells of LA31B T were slightly curved but became helical as their length increased. Preliminary characterization based on 16S rRNA gene sequence analysis showed that LA31B T shared 96·0 % identity with an Arcobacter sp. isolated from a cyanobacterial mat in hypersaline Lake Sinai, and 94 % identity with Arcobacter nitrofigilis , the type species of the genus Arcobacter . A polyphasic taxonomic study was conducted and confirmed the phylogenetic affiliation of strain LA31B T to the genus Arcobacter . However, LA31B T was found to be distinct from all recognized Arcobacter species, by a comprehensive biochemical test analysis, whole-cell fatty acid profiling, DNA G+C content (35 mol% in LA31B T ) and degree of DNA–DNA reassociation. Most notably, LA31B T was found to be an obligate halophile, a hitherto undescribed feature among recognized Arcobacter species. These data indicate that LA31B T should be considered to represent a novel species in the genus Arcobacter , for which the name Arcobacter halophilus sp. nov. is proposed. This is the first obligately halophilic member of the genus. The type strain is LA31B T (=ATCC BAA-1022 T =CIP 108450 T ).
Attached and planktonic listeria monocytogenes global proteomic responses and associated influence of strain genetics and temperature
Publisher: American Chemical Society (ACS)
Date: 09-01-2015
DOI: 10.1021/PR501114E
Abstract: Contamination of industrial and domestic food usage environments by the attachement of bacterial food-borne pathogen Listeria monocytogenes has public health and economic implications. Comprehensive proteomics experiments using label-free liquid chromatography/tandem mass spectrometry were used to compare the proteomes of two different L. monocytogenes strains (Siliken_1/2c and F2365_4b), which show very different capacities to attach to surfaces. Growth temperature and strain type were highly influential on the proteomes in both attached and planktonic cells. On the basis of the proteomic data, it is highly unlikely that specific surface proteins play a direct role in adherence to inanimate surfaces. Instead, strain-dependent responses related to cell envelope polymer biosynthesis and stress response regulation likely contribute to a different ability to attach and also to survive external stressors. Collectively, the ergent proteome-level responses observed define strain- and growth-temperature-dependent differences relevant to attachment efficacy, highlight relevant proteins involved in stress protection in attached cells, and suggest that strain differences and growth conditions are important in relation to environmental persistence.
Prolonged Heat Stress of Lactobacillus paracasei GCRL163 Improves Binding to Human Colorectal Adenocarcinoma HT-29 Cells and Modulates the Relative Abundance of Secreted and Cell Surface-Locate
Publisher: American Chemical Society (ACS)
Date: 28-02-2020
Can public works increase equilibrium wages? Evidence from India’s National Rural Employment Guarantee
Publisher: Elsevier BV
Date: 03-2018
Developments with Antarctic microorganisms: Culture collections, bioactivity screening, taxonomy, PUFA production and cold-adapted enzymes
Publisher: Elsevier BV
Date: 06-1999
Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family
Publisher: Microbiology Society
Date: 05-2002
Utility of gel-free, label-free shotgun proteomics approaches to investigate microorganisms
Publisher: Springer Science and Business Media LLC
Date: 25-02-2011
DOI: 10.1007/S00253-011-3172-Z
Abstract: This review will examine the current situation with label-free, quantitative, shotgun-oriented proteomics technology and discuss the advantages and limitations associated with its capability in capturing and quantifying large portions of proteomes of microorganisms. Such an approach allows (1) comparisons between physiological or genetic states of organisms at the protein level, (2) 'painting' of proteomic data onto genome data-based metabolic maps, (3) enhancement of the utility of genomic data and finally (4) surveying of non-genome sequenced microorganisms by taking advantage of available inferred protein data in order to gain new insights into strain-dependent metabolic or physiological capacities. The technology essentially is a powerful addition to systems biology with a capacity to be used to ask hypothesis-driven 'top-down' questions or for more empirical 'bottom-up' exploration.
Comparative genomic analysis reveals that the 20K and 38K prophages in listeria monocytogenes serovar 4a strains Lm850658 and M7 contribute to genetic diversity but not to virulence
Publisher: Korean Society for Microbiology and Biotechnology
Date: 28-01-2015
Abstract: Listeria monocytogenes is a foodborne pathogen of considerable genetic ersity with varying pathogenicity. Initially, we found that the strain M7 was far less pathogenic than the strain Lm850658 though both are serovar 4a strains belonging to the lineage III. Comparative genomic approaches were then attempted to decipher the genetic basis that might govern the strain-dependent pathotypes. There are 2,761 coding sequences of 100% nucleotide identity between the two strains, accounting for 95.7% of the total genes in Lm850658 and 92.7% in M7. Lm850658 contains 33 specific genes, including a novel 20K prophage whereas strain M7 has 130 specific genes, including two large prophages (38K and 44K). To examine the roles of these specific prophages in pathogenicity, the 20K and 38K prophages were deleted from their respective strains. There were virtually no differences of pathogenicity between the deletion mutants and their parent strains, although some putative virulent factors like VirB4 are present in the 20K region or holin-lysin in the 38K region. In silico PCR analysis of 29 listeria genomes show that only strain SLCC2540 has the same 18 bp integration hotspot as Lm850658, whereas the sequence identity of their 20K prophages is very low (21.3%). The 38K and 44K prophages are located in two other different hotspots and are conserved in low virulent strains M7, HCC23, and L99. In conclusion, the 20K and 38K prophages of L. monocytogenes serovar 4a strains Lm850658 and M7 are not related to virulence but contribute to genetic ersity.
Advantages and applications of gel-free proteomic approaches in the study of prokaryotes
Publisher: Elsevier
Date: 2014
Effect of glucose, pH and lactic acid on Carnobacterium maltaromaticum, Brochothrix thermosphacta and Serratia liquefaciens within a commercial heat-shrunk vacuum-package film
Publisher: Elsevier BV
Date: 10-2020
International Committee on Systematics of Prokaryotes: Subcommittee on the Taxonomy of Aerobic Bacteroidetes (formerly Flavobacterium and Cytophaga-like bacteria)
Publisher: Microbiology Society
Date: 11-2020
Abstract: Minutes of the meeting: 15 November 2017 (Skype meeting).
Information systems in food safety management
Publisher: Elsevier BV
Date: 12-2006
DOI: 10.1016/J.IJFOODMICRO.2006.04.048
Abstract: Information systems are concerned with data capture, storage, analysis and retrieval. In the context of food safety management they are vital to assist decision making in a short time frame, potentially allowing decisions to be made and practices to be actioned in real time. Databases with information on microorganisms pertinent to the identification of foodborne pathogens, response of microbial populations to the environment and characteristics of foods and processing conditions are the cornerstone of food safety management systems. Such databases find application in: Identifying pathogens in food at the genus or species level using applied systematics in automated ways. Identifying pathogens below the species level by molecular subtyping, an approach successfully applied in epidemiological investigations of foodborne disease and the basis for national surveillance programs. Predictive modelling software, such as the Pathogen Modeling Program and Growth Predictor (that took over the main functions of Food Micromodel) the raw data of which were combined as the genesis of an international web based searchable database (ComBase). Expert systems combining databases on microbial characteristics, food composition and processing information with the resulting "pattern match" indicating problems that may arise from changes in product formulation or processing conditions. Computer software packages to aid the practical application of HACCP and risk assessment and decision trees to bring logical sequences to establishing and modifying food safety management practices. In addition there are many other uses of information systems that benefit food safety more globally, including: Rapid dissemination of information on foodborne disease outbreaks via websites or list servers carrying commentary from many sources, including the press and interest groups, on the reasons for and consequences of foodborne disease incidents. Active surveillance networks allowing rapid dissemination of molecular subtyping information between public health agencies to detect foodborne outbreaks and limit the spread of human disease. Traceability of in idual animals or crops from (or before) conception or germination to the consumer as an integral part of food supply chain management. Provision of high quality, online educational packages to food industry personnel otherwise precluded from access to such courses.
The phylogenetic position of the family methylococcaceae
Publisher: Microbiology Society
Date: 1995
DOI: 10.1099/00207713-45-1-182
Abstract: The 16S ribosomal DNA-based phylogenetic positions of various members of the Methylococcaceae (group I methanotrophs) were investigated. The Methylococcaceae as a whole formed a distinct branch in the gamma sub ision of the Proteobacteria, and this branch had five distinct subbranches. On the basis of a number of phenotypic traits, phospholipid fatty acid patterns, and the results of a 16S ribosomal DNA analysis, we determined that the species belonging to one subbranch, Methylobacter albus, Methylobacter agilis, and Methylobacter pelagicus, formed a distinct group that could be differentiated from other members of the genus Methylobacter, which grouped in an adjacent subbranch. We propose that these species belong to a new taxon, Methylomicrobium gen. nov.
Application of Thin-Layer Chromatography-Flame Ionization Detection (TLC-FID) to Total Lipid Quantitation in Mycolic-Acid Synthesizing Rhodococcus and Williamsia Species
Publisher: MDPI AG
Date: 29-02-2020
DOI: 10.3390/IJMS21051670
Abstract: In addition to cell membrane phospholipids, Actinobacteria in the order Corynebacteriales possess a waxy cell envelope containing mycolic acids (MA). In optimized culture condition, some species can also accumulate high concentrations of intracellular triacylglycerols (TAG), which are a potential source of biodiesel. Bacterial lipid classes and composition alter in response to environmental stresses, including nutrient availability, thus understanding carbon flow into different lipid classes is important when optimizing TAG synthesis. Quantitative and qualitative analysis of lipid classes normally requires combinations of different extraction, derivatization, chromatographic and detection methods. In this study, a single-step thin-layer chromatography-flame ionization detection (TLC-FID) technique was applied to quantify lipid classes in six sub-Antarctic Corynebacteriales strains identified as Rhodococcus and Williamsia species. A hexane:diethyl-ether:acetic acid solvent system separated the total cellular lipids extracted from cells lysed by bead beating, which released more bound and unbound MA than sonication. Typical profiles included a major broad non-polar lipid peak, TAG and phospholipids, although trehalose dimycolates, when present, co-eluted with phospholipids. Ultra-performance liquid chromatography-tandem mass-spectrometry and nuclear magnetic resonance spectroscopy detected MA signatures in the non-polar lipid peak and indicated that these lipids were likely bound, at least in part, to sugars from cell wall arabinogalactan. Waxy esters were not detected. The single-solvent TLC-FID procedure provides a useful platform for the quantitation and preliminary screening of cellular lipid classes when testing the impacts of growth conditions on TAG synthesis.
Dark metabolism: a molecular insight into how the Antarctic sea‐ice diatom Fragilariopsis cylindrus survives long‐term darkness
Publisher: Wiley
Date: 07-05-2019
DOI: 10.1111/NPH.15843
Methylosphaera hansonii gen nov, sp nov, a psychrophilic, group I methanotroph from Antarctic marine-salinity, meromictic lakes
Publisher: Microbiology Society
Date: 04-1997
DOI: 10.1099/00221287-143-4-1451
Abstract: Methanotrophic bacteria were enumerated and isolated from the chemocline and surface sediments of marine-salinity Antarctic meromictic lakes located in the Vestfold Hills, Antarctica (68° S 78° E). Most probable number (MPN) analysis indicated that at the chemocline of Ace Lake the methanotroph population made up only a small proportion of the total microbial population and was sharply stratified, with higher populations detected in the surface sediments collected at the edge of Ace Lake and Burton Lake. Methanotrophs were not detected in Pendant Lake. Only a single phenotypic group of methanotrophs was successfully enriched, enumerated and isolated into pure culture from the lake s les. Strains of this group were non-motile, coccoidal in morphology, did not form resting cells, reproduced by constriction, and required seawater for growth. The strains were also psychrophilic, with optimal growth occurring at 10–13°C and maximum growth temperatures of 16–21°C. The ribulose monophosphate pathway but not the serine pathway for incorporation of C 1 compounds was detectable in the strains. The guanine plus cytosine (G+C) content of the genomic DNA was 43–46 mol%. Whole-cell fatty acid analysis indicated that 16:1 ω 8c (37–41%), 16:1 ω 6c (17–19%), 16:1ω7c (15–19%) and 16:0 (14–15%) were the major fatty acids in the strains. 16S rDNA sequence analysis revealed that the strains form a distinct line of descent in the family Methylococcaceae (group I methanotrophs), with the closest relative being the Louisiana Slope methanotrophic mytilid endosymbiont (91∙8–92∙3% sequence similarity). On the basis of polyphasic taxonomic characteristics the Antarctic lake isolates represent a novel group I methanotrophic genus with the proposed name Methylosphaera hansonii (type strain ACAM 549).
Ion transport and osmotic adjustment in Escherichia coli in response to ionic and non‐ionic osmotica
Publisher: Wiley
Date: 2009
DOI: 10.1111/J.1462-2920.2008.01748.X
Abstract: Bacteria respond to osmotic stress by a substantial increase in the intracellular osmolality, adjusting their cell turgor for altered growth conditions. Using Escherichia coli as a model organism we demonstrate here that bacterial responses to hyperosmotic stress specifically depend on the nature of osmoticum used. We show that increasing acute hyperosmotic NaCl stress above approximately 1.0 Os kg(-1) causes a dose-dependent K(+) leak from the cell, resulting in a substantial decrease in cytosolic K(+) content and a concurrent accumulation of Na(+) in the cell. At the same time, isotonic sucrose or mannitol treatment (non-ionic osmotica) results in a gradual increase of the net K(+) uptake. Ion flux data are consistent with growth experiments showing that bacterial growth is impaired by NaCl at the concentration resulting in a switch from net K(+) uptake to efflux. Microarray experiments reveal that about 40% of upregulated genes shared no similarity in their responses to NaCl and sucrose treatment, further suggesting specificity of osmotic adjustment in E. coli to ionic and non-ionic osmotica. The observed differences are explained by the specificity of the stress-induced changes in the membrane potential of bacterial cells highlighting the importance of voltage-gated K(+) transporters for bacterial adaptation to hyperosmotic stress.
Differential gene expression of Listeria monocytogenes during high hydrostatic pressure processing
Publisher: Microbiology Society
Date: 02-2008
DOI: 10.1099/MIC.0.2007/010314-0
Abstract: High hydrostatic pressure processing (HPP) is currently being used as a treatment for certain foods to control the presence of food-borne pathogens, such as Listeria monocytogenes. Genomic microarray analysis was performed to determine the effects of HPP on L. monocytogenes in order to understand how it responds to mechanical stress injury. Reverse transcriptase PCR analysis of tufA and rpoC indicated that the reduction of mRNA expression in HPP-treated cells was dependent on intensity and time of the treatment. Treatments of 400 and 600 MPa for 5 min on cells in the exponential growth phase, though leading to partial or complete cellular inactivation, still resulted in measurable relative differential gene expression. Gene set enrichment analysis indicated that HPP induced increased expression of genes associated with DNA repair mechanisms, transcription and translation protein complexes, the septal ring, the general protein translocase system, flagella assemblage and chemotaxis, and lipid and peptidoglycan biosynthetic pathways. On the other hand, HPP appears to suppress a wide range of energy production and conversion, carbohydrate metabolism and virulence-associated genes accompanied by strong suppression of the SigB and PrfA regulons. HPP also affected genes controlled by the pleotrophic regulator CodY. HPP-induced cellular damage appears to lead to increased expression of genes linked to sections of the cell previously shown in bacteria to be damaged or altered during HPP exposure and suppression of gene expression associated with cellular growth processes and virulence.
Molecules and morphology: Comparative developmental genetics of the Brassicaceae
Publisher: Springer Science and Business Media LLC
Date: 19-06-2006
Patterns of tolerance to heavy metals among methane‐utilizing bacteria
Publisher: Oxford University Press (OUP)
Date: 02-1990
Transcriptomic and Phenotypic Responses of Listeria monocytogenes Strains Possessing Different Growth Efficiencies under Acidic Conditions
Publisher: American Society for Microbiology
Date: 15-07-2010
DOI: 10.1128/AEM.00315-10
Abstract: In an experiment delineating aciduric strains, food and clinical Listeria monocytogenes isolates tended to produce the most biomass whereas ovine and avian strains produced comparatively less biomass when exposed to high levels of sodium diacetate (SD) and potassium sorbate. Compared to reference strains that exhibited greater acid sensitivity, representative food isolates with comparatively good growth capacities in the presence of 21 mM SD at pH 5.0 accumulated reduced levels of acetate anion and K + ion. The aciduric nature of SD-resistant strains was also reflected by comparatively high tolerance to pH 2.4 (HCl) acid challenges, a property boosted by the presence of SD. Exposure to elevated levels of SD (21 mM SD at pH 5.0) was found to have broad effects on gene expression, as differentiated from effects caused by mildly acidic conditions (pH 5.0). SD-resistant strain FW04/0025 was more responsive to elevated SD, increasing the expression of 222 genes ( -fold change [ P 0.05]), compared to the more sensitive EGD reference strain, which exhibited increases in expression of 112 genes. Key differences between the strains in relation to SD-enhanced transcripts were notably associated with the cell envelope, oxidative stress management, and intermediary metabolism. SD thus appears to differentially influence growth efficiency and survival of strains, under conditions relevant to acidic foods, that could be due to altered cell wall and metabolic phenotypes.
Isolation and characterization of two novel ethanol-tolerant facultative-anaerobic thermophilic bacteria strains from waste compost
Publisher: Springer Science and Business Media LLC
Date: 11-03-2006
DOI: 10.1007/S00792-006-0507-2
Abstract: In a search for potential ethanologens, waste compost was screened for ethanol-tolerant thermophilic microorganisms. Two thermophilic bacterial strains, M5EXG and M10EXG, with tolerance of 5 and 10% (v/v) ethanol, respectively, were isolated. Both isolates are facultative anaerobic, non-spore forming, non-motile, catalase-positive, oxidase-negative, Gram-negative rods that are capable of utilizing a range of carbon sources including arabinose, galactose, mannose, glucose and xylose and produce low amounts of ethanol, acetate and lactate. Growth of both isolates was observed in fully defined minimal media within the temperature range 50-80 degrees C and pH 6.0-8.0. Phylogenetic analysis of the 16S rDNA sequences revealed that both isolates clustered with members of subgroup 5 of the genus Bacillus. G+C contents and DNA-DNA relatedness of M5EXG and M10EXG revealed that they are strains belonging to Geobacillus thermoglucosidasius. However, physiological and biochemical differences were evident when isolates M5EXG and M10EXG were compared with G. thermoglucosidasius type strain (DSM 2542(T)). The new thermophilic, ethanol-tolerant strains of G. thermoglucosidasius may be candidates for ethanol production at elevated temperatures.
Ecological and biogeographic relationships of class Flavobacteria in the Southern Ocean
Publisher: Oxford University Press (OUP)
Date: 2005
DOI: 10.1016/J.FEMSEC.2004.09.001
Abstract: The abundance, spatial distribution and ersity of class Flavobacteria were investigated in the Southern Ocean euphotic zone across a latitudinal transect and in the ice pack off Eastern Antarctica. Surface seawater s les filter-fractionated into 0.8 mum particulate and 0.2 m planktonic fractions were investigated with different molecular techniques. The abundance of particle-associated Flavobacteria, ascertained with real-time PCR and DGGE band analysis using Flavobacteria-specific primers, was found to be significantly higher in Polar Front Zone (PFZ) and Antarctic Zone (AZ) water s les than in nutrient limited Temperate Zone (TZ) and Sub-Antarctic Zone (SAZ) waters. Abundance of particle-associated Flavobacteria correlated positively with seawater chlorophyll a and nutrient concentrations, suggesting that increased Flavobacteria abundance may relate to enhanced primary production in the PFZ and AZ. This is supported by comparison of DGGE profiles that demonstrated significant differences in the total Flavobacteria community structure and 16S rRNA gene ersity between s les from the PFZ and AZ and those from TZ and SAZ. Sequence analysis revealed a broad ersity amongst class Flavobacteria in the Southern Ocean with several Flavobacteria clades detected in PFZ and AZ waters not detected in TZ and SAZ waters that putatively represent psychrophilic taxa. Sequence data included a large, so far uncultivated, cosmopolitan phylogenetic clade ("DE cluster 2") that is distributed throughout the Southern Ocean.
Draft genome sequence of the psychrophilic gliding species Gelidibacter algens ACAM 536
Publisher: American Society for Microbiology
Date: 27-10-2016
Abstract: A draft genome sequence was obtained from the type strain of Gelidibacter algens (ACAM 536). This species was isolated from sea-ice diatom assemblages collected from Ellis Fjord, Eastern Antarctica. The genome of ACAM 536 is a single circular chromosome with an estimated size of 4.50 Mbp.
Composition and functionality of bacterioplankton communities in marine coastal zones adjacent to finfish aquaculture
Publisher: Cold Spring Harbor Laboratory
Date: 08-03-2022
DOI: 10.1101/2022.03.07.483349
Abstract: Finfish aquaculture is one of the fastest-growing primary industries globally and is increasingly common in coastal ecosystems. Bacterioplankton is ubiquitous in marine environment and respond rapidly to environmental changes. However, little is known about the effect of the aquaculture in the bacterioplankton community. This study aims to examine aquaculture effects in the composition and functional profiles of the bacterioplankton community using licon sequencing along a distance gradient from two finfish leases in a marine embayment. Our results revealed natural stratification in bacterioplankton strongly associated to NOx, conductivity, salinity, temperature and PO 4 . Among the differentially abundant bacteria in leases, we found members associated with nutrient enrichment and aquaculture activities. Abundant predicted functions near leases were assigned to organic matter degradation, fermentation, and antibiotic resistance. This study provides a first effort to describe changes in the bacterioplankton community composition and function due to finfish aquaculture in a semi-enclosed and highly stratified embayment.
Effects of organic perturbation on marine sediment betaproteobacterial ammonia oxidizers and on benthic nitrogen biogeochemistry
Publisher: Inter-Research Science Center
Date: 19-10-2009
DOI: 10.3354/MEPS08244
Novel Biocontrol Methods for Listeria monocytogenes Biofilms in Food Production Facilities
Publisher: Frontiers Media SA
Date: 03-04-2018
Effects of feed ration and temperature on Chinook salmon (Oncorhynchus tshawytscha) microbiota in freshwater recirculating aquaculture systems
Publisher: Elsevier BV
Date: 10-2021
MudPIT Profiling Reveals a Link between Anaerobic Metabolism and the Alkaline Adaptive Response of Listeria monocytogenes EGD-e
Publisher: Public Library of Science (PLoS)
Date: 14-01-2013
Proposal of Xanthomonas translucens pv. pistaciae pv. nov., pathogenic to pistachio (Pistacia vera)
Publisher: Elsevier BV
Date: 12-2009
DOI: 10.1016/J.SYAPM.2009.08.001
Abstract: Strains of Xanthomonas translucens have caused dieback in the Australian pistachio industry for the last 15 years. Such pathogenicity to a dicotyledonous woody host contrasts with that of other pathovars of X. translucens, which are characterized by their pathogenicity to monocotyledonous plant families. Further investigations, using DNA-DNA hybridization, gyrB gene sequencing and integron screening, were conducted to confirm the taxonomic status of the X. translucens pathogenic to pistachio. DNA-DNA hybridization provided a clear classification, at the species level, of the pistachio pathogen as a X. translucens. In the gyrB-based phylogeny, strains of the pistachio pathogen clustered among the X. translucens pathovars as two distinct lineages. Integron screening revealed that the cassette arrays of strains of the pistachio pathogen were different from those of other Xanthomonas species, and again distinguished two groups. Together with previously reported pathogenicity data, these results confirm that the pistachio pathogen is a new pathovar of X. translucens and allow hypotheses about its origin. The proposed name is Xanthomonas translucens pv. pistaciae pv. nov.
Understanding bacterial communities for informed biosecurity and improved larval survival in Pacific oysters
Publisher: Elsevier BV
Date: 12-2018
Auxin-dependent patterning and gamete specification in the Arabidopsis female gametophyte
Publisher: American Association for the Advancement of Science (AAAS)
Date: 26-06-2009
Abstract: The development of the specialized cells that make up the female reproductive unit in flowering plants, the gametophyte, requires the hormone auxin. However, auxin's function and movement to and within these cells are unclear. Pagnussat et al. (p. 1684 , published online 4 June see the Perspective Friedman ) provide evidence that auxin is synthesized at specific positions within the female gametophyte and exerts a positional effect and that a gradient of auxin controls patterning of these specialized cells.
International Committee on Systematics of Prokaryotes: Subcommittee on the Taxonomy of Aerobic Bacteroidetes (formerly Flavobacterium and Cytophaga-like bacteria). Minutes of the open meeting, 10 July 2019, Glasgow, UK
Publisher: Microbiology Society
Date: 14-08-2023
Chemical characterization of exopolysaccharides from Antarctic marine bacteria
Publisher: Springer Science and Business Media LLC
Date: 05-2005
DOI: 10.1007/S00248-004-0093-8
Abstract: Exopolysaccharides (EPS) may have an important role in the Antarctic marine environment, possibly acting as ligands for trace metal nutrients such as iron or providing cryoprotection for growth at low temperature and high salinity. Ten bacterial strains, isolated from Southern Ocean particulate material or from sea ice, were characterized. Whole cell fatty acid profiles and 16S rRNA gene sequences showed that the isolates included representatives of the genera Pseudoalteromonas, Shewanella, Polaribacter, and Flavobacterium as well as one strain, which constituted a new bacterial genus in the family Flavobacteriaceae. The isolates are, therefore, members of the "Gammaproteobacteria" and Cytophaga-Flexibacter-Bacteroides, the taxonomic groups that have been shown to dominate polar sea ice and seawater microbial communities. Exopolysaccharides produced by Antarctic isolates were characterized. Chemical composition and molecular weight data revealed that these EPS were very erse, even among six closely related Pseudoalteromonas isolates. Most of the EPS contained charged uronic acid residues several also contained sulfate groups. Some strain produced unusually large polymers (molecular weight up to 5.7 MDa) including one strain in which EPS synthesis is stimulated by low temperature. This study represents a first step in the understanding of the role of bacterial EPS in the Antarctic marine environment.
Bacterial community shifts in organically perturbed sediments
Publisher: Wiley
Date: 29-09-2007
DOI: 10.1111/J.1462-2920.2006.01110.X
Abstract: Bacterial abundance, ersity and sediment function were investigated in organically perturbed sediments under Tasmanian salmon (Salmo salar) farms and adjacent reference sites. Bacterial numbers increased as farming and organic loading progressed through the farm stocking cycle and declined during the fallow period, although not to prestocking levels. Bacterial numbers ranged between approximately 2 x 10(8) and 3 x 10(9) cells per gram of sediment and were higher at cage sites than reference sites. Microelectrode and respiration data also demonstrated a clear effect of organic loading on sediments. Denaturing gradient gel electrophoresis (DGGE) showed that bacterial communities shifted both in response to farm loading and its cessation. A seasonal effect on microbial communities was also evident. Although bacterial communities did shift again during the fallowing period, this shift was not necessarily a return to preloading communities. The complexity of community shifts may be affected by the vast functional redundancy of bacterial groups. All bacterial communities, including those at reference sites, were highly dynamic. Respiration studies of amended sediments indicated that fish farm sediments were at least as resilient and erse as reference site communities. The results of this study indicate that the functional redundancy of highly complex bacterial communities contributes to their robustness. The relationship between ersity and stability in bacterial communities remains unclear and requires further investigation before an understanding of bacterial response to perturbation is possible.
Prokaryotic metabolic activity and community structure in antarctic continental shelf sediments
Publisher: American Society for Microbiology
Date: 05-2003
DOI: 10.1128/AEM.69.5.2448-2462.2003
Abstract: The prokaryote community activity and structural characteristics within marine sediment s led across a continental shelf area located off eastern Antarctica (66°S, 143°E depth range, 709 to 964 m) were studied. Correlations were found between microbial biomass and aminopeptidase and chitinase rates, which were used as proxies for microbial activity. Biomass and activity were maximal within the 0- to 3-cm depth range and declined rapidly with sediment depths below 5 cm. Most-probable-number counting using a dilute carbohydrate-containing medium recovered 1.7 to 3.8% of the sediment total bacterial count, with mostly facultatively anaerobic psychrophiles cultured. The median optimal growth temperature for the sediment isolates was 15°C. Many of the isolates identified belonged to genera characteristic of deep-sea habitats, although most appear to be novel species. Phospholipid fatty acid (PLFA) and isoprenoid glycerol dialkyl glycerol tetraether analyses indicated that the s les contained lipid components typical of marine sediments, with profiles varying little between s les at the same depth however, significant differences in PLFA profiles were found between depths of 0 to 1 cm and 13 to 15 cm, reflecting the presence of a different microbial community. Denaturing gradient gel electrophoresis (DGGE) analysis of lified bacterial 16S rRNA genes revealed that between s les and across sediment core depths of 1 to 4 cm, the community structure appeared homogenous however, principal-component analysis of DGGE patterns revealed that at greater sediment depths, successional shifts in community structure were evident. Sequencing of DGGE bands and rRNA probe hybridization analysis revealed that the major community members belonged to delta proteobacteria, putative sulfide oxidizers of the gamma proteobacteria, Flavobacteria , Planctomycetales , and Archaea . rRNA hybridization analyses also indicated that these groups were present at similar levels in the top layer across the shelf region.
Draft Genome Sequences of Two Novel Sub-Antarctic Williamsia Species
Publisher: American Society for Microbiology
Date: 12-10-2017
Abstract: Illumina MiSeq shotgun sequencing technology was used to sequence the genomes of two novel sub-Antarctic Williamsia species, designated strains 1135 and 1138. The estimated genome sizes for strains 1135 and 1138 are 5.99 Mb and 6.08 Mb, respectively. This genome sequence information will aid in understanding the lipid metabolic pathways of cold-tolerant Williamsia species.
Sea-ice microbial communities
Publisher: Springer Berlin Heidelberg
Date: 2013
Characterisation of the Transcriptomes of Genetically Diverse Listeria monocytogenes Exposed to Hyperosmotic and Low Temperature Conditions Reveal Global Stress-Adaptation Mechanisms
Publisher: Public Library of Science (PLoS)
Date: 04-09-2013
Microbial ecology of Atlantic salmon (Salmo salar) hatcheries: impacts of the built environment on fish mucosal microbiota
Publisher: American Society for Microbiology
Date: 02-06-2020
DOI: 10.1128/AEM.00411-20
Abstract: Atlantic salmon, Salmo salar , is the most farmed marine fish worldwide, with an annual production of 2,248 million metric tons in 2016. Salmon hatcheries are increasingly changing from flowthrough toward recirculating aquaculture system (RAS) design to accommodate more control over production along with improved environmental sustainability due to lower impacts on water consumption. To date, microbiome studies of hatcheries have focused either on the fish mucosal microbiota or on the built environment microbiota but have not combined the two to understand their interactions. Our study evaluates how the water and tank biofilm microbiota influences the fish microbiota across three mucosal environments (gill, skin, and digesta). Results from this study highlight how the built environment is a unique source of microbes to colonize fish mucus and, furthermore, how this can influence fish health. Further studies can use this knowledge to engineer built environments to modulate fish microbiota for beneficial phenotypes.
Biogeographic and Quantitative Analyses of Abundant Uncultivated γ-Proteobacterial Clades from Marine Sediment
Publisher: Springer Science and Business Media LLC
Date: 04-2005
DOI: 10.1007/S00248-004-0070-2
Abstract: 16S rRNA gene-based molecular analyses revealed the presence of several large and so far uncultivated clades within class gamma-Proteobacteria, designated gamma-proteobacterial marine sediment (GMS) clades 1 to 4, in marine sediment. The GMS clades appear only indigenous to marine sediment and so far have an unknown functionality. SYBR Green-based real-time PCR analyses using GMS clade-specific primers indicated GMS clades were a significant part of the bacterial community (0.3-8.7% of total 16S rRNA genes) in both polar and temperate marine sediment s les. Univariate statistical analyses indicated that GMS clade communities were indistinguishable in two temperate coastal sediment s les even though these possessed very different mean grain sizes, organic contents, and organic loading rates. GMS clade communities were slightly different (p < 0.05) between polar and temperate sites, suggesting that psychrophilic adaptation among GMS clade taxa corresponds only to subtle phylogenetic differences. Similar levels of difference were also observed through a sediment core reflecting that through the sediment core history, which spanned approximately 3000 years, GMS clonal ersity shifted only marginally.
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