Profiling bacteriome associated with the sediments of a mangrove ecosystem in Kerala, India

Abstract

Microbiomes play an essential role in maintaining the health of an aquatic ecosystem. The present study is an attempt to analyze the bacteriome of a mangrove ecosystem in Cochin, Kerala, India. 16S rRNA gene-based high throughput sequencing revealed distinct and diverse bacterial communities present in the mangrove sediment sample. The taxonomic approaches applied revealed the dominance of Proteobacteria, Bacteroidetes and Firmicutes in the sample, followed by Actinobacteria, Cyanobacteria, Chloroflexi, Acidobacteria, Saccharibacteria (TM7) and Verrucomicrobia. At the genus level, Prevotella copri and Bacteroides fragilis dominated the sediment sample, which was followed by Pseudomonas, Bifidobacteria, Faecalibacterium, Agrobacterium, Acinetobacter, Streptococcus and Bacillus. Most of these organisms are predominantly found in the human intestine and human faeces and are found in polluted areas. Vibrio harveyi, a potential pathogen that results in mass mortality of mangrove associated organisms, could also be detected. Archaea only accounted for <1% of the metagenome and included Crenarchaeota, Euryarchaeota and unclassified ones. Unclassified bacteria also contributed a portion of the metagenome. The data obtained in the current study indicated that anthropogenic activities and micro-niche play an essential role in structuring the bacterial community. The results of the present study add valuable baseline data on the bacteriome of the mangrove sediments.