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Gios E, Verbruggen E, Audet J, Burns R, Butterbach-Bahl K, Espenberg M, Fritz C, Glatzel S, Jurasinski G, Larmola T, Mander Ü, Nielsen C, Rodriguez AF, Scheer C, Zak D, Silvennoinen HM. Unraveling microbial processes involved in carbon and nitrogen cycling and greenhouse gas emissions in rewetted peatlands by molecular biology. BIOGEOCHEMISTRY 2024; 167:609-629. [PMID: 38707517 PMCID: PMC11068585 DOI: 10.1007/s10533-024-01122-6] [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: 05/31/2023] [Accepted: 01/22/2024] [Indexed: 05/07/2024]
Abstract
Restoration of drained peatlands through rewetting has recently emerged as a prevailing strategy to mitigate excessive greenhouse gas emissions and re-establish the vital carbon sequestration capacity of peatlands. Rewetting can help to restore vegetation communities and biodiversity, while still allowing for extensive agricultural management such as paludiculture. Belowground processes governing carbon fluxes and greenhouse gas dynamics are mediated by a complex network of microbial communities and processes. Our understanding of this complexity and its multi-factorial controls in rewetted peatlands is limited. Here, we summarize the research regarding the role of soil microbial communities and functions in driving carbon and nutrient cycling in rewetted peatlands including the use of molecular biology techniques in understanding biogeochemical processes linked to greenhouse gas fluxes. We emphasize that rapidly advancing molecular biology approaches, such as high-throughput sequencing, are powerful tools helping to elucidate the dynamics of key biogeochemical processes when combined with isotope tracing and greenhouse gas measuring techniques. Insights gained from the gathered studies can help inform efficient monitoring practices for rewetted peatlands and the development of climate-smart restoration and management strategies. Supplementary Information The online version contains supplementary material available at 10.1007/s10533-024-01122-6.
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Affiliation(s)
- Emilie Gios
- NINA, Norwegian Institute for Nature Research, PO Box 5685, Torgarden, NO-7485 Trondheim, Norway
| | - Erik Verbruggen
- Plants and Ecosystems Research Group, Department of Biology, University of Antwerp, Universiteitsplein 1, Wilrijk, 2610 Antwerp, Belgium
| | - Joachim Audet
- Department of Ecoscience, Aarhus University, C.F. Møllers Allé, 8000 Aarhus, Denmark
| | - Rachel Burns
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Klaus Butterbach-Bahl
- Institute of Meteorology and Climate Research, Atmospheric Environmental Research, Karlsruhe Institute of Technology, 82467 Garmisch-Partenkirchen, Germany
- Department of Agroecology, Pioneer Center for Research in Sustainable Agricultural Futures (Land-CRAFT), Aarhus University, 8000 Aarhus, Denmark
| | - Mikk Espenberg
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 St., Vanemuise, 51003 Tartu, Estonia
| | - Christian Fritz
- Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Stephan Glatzel
- Department of Geography and Regional Research, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Gerald Jurasinski
- Faculty of Agriculture and Environment, Landscape Ecology and Site Evaluation, University of Rostock, Justus-von-Liebig-Weg 6, 18059 Rostock, Germany
- Department of Maritime Systems, Faculty of Interdisciplinary Research, University of Rostock, Albert- Einstein-Straße 3, 18059 Rostock, Germany
| | - Tuula Larmola
- Natural Resources Institute Finland (Luke), 00790 Helsinki, Finland
| | - Ülo Mander
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 St., Vanemuise, 51003 Tartu, Estonia
| | - Claudia Nielsen
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Blichers Alle 20, 8830 Tjele, Denmark
- CBIO, Centre for Circular Bioeconomy, Aarhus University, 8830 Tjele, Denmark
| | - Andres F. Rodriguez
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Blichers Alle 20, 8830 Tjele, Denmark
| | - Clemens Scheer
- Institute of Meteorology and Climate Research, Atmospheric Environmental Research, Karlsruhe Institute of Technology, 82467 Garmisch-Partenkirchen, Germany
| | - Dominik Zak
- Department of Ecoscience, Aarhus University, C.F. Møllers Allé, 8000 Aarhus, Denmark
- Department of Ecohydrology and Biogeochemistry, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, Germany
| | - Hanna M. Silvennoinen
- NINA, Norwegian Institute for Nature Research, PO Box 5685, Torgarden, NO-7485 Trondheim, Norway
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2
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Seward J, Bräuer S, Beckett P, Roy-Léveillée P, Emilson E, Watmough S, Basiliko N. Recovery of Smelter-Impacted Peat and Sphagnum Moss: a Microbial Perspective. MICROBIAL ECOLOGY 2023; 86:2894-2903. [PMID: 37632540 DOI: 10.1007/s00248-023-02289-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/15/2023] [Indexed: 08/28/2023]
Abstract
Peatlands store approximately one-half of terrestrial soil carbon and one-tenth of non-glacial freshwater. Some of these important ecosystems are located near heavy metal emitting smelters. To improve the understanding of smelter impacts and potential recovery after initial pollution controls in the 1970s (roughly 50 years of potential recovery), we sampled peatlands along a distance gradient of 134 km from a smelter in Sudbury, Ontario, Canada, an area with over a century of nickel (Ni) and copper (Cu) mining activity. This work is aimed at evaluating potential shifts in bacterial and archaeal community structures in Sphagnum moss and its underlying peat within smelter-impacted poor fens. In peat, total Ni and Cu concentrations were higher (0.062-0.067 and 0.110-0.208 mg/g, respectively) at sites close to the smelter and exponentially dropped with distance from the smelter. This exponential decrease in Ni concentrations was also observed in Sphagnum. 16S rDNA amplicon sequencing showed that peat and Sphagnum moss host distinct microbiomes with peat accommodating a more diverse community structure. The microbiomes of Sphagnum were dominated by Proteobacteria (62.5%), followed by Acidobacteria (11.9%), with no observable trends with distance from the smelter. Dominance of Acidobacteria (32.4%) and Proteobacteria (29.6%) in peat was reported across all sites. No drift in taxonomy was seen across the distance gradient or from the reference sites, suggesting a potential microbiome recovery toward that of the reference peatlands microbiomes after decades of pollution controls. These results advance the understanding of peat and Sphagnum moss microbiomes, as well as depict the sensitivities and the resilience of peatland ecosystems.
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Affiliation(s)
- James Seward
- Vale Living with Lakes Centre and the School of Natural Sciences, Laurentian University, 935 Ramsey Lake Rd, Sudbury, ON, P3E 2C6, Canada.
| | - Suzanna Bräuer
- Department of Biology, Appalachian State University, 572 Rivers Street, Boone, NC, 28608, USA
| | - Peter Beckett
- Vale Living with Lakes Centre and the School of Natural Sciences, Laurentian University, 935 Ramsey Lake Rd, Sudbury, ON, P3E 2C6, Canada
| | - Pascale Roy-Léveillée
- Department of Geography, Université Laval, Pavillon Abitibi-Price, Quebec, G1V 0A6, Canada
| | - Erik Emilson
- Natural Resources Canada, Great Lakes Forestry Centre, 1219 Queen St. East, Sault Ste. Marie, ON, P6A 2E5, Canada
| | - Shaun Watmough
- School of the Environment, Trent University, Peterborough, Ontario, Canada
| | - Nathan Basiliko
- Department of Natural Resources Management, Lakehead University, 955 Oliver Rd., Thunder Bay, ON, P7B 5E1, Canada
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3
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Roux S, Emerson JB. Diversity in the soil virosphere: to infinity and beyond? Trends Microbiol 2022; 30:1025-1035. [PMID: 35644779 DOI: 10.1016/j.tim.2022.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 01/13/2023]
Abstract
Viruses are key members of Earth's microbiomes, shaping microbial community composition and metabolism. Here, we describe recent advances in 'soil viromics', that is, virus-focused metagenome and metatranscriptome analyses that offer unprecedented windows into the soil virosphere. Given the emerging picture of high soil viral activity, diversity, and dynamics over short spatiotemporal scales, we then outline key eco-evolutionary processes that we hypothesize are the major diversity drivers for soil viruses. We argue that a community effort is needed to establish a 'global soil virosphere atlas' that can be used to address the roles of viruses in soil microbiomes and terrestrial biogeochemical cycles across spatiotemporal scales.
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Affiliation(s)
- Simon Roux
- DOE (Department of Energy) Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 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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4
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Muscatt G, Hilton S, Raguideau S, Teakle G, Lidbury IDEA, Wellington EMH, Quince C, Millard A, Bending GD, Jameson E. Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere. MICROBIOME 2022; 10:181. [PMID: 36280853 PMCID: PMC9590211 DOI: 10.1186/s40168-022-01371-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/18/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND The rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-microbe interactions in the rhizosphere, remains undetermined. Given the impact of viruses on the ecology and evolution of their host communities, determining how soil viruses influence microbiome dynamics is crucial to build a holistic understanding of rhizosphere functions. RESULTS Here, we aimed to investigate the influence of crop management on the composition and activity of bulk soil, rhizosphere soil, and root viral communities. We combined viromics, metagenomics, and metatranscriptomics on soil samples collected from a 3-year crop rotation field trial of oilseed rape (Brassica napus L.). By recovering 1059 dsDNA viral populations and 16,541 ssRNA bacteriophage populations, we expanded the number of underexplored Leviviricetes genomes by > 5 times. Through detection of viral activity in metatranscriptomes, we uncovered evidence of "Kill-the-Winner" dynamics, implicating soil bacteriophages in driving bacterial community succession. Moreover, we found the activity of viruses increased with proximity to crop roots, and identified that soil viruses may influence plant-microbe interactions through the reprogramming of bacterial host metabolism. We have provided the first evidence of crop rotation-driven impacts on soil microbial communities extending to viruses. To this aim, we present the novel principal of "viral priming," which describes how the consecutive growth of the same crop species primes viral activity in the rhizosphere through local adaptation. CONCLUSIONS Overall, we reveal unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil, and bulk soil compartments. Our work demonstrates that the roles of soil viruses need greater consideration to exploit the rhizosphere microbiome for food security, food safety, and environmental sustainability. Video Abstract.
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Affiliation(s)
- George Muscatt
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Sebastien Raguideau
- School of Life Sciences, University of Warwick, Coventry, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Graham Teakle
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Ian D E A Lidbury
- School of Life Sciences, University of Warwick, Coventry, UK
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, UK
| | | | - Christopher Quince
- School of Life Sciences, University of Warwick, Coventry, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, UK.
- School of Natural Sciences, Bangor University, Bangor, UK.
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5
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Chen KH, Nelson J. A scoping review of bryophyte microbiota: diverse microbial communities in small plant packages. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4496-4513. [PMID: 35536989 DOI: 10.1093/jxb/erac191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 05/05/2022] [Indexed: 06/14/2023]
Abstract
Plant health depends not only on the condition of the plant itself but also on its diverse community of microbes, or microbiota. Just like the better-studied angiosperms, bryophytes (mosses, liverworts, and hornworts) harbor diverse communities of bacteria, archaea, fungi, and other microbial eukaryotes. Bryophytes are increasingly recognized as important model systems for understanding plant evolution, development, physiology, and symbiotic interactions. Much of the work on bryophyte microbiota in the past focused on specific symbiont types for each bryophyte group, but more recent studies are taking a broader view acknowledging the coexistence of diverse microbial communities in bryophytes. Therefore, this review integrates studies of bryophyte microbes from both perspectives to provide a holistic view of the existing research for each bryophyte group and on key themes. The systematic search also reveals the taxonomic and geographic biases in this field, including a severe under-representation of the tropics, very few studies on viruses or eukaryotic microbes beyond fungi, and a focus on mycorrhizal fungi studies in liverworts. Such gaps may have led to errors in conclusions about evolutionary patterns in symbiosis. This analysis points to a wealth of future research directions that promise to reveal how the distinct life cycles and physiology of bryophytes interact with their microbiota.
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Affiliation(s)
- Ko-Hsuan Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jessica Nelson
- Maastricht Science Programme, Maastricht University, Maastricht, The Netherlands
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6
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Reboledo G, Agorio A, Ponce De León I. Moss transcription factors regulating development and defense responses to stress. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4546-4561. [PMID: 35167679 DOI: 10.1093/jxb/erac055] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Transcription factors control gene expression, leading to regulation of biological processes that determine plant development and adaptation to the environment. Land colonization by plants occurred 450-470 million years ago and was accompanied by an increase in the complexity of transcriptional regulation associated to transcription factor gene expansions. AP2/ERF, bHLH, MYB, NAC, GRAS, and WRKY transcription factor families increased in land plants compared with algae. In angiosperms, they play crucial roles in regulating plant growth and responses to environmental stressors. However, less information is available in bryophytes and only in a few cases is the functional role of moss transcription factors in stress mechanisms known. In this review, we discuss current knowledge of the transcription factor families involved in development and defense responses to stress in mosses and other bryophytes. By exploring and analysing the Physcomitrium patens public database and published transcriptional profiles, we show that a high number of AP2/ERF, bHLH, MYB, NAC, GRAS, and WRKY genes are differentially expressed in response to abiotic stresses and during biotic interactions. Expression profiles together with a comprehensive analysis provide insights into relevant transcription factors involved in moss defenses, and hint at distinct and conserved biological roles between bryophytes and angiosperms.
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Affiliation(s)
- Guillermo Reboledo
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Astrid Agorio
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Inés Ponce De León
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
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7
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Gilbert NE, LeCleir GR, Strzepek RF, Ellwood MJ, Twining BS, Roux S, Pennacchio C, Boyd PW, Wilhelm SW. Bioavailable iron titrations reveal oceanic Synechococcus ecotypes optimized for different iron availabilities. ISME COMMUNICATIONS 2022; 2:54. [PMID: 37938659 PMCID: PMC9723758 DOI: 10.1038/s43705-022-00132-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/24/2022] [Accepted: 06/09/2022] [Indexed: 04/18/2023]
Abstract
The trace metal iron (Fe) controls the diversity and activity of phytoplankton across the surface oceans, a paradigm established through decades of in situ and mesocosm experimental studies. Despite widespread Fe-limitation within high-nutrient, low chlorophyll (HNLC) waters, significant contributions of the cyanobacterium Synechococcus to the phytoplankton stock can be found. Correlations among differing strains of Synechococcus across different Fe-regimes have suggested the existence of Fe-adapted ecotypes. However, experimental evidence of high- versus low-Fe adapted strains of Synechococcus is lacking, and so we investigated the transcriptional responses of microbial communities inhabiting the HNLC, sub-Antarctic region of the Southern Ocean during the Spring of 2018. Analysis of metatranscriptomes generated from on-deck incubation experiments reflecting a gradient of Fe-availabilities reveal transcriptomic signatures indicative of co-occurring Synechococcus ecotypes adapted to differing Fe-regimes. Functional analyses comparing low-Fe and high-Fe conditions point to various Fe-acquisition mechanisms that may allow persistence of low-Fe adapted Synechococcus under Fe-limitation. Comparison of in situ surface conditions to the Fe-titrations indicate ecological relevance of these mechanisms as well as persistence of both putative ecotypes within this region. This Fe-titration approach, combined with transcriptomics, highlights the short-term responses of the in situ phytoplankton community to Fe-availability that are often overlooked by examining genomic content or bulk physiological responses alone. These findings expand our knowledge about how phytoplankton in HNLC Southern Ocean waters adapt and respond to changing Fe supply.
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Affiliation(s)
- Naomi E Gilbert
- Department of Microbiology, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Gary R LeCleir
- Department of Microbiology, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Robert F Strzepek
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7004, Australia
- Australian Antarctic Program Partnership (AAPP), Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Michael J Ellwood
- Research School of Earth Sciences, Australian National University, Canberra, ACT, Australia
| | | | - S Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - C Pennacchio
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Philip W Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, TN, 37996, USA.
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8
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Carrell AA, Lawrence TJ, Cabugao KGM, Carper DL, Pelletier DA, Lee JH, Jawdy SS, Grimwood J, Schmutz J, Hanson PJ, Shaw AJ, Weston DJ. Habitat-adapted microbial communities mediate Sphagnum peatmoss resilience to warming. THE NEW PHYTOLOGIST 2022; 234:2111-2125. [PMID: 35266150 PMCID: PMC9310625 DOI: 10.1111/nph.18072] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 02/21/2022] [Indexed: 05/19/2023]
Abstract
Sphagnum peatmosses are fundamental members of peatland ecosystems, where they contribute to the uptake and long-term storage of atmospheric carbon. Warming threatens Sphagnum mosses and is known to alter the composition of their associated microbiome. Here, we use a microbiome transfer approach to test if microbiome thermal origin influences host plant thermotolerance. We leveraged an experimental whole-ecosystem warming study to collect field-grown Sphagnum, mechanically separate the associated microbiome and then transfer onto germ-free laboratory Sphagnum for temperature experiments. Host and microbiome dynamics were assessed with growth analysis, Chla fluorescence imaging, metagenomics, metatranscriptomics and 16S rDNA profiling. Microbiomes originating from warming field conditions imparted enhanced thermotolerance and growth recovery at elevated temperatures. Metagenome and metatranscriptome analyses revealed that warming altered microbial community structure in a manner that induced the plant heat shock response, especially the HSP70 family and jasmonic acid production. The heat shock response was induced even without warming treatment in the laboratory, suggesting that the warm-microbiome isolated from the field provided the host plant with thermal preconditioning. Our results demonstrate that microbes, which respond rapidly to temperature alterations, can play key roles in host plant growth response to rapidly changing environments.
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Affiliation(s)
- Alyssa A. Carrell
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Travis J. Lawrence
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Kristine Grace M. Cabugao
- Bredesen Center for Interdisciplinary Research and Graduate EducationUniversity of Tennessee1502 Cumberland Ave.KnoxvilleTN37996USA
| | - Dana L. Carper
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Dale A. Pelletier
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Jun Hyung Lee
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Sara S. Jawdy
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology601 Genome WayHuntsvilleAL35806USA
- Department of Energy Joint Genome InstituteLawrence Berkeley National Lab1 Cyclotron Rd.BerkeleyCA94720USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology601 Genome WayHuntsvilleAL35806USA
- Department of Energy Joint Genome InstituteLawrence Berkeley National Lab1 Cyclotron Rd.BerkeleyCA94720USA
| | - Paul J. Hanson
- Environmental Sciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | | | - David J. Weston
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
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9
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Pound HL, Martin RM, Zepernick BN, Christopher CJ, Howard SM, Castro HF, Campagna SR, Boyer GL, Bullerjahn GS, Chaffin JD, Wilhelm SW. Changes in Microbiome Activity and Sporadic Viral Infection Help Explain Observed Variability in Microcosm Studies. Front Microbiol 2022; 13:809989. [PMID: 35369463 PMCID: PMC8966487 DOI: 10.3389/fmicb.2022.809989] [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: 11/05/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
The environmental conditions experienced by microbial communities are rarely fully simulated in the laboratory. Researchers use experimental containers ("bottles"), where natural samples can be manipulated and evaluated. However, container-based methods are subject to "bottle effects": changes that occur when enclosing the plankton community that are often times unexplained by standard measures like pigment and nutrient concentrations. We noted variability in a short-term, nutrient amendment experiment during a 2019 Lake Erie, Microcystis spp. bloom. We observed changes in heterotrophic bacteria activity (transcription) on a time-frame consistent with a response to experimental changes in nutrient availability, demonstrating how the often overlooked microbiome of cyanobacterial blooms can be altered. Samples processed at the time of collection (T0) contained abundant transcripts from Bacteroidetes, which reduced in abundance during incubation in all bottles, including controls. Significant biological variability in the expression of Microcystis-infecting phage was observed between replicates, with phosphate-amended treatments showing a 10-fold variation. The expression patterns of Microcystis-infecting phage were significantly correlated with ∼35% of Microcystis-specific functional genes and ∼45% of the cellular-metabolites measured across the entire microbial community, suggesting phage activity not only influenced Microcystis dynamics, but the biochemistry of the microbiome. Our observations demonstrate how natural heterogeneity among replicates can be harnessed to provide further insight on virus and host ecology.
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Affiliation(s)
- Helena L Pound
- Department of Microbiology, The University of Tennessee, Knoxville, TN, United States
| | - Robbie M Martin
- Department of Microbiology, The University of Tennessee, Knoxville, TN, United States
| | - Brittany N Zepernick
- Department of Microbiology, The University of Tennessee, Knoxville, TN, United States
| | - Courtney J Christopher
- Biological and Small Molecule Mass Spectrometry Core, The University of Tennessee, Knoxville, TN, United States
| | - Sara M Howard
- Biological and Small Molecule Mass Spectrometry Core, The University of Tennessee, Knoxville, TN, United States
| | - Hector F Castro
- Biological and Small Molecule Mass Spectrometry Core, The University of Tennessee, Knoxville, TN, United States
| | - Shawn R Campagna
- Biological and Small Molecule Mass Spectrometry Core, The University of Tennessee, Knoxville, TN, United States
| | - Gregory L Boyer
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, Syracuse, NY, United States
| | - George S Bullerjahn
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States
| | - Justin D Chaffin
- Stone Laboratory and Ohio Sea Grant, The Ohio State University, Put-In-Bay, OH, United States
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, TN, United States
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10
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Marttinen EM, Lehtonen MT, van Gessel N, Reski R, Valkonen JPT. Viral suppressor of RNA silencing in vascular plants also interferes with the development of the bryophyte Physcomitrella patens. PLANT, CELL & ENVIRONMENT 2022; 45:220-235. [PMID: 34564869 PMCID: PMC9135061 DOI: 10.1111/pce.14194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Plant viruses are important pathogens able to overcome plant defense mechanisms using their viral suppressors of RNA silencing (VSR). Small RNA pathways of bryophytes and vascular plants have significant similarities, but little is known about how viruses interact with mosses. This study elucidated the responses of Physcomitrella patens to two different VSRs. We transformed P. patens plants to express VSR P19 from tomato bushy stunt virus and VSR 2b from cucumber mosaic virus, respectively. RNA sequencing and quantitative PCR were used to detect the effects of VSRs on gene expression. Small RNA (sRNA) sequencing was used to estimate the influences of VSRs on the sRNA pool of P. patens. Expression of either VSR-encoding gene caused developmental disorders in P. patens. The transcripts of four different transcription factors (AP2/erf, EREB-11 and two MYBs) accumulated in the P19 lines. sRNA sequencing revealed that VSR P19 significantly changed the microRNA pool in P. patens. Our results suggest that VSR P19 is functional in P. patens and affects the abundance of specific microRNAs interfering with gene expression. The results open new opportunities for using Physcomitrella as an alternative system to study plant-virus interactions.
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Affiliation(s)
- Eeva M. Marttinen
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
| | - Mikko T. Lehtonen
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
- Plant Analytics UnitFinnish Food AuthorityHelsinkiFinland
| | - Nico van Gessel
- Plant Biotechnology, Faculty of BiologyUniversity of FreiburgFreiburgGermany
| | - Ralf Reski
- Plant Biotechnology, Faculty of BiologyUniversity of FreiburgFreiburgGermany
- Signalling Research Centres BIOSS and CIBSSUniversity of FreiburgFreiburgGermany
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11
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Abstract
The microorganisms associated with an organism, the microbiome, have a strong and wide impact in their host biology. In particular, the microbiome modulates both the host defense responses and immunity, thus influencing the fate of infections by pathogens. Indeed, this immune modulation and/or interaction with pathogenic viruses can be essential to define the outcome of viral infections. Understanding the interplay between the microbiome and pathogenic viruses opens future venues to fight viral infections and enhance the efficacy of antiviral therapies. An increasing number of researchers are focusing on microbiome-virus interactions, studying diverse combinations of microbial communities, hosts, and pathogenic viruses. Here, we aim to review these studies, providing an integrative overview of the microbiome impact on viral infection across different pathosystems.
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12
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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: 32] [Impact Index Per Article: 10.7] [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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13
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Ha AD, Moniruzzaman M, Aylward FO. High Transcriptional Activity and Diverse Functional Repertoires of Hundreds of Giant Viruses in a Coastal Marine System. mSystems 2021; 6:e0029321. [PMID: 34254826 PMCID: PMC8407384 DOI: 10.1128/msystems.00293-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/26/2021] [Indexed: 12/14/2022] Open
Abstract
Viruses belonging to the Nucleocytoviricota phylum are globally distributed and include members with notably large genomes and complex functional repertoires. Recent studies have shown that these viruses are particularly diverse and abundant in marine systems, but the magnitude of actively replicating Nucleocytoviricota present in ocean habitats remains unclear. In this study, we compiled a curated database of 2,431 Nucleocytoviricota genomes and used it to examine the gene expression of these viruses in a 2.5-day metatranscriptomic time-series from surface waters of the California Current. We identified 145 viral genomes with high levels of gene expression, including 90 Imitervirales and 49 Algavirales viruses. In addition to recovering high expression of core genes involved in information processing that are commonly expressed during viral infection, we also identified transcripts of diverse viral metabolic genes from pathways such as glycolysis, the TCA cycle, and the pentose phosphate pathway, suggesting that virus-mediated reprogramming of central carbon metabolism is common in oceanic surface waters. Surprisingly, we also identified viral transcripts with homology to actin, myosin, and kinesin domains, suggesting that viruses may use these gene products to manipulate host cytoskeletal dynamics during infection. We performed phylogenetic analysis on the virus-encoded myosin and kinesin proteins, which demonstrated that most belong to deep-branching viral clades, but that others appear to have been acquired from eukaryotes more recently. Our results highlight a remarkable diversity of active Nucleocytoviricota in a coastal marine system and underscore the complex functional repertoires expressed by these viruses during infection. IMPORTANCE The discovery of giant viruses has transformed our understanding of viral complexity. Although viruses have traditionally been viewed as filterable infectious agents that lack metabolism, giant viruses can reach sizes rivalling cellular lineages and possess genomes encoding central metabolic processes. Recent studies have shown that giant viruses are widespread in aquatic systems, but the activity of these viruses and the extent to which they reprogram host physiology in situ remains unclear. Here, we show that numerous giant viruses consistently express central metabolic enzymes in a coastal marine system, including components of glycolysis, the TCA cycle, and other pathways involved in nutrient homeostasis. Moreover, we found expression of several viral-encoded actin, myosin, and kinesin genes, indicating viral manipulation of the host cytoskeleton during infection. Our study reveals a high activity of giant viruses in a coastal marine system and indicates they are a diverse and underappreciated component of microbial diversity in the ocean.
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Affiliation(s)
- Anh D. Ha
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | | | - Frank O. Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
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14
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Correa AMS, Howard-Varona C, Coy SR, Buchan A, Sullivan MB, Weitz JS. Revisiting the rules of life for viruses of microorganisms. Nat Rev Microbiol 2021; 19:501-513. [PMID: 33762712 DOI: 10.1038/s41579-021-00530-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2021] [Indexed: 02/01/2023]
Abstract
Viruses that infect microbial hosts have traditionally been studied in laboratory settings with a focus on either obligate lysis or persistent lysogeny. In the environment, these infection archetypes are part of a continuum that spans antagonistic to beneficial modes. In this Review, we advance a framework to accommodate the context-dependent nature of virus-microorganism interactions in ecological communities by synthesizing knowledge from decades of virology research, eco-evolutionary theory and recent technological advances. We discuss that nuanced outcomes, rather than the extremes of the continuum, are particularly likely in natural communities given variability in abiotic factors, the availability of suboptimal hosts and the relevance of multitrophic partnerships. We revisit the 'rules of life' in terms of how long-term infections shape the fate of viruses and microbial cells, populations and ecosystems.
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Affiliation(s)
| | | | - Samantha R Coy
- BioSciences Department, Rice University, Houston, TX, USA
| | - Alison Buchan
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA.
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA. .,Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, USA.
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,School of Physics, Georgia Institute of Technology, Atlanta, GA, USA.
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15
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Zhang J, Cook J, Nearing JT, Zhang J, Raudonis R, Glick BR, Langille MGI, Cheng Z. Harnessing the plant microbiome to promote the growth of agricultural crops. Microbiol Res 2021; 245:126690. [PMID: 33460987 DOI: 10.1016/j.micres.2020.126690] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 12/11/2020] [Accepted: 12/30/2020] [Indexed: 12/11/2022]
Abstract
The rhizosphere microbiome is composed of diverse microbial organisms, including archaea, viruses, fungi, bacteria as well as eukaryotic microorganisms, which occupy a narrow region of soil directly associated with plant roots. The interactions between these microorganisms and the plant can be commensal, beneficial or pathogenic. These microorganisms can also interact with each other, either competitively or synergistically. Promoting plant growth by harnessing the soil microbiome holds tremendous potential for providing an environmentally friendly solution to the increasing food demands of the world's rapidly growing population, while also helping to alleviate the associated environmental and societal issues of large-scale food production. There recently have been many studies on the disease suppression and plant growth promoting abilities of the rhizosphere microbiome; however, these findings largely have not been translated into the field. Therefore, additional research into the dynamic interactions between crop plants, the rhizosphere microbiome and the environment are necessary to better guide the harnessing of the microbiome to increase crop yield and quality. This review explores the biotic and abiotic interactions that occur within the plant's rhizosphere as well as current agricultural practices, and how these biotic and abiotic factors, as well as human practices, impact the plant microbiome. Additionally, some limitations, safety considerations, and future directions to the study of the plant microbiome are discussed.
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Affiliation(s)
- Janie Zhang
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Jamie Cook
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Jacob T Nearing
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Junzeng Zhang
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Halifax, NS, Canada
| | - Renee Raudonis
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Morgan G I Langille
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada; Department of Pharmacology, Dalhousie University, Halifax, NS, Canada; CGEB-Integrated Microbiome Resource (IMR), Dalhousie University, Halifax, NS, Canada
| | - Zhenyu Cheng
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada.
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16
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Martinez-Hernandez F, Luo E, Tominaga K, Ogata H, Yoshida T, DeLong EF, Martinez-Garcia M. Diel cycling of the cosmopolitan abundant Pelagibacter virus 37-F6: one of the most abundant viruses on earth. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:214-219. [PMID: 31997562 DOI: 10.1111/1758-2229.12825] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/25/2020] [Indexed: 05/25/2023]
Abstract
The spatiotemporal dynamics for marine viral populations has only recently been explored. However, nothing is known about temporal activities of the uncultured Pelagibacter virus vSAG 37-F6, which was discovered by single-virus genomics as potentially the most abundant marine virus. Here, we investigate the diel cycling of 37-F6 virus and the putative SAR11 host using coastal and oceanic transcriptomic and viromic time-series data from Osaka Bay and North Pacific Subtropical Gyre. Virus 37-F6 and relatives displayed diel cycling of transcriptional activities synchronized with its putative host. In both virus and host, the lowest transcription rates were observed at 14:00-15:00, coinciding roughly with maximum solar irradiance, while higher transcriptional rates were detected during the night/early morning and afternoon. Diel abundance of free viruses of 37-F6 in seawater roughly mirrored the transcriptional activities of both virus and host. In Osaka Bay, among viral relatives (genus level), virus 37-F6 specifically showed the highest ratio of transcriptional activity to virome abundance, a proxy for viral transcriptional activity relative to free viral particle abundance. This high ratio suggests high infection rate efficiencies in vSAG 37-F6 virus compared to viral relatives. Thus, time-series data revealed temporal transcript activities in one of the most abundant viruses in Earth.
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Affiliation(s)
| | - Elaine Luo
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Manoa, Honolulu, HI, 96822, USA
| | - Kento Tominaga
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Uji, 611-0011, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Manoa, Honolulu, HI, 96822, USA
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
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17
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Pound HL, Gann ER, Tang X, Krausfeldt LE, Huff M, Staton ME, Talmy D, Wilhelm SW. The "Neglected Viruses" of Taihu: Abundant Transcripts for Viruses Infecting Eukaryotes and Their Potential Role in Phytoplankton Succession. Front Microbiol 2020; 11:338. [PMID: 32210938 PMCID: PMC7067694 DOI: 10.3389/fmicb.2020.00338] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/17/2020] [Indexed: 01/18/2023] Open
Abstract
Drivers of algal bloom dynamics remain poorly understood, but viruses have been implicated as important players. Research addressing bloom dynamics has generally been restricted to the virus-infection of the numerically dominant (i.e. bloom forming) taxa. Yet this approach neglects a broad diversity of viral groups, limiting our knowledge of viral interactions and constraints within these systems. We examined hallmark virus marker genes in metatranscriptomic libraries from a seasonal and spatial survey of a Microcystis aeruginosa bloom in Lake Tai (Taihu) China to identify active infections by nucleocytoplasmic large DNA viruses (NCLDVs), RNA viruses, ssDNA viruses, bacteriophage, and virophage. Phylogenetic analyses revealed a diverse virus population with seasonal and spatial variability. We observed disproportionately high expression of markers associated with NCLDVs and ssRNA viruses (consistent with viruses that infect photosynthetic protists) relative to bacteriophage infecting heterotrophic bacteria or cyanobacteria during the height of the Microcystis bloom event. Under a modified kill-the-winner scheme, we hypothesize viruses infecting protists help suppress the photosynthetic eukaryotic community and allow for the proliferation of cyanobacteria such as Microcystis. Our observations provide a foundation for a little considered factor promoting algal blooms.
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Affiliation(s)
- Helena L Pound
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Eric R Gann
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Lauren E Krausfeldt
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Matthew Huff
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Margaret E Staton
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - David Talmy
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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18
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Schulz F, Roux S, Paez-Espino D, Jungbluth S, Walsh DA, Denef VJ, McMahon KD, Konstantinidis KT, Eloe-Fadrosh EA, Kyrpides NC, Woyke T. Giant virus diversity and host interactions through global metagenomics. Nature 2020; 578:432-436. [PMID: 31968354 PMCID: PMC7162819 DOI: 10.1038/s41586-020-1957-x] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 01/09/2020] [Indexed: 12/11/2022]
Abstract
Our current knowledge about nucleocytoplasmic large DNA viruses (NCLDVs) is largely derived from viral isolates that are co-cultivated with protists and algae. Here we reconstructed 2,074 NCLDV genomes from sampling sites across the globe by building on the rapidly increasing amount of publicly available metagenome data. This led to an 11-fold increase in phylogenetic diversity and a parallel 10-fold expansion in functional diversity. Analysis of 58,023 major capsid proteins from large and giant viruses using metagenomic data revealed the global distribution patterns and cosmopolitan nature of these viruses. The discovered viral genomes encoded a wide range of proteins with putative roles in photosynthesis and diverse substrate transport processes, indicating that host reprogramming is probably a common strategy in the NCLDVs. Furthermore, inferences of horizontal gene transfer connected viral lineages to diverse eukaryotic hosts. We anticipate that the global diversity of NCLDVs that we describe here will establish giant viruses-which are associated with most major eukaryotic lineages-as important players in ecosystems across Earth's biomes.
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Affiliation(s)
- Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Paez-Espino
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sean Jungbluth
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David A Walsh
- Groupe de recherche interuniversitaire en limnologie, Department of Biology, Concordia University, Montréal, Québec, Canada
| | - Vincent J Denef
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Emiley A Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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19
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Starr EP, Nuccio EE, Pett-Ridge J, Banfield JF, Firestone MK. Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil. Proc Natl Acad Sci U S A 2019; 116:25900-25908. [PMID: 31772013 PMCID: PMC6926006 DOI: 10.1073/pnas.1908291116] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health, and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in soil, 1 of the most complex microbial systems. Here, we assembled 48 individual metatranscriptomes from 4 habitats within a planted soil sampled over a 22-d time series: Rhizosphere alone, detritosphere alone, rhizosphere with added root detritus, and unamended soil (4 time points and 3 biological replicates). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker genes. Based on viral phylogeny, much of the diversity was Narnaviridae that may parasitize fungi or Leviviridae, which may infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral and host communities were structured based on the presence of root litter. Clear temporal dynamics by Leviviridae and their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant, and active in soil. When viral infection causes host cell death, it may mobilize cell carbon in a process that may represent an overlooked component of soil carbon cycling.
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Affiliation(s)
- Evan P Starr
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Erin E Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA 94720;
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720
- Chan Zuckerberg Biohub, San Francisco, CA 94158
- Innovative Genomics Institute, Berkeley, CA 94720
| | - Mary K Firestone
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720
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