Bacterial Community And Diversity Of Post Larvae Wild Shrimps Along Merbok River Infer Using Metagenomic Approach
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Date
2019-08
Authors
Ahmad, Siti Zuliana
Journal Title
Journal ISSN
Volume Title
Publisher
Universiti Sains Malaysia
Abstract
The study describes the investigation of the bacterial community and diversity associated with post larvae wild shrimps along the mangrove-diverse Merbok River based on metagenomic approach. There are very few studies conducted on the microbiome associated with post larvae shrimps especially in wild species. Furthermore, there is knowledge gap of relationship between microbiome associated with host especially post larvae shrimps with environmental conditions. The goal of this study was identifying of microbial community diversity associated with the wild post larvae shrimps in Merbok Rivers and to determine key major abundance of the wild post larvae shrimp microbial species and overall microbial community structure. These objectives were addressed by using next generation sequencing of metagenomic 16S rRNA gene amplicon using the Illumina MiSeq platform. This was followed by the bioinformatics analysis using a 16S rRNA sequencing analysis pipeline. Relative abundance of bacterial diversity in the four different localities were compared by using a PRIMER6 and PERMANOVA+ softwares. Samples were obtained from four sites (stations); St 1 to St 4 from upstream freshwater habitat to downstream brackish water towards the marine waters. Water quality parameters were measured namely pH, salinity, dissolved oxygen, water depth, turbidity and surface temperature. Shrimps were found in abundance, a reflection that water parameters were in the range that were suitable to support post larvae shrimp survival. Metagenomic data detected a total of 171, 722 operational taxonomic units (OTUs) for all sites. Twenty-eight bacterium phyla were detected, dominated by phyla Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes at all four sites. The most abundant genera were the non-pathogenic bacteria for shrimps as example Streptomyces spp., Mesorhizobium spp., Rhizobium spp., Bacillus spp. and Pseudomonas spp.. The pathogenic Vibrio spp. that can cause infection in shrimps was only found in St 1 and St 4 but in low frequencies. As a conclusion, metagenomics approach 16S rRNA amplicon sequencing is able to identify the abundance and diversity of bacteria associated with post larvae wild shrimps along the Merbok River. Although analysis of a complex metagenomics data is challenging, it can be addressed with various designed pipelines to simplify the process. As for the Merbok River and its mangrove surroundings, despite being exposed to various human activities, it still can serve as a good spawning and nursery sites of shrimps and did not affect post larvae wild shrimp population. However, conservation and surveillance efforts on the wildlife populations are required to avoid the loss of shrimp diversity due to disease infections and to ensure that wild shrimps sources are sustainable.
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Keywords
Shrimp culture , Shellfish culture