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

Abstract

BackgroundBacterial 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.Methods and Principal FindingsIn 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.ConclusionThis 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.

Illumina-based analysis the microbial diversity associated with Thalassia hemprichii in Xincun Bay, South China Sea

“…and seagrass (Cymodocea sp. ), Karankadu coastal region, Indian (Aravindraja et al 2013). Proteobacteria can be observed in large amount in marine samples, which supported the phyla are ubiquity in the marine area, especially in the meadow habitats.…”

“…The bacteria inside of seagrass are nearly ten times more than the unvegetated areas (Delille et al 1996). The distribution of microbial communities is highly environmental correlation and ecological limitation (Crump and Koch 2008;Newby et al 2006), owing to abiotic (nutrients, dissolved organic carbon and physical parameters) and biotic (constraints in community ecology) factors (Sundqvist et al 2013), especially, the coastal and estuarine areas, where they are characterized by sharp physical and chemical gradients (Aravindraja et al 2013;Ning et al 2004). Diverse bacterias associated with Halodule, Thalassodendron, Thalassia and Cymodocea and various prokaryotic epiphytes associated with the seagrass have been found in the Western Indian Ocean (WIO) and the east Africa (Hamisi et al 2007;Uku 2007).…”

“…Denaturing gradient gel electrophoresis (DGGE), clone libraries and highthrough sequencing strategies have also been widely applied in marine costal seagrass investigations (Aravindraja et al 2013;Nubel et al 1996). The highthrough sequencing method can provide an effective alternative in identifying the microbial community structure of environment and host-associated samples with particular data software (Caporaso et al 2010;Zhang et al 2014).…”

Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities

“…Bacteria in the order Actinomycetales constitute a minor component of sediment communities (5,7,(31)(32)(33)(34)(35)(36), yet decades of culturing efforts have shown that they persist in most well-sampled sediments (37)(38)(39)(40). These bacteria are well known for secondary metabolite production (41), and their mycelial growth form creates the potential for the formation of large networks (42) that have yet to be spatially characterized.…”

Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach

“…Several recent works (Aravindraja et al 2013;Bartram et al 2014;Bowen et al 2012;Dohrmann et al 2013;Gibbons et al 2013;Kim et al 2013;Logares et al 2013;Oh et al 2013;Portillo et al 2013;Sánchez et al 2013;Székely and Langenheder 2014;Wegner et al 2013), mainly performed with nextgeneration sequencing technologies, have demonstrated that most bacterial communities are composed of a few abundant taxa and a plethora of rare ones (Pedrós-Alió 2012). Such different fractions may have in theory different taxonomic signatures (at the various taxonomic levels), in relation to the physiological features of the groups of taxa present.…”