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Sugiyama A, Nakata K, Hirano SI, Hasegawa T. Identification of groundwater microbes that decrease the concentration of the conservative tracer uranine. Heliyon 2024; 10:e27397. [PMID: 38496874 PMCID: PMC10944235 DOI: 10.1016/j.heliyon.2024.e27397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/20/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Fluorescent dyes are commonly used as conservative groundwater tracers to track the migration of water. Over- or underestimation of important parameters such as the water flow rate can occur if the concentration of a dye is changed by unexpected reactions. Because such errors may seriously affect the results of experiments, the reactions and processes that change fluorescent dye concentrations need to be understood. In this study, we focused on the widely used fluorescent dye uranine (UR) and aimed to identify microbes contributing to decreases in UR concentrations in groundwater. First, we identified the conditions (water temperature, pH, and salinity) under which significant decreases in UR concentrations occurred to show that the decrease in UR concentrations were caused by the effects of microbes in the groundwater. Next, we obtained information about the metabolism of organic matter by potential contributing microbes. These results were used to narrow down possible microbes that could decrease the UR concentration. Analysis of the microbial community in groundwater using 16S rRNA gene sequencing was then used to further identify contributing microbes. Finally, a verification experiment was conducted using a strain of one of the identified microbes (Parapontixanthobacter aurantiacus). Our results showed that conservation of the concentration of fluorescent dye solutions prepared with on-site groundwater was affected by several microbes with different metabolic characteristics, including P. aurantiacus. When fluorescent dye solutions prepared with on-site groundwater are used in field investigations or tracer tests, the pros and cons of using fluorescent dyes should be carefully evaluated because of the potential effects of microbes in the groundwater.
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Affiliation(s)
- Ayumi Sugiyama
- Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry (CRIEPI), 1646 Abiko, Abiko-shi, Chiba 270-1194, Japan
| | - Kotaro Nakata
- Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry (CRIEPI), 1646 Abiko, Abiko-shi, Chiba 270-1194, Japan
| | - Shin-Ichi Hirano
- Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry (CRIEPI), 1646 Abiko, Abiko-shi, Chiba 270-1194, Japan
| | - Takuma Hasegawa
- Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry (CRIEPI), 1646 Abiko, Abiko-shi, Chiba 270-1194, Japan
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2
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Worthan SB, McCarthy RDP, Delaleau M, Stikeleather R, Bratton BP, Boudvillain M, Behringer MG. Evolution of pH-sensitive transcription termination during adaptation to repeated long-term starvation. bioRxiv 2024:2024.03.01.582989. [PMID: 38464051 PMCID: PMC10925284 DOI: 10.1101/2024.03.01.582989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Fluctuating environments that consist of regular cycles of co-occurring stress are a common challenge faced by cellular populations. For a population to thrive in constantly changing conditions, an ability to coordinate a rapid cellular response is essential. Here, we identify a mutation conferring an arginine-to-histidine (Arg to His) substitution in the transcription terminator Rho. The rho R109H mutation frequently arose in E. coli populations experimentally evolved under repeated long-term starvation conditions, during which feast and famine result in drastic environmental pH fluctuations. Metagenomic sequencing revealed that populations containing the rho mutation also possess putative loss-of-function mutations in ydcI, which encodes a recently characterized transcription factor associated with pH homeostasis. Genetic reconstructions of these mutations show that the rho allele confers a plastic alkaline-induced reduction of Rho function that, when found in tandem with a ΔydcI allele, leads to intracellular alkalinization and genetic assimilation of Rho mutant function. We further identify Arg to His substitutions at analogous sites in rho alleles from species originating from fluctuating alkaline environments. Our results suggest that Arg to His substitutions in global regulators of gene expression can serve to rapidly coordinate complex responses through pH sensing and shed light on how cellular populations across the tree of life use environmental cues to coordinate rapid responses to complex, fluctuating environments.
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Affiliation(s)
- Sarah B Worthan
- Department of Biological Sciences, Vanderbilt University, Nashville, TN
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN
| | | | - Mildred Delaleau
- Centre de Biophysique Moléculaire, CNRS UPR4301, affiliated with Université d'Orléans, rue Charles Sadron, 45071 Orléans cedex 2, France
| | - Ryan Stikeleather
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ
| | - Benjamin P Bratton
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Marc Boudvillain
- Centre de Biophysique Moléculaire, CNRS UPR4301, affiliated with Université d'Orléans, rue Charles Sadron, 45071 Orléans cedex 2, France
| | - Megan G Behringer
- Department of Biological Sciences, Vanderbilt University, Nashville, TN
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ
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3
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Beaver RC, Vachon MA, Tully CS, Engel K, Spasov E, Binns WJ, Noël JJ, Neufeld JD. Impact of dry density and incomplete saturation on microbial growth in bentonite clay for nuclear waste storage. J Appl Microbiol 2024; 135:lxae053. [PMID: 38458234 DOI: 10.1093/jambio/lxae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 10/12/2023] [Accepted: 03/07/2024] [Indexed: 03/10/2024]
Abstract
AIMS Many countries are in the process of designing a deep geological repository (DGR) for long-term storage of used nuclear fuel. For several designs, used fuel containers will be placed belowground, with emplacement tunnels being backfilled using a combination of highly compacted powdered bentonite clay buffer boxes surrounded by a granulated "gapfill" bentonite. To limit the potential for microbiologically influenced corrosion of used fuel containers, identifying conditions that suppress microbial growth is critical for sustainable DGR design. This study investigated microbial communities in powdered and gapfill bentonite clay incubated in oxic pressure vessels at dry densities between 1.1 g cm-3 (i.e. below repository target) and 1.6 g cm-3 (i.e. at or above repository target) as a 1-year time series. RESULTS Our results showed an initial (i.e. 1 month) increase in the abundance of culturable heterotrophs associated with all dry densities <1.6 g cm-3, which reveals growth during transient low-pressure conditions associated with the bentonite saturation process. Following saturation, culturable heterotroph abundances decreased to those of starting material by the 6-month time point for all 1.4 and 1.6 g cm-3 pressure vessels, and the most probable numbers of culturable sulfate-reducing bacteria (SRB) remained constant for all vessels and time points. The 16S rRNA gene sequencing results showed a change in microbial community composition from the starting material to the 1-month time point, after which time most samples were dominated by sequences associated with Pseudomonas, Bacillus, Cupriavidus, and Streptomyces. Similar taxa were identified as dominant members of the culture-based community composition, demonstrating that the dominant members of the clay microbial communities are viable. Members of the spore-forming Desulfosporosinus genus were the dominant SRB for both clay and culture profiles. CONCLUSIONS After initial microbial growth while bentonite was below target pressure in the early phases of saturation, microbial growth in pressure vessels with dry densities of at least 1.4 g cm-3 was eventually suppressed as bentonite neared saturation.
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Affiliation(s)
- Rachel C Beaver
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Melody A Vachon
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Claire S Tully
- Department of Chemistry, Western University, London, Ontario, N6A 3K7, Canada
| | - Katja Engel
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Emilie Spasov
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - W Jeffrey Binns
- Nuclear Waste Management Organization, Toronto, Ontario, M4T 2S3, Canada
| | - James J Noël
- Department of Chemistry, Western University, London, Ontario, N6A 3K7, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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4
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Runzheimer K, Lozano C, Boy D, Boy J, Godoy R, Matus FJ, Engel D, Pavletic B, Leuko S, Armengaud J, Moeller R. Exploring Andean High-Altitude Lake Extremophiles through Advanced Proteotyping. J Proteome Res 2024; 23:891-904. [PMID: 38377575 PMCID: PMC10913102 DOI: 10.1021/acs.jproteome.3c00538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 02/22/2024]
Abstract
Quickly identifying and characterizing isolates from extreme environments is currently challenging while very important to explore the Earth's biodiversity. As these isolates may, in principle, be distantly related to known species, techniques are needed to reliably identify the branch of life to which they belong. Proteotyping these environmental isolates by tandem mass spectrometry offers a rapid and cost-effective option for their identification using their peptide profiles. In this study, we document the first high-throughput proteotyping approach for environmental extremophilic and halophilic isolates. Microorganisms were isolated from samples originating from high-altitude Andean lakes (3700-4300 m a.s.l.) in the Chilean Altiplano, which represent environments on Earth that resemble conditions on other planets. A total of 66 microorganisms were cultivated and identified by proteotyping and 16S rRNA gene amplicon sequencing. Both the approaches revealed the same genus identification for all isolates except for three isolates possibly representing not yet taxonomically characterized organisms based on their peptidomes. Proteotyping was able to indicate the presence of two potentially new genera from the families of Paracoccaceae and Chromatiaceae/Alteromonadaceae, which have been overlooked by 16S rRNA amplicon sequencing approach only. The paper highlights that proteotyping has the potential to discover undescribed microorganisms from extreme environments.
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Affiliation(s)
- Katharina Runzheimer
- Department
of Radiation Biology, Institute of Aerospace
Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany
| | - Clément Lozano
- Département
Médicaments et Technologies pour la Santé (DMTS), CEA,
INRAE, SPI, Université, Paris-Saclay, F-30200 Bagnols-sur-Cèze, France
| | - Diana Boy
- Institute
of Microbiology, Leibniz University Hannover, 30419 Hannover, Germany
| | - Jens Boy
- Institute
of Soil Science, Leibniz University Hannover, 30419 Hannover, Germany
| | - Roberto Godoy
- Instituto
de Ciencias Ambientales y Evolutivas, Universidad
Austral de Chile, 509000 Valdivia, Chile
| | - Francisco J. Matus
- Laboratory
of Conservation and Dynamics of Volcanic Soils, Department of Chemical
Sciences and Natural Resources, Universidad
de La Frontera, 4811230 Temuco, Chile
- Network
for Extreme Environmental Research (NEXER), Universidad de La Frontera, 4811230 Temuco, Chile
| | - Denise Engel
- Department
of Radiation Biology, Institute of Aerospace
Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany
| | - Bruno Pavletic
- Department
of Radiation Biology, Institute of Aerospace
Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany
| | - Stefan Leuko
- Department
of Radiation Biology, Institute of Aerospace
Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany
| | - Jean Armengaud
- Département
Médicaments et Technologies pour la Santé (DMTS), CEA,
INRAE, SPI, Université, Paris-Saclay, F-30200 Bagnols-sur-Cèze, France
| | - Ralf Moeller
- Department
of Radiation Biology, Institute of Aerospace
Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany
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5
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Skoog EJ, Bosak T. Predicted metabolic roles and stress responses provide insights into candidate phyla Hydrogenedentota and Sumerlaeota as members of the rare biosphere in biofilms from various environments. Environ Microbiol Rep 2024; 16:e13228. [PMID: 38192240 PMCID: PMC10866078 DOI: 10.1111/1758-2229.13228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/11/2023] [Indexed: 01/10/2024]
Abstract
Pustular mats from Shark Bay, Western Australia, host complex microbial communities bound within an organic matrix. These mats harbour many poorly characterized organisms with low relative abundances (<1%), such as candidate phyla Hydrogenedentota and Sumerlaeota. Here, we aim to constrain the metabolism and physiology of these candidate phyla by analyzing two representative metagenome-assembled genomes (MAGs) from a pustular mat. Metabolic reconstructions of these MAGs suggest facultatively anaerobic, chemoorganotrophic lifestyles of both organisms and predict that both MAGs can metabolize a diversity of carbohydrate substrates. Ca. Sumerlaeota possesses genes involved in degrading chitin, cellulose and other polysaccharides, while Ca. Hydrogenedentota can metabolize cellulose derivatives in addition to glycerol, fatty acids and phosphonates. Both Ca. phyla can respond to nitrosative stress and participate in nitrogen metabolism. Metabolic comparisons of MAGs from Shark Bay and those from various polyextreme environments (i.e., hot springs, hydrothermal vents, subsurface waters, anaerobic digesters, etc.) reveal similar metabolic capabilities and adaptations to hypersalinity, oxidative stress, antibiotics, UV radiation, nitrosative stress, heavy metal toxicity and life in surface-attached communities. These adaptations and capabilities may account for the widespread nature of these organisms and their contributions to biofilm communities in a range of extreme surface and subsurface environments.
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Affiliation(s)
- Emilie J. Skoog
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Integrative Oceanography DivisionScripps Institution of Oceanography, UC San DiegoLa JollaCaliforniaUSA
| | - Tanja Bosak
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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6
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Li S, Mosier D, Kouris A, Humez P, Mayer B, Strous M, Diao M. High diversity, abundance, and expression of hydrogenases in groundwater. ISME Commun 2024; 4:ycae023. [PMID: 38500700 PMCID: PMC10945355 DOI: 10.1093/ismeco/ycae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/02/2024] [Accepted: 02/09/2024] [Indexed: 03/20/2024]
Abstract
Hydrogen may be the most important electron donor available in the subsurface. Here we analyse the diversity, abundance and expression of hydrogenases in 5 proteomes, 25 metagenomes, and 265 amplicon datasets of groundwaters with diverse geochemistry. A total of 1545 new [NiFe]-hydrogenase gene sequences were recovered, which considerably increased the number of sequences (1999) in a widely used database. [NiFe]-hydrogenases were highly abundant, as abundant as the DNA-directed RNA polymerase. The abundance of hydrogenase genes increased with depth from 0 to 129 m. Hydrogenases were present in 481 out of 1245 metagenome-assembled genomes. The relative abundance of microbes with hydrogenases accounted for ~50% of the entire community. Hydrogenases were actively expressed, making up as much as 5.9% of methanogen proteomes. Most of the newly discovered diversity of hydrogenases was in "Group 3b", which has been associated with sulfur metabolism. "Group 3d", facilitating the interconversion of electrons between hydrogen and NAD, was the most abundant and mainly observed in methanotrophs and chemoautotrophs. "Group 3a", associated with methanogenesis, was the most abundant in proteomes. Two newly discovered groups of [NiFe]-hydrogenases, observed in Methanobacteriaceae and Anaerolineaceae, further expanded diversity. Our results highlight the vast diversity, abundance and expression of hydrogenases in groundwaters, suggesting a high potential for hydrogen oxidation in subsurface habitats.
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Affiliation(s)
- Shengjie Li
- Department of Earth, Energy and Environment, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
| | - Damon Mosier
- Department of Earth, Energy and Environment, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Angela Kouris
- Department of Earth, Energy and Environment, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Pauline Humez
- Department of Earth, Energy and Environment, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Bernhard Mayer
- Department of Earth, Energy and Environment, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Marc Strous
- Department of Earth, Energy and Environment, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Muhe Diao
- Department of Earth, Energy and Environment, University of Calgary, Calgary, AB T2N 1N4, Canada
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7
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Liu S, Hu R, Peng N, Zhou Z, Chen R, He Z, Wang C. Phylogenetic and ecophysiological novelty of subsurface mercury methylators in mangrove sediments. ISME J 2023; 17:2313-2325. [PMID: 37880540 PMCID: PMC10689504 DOI: 10.1038/s41396-023-01544-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023]
Abstract
Mangrove sediment is a crucial component in the global mercury (Hg) cycling and acts as a hotspot for methylmercury (MeHg) production. Early evidence has documented the ubiquity of well-studied Hg methylators in mangrove superficial sediments; however, their diversity and metabolic adaptation in the more anoxic and highly reduced subsurface sediments are lacking. Through MeHg biogeochemical assay and metagenomic sequencing, we found that mangrove subsurface sediments (20-100 cm) showed a less hgcA gene abundance but higher diversity of Hg methylators than superficial sediments (0-20 cm). Regional-scale investigation of mangrove subsurface sediments spanning over 1500 km demonstrated a prevalence and family-level novelty of Hg-methylating microbial lineages (i.e., those affiliated to Anaerolineae, Phycisphaerae, and Desulfobacterales). We proposed the candidate phylum Zixibacteria lineage with sulfate-reducing capacity as a currently understudied Hg methylator across anoxic environments. Unlike other Hg methylators, the Zixibacteria lineage does not use the Wood-Ljungdahl pathway but has unique capabilities of performing methionine synthesis to donate methyl groups. The absence of cobalamin biosynthesis pathway suggests that this Hg-methylating lineage may depend on its syntrophic partners (i.e., Syntrophobacterales members) for energy in subsurface sediments. Our results expand the diversity of subsurface Hg methylators and uncover their unique ecophysiological adaptations in mangrove sediments.
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Affiliation(s)
- Songfeng Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Nenglong Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhengyuan Zhou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Ruihan Chen
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, 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, 510006, 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, 510006, China.
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8
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Momper L, Casar CP, Osburn MR. A metagenomic view of novel microbial and metabolic diversity found within the deep terrestrial biosphere at DeMMO: A microbial observatory in South Dakota, USA. Environ Microbiol 2023; 25:3719-3737. [PMID: 37964716 DOI: 10.1111/1462-2920.16543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/31/2023] [Indexed: 11/16/2023]
Abstract
The deep terrestrial subsurface is a large and diverse microbial habitat and vast repository of biomass. However, in relation to its size and physical heterogeneity we have limited understanding of taxonomic and metabolic diversity in this realm. Here we present a detailed metagenomic analysis of samples from the Deep Mine Microbial Observatory (DeMMO) spanning depths from the surface to 1.5 km into the crust. From eight geochemically and spatially distinct fluid samples we reconstructed ~600 partial to near-complete metagenome-assembled genomes (MAGs), representing 50 distinct phyla and including 18 candidate phyla. These novel clades include members of the candidate phyla radiation, two new MAGs from OLB16, a phylum originally identified in DeMMO fluids and for which only one other MAG is currently available, and new MAGs from the Eisenbacteria, Omnitrophota, and Edwardsbacteria. We find that microbes spanning this expansive phylogenetic diversity and physical subsurface space gain a competitive edge by maintaining a wide variety of functional pathways, are often capable of numerous dissimilatory energy metabolisms and poised to take advantage of nutrients as they become available in isolated fracture fluids. Our results support and expand on emerging themes of tight nutrient cycling and genomic plasticity in deep subsurface biosphere taxa.
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Affiliation(s)
- Lily Momper
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
- Exponent, Inc, Menlo Park, California, USA
| | - Caitlin P Casar
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
| | - Magdalena R Osburn
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
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9
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Lemay-St-Denis C, Pelletier JN. From a binding module to essential catalytic activity: how nature stumbled on a good thing. Chem Commun (Camb) 2023; 59:12560-12572. [PMID: 37791701 DOI: 10.1039/d3cc04209j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Enzymes are complex macromolecules capable of catalyzing a wide variety of chemical reactions with high efficiency. Nonetheless, biological catalysis can be rudimentary. Here, we describe an enzyme that is built from a simple protein fold. This short protein sequence - almost a peptide - belongs to the ancient SH3 family of binding modules. Surprisingly, this binding module catalyzes the specific reduction of dihydrofolate using NADPH as a reducing cofactor, making this a dihydrofolate reductase. Too small to provide all the required binding and catalytic machinery on its own, it homotetramerizes, thus creating a large, central active site environment. Remarkably, none of the active site residues is essential to the catalytic function. Instead, backbone interactions juxtapose the reducing cofactor proximal to the target imine of the folate substrate, and a specific motion of the substrate promotes formation of the transition state. In this feature article, we describe the features that make this small protein a functional enzyme capable of catalyzing a metabolically essential reaction, highlighting the characteristics that make it a model for the evolution of primitive enzymes from binding modules.
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Affiliation(s)
- Claudèle Lemay-St-Denis
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
| | - Joelle N Pelletier
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
- Chemistry Department, Université de Montréal, Montreal, QC, Canada.
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10
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Esser SP, Rahlff J, Zhao W, Predl M, Plewka J, Sures K, Wimmer F, Lee J, Adam PS, McGonigle J, Turzynski V, Banas I, Schwank K, Krupovic M, Bornemann TLV, Figueroa-Gonzalez PA, Jarett J, Rattei T, Amano Y, Blaby IK, Cheng JF, Brazelton WJ, Beisel CL, Woyke T, Zhang Y, Probst AJ. A predicted CRISPR-mediated symbiosis between uncultivated archaea. Nat Microbiol 2023; 8:1619-1633. [PMID: 37500801 DOI: 10.1038/s41564-023-01439-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023]
Abstract
CRISPR-Cas systems defend prokaryotic cells from invasive DNA of viruses, plasmids and other mobile genetic elements. Here, we show using metagenomics, metatranscriptomics and single-cell genomics that CRISPR systems of widespread, uncultivated archaea can also target chromosomal DNA of archaeal episymbionts of the DPANN superphylum. Using meta-omics datasets from Crystal Geyser and Horonobe Underground Research Laboratory, we find that CRISPR spacers of the hosts Candidatus Altiarchaeum crystalense and Ca. A. horonobense, respectively, match putative essential genes in their episymbionts' genomes of the genus Ca. Huberiarchaeum and that some of these spacers are expressed in situ. Metabolic interaction modelling also reveals complementation between host-episymbiont systems, on the basis of which we propose that episymbionts are either parasitic or mutualistic depending on the genotype of the host. By expanding our analysis to 7,012 archaeal genomes, we suggest that CRISPR-Cas targeting of genomes associated with symbiotic archaea evolved independently in various archaeal lineages.
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Affiliation(s)
- Sarah P Esser
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Janina Rahlff
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Weishu Zhao
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI, USA
- Shanghai Jiao Tong University, School of Life Sciences and Biotechnology, International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, China
| | - Michael Predl
- Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Julia Plewka
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Katharina Sures
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Franziska Wimmer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany
| | - Janey Lee
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Panagiotis S Adam
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Julia McGonigle
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Victoria Turzynski
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Indra Banas
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Katrin Schwank
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
- University of Regensburg, Biochemistry III, Regensburg, Germany
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Till L V Bornemann
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Perla Abigail Figueroa-Gonzalez
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Jessica Jarett
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Thomas Rattei
- Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Yuki Amano
- Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Tokai, Japan
| | - Ian K Blaby
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany
- Medical faculty, University of Würzburg, Würzburg, Germany
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI, USA
| | - Alexander J Probst
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany.
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.
- Centre of Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany.
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11
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Barrera-Rojas J, Gurubel-Tun KJ, Ríos-Castro E, López-Méndez MC, Sulbarán-Rangel B. An Initial Proteomic Analysis of Biogas-Related Metabolism of Euryarchaeota Consortia in Sediments from the Santiago River, México. Microorganisms 2023; 11:1640. [PMID: 37512813 PMCID: PMC10384328 DOI: 10.3390/microorganisms11071640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/18/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
In this paper, sediments from the Santiago River were characterized to look for an alternative source of inoculum for biogas production. A proteomic analysis of methane-processing archaea present in these sediments was carried out. The Euryarchaeota superkingdom of archaea is responsible for methane production and methane assimilation in the environment. The Santiago River is a major river in México with great pollution and exceeded recovery capacity. Its sediments could contain nutrients and the anaerobic conditions for optimal growth of Euryarchaeota consortia. Batch bioreactor experiments were performed, and a proteomic analysis was conducted with current database information. The maximum biogas production was 266 NmL·L-1·g VS-1, with 33.34% of methane, and for proteomics, 3206 proteins were detected from 303 species of 69 genera. Most of them are metabolically versatile members of the genera Methanosarcina and Methanosarcinales, both with 934 and 260 proteins, respectively. These results showed a diverse euryarcheotic species with high potential to methane production. Although related proteins were found and could be feeding this metabolism through the methanol and acetyl-CoA pathways, the quality obtained from the biogas suggests that this metabolism is not the main one in carbon use, possibly the sum of several conditions including growth conditions and the pollution present in these sediments.
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Affiliation(s)
- Jesús Barrera-Rojas
- Department of Water and Energy, Campus Tonalá, University of Guadalajara, Tonalá 45425, Mexico
| | - Kelly Joel Gurubel-Tun
- Department of Water and Energy, Campus Tonalá, University of Guadalajara, Tonalá 45425, Mexico
| | - Emmanuel Ríos-Castro
- Laboratorios Nacionales de Servicios Experimentales, Centro de Investigación y Estudios Avanzados del IPN, Ciudad de México 07000, Mexico
| | - María Cristina López-Méndez
- Wetlands and Environmental Sustainability Laboratory, Division of Graduate Studies and Research, Tecnológico Nacional de México/ITS de Misantla, Veracruz 93850, Mexico
| | - Belkis Sulbarán-Rangel
- Department of Water and Energy, Campus Tonalá, University of Guadalajara, Tonalá 45425, Mexico
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12
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Nishimura H, Kouduka M, Fukuda A, Ishimura T, Amano Y, Beppu H, Miyakawa K, Suzuki Y. Anaerobic methane-oxidizing activity in a deep underground borehole dominantly colonized by Ca. Methanoperedenaceae. Environ Microbiol Rep 2023; 15:197-205. [PMID: 36779262 PMCID: PMC10464669 DOI: 10.1111/1758-2229.13146] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 01/24/2023] [Indexed: 05/06/2023]
Abstract
The family Ca. Methanoperedenaceae archaea mediates the anaerobic oxidation of methane (AOM) in different terrestrial environments. Using a newly developed high-pressure laboratory incubation system, we investigated 214- and 249-m deep groundwater samples at Horonobe Underground Research Laboratory, Japan, where the high and low abundances of Ca. Methanoperedenaceae archaea have been shown by genome-resolved metagenomics, respectively. The groundwater samples amended with 13 C-labelled methane and amorphous Fe(III) were incubated at a pressure of 1.6 MPa. After 3-7 days of incubation, the AOM rate was 45.8 ± 19.8 nM/day in 214-m groundwater. However, almost no activity was detected from 249-m groundwater. Based on the results from 16S rRNA gene analysis, the abundance of Ca. Methanoperedenaceae archaea was high in the 214-m deep groundwater sample, whereas Ca. Methanoperedenaceae archaea was undetected in the 249-m deep groundwater sample. These results support the in situ AOM activity of Ca. Methanoperedenaceae archaea in the 214-m deep subsurface borehole interval. Although the presence of Fe-bearing phyllosilicates was demonstrated in the 214-m deep groundwater, it needs to be determined whether Ca. Methanoperedenaceae archaea use the Fe-bearing phyllosilicates as in situ electron acceptors by high-pressure incubation amended with the Fe-bearing phyllosilicates.
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Affiliation(s)
- Hiroki Nishimura
- Department of Earth and Planetary ScienceThe University of TokyoTokyoJapan
| | - Mariko Kouduka
- Department of Earth and Planetary ScienceThe University of TokyoTokyoJapan
| | - Akari Fukuda
- Department of Earth and Planetary ScienceThe University of TokyoTokyoJapan
| | - Toyoho Ishimura
- Graduate School of Human and Environmental StudiesKyoto UniversityKyotoJapan
| | - Yuki Amano
- Horonobe Underground Research CenterJapan Atomic Energy AgencyHoronobe‐cho, HokkaidoJapan
- Nuclear Fuel Cycle Engineering LaboratoriesJapan Atomic Energy AgencyIbarakiJapan
| | - Hikari Beppu
- Nuclear Fuel Cycle Engineering LaboratoriesJapan Atomic Energy AgencyIbarakiJapan
| | - Kazuya Miyakawa
- Horonobe Underground Research CenterJapan Atomic Energy AgencyHoronobe‐cho, HokkaidoJapan
| | - Yohey Suzuki
- Department of Earth and Planetary ScienceThe University of TokyoTokyoJapan
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13
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
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14
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Soares A, Edwards A, An D, Bagnoud A, Bradley J, Barnhart E, Bomberg M, Budwill K, Caffrey SM, Fields M, Gralnick J, Kadnikov V, Momper L, Osburn M, Mu A, Moreau JW, Moser D, Purkamo L, Rassner SM, Sheik CS, Sherwood Lollar B, Toner BM, Voordouw G, Wouters K, Mitchell AC. A global perspective on bacterial diversity in the terrestrial deep subsurface. Microbiology (Reading) 2023; 169:001172. [PMID: 36748549 PMCID: PMC9993121 DOI: 10.1099/mic.0.001172] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/07/2022] [Indexed: 01/19/2023]
Abstract
While recent efforts to catalogue Earth's microbial diversity have focused upon surface and marine habitats, 12-20 % of Earth's biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8 % in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. An in silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.
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Affiliation(s)
- A. Soares
- Department of Geography and Earth Sciences (DGES), Aberystwyth University (AU), Aberystwyth, UK
- Institute of Biology, Environmental and Rural Sciences (IBERS), AU, Aberystwyth, UK
- Department of Plant and Microbial Biology, University of Minnesota, Minneapolis, MN, USA
- Present address: Group for Aquatic Microbial Ecology (GAME), University of Duisburg-Essen, Campus Essen - Environmental Microbiology and Biotechnology, Universitätsstr. 5, 45141 Essen, Germany
| | - A. Edwards
- Institute of Biology, Environmental and Rural Sciences (IBERS), AU, Aberystwyth, UK
- Interdisciplinary Centre for Environmental Microbiology (iCEM), AU, Aberystwyth, UK
| | - D. An
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - A. Bagnoud
- Institut de Génie Thermique (IGT), Haute École d'Ingénierie et de Gestion du Canton de Vaud (HEIG-VD), Yverdon-les-Bains, Switzerland
| | - J. Bradley
- School of Geography, Queen Mary University of London, London, UK
| | - E. Barnhart
- U.S. Geological Survey (USGS), USA, Reston, VA, USA
- Center for Biofilm Engineering (CBE), Montana State University, Bozeman, MT, USA
| | - M. Bomberg
- VTT Technical Research Centre of Finland, Finland
| | | | | | - M. Fields
- Center for Biofilm Engineering (CBE), Montana State University, Bozeman, MT, USA
- Department of Microbiology & Immunology, MSU, Bozeman, MT, USA
| | - J. Gralnick
- Department of Plant and Microbial Biology, University of Minnesota, Minneapolis, MN, USA
| | - V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Russia
| | - L. Momper
- Department of Earth, Atmospheric and Planetary Sciences (DEAPS), The Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - M. Osburn
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL, USA
| | - A. Mu
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - J. W. Moreau
- School of Earth Sciences, The University of Melbourne, Parkville, Australia
| | - D. Moser
- Division of Hydrologic Sciences, Desert Research Institute (DRI), Las Vegas, NV, USA
| | - L. Purkamo
- VTT Technical Research Centre of Finland, Finland
- School of Earth and Environmental Sciences (SEES), University of St. Andrews, St. Andrews, UK
- Geological Survey of Finland (GTK), Finland
| | - S. M. Rassner
- Department of Geography and Earth Sciences (DGES), Aberystwyth University (AU), Aberystwyth, UK
- Interdisciplinary Centre for Environmental Microbiology (iCEM), AU, Aberystwyth, UK
| | - C. S. Sheik
- Large Lakes Observatory, University of Minnesota, Duluth, MN, USA
| | | | - B. M. Toner
- Department of Soil, Water & Climate, University of Minnesota, Minneapolis/Saint Paul, MN, USA
| | - G. Voordouw
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - K. Wouters
- Institute for Environment, Health and Safety (EHS), Belgian Nuclear Research Centre SCK•CEN, Mol, Belgium
| | - A. C. Mitchell
- Department of Geography and Earth Sciences (DGES), Aberystwyth University (AU), Aberystwyth, UK
- Interdisciplinary Centre for Environmental Microbiology (iCEM), AU, Aberystwyth, UK
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15
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Mandal S, Bose H, Ramesh K, Sahu RP, Saha A, Sar P, Kazy SK. Depth wide distribution and metabolic potential of chemolithoautotrophic microorganisms reactivated from deep continental granitic crust underneath the Deccan Traps at Koyna, India. Front Microbiol 2022; 13:1018940. [PMID: 36504802 PMCID: PMC9731672 DOI: 10.3389/fmicb.2022.1018940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/01/2022] [Indexed: 11/25/2022] Open
Abstract
Characterization of inorganic carbon (C) utilizing microorganisms from deep crystalline rocks is of major scientific interest owing to their crucial role in global carbon and other elemental cycles. In this study we investigate the microbial populations from the deep [up to 2,908 meters below surface (mbs)] granitic rocks within the Koyna seismogenic zone, reactivated (enriched) under anaerobic, high temperature (50°C), chemolithoautotrophic conditions. Subsurface rock samples from six different depths (1,679-2,908 mbs) are incubated (180 days) with CO2 (+H2) or HCO3 - as the sole C source. Estimation of total protein, ATP, utilization of NO3 - and SO4 2- and 16S rRNA gene qPCR suggests considerable microbial growth within the chemolithotrophic conditions. We note a better response of rock hosted community towards CO2 (+H2) over HCO3 -. 16S rRNA gene amplicon sequencing shows a depth-wide distribution of diverse chemolithotrophic (and a few fermentative) Bacteria and Archaea. Comamonas, Burkholderia-Caballeronia-Paraburkholderia, Ralstonia, Klebsiella, unclassified Burkholderiaceae and Enterobacteriaceae are reactivated as dominant organisms from the enrichments of the deeper rocks (2335-2,908 mbs) with both CO2 and HCO3 -. For the rock samples from shallower depths, organisms of varied taxa are enriched under CO2 (+H2) and HCO3 -. Pseudomonas, Rhodanobacter, Methyloversatilis, and Thaumarchaeota are major CO2 (+H2) utilizers, while Nocardioides, Sphingomonas, Aeromonas, respond towards HCO3 -. H2 oxidizing Cupriavidus, Hydrogenophilus, Hydrogenophaga, CO2 fixing Cyanobacteria Rhodobacter, Clostridium, Desulfovibrio and methanogenic archaea are also enriched. Enriched chemolithoautotrophic members show good correlation with CO2, CH4 and H2 concentrations of the native rock environments, while the organisms from upper horizons correlate more to NO3 -, SO4 2- , Fe and TIC levels of the rocks. Co-occurrence networks suggest close interaction between chemolithoautotrophic and chemoorganotrophic/fermentative organisms. Carbon fixing 3-HP and DC/HB cycles, hydrogen, sulfur oxidation, CH4 and acetate metabolisms are predicted in the enriched communities. Our study elucidates the presence of live, C and H2 utilizing Bacteria and Archaea in deep subsurface granitic rocks, which are enriched successfully. Significant impact of depth and geochemical controls on relative distribution of various chemolithotrophic species enriched and their C and H2 metabolism are highlighted. These endolithic microorganisms show great potential for answering the fundamental questions of deep life and their exploitation in CO2 capture and conversion to useful products.
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Affiliation(s)
- Sunanda Mandal
- Environmental Microbiology and Biotechnology Laboratory, Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, India
| | - Himadri Bose
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, India
| | - Kheerthana Ramesh
- Environmental Microbiology and Biotechnology Laboratory, Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, India
| | - Rajendra Prasad Sahu
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, India
| | - Anumeha Saha
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, India
| | - Pinaki Sar
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, India
| | - Sufia Khannam Kazy
- Environmental Microbiology and Biotechnology Laboratory, Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, India,*Correspondence: Sufia Khannam Kazy,
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16
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Schoelmerich MC, Ouboter HT, Sachdeva R, Penev PI, Amano Y, West-Roberts J, Welte CU, Banfield JF. A widespread group of large plasmids in methanotrophic Methanoperedens archaea. Nat Commun 2022; 13:7085. [PMID: 36400771 DOI: 10.1038/s41467-022-34588-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
Anaerobic methanotrophic (ANME) archaea obtain energy from the breakdown of methane, yet their extrachromosomal genetic elements are little understood. Here we describe large plasmids associated with ANME archaea of the Methanoperedens genus in enrichment cultures and other natural anoxic environments. By manual curation we show that two of the plasmids are large (155,605 bp and 191,912 bp), circular, and may replicate bidirectionally. The plasmids occur in the same copy number as the main chromosome, and plasmid genes are actively transcribed. One of the plasmids encodes three tRNAs, ribosomal protein uL16 and elongation factor eEF2; these genes appear to be missing in the host Methanoperedens genome, suggesting an obligate interdependence between plasmid and host. Our work opens the way for the development of genetic vectors to shed light on the physiology and biochemistry of Methanoperedens, and potentially genetically edit them to enhance growth and accelerate methane oxidation rates.
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17
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Nouioui I, Sangal V. Advanced prokaryotic systematics: the modern face of an ancient science. New Microbes New Infect 2022. [DOI: 10.1016/j.nmni.2022.101036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 11/13/2022] Open
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18
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Terashima M, Endo T, Kimuro S, Beppu H, Nemoto K, Amano Y. Iron-induced association between selenium and humic substances in groundwater from deep sedimentary formations. J NUCL SCI TECHNOL 2022. [DOI: 10.1080/00223131.2022.2111376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
| | - Takashi Endo
- Japan Nuclear Fuel Chemical Analysis Co., Ltd, Aomori, Japan
| | | | - Hikari Beppu
- Inspection Development Company Ltd, Ibaraki, Japan
| | | | - Yuki Amano
- Japan Atomic Energy Agency (JAEA), Ibaraki, Japan
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19
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Johnson LA, Hug LA. Cloacimonadota metabolisms include adaptations in engineered environments that are reflected in the evolutionary history of the phylum. Environ Microbiol Rep 2022; 14:520-529. [PMID: 35365914 DOI: 10.1111/1758-2229.13061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
Phylum Cloacimonadota (previously Cloacimonetes, WWE1) is an understudied bacterial lineage frequently associated with engineered and wastewater systems. Cloacimonadota members were abundant and diverse in metagenomic datasets from a municipal landfill, prompting an examination of phylogenetic relationships, metabolic diversity, and pangenomic dynamics across the phylum, based on the 30 publicly available genomes and 24 new metagenome-assembled genomes (MAGs) from landfill samples. We found that Cloacimonadota have distinct evolutionary histories associated with engineered versus natural environments and identified genomic features and metabolic strategies that correlate to habitat of origin. Metabolic reconstructions for MAGs predict an anaerobic, acetogenic, and mixed fermentative and flavin-bifurcation-based anaerobic respiratory lifestyle for the majority of Cloacimonadota surveyed. Genomes from engineered ecosystems encode a suite of genes not typically found in genomes from natural environments including acetate kinase, genes for cysteine degradation to pyruvate, increased diversity of carbon utilization enzymes, and different mechanisms for generating membrane potential and ATP synthesis. This phylum-level examination also clarifies the distribution of functions previously observed for members of the phylum, where propionate oxidation and reverse TCA cycles are not common components of Cloacimonadota metabolism.
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Affiliation(s)
- Lisa A Johnson
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, ON, N2L 3G1, Canada
| | - Laura A Hug
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, ON, N2L 3G1, Canada
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20
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Singh A, Schnürer A. AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters. Database (Oxford) 2022; 2022:6609150. [PMID: 35708586 PMCID: PMC9216588 DOI: 10.1093/database/baac041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 11/14/2022]
Abstract
AcetoBase is a public repository and database of formyltetrahydrofolate synthetase (FTHFS) sequences. It is the first systematic collection of bacterial FTHFS nucleotide and protein sequences from genomes and metagenome-assembled genomes and of sequences generated by clone library sequencing. At its publication in 2019, AcetoBase (Version 1) was also the first database to establish connections between the FTHFS gene, the Wood–Ljungdahl pathway and 16S ribosomal RNA genes. Since the publication of AcetoBase, there have been significant improvements in the taxonomy of many bacterial lineages and accessibility/availability of public genomics and metagenomics data. The update to the AcetoBase reference database described here (Version 2) provides new sequence data and taxonomy, along with improvements in web functionality and user interface. The evaluation of this latest update by re-analysis of publicly accessible FTHFS amplicon sequencing data previously analysed with AcetoBase Version 1 revealed significant improvements in the taxonomic assignment of FTHFS sequences. Database URL: https://acetobase.molbio.slu.se
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Affiliation(s)
- Abhijeet Singh
- Department of Molecular Sciences, BioCenter, Anaerobic Microbiology and Biotechnology Group, Swedish University of Agricultural Sciences , Almas Allé 5, Uppsala SE-750 07, Sweden
| | - Anna Schnürer
- Department of Molecular Sciences, BioCenter, Anaerobic Microbiology and Biotechnology Group, Swedish University of Agricultural Sciences , Almas Allé 5, Uppsala SE-750 07, Sweden
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21
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Bell E, Lamminmäki T, Alneberg J, Qian C, Xiong W, Hettich RL, Frutschi M, Bernier-Latmani R. Active anaerobic methane oxidation and sulfur disproportionation in the deep terrestrial subsurface. ISME J 2022; 16:1583-1593. [PMID: 35173296 PMCID: PMC9123182 DOI: 10.1038/s41396-022-01207-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/19/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Microbial life is widespread in the terrestrial subsurface and present down to several kilometers depth, but the energy sources that fuel metabolism in deep oligotrophic and anoxic environments remain unclear. In the deep crystalline bedrock of the Fennoscandian Shield at Olkiluoto, Finland, opposing gradients of abiotic methane and ancient seawater-derived sulfate create a terrestrial sulfate-methane transition zone (SMTZ). We used chemical and isotopic data coupled to genome-resolved metaproteogenomics to demonstrate active life and, for the first time, provide direct evidence of active anaerobic oxidation of methane (AOM) in a deep terrestrial bedrock. Proteins from Methanoperedens (formerly ANME-2d) are readily identifiable despite the low abundance (≤1%) of this genus and confirm the occurrence of AOM. This finding is supported by 13C-depleted dissolved inorganic carbon. Proteins from Desulfocapsaceae and Desulfurivibrionaceae, in addition to 34S-enriched sulfate, suggest that these organisms use inorganic sulfur compounds as both electron donor and acceptor. Zerovalent sulfur in the groundwater may derive from abiotic rock interactions, or from a non-obligate syntrophy with Methanoperedens, potentially linking methane and sulfur cycles in Olkiluoto groundwater. Finally, putative episymbionts from the candidate phyla radiation (CPR) and DPANN archaea represented a significant diversity in the groundwater (26/84 genomes) with roles in sulfur and carbon cycling. Our results highlight AOM and sulfur disproportionation as active metabolisms and show that methane and sulfur fuel microbial activity in the deep terrestrial subsurface.
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Affiliation(s)
- Emma Bell
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland.
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.
| | | | - Johannes Alneberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, SE-17121, Sweden
| | - Chen Qian
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Weili Xiong
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Manon Frutschi
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland.
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22
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Abstract
Noncoding RNAs with secondary structures play important roles in CRISPR-Cas systems. Many of these structures likely remain undiscovered. We used a large-scale comparative genomics approach to predict 156 novel candidate structured RNAs from 36,111 CRISPR-Cas systems. A number of these were found to overlap with coding genes, including palindromic candidates that overlapped with a variety of Cas genes in type I and III systems. Among these 156 candidates, we identified 46 new models of CRISPR direct repeats and 1 tracrRNA. This tracrRNA model occasionally overlapped with predicted cas9 coding regions, emphasizing the importance of expanding our search windows for novel structure RNAs in coding regions. We also demonstrated that the antirepeat sequence in this tracrRNA model can be used to accurately assign thousands of predicted CRISPR arrays to type II-C systems. This study highlights the importance of unbiased identification of candidate structured RNAs across CRISPR-Cas systems.
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Affiliation(s)
- Brayon J. Fremin
- Department of Energy, Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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23
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Abstract
A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.
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Affiliation(s)
- Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People's Republic of China.
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
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24
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Bornemann TLV, Adam PS, Turzynski V, Schreiber U, Figueroa-Gonzalez PA, Rahlff J, Köster D, Schmidt TC, Schunk R, Krauthausen B, Probst AJ. Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing. Nat Commun 2022; 13:284. [PMID: 35022403 PMCID: PMC8755723 DOI: 10.1038/s41467-021-27783-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 12/02/2021] [Indexed: 12/30/2022] Open
Abstract
Earth’s mantle releases 38.7 ± 2.9 Tg/yr CO2 along with other reduced and oxidized gases to the atmosphere shaping microbial metabolism at volcanic sites across the globe, yet little is known about its impact on microbial life under non-thermal conditions. Here, we perform comparative metagenomics coupled to geochemical measurements of deep subsurface fluids from a cold-water geyser driven by mantle degassing. Key organisms belonging to uncultivated Candidatus Altiarchaeum show a global biogeographic pattern and site-specific adaptations shaped by gene loss and inter-kingdom horizontal gene transfer. Comparison of the geyser community to 16 other publicly available deep subsurface sites demonstrate a conservation of chemolithoautotrophic metabolism across sites. In silico replication measures suggest a linear relationship of bacterial replication with ecosystems depth with the exception of impacted sites, which show near surface characteristics. Our results suggest that subsurface ecosystems affected by geological degassing are hotspots for microbial life in the deep biosphere. Geological degassing can impact subsurface metabolism. Here, the authors describe microbial communities from a cold-water geyser are described and compared with other deep subsurface sites, finding a key role for an uncultivated archaeon.
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Affiliation(s)
- Till L V Bornemann
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Panagiotis S Adam
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Victoria Turzynski
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Ulrich Schreiber
- Department of Geology, University Duisburg-Essen, Essen, Germany
| | | | - Janina Rahlff
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany.,Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linneaus University, Kalmar, Sweden
| | - Daniel Köster
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Torsten C Schmidt
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.,Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, Essen, Germany
| | | | - Bernhard Krauthausen
- Institute of Applied Geosciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Alexander J Probst
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany. .,Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, Essen, Germany.
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25
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Chen L, Li L, Zhang S, Zhang W, Xue K, Wang Y, Dong X. Anaerobic methane oxidation linked to Fe(III) reduction in a Candidatus Methanoperedens-enriched consortium from the cold Zoige wetland at Tibetan Plateau. Environ Microbiol 2021; 24:614-625. [PMID: 34951085 DOI: 10.1111/1462-2920.15848] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/10/2021] [Accepted: 11/10/2021] [Indexed: 12/20/2022]
Abstract
Anaerobic oxidation of methane (AOM) is a microbial process degrading ample methane in anoxic environments, and Ca. Methanoperedens mediated nitrate- or metal-reduction linked AOM is believed important in freshwater systems. This work, via 16S rRNA gene diversity survey and 16S rRNA quantification, found abundant Ca. Methanoperedens along with iron in the cold Zoige wetland at Tibetan Plateau. The wetland soil microcosm performed Fe(III) reduction, rather than nitrate- nor sulphate-reduction, coupled methane oxidation (3.87 μmol d-1 ) with 32.33 μmol Fe(II) accumulation per day at 18°C, but not at 30°C. A metagenome-assembled genome (MAG) recovered from the microcosm exhibits ~74% average nucleotide identity with the reported Ca. Methanoperedens spp. that perform Fe(III) reduction linked AOM, thus a novel species Ca. Methanoperedens psychrophilus was proposed. Ca. M. psychrophilus contains the whole suite of CO2 reductive methanogenic genes presumably involving in AOM via a reverse direction, and comparative genome analysis revealed its unique gene categories: the multi-heme clusters (MHCs) cytochromes, the S-layer proteins highly homologous to those recovered from lower temperature environments and type IV pili, those could confer Ca. M. psychrophilus of cold adaptability. Therefore, this work reports the first methanotroph implementing AOM in an alpine wetland.
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Affiliation(s)
- Lin Chen
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Lingyan Li
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shengjie Zhang
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenting Zhang
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kai Xue
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Yanfen Wang
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Xiuzhu Dong
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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26
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Takamiya H, Kouduka M, Suzuki Y. The Deep Rocky Biosphere: New Geomicrobiological Insights and Prospects. Front Microbiol 2021; 12:785743. [PMID: 34917063 PMCID: PMC8670094 DOI: 10.3389/fmicb.2021.785743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/08/2021] [Indexed: 12/02/2022] Open
Abstract
Rocks that react with liquid water are widespread but spatiotemporally limited throughout the solar system, except for Earth. Rock-forming minerals with high iron content and accessory minerals with high amounts of radioactive elements are essential to support rock-hosted microbial life by supplying organics, molecular hydrogen, and/or oxidants. Recent technological advances have broadened our understanding of the rocky biosphere, where microbial inhabitation appears to be difficult without nutrient and energy inputs from minerals. In particular, microbial proliferation in igneous rock basements has been revealed using innovative geomicrobiological techniques. These recent findings have dramatically changed our perspective on the nature and the extent of microbial life in the rocky biosphere, microbial interactions with minerals, and the influence of external factors on habitability. This study aimed to gather information from scientific and/or technological innovations, such as omics-based and single-cell level characterizations, targeting deep rocky habitats of organisms with minimal dependence on photosynthesis. By synthesizing pieces of rock-hosted life, we can explore the evo-phylogeny and ecophysiology of microbial life on Earth and the life’s potential on other planetary bodies.
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Affiliation(s)
- Hinako Takamiya
- Department of Earth and Planetary Science, The University of Tokyo, Bunkyo, Japan
| | - Mariko Kouduka
- Department of Earth and Planetary Science, The University of Tokyo, Bunkyo, Japan
| | - Yohey Suzuki
- Department of Earth and Planetary Science, The University of Tokyo, Bunkyo, Japan
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27
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Sahu RP, Kazy SK, Bose H, Mandal S, Dutta A, Saha A, Roy S, Dutta Gupta S, Mukherjee A, Sar P. Microbial diversity and function in crystalline basement beneath the Deccan Traps explored in a 3 km borehole at Koyna, western India. Environ Microbiol 2021; 24:2837-2853. [PMID: 34897962 DOI: 10.1111/1462-2920.15867] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 12/20/2022]
Abstract
Deep terrestrial subsurface represents a huge repository of global prokaryotic biomass. Given its vastness and importance, microbial life within the deep subsurface continental crust remains under-represented in global studies. We characterize the microbial communities of deep, extreme and oligotrophic realm hosted by crystalline Archaean granitic rocks underneath the Deccan Traps, through sampling via 3000 m deep scientific borehole at Koyna, India through metagenomics, amplicon sequencing and cultivation-based analyses. Gene sequences 16S rRNA (7.37 × 106 ) show considerable bacterial diversity and the existence of a core microbiome (5724 operational taxonomic units conserved out of a total 118,064 OTUs) across the depths. Relative abundance of different taxa of core microbiome varies with depth in response to prevailing lithology and geochemistry. Co-occurrence network analysis and cultivation attempt to elucidate close interactions among autotrophic and organotrophic bacteria. Shotgun metagenomics reveals a major role of autotrophic carbon fixation via the Wood-Ljungdahl pathway and genes responsible for energy and carbon metabolism. Deeper analysis suggests the existence of an 'acetate switch', coordinating biosynthesis and cellular homeostasis. We conclude that the microbial life in the nutrient- and energy-limited deep granitic crust is constrained by the depth and managed by a few core members via a close interplay between autotrophy and organotrophy.
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Affiliation(s)
- Rajendra Prasad Sahu
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Sufia K Kazy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India
| | - Himadri Bose
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Sunanda Mandal
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India
| | - Avishek Dutta
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Anumeha Saha
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Sukanta Roy
- Ministry of Earth Sciences, Borehole Geophysics Research Laboratory, Karad, MH, 415114, India
| | - Srimanti Dutta Gupta
- School of Environmental Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Abhijit Mukherjee
- School of Environmental Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India.,Department of Geology and Geophysics, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Pinaki Sar
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
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28
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Beaver RC, Engel K, Binns WJ, Neufeld JD. Microbiology of barrier component analogues of a deep geological repository. Can J Microbiol 2021; 68:73-90. [PMID: 34648720 DOI: 10.1139/cjm-2021-0225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Canada is currently implementing a site selection process to identify a location for a deep geological repository (DGR) for the long-term storage of Canada's used nuclear fuel, wherein used nuclear fuel bundles will be sealed inside copper-coated carbon steel containers, encased in highly compacted bentonite clay buffer boxes, and sealed deep underground in a stable geosphere. Because a DGR must remain functional for a million years, it is important to examine ancient natural systems that serve as analogues for planned DGR components. Specifically, studying the microbiology of natural analogue components of a DGR is important for developing an understanding of the types of microorganisms that may be able to grow and influence the long-term stability of a DGR. This study explored the abundance, viability, and composition of microorganisms in several ancient natural analogues using a combination of cultivation and cultivation-independent approaches. Samples were obtained from the Tsukinuno bentonite deposit (Japan) that formed ∼10 mya, the Opalinus Clay formation (Switzerland) that formed ∼174 mya, and Canadian shield crystalline rock from Northern Ontario that formed ∼2.7 bya. Analysis of 16S rRNA gene amplicons revealed that three of the ten Tsukinuno bentonite samples analyzed were dominated by putative aerobic heterotrophs and fermenting bacteria from the phylum Actinobacteria, whereas five of the Tsukinuno bentonite samples were dominated by sequences associated with putative acidophilic chemolithoautotrophs capable of sulfur reduction. The remaining Tsukinuno bentonite samples, the Northern Ontario rock samples, and the Opalinus Clay samples generated inconsistent replicate 16S rRNA gene profiles and were associated primarily with contaminant sequences, suggesting that the microbial profiles detected were not sample-specific but spurious. Culturable aerobic heterotroph abundances were relatively low for all Tsukinuno bentonite samples, culturable anaerobic heterotrophs were only detected in half of the Tsukinuno samples, and sulfate-reducing bacteria (SRB) were only detected in one Tsukinuno sample by cultivation. Culture-specific 16S rRNA gene profiles from Tsukinuno clay samples demonstrated the presence of phyla Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes among aerobic heterotroph cultures and additional bacteria from the phyla Actinobacteria and Firmicutes from anaerobic heterotroph plate incubations. Only one nucleic acid sequence detected from a culture was also associated with its corresponding clay sample profile, suggesting that nucleic acids from culturable bacteria were relatively rare within the clay samples. Sequencing of DNA extracted from the SRB culture revealed that the taxon present in the culture was affiliated with the genus Desulfosporosinus, which has been found in related bentonite clay analyses. Although the crystalline rock and Opalinus Clay samples were associated with inconsistent, likely spurious 16S rRNA gene profiles, we show evidence for viable and detectable microorganisms within several Tsukinuno natural analogue bentonite samples.
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Affiliation(s)
- Rachel C Beaver
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Katja Engel
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - W Jeffrey Binns
- Nuclear Waste Management Organization, Toronto, Ontario, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
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29
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Abstract
Fe(II)-oxidizing microorganisms and Fe(III)-reducing microorganisms, which drive the biogeochemical Fe cycle on the Earth's surface, are phylogenetically and ecologically diverse. However, no single organism capable of aerobic Fe(II) oxidation and anaerobic Fe(III) reduction at circumneutral pH have been reported so far. Here, we report a novel neutrophilic Fe(II)-oxidizing Rhodoferax bacterium, strain MIZ03, isolated from an iron-rich wetland in Japan. Our cultivation experiments demonstrate that MIZ03 represents a much more versatile metabolism for energy acquisition than previously recognized in the genus Rhodoferax. MIZ03 can grow chemolithoautotrophically at circumneutral pH by oxidation of Fe(II), H2, or thiosulfate as the sole electron donor under (micro)aerobic conditions (i.e., using O2 as the sole electron acceptor). In addition, it can reduce Fe(III) or nitrate under anaerobic conditions. Thus, this is the first report demonstrating the presence of a single bacterium capable of both Fe(II) oxidation and Fe(III) reduction at circumneutral pH. The observed physiology was consistent with its 4.9-Mbp complete genome encoding key genes for iron oxidation/reduction (foxEY and mtrABC), for nitrate reduction (narGHI), for thiosulfate oxidation (soxABCDXYZ), and for carbon fixation via the Calvin cycle. Our metagenomic survey suggests that there are more Rhodoferax members capable of Fe(II) oxidation and Fe(III) reduction. Such bifunctional Rhodoferax may have an ecological advantage in suboxic/anoxic environments at circumneutral pH by recycling of Fe as the electron donor and acceptor. IMPORTANCE The biogeochemical cycle of iron (Fe) via reactions of oxidation, reduction, precipitation, and dissolution is involved in the cycle of other ecologically relevant elements, such as C, N, P, S, As, Co, Ni, and Pb. The Fe cycle on the Earth's surface is driven by a variety of Fe(II)-oxidizing microorganisms and Fe(III)-reducing microorganisms. Here, we discovered a novel bacterium, Rhodoferax sp. strain MIZ03, capable of both Fe(II) oxidation and Fe(III) reduction at circumneutral pH, and we report its physiological characteristics and complete genome sequence. The unexpected capability of this bacterium provides novel insights into the Fe cycle in the environment. Moreover, this bacterium will help to better understand the molecular mechanisms of microbial Fe redox cycling as a model organism.
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Affiliation(s)
- Shingo Kato
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
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30
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Jaffe AL, Thomas AD, He C, Keren R, Valentin-Alvarado LE, Munk P, Bouma-Gregson K, Farag IF, Amano Y, Sachdeva R, West PT, Banfield JF. Patterns of Gene Content and Co-occurrence Constrain the Evolutionary Path toward Animal Association in Candidate Phyla Radiation Bacteria. mBio 2021; 12:e0052121. [PMID: 34253055 PMCID: PMC8406219 DOI: 10.1128/mbio.00521-21] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/14/2021] [Indexed: 12/20/2022] Open
Abstract
Candidate Phyla Radiation (CPR) bacteria are small, likely episymbiotic organisms found across Earth's ecosystems. Despite their prevalence, the distribution of CPR lineages across habitats and the genomic signatures of transitions among these habitats remain unclear. Here, we expand the genome inventory for Absconditabacteria (SR1), Gracilibacteria, and Saccharibacteria (TM7), CPR bacteria known to occur in both animal-associated and environmental microbiomes, and investigate variation in gene content with habitat of origin. By overlaying phylogeny with habitat information, we show that bacteria from these three lineages have undergone multiple transitions from environmental habitats into animal microbiomes. Based on co-occurrence analyses of hundreds of metagenomes, we extend the prior suggestion that certain Saccharibacteria have broad bacterial host ranges and constrain possible host relationships for Absconditabacteria and Gracilibacteria. Full-proteome analyses show that animal-associated Saccharibacteria have smaller gene repertoires than their environmental counterparts and are enriched in numerous protein families, including those likely functioning in amino acid metabolism, phage defense, and detoxification of peroxide. In contrast, some freshwater Saccharibacteria encode a putative rhodopsin. For protein families exhibiting the clearest patterns of differential habitat distribution, we compared protein and species phylogenies to estimate the incidence of lateral gene transfer and genomic loss occurring over the species tree. These analyses suggest that habitat transitions were likely not accompanied by large transfer or loss events but rather were associated with continuous proteome remodeling. Thus, we speculate that CPR habitat transitions were driven largely by availability of suitable host taxa and were reinforced by acquisition and loss of some capacities. IMPORTANCE Studying the genetic differences between related microorganisms from different environment types can indicate factors associated with their movement among habitats. This is particularly interesting for bacteria from the Candidate Phyla Radiation because their minimal metabolic capabilities require associations with microbial hosts. We found that shifts of Absconditabacteria, Gracilibacteria, and Saccharibacteria between environmental ecosystems and mammalian mouths/guts probably did not involve major episodes of gene gain and loss; rather, gradual genomic change likely followed habitat migration. The results inform our understanding of how little-known microorganisms establish in the human microbiota where they may ultimately impact health.
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Affiliation(s)
- Alexander L Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
| | - Alex D Thomas
- Department of Environmental Science, Policy, and Management, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
- Rocky Mountain Biological Laboratory, Crested Butte, Colorado, USA
| | - Christine He
- Innovative Genomics Institute, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
| | - Ray Keren
- Department of Civil and Environmental Engineering, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
| | - Luis E Valentin-Alvarado
- Department of Plant and Microbial Biology, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
- Innovative Genomics Institute, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
| | - Patrick Munk
- National Food Institute, Technical University of Denmarkgrid.5170.3, Kongens Lyngby, Denmark
| | - Keith Bouma-Gregson
- Department of Earth and Planetary Science, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
- Department of Integrative Biology, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
| | - Ibrahim F Farag
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, USA
| | - Yuki Amano
- Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agencygrid.20256.33, Ibaraki, Japan
- Horonobe Underground Research Center, Japan Atomic Energy Agencygrid.20256.33, Hokkaido, Japan
| | - Rohan Sachdeva
- Innovative Genomics Institute, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
- Department of Earth and Planetary Science, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
| | - Patrick T West
- Department of Medicine (Hematology & Blood and Marrow Transplantation), Stanford University, Stanford, California, USA
| | - Jillian F Banfield
- Department of Environmental Science, Policy, and Management, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
- Innovative Genomics Institute, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
- Department of Earth and Planetary Science, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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31
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Rahlff J, Turzynski V, Esser SP, Monsees I, Bornemann TLV, Figueroa-Gonzalez PA, Schulz F, Woyke T, Klingl A, Moraru C, Probst AJ. Lytic archaeal viruses infect abundant primary producers in Earth's crust. Nat Commun 2021; 12:4642. [PMID: 34330907 PMCID: PMC8324899 DOI: 10.1038/s41467-021-24803-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 07/05/2021] [Indexed: 02/07/2023] Open
Abstract
The continental subsurface houses a major portion of life's abundance and diversity, yet little is known about viruses infecting microbes that reside there. Here, we use a combination of metagenomics and virus-targeted direct-geneFISH (virusFISH) to show that highly abundant carbon-fixing organisms of the uncultivated genus Candidatus Altiarchaeum are frequent targets of previously unrecognized viruses in the deep subsurface. Analysis of CRISPR spacer matches display resistances of Ca. Altiarchaea against eight predicted viral clades, which show genomic relatedness across continents but little similarity to previously identified viruses. Based on metagenomic information, we tag and image a putatively viral genome rich in protospacers using fluorescence microscopy. VirusFISH reveals a lytic lifestyle of the respective virus and challenges previous predictions that lysogeny prevails as the dominant viral lifestyle in the subsurface. CRISPR development over time and imaging of 18 samples from one subsurface ecosystem suggest a sophisticated interplay of viral diversification and adapting CRISPR-mediated resistances of Ca. Altiarchaeum. We conclude that infections of primary producers with lytic viruses followed by cell lysis potentially jump-start heterotrophic carbon cycling in these subsurface ecosystems.
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Affiliation(s)
- Janina Rahlff
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Victoria Turzynski
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany
| | - Sarah P Esser
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany
| | - Indra Monsees
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany
| | - Till L V Bornemann
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany
| | - Perla Abigail Figueroa-Gonzalez
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, CA, USA
| | - Andreas Klingl
- Plant Development & Electron Microscopy, Biocenter LMU Munich, Planegg-Martinsried, Germany
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky-University Oldenburg, Oldenburg, Germany
| | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany.
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Lovley DR, Holmes DE. Electromicrobiology: the ecophysiology of phylogenetically diverse electroactive microorganisms. Nat Rev Microbiol 2021; 20:5-19. [PMID: 34316046 DOI: 10.1038/s41579-021-00597-6] [Citation(s) in RCA: 153] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2021] [Indexed: 02/03/2023]
Abstract
Electroactive microorganisms markedly affect many environments in which they establish outer-surface electrical contacts with other cells and minerals or reduce soluble extracellular redox-active molecules such as flavins and humic substances. A growing body of research emphasizes their broad phylogenetic diversity and shows that these microorganisms have key roles in multiple biogeochemical cycles, as well as the microbiome of the gut, anaerobic waste digesters and metal corrosion. Diverse bacteria and archaea have independently evolved cytochrome-based strategies for electron exchange between the outer cell surface and the cell interior, but cytochrome-free mechanisms are also prevalent. Electrically conductive protein filaments, soluble electron shuttles and non-biological conductive materials can substantially extend the electronic reach of microorganisms beyond the surface of the cell. The growing appreciation of the diversity of electroactive microorganisms and their unique electronic capabilities is leading to a broad range of applications.
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Affiliation(s)
- Derek R Lovley
- Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China. .,Department of Microbiology, University of Massachusetts, Amherst, MA, USA. .,Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, MA, USA.
| | - Dawn E Holmes
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA.,Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, MA, USA.,Department of Physical and Biological Sciences, Western New England University, Springfield, MA, USA
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Glass JB, Ranjan P, Kretz CB, Nunn BL, Johnson AM, Xu M, McManus J, Stewart FJ. Microbial metabolism and adaptations in Atribacteria-dominated methane hydrate sediments. Environ Microbiol 2021; 23:4646-4660. [PMID: 34190392 DOI: 10.1111/1462-2920.15656] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/28/2021] [Indexed: 12/12/2022]
Abstract
Gas hydrates harbour gigatons of natural gas, yet their microbiomes remain understudied. We bioprospected 16S rRNA amplicons, metagenomes, and metaproteomes from methane hydrate-bearing sediments under Hydrate Ridge (offshore Oregon, USA, ODP Site 1244, 2-69 mbsf) for novel microbial metabolic and biosynthetic potential. Atribacteria sequences generally increased in relative sequence abundance with increasing sediment depth. Most Atribacteria ASVs belonged to JS-1-Genus 1 and clustered with other sequences from gas hydrate-bearing sediments. We recovered 21 metagenome-assembled genomic bins spanning three geochemical zones in the sediment core: the sulfate-methane transition zone, the metal (iron/manganese) reduction zone, and the gas hydrate stability zone. We found evidence for bacterial fermentation as a source of acetate for aceticlastic methanogenesis and as a driver of iron reduction in the metal reduction zone. In multiple zones, we identified a Ni-Fe hydrogenase-Na+ /H+ antiporter supercomplex (Hun) in Atribacteria and Firmicutes bins and in other deep subsurface bacteria and cultured hyperthermophiles from the Thermotogae phylum. Atribacteria expressed tripartite ATP-independent transporters downstream from a novel regulator (AtiR). Atribacteria also possessed adaptations to survive extreme conditions (e.g. high salt brines, high pressure and cold temperatures) including the ability to synthesize the osmolyte di-myo-inositol-phosphate as well as expression of K+ -stimulated pyrophosphatase and capsule proteins.
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Affiliation(s)
- Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Piyush Ranjan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Brook L Nunn
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Abigail M Johnson
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Manlin Xu
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - James McManus
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
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Mehrshad M, Lopez-Fernandez M, Sundh J, Bell E, Simone D, Buck M, Bernier-Latmani R, Bertilsson S, Dopson M. Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater. Nat Commun 2021; 12:4253. [PMID: 34253732 PMCID: PMC8275790 DOI: 10.1038/s41467-021-24549-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/23/2021] [Indexed: 02/06/2023] Open
Abstract
While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome.
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Affiliation(s)
- Maliheh Mehrshad
- grid.8993.b0000 0004 1936 9457Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden ,grid.6341.00000 0000 8578 2742Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Margarita Lopez-Fernandez
- grid.8148.50000 0001 2174 3522Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden ,grid.4489.10000000121678994Present Address: Department of Microbiology, University of Granada, Granada, Spain
| | - John Sundh
- grid.10548.380000 0004 1936 9377Dept of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Emma Bell
- grid.5333.60000000121839049Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland ,grid.22072.350000 0004 1936 7697Present Address: Department of Biological Sciences, University of Calgary, Calgary, Alberta Canada
| | - Domenico Simone
- grid.8148.50000 0001 2174 3522Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden ,grid.6341.00000 0000 8578 2742SLU Bioinformatics Infrastructure, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Moritz Buck
- grid.6341.00000 0000 8578 2742Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Rizlan Bernier-Latmani
- grid.5333.60000000121839049Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Stefan Bertilsson
- grid.8993.b0000 0004 1936 9457Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden ,grid.6341.00000 0000 8578 2742Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mark Dopson
- grid.8148.50000 0001 2174 3522Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
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Barrena R, Vargas-García MDC, Capell G, Barańska M, Puntes V, Moral-Vico J, Sánchez A, Font X. Sustained effect of zero-valent iron nanoparticles under semi-continuous anaerobic digestion of sewage sludge: Evolution of nanoparticles and microbial community dynamics. Sci Total Environ 2021; 777:145969. [PMID: 33676214 DOI: 10.1016/j.scitotenv.2021.145969] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 06/12/2023]
Abstract
The effects of adding zero-valent iron nanoparticles (nZVI) on the physicochemical, biological and biochemical responses of a semi-continuous anaerobic digestion of sewage sludge have been assessed. Two sets of consecutive experiments of 103 and 116 days, respectively, were carried out in triplicate. nZVI were magnetically retained in the reactors, and the effect of punctual doses (from 0.27 to 4.33 g L-1) over time was studied. Among the different parameters monitored, only methane content in the biogas was significantly higher when nZVI was added. However, this effect was progressively lost after the addition, and in 5-7 days, the methane content returned to initial values. The increase in the oxidation state of nanoparticles seems to be related to the loss of effect over time. Higher dose (4.33 g L-1) sustained positive effects for a longer time along with higher methane content, but this fact seems to be related to microbiome acclimation. Changes in microbial community structure could also play a role in the mechanisms involved in methane enhancement. In this sense, the microbial consortium analysis reported a shift in the balance among acetogenic eubacterial communities, and a marked increase in the relative abundance of members assigned to Methanothrix genus, recognized as acetoclastic species showing high affinity for acetate, which explain the rise in methane content in the biogas. This research demonstrates that biogas methane enrichment in semicontinuous anaerobic digesters can be achieved by using nZVI nanoparticles, thus increasing energy production or reducing costs of a later biogas upgrading process.
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Affiliation(s)
- Raquel Barrena
- GICOM research group, Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Edifici Q, Carrer de les Sitges, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain.
| | - María Del Carmen Vargas-García
- Department of Biology and Geology, CITE II-B, Universidad de Almería, Agrifood Campus of International Excellence ceiA3, 04120 Almería, Spain
| | - Georgina Capell
- GICOM research group, Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Edifici Q, Carrer de les Sitges, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Maja Barańska
- GICOM research group, Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Edifici Q, Carrer de les Sitges, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Victor Puntes
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), 08035 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), P. Lluís Companys 23, 08010 Barcelona, Spain
| | - Javier Moral-Vico
- GICOM research group, Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Edifici Q, Carrer de les Sitges, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Antoni Sánchez
- GICOM research group, Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Edifici Q, Carrer de les Sitges, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Xavier Font
- GICOM research group, Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Edifici Q, Carrer de les Sitges, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
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Zhao R, Biddle JF. Helarchaeota and co-occurring sulfate-reducing bacteria in subseafloor sediments from the Costa Rica Margin. ISME Commun 2021; 1:25. [PMID: 36737514 PMCID: PMC9723726 DOI: 10.1038/s43705-021-00027-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/11/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023]
Abstract
Deep sediments host many archaeal lineages, including the Asgard superphylum which contains lineages predicted to require syntrophic partnerships. Our knowledge about sedimentary archaeal diversity and their metabolic pathways and syntrophic partners is still very limited. We present here new genomes of Helarchaeota and the co-occurring sulfate-reducing bacteria (SRB) recovered from organic-rich sediments off Costa Rica Margin. Phylogenetic analyses revealed three new metagenome-assembled genomes (MAGs) affiliating with Helarchaeota, each of which has three variants of the methyl-CoM reductase-like (MCR-like) complex that may enable them to oxidize short-chain alkanes anaerobically. These Helarchaeota have no multi-heme cytochromes but have Group 3b and Group 3c [NiFe] hydrogenases, and formate dehydrogenase, and therefore have the capacity to transfer the reducing equivalents (in the forms of hydrogen and formate) generated from alkane oxidation to external partners. We also recovered five MAGs of SRB affiliated with the class of Desulfobacteria, two of which showed relative abundances (represented by genome coverages) positively correlated with those of the three Helarchaeota. Genome analysis suggested that these SRB bacteria have the capacity of H2 and formate utilization and could facilitate electron transfers from other organisms by means of these reduced substances. Their co-occurrence and metabolic features suggest that Helarchaeota may metabolize synergistically with some SRB, and together exert an important influence on the carbon cycle by mitigating the hydrocarbon emission from sediments to the overlying ocean.
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Affiliation(s)
- Rui Zhao
- School of Marine Science and Policy, University of Delaware, Lewes, DE, USA
| | - Jennifer F Biddle
- School of Marine Science and Policy, University of Delaware, Lewes, DE, USA.
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Lui LM, Nielsen TN, Arkin AP. A method for achieving complete microbial genomes and improving bins from metagenomics data. PLoS Comput Biol 2021; 17:e1008972. [PMID: 33961626 PMCID: PMC8172020 DOI: 10.1371/journal.pcbi.1008972] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 06/02/2021] [Accepted: 04/16/2021] [Indexed: 11/19/2022] Open
Abstract
Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete genomes from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Some studies have attempted to extract complete bacterial, archaeal, and viral genomes and often focus on species with circular genomes so they can help confirm completeness with circularity. However, less than 100 circularized bacterial and archaeal genomes have been assembled and published from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a semi-automated method called Jorg to help circularize small bacterial, archaeal, and viral genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one ribosomal RNA operon. In addition to 34 circular CPR genomes, we present one circular Margulisbacteria genome, one circular Chloroflexi genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA. Code and a tutorial for this method is available at https://github.com/lmlui/Jorg and is available on the DOE Systems Biology KnowledgeBase as a beta app.
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Affiliation(s)
- Lauren M. Lui
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Torben N. Nielsen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, CA, United States of America
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38
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Lemay-St-Denis C, Diwan SS, Pelletier JN. The Bacterial Genomic Context of Highly Trimethoprim-Resistant DfrB Dihydrofolate Reductases Highlights an Emerging Threat to Public Health. Antibiotics (Basel) 2021; 10:antibiotics10040433. [PMID: 33924456 PMCID: PMC8103504 DOI: 10.3390/antibiotics10040433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/08/2021] [Accepted: 04/12/2021] [Indexed: 01/21/2023] Open
Abstract
Type B dihydrofolate reductase (dfrb) genes were identified following the introduction of trimethoprim in the 1960s. Although they intrinsically confer resistance to trimethoprim (TMP) that is orders of magnitude greater than through other mechanisms, the distribution and prevalence of these short (237 bp) genes is unknown. Indeed, this knowledge has been hampered by systematic biases in search methodologies. Here, we investigate the genomic context of dfrbs to gain information on their current distribution in bacterial genomes. Upon searching publicly available databases, we identified 61 sequences containing dfrbs within an analyzable genomic context. The majority (70%) of those sequences also harbor virulence genes and 97% of the dfrbs are found near a mobile genetic element, representing a potential risk for antibiotic resistance genes. We further identified and confirmed the TMP-resistant phenotype of two new members of the family, dfrb10 and dfrb11. Dfrbs are found both in Betaproteobacteria and Gammaproteobacteria, a majority (59%) being in Pseudomonas aeruginosa. Previously labelled as strictly plasmid-borne, we found 69% of dfrbs in the chromosome of pathogenic bacteria. Our results demonstrate that the intrinsically TMP-resistant dfrbs are a potential emerging threat to public health and justify closer surveillance of these genes.
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Affiliation(s)
- Claudèle Lemay-St-Denis
- Department of Biochemistry and Molecular Medecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
| | - Sarah-Slim Diwan
- Department of Biochemistry and Molecular Medecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
| | - Joelle N Pelletier
- Department of Biochemistry and Molecular Medecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
- Chemistry Department, Université de Montréal, Montréal, QC H2V 0B3, Canada
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Fang Y, Yuan Y, Liu J, Wu G, Yang J, Hua Z, Han J, Zhang X, Li W, Jiang H. Casting Light on the Adaptation Mechanisms and Evolutionary History of the Widespread Sumerlaeota. mBio 2021; 12:e00350-21. [PMID: 33785617 DOI: 10.1128/mBio.00350-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In recent years, the tree of life has expanded substantially. Despite this, many abundant yet uncultivated microbial groups remain to be explored. Sumerlaeota is a mysterious, putative phylum-level lineage distributed globally but rarely reported. As such, their physiology, ecology, and evolutionary history remain unknown. The 16S rRNA gene survey reveals that Sumerlaeota is frequently detected in diverse environments globally, especially cold arid desert soils and deep-sea basin surface sediments, where it is one dominant microbial group. Here, we retrieved four Sumerlaeota metagenome-assembled genomes (MAGs) from two hot springs and one saline lake. Including another 12 publicly available MAGs, they represent six of the nine putative Sumerlaeota subgroups/orders, as indicated by 16S rRNA gene-based phylogeny. These elusive organisms likely obtain carbon mainly through utilization of refractory organics (e.g., chitin and cellulose) and proteinaceous compounds, suggesting that Sumerlaeota act as scavengers in nature. The presence of key bidirectional enzymes involved in acetate and hydrogen metabolisms in these MAGs suggests that they are acetogenic bacteria capable of both the production and consumption of hydrogen. The capabilities of dissimilatory nitrate and sulfate reduction, nitrogen fixation, phosphate solubilization, and organic phosphorus mineralization may confer these heterotrophs great advantages to thrive under diverse harsh conditions. Ancestral state reconstruction indicated that Sumerlaeota originated from chemotrophic and facultatively anaerobic ancestors, and their smaller and variably sized genomes evolved along dynamic pathways from a sizeable common ancestor (2,342 genes), leading to their physiological divergence. Notably, large gene gain and larger loss events occurred at the branch to the last common ancestor of the order subgroup 1, likely due to niche expansion and population size effects.
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Murphy TR, Xiao R, Hamilton-Brehm SD. Hybrid genome de novo assembly with methylome analysis of the anaerobic thermophilic subsurface bacterium Thermanaerosceptrum fracticalcis strain DRI-13 T. BMC Genomics 2021; 22:209. [PMID: 33757423 PMCID: PMC7988955 DOI: 10.1186/s12864-021-07535-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND There is a dearth of sequenced and closed microbial genomes from environments that exceed > 500 m below level terrestrial surface. Coupled with even fewer cultured isolates, study and understanding of how life endures in the extreme oligotrophic subsurface environments is greatly hindered. Using a de novo hybrid assembly of Illumina and Oxford Nanopore sequences we produced a circular genome with corresponding methylome profile of the recently characterized thermophilic, anaerobic, and fumarate-respiring subsurface bacterium, Thermanaerosceptrum fracticalcis, strain DRI-13T to understand how this microorganism survives the deep subsurface. RESULTS The hybrid assembly produced a single circular genome of 3.8 Mb in length with an overall GC content of 45%. Out of the total 4022 annotated genes, 3884 are protein coding, 87 are RNA encoding genes, and the remaining 51 genes were associated with regulatory features of the genome including riboswitches and T-box leader sequences. Approximately 24% of the protein coding genes were hypothetical. Analysis of strain DRI-13T genome revealed: 1) energy conservation by bifurcation hydrogenase when growing on fumarate, 2) four novel bacterial prophages, 3) methylation profile including 76.4% N6-methyladenine and 3.81% 5-methylcytosine corresponding to novel DNA methyltransferase motifs. As well a cluster of 45 genes of unknown protein families that have enriched DNA mCpG proximal to the transcription start sites, and 4) discovery of a putative core of bacteriophage exclusion (BREX) genes surrounded by hypothetical proteins, with predicted functions as helicases, nucleases, and exonucleases. CONCLUSIONS The de novo hybrid assembly of strain DRI-13T genome has provided a more contiguous and accurate view of the subsurface bacterium T. fracticalcis, strain DRI-13T. This genome analysis reveals a physiological focus supporting syntrophy, non-homologous double stranded DNA repair, mobility/adherence/chemotaxis, unique methylome profile/recognized motifs, and a BREX defense system. The key to microbial subsurface survival may not rest on genetic diversity, but rather through specific syntrophy niches and novel methylation strategies.
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Affiliation(s)
- Trevor R Murphy
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Rui Xiao
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Scott D Hamilton-Brehm
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, USA.
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McAllister SM, Vandzura R, Keffer JL, Polson SW, Chan CS. Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents. ISME J 2021; 15:1271-86. [PMID: 33328652 DOI: 10.1038/s41396-020-00849-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 11/06/2020] [Accepted: 11/18/2020] [Indexed: 12/02/2022]
Abstract
In principle, iron oxidation can fuel significant primary productivity and nutrient cycling in dark environments such as the deep sea. However, we have an extremely limited understanding of the ecology of iron-based ecosystems, and thus the linkages between iron oxidation, carbon cycling, and nitrate reduction. Here we investigate iron microbial mats from hydrothermal vents at Lōʻihi Seamount, Hawaiʻi, using genome-resolved metagenomics and metatranscriptomics to reconstruct potential microbial roles and interactions. Our results show that the aerobic iron-oxidizing Zetaproteobacteria are the primary producers, concentrated at the oxic mat surface. Their fixed carbon supports heterotrophs deeper in the mat, notably the second most abundant organism, Candidatus Ferristratum sp. (uncultivated gen. nov.) from the uncharacterized DTB120 phylum. Candidatus Ferristratum sp., described using nine high-quality metagenome-assembled genomes with similar distributions of genes, expressed nitrate reduction genes narGH and the iron oxidation gene cyc2 in situ and in response to Fe(II) in a shipboard incubation, suggesting it is an anaerobic nitrate-reducing iron oxidizer. Candidatus Ferristratum sp. lacks a full denitrification pathway, relying on Zetaproteobacteria to remove intermediates like nitrite. Thus, at Lōʻihi, anaerobic iron oxidizers coexist with and are dependent on aerobic iron oxidizers. In total, our work shows how key community members work together to connect iron oxidation with carbon and nitrogen cycling, thus driving the biogeochemistry of exported fluids.
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Szeinbaum N, Nunn BL, Cavazos AR, Crowe SA, Stewart FJ, DiChristina TJ, Reinhard CT, Glass JB. Novel insights into the taxonomic diversity and molecular mechanisms of bacterial Mn(III) reduction. Environ Microbiol Rep 2020; 12:583-593. [PMID: 32613749 PMCID: PMC7775658 DOI: 10.1111/1758-2229.12867] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 05/23/2023]
Abstract
Soluble ligand-bound Mn(III) can support anaerobic microbial respiration in diverse aquatic environments. Thus far, Mn(III) reduction has only been associated with certain Gammaproteobacteria. Here, we characterized microbial communities enriched from Mn-replete sediments of Lake Matano, Indonesia. Our results provide the first evidence for the biological reduction of soluble Mn(III) outside the Gammaproteobacteria. Metagenome assembly and binning revealed a novel betaproteobacterium, which we designate 'Candidatus Dechloromonas occultata.' This organism dominated the enrichment and expressed a porin-cytochrome c complex typically associated with iron-oxidizing Betaproteobacteria and a novel cytochrome c-rich protein cluster (Occ), including an undecaheme putatively involved in extracellular electron transfer. This occ gene cluster was also detected in diverse aquatic bacteria, including uncultivated Betaproteobacteria from the deep subsurface. These observations provide new insight into the taxonomic and functional diversity of microbially driven Mn(III) reduction in natural environments.
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Affiliation(s)
- Nadia Szeinbaum
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- NASA Astrobiology Institute, Alternative Earths Team, Mountain View, CA, USA
| | - Brook L. Nunn
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Amanda R. Cavazos
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Sean A. Crowe
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Frank J. Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - Christopher T. Reinhard
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- NASA Astrobiology Institute, Alternative Earths Team, Mountain View, CA, USA
| | - Jennifer B. Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- NASA Astrobiology Institute, Alternative Earths Team, Mountain View, CA, USA
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43
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Wong HL, MacLeod FI, White RA, Visscher PT, Burns BP. Microbial dark matter filling the niche in hypersaline microbial mats. Microbiome 2020; 8:135. [PMID: 32938503 PMCID: PMC7495880 DOI: 10.1186/s40168-020-00910-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/19/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Shark Bay, Australia, harbours one of the most extensive and diverse systems of living microbial mats that are proposed to be analogs of some of the earliest ecosystems on Earth. These ecosystems have been shown to possess a substantial abundance of uncultivable microorganisms. These enigmatic microbes, jointly coined as 'microbial dark matter' (MDM), are hypothesised to play key roles in modern microbial mats. RESULTS We reconstructed 115 metagenome-assembled genomes (MAGs) affiliated to MDM, spanning 42 phyla. This study reports for the first time novel microorganisms (Zixibacterial order GN15) putatively taking part in dissimilatory sulfate reduction in surface hypersaline settings, as well as novel eukaryote signature proteins in the Asgard archaea. Despite possessing reduced-size genomes, the MDM MAGs are capable of fermenting and degrading organic carbon, suggesting a role in recycling organic carbon. Several forms of RuBisCo were identified, allowing putative CO2 incorporation into nucleotide salvaging pathways, which may act as an alternative carbon and phosphorus source. High capacity of hydrogen production was found among Shark Bay MDM. Putative schizorhodopsins were also identified in Parcubacteria, Asgard archaea, DPANN archaea, and Bathyarchaeota, allowing these members to potentially capture light energy. Diversity-generating retroelements were prominent in DPANN archaea that likely facilitate the adaptation to a dynamic, host-dependent lifestyle. CONCLUSIONS This is the first study to reconstruct and describe in detail metagenome-assembled genomes (MAGs) affiliated with microbial dark matter in hypersaline microbial mats. Our data suggests that these microbial groups are major players in these systems. In light of our findings, we propose H2, ribose and CO/CO2 as the main energy currencies of the MDM community in these mat systems. Video Abstract.
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Affiliation(s)
- Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia
| | - Fraser I MacLeod
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia
| | - Richard Allen White
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia
- RAW Molecular Systems LLC, Spokane, WA, USA
- Department of Bioinformatics and Genomics, The University of North Carolina, Charlotte, NC, USA
| | - Pieter T Visscher
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia
- Department of Marine Sciences, University of Connecticut, Mansfield, USA
- Biogeosciences, the Université de Bourgogne Franche-Comté, Dijon, France
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia.
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia.
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Mardanov AV, Kadnikov VV, Beletsky AV, Ravin NV. Sulfur and Methane-Oxidizing Microbial Community in a Terrestrial Mud Volcano Revealed by Metagenomics. Microorganisms 2020; 8:microorganisms8091333. [PMID: 32878336 PMCID: PMC7565565 DOI: 10.3390/microorganisms8091333] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/15/2022] Open
Abstract
Mud volcanoes are prominent geological structures where fluids and gases from the deep subsurface are discharged along a fracture network in tectonically active regions. Microbial communities responsible for sulfur and methane cycling and organic transformation in terrestrial mud volcanoes remain poorly characterized. Using a metagenomics approach, we analyzed the microbial community of bubbling fluids retrieved from an active mud volcano in eastern Crimea. The microbial community was dominated by chemolithoautotrophic Campylobacterota and Gammaproteobacteria, which are capable of sulfur oxidation coupled to aerobic and anaerobic respiration. Methane oxidation could be enabled by aerobic Methylococcales bacteria and anaerobic methanotrophic archaea (ANME), while methanogens were nearly absent. The ANME community was dominated by a novel species of Ca. Methanoperedenaceae that lacked nitrate reductase and probably couple methane oxidation to the reduction of metal oxides. Analysis of two Ca. Bathyarchaeota genomes revealed the lack of mcr genes and predicted that they could grow on fatty acids, sugars, and proteinaceous substrates performing fermentation. Thermophilic sulfate reducers indigenous to the deep subsurface, Thermodesulfovibrionales (Nitrospirae) and Ca. Desulforudis (Firmicutes), were found in minor amounts. Overall, the results obtained suggest that reduced compounds delivered from the deep subsurface support the development of autotrophic microorganisms using various electron acceptors for respiration.
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Arbour TJ, Gilbert B, Banfield JF. Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities. Front Microbiol 2020; 11:1694. [PMID: 32849356 PMCID: PMC7399161 DOI: 10.3389/fmicb.2020.01694] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 06/29/2020] [Indexed: 11/17/2022] Open
Abstract
Extracellular electron transfer (EET) between microbes and iron minerals, and syntrophically between species, is a widespread process affecting biogeochemical cycles and microbial ecology. The distribution of this capacity among microbial taxa, and the thermodynamic controls on EET in complex microbial communities, are not fully known. Microbial electrochemical cells (MXCs), in which electrodes serve as the electron acceptor or donor, provide a powerful approach to enrich for organisms capable of EET and to study their metabolism. We used MXCs coupled with genome-resolved metagenomics to investigate the capacity for EET in microorganisms present in a well-studied aquifer near Rifle, CO. Electroactive biofilms were established and maintained for almost 4 years on anodes poised mostly at −0.2 to −0.25 V vs. SHE, a range that mimics the redox potential of iron-oxide minerals, using acetate as the sole carbon source. Here we report the metagenomic characterization of anode-biofilm and planktonic microbial communities from samples collected at timepoints across the study period. From two biofilm and 26 planktonic samples we reconstructed draft-quality and near-complete genomes for 84 bacteria and 2 archaea that represent the majority of organisms present. A novel Geobacter sp. with at least 72 putative multiheme c-type cytochromes (MHCs) was the dominant electrode-attached organism. However, a diverse range of other electrode-associated organisms also harbored putative MHCs with at least 10 heme-binding motifs, as well as porin-cytochrome complexes and e-pili, including Actinobacteria, Ignavibacteria, Chloroflexi, Acidobacteria, Firmicutes, Beta- and Gammaproteobacteria. Our results identify a small subset of the thousands of organisms previously detected in the Rifle aquifer that may have the potential to mediate mineral redox transformations.
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Affiliation(s)
- Tyler J Arbour
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, United States
| | - Benjamin Gilbert
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, United States.,Energy Geosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, United States.,Energy Geosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
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46
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Méheust R, Castelle CJ, Matheus Carnevali PB, Farag IF, He C, Chen LX, Amano Y, Hug LA, Banfield JF. Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog. ISME J 2020; 14:2907-2922. [PMID: 32681159 DOI: 10.1038/s41396-020-0716-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/15/2020] [Accepted: 07/08/2020] [Indexed: 01/09/2023]
Abstract
Currently described members of Elusimicrobia, a relatively recently defined phylum, are animal-associated and rely on fermentation. However, free-living Elusimicrobia have been detected in sediments, soils and groundwater, raising questions regarding their metabolic capacities and evolutionary relationship to animal-associated species. Here, we analyzed 94 draft-quality, non-redundant genomes, including 30 newly reconstructed genomes, from diverse animal-associated and natural environments. Genomes group into 12 clades, 10 of which previously lacked reference genomes. Groundwater-associated Elusimicrobia are predicted to be capable of heterotrophic or autotrophic lifestyles, reliant on oxygen or nitrate/nitrite-dependent respiration, or a variety of organic compounds and Rhodobacter nitrogen fixation (Rnf) complex-dependent acetogenesis with hydrogen and carbon dioxide as the substrates. Genomes from two clades of groundwater-associated Elusimicrobia often encode a new group of nitrogenase paralogs that co-occur with an extensive suite of radical S-Adenosylmethionine (SAM) proteins. We identified similar genomic loci in genomes of bacteria from the Gracilibacteria phylum and the Myxococcales order and predict that the gene clusters reduce a tetrapyrrole, possibly to form a novel cofactor. The animal-associated Elusimicrobia clades nest phylogenetically within two free-living-associated clades. Thus, we propose an evolutionary trajectory in which some Elusimicrobia adapted to animal-associated lifestyles from free-living species via genome reduction.
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Affiliation(s)
- Raphaël Méheust
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, Berkeley, CA, 94720, USA
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, Berkeley, CA, 94720, USA
| | - Paula B Matheus Carnevali
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, Berkeley, CA, 94720, USA
| | - Ibrahim F Farag
- School of Marine Science and Policy, University of Delaware, Lewes, DE, 19968, USA
| | - Christine He
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Lin-Xing Chen
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, Berkeley, CA, 94720, USA
| | - Yuki Amano
- Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Tokai-mura, Ibaraki, Japan
| | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA. .,Innovative Genomics Institute, Berkeley, CA, 94720, USA.
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Leu AO, McIlroy SJ, Ye J, Parks DH, Orphan VJ, Tyson GW. Lateral Gene Transfer Drives Metabolic Flexibility in the Anaerobic Methane-Oxidizing Archaeal Family Methanoperedenaceae. mBio 2020; 11:e01325-20. [PMID: 32605988 DOI: 10.1128/mBio.01325-20] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Anaerobic oxidation of methane (AOM) is an important biological process responsible for controlling the flux of methane into the atmosphere. Members of the archaeal family Methanoperedenaceae (formerly ANME-2d) have been demonstrated to couple AOM to the reduction of nitrate, iron, and manganese. Here, comparative genomic analysis of 16 Methanoperedenaceae metagenome-assembled genomes (MAGs), recovered from diverse environments, revealed novel respiratory strategies acquired through lateral gene transfer (LGT) events from diverse archaea and bacteria. Comprehensive phylogenetic analyses suggests that LGT has allowed members of the Methanoperedenaceae to acquire genes for the oxidation of hydrogen and formate and the reduction of arsenate, selenate, and elemental sulfur. Numerous membrane-bound multiheme c-type cytochrome complexes also appear to have been laterally acquired, which may be involved in the direct transfer of electrons to metal oxides, humic substances, and syntrophic partners.IMPORTANCE AOM by microorganisms limits the atmospheric release of the potent greenhouse gas methane and has consequent importance for the global carbon cycle and climate change modeling. While the oxidation of methane coupled to sulfate by consortia of anaerobic methanotrophic (ANME) archaea and bacteria is well documented, several other potential electron acceptors have also been reported to support AOM. In this study, we identify a number of novel respiratory strategies that appear to have been laterally acquired by members of the Methanoperedenaceae, as they are absent from related archaea and other ANME lineages. Expanding the known metabolic potential for members of the Methanoperedenaceae provides important insight into their ecology and suggests their role in linking methane oxidation to several global biogeochemical cycles.
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Kadnikov VV, Mardanov AV, Beletsky AV, Karnachuk OV, Ravin NV. Genome Analysis of a Member of the Uncultured Phylum Riflebacteria Revealed Pathways of Organotrophic Metabolism and Dissimilatory Iron Reduction. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720030078] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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49
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Atashgahi S. Discovered by genomics: putative reductive dehalogenases with N-terminus transmembrane helixes. FEMS Microbiol Ecol 2020; 95:5426821. [PMID: 30942854 PMCID: PMC6797604 DOI: 10.1093/femsec/fiz048] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/02/2019] [Indexed: 11/13/2022] Open
Abstract
Attempts for bioremediation of toxic organohalogens resulted in the identification of organohalide-respiring bacteria harbouring reductive dehalogenases (RDases) enzymes. RDases consist of the catalytic subunit (RdhA, encoded by rdhA) that does not have membrane-integral domains, and a small putative membrane anchor (RdhB, encoded by rdhB) that (presumably) locates the A subunit to the outside of the cytoplasmic membrane. Recent genomic studies identified a putative rdh gene in an uncultured deltaproteobacterial genome that was not accompanied by an rdhB gene, but contained transmembrane helixes in N-terminus. Therefore, rather than having a separate membrane anchor protein, this putative RDase is likely a hybrid of RdhA and RdhB, and directly connected to the membrane with transmembrane helixes. However, functionality of the hybrid putative RDase remains unknown. Further analysis showed that the hybrid putative rdh genes are present in the genomes of pure cultures and uncultured members of Bacteriodetes and Deltaproteobacteria, but also in the genomes of the candidate divisions. The encoded hybrid putative RDases have cytoplasmic or exoplasmic C-terminus localization, and cluster phylogenetically separately from the existing RDase groups. With increasing availability of (meta)genomes, more diverse and likely novel rdh genes are expected, but questions regarding their functionality and ecological roles remain open.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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50
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Leu AO, Cai C, McIlroy SJ, Southam G, Orphan VJ, Yuan Z, Hu S, Tyson GW. Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae. ISME J 2020; 14:1030-1041. [PMID: 31988473 PMCID: PMC7082337 DOI: 10.1038/s41396-020-0590-x] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 12/10/2019] [Accepted: 01/16/2020] [Indexed: 11/09/2022]
Abstract
Anaerobic oxidation of methane (AOM) is a major biological process that reduces global methane emission to the atmosphere. Anaerobic methanotrophic archaea (ANME) mediate this process through the coupling of methane oxidation to different electron acceptors, or in concert with a syntrophic bacterial partner. Recently, ANME belonging to the archaeal family Methanoperedenaceae (formerly known as ANME-2d) were shown to be capable of AOM coupled to nitrate and iron reduction. Here, a freshwater sediment bioreactor fed with methane and Mn(IV) oxides (birnessite) resulted in a microbial community dominated by two novel members of the Methanoperedenaceae, with biochemical profiling of the system demonstrating Mn(IV)-dependent AOM. Genomic and transcriptomic analyses revealed the expression of key genes involved in methane oxidation and several shared multiheme c-type cytochromes (MHCs) that were differentially expressed, indicating the likely use of different extracellular electron transfer pathways. We propose the names "Candidatus Methanoperedens manganicus" and "Candidatus Methanoperedens manganireducens" for the two newly described Methanoperedenaceae species. This study demonstrates the ability of members of the Methanoperedenaceae to couple AOM to the reduction of Mn(IV) oxides, which suggests their potential role in linking methane and manganese cycling in the environment.
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Affiliation(s)
- Andy O Leu
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Chen Cai
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, Brisbane, QLD, Australia
| | - Simon J McIlroy
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Gordon Southam
- School of Earth & Environmental Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Victoria J Orphan
- Department of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91106, USA
| | - Zhiguo Yuan
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, Brisbane, QLD, Australia
| | - Shihu Hu
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, Brisbane, QLD, Australia.
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
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