A Metagenomes-Based Investigation of the Impact of Natural Run-offs and Anthropogenesis on a Freshwater Ecosystem at Points of Use in Niger Delta, Nigeria

Abstract

A metagenomes-based approach was applied to investigate the impact of anthropogenic activities and run-offs to the diversity and relative abundance of bacterial community structure in a freshwater ecosystem at points of use across three referenced sites (RIK, RTM and RSW) in Yenagoa Metropolitan area of Bayelsa State, Nigeria. High throughput sequencing (HTS) on Illumina Miseq of the V₁ -V₃ hyper variable regions of the 16s rRNA gene revealed high bacterial diversity. In all, a total of 291,757 and 204,179 quality filtered reads describing ten distinct bacterial phyla from water and environmental soils respectively were generated at the top eight classifications. Proteobacteria was the modal abundant phylum in all communities with Betaproteobacteria as the most common class in all water samples and Alphaproteobacteria in the environmental soils. Differences in community structure were noted especially among the rare population. Proteobacteria, Actinobacteria, unclassified bacteria and Firmicutes were the most common and abundant phyla in the freshwater Metagenome. A comparative analysis of the environmental soils from settlements situated at river banks revealed Proteobacteria, Actinobacteria, unclassified bacteria, Firmicutes and Bacteriodetes as the most common and abundant phyla. The degree of abundance of the unclassified bacteria at phylum level significantly increased down to the specie level taxonomic categories in all the water and soil metagenomes across the sampling sites. The genera; Burkholderia, Leptothrix, Hebaspirillium, Novosphingobium and Thaurea detected in water samples are of public health risk. A progressive increase in the abundance of the Actinobacteria members in both water and environmental soil metagenomes across the three study sites indicates higher anthropogenic disturbance at the downstream site. The dominance of Betaproteobacteria in water samples and Alphaproteobacteria in soil samples further suggests that runoff discharges significantly impacted the community structure. This study reveals that run-off discharges and anthropogenesis from metropolitan activities could lead to variation in microbial community structure, diversity and distribution of pathogenic bacteria at points of use of a freshwater ecosystem. The study also reveals an abundance of unclassified bacterial sequences which may give rise to novel bacteria with unexploited microbial genetic diversity within the freshwater ecosystem in the Niger Delta region.