ORCID Profile
0000-0001-7616-0594
Current Organisation
Monash University
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Microbiology | Microbial Ecology | Environmental Chemistry (incl. Atmospheric Chemistry) | Isotope Geochemistry | Climate Change Processes | Other Chemical Sciences | Bacteriology | Biochemistry and cell biology | Chemical Oceanography | Marine Geoscience | Global Change Biology | Carbon capture engineering (excl. sequestration) | Enzymes | Microbial Genetics | Chemical and thermal processes in energy and combustion | Chemical engineering | Other Biological Sciences | Environmental Management | Microbial genetics | Bioprocessing bioproduction and bioproducts | Enzymes |
ANZSRC Socio-Economic Objective (SEO)
Effects of Climate Change and Variability on Antarctic and Sub-Antarctic Environments (excl. Social Impacts) | Atmospheric Processes and Dynamics | Ecosystem Assessment and Management of Antarctic and Sub-Antarctic Environments | Soils not elsewhere classified | Hydrogen-based Energy Systems (incl. Internal Hydrogen Combustion Engines) | Rehabilitation of Degraded Fresh, Ground and Surface Water Environments | Physical and Chemical Conditions of Water in Marine Environments | Environmental Policy, Legislation and Standards not elsewhere classified | Physical and Chemical Conditions of Water in Coastal and Estuarine Environments | Expanding Knowledge in the Environmental Sciences | Expanding Knowledge in the Biological Sciences | Coastal and Estuarine Water Management
Related Links
Publications
Microbial oxidation of atmospheric trace gases
Publisher: Springer Science and Business Media LLC
Date: 12-04-2022
DOI: 10.1038/S41579-022-00724-X
Abstract: The atmosphere has recently been recognized as a major source of energy sustaining life. Diverse aerobic bacteria oxidize the three most abundant reduced trace gases in the atmosphere, namely hydrogen (H
Technical note: Inexpensive modification of Exetainers for the reliable storage of trace-level hydrogen and carbon monoxide gas samples
Publisher: Copernicus GmbH
Date: 29-01-2021
Abstract: Abstract. Atmospheric trace gases such as dihydrogen (H2), carbon monoxide (CO) and methane (CH4) play important roles in microbial metabolism and biogeochemical cycles. Analysis of these gases at trace levels requires reliable storage of discrete s les of low volume. While commercial s ling vials such as Exetainers® have been tested for CH4 and other greenhouse gases, no information on reliable storage is available for H2 and CO. We show that vials sealed with butyl rubber stoppers are not suitable for storing H2 and CO due to release of these gases from rubber material. Treating butyl septa with NaOH reduced trace-gas release, but contamination was still substantial, with H2 and CO mixing ratios in air s les increasing by a factor of 3 and 10 after 30 d of storage in conventional 12 mL Exetainers. All tested materials showed a near-linear increase in H2 and CO mixing ratios, indicating a zero-order reaction and material degradation as the underlying cause. Among the rubber materials tested, silicone showed the lowest potential for H2 and CO release. We thus propose modifying Exetainers by closing them with a silicone plug to minimise contamination and sealing them with a stainless-steel bolt and O-ring as a secondary diffusion barrier for long-term storage. Such modified Exetainers exhibited stable mixing ratios of H2 and CH4 exceeding 60 d of storage at atmospheric and elevated (10 ppm) mixing ratios. The increase of CO was still measurable but was 9 times lower than in conventional Exetainers with treated septa this can be corrected for due to its linearity by storing a standard gas alongside the s les. The proposed modification is inexpensive, scalable and robust, and thus it enables reliable storage of large numbers of low-volume gas s les from remote field locations.
Physiology, Biochemistry, and Applications of F-420- and F-o-Dependent Redox Reactions
Publisher: American Society for Microbiology
Date: 06-2016
Abstract: 5-Deazaflavin cofactors enhance the metabolic flexibility of microorganisms by catalyzing a wide range of challenging enzymatic redox reactions. While structurally similar to riboflavin, 5-deazaflavins have distinctive and biologically useful electrochemical and photochemical properties as a result of the substitution of N-5 of the isoalloxazine ring for a carbon. 8-Hydroxy-5-deazaflavin (F o ) appears to be used for a single function: as a light-harvesting chromophore for DNA photolyases across the three domains of life. In contrast, its oligoglutamyl derivative F 420 is a taxonomically restricted but functionally versatile cofactor that facilitates many low-potential two-electron redox reactions. It serves as an essential catabolic cofactor in methanogenic, sulfate-reducing, and likely methanotrophic archaea. It also transforms a wide range of exogenous substrates and endogenous metabolites in aerobic actinobacteria, for ex le mycobacteria and streptomycetes. In this review, we discuss the physiological roles of F 420 in microorganisms and the biochemistry of the various oxidoreductases that mediate these roles. Particular focus is placed on the central roles of F 420 in methanogenic archaea in processes such as substrate oxidation, C 1 pathways, respiration, and oxygen detoxification. We also describe how two F 420 -dependent oxidoreductase superfamilies mediate many environmentally and medically important reactions in bacteria, including biosynthesis of tetracycline and pyrrolobenzodiazepine antibiotics by streptomycetes, activation of the prodrugs pretomanid and delamanid by Mycobacterium tuberculosis , and degradation of environmental contaminants such as picrate, aflatoxin, and malachite green. The biosynthesis pathways of F o and F 420 are also detailed. We conclude by considering opportunities to exploit deazaflavin-dependent processes in tuberculosis treatment, methane mitigation, bioremediation, and industrial biocatalysis.
Life without water: How do bacteria generate biomass in desert ecosystems?
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.
Concrete- and timber-filled tubes under axial compression – Numerical and theoretical study
Publisher: Elsevier BV
Date: 12-2021
HydDB: A web tool for hydrogenase classification and analysis.
Publisher: Springer Science and Business Media LLC
Date: 27-09-2016
DOI: 10.1038/SREP34212
Abstract: H 2 metabolism is proposed to be the most ancient and erse mechanism of energy-conservation. The metalloenzymes mediating this metabolism, hydrogenases, are encoded by over 60 microbial phyla and are present in all major ecosystems. We developed a classification system and web tool, HydDB, for the structural and functional analysis of these enzymes. We show that hydrogenase function can be predicted by primary sequence alone using an expanded classification scheme (comprising 29 [NiFe], 8 [FeFe] and 1 [Fe] hydrogenase classes) that defines 11 new classes with distinct biological functions. Using this scheme, we built a web tool that rapidly and reliably classifies hydrogenase primary sequences using a combination of k -nearest neighbors’ algorithms and CDD referencing. Demonstrating its capacity, the tool reliably predicted hydrogenase content and function in 12 newly-sequenced bacteria, archaea and eukaryotes. HydDB provides the capacity to browse the amino acid sequences of 3248 annotated hydrogenase catalytic subunits and also contains a detailed repository of physiological, biochemical and structural information about the 38 hydrogenase classes defined here. The database and classifier are freely and publicly available at services.birc.au.dk/hyddb/
Integrative Approaches for Studying Mitochondrial and Nuclear Genome Co-evolution in Oxidative Phosphorylation.
Publisher: Frontiers Media SA
Date: 03-03-2017
Structural basis for bacterial energy extraction from atmospheric hydrogen
Publisher: Springer Science and Business Media LLC
Date: 08-03-2023
DOI: 10.1038/S41586-023-05781-7
Abstract: Diverse aerobic bacteria use atmospheric H 2 as an energy source for growth and survival 1 . This globally significant process regulates the composition of the atmosphere, enhances soil bio ersity and drives primary production in extreme environments 2,3 . Atmospheric H 2 oxidation is attributed to uncharacterized members of the [NiFe] hydrogenase superfamily 4,5 . However, it remains unresolved how these enzymes overcome the extraordinary catalytic challenge of oxidizing picomolar levels of H 2 amid ambient levels of the catalytic poison O 2 and how the derived electrons are transferred to the respiratory chain 1 . Here we determined the cryo-electron microscopy structure of the Mycobacterium smegmatis hydrogenase Huc and investigated its mechanism. Huc is a highly efficient oxygen-insensitive enzyme that couples oxidation of atmospheric H 2 to the hydrogenation of the respiratory electron carrier menaquinone. Huc uses narrow hydrophobic gas channels to selectively bind atmospheric H 2 at the expense of O 2 , and 3 [3Fe–4S] clusters modulate the properties of the enzyme so that atmospheric H 2 oxidation is energetically feasible. The Huc catalytic subunits form an octameric 833 kDa complex around a membrane-associated stalk, which transports and reduces menaquinone 94 Å from the membrane. These findings provide a mechanistic basis for the biogeochemically and ecologically important process of atmospheric H 2 oxidation, uncover a mode of energy coupling dependent on long-range quinone transport, and pave the way for the development of catalysts that oxidize H 2 in ambient air.
Protein target highlights in CASP15 : Analysis of models by structure providers
Publisher: Wiley
Date: 26-07-2023
DOI: 10.1002/PROT.26545
Abstract: We present an in‐depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three‐dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.
Energetics of Pathogenic Bacteria and Opportunities for Drug Development
Publisher: Elsevier
Date: 2014
DOI: 10.1016/BS.AMPBS.2014.08.001
Abstract: The emergence and spread of drug-resistant pathogens and our inability to develop new antimicrobials to overcome resistance has inspired scientists to consider new targets for drug development. Cellular bioenergetics is an area showing promise for the development of new antimicrobials, particularly in the discovery of new anti-tuberculosis drugs where several new compounds have entered clinical trials. In this review, we have examined the bioenergetics of various bacterial pathogens, highlighting the versatility of electron donor and acceptor utilisation and the modularity of electron transport chain components in bacteria. In addition to re-examining classical concepts, we explore new literature that reveals the intricacies of pathogen energetics, for ex le, how Salmonella enterica and C ylobacter jejuni exploit host and microbiota to derive powerful electron donors and sinks the strategies Mycobacterium tuberculosis and Pseudomonas aeruginosa use to persist in lung tissues and the importance of sodium energetics and electron bifurcation in the chemiosmotic anaerobe Fusobacterium nucleatum. A combination of physiological, biochemical, and pharmacological data suggests that, in addition to the clinically-approved target F1Fo-ATP synthase, NADH dehydrogenase type II, succinate dehydrogenase, hydrogenase, cytochrome bd oxidase, and menaquinone biosynthesis pathways are particularly promising next-generation drug targets. The realisation of cellular energetics as a rich target space for the development of new antimicrobials will be dependent upon gaining increased understanding of the energetic processes utilised by pathogens in host environments and the ability to design bacterial-specific inhibitors of these processes.
An obligately aerobic soil bacterium activates fermentative hydrogen production to survive reductive stress during hypoxia
Publisher: Proceedings of the National Academy of Sciences
Date: 21-07-2014
Abstract: Obligate aerobes require survival strategies to persist in temporarily oxygen-deprived environments. In this article, we reveal a previously unidentified survival mechanism for obligately aerobic bacteria. Under oxygen-limiting conditions, the saprophytic actinomycete Mycobacterium smegmatis can rapidly switch between fermentative hydrogen production and hydrogen oxidation coupled to either oxygen or fumarate reduction depending on electron acceptor availability. To our knowledge, these results demonstrate for the first time (i) hydrogen production in an obligate aerobe, (ii) the unambiguous confirmation of fermentation in a mycobacterium and (iii) strong evidence that hydrogen has a role in survival and not just growth.
Pore water conditions driving calcium carbonate dissolution in reef sands
Publisher: Elsevier BV
Date: 06-2020
Atmospheric hydrogen oxidation extends to the domain archaea
Publisher: Cold Spring Harbor Laboratory
Date: 13-12-2022
DOI: 10.1101/2022.12.13.520232
Abstract: Diverse aerobic bacteria use atmospheric hydrogen (H 2 ) and carbon monoxide (CO) as energy sources to support growth and survival. Though recently discovered, trace gas oxidation is now recognised as a globally significant process that serves as the main sink in the biogeochemical H 2 cycle and sustains microbial bio ersity in oligotrophic ecosystems. While trace gas oxidation has been reported in nine phyla of bacteria, it was not known whether archaea also use atmospheric H 2 . Here we show that a thermoacidophilic archaeon, Acidianus brierleyi (Thermoproteota), constitutively consumes H 2 and CO to sub-atmospheric levels. Oxidation occurred during both growth and survival across a wide range of temperatures (10 to 70°C). Genomic analysis demonstrated that A. brierleyi encodes a canonical carbon monoxide dehydrogenase and, unexpectedly, four distinct [NiFe]-hydrogenases from subgroups not known to mediate aerobic H 2 uptake. Quantitative proteomic analyses showed that A. brierleyi differentially produced these enzymes in response to electron donor and acceptor availability. A previously unidentified group 1 [NiFe]-hydrogenase, with a unique genetic arrangement, is constitutively expressed and upregulated during stationary phase and aerobic hydrogenotrophic growth. Another archaeon, Metallosphaera sedula , was also found to oxidize atmospheric H 2 . These results suggest that trace gas oxidation is a common trait of aerobic archaea, which likely plays a role in their survival and niche expansion, including during dispersal through temperate environments. These findings also demonstrate that atmospheric H 2 consumption is a cross-domain phenomenon, suggesting an ancient origin of this trait, and identify previously unknown microbial and enzymatic sinks of atmospheric H 2 and CO.
Correction to: Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups
Publisher: Springer Science and Business Media LLC
Date: 22-11-2022
Experiments and design of concrete-filled steel tubes with timber chips under axial compression
Publisher: Elsevier BV
Date: 05-2023
Climate-driven mitochondrial selection: A test in Australian songbirds.
Publisher: Wiley
Date: 02-2018
DOI: 10.1111/MEC.14488
Abstract: Diversifying selection between populations that inhabit different environments can promote lineage ergence within species and ultimately drive speciation. The mitochondrial genome (mitogenome) encodes essential proteins of the oxidative phosphorylation (OXPHOS) system and can be a strong target for climate-driven selection (i.e., associated with inhabiting different climates). We investigated whether Pleistocene climate changes drove mitochondrial selection and evolution within Australian birds. First, using phylogeographic analyses of the mitochondrial ND2 gene for 17 songbird species, we identified mitochondrial clades (mitolineages). Second, using distance-based redundancy analyses, we tested whether climate predicts variation in intraspecific genetic ergence beyond that explained by geographic distances and geographic position. Third, we analysed 41 complete mitogenome sequences representing each mitolineage of 17 species using codon models in a phylogenetic framework and a biochemical approach to identify signals of selection on OXPHOS protein-coding genes and test for parallel selection in mitolineages of different species existing in similar climates. Of 17 species examined, 13 had multiple mitolineages (range: 2-6). Climate was a significant predictor of mitochondrial variation in eight species. At least two amino acid replacements in OXPHOS complex I could have evolved under positive selection in specific mitolineages of two species. Protein homology modelling showed one of these to be in the loop region of the ND6 protein channel and the other in the functionally critical helix HL region of ND5. These findings call for direct tests of the functional and evolutionary significance of mitochondrial protein candidates for climate-associated selection.
Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups
Publisher: Springer Science and Business Media LLC
Date: 30-07-2022
Oxidative Phosphorylation as a Target Space for Tuberculosis: Success, Caution, and Future Directions.
Publisher: American Society for Microbiology
Date: 19-05-2017
DOI: 10.1128/MICROBIOLSPEC.TBTB2-0014-2016
Abstract: The emergence and spread of drug-resistant pathogens, and our inability to develop new antimicrobials to combat resistance, have inspired scientists to seek out new targets for drug development. The Mycobacterium tuberculosis complex is a group of obligately aerobic bacteria that have specialized for inhabiting a wide range of intracellular and extracellular environments. Two fundamental features in this adaptation are the flexible utilization of energy sources and continued metabolism in the absence of growth. M. tuberculosis is an obligately aerobic heterotroph that depends on oxidative phosphorylation for growth and survival. However, several studies are redefining the metabolic breadth of the genus. Alternative electron donors and acceptors may provide the maintenance energy for the pathogen to maintain viability in hypoxic, nonreplicating states relevant to latent infection. This hidden metabolic flexibility may ultimately decrease the efficacy of drugs targeted against primary dehydrogenases and terminal oxidases. However, it may also open up opportunities to develop novel antimycobacterials targeting persister cells. In this review, we discuss the progress in understanding the role of energetic targets in mycobacterial physiology and pathogenesis and the opportunities for drug discovery.
Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts
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.
Dietary selection of metabolically distinct microorganisms drives hydrogen metabolism in ruminants
Publisher: Springer Science and Business Media LLC
Date: 05-08-2022
DOI: 10.1038/S41396-022-01294-9
Abstract: Ruminants are important for global food security but emit the greenhouse gas methane. Rumen microorganisms break down complex carbohydrates to produce volatile fatty acids and molecular hydrogen. This hydrogen is mainly converted into methane by archaea, but can also be used by hydrogenotrophic acetogenic and respiratory bacteria to produce useful metabolites. A better mechanistic understanding is needed on how dietary carbohydrates influence hydrogen metabolism and methanogenesis. We profiled the composition, metabolic pathways, and activities of rumen microbiota in 24 beef cattle adapted to either fiber-rich or starch-rich diets. The fiber-rich diet selected for fibrolytic bacteria and methanogens resulting in increased fiber utilization, while the starch-rich diet selected for amylolytic bacteria and lactate utilizers, allowing the maintenance of a healthy rumen and decreasing methane production ( p 0.05). Furthermore, the fiber-rich diet enriched for hydrogenotrophic methanogens and acetogens leading to increased electron-bifurcating [FeFe]-hydrogenases, methanogenic [NiFe]- and [Fe]-hydrogenases and acetyl-CoA synthase, with lower dissolved hydrogen (42%, p 0.001). In contrast, the starch-rich diet enriched for respiratory hydrogenotrophs with greater hydrogen-producing group B [FeFe]-hydrogenases and respiratory group 1d [NiFe]-hydrogenases. Parallel in vitro experiments showed that the fiber-rich selected microbiome enhanced acetate and butyrate production while decreasing methane production ( p 0.05), suggesting that the enriched hydrogenotrophic acetogens converted some hydrogen that would otherwise be used by methanogenesis. These insights into hydrogen metabolism and methanogenesis improve understanding of energy harvesting strategies, healthy rumen maintenance, and methane mitigation in ruminants.
Study design, rationale and methods of the Revitalising Informal Settlements and their Environments (RISE) study: a cluster randomised controlled trial to evaluate environmental and human health impac
Publisher: BMJ
Date: 2021
DOI: 10.1136/BMJOPEN-2020-042850
Abstract: Increasing urban populations have led to the growth of informal settlements, with contaminated environments linked to poor human health through a range of interlinked pathways. Here, we describe the design and methods for the Revitalising Informal Settlements and their Environments (RISE) study, a transdisciplinary randomised trial evaluating impacts of an intervention to upgrade urban informal settlements in two Asia-Pacific countries. RISE is a cluster randomised controlled trial among 12 settlements in Makassar, Indonesia, and 12 in Suva, Fiji. Six settlements in each country have been randomised to receive the intervention at the outset the remainder will serve as controls and be offered intervention delivery after trial completion. The intervention involves a water-sensitive approach, delivering site-specific, modular, decentralised infrastructure primarily aimed at improving health by decreasing exposure to environmental faecal contamination. Consenting households within each informal settlement site have been enrolled, with longitudinal assessment to involve health and well-being surveys, and human and environmental s ling. Primary outcomes will be evaluated in children under 5 years of age and include prevalence and ersity of gastrointestinal pathogens, abundance and ersity of antimicrobial resistance (AMR) genes in gastrointestinal microorganisms and markers of gastrointestinal inflammation. Diverse secondary outcomes include changes in microbial contamination abundance and ersity of pathogens and AMR genes in environmental s les impacts on ecological bio ersity and microclimates mosquito vector abundance anthropometric assessments, nutrition markers and systemic inflammation in children caregiver-reported and self-reported health symptoms and healthcare utilisation and measures of in idual and community psychological, emotional and economic well-being. The study aims to provide proof-of-concept evidence to inform policies on upgrading of informal settlements to improve environments and human health and well-being. Study protocols have been approved by ethics boards at Monash University, Fiji National University and Hasanuddin University. ACTRN12618000633280 Pre-results.
A soil actinobacterium scavenges atmospheric H2 using two membrane-associated, oxygen-dependent [NiFe] hydrogenases.
Publisher: Proceedings of the National Academy of Sciences
Date: 03-03-2014
Abstract: Molecular hydrogen is present in trace concentrations in the Earth’s lower atmosphere and is rapidly turned over through a biogeochemical cycle. Microbial soil processes are responsible for the majority of net uptake of H 2 from the atmosphere, but the enzymes involved have remained elusive. In this communication, we use genetic dissection and GC measurements to show that the soil actinobacterium Mycobacterium smegmatis can oxidize trace concentrations of H 2 . This process depends on two oxygen-dependent, membrane-associated [NiFe] hydrogenases with picomolar thresholds. Activity is most pronounced during carbon limitation, suggesting that mycobacteria oxidize a dependable trace gas to survive starvation. We propose that these enzymes and their homologs in other actinobacteria and soil phyla constitute the principal sink of global atmospheric H 2 .
Developing high-affinity, oxygen-insensitive [NiFe]-hydrogenases as biocatalysts for energy conversion
Publisher: Portland Press Ltd.
Date: 25-09-2023
DOI: 10.1042/BST20230120
A widely distributed hydrogenase oxidises atmospheric H(2)during bacterial growth
Publisher: Springer Science and Business Media LLC
Date: 09-07-2020
DOI: 10.1038/S41396-020-0713-4
Abstract: Diverse aerobic bacteria persist by consuming atmospheric hydrogen (H 2 ) using group 1h [NiFe]-hydrogenases. However, other hydrogenase classes are also distributed in aerobes, including the group 2a [NiFe]-hydrogenase. Based on studies focused on Cyanobacteria, the reported physiological role of the group 2a [NiFe]-hydrogenase is to recycle H 2 produced by nitrogenase. However, given this hydrogenase is also present in various heterotrophs and lithoautotrophs lacking nitrogenases, it may play a wider role in bacterial metabolism. Here we investigated the role of this enzyme in three species from different phylogenetic lineages and ecological niches: Acidithiobacillus ferrooxidans (phylum Proteobacteria), Chloroflexus aggregans (phylum Chloroflexota), and Gemmatimonas aurantiaca (phylum Gemmatimonadota). qRT-PCR analysis revealed that the group 2a [NiFe]-hydrogenase of all three species is significantly upregulated during exponential growth compared to stationary phase, in contrast to the profile of the persistence-linked group 1h [NiFe]-hydrogenase. Whole-cell biochemical assays confirmed that all three strains aerobically respire H 2 to sub-atmospheric levels, and oxidation rates were much higher during growth. Moreover, the oxidation of H 2 supported mixotrophic growth of the carbon-fixing strains C. aggregans and A. ferrooxidans . Finally, we used phylogenomic analyses to show that this hydrogenase is widely distributed and is encoded by 13 bacterial phyla. These findings challenge the current persistence-centric model of the physiological role of atmospheric H 2 oxidation and extend this process to two more phyla, Proteobacteria and Gemmatimonadota. In turn, these findings have broader relevance for understanding how bacteria conserve energy in different environments and control the biogeochemical cycling of atmospheric trace gases.
Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem
Publisher: Springer Science and Business Media LLC
Date: 13-03-2021
DOI: 10.1038/S41396-021-00988-W
Abstract: Ecological theory suggests that habitat disturbance differentially influences distributions of habitat generalist and specialist species. While well-established for macroorganisms, this theory has rarely been explored for microorganisms. Here we tested these principles in permeable (sandy) sediments, ecosystems with much spatiotemporal variation in resource availability and physicochemical conditions. Microbial community composition and function were profiled in intertidal and subtidal sediments using 16S rRNA gene licon sequencing and metagenomics, yielding 135 metagenome-assembled genomes. Community composition and metabolic traits modestly varied with sediment depth and s ling date. Several taxa were highly abundant and prevalent in all s les, including within the orders Woeseiales and Flavobacteriales, and classified as habitat generalists genome reconstructions indicate these taxa are highly metabolically flexible facultative anaerobes and adapt to resource variability by using different electron donors and acceptors. In contrast, obligately anaerobic taxa such as sulfate reducers and candidate lineage MBNT15 were less abundant overall and only thrived in more stable deeper sediments. We substantiated these findings by measuring three metabolic processes in these sediments whereas the habitat generalist-associated processes of sulfide oxidation and fermentation occurred rapidly at all depths, the specialist-associated process of sulfate reduction was restricted to deeper sediments. A manipulative experiment also confirmed habitat generalists outcompete specialist taxa during simulated habitat disturbance. Together, these findings show metabolically flexible habitat generalists become dominant in highly dynamic environments, whereas metabolically constrained specialists are restricted to narrower niches. Thus, an ecological theory describing distribution patterns for macroorganisms likely extends to microorganisms. Such findings have broad ecological and biogeochemical ramifications.
Critical thinking in healthcare and education
Publisher: BMJ
Date: 16-05-2017
DOI: 10.1136/BMJ.J2234
Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism
Publisher: Springer Science and Business Media LLC
Date: 04-2019
DOI: 10.1038/S41564-019-0406-9
Abstract: The origin of eukaryotes represents an unresolved puzzle in evolutionary biology. Current research suggests that eukaryotes evolved from a merger between a host of archaeal descent and an alphaproteobacterial endosymbiont. The discovery of the Asgard archaea, a proposed archaeal superphylum that includes Lokiarchaeota, Thorarchaeota, Odinarchaeota and Heimdallarchaeota suggested to comprise the closest archaeal relatives of eukaryotes, has helped to elucidate the identity of the putative archaeal host. Whereas Lokiarchaeota are assumed to employ a hydrogen-dependent metabolism, little is known about the metabolic potential of other members of the Asgard superphylum. We infer the central metabolic pathways of Asgard archaea using comparative genomics and phylogenetics to be able to refine current models for the origin of eukaryotes. Our analyses indicate that Thorarchaeota and Lokiarchaeota encode proteins necessary for carbon fixation via the Wood-Ljungdahl pathway and for obtaining reducing equivalents from organic substrates. By contrast, Heimdallarchaeum LC2 and LC3 genomes encode enzymes potentially enabling the oxidation of organic substrates using nitrate or oxygen as electron acceptors. The gene repertoire of Heimdallarchaeum AB125 and Odinarchaeum indicates that these organisms can ferment organic substrates and conserve energy by coupling ferredoxin reoxidation to respiratory proton reduction. Altogether, our genome analyses suggest that Asgard representatives are primarily organoheterotrophs with variable capacity for hydrogen consumption and production. On this basis, we propose the 'reverse flow model', an updated symbiogenetic model for the origin of eukaryotes that involves electron or hydrogen flow from an organoheterotrophic archaeal host to a bacterial symbiont.
Assessing the fitness consequences of mitonuclear interactions in natural populations
Publisher: Wiley
Date: 26-12-2019
DOI: 10.1111/BRV.12493
Acidobacteria are active and abundant members of diverse atmospheric H2-oxidizing communities detected in temperate soils
Publisher: Springer Science and Business Media LLC
Date: 06-10-2021
DOI: 10.1038/S41396-020-00750-8
Abstract: Significant rates of atmospheric dihydrogen (H 2 ) consumption have been observed in temperate soils due to the activity of high-affinity enzymes, such as the group 1h [NiFe]-hydrogenase. We designed broadly inclusive primers targeting the large subunit gene ( hhyL ) of group 1h [NiFe]-hydrogenases for long-read sequencing to explore its taxonomic distribution across soils. This approach revealed a erse collection of microorganisms harboring hhyL , including previously unknown groups and taxonomically not assignable sequences. Acidobacterial group 1h [NiFe]-hydrogenase genes were abundant and expressed in temperate soils. To support the participation of acidobacteria in H 2 consumption, we studied two representative mesophilic soil acidobacteria, which expressed group 1h [NiFe]-hydrogenases and consumed atmospheric H 2 during carbon starvation. This is the first time mesophilic acidobacteria, which are abundant in ubiquitous temperate soils, have been shown to oxidize H 2 down to below atmospheric concentrations. As this physiology allows bacteria to survive periods of carbon starvation, it could explain the success of soil acidobacteria. With our long-read sequencing approach of group 1h [NiFe]-hydrogenase genes, we show that the ability to oxidize atmospheric levels of H 2 is more widely distributed among soil bacteria than previously recognized and could represent a common mechanism enabling bacteria to persist during periods of carbon deprivation.
Nitrification in acidic and alkaline environments
Publisher: Portland Press Ltd.
Date: 08-2023
DOI: 10.1042/EBC20220194
Abstract: Aerobic nitrification is a key process in the global nitrogen cycle mediated by microorganisms. While nitrification has primarily been studied in near-neutral environments, this process occurs at a wide range of pH values, spanning ecosystems from acidic soils to soda lakes. Aerobic nitrification primarily occurs through the activities of ammonia-oxidising bacteria and archaea, nitrite-oxidising bacteria, and complete ammonia-oxidising (comammox) bacteria adapted to these environments. Here, we review the literature and identify knowledge gaps on the metabolic ersity, ecological distribution, and physiological adaptations of nitrifying microorganisms in acidic and alkaline environments. We emphasise that nitrifying microorganisms depend on a suite of physiological adaptations to maintain pH homeostasis, acquire energy and carbon sources, detoxify reactive nitrogen species, and generate a membrane potential at pH extremes. We also recognize the broader implications of their activities primarily in acidic environments, with a focus on agricultural productivity and nitrous oxide emissions, as well as promising applications in treating municipal wastewater.
H2 metabolism is widespread and diverse among human colonic microbes.
Publisher: Informa UK Limited
Date: 28-04-2016
Concordant divergence of mitogenomes and a mitonuclear gene cluster in bird lineages inhabiting different climates.
Publisher: Springer Science and Business Media LLC
Date: 09-07-2018
DOI: 10.1038/S41559-018-0606-3
Abstract: Metabolic processes in eukaryotic cells depend on interactions between mitochondrial and nuclear gene products (mitonuclear interactions). These interactions could have a direct role in population ergence. Here, we study mitonuclear co-evolution in a widespread bird that experienced population ergence followed by bidirectional mitochondrial introgression into different nuclear backgrounds. Using >60,000 single nucleotide polymorphisms, we quantify patterns of nuclear genetic differentiation between populations that occupy areas with different climates and harbour deeply ergent mitochondrial lineages despite ongoing nuclear gene flow. We find that strong genetic differentiation and sequence ergence in a region of ~15.4 megabases on chromosome 1A mirror the geographic pattern of mitochondrial DNA ergence. This result is seen in two different transects representing populations with different nuclear backgrounds. The chromosome 1A region is enriched for genes performing mitochondrial functions (N-mt genes). Molecular signatures of selective sweeps in this region alongside those in the mitochondrial genome suggest a history of adaptive mitonuclear co-introgression. Moreover, evidence for large linkage disequilibrium blocks in this genomic region suggests that low recombination could facilitate functional interactions between co-evolved nuclear alleles. Our results are consistent with mitonuclear co-evolution as an important mechanism for population ergence and local adaptation.
Uncovering the Metabolic Strategies of the Dormant Microbial Majority: towards Integrative Approaches.
Publisher: American Society for Microbiology
Date: 25-06-2019
DOI: 10.1128/MSYSTEMS.00107-19
Abstract: A grand challenge in microbiology is to understand how the dormant majority lives. In natural environments, most microorganisms are not growing and instead exist in a spectrum of dormant states.
Formation and function of bacterial organelles
Publisher: Springer Science and Business Media LLC
Date: 24-07-2020
Soil bacterial communities exhibit strong biogeographic patterns at fine taxonomic resolution
Publisher: American Society for Microbiology
Date: 25-08-2020
DOI: 10.1128/MSYSTEMS.00540-20
Abstract: It is commonly thought that bacterial distributions show lower spatial variation than for multicellular organisms. In this article, we present evidence that these inferences are artifacts caused by methodological limitations. Through leveraging innovations in s ling design, sequence processing, and ersity analysis, we provide multifaceted evidence that bacterial communities in fact exhibit strong distribution patterns. This is driven by selection due to factors such as local soil characteristics. Altogether, these findings suggest that the processes underpinning ersity patterns are more unified across all domains of life than previously thought, which has broad implications for the understanding and management of soil bio ersity.
P yrinomonas
Publisher: Wiley
Date: 12-12-2018
DOI: 10.1002/9781118960608.GBM01533
Abstract: Py.ri.no.mo'nas. Gr. adj. pyrinos born of fire, igneous, fiery Gr. fem. n. monas a unit, monad N.L. fem. n. Pyrinomonas fire unit (bacterium). Acidobacteria / Blastocatellia / Blastocatellales / Pyrinomonadaceae / Pyrinomonas The genus Pyrinomonas is represented by a single species, Pyrinomonas methylaliphatogenes . Cells are nonmotile, non‐spore‐forming rods. Gram‐negative, catalase‐ and oxidase‐positive. Cells ide by binary fission. Thermophilic and moderately acidophilic. Obligately aerobic and chemoheterotrophic. Growth on a limited selection of peptides, saccharides, and organic acids. Hydrogen is oxidized to subatmospheric concentrations when cells are carbon‐limited. The principal fatty acids are iso‐C 15:0 , iso‐C 17:0 , iso‐C 19:0 , and iso‐C 21:0 . Transmembrane and ether‐linked lipids, including iso‐diabolic acid and the glyceryl ethers of iso‐C 15:0 and iso‐diabolic acid, comprise up to 40% of cell lipid extract. Primary cellular lipids are phosphatidylcholine and phosphatidylethanolamine. MK‐8 is the primary respiratory quinone and G + C content of 59.36 mol%. Members of the class Blastocatellia , family Pyrinomonadaceae . The type strain was isolated from geothermally heated soils in New Zealand. DNA G + C content (mol%) : 59.36 (genome analysis). Type species : Pyrinomonas methylaliphatogenes Crowe, Power, Morgan, Dunfield, Lagutin, Rijpstra, Vyssotski, Sinninghe Damsté, Houghton, Ryan and Stott 2014, 225 VP .
Genome-resolved metagenomics reveals how soil bacterial communities respond to elevated H2 availability
Publisher: Elsevier BV
Date: 12-2021
Termite-engineered microbial communities of termite nest structures: a new dimension to the extended phenotype
Publisher: Oxford University Press (OUP)
Date: 05-07-2022
Abstract: Termites are a prototypical ex le of the ‘extended phenotype’ given their ability to shape their environments by constructing complex nesting structures and cultivating fungus gardens. Such engineered structures provide termites with stable, protected habitats, and nutritious food sources, respectively. Recent studies have suggested that these termite-engineered structures harbour Actinobacteria-dominated microbial communities. In this review, we describe the composition, activities, and consequences of microbial communities associated with termite mounds, other nests, and fungus gardens. Culture-dependent and culture-independent studies indicate that these structures each harbour specialized microbial communities distinct from those in termite guts and surrounding soils. Termites select microbial communities in these structures through various means: opportunistic recruitment from surrounding soils controlling physicochemical properties of nesting structures excreting hydrogen, methane, and other gases as bacterial energy sources and pretreating lignocellulose to facilitate fungal cultivation in gardens. These engineered communities potentially benefit termites by producing antimicrobial compounds, facilitating lignocellulose digestion, and enhancing energetic efficiency of the termite ‘metaorganism’. Moreover, mound-associated communities have been shown to be globally significant in controlling emissions of methane and enhancing agricultural fertility. Altogether, these considerations suggest that the microbiomes selected by some animals extend much beyond their bodies, providing a new dimension to the ‘extended phenotype’.
Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts
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.
Predicting nitroimidazole antibiotic resistance mutations in Mycobacterium tuberculosis with protein engineering
Publisher: Public Library of Science (PLoS)
Date: 07-02-2020
The Redox Cofactor F-420 Protects Mycobacteria from Diverse Antimicrobial Compounds and Mediates a Reductive Detoxification System
Publisher: American Society for Microbiology
Date: 12-2016
DOI: 10.1128/AEM.02500-16
Abstract: A defining feature of mycobacterial redox metabolism is the use of an unusual deazaflavin cofactor, F 420 . This cofactor enhances the persistence of environmental and pathogenic mycobacteria, including after antimicrobial treatment, although the molecular basis for this remains to be understood. In this work, we explored our hypothesis that F 420 enhances persistence by serving as a cofactor in antimicrobial-detoxifying enzymes. To test this, we performed a series of phenotypic, biochemical, and analytical chemistry studies in relation to the model soil bacterium Mycobacterium smegmatis . Mutant strains unable to synthesize or reduce F 420 were found to be more susceptible to a wide range of antibiotic and xenobiotic compounds. Compounds from three classes of antimicrobial compounds traditionally resisted by mycobacteria inhibited the growth of F 420 mutant strains at subnanomolar concentrations, namely, furanocoumarins (e.g., methoxsalen), arylmethanes (e.g., malachite green), and quinone analogues (e.g., menadione). We demonstrated that promiscuous F 420 H 2 -dependent reductases directly reduce these compounds by a mechanism consistent with hydride transfer. Moreover, M. smegmatis strains unable to make F 420 H 2 lost the capacity to reduce and detoxify representatives of the furanocoumarin and arylmethane compound classes in whole-cell assays. In contrast, mutant strains were only slightly more susceptible to clinical antimycobacterials, and this appeared to be due to indirect effects of F 420 loss of function (e.g., redox imbalance) rather than loss of a detoxification system. Together, these data show that F 420 enhances antimicrobial resistance in mycobacteria and suggest that one function of the F 420 H 2 -dependent reductases is to broaden the range of natural products that mycobacteria and possibly other environmental actinobacteria can reductively detoxify. IMPORTANCE This study reveals that a unique microbial cofactor, F 420 , is critical for antimicrobial resistance in the environmental actinobacterium Mycobacterium smegmatis . We show that a superfamily of redox enzymes, the F 420 H 2 -dependent reductases, can reduce erse antimicrobials in vitro and in vivo . M. smegmatis strains unable to make or reduce F 420 become sensitive to inhibition by these antimicrobial compounds. This suggests that mycobacteria have harnessed the unique properties of F 420 to reduce structurally erse antimicrobials as part of the antibiotic arms race. The F 420 H 2 -dependent reductases that facilitate this process represent a new class of antimicrobial-detoxifying enzymes with potential applications in bioremediation and biocatalysis.
Plumage redness signals mitochondrial function in the house finch
Publisher: The Royal Society
Date: 25-09-2019
Abstract: Carotenoid coloration is widely recognized as a signal of in idual condition in various animals, but despite decades of study, the mechanisms that link carotenoid coloration to condition remain unresolved. Most birds with red feathers convert yellow dietary carotenoids to red carotenoids in an oxidation process requiring the gene encoding the putative cytochrome P450 enzyme CYP2J19. Here, we tested the hypothesis that the process of carotenoid oxidation and feather pigmentation is functionally linked to mitochondrial performance. Consistent with this hypothesis, we observed high levels of red ketolated carotenoids associated with the hepatic mitochondria of moulting wild house finches ( Haemorhous mexicanus ), and upon fractionation, we found the highest concentration of ketolated carotenoids in the inner mitochondrial membrane. We further found that the redness of growing feathers was positively related to the performance of liver mitochondria. Structural modelling of CYP2J19 supports a direct role of this protein in carotenoid ketolation that may be functionally linked to cellular respiration. These observations suggest that feather coloration serves as a signal of core functionality through inexorable links to cellular respiration in the mitochondria.
Metabolism in anoxic permeable sediments is dominated by eukaryotic dark fermentation
Publisher: Springer Science and Business Media LLC
Date: 28-11-2017
DOI: 10.1038/NGEO2843
Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep
Publisher: Springer Science and Business Media LLC
Date: 17-11-2020
DOI: 10.1038/S41467-020-19648-2
Abstract: At marine cold seeps, gaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface. Cold seep sediments are known to host taxonomically erse microorganisms, but little is known about their metabolic potential and depth distribution in relation to hydrocarbon and electron acceptor availability. Here we combined geophysical, geochemical, metagenomic and metabolomic measurements to profile microbial activities at a newly discovered cold seep in the deep sea. Metagenomic profiling revealed compositional and functional differentiation between near-surface sediments and deeper subsurface layers. In both sulfate-rich and sulfate-depleted depths, various archaeal and bacterial community members are actively oxidizing thermogenic hydrocarbons anaerobically. Depth distributions of hydrocarbon-oxidizing archaea revealed that they are not necessarily associated with sulfate reduction, which is especially surprising for anaerobic ethane and butane oxidizers. Overall, these findings link subseafloor microbiomes to various biochemical mechanisms for the anaerobic degradation of deeply-sourced thermogenic hydrocarbons.
Persistence of the dominant soil phylum Acidobacteria by trace gas scavenging
Publisher: Proceedings of the National Academy of Sciences
Date: 03-08-2015
Abstract: The mechanisms that the “dormant microbial majority” use to remain energized in nutrient-starved soil ecosystems have long remained elusive. In this work, we used an isolate of the highly abundant but poorly understood soil phylum Acidobacteria as a model for understanding microbial persistence mechanisms. When the bacterium entered a persistent state due to nutrient-exhaustion, we showed it could scavenge the trace concentrations of molecular hydrogen gas (H 2 ) found in ambient air using a specialized high-affinity enzyme. These findings demonstrate that Acidobacteria can consume H 2 and contribute to global hydrogen cycling. We propose that consumption of trace gases such as H 2 provides a dependable general mechanism for dominant soil phyla to generate the maintenance energy required for long-term survival.
Two Chloroflexi classes independently evolved the ability to persist on atmospheric hydrogen and carbon monoxide
Publisher: Springer Science and Business Media LLC
Date: 14-03-2019
DOI: 10.1038/S41396-019-0393-0
Abstract: Most aerobic bacteria exist in dormant states within natural environments. In these states, they endure adverse environmental conditions such as nutrient starvation by decreasing metabolic expenditure and using alternative energy sources. In this study, we investigated the energy sources that support persistence of two aerobic thermophilic strains of the environmentally widespread but understudied phylum Chloroflexi. A transcriptome study revealed that Thermomicrobium roseum (class Chloroflexia) extensively remodels its respiratory chain upon entry into stationary phase due to nutrient limitation. Whereas primary dehydrogenases associated with heterotrophic respiration were downregulated, putative operons encoding enzymes involved in molecular hydrogen (H 2 ), carbon monoxide (CO), and sulfur compound oxidation were significantly upregulated. Gas chromatography and microsensor experiments showed that T. roseum aerobically respires H 2 and CO at a range of environmentally relevant concentrations to sub-atmospheric levels. Phylogenetic analysis suggests that the hydrogenases and carbon monoxide dehydrogenases mediating these processes are widely distributed in Chloroflexi genomes and have probably been horizontally acquired on more than one occasion. Consistently, we confirmed that the sporulating isolate Thermogemmatispora sp. T81 (class Ktedonobacteria) also oxidises atmospheric H 2 and CO during persistence, though further studies are required to determine if these findings extend to mesophilic strains. This study provides axenic culture evidence that atmospheric CO supports bacterial persistence and reports the third phylum, following Actinobacteria and Acidobacteria, to be experimentally shown to mediate the biogeochemically and ecologically important process of atmospheric H 2 oxidation. This adds to the growing body of evidence that atmospheric trace gases are dependable energy sources for bacterial persistence.
FAD-sequestering proteins protect mycobacteria against hypoxic and oxidative stress
Publisher: Elsevier BV
Date: 02-2018
Implementing baseline ecological and human health field assessments in the Revitalizing Informal Settlements and their Environments (RISE) programme in Makassar, Indonesia: an interdisciplinary study
Publisher: Elsevier BV
Date: 09-2019
BonA from Acinetobacter baumannii Forms a Divisome-Localized Decamer That Supports Outer Envelope Function
Publisher: American Society for Microbiology
Date: 31-08-2021
Abstract: The pathogen Acinetobacter baumannii is considered an urgent threat to human health. A. baumannii is highly resistant to treatment with antibiotics, in part due to its protective cell envelope. This bacterium is only distantly related to other bacterial pathogens, so its cell envelope has distinct properties and contains components distinct from those of other bacteria that support its function.
Cofactor Tail Length Modulates Catalysis of Bacterial F-420-Dependent Oxidoreductases
Publisher: Frontiers Media SA
Date: 27-09-2017
Termite gas emissions select for hydrogenotrophic microbial communities in termite mounds
Publisher: Proceedings of the National Academy of Sciences
Date: 20-07-2021
Abstract: Termites are textbook ex les of the “extended phenotype” given their ability to construct complex mounds and regulate environments. Here, we show that termites also control microbial composition and biogeochemical cycling in their mounds through their emissions of hydrogen. These emissions drive remarkable enrichments of mound bacteria that use hydrogen to drive aerobic respiration and sometimes carbon fixation (i.e., lithoautotrophs). Such mound communities efficiently consume all termite-produced hydrogen and even mediate atmospheric uptake, while termite-produced methane escapes to the atmosphere. This provides further evidence that hydrogen is a major substrate for aerobic bacteria and that the terrestrial hydrogen sink is highly responsive to elevated emissions.
Crushing of steel tubes with different infills under partial axial loading
Publisher: Elsevier BV
Date: 04-2020
Bark-dwelling methanotrophic bacteria decrease methane emissions from trees
Publisher: Research Square Platform LLC
Date: 03-12-2020
DOI: 10.21203/RS.3.RS-119818/V1
Abstract: Tree stems are an important and unconstrained source of methane, yet it is uncertain if there are internal microbial controls (i.e. methanotrophy) within tree bark, that may reduce methane emissions. Using multiple lines of evidence, we demonstrate here that unique microbial communities dominated by methane oxidising bacteria (MOB) dwell within bark of Melaleuca quinquenervia , a common, invasive and globally distributed lowland species. Laboratory incubations of methane inoculated M. quinquenervia bark reveal methane consumption (up to 96.3 µmol m -2 bark d -1 ) and distinct isotopic δ 13 C-CH 4 enrichment characteristic of MOB. Molecular analysis indicates unique microbial communities reside within the bark, with methane-oxidising bacteria primarily from the genus Methylomonas comprising up to 25 % of the total microbial community. Methanotroph abundance was linearly correlated to methane uptake rates (R 2 = 0.76, p = 0.006). Finally, field-based methane oxidation inhibition experiments demonstrate that bark-dwelling MOB reduce methane emissions by 36 ± 5 %. These multiple, complementary lines of evidence indicate that bark-dwelling MOB represent a novel and potentially significant methane sink, and an important frontier for further research.
Protease-associated import systems are widespread in Gram-negative bacteria
Publisher: Public Library of Science (PLoS)
Date: 15-10-2019
A revised biosynthetic pathway for the cofactor F420 in prokaryotes
Publisher: Springer Science and Business Media LLC
Date: 05-04-2019
DOI: 10.1038/S41467-019-09534-X
Abstract: Cofactor F 420 plays critical roles in primary and secondary metabolism in a range of bacteria and archaea as a low-potential hydride transfer agent. It mediates a variety of important redox transformations involved in bacterial persistence, antibiotic biosynthesis, pro-drug activation and methanogenesis. However, the biosynthetic pathway for F 420 has not been fully elucidated: neither the enzyme that generates the putative intermediate 2-phospho- l -lactate, nor the function of the FMN-binding C-terminal domain of the γ-glutamyl ligase (FbiB) in bacteria are known. Here we present the structure of the guanylyltransferase FbiD and show that, along with its archaeal homolog CofC, it accepts phosphoenolpyruvate, rather than 2-phospho- l -lactate, as the substrate, leading to the formation of the previously uncharacterized intermediate dehydro-F 420 -0. The C-terminal domain of FbiB then utilizes FMNH 2 to reduce dehydro-F 420 -0, which produces mature F 420 species when combined with the γ-glutamyl ligase activity of the N-terminal domain. These new insights have allowed the heterologous production of F 420 from a recombinant F 420 biosynthetic pathway in Escherichia coli .
Integration of hydrogenase expression and hydrogen sensing in bacterial cell physiology
Publisher: Elsevier BV
Date: 04-2014
DOI: 10.1016/J.MIB.2014.02.001
Abstract: Hydrogenases are ubiquitous in ecosystems and widespread in microorganisms. In bacteria, hydrogen metabolism is a facultative trait that is tightly regulated in response to both external factors (e.g. gas concentrations) and internal factors (e.g. redox state). Here we consider how environmental and pathogenic bacteria regulate [NiFe]-hydrogenases to adapt to chemical changes and meet physiological needs. We introduce this concept by exploring how Ralstonia eutropha switches between heterotrophic and lithotrophic growth modes by sensing hydrogen and electron availability. The regulation and integration of hydrogen metabolism in the virulence of Salmonella enterica and Helicobacter pylori, persistence of mycobacteria and streptomycetes, and differentiation of filamentous cyanobacteria are subsequently discussed. We also consider how these findings are extendable to other systems.
Fermentative Spirochaetes mediate necromass recycling in anoxic hydrocarbon-contaminated habitats
Publisher: Springer Science and Business Media LLC
Date: 30-05-2018
A nitrite-oxidising bacterium constitutively consumes atmospheric hydrogen
Publisher: Springer Science and Business Media LLC
Date: 25-06-2022
DOI: 10.1038/S41396-022-01265-0
Abstract: Chemolithoautotrophic nitrite-oxidising bacteria (NOB) of the genus Nitrospira contribute to nitrification in erse natural environments and engineered systems. Nitrospira are thought to be well-adapted to substrate limitation owing to their high affinity for nitrite and capacity to use alternative energy sources. Here, we demonstrate that the canonical nitrite oxidiser Nitrospira moscoviensis oxidises hydrogen (H 2 ) below atmospheric levels using a high-affinity group 2a nickel-iron hydrogenase [ K m(app) = 32 nM]. Atmospheric H 2 oxidation occurred under both nitrite-replete and nitrite-deplete conditions, suggesting low-potential electrons derived from H 2 oxidation promote nitrite-dependent growth and enable survival during nitrite limitation. Proteomic analyses confirmed the hydrogenase was abundant under both conditions and indicated extensive metabolic changes occur to reduce energy expenditure and growth under nitrite-deplete conditions. Thermodynamic modelling revealed that H 2 oxidation theoretically generates higher power yield than nitrite oxidation at low substrate concentrations and significantly contributes to growth at elevated nitrite concentrations. Collectively, this study suggests atmospheric H 2 oxidation enhances the growth and survival of NOB amid variability of nitrite supply, extends the phenomenon of atmospheric H 2 oxidation to an eighth phylum (Nitrospirota), and reveals unexpected new links between the global hydrogen and nitrogen cycles. Long classified as obligate nitrite oxidisers, our findings suggest H 2 may primarily support growth and survival of certain NOB in natural environments.
Hydrogen is a major lifeline for aerobic bacteria
Publisher: Elsevier BV
Date: 04-2022
Putative Iron-Sulfur Proteins Are Required for Hydrogen Consumption and Enhance Survival of Mycobacteria
Publisher: Frontiers Media SA
Date: 22-11-2019
Molecular hydrogen in seawater supports growth of diverse marine bacteria
Publisher: Springer Science and Business Media LLC
Date: 06-02-2023
DOI: 10.1038/S41564-023-01322-0
Abstract: Molecular hydrogen (H 2 ) is an abundant and readily accessible energy source in marine systems, but it remains unknown whether marine microbial communities consume this gas. Here we use a suite of approaches to show that marine bacteria consume H 2 to support growth. Genes for H 2 -uptake hydrogenases are prevalent in global ocean metagenomes, highly expressed in metatranscriptomes and found across eight bacterial phyla. Capacity for H 2 oxidation increases with depth and decreases with oxygen concentration, suggesting that H 2 is important in environments with low primary production. Biogeochemical measurements of tropical, temperate and subantarctic waters, and axenic cultures show that marine microbes consume H 2 supplied at environmentally relevant concentrations, yielding enough cell-specific power to support growth in bacteria with low energy requirements. Conversely, our results indicate that oxidation of carbon monoxide (CO) primarily supports survival. Altogether, H 2 is a notable energy source for marine bacteria and may influence oceanic ecology and biogeochemistry.
Diverse hydrogen production and consumption pathways influence methane production in ruminants
Publisher: Springer Science and Business Media LLC
Date: 26-06-2019
Mycobacteria tolerate carbon monoxide by remodelling their respiratory chain
Publisher: Cold Spring Harbor Laboratory
Date: 09-04-2020
DOI: 10.1101/2020.04.08.032912
Abstract: Carbon monoxide (CO) is a gas infamous for its acute toxicity. The toxicity of CO predominantly stems from its tendency to form carbonyl complexes with transition metals, thus inhibiting the heme-prosthetic groups of proteins, including the terminal oxidases of the respiratory chain. While CO has been proposed as an antibacterial agent, the evidence supporting its toxicity towards bacteria is equivocal, and its cellular targets remain poorly defined. In this work, we investigate the physiological response of mycobacteria to CO. We show that Mycobacterium smegmatis is highly resistant to the toxic effects of CO, exhibiting normal growth parameters when cultured in its presence. We profiled the proteome of M. smegmatis during growth in CO, identifying strong induction of cytochrome bd oxidase and members of the dos regulon, but relatively few other changes. We show that the activity of cytochrome bd oxidase is resistant to CO, whereas cytochrome bcc-aa 3 oxidase is strongly inhibited by this gas. Consistent with these findings, growth analysis shows that M. smegmatis lacking cytochrome bd oxidase displays a significant growth defect in the presence of CO, while induction of the dos regulon appears to be unimportant for adaption to CO. Altogether, our findings suggest that M. smegmatis has considerable resistance to CO and benefits from respiratory flexibility to withstand its inhibitory effects. Carbon monoxide has an infamous reputation as a toxic gas and it has been suggested that it has potential as an antibacterial agent. Despite this, the means by which bacteria resist its toxic effects are not well understood. In this study we determine the physiological response of Mycobacterium smegmatis to growth in CO. We show for the first time that the cytochrome bd oxidase is inherently resistant to CO and is deployed by M. smegmatis to tolerate the presence of this gas. Further, we show that aside from this remodelling of its respiratory chain, M. smegmatis makes few other functional changes to its proteome, suggesting it has a high level of inherent resistance to CO.
Cellular and Structural Basis of Synthesis of the Unique Intermediate Dehydro-F420-0 in Mycobacteria
Publisher: American Society for Microbiology
Date: 30-06-2020
DOI: 10.1128/MSYSTEMS.00389-20
Abstract: Mycobacteria are major environmental microorganisms and cause many significant diseases, including tuberculosis. Mycobacteria make an unusual vitamin-like compound, F 420 , and use it to both persist during stress and resist antibiotic treatment. Understanding how mycobacteria make F 420 is important, as this process can be targeted to create new drugs to combat infections like tuberculosis. In this study, we show that mycobacteria make F 420 in a way that is different from other bacteria. We studied the molecular machinery that mycobacteria use to make F 420 , determining the chemical mechanism for this process and identifying a novel chemical intermediate. These findings also have clinical relevance, given that two new prodrugs for tuberculosis treatment are activated by F 420 .
Hydrodynamic disturbance controls microbial community assembly and biogeochemical processes in coastal sediments
Publisher: Springer Science and Business Media LLC
Date: 28-09-2022
DOI: 10.1038/S41396-021-01111-9
Abstract: The microbial community composition and biogeochemical dynamics of coastal permeable (sand) sediments differs from cohesive (mud) sediments. Tide- and wave-driven hydrodynamic disturbance causes spatiotemporal variations in oxygen levels, which select for microbial generalists and disrupt redox cascades. In this work, we profiled microbial communities and biogeochemical dynamics in sediment profiles from three sites varying in their exposure to hydrodynamic disturbance. Strong variations in sediment geochemistry, biogeochemical activities, and microbial abundance, composition, and capabilities were observed between the sites. Most of these variations, except for microbial abundance and ersity, significantly correlated with the relative disturbance level of each s le. In line with previous findings, metabolically flexible habitat generalists (e.g., Flavobacteriaceae, Woeseaiceae, Rhodobacteraceae) dominated in all s les. However, we present evidence that aerobic specialists such as ammonia-oxidizing archaea (Nitrosopumilaceae) were more abundant and active in more disturbed s les, whereas bacteria capable of sulfate reduction (e.g., uncultured Desulfobacterales), dissimilatory nitrate reduction to ammonium (DNRA e.g., Ignavibacteriaceae), and sulfide-dependent chemolithoautotrophy (e.g., Sulfurovaceae) were enriched and active in less disturbed s les. These findings are supported by insights from nine deeply sequenced metagenomes and 169 derived metagenome-assembled genomes. Altogether, these findings suggest that hydrodynamic disturbance is a critical factor controlling microbial community assembly and biogeochemical processes in coastal sediments. Moreover, they strengthen our understanding of the relationships between microbial composition and biogeochemical processes in these unique environments.
Bark-dwelling methanotrophic bacteria decrease methane emissions from trees
Publisher: Springer Science and Business Media LLC
Date: 09-04-2021
DOI: 10.1038/S41467-021-22333-7
Abstract: Tree stems are an important and unconstrained source of methane, yet it is uncertain whether internal microbial controls (i.e. methanotrophy) within tree bark may reduce methane emissions. Here we demonstrate that unique microbial communities dominated by methane-oxidising bacteria (MOB) dwell within bark of Melaleuca quinquenervia , a common, invasive and globally distributed lowland species. In laboratory incubations, methane-inoculated M. quinquenervia bark mediated methane consumption (up to 96.3 µmol m −2 bark d −1 ) and reveal distinct isotopic δ 13 C-CH 4 enrichment characteristic of MOB. Molecular analysis indicates unique microbial communities reside within the bark, with MOB primarily from the genus Methylomonas comprising up to 25 % of the total microbial community. Methanotroph abundance was linearly correlated to methane uptake rates (R 2 = 0.76, p = 0.006). Finally, field-based methane oxidation inhibition experiments demonstrate that bark-dwelling MOB reduce methane emissions by 36 ± 5 %. These multiple complementary lines of evidence indicate that bark-dwelling MOB represent a potentially significant methane sink, and an important frontier for further research.
Understanding the transmission of Mycobacterium ulcerans: A step towards controlling Buruli ulcer
Publisher: Public Library of Science (PLoS)
Date: 26-08-2021
DOI: 10.1371/JOURNAL.PNTD.0009678
Abstract: Mycobacterium ulcerans is the causative agent of Buruli ulcer, a rare but chronic debilitating skin and soft tissue disease found predominantly in West Africa and Southeast Australia. While a moderate body of research has examined the distribution of M . ulcerans , the specific route(s) of transmission of this bacterium remain unknown, hindering control efforts. M . ulcerans is considered an environmental pathogen given it is associated with lentic ecosystems and human-to-human spread is negligible. However, the pathogen is also carried by various mammals and invertebrates, which may serve as key reservoirs and mechanical vectors, respectively. Here, we examine and review recent evidence from these endemic regions on potential transmission pathways, noting differences in findings between Africa and Australia, and summarising the risk and protective factors associated with Buruli ulcer transmission. We also discuss evidence suggesting that environmental disturbance and human population changes precede outbreaks. We note five key research priorities, including adoption of One Health frameworks, to resolve transmission pathways and inform control strategies to reduce the spread of Buruli ulcer.
Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments
Publisher: Springer Science and Business Media LLC
Date: 19-08-2022
DOI: 10.1038/S41467-022-32503-W
Abstract: Microbially mediated nitrogen cycling in carbon-dominated cold seep environments remains poorly understood. So far anaerobic methanotrophic archaea (ANME-2) and their sulfate-reducing bacterial partners (SEEP-SRB1 clade) have been identified as diazotrophs in deep sea cold seep sediments. However, it is unclear whether other microbial groups can perform nitrogen fixation in such ecosystems. To fill this gap, we analyzed 61 metagenomes, 1428 metagenome-assembled genomes, and six metatranscriptomes derived from 11 globally distributed cold seeps. These sediments contain phylogenetically erse nitrogenase genes corresponding to an expanded ersity of diazotrophic lineages. Diverse catabolic pathways were predicted to provide ATP for nitrogen fixation, suggesting diazotrophy in cold seeps is not necessarily associated with sulfate-dependent anaerobic oxidation of methane. Nitrogen fixation genes among various diazotrophic groups in cold seeps were inferred to be genetically mobile and subject to purifying selection. Our findings extend the capacity for diazotrophy to five candidate phyla (Altarchaeia, Omnitrophota, FCPU426, Caldatribacteriota and UBA6262), and suggest that cold seep diazotrophs might contribute substantially to the global nitrogen balance.
Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations
Publisher: American Society for Microbiology
Date: 29-06-2021
DOI: 10.1128/MSYSTEMS.01196-20
Abstract: The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from erse freshwater habitats that spanned oxic and anoxic zones, s ling seasons, and latitudes.
Functional basis of primary succession: Traits of the pioneer microbes
Publisher: Wiley
Date: 18-11-2023
Trace gas oxidizers are widespread and active members of soil microbial communities
Publisher: Springer Science and Business Media LLC
Date: 04-01-2021
DOI: 10.1038/S41564-020-00811-W
Abstract: Soil microorganisms globally are thought to be sustained primarily by organic carbon sources. Certain bacteria also consume inorganic energy sources such as trace gases, but they are presumed to be rare community members, except within some oligotrophic soils. Here we combined metagenomic, biogeochemical and modelling approaches to determine how soil microbial communities meet energy and carbon needs. Analysis of 40 metagenomes and 757 derived genomes indicated that over 70% of soil bacterial taxa encode enzymes to consume inorganic energy sources. Bacteria from 19 phyla encoded enzymes to use the trace gases hydrogen and carbon monoxide as supplemental electron donors for aerobic respiration. In addition, we identified a fourth phylum (Gemmatimonadota) potentially capable of aerobic methanotrophy. Consistent with the metagenomic profiling, communities within soil profiles from erse habitats rapidly oxidized hydrogen, carbon monoxide and to a lesser extent methane below atmospheric concentrations. Thermodynamic modelling indicated that the power generated by oxidation of these three gases is sufficient to meet the maintenance needs of the bacterial cells capable of consuming them. Diverse bacteria also encode enzymes to use trace gases as electron donors to support carbon fixation. Altogether, these findings indicate that trace gas oxidation confers a major selective advantage in soil ecosystems, where availability of preferred organic substrates limits microbial growth. The observation that inorganic energy sources may sustain most soil bacteria also has broad implications for understanding atmospheric chemistry and microbial bio ersity in a changing world.
Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient
Publisher: Springer Science and Business Media LLC
Date: 25-05-2021
DOI: 10.1038/S41396-021-01001-0
Abstract: Desert soils harbour erse communities of aerobic bacteria despite lacking substantial organic carbon inputs from vegetation. A major question is therefore how these communities maintain their bio ersity and biomass in these resource-limiting ecosystems. Here, we investigated desert topsoils and biological soil crusts collected along an aridity gradient traversing four climatic regions (sub-humid, semi-arid, arid, and hyper-arid). Metagenomic analysis indicated these communities vary in their capacity to use sunlight, organic compounds, and inorganic compounds as energy sources. Thermoleophilia, Actinobacteria, and Acidimicrobiia were the most abundant and prevalent bacterial classes across the aridity gradient in both topsoils and biocrusts. Contrary to the classical view that these taxa are obligate organoheterotrophs, genome-resolved analysis suggested they are metabolically flexible, with the capacity to also use atmospheric H 2 to support aerobic respiration and often carbon fixation. In contrast, Cyanobacteria were patchily distributed and only abundant in certain biocrusts. Activity measurements profiled how aerobic H 2 oxidation, chemosynthetic CO 2 fixation, and photosynthesis varied with aridity. Cell-specific rates of atmospheric H 2 consumption increased 143-fold along the aridity gradient, correlating with increased abundance of high-affinity hydrogenases. Photosynthetic and chemosynthetic primary production co-occurred throughout the gradient, with photosynthesis dominant in biocrusts and chemosynthesis dominant in arid and hyper-arid soils. Altogether, these findings suggest that the major bacterial lineages inhabiting hot deserts use different strategies for energy and carbon acquisition depending on resource availability. Moreover, they highlight the previously overlooked roles of Actinobacteriota as abundant primary producers and trace gases as critical energy sources supporting productivity and resilience of desert ecosystems.
Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf
Publisher: Springer Science and Business Media LLC
Date: 10-01-2022
DOI: 10.1038/S41467-021-27769-5
Abstract: Throughout coastal Antarctica, ice shelves separate oceanic waters from sunlight by hundreds of meters of ice. Historical studies have detected activity of nitrifying microorganisms in oceanic cavities below permanent ice shelves. However, little is known about the microbial composition and pathways that mediate these activities. In this study, we profiled the microbial communities beneath the Ross Ice Shelf using a multi-omics approach. Overall, beneath-shelf microorganisms are of comparable abundance and ersity, though distinct composition, relative to those in the open meso- and bathypelagic ocean. Production of new organic carbon is likely driven by aerobic lithoautotrophic archaea and bacteria that can use ammonium, nitrite, and sulfur compounds as electron donors. Also enriched were aerobic organoheterotrophic bacteria capable of degrading complex organic carbon substrates, likely derived from in situ fixed carbon and potentially refractory organic matter laterally advected by the below-shelf waters. Altogether, these findings uncover a taxonomically distinct microbial community potentially adapted to a highly oligotrophic marine environment and suggest that ocean cavity waters are primarily chemosynthetically-driven systems.
Termite mounds contain soil-derived methanotroph communities kinetically adapted to elevated methane concentrations
Publisher: Springer Science and Business Media LLC
Date: 24-07-2020
DOI: 10.1038/S41396-020-0722-3
Abstract: Termite mounds have recently been confirmed to mitigate approximately half of termite methane (CH 4 ) emissions, but the aerobic CH 4 oxidising bacteria (methanotrophs) responsible for this consumption have not been resolved. Here, we describe the abundance, composition and CH 4 oxidation kinetics of the methanotroph communities in the mounds of three distinct termite species s led from Northern Australia. Results from three independent methods employed show that methanotrophs are rare members of microbial communities in termite mounds, with a comparable abundance but distinct composition to those of adjoining soil s les. Across all mounds, the most abundant and prevalent methane monooxygenase sequences were affiliated with upland soil cluster α (USCα), with sequences homologous to Methylocystis and tropical upland soil cluster (TUSC) also detected. The reconstruction of a metagenome-assembled genome of a mound USCα representative highlighted the metabolic capabilities of this group of methanotrophs. The apparent Michaelis–Menten kinetics of CH 4 oxidation in mounds were estimated from in situ reaction rates. Methane affinities of the communities were in the low micromolar range, which is one to two orders of magnitude higher than those of upland soils, but significantly lower than those measured in soils with a large CH 4 source such as landfill cover soils. The rate constant of CH 4 oxidation, as well as the porosity of the mound material, were significantly positively correlated with the abundance of methanotroph communities of termite mounds. We conclude that termite-derived CH 4 emissions have selected for distinct methanotroph communities that are kinetically adapted to elevated CH 4 concentrations. However, factors other than substrate concentration appear to limit methanotroph abundance and hence these bacteria only partially mitigate termite-derived CH 4 emissions. Our results also highlight the predominant role of USCα in an environment with elevated CH 4 concentrations and suggest a higher functional ersity within this group than previously recognised.
Editorial: Microbial Hydrogen Metabolism
Publisher: Frontiers Media SA
Date: 30-01-2020
Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival
Publisher: Springer Science and Business Media LLC
Date: 29-07-2019
FreshwaterChlorobiaexhibit metabolic specialization among cosmopolitan and endemic populations
Publisher: Cold Spring Harbor Laboratory
Date: 11-09-2020
DOI: 10.1101/2020.09.10.291559
Abstract: Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi ) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on their functional ecology and local adaptations came from isolates and merely 26 sequenced genomes that are poor representatives of natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-cell genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs) or “species”. Of the 71 mOTUs, 57 were classified as genus Chlorobium and these mOTUs varied in relative abundance up to ~60% of the microbial communities in the s led anoxic waters. Several Chlorobium -associated mOTUs were globally distributed whereas others were endemic to in idual lakes. Although most clades encoded the ability to oxidize hydrogen, many were lacking genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian Chlorobium clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insights into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems. The reconstruction of genomes from metagenomes has enabled unprecedented insights into the ecology and evolution of environmental microbiomes. We applied this powerful approach to 274 metagenomes collected from erse freshwater habitats that spanned oxic and anoxic zones, s ling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia -associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and pinpoint nutrients that likely fuel their electron chains. Being photoautotrophs, these Chlorobia organisms also have the potential to serve as carbon sources that support metalimnetic and hypolimnetic food webs.
Energetic Basis of Microbial Growth and Persistence in Desert Ecosystems.
Publisher: American Society for Microbiology
Date: 28-04-2020
DOI: 10.1128/MSYSTEMS.00495-19
Abstract: Microbial life is surprisingly abundant and erse in global desert ecosystems. In these environments, microorganisms endure a multitude of physicochemical stresses, including low water potential, carbon and nitrogen starvation, and extreme temperatures. In this review, we summarize our current understanding of the energetic mechanisms and trophic dynamics that underpin microbial function in desert ecosystems. Accumulating evidence suggests that dormancy is a common strategy that facilitates microbial survival in response to water and carbon limitation.
Global and seasonal variation of marine phosphonate metabolism
Publisher: Springer Science and Business Media LLC
Date: 23-06-2022
DOI: 10.1038/S41396-022-01266-Z
Abstract: Marine microbial communities rely on dissolved organic phosphorus (DOP) remineralisation to meet phosphorus (P) requirements. We extensively surveyed the genomic and metagenomic distribution of genes directing phosphonate biosynthesis, substrate-specific catabolism of 2-aminoethylphosphonate (2-AEP, the most abundant phosphonate in the marine environment), and broad-specificity catabolism of phosphonates by the C-P lyase (including methylphosphonate, a major source of methane). We developed comprehensive enzyme databases by curating publicly available sequences and then screened metagenomes from TARA Oceans and Munida Microbial Observatory Time Series (MOTS) to assess spatial and seasonal variation in phosphonate metabolism pathways. Phosphonate cycling genes were encoded in erse gene clusters by 35 marine bacterial and archaeal classes. More than 65% of marine phosphonate cycling genes mapped to Proteobacteria with production demonstrating wider taxonomic ersity than catabolism. Hydrolysis of 2-AEP was the dominant phosphonate catabolism strategy, enabling microbes to assimilate carbon and nitrogen alongside P. Genes for broad-specificity catabolism by the C-P lyase were far less widespread, though enriched in the extremely P-deplete environment of the Mediterranean Sea. Phosphonate cycling genes were abundant in marine metagenomes, particularly from the mesopelagic zone and winter s ling dates. Disparity between prevalence of substrate-specific and broad-specificity catabolism may be due to higher resource expenditure from the cell to build and retain the C-P lyase. This study is the most comprehensive metagenomic survey of marine microbial phosphonate cycling to date and provides curated databases for 14 genes involved in phosphonate cycling.
Simultaneous detection of multiple pathogens with the TaqMan Array Card
Publisher: Elsevier BV
Date: 2022
Molecular hydrogen metabolism: A widespread trait of pathogenic bacteria and protists
Publisher: American Society for Microbiology
Date: 19-02-2020
Abstract: Pathogenic microorganisms use various mechanisms to conserve energy in host tissues and environmental reservoirs. One widespread but often overlooked means of energy conservation is through the consumption or production of molecular hydrogen (H 2 ). Here, we comprehensively review the distribution, biochemistry, and physiology of H 2 metabolism in pathogens.
A planetary health model for reducing exposure to faecal contamination in urban informal settlements: Baseline findings from Makassar, Indonesia
Publisher: Elsevier BV
Date: 10-2021
The growth and survival of Mycobacterium smegmatis is enhanced by co-metabolism of atmospheric H2
Publisher: Public Library of Science (PLoS)
Date: 24-07-2014
Mycobacterial F420H2-dependent reductases promiscuously reduce diverse compounds through a common mechanism
Publisher: Frontiers Media SA
Date: 31-05-2017
Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea
Publisher: Oxford University Press (OUP)
Date: 14-04-2021
Abstract: Many bacteria and archaea produce the redox cofactor F420. F420 is structurally similar to the cofactors FAD and FMN but is catalytically more similar to NAD and NADP. These properties allow F420 to catalyze challenging redox reactions, including key steps in methanogenesis, antibiotic biosynthesis and xenobiotic biodegradation. In the last 5 years, there has been much progress in understanding its distribution, biosynthesis, role and applications. Whereas F420 was previously thought to be confined to Actinobacteria and Euryarchaeota, new evidence indicates it is synthesized across the bacterial and archaeal domains, as a result of extensive horizontal and vertical biosynthetic gene transfer. F420 was thought to be synthesized through one biosynthetic pathway however, recent advances have revealed variants of this pathway and have resolved their key biosynthetic steps. In parallel, new F420-dependent biosynthetic and metabolic processes have been discovered. These advances have enabled the heterologous production of F420 and identified enantioselective F420H2-dependent reductases for biocatalysis. New research has also helped resolve how microorganisms use F420 to influence human and environmental health, providing opportunities for tuberculosis treatment and methane mitigation. A total of 50 years since its discovery, multiple paradigms associated with F420 have shifted, and new F420-dependent organisms and processes continue to be discovered.
Mixotrophy drives niche expansion of verrucomicrobial methanotrophs.
Publisher: Springer Science and Business Media LLC
Date: 04-08-2017
Rethinking CSR theory to incorporate microbial metabolic diversity and foraging traits
Publisher: Springer Science and Business Media LLC
Date: 18-08-2023
Hydrogen oxidation influences glycogen accumulation in a verrucomicrobial methanotroph
Publisher: Frontiers Media SA
Date: 16-08-2019
Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments
Publisher: Springer Science and Business Media LLC
Date: 11-03-2019
DOI: 10.1038/S41564-019-0391-Z
Abstract: Permeable (sandy) sediments cover half of the continental margin and are major regulators of oceanic carbon cycling. The microbial communities within these highly dynamic sediments frequently shift between oxic and anoxic states, and hence are less stratified than those in cohesive (muddy) sediments. A major question is, therefore, how these communities maintain metabolism during oxic-anoxic transitions. Here, we show that molecular hydrogen (H
Population mitogenomics provides insights into evolutionary history, source of invasions and diversifying selection in the House Crow (Corvus splendens).
Publisher: Springer Science and Business Media LLC
Date: 28-11-2017
An obligate aerobe adapts to hypoxia by hybridising fermentation with carbon storage
Publisher: Cold Spring Harbor Laboratory
Date: 12-09-2023
Mycobacteria Tolerate Carbon Monoxide by Remodeling Their Respiratory Chain
Publisher: American Society for Microbiology
Date: 29-06-2021
DOI: 10.1128/MSYSTEMS.01292-20
Abstract: Carbon monoxide has an infamous reputation as a toxic gas, and it has been suggested that it has potential as an antibacterial agent. Despite this, how bacteria resist its toxic effects is not well understood.
The methanogenic redox cofactor F-420 is widely synthesized by aerobic soil bacteria
Publisher: Springer Science and Business Media LLC
Date: 09-08-2017
Two uptake hydrogenases differentially interact with the aerobic respiratory chain during mycobacterial growth and persistence
Publisher: Elsevier BV
Date: 12-2019
Disease-specific loss of microbial cross-feeding interactions in the human gut
Publisher: Springer Science and Business Media LLC
Date: 20-10-2023
Occurrence and expression of genes encoding methyl-compound production in rumen bacteria
Publisher: Springer Science and Business Media LLC
Date: 14-11-2019
DOI: 10.1186/S42523-019-0016-0
Abstract: Digestive processes in the rumen lead to the release of methyl-compounds, mainly methanol and methylamines, which are used by methyltrophic methanogens to form methane, an important agricultural greenhouse gas. Methylamines are produced from plant phosphatidylcholine degradation, by choline trimethylamine lyase, while methanol comes from demethoxylation of dietary pectins via pectin methylesterase activity. We have screened rumen metagenomic and metatranscriptomic datasets, metagenome assembled genomes, and the Hungate1000 genomes to identify organisms capable of producing methyl-compounds. We also describe the enrichment of pectin-degrading and methane-forming microbes from sheep rumen contents and the analysis of their genomes via metagenomic assembly. Screens of metagenomic data using the protein domains of choline trimethylamine lyase (CutC), and activator protein (CutD) found good matches only to Olsenella umbonata and to Caecibacter , while the Hungate1000 genomes and metagenome assembled genomes from the cattle rumen found bacteria within the phyla Actinobacteria, Firmicutes and Proteobacteria. The cutC and cutD genes clustered with genes that encode structural components of bacterial microcompartment proteins. Prevotella was the dominant genus encoding pectin methyl esterases, with smaller numbers of sequences identified from other fibre-degrading rumen bacteria. Some large pectin methyl esterases ( 2100 aa) were found to be encoded in Butyrivibrio genomes. The pectin-utilising, methane-producing consortium was composed of (i) a putative pectin-degrading bacterium (phylum Tenericutes, class Mollicutes ), (ii) a galacturonate-using Sphaerochaeta sp. predicted to produce acetate, lactate, and ethanol, and (iii) a methylotrophic methanogen, Methanosphaera sp., with the ability to form methane via a primary ethanol-dependent, hydrogen-independent, methanogenesis pathway. The main bacteria that produce methyl-compounds have been identified in ruminants. Their enzymatic activities can now be targeted with the aim of finding ways to reduce the supply of methyl-compound substrates to methanogens, and thereby limit methylotrophic methanogenesis in the rumen.
Hydrogen-Oxidizing Bacteria Are Abundant in Desert Soils and Strongly Stimulated by Hydration
Publisher: American Society for Microbiology
Date: 22-12-2020
DOI: 10.1128/MSYSTEMS.01131-20
Abstract: Desert ecosystems, spanning a third of the earth’s surface, harbor remarkably erse microbial life despite having a low potential for photosynthesis. In this work, we reveal that atmospheric hydrogen serves as a major previously overlooked energy source for a large proportion of desert bacteria. We show that both chemoheterotrophic and photoautotrophic bacteria have the potential to oxidize hydrogen across deserts s led across four continents. Whereas hydrogen oxidation was slow in native dry deserts, it increased by three orders of magnitude together with photosynthesis following hydration. This study revealed that continual harvesting of atmospheric energy sources may be a major way that desert communities adapt to long periods of water and energy deprivation, with significant ecological and biogeochemical ramifications.
Isotopic evidence for axial tree stem methane oxidation within subtropical lowland forests
Publisher: Wiley
Date: 12-04-2021
DOI: 10.1111/NPH.17343
Abstract: Knowledge regarding mechanisms moderating methane (CH 4 ) sink/source behaviour along the soil–tree stem–atmosphere continuum remains incomplete. Here, we applied stable isotope analysis (δ 13 C‐CH 4 ) to gain insights into axial CH 4 transport and oxidation in two globally distributed subtropical lowland species ( Melaleuca quinquenervia and Casuarina glauca ). We found consistent trends in CH 4 flux (decreasing with height) and δ 13 C‐CH 4 enrichment (increasing with height) in relation to stem height from ground. The average lower tree stem δ 13 C‐CH 4 (0–40 cm) of Melaleuca and Casuarina (−53.96‰ and −65.89‰) were similar to adjacent flooded soil CH 4 ebullition (−52.87‰ and −62.98‰), suggesting that stem CH 4 is derived mainly by soil sources. Upper stems (81–200 cm) displayed distinct δ 13 C‐CH 4 enrichment ( Melaleuca −44.6‰ and Casuarina −46.5‰, respectively). Coupled 3D‐photogrammetry with novel 3D‐stem measurements revealed distinct hotspots of CH 4 flux and isotopic fractionation on Melaleuca , which were likely due to bark anomalies in which preferential pathways of gas efflux were enhanced. Diel experiments revealed greater δ 13 C‐CH 4 enrichment and higher oxidation rates in the afternoon, compared with the morning. Overall, we estimated that c . 33% of the methane was oxidised between lower and upper stems during axial transport, therefore potentially representing a globally significant, yet previously unaccounted for, methane sink.
Coupling between Nitrogen Fixation and Tetrachlorobiphenyl Dechlorination in a Rhizobium-Legume Symbiosis.
Publisher: American Chemical Society (ACS)
Date: 05-02-2018
Abstract: Legume-rhizobium symbioses have the potential to remediate soils contaminated with chlorinated organic compounds. Here, the model symbiosis between Medicago sativa and Sinorhizobium meliloti was used to explore the relationships between symbiotic nitrogen fixation and transformation of tetrachlorobiphenyl PCB 77 within this association. 45-day-old seedlings in vermiculite were pretreated with 5 mg L
A nitrite-oxidizing bacterium constitutively consumes atmospheric hydrogen
Publisher: Cold Spring Harbor Laboratory
Date: 20-08-2021
DOI: 10.1101/2021.08.20.457082
Abstract: Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) of the genus Nitrospira contribute to nitrification in erse natural environments and engineered systems. Nitrospira are thought to be well-adapted to substrate limitation owing to their high affinity for nitrite and capacity to use alternative energy sources. Here, we demonstrate that the canonical nitrite oxidizer Nitrospira moscoviensis oxidizes hydrogen (H 2 ) below atmospheric levels using a high-affinity group 2a nickel-iron hydrogenase [ K m(app) = 32 nM]. Atmospheric H 2 oxidation occurred under both nitrite-replete and nitrite-deplete conditions, suggesting low-potential electrons derived from H 2 oxidation promote nitrite-dependent growth and enable survival during nitrite limitation. Proteomic analyses confirmed the hydrogenase was abundant under both conditions and indicated extensive metabolic changes occur to reduce energy expenditure and growth under nitrite-deplete conditions. Respirometry analysis indicates the hydrogenase and nitrite oxidoreductase are bona fide components of the aerobic respiratory chain of N. moscoviensis , though they transfer electrons to distinct electron carriers in accord with the contrasting redox potentials of their substrates. Collectively, this study suggests atmospheric H 2 oxidation enhances the growth and survival of NOB in amid variability of nitrite supply. These findings also extend the phenomenon of atmospheric H 2 oxidation to a seventh phylum (Nitrospirota) and reveal unexpected new links between the global hydrogen and nitrogen cycles.
Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments
Publisher: Springer Science and Business Media LLC
Date: 18-04-2019
DOI: 10.1038/S41467-019-09747-0
Abstract: The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors erse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encode enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally erse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism.
Three different [NiFe] hydrogenases confer metabolic flexibility in the obligate aerobe Mycobacterium smegmatis.
Publisher: Wiley
Date: 25-11-2014
Abstract: M ycobacterium smegmatis is an obligate aerobe that harbours three predicted [ NiFe ] hydrogenases, Hyd 1 ( MSMEG _2262–2263), Hyd 2 ( MSMEG _2720‐2719) and Hyd 3 ( MSMEG _3931‐3928). We show here that these three enzymes differ in their phylogeny, regulation and catalytic activity. Phylogenetic analysis revealed that Hyd 1 groups with hydrogenases that oxidize H 2 produced by metabolic processes, and Hyd 2 is homologous to a novel group of putative high‐affinity hydrogenases. Hyd 1 and Hyd 2 respond to carbon and oxygen limitation, and, in the case of Hyd 1, hydrogen supplementation. Hydrogen consumption measurements confirmed that both enzymes can oxidize hydrogen. In contrast, the phylogenetic analysis and activity measurements of Hyd 3 are consistent with the enzyme evolving hydrogen. Hyd 3 is controlled by DosR , a regulator that responds to hypoxic conditions. The strict dependence of hydrogen oxidation of Hyd 1 and Hyd 2 on oxygen suggests that the enzymes are oxygen tolerant and linked to the respiratory chain. This unique combination of hydrogenases allows M . smegmatis to oxidize hydrogen at high ( Hyd 1) and potentially tropospheric ( Hyd 2) concentrations, as well as recycle reduced equivalents by evolving hydrogen ( Hyd 3). The distribution of these hydrogenases throughout numerous soil and marine species of actinomycetes suggests that oxic hydrogen metabolism provides metabolic flexibility in environments with changing nutrient fluxes.
Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils
Publisher: Proceedings of the National Academy of Sciences
Date: 03-11-2021
Abstract: Diverse microbial life has been detected in the cold desert soils of Antarctica once thought to be barren. Here, we provide metagenomic, biogeochemical, and culture-based evidence that Antarctic soil microorganisms are phylogenetically and functionally distinct from those in other soils and adopt various metabolic and ecological strategies. The most abundant community members are metabolically versatile aerobes that use ubiquitous atmospheric trace gases to potentially meet energy, carbon, and, through metabolic water production, hydration needs. Lineages capable of harvesting solar energy, oxidizing edaphic inorganic substrates, or adopting symbiotic lifestyles were also identified. Altogether, these findings provide insights into microbial adaptation to extreme water and energy limitation and will inform ongoing efforts to conserve the unique bio ersity on this continent.
Atmospheric trace gases support primary production in Antarctic desert surface soil
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
Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps
Publisher: Springer Science and Business Media LLC
Date: 28-02-2023
DOI: 10.1038/S41467-023-36877-3
Abstract: Deep sea cold seep sediments host abundant and erse microbial populations that significantly influence biogeochemical cycles. While numerous studies have revealed their community structure and functional capabilities, little is known about genetic heterogeneity within species. Here, we examine intraspecies ersity patterns of 39 abundant species identified in sediment layers down to 430 cm below the sea floor across six cold seep sites. These populations are grouped as aerobic methane-oxidizing bacteria, anaerobic methanotrophic archaea and sulfate-reducing bacteria. Different evolutionary trajectories are observed at the genomic level among these physiologically and phylogenetically erse populations, with generally low rates of homologous recombination and strong purifying selection. Functional genes related to methane ( pmoA and mcrA ) and sulfate ( dsrA ) metabolisms are under strong purifying selection in most species investigated. These genes differ in evolutionary trajectories across phylogenetic clades but are functionally conserved across sites. Intrapopulation ersification of genomes and their mcrA and dsrA genes is depth-dependent and subject to different selection pressure throughout the sediment column redox zones at different sites. These results highlight the interplay between ecological processes and the evolution of key bacteria and archaea in deep sea cold seep extreme environments, shedding light on microbial adaptation in the subseafloor biosphere.
Atmospheric H2 fuels plant–microbe interactions
Publisher: Wiley
Date: 18-01-2016
Atmospheric hydrogen scavenging: From enzymes to ecosystems
Publisher: American Society for Microbiology
Date: 15-02-2015
DOI: 10.1128/AEM.03364-14
Abstract: We have known for 40 years that soils can consume the trace amounts of molecular hydrogen (H 2 ) found in the Earth's atmosphere. This process is predicted to be the most significant term in the global hydrogen cycle. However, the organisms and enzymes responsible for this process were only recently identified. Pure culture experiments demonstrated that several species of Actinobacteria , including streptomycetes and mycobacteria, can couple the oxidation of atmospheric H 2 to the reduction of ambient O 2 . A combination of genetic, biochemical, and phenotypic studies suggest that these organisms primarily use this fuel source to sustain electron input into the respiratory chain during energy starvation. This process is mediated by a specialized enzyme, the group 5 [NiFe]-hydrogenase, which is unusual for its high affinity, oxygen insensitivity, and thermostability. Atmospheric hydrogen scavenging is a particularly dependable mode of energy generation, given both the ubiquity of the substrate and the stress tolerance of its catalyst. This minireview summarizes the recent progress in understanding how and why certain organisms scavenge atmospheric H 2 . In addition, it provides insight into the wider significance of hydrogen scavenging in global H 2 cycling and soil microbial ecology.
Microbial hydrogen cycling in agricultural systems – plant beneficial or detrimental?
Publisher: Wiley
Date: 24-06-2023
Abstract: Hydrogen‐oxidising bacteria play a key role in maintaining the composition of gases within the atmosphere and are ubiquitous in agricultural soils. While studies have shown that hydrogen accumulates in soil surrounding legume nodules and the soil surface, soils as a whole act as a net sink for hydrogen, raising questions about how hydrogen is internally recycled by soils. Can the energy derived from hydrogen oxidation be directly funnelled into plants to promote their growth or does it only act as a booster for other plant‐growth promoting bacteria? Moreover, while the fertilisation effect of hydrogen on plants has previously been shown to be beneficial, questions remain about the upper limit of hydrogen uptake by plants before it becomes detrimental. Agricultural practices such as fertilisation may impact the balance of hydrogen‐oxidisers and hydrogen‐producers in these ecosystems, potentially having detrimental effects on not only agricultural land but also global biogeochemical cycles. In this perspectives piece, we highlight the importance of understanding the contribution of hydrogen to agricultural soils and the effects of agricultural practices on the ability for bacteria to cycle hydrogen in agricultural soils. We propose a framework to gain better insights into microbial hydrogen cycling within agroecosystems, which could contribute to the development of new agricultural biotechnologies.
Narrowing down chain length effects on the antibacterial action of guanylated oligomers
Publisher: Royal Society of Chemistry (RSC)
Date: 2023
DOI: 10.1039/D3PY00203A
Abstract: Synthesis of discrete guanylated antimicrobial oligomers through reversible addition fragmentation chain transfer (RAFT) polymerization followed by flash chromatography is described.
BonA from Acinetobacter baumannii forms a divisome-localized decamer that supports outer envelope function
Publisher: Cold Spring Harbor Laboratory
Date: 02-09-2020
DOI: 10.1101/2020.09.01.278697
Abstract: Acinetobacter baumannii is a high-risk pathogen due to the rapid global spread of multi-drug resistant lineages. Its phylogenetic ergence from other ESKAPE pathogens means that determinants of its antimicrobial resistance can be difficult to extrapolate from other widely studied bacteria. A recent study showed that A. baumannii upregulates production of an outer-membrane lipoprotein, which we designate BonA, in response to challenge with polymyxins. Here we show that BonA has limited sequence similarity and distinct structural features compared to lipoproteins from other bacterial species. Analyses through X-ray crystallography, small-angle X-ray scattering, electron microscopy, and multiangle light scattering demonstrate that BonA has a dual BON-domain architecture and forms a decamer via an unusual oligomerization mechanism. This analysis also indicates this decamer is transient, suggesting dynamic oligomerization plays a role in BonA function. Antisera recognizing BonA shows it is an outer membrane protein localized to the isome. Loss of BonA modulates the density of the outer membrane, consistent with a change in its structure or link to the peptidoglycan, and prevents motility in a clinical strain (ATCC 17978). Consistent with these findings, the dimensions of the BonA decamer are sufficient to permeate the peptidoglycan layer, with the potential to form a membrane-spanning complex during cell ision.
A genome compendium reveals diverse metabolic adaptations of Antarctic soil microorganisms
Publisher: Cold Spring Harbor Laboratory
Date: 06-08-2020
DOI: 10.1101/2020.08.06.239558
Abstract: A surprising ersity and abundance of microorganisms resides in the cold desert soils of Antarctica. The metabolic processes that sustain them, however, are poorly understood. In this study, we used metagenomic and biogeochemical approaches to study the microbial communities in 16 physicochemically erse mountainous and glacial soils from remote sites in South Victoria Land, north of the Mackay Glacier. We assembled 451 metagenome-assembled genomes from 18 bacterial and archaeal phyla, constituting the largest resource of Antarctic soil microbial genomes to date. The most abundant and prevalent microorganisms are metabolically versatile aerobes that use atmospheric hydrogen and carbon monoxide to meet energy, carbon, and, through metabolic water production, hydration needs. Phylogenetic analysis and structural modelling infer that bacteria from nine phyla can scavenge atmospheric hydrogen using a previously unreported enzyme family, the group 1l [NiFe]-hydrogenases. Consistently, gas chromatography measurements confirmed most soils rapidly consume atmospheric hydrogen and carbon monoxide, and provide the first experimental evidence of methane oxidation in non-maritime Antarctica. We also recovered genomes of microorganisms capable of oxidizing other inorganic compounds, including nitrogen, sulfur, and iron compounds, as well as harvesting solar energy via photosystems and novel microbial rhodopsins. Bacterial lineages defined by symbiotic lifestyles, including Patescibacteria, Chlamydiae, and predatory Bdellovibrionota, were also surprisingly abundant. We conclude that the dominant microorganisms in Antarctic soils adopt mixotrophic strategies for energy and sometimes carbon acquisition, though they co-exist with erse bacteria and archaea that adopt more specialist lifestyles. These unprecedented insights and associated genome compendium will inform efforts to protect bio ersity in this continent.
Sequence--Structure--Function Classification of a Catalytically Diverse Oxidoreductase Superfamily in Mycobacteria
Publisher: Elsevier BV
Date: 11-2015
DOI: 10.1016/J.JMB.2015.09.021
Abstract: The deazaflavin cofactor F420 enhances the persistence of mycobacteria during hypoxia, oxidative stress, and antibiotic treatment. However, the identities and functions of the mycobacterial enzymes that utilize F420 under these conditions have yet to be resolved. In this work, we used sequence similarity networks to analyze the distribution of the largest F420-dependent protein family in mycobacteria. We show that these enzymes are part of a larger split β-barrel enzyme superfamily (flavin/deazaflavin oxidoreductases, FDORs) that include previously characterized pyridoxamine yridoxine-5'-phosphate oxidases and heme oxygenases. We show that these proteins variously utilize F420, flavin mononucleotide, flavin adenine dinucleotide, and heme cofactors. Functional annotation using phylogenetic, structural, and spectroscopic methods revealed their involvement in heme degradation, biliverdin reduction, fatty acid modification, and quinone reduction. Four novel crystal structures show that plasticity in substrate binding pockets and modifications to cofactor binding motifs enabled FDORs to carry out a variety of functions. This systematic classification and analysis provides a framework for further functional analysis of the roles of FDORs in mycobacterial pathogenesis and persistence.
Related Organisations
University Of Oxford
Location: United Kingdom of Great Britain and Northern Ireland
Commonwealth Scientific And Industrial Research Organisation
Location: Australia
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