PMC

Functional Annotation from pond sediment and sites across dumpsite. a) Extrapolation of taxonomic diversity of PS1 and PS2 (Fisher's Exact Test, P > 0.01) is the overall representation of phylum profiles using Pfam protein domains and the associated Gene Ontology (GO) in PS1 versus PS2 (R² = 0.985), b) Rare fraction analysis performed on the unique Pfam protein domains across pond sediment (PS1 and PS2) and three HCH gradients (1 Km, 5 Km, DS(Dumpsite) and SolexaDS), c) Principle Component Analysis (PCA) plot of NCBI COG categories of three HCH gradients and two samples of pond sediment metagenome to validate the functional profiling of matagenomic samples, d) Plot showing Shannon diversity across pond sediment (PS1 & PS2), 1 Km, 5 Km, DS(Dumpsite) and SolexaDS for functional and diversity (by EGT) analysis.

Differential taxonomic binning of pond sediment. a) Phylogenetic reassignment of metagenomic reads of PS1, PS2 and HCH gradient (1 Km, 5 Km, DS and SolexaDS) against the nr-database (ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr, June, 2015) (BLASTX, E-value = 1e-10), b) Stack area plot of the most abundant phyla present among PS1 and PS2 samples which were statistically computed using METASTATS (P value ≤ 0.05 and 1000 permutations), c) Depiction of genomic variation in pond sediment by principal component analysis of tetranucleotide frequency of essential single copy genes using R v. 3.2.2 via the ace function of ape. pc.comp1 and pc.comp2 are its two principle components. d) The plot was constructed along two principle components; X1 and X2 were composed of all terminal and internal phylogenetic nodes with the branches connecting adjacent nodes. X1 and X2 axis in the principle component plot are the eigenvectors with the highest eigenvalues for essential single copy genes of the most abundant bacterial phyla. Clustering of nodes represented the genomic variation in pond sediment and Cluster B was found to be abundant in pond sediment metagenome.