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Walker RM, Sanabria VC, Youk H. Microbial life in slow and stopped lanes. Trends Microbiol 2024; 32:650-662. [PMID: 38123400 PMCID: PMC11187706 DOI: 10.1016/j.tim.2023.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]
Abstract
Microbes in nature often lack nutrients and face extreme or widely fluctuating temperatures, unlike microbes in growth-optimized settings in laboratories that much of the literature examines. Slowed or suspended lives are the norm for microbes. Studying them is important for understanding the consequences of climate change and for addressing fundamental questions about life: are there limits to how slowly a cell's life can progress, and how long cells can remain viable without self-replicating? Recent studies began addressing these questions with single-cell-level measurements and mathematical models. Emerging principles that govern slowed or suspended lives of cells - including lives of dormant spores and microbes at extreme temperatures - are re-defining discrete cellular states as continuums and revealing intracellular dynamics at new timescales. Nearly inactive, lifeless-appearing microbes are transforming our understanding of life.
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Affiliation(s)
- Rachel M Walker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Valeria C Sanabria
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Hyun Youk
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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2
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Graham EB, Garayburu-Caruso VA, Wu R, Zheng J, McClure R, Jones GD. Genomic fingerprints of the world's soil ecosystems. mSystems 2024; 9:e0111223. [PMID: 38722174 PMCID: PMC11237643 DOI: 10.1128/msystems.01112-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/25/2024] [Indexed: 06/19/2024] Open
Abstract
Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes-more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.IMPORTANCEWe address a critical gap in our understanding of soil microorganisms and their functions, which have a profound impact on our environment. We analyzed 1,512 global soils with advanced analytics to create detailed genetic profiles (fingerprints) of soil microbiomes. Our work reveals novel patterns in how microorganisms are distributed across different soil environments. For instance, we discovered shifts in microbial potential to acquire nutrients in relation to soil acidity, as well as changes in stress responses and potential greenhouse gas emissions linked to soil structure. We also identified soils with putative high activity that had unique genomic characteristics surrounding resource acquisition, plant-microbe interactions, and fungal activity. Finally, we observed that closely related microorganisms tend to respond in similar ways to changes in their surroundings. Our work is a significant step toward comprehending the intricate world of soil microorganisms and its role in the global climate.
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Affiliation(s)
- Emily B. Graham
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | | | - Ruonan Wu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jianqiu Zheng
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Ryan McClure
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Gerrad D. Jones
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, Oregon, USA
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3
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Imminger S, Meier DV, Schintlmeister A, Legin A, Schnecker J, Richter A, Gillor O, Eichorst SA, Woebken D. Survival and rapid resuscitation permit limited productivity in desert microbial communities. Nat Commun 2024; 15:3056. [PMID: 38632260 DOI: 10.1038/s41467-024-46920-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
Microbial activity in drylands tends to be confined to rare and short periods of rain. Rapid growth should be key to the maintenance of ecosystem processes in such narrow activity windows, if desiccation and rehydration cause widespread cell death due to osmotic stress. Here, simulating rain with 2H2O followed by single-cell NanoSIMS, we show that biocrust microbial communities in the Negev Desert are characterized by limited productivity, with median replication times of 6 to 19 days and restricted number of days allowing growth. Genome-resolved metatranscriptomics reveals that nearly all microbial populations resuscitate within minutes after simulated rain, independent of taxonomy, and invest their activity into repair and energy generation. Together, our data reveal a community that makes optimal use of short activity phases by fast and universal resuscitation enabling the maintenance of key ecosystem functions. We conclude that desert biocrust communities are highly adapted to surviving rapid changes in soil moisture and solute concentrations, resulting in high persistence that balances limited productivity.
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Affiliation(s)
- Stefanie Imminger
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- University of Vienna, Doctoral School in Microbiology and Environmental Science, Vienna, Austria
| | - Dimitri V Meier
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Department of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anton Legin
- Faculty of Chemistry, Institute of Inorganic Chemistry, University of Vienna, Vienna, Austria
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Midreshet Ben Gurion, Israel
| | - Stephanie A Eichorst
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
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4
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Bradley JA, Trivedi CB, Winkel M, Mourot R, Lutz S, Larose C, Keuschnig C, Doting E, Halbach L, Zervas A, Anesio AM, Benning LG. Active and dormant microorganisms on glacier surfaces. GEOBIOLOGY 2023; 21:244-261. [PMID: 36450703 PMCID: PMC10099831 DOI: 10.1111/gbi.12535] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/08/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
Glacier and ice sheet surfaces host diverse communities of microorganisms whose activity (or inactivity) influences biogeochemical cycles and ice melting. Supraglacial microbes endure various environmental extremes including resource scarcity, frequent temperature fluctuations above and below the freezing point of water, and high UV irradiance during summer followed by months of total darkness during winter. One strategy that enables microbial life to persist through environmental extremes is dormancy, which despite being prevalent among microbial communities in natural settings, has not been directly measured and quantified in glacier surface ecosystems. Here, we use a combination of metabarcoding and metatranscriptomic analyses, as well as cell-specific activity (BONCAT) incubations to assess the diversity and activity of microbial communities from glacial surfaces in Iceland and Greenland. We also present a new ecological model for glacier microorganisms and simulate physiological state-changes in the glacial microbial community under idealized (i) freezing, (ii) thawing, and (iii) freeze-thaw conditions. We show that a high proportion (>50%) of bacterial cells are translationally active in-situ on snow and ice surfaces, with Actinomycetota, Pseudomonadota, and Planctomycetota dominating the total and active community compositions, and that glacier microorganisms, even when frozen, could resume translational activity within 24 h after thawing. Our data suggest that glacial microorganisms respond rapidly to dynamic and changing conditions typical of their natural environment. We deduce that the biology and biogeochemistry of glacier surfaces are shaped by processes occurring over short (i.e., daily) timescales, and thus are susceptible to change following the expected alterations to the melt-regime of glaciers driven by climate change. A better understanding of the activity of microorganisms on glacier surfaces is critical in addressing the growing concern of climate change in Polar regions, as well as for their use as analogues to life in potentially habitable icy worlds.
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Affiliation(s)
- James A. Bradley
- Queen Mary University of LondonLondonUK
- GFZ German Research Centre for GeosciencesBerlinGermany
| | | | - Matthias Winkel
- GFZ German Research Centre for GeosciencesBerlinGermany
- Bundesanstalt für Risikobewertung (BfR)BerlinGermany
| | - Rey Mourot
- GFZ German Research Centre for GeosciencesBerlinGermany
- Freie University BerlinBerlinGermany
| | - Stefanie Lutz
- GFZ German Research Centre for GeosciencesBerlinGermany
| | - Catherine Larose
- Environmental Microbial GenomicsUniversité de LyonEcully CedexFrance
| | | | - Eva Doting
- Environmental ScienceAarhus UniversityRoskildeDenmark
| | - Laura Halbach
- Environmental ScienceAarhus UniversityRoskildeDenmark
| | | | | | - Liane G. Benning
- GFZ German Research Centre for GeosciencesBerlinGermany
- Freie University BerlinBerlinGermany
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5
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Ni G, Lappan R, Hernández M, Santini T, Tomkins AG, Greening C. Functional basis of primary succession: Traits of the pioneer microbes. Environ Microbiol 2023; 25:171-176. [PMID: 36309943 PMCID: PMC10098604 DOI: 10.1111/1462-2920.16266] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 10/27/2022] [Indexed: 01/21/2023]
Affiliation(s)
- Gaofeng Ni
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Rachael Lappan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Marcela Hernández
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, United Kingdom
| | - Talitha Santini
- School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Andrew G Tomkins
- School of Earth, Atmosphere & Environment, Monash University, Clayton, Victoria, Australia
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Securing Antarctica's Environmental Future, Monash University, Clayton, Victoria, Australia
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6
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Ring-stage growth arrest: Metabolic basis of artemisinin tolerance in Plasmodium falciparum. iScience 2022; 26:105725. [PMID: 36579133 PMCID: PMC9791339 DOI: 10.1016/j.isci.2022.105725] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/09/2022] [Accepted: 11/30/2022] [Indexed: 12/09/2022] Open
Abstract
The emergence and spread of artemisinin-tolerant malaria parasites threatens malaria control programmes worldwide. Mutations in the propeller domain of the Kelch13 protein confer Plasmodium falciparum artemisinin resistance (ART-R). ART-R is linked to the reduced susceptibility of temporary growth-arrested ring-stage parasites, but the metabolic mechanisms remain elusive. We generated two PfKelch13 mutant lines via CRISPR-Cas9 gene editing which displayed a reduced susceptibility accompanied by an extended ring stage. The metabolome of ART-induced ring-stage growth arrest parasites carrying PfKelch13 mutations showed significant alterations in the tricarboxylic acid (TCA) cycle, glycolysis, and amino acids metabolism, pointing to altered energy and porphyrin metabolism with metabolic plasticity. The critical role of these pathways was further confirmed by altering metabolic flow or through chemical inhibition. Our findings uncover that the growth arrestment associated with ART-R is potentially attributed to the adaptative metabolic plasticity, indicating that the defined metabolic remodeling turns out to be the trigger for ART-R.
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7
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Ortiz M, Leung PM, Shelley G, Jirapanjawat T, Nauer PA, Van Goethem MW, Bay SK, Islam ZF, Jordaan K, Vikram S, Chown SL, Hogg ID, Makhalanyane TP, Grinter R, Cowan DA, Greening C. Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils. Proc Natl Acad Sci U S A 2021; 118:e2025322118. [PMID: 34732568 PMCID: PMC8609440 DOI: 10.1073/pnas.2025322118] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2021] [Indexed: 12/11/2022] Open
Abstract
Numerous diverse microorganisms reside in the cold desert soils of continental Antarctica, though we lack a holistic understanding of the metabolic processes that sustain them. Here, we profile the composition, capabilities, and activities of the microbial communities in 16 physicochemically diverse mountainous and glacial soils. We assembled 451 metagenome-assembled genomes from 18 microbial phyla and inferred through Bayesian divergence analysis that the dominant lineages present are likely native to Antarctica. In support of earlier findings, metagenomic analysis revealed that the most abundant and prevalent microorganisms are metabolically versatile aerobes that use atmospheric hydrogen to support aerobic respiration and sometimes carbon fixation. Surprisingly, however, hydrogen oxidation in this region was catalyzed primarily by a phylogenetically and structurally distinct enzyme, the group 1l [NiFe]-hydrogenase, encoded by nine bacterial phyla. Through gas chromatography, we provide evidence that both Antarctic soil communities and an axenic Bacteroidota isolate (Hymenobacter roseosalivarius) oxidize atmospheric hydrogen using this enzyme. Based on ex situ rates at environmentally representative temperatures, hydrogen oxidation is theoretically sufficient for soil communities to meet energy requirements and, through metabolic water production, sustain hydration. Diverse carbon monoxide oxidizers and abundant methanotrophs were also active in the soils. We also recovered genomes of microorganisms capable of oxidizing edaphic inorganic nitrogen, sulfur, and iron compounds and harvesting solar energy via microbial rhodopsins and conventional photosystems. Obligately symbiotic bacteria, including Patescibacteria, Chlamydiae, and predatory Bdellovibrionota, were also present. We conclude that microbial diversity in Antarctic soils reflects the coexistence of metabolically flexible mixotrophs with metabolically constrained specialists.
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Affiliation(s)
- Maximiliano Ortiz
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - Pok Man Leung
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia;
| | - Guy Shelley
- School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
| | - Thanavit Jirapanjawat
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia
| | - Philipp A Nauer
- School of Chemistry, Monash University, Clayton VIC 3800, Australia
| | - Marc W Van Goethem
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Sean K Bay
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia
- School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
| | - Zahra F Islam
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia
- School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
| | - Karen Jordaan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - Steven L Chown
- Securing Antarctica's Environmental Future, School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
| | - Ian D Hogg
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- School of Science, University of Waikato, Hamilton 3240, New Zealand
- Polar Knowledge Canada, Canadian High Arctic Research Station, Cambridge Bay NU X0B 0C0, Canada
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - Rhys Grinter
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa;
| | - Chris Greening
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia;
- School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
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8
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Chen YJ, Leung PM, Wood JL, Bay SK, Hugenholtz P, Kessler AJ, Shelley G, Waite DW, Franks AE, Cook PLM, Greening C. Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem. THE ISME JOURNAL 2021; 15:2986-3004. [PMID: 33941890 PMCID: PMC8443593 DOI: 10.1038/s41396-021-00988-w] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/25/2021] [Accepted: 04/09/2021] [Indexed: 02/03/2023]
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 amplicon sequencing and metagenomics, yielding 135 metagenome-assembled genomes. Community composition and metabolic traits modestly varied with sediment depth and sampling date. Several taxa were highly abundant and prevalent in all samples, 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.
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Affiliation(s)
- Ya-Jou Chen
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Natural Resources Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Pok Man Leung
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Jennifer L Wood
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Sean K Bay
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Adam J Kessler
- Water Studies Centre, School of Chemistry, Monash University, Clayton, VIC, Australia
- School of Earth, Atmosphere and Environment, Monash University, Clayton, VIC, Australia
| | - Guy Shelley
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - David W Waite
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Ashley E Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Perran L M Cook
- Water Studies Centre, School of Chemistry, Monash University, Clayton, VIC, Australia.
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, Australia.
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.
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9
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Greening C, Islam ZF, Bay SK. Hydrogen is a major lifeline for aerobic bacteria. Trends Microbiol 2021; 30:330-337. [PMID: 34462186 DOI: 10.1016/j.tim.2021.08.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 12/31/2022]
Abstract
Molecular hydrogen (H2) is available in trace amounts in most ecosystems through atmospheric, biological, geochemical, and anthropogenic sources. Aerobic bacteria use this energy-dense gas, including at atmospheric concentrations, to support respiration and carbon fixation. While it was thought that aerobic H2 consumers are rare community members, here we summarize evidence suggesting that they are dominant throughout soils and other aerated ecosystems. Bacterial cultures from at least eight major phyla can consume atmospheric H2. At the ecosystem scale, H2 consumers are abundant, diverse, and active across diverse soils and are key primary producers in extreme environments such as hyper-arid deserts. On this basis, we propose that H2 is a universally available energy source for the survival of aerobic bacteria.
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Affiliation(s)
- Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Securing Antarctica's Environmental Future, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia.
| | - Zahra F Islam
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; STEM College, RMIT University, Bundoora, VIC 3083, Australia
| | - Sean K Bay
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Securing Antarctica's Environmental Future, Monash University, Clayton, VIC 3800, Australia; School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
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10
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Cezar RM, Vezzani FM, Kaschuk G, Balsanelli E, de Souza EM, Vargas LK, Molin R. Crop rotation reduces the frequency of anaerobic soil bacteria in Red Latosol of Brazil. Braz J Microbiol 2021; 52:2169-2177. [PMID: 34319574 DOI: 10.1007/s42770-021-00578-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 07/11/2021] [Indexed: 10/20/2022] Open
Abstract
Crop diversity affects the processes of soil physical structuring and most likely provokes changes in the frequencies of soil microbial communities. The study was conducted for soil prokaryotic diversity sequencing 16S rDNA genes from a 25-year no-tillage experiment comprised of two crop systems: crop succession (Triticum aestivum-Glycine max) and rotation (Vicia sativa-Zea mays-Avena sativa-Glycine max-Triticum aestivum-Glycine max). The hypothesis was that a crop system with higher crop diversification (rotation) would affect the frequencies of prokaryotic taxa against a less diverse crop system (succession) altering the major soil functions guided by bacterial diversity. Soils in both crop systems were dominated by Proteobacteria (31%), Acidobacteria (23%), Actinobacteria (10%), and Gemmatimonadetes (7.2%), among other common copiotrophic soil bacteria. Crop systems did not affect the richness and diversity indexes of soil bacteria and soil archaea. However, the crop rotation system reduced only the frequencies of anaerobic metabolism bacteria Chloroacidobacteria, Holophagae, Spirochaetes, Euryarchaeota, and Crenarchaeota. It can be concluded that crop succession, a system that is poorer in root diversity over time, may have conditioned the soil to lower oxygen diffusion and built up ecological niches that suitable for anaerobic bacteria tolerating lower levels of oxygen. On the other hand, it appeared that crop rotation has restructured the soil over the years while enabling copiotrophic aerobic bacteria to dominate the soil ecosystem. The changes prompted by crop succession have implications for efficient soil organic matter decomposition, reduced greenhouse gas emissions, higher root activity, and overall soil productivity, which compromise to agriculture sustainability.
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Affiliation(s)
- Raul Matias Cezar
- Post-Graduate in Soil Science, Federal University of Paraná, Rua Dos Funcionários, 1540, Curitiba, PR, CEP 80035-050, Brazil
| | - Fabiane Machado Vezzani
- Post-Graduate in Soil Science, Federal University of Paraná, Rua Dos Funcionários, 1540, Curitiba, PR, CEP 80035-050, Brazil
| | - Glaciela Kaschuk
- Post-Graduate in Soil Science, Federal University of Paraná, Rua Dos Funcionários, 1540, Curitiba, PR, CEP 80035-050, Brazil.
| | - Eduardo Balsanelli
- Department of Biochemistry, Federal University of Paraná, Rua Francisco H. Dos Santos S/N, Curitiba, PR, CEP 81531-990, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry, Federal University of Paraná, Rua Francisco H. Dos Santos S/N, Curitiba, PR, CEP 81531-990, Brazil
| | - Luciano Kayser Vargas
- Department of Agricultural Diagnosis and Research, Secretary of Agriculture and Livestock of the State of Rio Grande Do Sul, Rua Gonçalves Dias, 570, Porto Alegre, RS, CEP 90130-060, Brazil
| | - Rudimar Molin
- ABC Foundation, Rod. PR 151 km 288, Caixa-postal: 1003, Castro, PR, CEP 84165-700, Brazil
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11
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Shu L, He Z, Guan X, Yang X, Tian Y, Zhang S, Wu C, He Z, Yan Q, Wang C, Shi Y. A dormant amoeba species can selectively sense and predate on different soil bacteria. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13824] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Longfei Shu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology Sun Yat‐Sen University Guangzhou China
| | - Zhenzhen He
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Xiaotong Guan
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Xueqin Yang
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Yuehui Tian
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Siyi Zhang
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Chenyuan Wu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Zhili He
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Qingyun Yan
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Cheng Wang
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Yijing Shi
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology Sun Yat‐Sen University Guangzhou China
- School of Environment Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment SCNU Environmental Research InstituteSouth China Normal University Guangzhou China
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12
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Doello S, Burkhardt M, Forchhammer K. The essential role of sodium bioenergetics and ATP homeostasis in the developmental transitions of a cyanobacterium. Curr Biol 2021; 31:1606-1615.e2. [PMID: 33571435 DOI: 10.1016/j.cub.2021.01.065] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/30/2020] [Accepted: 01/19/2021] [Indexed: 10/22/2022]
Abstract
The ability to resume growth after a dormant period is an important strategy for the survival and spreading of bacterial populations. Energy homeostasis is critical in the transition into and out of a quiescent state. Synechocystis sp. PCC 6803, a non-diazotrophic cyanobacterium, enters metabolic dormancy as a response to nitrogen starvation. We used Synechocystis as a model to investigate the regulation of ATP homeostasis during dormancy, and we unraveled a critical role for sodium bioenergetics in dormant cells. During nitrogen starvation, cells reduce their ATP levels and engage sodium bioenergetics to maintain the minimum ATP content required for viability. When nitrogen becomes available, energy requirements rise, and cells immediately increase ATP levels, employing sodium bioenergetics and glycogen catabolism. These processes allow them to restore the photosynthetic machinery and resume photoautotrophic growth. Our work reveals a precise regulation of the energy metabolism essential for bacterial survival during periods of nutrient deprivation.
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Affiliation(s)
- Sofia Doello
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Markus Burkhardt
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
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13
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Trace gas oxidizers are widespread and active members of soil microbial communities. Nat Microbiol 2021; 6:246-256. [PMID: 33398096 DOI: 10.1038/s41564-020-00811-w] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/08/2020] [Indexed: 01/24/2023]
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 diverse 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 biodiversity in a changing world.
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14
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Jordaan K, Lappan R, Dong X, Aitkenhead IJ, Bay SK, Chiri E, Wieler N, Meredith LK, Cowan DA, Chown SL, Greening C. Hydrogen-Oxidizing Bacteria Are Abundant in Desert Soils and Strongly Stimulated by Hydration. mSystems 2020; 5:e01131-20. [PMID: 33203691 PMCID: PMC7677003 DOI: 10.1128/msystems.01131-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 10/29/2020] [Indexed: 01/19/2023] Open
Abstract
How the diverse bacterial communities inhabiting desert soils maintain energy and carbon needs is much debated. Traditionally, most bacteria are thought to persist by using organic carbon synthesized by photoautotrophs following transient hydration events. Recent studies focused on Antarctic desert soils have revealed, however, that some bacteria use atmospheric trace gases, such as hydrogen (H2), to conserve energy and fix carbon independently of photosynthesis. In this study, we investigated whether atmospheric H2 oxidation occurs in four nonpolar desert soils and compared this process to photosynthesis. To do so, we first profiled the distribution, expression, and activities of hydrogenases and photosystems in surface soils collected from the South Australian desert over a simulated hydration-desiccation cycle. Hydrogenase-encoding sequences were abundant in the metagenomes and metatranscriptomes and were detected in actinobacterial, acidobacterial, and cyanobacterial metagenome-assembled genomes. Native dry soil samples mediated H2 oxidation, but rates increased 950-fold following wetting. Oxygenic and anoxygenic phototrophs were also detected in the community but at lower abundances. Hydration significantly stimulated rates of photosynthetic carbon fixation and, to a lesser extent, dark carbon assimilation. Hydrogenase genes were also widespread in samples from three other climatically distinct deserts, the Namib, Gobi, and Mojave, and atmospheric H2 oxidation was also greatly stimulated by hydration at these sites. Together, these findings highlight that H2 is an important, hitherto-overlooked energy source supporting bacterial communities in desert soils. Contrary to our previous hypotheses, however, H2 oxidation occurs simultaneously rather than alternately with photosynthesis in such ecosystems and may even be mediated by some photoautotrophs.IMPORTANCE Desert ecosystems, spanning a third of the earth's surface, harbor remarkably diverse 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 sampled 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.
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Affiliation(s)
- Karen Jordaan
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Rachael Lappan
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Ian J Aitkenhead
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Sean K Bay
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Eleonora Chiri
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | | | - Laura K Meredith
- School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, USA
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Steven L Chown
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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15
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Bay SK, McGeoch MA, Gillor O, Wieler N, Palmer DJ, Baker DJ, Chown SL, Greening C. Soil Bacterial Communities Exhibit Strong Biogeographic Patterns at Fine Taxonomic Resolution. mSystems 2020; 5:e00540-20. [PMID: 32694128 PMCID: PMC7566276 DOI: 10.1128/msystems.00540-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 01/04/2023] Open
Abstract
Bacteria have been inferred to exhibit relatively weak biogeographic patterns. To what extent such findings reflect true biological phenomena or methodological artifacts remains unclear. Here, we addressed this question by analyzing the turnover of soil bacterial communities from three data sets. We applied three methodological innovations: (i) design of a hierarchical sampling scheme to disentangle environmental from spatial factors driving turnover; (ii) resolution of 16S rRNA gene amplicon sequence variants to enable higher-resolution community profiling; and (iii) application of the new metric zeta diversity to analyze multisite turnover and drivers. At fine taxonomic resolution, rapid compositional turnover was observed across multiple spatial scales. Turnover was overwhelmingly driven by deterministic processes and influenced by the rare biosphere. The communities also exhibited strong distance decay patterns and taxon-area relationships, with z values within the interquartile range reported for macroorganisms. These biogeographical patterns were weakened upon applying two standard approaches to process community sequencing data: clustering sequences at 97% identity threshold and/or filtering the rare biosphere (sequences lower than 0.05% relative abundance). Comparable findings were made across local, regional, and global data sets and when using shotgun metagenomic markers. Altogether, these findings suggest that bacteria exhibit strong biogeographic patterns, but these signals can be obscured by methodological limitations. We advocate various innovations, including using zeta diversity, to advance the study of microbial biogeography.IMPORTANCE 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 sampling design, sequence processing, and diversity 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 diversity patterns are more unified across all domains of life than previously thought, which has broad implications for the understanding and management of soil biodiversity.
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Affiliation(s)
- Sean K Bay
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, Australia
| | - Melodie A McGeoch
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sde Boker, Israel
| | - Nimrod Wieler
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sde Boker, Israel
| | - David J Palmer
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - David J Baker
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Steven L Chown
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, Australia
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16
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A widely distributed hydrogenase oxidises atmospheric H 2 during bacterial growth. ISME JOURNAL 2020; 14:2649-2658. [PMID: 32647310 PMCID: PMC7784904 DOI: 10.1038/s41396-020-0713-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/25/2020] [Accepted: 06/30/2020] [Indexed: 11/09/2022]
Abstract
Diverse aerobic bacteria persist by consuming atmospheric hydrogen (H2) 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 H2 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 H2 to sub-atmospheric levels, and oxidation rates were much higher during growth. Moreover, the oxidation of H2 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 H2 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.
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17
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Sawers RG, Fischer M, Falke D. Anaerobic nitrate respiration in the aerobe Streptomyces coelicolor A3(2): helping maintain a proton gradient during dormancy. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:645-650. [PMID: 31268622 DOI: 10.1111/1758-2229.12781] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 06/30/2019] [Accepted: 07/02/2019] [Indexed: 06/09/2023]
Abstract
Respiratory nitrate reductases (Nar) catalyse the reduction of nitrate to nitrite, coupling this process to energy conservation. The obligate aerobic actinobacterium Streptomyces coelicolor synthesizes three Nar enzymes that contribute to maintenance of a membrane potential when either the mycelium or the spores become hypoxic or anoxic. No growth occurs under such conditions but the bacterium survives the lack of O2 by remaining metabolically active; reducing nitrate is one means whereby this process is aided. Nar1 is exclusive to spores, Nar2 to vegetative mycelium and Nar3 to stationary-phase mycelium, each making a distinct contribution to energy conservation. While Nar2 and Nar3 appear to function like conventional menaquinol oxidases, unusually, Nar1 is completely dependent for its activity on a cytochrome bcc-aa 3 oxidase supercomplex. This suggest that electrons within this supercomplex are diverted to Nar1 during O2 limitation. Receiving electrons from this supercomplex potentially allows nitrate reduction to be coupled to the Q-cycle of the cytochrome bcc complex. This modification likely improves the efficiency of energy conservation, extending longevity of spores under O2 limitation. Knowledge gained on the bioenergetics of NO3 - respiration in the actinobacteria will aid our understanding of how many microorganisms survive under conditions of extreme nutrient and energy restriction.
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Affiliation(s)
- R Gary Sawers
- Institute of Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Marco Fischer
- Institute of Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Dörte Falke
- Institute of Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
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