Linking regional variation of epibiotic bacterial diversity and trophic ecology in a new species of Kiwaidae (Decapoda, Anomura) from East Scotia Ridge (Antarctica) hydrothermal vents.

We analyzed the diversity of bacterial epibionts and trophic ecology of a new species of Kiwa yeti crab discovered at two hydrothermal vent fields (E2 and E9) on the East Scotia Ridge (ESR) in the Southern Ocean using a combination of 454 pyrosequencing, Sanger sequencing, and stable isotope analysis. The Kiwa epibiont communities were dominated by Epsilon- and Gammaproteobacteria. About 454 sequencing of the epibionts on 15 individual Kiwa specimen revealed large regional differences between the two hydrothermal vent fields: at E2, the bacterial community on the Kiwa ventral setae was dominated (up to 75%) by Gammaproteobacteria, whereas at E9 Epsilonproteobacteria dominated (up to 98%). Carbon stable isotope analysis of both Kiwa and the bacterial epibionts also showed distinct differences between E2 and E9 in mean and variability. Both stable isotope and sequence data suggest a dominance of different carbon fixation pathways of the epibiont communities at the two vent fields. At E2, epibionts were putatively fixing carbon via the Calvin-Benson-Bassham and reverse tricarboxylic acid cycle, while at E9 the reverse tricarboxylic acid cycle dominated. Co-varying epibiont diversity and isotope values at E2 and E9 also present further support for the hypothesis that epibionts serve as a food source for Kiwa.

Internal and external influences on near-surface microbial community structure in the vicinity of the Cape Verde Islands.

Microbial community structure in the subtropical north-east Atlantic Ocean was compared between 2 years and variation attributed to environmental variables. Surface seawater communities were analysed by flow cytometry and fluorescence in situ hybridisation. Probes specific to Alphaproteobacteria, Cyanobacteria, Gammaproteobacteria and Bacteroidetes identified 67-100% of cells. Due to natural variation in the study region due to the occurrence of major currents and islands, data could not be pooled but were instead divided between distinct water masses. Community structure did not differ greatly around the Cape Verde Islands between sampling periods but varied substantially in the open ocean, suggesting different environmental perturbations favour specific bacterial groups. Wind speed varied significantly between years, with moderate to strong breeze in winter 2008 and gales in winter 2006 (8.9 ± 0.2 ms(-1) and 16.0 ± 0.4 ms(-1), respectively). Enhanced wind-driven turbulence was associated with domination by the SAR11 clade of Alphaproteobacteria, which were present at 2.4-fold in the abundance of Prochlorococcus (41.8 ± 1.6% cells, compared to 17.7 ± 7.1%). Conversely, the calmer conditions of 2008 seemed to favour Prochlorococcus (40.0 ± 1.2% cells). Prochlorococcus high-light adapted clade HLI were only numerous during wind-driven turbulence, whereas oligotrophic-adapted clade HLII dominated under calm conditions. Bacteroidetes were most prominent in turbulent conditions (9.5 ± 1.3% cells as opposed to 4.7 ± 0.3%), as were Synechococcus. In 2008, a considerable dust deposition event occurred in the region, which may have led to the substantial Gammaproteobacteria population (22.5 ± 4.0% cells compared to 4.6 ± 0.6% in 2006). Wind-driven turbulence may have a significant impact on microbial community structure in the surface ocean. Therefore, community change following dust storm events may be linked to associated wind in addition to dust-derived nutrients.

Capturing diversity of marine heterotrophic protists: one cell at a time.

Recent applications of culture-independent, molecular methods have revealed unexpectedly high diversity in a variety of functional and phylogenetic groups of microorganisms in the ocean. However, none of the existing research tools are free from significant limitations, such as PCR and cloning biases, low phylogenetic resolution and others. Here, we employed novel, single-cell sequencing techniques to assess the composition of small (<10 µm diameter), heterotrophic protists from the Gulf of Maine. Single cells were isolated by flow cytometry, their genomes amplified, and 18S rRNA marker genes were amplified and sequenced. We compared the results to traditional environmental PCR cloning of sorted cells. The diversity of heterotrophic protists was significantly higher in the library of single amplified genomes (SAGs) than in environmental PCR clone libraries of the 18S rRNA gene, obtained from the same coastal sample. Libraries of SAGs, but not clones contained several recently discovered, uncultured groups, including picobiliphytes and novel marine stramenopiles. Clone, but not SAG, libraries contained several large clusters of identical and nearly identical sequences of Dinophyceae, Cercozoa and Stramenopiles. Similar results were obtained using two alternative primer sets, suggesting that PCR biases may not be the only explanation for the observed patterns. Instead, differences in the number of 18S rRNA gene copies among the various protist taxa probably had a significant role in determining the PCR clone composition. These results show that single-cell sequencing has the potential to more accurately assess protistan community composition than previously established methods. In addition, the creation of SAG libraries opens opportunities for the analysis of multiple genes or entire genomes of the uncultured protist groups.

Basin-scale distribution patterns of picocyanobacterial lineages in the Atlantic Ocean.

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are major contributors to oceanic primary production. The genera are genetically diverse, comprising several known ecotypes or lineages. However, little is known of the distribution of these lineages over large geographic areas. Here, we analysed the relative abundance of Prochlorococcus ecotypes and Synechococcus lineages at the ocean basin scale along an Atlantic Meridional Transect (AMT) using dot blot hybridization and fluorescence in situ hybridization (FISH) techniques. The transect covered several contrasting oceanic provinces (gyres, upwelling, temperate regions) as well as environmentally 'equivalent' regions in the northern and southern hemisphere (northern and southern gyres and temperate regions). Flow cytometric data revealed a discrete separation in abundance of major picocyanobacterial genera. Prochlorococcus reached highest abundance in oligotrophic regions, while more mesotrophic waters were dominated by Synechococcus. Individual genetic lineages of both Prochlorococcus and Synechococcus showed highly similar distributions in corresponding regions in the northern and southern hemisphere. In addition, Prochlorococcus showed a distinctive depth distribution, with HLI and HLII ecotypes near the surface and co-occurring LL ecotypes further down in the water column. Conversely, Synechococcus generally revealed no obvious depth preference, but did show highly specific distribution at the horizontal scale, with clades I and IV particularly dominating temperate, mesotrophic waters in both the northern and southern hemispheres. The data clearly reveal that specific picocyanobacterial lineages proliferate in similar oceanic provinces separated by large spatial scales. Furthermore, comparison with an earlier AMT dataset suggests that basin scale distribution patterns for Prochlorococcus ecotypes are remarkably reproducible from year to year.