Metagenomic approach to characterize soil microbial diversity of Phumdi at Loktak Lake.

Loktak, one of the largest freshwater lakes of India, is known for floating islands (Phumdi), being made up of a heterogeneous biomass of vegetation and soil. This ecological site represents an exclusive environmental habitat wherein the rhizospheric microbial community of Phumdi plays a key role in biogeochemical cycling of nutrients. A culture-independent whole genome shotgun sequencing based metagenomic approach was employed to unravel the composition of the microbial community and its corresponding functional potential at this environmental habitat. Proteobacteria (51%) was found to be the most dominant bacterial phylum followed by Acidobacteria (10%), Actinobacteria (9%) and Bacteroidetes (7%). Furthermore, Loktak metagenome data were compared with available metagenomes from four other aquatic habitats, varying from pristine to highly polluted eutrophic habitats. The comparative metagenomics approach aided by statistical analysis revealed that Candidatus Solibacter, Bradyrhizobium, Candidatus Koribacter, Pedosphaera, Methylobacterium, Anaeromyxobacter, Sorangium, Opitutus and Acidobacterium genera are selectively dominant at this habitat. Correspondingly, 12 different functional categories were found to be exclusively prevalent at Phumdi compared to other freshwater habitats. These differential features have been attributed to the unique habitat at Phumdi and correlated to the phenomenon of bioremediation at Loktak Lake.

In silico analysis for prediction of degradative capacity of Pseudomonas putida SF1.

The study employs draft genome sequence data to explore p-nitrophenol (PNP) degradation activity of Pseudomonas putida strain SF-1 at a genomic scale. Annotation analysis proposes that the strain SF1 not only possesses the gene cluster for PNP utilization but also for the utilization of benzoate, catechol, hydroxybenzoate, protocatechuate, and homogentisate. Further, the analysis was carried out to understand more details of PNP 4-monooxygenase and its regulator. A comparative analysis of PNP 4-monooxygenase from SF1 was carried out for prediction of its tertiary structure; and also its binding affinity with PNP, FAD, NADH and NADPH using FlexX docking. The tertiary structure of regulator was also predicted along with its conserved DNA binding residues. Regulator binding site (RBS) and promoter region were mapped for the PNP degradation gene cluster. Based on genome sequence analysis, the study unveiled the genomic attributes for a versatile catabolic potential of Pseudomonas putida strain SF-1 for different aromatic compounds.

Comparative metagenomics demonstrating different degradative capacity of activated biomass treating hydrocarbon contaminated wastewater.

This study demonstrates the diverse degradative capacity of activated biomass, when exposed to different levels of total dissolved solids (TDS) using a comparative metagenomics approach. The biomass was collected at two time points to examine seasonal variations. Four metagenomes were sequenced on Illumina Miseq platform and analysed using MG-RAST. STAMP tool was used to analyse statistically significant differences amongst different attributes of metagenomes. Metabolic pathways related to degradation of aromatics via the central and peripheral pathways were found to be dominant in low TDS metagenome, while pathways corresponding to central carbohydrate metabolism, nitrogen, organic acids were predominant in high TDS sample. Seasonal variation was seen to affect catabolic gene abundance as well as diversity of the microbial community. Degradation of model compounds using activated sludge demonstrated efficient utilisation of single aromatic ring compounds in both samples but cyclic compounds were not efficiently utilised by biomass exposed to high TDS.