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Brewer TE, Stroupe ME, Jones KM. The genome, proteome and phylogenetic analysis of Sinorhizobium meliloti phage ΦM12, the founder of a new group of T4-superfamily phages. Virology 2013; 450-451:84-97. [PMID: 24503070 DOI: 10.1016/j.virol.2013.11.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 11/14/2013] [Accepted: 11/19/2013] [Indexed: 01/21/2023]
Abstract
Phage ΦM12 is an important transducing phage of the nitrogen-fixing rhizobial bacterium Sinorhizobium meliloti. Here we report the genome, phylogenetic analysis, and proteome of ΦM12, the first report of the genome and proteome of a rhizobium-infecting T4-superfamily phage. The structural genes of ΦM12 are most similar to T4-superfamily phages of cyanobacteria. ΦM12 is the first reported T4-superfamily phage to lack genes encoding class I ribonucleotide reductase (RNR) and exonuclease dexA, and to possess a class II coenzyme B12-dependent RNR. ΦM12's novel collection of genes establishes it as the founder of a new group of T4-superfamily phages, fusing features of cyanophages and phages of enteric bacteria.
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Affiliation(s)
- Tess E Brewer
- Department of Biological Science, Florida State University, Biology Unit I, 230A, 89 Chieftain Way, Tallahassee, FL 32306-4370, United States
| | - M Elizabeth Stroupe
- Department of Biological Science, Florida State University, Biology Unit I, 230A, 89 Chieftain Way, Tallahassee, FL 32306-4370, United States; Institute of Molecular Biophysics, Florida State University, 91 Chieftan Way Tallahassee, FL 32306-4380 United States
| | - Kathryn M Jones
- Department of Biological Science, Florida State University, Biology Unit I, 230A, 89 Chieftain Way, Tallahassee, FL 32306-4370, United States.
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Labonté JM, Suttle CA. Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea. Front Microbiol 2013; 4:404. [PMID: 24399999 PMCID: PMC3871881 DOI: 10.3389/fmicb.2013.00404] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 12/06/2013] [Indexed: 01/20/2023] Open
Abstract
Much remains to be learned about single-stranded (ss) DNA viruses in natural systems, and the evolutionary relationships among them. One of the eight recognized families of ssDNA viruses is the Microviridae, a group of viruses infecting bacteria. In this study we used metagenomic analysis, genome assembly, and amplicon sequencing of purified ssDNA to show that bacteriophages belonging to the subfamily Gokushovirinae within the Microviridae are genetically diverse and widespread members of marine microbial communities. Metagenomic analysis of coastal samples from the Gulf of Mexico (GOM) and British Columbia, Canada, revealed numerous sequences belonging to gokushoviruses and allowed the assembly of five putative genomes with an organization similar to chlamydiamicroviruses. Fragment recruitment to these genomes from different metagenomic data sets is consistent with gokushovirus genotypes being restricted to specific oceanic regions. Conservation among the assembled genomes allowed the design of degenerate primers that target an 800 bp fragment from the gene encoding the major capsid protein. Sequences could be amplified from coastal temperate and subtropical waters, but not from samples collected from the Arctic Ocean, or freshwater lakes. Phylogenetic analysis revealed that most sequences were distantly related to those from cultured representatives. Moreover, the sequences fell into at least seven distinct evolutionary groups, most of which were represented by one of the assembled metagenomes. Our results greatly expand the known sequence space for gokushoviruses, and reveal biogeographic separation and new evolutionary lineages of gokushoviruses in the oceans.
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Affiliation(s)
- Jessica M Labonté
- Department of Microbiology and Immunology, University of British Columbia Vancouver, BC, Canada
| | - Curtis A Suttle
- Department of Microbiology and Immunology, University of British Columbia Vancouver, BC, Canada ; Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia Vancouver, BC, Canada ; Department of Botany, University of British Columbia Vancouver, BC, Canada ; Canadian Institute for Advanced Research, University of British Columbia Vancouver, BC, Canada
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Mizuno CM, Rodriguez-Valera F, Kimes NE, Ghai R. Expanding the marine virosphere using metagenomics. PLoS Genet 2013; 9:e1003987. [PMID: 24348267 PMCID: PMC3861242 DOI: 10.1371/journal.pgen.1003987] [Citation(s) in RCA: 183] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 10/15/2013] [Indexed: 11/19/2022] Open
Abstract
Viruses infecting prokaryotic cells (phages) are the most abundant entities of the biosphere and contain a largely uncharted wealth of genomic diversity. They play a critical role in the biology of their hosts and in ecosystem functioning at large. The classical approaches studying phages require isolation from a pure culture of the host. Direct sequencing approaches have been hampered by the small amounts of phage DNA present in most natural habitats and the difficulty in applying meta-omic approaches, such as annotation of small reads and assembly. Serendipitously, it has been discovered that cellular metagenomes of highly productive ocean waters (the deep chlorophyll maximum) contain significant amounts of viral DNA derived from cells undergoing the lytic cycle. We have taken advantage of this phenomenon to retrieve metagenomic fosmids containing viral DNA from a Mediterranean deep chlorophyll maximum sample. This method allowed description of complete genomes of 208 new marine phages. The diversity of these genomes was remarkable, contributing 21 genomic groups of tailed bacteriophages of which 10 are completely new. Sequence based methods have allowed host assignment to many of them. These predicted hosts represent a wide variety of important marine prokaryotic microbes like members of SAR11 and SAR116 clades, Cyanobacteria and also the newly described low GC Actinobacteria. A metavirome constructed from the same habitat showed that many of the new phage genomes were abundantly represented. Furthermore, other available metaviromes also indicated that some of the new phages are globally distributed in low to medium latitude ocean waters. The availability of many genomes from the same sample allows a direct approach to viral population genomics confirming the remarkable mosaicism of phage genomes.
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Affiliation(s)
- Carolina Megumi Mizuno
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
- * E-mail:
| | - Nikole E. Kimes
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Rohit Ghai
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
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Abstract
Long-distance host-independent virus dispersal is poorly understood, especially for viruses found in isolated ecosystems. To demonstrate a possible dispersal mechanism, we show that bacteriophage T4, archaeal virus Sulfolobus spindle-shaped virus Kamchatka, and vaccinia virus are reversibly inactivated by mineralization in silica under conditions similar to volcanic hot springs. In contrast, bacteriophage PRD1 is not silicified. Moreover, silicification provides viruses with remarkable desiccation resistance, which could allow extensive aerial dispersal.
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55
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Ge X, Wu Y, Wang M, Wang J, Wu L, Yang X, Zhang Y, Shi Z. Viral metagenomics analysis of planktonic viruses in East Lake, Wuhan, China. Virol Sin 2013; 28:280-90. [PMID: 24132758 DOI: 10.1007/s12250-013-3365-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 09/28/2013] [Indexed: 11/28/2022] Open
Abstract
East Lake (Lake Donghu), located in Wuhan, China, is a typical city freshwater lake that has been experiencing eutrophic conditions and algal blooming during recent years. Marine and fresh water are considered to contain a large number of viruses. However, little is known about their genetic diversity because of the limited techniques for culturing viruses. In this study, we conducted a viral metagenomic analysis using a high-throughput sequencing technique with samples collected from East Lake in Spring, Summer, Autumn, and Winter. The libraries from four samples each generated 234,669, 71,837, 12,820, and 34,236 contigs (> 90 bp each), respectively. The genetic structure of the viral community revealed a high genetic diversity covering 23 viral families, with the majority of contigs homologous to DNA viruses, including members of Myoviridae, Podoviridae, Siphoviridae, Phycodnaviridae, and Microviridae, which infect bacteria or algae, and members of Circoviridae, which infect invertebrates and vertebrates. The highest viral genetic diversity occurred in samples collected in August, then December and June, and the least diversity in March. Most contigs have low-sequence identities with known viruses. PCR detection targeting the conserved sequences of genes (g20, psbA, psbD, and DNApol) of cyanophages further confirmed that there are novel cyanophages in the East Lake. Our viral metagenomic data provide the first preliminary understanding of the virome in one freshwater lake in China and would be helpful for novel virus discovery and the control of algal blooming in the future.
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Affiliation(s)
- Xingyi Ge
- Center for Emerging Infectious Diseases, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
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56
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Xia H, Li T, Deng F, Hu Z. Freshwater cyanophages. Virol Sin 2013; 28:253-9. [PMID: 24132756 DOI: 10.1007/s12250-013-3370-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 09/25/2013] [Indexed: 12/01/2022] Open
Abstract
Cyanophages are double-stranded DNA viruses that infect cyanobacteria, and they can be found in both freshwater and marine environments. They have a complex pattern of host ranges and play important roles in controlling cyanobacteria population. Unlike marine cyanophages, for which there have been a number of recent investigations, very little attention has been paid to freshwater cyanophages. This review summarizes the taxonomy and morphology, host range, distribution, seasonal dynamics, and complete genomes of freshwater cyanophages, as well as diagnostic markers that can be used to identify them.
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Affiliation(s)
- Han Xia
- State Key Laboratory of Virology, Virus Resource and Bioinformatics Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
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57
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Prevalence of viral photosynthetic and capsid protein genes from cyanophages in two large and deep perialpine lakes. Appl Environ Microbiol 2013; 79:7169-78. [PMID: 24038692 DOI: 10.1128/aem.01914-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyanophages are important components of aquatic ecosystems, but their genetic diversity has been little investigated in freshwaters. A yearlong survey was conducted in surface waters of the two largest natural perialpine lakes in France (Lake Annecy and Lake Bourget) to investigate part of this cyanophage diversity through the analysis of both structural (e.g., g20) and functional (e.g., psbA) genes. We found that these cyanophage signature genes were prevalent throughout the year but that the community compositions of g20 cyanomyoviruses were significantly different between the two lakes. In contrast, psbA-containing cyanophages seemed to be more similar between the two ecosystems. We also found that a large proportion of g20 sequences grouped with cyanomyophage isolates. psbA sequences, belonging to phages of Synechococcus spp., were characterized by distinct triplet motifs (with a novel viral triplet motif, EFE). Thus, our results show that cyanophages (i) are a diverse viral community in alpine lakes and (ii) are clearly distinct from some other freshwater and marine environments, suggesting the influence of unique biogeographic factors.
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58
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Schmidt HF, Sakowski EG, Williamson SJ, Polson SW, Wommack KE. Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton. ISME JOURNAL 2013; 8:103-14. [PMID: 23985748 DOI: 10.1038/ismej.2013.124] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 06/07/2013] [Accepted: 06/18/2013] [Indexed: 02/07/2023]
Abstract
Virioplankton have a significant role in marine ecosystems, yet we know little of the predominant biological characteristics of aquatic viruses that influence the flow of nutrients and energy through microbial communities. Family A DNA polymerases, critical to DNA replication and repair in prokaryotes, are found in many tailed bacteriophages. The essential role of DNA polymerase in viral replication makes it a useful target for connecting viral diversity with an important biological feature of viruses. Capturing the full diversity of this polymorphic gene by targeted approaches has been difficult; thus, full-length DNA polymerase genes were assembled out of virioplankton shotgun metagenomic sequence libraries (viromes). Within the viromes novel DNA polymerases were common and found in both double-stranded (ds) DNA and single-stranded (ss) DNA libraries. Finding DNA polymerase genes in ssDNA viral libraries was unexpected, as no such genes have been previously reported from ssDNA phage. Surprisingly, the most common virioplankton DNA polymerases were related to a siphovirus infecting an α-proteobacterial symbiont of a marine sponge and not the podoviral T7-like polymerases seen in many other studies. Amino acids predictive of catalytic efficiency and fidelity linked perfectly to the environmental clades, indicating that most DNA polymerase-carrying virioplankton utilize a lower efficiency, higher fidelity enzyme. Comparisons with previously reported, PCR-amplified DNA polymerase sequences indicated that the most common virioplankton metagenomic DNA polymerases formed a new group that included siphoviruses. These data indicate that slower-replicating, lytic or lysogenic phage populations rather than fast-replicating, highly lytic phages may predominate within the virioplankton.
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Affiliation(s)
- Helen F Schmidt
- Department of Plant & Soil Science, College of Marine Studies, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Eric G Sakowski
- Department of Plant & Soil Science, College of Marine Studies, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | | | - Shawn W Polson
- Department of Plant & Soil Science, College of Marine Studies, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - K Eric Wommack
- Department of Plant & Soil Science, College of Marine Studies, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
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59
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Bellas CM, Anesio AM. High diversity and potential origins of T4-type bacteriophages on the surface of Arctic glaciers. Extremophiles 2013; 17:861-70. [PMID: 23907516 DOI: 10.1007/s00792-013-0569-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 07/18/2013] [Indexed: 10/26/2022]
Abstract
Tailed bacteriophages are the most abundant viruses in the biosphere. Here we examined the T4-type bacteriophage community inhabiting the surface of two glaciers in Svalbard. We used a molecular approach to target g23, the major capsid protein gene, to demonstrate that in the extreme cryoconite hole habitats the T4-type phages are surprisingly diverse. Phylogenetic analysis revealed that cryoconite hole sediments harbour a mixed phage community spanning multiple T4-type phage subgroups. The majority (71 %) of phage sequences clustered into three novel phylogenetically distinct groups, whilst the remainder clustered with known marine and soil derived phage sequences. The meltwater in cryoconite holes also contained a further distinct phage community which was related to previously detected marine phage variants. The ability of phages to move between marine and glacial habitats was tested in a transplantation experiment. Phages from the nearby marine fjord were found to be capable of initiating infection of supraglacial bacteria, suggesting suitable hosts could be found by non-native phages. Together this evidence suggests that the surface of glaciers contain both novel and cosmopolitan phages, some of which may have arrived in the cryosphere from other biomes.
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Affiliation(s)
- Christopher M Bellas
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, BS8 1SS, Bristol, UK.
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60
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Winter C, Matthews B, Suttle CA. Effects of environmental variation and spatial distance on bacteria, archaea and viruses in sub-polar and arctic waters. THE ISME JOURNAL 2013; 7:1507-18. [PMID: 23552622 PMCID: PMC3721122 DOI: 10.1038/ismej.2013.56] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 03/01/2013] [Accepted: 03/04/2013] [Indexed: 11/17/2022]
Abstract
We investigated the influence of environmental parameters and spatial distance on bacterial, archaeal and viral community composition from 13 sites along a 3200-km long voyage from Halifax to Kugluktuk (Canada) through the Labrador Sea, Baffin Bay and the Arctic Archipelago. Variation partitioning was used to disentangle the effects of environmental parameters, spatial distance and spatially correlated environmental parameters on prokaryotic and viral communities. Viral and prokaryotic community composition were related in the Labrador Sea, but were independent of each other in Baffin Bay and the Arctic Archipelago. In oceans, the dominant dispersal mechanism for prokaryotes and viruses is the movement of water masses, thus, dispersal for both groups is passive and similar. Nevertheless, spatial distance explained 7-19% of the variation in viral community composition in the Arctic Archipelago, but was not a significant predictor of bacterial or archaeal community composition in either sampling area, suggesting a decoupling of the processes regulating community composition within these taxonomic groups. According to the metacommunity theory, patterns in bacterial and archaeal community composition suggest a role for species sorting, while patterns of virus community composition are consistent with species sorting in the Labrador Sea and suggest a potential role of mass effects in the Arctic Archipelago. Given that, a specific prokaryotic taxon may be infected by multiple viruses with high reproductive potential, our results suggest that viral community composition was subject to a high turnover relative to prokaryotic community composition in the Arctic Archipelago.
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Affiliation(s)
- Christian Winter
- Department of Earth and Ocean Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.
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61
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Labonté JM, Suttle CA. Previously unknown and highly divergent ssDNA viruses populate the oceans. ISME JOURNAL 2013; 7:2169-77. [PMID: 23842650 DOI: 10.1038/ismej.2013.110] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 05/30/2013] [Accepted: 06/04/2013] [Indexed: 11/09/2022]
Abstract
Single-stranded DNA (ssDNA) viruses are economically important pathogens of plants and animals, and are widespread in oceans; yet, the diversity and evolutionary relationships among marine ssDNA viruses remain largely unknown. Here we present the results from a metagenomic study of composite samples from temperate (Saanich Inlet, 11 samples; Strait of Georgia, 85 samples) and subtropical (46 samples, Gulf of Mexico) seawater. Most sequences (84%) had no evident similarity to sequenced viruses. In total, 608 putative complete genomes of ssDNA viruses were assembled, almost doubling the number of ssDNA viral genomes in databases. These comprised 129 genetically distinct groups, each represented by at least one complete genome that had no recognizable similarity to each other or to other virus sequences. Given that the seven recognized families of ssDNA viruses have considerable sequence homology within them, this suggests that many of these genetic groups may represent new viral families. Moreover, nearly 70% of the sequences were similar to one of these genomes, indicating that most of the sequences could be assigned to a genetically distinct group. Most sequences fell within 11 well-defined gene groups, each sharing a common gene. Some of these encoded putative replication and coat proteins that had similarity to sequences from viruses infecting eukaryotes, suggesting that these were likely from viruses infecting eukaryotic phytoplankton and zooplankton.
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Affiliation(s)
- Jessica M Labonté
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
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62
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Zhong X, Berdjeb L, Jacquet S. Temporal dynamics and structure of picocyanobacteria and cyanomyoviruses in two large and deep peri-alpine lakes. FEMS Microbiol Ecol 2013; 86:312-26. [PMID: 23772675 DOI: 10.1111/1574-6941.12166] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 06/05/2013] [Accepted: 06/05/2013] [Indexed: 11/29/2022] Open
Abstract
We conducted a 1-year survey of the surface waters of two deep peri-alpine lakes, and investigated the abundances and community structure of picocyanobacteria and co-occurring cyanomyophages. Picocyanobacterial abundances ranged between 4.5 × 10(4) and 1.6 × 10(5) cells mL(-1) in Lake Annecy vs. 2.2 × 10(3) and 1.6 × 10(5) cells mL(-1) in Lake Bourget. Cyanomyoviruses ranged between 2.8 × 10(3) and 3.7 × 10(5) copies of g 20 mL(-1) in Lake Annecy vs. between 9.4 × 10(3) and 9.4 × 10(5) copies of g 20 mL(-1) in Lake Bourget. The structures of picocyanobacteria and cyanomyoviruses differed in the two lakes, and a more pronounced dynamic pattern with greater seasonality was observed in Lake Bourget. At the annual scale, there was no relationship between cyanomyovirus and picocyanobacterial abundances or structures, but we could observe that abundances of the two communities covaried in spring in Lake Bourget. We showed that (i) the changes of picocyanobacteria and cyanomyoviruses were caused by the combined effect of several environmental and biological factors the importance of which differed over time and between the lakes, and (ii) the viral control of the picocyanobacterial community was probably relatively weak at the scale of the investigation.
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Affiliation(s)
- Xu Zhong
- INRA, UMR CARRTEL, Thonon-les-Bains cx, France
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63
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Wilkins D, Yau S, Williams TJ, Allen MA, Brown MV, DeMaere MZ, Lauro FM, Cavicchioli R. Key microbial drivers in Antarctic aquatic environments. FEMS Microbiol Rev 2013; 37:303-35. [DOI: 10.1111/1574-6976.12007] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 08/11/2012] [Accepted: 10/01/2012] [Indexed: 11/27/2022] Open
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Rohwer F, Barott K. Viral information. BIOLOGY & PHILOSOPHY 2013; 28:283-297. [PMID: 23482918 PMCID: PMC3585991 DOI: 10.1007/s10539-012-9344-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 09/24/2012] [Indexed: 05/20/2023]
Abstract
Viruses are major drivers of global biogeochemistry and the etiological agents of many diseases. They are also the winners in the game of life: there are more viruses on the planet than cellular organisms and they encode most of the genetic diversity on the planet. In fact, it is reasonable to view life as a viral incubator. Nevertheless, most ecological and evolutionary theories were developed, and continue to be developed, without considering the virosphere. This means these theories need to be to reinterpreted in light of viral knowledge or we need to develop new theory from the viral point-of-view. Here we briefly introduce our viral planet and then address a major outstanding question in biology: why is most of life viral? A key insight is that during an infection cycle the original virus is completely broken down and only the associated information is passed on to the next generation. This is different for cellular organisms, which must pass on some physical part of themselves from generation to generation. Based on this premise, it is proposed that the thermodynamic consequences of physical information (e.g., Landauer's principle) are observed in natural viral populations. This link between physical and genetic information is then used to develop the Viral Information Hypothesis, which states that genetic information replicates itself to the detriment of system energy efficiency (i.e., is viral in nature). Finally, we show how viral information can be tested, and illustrate how this novel view can explain existing ecological and evolutionary theories from more fundamental principles.
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Affiliation(s)
- Forest Rohwer
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182 USA
| | - Katie Barott
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182 USA
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65
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Matteson AR, Rowe JM, Ponsero AJ, Pimentel TM, Boyd PW, Wilhelm SW. High abundances of cyanomyoviruses in marine ecosystems demonstrate ecological relevance. FEMS Microbiol Ecol 2013; 84:223-34. [PMID: 23240688 DOI: 10.1111/1574-6941.12060] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 09/11/2012] [Accepted: 12/03/2012] [Indexed: 12/01/2022] Open
Abstract
The distribution of cyanomyoviruses was estimated using a quantitative PCR (qPCR) approach that targeted the g20 gene as a proxy for phage. Samples were collected spatially during a > 3000 km transect through the Sargasso Sea and temporally during a gyre-constrained phytoplankton bloom within the southern Pacific Ocean. Cyanomyovirus abundances were lower in the Sargasso Sea than in the southern Pacific Ocean, ranging from 2.75 × 10(3) to 5.15 × 10(4) mL(-1) and correlating with the abundance of their potential hosts (Prochlorococcus and Synechococcus). Cyanomyovirus abundance in the southern Pacific Ocean (east of New Zealand) followed Synechococcus host populations in the system: this included a decrease in g20 gene copies (from 4.3 × 10(5) to 9.6 × 10(3) mL(-1) ) following the demise of a Synechococcus bloom. When compared with direct counts of viruses, observations suggest that the cyanomyoviruses comprised 0.5 to >25% of the total virus community. We estimated daily lysis rates of 0.2-46% of the standing stock of Synechococcus in the Pacific Ocean compared with c. < 1.0% in the Sargasso Sea. In total, our observations confirm this family of viruses is abundant in marine systems and that they are an important source of cyanobacterial mortality.
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Affiliation(s)
- Audrey R Matteson
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37996-0845, USA
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66
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Marston MF, Taylor S, Sme N, Parsons RJ, Noyes TJE, Martiny JBH. Marine cyanophages exhibit local and regional biogeography. Environ Microbiol 2012; 15:1452-63. [PMID: 23279166 DOI: 10.1111/1462-2920.12062] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 11/26/2012] [Accepted: 11/27/2012] [Indexed: 11/28/2022]
Abstract
Biogeographic patterns have been demonstrated for a wide range of microorganisms. Nevertheless, the biogeography of marine viruses has been slower to emerge. Here we investigate biogeographic patterns of marine cyanophages that infect Synechococcus sp. WH7803 across multiple spatial and temporal scales. We compared cyanophage myoviral communities from nine coastal sites in Southern New England (SNE), USA, one site in Long Island NY, and four sites from Bermuda's inshore waters by assaying cyanophage isolates using the myoviral g43 DNA polymerase gene. Cyanophage community composition varied temporally at each of the sites. Further, 6 years of sampling at one Narragansett Bay site revealed annual seasonal variations in community composition, driven by the seasonal reoccurrence of specific viral taxa. Although the four Bermuda communities were similar to one another, they were significantly different than the North American coastal communities, with almost no overlap of taxa between the two regions. Among the SNE sites, cyanophage community composition also varied significantly and was correlated with the body of water sampled (e.g. Narragansett Bay, Cape Cod Bay, Vineyard Sound), although here, the same viral taxa were found at multiple sites. This study demonstrates that marine cyanophages display striking seasonal and spatial biogeographic patterns.
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Affiliation(s)
- Marcia F Marston
- Department of Biology and Marine Biology, Roger Williams University, Bristol, RI 02809, USA.
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67
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Effects of patch connectivity and heterogeneity on metacommunity structure of planktonic bacteria and viruses. ISME JOURNAL 2012. [PMID: 23178674 DOI: 10.1038/ismej.2012.138] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Dispersal limitation is generally considered to have little influence on the spatial structure of biodiversity in microbial metacommunities. This notion derives mainly from the analysis of spatial patterns in the field, but experimental tests of dispersal limitation using natural communities are rare for prokaryotes and, to our knowledge, non-existent for viruses. We studied the effects of dispersal intensity (three levels) and patch heterogeneity (two levels) on the structure of replicate experimental metacommunities of bacteria and viruses using outdoor mesocosms with plankton communities from natural ponds and lakes. Low levels of dispersal resulted in a decrease in the compositional differences (beta diversity) among the communities of both bacteria and viruses, but we found no effects of patch heterogeneity. The reductions in beta diversity are unlikely to be a result of mass effects and only partly explained by indirect dispersal-mediated interactions with phytoplankton and zooplankton. Our results suggest that even a very limited exchange among local communities can alter the trajectory of bacterial and viral communities at small temporal and spatial scales.
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68
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Prophage carriage and diversity within clinically relevant strains of Clostridium difficile. Appl Environ Microbiol 2012; 78:6027-34. [PMID: 22706062 DOI: 10.1128/aem.01311-12] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Prophages are encoded in most genomes of sequenced Clostridium difficile strains. They are key components of the mobile genetic elements and, as such, are likely to influence the biology of their host strains. The majority of these phages are not amenable to propagation, and therefore the development of a molecular marker is a useful tool with which to establish the extent and diversity of C. difficile prophage carriage within clinical strains. To design markers, several candidate genes were analyzed including structural and holin genes. The holin gene is the only gene present in all sequenced phage genomes, conserved at both terminals, with a variable mid-section. This allowed us to design two sets of degenerate PCR primers specific to C. difficile myoviruses and siphoviruses. Subsequent PCR analysis of 16 clinical C. difficile ribotypes showed that 15 of them are myovirus positive, and 2 of them are also siphovirus positive. Antibiotic induction and transmission electron microscope analysis confirmed the molecular prediction of myoviruses and/or siphovirus presence. Phylogenetic analysis of the holin sequences identified three groups of C. difficile phages, two within the myoviruses and a divergent siphovirus group. The marker also produced tight groups within temperate phages that infect other taxa, including Clostridium perfringens, Clostridium botulinum, and Bacillus spp., which suggests the potential application of the holin gene to study prophage carriage in other bacteria. This study reveals the high incidence of prophage carriage in clinically relevant strains of C. difficile and correlates the molecular data to the morphological observation.
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69
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Abstract
Marine myoviruses (i.e. bacteriophages with a contractile tail sheath) are numerically abundant and genetically diverse. We developed a terminal restriction fragment length polymorphism assay (TRFLP) for g23, the conserved gene encoding the major capsid protein, to investigate T4-like myovirus communities at USC's Microbial Observatory at the San Pedro Ocean Time-series (SPOT), where we previously reported bacterial seasonality. Between 71 and 154 operational taxonomic units (OTUs) were observed monthly over 3 years. Roughly 25% of OTUs were detected in 31 or more months. T4-like myoviral community structure varied seasonally with some OTUs peaking repeatedly in spring-summer and others in fall-winter, while moderately abundant OTUs persisted year-round. Recurring community structure was demonstrated using discriminant function analysis (DFA, selecting taxa that best predict months) and average Bray-Curtis similarity. DFA showed communities from adjacent months or 12 months apart were positively auto-correlated, while communities 3-7 months apart were negatively auto-correlated. Bray-Curtis similarity was highest between adjacent months - with a local maximum at 12-month and local minima at 6- and 18- to 20-month lags. The T4-like virus community at SPOT exhibited seasonality, yet the somewhat unexpected persistence of moderately abundant OTUs and predictability of the community add new twists to existing conceptual models of marine viruses.
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Affiliation(s)
- Cheryl-Emiliane T Chow
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USA.
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70
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Roux S, Enault F, Robin A, Ravet V, Personnic S, Theil S, Colombet J, Sime-Ngando T, Debroas D. Assessing the diversity and specificity of two freshwater viral communities through metagenomics. PLoS One 2012; 7:e33641. [PMID: 22432038 PMCID: PMC3303852 DOI: 10.1371/journal.pone.0033641] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 02/14/2012] [Indexed: 01/21/2023] Open
Abstract
Transitions between saline and fresh waters have been shown to be infrequent for microorganisms. Based on host-specific interactions, the presence of specific clades among hosts suggests the existence of freshwater-specific viral clades. Yet, little is known about the composition and diversity of the temperate freshwater viral communities, and even if freshwater lakes and marine waters harbor distinct clades for particular viral sub-families, this distinction remains to be demonstrated on a community scale. To help identify the characteristics and potential specificities of freshwater viral communities, such communities from two lakes differing by their ecological parameters were studied through metagenomics. Both the cluster richness and the species richness of the Lake Bourget virome were significantly higher that those of the Lake Pavin, highlighting a trend similar to the one observed for microorganisms (i.e. the specie richness observed in mesotrophic lakes is greater than the one observed in oligotrophic lakes). Using 29 previously published viromes, the cluster richness was shown to vary between different environment types and appeared significantly higher in marine ecosystems than in other biomes. Furthermore, significant genetic similarity between viral communities of related environments was highlighted as freshwater, marine and hypersaline environments were separated from each other despite the vast geographical distances between sample locations within each of these biomes. An automated phylogeny procedure was then applied to marker genes of the major families of single-stranded (Microviridae, Circoviridae, Nanoviridae) and double-stranded (Caudovirales) DNA viruses. These phylogenetic analyses all spotlighted a very broad diversity and previously unknown clades undetectable by PCR analysis, clades that gathered sequences from the two lakes. Thus, the two freshwater viromes appear closely related, despite the significant ecological differences between the two lakes. Furthermore, freshwater viral communities appear genetically distinct from other aquatic ecosystems, demonstrating the specificity of freshwater viruses at a community scale for the first time.
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Affiliation(s)
- Simon Roux
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Francois Enault
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
- * E-mail:
| | - Agnès Robin
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Viviane Ravet
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Sébastien Personnic
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Sébastien Theil
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Jonathan Colombet
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Télesphore Sime-Ngando
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Didier Debroas
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
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71
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Dwivedi B, Schmieder R, Goldsmith DB, Edwards RA, Breitbart M. PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity. BMC Bioinformatics 2012; 13:37. [PMID: 22385976 PMCID: PMC3314551 DOI: 10.1186/1471-2105-13-37] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 03/04/2012] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Phages (viruses that infect bacteria) have gained significant attention because of their abundance, diversity and important ecological roles. However, the lack of a universal gene shared by all phages presents a challenge for phage identification and characterization, especially in environmental samples where it is difficult to culture phage-host systems. Homologous conserved genes (or "signature genes") present in groups of closely-related phages can be used to explore phage diversity and define evolutionary relationships amongst these phages. Bioinformatic approaches are needed to identify candidate signature genes and design PCR primers to amplify those genes from environmental samples; however, there is currently no existing computational tool that biologists can use for this purpose. RESULTS Here we present PhiSiGns, a web-based and standalone application that performs a pairwise comparison of each gene present in user-selected phage genomes, identifies signature genes, generates alignments of these genes, and designs potential PCR primer pairs. PhiSiGns is available at (http://www.phantome.org/phisigns/; http://phisigns.sourceforge.net/) with a link to the source code. Here we describe the specifications of PhiSiGns and demonstrate its application with a case study. CONCLUSIONS PhiSiGns provides phage biologists with a user-friendly tool to identify signature genes and design PCR primers to amplify related genes from uncultured phages in environmental samples. This bioinformatics tool will facilitate the development of novel signature genes for use as molecular markers in studies of phage diversity, phylogeny, and evolution.
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Affiliation(s)
- Bhakti Dwivedi
- College of Marine Science, University of South Florida, St, Petersburg, FL 33701, USA.
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72
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Ignacio-Espinoza JC, Sullivan MB. Phylogenomics of T4 cyanophages: lateral gene transfer in the 'core' and origins of host genes. Environ Microbiol 2012; 14:2113-26. [PMID: 22348436 DOI: 10.1111/j.1462-2920.2012.02704.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The last two decades have revealed that phages (viruses that infect bacteria) are abundant and play fundamental roles in the Earth System, with the T4-like myoviruses (herein T4-like phages) emerging as a dominant 'signal' in wild populations. Here we examine 27 T4-like phage genomes, with a focus on 17 that infect ocean picocyanobacteria (cyanophages), to evaluate lateral gene transfer (LGT) in this group. First, we establish a reference tree by evaluating concatenated core gene supertrees and whole genome gene content trees. Next, we evaluate what fraction of these 'core genes' shared by all 17 cyanophages appear prone to LGT. Most (47 out of 57 core genes) were vertically transferred as inferred from tree tests and genomic synteny. Of those 10 core genes that failed the tree tests, the bulk (8 of 10) remain syntenic in the genomes with only a few (3 of the 10) having identifiable signatures of mobile elements. Notably, only one of these 10 is shared not only by the 17 cyanophages, but also by all 27 T4-like phages (thymidylate synthase); its evolutionary history suggests cyanophages may be the origin of these genes to Prochlorococcus. Next, we examined intragenic recombination among the core genes and found that it did occur, even among these core genes, but that the rate was significantly higher between closely related phages, perhaps reducing any detectable LGT signal and leading to taxon cohesion. Finally, among 18 auxiliary metabolic genes (AMGs, a.k.a. 'host' genes), we found that half originated from their immediate hosts, in some cases multiple times (e.g. psbA, psbD, pstS), while the remaining have less clear evolutionary origins ranging from cyanobacteria (4 genes) or microbes (5 genes), with particular diversity among viral TalC and Hsp20 sequences. Together, these findings highlight the patterns and limits of vertical evolution, as well as the ecological and evolutionary roles of LGT in shaping T4-like phage genomes.
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73
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Abstract
Over the past two decades, marine virology has progressed from a curiosity to an intensely studied topic of critical importance to oceanography. At concentrations of approximately 10 million viruses per milliliter of surface seawater, viruses are the most abundant biological entities in the oceans. The majority of these viruses are phages (viruses that infect bacteria). Through lysing their bacterial hosts, marine phages control bacterial abundance, affect community composition, and impact global biogeochemical cycles. In addition, phages influence their hosts through selection for resistance, horizontal gene transfer, and manipulation of bacterial metabolism. Recent work has also demonstrated that marine phages are extremely diverse and can carry a variety of auxiliary metabolic genes encoding critical ecological functions. This review is structured as a scientific "truth or dare," revealing several well-established "truths" about marine viruses and presenting a few "dares" for the research community to undertake in future studies.
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Affiliation(s)
- Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, Florida 33701, USA.
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74
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Huang S, Wang K, Jiao N, Chen F. Genome sequences of siphoviruses infecting marine Synechococcus unveil a diverse cyanophage group and extensive phage-host genetic exchanges. Environ Microbiol 2011; 14:540-58. [DOI: 10.1111/j.1462-2920.2011.02667.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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75
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Jameson E, Mann NH, Joint I, Sambles C, Mühling M. The diversity of cyanomyovirus populations along a North-South Atlantic Ocean transect. THE ISME JOURNAL 2011; 5:1713-21. [PMID: 21633395 PMCID: PMC3197166 DOI: 10.1038/ismej.2011.54] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 03/24/2011] [Accepted: 03/26/2011] [Indexed: 11/08/2022]
Abstract
Viruses that infect the marine cyanobacterium Prochlorococcus have the potential to impact the growth, productivity, diversity and abundance of their hosts. In this study, changes in the microdiversity of cyanomyoviruses were investigated in 10 environmental samples taken along a North-South Atlantic Ocean transect using a myoviral-specific PCR-sequencing approach. Phylogenetic analyses of 630 viral g20 clones from this study, with 786 published g20 sequences, revealed that myoviral populations in the Atlantic Ocean had higher diversity than previously reported, with several novel putative g20 clades. Some of these clades were detected throughout the Atlantic Ocean. Multivariate statistical analyses did not reveal any significant correlations between myoviral diversity and environmental parameters, although myoviral diversity appeared to be lowest in samples collected from the north and south of the transect where Prochlorococcus diversity was also lowest. The results were correlated to the abundance and diversity of the co-occurring Prochlorococcus and Synechococcus populations, but revealed no significant correlations to either of the two potential host genera. This study provides evidence that cyanophages have extremely high and variable diversity and are distributed over large areas of the Atlantic Ocean.
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Affiliation(s)
- Eleanor Jameson
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, UK.
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76
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Danovaro R, Corinaldesi C, Dell'Anno A, Fuhrman JA, Middelburg JJ, Noble RT, Suttle CA. Marine viruses and global climate change. FEMS Microbiol Rev 2011; 35:993-1034. [DOI: 10.1111/j.1574-6976.2010.00258.x] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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77
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Development of phoH as a novel signature gene for assessing marine phage diversity. Appl Environ Microbiol 2011; 77:7730-9. [PMID: 21926220 DOI: 10.1128/aem.05531-11] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phages play a key role in the marine environment by regulating the transfer of energy between trophic levels and influencing global carbon and nutrient cycles. The diversity of marine phage communities remains difficult to characterize because of the lack of a signature gene common to all phages. Recent studies have demonstrated the presence of host-derived auxiliary metabolic genes in phage genomes, such as those belonging to the Pho regulon, which regulates phosphate uptake and metabolism under low-phosphate conditions. Among the completely sequenced phage genomes in GenBank, this study identified Pho regulon genes in nearly 40% of the marine phage genomes, while only 4% of nonmarine phage genomes contained these genes. While several Pho regulon genes were identified, phoH was the most prevalent, appearing in 42 out of 602 completely sequenced phage genomes. Phylogenetic analysis demonstrated that phage phoH sequences formed a cluster distinct from those of their bacterial hosts. PCR primers designed to amplify a region of the phoH gene were used to determine the diversity of phage phoH sequences throughout a depth profile in the Sargasso Sea and at six locations worldwide. phoH was present at all sites examined, and a high diversity of phoH sequences was recovered. Most phoH sequences belonged to clusters without any cultured representatives. Each depth and geographic location had a distinct phoH composition, although most phoH clusters were recovered from multiple sites. Overall, phoH is an effective signature gene for examining phage diversity in the marine environment.
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78
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Molecular enumeration of an ecologically important cyanophage in a Laurentian Great Lake. Appl Environ Microbiol 2011; 77:6772-9. [PMID: 21841023 DOI: 10.1128/aem.05879-11] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Considerable research has shown that cyanobacteria and the viruses that infect them (cyanophage) are pervasive and diverse in global lake populations. Few studies have seasonally analyzed freshwater systems, and little is known about the bacterial and viral communities that coexist during the harsh winters of the Laurentian Great Lakes. Here, we employed quantitative PCR to estimate the abundance of cyanomyoviruses in this system, using the portal vertex g20 gene as a proxy for cyanophage abundance and to determine the potential ecological relevance of these viruses. Cyanomyoviruses were abundant in both the summer and the winter observations, with up to 3.1 × 10(6) copies of g20 genes ml(-1) found at several stations and depths in both seasons, representing up to 4.6% of the total virus community. Lake Erie was productive during both our observations, with high chlorophyll a concentrations in the summer (up to 10.3 μg liter(-1)) and winter (up to 5.2 μg liter(-1)). Both bacterial and viral abundances were significantly higher during the summer than during the winter (P < 0.05). Summer bacterial abundances ranged from 3.3 × 10(6) to 1.6 × 10(7) ml(-1) while winter abundances ranged between ∼3.4 × 10(5) and 1.2 × 10(6) ml(-1). Total virus abundances were high during both months, with summer abundances significantly higher at most stations, ranging from 6.5 × 10(7) to 8.8 × 10(7) ml(-1), and with winter abundances ranging from 3.4 × 10(7) to 6.6 × 10(7) ml(-1). This work confirms that putative cyanomyoviruses are ubiquitous in both summer and winter months in this large freshwater lake system and that they are an abundant component of the virioplankton group.
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79
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Dreher TW, Brown N, Bozarth CS, Schwartz AD, Riscoe E, Thrash C, Bennett SE, Tzeng SC, Maier CS. A freshwater cyanophage whose genome indicates close relationships to photosynthetic marine cyanomyophages. Environ Microbiol 2011; 13:1858-74. [PMID: 21605306 PMCID: PMC4185292 DOI: 10.1111/j.1462-2920.2011.02502.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Bacteriophage S-CRM01 has been isolated from a freshwater strain of Synechococcus and shown to be present in the upper Klamath River valley in northern California and Oregon. The genome of this lytic T4-like phage has a 178,563 bp circular genetic map with 297 predicted protein-coding genes and 33 tRNA genes that represent all 20-amino-acid specificities. Analyses based on gene sequence and gene content indicate a close phylogenetic relationship to the 'photosynthetic' marine cyanomyophages infecting Synechococcus and Prochlorococcus. Such relatedness suggests that freshwater and marine phages can draw on a common gene pool. The genome can be considered as being comprised of three regions. Region 1 is populated predominantly with structural genes, recognized as such by homology to other T4-like phages and by identification in a proteomic analysis of purified virions. Region 2 contains most of the genes with roles in replication, recombination, nucleotide metabolism and regulation of gene expression, as well as 5 of the 6 signature genes of the photosynthetic cyanomyophages (hli03, hsp20, mazG, phoH and psbA; cobS is present in Region 3). Much of Regions 1 and 2 are syntenic with marine cyanomyophage genomes, except that a segment encompassing Region 2 is inverted. Region 3 contains a high proportion (85%) of genes that are unique to S-CRM01, as well as most of the tRNA genes. Regions 1 and 2 contain many predicted late promoters, with a combination of CTAAATA and ATAAATA core sequences. Two predicted genes that are unusual in phage genomes are homologues of cellular spoT and nusG.
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Affiliation(s)
- Theo W Dreher
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA.
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80
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Belcaid M, Bergeron A, Poisson G. Mosaic graphs and comparative genomics in phage communities. J Comput Biol 2011; 17:1315-26. [PMID: 20874413 DOI: 10.1089/cmb.2010.0108] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Comparing the genomes of two closely related viruses often produces mosaics where nearly identical sequences alternate with sequences that are unique to each genome. When several closely related genomes are compared, the unique sequences are likely to be shared with third genomes, leading to virus mosaic communities. Here we present comparative analysis of sets of Staphylococcus aureus phages that share large identical sequences with up to three other genomes, and with different partners along their genomes. We introduce mosaic graphs to represent these complex recombination events, and use them to illustrate the breath and depth of sequence sharing: some genomes are almost completely made up of shared sequences, while genomes that share very large identical sequences can adopt alternate functional modules. Mosaic graphs also allow us to identify breakpoints that could eventually be used for the construction of recombination networks. These findings have several implications on phage metagenomics assembly, on the horizontal gene transfer paradigm, and more generally on the understanding of the composition and evolutionary dynamics of virus communities.
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Affiliation(s)
- Mahdi Belcaid
- Information and Computer Sciences, University of Hawaii, Honolulu, HI, USA
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81
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Wang G, Asakawa S, Kimura M. Spatial and temporal changes of cyanophage communities in paddy field soils as revealed by the capsid assembly protein gene g20. FEMS Microbiol Ecol 2011; 76:352-9. [PMID: 21255050 DOI: 10.1111/j.1574-6941.2011.01052.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Bacteriophages are ubiquitous in various environments. Our previous study revealed the diversity of the cyanophage community in paddy floodwater. In this study, the phylogeny and genetic diversity of cyanophage communities in paddy field soils were reported. The viral capsid assembly protein gene (g20) of cyanophage was amplified with the primers CPS1 and CPS8 from soil DNA extracted during two different sampling times at three sampling sites in Japan. The sequencing results indicated that about 93% of the clones were g20 genes. In total, 70 clones of g20 genes were obtained in this study, of which 69 clones were of cyanophage origin. As evaluated by g20 sequence assemblages in paddy field soils, the unifrac analyses results indicated that cyanophage communities changed among the sampling sites and times and differed from those communities detected in paddy floodwater. The phylogenetic analysis showed that the g20 sequences in paddy field soils were very diverse and distributed into Clusters α, β and ɛ, as well as four newly formed clusters. Within Clusters β and ɛ, four unique subclusters were formed from the g20 clones that were only observed in this study. These findings suggested that the cyanophage communities in paddy field soils are different from those found in freshwater, marine water and paddy floodwater.
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Affiliation(s)
- Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China.
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82
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Are low temperature habitats hot spots of microbial evolution driven by viruses? Trends Microbiol 2010; 19:52-7. [PMID: 21130655 DOI: 10.1016/j.tim.2010.11.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 10/21/2010] [Accepted: 11/04/2010] [Indexed: 11/27/2022]
Abstract
There is an increasing body of evidence to show that viruses are important drivers of microbial evolution and that they can store a great deal of the Earth's microbial diversity in their genomes. Examination of microbial diversity in polar regions has revealed a higher than expected diversity of viruses, bacteria and eukaryotic microbes. Further, the few available studies in polar regions reveal that viral control of microbial mortality is important in these habitats. In this opinion article, we argue that strong relationships between viruses and their hosts in a range of polar habitats could be key in explaining why polar regions are in fact hot spots of microbial diversity and evolution. Further, we argue that periodic glaciations, and particularly the Neoproterozoic low-latitude glaciation, known as 'snowball Earth', could have been periods of intense diversification in aquatic refuges.
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83
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Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean. ISME JOURNAL 2010; 5:822-30. [PMID: 21124487 DOI: 10.1038/ismej.2010.188] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Knowledge of marine phages is highly biased toward double-stranded DNA (dsDNA) phages; however, recent metagenomic surveys have also identified single-stranded DNA (ssDNA) phages in the oceans. Here, we describe two complete ssDNA phage genomes that were reconstructed from a viral metagenome from 80 m depth at the Bermuda Atlantic Time-series Study (BATS) site in the northwestern Sargasso Sea and examine their spatial and temporal distributions. Both genomes (SARssφ1 and SARssφ2) exhibited similarity to known phages of the Microviridae family in terms of size, GC content, genome organization and protein sequence. PCR amplification of the replication initiation protein (Rep) gene revealed narrow and distinct depth distributions for the newly described ssDNA phages within the upper 200 m of the water column at the BATS site. Comparison of Rep gene sequences obtained from the BATS site over time revealed changes in the diversity of ssDNA phages over monthly time scales, although some nearly identical sequences were recovered from samples collected 4 years apart. Examination of ssDNA phage diversity along transects through the North Atlantic Ocean revealed a positive correlation between genetic distance and geographic distance between sampling sites. Together, the data suggest fundamental differences between the distribution of these ssDNA phages and the distribution of known marine dsDNA phages, possibly because of differences in host range, host distribution, virion stability, or viral evolution mechanisms and rates. Future work needs to elucidate the host ranges for oceanic ssDNA phages and determine their ecological roles in the marine ecosystem.
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84
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Clokie MRJ, Millard AD, Mann NH. T4 genes in the marine ecosystem: studies of the T4-like cyanophages and their role in marine ecology. Virol J 2010; 7:291. [PMID: 21029435 PMCID: PMC2984593 DOI: 10.1186/1743-422x-7-291] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 10/28/2010] [Indexed: 11/30/2022] Open
Abstract
From genomic sequencing it has become apparent that the marine cyanomyoviruses capable of infecting strains of unicellular cyanobacteria assigned to the genera Synechococcus and Prochlorococcus are not only morphologically similar to T4, but are also genetically related, typically sharing some 40-48 genes. The large majority of these common genes are the same in all marine cyanomyoviruses so far characterized. Given the fundamental physiological differences between marine unicellular cyanobacteria and heterotrophic hosts of T4-like phages it is not surprising that the study of cyanomyoviruses has revealed novel and fascinating facets of the phage-host relationship. One of the most interesting features of the marine cyanomyoviruses is their possession of a number of genes that are clearly of host origin such as those involved in photosynthesis, like the psbA gene that encodes a core component of the photosystem II reaction centre. Other host-derived genes encode enzymes involved in carbon metabolism, phosphate acquisition and ppGpp metabolism. The impact of these host-derived genes on phage fitness has still largely to be assessed and represents one of the most important topics in the study of this group of T4-like phages in the laboratory. However, these phages are also of considerable environmental significance by virtue of their impact on key contributors to oceanic primary production and the true extent and nature of this impact has still to be accurately assessed.
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Affiliation(s)
- Martha R J Clokie
- Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, UK
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85
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Butina TV, Belykh OI, Belikov SI. Molecular-genetic identification of T4 bacteriophages in Lake Baikal. DOKL BIOCHEM BIOPHYS 2010; 433:175-8. [PMID: 20714850 DOI: 10.1134/s1607672910040083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Indexed: 11/23/2022]
Affiliation(s)
- T V Butina
- Institute of Limnology, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
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86
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Rooks DJ, Smith DL, McDonald JE, Woodward MJ, McCarthy AJ, Allison HE. 454-pyrosequencing: a molecular battiscope for freshwater viral ecology. Genes (Basel) 2010; 1:210-26. [PMID: 24710042 PMCID: PMC3954088 DOI: 10.3390/genes1020210] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 07/08/2010] [Accepted: 07/20/2010] [Indexed: 02/06/2023] Open
Abstract
Viruses, the most abundant biological entities on the planet, are capable of infecting organisms from all three branches of life, although the majority infect bacteria where the greatest degree of cellular diversity lies. However, the characterization and assessment of viral diversity in natural environments is only beginning to become a possibility. Through the development of a novel technique for the harvest of viral DNA and the application of 454 pyrosequencing, a snapshot of the diversity of the DNA viruses harvested from a standing pond on a cattle farm has been obtained. A high abundance of viral genotypes (785) were present within the virome. The absolute numbers of lambdoid and Shiga toxin (Stx) encoding phages detected suggested that the depth of sequencing had enabled recovery of only ca. 8% of the total virus population, numbers that agreed within less than an order of magnitude with predictions made by rarefaction analysis. The most abundant viral genotypes in the pond were bacteriophages (93.7%). The predominant viral genotypes infecting higher life forms found in association with the farm were pathogens that cause disease in cattle and humans, e.g. members of the Herpesviridae. The techniques and analysis described here provide a fresh approach to the monitoring of viral populations in the aquatic environment, with the potential to become integral to the development of risk analysis tools for monitoring the dissemination of viral agents of animal, plant and human diseases.
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Affiliation(s)
- David J Rooks
- Microbiology Research Group, School of Biological Sciences, Biosciences Building, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.
| | - Darren L Smith
- Microbiology Research Group, School of Biological Sciences, Biosciences Building, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.
| | - James E McDonald
- Microbiology Research Group, School of Biological Sciences, Biosciences Building, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.
| | - Martin J Woodward
- Veterinary Laboratories Agency (Weybridge), New Haw, Addlestone, Surrey KT15 3NB, UK.
| | - Alan J McCarthy
- Microbiology Research Group, School of Biological Sciences, Biosciences Building, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.
| | - Heather E Allison
- Microbiology Research Group, School of Biological Sciences, Biosciences Building, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.
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87
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Butina TV, Belykh OI, Maksimenko SY, Belikov SI. Phylogenetic diversity of T4-like bacteriophages in Lake Baikal, East Siberia. FEMS Microbiol Lett 2010; 309:122-9. [PMID: 20579103 DOI: 10.1111/j.1574-6968.2010.02025.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Among the tailed phages, the myoviruses, those with contractile tails, are widespread and diverse. An important component of the Myoviridae family is the genus 'T4-like viruses'. The present study was aimed at elucidating the molecular diversity of T4-type bacteriophages in Lake Baikal by partial sequencing of g23 genes of T4-type bacteriophages. Our study revealed that the g23 gene sequences investigated were highly diverse and different from those of T4-like bacteriophages and from g23 clones obtained from different environments. Phylogenetic analysis showed that all g23 fragments from Lake Baikal, except for the one sequence, were more closely related to marine T4 cyanophages and to previously described subgroups of uncultured T4 phages from marine and rice field environments.
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88
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Huang S, Wilhelm SW, Jiao N, Chen F. Ubiquitous cyanobacterial podoviruses in the global oceans unveiled through viral DNA polymerase gene sequences. ISME JOURNAL 2010; 4:1243-51. [PMID: 20463765 DOI: 10.1038/ismej.2010.56] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As a major cyanophage group, cyanobacterial podoviruses are important in regulating the biomass and population structure of picocyanobacteria in the ocean. However, little is known about their biogeography in the open ocean. This study represents the first survey of the biodiversity of cyanopodoviruses in the global oceans based on the viral encoded DNA polymerase (pol) gene. A total of 303 DNA pol sequences were amplified by PCR from 10 virus communities collected in the Atlantic and Pacific oceans and the South China Sea. At least five subclusters of cyanopodoviruses were identified in these samples, and one subcluster (subcluster VIII) was found in all sampling sites and comprised approximately 50% of total sequences. The diversity index based on the DNA pol gene sequences recovered through PCR suggests that cyanopodoviruses are less diverse in these oceanic samples than in a previously studied estuarine environment. Although diverse podoviruses were present in the global ocean, each sample was dominated by one major group of cyanopodoviruses. No clear biogeographic patterns were observed using statistical analysis. A metagenomic analysis based on the Global Ocean Sampling database indicates that other types of cyanopodovirus-like DNA pol sequences were present in the global ocean. Together, our study results suggest that cyanopodoviruses are widely distributed in the ocean but their community composition varies with local environments.
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Affiliation(s)
- Sijun Huang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
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89
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Comeau AM, Arbiol C, Krisch HM. Gene network visualization and quantitative synteny analysis of more than 300 marine T4-like phage scaffolds from the GOS metagenome. Mol Biol Evol 2010; 27:1935-44. [PMID: 20231334 PMCID: PMC2908710 DOI: 10.1093/molbev/msq076] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bacteriophages (phages) are the most abundant biological entities in the biosphere and are the dominant "organisms" in marine environments, exerting an enormous influence on marine microbial populations. Metagenomic projects, such as the Global Ocean Sampling expedition (GOS), have demonstrated the predominance of tailed phages (Caudovirales), particularly T4 superfamily cyanophages (Cyano-T4s), in the marine milieu. Whereas previous metagenomic analyses were limited to gene content information, here we present a comparative analysis of over 300 phage scaffolds assembled from the viral fraction of the GOS data. This assembly permits the examination of synteny (organization) of the genes on the scaffolds and their comparison with the genome sequences from cultured Cyano-T4s. We employ comparative genomics and a novel usage of network visualization software to show that the scaffold phylogenies are similar to those of the traditional marker genes they contain. Importantly, these uncultured metagenomic scaffolds quite closely match the organization of the "core genome" of the known Cyano-T4s. This indicates that the current view of genome architecture in the Cyano-T4s is not seriously biased by being based on a small number of cultured phages, and we can be confident that they accurately reflect the diverse population of such viruses in marine surface waters.
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Affiliation(s)
- André M Comeau
- Centre National de la Recherche Scientifique, UMR5100, Toulouse, France
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90
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ROOSSINCK MARILYNJ, SAHA PRASENJIT, WILEY GRAHAMB, QUAN JIAXI, WHITE JAMESD, LAI HONGSHING, CHAVARRÍA FELIPE, SHEN GUOAN, ROE BRUCEA. Ecogenomics: using massively parallel pyrosequencing to understand virus ecology. Mol Ecol 2010; 19 Suppl 1:81-8. [DOI: 10.1111/j.1365-294x.2009.04470.x] [Citation(s) in RCA: 186] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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91
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92
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Abstract
Long-term Helicobacter pylori (H. pylori) infection is associated with a high risk of gastric cancer and peptic ulcer disease. Biological therapy is one of the most promising methods for control of H. pylori infection. Borrowing ideas from phage therapy of refractory bacterial infections, phages have been used to treat H. pylori infection. In this article, we will review the advances in phage therapy of H. pylori infection.
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93
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Marston MF, Amrich CG. Recombination and microdiversity in coastal marine cyanophages. Environ Microbiol 2009; 11:2893-903. [DOI: 10.1111/j.1462-2920.2009.02037.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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94
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Lavigne R, Darius P, Summer EJ, Seto D, Mahadevan P, Nilsson AS, Ackermann HW, Kropinski AM. Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiol 2009; 9:224. [PMID: 19857251 PMCID: PMC2771037 DOI: 10.1186/1471-2180-9-224] [Citation(s) in RCA: 210] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 10/26/2009] [Indexed: 11/30/2022] Open
Abstract
Background We advocate unifying classical and genomic classification of bacteriophages by integration of proteomic data and physicochemical parameters. Our previous application of this approach to the entirely sequenced members of the Podoviridae fully supported the current phage classification of the International Committee on Taxonomy of Viruses (ICTV). It appears that horizontal gene transfer generally does not totally obliterate evolutionary relationships between phages. Results CoreGenes/CoreExtractor proteome comparison techniques applied to 102 Myoviridae suggest the establishment of three subfamilies (Peduovirinae, Teequatrovirinae, the Spounavirinae) and eight new independent genera (Bcep781, BcepMu, FelixO1, HAP1, Bzx1, PB1, phiCD119, and phiKZ-like viruses). The Peduovirinae subfamily, derived from the P2-related phages, is composed of two distinct genera: the "P2-like viruses", and the "HP1-like viruses". At present, the more complex Teequatrovirinae subfamily has two genera, the "T4-like" and "KVP40-like viruses". In the genus "T4-like viruses" proper, four groups sharing >70% proteins are distinguished: T4-type, 44RR-type, RB43-type, and RB49-type viruses. The Spounavirinae contain the "SPO1-"and "Twort-like viruses." Conclusion The hierarchical clustering of these groupings provide biologically significant subdivisions, which are consistent with our previous analysis of the Podoviridae.
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Affiliation(s)
- Rob Lavigne
- Biosystems Department, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, Leuven, B-3001, Belgium.
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95
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Current insights into phage biodiversity and biogeography. Curr Opin Microbiol 2009; 12:582-7. [PMID: 19811946 DOI: 10.1016/j.mib.2009.08.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 08/06/2009] [Accepted: 08/19/2009] [Indexed: 11/20/2022]
Abstract
Phages exert tremendous ecological and evolutionary forces directly on their bacterial hosts. Phage induced cell lysis also indirectly contributes to organic and inorganic nutrient recycling. Phage abundance, diversity, and distribution are therefore important parameters in ecosystem function. The assumption that phage consortia are ubiquitous and homogenous across habitats (everything is everywhere) is currently being re-evaluated. New studies on phage biogeography have found that some phages are globally distributed while others are unique and perhaps endemic to specific environments. Furthermore, advances in technology have allowed scientists to conduct experiments aimed at analyzing phage consortia over temporal scales, and surprisingly have found reoccurring patterns. This review discusses currents in the field of phage ecology with particular focus on efforts to characterize phage diversity and biogeography across various spatial and temporal scales.
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96
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Djikeng A, Kuzmickas R, Anderson NG, Spiro DJ. Metagenomic analysis of RNA viruses in a fresh water lake. PLoS One 2009; 4:e7264. [PMID: 19787045 PMCID: PMC2746286 DOI: 10.1371/journal.pone.0007264] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Accepted: 07/24/2009] [Indexed: 01/29/2023] Open
Abstract
Freshwater lakes and ponds present an ecological interface between humans and a variety of host organisms. They are a habitat for the larval stage of many insects and may serve as a medium for intraspecies and interspecies transmission of viruses such as avian influenza A virus. Furthermore, freshwater bodies are already known repositories for disease-causing viruses such as Norwalk Virus, Coxsackievirus, Echovirus, and Adenovirus. While RNA virus populations have been studied in marine environments, to this date there has been very limited analysis of the viral community in freshwater. Here we present a survey of RNA viruses in Lake Needwood, a freshwater lake in Maryland, USA. Our results indicate that just as in studies of other aquatic environments, the majority of nucleic acid sequences recovered did not show any significant similarity to known sequences. The remaining sequences are mainly from viral types with significant similarity to approximately 30 viral families. We speculate that these novel viruses may infect a variety of hosts including plants, insects, fish, domestic animals and humans. Among these viruses we have discovered a previously unknown dsRNA virus closely related to Banna Virus which is responsible for a febrile illness and is endemic to Southeast Asia. Moreover we found multiple viral sequences distantly related to Israeli Acute Paralysis virus which has been implicated in honeybee colony collapse disorder. Our data suggests that due to their direct contact with humans, domestic and wild animals, freshwater ecosystems might serve as repositories of a wide range of viruses (both pathogenic and non-pathogenic) and possibly be involved in the spread of emerging and pandemic diseases.
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Affiliation(s)
- Appolinaire Djikeng
- Infectious Diseases Group, The J. Craig Venter Institute (JCVI), Rockville, Maryland, United States of America
- * E-mail: (AD); (DJS)
| | - Ryan Kuzmickas
- Infectious Diseases Group, The J. Craig Venter Institute (JCVI), Rockville, Maryland, United States of America
| | - Norman G. Anderson
- Viral Defense Foundation, Kensington, Maryland, United States of America
| | - David J. Spiro
- Infectious Diseases Group, The J. Craig Venter Institute (JCVI), Rockville, Maryland, United States of America
- * E-mail: (AD); (DJS)
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97
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Logares R, Bråte J, Bertilsson S, Clasen JL, Shalchian-Tabrizi K, Rengefors K. Infrequent marine–freshwater transitions in the microbial world. Trends Microbiol 2009; 17:414-22. [DOI: 10.1016/j.tim.2009.05.010] [Citation(s) in RCA: 253] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 04/28/2009] [Accepted: 05/13/2009] [Indexed: 12/21/2022]
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98
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Chen F, Wang K, Huang S, Cai H, Zhao M, Jiao N, Wommack KE. Diverse and dynamic populations of cyanobacterial podoviruses in the Chesapeake Bay unveiled through DNA polymerase gene sequences. Environ Microbiol 2009; 11:2884-92. [PMID: 19703219 DOI: 10.1111/j.1462-2920.2009.02033.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many podoviruses have been isolated which infect marine picocyanobacteria, and they may play a potentially important role in regulating the biomass and population composition of picocyanobacteria. However, little is known about the diversity and population dynamics of autochthonous cyanopodoviruses in marine environments. Using a set of newly designed PCR primers which specifically amplify the DNA pol from cyanopodoviruses, a total of 221 DNA pol sequences were retrieved from eight Chesapeake Bay virioplankton communities collected at different times and locations. All DNA pol sequences clustered with the eight known podoviruses that infect different marine picocyanobacteria, and could be divided into at least 10 different subclusters (I-X). The presence of these cyanopodovirus genotypes based on PCR-amplification of DNA pol gene sequences was supported by the existence of similar DNA pol genotypes with metagenome libraries of Chesapeake Bay virioplankton assemblages. The composition of cyanopodoviruses in the Bay also exhibited distinct winter and summer patterns which were likely related to corresponding seasonal changes in the composition of cyanobacterial populations. Our study suggests that diverse and dynamic populations of cyanopodoviruses are present in the estuarine environment. The PCR method developed in this study provides a specific and sensitive tool to explore the abundance, distribution and phylogenetic diversity of cyanopodoviruses in aquatic environments. Linking the dynamics of host and viral populations in the natural environment is critical to broader characterization of the ecological role of virioplankton within microbial communities.
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Affiliation(s)
- Feng Chen
- Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, MD 21202, USA.
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99
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Abstract
Marine viruses affect Bacteria, Archaea and eukaryotic organisms and are major components of the marine food web. Most studies have focused on their role as predators and parasites, but many of the interactions between marine viruses and their hosts are much more complicated. A series of recent studies has shown that viruses have the ability to manipulate the life histories and evolution of their hosts in remarkable ways, challenging our understanding of this almost invisible world.
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100
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Millard AD, Zwirglmaier K, Downey MJ, Mann NH, Scanlan DJ. Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence of Synechococcus host genes localized to a hyperplastic region: implications for mechanisms of cyanophage evolution. Environ Microbiol 2009; 11:2370-87. [PMID: 19508343 DOI: 10.1111/j.1462-2920.2009.01966.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The vast majority of cyanophages isolated to date are cyanomyoviruses, a group related to bacteriophage T4. Comparative genome analysis of five cyanomyoviruses, including a newly sequenced cyanophage S-RSM4, revealed a 'core genome' of 64 genes, the majority of which are also found in other T4-like phages. Subsequent comparative genomic hybridization analysis using a pilot microarray showed that a number of 'host' genes are widespread in cyanomyovirus isolates. Furthermore, a hyperplastic region was identified between genes g15-g18, within a highly conserved structural gene module, which contained a variable number of inserted genes that lacked conservation in gene order. Several of these inserted genes were host-like and included ptoX, gnd, zwf and petE encoding plastoquinol terminal oxidase, 6-phosphogluconate dehydrogenase, glucose 6-phosphate dehydrogenase and plastocyanin respectively. Phylogenetic analyses suggest that these genes were acquired independently of each other, even though they have become localized within the same genomic region. This hyperplastic region contains no detectable sequence features that might be mechanistically involved with the acquisition of host-like genes, but does appear to be a site specifically associated with the acquisition process and may represent a novel facet of the evolution of marine cyanomyoviruses.
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Affiliation(s)
- Andrew D Millard
- Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK.
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