Unveiling organohalide respiration potential in River Nile sediments via 16S rRNA gene amplicon sequencing of endogenous bacterial communities

Abstract Background Industrial waste, agricultural runoff and untreated sewage contaminate the Nile, leaving a toxic legacy in its sediments. Organohalides-polluted sediment in particular poses serious public health risks and detrimental effects on aquatic life. Sediment microbiomes may harbor bacterial strains that could be utilized in bioremediation of such toxic pollutants. Material and methods Two microbiomes from polluted River Nile sediments were analyzed by using 16S rRNA gene amplicon sequencing. In addition, PICRUSt analysis based on 16S rRNA data was used to explore the organohalide respiring bacteria (OHRB) genera and their corresponding organohalide respiration (OHR) activity. Microcosm studies were performed to validate the potential for dechlorination activity of River Nile sediment. Dechlorination of the parent chloroethenes into daughter end product were detected by gas chromatography coupled with flame ionization detection analysis. Results Analysis of 16S rRNA gene amplicon sequences using the EZ-biocloud server identified Proteobacteria as the dominant phylum in both microbiomes, with Bacteroidetes and Chloroflexi prevalent in RNS1 sediment and Chlorobi in RNS2 sediment. EZ-biocloud and PCR analyses detected several potential OHRB genera, including Dehalococcoides, Dehalogenimonas, Desulfomonile, Desulfovibrio, and Geobacter, suggesting potential OHR activity. Further evidence for potential OHR activity was provided by PICRUSt functional prediction analysis, which suggested the presence of reductive dehalogenases as functional biomarkers associated with OHR in the sediment samples. Specifically, PICRUSt analysis predicted the presence of potential genes of tetrachloroethene reductive dehalogenase and 3-chloro-4-hydroxyphenylacetate reductive dehalogenase, previously linked to OHR. Microcosm studies confirmed the dechlorination potential of tetrachloroethene to dichloroethene. Conclusion This study demonstrates that River Nile sediment in industrialized area harbors distinct microbiomes enclosing various OHRB genera, providing substantial evidence for potential reductive dechlorination activity. It also provides potential functional biomarkers for OHR activity.