The seasonal structure of microbial communities in the Western English Channel. Environ Microbiol

Plymouth Marine Laboratory, Prospect Place, Plymouth, PL1 3DH, UK.
Environmental Microbiology (Impact Factor: 6.2). 08/2009; 11(12):3132-9. DOI: 10.1111/j.1462-2920.2009.02017.x
Source: PubMed


Very few marine microbial communities are well characterized even with the weight of research effort presently devoted to it. Only a small proportion of this effort has been aimed at investigating temporal community structure. Here we present the first report of the application of high-throughput pyrosequencing to investigate intra-annual bacterial community structure. Microbial diversity was determined for 12 time points at the surface of the L4 sampling site in the Western English Channel. This was performed over 11 months during 2007. A total of 182 560 sequences from the V6 hyper-variable region of the small-subunit ribosomal RNA gene (16S rRNA) were obtained; there were between 11 327 and 17 339 reads per sample. Approximately 7000 genera were identified, with one in every 25 reads being attributed to a new genus; yet this level of sampling far from exhausted the total diversity present at any one time point. The total data set contained 17 673 unique sequences. Only 93 (0.5%) were found at all time points, yet these few lineages comprised 50% of the total reads sequenced. The most abundant phylum was Proteobacteria (50% of all sequenced reads), while the SAR11 clade comprised 21% of the ubiquitous reads and approximately 12% of the total sequenced reads. In contrast, 78% of all operational taxonomic units were only found at one time point and 67% were only found once, evidence of a large and transient rare assemblage. This time series shows evidence of seasonally structured community diversity. There is also evidence for seasonal succession, primarily reflecting changes among dominant taxa. These changes in structure were significantly correlated to a combination of temperature, phosphate and silicate concentrations.

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    • "To this end, the availability of molecular techniques such as ribosomal gene sequencing has enabled tremendous upgrades to the knowledge of environmental microbes by allowing comprehensive description of natural communities (Lane et al., 1985; Weisburg et al., 1991; Hugenholtz and Pace, 1996). Further advances in molecular methods have shed light on the immense diversity of complex bacterial communities (Sogin et al., 2006) and have allowed the detailed description of geographic and temporal patterns created by microbial populations (Lauber et al., 2009; Gilbert et al., 2009, 2011). High-throughput molecular methods are thus ideal to study intricate microbial communities such as those found in marine sediments (Nealson, 1997; Lozupone and Knight, 2007; Baker et al., 2015). "
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    • "Formosa, 15%) (Fig. 1A). These results agree with previous studies carried out at station L4 where Alphaproteobacteria 16S rRNA gene sequences, particularly those belonging to the SAR11 clade (Pelagibacteraceae), predominated (Gilbert et al., 2009; 2012; Sargeant, 2013). Potential methanol utilizers, such as Methylophaga, Ruegeria and Roseovarius, represented < 0.5% of the total 16S rRNA gene sequences analyzed (included in 'Others' in Fig. 1A). "
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    • "Both the number of OTUs and sequences affiliated to the Class increased in abundance during periods of high sediment chlorophyll content. Flavobacteria are aerobic members of the phylum Bacteroidetes, considered to be specialist degraders of complex organic matter in the marine environment (Cottrell and Kirchman, 2000; Teeling et al., 2012; Williams et al., 2013), and are found in abundance in both open ocean (Schattenhofer et al., 2009) and coastal (Eilers et al., 2001; O&apos;Sullivan et al., 2004) waters, including L4 (O'Sullivan et al., 2004; Gilbert et al., 2009), and on marine snow (DeLong et al., 1993; Woebken et al., 2007) where their high abundance has been linked to phytoplankton blooms and areas with high levels of POC during upwelling events (e.g. Riemann et al., 2000; Fandino et al., 2005; Alonso-Sáez et al., 2007; Schattenhofer et al., 2009; Gómez-Pereira et al., 2010; Teeling et al., 2012). "
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