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Rasmussen AN, Tolar BB, Bargar JR, Boye K, Francis CA. Metagenome-Assembled Genomes for Oligotrophic Nitrifiers From a Mountainous Gravelbed Floodplain. Environ Microbiol 2025; 27:e70060. [PMID: 40103293 DOI: 10.1111/1462-2920.70060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 12/09/2024] [Accepted: 01/08/2025] [Indexed: 03/20/2025]
Abstract
Riparian floodplains are important regions for biogeochemical cycling, including nitrogen. Here, we present MAGs from nitrifying microorganisms, including ammonia-oxidising archaea (AOA) and comammox bacteria from Slate River (SR) floodplain sediments (Crested Butte, CO, US). Additionally, we explore MAGs from potential nitrite-oxidising bacteria (NOB) from the Nitrospirales. AOA diversity in SR is lower than observed in other western US floodplain sediments and Nitrosotalea-like lineages such as the genus TA-20 are the dominant AOA. No ammonia-oxidising bacteria (AOB) MAGs were recovered. Microorganisms from the Palsa-1315 genus (clade B comammox) are the most abundant ammonia-oxidizers in SR floodplain sediments. Established NOB are conspicuously absent; however, we recovered MAGs from uncultured lineages of the NS-4 family (Nitrospirales) and Nitrospiraceae that we propose as putative NOB. Nitrite oxidation may be carried out by organisms sister to established Nitrospira NOB lineages based on the genomic content of uncultured Nitrospirales clades. Nitrifier MAGs recovered from SR floodplain sediments harbour genes for using alternative sources of ammonia, such as urea, cyanate, biuret, triuret and nitriles. The SR floodplain therefore appears to be a low ammonia flux environment that selects for oligotrophic nitrifiers.
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Affiliation(s)
- Anna N Rasmussen
- Department of Earth System Science, Stanford University, Stanford, California, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Bradley B Tolar
- Department of Earth System Science, Stanford University, Stanford, California, USA
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - John R Bargar
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kristin Boye
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Christopher A Francis
- Department of Earth System Science, Stanford University, Stanford, California, USA
- Oceans Department, Stanford University, Stanford, California, USA
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Schechter MS, Trigodet F, Veseli IA, Miller SE, Klein ML, Sever M, Maignien L, Delmont TO, Light SH, Eren AM. Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.15.633187. [PMID: 39868213 PMCID: PMC11760686 DOI: 10.1101/2025.01.15.633187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
The increasing availability of microbial genomes is essential to gain insights into microbial ecology and evolution that can propel biotechnological and biomedical advances. Recent advances in genome recovery have significantly expanded the catalogue of microbial genomes from diverse habitats. However, the ability to explain how well a set of genomes account for the diversity in a given environment remains challenging for individual studies or biome-specific databases. Here we present EcoPhylo, a computational workflow to characterize the phylogeography of any gene family through integrated analyses of genomes and metagenomes, and our application of this approach to ribosomal proteins to quantify phylogeny-aware genome recovery rates across three biomes. Our findings show that genome recovery rates vary widely across taxa and biomes, and that single amplified genomes, metagenome-assembled genomes, and isolate genomes have non-uniform yet quantifiable representation of environmental microbes. EcoPhylo reveals highly resolved, reference-free, multi-domain phylogenies in conjunction with distribution patterns of individual clades across environments, providing a means to assess genome recovery in individual studies and benchmark biome-level genome collections.
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Affiliation(s)
- Matthew S. Schechter
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Florian Trigodet
- Helmholtz Institute for Functional Marine Biodiversity, 26129 Oldenburg, Germany
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Iva A. Veseli
- Helmholtz Institute for Functional Marine Biodiversity, 26129 Oldenburg, Germany
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Samuel E. Miller
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Matthew L. Klein
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Metehan Sever
- Helmholtz Institute for Functional Marine Biodiversity, 26129 Oldenburg, Germany
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Loïs Maignien
- University of Brest, CNRS, IFREMER, EMR 6002 BIOMEX, Unité Biologie et Écologie des Écosystèmes Marins Profonds BEEP, F-29280 Plouzané, France
| | - Tom O. Delmont
- Génomique Métabolique du Genoscope, Institut François Jacob, CEA, CNRS, University of Évry Val d’Essonne, Université Paris-Saclay, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | - Samuel H. Light
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - A. Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity, 26129 Oldenburg, Germany
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129 Oldenburg, Germany
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
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Wang Y, Wang F, Ford R, Tang W, Zhou M, Ma B, Zhang M. Dicyandiamide Applications Mitigate the Destructive Effects of Graphene Oxide on Microbial Activity, Diversity, and Composition and Nitrous Oxide Emission in Agricultural Soil. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:21449-21460. [PMID: 39288293 DOI: 10.1021/acs.jafc.4c04761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
The widespread production and utilization of graphene oxide (GO) raise concerns about its environmental release and potential ecological impacts, particularly in agricultural soil. Effective nitrogen (N) management, especially through nitrification inhibitors like dicyandiamide (DCD), might mitigate the negative effects of GO exposure on soil microbes via N biostimulation. This study quantified changes in soil physicochemical properties, nitrous oxide (N2O) emissions, microbial activity, biomass, and community after treatments with GO and DCD. The GO exposure significantly reduced bacterial 16S rRNA gene abundance and the biomass of major bacterial phyla. It also stimulated pathways linked to human diseases. However, DCD application alleviated the negative effects of GO exposure on soil bacterial biomass. While DCD application significantly reduced soil N2O emission, the GO application tended to hinder the inhibiting performance of DCD. Our findings highlight the hazards of GO exposure to soil microbes and the potential mitigation strategy with soil N management.
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Affiliation(s)
- Yan Wang
- College of Environment and Ecology, Hunan Agricultural University, Changsha 410128, China
| | - Fang Wang
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rebecca Ford
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Brisbane, Queensland 4111, Australia
| | - Wenhui Tang
- College of Environment and Ecology, Hunan Agricultural University, Changsha 410128, China
| | - Minzhe Zhou
- College of Environment and Ecology, Hunan Agricultural University, Changsha 410128, China
| | - Bin Ma
- College of Environment and Ecology, Hunan Agricultural University, Changsha 410128, China
| | - Manyun Zhang
- College of Environment and Ecology, Hunan Agricultural University, Changsha 410128, China
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Brisbane, Queensland 4111, Australia
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Rasmussen AN, Tolar BB, Bargar JR, Boye K, Francis CA. Diverse and unconventional methanogens, methanotrophs, and methylotrophs in metagenome-assembled genomes from subsurface sediments of the Slate River floodplain, Crested Butte, CO, USA. mSystems 2024; 9:e0031424. [PMID: 38940520 PMCID: PMC11264602 DOI: 10.1128/msystems.00314-24] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/06/2024] [Indexed: 06/29/2024] Open
Abstract
We use metagenome-assembled genomes (MAGs) to understand single-carbon (C1) compound-cycling-particularly methane-cycling-microorganisms in montane riparian floodplain sediments. We generated 1,233 MAGs (>50% completeness and <10% contamination) from 50- to 150-cm depth below the sediment surface capturing the transition between oxic, unsaturated sediments and anoxic, saturated sediments in the Slate River (SR) floodplain (Crested Butte, CO, USA). We recovered genomes of putative methanogens, methanotrophs, and methylotrophs (n = 57). Methanogens, found only in deep, anoxic depths at SR, originate from three different clades (Methanoregulaceae, Methanotrichaceae, and Methanomassiliicoccales), each with a different methanogenesis pathway; putative methanotrophic MAGs originate from within the Archaea (Candidatus Methanoperedens) in anoxic depths and uncultured bacteria (Ca. Binatia) in oxic depths. Genomes for canonical aerobic methanotrophs were not recovered. Ca. Methanoperedens were exceptionally abundant (~1,400× coverage, >50% abundance in the MAG library) in one sample that also contained aceticlastic methanogens, indicating a potential C1/methane-cycling hotspot. Ca. Methylomirabilis MAGs from SR encode pathways for methylotrophy but do not harbor methane monooxygenase or nitrogen reduction genes. Comparative genomic analysis supports that one clade within the Ca. Methylomirabilis genus is not methanotrophic. The genetic potential for methylotrophy was widespread, with over 10% and 19% of SR MAGs encoding a methanol dehydrogenase or substrate-specific methyltransferase, respectively. MAGs from uncultured Thermoplasmata archaea in the Ca. Gimiplasmatales (UBA10834) contain pathways that may allow for anaerobic methylotrophic acetogenesis. Overall, MAGs from SR floodplain sediments reveal a potential for methane production and consumption in the system and a robust potential for methylotrophy.IMPORTANCEThe cycling of carbon by microorganisms in subsurface environments is of particular relevance in the face of global climate change. Riparian floodplain sediments contain high organic carbon that can be degraded into C1 compounds such as methane, methanol, and methylamines, the fate of which depends on the microbial metabolisms present as well as the hydrological conditions and availability of oxygen. In the present study, we generated over 1,000 MAGs from subsurface sediments from a montane river floodplain and recovered genomes for microorganisms that are capable of producing and consuming methane and other C1 compounds, highlighting a robust potential for C1 cycling in subsurface sediments both with and without oxygen. Archaea from the Ca. Methanoperedens genus were exceptionally abundant in one sample, indicating a potential C1/methane-cycling hotspot in the Slate River floodplain system.
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Affiliation(s)
- Anna N. Rasmussen
- Department of Earth System Science, Stanford University, Stanford, California, USA
- SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Bradley B. Tolar
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - John R. Bargar
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kristin Boye
- SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Christopher A. Francis
- Department of Earth System Science, Stanford University, Stanford, California, USA
- Oceans Department, Stanford University, Stanford, California, USA
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Hui C, Li Y, Yuan S, Zhang W. River connectivity determines microbial assembly processes and leads to alternative stable states in river networks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166797. [PMID: 37673267 DOI: 10.1016/j.scitotenv.2023.166797] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/29/2023] [Accepted: 09/01/2023] [Indexed: 09/08/2023]
Abstract
River network is a common form of lotic ecosystems. Variances in river connection modes would form networks with significantly different structures, and further affect aquatic organisms. Microbial communities are vital organisms of river networks, they participate in numerous biogeochemical processes. Identifying associations between microbial community and structural features of river networks are essential for maintaining environmental quality. Thus, dendritic (DRN) and trellised river networks (TRN) were studied by combining molecular biological tools, ecological theory and hydrodynamic calculation. Results illustrated that river connectivity, a vital structural feature exhibiting mass transport ability of river network, increased relative importance of homogeneous selection processes in microbial assembly, which would further shape community with alternative stable states. Between the two researched river networks, DRN possessed higher connectivity, which made homogeneous selection as the driving force in community assembly. The microbial communities in DRN were consisted of species occupying similar ecological niche, and exhibited two alternative stable states, which can decrease influences of environmental disturbance on community composition. On the contrary, lower connectivity of TRN decreased proportions of homogeneous selection in community assembly, which further led to species occupying varied ecological niche. The microbial community exhibited only one stable state, and environmental disturbance would cause loss of ecological niche and significantly alter community composition. This study could provide useful information for the optimization of river connection engineering.
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Affiliation(s)
- Cizhang Hui
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China.
| | - Saiyu Yuan
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Nanjing 210098, PR China.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
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Lacroix EM, Aeppli M, Boye K, Brodie E, Fendorf S, Keiluweit M, Naughton HR, Noël V, Sihi D. Consider the Anoxic Microsite: Acknowledging and Appreciating Spatiotemporal Redox Heterogeneity in Soils and Sediments. ACS EARTH & SPACE CHEMISTRY 2023; 7:1592-1609. [PMID: 37753209 PMCID: PMC10519444 DOI: 10.1021/acsearthspacechem.3c00032] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/07/2023] [Accepted: 07/21/2023] [Indexed: 09/28/2023]
Abstract
Reduction-oxidation (redox) reactions underlie essentially all biogeochemical cycles. Like most soil properties and processes, redox is spatiotemporally heterogeneous. However, unlike other soil features, redox heterogeneity has yet to be incorporated into mainstream conceptualizations of soil biogeochemistry. Anoxic microsites, the defining feature of redox heterogeneity in bulk oxic soils and sediments, are zones of oxygen depletion in otherwise oxic environments. In this review, we suggest that anoxic microsites represent a critical component of soil function and that appreciating anoxic microsites promises to advance our understanding of soil and sediment biogeochemistry. In sections 1 and 2, we define anoxic microsites and highlight their dynamic properties, specifically anoxic microsite distribution, redox gradient magnitude, and temporality. In section 3, we describe the influence of anoxic microsites on several key elemental cycles, organic carbon, nitrogen, iron, manganese, and sulfur. In section 4, we evaluate methods for identifying and characterizing anoxic microsites, and in section 5, we highlight past and current approaches to modeling anoxic microsites. Finally, in section 6, we suggest steps for incorporating anoxic microsites and redox heterogeneities more broadly into our understanding of soils and sediments.
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Affiliation(s)
- Emily M. Lacroix
- Institut
des Dynamiques de la Surface Terrestre (IDYST), Université de Lausanne, 1015 Lausanne, Switzerland
- Department
of Earth System Science, Stanford University, Stanford, California 94305, United States
| | - Meret Aeppli
- Institut
d’ingénierie de l’environnement (IIE), École Polytechnique Fédérale
de Lausanne, 1015 Lausanne, Switzerland
| | - Kristin Boye
- Environmental
Geochemistry Group, SLAC National Accelerator
Laboratory, Menlo Park, California 94025, United States
| | - Eoin Brodie
- Lawrence
Berkeley Laboratory, Earth and Environmental
Sciences Area, Berkeley, California 94720, United States
| | - Scott Fendorf
- Department
of Earth System Science, Stanford University, Stanford, California 94305, United States
| | - Marco Keiluweit
- Institut
des Dynamiques de la Surface Terrestre (IDYST), Université de Lausanne, 1015 Lausanne, Switzerland
| | - Hannah R. Naughton
- Lawrence
Berkeley Laboratory, Earth and Environmental
Sciences Area, Berkeley, California 94720, United States
| | - Vincent Noël
- Environmental
Geochemistry Group, SLAC National Accelerator
Laboratory, Menlo Park, California 94025, United States
| | - Debjani Sihi
- Department
of Environmental Sciences, Emory University, Atlanta, Georgia 30322, United States
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7
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Torgeson JM, Rosenfeld CE, Dunshee AJ, Duhn K, Schmitter R, O'Hara PA, Ng GHC, Santelli CM. Hydrobiogechemical interactions in the hyporheic zone of a sulfate-impacted, freshwater stream and riparian wetland ecosystem. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:1360-1382. [PMID: 35661843 DOI: 10.1039/d2em00024e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Coupled abiotic and biotic processes in the hyporheic zone, where surface water and groundwater mix, play a critical role in the biogeochemical cycling of carbon, nutrients, and trace elements in streams and wetlands. Dynamic hydrologic conditions and anthropogenic pollution can impact redox gradients and biogeochemical response, although few studies examine the resulting hydrobiogeochemical interactions generated within the hyporheic zone. This study examines the effect of hyporheic flux dynamics and anthropogenic sulfate loading on the biogeochemistry of a riparian wetland and stream system. The hydrologic gradient as well as sediment, surface water, and porewater geochemistry chemistry was characterized at multiple points throughout the 2017 spring-summer-fall season at a sulfate-impacted stream flanked by wetlands in northern Minnesota. Results show that organic-rich sediments largely buffer the geochemical responses to brief or low magnitude changes in hydrologic gradient, but sustained or higher magnitude fluxes may variably alter the redox regime and, ultimately, the environmental geochemistry. This has implications for a changing climate that is expected to dramatically alter the hydrological cycle. Further, increased sulfate loading and dissolved or adsorbed ferric iron complexes in the hyporheic zone may induce a cryptic sulfur cycle linked to iron and carbon cycling, as indicated by the abundance of intermediate valence sulfur compounds (e.g., polysulfide, elemental sulfur, thiosulfate) throughout the anoxic wetland and stream-channel sediment column. The observed deviation from a classical redox tower coupled with potential changes in hydraulic gradient in these organic-rich wetland and stream hyporheic zones has implications for nutrient, trace element, and greenhouse gas fluxes into surface water and groundwater, ultimately influencing water quality and global climate.
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Affiliation(s)
- Joshua M Torgeson
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Carla E Rosenfeld
- Section of Minerals and Earth Sciences, Carnegie Museum of Natural History, USA.
| | - Aubrey J Dunshee
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Kelly Duhn
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.
| | - Riley Schmitter
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Patrick A O'Hara
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
| | - G H Crystal Ng
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
- St. Anthony Falls Laboratory, University of Minnesota, Minneapolis, MN 55455, USA
| | - Cara M Santelli
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.
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Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities. mSystems 2021; 6:e0120520. [PMID: 34402646 PMCID: PMC8407418 DOI: 10.1128/msystems.01205-20] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Candidate Phyla Radiation (CPR) bacteria and nanoarchaea populate most ecosystems but are rarely detected in soil. We concentrated particles of less than 0.2 μm in size from grassland soil, enabling targeted metagenomic analysis of these organisms, which are almost totally unexplored in largely oxic environments such as soil. We recovered a diversity of CPR bacterial and some archaeal sequences but no sequences from other cellular organisms. The sampled sequences include Doudnabacteria (SM2F11) and Pacearchaeota, organisms rarely reported in soil, as well as Saccharibacteria, Parcubacteria, and Microgenomates. CPR and archaea of the phyla Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) were enriched 100- to 1,000-fold compared to that in bulk soil, in which we estimate each of these organisms comprises approximately 1 to 100 cells per gram of soil. Like most CPR and DPANN sequenced to date, we predict these microorganisms live symbiotic anaerobic lifestyles. However, Saccharibacteria, Parcubacteria, and Doudnabacteria genomes sampled here also harbor ubiquinol oxidase operons that may have been acquired from other bacteria, likely during adaptation to aerobic soil environments. We conclude that CPR bacteria and DPANN archaea are part of the rare soil biosphere and harbor unique metabolic platforms that potentially evolved to live symbiotically under relatively oxic conditions. IMPORTANCE Here, we investigated overlooked microbes in soil, Candidate Phyla Radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, by size fractionating small particles from soil, an approach typically used for the recovery of viral metagenomes. Concentration of these small cells (<0.2 μm) allowed us to identify these organisms as part of the rare soil biosphere and to sample genomes that were absent from non-size-fractionated metagenomes. We found that some of these predicted symbionts, which have been largely studied in anaerobic systems, have acquired aerobic capacity via lateral transfer that may enable adaptation to oxic soil environments. We estimate that there are approximately 1 to 100 cells of each of these lineages per gram of soil, highlighting that the approach provides a window into the rare soil biosphere and its associated genetic potential.
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