METAGENOMIC BARCODING OF MICROBIOMES FROM SEAGRASS FOUND IN COASTAL KENYA USING 16S rRNA SEQUENCING

Abstract

Sea grasses are unique flowering plants that live entirely in the marine environment. They form large meadows that provide habitats for marine life and physical anchoring systems. Microbes have been found to have a significant effect on many eukaryotic organisms’ health and has been proposed to be used as an indicator which can guide its sustainable exploitation. For economic exploitation of this resource, such as by establishing a healthy sea grass stand that can be harvested for human snack, livestock feed or fertilizer, its sustainability needs to assessed. This study proposed to characterize the abundance and diversity of microbiomes associated with Thalassodendron ciliatum, and Enhalus acoroides; leaves and roots and their surrounding water and sediment. Environmental DNA samples were extracted from the target microbiomes of the 2 species, using Mobio DNA extraction kits, PCR amplified using universal 16S primers, the amplicons purified and submitted to 16S sequencing. The resulting cleaned sequences were analyzed using the Quantitative Insight Into Microbial Ecology (QIIME) bioinformatics pipeline. Overall, the most dominant phyla associated with both species was Proteobacteria, Bacteriodes, Cyanobacteria, Actinobacteria Caldithrix and Acidobacteria. E. acoroides associated samples showed higher organism diversity compared to T. ciliatum associated samples, in all alpha diversity metrics. Beta diversity analyses showed that, rhizosphere samples tended to cluster closer together than phyllosphere samples, but water sample replicates did not group together at all in both sites on the PCoA plot. E. acoroides associated samples exhibited higher proportions of microbes present in primary nutrient cycles, and fewer microbes associated with pathogenicity and heavy metals than T. ciliatum associated samples. Fecal indicator bacteria were absent at both sampling sites. T. ciliatum will serve better as fertilizer than animal feed due to the relatively high proportion of suspected pathogenic bacteria genera as well as decomposer bacteria present in its microbiomes. E. acoroides, will be more feasible as human and animal feed due to the virtual absence of pathogenic bacteria genera and observed presence of large numbers of bacteria associated with primary nutrient cycles.