Comparative Evaluation of Microbial Diversity of Epipellic and Benthic Sediments using Cultural and Metagenomics Techniques

Abstract

Introduction: Studies have shown that molecular techniques are better in describing microbial diversity in various ecosystems than cultural techniques. The study was aimed at comparative evaluation of the microbial diversity of benthic and epipellic sediments using cultural and metagenomics techniques. Methodology: Benthic and epipellic sediments were collected in triplicates from five locations from the Iko River estuary in Eastern Obolo. Total heterotrophic bacterial and fungal counts, and characterization of microbial isolates were done using the standard microbiological technique. Metagenomic DNA was extracted using ZYMO soil DNA extraction Kit (Model D601, Zymo Research, USA). Following extraction and amplification, the resulting DNA was sequenced using next-generation sequence on Miseq Illumina platform. Data from cultured based techniques were analysed using analysis of variance (ANOVA) and student t-test while resulting metagenomic data were analyzed using web-based bioinformatics tools. Results: Bacteria and fungi counts ranged from 1.08 to 1.60 (x 106 CFU/g) and 0.10 to 2.2 (x 103 CFU/g) with benthic sediments having the highest abundance in both cases. Compared to cultural techniques which captured only bacterial and fungal kingdoms, metagenomics captured archaea, protozoa, viruses, plantae, and unknown kingdoms. Furthermore, 17 phyla were obtained using metagenomics compared to 3 phyla captured by cultural techniques. A total of 61 isolates were recovered spread across various genera (10 from benthic and 11 from epipellic). Most common isolates in both samples were Bacillus, Micrococcus and Pseudomonas. Although a total of 300 species were identified using metagenomics, about 78.92% and 71.19% of the species were uncultured bacterium for benthic and epipellic sediments, respectively. Furthermore, the species were dominated with species involved in nutrient recycling such as Thiobacillus prosperus, Sulfurimonas species and Marinobacterium nitratireducens. Surprisingly, 15(0.15%) of the reads showed sequence similar to Influenza A virus (H3N6) viral cRNA with accession number LC053487.1. Conclusion: The results show that metagenomic assessment is better in capturing the bacterial diversity of sediment than cultural methods.