ORCID Profile
0000-0002-8943-3499
Current Organisations
University of Nottingham
,
Macquarie University
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Publisher: MDPI AG
Date: 24-12-2022
DOI: 10.3390/MICROORGANISMS11010055
Abstract: Soil microbes play important roles in plant health and ecosystem functioning, however, they can often be disturbed or depleted in degraded lands. During seed-based revegetation of such sites there is often very low germination and seedling establishment success, with recruitment of beneficial microbes to the rhizosphere one potential contributor to this problem. Here we investigated whether Australian native plant species may benefit from planting seed encapsulated within extruded seed pellets amended with one of two microbe-rich products: a commercial vermicast extract biostimulant or a whole-soil inoculum from a healthy reference site of native vegetation. Two manipulative glasshouse trials assessing the performance of two Australian native plant species (Acacia parramattensis and Indigofera australis) were carried out in both unmodified field-collected soil (trial 1) and in the same soil reduced in nutrients and microbes (trial 2). Seedling emergence and growth were compared between pelleted and bare-seeded controls and analyzed alongside soil nutrient concentrations and culturable microbial community assessments. The addition of microbial amendments maintained, but did not improve upon, high levels of emergence in both plant species relative to unamended pellets. In trial 1, mean time to emergence of Acacia parramattensis seedlings was slightly shorter in both amended pellet types relative to the standard pellets, and in trial 2, whole-soil inoculum pellets showed significantly improved growth metrics. This work shows that there is potential for microbial amendments to positively affect native plant emergence and growth, however exact effects are dependent on the type of amendment, the plant species, and the characteristics of the planting site soil.
Publisher: Oxford University Press (OUP)
Date: 15-05-2009
Publisher: Microbiology Society
Date: 17-11-2021
Abstract: Competitive behaviours of plant growth promoting rhizobacteria (PGPR) are integral to their ability to colonize and persist on plant roots and outcompete phytopathogenic fungi, oomycetes and bacteria. PGPR engage in a range of antagonistic behaviours that have been studied in detail, such as the production and secretion of compounds inhibitory to other microbes. In contrast, their defensive activities that enable them to tolerate exposure to inhibitory compounds produced by their neighbours are less well understood. In this study, the genes involved in the Pseudomonas protegens Pf-5 response to metabolites from eight erse rhizosphere competitor organisms, Fusarium oxysporum , Rhizoctonia solani , Gaeumannomyces graminis var. tritici , Pythium spinosum , Bacillus subtilis QST713, Pseudomonas sp. Q2-87, Streptomyces griseus and Streptomyces bikiniensis subspecies bikiniensi , were examined. Proximity induced excreted metabolite responses were confirmed for Pf-5 with all partner organisms through HPLC before culturing a dense Pf-5 transposon mutant library adjacent to each of these microbes. This was followed by transposon-directed insertion site sequencing (TraDIS), which identified genes that influence Pf-5 fitness during these competitive interactions. A set of 148 genes was identified that were associated with increased fitness during competition, including cell surface modification, electron transport, nucleotide metabolism, as well as regulatory genes. In addition, 51 genes were identified for which loss of function resulted in fitness gains during competition. These included genes involved in flagella biosynthesis and cell ision. Considerable overlap was observed in the set of genes observed to provide a fitness benefit during competition with all eight test organisms, indicating commonalities in the competitive response to phylogenetically erse micro-organisms and providing new insight into competitive processes likely to take place in the rhizosphere.
Publisher: ACM
Date: 11-07-2023
Publisher: Public Library of Science (PLoS)
Date: 03-10-2008
Publisher: MDPI AG
Date: 08-09-2015
DOI: 10.3390/GENES6030841
Publisher: American Society for Microbiology
Date: 11-03-2021
DOI: 10.1128/MRA.01341-20
Abstract: Subsurface coal seams harbor an array of erse microbial species subsisting as a community on the organic matter present in coal. Here, we present the annotated genome sequence of Dietzia sp. strain SYD-A1, a bacterium isolated from a terrestrial subsurface coal seam in New South Wales (NSW), Australia.
Publisher: ACM
Date: 19-04-2023
Publisher: ACM
Date: 13-03-2023
Publisher: Elsevier BV
Date: 04-2016
Publisher: Springer Science and Business Media LLC
Date: 30-10-2017
DOI: 10.1038/S41598-017-14707-Z
Abstract: The introduction of different nutrient and energy sources during weaning leads to significant changes in the infant gut microbiota. We used an in vitro infant digestive and gut microbiota model system to investigate the effect of four commercially available cereal products based on either wheat, sorghum, rice or oats, on the gut microbiota of six infants. Our results indicated cereal additions induced numerous changes in the gut microbiota composition. The relative abundance of bacterial families associated with fibre degradation, Bacteroidaceae , Bifidobacteriaceae , Lactobacillaceae , Prevotellaceae , Ruminococcaceae and Veillonellaceae increased, whilst the abundance of Enterobacteriaceae decreased with cereal additions. Corresponding changes in the production of SCFAs showed higher concentrations of acetate following all cereal additions, whilst, propionate and butyrate varied between specific cereal additions. These cereal-specific variations in the concentrations of SCFAs showed a moderate correlation with the relative abundance of potential SCFA-producing bacterial families. Overall, our results demonstrated clear shifts in the abundance of bacterial groups associated with weaning and an increase in the production of SCFAs following cereal additions.
Publisher: Public Library of Science (PLoS)
Date: 18-06-2012
Publisher: Oxford University Press (OUP)
Date: 19-06-2019
Abstract: Microbial communities in subsurface coal seams are responsible for the conversion of coal organic matter to methane. This process has important implications for both energy production and our understanding of global carbon cycling. Despite the environmental and economic importance of this process, little is known about which components of the heterogeneous coal organic matter are biodegradable under methanogenic conditions. Similarly, little is known about which taxa in coal seams carry out the initial stages of coal organics degradation. To identify the biodegradable components of coal and the microorganisms responsible for their breakdown, a subbituminous coal was fractionated into a number of chemical compound classes which were used as the sole carbon source for growth by a coal seam microbial community. This study identifies 65 microbial taxa able to proliferate on specific coal fractions and demonstrates a surprising level of substrate specificity among members of this coal-degrading microbial consortia. Additionally, coal kerogen, the solvent-insoluble organic component of coal often considered recalcitrant to microbial degradation, appeared to be readily converted to methane by microbial degradation. These findings challenge our understanding of coal organic matter catabolism and provide insights into the catabolic roles of in idual coal seam bacteria.
Publisher: Cold Spring Harbor Laboratory
Date: 09-02-2023
DOI: 10.1101/2023.02.09.527782
Abstract: Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbour class 1 integrons. We developed a modified version of epicPCR ( e mulsion, p aired i solation and c oncatenation p olymerase c hain r eaction) that links class 1 integrons lified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water s les that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multi-gene loci of interest. We also identified the Rhizobacter genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts towards hotspots of class 1 integron-mediated dissemination of AMR. We present a novel single-cell genomic surveillance technology for identifying environmental bacterial hosts of a class of mobile genetic elements that are linked to anthropogenic pollution and contribute to the dissemination of antimicrobial resistance.
Publisher: Frontiers Media SA
Date: 02-12-2020
DOI: 10.3389/FMICB.2020.605952
Abstract: Acinetobacter species are emerging as major nosocomial pathogens, aided by their ability to acquire resistance to all classes of antibiotics. A key factor leading to their multi-drug resistance phenotypes is the acquisition of a wide variety of mobile genetic elements, particularly large conjugative plasmids. Here, we characterize a family of 21 multi-drug resistance mega-plasmids in 11 different Acinetobacter species isolated from various locations across the globe. The plasmid family exhibits a highly dynamic and erse accessory genome, including 221 antibiotic resistance genes (ARGs) that confer resistance to 13 classes of antibiotics. We show that plasmids isolated within the same geographic region are often evolutionarily ergent members of this family based on their core-genome, yet they exhibit a more similar accessory genome. In idual plasmids, therefore, can disseminate to different locations around the globe, where they then appear to acquire erse sets of accessory genes from their local surroundings. Further, we show that plasmids from several geographic regions were enriched with location-specific functional traits. Together, our findings show that these mega-plasmids can transmit across species boundaries, have the capacity for global dissemination, can accumulate a erse suite of location-specific accessory genes, and can confer multi-drug resistance phenotypes of significant concern for human health. We therefore highlight this previously undescribed plasmid family as a serious threat to healthcare systems worldwide. These findings also add to the growing concern that mega-plasmids are key disseminators of antibiotic resistance and require global surveillance.
Publisher: PeerJ
Date: 19-03-2020
DOI: 10.7717/PEERJ.8705
Abstract: Fish skin and gut microbiomes contribute to host health and growth and are often significantly different in aquaculture-reared fish compared to wild fish. Determining how factors associated with aquaculture, including altered diet and abiotic conditions, affect the microbiome will assist with optimizing farming practices and non-invasively assessing fish health. Here, juvenile yellowtail kingfish ( Seriola lalandi ) housed at optimal (22 °C) and non-optimal (26 °C) water temperature were fed a fishmeal control diet or the same diet substituted with 30% soy-protein concentrate (SPC) in order to investigate impacts on host health and the microbial community composition of the skin mucosa, gut mucosa and digesta. Each of these sites was observed to have a distinct microbiome composition. The combination of SPC and housing at 26 °C significantly reduced weight gain in yellowtail kingfish and affected immune parameters. The overall microbial composition and relative abundance of specific operational taxonomic units (OTUs) was also significantly altered by inclusion of SPC at 26 °C, with a notable increase in an OTU identified as Photobacterium in the skin mucosa and digesta. Increased relative abundance of Photobacterium sp. was significantly correlated with reduced levels of digesta myeloperoxidase in yellowtail kingfish a recognized innate immunity defense mechanism. The changes in the microbial communities of yellowtail kingfish fed a diet containing 30% SPC at 26 °C highlights the importance of considering the interactive effects of diet and environmental factors on microbiome health in farmed yellowtail kingfish.
Publisher: Cold Spring Harbor Laboratory
Date: 14-02-2023
DOI: 10.1101/2023.02.13.528379
Abstract: Plastic pollution is a serious global problem, with more than 12 million tonnes of plastic waste entering the oceans every year. Plastic debris can have considerable impacts on microbial community structure and functions in marine environments, and has been associated with an enrichment in pathogenic bacteria and antimicrobial resistance (AMR) genes. However, our understanding of these impacts is largely restricted to microbial assemblages on plastic surfaces. It is therefore unclear whether these effects are driven by the surface properties of plastics, providing an additional niche for certain microbes residing in biofilms, and/or chemicals leached from plastics, the effects of which could extend to surrounding planktonic bacteria. Here, we examine the effects of polyvinyl chloride (PVC) plastic leachate exposure on the relative abundance of genes associated with bacterial pathogenicity and AMR within a seawater microcosm community. We show that PVC leachate, in the absence of plastic surfaces, drives an enrichment in AMR and virulence genes. In particular, leachate exposure significantly enriches AMR genes that confer multidrug, aminoglycoside and peptide antibiotic resistance. Additionally, enrichment of genes involved in the extracellular secretion of virulence proteins was observed among pathogens of marine organisms. This study provides the first evidence that chemicals leached from plastic particles alone can enrich genes related to microbial pathogenesis within a bacterial community, expanding our knowledge of the environmental impacts of plastic pollution with potential consequences for human and ecosystem health.
Publisher: Cold Spring Harbor Laboratory
Date: 16-07-2020
DOI: 10.1101/2020.07.16.205906
Abstract: Gene essentiality studies have been performed on numerous bacterial pathogens, but essential gene sets have been determined for only a few plant-associated bacteria. Pseudomonas protegens Pf-5 is a plant-commensal, biocontrol bacteria that can control disease-causing pathogens on a wide range of crops. Work on Pf-5 has mostly focused on secondary metabolism and biocontrol genes, but genome-wide approaches such as high-throughput transposon mutagenesis have not yet been used in this species. Here we generated a dense P. protegens Pf-5 transposon mutant library and used transposon-directed insertion site sequencing (TraDIS) to identify 446 genes essential for growth on rich media. Genes required for fundamental cellular machinery were enriched in the essential gene set, while genes related to nutrient biosynthesis, stress responses and transport were under-represented. Comparison of the essential gene sets of Pf-5 and P. aeruginosa PA14, an opportunistic human pathogen, provides insight into the biological processes important for their different lifestyles. Key differences include cytochrome c biogenesis, formation of periplasmic disulfide bonds, lipid biosynthesis, ribonuclease activity, lipopolysaccharides and cell surface structures. Comparison of the Pf-5 in silico predicted and in vitro determined essential gene sets highlighted the essential cellular functions that are over- and underestimated by each method. Expanding essentiality studies into bacteria with a range of lifestyles can improve our understanding of the biological processes important for survival and growth in different environmental niches. Essential genes are those crucial for survival or normal growth rates in an organism. Essential gene sets have been identified in numerous bacterial pathogens, but only a few plant-associated bacteria. Employing genome-wide approaches, such as transposon insertion sequencing, allows for the concurrent analysis of all genes of a bacterial species and rapid determination of essential gene sets. We have used transposon insertion sequencing to systematically analyze thousands of Pseudomonas protegens Pf-5 genes and gain insights into gene functions and interactions that are not readily available using traditional methods. Comparing Pf-5 essential genes with those of P. aeruginosa PA14, an opportunistic human pathogen, provides insight into differences in gene essentiality which may be linked to their different lifestyles.
Publisher: Wiley
Date: 20-09-2022
DOI: 10.1002/PPP3.10329
Abstract: Mixed species plantings present an attractive alternative to monoculture reforestation through their added benefits to bio ersity. Yet there is ambiguity in the use of the term ‘bio ersity’ in carbon and bio ersity markets, which may create perverse outcomes when designing schemes and projects. Here, we review how the concept of bio ersity is defined and applied in reforestation projects, and restoration more broadly. Improved transparency around the use of the term bio ersity is urgently needed to provide rigour in emerging market mechanisms, which seek to benefit the environment and people. Reforestation to capture and store atmospheric carbon is increasingly ch ioned as a climate change mitigation policy response. Reforestation plantings have the potential to provide conservation co‐benefits when erse mixtures of native species are planted, and there are growing attempts to monetise bio ersity benefits from carbon reforestation projects, particularly within emerging carbon markets. But what is meant by ‘bio erse’ across different stakeholders and groups implementing and overseeing these projects and how do these perceptions compare with long‐standing scientific definitions? Here, we discuss approaches to, and definitions of, bio ersity in the context of reforestation for carbon sequestration. Our aim is to review how the concept of bio ersity is defined and applied among stakeholders (e.g., governments, carbon certifiers and farmers) and rights holders (i.e., First Nations people) engaging in reforestation, and to identify best‐practice methods for restoring bio ersity in these projects. We find that some stakeholders have a vague understanding of ersity across varying levels of biological organisation (genes to ecosystems). While most understand that bio ersity underpins ecosystem functions and services, many stakeholders may not appreciate the difficulties of restoring bio ersity akin to reference ecosystems. Consequently, bio ersity goals are rarely explicit, and project goals may never be achieved because the levels of restored bio ersity are inadequate to support functional ecosystems and desired ecosystem services. We suggest there is significant value in integrating bio ersity objectives into reforestation projects and setting specific restoration goals with transparent reporting outcomes will pave the way for ensuring reforestation projects have meaningful outcomes for bio ersity, and legitimate incentive payments for bio ersity and natural capital accounting.
Publisher: Wiley
Date: 03-01-2023
DOI: 10.1111/REC.13857
Abstract: Worldwide, there is a strong need for new, innovative, large‐scale approaches to restoring erse native vegetation. Seed‐based revegetation, while often employed, can suffer from low plant establishment. Various seed coating technologies have been widely employed for decades to promote efficient agricultural planting however, a significant obstacle to the implementation of this technology for native species revegetation is the limited access to the expertise and techniques which are mostly confidential to and specialized for the agrochemical industry. Here we investigated whether the seeds of Australian native species may benefit from extruded pelleting, measuring both seedling emergence and early growth, and testing the pellets with and without the addition of a commercial plant probiotic. A manipulative glasshouse experiment was carried out with three treatments (bare seeded standard pellets pellets amended with a probiotic) for four native plant species. Incorporation of seeds within standard pellets was shown to maintain high percentages of emergence and improve growth of three of the tested species ( Daviesia ulicifolia , Hardenbergia violacea , and Indigofera australis ) in the glasshouse setting, with increases in mean biomass of 83, 385, and 1,002%, respectively. However, emergence in the fourth species ( Bursaria spinosa ) was low in all seed treatments, perhaps due to excessive sowing depth (bare seeds), while combined with being encased inside a pellet. Relative to the standard pellets, probiotic amended pellets did not impart further detectable emergence or growth benefits. Ultimately, these results highlight exciting prospects for the application of extruded seed pellets in facilitating efficient use of seed in the revegetation of some native species.
Publisher: Wiley
Date: 30-10-2023
DOI: 10.1002/PPP3.10448
Publisher: American Society for Microbiology
Date: 08-03-2021
DOI: 10.1128/JB.00432-20
Abstract: Essential genes are those crucial for survival or normal growth rates in an organism. Essential gene sets have been identified in numerous bacterial pathogens but only a few plant-associated bacteria.
Publisher: Association for Computing Machinery (ACM)
Date: 05-01-2021
DOI: 10.1145/3432947
Abstract: Via audiovisual communications and a controllable physical embodiment, Mobile Robotic telePresence (MRP) systems aim to support enhanced collaboration between remote and local members of a given setting. But MRP systems also put the remote user in positions where they frequently rely on the help of local partners. Getting or 'recruiting' such help can be done with various verbal and embodied actions ranging in explicitness. In this paper, we look at how such recruitment occurs in video data drawn from an experiment where pairs of participants (one local, one remote) performed a timed searching task. We find a prevalence of implicit recruitment methods and outline obstacles to effective recruitment that emerge due to communicative asymmetries that are built into MRP design. In a future where remote work becomes widespread, assistance through remote work technology like MRPs needs close examination at a fundamental interactional level, taking into account how communicative asymmetries are at play in everyday use of such technologies.
Publisher: American Chemical Society (ACS)
Date: 13-03-2023
Publisher: Elsevier BV
Date: 06-2023
Publisher: Frontiers Media SA
Date: 21-03-2018
Publisher: Frontiers Media SA
Date: 23-06-2022
DOI: 10.3389/FMARS.2022.872082
Abstract: Bundera sinkhole, located in north-western Australia, is the only known continental anchialine system in the Southern Hemisphere. Anchialine environments are characterised by stratified water columns with complex physicochemical profiles spanning hypoxic and anoxic regions, often displaying high levels of endemism. Research on these systems has focused on eukaryotic fauna, however interest in the microbial ersity of these environments is growing, enabled by next-generation DNA sequencing. Here we report detailed analyses of the microbial communities across a depth profile within Bundera sinkhole (from 2 to 28 m), involving parallel physicochemical measurements, cell population counts and 16S rRNA licon analyses. We observed clear shifts in microbial cell counts, community ersity, structure and membership across the depth profile, reflecting changing levels of light, organic and inorganic energy sources as well as shifts in pH and salinity. While Proteobacteria were the most abundant phylum found, there was a high degree of taxonomic novelty within these microbial communities, with 13,028 unique licon sequence variants (ASVs) identified, belonging to 67 identifiable bacterial and archaeal phyla. Of these ~4,600, more than one third of the total, were unclassified below family level. A small number of ASVs were highly abundant at select depths, all of which were part of the set not classified below family level. The 2 m and 6 m s les had in common two highly abundant ASVs, belonging to the Ectothiorhodospiraceae and Thiotrichaceae families, while the 8 m community contained a single predominant ASV belonging to family Thioglobaceae. At lower depths a different Ectothiorhodospiraceae ASV comprised up to 68% relative abundance, peaking at 26 and 28 m. Canonical correspondence analyses indicated that community structure was strongly influenced by differences in key physicochemical parameters, particularly salinity, dissolved organic and inorganic carbon, phosphate and sulphate concentrations. This work highlights the potential for anchialine systems to house considerable microbial novelty, potentially driven by adaptations to the specific physicochemical makeup of their local environment. As only a small number of anchialine systems have been examined via microbial community studies to date, this work is particularly valuable, contributing new insight regarding the microbial residents of these important and sensitive environments.
Publisher: Oxford University Press (OUP)
Date: 28-11-2016
DOI: 10.1093/NAR/GKW1068
Publisher: Proceedings of the National Academy of Sciences
Date: 25-11-2013
Abstract: Drug resistance is an increasing problem in clinical settings with some bacterial pathogens now resistant to virtually all available drugs. Chlorhexidine is a commonly used antiseptic and disinfectant in hospital environments, and there is increasing resistance to chlorhexidine seen in some pathogenic bacteria, such as Acinetobacter baumannii . This paper examines the global gene expression of A. baumannii in response to chlorhexidine exposure and identifies a gene that we demonstrate to mediate chlorhexidine resistance. Biochemical investigation reveals that this gene encodes a previously uncharacterized type of drug efflux pump that actively transports chlorhexidine out of the cell.
Publisher: Elsevier BV
Date: 05-2015
DOI: 10.1016/J.RESMIC.2014.10.003
Abstract: Clostridium perfringens can be isolated from a range of environments, including soil, marine and fresh water sediments, and the gastrointestinal tracts of animals and humans. Some C. perfringens strains have attractive industrial applications, e.g., in the degradation of waste products or the production of useful chemicals. However, C. perfringens has been most studied as the causative agent of a range of enteric and soft tissue infections of varying severities in humans and animals. Host preference and disease type in C. perfringens are intimately linked to the production of key extracellular toxins and on this basis toxigenic C. perfringens strains have been classified into five toxinotypes (A-E). To date, twelve genome sequences have been generated for a erse collection of C. perfringens isolates, including strains associated with human and animal infections, a human commensal strain, and a strain with potential industrial utility. Most of the sequenced strains are classified as toxinotype A. However, genome sequences of representative strains from each of the other four toxinotypes have also been determined. Analysis of this collection of sequences has highlighted a lack of features differentiating toxinotype A strains from the other isolates, indicating that the primary defining characteristic of toxinotype A strains is their lack of key plasmid-encoded extracellular toxin genes associated with toxinotype B to E strains. The representative B-E strains sequenced to date each harbour many unique genes. Additional genome sequences are needed to determine if these genes are characteristic of their respective toxinotypes.
Publisher: Microbiology Society
Date: 25-06-2021
DOI: 10.1099/MIC.0.001064
Abstract: Marine plastic pollution is a growing concern worldwide and has the potential to impact marine life via leaching of chemicals, with zinc (Zn), a common plastic additive, observed at particularly high levels in plastic leachates in previous studies. At this time, however, little is known regarding how elevated Zn affects key groups of marine primary producers. Marine cyanobacterial genera Prochlorococcus and Synechococcus are considered to be some of the most abundant oxygenic phototrophs on earth, and together contribute significantly to oceanic primary productivity. Here we set out to investigate how two Prochlorococcus (MIT9312 and NATL2A) and two Synechococcus (CC9311 and WH8102) strains, representative of erse ecological niches, respond to exposure to high Zn concentrations. The two genera showed differences in the timing and degree of growth and physiological responses to elevated Zn levels, with Prochlorococcus strains showing declines in their growth rate and photophysiology following exposure to 27 µg l −1 Zn, while Synechococcus CC9311 and WH8102 growth rates declined significantly on exposure to 52 and 152 µg l −1 Zn, respectively. Differences were also observed in each strain’s capacity to maintain cell wall integrity on exposure to different levels of Zn. Our results indicate that excess Zn has the potential to pose a challenge to some marine picocyanobacteria and highlights the need to better understand how different marine Prochlorococcus and Synechococcus strains may respond to increasing concentrations of Zn in some marine regions.
Publisher: Elsevier BV
Date: 2013
DOI: 10.1016/J.NBT.2012.07.005
Abstract: Trichoderma reesei Rut-C30 is used widely as an expression host for various gene products. We have explored cellular effects caused by the expression of a mutant form of cellobiohydrolase I (CBHI), the major secreted protein of T. reesei using biochemical and transcriptomic analyses and confocal laser scanning microscopy. The mutated CBHI was tagged fluorescently with Venus to establish the subcellular location of the fusion protein and its potential association with the proteasome, an organelle assigned for the disposal of misfolded proteins. Expression of the mutant CBHI in the high protein-secreting host Rut-C30 caused physiological changes in the fungal hyphae, affected protein secretion and elicited ER stress. A massive upregulation of UPR- and ERAD-related genes sec61, der1, uba1, bip1, pdi1, prp1, cxl1 and lhs1 was observed by qRT-PCR in the CBHIΔ4-Venus strain with four mutations introduced in the DNA encoding the core domain of CBHI. Further stress was applied to this strain by inhibiting function of the proteasome with MG132 (N-benzoylcarbonyl(Cbz)-Leu-Leu-leucinal). The effect of MG132 was found to be specific to the proteasome-associated genes. There are no earlier reports on the effect of proteasome inhibition on protein quality control in filamentous fungi. Confocal fluorescence microscopy studies suggested that the mutant CBHI accumulated in the ER and colocalized with the fungal proteasome. These results provide an indication that there is a limit to how far T. reesei Rut-C30, already under secretion stress, can be pressed to produce higher protein yields.
Publisher: Cold Spring Harbor Laboratory
Date: 12-01-2023
DOI: 10.1101/2023.01.12.523705
Abstract: Swimming motility is a key bacterial trait, important to success in many niches, including assisting in colonization of host surfaces. Biocontrol bacteria, such as Pseudomonas protegens Pf-5 are increasingly being used as an agricultural tool to control crop diseases, where motility is a factor in successful colonization of the plant rhizosphere. Swimming motility has been studied in a range of bacteria and typically involves a suite of flagella and chemotaxis genes, however the specific gene set employed for both regulation and biogenesis can differ substantially between organisms. Here we used transposon directed insertion site sequencing (TraDIS), a genome-wide approach, to identify 249 genes involved in P. protegens Pf-5 swimming motility. As expected, flagella and chemotaxis genes comprised a large proportion of these genes. However we also identified a suite of additional genes important for swimming, including genes related to peptidoglycan turnover, O-antigen biosynthesis, cell ision, signal transduction, c-di-GMP turnover and phosphate transport, along with 27 conserved hypothetical proteins. Experimental gene knockout mutants and TraDIS data together suggest that defects in the Pst phosphate transporter lead to enhanced swimming motility. Overall, this study expands our knowledge of pseudomonad motility and highlights the utility of a TraDIS-based approach for systematically analyzing the functions of thousands of genes. This work sets a foundation for understanding how swimming motility may be related to the inconsistency in biocontrol bacteria effectiveness and reliability in the field. Biocontrol bacteria, such as Pseudomonas protegens Pf-5 are increasingly being used as an agricultural tool to control crop diseases, and motility is a key factor in their successful colonization of plant surfaces. Here we use a high-throughput approach to identify the suite of genes important for swimming motility in P. protegens Pf-5. These included flagella and chemotaxis genes, as well as a variety of cell surface, cell ision and signalling genes. We also show that defects in the Pst phosphate transporter lead to enhanced swimming motility, a hitherto unreported link between phosphate transport and swimming motility. Understanding the genetic basis of swimming motility enhances our knowledge of key processes in biocontrol bacteria that are needed to ensure their competitive success. This will contribute to developing strategies to increase the utility of biocontrol bacteria in agricultural settings to prevent crop losses.
Publisher: Springer Science and Business Media LLC
Date: 14-05-2019
DOI: 10.1038/S42003-019-0410-X
Abstract: Plastic pollution is a global threat to marine ecosystems. Plastic litter can leach a variety of substances into marine environments however, virtually nothing is known regarding how this affects photosynthetic bacteria at the base of the marine food web. To address this, we investigated the effect of plastic leachate exposure on marine Prochlorococcus , widely considered the most abundant photosynthetic organism on Earth and vital contributors to global primary production and carbon cycling. Two strains of Prochlorococcus representing distinct ecotypes were exposed to leachate from common plastic items: high-density polyethylene bags and polyvinyl chloride matting. We show leachate exposure strongly impairs Prochlorococcus in vitro growth and photosynthetic capacity and results in genome-wide transcriptional changes. The strains showed distinct differences in the extent and timing of their response to each leachate. Consequently, plastic leachate exposure could influence marine Prochlorococcus community composition and potentially the broader composition and productivity of ocean phytoplankton communities.
Publisher: American Society for Microbiology
Date: 15-06-2016
DOI: 10.1128/AEM.00192-16
Abstract: Gut microbiota play an important role in maintenance of mammalian metabolism and immune system regulation, and disturbances to this community can have adverse impacts on animal health. To better understand the composition of gut microbiota in marine mammals, fecal bacterial communities of the Australian sea lion ( Neophoca cinerea ), an endangered pinniped with localized distribution, were examined. A comparison of s les from in iduals across 11 wild colonies in South and Western Australia and three Australian captive populations showed five dominant bacterial phyla: Firmicutes , Proteobacteria , Bacteroidetes , Actinobacteria , and Fusobacteria . The phylum Firmicutes was dominant in both wild (76.4% ± 4.73%) and captive animals (61.4% ± 10.8%), while Proteobacteria contributed more to captive (29.3% ± 11.5%) than to wild (10.6% ± 3.43%) fecal communities. Qualitative differences were observed between fecal communities from wild and captive animals based on principal-coordinate analysis. SIMPER (similarity percentage procedure) analyses indicated that operational taxonomic units (OTU) from the bacterial families Clostridiaceae and Ruminococcaceae were more abundant in wild than in captive animals and contributed most to the average dissimilarity between groups (SIMPER contributions of 19.1% and 10.9%, respectively). Differences in the biological environment, the foraging site fidelity, and anthropogenic impacts may provide various opportunities for unique microbial establishment in Australian sea lions. As anthropogenic disturbances to marine mammals are likely to increase, understanding the potential for such disturbances to impact microbial community compositions and subsequently affect animal health will be beneficial for management of these vulnerable species. IMPORTANCE The Australian sea lion is an endangered species for which there is currently little information regarding disease and microbial ecology. In this work, we present an in-depth study of the fecal microbiota of a large number of Australian sea lions from geographically erse wild and captive populations. Colony location and captivity were found to influence the gut microbial community compositions of these animals. Our findings significantly extend the baseline knowledge of marine mammal gut microbiome composition and variability.
Publisher: Humana Press
Date: 2014
DOI: 10.1007/978-1-62703-712-9_8
Abstract: Microbial identification using 16S rDNA variable regions has become increasingly popular over the past decade. The application of next-generation licon sequencing to these regions allows microbial communities to be sequenced in far greater depth than previous techniques, as well as allowing for the identification of unculturable or rare organisms within a s le. Multiplexing can be used to sequence multiple s les in tandem through the use of s le-specific identification sequences which are attached to each licon, making this a cost-effective method for large-scale microbial identification experiments.
Publisher: Elsevier BV
Date: 02-2018
Publisher: Springer Science and Business Media LLC
Date: 26-08-2023
DOI: 10.1186/S40168-023-01633-8
Abstract: Anchialine environments, in which oceanic water mixes with freshwater in coastal aquifers, are characterised by stratified water columns with complex physicochemical profiles. These environments, also known as subterranean estuaries, support an abundance of endemic macro and microorganisms. There is now growing interest in characterising the metabolisms of anchialine microbial communities, which is essential for understanding how complex ecosystems are supported in extreme environments, and assessing their vulnerability to environmental change. However, the ersity of metabolic strategies that are utilised in anchialine ecosystems remains poorly understood. Here, we employ shotgun metagenomics to elucidate the key microorganisms and their dominant metabolisms along a physicochemical profile in Bundera Sinkhole, the only known continental subterranean estuary in the Southern Hemisphere. Genome-resolved metagenomics suggests that the communities are largely represented by novel taxonomic lineages, with 75% of metagenome-assembled genomes assigned to entirely new or uncharacterised families. These erse and novel taxa displayed depth-dependent metabolisms, reflecting distinct phases along dissolved oxygen and salinity gradients. In particular, the communities appear to drive nutrient feedback loops involving nitrification, nitrate ammonification, and sulphate cycling. Genomic analysis of the most highly abundant members in this system suggests that an important source of chemotrophic energy is generated via the metabolic coupling of nitrogen and sulphur cycling. These findings substantially contribute to our understanding of the novel and specialised microbial communities in anchialine ecosystems, and highlight key chemosynthetic pathways that appear to be important in these energy-limited environments. Such knowledge is essential for the conservation of anchialine ecosystems, and sheds light on adaptive processes in extreme environments.
Publisher: Microbiology Society
Date: 18-01-2023
Abstract: Membrane transporters are a large group of proteins that span cell membranes and contribute to critical cell processes, including delivery of essential nutrients, ejection of waste products, and assisting the cell in sensing environmental conditions. Obtaining an accurate and specific annotation of the transporter proteins encoded by a micro-organism can provide details of its likely nutritional preferences and environmental niche(s), and identify novel transporters that could be utilized in small molecule production in industrial biotechnology. The Transporter Automated Annotation Pipeline (TransAAP) ( ransportDB2/TransAAP_login.html ) is a fully automated web service for the prediction and annotation of membrane transport proteins in an organism from its genome sequence, by using comparisons with both curated databases such as the TCDB (Transporter Classification Database) and TDB, as well as selected Pfams and TIGRFAMs of transporter families and other methodologies. TransAAP was used to annotate transporter genes in the prokaryotic genomes in the National Center for Biotechnology Information (NCBI) RefSeq these are presented in the transporter database TransportDB ( www.membranetransport.org ) website, which has a suite of data visualization and analysis tools. Creation and maintenance of a bioinformatic database specific for transporters in all genomic datasets is essential for microbiology research groups and the general research/biotechnology community to obtain a detailed picture of membrane transporter systems in various environments, as well as comprehensive information on specific membrane transport proteins.
Publisher: Springer Science and Business Media LLC
Date: 31-03-2021
DOI: 10.1038/S41598-021-85946-4
Abstract: Effective implementation of antibiotic stewardship, especially in critical care, is limited by a lack of direct comparative investigations on how different antibiotics impact the microbiota and antibiotic resistance rates. We investigated the impact of two commonly used antibiotics, third-generation cephalosporins (3GC) and piperacillin/tazobactam (TZP) on the endotracheal, perineal and faecal microbiota of intensive care patients in Australia. Patients exposed to either 3GC, TZP, or no β-lactams (control group) were s led over time and 16S rRNA licon sequencing was performed to examine microbiota ersity and composition. While neither treatment significantly affected ersity, numerous changes to microbiota composition were associated with each treatment. The shifts in microbiota composition associated with 3GC exposure differed from those observed with TZP, consistent with previous reports in animal models. This included a significant increase in Enterobacteriaceae and Enterococcaceae abundance in endotracheal and perineal microbiota for those administered 3GC compared to the control group. Culture-based analyses did not identify any significant changes in the prevalence of specific pathogenic or antibiotic-resistant bacteria. Exposure to clinical antibiotics has previously been linked to reduced microbiota ersity and increased antimicrobial resistance, but our results indicate that these effects may not be immediately apparent after short-term real-world exposures.
Publisher: American Society for Microbiology
Date: 02-05-2013
Abstract: The neurotoxins produced by Clostridium botulinum strains are among the world's most potent toxins and are the causative agents of paralytic botulism. Here, we present the draft genome sequence of the group III C. botulinum strain Eklund-C, including a pseudolysogen-like bacteriophage that harbors the type C neurotoxin operon.
Publisher: Cold Spring Harbor Laboratory
Date: 03-04-2023
DOI: 10.1101/2023.04.03.535450
Abstract: Anchialine environments, in which oceanic water mixes with freshwater in coastal aquifers, are characterised by stratified water columns with complex physicochemical profiles. These environments, also known as subterranean estuaries, support an abundance of endemic macro and microorganisms. There is now growing interest in characterising the metabolisms of anchialine microbial communities, which is essential for understanding how complex ecosystems are supported in extreme environments, and assessing their vulnerability to environmental change. However, the ersity of metabolic strategies that are utilised in anchialine ecosystems remains poorly understood. Here, we employ shotgun metagenomics to elucidate the key microorganisms and their dominant metabolisms along a physicochemical profile in Bundera Sinkhole, the only known continental subterranean estuary in the Southern Hemisphere. Genome-resolved metagenomics suggests that the communities are largely represented by novel taxonomic lineages, with 75% of metagenome-assembled genomes assigned to entirely new or uncharacterised families. These erse and novel taxa displayed depth-dependent metabolisms, reflecting distinct phases along dissolved oxygen and salinity gradients. In particular, the communities appear to drive nutrient feedback loops involving nitrification, nitrate ammonification, and sulphate cycling. Genomic analysis of the most highly abundant members in this system suggests that an important source of chemotrophic energy is generated via the metabolic coupling of nitrogen and sulphur cycling. These findings substantially contribute to our understanding of the novel and specialised microbial communities in anchialine ecosystems, and highlight key chemosynthetic pathways that appear to be important in these energy-limited environments. Such knowledge is essential for the conservation of anchialine ecosystems, and sheds light on adaptive processes in extreme environments.
Publisher: Cold Spring Harbor Laboratory
Date: 08-09-2021
DOI: 10.1101/2021.09.08.459516
Abstract: Integrons are bacterial genetic elements that can integrate mobile gene cassettes. They are mostly known for spreading antibiotic resistance cassettes among human pathogens. However, beyond clinical settings, gene cassettes encode an extraordinarily erse range of functions important for bacterial adaptation. The recovery and sequencing of cassettes has promising applications, including: surveillance of clinically important genes, particularly antibiotic resistance determinants investigating the functional ersity of integron-carrying bacteria and novel enzyme discovery. Although gene cassettes can be directly recovered using PCR, there are no standardised methods for their lification and, importantly, for validating sequences as genuine integron gene cassettes. Here, we present reproducible methods for the PCR lification, sequence processing, and validation of gene cassette licons from complex communities. We describe two different PCR assays that either lify cassettes together with integron integrases, or gene cassettes together within cassette arrays. We compare the use of Nanopore and Illumina sequencing, and present bioinformatic pipelines that filter sequences to ensure that they represent licons from genuine integrons. Using a erse set of environmental DNAs, we show that our approach can consistently recover thousands of unique cassettes per s le and up to hundreds of different integron integrases. Recovered cassettes confer a wide range of functions, including antibiotic resistance, with as many as 300 resistance cassettes found in a single s le. In particular, we show that class 1 integrons appear to be collecting and concentrating antibiotic resistance genes out of the broader ersity of cassette functions. The methods described here can be applied to any environmental or clinical microbiome s le.
Publisher: Public Library of Science (PLoS)
Date: 19-03-2013
Publisher: Wiley
Date: 21-10-2016
DOI: 10.1111/NYAS.13268
Abstract: Antibiotic resistance arises as a consequence of complex interactions among genes, mobile elements, and their bacterial hosts, coupled with the intense selection pressures imposed by humans in an attempt to control bacterial growth. Understanding the evolution of resistance requires an understanding of interacting cellular and genetic components. Here, we review how DNA analysis has helped reconstruct the origins of the mosaic, multiresistant mobile elements that have spread through pathogens in the last 60 years. This history helps inform the future, such that resistance might be better managed. Whole-genome sequencing has great potential for epidemiological tracking and for understanding the development of resistance via experimental evolution. DNA analysis also offers the opportunity for constructing databases that record genes of interest, the mobile elements that move these genes, and the cells or species that acquire such genes. Linking these DNA elements to their human and animal hosts and to the environments where they occur should help us establish a more robust ecological and evolutionary framework for controlling and managing resistance. Such efforts need to be well coordinated because, like many other issues that face humanity, antibiotic resistance is a global problem that requires global solutions.
Publisher: Public Library of Science (PLoS)
Date: 22-01-2010
Publisher: American Society for Microbiology
Date: 26-06-2014
Abstract: Clostridium strains from six phylogenetic groups, C. botulinum groups I to IV, C. baratii , and C. butyricum , display the capacity to produce botulinum neurotoxin. Here, we present the genome sequence of a C. butyricum isolate, the neurotoxigenic strain 5521, which encodes the type E botulinum neurotoxin.
Publisher: Springer Science and Business Media LLC
Date: 08-04-2010
Abstract: Previous microarray analyses have shown a key role for the two-component system PhoBR (SYNW0947, SYNW0948) in the regulation of P transport and metabolism in the marine cyanobacterium Synechococcus sp. WH8102. However, there is some evidence that another regulator, SYNW1019 (PtrA), probably under the control of PhoBR, is involved in the response to P depletion. PtrA is a member of the cAMP receptor protein transcriptional regulator family that shows homology to NtcA, the global nitrogen regulator in cyanobacteria. To define the role of this regulator, we constructed a mutant by insertional inactivation and compared the physiology of wild-type Synechcococcus sp. WH8102 with the ptrA mutant under P-replete and P-stress conditions. In response to P stress the ptrA mutant failed to upregulate phosphatase activity. Microarrays and quantitative RT-PCR indicate that a subset of the Pho regulon is controlled by PtrA, including two phosphatases, a predicted phytase and a gene of unknown function psip1 (SYNW0165), all of which are highly upregulated during P limitation. Electrophoretic mobility shift assays indicate binding of overexpressed PtrA to promoter sequences upstream of the induced genes. This work suggests a two-tiered response to P depletion in this strain, the first being PhoB-dependent induction of high-affinity PO(4) transporters, and the second the PtrA-dependent induction of phosphatases for scavenging organic P. The levels of numerous other transcripts are also directly or indirectly influenced by PtrA, including those involved in cell-surface modification, metal uptake, photosynthesis, stress responses and other metabolic processes, which may indicate a wider role for PtrA in cellular regulation in marine picocyanobacteria.
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
Publisher: Wiley
Date: 02-02-2021
DOI: 10.1111/OIK.07912
Abstract: A recent compilation of traits across culturable species of bacteria and archaea allows relationships to be quantified between genome size and other traits and habitat. Cell morphology, size, motility, sporulation and doubling time were not strongly correlated with genome size. Aerobic species averaged ca 35% larger genomes than anaerobic, adjusted for growth temperature. Aerobes had a similar mix of gene functions compared to anaerobes of the same genome size. Shifting proportions of aerobes to anaerobes accounted for about half of previously‐known differences in mean genome size between habitats. One possible factor in these results could be if effective population sizes are larger for aerobes, reducing the potential for gene loss via genetic drift. Larger genomes also confer versatility. They can transport and metabolise a wider range of substrates. More of their genome is engaged in signal detection and response, indicating they benefit from different resources at different times or under different condition. Aerobic habitats might well present opportunities and challenges that vary through time more than anaerobic habitats. The genome size trait‐dimension contributes a useful quantitative descriptor for ecological strategies.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 18-11-2022
Abstract: Horizontal gene transfer between different domains of life is increasingly being recognized as an important evolutionary driver, with the potential to increase the pace of biochemical innovation and environmental adaptation. However, the mechanisms underlying the recruitment of exogenous genes from foreign domains are mostly unknown. Integrons are a family of genetic elements that facilitate this process within Bacteria. However, they have not been reported outside Bacteria, and thus their potential role in cross-domain gene transfer has not been investigated. Here, we discover that integrons are also present in 75 archaeal metagenome-assembled genomes from nine phyla, and are particularly enriched among Asgard archaea. Furthermore, we provide experimental evidence that integrons can facilitate the recruitment of archaeal genes by bacteria. Our findings establish a previously unknown mechanism of cross-domain gene transfer whereby bacteria can incorporate archaeal genes from their surrounding environment via integron activity. These findings have important implications for prokaryotic ecology and evolution.
Publisher: Frontiers Media SA
Date: 27-10-2020
Publisher: Springer Science and Business Media LLC
Date: 21-02-2013
Publisher: Elsevier BV
Date: 10-2023
Publisher: Springer Science and Business Media LLC
Date: 09-08-2021
DOI: 10.1038/S42003-021-02489-0
Abstract: Integrons are bacterial genetic elements that can capture mobile gene cassettes. They are mostly known for their role in the spread of antibiotic resistance cassettes, contributing significantly to the global resistance crisis. These resistance cassettes likely originated from sedentary chromosomal integrons, having subsequently been acquired and disseminated by mobilised integrons. However, their taxonomic and environmental origins are unknown. Here, we use cassette recombination sites ( attC s) to predict the origins of those resistance cassettes now spread by mobile integrons. We modelled the structure and sequence homology of 1,978 chromosomal attC s from 11 different taxa. Using these models, we show that at least 27% of resistance cassettes have attC s that are structurally conserved among one of three taxa (Xanthomonadales, Spirochaetes and Vibrionales). Indeed, we found some resistance cassettes still residing in sedentary chromosomal integrons of the predicted taxa. Further, we show that attC s cluster according to host environment rather than host phylogeny, allowing us to assign their likely environmental sources. For ex le, the majority of β-lactamases and aminoglycoside acetyltransferases, the two most prevalent resistance cassettes, appear to have originated from marine environments. Together, our data represent the first evidence of the taxonomic and environmental origins of resistance cassettes spread by mobile integrons.
Publisher: Public Library of Science (PLoS)
Date: 05-07-2012
Publisher: Springer Science and Business Media LLC
Date: 05-06-2020
DOI: 10.1038/S41597-020-0497-4
Abstract: A synthesis of phenotypic and quantitative genomic traits is provided for bacteria and archaea, in the form of a scripted, reproducible workflow that standardizes and merges 26 sources. The resulting unified dataset covers 14 phenotypic traits, 5 quantitative genomic traits, and 4 environmental characteristics for approximately 170,000 strain-level and 15,000 species-aggregated records. It spans all habitats including soils, marine and fresh waters and sediments, host-associated and thermal. Trait data can find use in clarifying major dimensions of ecological strategy variation across species. They can also be used in conjunction with species and abundance s ling to characterize trait mixtures in communities and responses of traits along environmental gradients.
Publisher: MDPI AG
Date: 25-10-2021
DOI: 10.3390/MICROORGANISMS9112212
Abstract: Integrons were first identified because of their central role in assembling and disseminating antibiotic resistance genes in commensal and pathogenic bacteria. However, these clinically relevant integrons represent only a small proportion of integron ersity. Integrons are now known to be ancient genetic elements that are hotspots for genomic ersity, helping to generate adaptive phenotypes. This perspective examines the ersity, functions, and activities of integrons within both natural and clinical environments. We show how the fundamental properties of integrons exquisitely pre-adapted them to respond to the selection pressures imposed by the human use of antimicrobial compounds. We then follow the extraordinary increase in abundance of one class of integrons (class 1) that has resulted from its acquisition by multiple mobile genetic elements, and subsequent colonisation of erse bacterial species, and a wide range of animal hosts. Consequently, this class of integrons has become a significant pollutant in its own right, to the extent that it can now be detected in most ecosystems. As human activities continue to drive environmental instability, integrons will likely continue to play key roles in bacterial adaptation in both natural and clinical settings. Understanding the ecological and evolutionary dynamics of integrons can help us predict and shape these outcomes that have direct relevance to human and ecosystem health.
Publisher: Frontiers Media SA
Date: 2013
Publisher: Frontiers Media SA
Date: 19-01-2023
DOI: 10.3389/FMICB.2023.1091391
Abstract: Bacteriophages are versatile mobile genetic elements that play key roles in driving the evolution of their bacterial hosts through horizontal gene transfer. Phages co-evolve with their bacterial hosts and have plastic genomes with extensive mosaicism. In this study, we present bioinformatic and experimental evidence that temperate and virulent (lytic) phages carry integrons, including integron-integrase genes, attC / attI recombination sites and gene cassettes. Integrons are normally found in Bacteria, where they capture, express and re-arrange mobile gene cassettes via integron-integrase activity. We demonstrate experimentally that a panel of attC sites carried in virulent phage can be recognized by the bacterial class 1 integron-integrase (IntI1) and then integrated into the paradigmatic attI1 recombination site using an attC x attI recombination assay. With an increasing number of phage genomes projected to become available, more phage-associated integrons and their components will likely be identified in the future. The discovery of integron components in bacteriophages establishes a new route for lateral transfer of these elements and their cargo genes between bacterial host cells.
Publisher: Microbiology Society
Date: 11-2004
Publisher: Oxford University Press (OUP)
Date: 11-05-2007
Publisher: Elsevier BV
Date: 02-2019
Publisher: Frontiers Media SA
Date: 18-03-2020
Publisher: Microbiology Society
Date: 17-03-2022
Abstract: Integrons are microbial genetic elements that can integrate mobile gene cassettes. They are mostly known for spreading antibiotic resistance cassettes among human pathogens. However, beyond clinical settings, gene cassettes encode an extraordinarily erse range of functions important for bacterial adaptation. The recovery and sequencing of cassettes has promising applications, including: surveillance of clinically important genes, particularly antibiotic resistance determinants investigating the functional ersity of integron-carrying bacteria and novel enzyme discovery. Although gene cassettes can be directly recovered using PCR, there are no standardised methods for their lification and, importantly, for validating sequences as genuine integron gene cassettes. Here, we present reproducible methods for the lification, sequence processing, and validation of gene cassette licons from complex communities. We describe two different PCR assays that either lify cassettes together with integron integrases, or gene cassettes together within cassette arrays. We compare the performance of Nanopore and Illumina sequencing, and present bioinformatic pipelines that filter sequences to ensure that they represent licons from genuine integrons. Using a erse set of environmental DNAs, we show that our approach can consistently recover thousands of unique cassettes per s le and up to hundreds of different integron integrases. Recovered cassettes confer a wide range of functions, including antibiotic resistance, with as many as 300 resistance cassettes found in a single s le. In particular, we show that class one integrons are collecting and concentrating resistance genes out of the broader ersity of cassette functions. The methods described here can be applied to any environmental or clinical microbiome s le.
Publisher: Wiley
Date: 16-03-2021
DOI: 10.1002/ECE3.7290
Publisher: Frontiers Media SA
Date: 20-07-2018
Publisher: Springer Science and Business Media LLC
Date: 24-10-2022
DOI: 10.1186/S40168-022-01369-X
Abstract: Each year, approximately 9.5 million metric tons of plastic waste enter the ocean with the potential to adversely impact all trophic levels. Until now, our understanding of the impact of plastic pollution on marine microorganisms has been largely restricted to the microbial assemblages that colonize plastic particles. However, plastic debris also leaches considerable amounts of chemical additives into the water, and this has the potential to impact key groups of planktonic marine microbes, not just those organisms attached to plastic surfaces. To investigate this, we explored the population and genetic level responses of a marine microbial community following exposure to leachate from a common plastic (polyvinyl chloride) or zinc, a specific plastic additive. Both the full mix of substances leached from polyvinyl chloride (PVC) and zinc alone had profound impacts on the taxonomic and functional ersity of our natural planktonic community. Microbial primary producers, both prokaryotic and eukaryotic, which comprise the base of the marine food web, were strongly impaired by exposure to plastic leachates, showing significant declines in photosynthetic efficiency, ersity, and abundance. Key heterotrophic taxa, such as SAR11, which are the most abundant planktonic organisms in the ocean, also exhibited significant declines in relative abundance when exposed to higher levels of PVC leachate. In contrast, many copiotrophic bacteria, including members of the Alteromonadales, dramatically increased in relative abundance under both exposure treatments. Moreover, functional gene and genome analyses, derived from metagenomes, revealed that PVC leachate exposure selects for fast-adapting, motile organisms, along with enrichment in genes usually associated with pathogenicity and an increased capacity to metabolize organic compounds leached from PVC. This study shows that substances leached from plastics can restructure marine microbial communities with the potential for significant impacts on trophodynamics and biogeochemical cycling. These findings substantially expand our understanding of the ways by which plastic pollution impact life in our oceans, knowledge which is particularly important given that the burden of plastic pollution in the marine environment is predicted to continue to rise.
Publisher: Frontiers Media SA
Date: 17-09-2020
Publisher: Springer New York
Date: 25-11-2017
DOI: 10.1007/978-1-4939-7454-2_12
Abstract: The core genomes of most bacterial species include a large number of genes encoding putative efflux pumps. The functional roles of most of these pumps are unknown, however, they are often under tight regulatory control and expressed in response to their substrates. Therefore, one way to identify pumps that function in antimicrobial resistance is to examine the transcriptional responses of efflux pump genes to antimicrobial shock. By conducting complete transcriptomic experiments following antimicrobial shock treatments, it may be possible to identify novel drug efflux pumps encoded in bacterial genomes. In this chapter we describe a complete workflow for conducting transcriptomic analyses by RNA sequencing, to determine transcriptional changes in bacteria responding to antimicrobials.
Publisher: ACM
Date: 26-09-2023
Publisher: Humana Press
Date: 2014
DOI: 10.1007/978-1-62703-712-9_10
Abstract: Biolog Phenotype MicroArrays for microorganisms provide a high-throughput method for the global analysis of microbial growth phenotypes. Using a colorimetric reaction that is indicative of respiration, these microplate assays measure the response of an in idual strain or microbial community to a large and erse range of nutrients and chemicals. Phenotype MicroArrays have been used to study gene function and to improve genome annotation in single microorganisms and for physiological profiling of bacterial communities. The microplate system can be used to obtain a comprehensive overview of metabolic capability, or it can be tailored, through the use of subsets of plates, to address specific research needs.
Publisher: Springer Science and Business Media LLC
Date: 11-12-2019
DOI: 10.1007/S00248-019-01471-Y
Abstract: Diverse microbial communities living in subsurface coal seams are responsible for important geochemical processes including the movement of carbon between the geosphere, biosphere and atmosphere. Microbial conversion of the organic matter in coal to methane involves a complex assemblage of bacteria and archaea working in syntrophic relationships. Despite the importance and value of this microbial process, very few of the microbial taxa have defined metabolic or ecological roles in these environments. Additionally, the genomic features mediating life in this chemically reduced, energy poor, deep subsurface environment are not well characterised. Here we describe the isolation and genomic and catabolic characterisation of three alphaproteobacterial Stappia indica species from three coal basins across Australia. S. indica genomes from coal seams were compared with those from closely related S. indica isolated from erse surface waters, revealing a coal seam-specific suite of genes associated with life in the subsurface. These genes are linked to processes including viral defence, secondary metabolite production, polyamine metabolism, polypeptide uptake membrane transporters and putative energy neutral pressure-dependent CO
Publisher: Wiley
Date: 24-04-2021
DOI: 10.1111/ELE.13742
Abstract: Bacteria and archaea have very different ecology compared to plants. One similarity, though, is that much discussion of their ecological strategies has invoked concepts such as oligotrophy or stress tolerance. For plants, so‐called ‘trait ecology’—strategy description reframed along measurable trait dimensions—has made global syntheses possible. Among widely measured trait dimensions for bacteria and archaea three main axes are evident. Maximum growth rate in association with rRNA operon copy number expresses a rate‐yield trade‐off that is analogous to the acquisitive–conservative spectrum in plants, though underpinned by different trade‐offs. Genome size in association with signal transduction expresses versatility. Cell size has influence on diffusive uptake and on relative wall costs. These trait dimensions, and potentially others, offer promise for interpreting ecology. At the same time, there are very substantial differences from plant trait ecology. Traits and their underpinning trade‐offs are different. Also, bacteria and archaea use a variety of different substrates. Bacterial strategies can be viewed both through the facet of substrate‐use pathways, and also through the facet of quantitative traits such as maximum growth rate. Preliminary evidence shows the quantitative traits vary widely within substrate‐use pathways. This indicates they convey information complementary to substrate use.
Publisher: American Society for Microbiology
Date: 12-2011
DOI: 10.1128/AAC.00639-11
Abstract: pJIE143 (34 kb), from an Escherichia coli ST131 isolate, carries bla CTX-M-15 but could not be typed using the standard PCR-based replicon-typing primer set. Complete sequencing revealed a backbone with similarity to IncX plasmids, including a pir -like gene encoding a π-like replication protein and iterons related to those of other IncX plasmids. The 2.971-kb IS Ecp1-bla CTX-M-15 -orf477Δ transposition unit often found within Tn 2 is inserted just beyond the end of pir , flanked by 5-bp direct repeats.
Publisher: International Union of Crystallography (IUCr)
Date: 25-09-2014
DOI: 10.1107/S2053230X14019785
Abstract: Over 15% of the genome of an Australian clinical isolate of Acinetobacter baumannii occurs within genomic islands. An uncharacterized protein encoded within one island feature common to this and other International Clone II strains has been studied by X-ray crystallography. The 2.4 Å resolution structure of SDR-WM99c reveals it to be a new member of the classical short-chain dehydrogenase/reductase (SDR) superfamily. The enzyme contains a nucleotide-binding domain and, like many other SDRs, is tetrameric in form. The active site contains a catalytic tetrad (Asn117, Ser146, Tyr159 and Lys163) and water molecules occupying the presumed NADP cofactor-binding pocket. An adjacent cleft is capped by a relatively mobile helical subdomain, which is well positioned to control substrate access.
Publisher: Springer Science and Business Media LLC
Date: 23-10-2015
Publisher: Cold Spring Harbor Laboratory
Date: 07-02-2022
DOI: 10.1101/2022.02.06.479319
Abstract: Horizontal gene transfer between different domains of life is increasingly being recognised as an important driver of evolution, with the potential to provide the recipient with new gene functionality and assist niche adaptation 1-3 . However, the molecular mechanisms underlying the integration of exogenous genes from foreign domains are mostly unknown. Integrons are a family of genetic elements that facilitate this process within Bacteria via site-specific DNA recombination 4-7 . Integrons, however, have not been reported outside Bacteria, and thus their potential role in cross-domain gene transfer has not been investigated. Here we show that integrons are also present among erse phyla within the domain Archaea. Further, we provide experimental evidence that integron-mediated recombination can facilitate the recruitment of archaeal genes by bacteria. Our findings establish a new mechanism that can facilitate horizontal gene transfer between the two domains of prokaryotes, which has important implications for prokaryotic evolution in both clinical and environmental contexts.
Publisher: Elsevier BV
Date: 06-2020
DOI: 10.1016/J.TIM.2019.12.002
Abstract: Integrons are bacterial genetic elements that can capture, rearrange, and express mobile gene cassettes. They are best known for their role in disseminating antibiotic-resistance genes among pathogens. Their ability to rapidly spread resistance phenotypes makes it important to consider what other integron-mediated traits might impact human health in the future, such as increased virulence, pathogenicity, or resistance to novel antimicrobial strategies. Exploring the functional ersity of cassettes and understanding their de novo creation will allow better pre-emptive management of bacterial growth, while also facilitating development of technologies that could harness integron activity. If we can control integrons and cassette formation, we could use integrons as a platform for enzyme discovery and to construct novel biochemical pathways, with applications in bioremediation or biosynthesis of industrial and therapeutic molecules. Integron activity thus holds both peril and promise for humans.
Publisher: Springer Science and Business Media LLC
Date: 07-11-2019
DOI: 10.1038/S41598-019-52846-7
Abstract: Microbes in subsurface coal seams are responsible for the conversion of the organic matter in coal to methane, resulting in vast reserves of coal seam gas. This process is important from both environmental and economic perspectives as coal seam gas is rapidly becoming a popular fuel source worldwide and is a less carbon intensive fuel than coal. Despite the importance of this process, little is known about the roles of in idual bacterial taxa in the microbial communities carrying out this process. Of particular interest is the role of members of the genus Pseudomonas , a typically aerobic taxa which is ubiquitous in coal seam microbial communities worldwide and which has been shown to be abundant at early time points in studies of ecological succession on coal. The current study performed aerobic isolations of coal seam microbial taxa generating ten facultative anaerobic isolates from three coal seam formation waters across eastern Australia. Subsequent genomic sequencing and phenotypic analysis revealed a range of ecological strategies and roles for these facultative anaerobes in biomass recycling, suggesting that this group of organisms is involved in the degradation of accumulated biomass in coal seams, funnelling nutrients back into the microbial communities degrading coal to methane.
Publisher: American Society for Microbiology
Date: 15-07-2008
DOI: 10.1128/JB.00229-08
Abstract: Integrons facilitate the evolution of complex phenotypes by physical and transcriptional linkage of genes. They can be categorized as chromosomal integrons (CIs) or mobile resistance integrons (MRIs). The significance of MRIs for the problem of multiple antibiotic resistance is well established. CIs are more widespread, but their only demonstrated significance is as a reservoir of gene cassettes for MRIs. In characterizing CIs associated with Pseudomonas , we discovered a subfamily of insertion sequences, termed the IS 1111 - attC group, that insert into the recombination sites of gene cassettes ( attC site) by site-specific recombination. IS 1111-attC elements appear to have recently spread from Pseudomonas species to clinical class 1 integrons. Such elements are expected to significantly impact integrons. To explore this further, we examined CIs in 24 strains representing multiple levels of evolutionary ergence within the genus Pseudomonas . Cassette arrays frequently had a degenerated “footprint” of an IS 1111-attC group element at their terminus and in three cases were occupied by multiple functional IS 1111-attC elements. Within Pseudomonas spp. the IS-integron interaction appears to follow an evolutionarily rapid cycle of infection, expansion, and extinction. The final outcome is extinction of the IS element and modification of the right-hand boundary of the integron. This system represents an unusual ex le of convergent evolution whereby heterologous families of site-specific recombinases of distinct genetic elements have adopted the same target site. The interactions described here represent a model for evolutionary processes that offer insights to a number of aspects of the biology of integrons and other mosaic genetic elements.
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Sasha Tetu.