Microbial diversity and bioremediation potential in mangrove sediments—a metagenomic analysis

Mangroves in Kuwait are exposed to increasing levels of polycyclic aromatic hydrocarbons (PAHs) originating from industrial activities and urban runoff. However, the potential of native mangrove microbial communities for PAH bioremediation has not yet been explored. Sediment samples were collected from three locations (Shuwaikh, Al Khiran, and Sulaibikhat) at varying distances from Avicennia marina roots. The concentration of PAHs was determined using GC–MS. To assess microbial diversity, a metagenomic approach was used to evaluate diversity metrics. The statistical analysis included the non-parametric Kruskal-Wallis test ( p < 0.05) to compare the median values of different groups and the non-parametric PERMANOVA test ( p -values 0.001–0.009) to assess the differences among groups. The results of the study showed the presence of naphthalene, fluorene, phenanthrene, fluoranthene, pyrene, and chrysene PAHs at varying concentrations across the studied sites. Naphthalene concentrations reached a maximum of 89.64 μg/kg at the Sulaibikhat site and a minimum of 12 μg/kg at the Shuwaikh site. Metagenomic analysis revealed significant differences in microbial diversity between root distances and sites. The rhizosphere samples had higher alpha diversity and richness than the other sediment samples. Beta diversity analysis clustered the samples into groups of sample types and sites. The pairwise comparison between rhizosphere and sediment samples revealed significant differences in microbial communities between rhizosphere and sediment samples in Shuwaikh ( p = 0.012) and Al Khiran ( p = 0.007) sites. The heatmap of gene presence/absence revealed the enrichment of genes involved in hydrocarbon degradation ( alkB , nahA , nahB , phnABC ) and plant growth promotion. Functional analysis using KEGG revealed the metabolic capabilities of the isolates, including the presence of peptide/nickel transporters. All bacterial strains were identified by 16S rRNA gene sequencing, and the major groups of bacteria identified were Pseudomonas , Burkholderia , and Rhodococcus , which are known to have the ability to degrade PAHs and promote plant growth. Microorganisms of different species at various sites of Kuwait mangroves showed higher diversity in rhizosphere areas. Microorganisms living in such zones possess the necessary genes to degrade oil as well as for plant growth and thus have the potential for bioremediation of polluted sites by oil. The high level of PAH contamination in the sediment close to the roots of mangroves indicates localized pollution.