Comparative assessment of bacterial diversity associated with co-occurring eukaryotic hosts of Palk Bay origin

417-423Epibacterial communities of co-occurring eukaryotic hosts of Palk Bay origin (five seaweed species (Gracilaria sp, Padina sp, Enteromorpha sp, Sargassum sp, and Turbinaria sp) and one seagrass [Cymodaceae sp]) were analyzed for diversity and compared using 16S rRNA based Denaturant Gradient Gel Electrophoresis analysis. Diversity index revealed that Turbinaria sp hosts highest bacterial diversity while it was least in Gracilaria sp. The DGGE band profile showed that the epibacterial community differed considerably among the studied species. Statistical assessment using cluster analysis and Non-metric multidimensional scale analysis also authenticated the observed variability. Despite huge overlap, the composition of bacterial community structure differed significantly among the three closely related species namely Sargassum, Turbinaria and Padina. In addition, Enteromorpha and Sargassum, one being chlorophyta and the other phaeophyta showed about 80% similarity in bacterial composition. This differs from the general notion that epibacterial community composition will vary widely depending on the host phyla. The results extended the phenomenon of host specific epibacterial community irrespective of phylogeny and similarity in geographical location

Overview of sequence information.

a<p>More than 70% of bases in a read with >20 phred score and reads which are of low quality were trimmed and used.</p>b<p>Number of reads after chimera and duplicate removal.</p

Quorum sensing mediated virulence inhibition of an opportunistic human pathogen <i>Serratia marcescens</i> from unexplored marine sediment of Palk Bay through function driven metagenomic approach

448-452Indiscriminate use of antibiotics in treatment strategies of infections caused by opportunistic pathogen, Serratia marcescens has made the specimen multidrug resistant (MDR). The present study is focused to identify novel metaclones that selectively target quorum sensing mediated virulence factors of S. marcescens through culture independent approach. Metagenomic DNA library was constructed for the isolated marine sediment (Karakadu coastal region, India) metagenome using a copy control Fosmid vector. Quorum quenching activity of the cell free culture supernatants of the obtained metaclones was identified using the reduction in violacein pigment production in Chromobacterium violaceum. Among the obtained metagenomic clones, ethyl acetate extracts (50 µg/mL) of MCS-3 and MCS-4 showed 98 and 100 % of prodigiosin pigment reduction, respectively in S. marcescens. The production of secreted caseinase was reduced significantly up to 70 and 78 % when treated with 50 µg/mL ethyl acetate extracts of MCS-3 and MCS-4, respectively. Significant decrease (77 and 73 %) in lipase production was also observed with 50 µg/mL ethyl acetate extract of MCS-3 and MCS-4. This is one of the few reports that highlight the potential of function driven metagenomic approach that explicates the unexplored marine sediment of Palk Bay coastal region as a novel source of anti-QS agents

Ultradeep 16S rRNA Sequencing Analysis of Geographically Similar but Diverse Unexplored Marine Samples Reveal Varied Bacterial Community Composition

<div><p>Background</p><p>Bacterial community composition in the marine environment differs from one geographical location to another. Reports that delineate the bacterial diversity of different marine samples from geographically similar location are limited. The present study aims to understand whether the bacterial community compositions from different marine samples harbour similar bacterial diversity since these are geographically related to each other.</p><p>Methods and Principal Findings</p><p>In the present study, 16S rRNA deep sequencing analysis targeting V3 region was performed using Illumina bar coded sequencing. A total of 22.44 million paired end reads were obtained from the metagenomic DNA of Marine sediment, Rhizosphere sediment, Seawater and the epibacterial DNA of Seaweed and Seagrass. Diversity index analysis revealed that Marine sediment has the highest bacterial diversity and the least bacterial diversity was observed in Rhizosphere sediment. Proteobacteria, Actinobacteria and Bacteroidetes were the dominant taxa present in all the marine samples. Nearly 62–71% of rare species were identified in all the samples and most of these rare species were unique to a particular sample. Further taxonomic assignment at the phylum and genus level revealed that the bacterial community compositions differ among the samples.</p><p>Conclusion</p><p>This is the first report that supports the fact that, bacterial community composition is specific for specific samples irrespective of its similar geographical location. Existence of specific bacterial community for each sample may drive overall difference in bacterial structural composition of each sample. Further studies like whole metagenomic sequencing will throw more insights to the key stone players and its interconnecting metabolic pathways. In addition, this is one of the very few reports that depicts the unexplored bacterial diversity of marine samples (Marine sediment, Rhizosphere sediment, Seawater) and the host associated marine samples (Seaweed and Seagrass) at higher depths from uncharacterised coastal region of Palk Bay, India using next generation sequencing technology.</p></div

Comparison of bacterial communities among the samples at genus level.

<p>The members of the phyla Alphaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Actinobacteria, Bacteriodetes and Cyanobacteria which are above 1% are compared among the samples. As evident all the samples had varying levels of different genera.</p

Analysis of abundant and rare species among the marine samples.

<p>A. <b>Percentage of abundant and rare species across the samples.</b> In all the five samples when compared to abundant species the percentage of rare species is significantly high indicating the importance of rare species in a community. B. <b>Shared and specific rare species among the marine samples.</b> Most of the rare species are unique to particular sample and only a few are shared by all the samples. C. <b>Shared and specific abundant species among the marine samples.</b> Most of the abundant species are common to all the samples and only a few are unique to particular sample.</p