Screening of a Fosmid Library of Marine Environmental Genomic DNA Fragments Reveals Four Clones Related to Members of the Order
            <i>Planctomycetales</i>

Vergin, Kevin L.; Urbach, Ena; Stein, Jeffery L.; DeLong, Edward F.; Lanoil, Brian; Giovannoni, Stephen J.

doi:10.1128/aem.64.8.3075-3078.1998

Cited by 150 publications

(67 citation statements)

References 19 publications

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“…Béja et al, 2000). Environmental shotgun clone libraries were initially developed for analysis of prokaryote communities (Vergin et al, 1998), but are now being applied to complex, natural assemblages of marine viruses (Breitbart et al, 2002(Breitbart et al, , 2004Steward et al, 2002;Angly et al, 2006). These latter studies have shown that natural assemblages of DNA viruses are extraordinarily diverse, making the reconstruction of a genome by random sequencing an improbable event except with extraordinary sequencing effort (Angly et al, 2006).…”

Section: Metagenomicsmentioning

confidence: 99%

RNA viruses in the sea

et al. 2009

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Viruses are ubiquitous in the sea and appear to outnumber all other forms of marine life by at least an order of magnitude. Through selective infection, viruses influence nutrient cycling, community structure, and evolution in the ocean. Over the past 20 years we have learned a great deal about the diversity and ecology of the viruses that constitute the marine virioplankton, but until recently the emphasis has been on DNA viruses. Along with expanding knowledge about RNA viruses that infect important marine animals, recent isolations of RNA viruses that infect single-celled eukaryotes and molecular analyses of the RNA virioplankton have revealed that marine RNA viruses are novel, widespread, and genetically diverse. Discoveries in marine RNA virology are broadening our understanding of the biology, ecology, and evolution of viruses, and the epidemiology of viral diseases, but there is still much that we need to learn about the ecology and diversity of RNA viruses before we can fully appreciate their contributions to the dynamics of marine ecosystems. As a step toward making sense of how RNA viruses contribute to the extraordinary viral diversity in the sea, we summarize in this review what is currently known about RNA viruses that infect marine organisms.

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Section: Metagenomicsmentioning

confidence: 99%

RNA viruses in the sea

et al. 2009

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“…A negative control with no sample added was included in the extraction procedure and yielded no detectable DNA. Primers 27f-HEX (5-AGRGTTT-GATCMTGGCTCAG-3) (Vergin et al, 1998) and 519r (5-GWATTACCGCGGCKGCTG-3) (Lane et al, 1985) were used for amplification of 16S rRNA gene fragments. The forward primer was labelled with hexachloro-fluoroscein (HEX; Sigma-Aldrich, Suffolk, U.K.) at the 5¢ end to allow for fluorescent detection of terminal restriction fragments.…”

Section: Bacterial Community Compositionmentioning

confidence: 99%

Temporal variation in freshwater viral and bacterial community composition

et al. 2007

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1. The goal of this study conducted in three lakes differing in nutrient content and size was to assess the temporal variation in viral community composition and possible co-variation with compositional changes in bacterial communities. 2. The viral community composition differed among lakes and changed over the season. Changes could also be detected on short-time scales, i.e. over a few days. These changes were comparable in magnitude to the changes detected between months or seasons. 3. The most important environmental factors co-varying with viral community composition, as determined by multivariate analysis, differed over the year and among lakes. Temperature and concentrations of dissolved organic carbon (DOC), total phosphorus and soluble reactive phosphorus were the most important factors. 4. Bacterial community composition also varied over the season and among lakes. The most important factors co-varying with bacterial community composition, as determined by multivariate analysis, were also temperature and DOC concentration. 5. Correlation between viral and bacterial community composition was weak and appeared to be a result of an indirect connection rather than a direct relationship between bacteria and viruses.

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“…Relationships were determined using the neighbour-joining method with Jukes-Cantor correction and checked for consistency using parsimony. The most variable regions (E. coli positions 452-463 and 849-850) were excluded from phylogenetic analyses of single representative Vergin et al (1998) by incorporating a degeneracy (T/C) at position 1508 (E. coli numbering).…”

Section: Sequence Analysismentioning

confidence: 99%

“…16S rRNA gene-targeted primers. TAC CTT GTT AYG ACT T Most Bacteria and ArchaeaLane (1991);Vergin et al (1998) a. 16S rRNA positions; E. coli numbering.…”

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confidence: 99%

High overall diversity and dominance of microdiverse relationships in salt marsh sulphate‐reducing bacteria

Klepac‐Ceraj

Bahr

Crump

et al. 2004

Environmental Microbiology

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The biogeochemistry of North Atlantic salt marshes is characterized by the interplay between the marsh grass Spartina and sulphate-reducing bacteria (SRB), which mineralize the diverse carbon substrates provided by the plants. It was hypothesized that SRB populations display high diversity within the sediment as a result of the rich spatial and chemical structuring provided by Spartina roots. A 2000-member 16S rRNA gene library, prepared with delta-proteobacterial SRB-selective primers, was analysed for diversity patterns and phylogenetic relationships. Sequence clustering detected 348 16S rRNA sequence types (ribotypes) related to delta-proteobacterial SRB, and it was estimated that a total of 623 ribotypes were present in the library. Similarity clustering showed that approximately 46% of these sequences fell into groups with < 1% divergence; thus, microheterogeneity accounts for a large portion of the observable genetic diversity. Phylogenetic comparison revealed that sequences most frequently recovered were associated with the Desulfobacteriaceae and Desulfobulbaceae families. Sequences from the Desulfovibrionaceae family were also observed, but were infrequent. Over 80% of the delta-proteobacterial ribotypes clustered with cultured representatives of Desulfosarcina, Desulfococcus and Desulfobacterium genera, suggesting that complete oxidizers with high substrate versatility dominate. The large-scale approach demonstrates the co-existence of numerous SRB-like sequences and reveals an unexpected amount of microdiversity.

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Screening of a Fosmid Library of Marine Environmental Genomic DNA Fragments Reveals Four Clones Related to Members of the Order Planctomycetales

Cited by 150 publications

References 19 publications

RNA viruses in the sea

RNA viruses in the sea

Temporal variation in freshwater viral and bacterial community composition

High overall diversity and dominance of microdiverse relationships in salt marsh sulphate‐reducing bacteria

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