Biomaterial Database

[Diversity of Bdellovibrio-and-like organisms from shrimp mariculture ponds in Zhanjiang]. 2015

Chongqing Wen, and Ming Xue, and Huafang Liang, and Shining Zhou

OBJECTIVE Bdellovibrio-and-like organisms (BALOs) are small-sized, parasitic bacteria that rely on other Gram-negative bacteria for survival. Our work aimed to characterize the community diversity of BALOs associated with tropical shrimp ponds. METHODS We collected water samples from eight shrimp ponds culturing Litopenaeus vannamei, in Zhanjiang, China, and extracted total DNA of the samples. Then the 16S rRNA gene clone libraries were constructed following PCR amplification with BALOs family-specific primers. The community composition and structure of BALOs were further analyzed based on phylogenetic analysis. RESULTS A total of 726 and 664 valid clones were obtained from the 16S rRNA gene libraries of families Halobacteriovoracaceae and Peredibacteraceae, respectively. Subsequently, they were respectively grouped into 68 and 44 OTUs (operational taxonomic units) at 99.5% sequence similarity, and assigned into 37 and 28 clusters at 97% similarity. For the Halobacteriovoracaceae libraries, most clusters were so far uncultured with the exception of 5 members, which accounting for 43.5% clones. And the cultivable cluster IX and the uncultured cluster B28 were the first and second dominant ones respectively. For the Peredibacteraceae libraries, the cluster pa12 and the only cultivable cluster A3.12 were the first and second dominant ones respectively. Notably, the values of Shannon diversity indices of Halobacteriovoracaceae and Peredibacteraceae tend to be reversed with the change of salinity, but the total BALOs diversities among the eight shrimp ponds were similar. CONCLUSIONS Shrimp mariculture ponds in Zhanjinag harbor a high diversity of BALOs comprising of Halobacteriovoracaceae and Peredibacteraceae, and salinity affect their community structure and composition greatly.

UI	MeSH Term	Description	Entries
D008969	Molecular Sequence Data	Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.	Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D010802	Phylogeny	The relationships of groups of organisms as reflected by their genetic makeup.	Community Phylogenetics,Molecular Phylogenetics,Phylogenetic Analyses,Phylogenetic Analysis,Phylogenetic Clustering,Phylogenetic Comparative Analysis,Phylogenetic Comparative Methods,Phylogenetic Distance,Phylogenetic Generalized Least Squares,Phylogenetic Groups,Phylogenetic Incongruence,Phylogenetic Inference,Phylogenetic Networks,Phylogenetic Reconstruction,Phylogenetic Relatedness,Phylogenetic Relationships,Phylogenetic Signal,Phylogenetic Structure,Phylogenetic Tree,Phylogenetic Trees,Phylogenomics,Analyse, Phylogenetic,Analysis, Phylogenetic,Analysis, Phylogenetic Comparative,Clustering, Phylogenetic,Community Phylogenetic,Comparative Analysis, Phylogenetic,Comparative Method, Phylogenetic,Distance, Phylogenetic,Group, Phylogenetic,Incongruence, Phylogenetic,Inference, Phylogenetic,Method, Phylogenetic Comparative,Molecular Phylogenetic,Network, Phylogenetic,Phylogenetic Analyse,Phylogenetic Clusterings,Phylogenetic Comparative Analyses,Phylogenetic Comparative Method,Phylogenetic Distances,Phylogenetic Group,Phylogenetic Incongruences,Phylogenetic Inferences,Phylogenetic Network,Phylogenetic Reconstructions,Phylogenetic Relatednesses,Phylogenetic Relationship,Phylogenetic Signals,Phylogenetic Structures,Phylogenetic, Community,Phylogenetic, Molecular,Phylogenies,Phylogenomic,Reconstruction, Phylogenetic,Relatedness, Phylogenetic,Relationship, Phylogenetic,Signal, Phylogenetic,Structure, Phylogenetic,Tree, Phylogenetic
D002681	China	A country spanning from central Asia to the Pacific Ocean.	Inner Mongolia,Manchuria,People's Republic of China,Sinkiang,Mainland China
D004269	DNA, Bacterial	Deoxyribonucleic acid that makes up the genetic material of bacteria.	Bacterial DNA
D000818	Animals	Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA.	Animal,Metazoa,Animalia
D001501	Bdellovibrio	A genus of bacteria capable of developing within other bacteria.
D012336	RNA, Ribosomal, 16S	Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.	16S Ribosomal RNA,16S rRNA,RNA, 16S Ribosomal,Ribosomal RNA, 16S,rRNA, 16S
D012758	Shellfish	Aquatic invertebrates belonging to the phylum MOLLUSCA or the subphylum CRUSTACEA, and used as food.
D044822	Biodiversity	The variety of all native living organisms and their various forms and interrelationships.	Biological Diversity,Diversity, Biological
D061005	Ponds	Inland bodies of standing FRESHWATER usually smaller than LAKES. They can be man-made or natural but there is no universal agreement as to their exact size. Some consider a pond to be a small body of water that is shallow enough for sunlight to reach the bottom.	Ponds, Freshwater,Freshwater Pond,Freshwater Ponds,Pond,Pond, Freshwater