Bacterial Communities in Informal Dump Sites: A Rich Source of Unique Diversity and Functional Potential for Bioremediation Applications

Abstract

In this study, high-throughput metagenomic amplicon sequencing and physicochemical analyses were used to evaluate the structural composition and functional diversity of the soil bacterial communities at different illegal waste dump sites. Results showed that while the litter-free soil was dominated by the phylum Proteobacteria, dumpsite soils were enriched with phylum Actinobacteria, followed by Proteobacteria, Firmicutes, Chloroflexi, Acidobacteria, Planctomycetes, Bacteroidetes, and Gemmatimonadetes. Bacterial diversity differed significantly (p > 0.05) between the litter-free and contaminated sites, with each dumpsite having distinct genera that demonstrate the impact of waste type on the bacterial community composition. Genus Nocardioides, a versatile organic and inorganic pollutant-degrading bacteria in the class Actinomycetia, was dominant in the dump site soils, raising the possibility that this genus could serve as a potential biomarker for dump site soil pollution. PICRUSt functional profiling also showed the presence of genes involved in putative degradative pathways in the dump site soils. Furthermore, community-level physiological profile (CLPP) analyses revealed that the dump site soils are habitats to active bacterial communities with significant catabolic and carbon utilization capacity. Overall, this study provides a theoretical insight into the diversity and unique soil bacterial assemblages in illegal dump sites that could encode biotechnologically significant genes for biosynthesis and biodegradation.