Diversity of bacteria and viruses in sea cucumbers and shrimps

Abstract

Various studies have been conducted about the diversity of both bacteria and viruses from marine environment. However, diversity of microbes in marine invertebrates has not been greatly explored. Being genetically diverse, both bacteria and viruses from marine invertebrates can be promising biological resources. In this study, the diversity and genetic resources of such microbes in intestine samples of sea cucumbers and shrimps were investigated by metagenomics. Bacterial DNA was isolated using the Power Soil DNA Extraction Kit (MOBIO) and the extracted DNA was amplified using barcoded primers (27F and 518R). PCR products were subjected to 454 pyrosequencing and the resulting sequences were analyzed using QIIME. Various analyses revealed that sea cucumbers and shrimps have different bacterial composition. Viruses were collected through sequential filtration and their abundance ranged from 108 to 109 per gram of intestine. Viral DNA was extracted and was amplified via the multiple displacement amplification (MDA) method using the phi29 polymerase, and was analyzed by 454 pyrosequencing. Results showed that three viral families with double stranded DNA genomes including Siphoviridae (14.2%, 33.2%), Podoviridae (11.3%, 5.2%) and Myoviridae (8.9%, 9%), and three viral families with single stranded DNA genomes including Microviridae (52.5%, 29.7%), Circoviridae (6.3%, 10.2%), Nanoviridae (3.4%, 9.2%) dominated in sea cucumbers and shrimps, respectively. Phylogenetic analyses revealed that a huge part of viromes are novel sequences and that most of the isolated viromes are distantly related to the previously known viruses. Thus, this study showed that the microflora in the intestine of both sea cucumbers and shrimps consisted of unknown bacteria and viruses.