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Dueholm MKD, Andersen KS, Korntved AKC, Rudkjøbing V, Alves M, Bajón-Fernández Y, Batstone D, Butler C, Cruz MC, Davidsson Å, Erijman L, Holliger C, Koch K, Kreuzinger N, Lee C, Lyberatos G, Mutnuri S, O'Flaherty V, Oleskowicz-Popiel P, Pokorna D, Rajal V, Recktenwald M, Rodríguez J, Saikaly PE, Tooker N, Vierheilig J, De Vrieze J, Wurzbacher C, Nielsen PH. MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters. Nat Commun 2024; 15:5361. [PMID: 38918384 PMCID: PMC11199495 DOI: 10.1038/s41467-024-49641-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84-99% and 18-61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.
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Affiliation(s)
- Morten Kam Dahl Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
| | - Kasper Skytte Andersen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Anne-Kirstine C Korntved
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Vibeke Rudkjøbing
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Madalena Alves
- Centre of Biological Engineering, University of Minho, Minho, Portugal
| | | | - Damien Batstone
- Australian Centre for Water and Environmental Biotechnology (ACWEB), The University of Queensland, Brisbane, Australia
| | - Caitlyn Butler
- Department of Civil and Environmental Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | - Mercedes Cecilia Cruz
- Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Salta, Argentina
| | - Åsa Davidsson
- Department of Chemical Engineering, Lund University, Lund, Sweden
| | - Leonardo Erijman
- INGEBI-CONICET, University of Buenos Aires, Buenos Aires, Argentina
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Konrad Koch
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), Garching, Germany
| | - Norbert Kreuzinger
- Institute of Water Quality and Resource Management, TU Wien, Vienna, Austria
| | - Changsoo Lee
- Department of Civil, Urban, Earth, and Environmental Engineering & Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Gerasimos Lyberatos
- School of Chemical Engineering, National Technical University of Athens, Zografou, Greece
| | - Srikanth Mutnuri
- Applied Environmental Biotechnology Laboratory, Birla Institute of Technology and Science (BITS-Pilani), Pilani, Goa campus, Goa, India
| | - Vincent O'Flaherty
- School of Biological and Chemical Sciences and Ryan Institute, University of Galway, Galway, Ireland
| | - Piotr Oleskowicz-Popiel
- Water Supply and Bioeconomy Division, Faculty of Environmental Engineering and Energy, Poznan University of Technology, Poznan, Poland
| | - Dana Pokorna
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Veronica Rajal
- Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Salta, Argentina
| | | | - Jorge Rodríguez
- Chemical Engineering Department, Khalifa University, Khalifa, UAE
| | - Pascal E Saikaly
- Environmental Science and Engineering Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Nick Tooker
- Department of Civil and Environmental Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | - Julia Vierheilig
- Institute of Water Quality and Resource Management, TU Wien, Vienna, Austria
| | - Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), Garching, Germany
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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Peng L, Jia M, Li S, Wang X, Liang C, Xu Y. Developing antibiotics-based strategies to efficiently enrich ammonia-oxidizing archaea from wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171479. [PMID: 38458444 DOI: 10.1016/j.scitotenv.2024.171479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/02/2024] [Accepted: 03/03/2024] [Indexed: 03/10/2024]
Abstract
The effects of five antibiotics (i.e., ampicillin, streptomycin, carbenicillin, kanamycin and tetracycline) on ammonia-oxidizing archaea (AOA) enrichment from anoxic activated sludge were investigated. The combined use of five antibiotics during 90-day cultivation could selectively inhibit nitrite-oxidizing bacteria (NOB) and ammonia-oxidizing bacteria (AOB) with AOA unaffected, as evidenced by the nitrite accumulation ratio of 100 % and the proportion of AOA in ammonia-oxidizing microbes over 91 %. The alternative use of five antibiotics was the optimal approach to screening for AOA during 348-day cultivation, which inhibited AOB growth at a level equivalent to the combined use of five antibiotics (the AOB-amoA gene decreased by over 99.90 %), further promoted AOA abundance (the much higher AOA-amoA to AOB-amoA gene copy number ratio (1453.30) than that in the groups with the combined use of five antibiotics (192.94)), eliminated bacterial adaptation to antibiotics and reduced antibiotic-resistant bacteria to form Nitrocosmicus-dominant community (42.35 % in abundance).
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Affiliation(s)
- Lai Peng
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan 430070, China; School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan 430070, China
| | - Mengwen Jia
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan 430070, China; School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan 430070, China
| | - Shengjun Li
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan 430070, China; School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan 430070, China.
| | - Xi Wang
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan 430070, China; School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan 430070, China
| | - Chuanzhou Liang
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan 430070, China; School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan 430070, China
| | - Yifeng Xu
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan 430070, China; School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan 430070, China
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3
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Bei Q, Reitz T, Schädler M, Hodgskiss LH, Peng J, Schnabel B, Buscot F, Eisenhauer N, Schleper C, Heintz-Buschart A. Metabolic potential of Nitrososphaera-associated clades. THE ISME JOURNAL 2024; 18:wrae086. [PMID: 38742714 PMCID: PMC11131427 DOI: 10.1093/ismejo/wrae086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/13/2024] [Accepted: 05/11/2024] [Indexed: 05/16/2024]
Abstract
Soil ammonia-oxidizing archaea (AOA) play a crucial role in converting ammonia to nitrite, thereby mobilizing reactive nitrogen species into their soluble form, with a significant impact on nitrogen losses from terrestrial soils. Yet, our knowledge regarding their diversity and functions remains limited. In this study, we reconstructed 97 high-quality AOA metagenome-assembled genomes (MAGs) from 180 soil samples collected in Central Germany during 2014-2019 summers. These MAGs were affiliated with the order Nitrososphaerales and clustered into four family-level clades (NS-α/γ/δ/ε). Among these MAGs, 75 belonged to the most abundant but least understood δ-clade. Within the δ-clade, the amoA genes in three MAGs from neutral soils showed a 99.5% similarity to the fosmid clone 54d9, which has served as representative of the δ-clade for the past two decades since even today no cultivated representatives are available. Seventy-two MAGs constituted a distinct δ sub-clade, and their abundance and expression activity were more than twice that of other MAGs in slightly acidic soils. Unlike the less abundant clades (α, γ, and ε), the δ-MAGs possessed multiple highly expressed intracellular and extracellular carbohydrate-active enzymes responsible for carbohydrate binding (CBM32) and degradation (GH5), along with highly expressed genes involved in ammonia oxidation. Together, these results suggest metabolic versatility of uncultured soil AOA and a potential mixotrophic or chemolithoheterotrophic lifestyle among 54d9-like AOA.
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Affiliation(s)
- Qicheng Bei
- Department of Soil Ecology, Helmholtz Centre for Environmental Research – UFZ, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, United States
| | - Thomas Reitz
- Department of Soil Ecology, Helmholtz Centre for Environmental Research – UFZ, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Martin Schädler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Department of Community Ecology, Helmholtz Centre for Environmental Research – UFZ, 06120 Halle (Saale), Germany
| | - Logan H Hodgskiss
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Vienna, Austria
| | - Jingjing Peng
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Beatrix Schnabel
- Department of Soil Ecology, Helmholtz Centre for Environmental Research – UFZ, 06120 Halle (Saale), Germany
| | - François Buscot
- Department of Soil Ecology, Helmholtz Centre for Environmental Research – UFZ, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, 04103 Leipzig, Germany
| | - Christa Schleper
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Vienna, Austria
| | - Anna Heintz-Buschart
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, the Netherlands
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4
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Kolovou M, Panagiotou D, Süße L, Loiseleur O, Williams S, Karpouzas DG, Papadopoulou ES. Assessing the activity of different plant-derived molecules and potential biological nitrification inhibitors on a range of soil ammonia- and nitrite-oxidizing strains. Appl Environ Microbiol 2023; 89:e0138023. [PMID: 37916825 PMCID: PMC10686072 DOI: 10.1128/aem.01380-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/26/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Synthetic nitrification inhibitors are routinely used with nitrogen fertilizers to reduce nitrogen losses from agroecosystems, despite having drawbacks like poor efficiency, cost, and entry into the food chain. Plant-derived BNIs constitute a more environmentally conducive alternative. Knowledge on the activity of BNIs to soil nitrifiers is largely based on bioassays with a single Nitrosomonas europaea strain which does not constitute a dominant member of the community of ammonia-oxidizing microorganisms (AOM) in soil. We determined the activity of several plant-derived molecules reported as having activity, including the recently discovered maize-isolated BNI, zeanone, and its natural analog, 2-methoxy-1,4-naphthoquinone, on a range of ecologically relevant AOM and one nitrite-oxidizing bacterial culture, expanding our knowledge on the intrinsic inhibition potential of BNIs toward AOM and highlighting the necessity for a deeper understanding of the effect of BNIs on the overall soil microbiome integrity before their further use in agricultural settings.
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Affiliation(s)
- Maria Kolovou
- Department of Environmental Sciences, Laboratory of Environmental Microbiology, University of Thessaly, Larissa, Greece
| | - Dimitra Panagiotou
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
| | - Lars Süße
- Syngenta Crop Protection AG, Basel, Switzerland
| | | | | | - Dimitrios G. Karpouzas
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
| | - Evangelia S. Papadopoulou
- Department of Environmental Sciences, Laboratory of Environmental Microbiology, University of Thessaly, Larissa, Greece
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5
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Zhao J, Huang L, Chakrabarti S, Cooper J, Choi E, Ganan C, Tolchinsky B, Triplett EW, Daroub SH, Martens-Habbena W. Nitrogen and phosphorous acquisition strategies drive coexistence patterns among archaeal lineages in soil. THE ISME JOURNAL 2023; 17:1839-1850. [PMID: 37596409 PMCID: PMC10579303 DOI: 10.1038/s41396-023-01493-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023]
Abstract
Soil represents the largest reservoir of Archaea on Earth. Present-day archaeal diversity in soils globally is dominated by members of the class Nitrososphaeria. The evolutionary radiation of this class is thought to reflect adaptations to a wide range of temperatures, pH, and other environmental conditions. However, the mechanisms that govern competition and coexistence among Nitrososphaeria lineages in soil remain poorly understood. Here we show that predominant soil Nitrososphaeria lineages compose a patchwork of gene inventory and expression profiles for ammonia, urea, and phosphate utilization. In contrast, carbon fixation, respiration, and ATP synthesis genes are conserved and expressed consistently among predominant phylotypes across 12 major evolutionary lineages commonly found in soil. In situ gene expression profiles closely resemble pure culture reference strains under optimal growth conditions. Together, these results reveal resource-based coexistence patterns among Nitrososphaeria lineages and suggest complementary ecophysiological niches associated with differential nutrient acquisition strategies among globally predominant archaeal lineages in soil.
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Affiliation(s)
- Jun Zhao
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Laibin Huang
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Seemanti Chakrabarti
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Jennifer Cooper
- Everglades Research and Education Center, Soil and Water Sciences Department, University of Florida, Belle Glade, FL, 33430, USA
| | - EunKyung Choi
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Carolina Ganan
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Bryn Tolchinsky
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Eric W Triplett
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Samira H Daroub
- Everglades Research and Education Center, Soil and Water Sciences Department, University of Florida, Belle Glade, FL, 33430, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA.
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6
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Wright CL, Lehtovirta-Morley LE. Nitrification and beyond: metabolic versatility of ammonia oxidising archaea. THE ISME JOURNAL 2023; 17:1358-1368. [PMID: 37452095 PMCID: PMC10432482 DOI: 10.1038/s41396-023-01467-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/09/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
Ammonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in the global nitrogen cycle. They carry out oxidation of ammonia to nitrite, and their activity is relevant for both food security and climate change. Since their discovery nearly 20 years ago, major insights have been gained into their nitrogen and carbon metabolism, growth preferences and their mechanisms of adaptation to the environment, as well as their diversity, abundance and activity in the environment. Despite significant strides forward through the cultivation of novel organisms and omics-based approaches, there are still many knowledge gaps on their metabolism and the mechanisms which enable them to adapt to the environment. Ammonia oxidising microorganisms are typically considered metabolically streamlined and highly specialised. Here we review the physiology of ammonia oxidising archaea, with focus on aspects of metabolic versatility and regulation, and discuss these traits in the context of nitrifier ecology.
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Affiliation(s)
- Chloe L Wright
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
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7
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Christel A, Dequiedt S, Chemidlin-Prevost-Bouré N, Mercier F, Tripied J, Comment G, Djemiel C, Bargeot L, Matagne E, Fougeron A, Mina Passi JB, Ranjard L, Maron PA. Urban land uses shape soil microbial abundance and diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 883:163455. [PMID: 37062324 DOI: 10.1016/j.scitotenv.2023.163455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 06/03/2023]
Abstract
Soil microbial biodiversity provides many useful services in cities. However, the ecology of microbial communities in urban soils remains poorly documented, and studies are required to better predict the impact of urban land use. We characterized microbial communities (archea/bacteria and fungi) in urban soils in Dijon (Burgundy, France). Three main land uses were considered - public leisure, traffic, and urban agriculture - sub-categorized in sub-land uses according to urban indexes and management practices. Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA. Variation partitioning analysis was used to rank soil physicochemical characteristics and land uses according to their relative contribution to the variation of soil microbial communities. Urban soils in Dijon harbored high levels of microbial biomass and diversity that varied according to land uses. Microbial biomass was 1.8 times higher in public leisure and traffic sites than in urban agriculture sites. Fungal richness increased by 25 % in urban agriculture soils, and bacterial richness was lower (by 20 %) in public leisure soils. Partitioning models explained 25.7 %, 46.2 % and 75.6 % of the variance of fungal richness, bacterial richness and microbial biomass, respectively. The organic carbon content and the C/N ratio were the best predictors of microbial biomass, whereas soil bacterial diversity was mainly explained by soil texture and land use. Neither metal trace elements nor polycyclic aromatic hydrocarbons contents explained variations of microbial communities, probably due to their very low concentration in the soils. The microbial composition results highlighted that leisure sites represented a stabilized habitat favoring specialized microbial groups and microbial plant symbionts, as opposed to urban agriculture sites that stimulated opportunistic populations able to face the impact of agricultural practices. Altogether, our results provide evidence that there is scope for urban planners to drive soil microbial diversity through sustainable urban land use and associated management practices.
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Affiliation(s)
- Amélie Christel
- AgroParisTech, 75732 Paris, France; Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Samuel Dequiedt
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | | | - Florian Mercier
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Julie Tripied
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Gwendoline Comment
- Platforme GenoSol, INRAE-Université de Bourgogne, CMSE, 21000 Dijon, France
| | - Christophe Djemiel
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | | | - Eric Matagne
- AGARIC-IG, 144 Rue Rambuteau, 71000 Macon, France
| | - Agnès Fougeron
- Jardin de l'Arquebuse Mairie de Dijon, CS 73310, 21033 Dijon Cedex, France
| | | | - Lionel Ranjard
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Pierre-Alain Maron
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France.
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8
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Huang L, Levintal E, Erikson CB, Coyotl A, Horwath WR, Dahlke HE, Mazza Rodrigues JL. Molecular and Dual-Isotopic Profiling of the Microbial Controls on Nitrogen Leaching in Agricultural Soils under Managed Aquifer Recharge. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37467434 PMCID: PMC10399200 DOI: 10.1021/acs.est.3c01356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Nitrate (NO3-) leaching is a serious health and ecological concern in global agroecosystems, particularly those under the application of agricultural-managed aquifer recharge (Ag-MAR); however, there is an absence of information on microbial controls affecting NO3- leaching outcomes. We combine natural dual isotopes of NO3- (15N/14N and 18O/16O) with metagenomics, quantitative polymerase chain reaction (PCR), and a threshold indicator taxa analysis (TITAN) to investigate the activities, taxon profiles, and environmental controls of soil microbiome associated with NO3- leaching at different depths from Californian vineyards under Ag-MAR application. The isotopic signatures demonstrated a significant priming effect (P < 0.01) of Ag-MAR on denitrification activities in the topsoil (0-10 cm), with a 12-25-fold increase of 15N-NO3- and 18O-NO3- after the first 24 h of flooding, followed by a sharp decrease in the enrichment of both isotopes with ∼80% decline in denitrification activities thereafter. In contrast, deeper soils (60-100 cm) showed minimal or no denitrification activities over the course of Ag-MAR application, thus resulting in 10-20-fold of residual NO3- being leached. Metagenomic profiling and laboratory microcosm demonstrated that both nitrifying and denitrifying groups, responsible for controlling NO3- leaching, decreased in abundance and potential activity rates with soil depth. TITAN suggested that Nitrosocosmicus and Bradyrhizobium, as the major nitrifier and denitrifier, had the highest and lowest tipping points with regard to the NO3- changes (P < 0.05), respectively. Overall, our study provides new insight into specific depth limitations of microbial controls on soil NO3- leaching in agroecosystems.
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Affiliation(s)
- Laibin Huang
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
| | - Elad Levintal
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
| | - Christian Bernard Erikson
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
| | - Adolfo Coyotl
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
| | - William R Horwath
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
| | - Helen E Dahlke
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
| | - Jorge L Mazza Rodrigues
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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9
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Ecological Aerobic Ammonia and Methane Oxidation Involved Key Metal Compounds, Fe and Cu. Life (Basel) 2022; 12:life12111806. [PMID: 36362966 PMCID: PMC9693385 DOI: 10.3390/life12111806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Interactions between metals and microbes are critical in geomicrobiology and vital in microbial ecophysiological processes. Methane-oxidizing bacteria (MOB) and ammonia-oxidizing microorganisms (AOM) are key members in aerobic environments to start the C and N cycles. Ammonia and methane are firstly oxidized by copper-binding metalloproteins, monooxygenases, and diverse iron and copper-containing enzymes that contribute to electron transportation in the energy gain pathway, which is evolutionally connected between MOB and AOM. In this review, we summarized recently updated insight into the diverse physiological pathway of aerobic ammonia and methane oxidation of different MOB and AOM groups and compared the metabolic diversity mediated by different metalloenzymes. The elevation of iron and copper concentrations in ecosystems would be critical in the activity and growth of MOB and AOM, the outcome of which can eventually influence the global C and N cycles. Therefore, we also described the impact of various concentrations of metal compounds on the physiology of MOB and AOM. This review study could give a fundamental strategy to control MOB and AOM in diverse ecosystems because they are significantly related to climate change, eutrophication, and the remediation of contaminated sites for detoxifying pollutants.
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10
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Wang P, Li M, Dong L, Zhang C, Xie W. Comparative Genomics of Thaumarchaeota From Deep-Sea Sponges Reveal Their Niche Adaptation. Front Microbiol 2022; 13:869834. [PMID: 35859738 PMCID: PMC9289680 DOI: 10.3389/fmicb.2022.869834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
Thaumarchaeota account for a large portion of microbial symbionts in deep-sea sponges and are even dominant in some cases. In this study, we investigated three new sponge-associated Thaumarchaeota from the deep West Pacific Ocean. Thaumarchaeota were found to be the most dominant phylum in this sponge by both prokaryotic 16S rRNA amplicons and metagenomic sequencing. Fifty-seven published Thaumarchaeota genomes from sponges and other habitats were included for genomic comparison. Similar to shallow sponge-associated Thaumarchaeota, those Thaumarchaeota in deep-sea sponges have extended genome sizes and lower coding density compared with their free-living lineages. Thaumarchaeota in deep-sea sponges were specifically enriched in genes related to stress adapting, symbiotic adhesion and stability, host–microbe interaction and protein transportation. The genes involved in defense mechanisms, such as the restriction-modification system, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system, and toxin-antitoxin system were commonly enriched in both shallow and deep sponge-associated Thaumarchaeota. Our study demonstrates the significant effects of both depth and symbiosis on forming genomic characteristics of Thaumarchaeota, and provides novel insights into their niche adaptation in deep-sea sponges.
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Affiliation(s)
- Peng Wang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Minchun Li
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Liang Dong
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Cheng Zhang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- *Correspondence: Wei Xie,
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11
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Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom. Nat Commun 2022; 13:3358. [PMID: 35688919 PMCID: PMC9187648 DOI: 10.1038/s41467-022-31038-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 05/30/2022] [Indexed: 12/31/2022] Open
Abstract
Archaea are common constituents of the gut microbiome of humans, ruminants, and termites but little is known about their diversity and abundance in other animals. Here, we analyse sequencing and quantification data of archaeal and bacterial 16S rRNA genes from 250 species of animals covering a large taxonomic spectrum. We detect the presence of archaea in 175 animal species belonging to invertebrates, fish, amphibians, birds, reptiles and mammals. We identify five dominant gut lineages, corresponding to Methanobrevibacter, Methanosphaera, Methanocorpusculum, Methanimicrococcus and "Ca. Methanomethylophilaceae". Some archaeal clades, notably within Methanobrevibacter, are associated to certain hosts, suggesting specific adaptations. The non-methanogenic lineage Nitrososphaeraceae (Thaumarchaeota) is frequently present in animal samples, although at low abundance, but may have also adapted to the gut environment. Host phylogeny, diet type, fibre content, and intestinal tract physiology are major drivers of the diversity and abundance of the archaeome in mammals. The overall abundance of archaea is more influenced by these factors than that of bacteria. Methanogens reducing methyl-compounds with H2 can represent an important fraction of the overall methanogens in many animals. Together with CO2-reducing methanogens, they are influenced by diet and composition of gut bacteria. Our results provide key elements toward our understanding of the ecology of archaea in the gut, an emerging and important field of investigation.
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12
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Hwang Y, Schulze-Makuch D, Arens FL, Saenz JS, Adam PS, Sager C, Bornemann TLV, Zhao W, Zhang Y, Airo A, Schloter M, Probst AJ. Leave no stone unturned: individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core. MICROBIOME 2021; 9:234. [PMID: 34836555 PMCID: PMC8627038 DOI: 10.1186/s40168-021-01177-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The hyperarid core of the Atacama Desert is an extremely harsh environment thought to be colonized by only a few heterotrophic bacterial species. Current concepts for understanding this extreme ecosystem are mainly based on the diversity of these few species, yet a substantial area of the Atacama Desert hyperarid topsoil is covered by expansive boulder accumulations, whose underlying microbiomes have not been investigated so far. With the hypothesis that these sheltered soils harbor uniquely adapted microbiomes, we compared metagenomes and geochemistry between soils below and beside boulders across three distantly located boulder accumulations in the Atacama Desert hyperarid core. RESULTS Genome-resolved metagenomics of eleven samples revealed substantially different microbial communities in soils below and beside boulders, despite the presence of shared species. Archaea were found in significantly higher relative abundance below the boulders across all samples within distances of up to 205 km. These key taxa belong to a novel genus of ammonia-oxidizing Thaumarchaeota, Candidatus Nitrosodeserticola. We resolved eight mid-to-high quality genomes of this genus and used comparative genomics to analyze its pangenome and site-specific adaptations. Ca. Nitrosodeserticola genomes contain genes for ammonia oxidation, the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway, and acetate utilization indicating a chemolithoautotrophic and mixotrophic lifestyle. They also possess the capacity for tolerating extreme environmental conditions as highlighted by the presence of genes against oxidative stress and DNA damage. Site-specific adaptations of the genomes included the presence of additional genes for heavy metal transporters, multiple types of ATP synthases, and divergent genes for aquaporins. CONCLUSION We provide the first genomic characterization of hyperarid soil microbiomes below the boulders in the Atacama Desert, and report abundant and highly adapted Thaumarchaeaota with ammonia oxidation and carbon fixation potential. Ca. Nitrosodeserticola genomes provide the first metabolic and physiological insight into a thaumarchaeal lineage found in globally distributed terrestrial habitats characterized by various environmental stresses. We consequently expand not only the known genetic repertoire of Thaumarchaeota but also the diversity and microbiome functioning in hyperarid ecosystems. Video Abstract.
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Affiliation(s)
- Yunha Hwang
- Astrobiology Group, Center for Astronomy & Astrophysics, Technische Universität Berlin, 10623, Berlin, Germany
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141, Essen, Germany
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Dirk Schulze-Makuch
- Astrobiology Group, Center for Astronomy & Astrophysics, Technische Universität Berlin, 10623, Berlin, Germany.
- Section Geomicrobiology, German Research Centre for Geosciences (GFZ), 14473, Potsdam, Germany.
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587, Stechlin, Germany.
- School of the Environment, Washington State University, Pullman, WA, 99164, USA.
| | - Felix L Arens
- Astrobiology Group, Center for Astronomy & Astrophysics, Technische Universität Berlin, 10623, Berlin, Germany
| | - Johan S Saenz
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, 85758, Oberschleißheim, Germany
| | - Panagiotis S Adam
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141, Essen, Germany
| | - Christof Sager
- Astrobiology Group, Center for Astronomy & Astrophysics, Technische Universität Berlin, 10623, Berlin, Germany
| | - Till L V Bornemann
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141, Essen, Germany
| | - Weishu Zhao
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI, USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI, USA
| | - Alessandro Airo
- Astrobiology Group, Center for Astronomy & Astrophysics, Technische Universität Berlin, 10623, Berlin, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, 85758, Oberschleißheim, Germany
| | - Alexander J Probst
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141, Essen, Germany.
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, 45141 , Essen, Germany.
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13
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Wang H, Bagnoud A, Ponce-Toledo RI, Kerou M, Weil M, Schleper C, Urich T. Linking 16S rRNA Gene Classification to amoA Gene Taxonomy Reveals Environmental Distribution of Ammonia-Oxidizing Archaeal Clades in Peatland Soils. mSystems 2021; 6:e0054621. [PMID: 34463572 DOI: 10.1128/msystems.00546-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 08/12/2021] [Indexed: 01/04/2023] Open
Abstract
A highly resolved taxonomy for ammonia-oxidizing archaea (AOA) based on the alpha subunit of ammonia monooxygenase (amoA) was recently established, which uncovered novel environmental patterns of AOA, challenging previous generalizations. However, many microbiome studies target the 16S rRNA gene as a marker; thus, the usage of this novel taxonomy is currently limited. Here, we exploited the phylogenetic congruence of archaeal amoA and 16S rRNA genes to link 16S rRNA gene classification to the novel amoA taxonomy. We screened publicly available archaeal genomes and contigs for the co-occurring amoA and 16S rRNA genes and constructed a 16S rRNA gene database with the corresponding amoA clade taxonomy. Phylogenetic trees of both marker genes confirmed congruence, enabling the identification of clades. We validated this approach with 16S rRNA gene amplicon data from peatland soils. We succeeded in linking 16S rRNA gene amplicon sequence variants belonging to the class Nitrososphaeria to seven different AOA (amoA) clades, including two of the most frequently detected clades (Nitrososphaerales γ and δ clades) for which no pure culture is currently available. Water status significantly impacted the distribution of the AOA clades as well as the whole AOA community structure, which was correlated with pH, nitrate, and ammonium, consistent with previous clade predictions. Our study emphasizes the need to distinguish among AOA clades with distinct ecophysiologies and environmental preferences, for a better understanding of the ecology of the globally abundant AOA. IMPORTANCE The recently established phylogeny of amoA provides a finer resolution than previous studies, allowing clustering of AOA beyond the order level and thus revealing novel clades. While the 16S rRNA gene is mostly appreciated in microbiome studies, this novel phylogeny is in limited use. Here, we provide an alternative path to identifying AOA with this novel and highly resolved amoA taxonomy by using 16S rRNA gene sequencing data. We constructed a 16S rRNA gene database with the associated amoA clade taxonomy based on their phylogenetic congruence. With this database, we were able to assign 16S rRNA gene amplicons from peatland soils to different AOA clades, with a level of resolution provided previously only by amoA phylogeny. As 16S rRNA gene amplicon sequencing is still widely employed in microbiome studies, our database may have a broad application for interpreting the ecology of globally abundant AOA.
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Affiliation(s)
- Haitao Wang
- Institute of Microbiology, University of Greifswaldgrid.5603.0, Greifswald, Germany
| | - Alexandre Bagnoud
- Department of Functional and Evolutionary Ecology, University of Viennagrid.10420.37, Vienna, Austria
| | - Rafael I Ponce-Toledo
- Department of Functional and Evolutionary Ecology, University of Viennagrid.10420.37, Vienna, Austria
| | - Melina Kerou
- Department of Functional and Evolutionary Ecology, University of Viennagrid.10420.37, Vienna, Austria
| | - Micha Weil
- Institute of Microbiology, University of Greifswaldgrid.5603.0, Greifswald, Germany
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, University of Viennagrid.10420.37, Vienna, Austria
| | - Tim Urich
- Institute of Microbiology, University of Greifswaldgrid.5603.0, Greifswald, Germany
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14
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Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities. ISME JOURNAL 2021; 16:272-283. [PMID: 34316016 PMCID: PMC8692354 DOI: 10.1038/s41396-021-01064-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/01/2021] [Accepted: 07/07/2021] [Indexed: 02/04/2023]
Abstract
Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major cultivated phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest affinity for both ammonia and total ammonium of any characterized AOA, and these values are similar to previously determined ammonia and total ammonium affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values supports the hypothesis that—like for AOB—ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.
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15
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Rodriguez J, Chakrabarti S, Choi E, Shehadeh N, Sierra-Martinez S, Zhao J, Martens-Habbena W. Nutrient-Limited Enrichments of Nitrifiers From Soil Yield Consortia of Nitrosocosmicus-Affiliated AOA and Nitrospira-Affiliated NOB. Front Microbiol 2021; 12:671480. [PMID: 34322099 PMCID: PMC8312096 DOI: 10.3389/fmicb.2021.671480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/22/2021] [Indexed: 11/21/2022] Open
Abstract
The discovery of ammonia-oxidizing archaea (AOA) and complete ammonia-oxidizing (comammox) bacteria widespread in terrestrial ecosystems indicates an important role of these organisms in terrestrial nitrification. Recent evidence indicated a higher ammonia affinity of comammox bacteria than of terrestrial AOA and ammonia-oxidizing bacteria (AOB), suggesting that comammox bacteria could potentially represent the most low-nutrient adapted nitrifiers in terrestrial systems. We hypothesized that a nutrient-limited enrichment strategy could exploit the differences in cellular kinetic properties and yield enrichments dominated by high affinity and high yield comammox bacteria. Using soil with a mixed community of AOA, AOB, and comammox Nitrospira, we compared performance of nutrient-limited chemostat enrichment with or without batch culture pre-enrichment in two different growth media without inhibitors or antibiotics. Monitoring of microbial community composition via 16S rRNA and amoA gene sequencing showed that batch enrichments were dominated by AOB, accompanied by low numbers of AOA and comammox Nitrospira. In contrast, nutrient-limited enrichment directly from soil, and nutrient-limited sub-cultivation of batch enrichments consistently yielded high enrichments of Nitrosocosmicus-affiliated AOA associated with multiple canonical nitrite-oxidizing Nitrospira strains, whereas AOB numbers dropped below 0.1% and comammox Nitrospira were lost completely. Our results reveal competitiveness of Nitrosocosmicus sp. under nutrient limitation, and a likely more complex or demanding ecological niche of soil comammox Nitrospira than simulated in our nutrient-limited chemostat experiments.
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Affiliation(s)
| | | | | | | | | | | | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, United States
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16
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Effects of Different Land Use Types on Active Autotrophic Ammonia and Nitrite Oxidizers in Cinnamon Soils. Appl Environ Microbiol 2021; 87:e0009221. [PMID: 33837020 DOI: 10.1128/aem.00092-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Land use types with different disturbance gradients show many variations in soil properties, but the effects of different land use types on soil nitrifying communities and their ecological implications remain poorly understood. Using 13CO2-DNA-based stable isotope probing (DNA-SIP), we examined the relative importance and active community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in soils under three land use types, forest, cropland, and greenhouse vegetable soil, representing three interference gradients. Soil net nitrification rate was in the order forest soil > cropland soil > greenhouse vegetable soil. DNA-SIP showed that active AOA outcompeted AOB in the forest soil, whereas AOB outperformed AOA in the cropland and greenhouse vegetable soils. Cropland soil was richer in NOB than in AOA and AOB. Phylogenetic analysis revealed that ammonia oxidation in the forest soil was predominantly catalyzed by the AOA Nitrosocosmicus franklandus cluster within the group 1.1b lineage. The 13C-labeled AOB were overwhelmingly dominated by Nitrosospira cluster 3 in the cropland soil. The active AOB Nitrosococcus watsonii lineage was observed in the greenhouse vegetable soil, and it played an important role in nitrification. Active NOB communities were closely affiliated with Nitrospira in the forest and cropland soils, and with Nitrolancea and Nitrococcus in the greenhouse vegetable soil. Canonical correlation analysis showed that soil pH and organic matter content significantly affected the active nitrifier community composition. These results suggest that land use types with different disturbance gradients alter the distribution of active nitrifier communities by affecting soil physicochemical properties. IMPORTANCE Nitrification plays an important role in the soil N cycle, and land use management has a profound effect on soil nitrifiers. It is unclear how different gradients of land use affect active ammonia-oxidizing archaea and bacteria and nitrite-oxidizing bacteria. Our research is significant because we determined the response of nitrifiers to human disturbance, which will greatly improve our understanding of the niche of nitrifiers and the differences in their physiology.
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17
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Yang Y, Herbold CW, Jung MY, Qin W, Cai M, Du H, Lin JG, Li X, Li M, Gu JD. Survival strategies of ammonia-oxidizing archaea (AOA) in a full-scale WWTP treating mixed landfill leachate containing copper ions and operating at low-intensity of aeration. WATER RESEARCH 2021; 191:116798. [PMID: 33444853 DOI: 10.1016/j.watres.2020.116798] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 05/04/2023]
Abstract
Recent studies indicate that ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal by wastewater treatment plants (WWTPs). However, our knowledge of the mechanisms employed by AOA for growth and survival in full-scale WWTPs is still limited. Here, metagenomic and metatranscriptomic analyses combined with a laboratory cultivation experiment revealed that three active AOAs (WS9, WS192, and WS208) belonging to family Nitrososphaeraceae were active in the deep oxidation ditch (DOD) of a full-scale WWTP treating landfill leachate, which is configured with three continuous aerobic-anoxic (OA) modules with low-intensity aeration (≤ 1.5 mg/L). AOA coexisted with AOB and complete ammonia oxidizers (Comammox), while the ammonia-oxidizing microbial (AOM) community was unexpectedly dominated by the novel AOA strain WS9. The low aeration, long retention time, and relatively high inputs of ammonium and copper might be responsible for the survival of AOA over AOB and Comammox, while the dominance of WS9, specifically may be enhanced by substrate preference and uniquely encoded retention strategies. The urease-negative WS9 is specifically adapted for ammonia acquisition as evidenced by the high expression of an ammonium transporter, whereas two metabolically versatile urease-positive AOA strains (WS192 and WS208) can likely supplement ammonia needs with urea. This study provides important information for the survival and application of the eutrophic Nitrososphaeraceae AOA and advances our understanding of archaea-dominated ammonia oxidation in a full-scale wastewater treatment system.
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Affiliation(s)
- Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - Craig W Herbold
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Althanstrasse 14, 1090 Vienna, Austria
| | - Man-Young Jung
- Division of Biology Education, Department of Science Education, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, South Korea; Interdisciplinary Graduate Programme in Advance Convergence Technology and Science, Faculty of Science Education, Jeju National University, Jeju 6324, South Korea
| | - Wei Qin
- School of Oceanography, University of Washington, Seattle, Washington, United States; Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Mingwei Cai
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Huan Du
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Xiaoyan Li
- Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China.
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, China; Southern Laboratory of Ocean Science and Engineering, Zhuhai, Guangdong, China.
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18
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Ammonia-oxidizing archaea in biological interactions. J Microbiol 2021; 59:298-310. [DOI: 10.1007/s12275-021-1005-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 10/22/2022]
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19
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Rhizosphere Microbiome Cooperations: Strategies for Sustainable Crop Production. Curr Microbiol 2021; 78:1069-1085. [PMID: 33611628 DOI: 10.1007/s00284-021-02375-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 02/05/2021] [Indexed: 01/29/2023]
Abstract
Interactions between microorganisms and host plants determine the growth and development as well as the health of the host plant. Various microbial groups inhabit the rhizosphere, each with its peculiar function. The survival of each microbial group depends to a large extent on its ability to colonize the plant root and outcompete the native organisms. The role of the rhizospheric microbiome in enhancing plant growth has not been fully maximized. An understanding of the complexities of microbial interactions and factors affecting their assembly in the community is necessary to benefit maximally from the cooperations of various microbial communities for sustainable crop production. In this review, we outline the various organisms associated with the plant rhizosphere with emphasis on their interactions and mechanisms used in plant growth promotion.
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20
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Su Q, Schittich AR, Jensen MM, Ng H, Smets BF. Role of Ammonia Oxidation in Organic Micropollutant Transformation during Wastewater Treatment: Insights from Molecular, Cellular, and Community Level Observations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:2173-2188. [PMID: 33543927 DOI: 10.1021/acs.est.0c06466] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Organic micropollutants (OMPs) are a threat to aquatic environments, and wastewater treatment plants may act as a source or a barrier of OMPs entering the environment. Understanding the fate of OMPs in wastewater treatment processes is needed to establish efficient OMP removal strategies. Enhanced OMP biotransformation has been documented during biological nitrogen removal and has been attributed to the cometabolic activity of ammonia-oxidizing bacteria (AOB) and, specifically, to the ammonia monooxygenase (AMO) enzyme. Yet, the exact mechanisms of OMP biotransformation are often unknown. This critical review aims to fundamentally and quantitatively evaluate the role of ammonia oxidation in OMP biotransformation during wastewater treatment processes. OMPs can be transformed by AOB via direct and indirect enzymatic reactions: AMO directly transforms OMPs primarily via hydroxylation, while biologically produced reactive nitrogen species (hydroxylamine (NH2OH), nitrite (NO2-), and nitric oxide (NO)) can chemically transform OMPs through nitration, hydroxylation, and deamination and can contribute significantly to the observed OMP transformations. OMPs containing alkyl, aliphatic hydroxyl, ether, and sulfide functional groups as well as substituted aromatic rings and aromatic primary amines can be biotransformed by AMO, while OMPs containing alkyl groups, phenols, secondary amines, and aromatic primary amines can undergo abiotic transformations mediated by reactive nitrogen species. Higher OMP biotransformation efficiencies and rates are obtained in AOB-dominant microbial communities, especially in autotrophic reactors performing nitrification or nitritation, than in non-AOB-dominant microbial communities. The biotransformations of OMPs in wastewater treatment systems can often be linked to ammonium (NH4+) removal following two central lines of evidence: (i) Similar transformation products (i.e., hydroxylated, nitrated, and desaminated TPs) are detected in wastewater treatment systems as in AOB pure cultures. (ii) Consistency in OMP biotransformation (rbio, μmol/g VSS/d) to NH4+ removal (rNH4+, mol/g VSS/d) rate ratios (rbio/rNH4+) is observed for individual OMPs across different systems with similar rNH4+ and AOB abundances. In this review, we conclude that AOB are the main drivers of OMP biotransformation during wastewater treatment processes. The importance of biologically driven abiotic OMP transformation is quantitatively assessed, and functional groups susceptible to transformations by AMO and reactive nitrogen species are systematically classified. This critical review will improve the prediction of OMP transformation and facilitate the design of efficient OMP removal strategies during wastewater treatment.
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Affiliation(s)
- Qingxian Su
- National University of Singapore Environmental Research Institute, 5A Engineering Drive 1, 117411 Singapore, Singapore
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
| | - Anna-Ricarda Schittich
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
| | - Marlene Mark Jensen
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
| | - Howyong Ng
- National University of Singapore Environmental Research Institute, 5A Engineering Drive 1, 117411 Singapore, Singapore
- Centre for Water Research, Department of Civil & Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, 117576 Singapore, Singapore
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
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21
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Production and Excretion of Polyamines To Tolerate High Ammonia, a Case Study on Soil Ammonia-Oxidizing Archaeon " Candidatus Nitrosocosmicus agrestis". mSystems 2021; 6:6/1/e01003-20. [PMID: 33594004 PMCID: PMC8573960 DOI: 10.1128/msystems.01003-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ammonia tolerance is a universal characteristic among the ammonia-oxidizing bacteria (AOB); in contrast, the known species of ammonia-oxidizing archaea (AOA) have been regarded as ammonia sensitive, until the identification of the genus “Candidatus Nitrosocosmicus.” However, the mechanism of its ammonia tolerance has not been reported. In this study, the AOA species “Candidatus Nitrosocosmicus agrestis,” obtained from agricultural soil, was determined to be able to tolerate high concentrations of NH3 (>1,500 μM). In the genome of this strain, which was recovered from metagenomic data, a full set of genes for the pathways of polysaccharide metabolism, urea hydrolysis, arginine synthesis, and polyamine synthesis was identified. Among them, the genes encoding cytoplasmic carbonic anhydrase (CA) and a potential polyamine transporter (drug/metabolite exporter [DME]) were found to be unique to the genus “Ca. Nitrosocosmicus.” When “Ca. Nitrosocosmicus agrestis” was grown with high levels of ammonia, the genes that participate in CO2/HCO3− conversion, glutamate/glutamine syntheses, arginine synthesis, polyamine synthesis, and polyamine excretion were significantly upregulated, and the polyamines, including putrescine and spermidine, had significant levels of production. Based on genome analysis, gene expression quantification, and polyamine determination, we propose that the production and excretion of polyamines is probably one of the reasons for the ammonia tolerance of “Ca. Nitrosocosmicus agrestis,” and even of the genus “Ca. Nitrosocosmicus.” IMPORTANCE Ammonia tolerance of AOA is usually much lower than that of the AOB, which makes the AOB rather than AOA a predominant ammonia oxidizer in agricultural soils, contributing to global N2O emission. Recently, some AOA species from the genus “Ca. Nitrosocosmicus” were also found to have high ammonia tolerance. However, the reported mechanism for the ammonia tolerance is very rare and indeterminate for AOB and for AOA species. In this study, an ammonia-tolerant AOA strain of the species “Ca. Nitrosocosmicus agrestis” was identified and its potential mechanisms for ammonia tolerance were explored. This study will be of benefit for determining more of the ecological role of AOA in agricultural soils or other environments.
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22
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Séneca J, Pjevac P, Canarini A, Herbold CW, Zioutis C, Dietrich M, Simon E, Prommer J, Bahn M, Pötsch EM, Wagner M, Wanek W, Richter A. Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and CO 2, but strongly affected by drought. THE ISME JOURNAL 2020; 14:3038-3053. [PMID: 32770119 PMCID: PMC7784676 DOI: 10.1038/s41396-020-00735-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/21/2020] [Accepted: 07/30/2020] [Indexed: 11/23/2022]
Abstract
Nitrification is a fundamental process in terrestrial nitrogen cycling. However, detailed information on how climate change affects the structure of nitrifier communities is lacking, specifically from experiments in which multiple climate change factors are manipulated simultaneously. Consequently, our ability to predict how soil nitrogen (N) cycling will change in a future climate is limited. We conducted a field experiment in a managed grassland and simultaneously tested the effects of elevated atmospheric CO2, temperature, and drought on the abundance of active ammonia-oxidizing bacteria (AOB) and archaea (AOA), comammox (CMX) Nitrospira, and nitrite-oxidizing bacteria (NOB), and on gross mineralization and nitrification rates. We found that N transformation processes, as well as gene and transcript abundances, and nitrifier community composition were remarkably resistant to individual and interactive effects of elevated CO2 and temperature. During drought however, process rates were increased or at least maintained. At the same time, the abundance of active AOB increased probably due to higher NH4+ availability. Both, AOA and comammox Nitrospira decreased in response to drought and the active community composition of AOA and NOB was also significantly affected. In summary, our findings suggest that warming and elevated CO2 have only minor effects on nitrifier communities and soil biogeochemical variables in managed grasslands, whereas drought favors AOB and increases nitrification rates. This highlights the overriding importance of drought as a global change driver impacting on soil microbial community structure and its consequences for N cycling.
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Affiliation(s)
- Joana Séneca
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Alberto Canarini
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Christos Zioutis
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Marlies Dietrich
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Eva Simon
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Judith Prommer
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Michael Bahn
- Department of Ecology, University of Innsbruck, 6020, Innsbruck, Austria
| | - Erich M Pötsch
- Agricultural Research and Education Centre Raumberg-Gumpenstein, Altirdning 11, 8952, Irdning, Austria
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Wolfgang Wanek
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
- International Institute for Applied Systems Analysis, Laxenburg, Austria.
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23
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Papadopoulou ES, Bachtsevani E, Lampronikou E, Adamou E, Katsaouni A, Vasileiadis S, Thion C, Menkissoglu-Spiroudi U, Nicol GW, Karpouzas DG. Comparison of Novel and Established Nitrification Inhibitors Relevant to Agriculture on Soil Ammonia- and Nitrite-Oxidizing Isolates. Front Microbiol 2020; 11:581283. [PMID: 33250872 PMCID: PMC7672009 DOI: 10.3389/fmicb.2020.581283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/16/2020] [Indexed: 01/04/2023] Open
Abstract
Nitrification inhibitors (NIs) applied to soil reduce nitrogen fertilizer losses from agro-ecosystems. NIs that are currently registered for use in agriculture appear to selectively inhibit ammonia-oxidizing bacteria (AOB), while their impact on other nitrifiers is limited or unknown. Ethoxyquin (EQ), a fruit preservative shown to inhibit ammonia-oxidizers (AO) in soil, is rapidly transformed to 2,6-dihydro-2,2,4-trimethyl-6-quinone imine (QI), and 2,4-dimethyl-6-ethoxy-quinoline (EQNL). We compared the inhibitory potential of EQ and its derivatives with that of dicyandiamide (DCD), nitrapyrin (NP), and 3,4-dimethylpyrazole-phosphate (DMPP), NIs that have been used in agricultural settings. The effect of each compound on the growth of AOB (Nitrosomonas europaea, Nitrosospira multiformis), ammonia-oxidizing archaea (AOA; "Candidatus Nitrosocosmicus franklandus," "Candidatus Nitrosotalea sinensis"), and a nitrite-oxidizing bacterium (NOB; Nitrobacter sp. NHB1), all being soil isolates, were determined in liquid culture over a range of concentrations by measuring nitrite production or consumption and qPCR of amoA and nxrB genes, respectively. The degradation of NIs in the liquid cultures was also determined. In all cultures, EQ was transformed to the short-lived QI (major derivative) and the persistent EQNL (minor derivative). They all showed significantly higher inhibition activity of AOA compared to AOB and NOB isolates. QI was the most potent AOA inhibitor (EC50 = 0.3-0.7 μM) compared to EQ (EC50 = 1-1.4 μM) and EQNL (EC50 = 26.6-129.5 μM). The formation and concentration of QI in EQ-amended cultures correlated with the inhibition patterns for all isolates suggesting that it was primarily responsible for inhibition after application of EQ. DCD and DMPP showed greater inhibition of AOB compared to AOA or NOB, with DMPP being more potent (EC50 = 221.9-248.7 μM vs EC50 = 0.6-2.1 μM). NP was the only NI to which both AOA and AOB were equally sensitive with EC50s of 0.8-2.1 and 1.0-6.7 μM, respectively. Overall, EQ, QI, and NP were the most potent NIs against AOA, NP, and DMPP were the most effective against AOB, while NP, EQ and its derivatives showed the highest activity against the NOB isolate. Our findings benchmark the activity range of known and novel NIs with practical implications for their use in agriculture and the development of NIs with broad or complementary activity against all AO.
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Affiliation(s)
- Evangelia S. Papadopoulou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Eleftheria Bachtsevani
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Eleni Lampronikou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Eleni Adamou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Afroditi Katsaouni
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Sotirios Vasileiadis
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Cécile Thion
- Laboratoire Ampère, École Centrale de Lyon, University of Lyon, Ecully, France
| | - Urania Menkissoglu-Spiroudi
- Pesticide Science Laboratory, School of Agriculture, Forestry and Environment, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Graeme W. Nicol
- Laboratoire Ampère, École Centrale de Lyon, University of Lyon, Ecully, France
| | - Dimitrios G. Karpouzas
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
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24
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Cardarelli EL, Bargar JR, Francis CA. Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States. MICROBIAL ECOLOGY 2020; 80:778-792. [PMID: 32535638 DOI: 10.1007/s00248-020-01534-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (< 30 cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤ 10 m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.
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Affiliation(s)
- Emily L Cardarelli
- Department of Earth System Science, Stanford University, Stanford, CA, 94305-4216, USA
| | - John R Bargar
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Christopher A Francis
- Department of Earth System Science, Stanford University, Stanford, CA, 94305-4216, USA.
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25
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Ancestral Reconstructions Decipher Major Adaptations of Ammonia-Oxidizing Archaea upon Radiation into Moderate Terrestrial and Marine Environments. mBio 2020; 11:mBio.02371-20. [PMID: 33051370 PMCID: PMC7554672 DOI: 10.1128/mbio.02371-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Unlike all other archaeal lineages, ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread and abundant in all moderate and oxic environments on Earth. The evolutionary adaptations that led to such unprecedented ecological success of a microbial clade characterized by highly conserved energy and carbon metabolisms have, however, remained underexplored. Here, we reconstructed the genomic content and growth temperature of the ancestor of all AOA, as well as the ancestors of the marine and soil lineages, based on 39 available complete or nearly complete genomes of AOA. Our evolutionary scenario depicts an extremely thermophilic, autotrophic, aerobic ancestor from which three independent lineages of a marine and two terrestrial groups radiated into moderate environments. Their emergence was paralleled by (i) a continuous acquisition of an extensive collection of stress tolerance genes mostly involved in redox maintenance and oxygen detoxification, (ii) an expansion of regulatory capacities in transcription and central metabolic functions, and (iii) an extended repertoire of cell appendages and modifications related to adherence and interactions with the environment. Our analysis provides insights into the evolutionary transitions and key processes that enabled the conquest of the diverse environments in which contemporary AOA are found.
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26
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Jung J, Kim JS, Taffner J, Berg G, Ryu CM. Archaea, tiny helpers of land plants. Comput Struct Biotechnol J 2020; 18:2494-2500. [PMID: 33005311 PMCID: PMC7516179 DOI: 10.1016/j.csbj.2020.09.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/01/2020] [Accepted: 09/05/2020] [Indexed: 01/02/2023] Open
Abstract
Archaea are members of most microbiomes. While archaea are highly abundant in extreme environments, they are less abundant and diverse in association with eukaryotic hosts. Nevertheless, archaea are a substantial constituent of plant-associated ecosystems in the aboveground and belowground phytobiome. Only a few studies have investigated the role of archaea in plant health and its potential symbiosis in ecosystems. This review discusses recent progress in identifying how archaea contribute to plant traits such as growth, adaptation to abiotic stresses, and immune activation. We synthesized the most recent functional and molecular data on archaea, including root colonization and the volatile emission to activate plant systemic immunity. These data represent a paradigm shift in our understanding of plant-microbiota interactions.
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Affiliation(s)
- Jihye Jung
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon 34141, South Korea
- Department of Biological Sciences, KAIST, Daejeon 34141, South Korea
| | - Jun-Seob Kim
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon 34141, South Korea
| | - Julian Taffner
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Choong-Min Ryu
- Molecular Phytobacteriology Laboratory, KRIBB, Daejeon 34141, South Korea
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27
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Genomic Characteristics of a Novel Species of Ammonia-Oxidizing Archaea from the Jiulong River Estuary. Appl Environ Microbiol 2020; 86:AEM.00736-20. [PMID: 32631866 DOI: 10.1128/aem.00736-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/30/2020] [Indexed: 11/20/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are ubiquitous in diverse ecosystems and play a pivotal role in global nitrogen and carbon cycling. Although AOA diversity and distribution are widely studied, mainly based on the amoA (alpha subunit of ammonia monooxygenase) genotypes, only limited investigations have addressed the relationship between AOA genetic adaptation, metabolic features, and ecological niches, especially in estuaries. Here, we describe the AOA communities along the Jiulong River estuary in southern China. Nine high-quality AOA metagenome-assembled genomes (MAGs) were obtained by metagenomics. Five of the MAGs are proposed to constitute a new species, "Candidatus Nitrosopumilus aestuariumsis" sp. nov., based on the phylogenies of the 16S and 23S rRNA genes and concatenated ribosomal proteins, as well as the average amino acid identity. Comparative genomic analysis revealed unique features of the new species, including a high number of genes related to diverse carbohydrate-active enzymes, phosphatases, heavy-metal transport systems, flagellation, and chemotaxis. These genes may be crucial for AOA adaptation to the eutrophic and heavy-metal-contaminated Jiulong River estuary. The uncovered detailed genomic characteristics of the new estuarine AOA species highlight AOA contributions to ammonia oxidation in the Jiulong River estuary.IMPORTANCE In this study, AOA communities along a river in southern China were characterized, and metagenome-assembled genomes (MAGs) of a novel AOA clade were also obtained. Based on the characterization of AOA genomes, the study suggests adaptation of the novel AOAs to estuarine environments, providing new information on the ecology of estuarine AOA and the nitrogen cycle in contaminated estuarine environments.
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28
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Adeleke BS, Babalola OO. The endosphere microbial communities, a great promise in agriculture. Int Microbiol 2020; 24:1-17. [PMID: 32737846 DOI: 10.1007/s10123-020-00140-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/20/2020] [Accepted: 07/24/2020] [Indexed: 12/20/2022]
Abstract
Agricultural food production and sustainability need intensification to address the current global food supply to meet human demand. The continuous human population increase and other anthropogenic activities threaten food security. Agrochemical inputs have long been used in conventional agricultural systems to boost crop productivity, but they are disadvantageous to a safe environment. Towards developing environmentally friendly agriculture, efforts are being directed in exploring biological resources from soil and plant microbes. The survival of the rhizosphere and endosphere microbiota is influenced by biotic and abiotic factors. Plant microbiota live interdependently with the host plants. Endophytes are regarded as colonizer microbes inhabiting and establishing microbial communities within the plant tissue. Their activities are varied and include fixing atmospheric nitrogen, solubilizing phosphate, synthesis of siderophores, secretion of metabolite-like compounds containing active biocontrol agents in the control of phytopathogens, and induced systemic resistance that stimulates plant response to withstand stress. Exploring beneficial endophyte resources in the formulation of bio-inoculants, such as biofertilizers, as an alternative to agrochemicals (fertilizers and pesticides) in developing environmentally friendly agriculture and for incorporation into crop breeding and disease control program is promising. Therefore, in this review, endosphere microbial ecology, associating environmental factors, and their roles that contribute to their effectiveness in promoting plant growth for maximum agricultural crop productivity were highlighted.
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Affiliation(s)
- Bartholomew Saanu Adeleke
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
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29
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Qin W, Zheng Y, Zhao F, Wang Y, Urakawa H, Martens-Habbena W, Liu H, Huang X, Zhang X, Nakagawa T, Mende DR, Bollmann A, Wang B, Zhang Y, Amin SA, Nielsen JL, Mori K, Takahashi R, Virginia Armbrust E, Winkler MKH, DeLong EF, Li M, Lee PH, Zhou J, Zhang C, Zhang T, Stahl DA, Ingalls AE. Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea. ISME JOURNAL 2020; 14:2595-2609. [PMID: 32636492 PMCID: PMC7490402 DOI: 10.1038/s41396-020-0710-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 06/16/2020] [Accepted: 06/25/2020] [Indexed: 12/29/2022]
Abstract
Ammonia-oxidizing archaea (AOA) are among the most abundant and ubiquitous microorganisms in the ocean, exerting primary control on nitrification and nitrogen oxides emission. Although united by a common physiology of chemoautotrophic growth on ammonia, a corresponding high genomic and habitat variability suggests tremendous adaptive capacity. Here, we compared 44 diverse AOA genomes, 37 from species cultivated from samples collected across diverse geographic locations and seven assembled from metagenomic sequences from the mesopelagic to hadopelagic zones of the deep ocean. Comparative analysis identified seven major marine AOA genotypic groups having gene content correlated with their distinctive biogeographies. Phosphorus and ammonia availabilities as well as hydrostatic pressure were identified as selective forces driving marine AOA genotypic and gene content variability in different oceanic regions. Notably, AOA methylphosphonate biosynthetic genes span diverse oceanic provinces, reinforcing their importance for methane production in the ocean. Together, our combined comparative physiological, genomic, and metagenomic analyses provide a comprehensive view of the biogeography of globally abundant AOA and their adaptive radiation into a vast range of marine and terrestrial habitats.
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Affiliation(s)
- Wei Qin
- School of Oceanography, University of Washington, Seattle, WA, USA.
| | - Yue Zheng
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Feng Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Hidetoshi Urakawa
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Davie, FL, USA
| | - Haodong Liu
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
| | - Xiaowu Huang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong, China
| | - Xinxu Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Tatsunori Nakagawa
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Daniel R Mende
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, USA
| | | | - Baozhan Wang
- Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Sciences and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Shady A Amin
- Department of Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Jeppe L Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Koji Mori
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Kisarazu, Chiba, Japan
| | - Reiji Takahashi
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | | | - Mari-K H Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, USA
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong, China.,Department of Civil and Environmental Engineering, Imperial College London, London, UK
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.,Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,School of Environment, Tsinghua University, Beijing, China
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, USA.
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30
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Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956-4042. [DOI: 10.1099/ijsem.0.003789] [Citation(s) in RCA: 782] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
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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
| | - George M. Garrity
- NamesforLife, LLC, PO Box 769, Okemos MI 48805-0769, USA
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | | | - Maria Chuvochina
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia QLD 4072, Brisbane, Australia
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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31
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Saad MM, Eida AA, Hirt H. Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3878-3901. [PMID: 32157287 PMCID: PMC7450670 DOI: 10.1093/jxb/eraa111] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/09/2020] [Indexed: 05/05/2023]
Abstract
Plants are now recognized as metaorganisms which are composed of a host plant associated with a multitude of microbes that provide the host plant with a variety of essential functions to adapt to the local environment. Recent research showed the remarkable importance and range of microbial partners for enhancing the growth and health of plants. However, plant-microbe holobionts are influenced by many different factors, generating complex interactive systems. In this review, we summarize insights from this emerging field, highlighting the factors that contribute to the recruitment, selection, enrichment, and dynamic interactions of plant-associated microbiota. We then propose a roadmap for synthetic community application with the aim of establishing sustainable agricultural systems that use microbial communities to enhance the productivity and health of plants independently of chemical fertilizers and pesticides. Considering global warming and climate change, we suggest that desert plants can serve as a suitable pool of potentially beneficial microbes to maintain plant growth under abiotic stress conditions. Finally, we propose a framework for advancing the application of microbial inoculants in agriculture.
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Affiliation(s)
- Maged M Saad
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdul Aziz Eida
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette Cedex, France
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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32
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Zhong H, Lehtovirta-Morley L, Liu J, Zheng Y, Lin H, Song D, Todd JD, Tian J, Zhang XH. Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms. MICROBIOME 2020; 8:78. [PMID: 32482169 PMCID: PMC7265257 DOI: 10.1186/s40168-020-00849-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/27/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Marine Group I (MGI) Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI Thaumarchaeota were present in the deepest part of oceans-the hadal zone (depth > 6000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the "shallower" deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water. RESULTS In this study, metagenomic data were obtained from 0-10,500 m deep seawater samples from the Mariana Trench. The distribution patterns of Thaumarchaeota derived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance of Thaumarchaeota peaked in bathypelagic zone (depth 1000-4000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics, we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H+ and Na+ respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition. We also found that hadal MGI have the genetic potential to import a far higher range of organic compounds than their shallower water counterparts. Despite this trait, hadal MDI ammonia oxidation and carbon fixation genes are highly transcribed providing evidence they are likely autotrophic, contributing to the primary production in the aphotic deep sea. CONCLUSIONS Our study reveals potentially novel adaptation mechanisms of deep-sea thaumarchaeotal clades and suggests key functions of deep-sea Thaumarchaeota in carbon and nitrogen cycling. Video Abstract.
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Affiliation(s)
- Haohui Zhong
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Laura Lehtovirta-Morley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Jiwen Liu
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yanfen Zheng
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Heyu Lin
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Delei Song
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100, China.
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Reyes C, Hodgskiss LH, Baars O, Kerou M, Bayer B, Schleper C, Kraemer SM. Copper limiting threshold in the terrestrial ammonia oxidizing archaeon Nitrososphaera viennensis. Res Microbiol 2020; 171:134-142. [PMID: 31991171 DOI: 10.1016/j.resmic.2020.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/20/2019] [Accepted: 01/09/2020] [Indexed: 11/25/2022]
Abstract
Ammonia oxidizing archaea (AOA) inhabiting soils have a central role in the global nitrogen cycle. Copper (Cu) is central to many enzymes in AOA including ammonia monooxygenase (AMO), the enzyme involved in the first step of ammonia oxidation. This study explored the physiological response of the AOA soil isolate, Nitrososphaera viennensis (EN76T) to Cu-limiting conditions in order to approach its limiting threshold under laboratory conditions. The chelator TETA (1,4,8,11-tetraazacyclotetradecane N, N', N″, N‴-tetraacetic acid hydrochloride hydrate) with selective affinity for Cu2+ was used to lower bioavailable Cu2+ in culture experiments as predicted by thermodynamic speciation calculations. Results show that N. viennensis is Cu-limited at concentrations ≤10-15 mol L-1 free Cu2+ compared to standard conditions (10-12 mol L-1). This Cu2+ limiting threshold is similar to pure cultures of denitrifying bacteria and other AOA and AOB inhabiting soils, freshwaters and sewage (<10-16 mol L-1), and lower than pure cultures of the marine AOA Nitrosopumilus maritimus (<10-12.7 mol L-1), which also possesses a high amount of Cu-dependent enzymes.
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Affiliation(s)
- Carolina Reyes
- University of Vienna, EDGE- Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, UZA2, 1090, Vienna, Austria; University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Logan H Hodgskiss
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Oliver Baars
- North Carolina State University, Department of Entomology and Plant Pathology, 840 Main Campus Drive, Raleigh, NC, 27695, USA.
| | - Melina Kerou
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Barbara Bayer
- Department of Limnology and Bio-Oceanography, Division of Bio-Oceanography, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Christa Schleper
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Stephan M Kraemer
- University of Vienna, EDGE- Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, UZA2, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
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34
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Hu A, Wang H, Cao M, Rashid A, Li M, Yu CP. Environmental Filtering Drives the Assembly of Habitat Generalists and Specialists in the Coastal Sand Microbial Communities of Southern China. Microorganisms 2019; 7:microorganisms7120598. [PMID: 31766562 PMCID: PMC6955893 DOI: 10.3390/microorganisms7120598] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/18/2019] [Accepted: 11/20/2019] [Indexed: 11/16/2022] Open
Abstract
Coastal sands harbor diverse microbial assemblages that play a critical role in the biogeochemical cycling of beach ecosystems. However, little is known about the relative importance of the different ecological processes underlying the assembly of communities of sand microbiota. Here, we employed 16S rDNA amplicon sequencing to investigate the sand microbiota of two coastal beaches, in southern China. The results showed that sand microbial assemblages at intertidal and supratidal zones exhibited contrasting compositions that can be attributed to environmental filtering by electric conductivity. A consistent pattern of habitat generalists and specialists of sand microbiota was observed among different beach zones. Null and neutral model analyses indicated that the environmental filtering was mainly responsible for supratidal microbial communities, while the neutral processes could partially influence the assembly of intertidal communities. Moreover, environmental filtering was found to shape the habitat specialists, while random dispersal played a major role in shaping generalists. The neutral model analysis revealed that the habitat generalists exceeding the neutral prediction harbored a relatively higher proportion of microbial taxa than the specialist counterparts. An opposite pattern was observed for taxa falling below the neutral prediction. Collectively, these findings offer a novel insight into the assembly mechanisms of coastal sand microbiota.
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Affiliation(s)
- Anyi Hu
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (H.W.); (M.C.); (A.R.); (C.-P.Y.)
- Correspondence: (A.H.); (M.L.); Tel.: +86-592-6190582 (A.H.); +86-596-2591356 (M.L.)
| | - Hongjie Wang
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (H.W.); (M.C.); (A.R.); (C.-P.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meixian Cao
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (H.W.); (M.C.); (A.R.); (C.-P.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Azhar Rashid
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (H.W.); (M.C.); (A.R.); (C.-P.Y.)
- Nuclear Institute for Food and Agriculture, Tarnab, Peshawar 446, Pakistan
| | - Mingfeng Li
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou 363000, China
- Correspondence: (A.H.); (M.L.); Tel.: +86-592-6190582 (A.H.); +86-596-2591356 (M.L.)
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (H.W.); (M.C.); (A.R.); (C.-P.Y.)
- Graduate Institute of Environmental Engineering, National Taiwan University, Taipei 106, Taiwan
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35
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Gwak JH, Jung MY, Hong H, Kim JG, Quan ZX, Reinfelder JR, Spasov E, Neufeld JD, Wagner M, Rhee SK. Archaeal nitrification is constrained by copper complexation with organic matter in municipal wastewater treatment plants. ISME JOURNAL 2019; 14:335-346. [PMID: 31624348 PMCID: PMC6976641 DOI: 10.1038/s41396-019-0538-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/24/2019] [Accepted: 09/27/2019] [Indexed: 01/08/2023]
Abstract
Consistent with the observation that ammonia-oxidizing bacteria (AOB) outnumber ammonia-oxidizing archaea (AOA) in many eutrophic ecosystems globally, AOB typically dominate activated sludge aeration basins from municipal wastewater treatment plants (WWTPs). In this study, we demonstrate that the growth of AOA strains inoculated into sterile-filtered wastewater was inhibited significantly, in contrast to uninhibited growth of a reference AOB strain. In order to identify possible mechanisms underlying AOA-specific inhibition, we show that complex mixtures of organic compounds, such as yeast extract, were highly inhibitory to all AOA strains but not to the AOB strain. By testing individual organic compounds, we reveal strong inhibitory effects of organic compounds with high metal complexation potentials implying that the inhibitory mechanism for AOA can be explained by the reduced bioavailability of an essential metal. Our results further demonstrate that the inhibitory effect on AOA can be alleviated by copper supplementation, which we observed for pure AOA cultures in a defined medium and for AOA inoculated into nitrifying sludge. Our study offers a novel mechanistic explanation for the relatively low abundance of AOA in most WWTPs and provides a basis for modulating the composition of nitrifying communities in both engineered systems and naturally occurring environments.
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Affiliation(s)
- Joo-Han Gwak
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Man-Young Jung
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Heeji Hong
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Jong-Geol Kim
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - John R Reinfelder
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Emilie Spasov
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria.,Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea.
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36
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Genome Sequence of " Candidatus Nitrosocosmicus franklandus" C13, a Terrestrial Ammonia-Oxidizing Archaeon. Microbiol Resour Announc 2019; 8:8/40/e00435-19. [PMID: 31582432 PMCID: PMC6776761 DOI: 10.1128/mra.00435-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
“Candidatus Nitrosocosmicus franklandus” C13 is an ammonia-oxidizing archaeon (AOA) isolated from soil. Its complete genome is 2.84 Mb and possesses predicted AOA metabolic pathways for energy generation and carbon dioxide fixation but no typical surface layer (S-layer) proteins, only one ammonium transporter, and divergent A-type ATP synthase genes. “Candidatus Nitrosocosmicus franklandus” C13 is an ammonia-oxidizing archaeon (AOA) isolated from soil. Its complete genome is 2.84 Mb and possesses predicted AOA metabolic pathways for energy generation and carbon dioxide fixation but no typical surface layer (S-layer) proteins, only one ammonium transporter, and divergent A-type ATP synthase genes.
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37
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Hu J, Liu S, Yang W, He Z, Wang J, Liu H, Zheng P, Xi C, Ma F, Hu B. Ecological Success of the Nitrosopumilus and Nitrosospira Clusters in the Intertidal Zone. MICROBIAL ECOLOGY 2019; 78:555-564. [PMID: 30903203 DOI: 10.1007/s00248-019-01359-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
The intertidal zone is an important buffer and a nitrogen sink between land and sea. Ammonia oxidation is the rate-limiting step of nitrification, conducted by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, it remains a debatable issue regarding dominant ammonia oxidizers in this region, and environmental factors driving their spatiotemporal niche differentiation have yet to be identified. In this study, intertidal and subtidal zones of Zhoushan Islands were selected for seasonal sampling. Ammonia-oxidizing activity, quantitative PCR, and 454 high-throughput sequencing were performed to study the nitrification potential, abundance, and community structure of ammonia-oxidizing archaea and bacteria. AOA and AOB amoA abundance (107-108amoA gene copies/g dry weight sediment) varied spatiotemporally independently of environmental factors. AOA surpassed AOB in most samples, driven by sediment temperature, moisture, and total nitrogen. The diversity of both AOA and AOB differed spatiotemporally. The Nitrosopumilus and Nitrosospira clusters accounted for an absolutely dominant percentage of AOA (> 99%) and AOB (> 99%) respectively, indicating a negligible contribution of other clusters to ammonia oxidation. However, there was no significant correlation between nitrification potential and the abundance of AOA or AOB. Overall, the present study showed that AOA dominated over AOB spatiotemporally in the intertidal zone of Zhoushan Islands due to fluctuations in environmental factors, and the Nitrosopumilus and Nitrosospira clusters ecologically succeeded in the intertidal zone of Zhoushan Islands.
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Affiliation(s)
- Jiajie Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Shuai Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Weiling Yang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Zhanfei He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Huan Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Chuanwu Xi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China.
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China.
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38
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Membrane Lipid Composition of the Moderately Thermophilic Ammonia-Oxidizing Archaeon " Candidatus Nitrosotenuis uzonensis" at Different Growth Temperatures. Appl Environ Microbiol 2019; 85:AEM.01332-19. [PMID: 31420340 PMCID: PMC6805073 DOI: 10.1128/aem.01332-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 08/12/2019] [Indexed: 11/20/2022] Open
Abstract
For Thaumarchaeota, the ratio of their glycerol dialkyl glycerol tetraether (GDGT) lipids depends on growth temperature, a premise that forms the basis of the widely applied TEX86 paleotemperature proxy. A thorough understanding of which GDGTs are produced by which Thaumarchaeota and what the effect of temperature is on their GDGT composition is essential for constraining the TEX86 proxy. “Ca. Nitrosotenuis uzonensis” is a moderately thermophilic thaumarchaeote enriched from a thermal spring, setting it apart in its environmental niche from the other marine mesophilic members of its order. Indeed, we found that the GDGT composition of “Ca. Nitrosotenuis uzonensis” cultures was distinct from those of other members of its order and was more similar to those of other thermophilic, terrestrial Thaumarchaeota. This suggests that while phylogeny has a strong influence on GDGT distribution, the environmental niche that a thaumarchaeote inhabits also shapes its GDGT composition. “Candidatus Nitrosotenuis uzonensis” is the only cultured moderately thermophilic member of the thaumarchaeotal order Nitrosopumilales (NP) that contains many mesophilic marine strains. We examined its membrane lipid composition at different growth temperatures (37°C, 46°C, and 50°C). Its lipids were all membrane-spanning glycerol dialkyl glycerol tetraethers (GDGTs), with 0 to 4 cyclopentane moieties. Crenarchaeol (cren), the characteristic thaumarchaeotal GDGT, and its isomer (crenʹ) were present in high abundance (30 to 70%). The GDGT polar headgroups were mono-, di-, and trihexoses and hexose/phosphohexose. The ratio of glycolipid to phospholipid GDGTs was highest in the cultures grown at 50°C. With increasing growth temperatures, the relative contributions of cren and crenʹ increased, while those of GDGT-0 to GDGT-4 (including isomers) decreased. TEX86 (tetraether index of tetraethers consisting of 86 carbons)-derived temperatures were much lower than the actual growth temperatures, further demonstrating that TEX86 does not accurately reflect the membrane lipid adaptation of thermophilic Thaumarchaeota. As the temperature increased, specific GDGTs changed relative to their isomers, possibly representing temperature adaption-induced changes in cyclopentane ring stereochemistry. Comparison of a wide range of thaumarchaeotal core lipid compositions revealed that the “Ca. Nitrosotenuis uzonensis” cultures clustered separately from other members of the NP order and the Nitrososphaerales (NS) order. While phylogeny generally seems to have a strong influence on GDGT distribution, our analysis of “Ca. Nitrosotenuis uzonensis” demonstrates that its terrestrial, higher-temperature niche has led to a lipid composition that clearly differentiates it from other NP members and that this difference is mostly driven by its high crenʹ content. IMPORTANCE For Thaumarchaeota, the ratio of their glycerol dialkyl glycerol tetraether (GDGT) lipids depends on growth temperature, a premise that forms the basis of the widely applied TEX86 paleotemperature proxy. A thorough understanding of which GDGTs are produced by which Thaumarchaeota and what the effect of temperature is on their GDGT composition is essential for constraining the TEX86 proxy. “Ca. Nitrosotenuis uzonensis” is a moderately thermophilic thaumarchaeote enriched from a thermal spring, setting it apart in its environmental niche from the other marine mesophilic members of its order. Indeed, we found that the GDGT composition of “Ca. Nitrosotenuis uzonensis” cultures was distinct from those of other members of its order and was more similar to those of other thermophilic, terrestrial Thaumarchaeota. This suggests that while phylogeny has a strong influence on GDGT distribution, the environmental niche that a thaumarchaeote inhabits also shapes its GDGT composition.
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39
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Wang B, Qin W, Ren Y, Zhou X, Jung MY, Han P, Eloe-Fadrosh EA, Li M, Zheng Y, Lu L, Yan X, Ji J, Liu Y, Liu L, Heiner C, Hall R, Martens-Habbena W, Herbold CW, Rhee SK, Bartlett DH, Huang L, Ingalls AE, Wagner M, Stahl DA, Jia Z. Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons. ISME JOURNAL 2019; 13:3067-3079. [PMID: 31462715 PMCID: PMC6863869 DOI: 10.1038/s41396-019-0493-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/01/2019] [Accepted: 07/29/2019] [Indexed: 01/04/2023]
Abstract
Thaumarchaeota are responsible for a significant fraction of ammonia oxidation in the oceans and in soils that range from alkaline to acidic. However, the adaptive mechanisms underpinning their habitat expansion remain poorly understood. Here we show that expansion into acidic soils and the high pressures of the hadopelagic zone of the oceans is tightly linked to the acquisition of a variant of the energy-yielding ATPases via horizontal transfer. Whereas the ATPase genealogy of neutrophilic Thaumarchaeota is congruent with their organismal genealogy inferred from concatenated conserved proteins, a common clade of V-type ATPases unites phylogenetically distinct clades of acidophilic/acid-tolerant and piezophilic/piezotolerant species. A presumptive function of pumping cytoplasmic protons at low pH is consistent with the experimentally observed increased expression of the V-ATPase in an acid-tolerant thaumarchaeote at low pH. Consistently, heterologous expression of the thaumarchaeotal V-ATPase significantly increased the growth rate of E. coli at low pH. Its adaptive significance to growth in ocean trenches may relate to pressure-related changes in membrane structure in which this complex molecular machine must function. Together, our findings reveal that the habitat expansion of Thaumarchaeota is tightly correlated with extensive horizontal transfer of atp operons.
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Affiliation(s)
- Baozhan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Wei Qin
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Yi Ren
- Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd, Shanghai, China
| | - Xue Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Man-Young Jung
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Ping Han
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Emiley A Eloe-Fadrosh
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.,Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yue Zheng
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Lu Lu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xin Yan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Junbin Ji
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Linmeng Liu
- Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd, Shanghai, China
| | | | | | - Willm Martens-Habbena
- Department of Microbiology and Cell Science & Fort Lauderdale Research and Education Center, University of Florida, Gainesville, FL, USA
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.,Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.
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Zhang S, Song W, Wemheuer B, Reveillaud J, Webster N, Thomas T. Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota. mSystems 2019; 4:e00288-19. [PMID: 31409660 PMCID: PMC6697440 DOI: 10.1128/msystems.00288-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/22/2019] [Indexed: 01/25/2023] Open
Abstract
Thaumarchaeota are frequently reported to associate with marine sponges (phylum Porifera); however, little is known about the features that distinguish them from their free-living thaumarchaeal counterparts. In this study, thaumarchaeal metagenome-assembled genomes (MAGs) were reconstructed from metagenomic data sets derived from the marine sponges Hexadella detritifera, Hexadella cf. detritifera, and Stylissa flabelliformis Phylogenetic and taxonomic analyses revealed that the three thaumarchaeal MAGs represent two new species within the genus Nitrosopumilus and one novel genus, for which we propose the names "Candidatus UNitrosopumilus hexadellus," "Candidatus UNitrosopumilus detritiferus," and "Candidatus UCenporiarchaeum stylissum" (the U superscript indicates that the taxon is uncultured). Comparison of these genomes to data from the Sponge Earth Microbiome Project revealed that "Ca UCenporiarchaeum stylissum" has been exclusively detected in sponges and can hence be classified as a specialist, while "Ca UNitrosopumilus detritiferus" and "Ca UNitrosopumilus hexadellus" are also detected outside the sponge holobiont and likely lead a generalist lifestyle. Comparison of the sponge-associated MAGs to genomes of free-living Thaumarchaeota revealed signatures that indicate functional features of a sponge-associated lifestyle, and these features were related to nutrient transport and metabolism, restriction-modification, defense mechanisms, and host interactions. Each species exhibited distinct functional traits, suggesting that they have reached different stages of evolutionary adaptation and/or occupy distinct ecological niches within their sponge hosts. Our study therefore offers new evolutionary and ecological insights into the symbiosis between sponges and their thaumarchaeal symbionts.IMPORTANCE Sponges represent ecologically important models to understand the evolution of symbiotic interactions of metazoans with microbial symbionts. Thaumarchaeota are commonly found in sponges, but their potential adaptations to a host-associated lifestyle are largely unknown. Here, we present three novel sponge-associated thaumarchaeal species and compare their genomic and predicted functional features with those of closely related free-living counterparts. We found different degrees of specialization of these thaumarchaeal species to the sponge environment that is reflected in their host distribution and their predicted molecular and metabolic properties. Our results indicate that Thaumarchaeota may have reached different stages of evolutionary adaptation in their symbiosis with sponges.
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Affiliation(s)
- Shan Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
| | - Weizhi Song
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
| | - Bernd Wemheuer
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Julie Reveillaud
- ASTRE, INRA, CIRAD, University of Montpellier, Montpellier, France
| | - Nicole Webster
- Australian Institute of Marine Science, Townsville, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
| | - Torsten Thomas
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
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Havig JR, Hamilton TL. Productivity and Community Composition of Low Biomass/High Silica Precipitation Hot Springs: A Possible Window to Earth's Early Biosphere? Life (Basel) 2019; 9:E64. [PMID: 31362401 PMCID: PMC6789502 DOI: 10.3390/life9030064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/10/2019] [Accepted: 07/24/2019] [Indexed: 01/14/2023] Open
Abstract
Terrestrial hot springs have provided a niche space for microbial communities throughout much of Earth's history, and evidence for hydrothermal deposits on the Martian surface suggest this could have also been the case for the red planet. Prior to the evolution of photosynthesis, life in hot springs on early Earth would have been supported though chemoautotrophy. Today, hot spring geochemical and physical parameters can preclude the occurrence of oxygenic phototrophs, providing an opportunity to characterize the geochemical and microbial components. In the absence of the photo-oxidation of water, chemoautotrophy in these hot springs (and throughout Earth's history) relies on the delivery of exogenous electron acceptors and donors such as H2, H2S, and Fe2+. Thus, systems fueled by chemoautotrophy are likely energy substrate-limited and support low biomass communities compared to those where oxygenic phototrophs are prevalent. Low biomass silica-precipitating systems have implications for preservation, especially over geologic time. Here, we examine and compare the productivity and composition of low biomass chemoautotrophic versus photoautotrophic communities in silica-saturated hot springs. Our results indicate low biomass chemoautotrophic microbial communities in Yellowstone National Park are supported primarily by sulfur redox reactions and, while similar in total biomass, show higher diversity in anoxygenic phototrophic communities compared to chemoautotrophs. Our data suggest productivity in Archean terrestrial hot springs may be directly linked to redox substrate availability, and there may be high potential for geochemical and physical biosignature preservation from these communities.
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Affiliation(s)
- Jeff R Havig
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Trinity L Hamilton
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA
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42
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Alves RJE, Kerou M, Zappe A, Bittner R, Abby SS, Schmidt HA, Pfeifer K, Schleper C. Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures. Front Microbiol 2019; 10:1571. [PMID: 31379764 PMCID: PMC6657660 DOI: 10.3389/fmicb.2019.01571] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/24/2019] [Indexed: 11/13/2022] Open
Abstract
Climate change is causing arctic regions to warm disproportionally faster than those at lower latitudes, leading to alterations in carbon and nitrogen cycling, and potentially higher greenhouse gas emissions. It is thus increasingly important to better characterize the microorganisms driving arctic biogeochemical processes and their potential responses to changing conditions. Here, we describe a novel thaumarchaeon enriched from an arctic soil, Candidatus Nitrosocosmicus arcticus strain Kfb, which has been maintained for seven years in stable laboratory enrichment cultures as an aerobic ammonia oxidizer, with ammonium or urea as substrates. Genomic analyses show that this organism harbors all genes involved in ammonia oxidation and in carbon fixation via the 3-hydroxypropionate/4-hydroxybutyrate cycle, characteristic of all AOA, as well as the capability for urea utilization and potentially also for heterotrophic metabolism, similar to other AOA. Ca. N. arcticus oxidizes ammonia optimally between 20 and 28°C, well above average temperatures in its native high arctic environment (-13-4°C). Ammonia oxidation rates were nevertheless much lower than those of most cultivated mesophilic AOA (20-45°C). Intriguingly, we repeatedly observed apparent faster growth rates (based on marker gene counts) at lower temperatures (4-8°C) but without detectable nitrite production. Together with potential metabolisms predicted from its genome content, these observations indicate that Ca. N. arcticus is not a strict chemolithotrophic ammonia oxidizer and add to cumulating evidence for a greater metabolic and physiological versatility of AOA. The physiology of Ca. N. arcticus suggests that increasing temperatures might drastically affect nitrification in arctic soils by stimulating archaeal ammonia oxidation.
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Affiliation(s)
- Ricardo J Eloy Alves
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Melina Kerou
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Anna Zappe
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, Medical University of Vienna, University of Vienna, Vienna, Austria
| | - Romana Bittner
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Sophie S Abby
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Heiko A Schmidt
- Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, Medical University of Vienna, University of Vienna, Vienna, Austria
| | - Kevin Pfeifer
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,Institute for Synthetic Bioarchitectures, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christa Schleper
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
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43
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Proteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic Alphaproteobacterium. mSystems 2019; 4:4/4/e00181-19. [PMID: 31239395 PMCID: PMC6593220 DOI: 10.1128/msystems.00181-19] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Ammonia-oxidizing archaea (AOA) are the most abundant chemolithoautotrophic microorganisms in the oxygenated water column of the global ocean. Although H2O2 appears to be a universal by-product of aerobic metabolism, genes encoding the hydrogen peroxide (H2O2)-detoxifying enzyme catalase are largely absent in genomes of marine AOA. Here, we provide evidence that closely related marine AOA have different degrees of sensitivity to H2O2, which may contribute to niche differentiation between these organisms. Furthermore, our results suggest that marine AOA rely on H2O2 detoxification during periods of high metabolic activity and release organic compounds, thereby potentially attracting heterotrophic prokaryotes that provide this missing function. In summary, this report provides insights into the metabolic interactions between AOA and heterotrophic bacteria in marine environments and suggests that AOA play an important role in the biogeochemical carbon cycle by making organic carbon available for heterotrophic microorganisms. Ammonia-oxidizing archaea (AOA) play an important role in the nitrogen cycle and account for a considerable fraction of the prokaryotic plankton in the ocean. Most AOA lack the hydrogen peroxide (H2O2)-detoxifying enzyme catalase, and some AOA have been shown to grow poorly under conditions of exposure to H2O2. However, differences in the degrees of H2O2 sensitivity of different AOA strains, the physiological status of AOA cells exposed to H2O2, and their molecular response to H2O2 remain poorly characterized. Further, AOA might rely on heterotrophic bacteria to detoxify H2O2, and yet the extent and variety of costs and benefits involved in these interactions remain unclear. Here, we used a proteomics approach to compare the protein profiles of three Nitrosopumilus strains grown in the presence and absence of catalase and in coculture with the heterotrophic alphaproteobacterium Oceanicaulis alexandrii. We observed that most proteins detected at a higher relative abundance in H2O2-exposed Nitrosopumilus cells had no known function in oxidative stress defense. Instead, these proteins were putatively involved in the remodeling of the extracellular matrix, which we hypothesize to be a strategy limiting the influx of H2O2 into the cells. Using RNA-stable isotope probing, we confirmed that O. alexandrii cells growing in coculture with the Nitrosopumilus strains assimilated Nitrosopumilus-derived organic carbon, suggesting that AOA could recruit H2O2-detoxifying bacteria through the release of labile organic matter. Our results contribute new insights into the response of AOA to H2O2 and highlight the potential ecological importance of their interactions with heterotrophic free-living bacteria in marine environments. IMPORTANCE Ammonia-oxidizing archaea (AOA) are the most abundant chemolithoautotrophic microorganisms in the oxygenated water column of the global ocean. Although H2O2 appears to be a universal by-product of aerobic metabolism, genes encoding the hydrogen peroxide (H2O2)-detoxifying enzyme catalase are largely absent in genomes of marine AOA. Here, we provide evidence that closely related marine AOA have different degrees of sensitivity to H2O2, which may contribute to niche differentiation between these organisms. Furthermore, our results suggest that marine AOA rely on H2O2 detoxification during periods of high metabolic activity and release organic compounds, thereby potentially attracting heterotrophic prokaryotes that provide this missing function. In summary, this report provides insights into the metabolic interactions between AOA and heterotrophic bacteria in marine environments and suggests that AOA play an important role in the biogeochemical carbon cycle by making organic carbon available for heterotrophic microorganisms.
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Ren M, Feng X, Huang Y, Wang H, Hu Z, Clingenpeel S, Swan BK, Fonseca MM, Posada D, Stepanauskas R, Hollibaugh JT, Foster PG, Woyke T, Luo H. Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution. ISME JOURNAL 2019; 13:2150-2161. [PMID: 31024152 DOI: 10.1038/s41396-019-0418-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 03/07/2019] [Accepted: 04/03/2019] [Indexed: 11/09/2022]
Abstract
Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in marine and terrestrial habitats, playing a major role in the global nitrogen cycle. However, their evolutionary history remains unexplored, which limits our understanding of their adaptation mechanisms. Here, our comprehensive phylogenomic tree of Thaumarchaeota supports three sequential events: origin of AOA from terrestrial non-AOA ancestors, colonization of the shallow ocean, and expansion to the deep ocean. Careful molecular dating suggests that these events coincided with the Great Oxygenation Event around 2300 million years ago (Mya), and oxygenation of the shallow and deep ocean around 800 and 635-560 Mya, respectively. The first transition was likely enabled by the gain of an aerobic pathway for energy production by ammonia oxidation and biosynthetic pathways for cobalamin and biotin that act as cofactors in aerobic metabolism. The first transition was also accompanied by the loss of dissimilatory nitrate and sulfate reduction, loss of oxygen-sensitive pyruvate oxidoreductase, which reduces pyruvate to acetyl-CoA, and loss of the Wood-Ljungdahl pathway for anaerobic carbon fixation. The second transition involved gain of a K+ transporter and of the biosynthetic pathway for ectoine, which may function as an osmoprotectant. The third transition was accompanied by the loss of the uvr system for repairing ultraviolet light-induced DNA lesions. We conclude that oxygen availability drove the terrestrial origin of AOA and their expansion to the photic and dark oceans, and that the stressors encountered during these events were partially overcome by gene acquisitions from Euryarchaeota and Bacteria, among other sources.
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Affiliation(s)
- Minglei Ren
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.,Shenzhen Research Institute, The Chinese University of Hong Kong, 518000, Shenzhen, China
| | - Xiaoyuan Feng
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yongjie Huang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.,Shenzhen Research Institute, The Chinese University of Hong Kong, 518000, Shenzhen, China
| | - Hui Wang
- Biology Department, College of Science, Shantou University, 515063, Shantou, China
| | - Zhong Hu
- Biology Department, College of Science, Shantou University, 515063, Shantou, China
| | | | - Brandon K Swan
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA.,National Biodefense Analysis and Countermeasures Center, Frederick, MD, 21702, USA
| | - Miguel M Fonseca
- CINBIO and Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
| | - David Posada
- CINBIO and Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
| | | | - James T Hollibaugh
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Peter G Foster
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong. .,Shenzhen Research Institute, The Chinese University of Hong Kong, 518000, Shenzhen, China.
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45
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Liu L, Li S, Han J, Lin W, Luo J. A Two-Step Strategy for the Rapid Enrichment of Nitrosocosmicus-Like Ammonia-Oxidizing Thaumarchaea. Front Microbiol 2019; 10:875. [PMID: 31105671 PMCID: PMC6491936 DOI: 10.3389/fmicb.2019.00875] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 04/04/2019] [Indexed: 12/03/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are widely distributed on the earth and play a significant role in the global nitrogen cycle. Although dozens of AOA strains were obtained in the last 13 years, it is still necessary to obtain more AOA strains for the entire exploration of their ecology, physiology, and underlying biochemistry in different environments. In this study, we designed a two-step strategy for the rapid enrichment of Nitrosocosmicus–like AOA from soils. Firstly, combination of kanamycin and ampicillin was chosen as the selective stress for bacteria and quartz sands were used as the attachment of AOA cells during the first step cultivation; only after 40–75 days cultivation, AOA enrichments with abundance >20% were obtained. Secondly, combination of ciprofloxacin and azithromycin was chosen as the selective stress for the following cultivation; it is able to penetrate the biofilms and kill the bacterial cells inside the aggregate, contributing to the AOA enrichments reached high abundances (90%) only after one-time cultivation. Basing on this strategy, three AOA strains were obtained from agricultural soils only after 90–150 days cultivation. Phylogenetic analysis suggested these AOA belong to the soil group I.1b Thaumarchaeota and are closely related to the genus Nitrosocosmicus. In general, AOA enrichment or isolation is very difficult and time-consuming (an average of 2–3 years). Here, we provide a new strategy for the rapid enrichment of high abundance of Nitrosocosmicus-like AOA from soil, which gives a new solution to the AOA enrichment and cultivation in a short period.
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Affiliation(s)
- Liangting Liu
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Surong Li
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jiamin Han
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Weitie Lin
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jianfei Luo
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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Zou D, Li Y, Kao S, Liu H, Li M. Genomic adaptation to eutrophication of ammonia‐oxidizing archaea in the Pearl River estuary. Environ Microbiol 2019; 21:2320-2332. [DOI: 10.1111/1462-2920.14613] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Dayu Zou
- SZU‐HKUST Joint PhD Program in Marine Environmental ScienceShenzhen University Shenzhen China
- Department of Ocean ScienceThe Hong Kong University of Science and Technology Hong Kong, SAR China
- Institute for Advanced Study, Shenzhen University Shenzhen China
| | - Yingdong Li
- Department of Ocean ScienceThe Hong Kong University of Science and Technology Hong Kong, SAR China
| | - Shuh‐Ji Kao
- State Key Laboratory of Marine Environmental ScienceXiamen University Xiamen China
| | - Hongbin Liu
- Department of Ocean ScienceThe Hong Kong University of Science and Technology Hong Kong, SAR China
| | - Meng Li
- SZU‐HKUST Joint PhD Program in Marine Environmental ScienceShenzhen University Shenzhen China
- Institute for Advanced Study, Shenzhen University Shenzhen China
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47
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Bayer B, Vojvoda J, Reinthaler T, Reyes C, Pinto M, Herndl GJ. Nitrosopumilus adriaticus sp. nov. and Nitrosopumilus piranensis sp. nov., two ammonia-oxidizing archaea from the Adriatic Sea and members of the class Nitrososphaeria. Int J Syst Evol Microbiol 2019; 69:1892-1902. [PMID: 30938665 DOI: 10.1099/ijsem.0.003360] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two mesophilic, neutrophilic and aerobic marine ammonia-oxidizing archaea, designated strains NF5T and D3CT, were isolated from coastal surface water of the Northern Adriatic Sea. Cells were straight small rods 0.20-0.25 µm wide and 0.49-2.00 µm long. Strain NF5T possessed archaella as cell appendages. Glycerol dibiphytanyl glycerol tetraethers with zero to four cyclopentane moieties (GDGT-0 to GDGT-4) and crenarchaeol were the major core lipids. Menaquinone MK6 : 0 was the major respiratory quinone. Both isolates gained energy by oxidizing ammonia (NH3) to nitrite (NO2-) and used bicarbonate as a carbon source. Strain D3CT was able use urea as a source of ammonia for energy production and growth. Addition of hydrogen peroxide (H2O2) scavengers (catalase or α-keto acids) was required to sustain growth. Optimal growth occurred between 30 and 32 °C, pH 7.1 and 7.3 and between 34 and 37‰ salinity. The cellular metal abundance ranking of both strains was Fe>Zn>Cu>Mn>Co. The genomes of strains NF5T and D3CT have a DNA G+C content of 33.4 and 33.8 mol%, respectively. Phylogenetic analyses of 16S rRNA gene sequences revealed that both strains are affiliated with the class Nitrososphaeria, sharing ~85 % 16S rRNA gene sequence identity with Nitrososphaera viennensis EN76T. The two isolates are separated by phenotypic and genotypic characteristics and are assigned to distinct species within the genus Nitrosopumilus gen. nov. according to average nucleotide identity thresholds of their closed genomes. Isolates NF5T (=JCM 32270T =NCIMB 15114T) and D3CT (=JCM 32271T =DSM 106147T =NCIMB 15115T) are type strains of the species Nitrosopumilusadriaticus sp. nov. and Nitrosopumiluspiranensis sp. nov., respectively.
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Affiliation(s)
- Barbara Bayer
- 1Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Jana Vojvoda
- 1Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Thomas Reinthaler
- 1Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Carolina Reyes
- 2Department of Environmental Geosciences, Environmental Science Research Network, University of Vienna, Vienna, Austria
| | - Maria Pinto
- 1Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Gerhard J Herndl
- 1Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria.,3Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, The Netherlands
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48
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Song GC, Im H, Jung J, Lee S, Jung M, Rhee S, Ryu C. Plant growth‐promoting archaea trigger induced systemic resistance inArabidopsis thalianaagainstPectobacterium carotovorumandPseudomonas syringae. Environ Microbiol 2019; 21:940-948. [DOI: 10.1111/1462-2920.14486] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 11/11/2018] [Accepted: 11/16/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Geun Cheol Song
- Molecular Phytobacteriology LaboratoryKRIBB Daejeon 34141 South Korea
| | - Hyunjoo Im
- Molecular Phytobacteriology LaboratoryKRIBB Daejeon 34141 South Korea
- Biosystems and Bioengineering ProgramUniversity of Science and Technology Daejeon 34113 South Korea
| | - Jihye Jung
- Molecular Phytobacteriology LaboratoryKRIBB Daejeon 34141 South Korea
- Department of Biological SciencesKorea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 South Korea
| | - Soohyun Lee
- Molecular Phytobacteriology LaboratoryKRIBB Daejeon 34141 South Korea
| | - Man‐Young Jung
- Department of MicrobiologyChungbuk National University Cheongju 28644 South Korea
| | - Sung‐Keun Rhee
- Department of MicrobiologyChungbuk National University Cheongju 28644 South Korea
| | - Choong‐Min Ryu
- Molecular Phytobacteriology LaboratoryKRIBB Daejeon 34141 South Korea
- Biosystems and Bioengineering ProgramUniversity of Science and Technology Daejeon 34113 South Korea
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Holmes DE, Dang Y, Smith JA. Nitrogen cycling during wastewater treatment. ADVANCES IN APPLIED MICROBIOLOGY 2019; 106:113-192. [PMID: 30798802 DOI: 10.1016/bs.aambs.2018.10.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrogen removal practices are much more environmentally friendly and cost effective. Therefore, interest in biological treatment is increasing. Biological approaches take advantage of specific groups of microorganisms involved in nitrogen cycling to remove reactive nitrogen from reactor systems by converting ammonia to nitrogen gas. Organisms known to be involved in this process include autotrophic ammonia-oxidizing bacteria, heterotrophic ammonia-oxidizing bacteria, ammonia-oxidizing archaea, anaerobic ammonia oxidizing bacteria (anammox), nitrite-oxidizing bacteria, complete ammonia oxidizers, and dissimilatory nitrate reducing microorganisms. For example, in nitrifying-denitrifying reactors, ammonia- and nitrite-oxidizing bacteria convert ammonia to nitrate and then denitrifying microorganisms reduce nitrate to nonreactive dinitrogen gas. Other nitrogen removal systems (anammox reactors) take advantage of anammox bacteria to convert ammonia to nitrogen gas using NO as an oxidant. A number of promising new biological treatment technologies are emerging and it is hoped that as the cost of these practices goes down more wastewater treatment plants will start to include a tertiary treatment step.
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Approaches to understanding the ecology and evolution of understudied terrestrial archaeal ammonia-oxidisers. Emerg Top Life Sci 2018; 2:619-628. [PMID: 33525821 DOI: 10.1042/etls20180018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/05/2018] [Accepted: 10/08/2018] [Indexed: 12/17/2022]
Abstract
Ammonia-oxidising archaea (AOA) form a phylogenetic group within the phylum Thaumarchaeota and are of ecological significance due to their role in nitrification, an important biogeochemical process. Previous research has provided information on their ecosystem role and potential physiological characteristics, for example, through analyses of their environmental distribution, ecological adaptation and evolutionary history. However, most AOA diversity, assessed using several environmental marker genes, is not represented in laboratory cultures, with consequent gaps in knowledge of their physiology and evolution. The present study critically reviews existing and developing approaches for the assessment of AOA function and diversity and their potential to provide a deeper understanding of these ecologically important, but understudied microorganisms.
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