A combined sequence-based and fragment-based characterization of microbial eukaryote assemblages provides taxonomic context for the Terminal Restriction Fragment Length Polymorphism (T-RFLP) method

Kim, Diane Y.; Countway, Peter D.; Yamashita, Warren; Caron, David A.

doi:10.1016/j.mimet.2012.09.026

Cited by 12 publications

(15 citation statements)

References 55 publications

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“…Top-down controls on bacterial communities C-ET Chow et al detected OTUs 40.1%; g23-TRFLP detected 4100 T4-like virus OTUs each month on average, each representing 40.1% of the total T4-like community (Chow and Fuhrman, 2012) and 18S rDNA TRFLP revealed dominant members (40.5%) of the protistan community (Kim et al, 2012). Community variability was predictable by environmental factors, but only to a limited extent; each microbial community was discerned by a unique set of environmental factors.…”

Section: Discussionmentioning

confidence: 99%

“…Seawater (B20 l) was collected approximately monthly at 0 or 5 m at the University of Southern California's Microbial Observatory at SPOT (33' 331 N,118' 241 W) and filtered for free-living protistan (0.7-20 mm), bacterial (0.22-1 mm) and viral (30 kDa-0.22 mm) community DNA from March 2008 to January 2011, as previously described (Countway et al, 2005;Fuhrman et al, 2006;Vigil et al, 2009;Countway et al, 2010;Steele et al, 2011;Chow and Fuhrman, 2012;Kim et al, 2012;Chow et al, 2013). Molecular data was unavailable for October 2008 (virus), January 2009 (all), March 2009 (bacteria), October-November 2009 (bacteria) and January 2011 (protist).…”

Section: Sample Collectionmentioning

confidence: 99%

“…and Phaeocystis globosa cultures were used as positive controls for calibrating and verifying fragment sizes. Protistan OTUs were identified from in silico digestion of 1341 18S rRNA gene sequences from October 2001 at SPOT (Kim et al, 2012).…”

Section: Fingerprinting Microbial Communitiesmentioning

confidence: 99%

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Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists

et al. 2013

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Characterizing ecological relationships between viruses, bacteria and protists in the ocean are critical to understanding ecosystem function, yet these relationships are infrequently investigated together. We evaluated these relationships through microbial association network analysis of samples collected approximately monthly from March 2008 to January 2011 in the surface ocean (0-5 m) at the San Pedro Ocean Time series station. Bacterial, T4-like myoviral and protistan communities were described by Automated Ribosomal Intergenic Spacer Analysis and terminal restriction fragment length polymorphism of the gene encoding the major capsid protein (g23) and 18S ribosomal DNA, respectively. Concurrent shifts in community structure suggested similar timing of responses to environmental and biological parameters. We linked T4-like myoviral, bacterial and protistan operational taxonomic units by local similarity correlations, which were then visualized as association networks. Network links (correlations) potentially represent synergistic and antagonistic relationships such as viral lysis, grazing, competition or other interactions. We found that virus-bacteria relationships were more cross-linked than protist-bacteria relationships, suggestive of increased taxonomic specificity in virus-bacteria relationships. We also found that 80% of bacterial-protist and 74% of bacterial-viral correlations were positive, with the latter suggesting that at monthly and seasonal timescales, viruses may be following their hosts more often than controlling host abundance.

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Section: Discussionmentioning

confidence: 99%

Section: Sample Collectionmentioning

confidence: 99%

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Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists

et al. 2013

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“…Commonly occurring OTUs, defined as OTUs that were present in more than half of the samples of each dataset (i.e. spatial and daily samples), were compared with reference fragments generated through in silico digestion of full-length 18S rRNA gene sequences from Kim et al (2012) (Table S1 in the Supplement at www. int-res.…”

Section: T-rflp Analysis Of the Protistan Community Compositionmentioning

confidence: 99%

“…Kim et al (2012) identified OTUs using the same reference fragments for a dataset of monthly samples collected at the SPOT over a period of 3 yr. The applicability of this reference dataset for year-round samples is attributed in part to the generally oligotrophic conditions at the SPOT station, which leads to a relatively more stable assemblage of protists ).…”

Section: Commonly Occurring Taxa In the Protistan Communitymentioning

confidence: 99%