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Liu J, Wang J, Zhang M, Wang X, Guo P, Li Q, Ren J, Wei Y, Wu T, Chai B. Protists play important roles in the assembly and stability of denitrifying bacterial communities in copper-tailings drainage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170386. [PMID: 38280613 DOI: 10.1016/j.scitotenv.2024.170386] [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: 11/26/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 01/29/2024]
Abstract
Unraveling the drivers controlling the assembly and stability of functional communities is a central issue in ecology. Despite extensive research and data, relatively little attention has been paid on the importance of biotic factors and, in particular, on the trophic interaction for explaining the assembly of microbial community. Here, we examined the diversity, assembly, and stability of nirS-, nirK-, and nosZ-type denitrifying bacterial communities in copper-tailings drainages of the Shibahe tailings reservoir in Zhongtiao Mountain, China's. We found that components of nirS-, nirK-, and nosZ-type denitrifying bacterial community diversity, such as taxon relative abundance, richness, and copy number, were strongly correlated with protist community composition and diversity. Assembly of the nirK-type denitrifying bacterial community was governed by dispersal limitation, whereas those of nirS- and nosZ-type communities were controlled by homogeneous selection. The relative importance of protist diversity in the assembly of nirK- and nosZ-type denitrifying bacterial communities was greater than that in nirS-type assembly. In addition, protists reduced the stability of the co-occurrence network of the nosZ-type denitrifying bacterial community. Compared with eukaryotic algae, protozoa had a greater impact on the stability of denitrifying bacterial community co-occurrence networks. Generally, protists affected the assembly and community stability of denitrifying bacteria in copper-tailings drainages. Our findings thus emphasize the importance of protists on affecting the assembly and community stability of denitrifying bacteria in copper-tailings drainages and may be useful for predicting changes in the ecological functions of microorganisms.
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Affiliation(s)
- Jinxian Liu
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Jiayi Wang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Meiting Zhang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Xue Wang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Ping Guo
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Qianru Li
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Jiali Ren
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Yuqi Wei
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Tiehang Wu
- Department of Biology, Georgia Southern University, Statesboro, GA 30460-8042, USA
| | - Baofeng Chai
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China.
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2
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McNichol J. Mineral-eating microorganisms at extinct hydrothermal vents. Nat Microbiol 2024; 9:589-590. [PMID: 38429423 DOI: 10.1038/s41564-024-01622-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Affiliation(s)
- Jesse McNichol
- Department of Biology, St Francis Xavier University, Antigonish, Nova Scotia, Canada.
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3
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Achberger AM, Jones R, Jamieson J, Holmes CP, Schubotz F, Meyer NR, Dekas AE, Moriarty S, Reeves EP, Manthey A, Brünjes J, Fornari DJ, Tivey MK, Toner BM, Sylvan JB. Inactive hydrothermal vent microbial communities are important contributors to deep ocean primary productivity. Nat Microbiol 2024; 9:657-668. [PMID: 38287146 DOI: 10.1038/s41564-024-01599-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/20/2023] [Indexed: 01/31/2024]
Abstract
Active hydrothermal vents are oases for productivity in the deep ocean, but the flow of dissolved substrates that fuel such abundant life ultimately ceases, leaving behind inactive mineral deposits. The rates of microbial activity on these deposits are largely unconstrained. Here we show primary production occurs on inactive hydrothermal deposits and quantify its contribution to new organic carbon production in the deep ocean. Measured incorporation of 14C-bicarbonate shows that microbial communities on inactive deposits fix inorganic carbon at rates comparable to those on actively venting deposits. Single-cell uptake experiments and nanoscale secondary ion mass spectrometry showed chemoautotrophs comprise a large fraction (>30%) of the active microbial cells. Metagenomic and lipidomic surveys of inactive deposits further revealed that the microbial communities are dominated by Alphaproteobacteria and Gammaproteobacteria using the Calvin-Benson-Bassham pathway for carbon fixation. These findings establish inactive vent deposits as important sites for microbial activity and organic carbon production on the seafloor.
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Affiliation(s)
- Amanda M Achberger
- Department of Oceanography, Texas A&M University, College Station, Texas, USA.
| | - Rose Jones
- Department of Soil, Water and Climate, University of Minnesota-Twin Cities, St Paul, MN, USA
| | - John Jamieson
- Department of Earth Sciences, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, Canada
| | - Charles P Holmes
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
| | - Florence Schubotz
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Nicolette R Meyer
- Department of Earth System Science, Stanford University, Stanford, CA, USA
| | - Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, USA
| | - Sarah Moriarty
- Department of Earth Sciences, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, Canada
| | - Eoghan P Reeves
- Department of Earth Science, Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Alex Manthey
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Jonas Brünjes
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Department of Earth Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Daniel J Fornari
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Margaret K Tivey
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Brandy M Toner
- Department of Soil, Water and Climate, University of Minnesota-Twin Cities, St Paul, MN, USA
| | - Jason B Sylvan
- Department of Oceanography, Texas A&M University, College Station, Texas, USA.
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4
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Hu SK, Anderson RE, Pachiadaki MG, Edgcomb VP, Serres MH, Sylva SP, German CR, Seewald JS, Lang SQ, Huber JA. Microbial eukaryotic predation pressure and biomass at deep-sea hydrothermal vents. THE ISME JOURNAL 2024; 18:wrae004. [PMID: 38366040 PMCID: PMC10939315 DOI: 10.1093/ismejo/wrae004] [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: 11/02/2023] [Revised: 12/22/2023] [Accepted: 01/12/2024] [Indexed: 02/18/2024]
Abstract
Deep-sea hydrothermal vent geochemistry shapes the foundation of the microbial food web by fueling chemolithoautotrophic microbial activity. Microbial eukaryotes (or protists) play a critical role in hydrothermal vent food webs as consumers and hosts of symbiotic bacteria, and as a nutritional source to higher trophic levels. We measured microbial eukaryotic cell abundance and predation pressure in low-temperature diffuse hydrothermal fluids at the Von Damm and Piccard vent fields along the Mid-Cayman Rise in the Western Caribbean Sea. We present findings from experiments performed under in situ pressure that show cell abundances and grazing rates higher than those done at 1 atmosphere (shipboard ambient pressure); this trend was attributed to the impact of depressurization on cell integrity. A relationship between the protistan grazing rate, prey cell abundance, and temperature of end-member hydrothermal vent fluid was observed at both vent fields, regardless of experimental approach. Our results show substantial protistan biomass at hydrothermally fueled microbial food webs, and when coupled with improved grazing estimates, suggest an important contribution of grazers to the local carbon export and supply of nutrient resources to the deep ocean.
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Affiliation(s)
- Sarah K Hu
- Department of Oceanography, Texas A&M University, College Station, TX 77843, United States
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Rika E Anderson
- Biology Department, Carleton College, Northfield, MN 55057, United States
| | - Maria G Pachiadaki
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Virginia P Edgcomb
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Margrethe H Serres
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Sean P Sylva
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Christopher R German
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Jeffrey S Seewald
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Susan Q Lang
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Julie A Huber
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
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5
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Anderson SR, Blanco-Bercial L, Carlson CA, Harvey EL. Role of Syndiniales parasites in depth-specific networks and carbon flux in the oligotrophic ocean. ISME COMMUNICATIONS 2024; 4:ycae014. [PMID: 38419659 PMCID: PMC10900894 DOI: 10.1093/ismeco/ycae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 03/02/2024]
Abstract
Microbial associations that result in phytoplankton mortality are important for carbon transport in the ocean. This includes parasitism, which in microbial food webs is dominated by the marine alveolate group, Syndiniales. Parasites are expected to contribute to carbon recycling via host lysis; however, knowledge on host dynamics and correlation to carbon export remain unclear and limit the inclusion of parasitism in biogeochemical models. We analyzed a 4-year 18S rRNA gene metabarcoding dataset (2016-19), performing network analysis for 12 discrete depths (1-1000 m) to determine Syndiniales-host associations in the seasonally oligotrophic Sargasso Sea. Analogous water column and sediment trap data were included to define environmental drivers of Syndiniales and their correlation with particulate carbon flux (150 m). Syndiniales accounted for 48-74% of network edges, most often associated with Dinophyceae and Arthropoda (mainly copepods) at the surface and Rhizaria (Polycystinea, Acantharea, and RAD-B) in the aphotic zone. Syndiniales were the only eukaryote group to be significantly (and negatively) correlated with particulate carbon flux, indicating their contribution to flux attenuation via remineralization. Examination of Syndiniales amplicons revealed a range of depth patterns, including specific ecological niches and vertical connection among a subset (19%) of the community, the latter implying sinking of parasites (infected hosts or spores) on particles. Our findings elevate the critical role of Syndiniales in marine microbial systems and reveal their potential use as biomarkers for carbon export.
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Affiliation(s)
- Sean R Anderson
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, United States
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Falmouth, MA 02543, United States
| | | | - Craig A Carlson
- Department of Ecology, Evolution and Marine Biology and the Marine Science Institute, University of California, Santa Barbara, CA 93106, United States
| | - Elizabeth L Harvey
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, United States
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6
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Hu SK, Smith AR, Anderson RE, Sylva SP, Setzer M, Steadmon M, Frank KL, Chan EW, Lim DSS, German CR, Breier JA, Lang SQ, Butterfield DA, Fortunato CS, Seewald JS, Huber JA. Globally-distributed microbial eukaryotes exhibit endemism at deep-sea hydrothermal vents. Mol Ecol 2023; 32:6580-6598. [PMID: 36302092 DOI: 10.1111/mec.16745] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/21/2022] [Accepted: 10/06/2022] [Indexed: 11/30/2022]
Abstract
Single-celled microbial eukaryotes inhabit deep-sea hydrothermal vent environments and play critical ecological roles in the vent-associated microbial food web. 18S rRNA amplicon sequencing of diffuse venting fluids from four geographically- and geochemically-distinct hydrothermal vent fields was applied to investigate community diversity patterns among protistan assemblages. The four vent fields include Axial Seamount at the Juan de Fuca Ridge, Sea Cliff and Apollo at the Gorda Ridge, all in the NE Pacific Ocean, and Piccard and Von Damm at the Mid-Cayman Rise in the Caribbean Sea. We describe species diversity patterns with respect to hydrothermal vent field and sample type, identify putative vent endemic microbial eukaryotes, and test how vent fluid geochemistry may influence microbial community diversity. At a semi-global scale, microbial eukaryotic communities at deep-sea vents were composed of similar proportions of dinoflagellates, ciliates, Rhizaria, and stramenopiles. Individual vent fields supported distinct and highly diverse assemblages of protists that included potentially endemic or novel vent-associated strains. These findings represent a census of deep-sea hydrothermal vent protistan communities. Protistan diversity, which is shaped by the hydrothermal vent environment at a local scale, ultimately influences the vent-associated microbial food web and the broader deep-sea carbon cycle.
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Affiliation(s)
- Sarah K Hu
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Amy R Smith
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
- Bard College at Simon's Rock, Great Barrington, Massachusetts, USA
| | - Rika E Anderson
- Biology Department, Carleton College, Northfield, Minnesota, USA
| | - Sean P Sylva
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Michaela Setzer
- Pacific Biosciences Research Center, Kewalo Marine Laboratory, University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA
- Department of Oceanography, University of Hawaii at Mānoa, Honolulu, Hawai'i, USA
| | - Maria Steadmon
- Pacific Biosciences Research Center, Kewalo Marine Laboratory, University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA
- Department of Oceanography, University of Hawaii at Mānoa, Honolulu, Hawai'i, USA
| | - Kiana L Frank
- Pacific Biosciences Research Center, Kewalo Marine Laboratory, University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA
| | - Eric W Chan
- School of Earth, Environmental, and Marine Sciences, The University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | | | - Christopher R German
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - John A Breier
- School of Earth, Environmental, and Marine Sciences, The University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | - Susan Q Lang
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
- School of the Earth, Ocean, and Environment, University of South Carolina, Columbia, South Carolina, USA
| | - David A Butterfield
- Cooperative Institute for Climate, Ocean, and Ecosystem Studies, University of Washington and NOAA/PMEL, Seattle, Washington, USA
| | | | - Jeffrey S Seewald
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Julie A Huber
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
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7
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Xu H, You C, Tan B, Xu L, Liu Y, Wang M, Xu Z, Sardans J, Peñuelas J. Effects of livestock grazing on the relationships between soil microbial community and soil carbon in grassland ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163416. [PMID: 37059137 DOI: 10.1016/j.scitotenv.2023.163416] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/23/2023] [Accepted: 04/06/2023] [Indexed: 06/01/2023]
Abstract
Livestock grazing of grassland ecosystems may induce shifts in microbe community traits and soil carbon (C) cycling; however, impacts of grassland management (grazing) on soil C- microbe community trait (microbial biomass, diversity, community structure, and enzyme activity) relationships are unclear. To address this, we conducted a global meta-analysis of 95 articles of livestock grazing studies that vary in grazing intensities (light, moderate, and high) and durations (<5 years, 5-10 years, and > 10 years). We found that gazing decreased soil organic carbon content (SOC; 10.1 %), and activities of the enzymes of saccharase (SA; 31.1 %), urease (UA; 7.0 %), and acid phosphatase (11.9 %) in topsoil. Meanwhile, the SOC, soil microbial biomass and enzyme activities consistently decreased as grazing intensity and duration prolonged. Furthermore, we observed strong linear relationships of microbe community traits with SOC (p < 0.05), but weak relationships with soil N or P (p > 0.05) in grasslands, which also depends on the grazing intensity and duration. In conclusion, our results indicate that traits of soil carbon content, soil microbe community, and in particular their relationships in global grasslands are overall significantly affected by livestock grazing, but the effects strongly depend on the grazing intensity and duration.
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Affiliation(s)
- Hongwei Xu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Chengming You
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Bo Tan
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lin Xu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yang Liu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Minggang Wang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China.
| | - Zhenfeng Xu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
| | - Jordi Sardans
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08913 Bellaterra, Catalonia, Spain; CREAF, 08913 Cerdanyola del Vallès, Catalonia, Spain; Nonlinear Analysis and Applied Mathematics (NAAM)-Research Group, Department of Mathematics, Faculty of Science, King Abdulaziz University, P.O. Box 80257, Jeddah 21589, Saudi Arabia
| | - Josep Peñuelas
- CREAF, 08913 Cerdanyola del Vallès, Catalonia, Spain; Nonlinear Analysis and Applied Mathematics (NAAM)-Research Group, Department of Mathematics, Faculty of Science, King Abdulaziz University, P.O. Box 80257, Jeddah 21589, Saudi Arabia
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8
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Tong D, Wang Y, Yu H, Shen H, Dahlgren RA, Xu J. Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil. THE ISME JOURNAL 2023:10.1038/s41396-023-01438-5. [PMID: 37248401 DOI: 10.1038/s41396-023-01438-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 05/13/2023] [Accepted: 05/22/2023] [Indexed: 05/31/2023]
Abstract
Viruses are critical for regulating microbial communities and biogeochemical processes affecting carbon/nutrient cycling. However, the role of soil phages in controlling microbial physiological traits and intrinsic dissolved organic matter (DOM) properties remains largely unknown. Herein, microcosm experiments with different soil phage concentrates (including no-added phages, inactive phages, and three dilutions of active phages) at two temperatures (15 °C and 25 °C) were conducted to disclose the nutrient and DOM dynamics associated with viral lysing. Results demonstrated three different phases of viral impacts on CO2 emission at both temperatures, and phages played a role in maintaining Q10 within bounds. At both temperatures, microbial nutrient limitations (especially P limitation) were alleviated by viral lysing as determined by extracellular enzyme activity (decreased Vangle with active phages). Additionally, the re-utilization of lysate-derived DOM by surviving microbes stimulated an increase of microbial metabolic efficiency and recalcitrant DOM components (e.g., SUV254, SUV260 and HIX). This research provides direct experimental evidence that the "viral shuttle" exists in soils, whereby soil phages increase recalcitrant DOM components. Our findings advance the understanding of viral controls on soil biogeochemical processes, and provide a new perspective for assessing whether soil phages provide a net "carbon sink" vs. "carbon source" in soils.
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Affiliation(s)
- Di Tong
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Youjing Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Haodan Yu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Haojie Shen
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Randy A Dahlgren
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China.
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9
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Hu R, Liu S, Saleem M, Xiong Z, Zhou Z, Luo Z, Shu L, He Z, Wang C. Environmentally‐induced reconstruction of microbial communities alters particulate carbon flux of deep chlorophyll maxima in the South China sea. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ruiwen Hu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Songfeng Liu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Muhammad Saleem
- Department of Biological Sciences Alabama State University Montgomery AL USA
| | - Zhiyao Xiong
- School of Marine Sciences Sun Yat‐sen University Zhuhai
| | - Zhengyuan Zhou
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Zhiwen Luo
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Longfei Shu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Zhili He
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
- College of Agronomy Hunan Agricultural University Changsha China
| | - Cheng Wang
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
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10
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Rocca JD, Yammine A, Simonin M, Gibert JP. Protist Predation Influences the Temperature Response of Bacterial Communities. Front Microbiol 2022; 13:847964. [PMID: 35464948 PMCID: PMC9022080 DOI: 10.3389/fmicb.2022.847964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/08/2022] [Indexed: 01/04/2023] Open
Abstract
Temperature strongly influences microbial community structure and function, in turn contributing to global carbon cycling that can fuel further warming. Recent studies suggest that biotic interactions among microbes may play an important role in determining the temperature responses of these communities. However, how predation regulates these microbiomes under future climates is still poorly understood. Here, we assess whether predation by a key global bacterial consumer—protists—influences the temperature response of the community structure and function of a freshwater microbiome. To do so, we exposed microbial communities to two cosmopolitan protist species—Tetrahymena thermophila and Colpidium sp.—at two different temperatures, in a month-long microcosm experiment. While microbial biomass and respiration increased with temperature due to community shifts, these responses changed over time and in the presence of protists. Protists influenced microbial biomass and respiration rate through direct and indirect effects on bacterial community structure, and predator presence actually reduced microbial respiration at elevated temperature. Indicator species analyses showed that these predator effects were mostly determined by phylum-specific bacterial responses to protist density and cell size. Our study supports previous findings that temperature is an important driver of microbial communities but also demonstrates that the presence of a large predator can mediate these responses to warming.
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Affiliation(s)
- Jennifer D Rocca
- Department of Biology, Duke University, Durham, NC, United States.,Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Andrea Yammine
- Department of Biology, Duke University, Durham, NC, United States
| | - Marie Simonin
- Department of Biology, Duke University, Durham, NC, United States.,University of Angers, Institut Agro, Institut National de la Recherche Agronomique, L'Institut de Recherche en Horticulture et Semences, Structure Fédérative de Recherche Qualité et Santé du Végétal, Angers, France
| | - Jean P Gibert
- Department of Biology, Duke University, Durham, NC, United States
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Chen X, Wei W, Xiao X, Wallace D, Hu C, Zhang L, Batt J, Liu J, Gonsior M, Zhang Y, LaRoche J, Hill P, Xu D, Wang J, Jiao N, Zhang R. Heterogeneous viral contribution to dissolved organic matter processing in a long-term macrocosm experiment. ENVIRONMENT INTERNATIONAL 2022; 158:106950. [PMID: 34715430 DOI: 10.1016/j.envint.2021.106950] [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: 12/31/2020] [Revised: 09/21/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
Viruses saturate environments throughout the world and play key roles in microbial food webs, yet how viral activities affect dissolved organic matter (DOM) processing in natural environments remains elusive. We established a large-scale long-term macrocosm experiment to explore viral dynamics and their potential impacts on microbial mortality and DOM quantity and quality in starved and stratified ecosystems. High viral infection dynamics and the virus-induced cell lysis (6.23-64.68% d-1) was found in the starved seawater macrocosm, which contributed to a significant transformation of microbial biomass into DOM (0.72-5.32 μg L-1 d-1). In the stratified macrocosm, a substantial amount of viral lysate DOM (2.43-17.87 μg L-1 d-1) was released into the upper riverine water, and viral lysis and DOM release (0.35-5.75 μg L-1 d-1) were reduced in the mixed water layer between riverine water and seawater. Viral lysis was stimulated at the bottom of stratified macrocosm, potentially fueled by the sinking of particulate organic carbon. Significant positive and negative associations between lytic viral production and different fluorescent DOM components were found in the starved and stratified macrocosm, indicating the potentially complex viral impacts on the production and utilization of DOM. Results also revealed the significant viral contribution to pools of both relatively higher molecular weight labile DOM and lower molecular weight recalcitrant DOM. Our study suggests that viruses have heterogeneous impact on the cycling and fate of DOM in aquatic environments.
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Affiliation(s)
- Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - Wei Wei
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China; College of the Environment and Ecology, Xiamen University, Xiamen 361102, PR China
| | - Xilin Xiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - Douglas Wallace
- Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China; Department of Oceanography, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Chen Hu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - Lianbao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - John Batt
- Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China; Department of Oceanography, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Jihua Liu
- Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China; Institute of Marine Science and Technology, Shandong University, Qingdao 266237, PR China
| | - Michael Gonsior
- Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, Solomons, MD 20688, United States
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - Julie LaRoche
- Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China; Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Paul Hill
- Department of Oceanography, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - Jianning Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China.
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China.
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