Copepods are the dominant members of the zooplankton community and the most abundant form of life. It is imperative to obtain insights into the copepod-associated bacteriobiomes (CAB) in order to identify specific bacterial taxa associated within a copepod, and to understand how they vary between different copepods. Analysing the potential genes within the CAB may reveal their intrinsic role in biogeochemical cycles. For this, machine-learning models and PICRUSt2 analysis were deployed to analyse 16S rDNA gene sequences (approximately 16 million reads) of CAB belonging to five different copepod genera viz., Acartia spp., Calanus spp., Centropages sp., Pleuromamma spp., and Temora spp.. Overall, we predict 50 sub-OTUs (s-OTUs) (gradient boosting classifiers) to be important in five copepod genera. Among these, 15 s-OTUs were predicted to be important in Calanus spp. and 20 s-OTUs as important in Pleuromamma spp.. Four bacterial s-OTUs Acinetobacter johnsonii, Phaeobacter, Vibrio shilonii and Piscirickettsiaceae were identified as important s-OTUs in Calanus spp., and the s-OTUs Marinobacter, Alteromonas, Desulfovibrio, Limnobacter, Sphingomonas, Methyloversatilis, Enhydrobacter and Coriobacteriaceae were predicted as important s-OTUs in Pleuromamma spp., for the first time. Our meta-analysis revealed that the CAB of Pleuromamma spp. had a high proportion of potential genes responsible for methanogenesis and nitrogen fixation, whereas the CAB of Temora spp. had a high proportion of potential genes involved in assimilatory sulphate reduction, and cyanocobalamin synthesis. The CAB of Pleuromamma spp. and Temora spp. have potential genes accountable for iron transport.
Bacterial diversity studies in hypersaline soil often yield novel organisms and contribute to our understanding of this extreme environment. Soil from Mad Boon is previously uncharacterized, with dense mangrove forest in one side and hypersaline soil in another side of backwater located in Southeast coast of Tamil Nadu, India. We surveyed to characterize the structure and diversity of the bacterial community. Samples were collected in a partially vegetated upland, exposed backwater sedimentation and water-logged location. In this study, we investigate the bacterial community structure using pyrosequence analysis of the V5- V9 gene region. After quality checks a total of 3919, 7298 and 7399 reads were obtained. About 42 phyla were observed, among them Proteobacteria were dominant phylum followed by Acidobacteria, Firmicutes and Chloroflexi. Classes including Deltaproteobacteria and Gammaproteobacteriawere observed. All sequences generated in this study were submitted to NCBI SRA under the accession numbers SRR627695, SRR63011 and SRR631012.
Strengthening the DNA barcode database is important for a species level identification, which was lacking for seaweeds. We made an effort to collect and barcode seaweeds occurring along Southeast coast of India. We barcoded 31 seaweeds species belonging to 21 genera, 14 family, 12 order of 3 phyla (viz., Chlorophyta, Ochrophyta and Rhodophyta). We found 10 species in 3 phyla and 2 genera (Anthophycus and Chnoospora) of Ochrophyta were barcoded for the first time. Uncorrected p-distance calculated using K2P, nucleotide diversity and Tajima’s test statistics reveals highest values among the species of Chlorophyta. Over all K2P distance was 0.36. The present study revealed the potentiality of rbcL gene sequences in identification of all 3 phyla of seaweeds. We also found that the present barcode reference libraries (GenBank and BOLD) were insufficient in seaweeds identification and more efforts were needed for strengthening local seaweed barcode library to benefit rapids developing field such as environmental DNA barcoding. We also show that the constructed barcode library could aid various industrial experts involved in seaweed bio-resource exploration and taxonomy/non-taxonomic researches involved in climate, agriculture and epigenetics research in precise seaweed identification. Since the rise of modern high-throughput sequencing technologies is significantly altering bio-monitoring applications and surveys, reference datasets such as ours will become essential in ecosystem’s health assessment and monitoring.
Understanding biota distribution in oxygen minimum zone can help guide further exploration of potentially unusual habitats. The present study explores the culturable bacterial fractions in the oxygen minimum zone sediments of Bay of Bengal. The 16S rRNA gene sequences of 30 morphologically distinct bacterial colonies isolated form oxygen minimum zone of Bay of Bengal reveals 25 phylo-types, predominated by Proteobacteria (83.3%) and Actinobacteria (16.6%). Over all, Alphaproteobacteria and Gammaproteobacteria dominated the culturable fraction in this study. The overall pair-wise distances of bacterial isolates of Bay of Bengal is two times lesser when compared to overall pair-wise distance of bacterial isolates from oxygen minimum zone of Arabian Sea indicating relatively low genetic distances in Bay of Bengal. Not even 1% of bacterial cells in oxygen minimum zone of Bay of Bengal are culturable. We found that oxygen concentration alone could not be a deciding factor of culturable bacterial diversity in oxygen minimum zone. More than 50% bacterial isolates of present study is an active degraders of hydrocarbons. Higher similarity of 16S rRNA sequences produced in this study with that of previously reported efficient hydrobonoclastic bacterial isolates like Vibrio diazotrophicus, Vibrio cyclotrophicus, Pseudomonas poae, Marinobacter hydrocarbonoclasticus, Marinobacter flavimaris and Alcanivorax borkumensis further strengthens the evidence of hydrocarbon presence in Bay of Bengal sediments. This study is first of its time addresses the diversity of culturable bacterial fractions in oxygen minimum zone sediments of Bay of Bengal. Higher number of bacterial isolates from oxygen minimum zone of Bay of Bengal has carbonoclastic potentialities implying that they may play an important role in in situ hydrocarbon degradation in oxygen minimum zone of Bay of Bengal.
Globally, mangrove coverings are disappearing at the rate of 1–2% per annum and 35% have been lost in the last 20 years. Changes in climate and human activities are affecting the mangrove habitats significantly. When the mangroves were transplanted artificially 25 years ago in the Vellar estuary, no mangrove-associated crabs were found. We sampled this mangrove ecosystem and intent to estimate the diversity, species abundance, composition and phylogenetic relationships of barchyuran crabs. We also intend to evaluate the efficacy of DNA barcoding technique in precisely identifying species of brachyuran crab associated with mangroves. Mangrove species such as, Avicennia marina, A. officinalis, Rhizophora apiculata, R. mucronata and R. annamalayana, Acanthus ilicifolius and salt marshes; Suaeda maritima and Prosopis juliflora constituted the artificially created mangrove ecosystem. A total of 2844 crabs were collected, representing 35 species belonging to 20 genera within 8 families. The four species of brachyuran crab, that is, Uca lactae, U. triangularis, Selatium brockii, and Neosarmatium asiaticum contribute >70% of total abundances. The present study recovered an estimated 87.5% of crab species. The maximum association index value (97.7%) was observed between Uca lactea and Uca triangularis. Cluster analysis, grouped the sampled stations according to the type of mangrove species present. It was clear that the type of mangrove species influences brachyuran crabs’ structure and species composition. Clustering analysis also clearly distinguished the mangrove stations and salt-marsh station (control) based on the composition of the brachyuran crab species. In general, the abundances of all collected species of crabs, and particularly Neosarmatium asiaticum, prefers vegetative cover composed of multiple species of mangroves. DNA barcoding analysis shows that 40% of the species collected in this study was barcoded for the first time. In near future, the advent of new high-throughput sequencing technologies will dramatically change bio-monitoring applications and surveys. This will make reference datasets such as ours important. Using the array of diversity and species estimator indices we presented useful data on brachyuran crab diversity associated with artificially created mangrove ecosystem, which will be useful for marine policy makers, coastal ecosystem designers and climate researchers.
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