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Gong X, Xu L, Langwig MV, Chen Z, Huang S, Zhao D, Su L, Zhang Y, Francis CA, Liu J, Li J, Baker BJ. Globally distributed marine Gemmatimonadota have unique genomic potentials. MICROBIOME 2024; 12:149. [PMID: 39123272 PMCID: PMC11316326 DOI: 10.1186/s40168-024-01871-4] [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: 02/24/2024] [Accepted: 07/09/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND Gemmatimonadota bacteria are widely distributed in nature, but their metabolic potential and ecological roles in marine environments are poorly understood. RESULTS Here, we obtained 495 metagenome-assembled genomes (MAGs), and associated viruses, from coastal to deep-sea sediments around the world. We used this expanded genomic catalog to compare the protein composition and update the phylogeny of these bacteria. The marine Gemmatimonadota are phylogenetically different from those previously reported from terrestrial environments. Functional analyses of these genomes revealed these marine genotypes are capable of degradation of complex organic carbon, denitrification, sulfate reduction, and oxidizing sulfide and sulfite. Interestingly, there is widespread genetic potential for secondary metabolite biosynthesis across Gemmatimonadota, which may represent an unexplored source of novel natural products. Furthermore, viruses associated with Gemmatimonadota have the potential to "hijack" and manipulate host metabolism, including the assembly of the lipopolysaccharide in their hosts. CONCLUSIONS This expanded genomic diversity advances our understanding of these globally distributed bacteria across a variety of ecosystems and reveals genetic distinctions between those in terrestrial and marine communities. Video Abstract.
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Affiliation(s)
- Xianzhe Gong
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, Guangdong, China.
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Austin, TX, 78373, USA.
| | - Le Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Marguerite V Langwig
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Austin, TX, 78373, USA
| | - Zhiyi Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Shujie Huang
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Duo Zhao
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Lei Su
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Yan Zhang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Christopher A Francis
- Departments of Earth System Science & Oceans, Stanford University, Stanford, CA, 94305, USA
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China.
| | - Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China.
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Austin, TX, 78373, USA.
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA.
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Su Y, Yu H, Gao C, Sun S, Liang Y, Liu G, Zhang X, Dong Y, Liu X, Chen G, Shao H, McMinn A, Wang M. Effects of vegetation cover and aquaculture pollution on viral assemblages in mangroves sediments. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135147. [PMID: 39029189 DOI: 10.1016/j.jhazmat.2024.135147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/07/2024] [Accepted: 07/06/2024] [Indexed: 07/21/2024]
Abstract
Mangrove forests, a critical coastal ecosystem, face numerous anthropogenic threats, particularly from aquaculture activities. Despite the acknowledged significance of viruses in local and global biogeochemical cycles, there is limited knowledge regarding the community structure, genomic diversity, and ecological roles of viruses in mangrove forests ecosystems, especially regarding their responses to aquaculture. In this study, we identified 17,755 viral operational taxonomic units (vOTUs) from nine sediments viromes across three distinct ecological regions of the mangrove forests ecosystem: mangrove, bare flat, and aquaculture regions. Viral assemblages varied among three regions, and the pathogenic viruses associated with marine animals, such as the white spot syndrome virus (WSSV) from Nimaviridae, were identified in this study. The relative abundance of Nimaviridae in the bare flat region was higher than in other regions. Furthermore, viruses in distinct mangrove forests sediments regions have adapted to their environments by adopting distinct survival strategies and encoding various auxiliary metabolic genes involved in carbon metabolism and antibiotic resistance. These adaptations may have profound impacts on biogeochemical cycles. This study provides the first insights into the effects of vegetation cover and aquaculture on the community structure and ecological roles of viruses in mangrove forests sediments. These findings are crucial for understanding the risks posed by anthropogenic threats to mangrove forests ecosystems and informing effective management strategies.
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Affiliation(s)
- Yue Su
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hao Yu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Chen Gao
- Haide College, Ocean University of China, Qingdao, China
| | - Shujuan Sun
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China.
| | - Gang Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Xinran Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yue Dong
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Xiaoshou Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Guangcheng Chen
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China; Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; Haide College, Ocean University of China, Qingdao, China; UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China; The Affiliated Hospital of Qingdao University, Qingdao 266000, China.
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3
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George NA, Zhou Z, Anantharaman K, Hug LA. Discarded diversity: Novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596742. [PMID: 38854013 PMCID: PMC11160803 DOI: 10.1101/2024.05.30.596742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Background Viruses are the most abundant microbial entity on the planet, impacting microbial community structure and ecosystem services. Despite outnumbering Bacteria and Archaea by an order of magnitude, viruses have been comparatively underrepresented in reference databases. Metagenomic examinations have illustrated that viruses of Bacteria and Archaea have been specifically understudied in engineered environments. Here we employed metagenomic and computational biology methods to examine the diversity, host interactions, and genetic systems of viruses predicted from 27 samples taken from three municipal landfills across North America. Results We identified numerous viruses that are not represented in reference databases, including the third largest bacteriophage genome identified to date (~678 kbp), and note a cosmopolitan diversity of viruses in landfills that are distinct from viromes in other systems. Host-virus interactions were examined via host CRISPR spacer to viral protospacer mapping which captured hyper-targeted viral populations and six viral populations predicted to infect across multiple phyla. Virally-encoded auxiliary metabolic genes (AMGs) were identified with the potential to augment hosts' methane, sulfur, and contaminant degradation metabolisms, including AMGs not previously reported in literature. CRISPR arrays and CRISPR-Cas systems were identified from predicted viral genomes, including the two largest bacteriophage genomes to contain these genetic features. Some virally encoded Cas effector proteins appear distinct relative to previously reported Cas systems and are interesting targets for potential genome editing tools. Conclusions Our observations indicate landfills, as heterogeneous contaminated sites with unique selective pressures, are key locations for diverse viruses and atypical virus-host dynamics.
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Affiliation(s)
- Nikhil A. George
- Department of Biology, University of Waterloo, Waterloo ON, Canada
| | - Zhichao Zhou
- Department of Bacteriology, University of Wisconsin – Madison, Madison, WI, USA
| | | | - Laura A. Hug
- Department of Biology, University of Waterloo, Waterloo ON, Canada
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Demin KA, Prazdnova EV, Minkina TM, Gorovtsov AV. Sulfate-reducing bacteria unearthed: ecological functions of the diverse prokaryotic group in terrestrial environments. Appl Environ Microbiol 2024; 90:e0139023. [PMID: 38551370 PMCID: PMC11022543 DOI: 10.1128/aem.01390-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024] Open
Abstract
Sulfate-reducing prokaryotes (SRPs) are essential microorganisms that play crucial roles in various ecological processes. Even though SRPs have been studied for over a century, there are still gaps in our understanding of their biology. In the past two decades, a significant amount of data on SRP ecology has been accumulated. This review aims to consolidate that information, focusing on SRPs in soils, their relation to the rare biosphere, uncultured sulfate reducers, and their interactions with other organisms in terrestrial ecosystems. SRPs in soils form part of the rare biosphere and contribute to various processes as a low-density population. The data reveal a diverse range of sulfate-reducing taxa intricately involved in terrestrial carbon and sulfur cycles. While some taxa like Desulfitobacterium and Desulfosporosinus are well studied, others are more enigmatic. For example, members of the Acidobacteriota phylum appear to hold significant importance for the terrestrial sulfur cycle. Many aspects of SRP ecology remain mysterious, including sulfate reduction in different bacterial phyla, interactions with bacteria and fungi in soils, and the existence of soil sulfate-reducing archaea. Utilizing metagenomic, metatranscriptomic, and culture-dependent approaches will help uncover the diversity, functional potential, and adaptations of SRPs in the global environment.
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Zheng Y, Gao Z, Wu S, Ruan A. Community Structure, Drivers, and Potential Functions of Different Lifestyle Viruses in Chaohu Lake. Viruses 2024; 16:590. [PMID: 38675931 PMCID: PMC11053968 DOI: 10.3390/v16040590] [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: 03/22/2024] [Revised: 04/06/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Viruses, as the most prolific entities on Earth, constitute significant ecological groups within freshwater lakes, exerting pivotal ecological roles. In this study, we selected Chaohu Lake, a representative eutrophic freshwater lake in China, as our research site to explore the community distribution, driving mechanisms, and potential ecological functions of diverse viral communities, the intricate virus-host interaction systems, and the overarching influence of viruses on global biogeochemical cycling.
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Affiliation(s)
- Yu Zheng
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210024, China; (Y.Z.); (Z.G.); (S.W.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Zihao Gao
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210024, China; (Y.Z.); (Z.G.); (S.W.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Shuai Wu
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210024, China; (Y.Z.); (Z.G.); (S.W.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Aidong Ruan
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210024, China; (Y.Z.); (Z.G.); (S.W.)
- College of Geography and Remote Sensing, Hohai University, Nanjing 210098, China
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6
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Liang H, Mower JP, Chia CP. Functional Prokaryotic-Like Deoxycytidine Triphosphate Deaminases and Thymidylate Synthase in Eukaryotic Social Amoebae: Vertical, Endosymbiotic, or Horizontal Gene Transfer? Mol Biol Evol 2023; 40:msad268. [PMID: 38064674 PMCID: PMC10733785 DOI: 10.1093/molbev/msad268] [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: 06/10/2023] [Revised: 10/22/2023] [Accepted: 11/30/2023] [Indexed: 12/22/2023] Open
Abstract
The de novo synthesis of deoxythymidine triphosphate uses several pathways: gram-negative bacteria use deoxycytidine triphosphate deaminase to convert deoxycytidine triphosphate into deoxyuridine triphosphate, whereas eukaryotes and gram-positive bacteria instead use deoxycytidine monophosphate deaminase to transform deoxycytidine monophosphate to deoxyuridine monophosphate. It is then unusual that in addition to deoxycytidine monophosphate deaminases, the eukaryote Dictyostelium discoideum has 2 deoxycytidine triphosphate deaminases (Dcd1Dicty and Dcd2Dicty). Expression of either DcdDicty can fully rescue the slow growth of an Escherichia coli dcd knockout. Both DcdDicty mitigate the hydroxyurea sensitivity of a Schizosaccharomyces pombe deoxycytidine monophosphate deaminase knockout. Phylogenies show that Dcd1Dicty homologs may have entered the common ancestor of the eukaryotic groups of Amoebozoa, Obazoa, Metamonada, and Discoba through an ancient horizontal gene transfer from a prokaryote or an ancient endosymbiotic gene transfer from a mitochondrion, followed by horizontal gene transfer from Amoebozoa to several other unrelated groups of eukaryotes. In contrast, the Dcd2Dicty homologs were a separate horizontal gene transfer from a prokaryote or a virus into either Amoebozoa or Rhizaria, followed by a horizontal gene transfer between them. ThyXDicty, the D. discoideum thymidylate synthase, another enzyme of the deoxythymidine triphosphate biosynthesis pathway, was suggested previously to be acquired from the ancestral mitochondria or by horizontal gene transfer from alpha-proteobacteria. ThyXDicty can fully rescue the E. coli thymidylate synthase knockout, and we establish that it was obtained by the common ancestor of social amoebae not from mitochondria but from a bacterium. We propose horizontal gene transfer and endosymbiotic gene transfer contributed to the enzyme diversity of the deoxythymidine triphosphate synthesis pathway in most social amoebae, many Amoebozoa, and other eukaryotes.
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Affiliation(s)
- Heng Liang
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Catherine P Chia
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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7
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Bansal S, Creed IF, Tangen BA, Bridgham SD, Desai AR, Krauss KW, Neubauer SC, Noe GB, Rosenberry DO, Trettin C, Wickland KP, Allen ST, Arias-Ortiz A, Armitage AR, Baldocchi D, Banerjee K, Bastviken D, Berg P, Bogard MJ, Chow AT, Conner WH, Craft C, Creamer C, DelSontro T, Duberstein JA, Eagle M, Fennessy MS, Finkelstein SA, Göckede M, Grunwald S, Halabisky M, Herbert E, Jahangir MMR, Johnson OF, Jones MC, Kelleway JJ, Knox S, Kroeger KD, Kuehn KA, Lobb D, Loder AL, Ma S, Maher DT, McNicol G, Meier J, Middleton BA, Mills C, Mistry P, Mitra A, Mobilian C, Nahlik AM, Newman S, O’Connell JL, Oikawa P, van der Burg MP, Schutte CA, Song C, Stagg CL, Turner J, Vargas R, Waldrop MP, Wallin MB, Wang ZA, Ward EJ, Willard DA, Yarwood S, Zhu X. Practical Guide to Measuring Wetland Carbon Pools and Fluxes. WETLANDS (WILMINGTON, N.C.) 2023; 43:105. [PMID: 38037553 PMCID: PMC10684704 DOI: 10.1007/s13157-023-01722-2] [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: 06/12/2023] [Accepted: 07/24/2023] [Indexed: 12/02/2023]
Abstract
Wetlands cover a small portion of the world, but have disproportionate influence on global carbon (C) sequestration, carbon dioxide and methane emissions, and aquatic C fluxes. However, the underlying biogeochemical processes that affect wetland C pools and fluxes are complex and dynamic, making measurements of wetland C challenging. Over decades of research, many observational, experimental, and analytical approaches have been developed to understand and quantify pools and fluxes of wetland C. Sampling approaches range in their representation of wetland C from short to long timeframes and local to landscape spatial scales. This review summarizes common and cutting-edge methodological approaches for quantifying wetland C pools and fluxes. We first define each of the major C pools and fluxes and provide rationale for their importance to wetland C dynamics. For each approach, we clarify what component of wetland C is measured and its spatial and temporal representativeness and constraints. We describe practical considerations for each approach, such as where and when an approach is typically used, who can conduct the measurements (expertise, training requirements), and how approaches are conducted, including considerations on equipment complexity and costs. Finally, we review key covariates and ancillary measurements that enhance the interpretation of findings and facilitate model development. The protocols that we describe to measure soil, water, vegetation, and gases are also relevant for related disciplines such as ecology. Improved quality and consistency of data collection and reporting across studies will help reduce global uncertainties and develop management strategies to use wetlands as nature-based climate solutions. Supplementary Information The online version contains supplementary material available at 10.1007/s13157-023-01722-2.
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Affiliation(s)
- Sheel Bansal
- U.S. Geological Survey, Northern Prairie Wildlife Research Center, Jamestown, ND USA
| | - Irena F. Creed
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON Canada
| | - Brian A. Tangen
- U.S. Geological Survey, Northern Prairie Wildlife Research Center, Jamestown, ND USA
| | - Scott D. Bridgham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR USA
| | - Ankur R. Desai
- Department of Atmospheric and Oceanic Sciences, University of Wisconsin-Madison, Madison, WI USA
| | - Ken W. Krauss
- U.S. Geological Survey, Wetland and Aquatic Research Center, Lafayette, LA USA
| | - Scott C. Neubauer
- Department of Biology, Virginia Commonwealth University, Richmond, VA USA
| | - Gregory B. Noe
- U.S. Geological Survey, Florence Bascom Geoscience Center, Reston, VA USA
| | | | - Carl Trettin
- U.S. Forest Service, Pacific Southwest Research Station, Davis, CA USA
| | - Kimberly P. Wickland
- U.S. Geological Survey, Geosciences and Environmental Change Science Center, Denver, CO USA
| | - Scott T. Allen
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, Reno, NV USA
| | - Ariane Arias-Ortiz
- Ecosystem Science Division, Department of Environmental Science, Policy and Management, University of California, Berkeley, CA USA
| | - Anna R. Armitage
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX USA
| | - Dennis Baldocchi
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA USA
| | - Kakoli Banerjee
- Department of Biodiversity and Conservation of Natural Resources, Central University of Odisha, Koraput, Odisha India
| | - David Bastviken
- Department of Thematic Studies – Environmental Change, Linköping University, Linköping, Sweden
| | - Peter Berg
- Department of Environmental Sciences, University of Virginia, Charlottesville, VA USA
| | - Matthew J. Bogard
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB Canada
| | - Alex T. Chow
- Earth and Environmental Sciences Programme, The Chinese University of Hong Kong, Shatin, Hong Kong SAR China
| | - William H. Conner
- Baruch Institute of Coastal Ecology and Forest Science, Clemson University, Georgetown, SC USA
| | - Christopher Craft
- O’Neill School of Public and Environmental Affairs, Indiana University, Bloomington, IN USA
| | - Courtney Creamer
- U.S. Geological Survey, Geology, Minerals, Energy and Geophysics Science Center, Menlo Park, CA USA
| | - Tonya DelSontro
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, ON Canada
| | - Jamie A. Duberstein
- Baruch Institute of Coastal Ecology and Forest Science, Clemson University, Georgetown, SC USA
| | - Meagan Eagle
- U.S. Geological Survey, Woods Hole Coastal & Marine Science Center, Woods Hole, MA USA
| | | | | | - Mathias Göckede
- Department for Biogeochemical Signals, Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Sabine Grunwald
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL USA
| | - Meghan Halabisky
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA USA
| | | | | | - Olivia F. Johnson
- U.S. Geological Survey, Northern Prairie Wildlife Research Center, Jamestown, ND USA
- Departments of Biology and Environmental Studies, Kent State University, Kent, OH USA
| | - Miriam C. Jones
- U.S. Geological Survey, Florence Bascom Geoscience Center, Reston, VA USA
| | - Jeffrey J. Kelleway
- School of Earth, Atmospheric and Life Sciences and Environmental Futures Research Centre, University of Wollongong, Wollongong, NSW Australia
| | - Sara Knox
- Department of Geography, McGill University, Montreal, Canada
| | - Kevin D. Kroeger
- U.S. Geological Survey, Woods Hole Coastal & Marine Science Center, Woods Hole, MA USA
| | - Kevin A. Kuehn
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS USA
| | - David Lobb
- Department of Soil Science, University of Manitoba, Winnipeg, MB Canada
| | - Amanda L. Loder
- Department of Geography, University of Toronto, Toronto, ON Canada
| | - Shizhou Ma
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK Canada
| | - Damien T. Maher
- Faculty of Science and Engineering, Southern Cross University, Lismore, NSW Australia
| | - Gavin McNicol
- Department of Earth and Environmental Sciences, University of Illinois Chicago, Chicago, IL USA
| | - Jacob Meier
- U.S. Geological Survey, Northern Prairie Wildlife Research Center, Jamestown, ND USA
| | - Beth A. Middleton
- U.S. Geological Survey, Wetland and Aquatic Research Center, Lafayette, LA USA
| | - Christopher Mills
- U.S. Geological Survey, Geology, Geophysics, and Geochemistry Science Center, Denver, CO USA
| | - Purbasha Mistry
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK Canada
| | - Abhijit Mitra
- Department of Marine Science, University of Calcutta, Kolkata, West Bengal India
| | - Courtney Mobilian
- O’Neill School of Public and Environmental Affairs, Indiana University, Bloomington, IN USA
| | - Amanda M. Nahlik
- Office of Research and Development, Center for Public Health and Environmental Assessments, Pacific Ecological Systems Division, U.S. Environmental Protection Agency, Corvallis, OR USA
| | - Sue Newman
- South Florida Water Management District, Everglades Systems Assessment Section, West Palm Beach, FL USA
| | - Jessica L. O’Connell
- Department of Ecosystem Science and Sustainability, Colorado State University, Fort Collins, CO USA
| | - Patty Oikawa
- Department of Earth and Environmental Sciences, California State University, East Bay, Hayward, CA USA
| | - Max Post van der Burg
- U.S. Geological Survey, Northern Prairie Wildlife Research Center, Jamestown, ND USA
| | - Charles A. Schutte
- Department of Environmental Science, Rowan University, Glassboro, NJ USA
| | - Changchun Song
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Camille L. Stagg
- U.S. Geological Survey, Wetland and Aquatic Research Center, Lafayette, LA USA
| | - Jessica Turner
- Freshwater and Marine Science, University of Wisconsin-Madison, Madison, WI USA
| | - Rodrigo Vargas
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE USA
| | - Mark P. Waldrop
- U.S. Geological Survey, Geology, Minerals, Energy and Geophysics Science Center, Menlo Park, CA USA
| | - Marcus B. Wallin
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Zhaohui Aleck Wang
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA USA
| | - Eric J. Ward
- U.S. Geological Survey, Wetland and Aquatic Research Center, Lafayette, LA USA
| | - Debra A. Willard
- U.S. Geological Survey, Florence Bascom Geoscience Center, Reston, VA USA
| | - Stephanie Yarwood
- Environmental Science and Technology, University of Maryland, College Park, MD USA
| | - Xiaoyan Zhu
- Key Laboratory of Songliao Aquatic Environment, Ministry of Education, Jilin Jianzhu University, Changchun, China
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8
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Skvorak K, Liu J, Kruse N, Mehmood R, Das S, Jenne S, Chng C, Lao UL, Duan D, Asfaha J, Du F, Teadt L, Sero A, Ching C, Riggins J, Pope L, Yan P, Mashiana H, Ismaili MHA, McCluskie K, Huisman G, Silverman AP. Oral enzyme therapy for maple syrup urine disease (MSUD) suppresses plasma leucine levels in intermediate MSUD mice and healthy nonhuman primates. J Inherit Metab Dis 2023; 46:1089-1103. [PMID: 37494004 DOI: 10.1002/jimd.12662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/06/2023] [Accepted: 07/25/2023] [Indexed: 07/27/2023]
Abstract
Maple syrup urine disease (MSUD) is an inborn error of branched-chain amino acid metabolism affecting several thousand individuals worldwide. MSUD patients have elevated levels of plasma leucine and its metabolic product α-ketoisocaproate (KIC), which can lead to severe neurotoxicity, coma, and death. Patients must maintain a strict diet of protein restriction and medical formula, and periods of noncompliance or illness can lead to acute metabolic decompensation or cumulative neurological impairment. Given the lack of therapeutic options for MSUD patients, we sought to develop an oral enzyme therapy that can degrade leucine within the gastrointestinal tract prior to its systemic absorption and thus enable patients to maintain acceptable plasma leucine levels while broadening their access to natural protein. We identified a highly active leucine decarboxylase enzyme from Planctomycetaceae bacterium and used directed evolution to engineer the enzyme for stability to gastric and intestinal conditions. Following high-throughput screening of over 12 000 enzyme variants over 9 iterative rounds of evolution, we identified a lead variant, LDCv10, which retains activity following simulated gastric or intestinal conditions in vitro. In intermediate MSUD mice or healthy nonhuman primates given a whey protein meal, oral treatment with LDCv10 suppressed the spike in plasma leucine and KIC and reduced the leucine area under the curve in a dose-dependent manner. Reduction in plasma leucine correlated with decreased brain leucine levels following oral LDCv10 treatment. Collectively, these data support further development of LDCv10 as a potential new therapy for MSUD patients.
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Affiliation(s)
| | - Joyce Liu
- Codexis, Inc., Redwood City, California, USA
| | - Nikki Kruse
- Codexis, Inc., Redwood City, California, USA
| | | | | | | | | | - U Loi Lao
- Codexis, Inc., Redwood City, California, USA
| | - Da Duan
- Codexis, Inc., Redwood City, California, USA
| | | | - Faye Du
- Codexis, Inc., Redwood City, California, USA
| | - Leann Teadt
- Codexis, Inc., Redwood City, California, USA
| | | | | | | | - Lianne Pope
- Codexis, Inc., Redwood City, California, USA
| | - Ping Yan
- Codexis, Inc., Redwood City, California, USA
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9
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Ter Horst AM, Fudyma JD, Sones JL, Emerson JB. Dispersal, habitat filtering, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography. THE ISME JOURNAL 2023; 17:2079-2089. [PMID: 37735616 PMCID: PMC10579374 DOI: 10.1038/s41396-023-01516-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/08/2023] [Indexed: 09/23/2023]
Abstract
Wetlands store 20-30% of the world's soil carbon, and identifying the microbial controls on these carbon reserves is essential to predicting feedbacks to climate change. Although viral infections likely play important roles in wetland ecosystem dynamics, we lack a basic understanding of wetland viral ecology. Here 63 viral size-fraction metagenomes (viromes) and paired total metagenomes were generated from three time points in 2021 at seven fresh- and saltwater wetlands in the California Bodega Marine Reserve. We recovered 12,826 viral population genomic sequences (vOTUs), only 4.4% of which were detected at the same field site two years prior, indicating a small degree of population stability or recurrence. Viral communities differed most significantly among the seven wetland sites and were also structured by habitat (plant community composition and salinity). Read mapping to a new version of our reference database, PIGEONv2.0 (515,763 vOTUs), revealed 196 vOTUs present over large geographic distances, often reflecting shared habitat characteristics. Wetland vOTU microdiversity was significantly lower locally than globally and lower within than between time points, indicating greater divergence with increasing spatiotemporal distance. Viruses tended to have broad predicted host ranges via CRISPR spacer linkages to metagenome-assembled genomes, and increased SNP frequencies in CRISPR-targeted major tail protein genes suggest potential viral eco-evolutionary dynamics in response to both immune targeting and changes in host cell receptors involved in viral attachment. Together, these results highlight the importance of dispersal, environmental selection, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography.
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Affiliation(s)
| | - Jane D Fudyma
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Jacqueline L Sones
- Bodega Marine Reserve, University of California, Davis, Bodega Bay, CA, USA
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, CA, USA.
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10
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Cleary DFR, de Voogd NJ, Stuij TM, Swierts T, Oliveira V, Polónia ARM, Louvado A, Gomes NCM, Coelho FJRC. A Study of Sponge Symbionts from Different Light Habitats. MICROBIAL ECOLOGY 2023; 86:2819-2837. [PMID: 37597041 PMCID: PMC10640470 DOI: 10.1007/s00248-023-02267-x] [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: 01/29/2023] [Accepted: 07/07/2023] [Indexed: 08/21/2023]
Abstract
The amount of available light plays a key role in the growth and development of microbial communities. In the present study, we tested to what extent sponge-associated prokaryotic communities differed between specimens of the sponge species Cinachyrella kuekenthali and Xestospongia muta collected in dimly lit (caves and at greater depths) versus illuminated (shallow water) habitats. In addition to this, we also collected samples of water, sediment, and another species of Cinachyrella, C. alloclada. Overall, the biotope (sponge host species, sediment, and seawater) proved the major driver of variation in prokaryotic community composition. The light habitat, however, also proved a predictor of compositional variation in prokaryotic communities of both C. kuekenthali and X. muta. We used an exploratory technique based on machine learning to identify features (classes, orders, and OTUs), which distinguished X. muta specimens sampled in dimly lit versus illuminated habitat. We found that the classes Alphaproteobacteria and Rhodothermia and orders Puniceispirillales, Rhodospirillales, Rhodobacterales, and Thalassobaculales were associated with specimens from illuminated, i.e., shallow water habitat, while the classes Dehalococcoidia, Spirochaetia, Entotheonellia, Nitrospiria, Schekmanbacteria, and Poribacteria, and orders Sneathiellales and Actinomarinales were associated with specimens sampled from dimly lit habitat. There was, however, considerable variation within the different light habitats highlighting the importance of other factors in structuring sponge-associated bacterial communities.
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Affiliation(s)
- D F R Cleary
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - N J de Voogd
- Naturalis Biodiversity Center, Leiden, The Netherlands.
- Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands.
| | - T M Stuij
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - T Swierts
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - V Oliveira
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - A R M Polónia
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - A Louvado
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - N C M Gomes
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - F J R C Coelho
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
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11
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Zhang R, Fu X, Zhong H, Sui X, Liu Y. Changes in Soil Bacterial Community and Function in Winter Following Long-Term Nitrogen (N) Deposition in Wetland Soil in Sanjiang Plain, China. Microorganisms 2023; 11:2634. [PMID: 38004646 PMCID: PMC10673031 DOI: 10.3390/microorganisms11112634] [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: 10/08/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
N deposition is a key factor affecting the composition and function of soil microbial communities in wetland ecosystems. Previous studies mainly focused on the effects of N deposition in the soil during the growing season (summer and autumn). Here, we focused on the response of the soil microbial community structure and function in winter. Soil from the Sanjiang Plain wetland, China, that had been treated for the past 11 years by using artificial N deposition at three levels (no intervention in N0, N deposition with 4 g N m-2 yr-1 in N1, and with 8 g N m-2 yr-1 in N2). Soil characteristics were determined and the bacterial composition and function was characterized using high-throughput sequence technology. The N deposition significantly reduced the soil bacterial diversity detected in winter compared with the control N0, and it significantly changed the composition of the bacterial community. At the phylum level, the high N deposition (N2) increased the relative abundance of Acidobacteria and decreased that of Myxococcota and Gemmatimonadota compared with N0. In soil from N2, the relative abundance of the general Candidatus_Solibacter and Bryobacter was significantly increased compared with N0. Soil pH, soil organic carbon (SOC), and total nitrogen (TN) were the key factors affecting the soil bacterial diversity and composition in winter. Soil pH was correlated with soil carbon cycling, probably due to its significant correlation with aerobic_chemoheterotrophy. The results show that a long-term N deposition reduces soil nutrients in winter wetlands and decreases soil bacterial diversity, resulting in a negative impact on the Sanjiang plain wetland. This study contributes to a better understanding of the winter responses of soil microbial community composition and function to the N deposition in temperate wetland ecosystems.
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Affiliation(s)
- Rongtao Zhang
- Institution of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China; (R.Z.); (X.F.); (H.Z.)
| | - Xiaoyu Fu
- Institution of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China; (R.Z.); (X.F.); (H.Z.)
| | - Haixiu Zhong
- Institution of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China; (R.Z.); (X.F.); (H.Z.)
| | - Xin Sui
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin 150040, China
| | - Yingnan Liu
- Institution of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China; (R.Z.); (X.F.); (H.Z.)
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12
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Trubl G, Stedman KM, Bywaters KF, Matula EE, Sommers P, Roux S, Merino N, Yin J, Kaelber JT, Avila-Herrera A, Johnson PA, Johnson JC, Borges S, Weber PK, Pett-Ridge J, Boston PJ. Astrovirology: how viruses enhance our understanding of life in the Universe. INTERNATIONAL JOURNAL OF ASTROBIOLOGY 2023; 22:247-271. [PMID: 38046673 PMCID: PMC10691837 DOI: 10.1017/s1473550423000058] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Viruses are the most numerically abundant biological entities on Earth. As ubiquitous replicators of molecular information and agents of community change, viruses have potent effects on the life on Earth, and may play a critical role in human spaceflight, for life-detection missions to other planetary bodies and planetary protection. However, major knowledge gaps constrain our understanding of the Earth's virosphere: (1) the role viruses play in biogeochemical cycles, (2) the origin(s) of viruses and (3) the involvement of viruses in the evolution, distribution and persistence of life. As viruses are the only replicators that span all known types of nucleic acids, an expanded experimental and theoretical toolbox built for Earth's viruses will be pivotal for detecting and understanding life on Earth and beyond. Only by filling in these knowledge and technical gaps we will obtain an inclusive assessment of how to distinguish and detect life on other planetary surfaces. Meanwhile, space exploration requires life-support systems for the needs of humans, plants and their microbial inhabitants. Viral effects on microbes and plants are essential for Earth's biosphere and human health, but virus-host interactions in spaceflight are poorly understood. Viral relationships with their hosts respond to environmental changes in complex ways which are difficult to predict by extrapolating from Earth-based proxies. These relationships should be studied in space to fully understand how spaceflight will modulate viral impacts on human health and life-support systems, including microbiomes. In this review, we address key questions that must be examined to incorporate viruses into Earth system models, life-support systems and life detection. Tackling these questions will benefit our efforts to develop planetary protection protocols and further our understanding of viruses in astrobiology.
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Affiliation(s)
- Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kenneth M. Stedman
- Center for Life in Extreme Environments, Department of Biology, Portland State University, Portland, OR, USA
| | | | | | | | - Simon Roux
- DOE Joint Genome Institute, Berkeley, CA, USA
| | - Nancy Merino
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - John Yin
- Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Jason T. Kaelber
- Institute for Quantitative Biomedicine, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Aram Avila-Herrera
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter Anto Johnson
- Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | | | | | - Peter K. Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, CA, USA
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13
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Liao H, Liu C, Ai C, Gao T, Yang QE, Yu Z, Gao S, Zhou S, Friman VP. Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting. THE ISME JOURNAL 2023; 17:916-930. [PMID: 37031344 DOI: 10.1038/s41396-023-01404-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/10/2023]
Abstract
While decomposition of organic matter by bacteria plays a major role in nutrient cycling in terrestrial ecosystems, the significance of viruses remains poorly understood. Here we combined metagenomics and metatranscriptomics with temporal sampling to study the significance of mesophilic and thermophilic bacteria and their viruses on nutrient cycling during industrial-scale hyperthermophilic composting (HTC). Our results show that virus-bacteria density dynamics and activity are tightly coupled, where viruses specific to mesophilic and thermophilic bacteria track their host densities, triggering microbial community succession via top-down control during HTC. Moreover, viruses specific to mesophilic bacteria encoded and expressed several auxiliary metabolic genes (AMGs) linked to carbon cycling, impacting nutrient turnover alongside bacteria. Nutrient turnover correlated positively with virus-host ratio, indicative of a positive relationship between ecosystem functioning, viral abundances, and viral activity. These effects were predominantly driven by DNA viruses as most detected RNA viruses were associated with eukaryotes and not associated with nutrient cycling during the thermophilic phase of composting. Our findings suggest that DNA viruses could drive nutrient cycling during HTC by recycling bacterial biomass through cell lysis and by expressing key AMGs. Viruses could hence potentially be used as indicators of microbial ecosystem functioning to optimize productivity of biotechnological and agricultural systems.
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Affiliation(s)
- Hanpeng Liao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Chen Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chaofan Ai
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tian Gao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qiu-E Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhen Yu
- Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Shaoming Gao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
| | - Ville-Petri Friman
- Department of Biology, University of York, Wentworth Way, YO10 5DD, York, UK.
- Department of Microbiology, University of Helsinki, Helsinki, 00014, Finland.
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14
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George NA, Hug LA. CRISPR-resolved virus-host interactions in a municipal landfill include non-specific viruses, hyper-targeted viral populations, and interviral conflicts. Sci Rep 2023; 13:5611. [PMID: 37019939 PMCID: PMC10076291 DOI: 10.1038/s41598-023-32078-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 03/22/2023] [Indexed: 04/07/2023] Open
Abstract
Viruses are the most abundant microbial guild on the planet, impacting microbial community structure and ecosystem services. Viruses are specifically understudied in engineered environments, including examinations of their host interactions. We examined host-virus interactions via host CRISPR spacer to viral protospacer mapping in a municipal landfill across two years. Viruses comprised ~ 4% of both the unassembled reads and assembled basepairs. A total of 458 unique virus-host connections captured hyper-targeted viral populations and host CRISPR array adaptation over time. Four viruses were predicted to infect across multiple phyla, suggesting that some viruses are far less host-specific than is currently understood. We detected 161 viral elements that encode CRISPR arrays, including one with 187 spacers, the longest virally-encoded CRISPR array described to date. Virally-encoded CRISPR arrays targeted other viral elements in interviral conflicts. CRISPR-encoding proviruses integrated into host chromosomes were latent examples of CRISPR-immunity-based superinfection exclusion. The bulk of the observed virus-host interactions fit the one-virus-one-host paradigm, but with limited geographic specificity. Our networks highlight rare and previously undescribed complex interactions influencing the ecology of this dynamic engineered system. Our observations indicate landfills, as heterogeneous contaminated sites with unique selective pressures, are key locations for atypical virus-host dynamics.
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Affiliation(s)
- Nikhil A George
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
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15
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Liu R, Li Z, Han G, Cun S, Hou D, Yu Z, Xue K, Liu X. Microbial density-dependent viral dynamics and low activity of temperate phages in the activated sludge process. WATER RESEARCH 2023; 232:119709. [PMID: 36764107 DOI: 10.1016/j.watres.2023.119709] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 01/31/2023] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
The ecological behavior of bacteriophages (phages), the most abundant biological entity in wastewater treatment systems, is poorly understood, especially that of temperate phages. Here, the temporal dynamics of lytic and temperate phages in a laboratory-scale activated sludge reactor with a sludge bulking issue was investigated using coupled sludge metagenomic and viromic analyses. The lysogenic fragments (prophages) identified were widely distributed in the reconstructed metagenome-assembled genomes (61.7%, n = 227). However, only 12.3% of the identified prophages experienced lysogenic-lytic switching, and the abundance contribution of prophages to free virus communities was only 0.02-0.3%, indicating low activity of temperate phages. Although the sludge community changed dramatically during reactor operation, no massive prophage induction events were detected. Statistical analyses showed strong correlations between sludge concentration and free virus and temperate phage communities, suggesting microbial density-dependent virus dynamics in the sludge microbiota.
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Affiliation(s)
- Ruyin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China; Binzhou Institute of Technology, Weiqiao-UCAS Science and Technology Park, Binzhou City, Shandong Province, China.
| | - Zong Li
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Ganghua Han
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Shujuan Cun
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Deyin Hou
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Xinchun Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China.
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16
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El-Baky NA, Rezk NMF, Amara AA. Arthrospira platensis Variants: A Comparative Study Based on C-phycocyanin Gene and Protein, Habitat, and Growth Conditions. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2023; 11:663. [DOI: 10.3390/jmse11030663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
This study aimed to map the differences between Arthrospira sp. and Arthrospira platensis strains and variants from the order Oscillatoriales at the gene and protein levels of C-phycocyanin alpha chain via multiple alignment, phylogenetic trees of species, and analysis of the nucleotide and amino acid composition of the studied sequences. The links between gene/protein and environmental features of the habitat or source of isolation were also investigated. Phycocyanin was extracted from three A. platensis strains: an Egyptian isolate cultivated in the laboratory under static conditions in a highly saline medium and two commercial products. The French commercial strain showed the highest extraction yield but the lowest C-phycocyanin purity, and the color intensity of the extracted pigment from the Egyptian isolate was significantly weaker than those of the two commercial strains. All the analyzed species and strains had GC content of more than 54.5% in C-phycocyanin alpha chain gene and showed high abundance of alanine, an amino acid encoded exclusively by GC-biased codons, in their protein. The frequencies of the acidic amino acids aspartic acid and glutamic acid were 5.2% and 5.0% on average, respectively, which were slightly higher than those of the basic residues (4.3% arginine, 0.6% histidine, and 5.0% lysine). Data relating to the isolation source of most of the analyzed species revealed harsh conditions, such as high alkalinity, salinity, CO2 saturation, and/or temperature. These findings may link the gene/protein of C-phycocyanin, which is one of the most important bioactive proteins of A. platensis, to the adaptation of this organism to harsh environmental conditions and associate the color of the pigment to cultivation conditions and/or isolation source.
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Affiliation(s)
- Nawal Abd El-Baky
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Alexandria P.O. Box 21934, Egypt
| | - Neama Mahmoud Fattouh Rezk
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Alexandria P.O. Box 21934, Egypt
| | - Amro A. Amara
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Alexandria P.O. Box 21934, Egypt
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17
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Lin Z, Lu P, Wang R, Liu X, Yuan T. Sulfur: a neglected driver of the increased abundance of antibiotic resistance genes in agricultural reclaimed subsidence land located in coal mines with high phreatic water levels. Heliyon 2023; 9:e14364. [PMID: 36994396 PMCID: PMC10040520 DOI: 10.1016/j.heliyon.2023.e14364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 03/01/2023] [Accepted: 03/01/2023] [Indexed: 03/09/2023] Open
Abstract
Due to the shallow burial of groundwater in coal mines with a high phreatic water level, a large area of subsidence lakes is formed after the mine collapses. Agricultural and fishery reclamation activities have been carried out, which introduced antibiotics and exacerbated the contamination of antibiotic resistance genes (ARGs), but this has received limited attention. This study analyzed ARG occurrence in reclaimed mining areas, the key impact factors, and the underlying mechanism. The results show that sulfur is the most critical factor impacting the abundance of ARGs in reclaimed soil, which is due to changes in the microbial community. The species and abundance of ARGs in the reclaimed soil were higher than those in the controlled soil. The relative abundances of most ARGs increased with the depth of reclaimed soil (from 0 to 80 cm). In addition, the microbial structures of the reclaimed and controlled soils were significantly different. Proteobacteria, was the most dominant microbial phylum in the reclaimed soil. This difference is likely related to the high abundance of sulfur metabolism functional genes in the reclaimed soil. Correlation analysis showed that the differences in ARGs and microorganisms in the two soil types were highly correlated with the sulfur content. High levels of sulfur promoted the proliferation of sulfur-metabolizing microbial populations such as Proteobacteria and Gemmatimonadetes in the reclaimed soils. Remarkably, these microbial phyla were the main antibiotic-resistant bacteria in this study, and their proliferation created conditions for the enrichment of ARGs. Overall, this study underscores the risk of the abundance and spread of ARGs driven by high-level sulfur in reclaimed soils and reveals the mechanisms.
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Roux S, Fischer MG, Hackl T, Katz LA, Schulz F, Yutin N. Updated Virophage Taxonomy and Distinction from Polinton-like Viruses. Biomolecules 2023; 13:204. [PMID: 36830574 PMCID: PMC9952930 DOI: 10.3390/biom13020204] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
Virophages are small dsDNA viruses that hijack the machinery of giant viruses during the co-infection of a protist (i.e., microeukaryotic) host and represent an exceptional case of "hyperparasitism" in the viral world. While only a handful of virophages have been isolated, a vast diversity of virophage-like sequences have been uncovered from diverse metagenomes. Their wide ecological distribution, idiosyncratic infection and replication strategy, ability to integrate into protist and giant virus genomes and potential role in antiviral defense have made virophages a topic of broad interest. However, one limitation for further studies is the lack of clarity regarding the nomenclature and taxonomy of this group of viruses. Specifically, virophages have been linked in the literature to other "virophage-like" mobile genetic elements and viruses, including polinton-like viruses (PLVs), but there are no formal demarcation criteria and proper nomenclature for either group, i.e., virophage or PLVs. Here, as part of the ICTV Virophage Study Group, we leverage a large set of genomes gathered from published datasets as well as newly generated protist genomes to propose delineation criteria and classification methods at multiple taxonomic ranks for virophages 'sensu stricto', i.e., genomes related to the prototype isolates Sputnik and mavirus. Based on a combination of comparative genomics and phylogenetic analyses, we show that this group of virophages forms a cohesive taxon that we propose to establish at the class level and suggest a subdivision into four orders and seven families with distinctive ecogenomic features. Finally, to illustrate how the proposed delineation criteria and classification method would be used, we apply these to two recently published datasets, which we show include both virophages and other virophage-related elements. Overall, we see this proposed classification as a necessary first step to provide a robust taxonomic framework in this area of the virosphere, which will need to be expanded in the future to cover other virophage-related viruses such as PLVs.
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Affiliation(s)
- Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Matthias G. Fischer
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, 69120 Heidelberg, Germany
| | - Thomas Hackl
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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Luo XQ, Wang P, Li JL, Ahmad M, Duan L, Yin LZ, Deng QQ, Fang BZ, Li SH, Li WJ. Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts. MICROBIOME 2022; 10:190. [PMID: 36333738 PMCID: PMC9636769 DOI: 10.1186/s40168-022-01384-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/04/2022] [Indexed: 06/02/2023]
Abstract
BACKGROUND Viral-encoded auxiliary metabolic genes (AMGs) are important toolkits for modulating their hosts' metabolisms and the microbial-driven biogeochemical cycles. Although the functions of AMGs have been extensively reported in numerous environments, we still know little about the drivers that shape the viral community-wide AMG compositions in natural ecosystems. Exploring the drivers of viral community-wide AMG compositions is critical for a deeper understanding of the complex interplays among viruses, hosts, and the environments. RESULTS Here, we investigated the impact of viral lifestyles (i.e., lytic and lysogenic), habitats (i.e., water, particle, and sediment), and prokaryotic hosts on viral AMG profiles by utilizing metagenomic and metatranscriptomic techniques. We found that viral lifestyles were the most important drivers, followed by habitats and host identities. Specifically, irrespective of what habitats viruses came from, lytic viruses exhibited greater AMG diversity and tended to encode AMGs for chaperone biosynthesis, signaling proteins, and lipid metabolism, which could boost progeny reproduction, whereas temperate viruses were apt to encode AMGs for host survivability. Moreover, the lytic and temperate viral communities tended to mediate the microbial-driven biogeochemical cycles, especially nitrogen metabolism, in different manners via AMGs. When focusing on each lifestyle, we further found clear dissimilarity in AMG compositions between water and sediment, as well the divergent AMGs encoded by viruses infecting different host orders. CONCLUSIONS Overall, our study provides a first systematic characterization of the drivers of viral community-wide AMG compositions and further expands our knowledge of the distinct interactions of lytic and temperate viruses with their prokaryotic hosts from an AMG perspective, which is critical for understanding virus-host-environment interactions in natural conditions. Video Abstract.
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Affiliation(s)
- Xiao-Qing 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, People's Republic of China
| | - Pandeng Wang
- 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, People's Republic of China.
- School of Ecology, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China.
| | - Jia-Ling 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, People's Republic of China
| | - Manzoor Ahmad
- 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, People's Republic of China
| | - Li Duan
- 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, People's Republic of China
| | - Ling-Zi Yin
- 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, People's Republic of China
| | - Qi-Qi Deng
- 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, People's Republic of China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Shan-Hui 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, People's Republic of 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, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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20
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Su H, Wu C, Han P, Liu Z, Liang M, Zhang Z, Wang Z, Guo G, He X, Pang J, Wang C, Weng S, He J. The microbiome and its association with antibiotic resistance genes in the hadal biosphere at the Yap Trench. JOURNAL OF HAZARDOUS MATERIALS 2022; 439:129543. [PMID: 35870206 DOI: 10.1016/j.jhazmat.2022.129543] [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: 04/27/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
The hadal biosphere, the deepest part of the ocean, is known as the least-explored aquatic environment and hosts taxonomically diverse microbial communities. However, the microbiome and its association with antibiotic resistance genes (ARGs) in the hadal ecosystem remain unknown. Here, we profiled the microbiome diversity and ARG occurrence in seawater and sediments of the Yap Trench (YT) using metagenomic sequencing. Within the prokaryote (bacteria and archaea) lineages, the main components of bacteria were Gammaproteobacteria (77.76 %), Firmicutes (8.36 %), and Alphaproteobacteria (2.25 %), whereas the major components of archaea were Nitrososphaeria (6.51 %), Nanoarchaeia (0.42 %), and Thermoplasmata (0.25 %), respectively. Taxonomy of viral contigs showed that the classified viral communities in YT seawater and sediments were dominated by Podoviridae (45.96 %), Siphoviridae (29.41 %), and Myoviridae (24.63 %). A large majority of viral contigs remained uncharacterized and exhibited endemicity. A total of 48 ARGs encoding resistance to 12 antibiotic classes were identified and their hosts were bacteria and viruses. Novel ARG subtypes mexFYTV-1, mexFYTV-2, mexFYTV-3, vanRYTV-1, vanSYTV-1 (carried by unclassified viruses), and bacAYTB-1 (carried by phylum Firmicutes) were detected in seawater samples. Overall, our findings imply that the hadal environment of the YT is a repository of viral and ARG diversity.
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Affiliation(s)
- Hualong Su
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China
| | - Chengcheng Wu
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Peiyun Han
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zixuan Liu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China
| | - Mincong Liang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China
| | - Zheng Zhang
- Baidu International Technology (Shenzhen), Shenzhen 518062, China
| | - Zhike Wang
- Hainan Guodun Information Development, Haikou 570206, China
| | - Guangyu Guo
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China
| | - Xinyi He
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jianhu Pang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Cheng Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Shaoping Weng
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jianguo He
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China; State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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21
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Zhou YL, Mara P, Vik D, Edgcomb VP, Sullivan MB, Wang Y. Ecogenomics reveals viral communities across the Challenger Deep oceanic trench. Commun Biol 2022; 5:1055. [PMID: 36192584 PMCID: PMC9529941 DOI: 10.1038/s42003-022-04027-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 09/23/2022] [Indexed: 11/23/2022] Open
Abstract
Despite the environmental challenges and nutrient scarcity, the geographically isolated Challenger Deep in Mariana trench, is considered a dynamic hotspot of microbial activity. Hadal viruses are the least explored microorganisms in Challenger Deep, while their taxonomic and functional diversity and ecological impact on deep-sea biogeochemistry are poorly described. Here, we collect 13 sediment cores from slope and bottom-axis sites across the Challenger Deep (down to ~11 kilometers depth), and identify 1,628 previously undescribed viral operational taxonomic units at species level. Community-wide analyses reveals 1,299 viral genera and distinct viral diversity across the trench, which is significantly higher at the bottom-axis vs. slope sites of the trench. 77% of these viral genera have not been previously identified in soils, deep-sea sediments and other oceanic settings. Key prokaryotes involved in hadal carbon and nitrogen cycling are predicted to be potential hosts infected by these viruses. The detected putative auxiliary metabolic genes suggest that viruses at Challenger Deep could modulate the carbohydrate and sulfur metabolisms of their potential hosts, and stabilize host's cell membranes under extreme hydrostatic pressures. Our results shed light on hadal viral metabolic capabilities, contribute to understanding deep sea ecology and on functional adaptions of hadal viruses for future research.
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Affiliation(s)
- Ying-Li Zhou
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Paraskevi Mara
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Dean Vik
- Department of Microbiology and Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Matthew B Sullivan
- Department of Microbiology and Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
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22
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Li JT, Jia P, Wang XJ, Ou SN, Yang TT, Feng SW, Lu JL, Fang Z, Liu J, Liao B, Shu WS, Liang JL. Metagenomic and metatranscriptomic insights into sulfate-reducing bacteria in a revegetated acidic mine wasteland. NPJ Biofilms Microbiomes 2022; 8:71. [PMID: 36068230 PMCID: PMC9448743 DOI: 10.1038/s41522-022-00333-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
The widespread occurrence of sulfate-reducing microorganisms (SRMs) in temporarily oxic/hypoxic aquatic environments indicates an intriguing possibility that SRMs can prevail in constantly oxic/hypoxic terrestrial sulfate-rich environments. However, little attention has been given to this possibility, leading to an incomplete understanding of microorganisms driving the terrestrial part of the global sulfur (S) cycle. In this study, genome-centric metagenomics and metatranscriptomics were employed to explore the diversity, metabolic potential, and gene expression profile of SRMs in a revegetated acidic mine wasteland under constantly oxic/hypoxic conditions. We recovered 16 medium- to high-quality metagenome-assembled genomes (MAGs) containing reductive dsrAB. Among them, 12 and four MAGs belonged to Acidobacteria and Deltaproteobacteria, respectively, harboring three new SRM genera. Comparative genomic analysis based on seven high-quality MAGs (completeness >90% and contamination <10%; including six acidobacterial and one deltaproteobacterial) and genomes of three additional cultured model species showed that Acidobacteria-related SRMs had more genes encoding glycoside hydrolases, oxygen-tolerant hydrogenases, and cytochrome c oxidases than Deltaproteobacteria-related SRMs. The opposite pattern was observed for genes encoding superoxide reductases and thioredoxin peroxidases. Using VirSorter, viral genome sequences were found in five of the 16 MAGs and in all three cultured model species. These prophages encoded enzymes involved in glycoside hydrolysis and antioxidation in their hosts. Moreover, metatranscriptomic analysis revealed that 15 of the 16 SRMs reported here were active in situ. An acidobacterial MAG containing a prophage dominated the SRM transcripts, expressing a large number of genes involved in its response to oxidative stress and competition for organic matter.
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Affiliation(s)
- Jin-Tian Li
- 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.,School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Pu Jia
- 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
| | - Xiao-Juan Wang
- 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
| | - Shu-Ning Ou
- 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
| | - Tao-Tao Yang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Shi-Wei Feng
- 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
| | - Jing-Li Lu
- 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
| | - Zhou Fang
- 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
| | - Jun Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Bin Liao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, 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
| | - Jie-Liang Liang
- 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.
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23
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Han Y, Wang Q, Li Q, Hu C. Active metabolism and biomass dynamics of biocrusts are shaped by variation in their successional state and seasonal energy sources. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 831:154756. [PMID: 35339556 DOI: 10.1016/j.scitotenv.2022.154756] [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: 12/06/2021] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Seasonal growth and changes in biomass within communities are the core of ecosystem dynamics. Biocrusts play a prominent role as pioneers in dryland soils. However, the seasonal dynamics of biocrusts remain poorly resolved. In this study, we collected biocrusts across a successional gradient (cyanobacteria, cyanolichen, chlorolichen, and moss-dominated) from southeastern Tengger Desert (China) during the summer and autumn seasons, and explored seasonal changes in metabolism and biomass using multi-omics approaches. We found that Cyanobacteria and Ascomycota were the dominant active taxa and both exhibited higher abundances in autumn. We also found that the dominant primary producers in biocrusts strongly affected community-wide characteristics of metabolism. Along with seasonal differences in light energy utilization, utilization of inorganic energy sources exhibited higher expression in the summer while for organic sources, in the autumn. We found that overall metabolism was significantly regulated by the ratio of intracellular to extracellular polymer degradation, and affected by NO3-, PO43- and EC (in the summer)/NO2- (in the autumn). In summary, biocrust growth varied with seasonal variation in light energy utilization and complementary chemical energy sources, with the most suitable season varying with biocrust successional type.
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Affiliation(s)
- Yingchun Han
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiong Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunxiang Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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24
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Hegarty B, Dai Z, Raskin L, Pinto A, Wigginton K, Duhaime M. A snapshot of the global drinking water virome: Diversity and metabolic potential vary with residual disinfectant use. WATER RESEARCH 2022; 218:118484. [PMID: 35504157 DOI: 10.1016/j.watres.2022.118484] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/01/2022] [Accepted: 04/19/2022] [Indexed: 05/22/2023]
Abstract
Viruses are important drivers of microbial community ecology and evolution, influencing microbial mortality, metabolism, and horizontal gene transfer. However, the effects of viruses remain largely unknown in many environments, including in drinking water systems. Drinking water metagenomic studies have offered a whole community perspective of bacterial impacts on water quality, but have not yet considered the influences of viruses. In this study, we address this gap by mining viral DNA sequences from publicly available drinking water metagenomes from distribution systems in six countries around the world. These datasets provide a snapshot of the taxonomic diversity and metabolic potential of the global drinking water virome; and provide an opportunity to investigate the effects of geography, climate, and drinking water treatment practices on viral diversity. Both environmental conditions and differences in sample processing were found to influence the viral composition. Using free chlorine as the residual disinfectant was associated with clear differences in viral taxonomic diversity and metabolic potential, with significantly fewer viral populations and less even viral community structures than observed in distribution systems without residual disinfectant. Additionally, drinking water viruses carry antibiotic resistance genes (ARGs), as well as genes to survive oxidative stress and nitrogen limitation. Through this study, we have demonstrated that viral communities are diverse across drinking water systems and vary with the use of residual disinfectant. Our findings offer directions for future research to develop a more robust understanding of how virus-bacteria interactions in drinking water distribution systems affect water quality.
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Affiliation(s)
- Bridget Hegarty
- Department of Civil and Environmental Engineering, Environmental and Water Resources Engineering Building, University of Michigan, 1351 Beal Ave. 181, Ann Arbor, MI 48109-2125, USA
| | - Zihan Dai
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering, Environmental and Water Resources Engineering Building, University of Michigan, 1351 Beal Ave. 181, Ann Arbor, MI 48109-2125, USA
| | - Ameet Pinto
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Georgia
| | - Krista Wigginton
- Department of Civil and Environmental Engineering, Environmental and Water Resources Engineering Building, University of Michigan, 1351 Beal Ave. 181, Ann Arbor, MI 48109-2125, USA.
| | - Melissa Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105N University Ave., 4068 Biological Sciences Building, Ann Arbor, MI 48109-1085, USA.
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25
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Bacterial, Phytoplankton, and Viral Distributions and Their Biogeochemical Contexts in Meromictic Lake Cadagno Offer Insights into the Proterozoic Ocean Microbial Loop. mBio 2022; 13:e0005222. [PMID: 35726916 PMCID: PMC9426590 DOI: 10.1128/mbio.00052-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lake Cadagno, a permanently stratified high-alpine lake with a persistent microbial bloom in its chemocline, has long been considered a model for the low-oxygen, high-sulfide Proterozoic ocean. Although the lake has been studied for over 25 years, the absence of concerted study of the bacteria, phytoplankton, and viruses, together with primary and secondary production, has hindered a comprehensive understanding of its microbial food web. Here, the identities, abundances, and productivity of microbes were evaluated in the context of Lake Cadagno biogeochemistry. Photosynthetic pigments together with 16S rRNA gene phylogenies suggest the prominence of eukaryotic phytoplankton chloroplasts, primarily chlorophytes. Chloroplasts closely related to those of high-alpine-adapted Ankyra judayi persisted with oxygen in the mixolimnion, where photosynthetic efficiency was high, while chloroplasts of Closteriopsis-related chlorophytes peaked in the chemocline and monimolimnion. The anoxygenic phototrophic sulfur bacterium Chromatium dominated the chemocline along with Lentimicrobium, a genus of known fermenters. Secondary production peaked in the chemocline, which suggested that anoxygenic primary producers depended on heterotrophic nutrient remineralization. The virus-to-microbe ratio peaked with phytoplankton abundances in the mixolimnion and were at a minimum where Chromatium abundance was highest, trends that suggest that viruses may play a role in the modulation of primary production. Through the combined analysis of bacterial, eukaryotic, viral, and biogeochemical spatial dynamics, we provide a comprehensive synthesis of the Lake Cadagno microbial loop. This study offers a new ecological perspective on how biological and geochemical connections may have occurred in the chemocline of the Proterozoic ocean, where eukaryotic microbial life is thought to have evolved.
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Lu M, Schneider D, Daniel R. Metagenomic Screening for Lipolytic Genes Reveals an Ecology-Clustered Distribution Pattern. Front Microbiol 2022; 13:851969. [PMID: 35756004 PMCID: PMC9226776 DOI: 10.3389/fmicb.2022.851969] [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: 01/10/2022] [Accepted: 04/28/2022] [Indexed: 12/02/2022] Open
Abstract
Lipolytic enzymes are one of the most important enzyme types for application in various industrial processes. Despite the continuously increasing demand, only a small portion of the so far encountered lipolytic enzymes exhibit adequate stability and activities for biotechnological applications. To explore novel and/or extremophilic lipolytic enzymes, microbial consortia in two composts at thermophilic stage were analyzed using function-driven and sequence-based metagenomic approaches. Analysis of community composition by amplicon-based 16S rRNA genes and transcripts, and direct metagenome sequencing revealed that the communities of the compost samples were dominated by members of the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Chloroflexi. Function-driven screening of the metagenomic libraries constructed from the two samples yielded 115 unique lipolytic enzymes. The family assignment of these enzymes was conducted by analyzing the phylogenetic relationship and generation of a protein sequence similarity network according to an integrated classification system. The sequence-based screening was performed by using a newly developed database, containing a set of profile Hidden Markov models, highly sensitive and specific for detection of lipolytic enzymes. By comparing the lipolytic enzymes identified through both approaches, we demonstrated that the activity-directed complements sequence-based detection, and vice versa. The sequence-based comparative analysis of lipolytic genes regarding diversity, function and taxonomic origin derived from 175 metagenomes indicated significant differences between habitats. Analysis of the prevalent and distinct microbial groups providing the lipolytic genes revealed characteristic patterns and groups driven by ecological factors. The here presented data suggests that the diversity and distribution of lipolytic genes in metagenomes of various habitats are largely constrained by ecological factors.
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Affiliation(s)
| | | | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg August University of Göttingen, Göttingen, Germany
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27
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Yu RQ, Barkay T. Microbial mercury transformations: Molecules, functions and organisms. ADVANCES IN APPLIED MICROBIOLOGY 2022; 118:31-90. [PMID: 35461663 DOI: 10.1016/bs.aambs.2022.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Mercury (Hg) methylation, methylmercury (MeHg) demethylation, and inorganic redox transformations of Hg are microbe-mediating processes that determine the fate and cycling of Hg and MeHg in many environments, and by doing so influence the health of humans and wild life. The discovery of the Hg methylation genes, hgcAB, in the last decade together with advances in high throughput and genome sequencing methods, have resulted in an expanded appreciation of the diversity of Hg methylating microbes. This review aims to describe experimentally confirmed and recently discovered hgcAB gene-carrying Hg methylating microbes; phylogenetic and taxonomic analyses are presented. In addition, the current knowledge on transformation mechanisms, the organisms that carry them out, and the impact of environmental parameters on Hg methylation, MeHg demethylation, and inorganic Hg reduction and oxidation is summarized. This knowledge provides a foundation for future action toward mitigating the impact of environmental Hg pollution.
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Affiliation(s)
- Ri-Qing Yu
- Department of Biology, University of Texas at Tyler, Tyler, TX, United States.
| | - Tamar Barkay
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
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Wang Y, Liu Y, Wu Y, Wu N, Liu W, Wang X. Heterogeneity of soil bacterial and bacteriophage communities in three rice agroecosystems and potential impacts of bacteriophage on nutrient cycling. ENVIRONMENTAL MICROBIOME 2022; 17:17. [PMID: 35387674 PMCID: PMC8985318 DOI: 10.1186/s40793-022-00410-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND As genetic entities infecting and replicating only in bacteria, bacteriophages can regulate the community structure and functions of their host bacteria. The ecological roles of bacteriophages in aquatic and forest environments have been widely explored, but those in agroecosystems remains limited. Here, we used metagenomic sequencing to analyze the diversity and interactions of bacteriophages and their host bacteria in soils from three typical rice agroecosystems in China: double cropping in Guangzhou, southern China, rice-wheat rotation cropping in Nanjing, eastern China and early maturing single cropping in Jiamusi, northeastern China. Enterobacter phage-NJ was isolated and its functions on soil nitrogen cycling and effect on soil bacterial community structure were verified in pot inoculation experiments and 16S rRNA gene sequencing. RESULTS Soil bacterial and viral diversity and predicted functions varied among the three agroecosystems. Genes detected in communities from the three agroecosystems were associated with typical functions: soil bacteria in Jiamusi were significantly enriched in genes related to carbohydrate metabolism, in Nanjing with xenobiotics biodegradation and metabolism, and in Guangzhou with virulence factors and scarce in secondary metabolite biosynthesis, which might lead to a significant occurrence of rice bacterial diseases. The virus community structure varies significantly among the three ecosystems, only 13.39% of the total viral species were shared by the three rice agroecosystems, 59.56% of the viral species were specific to one agroecosystem. Notably, over-represented auxiliary carbohydrate-active enzyme (CAZyme) genes were identified in the viruses, which might assist host bacteria in metabolizing carbon, and 67.43% of these genes were present in Jiamusi. In bacteriophage isolation and inoculation experiments, Enterobacter bacteriophage-NJ reduced the nitrogen fixation capacity of soil by lysing N-fixing host bacteria and changed the soil bacterial diversity and community structure. CONCLUSION Our results showed that diversity and function predicted of paddy soil bacteria and viruses varied in the three agroecosystems. Soil bacteriophages can affect nutrient cycling by boosting host metabolism through the carried auxiliary metabolic genes (AMGs) and lysing the host bacteria that are involved in biogeochemical cycles. These findings form a basis for better understanding bacterial and bacteriophage diversity in different rice agroecosystems, laying a solid foundation for further studies of soil microbial communities that support ecofriendly production of healthy rice.
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Affiliation(s)
- Yajiao Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Baoding, 071000, China
| | - Yu Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yuxing Wu
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Baoding, 071000, China
| | - Nan Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wenwen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Dalcin Martins P, Echeveste Medrano MJ, Arshad A, Kurth JM, Ouboter HT, Op den Camp HJM, Jetten MSM, Welte CU. Unraveling Nitrogen, Sulfur, and Carbon Metabolic Pathways and Microbial Community Transcriptional Responses to Substrate Deprivation and Toxicity Stresses in a Bioreactor Mimicking Anoxic Brackish Coastal Sediment Conditions. Front Microbiol 2022; 13:798906. [PMID: 35283857 PMCID: PMC8906906 DOI: 10.3389/fmicb.2022.798906] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/12/2022] [Indexed: 12/25/2022] Open
Abstract
Microbial communities are key drivers of carbon, sulfur, and nitrogen cycling in coastal ecosystems, where they are subjected to dynamic shifts in substrate availability and exposure to toxic compounds. However, how these shifts affect microbial interactions and function is poorly understood. Unraveling such microbial community responses is key to understand their environmental distribution and resilience under current and future disturbances. Here, we used metagenomics and metatranscriptomics to investigate microbial community structure and transcriptional responses to prolonged ammonium deprivation, and sulfide and nitric oxide toxicity stresses in a controlled bioreactor system mimicking coastal sediment conditions. Ca. Nitrobium versatile, identified in this study as a sulfide-oxidizing denitrifier, became a rare community member upon ammonium removal. The ANaerobic Methanotroph (ANME) Ca. Methanoperedens nitroreducens showed remarkable resilience to both experimental conditions, dominating transcriptional activity of dissimilatory nitrate reduction to ammonium (DNRA). During the ammonium removal experiment, increased DNRA was unable to sustain anaerobic ammonium oxidation (anammox) activity. After ammonium was reintroduced, a novel anaerobic bacterial methanotroph species that we have named Ca. Methylomirabilis tolerans outcompeted Ca. Methylomirabilis lanthanidiphila, while the anammox Ca. Kuenenia stuttgartiensis outcompeted Ca. Scalindua rubra. At the end of the sulfide and nitric oxide experiment, a gammaproteobacterium affiliated to the family Thiohalobacteraceae was enriched and dominated transcriptional activity of sulfide:quinone oxidoreductases. Our results indicate that some community members could be more resilient to the tested experimental conditions than others, and that some community functions such as methane and sulfur oxidation coupled to denitrification can remain stable despite large shifts in microbial community structure. Further studies on complex bioreactor enrichments are required to elucidate coastal ecosystem responses to future disturbances.
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Affiliation(s)
| | | | - Arslan Arshad
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Julia M Kurth
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Heleen T Ouboter
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | | | - Mike S M Jetten
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Cornelia U Welte
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
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Zhao J, Jing H, Wang Z, Wang L, Jian H, Zhang R, Xiao X, Chen F, Jiao N, Zhang Y. Novel Viral Communities Potentially Assisting in Carbon, Nitrogen, and Sulfur Metabolism in the Upper Slope Sediments of Mariana Trench. mSystems 2022; 7:e0135821. [PMID: 35089086 PMCID: PMC8725595 DOI: 10.1128/msystems.01358-21] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/08/2021] [Indexed: 01/12/2023] Open
Abstract
Viruses are ubiquitous in the oceans. Even in the deep sediments of the Mariana Trench, viruses have high productivity. However, little is known about their species composition and survival strategies in that environment. Here, we uncovered novel viral communities (3,206 viral scaffolds) in the upper slope sediments of the Mariana Trench via metagenomic analysis of 15 sediment samples. Most (99%) of the viral scaffolds lack known viral homologs, and ca. 59% of the high-quality viral genomes (total of 111 with completeness of >90%) represent novel genera, including some Phycodnaviridae and jumbo phages. These viruses contain various auxiliary metabolic genes (AMGs) potentially involved in organic carbon degradation, inorganic carbon fixation, denitrification, and assimilatory sulfate reduction, etc. This study provides novel insight into the almost unknown benthic viral communities in the Mariana Trench. IMPORTANCE The Mariana Trench harbors a substantial number of infective viral particles. However, very little is known about the identity, survival strategy, and potential functions of viruses in the trench sediments. Here, through metagenomic analysis, unusual benthic viral communities with high diversity and novelty were discovered. Among them, 59% of the viruses with a genome completeness of >90% represent novel genera. Various auxiliary metabolic genes carried by these viruses reflect the potential adaptive characteristics of viruses in this extreme environment and the biogeochemical cycles that they may participate in. This study gives us a deeper understanding of the peculiarities of viral communities in deep-sea/hadal sediments.
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Affiliation(s)
- Jiulong Zhao
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zengmeng Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Long Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- State Key Laboratory for Marine Environmental Science, Xiamen University, Xiamen, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rui Zhang
- State Key Laboratory for Marine Environmental Science, Xiamen University, Xiamen, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Chen
- University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Xiamen University, Xiamen, China
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
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The DsrD functional marker protein is an allosteric activator of the DsrAB dissimilatory sulfite reductase. Proc Natl Acad Sci U S A 2022; 119:2118880119. [PMID: 35064091 PMCID: PMC8794893 DOI: 10.1073/pnas.2118880119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 11/26/2022] Open
Abstract
Metagenomic data have recently transformed our view of the role played by sulfur metabolism in anoxic environments by showing that this trait is much more widespread than previously believed. A key enzyme in sulfur metabolism is the dissimilatory sulfite reductase DsrAB that is ubiquitous in organisms with a reductive, oxidative, or disproportionating activity. However, the function of some dsr genes, such as dsrD, has so far been unknown despite its use as a functional marker to genomically assign the type of sulfur energy metabolism, sometimes with unclear results. Here, we disclose the function of DsrD as an activator of DsrAB that significantly increases its activity, providing important insights into the mechanism of this enzyme in different types of sulfur metabolism. Dissimilatory sulfur metabolism was recently shown to be much more widespread among bacteria and archaea than previously believed. One of the key pathways involved is the dsr pathway that is responsible for sulfite reduction in sulfate-, sulfur-, thiosulfate-, and sulfite-reducing organisms, sulfur disproportionators and organosulfonate degraders, or for the production of sulfite in many photo- and chemotrophic sulfur-oxidizing prokaryotes. The key enzyme is DsrAB, the dissimilatory sulfite reductase, but a range of other Dsr proteins is involved, with different gene sets being present in organisms with a reductive or oxidative metabolism. The dsrD gene codes for a small protein of unknown function and has been widely used as a functional marker for reductive or disproportionating sulfur metabolism, although in some cases this has been disputed. Here, we present in vivo and in vitro studies showing that DsrD is a physiological partner of DsrAB and acts as an activator of its sulfite reduction activity. DsrD is expressed in respiratory but not in fermentative conditions and a ΔdsrD deletion strain could be obtained, indicating that its function is not essential. This strain grew less efficiently during sulfate and sulfite reduction. Organisms with the earliest forms of dsrAB lack the dsrD gene, revealing that its activating role arose later in evolution relative to dsrAB.
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ter Horst AM, Santos-Medellín C, Sorensen JW, Zinke LA, Wilson RM, Johnston ER, Trubl G, Pett-Ridge J, Blazewicz SJ, Hanson PJ, Chanton JP, Schadt CW, Kostka JE, Emerson JB. Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations. MICROBIOME 2021; 9:233. [PMID: 34836550 PMCID: PMC8626947 DOI: 10.1186/s40168-021-01156-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/02/2021] [Indexed: 05/31/2023]
Abstract
BACKGROUND Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems. RESULTS Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH4 and CO2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes. CONCLUSIONS Results suggest strong viral "species" boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics. Video abstract The importance of Minnesota peat viromes in revealing terrestrial and aquatic niche partitioning for viral populations.
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Affiliation(s)
| | | | - Jackson W. Sorensen
- Department of Plant Pathology, University of California, Davis, Davis, CA USA
| | - Laura A. Zinke
- Department of Plant Pathology, University of California, Davis, Davis, CA USA
| | - Rachel M. Wilson
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL USA
| | - Eric R. Johnston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Steven J. Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Paul J. Hanson
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Jeffrey P. Chanton
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL USA
| | | | - Joel E. Kostka
- Schools of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Joanne B. Emerson
- Department of Plant Pathology, University of California, Davis, Davis, CA USA
- Genome Center, University of California, Davis, Davis, CA USA
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Wang Y, Wei D, Li P, Jiang Z, Liu H, Qing C, Wang H. Diversity and arsenic-metabolizing gene clusters of indigenous arsenate-reducing bacteria in high arsenic groundwater of the Hetao Plain, Inner Mongolia. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1680-1688. [PMID: 33196984 DOI: 10.1007/s10646-020-02305-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/27/2020] [Indexed: 06/11/2023]
Abstract
Dissimilatory arsenate reduction from arsenic (As)-bearing minerals into highly mobile arsenite is one of the key mechanisms of As release into groundwater. To detect the microbial diversity and As-metabolizing gene clusters of indigenous arsenate-reducing bacteria in high As groundwater in the Hetao Plain of Inner Mongolia, China, three anaerobic arsenate-reducing bacteria were isolated and arrA and arsC gene-based clone libraries of four in situ groundwater samples were constructed. The strains IMARCUG-11(G-11), IMARCUG-C1(G-C1) and IMARCUG-12(G-12) were phylogenetically belonged to genera Paraclostridium, Citrobacter and Klebsiella, respectively. They could reduce >99% of 1 mM arsenate under anoxic conditions with lactate as a carbon source in 60 h, 72 h and 84 h, respectively. As far as we know, this was the first report of arsenate reduction by genus Paraclostridium. Compared with strain G-11 (arsC) and G-C1 (arsRBC), strain G-12 contained two incomplete ars operons (operon1: arsABC, operon2: arsBC), indicating that these strains might present different strategies to resist As toxicity. Phylogenetic analysis illuminating by the arrA genes showed that in situ arsenate-reducing bacterial communities were diverse and mainly composed of Desulfobacterales (53%, dominated by Geobacter), Betaproteobacteria (12%), and unidentified groups (35%). Based on the arsC gene analysis, the indigenous arsenate-reducing bacterial communities were mainly affiliated with Omnitrophica (88%) and Deltaproteobacteria (11%, dominated by Geobacter and Syntrophobacterales). Results of this study expanded our understanding of indigenous arsenic-reducing bacteria in high As groundwater aquifers.
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Affiliation(s)
- Yanhong Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China
| | - Dazhun Wei
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China
| | - Ping Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China.
| | - Zhou Jiang
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, PR China
| | - Han Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China
| | - Chun Qing
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China
| | - Helin Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China
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Pereira J, Alva V. How do I get the most out of my protein sequence using bioinformatics tools? Acta Crystallogr D Struct Biol 2021; 77:1116-1126. [PMID: 34473083 PMCID: PMC8411974 DOI: 10.1107/s2059798321007907] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/02/2021] [Indexed: 12/21/2022] Open
Abstract
Biochemical and biophysical experiments are essential for uncovering the three-dimensional structure and biological role of a protein of interest. However, meaningful predictions can frequently also be made using bioinformatics resources that transfer knowledge from a well studied protein to an uncharacterized protein based on their evolutionary relatedness. These predictions are helpful in developing specific hypotheses to guide wet-laboratory experiments. Commonly used bioinformatics resources include methods to identify and predict conserved sequence motifs, protein domains, transmembrane segments, signal sequences, and secondary as well as tertiary structure. Here, several such methods available through the MPI Bioinformatics Toolkit (https://toolkit.tuebingen.mpg.de) are described and how their combined use can provide meaningful information on a protein of unknown function is demonstrated. In particular, the identification of homologs of known structure using HHpred, internal repeats using HHrepID, coiled coils using PCOILS and DeepCoil, and transmembrane segments using Quick2D are focused on.
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Affiliation(s)
- Joana Pereira
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
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Li Z, Pan D, Wei G, Pi W, Zhang C, Wang JH, Peng Y, Zhang L, Wang Y, Hubert CRJ, Dong X. Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity. THE ISME JOURNAL 2021; 15:2366-2378. [PMID: 33649554 PMCID: PMC8319345 DOI: 10.1038/s41396-021-00932-y] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/11/2022]
Abstract
In marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse microbial communities, but little is known about viruses infecting these microorganisms. Here, we probed metagenomes from seven geographically diverse cold seeps across global oceans to assess viral diversity, virus-host interaction, and virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons with viruses inhabiting other ecosystems reveal that cold seep sediments harbour considerable unexplored viral diversity. Most cold seep viruses display high degrees of endemism with seep fluid flux being one of the main drivers of viral community composition. In silico predictions linked 14.2% of the viruses to microbial host populations with many belonging to poorly understood candidate bacterial and archaeal phyla. Lysis was predicted to be a predominant viral lifestyle based on lineage-specific virus/host abundance ratios. Metabolic predictions of prokaryotic host genomes and viral AMGs suggest that viruses influence microbial hydrocarbon biodegradation at cold seeps, as well as other carbon, sulfur and nitrogen cycling via virus-induced mortality and/or metabolic augmentation. Overall, these findings reveal the global diversity and biogeography of cold seep viruses and indicate how viruses may manipulate seep microbial ecology and biogeochemistry.
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Affiliation(s)
- Zexin Li
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Donald Pan
- Department of Ecology and Environmental Studies, The Water School, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Guangshan Wei
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Weiling Pi
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Chuwen Zhang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Jiang-Hai Wang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Yongyi Peng
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Lu Zhang
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yong Wang
- Department of Life Science, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China.
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Wu B, Liu F, Fang W, Yang T, Chen GH, He Z, Wang S. Microbial sulfur metabolism and environmental implications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 778:146085. [PMID: 33714092 DOI: 10.1016/j.scitotenv.2021.146085] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
Sulfur as a macroelement plays an important role in biochemistry in both natural environments and engineering biosystems, which can be further linked to other important element cycles, e.g. carbon, nitrogen and iron. Consequently, the sulfur cycling primarily mediated by sulfur compounds oxidizing microorganisms and sulfur compounds reducing microorganisms has enormous environmental implications, particularly in wastewater treatment and pollution bioremediation. In this review, to connect the knowledge in microbial sulfur metabolism to environmental applications, we first comprehensively review recent advances in understanding microbial sulfur metabolisms at molecular-, cellular- and ecosystem-levels, together with their energetics. We then discuss the environmental implications to fight against soil and water pollution, with four foci: (1) acid mine drainage, (2) water blackening and odorization in urban rivers, (3) SANI® and DS-EBPR processes for sewage treatment, and (4) bioremediation of persistent organic pollutants. In addition, major challenges and further developments toward elucidation of microbial sulfur metabolisms and their environmental applications are identified and discussed.
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Affiliation(s)
- Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Feifei Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China
| | - Wenwen Fang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Tony Yang
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK S9H 3X2, Canada
| | - Guang-Hao Chen
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China.
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Zhou H, Chen P, Zhang M, Chen J, Fang J, Li X. Revealing the Viral Community in the Hadal Sediment of the New Britain Trench. Genes (Basel) 2021; 12:genes12070990. [PMID: 34209474 PMCID: PMC8306916 DOI: 10.3390/genes12070990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 12/24/2022] Open
Abstract
Marine viruses are widely distributed and influence matter and energy transformation in ecosystems by modulating hosts’ metabolism. The hadal trenches represent the deepest marine habitat on Earth, for which the viral communities and related biogeochemical functions are least explored and poorly understood. Here, using the sediment samples (8720 m below sea level) collected from the New Britain Trench (NBT), we investigated the viral community, diversity, and genetic potentials in the hadal sediment habitat for the first time by deep shotgun metagenomic sequencing. We found the NBT sediment viral community was dominated by Siphoviridae, Myoviridae, Podoviridae, Mimiviridae, and Phycodnaviridae, which belong to the dsDNA viruses. However, the large majority of them remained uncharacterized. We found the hadal sediment virome had some common components by comparing the hadal sediment viruses with those of hadal aquatic habitats and those of bathypelagic and terrestrial habitats. It was also distinctive in community structure and had many novel viral clusters not associated with the other habitual virome included in our analyses. Further phylogenetic analysis on its Caudovirales showed novel diversities, including new clades specially evolved in the hadal sediment habitat. Annotation of the NBT sediment viruses indicated the viruses might influence microbial hydrocarbon biodegradation and carbon and sulfur cycling via metabolic augmentation through auxiliary metabolic genes (AMGs). Our study filled in the knowledge gaps on the virome of the hadal sediment habitats and provided insight into the evolution and the potential metabolic functions of the hadal sediment virome.
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Affiliation(s)
- Hui Zhou
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (H.Z.); (P.C.); (M.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Chen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (H.Z.); (P.C.); (M.Z.)
| | - Mengjie Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (H.Z.); (P.C.); (M.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawang Chen
- Ocean College, Zhejiang University, Zhoushan 316021, China
- Correspondence: (J.C.); (J.F.); (X.L.)
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
- Correspondence: (J.C.); (J.F.); (X.L.)
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (H.Z.); (P.C.); (M.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (J.C.); (J.F.); (X.L.)
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Global overview and major challenges of host prediction methods for uncultivated phages. Curr Opin Virol 2021; 49:117-126. [PMID: 34126465 DOI: 10.1016/j.coviro.2021.05.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/20/2021] [Accepted: 05/22/2021] [Indexed: 12/14/2022]
Abstract
Bacterial communities play critical roles across all of Earth's biomes, affecting human health and global ecosystem functioning. They do so under strong constraints exerted by viruses, that is, bacteriophages or 'phages'. Phages can reshape bacterial communities' structure, influence long-term evolution of bacterial populations, and alter host cell metabolism during infection. Metagenomics approaches, that is, shotgun sequencing of environmental DNA or RNA, recently enabled large-scale exploration of phage genomic diversity, yielding several millions of phage genomes now to be further analyzed and characterized. One major challenge however is the lack of direct host information for these phages. Several methods and tools have been proposed to bioinformatically predict the potential host(s) of uncultivated phages based only on genome sequence information. Here we review these different approaches and highlight their distinct strengths and limitations. We also outline complementary experimental assays which are being proposed to validate and refine these bioinformatic predictions.
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Zheng L, Liang X, Shi R, Li P, Zhao J, Li G, Wang S, Han S, Radosevich M, Zhang Y. Viral Abundance and Diversity of Production Fluids in Oil Reservoirs. Microorganisms 2020; 8:microorganisms8091429. [PMID: 32957569 PMCID: PMC7563284 DOI: 10.3390/microorganisms8091429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 11/16/2022] Open
Abstract
Viruses are widely distributed in various ecosystems and have important impacts on microbial evolution, community structure and function and nutrient cycling in the environment. Viral abundance, diversity and distribution are important for a better understanding of ecosystem functioning and have often been investigated in marine, soil, and other environments. Though microbes have proven useful in oil recovery under extreme conditions, little is known about virus community dynamics in such systems. In this study, injection water and production fluids were sampled in two blocks of the Daqing oilfield limited company where water flooding and microbial flooding were continuously used to improve oil recovery. Virus-like particles (VLPs) and bacteria in these samples were extracted and enumerated with epifluorescence microscopy, and viromes of these samples were also sequenced with Illumina Hiseq PE150. The results showed that a large number of viruses existed in the oil reservoir, and VLPs abundance of production wells was 3.9 ± 0.7 × 108 mL-1 and virus to bacteria ratio (VBR) was 6.6 ± 1.1 during water flooding. Compared with water flooding, the production wells of microbial flooding had relative lower VLPs abundance (3.3 ± 0.3 × 108 mL-1) but higher VBR (7.9 ± 2.2). Assembled viral contigs were mapped to an in-house virus reference data separate from the GenBank non-redundant nucleotide (NT) database, and the sequences annotated as virus accounted for 35.34 and 55.04% of total sequences in samples of water flooding and microbial flooding, respectively. In water flooding, 7 and 6 viral families were identified in the injection and production wells, respectively. In microbial flooding, 6 viral families were identified in the injection and production wells. The total number of identified viral species in the injection well was higher than that in the production wells for both water flooding and microbial flooding. The Shannon diversity index was higher in the production well of water flooding than in the production well of microbial flooding. These results show that viruses are very abundant and diverse in the oil reservoir's ecosystem, and future efforts are needed to reveal the potential function of viral communities in this extreme environment.
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Affiliation(s)
- Liangcan Zheng
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolong Liang
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, TN 37996, USA; (X.L.); (M.R.)
| | - Rongjiu Shi
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
| | - Ping Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinyi Zhao
- No. 2 Oil Production Company, Daqing Oilfield Limited Company, Daqing 163414, China; (J.Z.); (G.L.)
| | - Guoqiao Li
- No. 2 Oil Production Company, Daqing Oilfield Limited Company, Daqing 163414, China; (J.Z.); (G.L.)
| | - Shuang Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
| | - Siqin Han
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
| | - Mark Radosevich
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, TN 37996, USA; (X.L.); (M.R.)
| | - Ying Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
- Correspondence:
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Roy K, Ghosh D, DeBruyn JM, Dasgupta T, Wommack KE, Liang X, Wagner RE, Radosevich M. Temporal Dynamics of Soil Virus and Bacterial Populations in Agricultural and Early Plant Successional Soils. Front Microbiol 2020; 11:1494. [PMID: 32733413 PMCID: PMC7358527 DOI: 10.3389/fmicb.2020.01494] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/08/2020] [Indexed: 12/15/2022] Open
Abstract
As reported in many aquatic environments, recent studies in terrestrial ecosystems implicate a role for viruses in shaping the structure, function, and evolution of prokaryotic soil communities. However, given the heterogeneity of soil and the physical constraints (i.e., pore-scale hydrology and solid-phase adsorption of phage and host cells) on the mobility of viruses and bacteria, phage-host interactions likely differ from those in aquatic systems. In this study, temporal changes in the population dynamics of viruses and bacteria in soils under different land management practices were examined. The results showed that bacterial abundance was significantly and positively correlated to both virus and inducible prophage abundance. Bacterial and viral abundance were also correlated with soil organic carbon and nitrogen content as well as with C:N ratio. The seasonal variability in viral abundance increased with soil organic carbon content. The prokaryotic community structure was influenced more by land use than by seasonal variation though considerable variation was evident in the early plant successional and grassland sites. The free extracellular viral communities were also separated by land use, and the forest soil viral assemblage exhibiting the most seasonal variability was more distinct from the other sites. Viral assemblages from the agricultural soils exhibited the least seasonal variability. Similar patterns were observed for inducible prophage viral assemblages. Seasonal variability of viral assemblages was greater in mitomycin-C (mitC) induced prophages than in extracellular viruses irrespective of land use and management. Taken together, the data suggest that soil viral production and decay are likely balanced but there was clear evidence that the structure of viral assemblages is influenced by land use and by season.
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Affiliation(s)
- Krishnakali Roy
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Dhritiman Ghosh
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jennifer M DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | | | - K Eric Wommack
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, United States
| | - Xiaolong Liang
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Regan E Wagner
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Mark Radosevich
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
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41
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Atashgahi S. Discovered by genomics: putative reductive dehalogenases with N-terminus transmembrane helixes. FEMS Microbiol Ecol 2020; 95:5426821. [PMID: 30942854 PMCID: PMC6797604 DOI: 10.1093/femsec/fiz048] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/02/2019] [Indexed: 11/13/2022] Open
Abstract
Attempts for bioremediation of toxic organohalogens resulted in the identification of organohalide-respiring bacteria harbouring reductive dehalogenases (RDases) enzymes. RDases consist of the catalytic subunit (RdhA, encoded by rdhA) that does not have membrane-integral domains, and a small putative membrane anchor (RdhB, encoded by rdhB) that (presumably) locates the A subunit to the outside of the cytoplasmic membrane. Recent genomic studies identified a putative rdh gene in an uncultured deltaproteobacterial genome that was not accompanied by an rdhB gene, but contained transmembrane helixes in N-terminus. Therefore, rather than having a separate membrane anchor protein, this putative RDase is likely a hybrid of RdhA and RdhB, and directly connected to the membrane with transmembrane helixes. However, functionality of the hybrid putative RDase remains unknown. Further analysis showed that the hybrid putative rdh genes are present in the genomes of pure cultures and uncultured members of Bacteriodetes and Deltaproteobacteria, but also in the genomes of the candidate divisions. The encoded hybrid putative RDases have cytoplasmic or exoplasmic C-terminus localization, and cluster phylogenetically separately from the existing RDase groups. With increasing availability of (meta)genomes, more diverse and likely novel rdh genes are expected, but questions regarding their functionality and ecological roles remain open.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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42
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Bi L, Yu DT, Du S, Zhang LM, Zhang LY, Wu CF, Xiong C, Han LL, He JZ. Diversity and potential biogeochemical impacts of viruses in bulk and rhizosphere soils. Environ Microbiol 2020; 23:588-599. [PMID: 32249528 DOI: 10.1111/1462-2920.15010] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 12/31/2022]
Abstract
Viruses can affect microbial dynamics, metabolism and biogeochemical cycles in aquatic ecosystems. However, viral diversity and functions in agricultural soils are poorly known, especially in the rhizosphere. We used virome analysis of eight rhizosphere and bulk soils to study viral diversity and potential biogeochemical impacts in an agro-ecosystem. The order Caudovirales was the predominant viral type in agricultural soils, with Siphoviridae being the most abundant family. Phylogenetic analysis of the terminase large subunit of Caudovirales identified high viral diversity and three novel groups. Viral community composition differed significantly between bulk and rhizosphere soils. Soil pH was the main environmental driver of the viral community structure. Remarkably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes were detected in viromes, including glycoside hydrolases, carbohydrate esterases and carbohydrate-binding modules. These results demonstrate that virus-encoded putative auxiliary metabolic genes or metabolic genes that may change bacterial metabolism and indirectly contribute to biogeochemical cycling, especially carbon cycling, in agricultural soil.
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Affiliation(s)
- Li Bi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dan-Ting Yu
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China
| | - Shuai Du
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Yu Zhang
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Chuan-Fa Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - Chao Xiong
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ji-Zheng He
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
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43
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Braga LPP, Spor A, Kot W, Breuil MC, Hansen LH, Setubal JC, Philippot L. Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios. MICROBIOME 2020; 8:52. [PMID: 32252805 PMCID: PMC7137350 DOI: 10.1186/s40168-020-00822-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/03/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Bacteriophages, the viruses infecting bacteria, are biological entities that can control their host populations. The ecological relevance of phages for microbial systems has been widely explored in aquatic environments, but the current understanding of the role of phages in terrestrial ecosystems remains limited. Here, our objective was to quantify the extent to which phages drive the assembly and functioning of soil bacterial communities. We performed a reciprocal transplant experiment using natural and sterilized soil incubated with different combinations of two soil microbial communities, challenged against native and non-native phage suspensions as well as against a cocktail of phage isolates. We tested three different community assembly scenarios by adding phages: (a) during soil colonization, (b) after colonization, and (c) in natural soil communities. One month after inoculation with phage suspensions, bacterial communities were assessed by 16S rRNA amplicon gene sequencing. RESULTS By comparing the treatments inoculated with active versus autoclaved phages, our results show that changes in phage pressure have the potential to impact soil bacterial community composition and diversity. We also found a positive effect of active phages on the soil ammonium concentration in a few treatments, which indicates that increased phage pressure may also be important for soil functions. CONCLUSIONS Overall, the present work contributes to expand the current knowledge about soil phages and provide some empirical evidence supporting their relevance for soil bacterial community assembly and functioning. Video Abstract.
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Affiliation(s)
- Lucas P P Braga
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, 21000, Dijon, France.
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
| | - Aymé Spor
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, 21000, Dijon, France
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Marie-Christine Breuil
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, 21000, Dijon, France
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - João C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Laurent Philippot
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, 21000, Dijon, France.
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44
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Revon Liu B, Huang YW, Lee HJ. Hypotoxic Fluorescent Nanoparticles Delivery by Cell-Penetrating Peptides in Multiple Organisms: From Prokaryotes to Mammalians Cells. Biotechnol Bioeng 2019. [DOI: 10.5772/intechopen.83818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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45
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Chen LX, Zhao Y, McMahon KD, Mori JF, Jessen GL, Nelson TC, Warren LA, Banfield JF. Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria. mSystems 2019. [PMID: 31641047 DOI: 10.1101/672428v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023] Open
Abstract
Fonsibacter (LD12 subclade) is among the most abundant bacterioplankton in freshwater ecosystems. These bacteria belong to the order Pelagibacterales (SAR11) and are related to Pelagibacter (marine SAR11), which dominates many marine habitats. Although a few Pelagibacter phage (Pelagiphage) have been described, no phage that infect Fonsibacter have been reported. In this study, we describe two groups of Podoviridae phage that infect Fonsibacter A complete Fonsibacter genome containing a prophage was reconstructed from metagenomic data. A circularized and complete genome related to the prophage, referred to as uv-Fonsiphage-EPL (lysogenic strategy), shows high similarity to marine Pelagiphage HTVC025P. Additionally, we reconstructed three complete genomes and one draft genome of phage related to marine Pelagiphage HTVC010P and predicted a lytic strategy. The similarity in codon usage and cooccurrence patterns of HTVC010P-related phage and Fonsibacter suggested that these phage infect Fonsibacter Similar phage were detected in Lake Mendota, Wisconsin, where Fonsibacter is also present. A search of related phage revealed the worldwide distribution of some genotypes in freshwater ecosystems, suggesting their substantial role in shaping indigenous microbial assemblages and influence on biogeochemical cycling. However, the uv-Fonsiphage-EPL and one group of HTVC010P-related phage have a more limited distribution in freshwater ecosystems. Overall, the findings provide insights into the genomic features of phage that infect Fonsibacter and expand understanding of the ecology and evolution of these important bacteria.IMPORTANCE Fonsibacter represents a significant microbial group of freshwater ecosystems. Although the genomic and metabolic features of these bacteria have been well studied, no phage infecting them has been reported. In this study, we reconstructed complete genomes of Fonsibacter and infecting phage and revealed their close relatedness to the phage infecting marine SAR11 members. Also, we illustrated that phage that infect Fonsibacter are widely distributed in freshwater habitats. In summary, the results contribute new insights into the ecology and evolution of Fonsibacter and phage.
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Affiliation(s)
- Lin-Xing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, California, USA
| | - Yanlin Zhao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Katherine D McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
| | - Jiro F Mori
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, Canada
| | - Gerdhard L Jessen
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, Canada
| | | | - Lesley A Warren
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, Canada
- School of Geography and Earth Science, McMaster University, Hamilton, Canada
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, California, USA
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Innovative Genomics Institute at UC Berkeley, Berkeley, California, USA
- The University of Melbourne, Melbourne, Australia
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Abstract
Fonsibacter represents a significant microbial group of freshwater ecosystems. Although the genomic and metabolic features of these bacteria have been well studied, no phage infecting them has been reported. In this study, we reconstructed complete genomes of Fonsibacter and infecting phage and revealed their close relatedness to the phage infecting marine SAR11 members. Also, we illustrated that phage that infect Fonsibacter are widely distributed in freshwater habitats. In summary, the results contribute new insights into the ecology and evolution of Fonsibacter and phage. Fonsibacter (LD12 subclade) is among the most abundant bacterioplankton in freshwater ecosystems. These bacteria belong to the order Pelagibacterales (SAR11) and are related to Pelagibacter (marine SAR11), which dominates many marine habitats. Although a few Pelagibacter phage (Pelagiphage) have been described, no phage that infect Fonsibacter have been reported. In this study, we describe two groups of Podoviridae phage that infect Fonsibacter. A complete Fonsibacter genome containing a prophage was reconstructed from metagenomic data. A circularized and complete genome related to the prophage, referred to as uv-Fonsiphage-EPL (lysogenic strategy), shows high similarity to marine Pelagiphage HTVC025P. Additionally, we reconstructed three complete genomes and one draft genome of phage related to marine Pelagiphage HTVC010P and predicted a lytic strategy. The similarity in codon usage and cooccurrence patterns of HTVC010P-related phage and Fonsibacter suggested that these phage infect Fonsibacter. Similar phage were detected in Lake Mendota, Wisconsin, where Fonsibacter is also present. A search of related phage revealed the worldwide distribution of some genotypes in freshwater ecosystems, suggesting their substantial role in shaping indigenous microbial assemblages and influence on biogeochemical cycling. However, the uv-Fonsiphage-EPL and one group of HTVC010P-related phage have a more limited distribution in freshwater ecosystems. Overall, the findings provide insights into the genomic features of phage that infect Fonsibacter and expand understanding of the ecology and evolution of these important bacteria. IMPORTANCEFonsibacter represents a significant microbial group of freshwater ecosystems. Although the genomic and metabolic features of these bacteria have been well studied, no phage infecting them has been reported. In this study, we reconstructed complete genomes of Fonsibacter and infecting phage and revealed their close relatedness to the phage infecting marine SAR11 members. Also, we illustrated that phage that infect Fonsibacter are widely distributed in freshwater habitats. In summary, the results contribute new insights into the ecology and evolution of Fonsibacter and phage.
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47
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High-Level Abundances of Methanobacteriales and Syntrophobacterales May Help To Prevent Corrosion of Metal Sheet Piles. Appl Environ Microbiol 2019; 85:AEM.01369-19. [PMID: 31420342 DOI: 10.1128/aem.01369-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/11/2019] [Indexed: 11/20/2022] Open
Abstract
Iron sheet piles are widely used in flood protection, dike construction, and river bank reinforcement. Their corrosion leads to gradual deterioration and often makes replacement necessary. Natural deposit layers on these sheet piles can prevent degradation and significantly increase their life span. However, little is known about the mechanisms of natural protective layer formation. Here, we studied the microbially diverse populations of corrosion-protective deposit layers on iron sheet piles at the Gouderak pumping station in Zuid-Holland, the Netherlands. Deposit layers, surrounding sediment and top sediment samples were analyzed for soil physicochemical parameters, microbially diverse populations, and metabolic potential. Methanogens appeared to be enriched 18-fold in the deposit layers. After sequencing, metagenome assembly and binning, we obtained four nearly complete draft genomes of microorganisms (Methanobacteriales, two Coriobacteriales, and Syntrophobacterales) that were highly enriched in the deposit layers, strongly indicating a potential role in corrosion protection. Coriobacteriales and Syntrophobacterales could be part of a microbial food web degrading organic matter to supply methanogenic substrates. Methane-producing Methanobacteriales could metabolize iron, which may initially lead to mild corrosion but potentially stimulates the formation of a carbonate-rich protective deposit layer in the long term. In addition, Methanobacteriales and Coriobacteriales have the potential to interact with metal surfaces via direct interspecies or extracellular electron transfer. In conclusion, our study provides valuable insights into microbial populations involved in iron corrosion protection and potentially enables the development of novel strategies for in situ screening of iron sheet piles in order to reduce risks and develop more sustainable replacement practices.IMPORTANCE Iron sheet piles are widely used to reinforce dikes and river banks. Damage due to iron corrosion poses a significant safety risk and has significant economic impact. Different groups of microorganisms are known to either stimulate or inhibit the corrosion process. Recently, natural corrosion-protective deposit layers were found on sheet piles. Analyses of the microbial composition indicated a potential role for methane-producing archaea. However, the full metabolic potential of the microbial communities within these protective layers has not been determined. The significance of this work lies in the reconstruction of the microbial food web of natural corrosion-protective layers isolated from noncorroding metal sheet piles. With this work, we provide insights into the microbiological mechanisms that potentially promote corrosion protection in freshwater ecosystems. Our findings could support the development of screening protocols to assess the integrity of iron sheet piles to decide whether replacement is required.
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Danczak RE, Johnston MD, Kenah C, Slattery M, Wilkins MJ. Capability for arsenic mobilization in groundwater is distributed across broad phylogenetic lineages. PLoS One 2019; 14:e0221694. [PMID: 31490939 PMCID: PMC6730927 DOI: 10.1371/journal.pone.0221694] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 08/13/2019] [Indexed: 01/24/2023] Open
Abstract
Despite the importance of microbial activity in mobilizing arsenic in groundwater aquifers, the phylogenetic distribution of contributing microbial metabolisms is understudied. Groundwater samples from Ohio aquifers were analyzed using metagenomic sequencing to identify functional potential that could drive arsenic cycling, and revealed mechanisms for direct (i.e., Ars system) and indirect (i.e., iron reduction) arsenic mobilization in all samples, despite differing geochemical conditions. Analyses of 194 metagenome-assembled genomes (MAGs) revealed widespread functionality related to arsenic mobilization throughout the bacterial tree of life. While arsB and arsC genes (components of an arsenic resistance system) were found in diverse lineages with no apparent phylogenetic bias, putative aioA genes (aerobic arsenite oxidase) were predominantly identified in Methylocystaceae MAGs. Both previously described and undescribed respiratory arsenate reduction potential via arrA was detected in Betaproteobacteria, Deltaproteobacteria, and Nitrospirae MAGs, whereas sulfate reduction potential was primarily limited to members of the Deltaproteobacteria and Nitrospirae. Lastly, iron reduction potential was detected in the Ignavibacteria, Deltaproteobacteria, and Nitrospirae. These results expand the phylogenetic distribution of taxa that may play roles in arsenic mobilization in subsurface systems. Specifically, the Nitrospirae are a much more functionally diverse group than previously assumed and may play key biogeochemical roles in arsenic-contaminated ecosystems.
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Affiliation(s)
- Robert E. Danczak
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Michael D. Johnston
- School of Earth Sciences, Ohio State University, Columbus, OH, United States of America
| | - Chris Kenah
- Ohio Environmental Protection Agency, Columbus, OH, United States of America
| | - Michael Slattery
- Ohio Environmental Protection Agency, Columbus, OH, United States of America
| | - Michael J. Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States of America
- * E-mail:
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Bonetti G, Trevathan-Tackett SM, Carnell PE, Macreadie PI. Implication of Viral Infections for Greenhouse Gas Dynamics in Freshwater Wetlands: Challenges and Perspectives. Front Microbiol 2019; 10:1962. [PMID: 31507569 PMCID: PMC6718870 DOI: 10.3389/fmicb.2019.01962] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 08/09/2019] [Indexed: 01/07/2023] Open
Abstract
Viruses are non-living, acellular entities, and the most abundant biological agents on earth. They are widely acknowledged as having the capacity to influence global biogeochemical cycles by infecting the bacterial and archaeal populations that regulate carbon and nutrient turnover. Evidence suggests that the majority of viruses in wetlands are bacteriophages, but despite their importance, studies on how viruses control the prokaryotic community and the concomitant impacts on ecosystem function (such as carbon cycling and greenhouse gas flux) in wetlands are rare. Here we investigate virus-prokaryote interactions in freshwater wetland ecosystems in the context of their potential influence on biogeochemical cycling. Specifically, we (1) synthesize existing literature to establish current understanding of virus-prokaryote interactions, focusing on the implications for wetland greenhouse gas dynamics and (2) identify future research priorities. Viral dynamics in freshwater wetlands have received much less attention compared to those in marine ecosystems. However, based on our literature review, within the last 10 years, viral ecology studies on freshwater wetlands have increased twofold. Despite this increase in literature, the potential implication of viral infections on greenhouse gas emission dynamics is still a knowledge gap. We hypothesize that the rate of greenhouse gas emissions and the pool of sequestered carbon could be strongly linked to the type and rate of viral infection. Viral replication mechanism choice will consequently influence the microbial efficiency of organic matter assimilation and thus the ultimate fate of carbon as a greenhouse gas or stored in soils.
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Affiliation(s)
- Giuditta Bonetti
- Faculty of Science, Engineering and Built Environment, School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, VIC, Australia
| | - Stacey M Trevathan-Tackett
- Faculty of Science, Engineering and Built Environment, School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, VIC, Australia
| | - Paul E Carnell
- Faculty of Science, Engineering and Built Environment, School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, VIC, Australia
| | - Peter I Macreadie
- Faculty of Science, Engineering and Built Environment, School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, VIC, Australia
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Jiang Y, Huang H, Ma T, Ru J, Blank S, Kurmayer R, Deng L. Temperature Response of Planktonic Microbiota in Remote Alpine Lakes. Front Microbiol 2019; 10:1714. [PMID: 31417513 PMCID: PMC6685043 DOI: 10.3389/fmicb.2019.01714] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 07/11/2019] [Indexed: 02/01/2023] Open
Abstract
Alpine lakes are considered pristine freshwater ecosystems and sensitive to direct and indirect changes in water temperature as induced by climate change. The bacterial plankton constitutes a key component in the water column and bacterial metabolic activity has direct consequences for water quality. In order to understand bacterial response to global temperature rise in five alpine lakes located in the Austrian Alps (1700-2188 m a.S.L.) water temperature was compared within a decadal period. Depth-integrated samples were characterized in community composition by 16S rDNA deep-amplicon sequencing early [56 ± 16 (SD) days after ice break up] and later (88 ± 16 days) in the growing season. Within the 10 years period, temperature rise was observed through reduced ice cover duration and increased average water temperature. During the early growing season, the average water temperature recorded between circulation in spring until sampling date (WAS), and the day of autumn circulation, as well as chemical composition including dissolved organic carbon influenced bacterial community composition. In contrast, only nutrients (such as nitrate) were found influential later in the growing season. Metabolic theory of ecology (MTE) was applied to explain the dependence of taxonomic richness on WAS in mathematical terms. The calculated activation energy exceeded the frequently reported prediction emphasizing the role of WAS during early growing season. Accordingly, the relative abundance of predicted metabolism related genes increased with WAS. Thus, the dominant influence of temperature after ice break up could be explained by overall climate change effects, such as a more intense warming in spring and an overall higher amplitude of temperature variation.
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Affiliation(s)
- Yiming Jiang
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Haiying Huang
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Tianli Ma
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Jinlong Ru
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Stephan Blank
- Research Department for Limnology, Mondsee, University of Innsbruck, Innsbruck, Austria
| | - Rainer Kurmayer
- Research Department for Limnology, Mondsee, University of Innsbruck, Innsbruck, Austria
| | - Li Deng
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Virology, Technical University of Munich, Munich, Germany
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