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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.
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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.
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Pérez-Losada M, Arenas M, Galán JC, Bracho MA, Hillung J, García-González N, González-Candelas F. High-throughput sequencing (HTS) for the analysis of viral populations. INFECTION GENETICS AND EVOLUTION 2020; 80:104208. [PMID: 32001386 DOI: 10.1016/j.meegid.2020.104208] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 12/12/2022]
Abstract
The development of High-Throughput Sequencing (HTS) technologies is having a major impact on the genomic analysis of viral populations. Current HTS platforms can capture nucleic acid variation across millions of genes for both selected amplicons and full viral genomes. HTS has already facilitated the discovery of new viruses, hinted new taxonomic classifications and provided a deeper and broader understanding of their diversity, population and genetic structure. Hence, HTS has already replaced standard Sanger sequencing in basic and applied research fields, but the next step is its implementation as a routine technology for the analysis of viruses in clinical settings. The most likely application of this implementation will be the analysis of viral genomics, because the huge population sizes, high mutation rates and very fast replacement of viral populations have demonstrated the limited information obtained with Sanger technology. In this review, we describe new technologies and provide guidelines for the high-throughput sequencing and genetic and evolutionary analyses of viral populations and metaviromes, including software applications. With the development of new HTS technologies, new and refurbished molecular and bioinformatic tools are also constantly being developed to process and integrate HTS data. These allow assembling viral genomes and inferring viral population diversity and dynamics. Finally, we also present several applications of these approaches to the analysis of viral clinical samples including transmission clusters and outbreak characterization.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, USA; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain; Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain.
| | - Juan Carlos Galán
- Microbiology Service, Hospital Ramón y Cajal, Madrid, Spain; CIBER in Epidemiology and Public Health, Spain.
| | - Mª Alma Bracho
- CIBER in Epidemiology and Public Health, Spain; Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain.
| | - Julia Hillung
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| | - Neris García-González
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| | - Fernando González-Candelas
- CIBER in Epidemiology and Public Health, Spain; Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
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4
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Liang Y, Wang L, Wang Z, Zhao J, Yang Q, Wang M, Yang K, Zhang L, Jiao N, Zhang Y. Metagenomic Analysis of the Diversity of DNA Viruses in the Surface and Deep Sea of the South China Sea. Front Microbiol 2019; 10:1951. [PMID: 31507563 PMCID: PMC6716333 DOI: 10.3389/fmicb.2019.01951] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/08/2019] [Indexed: 11/13/2022] Open
Abstract
A metagenomic analysis of the viral community from five surface and five deep sea water (>2000 m below the surface, mbs) samples collected from the central basin of the South China Sea and adjacent Northwest Pacific Ocean during July-August 2017 was conducted herein. We builded up a South China Sea DNA virome (SCSV) dataset of 29,967 viral Operational Taxonomic Units (vOTUs), which is comparable to the viral populations from the original Tara Ocean and Malaspina expeditions. The most abundant and widespread viral populations were from the uncultivated viruses annotated from the viral metagenomics. Only 74 and 37 vOTUs have similarity with the reported genomes from the cultivated viruses and the single-virus genomics, respectively. The community structures of deep sea viromes in the SCSV were generally different from the surface viromes. The carbon flux and nutrients (PO4 and NOx) were related to the surface and deep sea viromes in the SCSV, respectively. In the SCSV, the annotated vOTUs could be affiliated to the cultivated viruses mainly including Pelagibacter (SAR11) phage HTVC010P, Prochlorococcus phages (P-GSP1, P-SSM4, and P-TIM68), Cyanophages (MED4-184 and MED4-117) and Mycobacterium phages (Sparky and Squirty). It indicated that phage infection to the SAR11 cluster may occur ubiquitously and has significant impacts on bathypelagic SAR11 communities in the deep sea. Meanwhile, as Prochlorococcus is prominently distributed in the euphotic ocean, the existence of their potential phages in the deep sea suggested the sedimentation mechanism might contribute to the formation of the deep sea viromes. Intriguingly, the presence of Mycobacterium phages only in the deep sea viromes, suggests inhabitance of endemic viral populations in the deep sea viromes in the SCSV. This study provided an insight of the viral community in the South China Sea and for the first time uncovered the deep sea viral diversity in the central basin of the South China Sea.
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Affiliation(s)
- Yantao Liang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.,State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Long Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Zengmeng Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Jiulong Zhao
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Qingwei Yang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Kaiguang Yang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Lihua Zhang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
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Yahya RZ, Arrieta JM, Cusack M, Duarte CM. Airborne Prokaryote and Virus Abundance Over the Red Sea. Front Microbiol 2019; 10:1112. [PMID: 31214129 PMCID: PMC6554326 DOI: 10.3389/fmicb.2019.01112] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 05/01/2019] [Indexed: 11/13/2022] Open
Abstract
Aeolian dust exerts a considerable influence on atmospheric and oceanic conditions negatively impacting human health, particularly in arid and semi-arid regions like Saudi Arabia. Aeolian dust is often characterized by its mineral and chemical composition; however, there is a microbiological component of natural aerosols that has received comparatively little attention. Moreover, the amount of materials suspended in the atmosphere is highly variable from day to day. Thus, understanding the variability of atmospheric dust loads and suspended microbes throughout the year is essential to clarify the possible effects of dust on the Red Sea ecosystem. Here, we present the first estimates of dust and microbial loads at a coastal site on the Red Sea over a 2-year period, supplemented with measurements from dust samples collected along the Red Sea basin in offshore waters. Weekly average dust loads from a coastal site on the Red Sea ranged from 4.6 to 646.11 μg m-3, while the abundance of airborne prokaryotic cells and viral-like particles (VLPs) ranged from 77,967 to 1,203,792 cells m-3 and from 69,615 to 3,104,758 particles m-3, respectively. To the best of our knowledge, these are the first estimates of airborne microbial abundance in this region. The elevated concentrations of resuspended dust particles and suspended microbes found in the air indicate that airborne microbes may potentially have a large impact on human health and on the Red Sea ecosystem.
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Affiliation(s)
- Razan Z Yahya
- Division of Biological and Environmental Science and Engineering, Red Sea Research Centre and Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Jesús M Arrieta
- Spanish Institute of Oceanography (IEO), Oceanographic Center of The Canary Islands, Santa Cruz de Tenerife, Spain
| | - Michael Cusack
- Division of Biological and Environmental Science and Engineering, Red Sea Research Centre and Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Carlos M Duarte
- Division of Biological and Environmental Science and Engineering, Red Sea Research Centre and Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Gong Z, Liang Y, Wang M, Jiang Y, Yang Q, Xia J, Zhou X, You S, Gao C, Wang J, He J, Shao H, McMinn A. Viral Diversity and Its Relationship With Environmental Factors at the Surface and Deep Sea of Prydz Bay, Antarctica. Front Microbiol 2018; 9:2981. [PMID: 30559737 PMCID: PMC6287040 DOI: 10.3389/fmicb.2018.02981] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 11/19/2018] [Indexed: 12/31/2022] Open
Abstract
A viral metagenomic analysis of five surface and two bottom water (878 meters below surface, mbs, and 3,357 mbs) samples from Prydz Bay, was conducted during February-March 2015. The results demonstrated that most of the DNA viruses were dsDNA viruses (79.73-94.06%, except at PBI1, 37.51%). Of these, Caudovirales (Siphoviridae, Myoviridae, and Podoviridae) phages were most abundant in surface seawater (67.67-71.99%), while nucleocytoplasmic large DNA viruses (NCLDVs) (Phycodnaviridae, Mimiviridae, and Pandoraviridae accounted for >30% of dsDNA viruses) were most abundant in the bottom water (3,357 mbs). Of the ssDNA viruses, Microviridae was the dominant family in PBI2, PBI3, PBOs, and PBI4b (57.09-87.55%), while Inoviridae (58.16%) was the dominant family in PBI1. Cellulophaga phages (phi38:1 and phi10:1) and Flavobacterium phage 11b, infecting the possible host strains affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes, were abundant in surface water dsDNA viromes. The long contig (PBI2_1_C) from the viral metagenomes were most similar to the genome architectures of Cellulophaga phage phi10:1 and Flavobacterium phage 11b from the Arctic Ocean. Comparative analysis showed that the surface viral community of Prydz Bay could be clearly separated from other marine and freshwater environments. The deep sea viral community was similar to the deep sea viral metagenome at A Long-term Oligotrophic Habitat Assessment Station (ALOHA, at 22°45'N, 158°00'W). The multivariable analysis indicated that nutrients probably played an important role in shaping the local viral community structure. This study revealed the preliminary characteristics of the viral community in Prydz Bay, from both the surface and the deep sea. It provided evidence of the relationships between the virome and the environment in Prydz Bay and provided the first data from the deep sea viral community of the Southern Ocean.
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Affiliation(s)
- Zheng Gong
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Qingwei Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jun Xia
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xinhao Zhou
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Siyuan You
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chen Gao
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jian Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jianfeng He
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
| | - Hongbing Shao
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
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7
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Hewson I, Bistolas KSI, Button JB, Jackson EW. Occurrence and seasonal dynamics of RNA viral genotypes in three contrasting temperate lakes. PLoS One 2018; 13:e0194419. [PMID: 29543885 PMCID: PMC5854377 DOI: 10.1371/journal.pone.0194419] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/04/2018] [Indexed: 11/18/2022] Open
Abstract
Decades of research have demonstrated the crucial importance of viruses in freshwater ecosystems. However, few studies have focused on the seasonal dynamics and potential hosts of RNA viruses. We surveyed microbial-sized (i.e. 5-0.2 μm) mixed community plankton transcriptomes for RNA viral genomes and investigated their distribution between microbial and macrobial plankton over a seasonal cycle across three temperate lakes by quantitative reverse transcriptase PCR (qRT-PCR). A total of 30 contigs bearing similarity to RNA viral genomes were recovered from a global assembly of 30 plankton RNA libraries. Of these, only 13 were found in >2 libraries and recruited >100 reads (of 9.13 x 107 total reads), representing several picornaviruses, two tobamoviruses and a reovirus. We quantified the abundance of four picornaviruses and the reovirus monthly from August 2014 to May 2015. Patterns of viral abundance in the >5 μm size fraction and representation in microbial-sized community RNA libraries over time suggest that one picornavirus genotype (TS24835) and the reovirus (TS148892) may infect small (<5 μm) eukaryotic microorganisms, while two other picornaviruses (TS24641 and TS4340) may infect larger (>5 μm) eukaryotic microorganisms or metazoa. Our data also suggest that picornavirus TS152062 may originate from an allochthonous host. All five viral genotypes were present in at least one size fraction across all 3 lakes during the year, suggesting that RNA viruses may easily disperse between adjacent aquatic habitats. Our data therefore demonstrate that RNA viruses are widespread in temperate lacustrine ecosystems, and may provide evidence of viral infection in larger eukaryotes (including metazoa) inhabiting the lakes.
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Affiliation(s)
- Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
| | - Kalia S. I. Bistolas
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
| | - Jason B. Button
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
| | - Elliot W. Jackson
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
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Corinaldesi C, Tangherlini M, Dell'Anno A. From virus isolation to metagenome generation for investigating viral diversity in deep-sea sediments. Sci Rep 2017; 7:8355. [PMID: 28827715 PMCID: PMC5566222 DOI: 10.1038/s41598-017-08783-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 07/13/2017] [Indexed: 11/09/2022] Open
Abstract
Viruses are the most abundant and, likely, one of the most diverse biological components in the oceans. By infecting their hosts, they play key roles in biogeochemical cycles and ecosystem functioning at a global scale. The ocean interior hosts most of the microbial life, and, despite deep-sea sediments represent the main repository of this component and the largest biome on Earth, viral diversity in these ecosystems remains almost completely unknown. We compared a physical-chemical procedure and a previously published sediment washing-based procedure for isolating viruses from benthic deep-sea ecosystems to generate viromes through high-throughput sequencing. The procedure based on a physical-chemical dislodgment of viral particles from the sediments, followed by vacuum filtration was much more efficient allowing us to recover >85% of the extractable viruses. By using this procedure, a high fraction of viral DNA was recovered and new viromes from different benthic deep-sea sites were generated. Such viromes were diversified in terms of both viral families and putative functions. Overall, the results presented here provide new insights for evaluating benthic deep-sea viral diversity through metagenomic analyses, and reveal that deep-sea sediments are a hot spot of novel viral genotypes and functions.
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Affiliation(s)
- Cinzia Corinaldesi
- Department of Sciences and Engineering of Materials, Environment and Urbanistics, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Michael Tangherlini
- Department of Environmental and Life Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Antonio Dell'Anno
- Department of Environmental and Life Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
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Abstract
Viruses are believed to be responsible for the mortality of host organisms. However, some recent investigations reveal that viruses may be essential for host survival. To date, it remains unclear whether viruses are beneficial or harmful to their hosts. To reveal the roles of viruses in the virus-host interactions, viromes and microbiomes of sediment samples from three deep-sea hydrothermal vents were explored in this study. To exclude the influence of exogenous DNAs on viromes, the virus particles were purified with nuclease (DNase I and RNase A) treatments and cesium chloride density gradient centrifugation. The metagenomic analysis of viromes without exogenous DNA contamination and microbiomes of vent samples indicated that viruses had compensation effects on the metabolisms of their host microorganisms. Viral genes not only participated in most of the microbial metabolic pathways but also formed branched pathways in microbial metabolisms, including pyrimidine metabolism; alanine, aspartate, and glutamate metabolism; nitrogen metabolism and assimilation pathways of the two-component system; selenocompound metabolism; aminoacyl-tRNA biosynthesis; and amino sugar and nucleotide sugar metabolism. As is well known, deep-sea hydrothermal vent ecosystems exist in relatively isolated environments which are barely influenced by other ecosystems. The metabolic compensation of hosts mediated by viruses might represent a very important aspect of virus-host interactions. Viruses are the most abundant biological entities in the oceans and have very important roles in regulating microbial community structure and biogeochemical cycles. The relationship between virus and host microbes is broadly thought to be that of predator and prey. Viruses can lyse host cells to control microbial population sizes and affect community structures of hosts by killing specific microbes. However, viruses also influence their hosts through manipulation of bacterial metabolism. We found that viral genes not only participated in most microbial metabolic pathways but also formed branched pathways in microbial metabolisms. The metabolic compensation of hosts mediated by viruses may help hosts to adapt to extreme environments and may be essential for host survival.
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Miranda JA, Culley AI, Schvarcz CR, Steward GF. RNA viruses as major contributors to Antarctic virioplankton. Environ Microbiol 2016; 18:3714-3727. [PMID: 26950773 DOI: 10.1111/1462-2920.13291] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 03/05/2016] [Indexed: 11/28/2022]
Abstract
Early work on marine algal viruses focused exclusively on those having DNA genomes, but recent studies suggest that RNA viruses, especially those with positive-sense, single-stranded RNA (+ssRNA) genomes, are abundant in tropical and temperate coastal seawater. To test whether this was also true of polar waters, we estimated the relative abundances of RNA and DNA viruses using a mass ratio approach and conducted shotgun metagenomics on purified viral samples collected from a coastal site near Palmer Station, Antarctica on six occasions throughout a summer phytoplankton bloom (November-March). Our data suggest that RNA viruses contributed up to 65% of the total virioplankton (8-65%), and that, as observed previously in warmer waters, the majority of RNA viruses in these Antarctic RNA virus metagenomes had +ssRNA genomes most closely related to viruses in the order Picornavirales. Assembly of the metagenomic reads resulted in five novel, nearly complete genomes, three of which had features similar to diatom-infecting viruses. Our data are consistent with the hypothesis that RNA viruses influence diatom bloom dynamics in Antarctic waters.
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Affiliation(s)
- Jaclyn A Miranda
- Department of Oceanography, Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, 1950 East-West Road, Honolulu, HI, 96822, USA
| | - Alexander I Culley
- Department of Oceanography, Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, 1950 East-West Road, Honolulu, HI, 96822, USA
| | - Christopher R Schvarcz
- Department of Oceanography, Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, 1950 East-West Road, Honolulu, HI, 96822, USA
| | - Grieg F Steward
- Department of Oceanography, Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, 1950 East-West Road, Honolulu, HI, 96822, USA
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11
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Rising to the challenge: accelerated pace of discovery transforms marine virology. Nat Rev Microbiol 2015; 13:147-59. [PMID: 25639680 DOI: 10.1038/nrmicro3404] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Marine viruses have important roles in microbial mortality, gene transfer, metabolic reprogramming and biogeochemical cycling. In this Review, we discuss recent technological advances in marine virology including the use of near-quantitative, reproducible metagenomics for large-scale investigation of viral communities and the emergence of gene-based viral ecology. We also describe the reprogramming of microbially driven processes by viral metabolic genes, the identification of novel viruses using cultivation-dependent and cultivation-independent tools, and the potential for modelling studies to provide a framework for studying virus-host interactions. These transformative advances have set a rapid pace in exploring and predicting how marine viruses manipulate and respond to their environment.
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12
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Efficient purification and concentration of viruses from a large body of high turbidity seawater. MethodsX 2014; 1:197-206. [PMID: 26150953 PMCID: PMC4473021 DOI: 10.1016/j.mex.2014.09.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 09/11/2014] [Accepted: 09/12/2014] [Indexed: 11/29/2022] Open
Abstract
Marine viruses are the most abundant entities in the ocean and play crucial roles in the marine ecological system. However, understanding of viral diversity on large scale depends on efficient and reliable viral purification and concentration techniques. Here, we report on developing an efficient method to purify and concentrate viruses from large body of high turbidity seawater. The developed method characterizes with high viral recovery efficiency, high concentration factor, high viral particle densities and high-throughput, and is reliable for viral concentration from high turbidity seawater. Recovered viral particles were used directly for subsequent analysis by epifluorescence microscopy, transmission electron microscopy and metagenomic sequencing. Three points are essential for this method:The sampled seawater (>150 L) was initially divided into two parts, water fraction and settled matter fraction, after natural sedimentation. Both viruses in the water fraction concentrated by tangential flow filtration (TFF) and viruses isolated from the settled matter fraction were considered as the whole viral community in high turbidity seawater. The viral concentrates were re-concentrated by using centrifugal filter device in order to obtain high density of viral particles.
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13
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Hurwitz BL, Brum JR, Sullivan MB. Depth-stratified functional and taxonomic niche specialization in the 'core' and 'flexible' Pacific Ocean Virome. ISME JOURNAL 2014; 9:472-84. [PMID: 25093636 DOI: 10.1038/ismej.2014.143] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 06/22/2014] [Accepted: 06/24/2014] [Indexed: 11/09/2022]
Abstract
Microbes drive myriad ecosystem processes, and their viruses modulate microbial-driven processes through mortality, horizontal gene transfer, and metabolic reprogramming by viral-encoded auxiliary metabolic genes (AMGs). However, our knowledge of viral roles in the oceans is primarily limited to surface waters. Here we assess the depth distribution of protein clusters (PCs) in the first large-scale quantitative viral metagenomic data set that spans much of the pelagic depth continuum (the Pacific Ocean Virome; POV). This established 'core' (180 PCs; one-third new to science) and 'flexible' (423K PCs) community gene sets, including niche-defining genes in the latter (385 and 170 PCs are exclusive and core to the photic and aphotic zones, respectively). Taxonomic annotation suggested that tailed phages are ubiquitous, but not abundant (<5% of PCs) and revealed depth-related taxonomic patterns. Functional annotation, coupled with extensive analyses to document non-viral DNA contamination, uncovered 32 new AMGs (9 core, 20 photic and 3 aphotic) that introduce ways in which viruses manipulate infected host metabolism, and parallel depth-stratified host adaptations (for example, photic zone genes for iron-sulphur cluster modulation for phage production, and aphotic zone genes for high-pressure deep-sea survival). Finally, significant vertical flux of photic zone viruses to the deep sea was detected, which is critical for interpreting depth-related patterns in nature. Beyond the ecological advances outlined here, this catalog of viral core, flexible and niche-defining genes provides a resource for future investigation into the organization, function and evolution of microbial molecular networks to mechanistically understand and model viral roles in the biosphere.
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Affiliation(s)
- Bonnie L Hurwitz
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Jennifer R Brum
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
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14
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Abstract
UNLABELLED Viruses have a profound influence on the ecology and evolution of plankton, but our understanding of the composition of the aquatic viral communities is still rudimentary. This is especially true of those viruses having RNA genomes. The limited data that have been published suggest that the RNA virioplankton is dominated by viruses with positive-sense, single-stranded (+ss) genomes that have features in common with those of eukaryote-infecting viruses in the order Picornavirales (picornavirads). In this study, we investigated the diversity of the RNA virus assemblages in tropical coastal seawater samples using targeted PCR and metagenomics. Amplification of RNA-dependent RNA polymerase (RdRp) genes from fractions of a buoyant density gradient suggested that the distribution of two major subclades of the marine picornavirads was largely congruent with the distribution of total virus-like RNA, a finding consistent with their proposed dominance. Analyses of the RdRp sequences in the library revealed the presence of many diverse phylotypes, most of which were related only distantly to those of cultivated viruses. Phylogenetic analysis suggests that there were hundreds of unique picornavirad-like phylotypes in one 35-liter sample that differed from one another by at least as much as the differences among currently recognized species. Assembly of the sequences in the metagenome resulted in the reconstruction of six essentially complete viral genomes that had features similar to viruses in the families Bacillarna-, Dicistro-, and Marnaviridae. Comparison of the tropical seawater metagenomes with those from other habitats suggests that +ssRNA viruses are generally the most common types of RNA viruses in aquatic environments, but biases in library preparation remain a possible explanation for this observation. IMPORTANCE Marine plankton account for much of the photosynthesis and respiration on our planet, and they influence the cycling of carbon and the distribution of nutrients on a global scale. Despite the fundamental importance of viruses to plankton ecology and evolution, most of the viruses in the sea, and the identities of their hosts, are unknown. This report is one of very few that delves into the genetic diversity within RNA-containing viruses in the ocean. The data expand the known range of viral diversity and shed new light on the physical properties and genetic composition of RNA viruses in the ocean.
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15
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Sachsenröder J, Twardziok SO, Scheuch M, Johne R. The general composition of the faecal virome of pigs depends on age, but not on feeding with a probiotic bacterium. PLoS One 2014; 9:e88888. [PMID: 24586429 PMCID: PMC3929612 DOI: 10.1371/journal.pone.0088888] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/13/2014] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The pig faecal virome, which comprises the community of viruses present in pig faeces, is complex and consists of pig viruses, bacteriophages, transiently passaged plant viruses and other minor virus species. Only little is known about factors influencing its general composition. Here, the effect of the probiotic bacterium Enterococcus faecium (E. faecium) NCIMB 10415 on the pig faecal virome composition was analysed in a pig feeding trial with sows and their piglets, which received either the probiotic bacterium or not. RESULTS From 8 pooled faecal samples derived from the feeding trial, DNA and RNA virus particles were prepared and subjected to process-controlled Next Generation Sequencing resulting in 390,650 sequence reads. In average, 14% of the reads showed significant sequence identities to known viruses. The percentage of detected mammalian virus sequences was highest (55-77%) in the samples of the youngest piglets and lowest (8-10%) in the samples of the sows. In contrast, the percentage of bacteriophage sequences increased from 22-44% in the youngest piglets to approximately 90% in the sows. The dominating mammalian viruses differed remarkably among 12 day-old piglets (kobuvirus), 54 day-old piglets (boca-, dependo- and pig stool-associated small circular DNA virus [PigSCV]) and the sows (PigSCV, circovirus and "circovirus-like" viruses CB-A and RW-A). In addition, the Shannon index, which reflects the diversity of sequences present in a sample, was generally higher for the sows as compared to the piglets. No consistent differences in the virome composition could be identified between the viromes of the probiotic bacterium-treated group and the control group. CONCLUSION The analysis indicates that the pig faecal virome shows a high variability and that its general composition is mainly dependent on the age of the pigs. Changes caused by feeding with the probiotic bacterium E. faecium could not be demonstrated using the applied metagenomics method.
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Affiliation(s)
| | - Sven O. Twardziok
- Institute for Molecular Biology and Bioinformatic, Charité Berlin, Berlin, Germany
| | | | - Reimar Johne
- Federal Institute for Risk Assessment, Berlin, Germany
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16
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Martínez Martínez J, Swan BK, Wilson WH. Marine viruses, a genetic reservoir revealed by targeted viromics. ISME JOURNAL 2013; 8:1079-88. [PMID: 24304671 DOI: 10.1038/ismej.2013.214] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 10/01/2013] [Accepted: 10/31/2013] [Indexed: 11/09/2022]
Abstract
Metagenomics has opened new windows on investigating viral diversity and functions. Viromic studies typically require large sample volumes and filtration through 0.2 μm pore-size filters, consequently excluding or under-sampling tailed and very large viruses. We have optimized a targeted viromic approach that employs fluorescence-activated sorting and whole genome amplification to produce dsDNA-enriched libraries from discrete viral populations from a 1-ml water sample. Using this approach on an environmental sample from the Patagonian Shelf, we produced three distinct libraries. One of the virus libraries was dominated (79.65% of sequences with known viral homology) by giant viruses from the Mimiviridae and Phycodnaviridae families, while the two other viromes were dominated by smaller phycodnaviruses, cyanophages and other bacteriophages. The estimated genotypic richness and diversity in our sorted viromes, with 52-163 estimated genotypes, was much lower than in previous virome reports. Fragment recruitment of metagenome reads to selected reference viral genomes yields high genome coverage, suggesting little amplification and sequencing bias against some genomic regions. These results underscore the value of our approach as an effective way to target and investigate specific virus groups. In particular, it will help reveal the diversity and abundance of giant viruses in marine ecosystems.
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Affiliation(s)
| | - Brandon K Swan
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
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Pagnier I, Reteno DGI, Saadi H, Boughalmi M, Gaia M, Slimani M, Ngounga T, Bekliz M, Colson P, Raoult D, La Scola B. A decade of improvements in Mimiviridae and Marseilleviridae isolation from amoeba. Intervirology 2013; 56:354-63. [PMID: 24157882 DOI: 10.1159/000354556] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Since the isolation of the first giant virus, the Mimivirus, by T.J. Rowbotham in a cooling tower in Bradford, UK, and after its characterisation by our group in 2003, we have continued to develop novel strategies to isolate additional strains. By first focusing on cooling towers using our original time-consuming procedure, we were able to isolate a new lineage of giant virus called Marseillevirus and a new Mimivirus strain called Mamavirus. In the following years, we have accumulated the world's largest unique collection of giant viruses by improving the use of antibiotic combinations to avoid bacterial contamination of amoeba, developing strategies of preliminary screening of samples by molecular methods, and using a high-throughput isolation method developed by our group. Based on the inoculation of nearly 7,000 samples, our collection currently contains 43 strains of Mimiviridae (14 in lineage A, 6 in lineage B, and 23 in lineage C) and 17 strains of Marseilleviridae isolated from various environments, including 3 of human origin. This study details the procedures used to build this collection and paves the way for the high-throughput isolation of new isolates to improve the record of giant virus distribution in the environment and the determination of their pangenome.
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Affiliation(s)
- Isabelle Pagnier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Aix-Marseille Université, Marseille, France
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18
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Orsini M, Carcangiu S, Cuccuru G, Uva P, Tramontano A. The PARIGA server for real time filtering and analysis of reciprocal BLAST results. PLoS One 2013; 8:e62224. [PMID: 23667459 PMCID: PMC3646873 DOI: 10.1371/journal.pone.0062224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Accepted: 03/19/2013] [Indexed: 12/03/2022] Open
Abstract
BLAST-based similarity searches are commonly used in several applications involving both nucleotide and protein sequences. These applications span from simple tasks such as mapping sequences over a database to more complex procedures as clustering or annotation processes. When the amount of analysed data increases, manual inspection of BLAST results become a tedious procedure. Tools for parsing or filtering BLAST results for different purposes are then required. We describe here PARIGA (http://resources.bioinformatica.crs4.it/pariga/), a server that enables users to perform all-against-all BLAST searches on two sets of sequences selected by the user. Moreover, since it stores the two BLAST output in a python-serialized-objects database, results can be filtered according to several parameters in real-time fashion, without re-running the process and avoiding additional programming efforts. Results can be interrogated by the user using logical operations, for example to retrieve cases where two queries match same targets, or when sequences from the two datasets are reciprocal best hits, or when a query matches a target in multiple regions. The Pariga web server is designed to be a helpful tool for managing the results of sequence similarity searches. The design and implementation of the server renders all operations very fast and easy to use.
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Affiliation(s)
- Massimiliano Orsini
- CRS4 Bioinformatics Laboratory, Science and Technology Park Polaris, Pula, Italy.
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19
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He B, Li Z, Yang F, Zheng J, Feng Y, Guo H, Li Y, Wang Y, Su N, Zhang F, Fan Q, Tu C. Virome profiling of bats from Myanmar by metagenomic analysis of tissue samples reveals more novel Mammalian viruses. PLoS One 2013; 8:e61950. [PMID: 23630620 PMCID: PMC3632529 DOI: 10.1371/journal.pone.0061950] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 03/11/2013] [Indexed: 02/07/2023] Open
Abstract
Bats are reservoir animals harboring many important pathogenic viruses and with the capability of transmitting these to humans and other animals. To establish an effective surveillance to monitor transboundary spread of bat viruses between Myanmar and China, complete organs from the thorax and abdomen from 853 bats of six species from two Myanmar counties close to Yunnan province, China, were collected and tested for their virome through metagenomics by Solexa sequencing and bioinformatic analysis. In total, 3,742,314 reads of 114 bases were generated, and over 86% were assembled into 1,649,512 contigs with an average length of 114 bp, of which 26,698 (2%) contigs were recognizable viral sequences belonging to 24 viral families. Of the viral contigs 45% (12,086/26,698) were related to vertebrate viruses, 28% (7,443/26,698) to insect viruses, 27% (7,074/26,698) to phages and 95 contigs to plant viruses. The metagenomic results were confirmed by PCR of selected viruses in all bat samples followed by phylogenetic analysis, which has led to the discovery of some novel bat viruses of the genera Mamastrovirus, Bocavirus, Circovirus, Iflavirus and Orthohepadnavirus and to their prevalence rates in two bat species. In conclusion, the present study aims to present the bat virome in Myanmar, and the results obtained further expand the spectrum of viruses harbored by bats.
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Affiliation(s)
- Biao He
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Zuosheng Li
- Center for Disease Control and Prevention, Chengdu Military Region of the People’s Liberation Army, Kunming, Yunnan, China
| | - Fanli Yang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Junfeng Zheng
- Center for Disease Control and Prevention, Chengdu Military Region of the People’s Liberation Army, Kunming, Yunnan, China
| | - Ye Feng
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Huancheng Guo
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Yingying Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Yiyin Wang
- Center for Disease Control and Prevention, Chengdu Military Region of the People’s Liberation Army, Kunming, Yunnan, China
| | - Nan Su
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Fuqiang Zhang
- Center for Disease Control and Prevention, Chengdu Military Region of the People’s Liberation Army, Kunming, Yunnan, China
| | - Quanshui Fan
- Center for Disease Control and Prevention, Chengdu Military Region of the People’s Liberation Army, Kunming, Yunnan, China
- * E-mail: (QF); (CT)
| | - Changchun Tu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin, China
- * E-mail: (QF); (CT)
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20
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Assembly of a marine viral metagenome after physical fractionation. PLoS One 2013; 8:e60604. [PMID: 23580170 PMCID: PMC3620275 DOI: 10.1371/journal.pone.0060604] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 02/28/2013] [Indexed: 11/19/2022] Open
Abstract
Metagenomic analyses of marine viruses generate an overview of viral genes present in a sample, but the percentage of the resulting sequence fragments that can be reassembled is low and the phenotype of the virus from which a given sequence derives is usually unknown. In this study, we employed physical fractionation to characterize the morphological and genomic traits of a subset of uncultivated viruses from a natural marine assemblage. Viruses from Kāne‘ohe Bay, Hawai‘i were fractionated by equilibrium buoyant density centrifugation in a cesium chloride (CsCl) gradient, and one fraction from the CsCl gradient was then further fractionated by strong anion-exchange chromatography. One of the fractions resulting from this two-dimensional separation appeared to be dominated by only a few virus types based on genome sizes and morphology. Sequences generated from a shotgun clone library of the viruses in this fraction were assembled into significantly more numerous contigs than have been generated with previous metagenomic investigations of whole DNA viral assemblages with comparable sequencing effort. Analysis of the longer contigs (up to 6.5 kb) assembled from our metagenome allowed us to assess gene arrangement in this subset of marine viruses. Our results demonstrate the potential for physical fractionation to facilitate sequence assembly from viral metagenomes and permit linking of morphological and genomic data for uncultivated viruses.
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21
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Hurwitz BL, Sullivan MB. The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One 2013; 8:e57355. [PMID: 23468974 PMCID: PMC3585363 DOI: 10.1371/journal.pone.0057355] [Citation(s) in RCA: 239] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 01/21/2013] [Indexed: 01/17/2023] Open
Abstract
Bacteria and their viruses (phage) are fundamental drivers of many ecosystem processes including global biogeochemistry and horizontal gene transfer. While databases and resources for studying function in uncultured bacterial communities are relatively advanced, many fewer exist for their viral counterparts. The issue is largely technical in that the majority (often 90%) of viral sequences are functionally 'unknown' making viruses a virtually untapped resource of functional and physiological information. Here, we provide a community resource that organizes this unknown sequence space into 27 K high confidence protein clusters using 32 viral metagenomes from four biogeographic regions in the Pacific Ocean that vary by season, depth, and proximity to land, and include some of the first deep pelagic ocean viral metagenomes. These protein clusters more than double currently available viral protein clusters, including those from environmental datasets. Further, a protein cluster guided analysis of functional diversity revealed that richness decreased (i) from deep to surface waters, (ii) from winter to summer, (iii) and with distance from shore in surface waters only. These data provide a framework from which to draw on for future metadata-enabled functional inquiries of the vast viral unknown.
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Affiliation(s)
- Bonnie L. Hurwitz
- Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Matthew B. Sullivan
- Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
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22
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Ocean viruses: rigorously evaluating the metagenomic sample-to-sequence pipeline. Virology 2012; 434:181-6. [PMID: 23084423 DOI: 10.1016/j.virol.2012.09.036] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 09/26/2012] [Accepted: 09/27/2012] [Indexed: 11/21/2022]
Abstract
As new environments are studied, viruses consistently emerge as important and prominent players in natural and man-made ecosystems. However, much of what we know is built both upon the foundation of the culturable minority and using methods that are often insufficiently ground-truthed. Here, we review the modern culture-independent viral metagenomic sample-to-sequence pipeline and how next-generation sequencing techniques are drastically altering our ability to systematically and rigorously evaluate them. Together, a series of studies quantitatively evaluate existing and new methods that allow-even for ultra-low DNA samples-the generation of replicable, near-quantitative datasets that maximize inter-comparability and biological inference.
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23
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Cassman N, Prieto-Davó A, Walsh K, Silva GGZ, Angly F, Akhter S, Barott K, Busch J, McDole T, Haggerty JM, Willner D, Alarcón G, Ulloa O, DeLong EF, Dutilh BE, Rohwer F, Dinsdale EA. Oxygen minimum zones harbour novel viral communities with low diversity. Environ Microbiol 2012; 14:3043-65. [PMID: 23039259 DOI: 10.1111/j.1462-2920.2012.02891.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 08/23/2012] [Accepted: 09/02/2012] [Indexed: 01/03/2023]
Abstract
Oxygen minimum zones (OMZs) are oceanographic features that affect ocean productivity and biodiversity, and contribute to ocean nitrogen loss and greenhouse gas emissions. Here we describe the viral communities associated with the Eastern Tropical South Pacific (ETSP) OMZ off Iquique, Chile for the first time through abundance estimates and viral metagenomic analysis. The viral-to-microbial ratio (VMR) in the ETSP OMZ fluctuated in the oxycline and declined in the anoxic core to below one on several occasions. The number of viral genotypes (unique genomes as defined by sequence assembly) ranged from 2040 at the surface to 98 in the oxycline, which is the lowest viral diversity recorded to date in the ocean. Within the ETSP OMZ viromes, only 4.95% of genotypes were shared between surface and anoxic core viromes using reciprocal BLASTn sequence comparison. ETSP virome comparison with surface marine viromes (Sargasso Sea, Gulf of Mexico, Kingman Reef, Chesapeake Bay) revealed a dissimilarity of ETSP OMZ viruses to those from other oceanic regions. From the 1.4 million non-redundant DNA sequences sampled within the altered oxygen conditions of the ETSP OMZ, more than 97.8% were novel. Of the average 3.2% of sequences that showed similarity to the SEED non-redundant database, phage sequences dominated the surface viromes, eukaryotic virus sequences dominated the oxycline viromes, and phage sequences dominated the anoxic core viromes. The viral community of the ETSP OMZ was characterized by fluctuations in abundance, taxa and diversity across the oxygen gradient. The ecological significance of these changes was difficult to predict; however, it appears that the reduction in oxygen coincides with an increased shedding of eukaryotic viruses in the oxycline, and a shift to unique viral genotypes in the anoxic core.
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Affiliation(s)
- Noriko Cassman
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
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Anderson RE, Brazelton WJ, Baross JA. Is the genetic landscape of the deep subsurface biosphere affected by viruses? Front Microbiol 2011; 2:219. [PMID: 22084639 PMCID: PMC3211056 DOI: 10.3389/fmicb.2011.00219] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 10/14/2011] [Indexed: 12/26/2022] Open
Abstract
Viruses are powerful manipulators of microbial diversity, biogeochemistry, and evolution in the marine environment. Viruses can directly influence the genetic capabilities and the fitness of their hosts through the use of fitness factors and through horizontal gene transfer. However, the impact of viruses on microbial ecology and evolution is often overlooked in studies of the deep subsurface biosphere. Subsurface habitats connected to hydrothermal vent systems are characterized by constant fluid flux, dynamic environmental variability, and high microbial diversity. In such conditions, high adaptability would be an evolutionary asset, and the potential for frequent host-virus interactions would be high, increasing the likelihood that cellular hosts could acquire novel functions. Here, we review evidence supporting this hypothesis, including data indicating that microbial communities in subsurface hydrothermal fluids are exposed to a high rate of viral infection, as well as viral metagenomic data suggesting that the vent viral assemblage is particularly enriched in genes that facilitate horizontal gene transfer and host adaptability. Therefore, viruses are likely to play a crucial role in facilitating adaptability to the extreme conditions of these regions of the deep subsurface biosphere. We also discuss how these results might apply to other regions of the deep subsurface, where the nature of virus-host interactions would be altered, but possibly no less important, compared to more energetic hydrothermal systems.
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Affiliation(s)
- Rika E Anderson
- School of Oceanography and Astrobiology Program, University of Washington Seattle, WA, USA
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