Dataset Information

Dataset of blood cockle (Anadara granosa) microbiota from coastal areas and earthen-pond farms around the upper Gulf of Thailand.

ABSTRACT: The blood cockle (Anadara granosa), a bivalve mollusc, is a unique seafood item in Southeast Asia. Bivalve molluscs are filter feeders upon plankton, and so they may bioaccumulate microbes and heavy metals in their tissues. Bacteria survival can be enhanced by living inside the shell and they can subsequently infect humans and higher vertebrates after ingestion of the bivalve. This study presented a metagenomics analysis of the bacteria associated with A. granosa from six farms around the Gulf of Thailand. Three farms were located on the coast and the other three were from earthen ponds. Genomic DNA was extracted from the samples and analysed via sequencing of the V3-V4 region of the 16S rRNA gene, and then using a 97% DNA sequence similarity cut-off for designation of the operational taxonomic units. The environmental parameters, including temperature, pH, salinity, dissolved oxygen, and the concentration of three heavy metals (Cu, Cr, and Hg) and one metalloid (As) were investigated. The raw sequence data is available at the NCBI Sequence Read Archive accession number PRJNA592226. The Proteobacteria, Bacteroidetes and Cyanobacteria were common components of the microbiota in all six habitats and together comprised more than 77% of the relative abundance in all the samples. This is the first report on the microbiome in blood cockles in Thailand by a culture independent method. The data can be applied for efficiently controlling and improving seafood safety management.

SUBMITTER: Theerachat M

PROVIDER: S-EPMC7083786 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Dataset of blood cockle (Anadara granosa) microbiota from coastal areas and earthen-pond farms around the upper Gulf of Thailand.

Theerachat Monnat M Glinwong Chompunuch C Chulalaksananukul Warawut W

Data in brief 20200310

The blood cockle (Anadara granosa), a bivalve mollusc, is a unique seafood item in Southeast Asia. Bivalve molluscs are filter feeders upon plankton, and so they may bioaccumulate microbes and heavy metals in their tissues. Bacteria survival can be enhanced by living inside the shell and they can subsequently infect humans and higher vertebrates after ingestion of the bivalve. This study presented a metagenomics analysis of the bacteria associated with A. granosa from six farms aro ...[more]

PMID: 32215305

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Project description:Background:It has been suggested that aquaculture ponds on the Chinese coast could act as breeding grounds for scyphozoans. Here, we present the first record of the scyphomedusa Phyllorhiza sp. in an aquaculture pond on the coast of the southern Yellow Sea, based on a combination of morphological characteristics and mitochondrial 16S DNA sequence data. Methods:A field survey was performed on June 29, 2017 in a pond used for culturing the shrimp Penaeus japonicus, located in the southern Yellow Sea, China. Jellyfish specimens were collected for morphological and genetic analysis. The morphological characters of the jellyfish specimens were compared to taxonomic literature. Additionally, phylogenetic analysis of the mitochondrial 16S fragments of these specimens were also conducted. Results:These specimens had the following morphological characters: hemispherical umbrella without scapulets; J-shaped oral arms; a single larger terminal club on each arm; bluish colored with a slightly expanded white tip; and mouthlets present only in the lower half to one-third of each arm. These morphological features of the medusae indicated that the specimens found in the shrimp culture ponds belong to the genus Phyllorhiza Agassiz, 1862, but did not match with the description of any of the known species of the genus Phyllorhiza. Phylogenetic analyses of the mtDNA 16S regions revealed that these specimens, together with Phyllorhiza sp. from Malaysian coastal waters, belong to a sister group of Phyllorhiza punctata. Juveniles and ephyrae of Phyllorhiza sp. were observed in the aquaculture pond. The mean density of Phyllorhiza sp. medusa in the surface water within the pond was estimated to be 0.05 individuals/m2. Discussion:Based on our observations of the gross morphology and molecular data, we state that the specimens collected in the aquaculture pond can be identified as Phyllorhiza sp. This is the first record of Phyllorhiza sp. in Chinese seas. Large scale dispersal through ballast water or the expansion of jellyfish aquarium exhibitions are possible pathways of invasion, but this needs to be confirmed in further studies.

Project description:BackgroundEarthen sites are immobile cultural relics and an important part of cultural heritage with historical, artistic and scientific values. The deterioration of features in earthen sites result in permanent loss of cultural information, causing immeasurable damage to the study of history and culture. Most research on the deterioration of earthen sites has concentrated on physicochemical factors, and information on microbial communities in earthen sites and their relationship with the earthen site deterioration is scarce. We used high-throughput sequencing to analyze bacterial and fungal communities in soils from earthen walls with different degree of deterioration at Jinsha earthen site to characterize the microbial communities and their correlation with environmental factors, and to compare microbial community structures and the relative abundances of individual taxa associated with different degree of deterioration for identifying possible marker taxa.ResultsThe relative abundances of Proteobacteria and Firmicutes were higher and that of Actinobacteria lower with higher degree of deterioration. At the genus level, the relative abundances of Rubrobacter were highest in all sample groups except in the most deteriorated samples where that of Bacteroides was highest. The relative abundance of the yeast genus Candida was highest in the severely deteriorated sample group. The bacterial phylum Bacteroidetes and genus Bacteroides, and fungal class Saccharomycetes that includes Candida sp. were specific for the most deteriorated samples. For both bacteria and fungi, the differences in community composition were associated with differences in EC, moisture, pH, and the concentrations of NH4+, K+, Mg2+, Ca2+ and SO42-.ConclusionThe microbial communities in soil with different degree of deterioration were distinctly different, and deterioration was accompanied with bigger changes in the bacterial than in the fungal community. In addition, the deteriorated soil contained higher concentrations of soluble salts. Potentially, the accumulation of Bacteroides and Candida plays an important role in the deterioration of earthen features. Further work is needed to conclude whether controlling the growth of the bacteria and fungi with high relative abundances in the deteriorated samples can be applied to alleviate deterioration.

Dataset Information

Dataset of blood cockle (Anadara granosa) microbiota from coastal areas and earthen-pond farms around the upper Gulf of Thailand.

Publications

Dataset of blood cockle (<i>Anadara granosa</i>) microbiota from coastal areas and earthen-pond farms around the upper Gulf of Thailand.

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