They observed that different provinces harbored distinct flavobacterial communities which displayed distinct niches and different lifestyle strategies, revealing basin scale taxonomy and trait biogeographic patterns. Tanespimycin This highlights another factor complicating marine microbial biogeography: specific biogeographical patterns may emerge at some scales but not others. Indeed the geographic distribution of samples collected (e.g. micro, local, regional, basin, global),
the number of samples examined and the depth of interrogation (e.g. number of sequences obtained per samples) may determine which patterns are revealed, and this effect is particularly pronounced for taxa belonging to the rare biosphere (Woodcock et al., 2006 and Zinger et al., 2014). It has been shown that much of the microbial diversity
in the marine system can be determined present at a single given site if enough sequences are examined (Gibbons et al., 2013) so biogeographic patterns may be the result of “shallow” sequencing. However, determination of presence should not negate the importance of patterns in the abundance of microorganisms, especially the relative Fulvestrant abundance of different ecotypes within a given taxa. Hence, the taxonomic scale of sampling is a critical component to consider. To date, most microbial biogeography studies rely on comparison of 16S rRNA gene sequences. Due to a lack of a consensus model for what constitutes a bacterial species, patterns are derived from comparison of operational taxonomic units (OTU’s) (e.g. Schloss and Handelsman, 2005). Using next generation sequencing technology these OTU’s are generally based on sequence similarity of a small variable region of the ribosomal operon (e.g. Caporaso et al., 2012a). What
divergence in these variable regions means in terms of historically defined 97% 16S rRNA gene sequence similarity or 70% DNA/DNA hybridization (Stakebrandt and Goebel, 1994), or in terms of organismal GBA3 ecology (e.g. Eren et al., 2013), is rarely considered. For example, Synechococcus clades IV and III which proliferate under distinctly different oceanic conditions (temperate versus subtropical oligotrophic oceans respectively, discussed below) cannot be resolved on the basis of the V6 hypervariable region of the SSU rRNA gene ( Post et al., 2011). Moreover, there can be much phylogenetic and ecological heterogeneity obscured within OTU’s, even those that are highly stringent ( Brown et al., 2009 and Koeppel and Wu, 2013). Some of this heterogeneity may be resolved using higher resolution molecular markers such as the internal transcribed spacer region (e.g. Brown et al., 2012), while some requires whole genome sequencing to unmask. For instance, in the marine Synechococcus clade III, genes found on genomic islands ( Dufresne et al.