1
|
Sbardellati DL, Vannette RL. Targeted viromes and total metagenomes capture distinct components of bee gut phage communities. MICROBIOME 2024; 12:155. [PMID: 39175056 PMCID: PMC11342477 DOI: 10.1186/s40168-024-01875-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 07/16/2024] [Indexed: 08/24/2024]
Abstract
BACKGROUND Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey bee Apis mellifera and the eastern bumble bee Bombus impatiens. RESULTS We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low occupancy phage, while total metagenomes were biased towards sampling temperate phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments. CONCLUSIONS Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage. Video Abstract.
Collapse
Affiliation(s)
| | - Rachel Lee Vannette
- Department of Entomology and Nematology, University of California Davis, Davis, CA, USA
| |
Collapse
|
2
|
He Y, Zhuo S, Gao D, Pan Y, Li M, Pan J, Jiang Y, Hu Y, Guo J, Lin Q, Sanford RA, Sun W, Shang J, Wei N, Peng S, Jiang Z, Li S, Li Y, Dong Y, Shi L. Viral communities in a pH>10 serpentinite-like environment: insight into diversity and potential roles in modulating the microbiomes by bioactive vitamin B 9 synthesis. Appl Environ Microbiol 2024; 90:e0085024. [PMID: 39016614 PMCID: PMC11337834 DOI: 10.1128/aem.00850-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/26/2024] [Indexed: 07/18/2024] Open
Abstract
Viral communities exist in a variety of ecosystems and play significant roles in mediating biogeochemical processes, whereas viruses inhabiting strongly alkaline geochemical systems remain underexplored. In this study, the viral diversity, potential functionalities, and virus-host interactions in a strongly alkaline environment (pH = 10.4-12.4) exposed to the leachates derived from the serpentinization-like reactions of smelting slags were investigated. The viral populations (e.g., Herelleviridae, Queuovirinae, and Inoviridae) were closely associated with the dominating prokaryotic hosts (e.g., Meiothermus, Trueperaceae, and Serpentinomonas) in this ultrabasic environment. Auxiliary metabolic genes (AMGs) suggested that viruses may enhance hosts' fitness by facilitating cofactor biosynthesis, hydrogen metabolism, and carbon cycling. To evaluate the activity of synthesis of essential cofactor vitamin B9 by the viruses, a viral folA (vfolA) gene encoding dihydrofolate reductase (DHFR) was introduced into a thymidine-auxotrophic strain Escherichia coli MG1655 ΔfolA mutant, which restored the growth of the latter in the absence of thymidine. Notably, the homologs of the validated vDHFR were globally distributed in the viromes across various ecosystems. The present study sheds new light on the unique viral communities in hyperalkaline ecosystems and their potential beneficial impacts on the coexisting microbial consortia by supplying essential cofactors. IMPORTANCE This study presents a comprehensive investigation into the diversity, potential functionalities, and virus-microbe interactions in an artificially induced strongly alkaline environment. Functional validation of the detected viral folA genes encoding dihydrofolate reductase substantiated the synthesis of essential cofactors by viruses, which may be ubiquitous, considering the broad distribution of the viral genes associated with folate cycling.
Collapse
Affiliation(s)
- Yu He
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Shiyan Zhuo
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Donghao Gao
- School of Environmental Studies, China University of Geosciences, Wuhan, China
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Yue Pan
- College of Land Science and Technology, China Agricultural University, Beijing, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Studies, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Studies, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yongguang Jiang
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yidan Hu
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Jinzhi Guo
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Qin Lin
- Shanghai Biozeron Biological Technology Co. Ltd, China, Shanghai, China
| | - Robert A. Sanford
- Department of Earth Science & Environmental Change, University of Illinois Urbana-Champaign, Urbana, llinois, USA
| | - Weimin Sun
- Guangdong Institute of Eco-environmental and Soil Science, Guangdong, China
| | - Jianying Shang
- College of Land Science and Technology, China Agricultural University, Beijing, China
- Key Laboratory of Arable Land Conservation in North China, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Na Wei
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Shuming Peng
- Institute of Ecological Environment, Chengdu University of Technology, Chengdu, China
| | - Zhou Jiang
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Shuyi Li
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yongzhe Li
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, Beijing, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, Wuhan, China
| | - Liang Shi
- School of Environmental Studies, China University of Geosciences, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, Beijing, China
| |
Collapse
|
3
|
An L, Liu X, Wang J, Xu J, Chen X, Liu X, Hu B, Nie Y, Wu XL. Global diversity and ecological functions of viruses inhabiting oil reservoirs. Nat Commun 2024; 15:6789. [PMID: 39117673 PMCID: PMC11310422 DOI: 10.1038/s41467-024-51101-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
Oil reservoirs, being one of the significant subsurface repositories of energy and carbon, host diverse microbial communities affecting energy production and carbon emissions. Viruses play crucial roles in the ecology of microbiomes, however, their distribution and ecological significance in oil reservoirs remain undetermined. Here, we assemble a catalogue encompassing viral and prokaryotic genomes sourced from oil reservoirs. The catalogue comprises 7229 prokaryotic genomes and 3,886 viral Operational Taxonomic Units (vOTUs) from 182 oil reservoir metagenomes. The results show that viruses are widely distributed in oil reservoirs, and 85% vOTUs in oil reservoir are detected in less than 10% of the samples, highlighting the heterogeneous nature of viral communities within oil reservoirs. Through combined microcosm enrichment experiments and bioinformatics analysis, we validate the ecological roles of viruses in regulating the community structure of sulfate reducing microorganisms, primarily through a virulent lifestyle. Taken together, this study uncovers a rich diversity of viruses and their ecological functions within oil reservoirs, offering a comprehensive understanding of the role of viral communities in the biogeochemical cycles of the deep biosphere.
Collapse
Affiliation(s)
- Liyun An
- College of architecture and environment, Sichuan University, Chengdu, 610065, China
| | - Xinwu Liu
- College of Engineering, Peking University, Beijing, 100871, China
| | - Jianwei Wang
- College of Engineering, Peking University, Beijing, 100871, China
| | - Jinbo Xu
- School of Earth and Space Sciences, Peking University, Beijing, 100871, China
| | - Xiaoli Chen
- College of Engineering, Peking University, Beijing, 100871, China
- Institute of Ocean Research, Peking University, Beijing, 100871, China
| | - Xiaonan Liu
- College of Engineering, Peking University, Beijing, 100871, China
| | - Bingxin Hu
- College of Engineering, Peking University, Beijing, 100871, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing, 100871, China.
| | - Xiao-Lei Wu
- College of architecture and environment, Sichuan University, Chengdu, 610065, China.
- College of Engineering, Peking University, Beijing, 100871, China.
- School of Earth and Space Sciences, Peking University, Beijing, 100871, China.
- Institute of Ocean Research, Peking University, Beijing, 100871, China.
- Institute of Ecology, Peking University, Beijing, 100871, China.
| |
Collapse
|
4
|
Liang JL, Feng SW, Jia P, Lu JL, Yi X, Gao SM, Wu ZH, Liao B, Shu WS, Li JT. Unraveling the habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses across China. MICROBIOME 2024; 12:136. [PMID: 39039586 PMCID: PMC11265010 DOI: 10.1186/s40168-024-01851-8] [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: 09/20/2023] [Accepted: 05/30/2024] [Indexed: 07/24/2024]
Abstract
BACKGROUND Soil giant viruses are increasingly believed to have profound effects on ecological functioning by infecting diverse eukaryotes. However, their biogeography and ecology remain poorly understood. RESULTS In this study, we analyzed 333 soil metagenomes from 5 habitat types (farmland, forest, grassland, Gobi desert, and mine wasteland) across China and identified 533 distinct giant virus phylotypes affiliated with nine families, thereby greatly expanding the diversity of soil giant viruses. Among the nine families, Pithoviridae were the most diverse. The majority of phylotypes exhibited a heterogeneous distribution among habitat types, with a remarkably high proportion of unique phylotypes in mine wasteland. The abundances of phylotypes were negatively correlated with their environmental ranges. A total of 76 phylotypes recovered in this study were detectable in a published global topsoil metagenome dataset. Among climatic, geographical, edaphic, and biotic characteristics, soil eukaryotes were identified as the most important driver of beta-diversity of giant viral communities across habitat types. Moreover, co-occurrence network analysis revealed some pairings between giant viral phylotypes and eukaryotes (protozoa, fungi, and algae). Analysis of 44 medium- to high-quality giant virus genomes recovered from our metagenomes uncovered not only their highly shared functions but also their novel auxiliary metabolic genes related to carbon, sulfur, and phosphorus cycling. CONCLUSIONS These findings extend our knowledge of diversity, habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses. Video Abstract.
Collapse
Affiliation(s)
- Jie-Liang Liang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Shi-Wei Feng
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Pu Jia
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Jing-Li Lu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Xinzhu Yi
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Shao-Ming Gao
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zhuo-Hui Wu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Bin Liao
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wen-Sheng Shu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Jin-Tian Li
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China.
| |
Collapse
|
5
|
Sun CL, Pratama AA, Gazitúa MC, Cronin D, McGivern BB, Wainaina JM, Vik DR, Zayed AA, Bolduc B, Wrighton KC, Rich VI, Sullivan MB. Virus ecology and 7-year temporal dynamics across a permafrost thaw gradient. Environ Microbiol 2024; 26:e16665. [PMID: 39101434 DOI: 10.1111/1462-2920.16665] [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: 01/01/2024] [Accepted: 05/16/2024] [Indexed: 08/06/2024]
Abstract
Soil microorganisms are pivotal in the global carbon cycle, but the viruses that affect them and their impact on ecosystems are less understood. In this study, we explored the diversity, dynamics, and ecology of soil viruses through 379 metagenomes collected annually from 2010 to 2017. These samples spanned the seasonally thawed active layer of a permafrost thaw gradient, which included palsa, bog, and fen habitats. We identified 5051 virus operational taxonomic units (vOTUs), doubling the known viruses for this site. These vOTUs were largely ephemeral within habitats, suggesting a turnover at the vOTU level from year to year. While the diversity varied by thaw stage and depth-related patterns were specific to each habitat, the virus communities did not significantly change over time. The abundance ratios of virus to host at the phylum level did not show consistent trends across the thaw gradient, depth, or time. To assess potential ecosystem impacts, we predicted hosts in silico and found viruses linked to microbial lineages involved in the carbon cycle, such as methanotrophy and methanogenesis. This included the identification of viruses of Candidatus Methanoflorens, a significant global methane contributor. We also detected a variety of potential auxiliary metabolic genes, including 24 carbon-degrading glycoside hydrolases, six of which are uniquely terrestrial. In conclusion, these long-term observations enhance our understanding of soil viruses in the context of climate-relevant processes and provide opportunities to explore their role in terrestrial carbon cycling.
Collapse
Affiliation(s)
- Christine L Sun
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | - Akbar Adjie Pratama
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | | | - Dylan Cronin
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | - Bridget B McGivern
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
- Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - James M Wainaina
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
| | - Dean R Vik
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | - Kelly C Wrighton
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
- Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Virginia I Rich
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
- Byrd Polar and Climate Research Center, The Ohio State University, Columbus, Ohio, USA
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
- Byrd Polar and Climate Research Center, The Ohio State University, Columbus, Ohio, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
6
|
Wen Q, Yin X, Moming A, Liu G, Jiang B, Wang J, Fan Z, Sajjad W, Ge Y, Kang S, Shen S, Deng F. Viral communities locked in high elevation permafrost up to 100 m in depth on the Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:172829. [PMID: 38692332 DOI: 10.1016/j.scitotenv.2024.172829] [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: 12/18/2023] [Revised: 04/02/2024] [Accepted: 04/25/2024] [Indexed: 05/03/2024]
Abstract
Permafrost serves as a natural cold reservoir for viral communities. However, little is known about the viromes in deep permafrost soil, as most studies of permafrost were restricted to shallow areas. Here, permafrost soil samples of up to 100 m in depth were collected from two sites in the Tuotuo River permafrost area on the Tibetan Plateau. We investigated the viral composition in these permafrost soil samples and analyzed the relationship of viral composition and diversity along with depths. Our study revealed that greater permafrost thickness corresponds to higher diversity within the viral community. Bacteriophages were found to be the dominant viral communities, with "kill the winner" dynamics observed within the Siphoviridae and Myoviridae. The abundance and diversity of viral communities may follow a potential pattern along soil layers and depths, influenced by pH, trace elements, and permafrost thickness. Notably, strong correlations were discovered between the content of inorganic elements, including B, Mg, Cr, Bi, Ti, Na, Ni, and Cu, and the viral composition. Moreover, we discovered highly conserved sequences of giant viruses at depth of 10, 20, and 50 m in permafrost, which play a crucial role in evolutionary processes. These findings provide valuable insights into the viral community patterns from shallow to 100-m-depth in high-elevation permafrost, offering crucial data support for the formulation of strategies for permafrost thaw caused by climate change and anthropogenic activities.
Collapse
Affiliation(s)
- Qian Wen
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071 Wuhan, China; University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Xiufeng Yin
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, 730000 Lanzhou, China
| | - Abulimiti Moming
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071 Wuhan, China
| | - Guanyue Liu
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, 730000 Lanzhou, China
| | - Boyong Jiang
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071 Wuhan, China
| | - Jun Wang
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071 Wuhan, China
| | - Zhaojun Fan
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071 Wuhan, China
| | - Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, 730000 Lanzhou, China
| | - Yingying Ge
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071 Wuhan, China
| | - Shichang Kang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, 730000 Lanzhou, China; University of Chinese Academy of Sciences, 100049 Beijing, China.
| | - Shu Shen
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071 Wuhan, China; Hubei Jiangxia Laboratory, 430200 Wuhan, China.
| | - Fei Deng
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071 Wuhan, China.
| |
Collapse
|
7
|
Li W, Wang Y, Zhao K, Xu L, Shi T, Ma B, Lv X. Host-virus coevolution drives soil microbial function succession along a millennium land reclamation chronosequence. J Adv Res 2024:S2090-1232(24)00258-3. [PMID: 38960277 DOI: 10.1016/j.jare.2024.06.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/05/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024] Open
Abstract
INTRODUCTION Gene exchange between viruses and hosts plays an important role in driving virus-host coevolution, enabling adaptation of both viruses and hosts to environmental changes. However, the mechanisms and functional significance of virus-host gene exchanges over long-term scales remain largely unexplored. OBJECTIVE The present study aimed to gain insights into the role of viruses in virus-host interactions and coevolution by monitoring virome dynamics along a millennium-long land reclamation chronosequence. METHODS We collected 24 soil samples from 8 stages of a millennium-long land reclamation chronosequence, including non-reclamation, and reclamation periods of 10, 50, 100, 300, 500, 700, and 1000 years. We characterized their metagenomes, and identified DNA viruses within these metagenomes. RESULTS Our findings reveal a significant shift in viral community composition after 50 years of land reclamation, but soil viral diversity reached a stable phase approximately 300 years after the initial reclamation. Analysis of the virus-host network showed a scale-free degree distribution and a reduction in complexity over time, with generalist viruses emerging as key facilitators of horizontal gene transfer. CONCLUSION These findings highlight the integral role of viruses, especially generalist types, in mediating gene exchanges between viruses and hosts, thereby influencing the coevolutionary dynamics in soil ecosystems over significant timescales. This study offers novel insights into long-term virus-host interactions, showing how the virome responds to environmental changes, driving shifts in various microbial functions in reclaimed land.
Collapse
Affiliation(s)
- Wenbing Li
- School of Engineering, Hangzhou Normal University, Hangzhou 310018, China; School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China.
| | - Yiling 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
| | - Kankan Zhao
- 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
| | - Linya 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
| | - Tingfeng Shi
- 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
| | - Bin Ma
- 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; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Xiaofei Lv
- Department of Environmental Engineering, China Jiliang University, Hangzhou 310018, China.
| |
Collapse
|
8
|
Wang Y, Zhang Z, Kang J, Chen B, Hong W, Lv B, Wang T, Qian H. Phages in different habitats and their ability to carry antibiotic resistance genes. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133941. [PMID: 38447371 DOI: 10.1016/j.jhazmat.2024.133941] [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: 07/26/2023] [Revised: 02/19/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024]
Abstract
As the most abundant organisms on Earth, phages play a key role in the evolution of bacterial antibiotic resistance. Although previous studies have demonstrated the molecular mechanisms of horizontal gene transfer mediated by mobile genetic elements, our understanding of the intertwined relationships between antibiotic resistance genes (ARGs) and phages is limited. In this study, we analysed 2781 metagenomic samples to reveal the composition and species interactions of phage communities in different habitats as well as their capacity to carry ARGs with health risks. The composition of phage communities varies in different habitats and mainly depends on environmental conditions. Terrestrial habitats display more complex and robust interactions between phages than aquatic and human-associated habitats, resulting in the highest biodiversity of phages. Several types of phages in certain taxa (4.95-7.67%, mainly belonging to Caudoviricetes) have the capacity to carry specific ARGs and display a high potential risk to human health, especially in human-associated habitats. Overall, our results provide insights into the assembly mechanisms of phage communities and their effects on the dissemination of antibiotic resistance.
Collapse
Affiliation(s)
- Yan Wang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Jian Kang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China; College of Ecology and Environment, Anhui Normal University, Wuhu 241002, PR China
| | - Bingfeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Wenjie Hong
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, PR China
| | - Binghai Lv
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, PR China.
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China.
| |
Collapse
|
9
|
Coleine C, Delgado-Baquerizo M, DiRuggiero J, Guirado E, Harfouche AL, Perez-Fernandez C, Singh BK, Selbmann L, Egidi E. Dryland microbiomes reveal community adaptations to desertification and climate change. THE ISME JOURNAL 2024; 18:wrae056. [PMID: 38552152 PMCID: PMC11031246 DOI: 10.1093/ismejo/wrae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/21/2024]
Abstract
Drylands account for 45% of the Earth's land area, supporting ~40% of the global population. These regions support some of the most extreme environments on Earth, characterized by extreme temperatures, low and variable rainfall, and low soil fertility. In these biomes, microorganisms provide vital ecosystem services and have evolved distinctive adaptation strategies to endure and flourish in the extreme. However, dryland microbiomes and the ecosystem services they provide are under threat due to intensifying desertification and climate change. In this review, we provide a synthesis of our current understanding of microbial life in drylands, emphasizing the remarkable diversity and adaptations of these communities. We then discuss anthropogenic threats, including the influence of climate change on dryland microbiomes and outline current knowledge gaps. Finally, we propose research priorities to address those gaps and safeguard the sustainability of these fragile biomes.
Collapse
Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, E-41012, Spain
| | - Jocelyne DiRuggiero
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, United States
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Emilio Guirado
- Multidisciplinary Institute for Environment Studies “Ramón Margalef”, Universidad de Alicante, Alicante E-03071, Spain
| | - Antoine L Harfouche
- Department for Innovation in Biological, Agro-Food and Forest systems, University of Tuscia, Viterbo 01100, Italy
| | | | - Brajesh K Singh
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith 2750, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith 2750, Australia
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy
- Mycological Section, Italian Antarctic National Museum (MNA), Genoa 16128, Italy
| | - Eleonora Egidi
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith 2750, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith 2750, Australia
| |
Collapse
|
10
|
Heinrichs ME, Piedade GJ, Popa O, Sommers P, Trubl G, Weissenbach J, Rahlff J. Breaking the Ice: A Review of Phages in Polar Ecosystems. Methods Mol Biol 2024; 2738:31-71. [PMID: 37966591 DOI: 10.1007/978-1-0716-3549-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Bacteriophages, or phages, are viruses that infect and replicate within bacterial hosts, playing a significant role in regulating microbial populations and ecosystem dynamics. However, phages from extreme environments such as polar regions remain relatively understudied due to challenges such as restricted ecosystem access and low biomass. Understanding the diversity, structure, and functions of polar phages is crucial for advancing our knowledge of the microbial ecology and biogeochemistry of these environments. In this review, we will explore the current state of knowledge on phages from the Arctic and Antarctic, focusing on insights gained from -omic studies, phage isolation, and virus-like particle abundance data. Metagenomic studies of polar environments have revealed a high diversity of phages with unique genetic characteristics, providing insights into their evolutionary and ecological roles. Phage isolation studies have identified novel phage-host interactions and contributed to the discovery of new phage species. Virus-like particle abundance and lysis rate data, on the other hand, have highlighted the importance of phages in regulating bacterial populations and nutrient cycling in polar environments. Overall, this review aims to provide a comprehensive overview of the current state of knowledge about polar phages, and by synthesizing these different sources of information, we can better understand the diversity, dynamics, and functions of polar phages in the context of ongoing climate change, which will help to predict how polar ecosystems and residing phages may respond to future environmental perturbations.
Collapse
Affiliation(s)
- Mara Elena Heinrichs
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Gonçalo J Piedade
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Ovidiu Popa
- Institute of Quantitative and Theoretical Biology Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | | | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Julia Weissenbach
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Janina Rahlff
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.
- Aero-Aquatic Virus Research Group, Friedrich Schiller University Jena, Jena, Germany.
| |
Collapse
|
11
|
Coclet C, Sorensen PO, Karaoz U, Wang S, Brodie EL, Eloe-Fadrosh EA, Roux S. Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem. MICROBIOME 2023; 11:237. [PMID: 37891627 PMCID: PMC10604447 DOI: 10.1186/s40168-023-01666-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 09/07/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time and their response to strong seasonal changes in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental soil DNA and RNA viruses, focusing especially on bacteriophages, across dynamics' seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes. RESULTS We identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of fungal RNA viruses, and a large and unsuspected diversity of positive single-stranded RNA phages (Leviviricetes), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active DNA and RNA phages that changed across seasons, consistent with a "seed-bank" viral community structure in which new phage activity, for example, replication and host lysis, is sequentially triggered by changes in environmental conditions. At the population level, we further identified virus-host dynamics matching two existing ecological models: "Kill-The-Winner" which proposes that lytic phages are actively infecting abundant bacteria, and "Piggyback-The-Persistent" which argues that when the host is growing slowly, it is more beneficial to remain in a dormant state. The former was associated with summer months of high and rapid microbial activity, and the latter with winter months of limited and slow host growth. CONCLUSION Taken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. As our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry. Video Abstract.
Collapse
Affiliation(s)
- Clement Coclet
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Patrick O Sorensen
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Shi Wang
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Emiley A Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| |
Collapse
|
12
|
Zhu Y, Zhang Y, Yan S, Chen X, Xie S. Viral community structure and functional potential vary with lifestyle and altitude in soils of Mt. Everest. ENVIRONMENT INTERNATIONAL 2023; 178:108055. [PMID: 37356309 DOI: 10.1016/j.envint.2023.108055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/13/2023] [Accepted: 06/17/2023] [Indexed: 06/27/2023]
Abstract
More and more focus has been placed on the processes by which viruses interact with bacteria to influence the biogeochemical cycles. The intricacy of soil matrix and the incompleteness of databases, however, constrains the investigation on the mechanisms of soil viruses exerting ecological functions. The modification of ICTV classification system in 2021 was also a huge shock to the results of the existing studies on virome. We used viral metagenomes combined with soil properties to investigate the viral community composition and auxiliary metabolic genes (AMGs) profiles of various lifestyles in soils of Mount Everest at different altitudes. Viral lifestyles and soil nutrient levels were found to significantly influence the diversity and composition of viral communities. Temperate virus lifestyle dominated in high-altitude soils with lower level of nutrients because of its stronger survival adaptability, and the structural and functional diversity of viral communities was positively correlated with the contents of nutrients (total carbon and total nitrogen). The primary types of AMGs carried by temperate and virulent viruses differed, while a variety of genes involved in carbon metabolism highlighted the potential importance of viruses in the soil carbon cycle of Mount Everest. Moreover, the abundance of AMGs encoding carbohydrate-active enzymes had a significant and positive correlation with soil C/N ratio. Overall, these findings provide a context for further exploration on the regulatory mechanisms of viruses in carbon cycle via interactions with microorganisms.
Collapse
Affiliation(s)
- Ying Zhu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yi Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Shuang Yan
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xiuli Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
| |
Collapse
|
13
|
Mashamaite L, Lebre PH, Varliero G, Maphosa S, Ortiz M, Hogg ID, Cowan DA. Microbial diversity in Antarctic Dry Valley soils across an altitudinal gradient. Front Microbiol 2023; 14:1203216. [PMID: 37555066 PMCID: PMC10406297 DOI: 10.3389/fmicb.2023.1203216] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/23/2023] [Indexed: 08/10/2023] Open
Abstract
INTRODUCTION The Antarctic McMurdo Dry Valleys are geologically diverse, encompassing a wide variety of soil habitats. These environments are largely dominated by microorganisms, which drive the ecosystem services of the region. While altitude is a well-established driver of eukaryotic biodiversity in these Antarctic ice-free areas (and many non-Antarctic environments), little is known of the relationship between altitude and microbial community structure and functionality in continental Antarctica. METHODS We analysed prokaryotic and lower eukaryotic diversity from soil samples across a 684 m altitudinal transect in the lower Taylor Valley, Antarctica and performed a phylogenic characterization of soil microbial communities using short-read sequencing of the 16S rRNA and ITS marker gene amplicons. RESULTS AND DISCUSSION Phylogenetic analysis showed clear altitudinal trends in soil microbial composition and structure. Cyanobacteria were more prevalent in higher altitude samples, while the highly stress resistant Chloroflexota and Deinococcota were more prevalent in lower altitude samples. We also detected a shift from Basidiomycota to Chytridiomycota with increasing altitude. Several genera associated with trace gas chemotrophy, including Rubrobacter and Ornithinicoccus, were widely distributed across the entire transect, suggesting that trace-gas chemotrophy may be an important trophic strategy for microbial survival in oligotrophic environments. The ratio of trace-gas chemotrophs to photoautotrophs was significantly higher in lower altitude samples. Co-occurrence network analysis of prokaryotic communities showed some significant differences in connectivity within the communities from different altitudinal zones, with cyanobacterial and trace-gas chemotrophy-associated taxa being identified as potential keystone taxa for soil communities at higher altitudes. By contrast, the prokaryotic network at low altitudes was dominated by heterotrophic keystone taxa, thus suggesting a clear trophic distinction between soil prokaryotic communities at different altitudes. Based on these results, we conclude that altitude is an important driver of microbial ecology in Antarctic ice-free soil habitats.
Collapse
Affiliation(s)
- Lefentse Mashamaite
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Pedro H. Lebre
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Gilda Varliero
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Silindile Maphosa
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Max Ortiz
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- Clemson University Genomics & Bioinformatics Facility, Clemson University, Clemson, SC, United States
| | - Ian D. Hogg
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- School of Science, University of Waikato, Hamilton, New Zealand
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, NU, Canada
| | - Don A. Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| |
Collapse
|
14
|
Zhang Q, Zhou L, Zhao Y, Gao S, Yang Y, Chen Q, Li W, Qi Q, Dong Q, Lei J, Guo X, Gao Q, Yang Y. Uncovering the virome and its interaction with antibiotic resistome during compost fertilization. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131763. [PMID: 37311294 DOI: 10.1016/j.jhazmat.2023.131763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/26/2023] [Accepted: 06/01/2023] [Indexed: 06/15/2023]
Abstract
Antibiotic resistance is a pressing global health issue, leading to increased illnesses and fatalities. The contribution of viruses to the acquisition, preservation, and dissemination of antibiotic resistance genes (ARGs) is not yet fully understood. By using a high-throughput functional gene-based microarray (GeoChip 5.0), this study examines the prevalence and relative abundance of bacteriophage and eukaryotic viral genes in swine manure, compost, compost-amended agricultural soil, and unamended soil from suburban regions of Beijing, China. Our findings reveal a significantly elevated presence of biomarker viral genes in compost-amended soils compared to unamended soils, suggesting potential health risks associated with compost fertilization. We also observed stronger ecological interactions between ARGs and viral genes in manure and compost than in soils. Network analysis identified arabinose efflux permeases and EmrB/QacA resistance genes, linked to CRISPR encoding sequences, as keystone nodes, indicating possible ARG acquisition via virus infections. Moreover, positive correlations were found between viral genes, antibiotic concentrations, and ARG diversity in manure, compost, and compost-amended soils, highlighting a likely pathway for virus-mediated ARG transfer. In summary, our results indicate that use of compost as a fertilizer in agricultural settings could facilitate the spread of ARGs through viral mechanisms, allowing for time-delayed genetic exchanges over broader temporal and spatial scales than ARGs within bacterial genomes.
Collapse
Affiliation(s)
- Qingxia Zhang
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Lei Zhou
- Center for professional training and service, China Association for Science and Technology, China
| | - Yilong Zhao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Shuhong Gao
- School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Yanjun Yang
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Qingyun Chen
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Wenhui Li
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Qi Qi
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Dong
- Institute of Chemical Defense, Beijing 102205, China
| | - Jiesi Lei
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
15
|
Tang X, Zhong L, Tang L, Fan C, Zhang B, Wang M, Dong H, Zhou C, Rensing C, Zhou S, Zeng G. Lysogenic bacteriophages encoding arsenic resistance determinants promote bacterial community adaptation to arsenic toxicity. THE ISME JOURNAL 2023:10.1038/s41396-023-01425-w. [PMID: 37161002 DOI: 10.1038/s41396-023-01425-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023]
Abstract
Emerging evidence from genomics gives us a glimpse into the potential contribution of lysogenic bacteriophages (phages) to the environmental adaptability of their hosts. However, it is challenging to quantify this kind of contribution due to the lack of appropriate genetic markers and the associated controllable environmental factors. Here, based on the unique transformable nature of arsenic (the controllable environmental factor), a series of flooding microcosms was established to investigate the contribution of arsM-bearing lysogenic phages to their hosts' adaptation to trivalent arsenic [As(III)] toxicity, where arsM is the marker gene associated with microbial As(III) detoxification. In the 15-day flooding period, the concentration of As(III) was significantly increased, and this elevated As(III) toxicity visibly inhibited the bacterial population, but the latter quickly adapted to As(III) toxicity. During the flooding period, some lysogenic phages re-infected new hosts after an early burst, while others persistently followed the productive cycle (i.e., lytic cycle). The unique phage-host interplay contributed to the rapid spread of arsM among soil microbiota, enabling the quick recovery of the bacterial community. Moreover, the higher abundance of arsM imparted a greater arsenic methylation capability to soil microbiota. Collectively, this study provides experimental evidence for lysogenic phages assisting their hosts in adapting to an extreme environment, which highlights the ecological perspectives on lysogenic phage-host mutualism.
Collapse
Affiliation(s)
- Xiang Tang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, P. R. China
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
| | - Linrui Zhong
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, P. R. China
| | - Lin Tang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, P. R. China
| | - Changzheng Fan
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, P. R. China.
| | - Baowei Zhang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, P. R. China
| | - Mier Wang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, P. R. China
| | - Haoran Dong
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, P. R. China
| | - Chengyun Zhou
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, P. R. China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, P. R. China.
| |
Collapse
|
16
|
Ettinger CL, Saunders M, Selbmann L, Delgado-Baquerizo M, Donati C, Albanese D, Roux S, Tringe S, Pennacchio C, Del Rio TG, Stajich JE, Coleine C. Highly diverse and unknown viruses may enhance Antarctic endoliths' adaptability. MICROBIOME 2023; 11:103. [PMID: 37158954 PMCID: PMC10165816 DOI: 10.1186/s40168-023-01554-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND Rock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology, and further still, viruses in these communities have been largely unexplored despite important roles related to host metabolism and nutrient cycling. To begin to address this, we present a large-scale viral catalog from Antarctic rock microbial communities. RESULTS We performed metagenomic analyses on rocks from across Antarctica representing a broad range of environmental and spatial conditions, and which resulted in a predicted viral catalog comprising > 75,000 viral operational taxonomic units (vOTUS). We found largely undescribed, highly diverse and spatially structured virus communities which had predicted auxiliary metabolic genes (AMGs) with functions indicating that they may be potentially influencing bacterial adaptation and biogeochemistry. CONCLUSION This catalog lays the foundation for expanding knowledge of virosphere diversity, function, spatial ecology, and dynamics in extreme environments. This work serves as a step towards exploring adaptability of microbial communities in the face of a changing climate. Video Abstract.
Collapse
Affiliation(s)
- Cassandra L Ettinger
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.
| | - Morgan Saunders
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA, USA
- The University of Arizona, Tucson, AZ, USA
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad Y Funcionamiento Ecosistémico, Instituto de Recursos Naturales Y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, Seville, E-41012, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Seville, 41013, Spain
| | - Claudio Donati
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele All'Adige, 38098, Italy
| | - Davide Albanese
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele All'Adige, 38098, Italy
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Susannah Tringe
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Christa Pennacchio
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Tijana G Del Rio
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Claudia Coleine
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.
- Laboratorio de Biodiversidad Y Funcionamiento Ecosistémico, Instituto de Recursos Naturales Y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, Seville, E-41012, Spain.
| |
Collapse
|
17
|
Abstract
Soil viruses are highly abundant and have important roles in the regulation of host dynamics and soil ecology. Climate change is resulting in unprecedented changes to soil ecosystems and the life forms that reside there, including viruses. In this Review, we explore our current understanding of soil viral diversity and ecology, and we discuss how climate change (such as extended and extreme drought events or more flooding and altered precipitation patterns) is influencing soil viruses. Finally, we provide our perspective on future research needs to better understand how climate change will impact soil viral ecology.
Collapse
Affiliation(s)
- Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Ruonan Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| |
Collapse
|
18
|
Tundra Soil Viruses Mediate Responses of Microbial Communities to Climate Warming. mBio 2023; 14:e0300922. [PMID: 36786571 PMCID: PMC10127799 DOI: 10.1128/mbio.03009-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
The rise of global temperature causes the degradation of the substantial reserves of carbon (C) stored in tundra soils, in which microbial processes play critical roles. Viruses are known to influence the soil C cycle by encoding auxiliary metabolic genes and infecting key microorganisms, but their regulation of microbial communities under climate warming remains unexplored. In this study, we evaluated the responses of viral communities for about 5 years of experimental warming at two depths (15 to 25 cm and 45 to 55 cm) in the Alaskan permafrost region. Our results showed that the viral community and functional gene composition and abundances (including viral functional genes related to replication, structure, infection, and lysis) were significantly influenced by environmental conditions such as total nitrogen (N), total C, and soil thawing duration. Although long-term warming did not impact the viral community composition at the two depths, some glycoside hydrolases encoded by viruses were more abundant at both depths of the warmed plots. With the continuous reduction of total C, viruses may alleviate methane release by altering infection strategies on methanogens. Importantly, viruses can adopt lysogenic and lytic lifestyles to manipulate microbial communities at different soil depths, respectively, which could be one of the major factors causing the differences in microbial responses to warming. This study provides a new ecological perspective on how viruses regulate the responses of microbes to warming at community and functional scales. IMPORTANCE Permafrost thawing causes microbial release of greenhouse gases, exacerbating climate warming. Some previous studies examined the responses of the microbial communities and functions to warming in permafrost region, but the roles of viruses in mediating the responses of microbial communities to warming are poorly understood. This study revealed that warming induced changes in some viral functional classes and in the virus/microbe ratios for specific lineages, which might influence the entire microbial community. Furthermore, differences in viral communities and functions, along with soil depths, are important factors influencing microbial responses to warming. Collectively, our study revealed the regulation of microbial communities by viruses and demonstrated the importance of viruses in the microbial ecology research.
Collapse
|
19
|
Shin H, Kim Y, Unno T, Hur HG. Prevalence and Characterization of CRISPR Locus 2.1 Spacers in Escherichia coli Isolates Obtained from Feces of Animals and Humans. Microbiol Spectr 2023; 11:e0493422. [PMID: 36719193 PMCID: PMC10101085 DOI: 10.1128/spectrum.04934-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/10/2023] [Indexed: 02/01/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR) has been studied as an immune system in prokaryotes for the survival of bacteriophages. The CRISPR system in prokaryotes records the invasion of bacteriophages or other genetic materials in CRISPR loci. Accordingly, CRISPR loci can reveal a history of infection records of bacteriophages and other genetic materials. Therefore, identification of the CRISPR array may help trace the events that bacteria have undergone. In this study, we characterized and identified the spacers of the CRISPR loci in Escherichia coli isolates obtained from the feces of animals and humans. Most CRISPR spacers were found to stem from phages. Although we did not find any patterns in CRISPR spacers according to sources, our results showed that phage-derived spacers mainly originated from the families Inoviridae, Myoviridae, Podoviridae, and Siphoviridae and the order Caudovirales, whereas plasmid-derived CRISPR spacers were mainly from the Enterobacteriaceae family. In addition, it is worth noting that the isolates from each animal and human source harbored source-specific spacers. Considering that some of these taxa are likely found in the gut of mammalian animals, CRISPR spacers identified in these E. coli isolates were likely derived from the bacteriophageome and microbiome in closed gut environments. Although the bacteriophageome database limits the characterization of CRISPR arrays, the present study showed that some spacers were specifically found in both animal and human sources. Thus, this finding may suggest the possible use of E. coli CRISPR spacers as a microbial source tracking tool. IMPORTANCE We characterized spacers of CRISPR locus 2.1 in E. coli isolates obtained from the feces of various sources. Phage-derived CRISPR spacers are mainly acquired from the order Caudovirales, and plasmid-derived CRISPR spacers are mostly from the Enterobacteriaceae family. This is thought to reflect the microbiome and phageome of the gut environment of the sources. Hence, spacers may help track the encounter of bacterial cells with bacterial cells, viruses, or other genetic materials. Interestingly, source-specific spacers are also observed. The identification of source-specific spacers is thought to help develop the methodology of microbial source tracking and understanding the interactions between viruses and bacteria. However, very few spacers have been uncovered to track where they originate. The accumulation of genome sequences can help identify the hosts of spacers and can be applied for microbial source tracking.
Collapse
Affiliation(s)
- Hanseob Shin
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Yongjin Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Tatsuya Unno
- Faculty of Biotechnology, College of Applied Life Sciences, SARI, Jeju National University, Jeju, Republic of Korea
| | - Hor-Gil Hur
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| |
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Tang X, Fan C, Zeng G, Zhong L, Li C, Ren X, Song B, Liu X. Phage-host interactions: The neglected part of biological wastewater treatment. WATER RESEARCH 2022; 226:119183. [PMID: 36244146 DOI: 10.1016/j.watres.2022.119183] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/29/2022] [Accepted: 09/29/2022] [Indexed: 05/25/2023]
Abstract
In wastewater treatment plants (WWTPs), the stable operation of biological wastewater treatment is strongly dependent on the stability of associated microbiota. Bacteriophages (phages), viruses that specifically infect bacteria and archaea, are highly abundant and diverse in WWTPs. Although phages do not have known metabolic functions for themselves, they can shape functional microbiota via various phage-host interactions to impact biological wastewater treatment. However, the developments of phage-host interaction in WWTPs and their impact on biological wastewater treatment are overlooked. Here, we review the current knowledge regarding the phage-host interactions in biological wastewater treatment, mainly focusing on the characteristics of different phage populations, the phage-driven changes in functional microbiota, and the potential driving factors of phage-host interactions. We also discuss the efforts required further to understand and manipulate the phage-host interactions in biological wastewater treatment. Overall, this review advocates more attention to the phage dynamics in WWTPs.
Collapse
Affiliation(s)
- Xiang Tang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Changzheng Fan
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China.
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Linrui Zhong
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Chao Li
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China; Nova Skantek (Hunan) Environ Energy Co., Ltd., Changsha 410100, P.R. China
| | - Xiaoya Ren
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Biao Song
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Xigui Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| |
Collapse
|
22
|
Liao H, Li H, Duan CS, Zhou XY, Luo QP, An XL, Zhu YG, Su JQ. Response of soil viral communities to land use changes. Nat Commun 2022; 13:6027. [PMID: 36224209 PMCID: PMC9556555 DOI: 10.1038/s41467-022-33771-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/30/2022] [Indexed: 02/07/2023] Open
Abstract
Soil viruses remain understudied when compared to virus found in aquatic ecosystems. Here, we investigate the ecological patterns of soil viral communities across various land use types encompassing forest, agricultural, and urban soil in Xiamen, China. We recovered 59,626 viral operational taxonomic units (vOTUs) via size-fractioned viromic approach with additional mitomycin C treatment to induce virus release from bacterial fraction. Our results show that viral communities are significantly different amongst the land use types considered. A microdiversity analysis indicates that selection act on soil vOTUs, resulting in disparities between land use associated viral communities. Soil pH is one of the major determinants of viral community structure, associated with changes of in-silico predicted host compositions of soil vOTUs. Habitat disturbance and variation of soil moisture potentially contribute to the dynamics of putative lysogenic vOTUs. These findings provide mechanistic understandings of the ecology and evolution of soil viral communities in changing environments.
Collapse
Affiliation(s)
- Hu Liao
- grid.9227.e0000000119573309Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Hu Li
- grid.9227.e0000000119573309Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, China
| | - Chen-Song Duan
- grid.9227.e0000000119573309Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Xin-Yuan Zhou
- grid.9227.e0000000119573309Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Qiu-Ping Luo
- grid.9227.e0000000119573309Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Xin-Li An
- grid.9227.e0000000119573309Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, China
| | - Yong-Guan Zhu
- grid.9227.e0000000119573309Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, China ,grid.9227.e0000000119573309State Key Lab of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China
| | - Jian-Qiang Su
- grid.9227.e0000000119573309Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| |
Collapse
|
23
|
Elbehery AHA, Deng L. Insights into the global freshwater virome. Front Microbiol 2022; 13:953500. [PMID: 36246212 PMCID: PMC9554406 DOI: 10.3389/fmicb.2022.953500] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022] Open
Abstract
Viruses are by far the most abundant life forms on this planet. Yet, the full viral diversity remains mostly unknown, especially in environments like freshwater. Therefore, we aimed to study freshwater viruses in a global context. To this end, we downloaded 380 publicly available viral metagenomes (>1 TB). More than 60% of these metagenomes were discarded based on their levels of cellular contamination assessed by ribosomal DNA content. For the remaining metagenomes, assembled contigs were decontaminated using two consecutive steps, eventually yielding 273,365 viral contigs longer than 1,000 bp. Long enough contigs (≥ 10 kb) were clustered to identify novel genomes/genome fragments. We could recover 549 complete circular and high-quality draft genomes, out of which 10 were recognized as being novel. Functional annotation of these genomes showed that most of the annotated coding sequences are DNA metabolic genes or phage structural genes. On the other hand, taxonomic analysis of viral contigs showed that most of the assigned contigs belonged to the order Caudovirales, particularly the families of Siphoviridae, Myoviridae, and Podoviridae. The recovered viral contigs contained several auxiliary metabolic genes belonging to several metabolic pathways, especially carbohydrate and amino acid metabolism in addition to photosynthesis as well as hydrocarbon degradation and antibiotic resistance. Overall, we present here a set of prudently chosen viral contigs, which should not only help better understanding of freshwater viruses but also be a valuable resource for future virome studies.
Collapse
Affiliation(s)
- Ali H. A. Elbehery
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt
- *Correspondence: Ali H. A. Elbehery,
| | - Li Deng
- Helmholtz Centre Munich – German Research Centre for Environmental Health, Institute of Virology, Neuherberg, Germany
- Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, Freising, Germany
- Li Deng,
| |
Collapse
|
24
|
Busse L, Tisza M, DiRuggiero J. Viruses Ubiquity and Diversity in Atacama Desert Endolithic Communities. Viruses 2022; 14:1983. [PMID: 36146789 PMCID: PMC9500819 DOI: 10.3390/v14091983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Viruses are key players in the environment, and recent metagenomic studies have revealed their diversity and genetic complexity. Despite progress in understanding the ecology of viruses in extreme environments, viruses' dynamics and functional roles in dryland ecosystems, which cover about 45% of the Earth's land surfaces, remain largely unexplored. This study characterizes virus sequences in the metagenomes of endolithic (within rock) microbial communities ubiquitously found in hyper-arid deserts. Taxonomic classification and network construction revealed the presence of novel and diverse viruses in communities inhabiting calcite, gypsum, and ignimbrite rocks. Viral genome maps show a high level of protein diversity within and across endolithic communities and the presence of virus-encoded auxiliary metabolic genes. Phage-host relationships were predicted by matching tRNA, CRISPR spacer, and protein sequences in the viral and microbial metagenomes. Primary producers and heterotrophic bacteria were found to be putative hosts to some viruses. Intriguingly, viral diversity was not correlated with microbial diversity across rock substrates.
Collapse
Affiliation(s)
- Leora Busse
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Mike Tisza
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jocelyne DiRuggiero
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
| |
Collapse
|
25
|
Wang J, Xiao J, Zhu Z, Wang S, Zhang L, Fan Z, Deng Y, Hu Z, Peng F, Shen S, Deng F. Diverse viromes in polar regions: A retrospective study of metagenomic data from Antarctic animal feces and Arctic frozen soil in 2012-2014. Virol Sin 2022; 37:883-893. [PMID: 36028202 PMCID: PMC9797369 DOI: 10.1016/j.virs.2022.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/17/2022] [Indexed: 01/01/2023] Open
Abstract
Antarctica and the Arctic are the coldest places, containing a high diversity of microorganisms, including viruses, which are important components of polar ecosystems. However, owing to the difficulties in obtaining access to animal and environmental samples, the current knowledge of viromes in polar regions is still limited. To better understand polar viromes, this study performed a retrospective analysis using metagenomic sequencing data of animal feces from Antarctica and frozen soil from the Arctic collected during 2012-2014. The results reveal diverse communities of DNA and RNA viruses from at least 23 families from Antarctic animal feces and 16 families from Arctic soils. Although the viral communities from Antarctica and the Arctic show a large diversity, they have genetic similarities with known viruses from different ecosystems and organisms with similar viral proteins. Phylogenetic analysis of Microviridae, Parvoviridae, and Larvidaviridae was further performed, and complete genomic sequences of two novel circular replication-associated protein (rep)-encoding single-stranded (CRESS) DNA viruses closely related to Circoviridae were identified. These results reveal the high diversity, complexity, and novelty of viral communities from polar regions, and suggested the genetic similarity and functional correlations of viromes between the Antarctica and Arctic. Variations in viral families in Arctic soils, Arctic freshwater, and Antarctic soils are discussed. These findings improve our understanding of polar viromes and suggest the importance of performing follow-up in-depth investigations of animal and environmental samples from Antarctica and the Arctic, which would reveal the substantial role of these viruses in the global viral community.
Collapse
Affiliation(s)
- Jun Wang
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jian Xiao
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zheng Zhu
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Siyuan Wang
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China,Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Lei Zhang
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zhaojun Fan
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yali Deng
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zhihong Hu
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Fang Peng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, 430072, China,Corresponding authors.
| | - Shu Shen
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China,Corresponding authors.
| | - Fei Deng
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China,Corresponding authors.
| |
Collapse
|
26
|
The potential of mineral weathering of halophilic-endophytic bacteria isolated from Suaeda salsa and Spartina anglica. Arch Microbiol 2022; 204:561. [PMID: 35978053 PMCID: PMC9385829 DOI: 10.1007/s00203-022-03129-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 06/02/2022] [Accepted: 06/13/2022] [Indexed: 11/02/2022]
Abstract
Bacteria have the abilities of salt tolerant, mineral weathering and plant growth promoting can promote the growth of plants in saline lands. However, few reports of the mineral weathering capacity of halophilic-endophytic bacteria, raising the question of whether the halophilic-endophytic weathering bacteria are fundamentally distinct from those in plants communities. In this study, we isolated and characterized halophilic bacterial strains from the roots and leaves of Suaeda salsa and Spartina anglica with respect to their mineral weathering pattern, role in the promoting plant growth, community structure, and their changes in these two plants. Using improved Gibbson medium, we obtained 156 halophilic bacterial strains, among which 92 and 64 strains were isolated from the S. salsa and S. anglica samples, respectively. The rock weathering patterns of the isolates were characterized using batch cultures that measure the quantity of Si, Al, K, and Fe released from crystal biotite under aerobic conditions. Significantly, the biomass and capacity of the mineral weathering of the halophilic-endophytic bacteria were different in the plants. The abundance of the halophilic-endophytic bacterials in the Suaeda salsa was significantly greater than Spartina anglica, whereas the mineral weathering bacterial in the Suaeda salsa was similar to the Spartina anglica. Furthermore, the proportion of plant growth-promoting bacteria in the Suaeda salsa was higher than Spartina anglica. Phylogenetic analyses show that the weathered minerals were inhabited by specific functional groups of bacteria (Halomonas, Acinetobacter, Burkholderia, Alcaligenes, Sphingobium, Arthrobacter, Chryseobacterium, Paenibacillus, Microbacterium, Ensifer, Ralstonia and Enterobacter) that contribute to the mineral weathering. The changes in halophilic endophytes weathering communities between the two plants were attributable not only to major bacterial groups but also to a change in the minor population structure.
Collapse
|
27
|
Zhang Y, Guo Y, Qiu T, Gao M, Wang X. Bacteriophages: Underestimated vehicles of antibiotic resistance genes in the soil. Front Microbiol 2022; 13:936267. [PMID: 35992716 PMCID: PMC9386270 DOI: 10.3389/fmicb.2022.936267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022] Open
Abstract
Bacteriophages (phages), the most abundant biological entities on Earth, have a significant effect on the composition and dynamics of microbial communities, biogeochemical cycles of global ecosystems, and bacterial evolution. A variety of antibiotic resistance genes (ARGs) have been identified in phage genomes in different soil samples. Phages can mediate the transfer of ARGs between bacteria via transduction. Recent studies have suggested that anthropogenic activities promote phage-mediated horizontal gene transfer events. Therefore, the role of phages in the dissemination of ARGs, which are a potential threat to human health, may be underestimated. However, the contribution of phages to the transfer of ARGs is still poorly understood. Considering the growing and wide concerns of antibiotic resistance, phages should be considered a research focus in the mobile resistome. This review aimed to provide an overview of phages as vehicles of ARGs in soil. Here, we summarized the current knowledge on the diversity and abundance of ARGs in soilborne phages and analyzed the contribution of phages to the horizontal transfer of ARGs. Finally, research deficiencies and future perspectives were discussed. This study provides a reference for preventing and controlling ARG pollution in agricultural systems.
Collapse
|
28
|
Hernández-Guzmán M, Pérez-Hernández V, Gómez-Acata S, Jiménez-Bueno N, Verhulst N, Muñoz-Arenas LC, Navarro-Noya YE, Luna-Guido ML, Dendooven L. Application of young maize plant residues alters the microbiome composition and its functioning in a soil under conservation agriculture: a metagenomics study. Arch Microbiol 2022; 204:458. [PMID: 35788780 DOI: 10.1007/s00203-022-03060-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 05/01/2022] [Accepted: 06/07/2022] [Indexed: 12/24/2022]
Abstract
To increase our knowledge on how application of organic material alters soil microbial populations and functionality, shotgun metagenomic sequencing was used to determine the microbial communities and their potential functionality in an arable soil amended with young maize plants (Zea mays L.) in a laboratory experiment after 3 days. The relative abundance of bacterial and viral groups was strongly affected by organic material application, whereas that of the archaeal, protist and fungal groups was less affected. Cellulose degraders with copiotrophic lifestyle (e.g., Betaproteobacteria) were enriched in the amended soil, whereas the groups with slow growing oligotrophic and chemolithoautotrophic metabolism within Bacteria and Archaea were greater in the unamended than in the amended soil. The soil viral structure and richness were also affected. Caudovirales was the dominant viral family, with members of Siphoviridae enriched in the amended soil and members of Myoviridae in the unamended soil. More specialized metabolic traits related to both the degradation of complex C compounds and denitrification related genes were enriched in the young maize plant amended soil than in the unamended soil, whereas nitrification related genes were enriched in the latter. Copiotrophic life-style bacterial groups were enriched in the amended soil, whereas oligotrophic life-style bacterial groups in the unamended soil. Many bacterial and viral phylotypes were affected by the application of young maize plants, but the number of soil fungi, archaea and protists affected was smaller. Metabolic functionality was affected by the application of organic material as the relative abundance of genes involved in the denitrification process was higher in the maize plant amended soil than in the unamended soil and those involved in the nitrification process was higher in the unamended soil.
Collapse
Affiliation(s)
| | | | - Selene Gómez-Acata
- Laboratory of Soil Ecology, ABACUS, CINVESTAV, 07360, Mexico City, Mexico
| | | | - Nele Verhulst
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, Mexico
| | | | | | - Marco L Luna-Guido
- Laboratory of Soil Ecology, ABACUS, CINVESTAV, 07360, Mexico City, Mexico
| | - Luc Dendooven
- Laboratory of Soil Ecology, ABACUS, CINVESTAV, 07360, Mexico City, Mexico.
| |
Collapse
|
29
|
Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China. Nat Commun 2022; 13:2389. [PMID: 35501347 PMCID: PMC9061769 DOI: 10.1038/s41467-022-30049-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 04/14/2022] [Indexed: 11/09/2022] Open
Abstract
Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses in natural settings. Yet, our knowledge of viral biogeographic patterns and the corresponding drivers is still limited. Here, we perform metagenomic deep sequencing on 90 acid mine drainage (AMD) sediments sampled across Southern China and examine the biogeography of viruses in this extreme environment. The results demonstrate that prokaryotic communities dictate viral taxonomic and functional diversity, abundance and structure, whereas other factors especially latitude and mean annual temperature also impact viral populations and functions. In silico predictions highlight lineage-specific virus-host abundance ratios and richness-dependent virus-host interaction structure. Further functional analyses reveal important roles of environmental conditions and horizontal gene transfers in shaping viral auxiliary metabolic genes potentially involved in phosphorus assimilation. Our findings underscore the importance of both abiotic and biotic factors in predicting the taxonomic and functional biogeographic dynamics of viruses in the AMD sediments. The biogeography of viral communities in extreme environments remains understudied. Here, the authors use metagenomic sequencing on 90 acid mine drainage sediments sampled across Southern China, showing the predominant effects of prokaryotic communities and the influence of environmental variables on viral taxonomy and function.
Collapse
|
30
|
Zheng X, Jahn MT, Sun M, Friman VP, Balcazar JL, Wang J, Shi Y, Gong X, Hu F, Zhu YG. Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes. THE ISME JOURNAL 2022; 16:1397-1408. [PMID: 35039616 PMCID: PMC9038774 DOI: 10.1038/s41396-022-01188-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 12/29/2021] [Accepted: 01/06/2022] [Indexed: 12/13/2022]
Abstract
Viruses significantly influence local and global biogeochemical cycles and help bacteria to survive in different environments by encoding various auxiliary metabolic genes (AMGs) associated with energy acquisition, stress tolerance and degradation of xenobiotics. Here we studied whether bacterial (dsDNA) virus encoded AMGs are enriched in organochlorine pesticide (OCP) contaminated soil in China and if viral AMGs include genes linked to OCP biodegradation. Using metagenomics, we found that OCP-contaminated soils displayed a lower bacterial, but higher diversity of viruses that harbored a higher relative abundance of AMGs linked to pesticide degradation and metabolism. Furthermore, the diversity and relative abundance of AMGs significantly increased along with the severity of pesticide contamination, and several biodegradation genes were identified bioinformatically in viral metagenomes. Functional assays were conducted to experimentally demonstrate that virus-encoded L-2-haloacid dehalogenase gene (L-DEX) is responsible for the degradation of L-2-haloacid pesticide precursors, improving bacterial growth at sub-inhibitory pesticide concentrations. Taken together, these results demonstrate that virus-encoded AMGs are linked to bacterial metabolism and biodegradation, being more abundant and diverse in soils contaminated with pesticides. Moreover, our findings highlight the importance of virus-encoded accessory genes for bacterial ecology in stressful environments, providing a novel avenue for using viruses in the bioremediation of contaminated soils.
Collapse
Affiliation(s)
- Xiaoxuan Zheng
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Martin T Jahn
- Departments of Biochemistry, Zoology and Chemistry, University of Oxford, Oxford, OX1 3SZ, United Kingdom
| | - Mingming Sun
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
- Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing, 210095, China.
| | - Ville-Petri Friman
- University of York, Department of Biology, Wentworth Way, York, Y010 5DD, United Kingdom.
| | - Jose Luis Balcazar
- Catalan Institute for Water Research (ICRA), Girona, 17003, Spain
- University of Girona, Girona, 17004, Spain
| | - Jinfeng Wang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008, China
| | - Xin Gong
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Hu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yong-Guan Zhu
- Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian, 100085, Beijing, China
| |
Collapse
|
31
|
Cao MM, Liu SY, Bi L, Chen SJ, Wu HY, Ge Y, Han B, Zhang LM, He JZ, Han LL. Distribution Characteristics of Soil Viruses Under Different Precipitation Gradients on the Qinghai-Tibet Plateau. Front Microbiol 2022; 13:848305. [PMID: 35464951 PMCID: PMC9022101 DOI: 10.3389/fmicb.2022.848305] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Viruses are extremely abundant in the soil environment and have potential roles in impacting on microbial population, evolution, and nutrient biogeochemical cycles. However, how environment and climate changes affect soil viruses is still poorly understood. Here, a metagenomic approach was used to investigate the distribution, diversity, and potential biogeochemical impacts of DNA viruses in 12 grassland soils under three precipitation gradients on the Qinghai-Tibet Plateau, which is one of the most sensitive areas to climate change. A total of 557 viral operational taxonomic units were obtained, spanning 152 viral families from the 30 metagenomes. Both virus-like particles (VLPs) and microbial abundance increased with average annual precipitation. A significant positive correlation of VLP counts was observed with soil water content, total carbon, total nitrogen, soil organic matter, and total phosphorus. Among these biological and abiotic factors, SWC mainly contributed to the variability in VLP abundance. The order Caudovirales (70.1% of the identified viral order) was the predominant viral type in soils from the Qinghai-Tibet Plateau, with the Siphoviridae family being the most abundant. Remarkably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes represented by glycoside hydrolases were identified, indicating that soil viruses may play a potential role in the carbon cycle on the Qinghai-Tibet Plateau. There were more diverse hosts and abundant CAZyme genes in soil with moderate precipitation. Our study provides a strong evidence that changes in precipitation impact not only viral abundance and virus–host interactions in soil but also the viral functional potential, especially carbon cycling.
Collapse
Affiliation(s)
- Miao-Miao Cao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Si-Yi Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,The Zhongke-Ji'an Institute for Eco-Environmental Sciences, Ji'an, China
| | - Li Bi
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Shu-Jun Chen
- Information Technology Center, Tsinghua University, Beijing, China
| | - Hua-Yong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Bing Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ji-Zheng He
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.,Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
32
|
Hillary LS, Adriaenssens EM, Jones DL, McDonald JE. RNA-viromics reveals diverse communities of soil RNA viruses with the potential to affect grassland ecosystems across multiple trophic levels. ISME COMMUNICATIONS 2022; 2:34. [PMID: 36373138 PMCID: PMC8992426 DOI: 10.1038/s43705-022-00110-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 02/08/2023]
Abstract
The distribution and diversity of RNA viruses in soil ecosystems are largely unknown, despite their significant impact on public health, ecosystem functions, and food security. Here, we characterise soil RNA viral communities along an altitudinal productivity gradient of peat, managed grassland and coastal soils. We identified 3462 viral contigs in RNA viromes from purified virus-like-particles in five soil-types and assessed their spatial distribution, phylogenetic diversity and potential host ranges. Soil types exhibited minimal similarity in viral community composition, but with >10-fold more viral contigs shared between managed grassland soils when compared with peat or coastal soils. Phylogenetic analyses predicted soil RNA viral communities are formed from viruses of bacteria, plants, fungi, vertebrates and invertebrates, with only 12% of viral contigs belonging to the bacteria-infecting Leviviricetes class. 11% of viral contigs were found to be most closely related to members of the Ourmiavirus genus, suggesting that members of this clade of plant viruses may be far more widely distributed and diverse than previously thought. These results contrast with soil DNA viromes which are typically dominated by bacteriophages. RNA viral communities, therefore, have the potential to exert influence on inter-kingdom interactions across terrestrial biomes.
Collapse
Affiliation(s)
- Luke S. Hillary
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW UK
| | | | - David L. Jones
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW UK
- SoilsWest, Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, Murdoch, WA 6105 Australia
| | - James E. McDonald
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW UK
| |
Collapse
|
33
|
Wang Y, Liu Y, Wu Y, Wu N, Liu W, Wang X. Heterogeneity of soil bacterial and bacteriophage communities in three rice agroecosystems and potential impacts of bacteriophage on nutrient cycling. ENVIRONMENTAL MICROBIOME 2022; 17:17. [PMID: 35387674 PMCID: PMC8985318 DOI: 10.1186/s40793-022-00410-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND As genetic entities infecting and replicating only in bacteria, bacteriophages can regulate the community structure and functions of their host bacteria. The ecological roles of bacteriophages in aquatic and forest environments have been widely explored, but those in agroecosystems remains limited. Here, we used metagenomic sequencing to analyze the diversity and interactions of bacteriophages and their host bacteria in soils from three typical rice agroecosystems in China: double cropping in Guangzhou, southern China, rice-wheat rotation cropping in Nanjing, eastern China and early maturing single cropping in Jiamusi, northeastern China. Enterobacter phage-NJ was isolated and its functions on soil nitrogen cycling and effect on soil bacterial community structure were verified in pot inoculation experiments and 16S rRNA gene sequencing. RESULTS Soil bacterial and viral diversity and predicted functions varied among the three agroecosystems. Genes detected in communities from the three agroecosystems were associated with typical functions: soil bacteria in Jiamusi were significantly enriched in genes related to carbohydrate metabolism, in Nanjing with xenobiotics biodegradation and metabolism, and in Guangzhou with virulence factors and scarce in secondary metabolite biosynthesis, which might lead to a significant occurrence of rice bacterial diseases. The virus community structure varies significantly among the three ecosystems, only 13.39% of the total viral species were shared by the three rice agroecosystems, 59.56% of the viral species were specific to one agroecosystem. Notably, over-represented auxiliary carbohydrate-active enzyme (CAZyme) genes were identified in the viruses, which might assist host bacteria in metabolizing carbon, and 67.43% of these genes were present in Jiamusi. In bacteriophage isolation and inoculation experiments, Enterobacter bacteriophage-NJ reduced the nitrogen fixation capacity of soil by lysing N-fixing host bacteria and changed the soil bacterial diversity and community structure. CONCLUSION Our results showed that diversity and function predicted of paddy soil bacteria and viruses varied in the three agroecosystems. Soil bacteriophages can affect nutrient cycling by boosting host metabolism through the carried auxiliary metabolic genes (AMGs) and lysing the host bacteria that are involved in biogeochemical cycles. These findings form a basis for better understanding bacterial and bacteriophage diversity in different rice agroecosystems, laying a solid foundation for further studies of soil microbial communities that support ecofriendly production of healthy rice.
Collapse
Affiliation(s)
- Yajiao Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Baoding, 071000, China
| | - Yu Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yuxing Wu
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Baoding, 071000, China
| | - Nan Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wenwen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| |
Collapse
|
34
|
Nair A, Ghugare GS, Khairnar K. An Appraisal of Bacteriophage Isolation Techniques from Environment. MICROBIAL ECOLOGY 2022; 83:519-535. [PMID: 34136953 DOI: 10.1007/s00248-021-01782-z] [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: 01/18/2021] [Accepted: 05/23/2021] [Indexed: 06/12/2023]
Abstract
Researchers have recently renewed interest in bacteriophages. Being valuable models for the study of eukaryotic viruses, and more importantly, natural killers of bacteria, bacteriophages are being tapped for their potential role in multiple applications. Bacteriophages are also being increasingly sought for bacteriophage therapy due to rising antimicrobial resistance among pathogens. Reports show that there is an increasing trend in therapeutic application of natural bacteriophages, genetically engineered bacteriophages, and bacteriophage-encoded products as antimicrobial agents. In view of these applications, the isolation and characterization of bacteriophages from the environment has caught attention. In this review, various methods for isolation of bacteriophages from environmental sources like water, soil, and air are comprehensively described. The review also draws attention towards a handful on-field bacteriophage isolation techniques and the need for their further rapid development.
Collapse
Affiliation(s)
- Aparna Nair
- Environmental Virology Cell, Council of Scientific and Industrial Research-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Gaurav S Ghugare
- Environmental Virology Cell, Council of Scientific and Industrial Research-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Krishna Khairnar
- Environmental Virology Cell, Council of Scientific and Industrial Research-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| |
Collapse
|
35
|
Bi L, Yu DT, Han LL, Du S, Yuan CY, He JZ, Hu HW. Unravelling the ecological complexity of soil viromes: Challenges and opportunities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 812:152217. [PMID: 34890674 DOI: 10.1016/j.scitotenv.2021.152217] [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: 11/02/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 06/13/2023]
Abstract
Viruses are extremely abundant and ubiquitous in soil, and significantly contribute to various terrestrial ecosystem processes such as biogeochemical nutrient cycling, microbiome regulation and community assembly, and host evolutionary dynamics. Despite their numerous dominance and functional importance, understanding soil viral ecology is a formidable challenge, because of the technological challenges to characterize the abundance, diversity and community compositions of viruses, and their interactions with other organisms in the complex soil environment. Viruses may engage in a myriad of biological interactions within soil food webs across a broad range of spatiotemporal scales and are exposed to various biotic and abiotic disturbances. Current studies on the soil viromes, however, often describe the complexity of their tremendous diversity, but lack of exploring their potential ecological roles. In this article, we summarized the major methods to decipher the ecology of soil viruses, discussed biotic and abiotic factors and global change factors that shape the diversity and composition of soil viromes, and the ecological roles of soil viruses. We also proposed a new framework to understand the ecological complexity of viruses from micro to macro ecosystem scales and to predict and unravel their activities in terrestrial ecosystems.
Collapse
Affiliation(s)
- Li Bi
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Dan-Ting Yu
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, Fujian Normal University, Fujian 350007, China; School of Geographical Sciences, Fujian Normal University, Fujian 350007, China.
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shuai Du
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng-Yu Yuan
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, Fujian Normal University, Fujian 350007, China; School of Geographical Sciences, Fujian Normal University, Fujian 350007, China
| | - Ji-Zheng He
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| |
Collapse
|
36
|
Han LL, Yu DT, Bi L, Du S, Silveira C, Cobián Güemes AG, Zhang LM, He JZ, Rohwer F. Distribution of soil viruses across China and their potential role in phosphorous metabolism. ENVIRONMENTAL MICROBIOME 2022; 17:6. [PMID: 35130971 PMCID: PMC8822697 DOI: 10.1186/s40793-022-00401-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Viruses are the most abundant biological entities on the planet and drive biogeochemical cycling on a global scale. Our understanding of biogeography of soil viruses and their ecological functions lags significantly behind that of Bacteria and Fungi. Here, a viromic approach was used to investigate the distribution and ecological functions of viruses from 19 soils across China. RESULTS Soil viral community were clustered more significantly by geographical location than type of soil (agricultural and natural). Three clusters of viral communities were identified from North, Southeast and Southwest regions; these clusters differentiated using taxonomic composition and were mainly driven by geographic location and climate factors. A total of 972 viral populations (vOTUs) were detected spanning 23 viral families from the 19 viromes. Phylogenetic analyses of the phoH gene showed a remarkable diversity and the distribution of viral phoH genes was more dependent on the environment. Notably, five proteins involved in phosphorus (P) metabolism-related nucleotide synthesis functions, including dUTPase, MazG, PhoH, Thymidylate synthase complementing protein (Thy1), and Ribonucleoside reductase (RNR), were mainly identified in agricultural soils. CONCLUSIONS The present work revealed that soil viral communities were distributed across China according to geographical location and climate factors. In addition, P metabolism genes encoded by these viruses probably drive the synthesis of nucleotides for their own genomes inside bacterial hosts, thereby affecting P cycling in the soil ecosystems.
Collapse
Affiliation(s)
- Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA.
| | - Dan-Ting Yu
- Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, Fujian, China.
| | - Li Bi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuai Du
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cynthia Silveira
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
- Viral Information Institute at San Diego State University, San Diego, CA, 92182, USA
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Ana Georgina Cobián Güemes
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
- Viral Information Institute at San Diego State University, San Diego, CA, 92182, USA
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ji-Zheng He
- Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, Fujian, China
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
- Viral Information Institute at San Diego State University, San Diego, CA, 92182, USA
| |
Collapse
|
37
|
Gu C, Liang Y, Li J, Shao H, Jiang Y, Zhou X, Gao C, Li X, Zhang W, Guo C, He H, Wang H, Sung YY, Mok WJ, Wong LL, Suttle CA, McMinn A, Tian J, Wang M. Saline lakes on the Qinghai-Tibet Plateau harbor unique viral assemblages mediating microbial environmental adaption. iScience 2021; 24:103439. [PMID: 34988389 PMCID: PMC8710556 DOI: 10.1016/j.isci.2021.103439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/10/2021] [Accepted: 11/10/2021] [Indexed: 12/21/2022] Open
Abstract
The highest plateau on Earth, Qinghai-Tibet Plateau, contains thousands of lakes with broad salinity and diverse and unique microbial communities. However, little is known about their co-occurring viruses. Herein, we identify 4,560 viral Operational Taxonomic Units (vOTUs) from six viromes of three saline lakes on Qinghai-Tibet Plateau, with less than 1% that could be classified. Most of the predicted vOTUs were associated with the dominant bacterial and archaeal phyla. Virus-encoded auxiliary metabolic genes suggest that viruses influence microbial metabolisms of carbon, nitrogen, sulfur, and lipid; the antibiotic resistance mediation; and their salinity adaption. The six viromes clustered together with the ice core viromes and bathypelagic ocean viromes and might represent a new viral habitat. This study has revealed the unique characteristics and potential ecological roles of DNA viromes in the lakes of the highest plateau and established a foundation for the recognition of the viral roles in plateau lake ecosystems.
Collapse
Affiliation(s)
- Chengxiang Gu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Jiansen Li
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China
- Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Yong Jiang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Xinhao Zhou
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Chen Gao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Xianrong Li
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Wenjing Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Cui Guo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Hui He
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Hualong Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Yeong Yik Sung
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), 21030 Kuala Nerus, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), 21030 Kuala Nerus, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), 21030 Kuala Nerus, Malaysia
| | - Curtis A. Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Microbiology and Immunology, and Botany and Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7001, Australia
| | - Jiwei Tian
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
- The affiliated hospital of Qingdao University, Qingdao 266000, China
| |
Collapse
|
38
|
Nwokolo NL, Enebe MC. Shotgun metagenomics evaluation of soil fertilization effect on the rhizosphere viral community of maize plants. Antonie van Leeuwenhoek 2021; 115:69-78. [PMID: 34762236 DOI: 10.1007/s10482-021-01679-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 10/19/2021] [Indexed: 11/30/2022]
Abstract
The need for sustainability in food supply has led to progressive increase in soil nutrient enrichment. Fertilizer application effects both biological and abiotic processes in the soil, of which the bacterial community that support viral multiplication are equally influenced. Nevertheless, little is known on the effect of soil fertilization on the Soil viral community composition and dynamics. In this study, we evaluated the influence of soil fertilization on the maize rhizosphere viral community growing in Luvisolic soil. The highest abundance of bacteriophages were detected in soil treated with 8 tons/ha compost manure (Cp8), 60 kg/ha inorganic fertilizer (N1), 4 tons/ha compost manure (Cp4) and the unfertilized control (Cn0). Our result showed higher relative abundance of Myoviridae, Podoviridae and Siphoviridae in 8 tons/ha organic manure (Cp8) fertilized compared to others. While Inoviridae and Microviridae were the most relative abundant phage families in 4 tons/ha organic manure (Cp4) fertilized soil. This demonstrate that soil fertilization with organic manure increases the abundance and diversity of viruses in the soil due to its soil conditioning effects.
Collapse
Affiliation(s)
| | - Matthew Chekwube Enebe
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
| |
Collapse
|
39
|
Ortiz M, Leung PM, Shelley G, Jirapanjawat T, Nauer PA, Van Goethem MW, Bay SK, Islam ZF, Jordaan K, Vikram S, Chown SL, Hogg ID, Makhalanyane TP, Grinter R, Cowan DA, Greening C. Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils. Proc Natl Acad Sci U S A 2021; 118:e2025322118. [PMID: 34732568 PMCID: PMC8609440 DOI: 10.1073/pnas.2025322118] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2021] [Indexed: 12/11/2022] Open
Abstract
Numerous diverse microorganisms reside in the cold desert soils of continental Antarctica, though we lack a holistic understanding of the metabolic processes that sustain them. Here, we profile the composition, capabilities, and activities of the microbial communities in 16 physicochemically diverse mountainous and glacial soils. We assembled 451 metagenome-assembled genomes from 18 microbial phyla and inferred through Bayesian divergence analysis that the dominant lineages present are likely native to Antarctica. In support of earlier findings, metagenomic analysis revealed that the most abundant and prevalent microorganisms are metabolically versatile aerobes that use atmospheric hydrogen to support aerobic respiration and sometimes carbon fixation. Surprisingly, however, hydrogen oxidation in this region was catalyzed primarily by a phylogenetically and structurally distinct enzyme, the group 1l [NiFe]-hydrogenase, encoded by nine bacterial phyla. Through gas chromatography, we provide evidence that both Antarctic soil communities and an axenic Bacteroidota isolate (Hymenobacter roseosalivarius) oxidize atmospheric hydrogen using this enzyme. Based on ex situ rates at environmentally representative temperatures, hydrogen oxidation is theoretically sufficient for soil communities to meet energy requirements and, through metabolic water production, sustain hydration. Diverse carbon monoxide oxidizers and abundant methanotrophs were also active in the soils. We also recovered genomes of microorganisms capable of oxidizing edaphic inorganic nitrogen, sulfur, and iron compounds and harvesting solar energy via microbial rhodopsins and conventional photosystems. Obligately symbiotic bacteria, including Patescibacteria, Chlamydiae, and predatory Bdellovibrionota, were also present. We conclude that microbial diversity in Antarctic soils reflects the coexistence of metabolically flexible mixotrophs with metabolically constrained specialists.
Collapse
Affiliation(s)
- Maximiliano Ortiz
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - Pok Man Leung
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia;
| | - Guy Shelley
- School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
| | - Thanavit Jirapanjawat
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia
| | - Philipp A Nauer
- School of Chemistry, Monash University, Clayton VIC 3800, Australia
| | - Marc W Van Goethem
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Sean K Bay
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia
- School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
| | - Zahra F Islam
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia
- School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
| | - Karen Jordaan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - Steven L Chown
- Securing Antarctica's Environmental Future, School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
| | - Ian D Hogg
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- School of Science, University of Waikato, Hamilton 3240, New Zealand
- Polar Knowledge Canada, Canadian High Arctic Research Station, Cambridge Bay NU X0B 0C0, Canada
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - Rhys Grinter
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa;
| | - Chris Greening
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia;
- School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
| |
Collapse
|
40
|
Merges D, Dal Grande F, Greve C, Otte J, Schmitt I. Virus diversity in metagenomes of a lichen symbiosis (Umbilicaria phaea): complete viral genomes, putative hosts and elevational distributions. Environ Microbiol 2021; 23:6637-6650. [PMID: 34697892 DOI: 10.1111/1462-2920.15802] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 10/01/2021] [Indexed: 11/28/2022]
Abstract
Viruses can play critical roles in symbioses by initiating horizontal gene transfer, affecting host phenotypes, or expanding their host's ecological niche. However, knowledge of viral diversity and distribution in symbiotic organisms remains elusive. Here we use deep-sequenced metagenomic DNA (PacBio Sequel II; two individuals), paired with a population genomics approach (Pool-seq; 11 populations, 550 individuals) to understand viral distributions in the lichen Umbilicaria phaea. We assess (i) viral diversity in lichen thalli, (ii) putative viral hosts (fungi, algae, bacteria) and (iii) viral distributions along two replicated elevation gradients. We identified five novel viruses, showing 28%-40% amino acid identity to known viruses. They tentatively belong to the families Caulimoviridae, Myoviridae, Podoviridae and Siphoviridae. Our analysis suggests that the Caulimovirus is associated with green algal photobionts (Trebouxia) of the lichen, and the remaining viruses with bacterial hosts. We did not detect viral sequences in the mycobiont. Caulimovirus abundance decreased with increasing elevation, a pattern reflected by a specific algal lineage hosting this virus. Bacteriophages showed population-specific patterns. Our work provides the first comprehensive insights into viruses associated with a lichen holobiont and suggests an interplay of viral hosts and environment in structuring viral distributions.
Collapse
Affiliation(s)
- Dominik Merges
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany.,Department of Biological Sciences, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| |
Collapse
|
41
|
Chen ML, An XL, Liao H, Yang K, Su JQ, Zhu YG. Viral Community and Virus-Associated Antibiotic Resistance Genes in Soils Amended with Organic Fertilizers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:13881-13890. [PMID: 34596377 DOI: 10.1021/acs.est.1c03847] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Antibiotic resistance is a global health concern. Long-term organic fertilization can influence the antibiotic resistome of agricultural soils, posing potential risks to human health. However, little is known about the contribution of viruses to the dissemination of antibiotic resistance genes (ARGs) in this context. Here, we profiled the viral communities and virus-associated ARGs in a long-term (over 10 years) organic fertilized field by viral metagenomic analysis. A total of 61,520 viral populations (viral operational taxonomic units, vOTUs) were retrieved, of which 21,308 were assigned at the family level. The viral community structures were significantly correlated with the bacterial community structures (P < 0.001) and the dosage of applied sewage sludge (r2 = 0.782). A total of 16 unique ARGs were detected in soil viromes, and the number of virus-associated ARG subtypes was higher in sewage sludge treatments (except for 1 SS) than others. The network analysis showed that the application of the organic fertilizer increased the bacteria-virus interactions, suggesting that the chances of ARG exchange between viruses and their hosts may increase. Overall, our results provide a novel understanding about virus-associated ARGs and factors affecting the profile of viral community in fertilized soil.
Collapse
Affiliation(s)
- Mo-Lian Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xin-Li An
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hu Liao
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Kai Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| |
Collapse
|
42
|
Trubl G, Kimbrel JA, Liquet-Gonzalez J, Nuccio EE, Weber PK, Pett-Ridge J, Jansson JK, Waldrop MP, Blazewicz SJ. Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. MICROBIOME 2021; 9:208. [PMID: 34663463 PMCID: PMC8522061 DOI: 10.1186/s40168-021-01154-2] [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: 04/01/2021] [Accepted: 08/19/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures). RESULTS We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H218O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO2) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up 18O in soil and respired CO2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients. CONCLUSIONS Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks. Video abstract.
Collapse
Affiliation(s)
- Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Jeffrey A Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jose Liquet-Gonzalez
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Erin E Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Life and Environmental Sciences, University of California, Merced, CA, 95343, USA
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mark P Waldrop
- U.S. Geological Survey, Geology, Minerals, Energy, and Geophysics Science Center, Menlo Park, CA, USA
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| |
Collapse
|
43
|
Li X, Yang J, Fan Y, Xie M, Qian X, Li H. Rapid monitoring of heavy metal pollution in lake water using nitrogen and phosphorus nutrients and physicochemical indicators by support vector machine. CHEMOSPHERE 2021; 280:130599. [PMID: 33940448 DOI: 10.1016/j.chemosphere.2021.130599] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/26/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
A novel method of predicting heavy metal concentration in lake water by support vector machine (SVM) model was developed, combined with low-cost, easy to obtain nutrients and physicochemical indicators as input variables. 115 surface water samples were collected from 23 sites in Chaohu Lake, China, during different hydrological periods. The particulate concentrations of heavy metals in water were much higher than the dissolved concentrations. According to Nemerow pollution index (Pi), pollution degrees by Fe, V, Mn and As ranged from heavy (2 ≤ Pi < 4) to serious (Pi ≥ 4). The concentrations of most heavy metals were the highest during the medium-water period and the lowest during the dry season. Non-metric Multidimensional Scaling Analysis confirmed heavy metal concentrations had slight spatial difference but relatively large seasonal variation. Redundancy Analysis indicated the close associations of heavy metals with nutrient and physicochemical indicators. When both nutrient and physicochemical indicators were used as input variables, the simulation effects for most elements in total and particulate were relatively better than those obtained using only nutrient or only physicochemical indicators. The simulation effects for As, Ba, Fe, Ti, V and Zn were generally good, based on their training R values of 0.847, 0.828, 0.856, 0.867, 0.817 and 0.893, respectively, as well as their test R values of 0.811, 0.836, 0.843, 0.873, 0.829 and 0.826, respectively; and meanwhile, in both the training and test stages, these metals also had relatively lower errors. The spatial distribution of heavy metals in Chaohu Lake was then predicted using the fully trained SVM models.
Collapse
Affiliation(s)
- Xiaolong Li
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China; School of Earth and Environment, Anhui University of Science and Technology, Huainan, 232001, PR China
| | - Jinxiang Yang
- School of Earth and Environment, Anhui University of Science and Technology, Huainan, 232001, PR China
| | - Yifan Fan
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Mengxing Xie
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Xin Qian
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China.
| | - Huiming Li
- School of Environment, Nanjing Normal University, Nanjing, 210023, PR China.
| |
Collapse
|
44
|
Li X, Yang B, Yang J, Fan Y, Qian X, Li H. Magnetic properties and its application in the prediction of potentially toxic elements in aquatic products by machine learning. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 783:147083. [PMID: 34088131 DOI: 10.1016/j.scitotenv.2021.147083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/04/2021] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
Magnetic measurement was provided to substitute for time-consuming conventional methods for determination of potentially toxic elements. Both the concentrations of 12 elements and 9 magnetic parameters were determined in 700 muscle tissue samples from the snail Bellamya aeruginosa, shrimp species Exopalaemon modestus and Macrobrachium nipponense, and fish species Hemisalanx prognathous Regan, Coilia ectenes taihuensis, and Culer alburnus Basilewsky collected from Chaohu Lake during different hydrological periods. Spherical and irregular iron oxide particles were observed in the muscle tissues of the studied aquatic products. A field survey of the exposure parameters in humans, such as per capita intake dose of local aquatic products, found no evidence that consumption of the tested species poses a potential health risk. Redundancy analysis revealed different degrees of correlation between the magnetic parameters and concentrations of elements in aquatic products. Back-propagation artificial neural network (BP-ANN) and support vector machine (SVM) models were applied to predict elemental concentrations in aquatic products, using magnetic parameters as input. SVM models performed well in predicting the presence of Cr and Ni, with R and index of agreement values of >0.8 in both training and validation stages as well as relatively low errors. The BP-ANN and SVM models both performed relatively poorly in predicting the presence of Cd and Zn in aquatic products, with R values between 0.333 and 0.718 for Cd and between 0.454 and 0.664 for Zn in training and validation stages. For most of the elements, a better R value was obtained with the SVM than with BP-ANN model. The R of Co, Cr, Cu, Ni, and Ti in the training and validation stages of snail in the SVM model were >0.8. This study is a first step in developing a novel approach allowing the rapid monitoring of potentially toxic elements concentrations in aquatic products.
Collapse
Affiliation(s)
- Xiaolong Li
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China; School of Earth and Environment, Anhui University of Science and Technology, Huainan 232001, PR China
| | - Biying Yang
- School of Earth and Environment, Anhui University of Science and Technology, Huainan 232001, PR China
| | - Jinxiang Yang
- School of Earth and Environment, Anhui University of Science and Technology, Huainan 232001, PR China
| | - Yifan Fan
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Xin Qian
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China.
| | - Huiming Li
- School of Environment, Nanjing Normal University, Nanjing 210023, PR China.
| |
Collapse
|
45
|
Li X, Yang Y, Yang J, Fan Y, Qian X, Li H. Rapid diagnosis of heavy metal pollution in lake sediments based on environmental magnetism and machine learning. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:126163. [PMID: 34492941 DOI: 10.1016/j.jhazmat.2021.126163] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 05/10/2021] [Accepted: 05/16/2021] [Indexed: 06/13/2023]
Abstract
Environmental magnetism in combination with machine learning can be used to monitor heavy metal pollution in sediments. Magnetic parameters and heavy metal concentrations of sediments from Chaohu Lake (China) were analyzed. The magnetic measurements, high- and low-temperature curves, and hysteresis loops showed the primary magnetic minerals were ferrimagnetic minerals in sediments. For most metals, their concentrations were highest during the wet season and lowest during the medium-water period. Cd, Hg, and Zn were moderately enriched and Cd and Hg posed a considerable ecological risk. A redundancy analysis indicated a relationship between physicochemical indexes and magnetic parameters and heavy metal concentrations. An artificial neural network (ANN) and support vector machine (SVM) were used to construct six models to predict the heavy metal concentrations and ecological risk index. The inclusion of both the physicochemical indexes and magnetic parameters as input factors in the models were significantly ameliorated the simulation accuracy for the majority of heavy metals. The training and test R, for Be, Fe, Pb, Zn, As, Cu, and Cr were > 0.8. The SVM showed better performance and hence it has potential for the efficient and economical long-term tracking and monitoring of heavy metal pollution in lake sediments.
Collapse
Affiliation(s)
- Xiaolong Li
- School of Earth and Environment, Anhui University of Science and Technology, Huainan 232001, PR China; State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Yang Yang
- School of Earth and Environment, Anhui University of Science and Technology, Huainan 232001, PR China
| | - Jinxiang Yang
- School of Earth and Environment, Anhui University of Science and Technology, Huainan 232001, PR China
| | - Yifan Fan
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Xin Qian
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China.
| | - Huiming Li
- School of Environment, Nanjing Normal University, Nanjing 210023, PR China.
| |
Collapse
|
46
|
Huang D, Yu P, Ye M, Schwarz C, Jiang X, Alvarez PJJ. Enhanced mutualistic symbiosis between soil phages and bacteria with elevated chromium-induced environmental stress. MICROBIOME 2021; 9:150. [PMID: 34183048 PMCID: PMC8240259 DOI: 10.1186/s40168-021-01074-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/07/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND Microbe-virus interactions have broad implications on the composition, function, and evolution of microbiomes. Elucidating the effects of environmental stresses on these interactions is critical to identify the ecological function of viral communities and understand microbiome environmental adaptation. Heavy metal-contaminated soils represent a relevant ecosystem to study the interplay between microbes, viruses, and environmental stressors. RESULTS Metagenomic analysis revealed that Cr pollution adversely altered the abundance, diversity, and composition of viral and bacterial communities. Host-phage linkage based on CRISPR indicated that, in soils with high Cr contamination, the abundance of phages associated with heavy metal-tolerant hosts increased, as did the relative abundance of phages with broad host ranges (identified as host-phage linkages across genera), which would facilitate transfection and broader distribution of heavy metal resistance genes in the bacterial community. Examining variations along the pollutant gradient, enhanced mutualistic phage-bacterium interactions were observed in the face of greater environmental stresses. Specifically, the fractions of lysogens in bacterial communities (identified by integrase genes within bacterial genomes and prophage induction assay by mitomycin-C) were positively correlated with Cr contamination levels. Furthermore, viral genomic analysis demonstrated that lysogenic phages under higher Cr-induced stresses carried more auxiliary metabolic genes regulating microbial heavy metal detoxification. CONCLUSION With the intensification of Cr-induced environmental stresses, the composition, replication strategy, and ecological function of the phage community all evolve alongside the bacterial community to adapt to extreme habitats. These result in a transformation of the phage-bacterium interaction from parasitism to mutualism in extreme environments and underscore the influential role of phages in bacterial adaptation to pollution-related stress and in related biogeochemical processes. Video Abstract.
Collapse
Affiliation(s)
- Dan Huang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Pingfeng Yu
- Department of Civil and Environmental Engineering, Rice University, Houston, 77005, USA.
| | - Mao Ye
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China.
| | - Cory Schwarz
- Department of Civil and Environmental Engineering, Rice University, Houston, 77005, USA
| | - Xin Jiang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, 77005, USA
| |
Collapse
|
47
|
Gil P, Dupuy V, Koual R, Exbrayat A, Loire E, Fall AG, Gimonneau G, Biteye B, Talla Seck M, Rakotoarivony I, Marie A, Frances B, Lambert G, Reveillaud J, Balenghien T, Garros C, Albina E, Eloit M, Gutierrez S. A library preparation optimized for metagenomics of RNA viruses. Mol Ecol Resour 2021; 21:1788-1807. [PMID: 33713395 DOI: 10.1111/1755-0998.13378] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 11/28/2022]
Abstract
Our understanding of the viral communities associated to animals has not yet reached the level attained on the bacteriome. This situation is due to, among others, technical challenges in adapting metagenomics using high-throughput sequencing to the study of RNA viromes in animals. Although important developments have been achieved in most steps of viral metagenomics, there is yet a key step that has received little attention: the library preparation. This situation differs from bacteriome studies in which developments in library preparation have largely contributed to the democratisation of metagenomics. Here, we present a library preparation optimized for metagenomics of RNA viruses from insect vectors of viral diseases. The library design allows a simple PCR-based preparation, such as those routinely used in bacterial metabarcoding, that is adapted to shotgun sequencing as required in viral metagenomics. We first optimized our library preparation using mock viral communities and then validated a full metagenomic approach incorporating our preparation in two pilot studies with field-caught insect vectors; one including a comparison with a published metagenomic protocol. Our approach provided a fold increase in virus-like sequences compared to other studies, and nearly-full genomes from new virus species. Moreover, our results suggested conserved trends in virome composition within a population of a mosquito species. Finally, the sensitivity of our approach was compared to a commercial diagnostic PCR for the detection of an arbovirus in field-caught insect vectors. Our approach could facilitate studies on viral communities from animals and the democratization of metagenomics in community ecology of viruses.
Collapse
Affiliation(s)
- Patricia Gil
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Virginie Dupuy
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Rachid Koual
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Antoni Exbrayat
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Etienne Loire
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Assane G Fall
- Laboratoire National de l'Elevage et de Recherches Vétérinaires, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar-Hann, Senegal
| | - Geoffrey Gimonneau
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France.,Laboratoire National de l'Elevage et de Recherches Vétérinaires, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar-Hann, Senegal
| | - Biram Biteye
- Laboratoire National de l'Elevage et de Recherches Vétérinaires, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar-Hann, Senegal
| | - Momar Talla Seck
- Laboratoire National de l'Elevage et de Recherches Vétérinaires, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar-Hann, Senegal
| | - Ignace Rakotoarivony
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | | | | | | | - Julie Reveillaud
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France
| | - Thomas Balenghien
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Claire Garros
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Emmanuel Albina
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France.,The OIE Collaborating Centre for Detection and Identification in Humans of Emerging Animal Pathogens, Institut Pasteur, Paris, France.,École nationale vétérinaire d'Alfort, Maisons-Alfort, France
| | - Serafin Gutierrez
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| |
Collapse
|
48
|
Labadie T, Batéjat C, Leclercq I, Manuguerra JC. Historical Discoveries on Viruses in the Environment and Their Impact on Public Health. Intervirology 2020; 63:17-32. [PMID: 33238280 DOI: 10.1159/000511575] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 09/14/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Transmission of many viruses occurs by direct transmission during a close contact between two hosts, or by an indirect transmission through the environment. Several and often interconnected factors, both abiotic and biotic, determine the persistence of these viruses released in the environment, which can last from a few seconds to several years. Moreover, viruses in the environment are able to travel short to very long distances, especially in the air or in water. SUMMARY Although well described now, the role of these environments as intermediaries or as reservoirs in virus transmission has been extensively studied and debated in the last century. The majority of these discoveries, such as the pioneer work on bacteria transmission, the progressive discoveries of viruses, as well as the persistence of the influenza virus in the air varying along with droplet sizes, or the role of water in the transmission of poliovirus, have contributed to the improvement of public health. Recent outbreaks of human coronavirus, influenza virus, and Ebola virus have also demonstrated the contemporaneity of these research studies and the need to study virus persistence in the environment. Key Messages: In this review, we discuss historical discoveries that contributed to describe biotic and abiotic factors determining viral persistence in the environment.
Collapse
Affiliation(s)
- Thomas Labadie
- Unité Environnement et Risques Infectieux, Institut Pasteur, Cellule d'Intervention Biologique d'Urgence (CIBU), Paris, France.,Centre de Biochimie Structurale (CBS), UMR 5048, University of Montpellier, CNRS, Montpellier, France
| | - Christophe Batéjat
- Unité Environnement et Risques Infectieux, Institut Pasteur, Cellule d'Intervention Biologique d'Urgence (CIBU), Paris, France
| | - India Leclercq
- Unité Environnement et Risques Infectieux, Institut Pasteur, Cellule d'Intervention Biologique d'Urgence (CIBU), Paris, France, .,Université de Paris, Cellule Pasteur, Paris, France,
| | - Jean-Claude Manuguerra
- Unité Environnement et Risques Infectieux, Institut Pasteur, Cellule d'Intervention Biologique d'Urgence (CIBU), Paris, France
| |
Collapse
|
49
|
Ortiz M, Bosch J, Coclet C, Johnson J, Lebre P, Salawu-Rotimi A, Vikram S, Makhalanyane T, Cowan D. Microbial Nitrogen Cycling in Antarctic Soils. Microorganisms 2020; 8:E1442. [PMID: 32967081 PMCID: PMC7564152 DOI: 10.3390/microorganisms8091442] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 01/19/2023] Open
Abstract
The Antarctic continent is widely considered to be one of the most hostile biological habitats on Earth. Despite extreme environmental conditions, the ice-free areas of the continent, which constitute some 0.44% of the total continental land area, harbour substantial and diverse communities of macro-organisms and especially microorganisms, particularly in the more "hospitable" maritime regions. In the more extreme non-maritime regions, exemplified by the McMurdo Dry Valleys of South Victoria Land, nutrient cycling and ecosystem servicing processes in soils are largely driven by microbial communities. Nitrogen turnover is a cornerstone of ecosystem servicing. In Antarctic continental soils, specifically those lacking macrophytes, cold-active free-living diazotrophic microorganisms, particularly Cyanobacteria, are keystone taxa. The diazotrophs are complemented by heterotrophic bacterial and archaeal taxa which show the genetic capacity to perform elements of the entire N cycle, including nitrification processes such as the anammox reaction. Here, we review the current literature on nitrogen cycling genes, taxa, processes and rates from studies of Antarctic soils. In particular, we highlight the current gaps in our knowledge of the scale and contribution of these processes in south polar soils as critical data to underpin viable predictions of how such processes may alter under the impacts of future climate change.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Don Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa; (M.O.); (J.B.); (C.C.); (J.J.); (P.L.); (A.S.-R.); (S.V.); (T.M.)
| |
Collapse
|
50
|
Identification and Distribution of Novel Cressdnaviruses and Circular molecules in Four Penguin Species in South Georgia and the Antarctic Peninsula. Viruses 2020; 12:v12091029. [PMID: 32947826 PMCID: PMC7551938 DOI: 10.3390/v12091029] [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: 08/03/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/26/2022] Open
Abstract
There is growing interest in uncovering the viral diversity present in wild animal species. The remote Antarctic region is home to a wealth of uncovered microbial diversity, some of which is associated with its megafauna, including penguin species, the dominant avian biota. Penguins interface with a number of other biota in their roles as marine mesopredators and several species overlap in their ranges and habitats. To characterize the circular single-stranded viruses related to those in the phylum Cressdnaviricota from these environmental sentinel species, cloacal swabs (n = 95) were obtained from King Penguins in South Georgia, and congeneric Adélie Penguins, Chinstrap Penguins, and Gentoo Penguins across the South Shetland Islands and Antarctic Peninsula. Using a combination of high-throughput sequencing, abutting primers-based PCR recovery of circular genomic elements, cloning, and Sanger sequencing, we detected 97 novel sequences comprising 40 ssDNA viral genomes and 57 viral-like circular molecules from 45 individual penguins. We present their detection patterns, with Chinstrap Penguins harboring the highest number of new sequences. The novel Antarctic viruses identified appear to be host-specific, while one circular molecule was shared between sympatric Chinstrap and Gentoo Penguins. We also report viral genotype sharing between three adult-chick pairs, one in each Pygoscelid species. Sequence similarity network approaches coupled with Maximum likelihood phylogenies of the clusters indicate the 40 novel viral genomes do not fall within any known viral families and likely fall within the recently established phylum Cressdnaviricota based on their replication-associated protein sequences. Similarly, 83 capsid protein sequences encoded by the viruses or viral-like circular molecules identified in this study do not cluster with any of those encoded by classified viral groups. Further research is warranted to expand knowledge of the Antarctic virome and would help elucidate the importance of viral-like molecules in vertebrate host evolution.
Collapse
|