1
|
Han S, Kim S, Sedlacek CJ, Farooq A, Song C, Lee S, Liu S, Brüggemann N, Rohe L, Kwon M, Rhee SK, Jung MY. Adaptive traits of Nitrosocosmicus clade ammonia-oxidizing archaea. mBio 2024:e0216924. [PMID: 39360821 DOI: 10.1128/mbio.02169-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Accepted: 09/03/2024] [Indexed: 10/05/2024] Open
Abstract
Nitrification is a core process in the global nitrogen (N) cycle mediated by ammonia-oxidizing microorganisms, including ammonia-oxidizing archaea (AOA) as a key player. Although much is known about AOA abundance and diversity across environments, the genetic drivers of the ecophysiological adaptations of the AOA are often less clearly defined. This is especially true for AOA within the genus Nitrosocosmicus, which have several unique physiological traits (e.g., high substrate tolerance, low substrate affinity, and large cell size). To better understand what separates the physiology of Nitrosocosmicus AOA, we performed comparative genomics with genomes from 39 cultured AOA, including five Nitrosocosmicus AOA. The absence of a canonical high-affinity type ammonium transporter and typical S-layer structural genes was found to be conserved across all Nitrosocosmicus AOA. In agreement, cryo-electron tomography confirmed the absence of a visible outermost S-layer structure, which has been observed in other AOA. In contrast to other AOA, the cryo-electron tomography highlighted the possibility that Nitrosocosmicus AOA may possess a glycoprotein or glycolipid-based glycocalyx cell covering outer layer. Together, the genomic, physiological, and metabolic properties revealed in this study provide insight into niche adaptation mechanisms and the overall ecophysiology of members of the Nitrosocosmicus clade in various terrestrial ecosystems. IMPORTANCE Nitrification is a vital process within the global biogeochemical nitrogen cycle but plays a significant role in the eutrophication of aquatic ecosystems and the production of the greenhouse gas nitrous oxide (N2O) from industrial agriculture ecosystems. While various types of ammonia-oxidizing microorganisms play a critical role in the N cycle, ammonia-oxidizing archaea (AOA) are often the most abundant nitrifiers in natural environments. Members of the genus Nitrosocosmicus are one of the prevalent AOA groups detected in undisturbed terrestrial ecosystems and have previously been reported to possess a range of physiological characteristics that set their physiology apart from other AOA species. This study provides significant progress in understanding these unique physiological traits and their genetic drivers. Our results highlight how physiological studies based on comparative genomics-driven hypotheses can contribute to understanding the unique niche of Nitrosocosmicus AOA.
Collapse
Affiliation(s)
- Saem Han
- Interdisciplinary Graduate Program in Advance Convergence Technology and Science, Jeju National University, Jeju, South Korea
| | - Seongwook Kim
- Interdisciplinary Graduate Program in Advance Convergence Technology and Science, Jeju National University, Jeju, South Korea
| | - Christopher J Sedlacek
- Division of Microbial Ecology, Centre for Microbiology and Environmental System Science, University of Vienna, Vienna, Austria
- Department of Biology, University of Southern Indiana, Evansville, Indiana, USA
| | - Adeel Farooq
- Department of Biology Education, Jeju National University, Jeju, South Korea
| | - Chihong Song
- Core Research Facility, Pusan National University, Yangsan, South Korea
| | - Sujin Lee
- Core Research Facility, Pusan National University, Yangsan, South Korea
| | - Shurong Liu
- School of Agriculture, Sun Yat-Sen University, Shenzhen, China
| | - Nicolas Brüggemann
- Agrosphäre (IBG-3), Institut für Bio- und Geowissenschaften (IBG), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Lena Rohe
- Thünen Institute of Climate-Smart Agriculture, Braunschweig, Germany
| | - Miye Kwon
- Biodiversity Research Institute, Jeju Technopark, Jeju, South Korea
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Chungdae-ro,Seowon-Gu, Cheongju, South Korea
| | - Man-Young Jung
- Interdisciplinary Graduate Program in Advance Convergence Technology and Science, Jeju National University, Jeju, South Korea
- Department of Biology Education, Jeju National University, Jeju, South Korea
| |
Collapse
|
2
|
Zheng X, Huang L. Diverse non-canonical electron bifurcating [FeFe]-hydrogenases of separate evolutionary origins in Hydrogenedentota. mSystems 2024; 9:e0099924. [PMID: 39189956 PMCID: PMC11406978 DOI: 10.1128/msystems.00999-24] [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: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/28/2024] Open
Abstract
Hydrogenedentota, a globally distributed bacterial phylum-level lineage, is poorly understood. Here, we established a comprehensive genomic catalog of Hydrogenedentota, including a total of seven clades (or families) with 179 genomes, and explored the metabolic potential and evolutionary history of these organisms. We show that a single genome, especially those belonging to Clade 6, often encodes multiple hydrogenases with genomes in Clade 2, which rarely encode hydrogenases being the exception. Notably, most members of Hydrogenedentota contain a group A3 [FeFe]-hydrogenase (BfuABC) with a non-canonical electron bifurcation mechanism, in addition to substrate-level phosphorylation and electron transport-linked phosphorylation pathways, in energy conservation. Furthermore, we show that BfuABC from Hydrogenedentota fall into five sub-types. Phylogenetic analysis reveals five independent routes for the evolution of BfuABC homologs in Hydrogenedentota. We speculate that the five sub-types of BfuABC might be acquired from Bacillota (synonym Firmicutes) through separate horizontal gene transfer events. These data shed light on the diversity and evolution of bifurcating [FeFe]-hydrogenases and provide insight into the strategy of Hydrogenedentota to adapt to survival in various habitats. IMPORTANCE The phylum Hydrogenedentota is widely distributed in various environments. However, their physiology, ecology, and evolutionary history remain unknown, primarily due to the limited availability of the genomes and the lack of cultured representatives of the phylum. Our results have increased the knowledge of the genetic and metabolic diversity of these organisms and shed light on their diverse energy conservation strategies, especially those involving electron bifurcation with a non-canonical mechanism, which are likely responsible for their wide distribution. Besides, the organization and phylogenetic relationships of gene clusters coding for BfuABC in Hydrogenedentota provide valuable clues to the evolutionary history of group A3 electron bifurcating [FeFe]-hydrogenases.
Collapse
Affiliation(s)
- Xiaowei Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
3
|
Pereira O, Qin W, Galand PE, Debroas D, Lami R, Hochart C, Zhou Y, Zhou J, Zhang C. Metabolic activities of marine ammonia-oxidizing archaea orchestrated by quorum sensing. MLIFE 2024; 3:417-429. [PMID: 39359677 PMCID: PMC11442133 DOI: 10.1002/mlf2.12144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/22/2024] [Accepted: 06/18/2024] [Indexed: 10/04/2024]
Abstract
Ammonia-oxidizing archaea (AOA) play crucial roles in marine carbon and nitrogen cycles by fixing inorganic carbon and performing the initial step of nitrification. Evaluation of carbon and nitrogen metabolism popularly relies on functional genes such as amoA and accA. Increasing studies suggest that quorum sensing (QS) mainly studied in biofilms for bacteria may serve as a universal communication and regulatory mechanism among prokaryotes; however, this has yet to be demonstrated in marine planktonic archaea. To bridge this knowledge gap, we employed a combination of metabolic activity markers (amoA, accA, and grs) to elucidate the regulation of AOA-mediated nitrogen, carbon processes, and their interactions with the surrounding heterotrophic population. Through co-transcription investigations linking metabolic markers to potential key QS genes, we discovered that QS molecules could regulate AOA's carbon, nitrogen, and lipid metabolisms under different conditions. Interestingly, specific AOA ecotypes showed a preference for employing distinct QS systems and a distinct QS circuit involving a typical population. Overall, our data demonstrate that QS orchestrates nitrogen and carbon metabolism, including the exchange of organic metabolites between AOA and surrounding heterotrophic bacteria, which has been previously overlooked in marine AOA research.
Collapse
Affiliation(s)
- Olivier Pereira
- Shenzhen Key Laboratory of Marine Geo-Omics of Archaea, Department of Science and Engineering Southern University of Science and Technology Shenzhen China
- Institut WUT-AMU Wuhan University of Technology and Aix-Marseille Université Wuhan China
| | - Wei Qin
- School of Biological Sciences, Institute for Environmental Genomics University of Oklahoma Norman Oklahoma USA
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB) Banyuls sur Mer France
| | - Didier Debroas
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement Clermont-Ferrand France
| | - Raphael Lami
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM) Banyuls sur Mer France
| | - Corentin Hochart
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB) Banyuls sur Mer France
| | - Yangkai Zhou
- Shenzhen Key Laboratory of Marine Geo-Omics of Archaea, Department of Science and Engineering Southern University of Science and Technology Shenzhen China
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School Tsinghua University Shenzhen China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Geo-Omics of Archaea, Department of Science and Engineering Southern University of Science and Technology Shenzhen China
- Shanghai Sheshan National Geophysical Observatory Shanghai Earthquake Agency Shanghai China
| |
Collapse
|
4
|
Pan J, Li J, Zhang T, Liu T, Xu K, Wang C, Zheng M. Complete ammonia oxidation (comammox) at pH 3-4 supports stable production of ammonium nitrate from urine. WATER RESEARCH 2024; 257:121686. [PMID: 38705065 DOI: 10.1016/j.watres.2024.121686] [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: 09/17/2023] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 05/07/2024]
Abstract
This study developed a new process that stably produced ammonium nitrate (NH4NO3), an important and commonly used fertilizer, from the source-separated urine by comammox Nitrospira. In the first stage, the complete conversion of ammonium to nitrate was achieved by comammox Nitrospira. In this scenario, the pH was maintained at 6 by adding external alkali, which also provided sufficient alkalinity for full nitrification. In the second stage, the NH4NO3 was produced directly by comammox Nitropsira by converting half of the ammonium in urine into nitrate. In this case, no alkali was added and pH automatically dropped and self-maintained at an extremely acidic level (pH 3-4). In both scenarios, negligible nitrite accumulation was observed, while the final product of the second stage contained ammonium and nitrate at the molar ratio of 1:1. The dominance of comammox Nitrospira over canonical ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) was systematically proved by the combination of 16S rRNA gene amplicon sequencing, quantitative polymerase chain reaction, and metagenomics. Notably, metagenomic sequencing suggested that the relative abundance of comammox Nitrospira was over 20 % under the acidic condition at pH 3-4, while canonical AOB and NOB were undetectable. Batch experiments showed that the optimal pH for the enriched comammox Nitrospira was ∼7, which could sustain their activity in a wider pH range from 4 to 8 surprisingly but lost activity at pH 3 and 9. The findings not only present an application potential of comammox Nitrospira in nitrogen recovery from urine wastewater but also report the survivability of comammox bacteria in acidic environments.
Collapse
Affiliation(s)
- Junhao Pan
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiyun Li
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Tingting Zhang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Tao Liu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Kangning Xu
- Beijing Key Laboratory for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, China
| | - Chengwen Wang
- School of Environment, Tsinghua University, Beijing 100084, China.
| | - Min Zheng
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales 2052, Australia.
| |
Collapse
|
5
|
Wang S, Lan B, Yu L, Xiao M, Jiang L, Qin Y, Jin Y, Zhou Y, Armanbek G, Ma J, Wang M, Jetten MSM, Tian H, Zhu G, Zhu YG. Ammonium-derived nitrous oxide is a global source in streams. Nat Commun 2024; 15:4085. [PMID: 38744837 PMCID: PMC11094135 DOI: 10.1038/s41467-024-48343-9] [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: 05/30/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
Global riverine nitrous oxide (N2O) emissions have increased more than 4-fold in the last century. It has been estimated that the hyporheic zones in small streams alone may contribute approximately 85% of these N2O emissions. However, the mechanisms and pathways controlling hyporheic N2O production in stream ecosystems remain unknown. Here, we report that ammonia-derived pathways, rather than the nitrate-derived pathways, are the dominant hyporheic N2O sources (69.6 ± 2.1%) in agricultural streams around the world. The N2O fluxes are mainly in positive correlation with ammonia. The potential N2O metabolic pathways of metagenome-assembled genomes (MAGs) provides evidence that nitrifying bacteria contain greater abundances of N2O production-related genes than denitrifying bacteria. Taken together, this study highlights the importance of mitigating agriculturally derived ammonium in low-order agricultural streams in controlling N2O emissions. Global models of riverine ecosystems need to better represent ammonia-derived pathways for accurately estimating and predicting riverine N2O emissions.
Collapse
Affiliation(s)
- Shanyun Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bangrui Lan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Longbin Yu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Manyi Xiao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Liping Jiang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Qin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yucheng Jin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yuting Zhou
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Gawhar Armanbek
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingchen Ma
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Manting Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Mike S M Jetten
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, AJ, 6525, the Netherlands
| | - Hanqin Tian
- Center for Earth System Science and Global Sustainability, Schiller Institute for Integrated Science and Society, Boston College, Chestnut Hill, MA, 02467, USA
- Department of Earth and Environmental Sciences, Boston College, Chestnut Hill, MA, 02467, USA
| | - Guibing Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yong-Guan Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
6
|
Wang S, Narsing Rao MP, Quadri SR. Assessing the metabolism, phylogenomic, and taxonomic classification of the halophilic genus Halarchaeum. FEMS Microbiol Lett 2024; 371:fnae001. [PMID: 38192037 DOI: 10.1093/femsle/fnae001] [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: 11/16/2023] [Revised: 01/01/2024] [Accepted: 01/05/2024] [Indexed: 01/10/2024] Open
Abstract
In this study, a genomic approach was employed to evaluate the metabolic potentials and taxonomic classification of the halophilic genus Halarchaeum. Genomic analysis revealed that Halarchaeum members exhibit a predilection for amino acids as their primary energy source in high-salinity environments over carbohydrates. Genome analysis unveiled the presence of crucial genes associated with metabolic pathways, including the Embden-Meyerhof pathway, semi-phosphorylative Entner-Doudoroff pathway, and the urea cycle. Furthermore, the genomic analysis indicated that Halarchaeum members employ diverse mechanisms for osmotic regulation (encompassing both salt-in and salt-out strategies). Halarchaeum members also encode genes to alleviate acid and heat stress. The average nucleotide identity value between Halarchaeum solikamskense and Halarchaeum nitratireducens exceeded the established threshold (95%-96%) for defining distinct species. This high similarity suggests a close relationship between these two species, prompting the proposal to reclassify Halarchaeum solikamskense as a heterotypic synonym of Halarchaeum nitratireducens. The results of this study contribute to our knowledge of taxonomic classification and shed light on the adaptive strategies employed by Halarchaeum species in their specific ecological niches.
Collapse
Affiliation(s)
- Shuang Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization/Heilongjiang Black Soil Conservation Engineering and Technology Research Center, Harbin 150086, People's Republic of China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, People's Republic of China
| | - Manik Prabhu Narsing Rao
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Sede Talca, Talca 3460000, Chile
| | - Syed Raziuddin Quadri
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Northern Border University, Arar-91431 Northern Borders, Kingdom of Saudi Arabia
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Zheng Y, Wang B, Gao P, Yang Y, Xu B, Su X, Ning D, Tao Q, Li Q, Zhao F, Wang D, Zhang Y, Li M, Winkler MKH, Ingalls AE, Zhou J, Zhang C, Stahl DA, Jiang J, Martens-Habbena W, Qin W. Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments. THE ISME JOURNAL 2024; 18:wrad002. [PMID: 38365232 PMCID: PMC10811736 DOI: 10.1093/ismejo/wrad002] [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: 10/20/2023] [Revised: 11/03/2023] [Accepted: 10/28/2023] [Indexed: 02/18/2024]
Abstract
Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.
Collapse
Affiliation(s)
- Yue Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Baozhan Wang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Gao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiyan Yang
- National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States
| | - Bu Xu
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen 518055, China
- Shanghai Sheshan National Geophysical Observatory , Shanghai 201602, China
| | - Xiaoquan Su
- College of Computer Science and Technology, Qingdao University , Qingdao 266101, China
| | - Daliang Ning
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
| | - Qing Tao
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
| | - Qian Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Feng Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Mari-K H Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, United States
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA 98195, United States
| | - Jizhong Zhou
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK 73019, United States
- Department of Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen 518055, China
- Shanghai Sheshan National Geophysical Observatory , Shanghai 201602, China
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, United States
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Willm Martens-Habbena
- Department of Microbiology and Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL 33314, United States
| | - Wei Qin
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
| |
Collapse
|
9
|
Luo ZH, Li Q, Xie YG, Lv AP, Qi YL, Li MM, Qu YN, Liu ZT, Li YX, Rao YZ, Jiao JY, Liu L, Narsing Rao MP, Hedlund BP, Evans PN, Fang Y, Shu WS, Huang LN, Li WJ, Hua ZS. Temperature, pH, and oxygen availability contributed to the functional differentiation of ancient Nitrososphaeria. THE ISME JOURNAL 2024; 18:wrad031. [PMID: 38365241 PMCID: PMC10833072 DOI: 10.1093/ismejo/wrad031] [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: 12/01/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 02/18/2024]
Abstract
Ammonia-oxidizing Nitrososphaeria are among the most abundant archaea on Earth and have profound impacts on the biogeochemical cycles of carbon and nitrogen. In contrast to these well-studied ammonia-oxidizing archaea (AOA), deep-branching non-AOA within this class remain poorly characterized because of a low number of genome representatives. Here, we reconstructed 128 Nitrososphaeria metagenome-assembled genomes from acid mine drainage and hot spring sediment metagenomes. Comparative genomics revealed that extant non-AOA are functionally diverse, with capacity for carbon fixation, carbon monoxide oxidation, methanogenesis, and respiratory pathways including oxygen, nitrate, sulfur, or sulfate, as potential terminal electron acceptors. Despite their diverse anaerobic pathways, evolutionary history inference suggested that the common ancestor of Nitrososphaeria was likely an aerobic thermophile. We further surmise that the functional differentiation of Nitrososphaeria was primarily shaped by oxygen, pH, and temperature, with the acquisition of pathways for carbon, nitrogen, and sulfur metabolism. Our study provides a more holistic and less biased understanding of the diversity, ecology, and deep evolution of the globally abundant Nitrososphaeria.
Collapse
Affiliation(s)
- Zhen-Hao Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Qi Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yuan-Guo Xie
- Chinese Academy of Sciences, Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, PR China
| | - Ai-Ping Lv
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yan-Ling Qi
- Chinese Academy of Sciences, Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, PR China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yan-Ni Qu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Ze-Tao Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yu-Xian Li
- Chinese Academy of Sciences, Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, PR China
| | - Yang-Zhi Rao
- Chinese Academy of Sciences, Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, PR China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Manik Prabhu Narsing Rao
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Sede Talca, 3460000 Talca, Chile
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, United States
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, United States
| | - Paul N Evans
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Yuan Fang
- Chinese Academy of Sciences, Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, PR China
| | - Wen-Sheng Shu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
- Guangdong Provincial Key Laboratory of Chemical Pollution, South China Normal University, Guangzhou 510006, PR China
| | - Li-Nan Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences, Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, PR China
| |
Collapse
|
10
|
Zhang RY, Wang YR, Liu RL, Rhee SK, Zhao GP, Quan ZX. Metagenomic characterization of a novel non-ammonia-oxidizing Thaumarchaeota from hadal sediment. MICROBIOME 2024; 12:7. [PMID: 38191433 PMCID: PMC10773090 DOI: 10.1186/s40168-023-01728-2] [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: 07/01/2023] [Accepted: 11/20/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND The hadal sediment, found at an ocean depth of more than 6000 m, is geographically isolated and under extremely high hydrostatic pressure, resulting in a unique ecosystem. Thaumarchaeota are ubiquitous marine microorganisms predominantly present in hadal environments. While there have been several studies on Thaumarchaeota there, most of them have primarily focused on ammonia-oxidizing archaea (AOA). However, systematic metagenomic research specifically targeting heterotrophic non-AOA Thaumarchaeota is lacking. RESULTS In this study, we explored the metagenomes of Challenger Deep hadal sediment, focusing on the Thaumarchaeota. Functional analysis of sequence reads revealed the potential contribution of Thaumarchaeota to recalcitrant dissolved organic matter degradation. Metagenome assembly binned one new group of hadal sediment-specific and ubiquitously distributed non-AOA Thaumarchaeota, named Group-3.unk. Pathway reconstruction of this new type of Thaumarchaeota also supports heterotrophic characteristics of Group-3.unk, along with ABC transporters for the uptake of amino acids and carbohydrates and catabolic utilization of these substrates. This new clade of Thaumarchaeota also contains aerobic oxidation of carbon monoxide-related genes. Complete glyoxylate cycle is a distinctive feature of this clade in supplying intermediates of anabolic pathways. The pan-genomic and metabolic analyses of metagenome-assembled genomes belonging to Group-3.unk Thaumarchaeota have highlighted distinctions, including the dihydroxy phthalate decarboxylase gene associated with the degradation of aromatic compounds and the absence of genes related to the synthesis of some types of vitamins compared to AOA. Notably, Group-3.unk shares a common feature with deep ocean AOA, characterized by their high hydrostatic pressure resistance, potentially associated with the presence of V-type ATP and di-myo-inositol phosphate syntheses-related genes. The enrichment of organic matter in hadal sediments might be attributed to the high recruitment of sequence reads of the Group-3.unk clade of heterotrophic Thaumarchaeota in the trench sediment. Evolutionary and genetic dynamic analyses suggest that Group-3 non-AOA consists of mesophilic Thaumarchaeota organisms. These results indicate a potential role in the transition from non-AOA to AOA Thaumarchaeota and from thermophilic to mesophilic Thaumarchaeota, shedding light on recent evolutionary pathways. CONCLUSIONS One novel clade of heterotrophic non-AOA Thaumarchaeota was identified through metagenome analysis of sediments from Challenger Deep. Our study provides insight into the ecology and genomic characteristics of the new sub-group of heterotrophic non-AOA Thaumarchaeota, thereby extending the knowledge of the evolution of Thaumarchaeota. Video Abstract.
Collapse
Affiliation(s)
- Ru-Yi Zhang
- Fudan Microbiome Center, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Yan-Ren Wang
- Fudan Microbiome Center, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Ru-Long Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, Republic of Korea
| | - Guo-Ping Zhao
- Fudan Microbiome Center, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhe-Xue Quan
- Fudan Microbiome Center, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China.
| |
Collapse
|
11
|
Kop LFM, Koch H, Jetten MSM, Daims H, Lücker S. Metabolic and phylogenetic diversity in the phylum Nitrospinota revealed by comparative genome analyses. ISME COMMUNICATIONS 2024; 4:ycad017. [PMID: 38317822 PMCID: PMC10839748 DOI: 10.1093/ismeco/ycad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
The most abundant known nitrite-oxidizing bacteria in the marine water column belong to the phylum Nitrospinota. Despite their importance in marine nitrogen cycling and primary production, there are only few cultured representatives that all belong to the class Nitrospinia. Moreover, although Nitrospinota were traditionally thought to be restricted to marine environments, metagenome-assembled genomes have also been recovered from groundwater. Over the recent years, metagenomic sequencing has led to the discovery of several novel classes of Nitrospinota (UBA9942, UBA7883, 2-12-FULL-45-22, JACRGO01, JADGAW01), which remain uncultivated and have not been analyzed in detail. Here, we analyzed a nonredundant set of 98 Nitrospinota genomes with focus on these understudied Nitrospinota classes and compared their metabolic profiles to get insights into their potential role in biogeochemical element cycling. Based on phylogenomic analysis and average amino acid identities, the highly diverse phylum Nitrospinota could be divided into at least 33 different genera, partly with quite distinct metabolic capacities. Our analysis shows that not all Nitrospinota are nitrite oxidizers and that members of this phylum have the genomic potential to use sulfide and hydrogen for energy conservation. This study expands our knowledge of the phylogeny and potential ecophysiology of the phylum Nitrospinota and offers new avenues for the isolation and cultivation of these elusive bacteria.
Collapse
Affiliation(s)
- Linnea F M Kop
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, Vienna 1030, Austria
| | - Hanna Koch
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, Tulln an der Donau 3430, Austria
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Holger Daims
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, Vienna 1030, Austria
| | - Sebastian Lücker
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| |
Collapse
|
12
|
Mahendrarajah TA, Moody ERR, Schrempf D, Szánthó LL, Dombrowski N, Davín AA, Pisani D, Donoghue PCJ, Szöllősi GJ, Williams TA, Spang A. ATP synthase evolution on a cross-braced dated tree of life. Nat Commun 2023; 14:7456. [PMID: 37978174 PMCID: PMC10656485 DOI: 10.1038/s41467-023-42924-w] [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: 04/21/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023] Open
Abstract
The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. We reconstruct the evolutionary history of ATP synthases using an expanded taxon sampling set and develop a phylogenetic cross-bracing approach, constraining equivalent speciation nodes to be contemporaneous, based on the phylogenetic imprint of endosymbioses and ancient gene duplications. This approach results in a highly resolved, dated species tree and establishes an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of ATP synthase into F- and A/V-type lineages was a very early event in cellular evolution dating back to more than 4 Ga, potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19 Ga) and bacterial (2.58-2.12 Ga) relatives at approximately the same time, with a slightly longer nuclear stem-lineage.
Collapse
Affiliation(s)
- Tara A Mahendrarajah
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - Edmund R R Moody
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Dominik Schrempf
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
| | - Lénárd L Szánthó
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- Institute of Evolution, Centre for Ecological Research, Karolina ut 29, H-1113, Budapest, Hungary
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - Adrián A Davín
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Gergely J Szöllősi
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- Model-Based Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK.
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands.
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
13
|
Vos M, Padfield D, Quince C, Vos R. Adaptive radiations in natural populations of prokaryotes: innovation is key. FEMS Microbiol Ecol 2023; 99:fiad154. [PMID: 37996397 PMCID: PMC10710302 DOI: 10.1093/femsec/fiad154] [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: 09/13/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
Prokaryote diversity makes up most of the tree of life and is crucial to the functioning of the biosphere and human health. However, the patterns and mechanisms of prokaryote diversification have received relatively little attention compared to animals and plants. Adaptive radiation, the rapid diversification of an ancestor species into multiple ecologically divergent species, is a fundamental process by which macrobiological diversity is generated. Here, we discuss whether ecological opportunity could lead to similar bursts of diversification in bacteria. We explore how adaptive radiations in prokaryotes can be kickstarted by horizontally acquired key innovations allowing lineages to invade new niche space that subsequently is partitioned among diversifying specialist descendants. We discuss how novel adaptive zones are colonized and exploited after the evolution of a key innovation and whether certain types of are more prone to adaptive radiation. Radiation into niche specialists does not necessarily lead to speciation in bacteria when barriers to recombination are absent. We propose that in this scenario, niche-specific genes could accumulate within a single lineage, leading to the evolution of an open pangenome.
Collapse
Affiliation(s)
- Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
- Environment and Sustainability Institute, University of Exeter, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
| | - Daniel Padfield
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
- Environment and Sustainability Institute, University of Exeter, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
- Gut Microbes and Health, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
| | - Rutger Vos
- Naturalis Biodiversity Center, Understanding Evolution, Darwinweg 2, Leiden 2333 CR, the Netherlands
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, Leiden 2333 BE, the Netherlands
| |
Collapse
|
14
|
Sarkar S, Kazarina A, Hansen PM, Ward K, Hargreaves C, Reese N, Ran Q, Kessler W, de Souza LF, Loecke TD, Sarto MVM, Rice CW, Zeglin LH, Sikes BA, Lee ST. Ammonia-oxidizing archaea and bacteria differentially contribute to ammonia oxidation in soil under precipitation gradients and land legacy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566028. [PMID: 37987001 PMCID: PMC10659370 DOI: 10.1101/2023.11.08.566028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Background Global change has accelerated the nitrogen cycle. Soil nitrogen stock degradation by microbes leads to the release of various gases, including nitrous oxide (N2O), a potent greenhouse gas. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) participate in the soil nitrogen cycle, producing N2O. There are outstanding questions regarding the impact of environmental processes such as precipitation and land use legacy on AOA and AOB structurally, compositionally, and functionally. To answer these questions, we analyzed field soil cores and soil monoliths under varying precipitation profiles and land legacies. Results We resolved 28 AOA and AOB metagenome assembled genomes (MAGs) and found that they were significantly higher in drier environments and differentially abundant in different land use legacies. We further dissected AOA and AOB functional potentials to understand their contribution to nitrogen transformation capabilities. We identified the involvement of stress response genes, differential metabolic functional potentials, and subtle population dynamics under different environmental parameters for AOA and AOB. We observed that AOA MAGs lacked a canonical membrane-bound electron transport chain and F-type ATPase but possessed A/A-type ATPase, while AOB MAGs had a complete complex III module and F-type ATPase, suggesting differential survival strategies of AOA and AOB. Conclusions The outcomes from this study will enable us to comprehend how drought-like environments and land use legacies could impact AOA- and AOB-driven nitrogen transformations in soil.
Collapse
Affiliation(s)
- Soumyadev Sarkar
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Anna Kazarina
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Paige M. Hansen
- PMH Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado USA
| | - Kaitlyn Ward
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | | | - Nicholas Reese
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Qinghong Ran
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Willow Kessler
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Ligia F.T. de Souza
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Terry D. Loecke
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
- Environmental Studies Program, University of Kansas, Lawrence, Kansas, USA
| | | | - Charles W. Rice
- Department of Agronomy, Kansas State University, Manhattan, Kansas, USA
| | - Lydia H. Zeglin
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Benjamin A. Sikes
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
| | - Sonny T.M. Lee
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| |
Collapse
|
15
|
Sheridan PO, Meng Y, Williams TA, Gubry-Rangin C. Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae. Nat Commun 2023; 14:7305. [PMID: 37951938 PMCID: PMC10640624 DOI: 10.1038/s41467-023-43196-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023] Open
Abstract
Knowledge of deeply-rooted non-ammonia oxidising Thaumarchaeota lineages from terrestrial environments is scarce, despite their abundance in acidic soils. Here, 15 new deeply-rooted thaumarchaeotal genomes were assembled from acidic topsoils (0-15 cm) and subsoils (30-60 cm), corresponding to two genera of terrestrially prevalent Gagatemarchaeaceae (previously known as thaumarchaeotal Group I.1c) and to a novel genus of heterotrophic terrestrial Thaumarchaeota. Unlike previous predictions, metabolic annotations suggest Gagatemarchaeaceae perform aerobic respiration and use various organic carbon sources. Evolutionary divergence between topsoil and subsoil lineages happened early in Gagatemarchaeaceae history, with significant metabolic and genomic trait differences. Reconstruction of the evolutionary mechanisms showed that the genome expansion in topsoil Gagatemarchaeaceae resulted from extensive early lateral gene acquisition, followed by progressive gene duplication throughout evolutionary history. Ancestral trait reconstruction using the expanded genomic diversity also did not support the previous hypothesis of a thermophilic last common ancestor of the ammonia-oxidising archaea. Ultimately, this study provides a good model for studying mechanisms driving niche partitioning between spatially related ecosystems.
Collapse
Affiliation(s)
- Paul O Sheridan
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Yiyu Meng
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | |
Collapse
|
16
|
Zou D, Chen J, Zhang C, Kao SJ, Liu H, Li M. Diversity and salinity adaptations of ammonia oxidizing archaea in three estuaries of China. Appl Microbiol Biotechnol 2023; 107:6897-6909. [PMID: 37702790 DOI: 10.1007/s00253-023-12761-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/22/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
Ammonia-oxidizing archaea (AOA) are ubiquitously found in diverse habitats and play pivotal roles in the nitrogen and carbon cycle, especially in estuarine and coastal environments. Despite the fact that the diversity and distribution of AOA are thought to be tightly linked to habitats, little is known about the relationship that underpins their genomic traits, adaptive potentials, and ecological niches. Here, we have characterized and compared the AOA community in three estuaries of China using metagenomics. AOA were the dominant ammonia oxidizers in the three estuaries. Through phylogenetic analyses, five major AOA groups were identified, including the Nitrosomarinus-like, Nitrosopumilus-like, Aestuariumsis-like, Nitrosarchaeum-like, and Nitrosopelagicus-like groups. Statistical analyses showed that the aquatic and sedimentary AOA communities were mainly influenced by spatial factors (latitude and water depth) and environmental factors (salinity, pH, and dissolved oxygen) in estuaries, respectively. Compared to AOA dwelling in terrestrial and marine habitats, estuarine AOA encoded more genes involved in glucose and amino acid metabolism, transport systems, osmotic control, and cell motility. The low proteome isoelectric points (pI), high content of acidic amino acids, and the presence of potassium ion and mechanosensitive channels suggest a "salt-in" strategy for estuarine AOA to counteract high osmolarity in their surroundings. Our findings have indicated potential adaptation strategies and highlighted their importance in the estuarine nitrogen and carbon cycles. KEY POINTS: • Spatial and environmental factors influence water and sediment AOA respectively. • Estuarine AOA share low proteome isoelectric value and high acid amino acids content. • AOA adaptation to estuaries is likely resulted from their unique genomic features.
Collapse
Affiliation(s)
- Dayu Zou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Jianfang Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, 518000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361000, China
| | - Hongbin Liu
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
| |
Collapse
|
17
|
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.
Collapse
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.
| |
Collapse
|
18
|
Ni G, Leung PM, Daebeler A, Guo J, Hu S, Cook P, Nicol GW, Daims H, Greening C. Nitrification in acidic and alkaline environments. Essays Biochem 2023; 67:753-768. [PMID: 37449414 PMCID: PMC10427799 DOI: 10.1042/ebc20220194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
Aerobic nitrification is a key process in the global nitrogen cycle mediated by microorganisms. While nitrification has primarily been studied in near-neutral environments, this process occurs at a wide range of pH values, spanning ecosystems from acidic soils to soda lakes. Aerobic nitrification primarily occurs through the activities of ammonia-oxidising bacteria and archaea, nitrite-oxidising bacteria, and complete ammonia-oxidising (comammox) bacteria adapted to these environments. Here, we review the literature and identify knowledge gaps on the metabolic diversity, ecological distribution, and physiological adaptations of nitrifying microorganisms in acidic and alkaline environments. We emphasise that nitrifying microorganisms depend on a suite of physiological adaptations to maintain pH homeostasis, acquire energy and carbon sources, detoxify reactive nitrogen species, and generate a membrane potential at pH extremes. We also recognize the broader implications of their activities primarily in acidic environments, with a focus on agricultural productivity and nitrous oxide emissions, as well as promising applications in treating municipal wastewater.
Collapse
Affiliation(s)
- Gaofeng Ni
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Pok Man Leung
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Anne Daebeler
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, Ceske Budejovice, Czechia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (Formerly AWMC), The University of Queensland, Brisbane, Queensland, Australia
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology (Formerly AWMC), The University of Queensland, Brisbane, Queensland, Australia
| | - Perran Cook
- School of Chemistry, Monash University, Melbourne, Victoria, Australia
| | - Graeme W Nicol
- Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, Ecole Centrale de Lyon, Ampère, UMR5005, 69134 Ecully, France
| | - Holger Daims
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- The Comammox Research Platform, University of Vienna, Vienna, Austria
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Securing Antarctica's Environmental Future, Monash University, Melbourne, Victoria, Australia
- Centre to Impact AMR, Monash University, Melbourne, Victoria, Australia
| |
Collapse
|
19
|
Zhou J, Zheng Y, Hou L, An Z, Chen F, Liu B, Wu L, Qi L, Dong H, Han P, Yin G, Liang X, Yang Y, Li X, Gao D, Li Y, Liu Z, Bellerby R, Liu M. Effects of acidification on nitrification and associated nitrous oxide emission in estuarine and coastal waters. Nat Commun 2023; 14:1380. [PMID: 36914644 PMCID: PMC10011576 DOI: 10.1038/s41467-023-37104-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/28/2023] [Indexed: 03/16/2023] Open
Abstract
In the context of an increasing atmospheric carbon dioxide (CO2) level, acidification of estuarine and coastal waters is greatly exacerbated by land-derived nutrient inputs, coastal upwelling, and complex biogeochemical processes. A deeper understanding of how nitrifiers respond to intensifying acidification is thus crucial to predict the response of estuarine and coastal ecosystems and their contribution to global climate change. Here, we show that acidification can significantly decrease nitrification rate but stimulate generation of byproduct nitrous oxide (N2O) in estuarine and coastal waters. By varying CO2 concentration and pH independently, an expected beneficial effect of elevated CO2 on activity of nitrifiers ("CO2-fertilization" effect) is excluded under acidification. Metatranscriptome data further demonstrate that nitrifiers could significantly up-regulate gene expressions associated with intracellular pH homeostasis to cope with acidification stress. This study highlights the molecular underpinnings of acidification effects on nitrification and associated greenhouse gas N2O emission, and helps predict the response and evolution of estuarine and coastal ecosystems under climate change and human activities.
Collapse
Affiliation(s)
- Jie Zhou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, East China Normal University, Shanghai, 200241, China
| | - Yanling Zheng
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, East China Normal University, Shanghai, 200241, China. .,School of Geographic Sciences, East China Normal University, Shanghai, 200241, China. .,Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China. .,Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai, 200241, China.
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, East China Normal University, Shanghai, 200241, China.
| | - Zhirui An
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, East China Normal University, Shanghai, 200241, China
| | - Feiyang Chen
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, East China Normal University, Shanghai, 200241, China
| | - Bolin Liu
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, East China Normal University, Shanghai, 200241, China
| | - Li Wu
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China.,Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China
| | - Lin Qi
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China.,Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, East China Normal University, Shanghai, 200241, China
| | - Ping Han
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China.,Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China.,Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai, 200241, China
| | - Guoyu Yin
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China.,Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China.,Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai, 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, East China Normal University, Shanghai, 200241, China
| | - Yi Yang
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China.,Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China.,Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai, 200241, China
| | - Xiaofei Li
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, East China Normal University, Shanghai, 200241, China
| | - Dengzhou Gao
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, East China Normal University, Shanghai, 200241, China
| | - Ye Li
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China.,Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China.,Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai, 200241, China
| | - Zhanfei Liu
- The University of Texas at Austin Marine Science Institute, Port Aransas, TX, 78373, USA
| | - Richard Bellerby
- Norwegian Institute for Water Research, Thormøhlensgt 53D, 5006, Bergen, Norway
| | - Min Liu
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China. .,Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China. .,Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai, 200241, China.
| |
Collapse
|
20
|
Zhao J, Rodriguez J, Martens-Habbena W. Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils. Front Microbiol 2023; 14:1140487. [PMID: 36910167 PMCID: PMC9995467 DOI: 10.3389/fmicb.2023.1140487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 01/30/2023] [Indexed: 02/25/2023] Open
Abstract
The advance of high-throughput molecular biology tools allows in-depth profiling of microbial communities in soils, which possess a high diversity of prokaryotic microorganisms. Amplicon-based sequencing of 16S rRNA genes is the most common approach to studying the richness and composition of soil prokaryotes. To reliably detect different taxonomic lineages of microorganisms in a single soil sample, an adequate pipeline including DNA isolation, primer selection, PCR amplification, library preparation, DNA sequencing, and bioinformatic post-processing is required. Besides DNA sequencing quality and depth, the selection of PCR primers and PCR amplification reactions arguably have the largest influence on the results. This study tested the performance and potential bias of two primer pairs, i.e., 515F (Parada)-806R (Apprill) and 515F (Parada)-926R (Quince) in the standard pipelines of 16S rRNA gene Illumina amplicon sequencing protocol developed by the Earth Microbiome Project (EMP), against shotgun metagenome-based 16S rRNA gene reads. The evaluation was conducted using five differently managed soils. We observed a higher richness of soil total prokaryotes by using reverse primer 806R compared to 926R, contradicting to in silico evaluation results. Both primer pairs revealed various degrees of taxon-specific bias compared to metagenome-derived 16S rRNA gene reads. Nonetheless, we found consistent patterns of microbial community variation associated with different land uses, irrespective of primers used. Total microbial communities, as well as ammonia oxidizing archaea (AOA), the predominant ammonia oxidizers in these soils, shifted along with increased soil pH due to agricultural management. In the unmanaged low pH plot abundance of AOA was dominated by the acid-tolerant NS-Gamma clade, whereas limed agricultural plots were dominated by neutral-alkaliphilic NS-Delta/NS-Alpha clades. This study stresses how primer selection influences community composition and highlights the importance of primer selection for comparative and integrative studies, and that conclusions must be drawn with caution if data from different sequencing pipelines are to be compared.
Collapse
Affiliation(s)
| | | | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, United States
| |
Collapse
|
21
|
Ngugi DK, Salcher MM, Andrei AS, Ghai R, Klotz F, Chiriac MC, Ionescu D, Büsing P, Grossart HP, Xing P, Priscu JC, Alymkulov S, Pester M. Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes. SCIENCE ADVANCES 2023; 9:eadc9392. [PMID: 36724220 PMCID: PMC9891703 DOI: 10.1126/sciadv.adc9392] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their genetic diversity is viewed as the outcome of evolutionary processes that shaped ancestral transition from terrestrial to marine habitats. However, current genome-wide insights into AOA evolution rarely consider brackish and freshwater representatives or provide their divergence timeline in lacustrine systems. An unbiased global assessment of lacustrine AOA diversity is critical for understanding their origins, dispersal mechanisms, and ecosystem roles. Here, we leveraged continental-scale metagenomics to document that AOA species diversity in freshwater systems is remarkably low compared to marine environments. We show that the uncultured freshwater AOA, "Candidatus Nitrosopumilus limneticus," is ubiquitous and genotypically static in various large European lakes where it evolved 13 million years ago. We find that extensive proteome remodeling was a key innovation for freshwater colonization of AOA. These findings reveal the genetic diversity and adaptive mechanisms of a keystone species that has survived clonally in lakes for millennia.
Collapse
Affiliation(s)
- David Kamanda Ngugi
- Leibniz Institute DSMZ–German Collection of Cell Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
- Corresponding author.
| | - Michaela M. Salcher
- Institute of Hydrobiology, Biology Center CAS, Na Sádkách 7, 37005 České Budejovice, Czech Republic
| | - Adrian-Stefan Andrei
- Microbial Evogenomics Lab, Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Rohit Ghai
- Institute of Hydrobiology, Biology Center CAS, Na Sádkách 7, 37005 České Budejovice, Czech Republic
| | - Franziska Klotz
- Department of Biology, University of Konstanz, D-78457 Constance, Germany
| | - Maria-Cecilia Chiriac
- Institute of Hydrobiology, Biology Center CAS, Na Sádkách 7, 37005 České Budejovice, Czech Republic
| | - Danny Ionescu
- Department of Experimental Limnology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, D-12587 Stechlin, Germany
| | - Petra Büsing
- Leibniz Institute DSMZ–German Collection of Cell Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, D-12587 Stechlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, D-14469 Potsdam, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Free University, D-14195 Berlin, Germany
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - John C. Priscu
- Department of Land Resources and Environmental Sciences, Montana State University, 334 Leon Johnson Hall, Bozeman, MT 59717, USA
| | - Salmor Alymkulov
- Institute of Physics, National Academy of Sciences of Kyrgyz Republic, Chui Avenue, 265-a, Bishkek 720071, Kyrgyzstan
| | - Michael Pester
- Leibniz Institute DSMZ–German Collection of Cell Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
- Institute of Microbiology, Technical University of Braunschweig, D-38108 Braunschweig, Germany
| |
Collapse
|
22
|
Wang D, Meng Y, Meng F. Genome-centric metagenomics insights into functional divergence and horizontal gene transfer of denitrifying bacteria in anammox consortia. WATER RESEARCH 2022; 224:119062. [PMID: 36116192 DOI: 10.1016/j.watres.2022.119062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/21/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
Denitrifying bacteria with high abundances in anammox communities play crucial roles in achieving stable anammox-based systems. Despite the relative constant composition of denitrifying bacteria, their functional diversity remains to be explored in anammox communities. Herein, a total of 77 high-quality metagenome-assembled genomes (MAGs) of denitrifying bacteria were recovered from the anammox community in a full-scale swine wastewater treatment plant. Among these microbes, a total of 26 MAGs were affiliated with the seven dominant denitrifying genera that have total abundances higher than 1%. A meta-analysis of these species suggested that external organics reduced the abundances of genus Ignavibacterium and species MAG.305 of UTPRO2 in anammox communities. Comparative genome analysis revealed functional divergence across different denitrifying bacteria, largely owing to their distinct capabilities for carbohydrate (including endogenous and exogenous) utilization and vitamin (e.g., pantothenate and thiamine) biosynthesis. Serval microbes in this system contained fewer genes encoding biotin, pantothenate and methionine biosynthesis compared with their related species from other habitats. In addition, the genes encoding energy production and conversion (73 genes) and inorganic ion transport (53 genes) putatively transferred from other species to denitrifying bacteria, while these denitrifying bacteria (especially genera UTPRO2 and SCN-69-89) likely donated the genes encoding nutrients (e.g., inorganic ion and amino acid) transporter (64 genes) for other members to utilize new metabolites. Collectively, these findings highlighted the functional divergence of these denitrifying bacteria and speculated that the genetic interactions within anammox communities through horizontal gene transfer may be one of the reasons for their functional divergence.
Collapse
Affiliation(s)
- Depeng Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China
| | - Yabing Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China.
| |
Collapse
|
23
|
Sheridan PO, Meng Y, Williams TA, Gubry-Rangin C. Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota. Nat Commun 2022; 13:4110. [PMID: 35840579 PMCID: PMC9287336 DOI: 10.1038/s41467-022-31847-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/06/2022] [Indexed: 11/09/2022] Open
Abstract
The Terrestrial Miscellaneous Euryarchaeota Group has been identified in various environments, and the single genome investigated thus far suggests that these archaea are anaerobic sulfite reducers. We assemble 35 new genomes from this group that, based on genome analysis, appear to possess aerobic and facultative anaerobic lifestyles and may oxidise rather than reduce sulfite. We propose naming this order (representing 16 genera) "Lutacidiplasmatales" due to their occurrence in various acidic environments and placement within the phylum Thermoplasmatota. Phylum-level analysis reveals that Thermoplasmatota evolution had been punctuated by several periods of high levels of novel gene family acquisition. Several essential metabolisms, such as aerobic respiration and acid tolerance, were likely acquired independently by divergent lineages through convergent evolution rather than inherited from a common ancestor. Ultimately, this study describes the terrestrially prevalent Lutacidiciplasmatales and highlights convergent evolution as an important driving force in the evolution of archaeal lineages.
Collapse
Affiliation(s)
- Paul O Sheridan
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Yiyu Meng
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | |
Collapse
|
24
|
Ren M, Wang J. Phylogenetic divergence and adaptation of Nitrososphaeria across lake depths and freshwater ecosystems. THE ISME JOURNAL 2022; 16:1491-1501. [PMID: 35091647 PMCID: PMC9123079 DOI: 10.1038/s41396-022-01199-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 01/05/2022] [Accepted: 01/17/2022] [Indexed: 04/29/2023]
Abstract
Thaumarchaeota (now the class Nitrososphaeria in the phylum Thermoproteota in GTDB taxonomy) are abundant across marine and soil habitats; however, their genomic diversity and evolutionary history in freshwater environments remain elusive. Here, we reconstructed 17 high-quality metagenome-assembled genomes of Nitrososphaeria from a deep lake and two great rivers, and compared all available genomes between freshwater and marine habitats regarding their phylogenetic positions, relative abundance, and genomic content. We found that freshwater Nitrososphaeria were dominated by the family Nitrosopumilaceae and could be grouped into three distinct clades closely related to the genera Nitrosopumilus, Nitrosoarchaeum, and Nitrosotenuis. The Nitrosopumilus-like clade was exclusively from deep lakes, while the Nitrosoarchaeum-like clade was dominated by species from deep lakes and rivers, and the Nitrosotenuis-like clade was mainly from rivers, deep lakes, and estuaries. Interestingly, there was vertical niche separation between two clades in deep lakes, showing that the Nitrosopumilus-like species dominated shallow layers, whereas the relative abundance of the Nitrosoarchaeum-like clade increased toward deep waters. Phylogenetic clustering patterns in the Nitrosopumilaceae supported at least one freshwater-to-marine and two marine-to-freshwater transitions, the former of which refined the potential terrestrial-to-marine evolutionary path as previously proposed. The occurrence of the two marine-to-freshwater transitions were accompanied by horizontal transfer of the genes involved in nutrition regulation, osmoregulation, and cell motility during their colonization to freshwater habitats. Specifically, the Nitrosopumilus-like clade showed losses of genes encoding flagella assembly and ion transport, whereas the Nitrosoarchaeum-like clade had losses of intact genes involved in urea uptake and utilization and gains of genes encoding osmolarity-mediated mechanosensitive channels. Collectively, our results reveal for the first time the high genomic diversity of the class Nitrososphaeria across freshwater ecosystems and provide novel insights into their adaptive mechanisms and evolutionary histories.
Collapse
Affiliation(s)
- Minglei Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
25
|
Li Y, Wei J, Yang H, Zhang D, Hu C. Biogeographic, Driving Factors, Assembly, and Co-occurrence Patterns of Archaeal Community in Biocrusts. Front Microbiol 2022; 13:848908. [PMID: 35495652 PMCID: PMC9042396 DOI: 10.3389/fmicb.2022.848908] [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: 01/05/2022] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Archaea exhibit strong community heterogeneity with microhabitat gradients and are a non-negligible part of biocrust's microorganisms. The study on archaeal biogeography in biocrusts could provide new insights for its application in environmental restoration. However, only a few studies on assembly processes and co-occurrence patterns of the archaeal community in patchy biocrusts have been reported, especially considering the number of species pools (SPs). Here, we comprehensively collected biocrusts across 3,500 km of northern China. Different successional biocrusts from various regions contain information of local climate and microenvironments, which can shape multiple unique archaeal SPs. The archaeal community differences in the same successional stage exceeded the variations between successional stages, which was due to the fact that the heterogeneous taxa tended to exchange between unknown patches driven by drift. We also comparatively studied the driving forces of community heterogeneity across three to ten SPs, and assembly and co-occurrence patterns were systematically analyzed. The results revealed that the impact of spatial factors on biogeographic patterns was greater than that of environmental and successional factors and that impact decreased with the number of SPs considered. Meanwhile, community heterogeneity at the phylogenetic facet was more sensitive to these driving factors than the taxonomic facet. Subgroups 1 (SG1) and 2 (SG2) of the archaeal communities in biocrusts were dominated by Nitrososphaeraceae and Haloarchaea, respectively. The former distribution pattern was associated with non-salinity-related variables and primarily assembled by drift, whereas the latter was associated with salinity-related variables and primarily assembled by homogeneous selection. Finally, network analysis indicated that the SG1 network had a higher proportion of competition and key taxa than the SG2 network, but the network of SG2 was more complex. Our study suggested that the development of the archaeal community was not consistent with biocrusts succession. The dominant taxa may determine the patterns of community biogeography, assembly, and co-occurrence.
Collapse
Affiliation(s)
- Yuanlong Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingyi Wei
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haijian Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Delu Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chunxiang Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| |
Collapse
|
26
|
Fiard M, Cuny P, Sylvi L, Hubas C, Jézéquel R, Lamy D, Walcker R, El Houssainy A, Heimbürger-Boavida LE, Robinet T, Bihannic I, Gilbert F, Michaud E, Dirberg G, Militon C. Mangrove microbiota along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America): Drivers and potential bioindicators. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150667. [PMID: 34599952 DOI: 10.1016/j.scitotenv.2021.150667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/13/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
The microbial communities inhabiting the Atlantic-East Pacific (AEP) mangroves have been poorly studied, and mostly comprise chronically polluted mangroves. In this study, we characterized changes in the structure and diversity of microbial communities of mangroves along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America) that experience low human impact. The microbial communities were assigned into 50 phyla. Proteobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Planctomycetes were the most abundant taxa. The environmental determinants found to significantly correlated to the microbial communities at these mangroves were granulometry, dieldrin concentration, pH, and total carbon (TC) content. Furthermore, a precise analysis of the sediment highlights the existence of three types of anthropogenic pressure among the stations: (i) organic matter (OM) enrichment due to the proximity to the city and its wastewater treatment plant, (ii) dieldrin contamination, and (iii) naphthalene contamination. These forms of weak anthropogenic pressure seemed to impact the bacterial population size and microbial assemblages. A decrease in Bathyarchaeota, "Candidatus Nitrosopumilus", and Nitrospira genera was observed in mangroves subjected to OM enrichment. Mangroves polluted with organic contaminants were enriched in Desulfobacteraceae, Desulfarculaceae, and Acanthopleuribacteraceae (with dieldrin or polychlorobiphenyl contamination), and Chitinophagaceae and Geobacteraceae (with naphthalene contamination). These findings provide insights into the main environmental factors shaping microbial communities of mangroves in the AEP that experience low human impact and allow for the identification of several potential microbial bioindicators of weak anthropogenic pressure.
Collapse
Affiliation(s)
- Maud Fiard
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Philippe Cuny
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Léa Sylvi
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Cédric Hubas
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Station Marine de Concarneau, 29900 Concarneau, France.
| | | | - Dominique Lamy
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France; Institute of Ecology and Environmental Sciences of Paris (iEES-Paris), Sorbonne Université, Univ Paris Est Créteil, IRD, CNRS, INRA, 4 place Jussieu, 75005 Paris, France.
| | - Romain Walcker
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France.
| | - Amonda El Houssainy
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | | | - Tony Robinet
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Station Marine de Concarneau, 29900 Concarneau, France.
| | | | - Franck Gilbert
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France.
| | - Emma Michaud
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Guillaume Dirberg
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France.
| | - Cécile Militon
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| |
Collapse
|
27
|
Zhao J, Wang B, Zhou X, Alam MS, Fan J, Guo Z, Zhang H, Gubry-Rangin C, Zhongjun J. Long-Term Adaptation of Acidophilic Archaeal Ammonia Oxidisers Following Different Soil Fertilisation Histories. MICROBIAL ECOLOGY 2022; 83:424-435. [PMID: 33970312 PMCID: PMC8891100 DOI: 10.1007/s00248-021-01763-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/21/2021] [Indexed: 06/01/2023]
Abstract
Ammonia oxidising archaea (AOA) are ecologically important nitrifiers in acidic agricultural soils. Two AOA phylogenetic clades, belonging to order-level lineages of Nitrososphaerales (clade C11; also classified as NS-Gamma-2.3.2) and family-level lineage of Candidatus Nitrosotaleaceae (clade C14; NT-Alpha-1.1.1), usually dominate AOA population in low pH soils. This study aimed to investigate the effect of different fertilisation histories on community composition and activity of acidophilic AOA in soils. High-throughput sequencing of ammonia monooxygenase gene (amoA) was performed on six low pH agricultural plots originating from the same soil but amended with different types of fertilisers for over 20 years and nitrification rates in those soils were measured. In these fertilised acidic soils, nitrification was likely dominated by Nitrososphaerales AOA and ammonia-oxidising bacteria, while Ca. Nitrosotaleaceae AOA activity was non-significant. Within Nitrososphaerales AOA, community composition differed based on the fertilisation history, with Nitrososphaerales C11 only representing a low proportion of the community. This study revealed that long-term soil fertilisation selects for different acidophilic nitrifier communities, potentially through soil pH change or through direct effect of nitrogen, potassium and phosphorus. Comparative community composition among the differently fertilised soils also highlighted the existence of AOA phylotypes with different levels of stability to environmental changes, contributing to the understanding of high AOA diversity maintenance in terrestrial ecosystems.
Collapse
Affiliation(s)
- Jun Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen, AB24 3UU, UK
| | - Baozhan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xue Zhou
- College of Agricultural Science and Engineering, Hohai University, Nanjing, 210098, China
| | - Mohammad Saiful Alam
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Department of Soil Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Jianbo Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zhiying Guo
- Soil Subcenter of Chinese Ecological Research Network, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Huimin Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Cécile Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen, AB24 3UU, UK.
| | - Jia Zhongjun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| |
Collapse
|
28
|
Fan S, Wang M, Ding W, Li YX, Zhang YZ, Zhang W. Scientific and technological progress in the microbial exploration of the hadal zone. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:127-137. [PMID: 37073349 PMCID: PMC10077178 DOI: 10.1007/s42995-021-00110-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 05/11/2021] [Indexed: 05/03/2023]
Abstract
The hadal zone is the deepest point in the ocean with a depth that exceeds 6000 m. Exploration of the biological communities in hadal zone began in the 1950s (the first wave of hadal exploration) and substantial advances have been made since the turn of the twenty-first century (the second wave of hadal exploration), resulting in a focus on the hadal sphere as a research hotspot because of its unique physical and chemical conditions. A variety of prokaryotes are found in the hadal zone. The mechanisms used by these prokaryotes to manage the high hydrostatic pressures and acquire energy from the environment are of substantial interest. Moreover, the symbioses between microbes and hadal animals have barely been studied. In addition, equipment has been developed that can now mimic hadal environments in the laboratory and allow cultivation of microbes under simulated in situ pressure. This review provides a brief summary of recent progress in the mechanisms by which microbes adapt to high hydrostatic pressures, manage limited energy resources and coexist with animals in the hadal zone, as well as technical developments in the exploration of hadal microbial life.
Collapse
Affiliation(s)
- Shen Fan
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Meng Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Wei Ding
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Yong-Xin Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Weipeng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| |
Collapse
|
29
|
Kajan K, Cukrov N, Cukrov N, Bishop-Pierce R, Orlić S. Microeukaryotic and Prokaryotic Diversity of Anchialine Caves from Eastern Adriatic Sea Islands. MICROBIAL ECOLOGY 2022; 83:257-270. [PMID: 33903927 PMCID: PMC8891109 DOI: 10.1007/s00248-021-01760-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/19/2021] [Indexed: 05/13/2023]
Abstract
Anchialine ecosystems in the eastern Adriatic Sea are diverse both morphologically and biologically. In this study, for the first time, we explored the microeukaryotic and prokaryotic community of anchialine caves in the Mediterranean region using high-throughput sequencing. Four anchialine caves located on nearby islands with a well-pronounced salinity gradient were sampled at the surface freshwater area, halocline area, and seawater area. Sequencing revealed a surprisingly wide diversity of the microeukaryotic and prokaryotic community with the relative abundance of major phyla differing within the salinity gradient and between the caves. Interestingly, microeukaryotic and prokaryotic communities clustered into four groups based on location, pointing out that sampled anchialine caves have different microbial community patterns and high microbial endemism. Our results indicate that even with the halocline acting as a selecting barrier, the salinity is not the only community structuring factor. Despite the short geographical distance, the isolation of anchialine caves facilitated high microbial community adaptation and endemism. Our study suggests that anchialine caves represent reservoirs of new biodiversity, maintaining unique and complex microbial diversity influenced by biotic interactions and abiotic environmental conditions.
Collapse
Affiliation(s)
- Katarina Kajan
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Zagreb, Croatia
| | - Neven Cukrov
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia
| | - Nuša Cukrov
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia
| | | | - Sandi Orlić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia.
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Zagreb, Croatia.
| |
Collapse
|
30
|
Genome-Resolved Metagenomic Insights into Massive Seasonal Ammonia-Oxidizing Archaea Blooms in San Francisco Bay. mSystems 2022; 7:e0127021. [PMID: 35076275 PMCID: PMC8788347 DOI: 10.1128/msystems.01270-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are key for the transformation of ammonia to oxidized forms of nitrogen in aquatic environments around the globe, including nutrient-rich coastal and estuarine waters such as San Francisco Bay (SFB). Using metagenomics and 16S rRNA gene amplicon libraries, we found that AOA are more abundant than ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), except in the freshwater stations in SFB. In South SFB, we observed recurrent AOA blooms of “Candidatus Nitrosomarinus catalina” SPOT01-like organisms, which account for over 20% of 16S rRNA gene amplicons in both surface and bottom waters and co-occur with weeks of high nitrite concentrations (>10 μM) in the oxic water column. We observed pronounced nitrite peaks occurring in the autumn for 7 of the last 9 years (2012 to 2020), suggesting that seasonal AOA blooms are common in South SFB. We recovered two high-quality AOA metagenome-assembled genomes (MAGs), including a Nitrosomarinus-like genome from the South SFB bloom and another Nitrosopumilus genome originating from Suisun Bay in North SFB. Both MAGs cluster with genomes from other estuarine/coastal sites. Analysis of Nitrosomarinus-like genomes show that they are streamlined, with low GC content and high coding density, and harbor urease genes. Our findings support the unique niche of Nitrosomarinus-like organisms which dominate coastal/estuarine waters and provide insights into recurring AOA blooms in SFB. IMPORTANCE Ammonia-oxidizing archaea (AOA) carry out key transformations of ammonia in estuarine systems such as San Francisco Bay (SFB)—the largest estuary on the west coast of North America—and play a significant role in both local and global nitrogen cycling. Using metagenomics and 16S rRNA gene amplicon libraries, we document a massive, recurrent AOA bloom in South SFB that co-occurs with months of high nitrite concentrations in the oxic water column. Our study is the first to generate metagenome-assembled genomes (MAGs) from SFB, and through this process we recovered two high-quality AOA MAGs, one of which originated from bloom samples. These AOA MAGs yield new insight into the Nitrosopumilus and Nitrosomarinus-like lineages and their potential niches in coastal and estuarine systems. Nitrosomarinus-like AOA are abundant in coastal regions around the globe, and we highlight the common occurrence of urease genes, low GC content, and range of salinity tolerances within this lineage.
Collapse
|
31
|
Zhu J, Yan X, Zhou L, Li N, Liao C, Wang X. Insight of bacteria and archaea in Feammox community enriched from different soils. ENVIRONMENTAL RESEARCH 2022; 203:111802. [PMID: 34343555 DOI: 10.1016/j.envres.2021.111802] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Anaerobic ammonium oxidation coupled to Fe(III) reduction, known as Feammox, is a newly discovered nitrogen-cycling process, which serves an important role in the pathways of nitrogen loss in the environment. However, the specific types of microorganisms involved in Feammox currently remain unclear. In this study, we selected two groups of soil samples (paddy and mine), from considerably different habitats in South China, to acclimate Feammox colonies. The Paddy Group had a shorter lag period than the Mine Group, while the ammonium transformation rate was nearly equal in both groups in the mature period. The emergence of the Feammox activity was found to be associated with the increased abundance of iron-reducing bacteria, especially Clostridium_sensu_stricto_12, Desulfitobacterium, Thermoanaerobaculum, Anaeromyxobacter and Geobacter. Ammonium oxidizing archaea and methanogens were dominant among the known archaea. These findings extend our knowledge of the microbial community composition of the potential Feammox microbes from soils under different environmental conditions, which broadens our understanding of this important Fe/N transformation process.
Collapse
Affiliation(s)
- Jiaxuan Zhu
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin, 300350, China
| | - Xuejun Yan
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin, 300350, China
| | - Lean Zhou
- School of Hydraulic Engineering, Changsha University of Science & Technology, Changsha, 410114, China
| | - Nan Li
- School of Environmental Science and Engineering, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Chengmei Liao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin, 300350, China.
| | - Xin Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin, 300350, China.
| |
Collapse
|
32
|
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: 12] [Impact Index Per Article: 4.0] [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.
Collapse
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.
| |
Collapse
|
33
|
Kerou M, Ponce-Toledo RI, Zhao R, Abby SS, Hirai M, Nomaki H, Takaki Y, Nunoura T, Jørgensen SL, Schleper C. Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages. THE ISME JOURNAL 2021; 15:2792-2808. [PMID: 33795828 PMCID: PMC8397731 DOI: 10.1038/s41396-021-00962-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 01/12/2021] [Accepted: 03/11/2021] [Indexed: 02/01/2023]
Abstract
Marine sediments represent a vast habitat for complex microbiomes. Among these, ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are one of the most common, yet little explored, inhabitants, which seem extraordinarily well adapted to the harsh conditions of the subsurface biosphere. We present 11 metagenome-assembled genomes of the most abundant AOA clades from sediment cores obtained from the Atlantic Mid-Ocean ridge flanks and Pacific abyssal plains. Their phylogenomic placement reveals three independently evolved clades within the order Nitrosopumilales, of which no cultured representative is known yet. In addition to the gene sets for ammonia oxidation and carbon fixation known from other AOA, all genomes encode an extended capacity for the conversion of fermentation products that can be channeled into the central carbon metabolism, as well as uptake of amino acids probably for protein maintenance or as an ammonia source. Two lineages encode an additional (V-type) ATPase and a large repertoire of DNA repair systems that may allow to overcome the challenges of high hydrostatic pressure. We suggest that the adaptive radiation of AOA into marine sediments occurred more than once in evolution and resulted in three distinct lineages with particular adaptations to this extremely energy-limiting and high-pressure environment.
Collapse
Affiliation(s)
- Melina Kerou
- grid.10420.370000 0001 2286 1424Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Vienna, Austria
| | - Rafael I. Ponce-Toledo
- grid.10420.370000 0001 2286 1424Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Vienna, Austria
| | - Rui Zhao
- grid.7914.b0000 0004 1936 7443Department of Earth Science, K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway ,grid.33489.350000 0001 0454 4791Present Address: School of Marine Science and Policy, University of Delaware, Lewes, DE USA
| | - Sophie S. Abby
- grid.10420.370000 0001 2286 1424Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Vienna, Austria ,grid.463716.10000 0004 4687 1979Present Address: University Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Miho Hirai
- grid.410588.00000 0001 2191 0132Super-cutting-edge Grand and Advanced Research (SUGAR) Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Hidetaka Nomaki
- grid.410588.00000 0001 2191 0132Super-cutting-edge Grand and Advanced Research (SUGAR) Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshihiro Takaki
- grid.410588.00000 0001 2191 0132Super-cutting-edge Grand and Advanced Research (SUGAR) Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Takuro Nunoura
- grid.410588.00000 0001 2191 0132Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Steffen L. Jørgensen
- grid.7914.b0000 0004 1936 7443Department of Earth Science, K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Christa Schleper
- grid.10420.370000 0001 2286 1424Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Vienna, Austria
| |
Collapse
|
34
|
Tahon G, Patricia Geesink, Ettema TJG. Expanding Archaeal Diversity and Phylogeny: Past, Present, and Future. Annu Rev Microbiol 2021; 75:359-381. [PMID: 34351791 DOI: 10.1146/annurev-micro-040921-050212] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The discovery of the Archaea is a major scientific hallmark of the twentieth century. Since then, important features of their cell biology, physiology, ecology, and diversity have been revealed. Over the course of some 40 years, the diversity of known archaea has expanded from 2 to about 30 phyla comprising over 20,000 species. Most of this archaeal diversity has been revealed by environmental 16S rRNA amplicon sequencing surveys using a broad range of universal and targeted primers. Of the few primers that target a large fraction of known archaeal diversity, all display a bias against recently discovered lineages, which limits studies aiming to survey overall archaeal diversity. Induced by genomic exploration of archaeal diversity, and improved phylogenomics approaches, archaeal taxonomic classification has been frequently revised. Due to computational limitations and continued discovery of new lineages, a stable archaeal phylogeny is not yet within reach. Obtaining phylogenetic and taxonomic consensus of archaea should be a high priority for the archaeal research community. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Guillaume Tahon
- Laboratory of Microbiology, Wageningen University and Research, 6700 EH Wageningen, The Netherlands; , ,
| | - Patricia Geesink
- Laboratory of Microbiology, Wageningen University and Research, 6700 EH Wageningen, The Netherlands; , ,
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University and Research, 6700 EH Wageningen, The Netherlands; , ,
| |
Collapse
|
35
|
Chen Z, Liu WS, Zhong X, Zheng M, Fei YH, He H, Ding K, Chao Y, Tang YT, Wang S, Qiu R. Genome- and community-level interaction insights into the ecological role of archaea in rare earth element mine drainage in South China. WATER RESEARCH 2021; 201:117331. [PMID: 34153824 DOI: 10.1016/j.watres.2021.117331] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 06/13/2023]
Abstract
Microbial communities play crucial roles in mine drainage generation and remediation. Despite the wide distribution of archaea in the mine ecosystem, their diversity and ecological roles remain less understood than bacteria. Here, we retrieved 56 archaeal metagenome-assembled genomes from a river impacted by rare earth element (REE) mining activities in South China. Genomic analysis showed that archaea represented four distinct lineages, including phyla of Thaumarchaeota, Micrarchaeota, Nanoarchaeota and Thermoplasmata. These archaea represented a considerable fraction (up to 40%) of the total prokaryote community, which might contribute to nitrogen and sulfur cycling in the REE mine drainage. Reconstructed metabolic potential among diverse archaea taxa revealed that archaea were involved in the network of ammonia oxidation, denitrification, sulfate redox reaction, and required substrates supplied by other community members. As the dominant driver of ammonia oxidation, Thaumarchaeota might provide substrates to support the survival of two nano-sized archaea belonging to Micrarchaeota and Nanoarchaeota. Despite the absence of biosynthesis pathways for amino acids and nucleotides, the potential capacity for nitrite reduction (nirD) was observed in Micrarchaeota, indicating that these nano-sized archaea encompassed diverse metabolisms. Moreover, Thermoplasmata, as keystone taxa in community, might be the main genetic donor for the other three archaeal phyla, transferring many environmental resistance related genes (e.g., V/A-type ATPase and Vitamin B12-transporting ATPase). The genetic interactions within archaeal community through horizontal gene transfer might be the key to the formation of archaeal resistance and functional partitioning. This study provides putative metabolic and genetic insights into the diverse archaea taxa from community-level perspectives, and highlights the ecological roles of archaea in REE contaminated aquatic environment.
Collapse
Affiliation(s)
- Ziwu Chen
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Wen-Shen Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Xi Zhong
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Mengyuan Zheng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Ying-Heng Fei
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Huan He
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Kengbo Ding
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuanqing Chao
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China.
| | - Ye-Tao Tang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Shizhong Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Rongliang Qiu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
| |
Collapse
|
36
|
Feng Y, Neri U, Gosselin S, Louyakis AS, Papke RT, Gophna U, Gogarten JP. The Evolutionary Origins of Extreme Halophilic Archaeal Lineages. Genome Biol Evol 2021; 13:6320066. [PMID: 34255041 PMCID: PMC8350355 DOI: 10.1093/gbe/evab166] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2021] [Indexed: 12/12/2022] Open
Abstract
Interest and controversy surrounding the evolutionary origins of extremely halophilic Archaea has increased in recent years, due to the discovery and characterization of the Nanohaloarchaea and the Methanonatronarchaeia. Initial attempts in explaining the evolutionary placement of the two new lineages in relation to the classical Halobacteria (also referred to as Haloarchaea) resulted in hypotheses that imply the new groups share a common ancestor with the Haloarchaea. However, more recent analyses have led to a shift: the Nanohaloarchaea have been largely accepted as being a member of the DPANN superphylum, outside of the euryarchaeota; whereas the Methanonatronarchaeia have been placed near the base of the Methanotecta (composed of the class II methanogens, the Halobacteriales, and Archaeoglobales). These opposing hypotheses have far-reaching implications on the concepts of convergent evolution (distantly related groups evolve similar strategies for survival), genome reduction, and gene transfer. In this work, we attempt to resolve these conflicts with phylogenetic and phylogenomic data. We provide a robust taxonomic sampling of Archaeal genomes that spans the Asgardarchaea, TACK Group, euryarchaeota, and the DPANN superphylum. In addition, we assembled draft genomes from seven new representatives of the Nanohaloarchaea from distinct geographic locations. Phylogenies derived from these data imply that the highly conserved ATP synthase catalytic/noncatalytic subunits of Nanohaloarchaea share a sisterhood relationship with the Haloarchaea. We also employ a novel gene family distance clustering strategy which shows this sisterhood relationship is not likely the result of a recent gene transfer. In addition, we present and evaluate data that argue for and against the monophyly of the DPANN superphylum, in particular, the inclusion of the Nanohaloarchaea in DPANN.
Collapse
Affiliation(s)
- Yutian Feng
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Uri Neri
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Israel
| | - Sean Gosselin
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Artemis S Louyakis
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Uri Gophna
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Israel
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
| |
Collapse
|
37
|
Vuong P, Lim DJ, Murphy DV, Wise MJ, Whiteley AS, Kaur P. Developing Bioprospecting Strategies for Bioplastics Through the Large-Scale Mining of Microbial Genomes. Front Microbiol 2021; 12:697309. [PMID: 34322108 PMCID: PMC8312272 DOI: 10.3389/fmicb.2021.697309] [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: 04/19/2021] [Accepted: 06/21/2021] [Indexed: 11/22/2022] Open
Abstract
The accumulation of petroleum-based plastic waste has become a major issue for the environment. A sustainable and biodegradable solution can be found in Polyhydroxyalkanoates (PHAs), a microbially produced biopolymer. An analysis of the global phylogenetic and ecological distribution of potential PHA producing bacteria and archaea was carried out by mining a global genome repository for PHA synthase (PhaC), a key enzyme involved in PHA biosynthesis. Bacteria from the phylum Actinobacteria were found to contain the PhaC Class II genotype which produces medium-chain length PHAs, a physiology until now only found within a few Pseudomonas species. Further, several PhaC genotypes were discovered within Thaumarchaeota, an archaeal phylum with poly-extremophiles and the ability to efficiently use CO2 as a carbon source, a significant ecological group which have thus far been little studied for PHA production. Bacterial and archaeal PhaC genotypes were also observed in high salinity and alkalinity conditions, as well as high-temperature geothermal ecosystems. These genome mining efforts uncovered previously unknown candidate taxa for biopolymer production, as well as microbes from environmental niches with properties that could potentially improve PHA production. This in silico study provides valuable insights into unique PHA producing candidates, supporting future bioprospecting efforts toward better targeted and relevant taxa to further enhance the diversity of exploitable PHA production systems.
Collapse
Affiliation(s)
- Paton Vuong
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Daniel J. Lim
- Department of Physics and Astronomy, Curtin University, Perth, WA, Australia
| | - Daniel V. Murphy
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Michael J. Wise
- School of Physics, Mathematics and Computing, The University of Western Australia, Perth, WA, Australia
- Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Perth, WA, Australia
| | | | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| |
Collapse
|
38
|
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.
Collapse
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.
| |
Collapse
|
39
|
Ando N, Barquera B, Bartlett DH, Boyd E, Burnim AA, Byer AS, Colman D, Gillilan RE, Gruebele M, Makhatadze G, Royer CA, Shock E, Wand AJ, Watkins MB. The Molecular Basis for Life in Extreme Environments. Annu Rev Biophys 2021; 50:343-372. [PMID: 33637008 DOI: 10.1146/annurev-biophys-100120-072804] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sampling and genomic efforts over the past decade have revealed an enormous quantity and diversity of life in Earth's extreme environments. This new knowledge of life on Earth poses the challenge of understandingits molecular basis in such inhospitable conditions, given that such conditions lead to loss of structure and of function in biomolecules from mesophiles. In this review, we discuss the physicochemical properties of extreme environments. We present the state of recent progress in extreme environmental genomics. We then present an overview of our current understanding of the biomolecular adaptation to extreme conditions. As our current and future understanding of biomolecular structure-function relationships in extremophiles requires methodologies adapted to extremes of pressure, temperature, and chemical composition, advances in instrumentation for probing biophysical properties under extreme conditions are presented. Finally, we briefly discuss possible future directions in extreme biophysics.
Collapse
Affiliation(s)
- Nozomi Ando
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA.,Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Blanca Barquera
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202, USA
| | - Eric Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
| | - Audrey A Burnim
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Amanda S Byer
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Daniel Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
| | - Richard E Gillilan
- Center for High Energy X-ray Sciences (CHEXS), Ithaca, New York 14853, USA
| | - Martin Gruebele
- Department of Chemistry, University of Illinois, Urbana-Champaign, Illinois 61801, USA.,Department of Physics, University of Illinois, Urbana-Champaign, Illinois 61801, USA.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana-Champaign, Illinois 61801, USA
| | - George Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Everett Shock
- GEOPIG, School of Earth & Space Exploration, School of Molecular Sciences, Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona 85287, USA
| | - A Joshua Wand
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77845, USA.,Department of Chemistry, Texas A&M University, College Station, Texas 77845, USA.,Department of Molecular & Cellular Medicine, Texas A&M University, College Station, Texas 77845, USA
| | - Maxwell B Watkins
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA.,Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| |
Collapse
|
40
|
Stahl DA. The path leading to the discovery of the ammoniaoxidizing archaea. Environ Microbiol 2020; 22:4507-4519. [PMID: 32955155 DOI: 10.1111/1462-2920.15239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 11/28/2022]
Affiliation(s)
- David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
| |
Collapse
|
41
|
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.
Collapse
|
42
|
Zou D, Liu H, Li M. Community, Distribution, and Ecological Roles of Estuarine Archaea. Front Microbiol 2020; 11:2060. [PMID: 32983044 PMCID: PMC7484942 DOI: 10.3389/fmicb.2020.02060] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/05/2020] [Indexed: 12/04/2022] Open
Abstract
Archaea are diverse and ubiquitous prokaryotes present in both extreme and moderate environments. Estuaries, serving as links between the land and ocean, harbor numerous microbes that are relatively highly active because of massive terrigenous input of nutrients. Archaea account for a considerable portion of the estuarine microbial community. They are diverse and play key roles in the estuarine biogeochemical cycles. Ammonia-oxidizing archaea (AOA) are an abundant aquatic archaeal group in estuaries, greatly contributing estuarine ammonia oxidation. Bathyarchaeota are abundant in sediments, and they may involve in sedimentary organic matter degradation, acetogenesis, and, potentially, methane metabolism, based on genomics. Other archaeal groups are also commonly detected in estuaries worldwide. They include Euryarchaeota, and members of the DPANN and Asgard archaea. Based on biodiversity surveys of the 16S rRNA gene and some functional genes, the distribution and abundance of estuarine archaea are driven by physicochemical factors, such as salinity and oxygen concentration. Currently, increasing amount of genomic information for estuarine archaea is becoming available because of the advances in sequencing technologies, especially for AOA and Bathyarchaeota, leading to a better understanding of their functions and environmental adaptations. Here, we summarized the current knowledge on the community composition and major archaeal groups in estuaries, focusing on AOA and Bathyarchaeota. We also highlighted the unique genomic features and potential adaptation strategies of estuarine archaea, pointing out major unknowns in the field and scope for future research.
Collapse
Affiliation(s)
- Dayu Zou
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Meng Li
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| |
Collapse
|
43
|
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.
Collapse
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.
| |
Collapse
|
44
|
Aylward FO, Santoro AE. Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean. mSystems 2020; 5:e00415-20. [PMID: 32546674 PMCID: PMC7300363 DOI: 10.1128/msystems.00415-20] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 05/28/2020] [Indexed: 01/01/2023] Open
Abstract
The Thaumarchaeota is a diverse archaeal phylum comprising numerous lineages that play key roles in global biogeochemical cycling, particularly in the ocean. To date, all genomically characterized marine thaumarchaea are reported to be chemolithoautotrophic ammonia oxidizers. In this study, we report a group of putatively heterotrophic marine thaumarchaea (HMT) with small genome sizes that is globally abundant in the mesopelagic, apparently lacking the ability to oxidize ammonia. We assembled five HMT genomes from metagenomic data and show that they form a deeply branching sister lineage to the ammonia-oxidizing archaea (AOA). We identify this group in metagenomes from mesopelagic waters in all major ocean basins, with abundances reaching up to 6% of that of AOA. Surprisingly, we predict the HMT have small genomes of ∼1 Mbp, and our ancestral state reconstruction indicates this lineage has undergone substantial genome reduction compared to other related archaea. The genomic repertoire of HMT indicates a versatile metabolism for aerobic chemoorganoheterotrophy that includes a divergent form III-a RuBisCO, a 2M respiratory complex I that has been hypothesized to increase energetic efficiency, and a three-subunit heme-copper oxidase complex IV that is absent from AOA. We also identify 21 pyrroloquinoline quinone (PQQ)-dependent dehydrogenases that are predicted to supply reducing equivalents to the electron transport chain and are among the most highly expressed HMT genes, suggesting these enzymes play an important role in the physiology of this group. Our results suggest that heterotrophic members of the Thaumarchaeota are widespread in the ocean and potentially play key roles in global chemical transformations.IMPORTANCE It has been known for many years that marine Thaumarchaeota are abundant constituents of dark ocean microbial communities, where their ability to couple ammonia oxidation and carbon fixation plays a critical role in nutrient dynamics. In this study, we describe an abundant group of putatively heterotrophic marine Thaumarchaeota (HMT) in the ocean with physiology distinct from those of their ammonia-oxidizing relatives. HMT lack the ability to oxidize ammonia and fix carbon via the 3-hydroxypropionate/4-hydroxybutyrate pathway but instead encode a form III-a RuBisCO and diverse PQQ-dependent dehydrogenases that are likely used to conserve energy in the dark ocean. Our work expands the scope of known diversity of Thaumarchaeota in the ocean and provides important insight into a widespread marine lineage.
Collapse
Affiliation(s)
- Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USA
| |
Collapse
|
45
|
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: 41] [Impact Index Per Article: 10.3] [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.
Collapse
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.
| |
Collapse
|
46
|
Yang Y, Daims H, Liu Y, Herbold CW, Pjevac P, Lin JG, Li M, Gu JD. Activity and Metabolic Versatility of Complete Ammonia Oxidizers in Full-Scale Wastewater Treatment Systems. mBio 2020; 11:e03175-19. [PMID: 32184251 PMCID: PMC7078480 DOI: 10.1128/mbio.03175-19] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/06/2020] [Indexed: 11/20/2022] Open
Abstract
The recent discovery of complete ammonia oxidizers (comammox) contradicts the paradigm that chemolithoautotrophic nitrification is always catalyzed by two different microorganisms. However, our knowledge of the survival strategies of comammox in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Analyses of genomes and in situ transcriptomes of four comammox organisms from two full-scale WWTPs revealed that comammox were active and showed a surprisingly high metabolic versatility. A gene cluster for the utilization of urea and a gene encoding cyanase suggest that comammox may use diverse organic nitrogen compounds in addition to free ammonia as the substrates. The comammox organisms also encoded the genomic potential for multiple alternative energy metabolisms, including respiration with hydrogen, formate, and sulfite as electron donors. Pathways for the biosynthesis and degradation of polyphosphate, glycogen, and polyhydroxyalkanoates as intracellular storage compounds likely help comammox survive unfavorable conditions and facilitate switches between lifestyles in fluctuating environments. One of the comammox strains acquired from the anaerobic tank encoded and transcribed genes involved in homoacetate fermentation or in the utilization of exogenous acetate, both pathways being unexpected in a nitrifying bacterium. Surprisingly, this strain also encoded a respiratory nitrate reductase which has not yet been found in any other Nitrospira genome and might confer a selective advantage to this strain over other Nitrospira strains in anoxic conditions.IMPORTANCE The discovery of comammox in the genus Nitrospira changes our perception of nitrification. However, genomes of comammox organisms have not been acquired from full-scale WWTPs, and very little is known about their survival strategies and potential metabolisms in complex wastewater treatment systems. Here, four comammox metagenome-assembled genomes and metatranscriptomic data sets were retrieved from two full-scale WWTPs. Their impressive and-among nitrifiers-unsurpassed ecophysiological versatility could make comammox Nitrospira an interesting target for optimizing nitrification in current and future bioreactor configurations.
Collapse
Affiliation(s)
- Yuchun Yang
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, Hong Kong, People's Republic of China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, People's Republic of China
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Holger Daims
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- University of Vienna, The Comammox Research Platform, Vienna, Austria
| | - Yang Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, People's Republic of China
| | - Craig W Herbold
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Petra Pjevac
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Chiao Tung University, Hsinchu City, Taiwan
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, People's Republic of China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, Hong Kong, People's Republic of China
| |
Collapse
|
47
|
Whelan FJ, Rusilowicz M, McInerney JO. Coinfinder: detecting significant associations and dissociations in pangenomes. Microb Genom 2020; 6:e000338. [PMID: 32100706 PMCID: PMC7200068 DOI: 10.1099/mgen.0.000338] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 01/23/2020] [Indexed: 12/16/2022] Open
Abstract
The accessory genes of prokaryote and eukaryote pangenomes accumulate by horizontal gene transfer, differential gene loss, and the effects of selection and drift. We have developed Coinfinder, a software program that assesses whether sets of homologous genes (gene families) in pangenomes associate or dissociate with each other (i.e. are 'coincident') more often than would be expected by chance. Coinfinder employs a user-supplied phylogenetic tree in order to assess the lineage-dependence (i.e. the phylogenetic distribution) of each accessory gene, allowing Coinfinder to focus on coincident gene pairs whose joint presence is not simply because they happened to appear in the same clade, but rather that they tend to appear together more often than expected across the phylogeny. Coinfinder is implemented in C++, Python3 and R and is freely available under the GNU license from https://github.com/fwhelan/coinfinder.
Collapse
Affiliation(s)
- Fiona Jane Whelan
- School of Life Sciences, The University of Nottingham, Nottingham, UK
| | - Martin Rusilowicz
- Faculty of Biology, Medicine & Health, The University of Manchester, Manchester, UK
| | - James Oscar McInerney
- School of Life Sciences, The University of Nottingham, Nottingham, UK
- Faculty of Biology, Medicine & Health, The University of Manchester, Manchester, UK
| |
Collapse
|
48
|
Barnett SE, Buckley DH. Simulating metagenomic stable isotope probing datasets with MetaSIPSim. BMC Bioinformatics 2020; 21:37. [PMID: 32000676 PMCID: PMC6993524 DOI: 10.1186/s12859-020-3372-6] [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: 08/13/2019] [Accepted: 01/16/2020] [Indexed: 11/10/2022] Open
Abstract
Background DNA-stable isotope probing (DNA-SIP) links microorganisms to their in-situ function in diverse environmental samples. Combining DNA-SIP and metagenomics (metagenomic-SIP) allows us to link genomes from complex communities to their specific functions and improves the assembly and binning of these targeted genomes. However, empirical development of metagenomic-SIP methods is hindered by the complexity and cost of these studies. We developed a toolkit, ‘MetaSIPSim,’ to simulate sequencing read libraries for metagenomic-SIP experiments. MetaSIPSim is intended to generate datasets for method development and testing. To this end, we used MetaSIPSim generated data to demonstrate the advantages of metagenomic-SIP over a conventional shotgun metagenomic sequencing experiment. Results Through simulation we show that metagenomic-SIP improves the assembly and binning of isotopically labeled genomes relative to a conventional metagenomic approach. Improvements were dependent on experimental parameters and on sequencing depth. Community level G + C content impacted the assembly of labeled genomes and subsequent binning, where high community G + C generally reduced the benefits of metagenomic-SIP. Furthermore, when a high proportion of the community is isotopically labeled, the benefits of metagenomic-SIP decline. Finally, the choice of gradient fractions to sequence greatly influences method performance. Conclusions Metagenomic-SIP is a valuable method for recovering isotopically labeled genomes from complex communities. We show that metagenomic-SIP performance depends on optimization of experimental parameters. MetaSIPSim allows for simulation of metagenomic-SIP datasets which facilitates the optimization and development of metagenomic-SIP experiments and analytical approaches for dealing with these data.
Collapse
Affiliation(s)
- Samuel E Barnett
- School of Integrative Plant Science, Cornell University, Bradfield Hall, room 705, 306 Tower Rd, Ithaca, NY, 14853, USA
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Bradfield Hall, room 705, 306 Tower Rd, Ithaca, NY, 14853, USA.
| |
Collapse
|