Cross-biome metagenomic analyses of the impact of pollutants on taxonomic and functional diversity of bacterial communities from different geographical regions

Abstract

Due to anthropogenic activities, a large number of pollutants are disposed into the environment. The microbial communities in the environment are immensely diverse and critical mediators of various ecosystem processes. But it is not clearly known to what extent xenobiotics effect the composition and functionality of environmental microorganisms, across biomes in different geographic locations, with varying contaminating sources, categories of chemical pollutants, and their application types. Here, we investigated the impact of xenobiotics by metagenomic analysis of 16S rRNA from seawater, soil, sludge and sediment, for deciphering microbial diversity, community structure, functional enrichment and metabolic potentiality in relation to the application of pesticide (metaldehyde), herbicide (2,4-dichlorophenoxyacetic acid; DCPAA), insecticide (chlordecone) and flame retardant additives (organophosphate triesters; OPT and tris 2 chloroethyl phosphate; TCEP). Firmicutes was the most abundant phylum consisting of Clostridia, in association with DCPAA (Lutispora sp.), metaldehyde and TCEP treatments. The next two abundant phyla were Proteobacteria [class Deltaproteobacteria, Alphaproteobacteria (Pelagibacter ubique with OPT treatment) and Gammaproteobacteria], and Euryarchaeota consisting mostly of Methanobacteria with chlordecone and DCPAA. Both Desulfomicrobium and Sedimentibacter were predominant in the subtropical moist forest sediment, while Synechococcus and Pelagibacter dominated the temperate Mediterranean Sea. Ruminococcus and Lutispora were more abundant in rain forest compared to waste water solid, while Anaerovorax predominated subtropical moist forest. Sequences involved in house-keeping genes comprised the most abundant hits. The genes involved in environmental information processing such as ABC transporters catalyzing carbohydrate uptake, membrane transport and quorum sensing were over-represented with TCEP, DCPAA, OPT and metaldehyde. Exposure to different classes of xenobiotics revealed major differences in microbial structure and function abundances, mainly driven by environmental sources and biomes. Preponderance of core metabolic functional genes across all the metagenomes analysed is indicative of microbial community responding and adjusting itself to deal with these treatments and maintain its balance.