Abstract

Aquaculture production of the Pacific white shrimp is the largest in the world for crustacean species. Crucial to the sustainable global production of this important seafood species is a fundamental understanding of the shrimp gut microbiota and its relationship to the microbial ecology of shrimp pond. This is especially true, given the recently recognized role of beneficial microbes in promoting shrimp nutrient intake and in conferring resistance against pathogens. Unfortunately, aquaculture-related microbiome studies are scarce in Southeast Asia countries despite the severe impact of early mortality syndrome outbreaks on shrimp production in the region. In this study, we employed the 16S rRNA amplicon (V3–V4 region) sequencing and amplicon sequence variants (ASV) method to investigate the microbial diversity of shrimp guts and pond water samples collected from aquaculture farms located in Malaysia and Vietnam. Substantial differences in the pond microbiota were observed between countries with the presence and absence of several taxa extending to the family level. Microbial diversity of the shrimp gut was found to be generally lower than that of the pond environments with a few ubiquitous genera representing a majority of the shrimp gut microbial diversity such as Vibrio and Photobacterium, indicating host-specific selection of microbial species. Given the high sequence conservation of the 16S rRNA gene, we assessed its veracity at distinguishing Vibrio species based on nucleotide alignment against type strain reference sequences and demonstrated the utility of ASV approach in uncovering a wider diversity of Vibrio species compared to the conventional OTU clustering approach.

Highlights

  • Litopenaeus vannamei (Boone, 1931), known as the Pacific white shrimp or Whiteleg shrimp, is a major aquaculture commodity with a production of 3.69 million tonnes valued at 18 billion USD revenue (FAO, 2016)

  • A total of 2,731,818 successfully merged reads were generated in this study with 2,144,192 reads confidently mapped to the amplicon sequence variants (ASV). 92.12% and 7.77% of the mapped reads correspond to RDP-classified and SINAclassified ASVs respectively, while the remaining mapped reads belong to ASVs without confident taxonomic assignment at the kingdom rank

  • Malaysian shrimp intestinal microbiome contains more reads mapping to the phylum Fusobacteria (p < 0.01). This phylum is near absent in three out of four Malaysian shrimps noted to be unhealthy based on morphological observation by the aquaculture manager (Fig. 1)

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Summary

Introduction

Litopenaeus vannamei (Boone, 1931), known as the Pacific white shrimp or Whiteleg shrimp, is a major aquaculture commodity with a production of 3.69 million tonnes valued at 18 billion USD revenue (FAO, 2016). The importance of microbial communities in influencing or responding to variation in aquaculture pond water quality has only been recognized in recent years (Bentzon-Tilia, Sonnenschein & Gram, 2016). This is especially relevant to managing the water quality of aquaculture ponds and their cultured biomass because microbes carry out important biological services in aquaculture environment including nutrient cycling, probiotic/pathogenic activity and nutrient acquisition in addition to potentially acting as a rapid biological indicator of critical chemical changes in the rearing water (Cardona et al, 2016; Cornejo-Granados et al, 2017; Costa, Pérez & Kreft, 2006; Emerenciano, Gaxiola & Cuzon, 2013; Grotkjær et al, 2016; Jinbo et al, 2017; Liu et al, 2015; Wright, Konwar & Hallam, 2012; Zeng et al, 2017; Zhu et al, 2016). Adding denitrifying bacteria to biofilters has been shown to reduce the concentration of ammonia and its immediate derivatives, which are detrimental to shrimp health (Saffran et al, 2001)

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