ORCID Profile
0000-0001-5043-3726
Current Organisation
UNSW Sydney
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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.
Microbiology | Microbial Ecology | Soil Biology | Environmental Science and Management | Genetics Not Elsewhere Classified | Synthetic biology | Biochemistry and Cell Biology | Public Health and Health Services | Epidemiology | Microbiology Not Elsewhere Classified | Genetics | Biological Oceanography | Genetics | Synthetic Biology | Parasitology | Microbial Genetics | Terrestrial Ecology | Genomics | Gene Expression | Conservation and Biodiversity | Molecular Evolution | Microbial genetics | Microbial Ecology | Microbial Systematics, Taxonomy And Phylogeny | Atmospheric Sciences Not Elsewhere Classified | Genomics
Expanding Knowledge in the Biological Sciences | Antarctic and Sub-Antarctic Flora, Fauna and Biodiversity | Biological sciences | Effects of Climate Change and Variability on Antarctic and Sub-Antarctic Environments (excl. Social Impacts) | Ecosystem Adaptation to Climate Change | Ecosystem Assessment and Management of Coastal and Estuarine Environments | Higher education | Manufacturing not elsewhere classified | Diagnostic methods | Inherited diseases (incl. gene therapy) | Rural health | Disease distribution and transmission | Marine Flora, Fauna and Biodiversity | Ecosystem Assessment and Management of Marine Environments |
Publisher: American Society for Microbiology
Date: 2009
DOI: 10.1128/AEM.01341-08
Abstract: Effective management of human cryptosporidiosis requires efficient methods for detection and identification of the species of Cryptosporidium isolates. Identification of isolates to the species level is not routine for diagnostic assessment of cryptosporidiosis, which leads to uncertainty about the epidemiology of the Cryptosporidium species that cause human disease. We developed a rapid and reliable method for species identification of Cryptosporidium oocysts from human fecal s les using terminal restriction fragment polymorphism (T-RFLP) analysis of the 18S rRNA gene. This method generated diagnostic fragments unique to the species of interest. A panel of previously identified isolates of species was blind tested to validate the method, which determined the correct species identity in every case. The T-RFLP profiles obtained for s les spiked with known amounts of Cryptosporidium hominis and Cryptosporidium parvum oocysts generated the two expected diagnostic peaks. The detection limit for an in idual species was 1% of the total DNA. This is the first application of T-RFLP to protozoa, and the method which we developed is a rapid, repeatable, and cost-effective method for species identification.
Publisher: Elsevier BV
Date: 12-2008
DOI: 10.1016/J.CBPA.2008.08.028
Abstract: Our prior work has shown that the catecholamine hormone, noradrenaline, mediates environmental stress responses in Sydney rock oysters, resulting in impaired immunological function. In the current study, we tested the cellular basis of this stress response. Hemocytes were exposed to noradrenaline in vitro before cell morphology and viability were analyzed. Noradrenaline was shown to induce apoptotic markers, including the loss of mitochondrial membrane potential, DNA fragmentation and plasma membrane blebbing. F-actin appeared to play an important role in the changes observed in hemocytes, being concentrated mostly in the plasma membrane blebs of noradrenaline-treated hemocytes. This may explain why hemocyte adhesion and pseudopodia formation were inhibited by noradrenaline. Cellular dysfunction induced by norarenaline mainly affected the hyalinocyte sub-population of hemocytes, whilst the other major cell type, granulocytes, remained unaffected. Given that hyalinocytes are important immunological effectors, the results of this study help to explain why immunosuppression accompanies noradrenaline-mediated stress responses in oysters.
Publisher: Wiley
Date: 10-11-2021
Abstract: Actinobacteria and Proteobacteria are important producers of bioactive natural products (NP), and these phyla dominate in the arid soils of Antarctica, where metabolic adaptations influence survival under harsh conditions. Biosynthetic gene clusters (BGCs) which encode NPs, are typically long and repetitious high G + C regions difficult to sequence with short‐read technologies. We sequenced 17 Antarctic soil bacteria from multi‐genome libraries, employing the long‐read PacBio platform, to optimize capture of BGCs and to facilitate a comprehensive analysis of their NP capacity. We report 13 complete bacterial genomes of high quality and contiguity, representing 10 different cold‐adapted genera including novel species. Antarctic BGCs exhibited low similarity to known compound BGCs (av. 31%), with an abundance of terpene, non‐ribosomal peptide and polyketide‐encoding clusters. Comparative genome analysis was used to map BGC variation between closely related strains from geographically distant environments. Results showed the greatest biosynthetic differences to be in a psychrotolerant Streptomyces strain, as well as a rare Actinobacteria genus, Kribbella , while two other Streptomyces spp. were surprisingly similar to known genomes. Streptomyces and Kribbella BGCs were predicted to encode antitumour, antifungal, antibacterial and biosurfactant‐like compounds, and the synthesis of NPs with antibacterial, antifungal and surfactant properties was confirmed through bioactivity assays.
Publisher: Elsevier BV
Date: 06-2009
DOI: 10.1016/J.EXPPARA.2009.02.006
Abstract: Management and control of cryptosporidiosis in human requires knowledge of Cryptosporidium species contributing to human disease. Markers that are able to provide information below the species level have become important tools for source tracking. Using the hypervariable surface antigen, glycoprotein 60 (GP60), C. hominis (n=37) and C. parvum (n=32) isolates from cryptosporidiosis cases in New South Wales, Australia, were characterised. Extensive variation was observed within this locus and the isolates could be ided into 8 families and 24 different subtypes. The subtypes identified have global distributions and indicate that anthroponotic and zoonotic transmission routes contribute to sporadic human cryptosporidiosis in NSW.
Publisher: Elsevier BV
Date: 12-2008
DOI: 10.1016/J.MIMET.2008.08.007
Abstract: Cryptosporidium is the most common non-viral cause of diarrhea worldwide. Of the 5 described species that contribute to the majority of human infections, C. parvum is of major interest due to its zoonotic potential. A species-specific fluorescence in situ hybridisation probe was designed to the variable region in the small subunit of the 18S rRNA of C. parvum and labeled with Cy3. Probe specificity was validated against a panel of 7 other Cryptosporidium spp. before it was applied to 33 human faecal s les positive for cryptosporidiosis which were obtained during the period from 2006-2007. Results were compared to PCR-RFLP targeting the 18S rDNA. FISH results revealed that 19 of the 33 isolates analysed were identified as C. parvum. Correlation of PCR-RFLP and FISH was statistically significant (P<0.05), resulting in a calculated correlation coefficient of 0.994. In this study, species identification by FISH and PCR-RFLP provided preliminary evidence to support both anthroponotic and zoonotic transmission of sporadic cases of cryptosporidiosis in the Sydney basin. In conclusion, FISH using a C. parvum-specific probe provided an alternative tool for accurate identification of zoonotic Cryptosporidium which will be applied in the future to both epidemiological and outbreak investigations.
Publisher: Springer Science and Business Media LLC
Date: 04-02-2014
DOI: 10.1038/SREP03957
Publisher: American Society for Microbiology
Date: 11-2011
DOI: 10.1128/AEM.00616-11
Abstract: Cryptosporidiosis is one of the most common waterborne diseases reported worldwide. Outbreaks of this gastrointestinal disease, which is caused by the Cryptosporidium parasite, are often attributed to public swimming pools and municipal water supplies. Between the months of January and April in 2009, New South Wales, Australia, experienced the largest waterborne cryptosporidiosis outbreak reported in Australia to date. Through the course of the contamination event, 1,141 in iduals became infected with Cryptosporidium . Health authorities in New South Wales indicated that public swimming pool use was a contributing factor in the outbreak. To identify the Cryptosporidium species responsible for the outbreak, fecal s les from infected patients were collected from hospitals and pathology companies throughout New South Wales for genetic analyses. Genetic characterization of Cryptosporidium oocysts from the fecal s les identified the anthroponotic Cryptosporidium hominis IbA10G2 subtype as the causative parasite. Equal proportions of infections were found in males and females, and an increased susceptibility was observed in the 0- to 4-year age group. Spatiotemporal analysis indicated that the outbreak was primarily confined to the densely populated coastal cities of Sydney and Newcastle.
Publisher: CSIRO Publishing
Date: 2018
DOI: 10.1071/MA18008
Abstract: Many of the world's most arid deserts harbour surprisingly erse communities of heterotrophic bacteria. These organisms persist in surface soils under extreme climatic conditions, despite lacking obvious energy inputs from phototrophic primary producers. A longstanding conundrum has been how these communities sustain enough energy to maintain their ersity and biomass. We recently helped to resolve this conundrum by demonstrating that some desert communities are structured by a minimalistic mode of chemosynthetic primary production, where atmospheric trace gases, not sunlight, serve as the main energy sources. These findings are supported by pure culture studies that suggest atmospheric trace gases are dependable energy sources for the long-term survival of dormant soil bacteria. We predict that atmospheric trace gases may be a major energy source for desert ecosystems worldwide.
Publisher: The World Academic Publishing
Date: 26-06-2013
DOI: 10.5963/PHF0202007
Publisher: Frontiers Media SA
Date: 15-07-2014
Publisher: Frontiers Media SA
Date: 21-08-2020
Publisher: Elsevier BV
Date: 09-2011
Publisher: Springer Science and Business Media LLC
Date: 09-01-2021
DOI: 10.1186/S12866-020-02076-Z
Abstract: The analysis of blow microbiota has been proposed as a biomarker for respiratory health analysis in cetaceans. Yet, we lack crucial knowledge on the long-term stability of the blow microbiota and its potential changes during disease. Research in humans and mice have provided evidence that respiratory disease is accompanied by a shift in microbial communities of the airways. We investigate here the stability of the community composition of the blow microbiota for 13 captive bottlenose dolphins over eight months including both sick and healthy in iduals. We used barcoded tag sequencing of the bacterial 16S rRNA gene. Four of the dolphins experienced distinct medical conditions and received systemic antimicrobial treatment during the study. We showed that each dolphin harboured a unique community of zero-radius operational taxonomic units (zOTUs) that was present throughout the entire s ling period (‘intra-core’). Although for most dolphins there was significant variation over time, overall the intra-core accounted for an average of 73% of relative abundance of the blow microbiota. In addition, the dolphins shared between 8 and 66 zOTUs on any of the s ling occasions (‘inter-core’), accounting for a relative abundance between 17 and 41% of any dolphin’s airway microbiota. The majority of the intra-core and all of the inter-core zOTUs in this study are commonly found in captive and free-ranging dolphins and have previously been reported from several different body sites. While we did not find a clear effect of microbial treatment on blow microbiota, age and sex of the dolphins did have such an effect. The airways of dolphins were colonized by an in idual intra-core ‘signature’ that varied in abundance relative to more temporary bacteria. We speculate that the intra-core bacteria interact with the immune response of the respiratory tract and support its function. This study provides the first evidence of in idual-specific airway microbiota in cetaceans that is stable over eight months.
Publisher: Elsevier BV
Date: 2200
DOI: 10.1016/S0167-7012(02)00130-6
Abstract: Beljian red (BR) is a novel long Stokes shift fluorescent dye that fluoresces orange when illuminated with UV or blue light. Due to its long Stokes shift, and the fact that it is excitable at 488 nm, BR has particular utility in multi-colour applications with short Stokes shift fluorophores such as fluorescein. Here we have demonstrated that BR can be used to discriminate Giardia cysts seeded into water s les from those naturally present in the s le. We show that the dye does not interfere with other staining methods such as DAPI, and is compatible with mAb-FITC staining in a multi-colour fluorescence technique. This should be useful in determining the specific recovery of protozoan parasites from environmental s les.
Publisher: SPIE-Intl Soc Optical Eng
Date: 2009
DOI: 10.1117/1.3103770
Abstract: A fundamental problem for rare-event cell analysis is auto-fluorescence from nontarget particles and cells. Time-gated flow cytometry is based on the temporal-domain discrimination of long-lifetime (>1 micros) luminescence-stained cells and can render invisible all nontarget cell and particles. We aim to further evaluate the technique, focusing on detection of ultra-rare-event 5-microm calibration beads in environmental water dirt s les. Europium-labeled 5-microm calibration beads with improved luminescence homogeneity and reduced aggregation were evaluated using the prototype UV LED excited time-gated luminescence (TGL) flow cytometer (FCM). A BD FACSAria flow cytometer was used to sort accurately a very low number of beads (<100 events), which were then spiked into concentrated s les of environmental water. The use of europium-labeled beads permitted the demonstration of specific detection rates of 100%+/-30% and 91%+/-3% with 10 and 100 target beads, respectively, that were mixed with over one million nontarget autofluorescent background particles. Under the same conditions, a conventional FCM was unable to recover rare-event fluorescein isothiocyanate (FITC) calibration beads. Preliminary results on Giardia detection are also reported. We have demonstrated the scientific value of lanthanide-complex biolabels in flow cytometry. This approach may augment the current method that uses multifluorescence-channel flow cytometry gating.
Publisher: Elsevier BV
Date: 12-2021
Publisher: Springer Science and Business Media LLC
Date: 27-05-2020
DOI: 10.1038/S41597-020-0496-5
Abstract: Real-world observational datasets that record and quantify pressure-stressor-response linkages between effluent discharges and natural aquatic systems are rare. With global wastewater volumes increasing at unprecedented rates, it is urgent that the present dataset is available to provide the necessary information about microbial community structure and functioning. Field studies were performed at two time-points in the Austral summer. Single-species and microbial community whole effluent toxicity (WET) testing was performed at a complete range of effluent concentrations and two salinities, with accompanying environmental data to provide new insights into nutrient and organic matter cycling, and to identify ecotoxicological tipping points. The two salinity regimes were chosen to investigate future scenarios based on a predicted salinity increase at the study site, typical of coastal regions with rising sea levels globally. Flow cytometry, licon sequencing of 16S and 18S rRNA genes and micro-fluidic quantitative polymerase-chain reactions (MFQPCR) were used to determine chlorophyll-a and total bacterial cell numbers and size, as well as taxonomic and functional ersity of pelagic microbial communities. This strong pilot dataset could be replicated in other regions globally and would be of high value to scientists and engineers to support the next advances in microbial ecotoxicology, environmental biomonitoring and estuarine water quality modelling.
Publisher: Springer Science and Business Media LLC
Date: 22-03-2021
Publisher: American Society for Microbiology
Date: 13-12-2019
DOI: 10.1128/AEM.01968-19
Abstract: Quorum sensing, a type of bacterial communication, is widely known to regulate many processes, including those that confer a survival advantage. However, little is known about communication by bacteria residing within Antarctic soils. Employing a combination of bacterial biosensors, analytical techniques, and genome mining, we found a variety of Antarctic soil bacteria speaking a common language, via LuxI/LuxR-based quorum sensing, thus potentially supporting survival in a mixed microbial community. This study reports potential quorum sensing activity in Antarctic soils and has provided a platform for studying physiological adaptations of microorganisms that allow them to survive in the harsh Antarctic environment.
Publisher: Elsevier BV
Date: 11-2020
Publisher: MDPI AG
Date: 17-12-2008
DOI: 10.3390/IJMS9122622
Publisher: Springer International Publishing
Date: 2017
Publisher: Wiley
Date: 05-02-2007
DOI: 10.1002/CYTO.A.20381
Abstract: Significant developments in biological applications are occurring through the incorporation of Quantum Dots (QDs) as biological labels. The demonstration of QDs unique optical properties may have important implications for the study of environmental s les, where microorganisms of interest need to be isolated away from the background debris. Flow cytometric analysis was used to determine the fluorescence intensity of oocysts after mAb staining by QDs or organic fluorophore conjugates. In addition, the level of non-specific binding to detrital particles within a control water concentrate was estimated using the optimal staining concentration determined for each mAb analyzed. Under 488 nm excitation, oocysts stained with QD-conjugates exhibited significantly lower fluorescence intensity than organic conjugates. Moreover, the level of non-specific binding by QD-conjugates to detrital particles present in the water concentrate was significantly higher that of the organic conjugates. While QDs are noted for their superior spectral characteristics, they have been shown here to be unsuitable for conventional flow cytometric detection of Cryptosporidium. Therefore, we conclude that in their current form, QD's are severely limited for fluorescent detection of pathogens in environmental applications.
Publisher: Wiley
Date: 12-2003
Abstract: Lightning Fast is a sensitive fluorescence-based stain for detecting proteins in one-dimensional and two-dimensional polyacrylamide electrophoresis gels. It contains the fluorophore epicocconone from the fungus Epicoccum nigrum that interacts noncovalently with sodium dodecyl sulfate and protein. Stained proteins can be excited optimally by near-ultraviolet light of about 395 nm or with visible light of about 520 nm. The stain can be excited using a range of sources used in image analysis systems including UVA (ca. 365 nm) and UVB (ca. 302 nm) transilluminators Xenon-arc l s 488 nm and 457 nm Argon-ion lasers 473 nm and 532 nm neodymium: yttrium aluminum garnet (Nd:YAG) solid-state lasers 543 nm helium-neon lasers, and emerging violet, blue and green diode lasers. Maximum fluorescence emission of the dye is at approximately 610 nm. The limit of detection in one-dimensional gels stained with Lightning Fast protein gel stain is less than 100 pg of protein, rivaling the current limits of matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS). Lightning Fast was found to be considerably more sensitive than SYPRO Ruby, SYPRO Orange, silver and Coomassie Brilliant Blue G-250 in matched experiments. Staining takes as little as 3.5 h and stained proteins displayed quantitative linearity over more than four orders of magnitude, thereby allowing visualization of entire proteomes. Lightning Fast protein gel staining is compatible with subsequent peptide mass fingerprinting using MALDI-MS and Edman-based sequencing chemistry.
Publisher: Wiley
Date: 03-06-2021
Abstract: Candidatus Dormibacterota is an uncultured bacterial phylum found predominantly in soil that is present in high abundances within cold desert soils. Here, we interrogate nine metagenome‐assembled genomes ( MAGs ), including six new MAGs derived from soil metagenomes obtained from two eastern Antarctic sites. Phylogenomic and taxonomic analyses revealed these MAGs represent four genera and five species, representing two order‐level clades within Ca . Dormibacterota. Metabolic reconstructions of these MAGs revealed the potential for aerobic metabolism, and versatile adaptations enabling persistence in the ‘extreme’ Antarctic environment. Primary amongst these adaptations were abilities to scavenge atmospheric H 2 and CO as energy sources, as well as using the energy derived from H 2 oxidation to fix atmospheric CO 2 via the Calvin–Bassham–Benson cycle, using a RuBisCO type IE . We propose that these allow Ca . Dormibacterota to persist using H 2 oxidation and grow using atmospheric chemosynthesis in terrestrial Antarctica. Fluorescence in situ hybridization revealed Ca . Dormibacterota to be coccoid cells, 0.3–1.4 μm in diameter, with some cells exhibiting the potential for a symbiotic or syntrophic lifestyle.
Publisher: Springer Science and Business Media LLC
Date: 30-08-2016
Publisher: Frontiers Media SA
Date: 07-04-2017
Publisher: Wiley
Date: 14-10-2016
Abstract: Landscape heterogeneity impacts community assembly in animals and plants, but it is not clear if this ecological concept extends to microbes. To examine this question, we chose to investigate polar soil environments from the Antarctic and Arctic, where microbes often form the major component of biomass. We examined soil environments that ranged in connectivity from relatively well-connected slopes to patchy, fragmented landforms that comprised isolated frost boils. We found landscape connectedness to have a significant correlation with microbial community structure and connectivity, as measured by co-occurrence networks. Soils from within fragmented landforms appeared to exhibit less local environmental heterogeneity, harboured more similar communities, but fewer biological associations than connected landforms. This effect was observed at both poles, despite the geographical distances and ecological differences between them. We suggest that microbial communities inhabiting well-connected landscape elements respond consistently to regional-scale gradients in biotic and edaphic factors. Conversely, the repeated freeze thaw cycles that characterize fragmented landscapes create barriers within the landscape and act to homogenize the soil environment within in idual frost boils and consequently the microbial communities. We propose that lower microbial connectivity in the fragmented landforms is a function of smaller patch size and continual disturbances following soil mixing.
Publisher: Cold Spring Harbor Laboratory
Date: 23-09-2021
DOI: 10.1101/2021.09.22.461446
Abstract: Microorganisms are key to sustaining core ecosystem processes across terrestrial Antarctica but they are rarely considered in conservation frameworks. Whilst greater advocacy has been made towards the inclusion of microbial data in this context, there is still a need for better tools to quantify multispecies responses to environmental change. Here, we extend the scope of Gradient Forest modelling beyond macroorganisms and small datasets to the comprehensive polar soil microbiome encompassing , 000 sequence variants for bacteria, micro-eukarya and archaea throughout the hyperarid Vestfold Hills of Eastern Antarctica. Quantification of microbial ersity against 79 physiochemical variables revealed that whilst rank-order importance differed, predictors were broadly consistent between domains, with greatest sharing occurring between bacteria and micro-eukarya. Moisture was identified as the most robust predictor for shaping the regional soil microbiome, with highest compositional turnover or “splits” occurring within the 10 – 12 % moisture content range. Often the most responsive taxa were rarer lineages of bacteria and micro-eukarya with phototrophic and nutrient-cycling capacities such as Cyanobacteria (up to 61.81 % predictive capacity), Chlorophyta (62.17 %) and Ochrophyta (57.81 %). These taxa groups are thus at greater risk of bio ersity loss or gain to projected climate trajectories, which will inevitably disturb current ecosystem dynamics. Better understanding of these threshold tipping points will positively aid conservation efforts across Eastern Antarctica. Furthermore, the successful implementation of an improved Gradient Forest model also presents an exciting opportunity to broaden its use on microbial systems globally.
Publisher: Elsevier BV
Date: 09-2000
DOI: 10.1016/S0022-1759(00)00234-9
Abstract: Large numbers of microbiological s les are analysed annually using traditional culture-based techniques. These techniques take hours to days to yield a result, are tedious and are not suitable for non-culturable microorganisms. Further, culture-based techniques do not provide real-time information on the physiological status of the organism in situ which is important in the industrial manufacture of many microbial products. Flow cytometry offers the prospect of real-time microbial analysis of in idual microorganisms, without dependency on microbial culture. However, flow cytometry has not been extensively used as a tool for routine microbial analysis. This has been mainly due to the high cost and complexity of instrumentation, the need for trained flow cytometrists and the lack of assay kits with appropriate biological reagents for specific applications. Many modern instruments are now relatively simple to operate, due to improvements in the user-interface, and no longer need a specialist operator. However, most cytometers are still reliant on analogue technology first developed 20-30 years ago. The incorporation of modern, solid state opto-electronics combined with micro-fabrication and digital signal processing technology offers the prospect of simple to use, low cost and robust instruments suitable for microbial analyses. Advances are being made in the development of a range of biological reagents and these are now being formulated into simple to use kits for microbiological applications. Currently, these kits are largely restricted to simple analyses, for ex le to assay for total or viable numbers of microorganisms present. However, technologies are available to selectively label specific types of microorganisms. For ex le, fluorescent antibodies can be used to label microorganisms according to expression of particular antigens, fluorescent in situ hybridisation to label according to phylogeny and fluorogenic enzymatic substrates to label according to expression of specific enzyme activities. Reagents are also available that stain viruses sufficiently brightly to enable their direct detection in environments such as sea water. Microorganisms need to be detected in a variety of different matrices (e.g., water, mud, food, and beverages) and these matrices may be highly variable in nature (e.g., tap water compared to river water). Many matrices have high background autofluorescence (e.g., algae and minerals in water s les) or may bind non-specifically to the fluorescent biological reagents used (e.g., protein micelles in milk). Formulation of biological reagents and s le pre-treatments are critical to the development of suitable microbiological assays. Here, developments in instrumentation and biological reagents for microbiological applications are reviewed with specific ex les from environmental or industrial microbiology. The broader considerations for the development of microbial assays for flow cytometry are also considered.
Publisher: Mary Ann Liebert Inc
Date: 02-2022
Publisher: American Society for Microbiology
Date: 15-08-2012
DOI: 10.1128/AEM.01299-12
Abstract: A large proportion of “universal” 16S PCR primers lack sequence homology to many of the “candidate” isions, severely limiting bacterial ersity assessments. We designed a primer set that offers a 50% increase in silico in coverage of the domain Bacteria over the commonly used primer combination 27F/519R. Comparisons using pyrosequencing on soil environments showed a significant increase in recovery of taxonomic ersity with around a 3-fold increase in recovery of sequences from candidate isions.
Publisher: Humana Press
Date: 2012
DOI: 10.1007/978-1-61779-827-6_1
Abstract: The isolation and subsequent characterization of microbial cells from within environmental s les is a difficult process. Flow cytometry and cell sorting, when combined with the application of fluorescent probes, have the capability for the detection and separation of erse microbial populations from within complex mixtures. The isolation of single cells allows for downstream investigations towards system-level characterization of unknown Bacterial Phyla to occur. We describe here the combination of fluorescent in situ hybridization and cell sorting for the detection and isolation of Candidate Division TM7 bacteria from an enriched soil s le. The result is the isolation of rare cells suitable for advanced molecular analysis including whole genome lification and high-throughput pyrosequencing.
Publisher: Springer Science and Business Media LLC
Date: 06-08-2022
DOI: 10.1038/S41396-022-01298-5
Abstract: Cold desert soil microbiomes thrive despite severe moisture and nutrient limitations. In Eastern Antarctic soils, bacterial primary production is supported by trace gas oxidation and the light-independent RuBisCO form IE. This study aims to determine if atmospheric chemosynthesis is widespread within Antarctic, Arctic and Tibetan cold deserts, to identify the breadth of trace gas chemosynthetic taxa and to further characterize the genetic determinants of this process. H 2 oxidation was ubiquitous, far exceeding rates reported to fulfill the maintenance needs of similarly structured edaphic microbiomes. Atmospheric chemosynthesis occurred globally, contributing significantly ( p 0.05) to carbon fixation in Antarctica and the high Arctic. Taxonomic and functional analyses were performed upon 18 cold desert metagenomes, 230 dereplicated medium-to-high-quality derived metagenome-assembled genomes (MAGs) and an additional 24,080 publicly available genomes. Hydrogenotrophic and carboxydotrophic growth markers were widespread. RuBisCO IE was discovered to co-occur alongside trace gas oxidation enzymes in representative Chloroflexota , Firmicutes , Deinococcota and Verrucomicrobiota genomes. We identify a novel group of high-affinity [NiFe]-hydrogenases, group 1m, through phylogenetics, gene structure analysis and homology modeling, and reveal substantial genetic ersity within RuBisCO form IE ( rbcL1E ), and high-affinity 1h and 1l [NiFe]-hydrogenase groups. We conclude that atmospheric chemosynthesis is a globally-distributed phenomenon, extending throughout cold deserts, with significant implications for the global carbon cycle and bacterial survival within environmental reservoirs.
Publisher: American Society for Microbiology
Date: 15-05-2009
DOI: 10.1128/AEM.02407-08
Abstract: Soil substrate membrane systems allow for microcultivation of fastidious soil bacteria as mixed microbial communities. We isolated established microcolonies from these membranes by using fluorescence viability staining and micromanipulation. This approach facilitated the recovery of erse, novel isolates, including the recalcitrant bacterium Leifsonia xyli , a plant pathogen that has never been isolated outside the host.
Publisher: American Society for Microbiology
Date: 12-2005
DOI: 10.1128/AEM.71.12.8714-8720.2005
Abstract: Traditional microbiological methods of cultivation recover less than 1% of the total bacterial species, and the culturable portion of bacteria is not representative of the total phylogenetic ersity. Classical cultivation strategies are now known to supply excessive nutrients to a system and therefore select for fast-growing bacteria that are capable of colony or biofilm formation. New approaches to the cultivation of bacteria which rely on growth in dilute nutrient media or simulated environments are beginning to address this problem of selection. Here we describe a novel microcultivation method for soil bacteria that mimics natural conditions. Our soil slurry membrane system combines a polycarbonate membrane as a growth support and soil extract as the substrate. The result is abundant growth of uncharacterized bacteria as microcolonies. By combining microcultivation with fluorescent in situ hybridization, previously “unculturable” organisms belonging to cultivated and noncultivated isions, including candidate ision TM7, can be identified by fluorescence microscopy. Successful growth of soil bacteria as microcolonies confirmed that the missing culturable majority may have a growth strategy that is not observed when traditional cultivation indicators are used.
Publisher: Wiley
Date: 2000
DOI: 10.1002/1097-0320(20001101)41:3<216::AID-CYTO9>3.0.CO;2-R
Publisher: Elsevier BV
Date: 02-2006
DOI: 10.1016/J.WATRES.2005.11.037
Abstract: As increasing water shortages continue, water re-use is posing new challenges with treated wastewater becoming a significant source of non-potable water. Rapid detection strategies that target waterborne pathogens of concern to industry are gaining importance in the assessment of water quality. This study reports on the ability to recover spiked Cryptosporidium and Giardia from a variety of industrial wastewater streams of varied water quality. Incorporation of an internal quality control used commonly in finished water-enabled quantitative assessments of pathogen loads and we describe successful analysis of pre- and part-treated wastewater s les from four industrial sites. The method used combined calcium carbonate flocculation followed by flow cytometry and epifluorescence microscopy. Our focus will now aim at characterising the ambient parasites isolated from industrial wastewater with the objective of developing a suite of highly specific platform detection technologies targeted to industrial needs.
Publisher: Elsevier BV
Date: 04-2020
Publisher: MDPI AG
Date: 27-06-2023
DOI: 10.3390/MICROORGANISMS11071670
Abstract: Water availability is the dominant driver of microbial community structure and function in desert soils. However, these habitats typically only receive very infrequent large-scale water inputs (e.g., from precipitation and/or run-off). In light of recent studies, the paradigm that desert soil microorganisms are largely dormant under xeric conditions is questionable. Gene expression profiling of microbial communities in desert soils suggests that many microbial taxa retain some metabolic functionality, even under severely xeric conditions. It, therefore, follows that other, less obvious sources of water may sustain the microbial cellular and community functionality in desert soil niches. Such sources include a range of precipitation and condensation processes, including rainfall, snow, dew, fog, and nocturnal distillation, all of which may vary quantitatively depending on the location and geomorphological characteristics of the desert ecosystem. Other more obscure sources of bioavailable water may include groundwater-derived water vapour, hydrated minerals, and metabolic hydro-genesis. Here, we explore the possible sources of bioavailable water in the context of microbial survival and function in xeric desert soils. With global climate change projected to have profound effects on both hot and cold deserts, we also explore the potential impacts of climate-induced changes in water availability on soil microbiomes in these extreme environments.
Publisher: Elsevier BV
Date: 2021
Publisher: Springer Science and Business Media LLC
Date: 17-07-2008
Abstract: Most bacteria are recalcitrant to traditional cultivation in the laboratory. The soil substrate membrane system provides a simulated environment for the cultivation of previously undescribed soil bacteria as microcolonies. The system uses a polycarbonate membrane as a solid support for growth and soil extract as the substrate. Diverse microcolonies can be visualized using total bacterial staining combined with fluorescence in situ hybridization (FISH) after 7-10-d incubation. Molecular typing shows that the majority of microcolony-forming bacteria recovered using this protocol were resistant to growth using standard methods. The protocol takes <4 h of bench time over the 10-d period.
Publisher: Wiley
Date: 31-03-2020
Publisher: Frontiers Media SA
Date: 26-11-2018
Publisher: Springer Science and Business Media LLC
Date: 16-03-2020
DOI: 10.1186/S40168-020-00809-W
Abstract: Resident soil microbiota play key roles in sustaining the core ecosystem processes of terrestrial Antarctica, often involving unique taxa with novel functional traits. However, the full scope of bio ersity and the niche-neutral processes underlying these communities remain unclear. In this study, we combine multivariate analyses, co-occurrence networks and fitted species abundance distributions on an extensive set of bacterial, micro-eukaryote and archaeal licon sequencing data to unravel soil microbiome patterns of nine sites across two east Antarctic regions, the Vestfold Hills and Windmill Islands. To our knowledge, this is the first microbial bio ersity report on the hyperarid Vestfold Hills soil environment. Our findings reveal distinct regional differences in phylogenetic composition, abundance and richness amongst microbial taxa. Actinobacteria dominated soils in both regions, yet Bacteroidetes were more abundant in the Vestfold Hills compared to the Windmill Islands, which contained a high abundance of novel phyla. However, intra-region comparisons demonstrate greater homogeneity of soil microbial communities and measured environmental parameters between sites at the Vestfold Hills. Community richness is largely driven by a variable suite of parameters but robust associations between co-existing members highlight potential interactions and sharing of niche space by erse taxa from all three microbial domains of life examined. Overall, non-neutral processes appear to structure the polar soil microbiomes studied here, with niche partitioning being particularly strong for bacterial communities at the Windmill Islands. Eukaryotic and archaeal communities reveal weaker niche-driven signatures accompanied by multimodality, suggesting the emergence of neutrality. We provide new information on assemblage patterns, environmental drivers and non-random occurrences for Antarctic soil microbiomes, particularly the Vestfold Hills, where basic ersity, ecology and life history strategies of resident microbiota are largely unknown. Greater understanding of these basic ecological concepts is a pivotal step towards effective conservation management.
Publisher: Elsevier BV
Date: 04-2016
Publisher: Elsevier BV
Date: 03-2022
Publisher: Elsevier BV
Date: 05-1999
Publisher: Oxford University Press (OUP)
Date: 21-03-2014
Abstract: Despite decreasing costs, generating large-scale, well-replicated and multivariate microbial ecology investigations with sequencing remains an expensive and time-consuming option. As a result, many microbial ecology investigations continue to suffer from a lack of appropriate replication. We evaluated two fingerprinting approaches - terminal restriction fragment length polymorphism (T-RFLP) and automated ribosomal intergenic spacer analysis (ARISA) against 454 pyrosequencing, by applying them to 225 polar soil s les from East Antarctica and the high Arctic. By incorporating local and global spatial scales into the dataset, our aim was to determine whether various approaches differed in their ability and hence utility, to identify ecological patterns. Through the reduction in the 454 sequencing data to the most dominant OTUs, we revealed that a surprisingly small proportion of abundant OTUs (< 0.25%) was driving the biological patterns observed. Overall, ARISA and T-RFLP had a similar capacity as sequencing to separate s les according to distance at a local scale, and to correlate environmental variables with microbial community structure. Pyrosequencing had a greater resolution at the global scale but all methods were capable of significantly differentiating the polar sites. We conclude fingerprinting remains a legitimate approach to generating large datasets as well as a cost-effective rapid method to identify s les for elucidating taxonomic information or ersity estimates with sequencing methods.
Publisher: Wiley
Date: 02-04-2020
Publisher: Wiley
Date: 20-01-2011
DOI: 10.1111/J.1462-2920.2010.02412.X
Abstract: Toxin production during cyanobacterial blooms poses a significant public health threat in water bodies globally and requires the development of effective bloom management strategies. Previously, synthesis of the hepatotoxin microcystin has been proposed to be regulated by iron availability, but the contribution of the toxin to the adaptation of cyanobacteria to environmental stresses, such as changing light intensity and nutrient limitation, remains unclear. The aim of this study was to compare the iron stress response in toxic and non-toxic strains of Microcystis aeruginosa subjected to moderate and severe iron limitation. The transcription of a number of genes involved in iron uptake, oxidative stress response, toxin synthesis and transcriptional control of these processes was accessed by quantitative real-time PCR (qRT-PCR). The process of adaptation of M. aeruginosa to iron stress was found to be highly dynamic and strain-specific. Toxin production in PCC 7806 increased in an iron-dependent manner and appeared to be regulated by FurA. The inability to produce microcystin, either due to natural mutations in the mcy gene cluster or due to insertional inactivation of mcyH, affected the remodelling of the photosynthetic machinery in iron-stressed cells, the transport of Fe(II) and transcription of the Fur family of transcriptional regulators. The presence of the toxin appears to give an advantage to microcystin-producing cyanobacteria in the early stages of exposure to severe iron stress and may protect the cell from reactive oxygen species-induced damage.
Publisher: Elsevier BV
Date: 04-2020
DOI: 10.1016/J.ENVPOL.2019.113780
Abstract: Microorganisms are useful biological indicators of toxicity and play a key role in the functioning of healthy soils. In this study, we investigated the residual toxicity of hydrocarbons in aged contaminated soils and determined the extent of microbial community recovery during in-situ bioremediation at subantarctic Macquarie Island. Previously identified microbial indicators of hydrocarbon toxicity were used to understand interactions between hydrocarbon concentrations, soil physicochemical parameters and the microbial community. Despite the complexity of the field sites, which included active fuel storage areas with high levels of soil heterogeneity, multiple spill events and variable fuel sources, we observed consistent microbial community traits associated with exposure to high concentrations of hydrocarbons. These included reductions in alpha ersity, inhibition of nitrification potential and a reduction in the ratio of oligotrophic to copiotrophic species. These observed responses and the sensitivity of microbial communities in the field, were comparable to sensitivity estimates obtained in a previous lab-based mesocosm study with hydrocarbon spiked soils. This study provides a valuable and often missing link between the quite disparate conditions of controlled lab-based spiking experiments and the complexity presented by 'real-world' contaminated field sites.
Publisher: The Royal Society
Date: 29-08-2000
Abstract: Hepatitis C virus (HCV) infection is a major public health problem, affecting an estimated 3% of the world's population, and over 10% in some countries. Infection in most cases becomes persistent, and can lead to hepatic inflammation, fibrosis and liver failure. The T lymphocyte reponse, in particular that mediated by cytotoxic T lymphocytes (CTLs), is likely to be involved in determining the outcome of infection, although its overall role is not clear. The use of major histocompatibility complex (MHC) class I peptide tetrameric complexes (tetramers) to study antiviral CTL responses has revolutionized our approach to the study of human infection. We have used a panel of MHC class I tetramers to analyse immune responses in HCV–infected in iduals at various stages of disease. We find that the CTL response against HCV is vigorous in its early phases but dwindles over time both in terms of lymphocyte number and function. A number of potential explanations for this ‘CTL failure’ are discussed.
Publisher: Springer Science and Business Media LLC
Date: 28-07-2020
DOI: 10.1038/S41598-020-69602-X
Abstract: Humpback whales endure several months of fasting while undertaking one of the longest annual migrations of any mammal, which depletes the whales’ energy stores and likely compromises their physiological state. Airway microbiota are linked to respiratory health in mammals. To illuminate the dynamics of airway microbiota in a physiologically challenged mammal, we investigated the bacterial communities in the blow of East Australian humpback whales at two stages of their migration: at the beginning (n = 20) and several months into their migration (n = 20), using barcoded tag sequencing of the bacterial 16S rRNA gene. We show that early in the fasting the whale blow s les had a higher ersity and richness combined with a larger number of core taxa and a different bacterial composition than later in the fasting. This study provides some evidence that the rich blow microbiota at the beginning of their fasting might reflect the whales’ uncompromised physiology and that changes in the microbiota occur during the whales’ migration.
Publisher: American Society for Microbiology
Date: 08-2006
DOI: 10.1128/AEM.00546-06
Abstract: In the ubiquitous marine bacterium Pseudoalteromonas tunicata , subpopulations of cells are killed by the production of an autocidal protein, AlpP, during biofilm development. Our data demonstrate an involvement of this process in two parameters, dispersal and phenotypic ersification, which are of importance for the ecology of this organism and for its survival within the environment. Cell death in P. tunicata wild-type biofilms led to a major reproducible dispersal event after 192 h of biofilm development. The dispersal was not observed with a ΔAlpP mutant strain. Using flow cytometry and the fluorescent dye DiBAC 4 (3), we also show that P. tunicata wild-type cells that disperse from biofilms have enhanced metabolic activity compared to those cells that disperse from ΔAlpP mutant biofilms, possibly due to nutrients released from dead cells. Furthermore, we report that there was considerable phenotypic variation among cells dispersing from wild-type biofilms but not from the ΔAlpP mutant. Wild-type cells that dispersed from biofilms showed significantly increased variations in growth, motility, and biofilm formation, which may be important for successful colonization of new surfaces. These findings suggest for the first time that the autocidal events mediated by an antibacterial protein can confer ecological advantages to the species by generating a metabolically active and phenotypically erse subpopulation of dispersal cells.
Publisher: Frontiers Media SA
Date: 12-08-2020
Publisher: American Society for Microbiology
Date: 2006
DOI: 10.1128/AEM.72.1.918-922.2006
Abstract: Advances in the growth of hitherto unculturable soil bacteria have emphasized the requirement for rapid bacterial identification methods. Due to the slow-growing strategy of microcolony-forming soil bacteria, successful fluorescence in situ hybridization (FISH) requires an rRNA enrichment step for visualization. In this study, catalyzed reporter deposition (CARD)-FISH was employed as an alternative method to rRNA enhancement and was found to be superior to conventional FISH for the detection of microcolonies that are cultivated by using the soil substrate membrane system. CARD-FISH enabled real-time identification of oligophilic microcolony-forming soil bacteria without the requirement for enrichment on complex media and the associated shifts in community composition.
Publisher: Elsevier BV
Date: 11-2019
DOI: 10.1016/J.SCITOTENV.2019.06.389
Abstract: Hydrocarbon polar metabolites are gaining interest from industry and the remediation community due to their ubiquity and uncertainty around their toxicity. In this study, we used headspace-gas chromatography/mass spectrometry (HS-GC/MS) to characterize polar metabolites present in elutriates derived from uncontaminated, freshly hydrocarbon contaminated and partially remediated Antarctic soils. Elutriates represent the bioavailable fraction and may be used as a proxy for leachate runoff in environmental risk assessments. Control and contaminated soil elutriates were analysed for the presence of 12 aldehydes and two ketones, which cover a broad spectrum of metabolites, ranging from nC
Publisher: Elsevier BV
Date: 06-2006
DOI: 10.1016/J.IJPARA.2006.02.023
Abstract: With the recent publication of the Cryptosporidium genome, investigation of the proteins expressed by Cryptosporidium parvum will provide complementary information on the biology of this complex organism. Proteomic studies on this apicomplexan parasite have been h ered due to the inability to culture or isolate high numbers required for 2D gel analysis. Neonatal calves are a common source of Cryptosporidium oocysts and we report on the development of a sucrose-Percoll purification procedure which produced the high yield and purity (free from faecal and bacterial contaminants) that is required for successful proteomic studies from neonatal calves. We report on the development of quantitative and qualitative flow cytometric methods which were confirmed by epifluorescence microscopy. A comparison of five common purification procedures was carried out to determine the efficiency of the sucrose-Percoll gradient. 2D-PAGE results strongly support the sucrose-Percoll procedure as the most suitable method for applications like proteomics which require the recovery of high numbers of isolated oocysts with minimal faecal and bacterial contaminants.
Publisher: American Society for Microbiology
Date: 07-2014
DOI: 10.1128/AEM.03939-13
Abstract: Appropriate remediation targets or universal guidelines for polar regions do not currently exist, and a comprehensive understanding of the effects of diesel fuel on the natural microbial populations in polar and subpolar soils is lacking. Our aim was to investigate the response of the bacterial community to diesel fuel and to evaluate if these responses have the potential to be used as indicators of soil toxicity thresholds. We set up short- and long-exposure tests across a soil organic carbon gradient. Utilizing broad and targeted community indices, as well as functional genes involved in the nitrogen cycle, we investigated the bacterial community structure and its potential functioning in response to special Antarctic blend (SAB) diesel fuel. We found the primary effect of diesel fuel toxicity was a reduction in species richness, evenness, and phylogenetic ersity, with the resulting community heavily dominated by a few species, principally Pseudomonas . The decline in richness and phylogenetic ersity was linked to disruption of the nitrogen cycle, with species and functional genes involved in nitrification significantly reduced. Of the 11 targets we evaluated, we found the bacterial amoA gene indicative of potential ammonium oxidation, the most suitable indicator of toxicity. Dose-response modeling for this target generated an average effective concentration responsible for 20% change (EC 20 ) of 155 mg kg −1 , which is consistent with previous Macquarie Island ecotoxicology assays. Unlike traditional single-species tolerance testing, bacterial targets allowed us to simultaneously evaluate more than 1,700 species from 39 phyla, inclusive of rare, sensitive, and functionally relevant portions of the community.
Publisher: Elsevier BV
Date: 02-2019
DOI: 10.1016/J.FUNBIO.2018.11.011
Abstract: A new black yeast species, Exophiala macquariensis is described that is a member of the ascomycete family Herpotrichiellaceae, order Chaetothyriales. The genus Exophiala is comprised of opportunistic pathogens isolated from clinical specimens as well as species recovered from hydrocarbon contaminated environments. Several species have been reported to be able to degrade benzene, toluene, ethylbenzene and xylenes. Here, a novel species of Exophiala (CZ06) previously isolated from a Sub-Antarctic, Macquarie Island soil that was spiked with Special Antarctic Blend diesel fuel (SAB) is described. This isolate has the capacity of toluene biodegradation at cold temperatures. Multilocus sequence typing showed that this fungus was closely related to the pathogenic species Exophiala salmonis and Exophiala equina. With the capacity to utilise hydrocarbons as a sole carbon source at 10 °C, this fungus has great potential for future bioremediation applications.
Publisher: Wiley
Date: 13-06-2017
DOI: 10.1111/NPH.14634
Abstract: The current theoretical framework suggests that tripartite positive feedback relationships between soil bio ersity, fertility and plant productivity are universal. However, empirical evidence for these relationships at the continental scale and across different soil depths is lacking. We investigate the continental‐scale relationships between the ersity of microbial and invertebrate‐based soil food webs, fertility and above‐ground plant productivity at 289 sites and two soil depths, that is 0–10 and 20–30 cm, across Australia. Soil bio ersity, fertility and plant productivity are strongly positively related in surface soils. Conversely, in the deeper soil layer, the relationships between soil bio ersity, fertility and plant productivity weaken considerably, probably as a result of a reduction in bio ersity and fertility with depth. Further modeling suggested that strong positive associations among soil bio ersity–fertility and fertility–plant productivity are limited to the upper soil layer (0–10 cm), after accounting for key factors, such as distance from the equator, altitude, climate and physicochemical soil properties. These findings highlight the importance of surface soil bio ersity for soil fertility, and suggest that any loss of surface soil could potentially break the links between soil bio ersity–fertility and/or fertility–plant productivity, which can negatively impact nutrient cycling and food production, upon which future generations depend.
Publisher: Springer Science and Business Media LLC
Date: 13-07-2022
DOI: 10.1007/S00792-022-01271-2
Abstract: Antimicrobial resistance is an escalating health crisis requiring urgent action. Most antimicrobials are natural products (NPs) sourced from Actinomycetota , particularly the Streptomyces . Underexplored and extreme environments are predicted to harbour novel microorganisms with the capacity to synthesise unique metabolites. Herring Island is a barren and rocky cold desert in East Antarctica, remote from anthropogenic impact. We aimed to recover rare and cold-adapted NP-producing bacteria, by employing two culturing methods which mimic the natural environment: direct soil culturing and the soil substrate membrane system. First, we analysed 16S rRNA gene licon sequencing data from 18 Herring Island soils and selected the soil s le with the highest Actinomycetota relative abundance (78%) for culturing experiments. We isolated 166 strains across three phyla, including novel and rare strains, with 94% of strains belonging to the Actinomycetota . These strains encompassed thirty-five ‘species’ groups, 18 of which were composed of Streptomyces strains. We screened representative strains for genes which encode polyketide synthases and non-ribosomal peptide synthetases, indicating that 69% have the capacity to synthesise polyketide and non-ribosomal peptide NPs. Fourteen Streptomyces strains displayed antimicrobial activity against selected bacterial and yeast pathogens using an in situ assay. Our results confirm that the cold-adapted bacteria of the harsh East Antarctic deserts are worthy targets in the search for bioactive compounds.
Publisher: Frontiers Media SA
Date: 2011
Publisher: Oxford University Press (OUP)
Date: 08-03-2019
Abstract: The severity of environmental conditions at Earth's frigid zones present attractive opportunities for microbial biomining due to their heightened potential as reservoirs for novel secondary metabolites. Arid soil microbiomes within the Antarctic and Arctic circles are remarkably rich in Actinobacteria and Proteobacteria, bacterial phyla known to be prolific producers of natural products. Yet the ersity of secondary metabolite genes within these cold, extreme environments remain largely unknown. Here, we employed licon sequencing using PacBio RS II, a third generation long-read platform, to survey over 200 soils spanning twelve east Antarctic and high Arctic sites for natural product-encoding genes, specifically targeting non-ribosomal peptides (NRPS) and Type I polyketides (PKS). NRPS-encoding genes were more widespread across the Antarctic, whereas PKS genes were only recoverable from a handful of sites. Many recovered sequences were deemed novel due to their low amino acid sequence similarity to known protein sequences, particularly throughout the east Antarctic sites. Phylogenetic analysis revealed that a high proportion were most similar to antifungal and biosurfactant-type clusters. Multivariate analysis showed that soil fertility factors of carbon, nitrogen and moisture displayed significant negative relationships with natural product gene richness. Our combined results suggest that secondary metabolite production is likely to play an important physiological component of survival for microorganisms inhabiting arid, nutrient-starved soils.
Publisher: SPIE
Date: 07-02-2008
DOI: 10.1117/12.762077
Publisher: Oxford University Press (OUP)
Date: 05-2017
Publisher: Research Square Platform LLC
Date: 13-10-2021
DOI: 10.21203/RS.3.RS-948000/V1
Abstract: Cold desert soil microbiomes thrive despite severe moisture and nutrient limitations. In Eastern Antarctic soils, hydrogen oxidising bacteria support primary production through a novel carbon fixation process reliant on the chemoautotrophy-associated RuBisCO form IE. Here, biochemical assays show that atmospheric chemosynthesis occurs globally for primary production, contributing significantly to autotrophic carbon fixation throughout arid to hyperarid deserts in Antarctica, the high Arctic, and the Tibetan Plateau. Taxonomic and functional analyses were performed on 230 dereplicated medium-to-high quality metagenome-assembled genomes (MAGs) derived from 18 cold desert metagenomes and an additional 24,080 publicly available genomes. We infer that atmospheric chemosynthetic bacteria are widespread across environmental and clinical s les, increasing our knowledge of the bacterial phyla genetically capable of atmospheric chemosynthesis to seven, with key enzymes co-occurring within MAGs from four previously unidentified phyla Chloroflexota, Firmicutes, Deinococcota and Verrucomicrobiota. We informatically identify an additional group of high-affinity hydrogenases, group 1m [NiFe]-hydrogenase using phylogenetics, gene structure analysis and homology modelling and reveal substantial new genetic ersity within RuBisCO form IE ( rbcL1E ), and high-affinity groups 1h and 1l [NiFe]-hydrogenases. Finally, we conclude that atmospheric chemosynthesis is a global phenomenon, extending throughout and beyond cold deserts, with significant implications for the global carbon cycle and bacterial survival within environmental and clinical reservoirs.
Publisher: American Society for Microbiology
Date: 24-10-2013
DOI: 10.1128/AEM.00643-09
Abstract: A two-color fluorescence in situ hybridization assay that allows for the simultaneous identification of Cryptosporidium parvum and C. hominis was developed. The assay is a simple, rapid, and cost-effective tool for the detection of the major Cryptosporidium species of concern to public health.
Publisher: American Society for Microbiology
Date: 12-2006
DOI: 10.1128/AEM.01040-06
Abstract: A novel Escherichia coli outer membrane protein A (OmpA) was discovered through a proteomic investigation of cell surface proteins. DNA polymorphisms were localized to regions encoding the protein's surface-exposed loops which are known phage receptor sites. Bacteriophage sensitivity testing indicated an association between bacteriophage resistance and isolates having the novel ompA allele.
Publisher: American Society for Microbiology
Date: 08-2203
DOI: 10.1128/AEM.67.1.239-244.2001
Abstract: Combining the high specificity of bacterial biosensors and the resolution power of fluorescence-activated cell sorting (FACS) provided qualitative detection of oxytetracycline production by Streptomyces rimosus in soil microcosms. A plasmid containing a transcriptional fusion between the tetR -regulated P tet promoter from Tn 10 and a FACS-optimized gfp gene was constructed. When harbored by Escherichia coli , this plasmid produces large amounts of green fluorescent protein (GFP) in the presence of tetracycline. This tetracycline biosensor was used to detect the production of oxytetracycline by S. rimosus introduced into sterile soil. The tetracycline-induced GFP-producing biosensors were detected by FACS analysis, enabling the detection of oxytetracycline encounters by single biosensor cells. This approach can be used to study interactions between antibiotic producers and their target organisms in soil.
Publisher: American Society for Microbiology
Date: 11-2011
DOI: 10.1128/AEM.00615-11
Abstract: Parasites from the Cryptosporidium genus are the most common cause of waterborne disease around the world. Successful management and prevention of this emerging disease requires knowledge of the ersity of species causing human disease and their zoonotic sources. This study employed a spatiotemporal approach to investigate sporadic human cryptosporidiosis in New South Wales, Australia, between January 2008 and December 2010. Analysis of 261 human fecal s les showed that sporadic human cryptosporidiosis is caused by four species C. hominis , C. parvum , C. andersoni , and C. fayeri . Sequence analysis of the gp60 gene identified 5 subtype families and 31 subtypes. Cryptosporidium hominis IbA10G2 and C. parvum IIaA18G3R1 were the most frequent causes of human cryptosporidiosis in New South Wales, with 59% and 16% of infections, respectively, attributed to them. The results showed that infections were most prevalent in 0- to 4-year-olds. No gender bias or regional segregation was observed between the distribution of C. hominis and C. parvum infections. To determine the role of cattle in sporadic human infections in New South Wales, 205 cattle fecal s les were analyzed. Four Cryptosporidium species were identified, C. hominis , C. parvum , C. bovis , and C. ryanae. C. parvum subtype IIaA18G3R1 was the most common cause of cryptosporidiosis in cattle, with 47% of infections attributed to it. C. hominis subtype IbA10G2 was also identified in cattle isolates.
Publisher: Springer Science and Business Media LLC
Date: 12-2017
DOI: 10.1038/NATURE25014
Abstract: Cultivation-independent surveys have shown that the desert soils of Antarctica harbour surprisingly rich microbial communities. Given that phototroph abundance varies across these Antarctic soils, an enduring question is what supports life in those communities with low photosynthetic capacity. Here we provide evidence that atmospheric trace gases are the primary energy sources of two Antarctic surface soil communities. We reconstructed 23 draft genomes from metagenomic reads, including genomes from the candidate bacterial phyla WPS-2 and AD3. The dominant community members encoded and expressed high-affinity hydrogenases, carbon monoxide dehydrogenases, and a RuBisCO lineage known to support chemosynthetic carbon fixation. Soil microcosms aerobically scavenged atmospheric H
Publisher: Oxford University Press (OUP)
Date: 28-09-2021
Publisher: Springer Berlin Heidelberg
Date: 2014
Publisher: Microbiology Society
Date: 11-2017
Abstract: A Gram-stain-negative, rod-shaped, non-motile bacterium, designated D4N98
Publisher: Springer Science and Business Media LLC
Date: 09-11-2016
DOI: 10.1038/SREP36724
Abstract: The soil substrate membrane system (SSMS) is a novel micro-culturing technique targeted at terrestrial soil systems. We applied the SSMS to pristine and diesel fuel spiked polar soils, along with traditional solid media culturing and culture independent 454 tag pyrosequencing to elucidate the effects of diesel fuel on the soil community. The SSMS enriched for up to 76% of the total soil ersity within high diesel fuel concentration soils, in contrast to only 26% of the total ersity for the control soils. The majority of organisms originally recovered with the SSMS were lost in the transfer to solid media, with all 300 isolates belonging to Proteobacteria , Firmicutes , Actinobacteria or Bacteroidetes , the four phyla most frequently associated with soil culturing efforts. The soils spiked with high diesel fuel concentrations exhibited reduced species richness, ersity and a selection towards heterotrophs and hydrocarbon degraders in comparison to the control soils. Based on these observations and the unusually high level of overlap in microbial taxa observed between methods, we suggest the SSMS holds potential to exploit hydrocarbon degraders and other targets within simplified bacterial systems, yet is inadequate for soil ecology and ecotoxicology studies where identifying rare oligotrophic species is paramount.
Publisher: American Society for Microbiology
Date: 09-2000
DOI: 10.1128/CDLI.7.5.745-750.2000
Abstract: The detection of Cryptosporidium oocysts in drinking water is critically dependent on the quality of immunofluorescent reagents. Experiments were performed to develop a method for producing highly specific antibodies to Cryptosporidium oocysts that can be used for water testing. BALB/c mice were immunized with six different antigen preparations and monitored for immunoglobulin G (IgG) and IgM responses to the surface of Cryptosporidium oocysts. One group of mice received purified oocyst walls, a second group received a soluble protein preparation extracted from the outside of the oocyst wall, and the third group received whole inactivated oocysts. Three additional groups were immunized with sequentially prepared oocyst extracts to provide for a comparison of the immune response. Mice injected with the soluble protein extract demonstrated an IgG response to oocysts surface that was not seen in the whole-oocyst group. Mice injected with whole oocysts showed an IgM response only, while mice injected with purified oocyst walls showed little increase in IgM or IgG levels. Of the additional reported preparations only one, BME (2-mercaptoethanol treated), produced a weak IgM response to the oocyst wall. A mouse from the soluble oocyst extract group yielding a high IgG response was utilized to produce a highly specific IgG 1 monoclonal antibody (Cry104) specific to the oocyst surface. Comparative flow cytometric analysis indicated that Cry104 has a higher avidity and specificity to oocysts in water concentrates than other commercially available antibodies.
Publisher: Inderscience Publishers
Date: 2011
Publisher: Elsevier BV
Date: 11-2014
Publisher: Cold Spring Harbor Laboratory
Date: 24-02-2019
DOI: 10.1101/559666
Abstract: Terrestrial Antarctica, a predominantly microbial realm, encompasses some of the most unique environments on Earth where resident soil microbiota play key roles in the sustainability and evolution of the ecosystem. Yet the fundamental ecological processes that govern the assemblage of these natural communities remain unclear. Here, we combined multivariate analyses, co-occurrence networks and fitted species abundance distributions of licon sequencing data to disentangle community assemblage patterns of polar soil microbiomes across two ice-free deserts (Windmill Islands and Vestfold Hills) situated along the coastline of eastern Antarctica. Our findings report that communities were predominantly structured by non-neutral processes, with niche partitioning being particularly strong for bacterial communities at the Windmill Islands. In contrast, both eukaryotic and archaeal communities exhibited multimodal distributions, indicating the potential emergence of neutrality. Between the three microbial domains, polar soil bacterial communities consistently demonstrated the greatest taxonomic ersity, estimated richness, network connectivity and linear response to contemporary environmental soil parameters. We propose that reduced niche overlap promotes greater phylogenetic ersity enabling more bacterial species to co-exist and essentially thrive under adversity. However, irrespective of overall relative abundance, consistent and robust associations between co-existing community members from all three domains of life highlights the key roles that erse taxa play in ecosystem dynamics. In the face of a warming Antarctica, contemporary dynamics between polar soil microbial communities will inevitably change due to the climate-induced expansion of new ice-free areas. Increasing concern about disturbance and rapid bio ersity loss has intensified the need to better understand microbial community structure and function in high-latitude soils. We have taken an integrated approach to elucidate domain-level assemblage patterns across east Antarctic soil microbiomes. These assemblage patterns will be available to feed into policy management and conservation planning frameworks to potentially mitigate future bio ersity loss.
Publisher: Wiley
Date: 04-08-2016
Abstract: The bloom-forming cyanobacteria species Microcystis aeruginosa includes toxic and non-toxic (microcystin-producing) strains. Certain stress conditions stimulate synthesis of microcystin (MCYST) and enhance the binding of the MCYST molecule to proteins. In this quantitative proteomic study, we compared the response of a wild-type toxic strain PCC 7806, an mcyH(-) knockout non-toxic strain, and a naturally occurring non-toxic strain, PCC 7005, after 8 days in low iron (Fe) and nitrogen (N) starvation in order to assess the benefit of MCYST synthesis in non-optimal conditions. Fe limitation increased MCYST synthesis and caused an accumulation of phycobilisome proteins and the ferric iron transporter FutA only in the toxic PCC 7806 but not the non-toxic strains. In N starvation, photosynthetic, C and N metabolism proteins were more abundant in the non-toxic strains, as were chaperones and proteases. Significant interaction between nutrient availability and toxicity existed for thioredoxin peroxidase and several thioredoxin-regulated proteins. We propose a competition of MCYST for binding sites in thioredoxin-regulated proteins during oxidative stress (low Fe) but not in growth-limiting conditions (low N). This then leads to differences in the regulation of C:N metabolism in toxic and non-toxic M. aeruginosa in nutrient-replete and nutrient-limited conditions.
Publisher: Springer Science and Business Media LLC
Date: 27-05-2004
DOI: 10.1007/S00248-003-1069-9
Abstract: Exciting opportunities exist for the application of simple fluorescence-activated cell sorting (FACS) to microbiology. The technology is widely available, but critical reports on the efficiency of cell sorting using benchtop instruments are lacking. It is vital that single cell sorting be of the highest purity possible. If purity is compromised detrital material or unwanted cells will be captured along with target cells of interest. Here, the isolation of fluorescent bacteria using a benchtop FACSCalibur-sort flow cytometer is described. The efficiency and purity of isolated cells was determined using fluorescence microscopy, culturing, and molecular analysis. To achieve high purity it was essential that the total event rate did not exceed 300 cells per second. This instrument was capable of recovering >55% sorted Escherichia coli cells, coupled with a purity exceeding 99%. However, the purity of recovered cells was substantially reduced (<25%) when the event rate increased. Cell sorting onto polycarbonate membranes did not reduce the ability of E. coli to form colonies, and sorting of ~1000 E. coli cells was sufficient for 16S rDNA lification. Additionally, as few as 100 isolated Erwinia sp. carrying the gfp gene were lified using seminested PCR targeting the single copy gfp gene. With such low numbers of bacteria being required for molecular identification, FACS can be achieved without the requirement for high-speed droplet cell sorters.
Publisher: Springer Science and Business Media LLC
Date: 27-07-2007
DOI: 10.1007/S10529-007-9487-2
Abstract: Current DNA extraction methods for parasites are labour-intensive and usually involve several steps, increasing the potential for cross-contamination. We describe here a closed-tube DNA extraction procedure based upon the use of a thermostable proteinase that enabled sensitive lification of target loci from parasites from erse lineages including Apicomplexa, Sarcomastgophora and Nematoda. Moreover, this procedure is not subject to cross-contamination and is readily adaptable to automation.
Publisher: Wiley
Date: 10-2022
DOI: 10.1002/IMT2.91
Publisher: Oxford University Press (OUP)
Date: 12-06-2016
Abstract: Seasonally, snow environments cover up to 50% of the land's surface, yet the microbial ersity and ecosystem functioning within snow, particularly from alpine regions are not well described. This study explores the bacterial ersity in snow using next-generation sequencing technology. Our data expand the global inventory of snow microbiomes by focusing on two understudied regions, the Swiss Alps and the Australian Alps. A total biomass similar to cell numbers in polar snow was detected, with 5.2 to 10.5 × 10(3) cells mL(-1) of snow. We found that microbial community structure of surface snow varied by country and site and along the altitudinal range (alpine and sub-alpine). The bacterial communities present were erse, spanning 25 distinct phyla, but the six phyla Proteobacteria (Alpha- and Betaproteobacteria), Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and Firmicutes, accounted for 72%-98% of the total relative abundance. Taxa such as Acidobacteriaceae and Methylocystaceae, associated with cold soils, may be part of the atmospherically sourced snow community, while families like Sphingomonadaceae were detected in every snow s le and are likely part of the common snow biome.
Start Date: 12-2017
End Date: 07-2023
Amount: $924,105.00
Funder: Australian Research Council
View Funded ActivityStart Date: 07-2022
End Date: 07-2025
Amount: $466,656.00
Funder: Australian Research Council
View Funded ActivityStart Date: 01-2008
End Date: 05-2011
Amount: $229,052.00
Funder: Australian Research Council
View Funded ActivityStart Date: 2013
End Date: 12-2014
Amount: $580,000.00
Funder: Australian Research Council
View Funded ActivityStart Date: 2007
End Date: 12-2007
Amount: $532,000.00
Funder: Australian Research Council
View Funded ActivityStart Date: 2022
End Date: 12-2024
Amount: $490,649.00
Funder: Australian Research Council
View Funded ActivityStart Date: 2023
End Date: 12-2023
Amount: $682,792.00
Funder: Australian Research Council
View Funded ActivityStart Date: 2005
End Date: 12-2008
Amount: $230,000.00
Funder: Australian Research Council
View Funded ActivityStart Date: 06-2020
End Date: 06-2021
Amount: $400,000.00
Funder: Australian Research Council
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