1
|
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
|
2
|
Warwick-Dugdale J, Tian F, Michelsen ML, Cronin DR, Moore K, Farbos A, Chittick L, Bell A, Zayed AA, Buchholz HH, Bolanos LM, Parsons RJ, Allen MJ, Sullivan MB, Temperton B. Long-read powered viral metagenomics in the oligotrophic Sargasso Sea. Nat Commun 2024; 15:4089. [PMID: 38744831 PMCID: PMC11094077 DOI: 10.1038/s41467-024-48300-6] [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: 03/30/2023] [Accepted: 04/24/2024] [Indexed: 05/16/2024] Open
Abstract
Dominant microorganisms of the Sargasso Sea are key drivers of the global carbon cycle. However, associated viruses that shape microbial community structure and function are not well characterised. Here, we combined short and long read sequencing to survey Sargasso Sea phage communities in virus- and cellular fractions at viral maximum (80 m) and mesopelagic (200 m) depths. We identified 2,301 Sargasso Sea phage populations from 186 genera. Over half of the phage populations identified here lacked representation in global ocean viral metagenomes, whilst 177 of the 186 identified genera lacked representation in genomic databases of phage isolates. Viral fraction and cell-associated viral communities were decoupled, indicating viral turnover occurred across periods longer than the sampling period of three days. Inclusion of long-read data was critical for capturing the breadth of viral diversity. Phage isolates that infect the dominant bacterial taxa Prochlorococcus and Pelagibacter, usually regarded as cosmopolitan and abundant, were poorly represented.
Collapse
Affiliation(s)
- Joanna Warwick-Dugdale
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK.
- Plymouth Marine Laboratory, Plymouth, Devon, PL1 3DH, UK.
| | - Funing Tian
- Center of Microbiome Science and Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | | | - Dylan R Cronin
- Center of Microbiome Science and Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH, 43210, USA
| | - Karen Moore
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
| | - Audrey Farbos
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
| | - Lauren Chittick
- Center of Microbiome Science and Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | - Ashley Bell
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
| | - Ahmed A Zayed
- Center of Microbiome Science and Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH, 43210, USA
| | - Holger H Buchholz
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA
| | - Luis M Bolanos
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
| | - Rachel J Parsons
- Bermuda Institute of Ocean Sciences, St.George's, GE, 01, Bermuda
- School of Ocean Futures, Arizona State University, Tempe, AZ, US
| | - Michael J Allen
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
| | - Matthew B Sullivan
- Center of Microbiome Science and Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH, 43210, USA
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH, 43210, USA
| | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK.
| |
Collapse
|
3
|
Zhou K, Zhou H. Distribution patterns and functional diversity of DNA viruses determined by ecological niches in huge river ecosystems. Virology 2024; 593:110015. [PMID: 38359578 DOI: 10.1016/j.virol.2024.110015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/13/2024] [Accepted: 02/07/2024] [Indexed: 02/17/2024]
Abstract
While the vast number of DNA and RNA viruses participate in biogeochemical cycles in natural systems, little is known about virome in river ecosystems. Here, we analyzed the DNA viral composition and its metabolic potential in the Yangtze River, including freshwater (FW) and freshwater sediments (FWS). A total of 1237 river-derived virus contigs (RVCs) were obtained following de novo assembly from 62 metagenomics. We found that the viral diversity is significantly positively correlated longitudinally. Moreover, FW exhibited a greater viral variety and significantly different composition than FWS. The viral co-occurrence network suggested that positive correlations predominate between RVCs. Lastly, 1657 viral functions were predicted by gene ontology. Notably, 96 of 150 RVCs with higher weights identified by random-forest classier were more abundant in FW, which most engage organic cyclic compound metabolic processes and hydrolase activity. Together, this study highlights the previously unrecognized viruses and the importance of their distributions and functions in major river systems.
Collapse
Affiliation(s)
- Kang Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Hui Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| |
Collapse
|
4
|
He T, Jin M, Cui P, Sun X, He X, Huang Y, Xiao X, Zhang T, Zhang X. Environmental viromes reveal the global distribution signatures of deep-sea DNA viruses. J Adv Res 2024; 57:107-117. [PMID: 37075861 PMCID: PMC10918349 DOI: 10.1016/j.jare.2023.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 04/11/2023] [Accepted: 04/11/2023] [Indexed: 04/21/2023] Open
Abstract
INTRODUCTION Viruses are abundant and ecologically significant in marine ecosystems. However, the virome of deep-sea sediments is not extensively investigated. OBJECTIVES To explore the distribution pattern of deep-sea viruses on a global scale, the viromes of DNA viruses isolated from 138 sediments of 5 deep-sea ecosystems were characterized. METHODS The viral particles were purified from each sediment sample. Then the viral DNAs were extracted and subjected to viral metagenomic analysis. RESULTS Here, we constructed a global deep-sea environmental virome dataset by analyzing the viral DNA of 138 sediment samples. A total of 347,737 viral operational taxonomic units (vOTUs) were identified, of which 84.94% were hitherto unknown, indicating that deep sea was a reservoir of novel DNA viruses. Furthermore, circular viral genome analysis revealed 98,581 complete genomes. The classified vOTUs included eukaryotic (44.55%) and prokaryotic (25.75%) viruses, and were taxonomically assigned to 63 viral families. The composition and abundance of the deep-sea sediment viromes were dependent on the deep-sea ecosystem as opposed to geographical region. Further analysis revealed that the viral community differentiation in different deep-sea ecosystems was driven by the virus-mediated energy metabolism. CONCLUSION Our findings showed that deep-sea ecosystems are a reservoir of novel DNA viruses and the viral community is shaped by the environmental characteristics of deep-sea ecosystems, thus presenting critical information for determining the ecological significance of viruses in global deep-sea ecosystems.
Collapse
Affiliation(s)
- Tianliang He
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Min Jin
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Pei Cui
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, China
| | - Xumei Sun
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, China
| | - Xuebao He
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Yaqin Huang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Xi Xiao
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou 510760, China
| | - Tingting Zhang
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou 510760, China
| | - Xiaobo Zhang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
5
|
Tastassa AC, Sharaby Y, Lang-Yona N. Aeromicrobiology: A global review of the cycling and relationships of bioaerosols with the atmosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168478. [PMID: 37967625 DOI: 10.1016/j.scitotenv.2023.168478] [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: 09/10/2023] [Revised: 10/31/2023] [Accepted: 11/08/2023] [Indexed: 11/17/2023]
Abstract
Airborne microorganisms and biological matter (bioaerosols) play a key role in global biogeochemical cycling, human and crop health trends, and climate patterns. Their presence in the atmosphere is controlled by three main stages: emission, transport, and deposition. Aerial survival rates of bioaerosols are increased through adaptations such as ultra-violet radiation and desiccation resistance or association with particulate matter. Current research into modern concerns such as climate change, global gene transfer, and pathogenicity often neglects to consider atmospheric involvement. This comprehensive review outlines the transpiring of bioaerosols across taxa in the atmosphere, with significant focus on their interactions with environmental elements including abiotic factors (e.g., atmospheric composition, water cycle, and pollution) and events (e.g., dust storms, hurricanes, and wildfires). The aim of this review is to increase understanding and shed light on needed research regarding the interplay between global atmospheric phenomena and the aeromicrobiome. The abundantly documented bacteria and fungi are discussed in context of their cycling and human health impacts. Gaps in knowledge regarding airborne viral community, the challenges and importance of studying their composition, concentrations and survival in the air are addressed, along with understudied plant pathogenic oomycetes, and archaea cycling. Key methodologies in sampling, collection, and processing are described to provide an up-to-date picture of ameliorations in the field. We propose optimization to microbiological methods, commonly used in soil and water analysis, that adjust them to the context of aerobiology, along with other directions towards novel and necessary advancements. This review offers new perspectives into aeromicrobiology and calls for advancements in global-scale bioremediation, insights into ecology, climate change impacts, and pathogenicity transmittance.
Collapse
Affiliation(s)
- Ariel C Tastassa
- Civil and Environmental Engineering, Technion - Israel Institute of Technology, 3200003 Haifa, Israel
| | - Yehonatan Sharaby
- Civil and Environmental Engineering, Technion - Israel Institute of Technology, 3200003 Haifa, Israel
| | - Naama Lang-Yona
- Civil and Environmental Engineering, Technion - Israel Institute of Technology, 3200003 Haifa, Israel.
| |
Collapse
|
6
|
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
|
7
|
Bezuidt OKI, Makhalanyane TP. Phylogenomic analysis expands the known repertoire of single-stranded DNA viruses in benthic zones of the South Indian Ocean. ISME COMMUNICATIONS 2024; 4:ycae065. [PMID: 38800127 PMCID: PMC11128263 DOI: 10.1093/ismeco/ycae065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024]
Abstract
Single-stranded (ss) DNA viruses are ubiquitous and constitute some of the most diverse entities on Earth. Most studies have focused on ssDNA viruses from terrestrial environments resulting in a significant deficit in benthic ecosystems including aphotic zones of the South Indian Ocean (SIO). Here, we assess the diversity and phylogeny of ssDNA in deep waters of the SIO using a combination of established viral taxonomy tools and a Hidden Markov Model based approach. Replication initiator protein-associated (Rep) phylogenetic reconstruction and sequence similarity networks were used to show that the SIO hosts divergent and as yet unknown circular Rep-encoding ssDNA viruses. Several sequences appear to represent entirely novel families, expanding the repertoire of known ssDNA viruses. Results suggest that a small proportion of these viruses may be circular genetic elements, which may strongly influence the diversity of both eukaryotes and prokaryotes in the SIO. Taken together, our data show that the SIO harbours a diverse assortment of previously unknown ssDNA viruses. Due to their potential to infect a variety of hosts, these viruses may be crucial for marine nutrient recycling through their influence of the biological carbon pump.
Collapse
Affiliation(s)
- Oliver K I Bezuidt
- DSI/NRF South African Research Chair in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, microbiome@UP, University of Pretoria, Pretoria, 0028, South Africa
- Department of Microbiology, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Thulani P Makhalanyane
- Department of Microbiology, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa
- Centre for Epidemic Response and Innovation, The School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
| |
Collapse
|
8
|
Larsen F, Offersen SM, Li VR, Deng L, Nielsen DS, Rasmussen TS. Choice of Ultrafilter Affects Recovery Rate of Bacteriophages. Viruses 2023; 15:2051. [PMID: 37896828 PMCID: PMC10612031 DOI: 10.3390/v15102051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
Studies into the viral fraction of complex microbial communities, like in the mammalian gut, have recently garnered much interest. Yet there is still no standardized protocol for extracting viruses from such samples, and the protocols that exist employ procedures that skew the viral community of the sample one way or another. The first step of the extraction pipeline often consists of the basic filtering of macromolecules and bacteria, yet even this affects the viruses in a strain-specific manner. In this study, we investigate a protocol for viral extraction based on ultrafiltration and how the choice of ultrafilter might influence the extracted viral community. Clinical samples (feces, vaginal swabs, and tracheal suction samples) were spiked with a mock community of known phages (T4, c2, Φ6, Φ29, Φx174, and Φ2972), filtered, and quantified using spot and plaque assays to estimate the loss in recovery. The enveloped Φ6 phage is especially severely affected by the choice of filter, but also tailed phages such as T4 and c2 have a reduced infectivity after ultrafiltration. We conclude that the pore size of ultrafilters may affect the recovery of phages in a strain- and sample-dependent manner, suggesting the need for greater thought when selecting filters for virus extraction.
Collapse
Affiliation(s)
- Frej Larsen
- Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark; (L.D.); (D.S.N.)
| | - Simone Margaard Offersen
- Section for Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark; (S.M.O.)
| | - Viktoria Rose Li
- Section for Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark; (S.M.O.)
| | - Ling Deng
- Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark; (L.D.); (D.S.N.)
| | - Dennis Sandris Nielsen
- Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark; (L.D.); (D.S.N.)
| | - Torben Sølbeck Rasmussen
- Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark; (L.D.); (D.S.N.)
| |
Collapse
|
9
|
Abstract
Two decades of metagenomic analyses have revealed that in many environments, small (∼5 kb), single-stranded DNA phages of the family Microviridae dominate the virome. Although the emblematic microvirus phiX174 is ubiquitous in the laboratory, most other microviruses, particularly those of the gokushovirus and amoyvirus lineages, have proven to be much more elusive. This puzzling lack of representative isolates has hindered insights into microviral biology. Furthermore, the idiosyncratic size and nature of their genomes have resulted in considerable misjudgments of their actual abundance in nature. Fortunately, recent successes in microvirus isolation and improved metagenomic methodologies can now provide us with more accurate appraisals of their abundance, their hosts, and their interactions. The emerging picture is that phiX174 and its relatives are rather rare and atypical microviruses, and that a tremendous diversity of other microviruses is ready for exploration.
Collapse
Affiliation(s)
- Paul C Kirchberger
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA;
| | - Howard Ochman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| |
Collapse
|
10
|
Cisneros-Martínez AM, Eguiarte LE, Souza V. Metagenomic comparisons reveal a highly diverse and unique viral community in a seasonally fluctuating hypersaline microbial mat. Microb Genom 2023; 9:mgen001063. [PMID: 37459167 PMCID: PMC10438804 DOI: 10.1099/mgen.0.001063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 06/15/2023] [Indexed: 07/20/2023] Open
Abstract
In spring 2016, a shallow hypersaline pond (50×25 m) was found in the Cuatro Cienegas Basin (CCB). This pond, known as Archaean Domes (AD) because of its elastic microbial mats that form dome-shaped structures due to the production of reducing gases reminiscent of the Archaean eon, such as methane and hydrogen sulfide, harbour a highly diverse microbial community, rich in halophilic and methanogenic archaea. AD is a seasonally fluctuating hypersaline site, with salinity ranging from low hypersaline (5.3%) during the wet season to high hypersaline (saturation) during the dry season. To characterize the viral community and to test whether it resembles those of other hypersaline sites (whose diversity is conditioned by salinity), or if it is similar to other CCB sites (with which it shares a common geological history), we generated 12 metagenomes from different seasons and depths over a 4 year period and compared them to 35 metagenomes from varied environments. Haloarchaeaviruses were detected, but were never dominant (average of 15.37 % of the total viral species), and the viral community structure and diversity were not affected by environmental fluctuations. In fact, unlike other viral communities at hypersaline sites, AD remained more diverse than other environments regardless of season. β-Diversity analyses show that AD is closely related to other CCB sites, although it has a unique viral community that forms a cluster of its own. The similarity of two surface samples to the 30 and 50 cm depth samples, as well as the observed increase in diversity at greater depths, supports the hypothesis that the diversity of CCB has evolved as a result of a long time environmental stability of a deep aquifer that functions as a 'seed bank' of great microbial diversity that is transported to the surface by sporadic groundwater upwelling events.
Collapse
Affiliation(s)
- Alejandro Miguel Cisneros-Martínez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Centro de Estudios del Cuaternario de Fuego-Patagonia y Antártica (CEQUA), Punta Arenas, Chile
| |
Collapse
|
11
|
Jung SW, Kim KE, Kim HJ, Lee TK. Metavirome Profiling and Dynamics of the DNA Viral Community in Seawater in Chuuk State, Federated States of Micronesia. Viruses 2023; 15:1293. [PMID: 37376592 DOI: 10.3390/v15061293] [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: 05/13/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Despite their abundance and ecological importance, little is known about the diversity of marine viruses, in part because most cannot be cultured in the laboratory. Here, we used high-throughput viral metagenomics of uncultivated viruses to investigate the dynamics of DNA viruses in tropical seawater sampled from Chuuk State, Federated States of Micronesia, in March, June, and December 2014. Among the identified viruses, 71-79% were bacteriophages belonging to the families Myoviridae, Siphoviridae, and Podoviridae (Caudoviriales), listed in order of abundance at all sampling times. Although the measured environmental factors (temperature, salinity, and pH) remained unchanged in the seawater over time, viral dynamics changed. The proportion of cyanophages (34.7%) was highest in June, whereas the proportion of mimiviruses, phycodnaviruses, and other nucleo-cytoplasmic large DNA viruses (NCLDVs) was higher in March and December. Although host species were not analysed, the dramatic viral community change observed in June was likely due to changes in the abundance of cyanophage-infected cyanobacteria, whereas that in NCLDVs was likely due to the abundance of potential eukaryote-infected hosts. These results serve as a basis for comparative analyses of other marine viral communities, and guide policy-making when considering marine life care in Chuuk State.
Collapse
Affiliation(s)
- Seung Won Jung
- Library of Marine Samples, Korea Institute of Ocean Science and Technology, Geoje 53201, Republic of Korea
- Department of Ocean Science, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Kang Eun Kim
- Library of Marine Samples, Korea Institute of Ocean Science and Technology, Geoje 53201, Republic of Korea
- Department of Ocean Science, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Hyun-Jung Kim
- Library of Marine Samples, Korea Institute of Ocean Science and Technology, Geoje 53201, Republic of Korea
| | - Taek-Kyun Lee
- Department of Ocean Science, University of Science and Technology, Daejeon 34113, Republic of Korea
- Risk Assessment Research Center, Korea Institute of Ocean Science and Technology, Geoje 53201, Republic of Korea
| |
Collapse
|
12
|
Liu Y, Guo L, Wang G, Gao F, Tu Z, Xu D, Sun L, Yi L, Zhu G, Tu C, He B. DNA virome of ticks in the Northeast and Hubei provinces of China reveals diverse single-stranded circular DNA viruses. Parasit Vectors 2023; 16:61. [PMID: 36759895 PMCID: PMC9912487 DOI: 10.1186/s13071-023-05684-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND Ticks are medically important vectors capable of transmitting a variety of pathogens to and between host species. Although the spectrum of tick-borne RNA viruses has been frequently investigated, the diversity of tick-borne DNA viruses remains largely unknown. METHODS A total of 1571 ticks were collected from forests and infested animals, and the diversity of the viruses they harbored was profiled using a DNA-specific virome method. The viromic data were phylogenetically analyzed and validated by PCR assays. RESULTS Although diverse and abundant prokaryotic viruses were identified in the collected ticks, only eukaryotic DNA viruses with single-stranded circular genomes covering the anelloviruses and circular replication-associated (Rep) protein-encoding single-stranded (CRESS) DNA viruses were recovered from ticks. Anelloviruses were detected only in two tick pools, but CRESS DNA viruses were prevalent across these ticks except in one pool of Dermacentor spp. ticks. Phylogenetic analyses revealed that these tick-borne CRESS DNA viruses were related to viruses recovered from animal feces, tissues and even environmental samples, suggesting that their presence may be largely explained by environmental factors rather than by tick species and host blood meals. CONCLUSIONS Based on the results, tick-borne eukaryotic DNA viruses appear to be much less common than eukaryotic RNA viruses. Investigations involving a wider collection area and more diverse tick species are required to further support this speculation.
Collapse
Affiliation(s)
- Yuhang Liu
- grid.268415.cJiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu China ,grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin China
| | - Lei Guo
- grid.454880.50000 0004 0596 3180Division of Wildlife and Plant Conservation, State Forestry and Grassland Administration, Changchun, Jilin China
| | - Guoshuai Wang
- grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin China
| | - Fei Gao
- Section of Wildlife Conservation, Greater Xing’an Mountains Forestry Group Corporation, Jiagedaqi, Heilongjiang China
| | - Zhongzhong Tu
- grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin China
| | - Deming Xu
- Forestry Bureau of Linjiang City, Linjiang, Jilin China
| | - Lanshun Sun
- Provincial Wildlife Disease Monitoring Station of Shuanghe, Xunke, Heilongjiang China
| | - Le Yi
- grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin China
| | - Guoqiang Zhu
- grid.268415.cJiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu China
| | - Changchun Tu
- grid.268415.cJiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu China ,grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin China
| | - Biao He
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China. .,Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China.
| |
Collapse
|
13
|
Kim KE, Joo HM, Lee TK, Kim HJ, Kim YJ, Kim BK, Ha SY, Jung SW. Covariance of Marine Nucleocytoplasmic Large DNA Viruses with Eukaryotic Plankton Communities in the Sub-Arctic Kongsfjorden Ecosystem: A Metagenomic Analysis of Marine Microbial Ecosystems. Microorganisms 2023; 11:microorganisms11010169. [PMID: 36677461 PMCID: PMC9862967 DOI: 10.3390/microorganisms11010169] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/31/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Nucleocytoplasmic large DNA viruses (NCLDVs) infect various marine eukaryotes. However, little is known about NCLDV diversity and their relationships with eukaryotic hosts in marine environments, the elucidation of which will advance the current understanding of marine ecosystems. This study characterizes the interplay between NCLDVs and the eukaryotic plankton community (EPC) in the sub-Arctic area using metagenomics and metabarcoding to investigate NCLDVs and EPC, respectively, in the Kongsfjorden ecosystem of Svalbard (Norway) in April and June 2018. Gyrodinium helveticum (Dinophyceae) is the most prevalent eukaryotic taxon in the EPC in April, during which time Mimiviridae (31.8%), Poxviridae (25.1%), Phycodnaviridae (14.7%) and Pandoraviridae (13.1%) predominate. However, in June, the predominant taxon is Aureococcus anophagefferens (Pelagophyceae), and the NCLDVs, Poxviridae (32.9%), Mimiviridae (29.1%), and Phycodnaviridae (18.5%) appear in higher proportions with an increase in Pelagophyceae, Bacillariophyceae, and Chlorophyta groups. Thus, differences in NCLDVs may be caused by changes in EPC composition in response to environmental changes, such as increases in water temperature and light intensity. Taken together, these findings are particularly relevant considering the anticipated impact of NCLDV-induced EPC control mechanisms on polar regions and, therefore, improve the understanding of the Sub-Arctic Kongsfjorden ecosystem.
Collapse
Affiliation(s)
- Kang Eun Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Hyoung Min Joo
- Unit of Next Generation IBRV Building Program, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Taek-Kyun Lee
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea
- Risk Assessment Research Center, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea
| | - Hyun-Jung Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea
| | - Yu Jin Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Bo Kyung Kim
- Division of Polar Ocean Science Research, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Sun-Yong Ha
- Division of Polar Ocean Science Research, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Correspondence: (S.-Y.H.); (S.W.J.)
| | - Seung Won Jung
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea
- Correspondence: (S.-Y.H.); (S.W.J.)
| |
Collapse
|
14
|
Baran N, Carlson MCG, Sabehi G, Peleg M, Kondratyeva K, Pekarski I, Lindell D. Widespread yet persistent low abundance of TIM5-like cyanophages in the oceans. Environ Microbiol 2022; 24:6476-6492. [PMID: 36116015 PMCID: PMC10087341 DOI: 10.1111/1462-2920.16210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 09/12/2022] [Indexed: 01/12/2023]
Abstract
Ocean ecosystems are inhabited by a diverse set of viruses that impact microbial mortality and evolution. However, the distribution and abundances of specific viral lineages, particularly those from the large bank of rare viruses, remains largely unknown. Here, we assessed the diversity and abundance of the TIM5-like cyanophages. The sequencing of three new TIM5-like cyanophage genomes and environmental amplicons of a signature gene from the Red Sea revealed highly conserved gene content and sequence similarity. We adapted the polony method, a solid-phase polymerase chain reaction assay, to quantify TIM5-like cyanophages during three 2000 km expeditions in the Pacific Ocean and four annual cycles in the Red Sea. TIM5-like cyanophages were widespread, detected at all latitudes and seasons surveyed throughout the photic zone. Yet they were generally rare, ranging between <100 and 4000 viruses·ml-1 . Occasional peaks in abundance of 10- to 100-fold were observed, reaching 71,000 viruses·ml-1 . These peaks were ephemeral and seasonally variable in the Red Sea. Infection levels, quantified during one such peak, were very low. These characteristics of low diversity and abundance, as well as variable outbreaks, distinguishes the TIM5-like lineage from other major cyanophage lineages and illuminates that rare virus lineages can be persistent and widespread in the oceans.
Collapse
Affiliation(s)
- Nava Baran
- Technion - Israel Institute of Technology, Faculty of Biology, Haifa, Israel
| | - Michael C G Carlson
- Technion - Israel Institute of Technology, Faculty of Biology, Haifa, Israel
| | - Gazalah Sabehi
- Technion - Israel Institute of Technology, Faculty of Biology, Haifa, Israel
| | - Margalit Peleg
- Technion - Israel Institute of Technology, Faculty of Biology, Haifa, Israel
| | - Kira Kondratyeva
- Technion - Israel Institute of Technology, Faculty of Biology, Haifa, Israel
| | - Irena Pekarski
- Technion - Israel Institute of Technology, Faculty of Biology, Haifa, Israel
| | - Debbie Lindell
- Technion - Israel Institute of Technology, Faculty of Biology, Haifa, Israel
| |
Collapse
|
15
|
Zhou YL, Mara P, Vik D, Edgcomb VP, Sullivan MB, Wang Y. Ecogenomics reveals viral communities across the Challenger Deep oceanic trench. Commun Biol 2022; 5:1055. [PMID: 36192584 PMCID: PMC9529941 DOI: 10.1038/s42003-022-04027-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 09/23/2022] [Indexed: 11/23/2022] Open
Abstract
Despite the environmental challenges and nutrient scarcity, the geographically isolated Challenger Deep in Mariana trench, is considered a dynamic hotspot of microbial activity. Hadal viruses are the least explored microorganisms in Challenger Deep, while their taxonomic and functional diversity and ecological impact on deep-sea biogeochemistry are poorly described. Here, we collect 13 sediment cores from slope and bottom-axis sites across the Challenger Deep (down to ~11 kilometers depth), and identify 1,628 previously undescribed viral operational taxonomic units at species level. Community-wide analyses reveals 1,299 viral genera and distinct viral diversity across the trench, which is significantly higher at the bottom-axis vs. slope sites of the trench. 77% of these viral genera have not been previously identified in soils, deep-sea sediments and other oceanic settings. Key prokaryotes involved in hadal carbon and nitrogen cycling are predicted to be potential hosts infected by these viruses. The detected putative auxiliary metabolic genes suggest that viruses at Challenger Deep could modulate the carbohydrate and sulfur metabolisms of their potential hosts, and stabilize host's cell membranes under extreme hydrostatic pressures. Our results shed light on hadal viral metabolic capabilities, contribute to understanding deep sea ecology and on functional adaptions of hadal viruses for future research.
Collapse
Affiliation(s)
- Ying-Li Zhou
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Paraskevi Mara
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Dean Vik
- Department of Microbiology and Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Matthew B Sullivan
- Department of Microbiology and Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
| |
Collapse
|
16
|
Wirth J, Young M. Viruses in Subsurface Environments. Annu Rev Virol 2022; 9:99-119. [PMID: 36173700 DOI: 10.1146/annurev-virology-093020-015957] [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: 11/09/2022]
Abstract
Over the past 20 years, our knowledge of virus diversity and abundance in subsurface environments has expanded dramatically through application of quantitative metagenomic approaches. In most subsurface environments, viral diversity and abundance rival viral diversity and abundance observed in surface environments. Most of these viruses are uncharacterized in terms of their hosts and replication cycles. Analysis of accessory metabolic genes encoded by subsurface viruses indicates that they evolved to replicate within the unique features of their environments. The key question remains: What role do these viruses play in the ecology and evolution of the environments in which they replicate? Undoubtedly, as more virologists examine the role of viruses in subsurface environments, new insights will emerge.
Collapse
Affiliation(s)
- Jennifer Wirth
- Department of Plant Science and Plant Pathology and Thermal Biology Institute, Montana State University, Bozeman, Montana, USA;
| | - Mark Young
- Department of Plant Science and Plant Pathology and Thermal Biology Institute, Montana State University, Bozeman, Montana, USA;
| |
Collapse
|
17
|
Liu Z, Ding X, Haider MS, Ali F, Yu H, Chen X, Tan S, Zu Y, Liu W, Ding B, Zheng A, Zheng J, Qian Z, Ashfaq H, Yu D, Li K. A metagenomic insight into the Yangtze finless porpoise virome. Front Vet Sci 2022; 9:922623. [PMID: 36118360 PMCID: PMC9478467 DOI: 10.3389/fvets.2022.922623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
The Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis) inhabiting the Yantze River, China is critically endangered because of the influences of infectious disease, human activity, and water contamination. Viral diseases are one of the crucial factors that threatening the health of Yangtze finless porpoise. However, there are few studies which elaborate the viral diversity of Yangtze finless. Therefore, this study was performed to investigate the viral diversity of Yangtze finless by metagenomics. Results indicated that a total of 12,686,252 high-quality valid sequences were acquired and 2,172 virus reads were recognized. Additionally, we also obtained a total of 10,600 contigs. Phages was the most abundant virus in the samples and the ratio of DNA and RNA viruses were 69.75 and 30.25%, respectively. Arenaviridae, Ackermannviridae and Siphoviridae were the three most predominant families in all the samples. Moreover, the majority of viral genus were Mammarenavirus, Limestonevirus and Lambdavirus. The results of gene prediction indicated that these viruses play vital roles in biological process, cellular component, molecular function, and disease. To the best of our knowledge, this is the first report on the viral diversity of Yangtze finless porpoise, which filled the gaps in its viral information. Meanwhile, this study can also provide a theoretical basis for the establishment of the prevention and protection system for virus disease of Yangtze finless porpoise.
Collapse
Affiliation(s)
- Zhigang Liu
- College of Life Science, Anqing Normal University, Anqing, China
- Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, Anqing Normal University, Anqing, China
- Zhigang Liu
| | - Xin Ding
- College of Life Science, Anqing Normal University, Anqing, China
| | | | - Farah Ali
- Department of Theriogenology, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Han Yu
- College of Life Science, Anqing Normal University, Anqing, China
| | - Xin Chen
- College of Life Science, Anqing Normal University, Anqing, China
| | - Shuaishuai Tan
- College of Life Science, Anqing Normal University, Anqing, China
| | - Yuan Zu
- College of Life Science, Anqing Normal University, Anqing, China
| | - Wenlong Liu
- College of Life Science, Anqing Normal University, Anqing, China
| | - Bangzhi Ding
- College of Life Science, Anqing Normal University, Anqing, China
| | - Aifang Zheng
- College of Life Science, Anqing Normal University, Anqing, China
| | - Jinsong Zheng
- Institute of Hydrobiology, Chinese Academy of Sciences, Beijing, China
| | - Zhengyi Qian
- Hubei Yangtze River Ecological Protection Foundation, Wuhan, China
| | - Hassan Ashfaq
- Institute of Continuing Education and Extension, University of Veterinary Animal Sciences, Lahore, Pakistan
| | - Daoping Yu
- College of Life Science, Anqing Normal University, Anqing, China
- Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, Anqing Normal University, Anqing, China
| | - Kun Li
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Kun Li
| |
Collapse
|
18
|
Comprehensive Evaluation of RNA and DNA Viromic Methods Based on Species Richness and Abundance Analyses Using Marmot Rectal Samples. mSystems 2022; 7:e0043022. [PMID: 35862817 PMCID: PMC9426427 DOI: 10.1128/msystems.00430-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Viral metagenomics is the most powerful tool to profile viromic composition for a given sample. Different viromic methods, including amplification-free ones, have been developed, but choosing them for different purposes requires comprehensive benchmarks. Here, we assessed the performance of four routinely used methods, i.e., multiple displacement amplification (MDA), direct metagenomic sequencing (MTG), sequence-independent single-primer amplification (SIA), and metatranscriptomic sequencing (MTT), using marmot rectal samples as the templates spiked with five known viruses of different genome types. The obtained clean data were differently contaminated by host and bacterial genomes, resulting in MDA having the most, with ~72.1%, but MTT had only ~7.5% data, useful for follow-up viromic analysis. MDA showed a broader spectrum with higher efficiency to profile the DNA virome, and MTT captured almost all RNA viruses with extraordinary sensitivity; hence, they are advisable in richness-based viromic studies. MTG was weak in capturing single-stranded DNA viruses, and SIA could detect both RNA and DNA viruses but with high randomness. Due to biases to certain types of viruses, the four methods caused different alterations to species abundance compared to the initial virus composition. SIA and MDA introduced greater stochastic errors to relative abundances of species, genus, and family taxa, whereas the two amplification-free methods were more tolerant toward such errors and thus are recommendable in abundance-based analyses. In addition, genus taxon is a compromising analytic level that ensures technically supported and biologically and/or ecologically meaningful viromic conclusions. IMPORTANCE Viral metagenomics can be roughly divided into species richness-based studies and species abundance-based analyses. Viromic methods with different principles have been developed, but rational selection of these techniques according to different purposes requires comprehensive understanding of their properties. By assessing the four most widely used methods using template samples, we found that multiple displacement amplification (MDA) and metatranscriptomic sequencing (MTT) are advisable for species richness-based viromic studies, as they show excellent efficiency to detect DNA and RNA viruses. Meanwhile, metagenomic sequencing (MTG) and MTT are more compatible with stochastic errors of methods introduced into relative abundance of viromic taxa and hence are rational choices in species abundance-based analyses. This study also highlights that MTG needs to tackle host genome contamination and ameliorate the capacity to detect single-stranded DNA viruses in the future, and the MTT method requires an improvement in bacterial rRNA depletion prior to library preparation.
Collapse
|
19
|
Gao C, Liang Y, Jiang Y, Paez-Espino D, Han M, Gu C, Wang M, Yang Y, Liu F, Yang Q, Gong Z, Zhang X, Luo Z, He H, Guo C, Shao H, Zhou C, Shi Y, Xin Y, Xing J, Tang X, Qin Q, Zhang YZ, He J, Jiao N, McMinn A, Tian J, Suttle CA, Wang M. Virioplankton assemblages from challenger deep, the deepest place in the oceans. iScience 2022; 25:104680. [PMID: 35942087 PMCID: PMC9356048 DOI: 10.1016/j.isci.2022.104680] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/25/2022] [Accepted: 06/23/2022] [Indexed: 11/26/2022] Open
Abstract
Hadal ocean biosphere, that is, the deepest part of the world's oceans, harbors a unique microbial community, suggesting a potential uncovered co-occurring virioplankton assemblage. Herein, we reveal the unique virioplankton assemblages of the Challenger Deep, comprising 95,813 non-redundant viral contigs from the surface to the hadal zone. Almost all of the dominant viral contigs in the hadal zone were unclassified, potentially related to Alteromonadales and Oceanospirillales. 2,586 viral auxiliary metabolic genes from 132 different KEGG orthologous groups were mainly related to the carbon, nitrogen, sulfur, and arsenic metabolism. Lysogenic viral production and integrase genes were augmented in the hadal zone, suggesting the prevalence of viral lysogenic life strategy. Abundant rve genes in the hadal zone, which function as transposase in the caudoviruses, further suggest the prevalence of viral-mediated horizontal gene transfer. This study provides fundamental insights into the virioplankton assemblages of the hadal zone, reinforcing the necessity of incorporating virioplankton into the hadal biogeochemical cycles.
Collapse
Affiliation(s)
- Chen Gao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, 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, 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, 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
| | - David Paez-Espino
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Mammoth Biosciences, Inc., South San Francisco, CA, USA
| | - Meiaoxue Han
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, 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
| | - Chengxiang Gu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, 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
| | - Meiwen Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, 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
| | - Yumei Yang
- Inquire Life Diagnostics, Inc, Xi’an 710100, China
| | - Fengjiao Liu
- The Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Qingwei Yang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, 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
| | - Zheng Gong
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, 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
| | - Xinran Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, 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
| | - Zhixiang Luo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, 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, 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, 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
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, 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
| | - Chun Zhou
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Yang Shi
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Yu Xin
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Institute for Advanced Ocean Study, Ocean University of China, Qingdao 266100, China
| | - Jinyan Xing
- The Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Xuexi Tang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
| | - Qilong Qin
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China
| | - Jianfeng He
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, China
| | - Nianzhi Jiao
- Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, 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, Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao 266100, China
- Laboratory for Ocean and Climate Dynamics, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - 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
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, 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
|
20
|
Du K, Yang F, Zhang JT, Yu RC, Deng Z, Li WF, Chen Y, Li Q, Zhou CZ. Comparative genomic analysis of five freshwater cyanophages and reference-guided metagenomic data mining. MICROBIOME 2022; 10:128. [PMID: 35974417 PMCID: PMC9382816 DOI: 10.1186/s40168-022-01324-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND As important producers using photosynthesis on Earth, cyanobacteria contribute to the oxygenation of atmosphere and the primary production of biosphere. However, due to the eutrophication of urban waterbodies and global warming, uncontrollable growth of cyanobacteria usually leads to the seasonal outbreak of cyanobacterial blooms. Cyanophages, a group of viruses that specifically infect and lyse cyanobacteria, are considered as potential environment-friendly agents to control the harmful blooms. Compared to the marine counterparts, only a few freshwater cyanophages have been isolated and genome sequenced to date, largely limiting their characterizations and applications. RESULTS Here, we isolated five freshwater cyanophages varying in tail morphology, termed Pam1~Pam5, all of which infect the cyanobacterium Pseudanabaena mucicola Chao 1806 that was isolated from the bloom-suffering Lake Chaohu in Anhui, China. The whole-genome sequencing showed that cyanophages Pam1~Pam5 all contain a dsDNA genome, varying in size from 36 to 142 Kb. Phylogenetic analyses suggested that Pam1~Pam5 possess different DNA packaging mechanisms and are evolutionarily distinct from each other. Notably, Pam1 and Pam5 have lysogeny-associated gene clusters, whereas Pam2 possesses 9 punctuated DNA segments identical to the CRISPR spacers in the host genome. Metagenomic data-based calculation of the relative abundance of Pam1~Pam5 at the Nanfei estuary towards the Lake Chaohu revealed that the short-tailed Pam1 and Pam5 account for the majority of the five cyanophages. Moreover, comparative analyses of the reference genomes of Pam1~Pam5 and previously reported cyanophages enabled us to identify three circular and seven linear contigs of virtual freshwater cyanophages from the metagenomic data of the Lake Chaohu. CONCLUSIONS We propose a high-throughput strategy to systematically identify cyanophages based on the currently available metagenomic data and the very limited reference genomes of experimentally isolated cyanophages. This strategy could be applied to mine the complete or partial genomes of unculturable bacteriophages and viruses. Transformation of the synthesized whole genomes of these virtual phages/viruses to proper hosts will enable the rescue of bona fide viral particles and eventually enrich the library of microorganisms that exist on Earth. Video abstract.
Collapse
Affiliation(s)
- Kang Du
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Feng Yang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Jun-Tao Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Rong-Cheng Yu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Ziqing Deng
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI-Beijing, BGI-Shenzhen, Beijing, 100101, China
| | - Wei-Fang Li
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Yuxing Chen
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Qiong Li
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
| | - Cong-Zhao Zhou
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
| |
Collapse
|
21
|
Zucker F, Bischoff V, Olo Ndela E, Heyerhoff B, Poehlein A, Freese HM, Roux S, Simon M, Enault F, Moraru C. New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria. Virus Evol 2022; 8:veac070. [PMID: 36533142 PMCID: PMC9753089 DOI: 10.1093/ve/veac070] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/24/2022] [Accepted: 07/28/2022] [Indexed: 10/01/2023] Open
Abstract
The Microviridae family represents one of the major clades of single-stranded DNA (ssDNA) phages. Their cultivated members are lytic and infect Proteobacteria, Bacteroidetes, and Chlamydiae. Prophages have been predicted in the genomes from Bacteroidales, Hyphomicrobiales, and Enterobacteriaceae and cluster within the 'Alpavirinae', 'Amoyvirinae', and Gokushovirinae. We have isolated 'Ascunsovirus oldenburgi' ICBM5, a novel phage distantly related to known Microviridae. It infects Sulfitobacter dubius SH24-1b and uses both a lytic and a carrier-state life strategy. Using ICBM5 proteins as a query, we uncovered in publicly available resources sixty-five new Microviridae prophages and episomes in bacterial genomes and retrieved forty-seven environmental viral genomes (EVGs) from various viromes. Genome clustering based on protein content and phylogenetic analysis showed that ICBM5, together with Rhizobium phages, new prophages, episomes, and EVGs cluster within two new phylogenetic clades, here tentatively assigned the rank of subfamily and named 'Tainavirinae' and 'Occultatumvirinae'. They both infect Rhodobacterales. Occultatumviruses also infect Hyphomicrobiales, including nitrogen-fixing endosymbionts from cosmopolitan legumes. A biogeographical assessment showed that tainaviruses and occultatumviruses are spread worldwide, in terrestrial and marine environments. The new phage isolated here sheds light onto new and diverse branches of the Microviridae tree, suggesting that much of the ssDNA phage diversity remains in the dark.
Collapse
Affiliation(s)
- Falk Zucker
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| | - Vera Bischoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| | - Eric Olo Ndela
- Laboratoire Microorganismes: Genome Environment (LMGE), Université Clermont Auvergne, CNRS, 1 Imp. Amélie Murat, Aubière 63170, Frankreich
| | - Benedikt Heyerhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August-University Göttingen, Institute of Microbiology and Genetics, Grisebachstr. 8, Göttingen D-37077, Germany
| | - Heike M Freese
- Leibniz-Institut DSMZ, Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7 B, Braunschweig D-38124, Germany
| | - Simon Roux
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA 94720, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| | - Francois Enault
- Laboratoire Microorganismes: Genome Environment (LMGE), Université Clermont Auvergne, CNRS, 1 Imp. Amélie Murat, Aubière 63170, Frankreich
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| |
Collapse
|
22
|
Ferchiou S, Caza F, de Boissel PGJ, Villemur R, St-Pierre Y. Applying the concept of liquid biopsy to monitor the microbial biodiversity of marine coastal ecosystems. ISME COMMUNICATIONS 2022; 2:61. [PMID: 37938655 PMCID: PMC9723566 DOI: 10.1038/s43705-022-00145-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 06/28/2022] [Accepted: 07/08/2022] [Indexed: 10/04/2023]
Abstract
Liquid biopsy (LB) is a concept that is rapidly gaining ground in the biomedical field. Its concept is largely based on the detection of circulating cell-free DNA (ccfDNA) fragments that are mostly released as small fragments following cell death in various tissues. A small percentage of these fragments are from foreign (nonself) tissues or organisms. In the present work, we applied this concept to mussels, a sentinel species known for its high filtration capacity of seawater. We exploited the capacity of mussels to be used as natural filters to capture environmental DNA fragments of different origins to provide information on the biodiversity of marine coastal ecosystems. Our results showed that hemolymph of mussels contains DNA fragments that varied considerably in size, ranging from 1 to 5 kb. Shotgun sequencing revealed that a significant amount of DNA fragments had a nonself microbial origin. Among these, we found DNA fragments derived from bacteria, archaea, and viruses, including viruses known to infect a variety of hosts that commonly populate coastal marine ecosystems. Taken together, our study shows that the concept of LB applied to mussels provides a rich and yet unexplored source of knowledge regarding the microbial biodiversity of a marine coastal ecosystem.
Collapse
Affiliation(s)
- Sophia Ferchiou
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada
| | - France Caza
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada
| | | | - Richard Villemur
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada
| | - Yves St-Pierre
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada.
| |
Collapse
|
23
|
Mostafa-Hedeab G, Allayeh AK, Elhady HA, Eledrdery AY, Mraheil MA, Mostafa A. Viral Eco-Genomic Tools: Development and Implementation for Aquatic Biomonitoring. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:7707. [PMID: 35805367 PMCID: PMC9265447 DOI: 10.3390/ijerph19137707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 12/17/2022]
Abstract
Enteric viruses (EVs) occurrence within aquatic environments varies and leads to significant risk on public health of humans, animals, and diversity of aquatic taxa. Early and efficacious recognition of cultivable and fastidious EVs in aquatic systems are important to ensure the sanitary level of aquatic water and implement required treatment strategies. Herein, we provided a comprehensive overview of the conventional and up-to-date eco-genomic tools for aquatic biomonitoring of EVs, aiming to develop better water pollution monitoring tools. In combination with bioinformatics techniques, genetic tools including cloning sequencing analysis, DNA microarray, next-generation sequencing (NGS), and metagenomic sequencing technologies are implemented to make informed decisions about the global burden of waterborne EVs-associated diseases. The data presented in this review are helpful to recommend that: (1) Each viral pollution detection method has its own merits and demerits; therefore, it would be advantageous for viral pollution evaluation to be integrated as a complementary platform. (2) The total viral genome pool extracted from aquatic environmental samples is a real reflection of pollution status of the aquatic eco-systems; therefore, it is recommended to conduct regular sampling through the year to establish an updated monitoring system for EVs, and quantify viral peak concentrations, viral typing, and genotyping. (3) Despite that conventional detection methods are cheaper, it is highly recommended to implement molecular-based technologies to complement aquatic ecosystems biomonitoring due to numerous advantages including high-throughput capability. (4) Continuous implementation of the eco-genetic detection tools for monitoring the EVs in aquatic ecosystems is recommended.
Collapse
Affiliation(s)
- Gomaa Mostafa-Hedeab
- Pharmacology Department and Health Research Unit, Medical College, Jouf University, Skaka 11564, Saudi Arabia
| | - Abdou Kamal Allayeh
- Water Pollution Department, Virology Laboratory, National Research Centre, Dokki, Giza 12622, Egypt;
| | | | - Abozer Y. Eledrdery
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 11564, Saudi Arabia;
| | - Mobarak Abu Mraheil
- German Center for Infection Research (DZIF), Institute of Medical Microbiology, Justus-Liebig University, 35392 Giessen, Germany
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
| |
Collapse
|
24
|
Stenglein MD. The Case for Studying New Viruses of New Hosts. Annu Rev Virol 2022; 9:157-172. [PMID: 35671564 DOI: 10.1146/annurev-virology-100220-112915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Virology has largely focused on viruses that are pathogenic to humans or to the other species that we care most about. There is no doubt that this has been a worthwhile investment. But many transformative advances have been made through the in-depth study of relatively obscure viruses that do not appear on lists of prioritized pathogens. In this review, I highlight the benefits that can accrue from the study of viruses and hosts off the beaten track. I take stock of viral sequence diversity across host taxa as an estimate of the bias that exists in our understanding of host-virus interactions. I describe the gains that have been made through the metagenomic discovery of thousands of new viruses in previously unsampled hosts as well as the limitations of metagenomic surveys. I conclude by suggesting that the study of viruses that naturally infect existing and emerging model organisms represents an opportunity to push virology forward in useful and hard to predict ways.Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Mark D Stenglein
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA;
| |
Collapse
|
25
|
Buchholz HH, Bolaños LM, Bell AG, Michelsen ML, Allen MJ, Temperton B. A Novel and Ubiquitous Marine Methylophage Provides Insights into Viral-Host Coevolution and Possible Host-Range Expansion in Streamlined Marine Heterotrophic Bacteria. Appl Environ Microbiol 2022; 88:e0025522. [PMID: 35311512 PMCID: PMC9004378 DOI: 10.1128/aem.00255-22] [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: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 11/25/2022] Open
Abstract
The methylotrophic OM43 clade are Gammaproteobacteria that comprise some of the smallest free-living cells known and have highly streamlined genomes. OM43 represents an important microbial link between marine primary production and remineralization of carbon back to the atmosphere. Bacteriophages shape microbial communities and are major drivers of mortality and global marine biogeochemistry. Recent cultivation efforts have brought the first viruses infecting members of the OM43 clade into culture. Here, we characterize a novel myophage infecting OM43 called Melnitz. Melnitz was isolated independently from water samples from a subtropical ocean gyre (Sargasso Sea) and temperate coastal (Western English Channel) systems. Metagenomic recruitment from global ocean viromes confirmed that Melnitz is globally ubiquitous, congruent with patterns of host abundance. Bacteria with streamlined genomes such as OM43 and the globally dominant SAR11 clade use riboswitches as an efficient method to regulate metabolism. Melnitz encodes a two-piece tmRNA (ssrA), controlled by a glutamine riboswitch, providing evidence that riboswitch use also occurs for regulation during phage infection of streamlined heterotrophs. Virally encoded tRNAs and ssrA found in Melnitz were phylogenetically more closely related to those found within the alphaproteobacterial SAR11 clade and their associated myophages than those within their gammaproteobacterial hosts. This suggests the possibility of an ancestral host transition event between SAR11 and OM43. Melnitz and a related myophage that infects SAR11 were unable to infect hosts of the SAR11 and OM43, respectively, suggesting host transition rather than a broadening of host range. IMPORTANCE Isolation and cultivation of viruses are the foundations on which the mechanistic understanding of virus-host interactions and parameterization of bioinformatic tools for viral ecology are based. This study isolated and characterized the first myophage known to infect the OM43 clade, expanding our knowledge of this understudied group of microbes. The nearly identical genomes of four strains of Melnitz isolated from different marine provinces and the global abundance estimations from metagenomic data suggest that this viral population is globally ubiquitous. Genome analysis revealed several unusual features in Melnitz and related genomes recovered from viromes, such as a curli operon and virally encoded tmRNA controlled by a glutamine riboswitch, neither of which are found in the host. Further phylogenetic analysis of shared genes indicates that this group of viruses infecting the gammaproteobacterial OM43 shares a recent common ancestor with viruses infecting the abundant alphaproteobacterial SAR11 clade. Host ranges are affected by compatible cell surface receptors, successful circumvention of superinfection exclusion systems, and the presence of required accessory proteins, which typically limits phages to singular narrow groups of closely related bacterial hosts. This study provides intriguing evidence that for streamlined heterotrophic bacteria, virus-host transitioning may not be necessarily restricted to phylogenetically related hosts but is a function of shared physical and biochemical properties of the cell.
Collapse
Affiliation(s)
| | | | | | | | - Michael J. Allen
- University of Exeter, School of Biosciences, Exeter, UK
- Plymouth Marine Laboratory, Plymouth, UK
| | - Ben Temperton
- University of Exeter, School of Biosciences, Exeter, UK
| |
Collapse
|
26
|
Record-Breaking Rain Event Altered Estuarine Viral Assemblages. Microorganisms 2022; 10:microorganisms10040729. [PMID: 35456780 PMCID: PMC9025952 DOI: 10.3390/microorganisms10040729] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023] Open
Abstract
Viruses are the dominant biological entity in the ocean, play a vital role in biogeochemical cycles, and provide their hosts with novel metabolic capabilities through auxiliary metabolic genes (AMGs). Hurricane Harvey was a category 4 hurricane that made landfall on the Texas coast in 2017 and lashed the Houston area with 1.4–1.7 × 1010 m3 of rainfall. In this paper, we aim to characterize how the changes in abiotic conditions brought by Hurricane Harvey altered the viral assemblages of Galveston Bay at the taxonomic level and determine how viral ecosystem functions were altered. Metagenomes of the viruses and their hosts were sequenced from a transect in Galveston Bay over the five weeks following the storm. Our results show that the viral assemblages of Galveston Bay dramatically changed following Hurricane Harvey’s landfall. Of the abiotic parameters measured, salinity had the strongest effect on shaping the viral assemblages. In the five weeks following Hurricane Harvey, there was a steady increase of metabolic genes and putative viral infections. Our study provides the first in-depth look at how marine viral assemblages respond and recover from extreme rainfall events, which models predict will become more frequent and intense with climate change.
Collapse
|
27
|
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
|
28
|
Oral Toxicity Study for Salmonella Killing Lytic Bacteriophage NINP13076 in BALB/c Mice and Its Effect on Probiotic Microbiota. Curr Microbiol 2022; 79:89. [PMID: 35129700 DOI: 10.1007/s00284-021-02754-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 12/24/2021] [Indexed: 11/03/2022]
Abstract
Viruses that infect bacteria are emerging as attractive biocontrol agents and biopreservatives for foods. Since these bacteriophages kill the target pathogens by lysis and are also consumed along with food, it is essential to evaluate their collateral toxicity on the probiotic gut microbiota. In this study, we examined the acute oral toxicity of a Salmonella phage isolated from sewage in mice. Acute oral administration of the Salmonella phage for five consecutive days did not show any significant pathological changes in the vital organs like lung, kidneys, heart, liver, and intestine. In addition, growth of typical probiotic microbiota remained unaffected even after incubation up to 24 h with the Salmonella phage. The results of this study clearly showed that oral administration of the lytic Salmonella phage did not have any significant adverse effects on the animals, may not harm the probiotic gut microbiota, and are likely to be safe for use in food preservation.
Collapse
|
29
|
Transcriptional Organization of the Salmonella Typhimurium Phage P22 pid ORFan Locus. Int J Mol Sci 2022; 23:ijms23031253. [PMID: 35163175 PMCID: PMC8835761 DOI: 10.3390/ijms23031253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/20/2022] Open
Abstract
Many phage genes lack sequence similarity to any other open reading frame (ORF) in current databases. These enigmatic ORFan genes can have a tremendous impact on phage propagation and host interactions but often remain experimentally unexplored. We previously revealed a novel interaction between phage P22 and its Salmonella Typhimurium host, instigated by the ORFan gene pid (for phage P22 encoded instigator of dgo expression) and resulting in derepression of the host dgoRKAT operon. The pid gene is highly expressed in phage carrier cells that harbor a polarly located P22 episome that segregates asymmetrically among daughter cells. Here, we discovered that the pid locus is fitted with a weak promoter, has an exceptionally long 5′ untranslated region that is instructive for a secondary pid mRNA species, and has a 3′ Rho-independent termination loop that is responsible for stability of the pid transcript.
Collapse
|
30
|
Runa V, Wenk J, Bengtsson S, Jones BV, Lanham AB. Bacteriophages in Biological Wastewater Treatment Systems: Occurrence, Characterization, and Function. Front Microbiol 2021; 12:730071. [PMID: 34803947 PMCID: PMC8600467 DOI: 10.3389/fmicb.2021.730071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/25/2021] [Indexed: 12/20/2022] Open
Abstract
Phage bacteria interactions can affect structure, dynamics, and function of microbial communities. In the context of biological wastewater treatment (BWT), the presence of phages can alter the efficiency of the treatment process and influence the quality of the treated effluent. The active role of phages in BWT has been demonstrated, but many questions remain unanswered regarding the diversity of phages in these engineered environments, the dynamics of infection, the determination of bacterial hosts, and the impact of their activity in full-scale processes. A deeper understanding of the phage ecology in BWT can lead the improvement of process monitoring and control, promote higher influent quality, and potentiate the use of phages as biocontrol agents. In this review, we highlight suitable methods for studying phages in wastewater adapted from other research fields, provide a critical overview on the current state of knowledge on the effect of phages on structure and function of BWT bacterial communities, and highlight gaps, opportunities, and priority questions to be addressed in future research.
Collapse
Affiliation(s)
- Viviane Runa
- Centre for Sustainable and Circular Technologies, University of Bath, Bath, United Kingdom.,Department of Chemical Engineering, University of Bath, Bath, United Kingdom
| | - Jannis Wenk
- Department of Chemical Engineering, University of Bath, Bath, United Kingdom.,Water Innovation and Research Centre, University of Bath, Bath, United Kingdom
| | | | - Brian V Jones
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Ana B Lanham
- Centre for Sustainable and Circular Technologies, University of Bath, Bath, United Kingdom.,Department of Chemical Engineering, University of Bath, Bath, United Kingdom.,Water Innovation and Research Centre, University of Bath, Bath, United Kingdom
| |
Collapse
|
31
|
Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts. THE ISME JOURNAL 2021; 15:3129-3147. [PMID: 33972727 PMCID: PMC8528832 DOI: 10.1038/s41396-021-00989-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 03/08/2021] [Accepted: 04/14/2021] [Indexed: 02/03/2023]
Abstract
The marine picoeukaryote Bathycoccus prasinos has been considered a cosmopolitan alga, although recent studies indicate two ecotypes exist, Clade BI (B. prasinos) and Clade BII. Viruses that infect Bathycoccus Clade BI are known (BpVs), but not that infect BII. We isolated three dsDNA prasinoviruses from the Sargasso Sea against Clade BII isolate RCC716. The BII-Vs do not infect BI, and two (BII-V2 and BII-V3) have larger genomes (~210 kb) than BI-Viruses and BII-V1. BII-Vs share ~90% of their proteins, and between 65% to 83% of their proteins with sequenced BpVs. Phylogenomic reconstructions and PolB analyses establish close-relatedness of BII-V2 and BII-V3, yet BII-V2 has 10-fold higher infectivity and induces greater mortality on host isolate RCC716. BII-V1 is more distant, has a shorter latent period, and infects both available BII isolates, RCC716 and RCC715, while BII-V2 and BII-V3 do not exhibit productive infection of the latter in our experiments. Global metagenome analyses show Clade BI and BII algal relative abundances correlate positively with their respective viruses. The distributions delineate BI/BpVs as occupying lower temperature mesotrophic and coastal systems, whereas BII/BII-Vs occupy warmer temperature, higher salinity ecosystems. Accordingly, with molecular diagnostic support, we name Clade BII Bathycoccus calidus sp. nov. and propose that molecular diversity within this new species likely connects to the differentiated host-virus dynamics observed in our time course experiments. Overall, the tightly linked biogeography of Bathycoccus host and virus clades observed herein supports species-level host specificity, with strain-level variations in infection parameters.
Collapse
|
32
|
Viral Characteristics of the Warm Atlantic and Cold Arctic Water Masses in the Nordic Seas. Appl Environ Microbiol 2021; 87:e0116021. [PMID: 34469192 DOI: 10.1128/aem.01160-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nordic Seas are the subarctic seas connecting the Arctic Ocean and North Atlantic Ocean with complex water masses, experiencing an abrupt climate change. Though knowledge of the marine virosphere has expanded rapidly, the diversity of viruses and their relationships with host cells and water masses in the Nordic Seas remain to be fully revealed. Here, we establish the Nordic Sea DNA virome (NSV) data set of 55,315 viral contigs including 1,478 unique viral populations from seven stations influenced by both the warm Atlantic and cold Arctic water masses. Caudovirales dominated in the seven NSVs, especially in the warm Atlantic waters. The major giant nucleocytoplasmic large DNA viruses (NCLDVs) contributed a significant proportion of the classified viral contigs in the NSVs (32.2%), especially in the cold Arctic waters (44.9%). The distribution patterns of Caudovirales and NCLDVs were a reflection of the community structure of their hosts in the corresponding water masses and currents. Latitude, pH, and flow speed were found to be key factors influencing the microbial communities and coinfluencing the variation of viral communities. Network analysis illustrated the tight coupling between the variation of viral communities and microbial communities in the Nordic Seas. This study suggests a probable linkage between viromes, host cells, and surface water masses from both the cool Arctic and warm Atlantic Oceans. IMPORTANCE This is a systematic study of Nordic Sea viromes using metagenomic analysis. The viral diversity, community structure, and their relationships with host cells and the complex water masses from both the cool Arctic and the warm Atlantic oceans were illustrated. The NCLDVs and Caudovirales are proposed as the viral characteristics of the cold Arctic and warm Atlantic waters, respectively. This study provides an important background for the viromes in the subarctic seas connecting the Arctic Ocean and North Atlantic Ocean and sheds light on their responses to abrupt climate change in the future.
Collapse
|
33
|
Bhattarai B, Bhattacharjee AS, Coutinho FH, Goel RK. Viruses and Their Interactions With Bacteria and Archaea of Hypersaline Great Salt Lake. Front Microbiol 2021; 12:701414. [PMID: 34650523 PMCID: PMC8506154 DOI: 10.3389/fmicb.2021.701414] [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: 04/27/2021] [Accepted: 09/06/2021] [Indexed: 01/15/2023] Open
Abstract
Viruses play vital biogeochemical and ecological roles by (a) expressing auxiliary metabolic genes during infection, (b) enhancing the lateral transfer of host genes, and (c) inducing host mortality. Even in harsh and extreme environments, viruses are major players in carbon and nutrient recycling from organic matter. However, there is much that we do not yet understand about viruses and the processes mediated by them in the extreme environments such as hypersaline habitats. The Great Salt Lake (GSL) in Utah, United States is a hypersaline ecosystem where the biogeochemical role of viruses is poorly understood. This study elucidates the diversity of viruses and describes virus–host interactions in GSL sediments along a salinity gradient. The GSL sediment virosphere consisted of Haloviruses (32.07 ± 19.33%) and members of families Siphoviridae (39.12 ± 19.8%), Myoviridae (13.7 ± 6.6%), and Podoviridae (5.43 ± 0.64%). Our results demonstrate that salinity alongside the concentration of organic carbon and inorganic nutrients (nitrogen and phosphorus) governs the viral, bacteria, and archaeal diversity in this habitat. Computational host predictions for the GSL viruses revealed a wide host range with a dominance of viruses that infect Proteobacteria, Actinobacteria, and Firmicutes. Identification of auxiliary metabolic genes for photosynthesis (psbA), carbon fixation (rbcL, cbbL), formaldehyde assimilation (SHMT), and nitric oxide reduction (NorQ) shed light on the roles played by GSL viruses in biogeochemical cycles of global relevance.
Collapse
Affiliation(s)
- Bishav Bhattarai
- Department of Civil and Environmental Engineering, The University of Utah, Salt Lake City, UT, United States
| | - Ananda S Bhattacharjee
- Carl R. Woese Institute for Genomic Biology, The University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Felipe H Coutinho
- Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Ramesh K Goel
- Department of Civil and Environmental Engineering, The University of Utah, Salt Lake City, UT, United States
| |
Collapse
|
34
|
Sawaya NA, Baran N, Mahank S, Varsani A, Lindell D, Breitbart M. Adaptation of the polony technique to quantify Gokushovirinae, a diverse group of single-stranded DNA phage. Environ Microbiol 2021; 23:6622-6636. [PMID: 34623742 DOI: 10.1111/1462-2920.15805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/09/2021] [Accepted: 10/03/2021] [Indexed: 12/29/2022]
Abstract
Advances in metagenomics have revealed the ubiquity of single-stranded DNA (ssDNA) phage belonging to the subfamily Gokushovirinae in the oceans; however, the abundance and ecological roles of this group are unknown. Here, we quantify gokushoviruses through adaptation of the polony method, in which viral template DNA is immobilized in a gel, amplified by PCR, and subsequently detected by hybridization. Primers and probes for this assay were designed based on PCR amplicon diversity of gokushovirus major capsid protein gene sequences from a depth profile in the Gulf of Aqaba, Red Sea sampled in September 2015. At ≥95% identity, these 87 gokushovirus sequences formed 14 discrete clusters with the largest clades showing distinct depth distributions. The application of the polony method enabled the first quantification of gokushoviruses in any environment. The gokushoviruses were most abundant in the upper 40 m of the stratified water column, with a subsurface peak in abundance of 1.26 × 105 viruses ml-1 . These findings suggest that discrete gokushovirus genotypes infect bacterial hosts that differentially partition in the water column. Since the designed primers and probe are conserved across marine ecosystems, this polony method can be applied broadly for the quantification of gokushoviruses throughout the global oceans.
Collapse
Affiliation(s)
- Natalie A Sawaya
- University of South Florida, College of Marine Science, Saint Petersburg, FL, USA
| | - Nava Baran
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Shelby Mahank
- University of South Florida, College of Marine Science, Saint Petersburg, FL, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA.,Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Debbie Lindell
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Mya Breitbart
- University of South Florida, College of Marine Science, Saint Petersburg, FL, USA
| |
Collapse
|
35
|
Arisdakessian CG, Nigro OD, Steward GF, Poisson G, Belcaid M. CoCoNet: an efficient deep learning tool for viral metagenome binning. Bioinformatics 2021; 37:2803-2810. [PMID: 33822891 DOI: 10.1093/bioinformatics/btab213] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 03/24/2021] [Accepted: 04/02/2021] [Indexed: 02/02/2023] Open
Abstract
MOTIVATION Metagenomic approaches hold the potential to characterize microbial communities and unravel the intricate link between the microbiome and biological processes. Assembly is one of the most critical steps in metagenomics experiments. It consists of transforming overlapping DNA sequencing reads into sufficiently accurate representations of the community's genomes. This process is computationally difficult and commonly results in genomes fragmented across many contigs. Computational binning methods are used to mitigate fragmentation by partitioning contigs based on their sequence composition, abundance or chromosome organization into bins representing the community's genomes. Existing binning methods have been principally tuned for bacterial genomes and do not perform favorably on viral metagenomes. RESULTS We propose Composition and Coverage Network (CoCoNet), a new binning method for viral metagenomes that leverages the flexibility and the effectiveness of deep learning to model the co-occurrence of contigs belonging to the same viral genome and provide a rigorous framework for binning viral contigs. Our results show that CoCoNet substantially outperforms existing binning methods on viral datasets. AVAILABILITY AND IMPLEMENTATION CoCoNet was implemented in Python and is available for download on PyPi (https://pypi.org/). The source code is hosted on GitHub at https://github.com/Puumanamana/CoCoNet and the documentation is available at https://coconet.readthedocs.io/en/latest/index.html. CoCoNet does not require extensive resources to run. For example, binning 100k contigs took about 4 h on 10 Intel CPU Cores (2.4 GHz), with a memory peak at 27 GB (see Supplementary Fig. S9). To process a large dataset, CoCoNet may need to be run on a high RAM capacity server. Such servers are typically available in high-performance or cloud computing settings. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Cédric G Arisdakessian
- Department of Information and Computer Sciences, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Olivia D Nigro
- Department of Natural Science, Hawai'i Pacific University, Honolulu, HI 96813, USA
| | - Grieg F Steward
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Guylaine Poisson
- Department of Information and Computer Sciences, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Mahdi Belcaid
- Department of Information and Computer Sciences, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA.,Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Honolulu, HI 96816, USA
| |
Collapse
|
36
|
Le Gratiet T, Le Marechal C, Devaere M, Chemaly M, Woudstra C. Exploration of the Diversity of Clustered Regularly Interspaced Short Palindromic Repeats-Cas Systems in Clostridium novyi sensu lato. Front Microbiol 2021; 12:711413. [PMID: 34589070 PMCID: PMC8473940 DOI: 10.3389/fmicb.2021.711413] [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: 05/18/2021] [Accepted: 08/16/2021] [Indexed: 11/13/2022] Open
Abstract
Classified as the genospecies Clostridium novyi sensu lato and distributed into four lineages (I-IV), Clostridium botulinum (group III), Clostridium novyi, and Clostridium haemolyticum are clostridial pathogens that cause animal diseases. Clostridium novyi sensu lato contains a large mobilome consisting of plasmids and circular bacteriophages. Here, we explored clustered regularly interspaced short palindromic repeats (CRISPR) arrays and their associated proteins (Cas) to shed light on the link between evolution of CRISPR-Cas systems and the plasmid and phage composition in a study of 58 Clostridium novyi sensu lato genomes. In 55 of these genomes, types I-B (complete or partial), I-D, II-C, III-B, III-D, or V-U CRISPR-Cas systems were detected in chromosomes as well as in mobile genetic elements (MGEs). Type I-B predominated (67.2%) and was the only CRISPR type detected in the Ia, III, and IV genomic lineages. Putative type V-U CRISPR Cas14a genes were detected in two different cases: next to partial type-IB CRISPR loci on the phage encoding the botulinum neurotoxin (BoNT) in lineage Ia and in 12 lineage II genomes, as part of a putative integrative element related to a phage-inducible chromosomal island (PICI). In the putative PICI, Cas14a was associated with CRISPR arrays and restriction modification (RM) systems as part of an accessory locus. This is the first time a PICI containing such locus has been detected in C. botulinum. Mobilome composition and dynamics were also investigated based on the contents of the CRISPR arrays and the study of spacers. A large proportion of identified protospacers (20.2%) originated from Clostridium novyi sensu lato (p1_Cst, p4_BKT015925, p6_Cst, CWou-2020a, p1_BKT015925, and p2_BKT015925), confirming active exchanges within this genospecies and the key importance of specific MGEs in Clostridium novyi sensu lato.
Collapse
Affiliation(s)
- Thibault Le Gratiet
- Hygiene and Quality of Poultry and Pig Products Unit, ANSES, French Agency for Food, Environmental and Occupational Health Safety, Ploufragan, France
- UFR of Life Sciences and Environment, University of Rennes, Rennes, France
| | - Caroline Le Marechal
- Hygiene and Quality of Poultry and Pig Products Unit, ANSES, French Agency for Food, Environmental and Occupational Health Safety, Ploufragan, France
| | - Marie Devaere
- Hygiene and Quality of Poultry and Pig Products Unit, ANSES, French Agency for Food, Environmental and Occupational Health Safety, Ploufragan, France
| | - Marianne Chemaly
- Hygiene and Quality of Poultry and Pig Products Unit, ANSES, French Agency for Food, Environmental and Occupational Health Safety, Ploufragan, France
| | - Cédric Woudstra
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| |
Collapse
|
37
|
Jacobson TB, Callaghan MM, Amador-Noguez D. Hostile Takeover: How Viruses Reprogram Prokaryotic Metabolism. Annu Rev Microbiol 2021; 75:515-539. [PMID: 34348026 DOI: 10.1146/annurev-micro-060621-043448] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To reproduce, prokaryotic viruses must hijack the cellular machinery of their hosts and redirect it toward the production of viral particles. While takeover of the host replication and protein synthesis apparatus has long been considered an essential feature of infection, recent studies indicate that extensive reprogramming of host primary metabolism is a widespread phenomenon among prokaryotic viruses that is required to fulfill the biosynthetic needs of virion production. In this review we provide an overview of the most significant recent findings regarding virus-induced reprogramming of prokaryotic metabolism and suggest how quantitative systems biology approaches may be used to provide a holistic understanding of metabolic remodeling during lytic viral infection. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Tyler B Jacobson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Melanie M Callaghan
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| |
Collapse
|
38
|
Abstract
Viruses are the most abundant biological entity on Earth, infect cellular organisms from all domains of life, and are central players in the global biosphere. Over the last century, the discovery and characterization of viruses have progressed steadily alongside much of modern biology. In terms of outright numbers of novel viruses discovered, however, the last few years have been by far the most transformative for the field. Advances in methods for identifying viral sequences in genomic and metagenomic datasets, coupled to the exponential growth of environmental sequencing, have greatly expanded the catalog of known viruses and fueled the tremendous growth of viral sequence databases. Development and implementation of new standards, along with careful study of the newly discovered viruses, have transformed and will continue to transform our understanding of microbial evolution, ecology, and biogeochemical cycles, leading to new biotechnological innovations across many diverse fields, including environmental, agricultural, and biomedical sciences.
Collapse
Affiliation(s)
- Lee Call
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; ,
| | - Stephen Nayfach
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; ,
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; ,
| |
Collapse
|
39
|
Zhong ZP, Tian F, Roux S, Gazitúa MC, Solonenko NE, Li YF, Davis ME, Van Etten JL, Mosley-Thompson E, Rich VI, Sullivan MB, Thompson LG. Glacier ice archives nearly 15,000-year-old microbes and phages. MICROBIOME 2021; 9:160. [PMID: 34281625 PMCID: PMC8290583 DOI: 10.1186/s40168-021-01106-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/31/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Glacier ice archives information, including microbiology, that helps reveal paleoclimate histories and predict future climate change. Though glacier-ice microbes are studied using culture or amplicon approaches, more challenging metagenomic approaches, which provide access to functional, genome-resolved information and viruses, are under-utilized, partly due to low biomass and potential contamination. RESULTS We expand existing clean sampling procedures using controlled artificial ice-core experiments and adapted previously established low-biomass metagenomic approaches to study glacier-ice viruses. Controlled sampling experiments drastically reduced mock contaminants including bacteria, viruses, and free DNA to background levels. Amplicon sequencing from eight depths of two Tibetan Plateau ice cores revealed common glacier-ice lineages including Janthinobacterium, Polaromonas, Herminiimonas, Flavobacterium, Sphingomonas, and Methylobacterium as the dominant genera, while microbial communities were significantly different between two ice cores, associating with different climate conditions during deposition. Separately, ~355- and ~14,400-year-old ice were subject to viral enrichment and low-input quantitative sequencing, yielding genomic sequences for 33 vOTUs. These were virtually all unique to this study, representing 28 novel genera and not a single species shared with 225 environmentally diverse viromes. Further, 42.4% of the vOTUs were identifiable temperate, which is significantly higher than that in gut, soil, and marine viromes, and indicates that temperate phages are possibly favored in glacier-ice environments before being frozen. In silico host predictions linked 18 vOTUs to co-occurring abundant bacteria (Methylobacterium, Sphingomonas, and Janthinobacterium), indicating that these phages infected ice-abundant bacterial groups before being archived. Functional genome annotation revealed four virus-encoded auxiliary metabolic genes, particularly two motility genes suggest viruses potentially facilitate nutrient acquisition for their hosts. Finally, given their possible importance to methane cycling in ice, we focused on Methylobacterium viruses by contextualizing our ice-observed viruses against 123 viromes and prophages extracted from 131 Methylobacterium genomes, revealing that the archived viruses might originate from soil or plants. CONCLUSIONS Together, these efforts further microbial and viral sampling procedures for glacier ice and provide a first window into viral communities and functions in ancient glacier environments. Such methods and datasets can potentially enable researchers to contextualize new discoveries and begin to incorporate glacier-ice microbes and their viruses relative to past and present climate change in geographically diverse regions globally. Video Abstract.
Collapse
Affiliation(s)
- Zhi-Ping Zhong
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | - Funing Tian
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Natalie E Solonenko
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | - Yueh-Fen Li
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | - Mary E Davis
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA
| | - James L Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Ellen Mosley-Thompson
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
- Department of Geography, Ohio State University, Columbus, OH, USA
| | - Virginia I Rich
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | - Matthew B Sullivan
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA.
- Department of Microbiology, Ohio State University, Columbus, OH, USA.
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA.
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA.
| | - Lonnie G Thompson
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA.
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA.
- School of Earth Sciences, Ohio State University, Columbus, OH, USA.
| |
Collapse
|
40
|
Viral footprints across Gulfs of Kathiawar Peninsula and Arabian Sea: Unraveled from pelagic sediment metagenomic data. Virus Res 2021; 302:198485. [PMID: 34146609 DOI: 10.1016/j.virusres.2021.198485] [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: 11/19/2020] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 11/21/2022]
Abstract
Marine biosphere is one of the largest, diverse and dynamic system hosting numerous of microorganisms. Viruses being the most abundant under explored lifeforms in ocean, represent a reservoir of great genetic diversity. We report the metagenomic insights on the viral communities in the deep sediments of the two Gulfs of Gujarat i.e. Gulf of Khambhat and Gulf of Kutch, with one sample from Arabian Sea, treated as open sea control. The viral reads were filtered from the whole dataset, assembled and studied for viral diversity, which was visualized by Pavian. The sequences were checked for the viral abundance, diversity and functionality. The resulting viral taxonomic classification contained 6 orders, 8 families and 47 genera. The results revealed that the phages infecting Cyanobacterium, Bacillus and Vibrio dominated the sediments. Further, it was observed that majority of viral sequences belonged to double-stranded DNA phages. The present study attempts to provide a primary insight of the viral signals and potential genetic content in the Gulfs of Kathiawar.
Collapse
|
41
|
Aevarsson A, Kaczorowska AK, Adalsteinsson BT, Ahlqvist J, Al-Karadaghi S, Altenbuchner J, Arsin H, Átlasson ÚÁ, Brandt D, Cichowicz-Cieślak M, Cornish KAS, Courtin J, Dabrowski S, Dahle H, Djeffane S, Dorawa S, Dusaucy J, Enault F, Fedøy AE, Freitag-Pohl S, Fridjonsson OH, Galiez C, Glomsaker E, Guérin M, Gundesø SE, Gudmundsdóttir EE, Gudmundsson H, Håkansson M, Henke C, Helleux A, Henriksen JR, Hjörleifdóttir S, Hreggvidsson GO, Jasilionis A, Jochheim A, Jónsdóttir I, Jónsdóttir LB, Jurczak-Kurek A, Kaczorowski T, Kalinowski J, Kozlowski LP, Krupovic M, Kwiatkowska-Semrau K, Lanes O, Lange J, Lebrat J, Linares-Pastén J, Liu Y, Lorentsen SA, Lutterman T, Mas T, Merré W, Mirdita M, Morzywołek A, Ndela EO, Karlsson EN, Olgudóttir E, Pedersen C, Perler F, Pétursdóttir SK, Plotka M, Pohl E, Prangishvili D, Ray JL, Reynisson B, Róbertsdóttir T, Sandaa RA, Sczyrba A, Skírnisdóttir S, Söding J, Solstad T, Steen IH, Stefánsson SK, Steinegger M, Overå KS, Striberny B, Svensson A, Szadkowska M, Tarrant EJ, Terzian P, Tourigny M, Bergh TVD, Vanhalst J, Vincent J, Vroling B, Walse B, Wang L, Watzlawick H, Welin M, Werbowy O, Wons E, Zhang R. Going to extremes - a metagenomic journey into the dark matter of life. FEMS Microbiol Lett 2021; 368:6296640. [PMID: 34114607 DOI: 10.1093/femsle/fnab067] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 06/08/2021] [Indexed: 02/06/2023] Open
Abstract
The Virus-X-Viral Metagenomics for Innovation Value-project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. Specifically, the project was set to analyse and exploit viral metagenomes with the ultimate goal of developing new gene products with high innovation value for applications in biotechnology, pharmaceutical, medical, and the life science sectors. Viral gene pool analysis is also essential to obtain fundamental insight into ecosystem dynamics and to investigate how viruses influence the evolution of microbes and multicellular organisms. The Virus-X Consortium, established in 2016, included experts from eight European countries. The unique approach based on high throughput bioinformatics technologies combined with structural and functional studies resulted in the development of a biodiscovery pipeline of significant capacity and scale. The activities within the Virus-X consortium cover the entire range from bioprospecting and methods development in bioinformatics to protein production and characterisation, with the final goal of translating our results into new products for the bioeconomy. The significant impact the consortium made in all of these areas was possible due to the successful cooperation between expert teams that worked together to solve a complex scientific problem using state-of-the-art technologies as well as developing novel tools to explore the virosphere, widely considered as the last great frontier of life.
Collapse
Affiliation(s)
| | - Anna-Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | | | - Josefin Ahlqvist
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | | | - Joseph Altenbuchner
- Institute for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Hasan Arsin
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | | | - David Brandt
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Magdalena Cichowicz-Cieślak
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Katy A S Cornish
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | | | | | - Håkon Dahle
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway.,Department of Informatics, University of Bergen, PO Box 7803, Thormøhlens gate 53 A/B, N-5020 Bergen, Norway
| | | | - Sebastian Dorawa
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | | | - Francois Enault
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | - Anita-Elin Fedøy
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | - Stefanie Freitag-Pohl
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | | | - Clovis Galiez
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Eirin Glomsaker
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | | | - Sigurd E Gundesø
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | | | | | - Maria Håkansson
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Christian Henke
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany.,Computational Metagenomics, Bielefeld University, Universitätsstraße 27, 30501 Bielefeld, Germany
| | | | | | | | - Gudmundur O Hreggvidsson
- Matis ohf, Vinlandsleid 12, Reykjavik 113, Iceland.,Faculty of Life and Environmental Sciences, University of Iceland, Askja-Sturlugata 7, Reykjavik, Iceland
| | - Andrius Jasilionis
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | - Annika Jochheim
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | | | - Agata Jurczak-Kurek
- Department of Molecular Evolution, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Tadeusz Kaczorowski
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Lukasz P Kozlowski
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.,Institute of Informatics, Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Banacha 2, Warsaw 02-097, Poland
| | - Mart Krupovic
- Institute Pasteur, Department of Microbiology, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Karolina Kwiatkowska-Semrau
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Olav Lanes
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Joanna Lange
- Bio-Prodict, Nieuwe Marktstraat 54E 6511AA Nijmegen, Netherlands
| | | | - Javier Linares-Pastén
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | - Ying Liu
- Institute Pasteur, Department of Microbiology, 25-28 Rue du Dr Roux, 75015 Paris, France
| | | | - Tobias Lutterman
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Thibaud Mas
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | | | - Milot Mirdita
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Agnieszka Morzywołek
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Eric Olo Ndela
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | - Eva Nordberg Karlsson
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | | | - Cathrine Pedersen
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Francine Perler
- Perls of Wisdom Biotech Consulting, 74 Fuller Street, Brookline, MA 02446, USA
| | | | - Magdalena Plotka
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ehmke Pohl
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom.,Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - David Prangishvili
- Institute Pasteur, Department of Microbiology, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Jessica L Ray
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway.,NORCE Environment, NORCE Norwegian Research Centre AS, Nygårdsgaten 112, 5008 Bergen, Norway
| | | | | | - Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | - Alexander Sczyrba
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany.,Computational Metagenomics, Bielefeld University, Universitätsstraße 27, 30501 Bielefeld, Germany
| | | | - Johannes Söding
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Terese Solstad
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Ida H Steen
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | | | - Martin Steinegger
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | - Bernd Striberny
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Anders Svensson
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Monika Szadkowska
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Emma J Tarrant
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Paul Terzian
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | | | | | | | - Jonathan Vincent
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | - Bas Vroling
- Bio-Prodict, Nieuwe Marktstraat 54E 6511AA Nijmegen, Netherlands
| | - Björn Walse
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Lei Wang
- Institute for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Hildegard Watzlawick
- Institute for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Martin Welin
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Olesia Werbowy
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ewa Wons
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ruoshi Zhang
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| |
Collapse
|
42
|
Exploring Viral Diversity in a Gypsum Karst Lake Ecosystem Using Targeted Single-Cell Genomics. Genes (Basel) 2021; 12:genes12060886. [PMID: 34201311 PMCID: PMC8226683 DOI: 10.3390/genes12060886] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 12/14/2022] Open
Abstract
Little is known about the diversity and distribution of viruses infecting green sulfur bacteria (GSB) thriving in euxinic (sulfuric and anoxic) habitats, including gypsum karst lake ecosystems. In this study, we used targeted cell sorting combined with single-cell sequencing to gain insights into the gene content and genomic potential of viruses infecting sulfur-oxidizing bacteria Chlorobium clathratiforme, obtained from water samples collected during summer stratification in gypsum karst Lake Kirkilai (Lithuania). In total, 82 viral contigs were bioinformatically identified in 62 single amplified genomes (SAGs) of C. clathratiforme. The majority of viral gene and protein sequences showed little to no similarity with phage sequences in public databases, uncovering the vast diversity of previously undescribed GSB viruses. We observed a high level of lysogenization in the C. clathratiforme population, as 87% SAGs contained intact prophages. Among the thirty identified auxiliary metabolic genes (AMGs), two, thiosulfate sulfurtransferase (TST) and thioredoxin-dependent phosphoadenosine phosphosulfate (PAPS) reductase (cysH), were found to be involved in the oxidation of inorganic sulfur compounds, suggesting that viruses can influence the metabolism and cycling of this essential element. Finally, the analysis of CRISPR spacers retrieved from the consensus C. clathratiforme genome imply persistent and active virus–host interactions for several putative phages prevalent among C. clathratiforme SAGs. Overall, this study provides a glimpse into the diversity of phages associated with naturally occurring and highly abundant sulfur-oxidizing bacteria.
Collapse
|
43
|
Temporal Changes of Virus-Like Particle Abundance and Metagenomic Comparison of Viral Communities in Cropland and Prairie Soils. mSphere 2021; 6:e0116020. [PMID: 34077260 PMCID: PMC8265675 DOI: 10.1128/msphere.01160-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
During the last several decades, viruses have been increasingly recognized for their abundance, ubiquity, and important roles in different ecosystems. Despite known contributions to aquatic systems, few studies examine viral abundance and community structure over time in terrestrial ecosystems. The effects of land conversion and land management on soil microbes have been previously investigated, but their effects on virus population are not well studied. This study examined annual dynamics of viral abundance in soils from a native tallgrass prairie and two croplands, conventional till winter wheat and no-till canola, in Oklahoma. Virus-like particle (VLP) abundance varied across sites, and showed clear seasonal shifts. VLP abundance significantly correlated with environmental variables that were generally reflective of land use, including air temperature, soil nitrogen, and plant canopy coverage. Structural equation modeling supported the effects of land use on soil communities by emphasizing interactions between management, environmental factors, and viral and bacterial abundance. Between the viral metagenomes from the prairie and tilled wheat field, 1,231 unique viral operational taxonomic units (vOTUs) were identified, and only five were shared that were rare in the contrasting field. Only 13% of the vOTUs had similarity to previously identified viruses in the RefSeq database, with only 7% having known taxonomic classification. Together, our findings indicated land use and tillage practices influence virus abundance and community structure. Analyses of viromes over time and space are vital to viral ecology in providing insight on viral communities and key information on interactions between viruses, their microbial hosts, and the environment. IMPORTANCE Conversion of land alters the physiochemical and biological environments by not only changing the aboveground community, but also modifying the soil environment for viruses and microbes. Soil microbial communities are critical to nutrient cycling, carbon mineralization, and soil quality; and viruses are known for influencing microbial abundance, community structure, and evolution. Therefore, viruses are considered an important part of soil functions in terrestrial ecosystems. In aquatic environments, virus abundance generally exceeds bacterial counts by an order of magnitude, and they are thought to be one of the greatest genetic reservoirs on the planet. However, data are extremely limited on viruses in soils, and even less is known about their responses to the disturbances associated with land use and management. The study provides important insights into the temporal dynamics of viral abundance and the structure of viral communities in response to the common practice of turning native habitats into arable soils.
Collapse
|
44
|
Forcone K, Coutinho FH, Cavalcanti GS, Silveira CB. Prophage Genomics and Ecology in the Family Rhodobacteraceae. Microorganisms 2021; 9:microorganisms9061115. [PMID: 34064105 PMCID: PMC8224337 DOI: 10.3390/microorganisms9061115] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022] Open
Abstract
Roseobacters are globally abundant bacteria with critical roles in carbon and sulfur biogeochemical cycling. Here, we identified 173 new putative prophages in 79 genomes of Rhodobacteraceae. These prophages represented 1.3 ± 0.15% of the bacterial genomes and had no to low homology with reference and metagenome-assembled viral genomes from aquatic and terrestrial ecosystems. Among the newly identified putative prophages, 35% encoded auxiliary metabolic genes (AMGs), mostly involved in secondary metabolism, amino acid metabolism, and cofactor and vitamin production. The analysis of integration sites and gene homology showed that 22 of the putative prophages were actually gene transfer agents (GTAs) similar to a GTA of Rhodobacter capsulatus. Twenty-three percent of the predicted prophages were observed in the TARA Oceans viromes generated from free viral particles, suggesting that they represent active prophages capable of induction. The distribution of these prophages was significantly associated with latitude and temperature. The prophages most abundant at high latitudes encoded acpP, an auxiliary metabolic gene involved in lipid synthesis and membrane fluidity at low temperatures. Our results show that prophages and gene transfer agents are significant sources of genomic diversity in roseobacter, with potential roles in the ecology of this globally distributed bacterial group.
Collapse
Affiliation(s)
- Kathryn Forcone
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
| | - Felipe H. Coutinho
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche, Aptdo. 18, Ctra. Alicante-Valencia, s/n, 03550 San Juan de Alicante, Spain;
| | - Giselle S. Cavalcanti
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
| | - Cynthia B. Silveira
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
- Correspondence:
| |
Collapse
|
45
|
Kumar N, Gupta AK, Sudan SK, Pal D, Randhawa V, Sahni G, Mayilraj S, Kumar M. Abundance and Diversity of Phages, Microbial Taxa, and Antibiotic Resistance Genes in the Sediments of the River Ganges Through Metagenomic Approach. Microb Drug Resist 2021; 27:1336-1354. [PMID: 33913739 DOI: 10.1089/mdr.2020.0431] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In this study, we have analyzed the metagenomic DNA from the pooled sediment sample of the river Ganges to explore the abundance and diversity of phages, microbial community, and antibiotic resistance genes (ARGs). Utilizing data from Illumina platform, 4,174 (∼0.0013%) reads were classified for the 285 different DNA viruses largely dominated by the group of 260 distinctive phages (3,602 reads, ∼86.3%). Among all, Microcystis (782 hits), Haemophilus (403), Synechococcus (386), Pseudomonas (279), Enterococcus (232), Bacillus (196), Rhodococcus (166), Caulobacter (163), Salmonella (146), Enterobacteria (143), Mycobacterium and (128) phages show the highest abundance and account for ∼90% of the total identified phages. In addition, we have also identified corresponding host pertaining to these phages. Mainly, Proteobacteria (∼69.3%) dominates the microbial population structure. Primarily, orders such as Caulobacterales (∼28%), Burkholderiales (∼13.9%), Actinomycetales (∼13.7%), and Pseudomonadales (∼7.5%) signify the core section. Furthermore, 21,869 (∼0.00695%) reads were classified in 20 ARG types (classes) and 240 ARGs (subtypes), among which 4 ARG types, namely multidrug resistance (12,041 reads, ∼55%), bacitracin (3,202 reads, ∼15%), macrolide-lincosamide-streptogramin (1,744 reads, ∼7.98%), and fosmidomycin (990 reads, ∼4.53%), have the highest abundance. Simultaneously, six resistance mechanisms were also recognized with the dominance of antibiotic efflux (72.8%, 15,919 reads). The results unveil the distribution of (pro)-phages; microbial community; and various ARGs in the Ganges river sediments.
Collapse
Affiliation(s)
- Narender Kumar
- Division of Protein Science and Engineering, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Amit Kumar Gupta
- Virology Unit and Bioinformatics Centre, and Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Sarabjeet Kour Sudan
- Division of Protein Science and Engineering, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Deepika Pal
- MTCC-Microbial Type Culture Collection and Gene Bank, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Vinay Randhawa
- Virology Unit and Bioinformatics Centre, and Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Girish Sahni
- Division of Protein Science and Engineering, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Shanmugam Mayilraj
- MTCC-Microbial Type Culture Collection and Gene Bank, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Manoj Kumar
- Virology Unit and Bioinformatics Centre, and Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| |
Collapse
|
46
|
Butina TV, Bukin YS, Petrushin IS, Tupikin AE, Kabilov MR, Belikov SI. Extended Evaluation of Viral Diversity in Lake Baikal through Metagenomics. Microorganisms 2021; 9:760. [PMID: 33916464 PMCID: PMC8066274 DOI: 10.3390/microorganisms9040760] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/22/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022] Open
Abstract
Lake Baikal is a unique oligotrophic freshwater lake with unusually cold conditions and amazing biological diversity. Studies of the lake's viral communities have begun recently, and their full diversity is not elucidated yet. Here, we performed DNA viral metagenomic analysis on integral samples from four different deep-water and shallow stations of the southern and central basins of the lake. There was a strict distinction of viral communities in areas with different environmental conditions. Comparative analysis with other freshwater lakes revealed the highest similarity of Baikal viromes with those of the Asian lakes Soyang and Biwa. Analysis of new data, together with previously published data allowed us to get a deeper insight into the diversity and functional potential of Baikal viruses; however, the true diversity of Baikal viruses in the lake ecosystem remains still unknown. The new metaviromic data will be useful for future studies of viral composition, distribution, and the dynamics associated with global climatic and anthropogenic impacts on this ecosystem.
Collapse
Affiliation(s)
- Tatyana V. Butina
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia; (I.S.P.); (S.I.B.)
| | - Yurij S. Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia; (I.S.P.); (S.I.B.)
| | - Ivan S. Petrushin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia; (I.S.P.); (S.I.B.)
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.E.T.); (M.R.K.)
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.E.T.); (M.R.K.)
| | - Sergey I. Belikov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia; (I.S.P.); (S.I.B.)
| |
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
|
Abstract
The term “microbiome” is currently applied predominantly to assemblages of organisms with 16S rRNA genes. In this context, “microbiome” is a misnomer that has been conferred a wide-ranging primacy over terms for community members lacking such genes, e.g., mycobiome, eukaryome, and virome, yet these are also important subsets of microbial communities. Widespread convenient and affordable 16S rRNA sequencing pipelines have accelerated continued use of such a “microbiome”, but at what intellectual and practical costs? Here we show that the use of “microbiome” in ribosomal gene-based studies has been egregiously misapplied, and discuss potential impacts. We argue that the current focus of “microbiome” research, predominantly on only ‘bacteria’, presents a dangerous narrowing of scope which encourages dismissal and even ignorance of other organisms’ contributions to microbial diversity, sensu stricto, and as etiologic agents; we put this in context by discussing cases in both marine microbial diversity and the role of pathogens in global amphibian decline. Fortunately, the solution is simple. We must use descriptive nouns that strictly reflect the outcomes attainable by the methods used. “Microbiome”, as a descriptive noun, should only be used when diversity in the three recognized domains is explored.
Collapse
|
49
|
Abstract
Viruses are ubiquitous and abundant in the oceans, and viral metagenomes (viromes) have been investigated extensively via several large-scale ocean sequencing projects. However, there have not been any systematic viromic studies in estuaries. Here, we investigated the viromes of the Delaware Bay and Chesapeake Bay, two Mid-Atlantic estuaries. Deep sequencing generated a total of 48,190 assembled viral sequences (>5 kb) and 26,487 viral populations (9,204 virus clusters and 17,845 singletons), including 319 circular viral contigs between 7.5 kb and 161.8 kb. Unknown viruses represented the vast majority of the dominant populations, while the composition of known viruses, such as pelagiphage and cyanophage, appeared to be relatively consistent across a wide range of salinity gradients and in different seasons. A difference between estuarine and ocean viromes was reflected by the proportions of Myoviridae, Podoviridae, Siphoviridae, Phycodnaviridae, and a few well-studied virus representatives. The difference in viral community between the Delaware Bay and Chesapeake Bay is significantly more pronounced than the difference caused by temperature or salinity, indicating strong local profiles caused by the unique ecology of each estuary. Interestingly, a viral contig similar to phages infecting Acinetobacter baumannii (“Iraqibacter”) was found to be highly abundant in the Delaware Bay but not in the Chesapeake Bay, the source of which is yet to be identified. Highly abundant viruses in both estuaries have close hits to viral sequences derived from the marine single-cell genomes or long-read single-molecule sequencing, suggesting that important viruses are still waiting to be discovered in the estuarine environment. IMPORTANCE This is the first systematic study about spatial and temporal variation of virioplankton communities in estuaries using deep metagenomics sequencing. It is among the highest-quality viromic data sets to date, showing remarkably consistent sequencing depth and quality across samples. Our results indicate that there exists a large pool of abundant and diverse viruses in estuaries that have not yet been cultivated, their genomes only available thanks to single-cell genomics or single-molecule sequencing, demonstrating the importance of these methods for viral discovery. The spatiotemporal pattern of these abundant uncultivated viruses is more variable than that of cultured viruses. Despite strong environmental gradients, season and location had surprisingly little impact on the viral community within an estuary, but we saw a significant distinction between the two estuaries and also between estuarine and open ocean viromes.
Collapse
|
50
|
The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles. Commun Biol 2021; 4:307. [PMID: 33686191 PMCID: PMC7940616 DOI: 10.1038/s42003-021-01810-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/08/2021] [Indexed: 12/22/2022] Open
Abstract
The deep biosphere contains members from all three domains of life along with viruses. Here we investigate the deep terrestrial virosphere by sequencing community nucleic acids from three groundwaters of contrasting chemistries, origins, and ages. These viromes constitute a highly unique community compared to other environmental viromes and sequenced viral isolates. Viral host prediction suggests that many of the viruses are associated with Firmicutes and Patescibacteria, a superphylum lacking previously described active viruses. RNA transcript-based activity implies viral predation in the shallower marine water-fed groundwater, while the deeper and more oligotrophic waters appear to be in ‘metabolic standby’. Viral encoded antibiotic production and resistance systems suggest competition and antagonistic interactions. The data demonstrate a viral community with a wide range of predicted hosts that mediates nutrient recycling to support a higher microbial turnover than previously anticipated. This suggests the presence of ‘kill-the-winner’ oscillations creating slow motion ‘boom and burst’ cycles. Karin Holmfeldt et al. sequence metagenomes and metatranscriptomes of viruses in deep groundwaters down to 448 m below the surface. The results reveal ecological dynamics of viruses including slow motion ‘boom and burst’ cycles and a ‘kill the winner’ model potentially driven by viral predation.
Collapse
|