scholarly journals Environmental DNA Sequencing Reveals a Highly Complex Eukaryote Community in Sansha Yongle Blue Hole, Xisha, South China Sea

2019 ◽  
Vol 7 (12) ◽  
pp. 624
Author(s):  
Yueteng Liu ◽  
Hui He ◽  
Liang Fu ◽  
Qian Liu ◽  
Zuosheng Yang ◽  
...  
Keyword(s):  
South China Sea ◽  
South China ◽  
High Throughput Sequencing ◽  
Water Layer ◽  
Small Subunit ◽  
Reef Slope ◽  
Rrna Gene ◽  
Outer Reef ◽  
China Sea ◽  
Blue Hole

We report an Illumina high-throughput sequencing protocol of eukaryotic microbes in the world’s deepest marine blue hole, Sansha Yongle Blue Hole, Xisha, South China Sea. The variable V9 region of small subunit (SSU) rDNA, was sequenced using this approach from the waters of blue hole and outer reef slope. 917,771 unique eukaryotic 18S rRNA gene sequences and 6093 operational taxonomic units (OTUs) were identified. Significant differences in the eukaryotic composition were observed between the blue hole and outer reef slope, and the richness in the blue hole was much higher than that in the outer reef slope. The richness and diversity of eukaryotes in the blue hole were both lowest at 60 m and highest at 100 m depth. Eukaryotic microalgae assemblages dominated by Dinophyceae were the most abundant in the 10–20 m water column in the hole. Fauna was the main group at and below a depth of 60 m, where Araneae and Cyclopoida were dominant in the 60 m and 80 m water layer, respectively. There was a large number of Entoprocta at a depth of 180 m in the hole, where little oxygen was detected. Turbidity and nitrite concentration had a significant effect on the eukaryote community structure (p < 0.01).

scholarly journals The Diversity, Composition, and Putative Functions of Gill-Associated Bacteria of Bathymodiolin Mussel and Vesicomyid Clam from Haima Cold Seep, South China Sea

2020 ◽  
Vol 8 (11) ◽  
pp. 1699
Author(s):  
Juan Ling ◽  
Hongxiang Guan ◽  
Lihua Liu ◽  
Jun Tao ◽  
Jie Li ◽  
...  
Keyword(s):  
South China Sea ◽  
South China ◽  
Phylogenetic Diversity ◽  
High Throughput Sequencing ◽  
Cold Seep ◽  
Rrna Gene ◽  
Cold Seeps ◽  
Element Cycling ◽  
China Sea ◽  
Vesicomyid Clam

The Haima cold seep, which is one of the two active cold seeps in the South China Sea, is known for its great ecological importance. The seep bivalves are assumed to depend mainly on their bacterial symbiosis for survival and growth. However, information on the bacterial diversity, composition, and putative function of gill-associated of dominant dwelling animals in Haima cold seep remain elusive. Herein, we adopted a high-throughput sequencing of 16S rRNA gene amplicons, and function prediction methods (Functional Annotation of Prokaryotic Taxa (FAPROTAX) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICURUSTs)) to purposely illustrate the taxonomic and phylogenetic diversity, composition, and putative functions of the symbionts in bathymodiolin mussel Gigantidas haimaensis (Bivalvia: Mytilidae: Gigantidas) and vesicomyid clam Archivesica marissinica (Bivalvia: Glossoidea: Vesicomyidae). The predominant microbes of both species were Proteobacteria and Gammaproteobacteria on the phylum and class level, respectively. The taxonomic and phylogenetic diversity of gill microbial communities in G. haimaensis were significantly different from those in A. marissinica (p < 0.05). Nine functional groups, including seven carbon-related biogeochemical groups, were identified through the FAPROTAX analysis. However, the most dominant groups for G. haimaensis and A. marissinica were both chemoheterotrophic. G. haimaensis and A. marissinica shared many pathways, however, 16 obtained Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologous groups (42.11%) significantly differed between the two species (p < 0.05). These findings would provide insight into the functions of microbes in the element cycling and energy flow as well as the host-symbiont relationship of bivalves in the Haima cold seep environment.

scholarly journals Salegentibacter catena sp. nov., isolated from sediment of the South China Sea, and emended description of the genus Salegentibacter

2007 ◽  
Vol 57 (2) ◽  
pp. 219-222 ◽  
Author(s):  
Jiao-Yan Ying ◽  
Zhi-Pei Liu ◽  
Bao-Jun Wang ◽  
Xin Dai ◽  
Su-Sheng Yang ◽  
...  
Keyword(s):  
Fatty Acids ◽  
South China Sea ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
South China ◽  
The South China Sea ◽  
Rrna Gene ◽  
The South ◽  
China Sea ◽  
Emended Description

A novel marine bacterial strain, HY1T, was isolated from sediment of the South China Sea. The strain was aerobic and heterotrophic and formed saffron yellow-pigmented colonies on marine agar 2216. Cells were non-motile, Gram-negative rods, frequently occurring in chains. blastn searches revealed that the 16S rRNA gene sequence of strain HY1T showed high similarity with those of members of the genera Gillisia (91.7–93.8 %) and Salegentibacter (92.6–93.5 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain clustered with members of both Salegentibacter and Gillisia and phylogenetic trees constructed using three different methods (neighbour-joining, maximum-parsimony and minimum-evolution) indicated that strain HY1T clustered more frequently with members of the genus Salegentibacter. The DNA G+C content of strain HY1T was 44.4 mol% and its major cellular fatty acids (⩾5 % of the total fatty acids) were iso-15 : 1 (5.0 %), iso-15 : 0 (6.8 %), anteiso-15 : 0 (6.4 %), 15 : 0 (10.4 %), iso-16 : 0 (13.5 %), summed feature 3 (comprising iso-15 : 0 2-OH and/or 16 : 1ω7c; 6.3 %), iso-17 : 0 3-OH (5.2 %) and 17 : 0 2-OH (5.0 %). Cells contained menaquinone 6. Based on the phylogenetic and phenotypic analyses, strain HY1T should be classified as representing a novel species within the genus Salegentibacter, for which the name Salegentibacter catena sp. nov. is proposed. The type strain is HY1T (=CGMCC 1.6101T=JCM 14015T). Based on this study and on previously described Salegentibacter species, an emended description of the genus Salegentibacter is given.

Morphological and molecular characterization of Cucullanus hainanensis sp. nov. (Ascaridida: Cucullanidae) from Muraenichthys gymnopterus (Bleeker) (Anguilliformes: Ophichthidae) in the South China Sea

2014 ◽  
Vol 59 (4) ◽  
Author(s):  
Zhen Xu ◽  
Lu-Ping Zhang ◽  
Liang Li
Keyword(s):  
New Species ◽  
South China Sea ◽  
South China ◽  
Small Subunit ◽  
The South China Sea ◽  
Nuclear Ribosomal Dna ◽  
The South ◽  
China Sea ◽  
Second Internal Transcribed Spacer

AbstractCucullanus hainanensis sp. nov., collected from Muraenichthys gymnopterus (Bleeker) (Anguilliformes: Ophichthidae) in the South China Sea, was described using both light and scanning electron microscopy. The new species can be readily distinguished from its congeners by the large pseudobuccal capsule, the position of excretory pore and deirids, the length of spicules (0.64–0.76 mm, 5.84–6.67% of body length) and gubernaculum (0.21–0.24 mm), the number and arrangement of caudal papillae and the particular morphology of cloacal region in male. The new species was also characterized using molecular methods by sequencing and analysing the small subunit (18S) and the second internal transcribed spacer (ITS-2) of nuclear ribosomal DNA (rDNA). In addition, Cucullanus muraenesocis (Yin et Zhang, 1983) was regarded a homonym of C. muraenesocis Yamaguti, 1961, and a new name, Cucullanus wangi nom. nov. was given to it.

Hydrochemical properties and chemocline of the Sansha Yongle Blue Hole in the South China Sea

2019 ◽  
Vol 649 ◽  
pp. 1281-1292 ◽  
Author(s):  
Linping Xie ◽  
Baodong Wang ◽  
Xinming Pu ◽  
Ming Xin ◽  
Peiqing He ◽  
...  
Keyword(s):  
South China Sea ◽  
South China ◽  
The South China Sea ◽  
The South ◽  
China Sea ◽  
Blue Hole

scholarly journals Marivirga lumbricoides sp. nov., a marine bacterium isolated from the South China Sea

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 452-456 ◽  
Author(s):  
Yongle Xu ◽  
Rui Zhang ◽  
Qipei Li ◽  
Keshao Liu ◽  
Nianzhi Jiao
Keyword(s):  
South China Sea ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
South China ◽  
Type Species ◽  
The South China Sea ◽  
Rrna Gene ◽  
Content Type ◽  
China Sea ◽  
Link Type

A novel, aerobic, heterotrophic, orange-pigmented, Gram-staining-negative, rod-shaped, gliding bacterial strain, designated JLT2000T, was isolated from surface water of the South China Sea. The strain was oxidase- and catalase-positive. The major cellular fatty acids of strain JLT2000 T were C12 : 0, iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 0. MK-7 was the major respiratory quinone and the major polar lipids were phosphatidylcholine and phosphatidylethanolamine. The genomic DNA G+C content of strain JLT2000T was 37.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JLT2000T formed a branch within the genus Marivirga , but was clearly separated from the two established species of this genus, Marivirga tractuosa and Marivirga sericea . The 16S rRNA gene sequence similarity of strain JLT2000T with the type strains of these two species was 95.8 % and 96.1 %, respectively. Strain JLT2000T had a shorter cell length and wider growth range in different temperatures and salinities than those of Marivirga tractuosa NBRC 15989T and Marivirga sericea NBRC 15983T. In addition, strain JLT2000T could utilize more carbon sources and hydrolyse more polymers than Marivirga tractuosa NBRC 15989T and Marivirga sericea NBRC 15983T. Based on this polyphasic analysis, strain JLT2000T represents a novel species of the genus Marivirga , for which the name Marivirga lumbricoides sp. nov. is proposed. The type strain is JLT2000T ( = JCM 18012T = CGMCC 1.10832T).

Erythrobacter nanhaisediminis sp. nov., isolated from marine sediment of the South China Sea

2010 ◽  
Vol 60 (9) ◽  
pp. 2215-2220 ◽  
Author(s):  
Mingshuang Xu ◽  
Yuhua Xin ◽  
Yong Yu ◽  
Jianli Zhang ◽  
Yuguang Zhou ◽  
...  
Keyword(s):  
South China Sea ◽  
South China ◽  
Gene Sequence ◽  
The South China Sea ◽  
Rrna Gene ◽  
The South ◽  
China Sea ◽  
Bacterium Strain ◽  
Ubiquinone 10 ◽  
Sequence Similarities

A novel Gram-negative, orange-pigmented, slightly halophilic, rod-shaped bacterium, strain T30T, was isolated from sediment from the South China Sea. Phylogenetic analysis showed that strain T30T was a member of the genus Erythrobacter, sharing highest 16S rRNA gene sequence similarities with Erythrobacter aquimaris JCM 12189T (99.5 %) and Erythrobacter vulgaris DSM 17792T (99.0 %). Levels of DNA–DNA relatedness between strain T30T and closely related strains of Erythrobacter species ranged from 14.5 to 56.9 %.The isolate lacked bacteriochlorophyll a and contained ubiquinone-10 as the predominant respiratory lipoquinone. The major fatty acids of this strain were C18 : 1 ω7c (38.2 %) and C16 : 1 ω7c /C16 : 1 ω6c (17.4 %). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine and phosphatidylglycerol. The DNA G+C content of strain T30T was 59.5 mol%. On the basis of phenotypic and phylogenetic data, a novel species, Erythrobacter nanhaisediminis sp. nov., is proposed; the type strain is T30T (=CGMCC 1.7715T=JCM 16125T).

scholarly journals Arenibacter nanhaiticus sp. nov., isolated from marine sediment of the South China Sea

2010 ◽  
Vol 60 (1) ◽  
pp. 78-83 ◽  
Author(s):  
Fengqin Sun ◽  
Baojiang Wang ◽  
Yaping Du ◽  
Xiupian Liu ◽  
Qiliang Lai ◽  
...  
Keyword(s):  
South China Sea ◽  
South China ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
The South China Sea ◽  
Rrna Gene ◽  
Sandy Sediment ◽  
The South ◽  
China Sea ◽  
Gene Sequence Analysis

An aerobic, Gram-stain-negative, rod-shaped bacterial isolate, strain NH36AT, was isolated from a sandy sediment sample from the South China Sea. Colonies of the isolate were dark orange on M2 agar. Optimal growth was observed at pH 7.0–8.5, 30 °C and in the presence of 0.5–4.0 % (w/v) NaCl. The major fatty acids were C15 : 0, iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c). The DNA G+C content was 38.9 mol%. 16S rRNA gene sequence analysis revealed that strain NH36AT was most closely related to members of the genus Arenibacter, exhibiting 94.3–96.2 % sequence similarity to the type strains of Arenibacter species. On the basis of phenotypic, chemotaxonomic and phylogenetic data, this organism should be classified as a representative of a novel species in the genus Arenibacter. The name Arenibacter nanhaiticus sp. nov. is proposed and the type strain is NH36AT (=LMG 24842T=CCTCC AB 208315T=MCCC 1A04137T).

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