Sr, Pb, Cu, and Zn isotope variations in deep-sea sediments from Southern Okinawa Trough over the last 35ka

2006 ◽  
Vol 70 (18) ◽  
pp. A47 ◽  
Author(s):  
Y. Bentahila ◽  
D. Ben Othman ◽  
J.M. Luck
Keyword(s):  
Deep Sea ◽  
Okinawa Trough ◽  
Southern Okinawa Trough ◽  
Deep Sea Sediments ◽  
Cu And Zn

scholarly journals Combining Multiple Markers in Environmental DNA Metabarcoding to Assess Deep-Sea Benthic Biodiversity

2021 ◽  
Vol 8 ◽  
Author(s):  
Jun Liu ◽  
Haibin Zhang
Keyword(s):  
Deep Sea ◽  
Okinawa Trough ◽  
Environmental Dna ◽  
Rrna Gene ◽  
28S Rrna ◽  
Eukaryotic Diversity ◽  
The Okinawa Trough ◽  
Marine Diversity ◽  
Deep Sea Sediments ◽  
Reference Databases

Environmental DNA (eDNA) metabarcoding is an emerging tool to estimate diversity by combining DNA from the environmental samples and the high-throughput sequencing. Despite its wide use in estimating eukaryotic diversity, many factors may bias the results. Maker choice and reference databases are among the key issues in metabarcoding analyses. In the present study, we compared the performance of a novel 28S rRNA gene marker designed in this study and two commonly used 18S rRNA gene markers (V1-2 and V9) in estimating the eukaryotic diversity in the deep-sea sediments. The metabarcoding analyses based on the sediment surveys of the Okinawa Trough found that more eukaryotic taxa were discovered by 18S V9 than 28S and 18S V1-2, and that 18S V9 also performed better in metazoan recovery than the other two markers. Although a broad range of taxa were detected by the three metabarcoding markers, only a small proportion of taxa were shared between them even at the phylum level. The non-metric multidimensional scaling (NMDS) analysis also supported that communities detected by the three markers were distinct from each other. In addition, different communities were resolved by different reference databases (NCBI nt vs. SILVA) for the two 18S markers. Combining the three markers, annelids were found to be the most abundant (44.9%) and diverse [179 operational taxonomic units (OTUs)] metazoan group in the sediments of the Okinawa Trough. Therefore, multiple independent markers are recommended to be used in metabarcoding analyses during marine diversity surveys, especially for the poorly understood deep-sea sediments.

scholarly journals Marinitoga okinawensis sp. nov., a novel thermophilic and anaerobic heterotroph isolated from a deep-sea hydrothermal field, Southern Okinawa Trough

2007 ◽  
Vol 57 (3) ◽  
pp. 467-471 ◽  
Author(s):  
Takuro Nunoura ◽  
Hanako Oida ◽  
Masayuki Miyazaki ◽  
Yohey Suzuki ◽  
Ken Takai ◽  
...  
Keyword(s):  
Deep Sea ◽  
Gene Sequence ◽  
Okinawa Trough ◽  
Heterotrophic Bacterium ◽  
Fatty Acid Content ◽  
Hydrothermal Field ◽  
Rrna Gene ◽  
Southern Okinawa Trough ◽  
Gene Sequence Analysis ◽  
Bacterium Strain

A novel thermophilic and sulfur-reducing heterotrophic bacterium, strain TFS10-5T, was isolated from a deep-sea hydrothermal field in Yonaguni Knoll IV, Southern Okinawa Trough. Cells of strain TFS10-5T were motile rods, 1.5–5 μm in length and 0.5–0.8 μm in width. Strain TFS10-5T was an obligately anaerobic heterotroph and sulfur-reduction stimulated growth. Growth was observed between 30 and 70 °C (optimum at 55–60 °C), pH 5.0–7.4 (optimum at pH 5.5–5.8), 1.0–5.5 NaCl % (optimum at 3.0–3.5 %). The fatty acid content was C16 : 0 (71.0 %), C16 : 1 (6.0 %), C18 : 0 (21.4 %) and C18 : 1 (1.6 %). The G+C content of the genomic DNA was 28 mol%. 16S rRNA gene sequence analysis indicated that strain TFS10-5T belongs to the genus Marinitoga. Based on the physiological and phylogenetic features of the new isolate, strain TFS10-5T represents a novel species in the genus Marinitoga for which the name Marinitoga okinawensis sp. nov. is proposed. The type strain is TFS10-5T (=JCM 13303T=DSM 17373T).

Exploring fungal diversity in deep-sea sediments from Okinawa Trough using high-throughput Illumina sequencing

2016 ◽  
Vol 116 ◽  
pp. 99-105 ◽  
Author(s):  
Xiao-Yong Zhang ◽  
Guang-Hua Wang ◽  
Xin-Ya Xu ◽  
Xu-Hua Nong ◽  
Jie Wang ◽  
...  
Keyword(s):  
High Throughput ◽  
Illumina Sequencing ◽  
Deep Sea ◽  
Fungal Diversity ◽  
Okinawa Trough ◽  
Deep Sea Sediments

scholarly journals Thermotomaculum hydrothermale gen. nov., sp. nov., a novel heterotrophic thermophile within the phylum Acidobacteria from a deep-sea hydrothermal vent chimney in the Southern Okinawa Trough

Extremophiles ◽  
2012 ◽  
Vol 16 (2) ◽  
pp. 245-253 ◽  
Author(s):  
Hiroshi Izumi ◽  
Takuro Nunoura ◽  
Masayuki Miyazaki ◽  
Sayaka Mino ◽  
Tomohiro Toki ◽  
...  
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Okinawa Trough ◽  
Southern Okinawa Trough

scholarly journals Myroides profundisp. nov., isolated from deep-sea sediment of the southern Okinawa Trough

2008 ◽  
Vol 287 (1) ◽  
pp. 108-112 ◽  
Author(s):  
Xi-Ying Zhang ◽  
Yan-Jiao Zhang ◽  
Xiu-Lan Chen ◽  
Qi-Long Qin ◽  
Dian-Li Zhao ◽  
...  
Keyword(s):  
Deep Sea ◽  
Okinawa Trough ◽  
Deep Sea Sediment ◽  
Southern Okinawa Trough

scholarly journals Archaeal Diversity and Distribution along Thermal and Geochemical Gradients in Hydrothermal Sediments at the Yonaguni Knoll IV Hydrothermal Field in the Southern Okinawa Trough

2009 ◽  
Vol 76 (4) ◽  
pp. 1198-1211 ◽  
Author(s):  
Takuro Nunoura ◽  
Hanako Oida ◽  
Miwako Nakaseama ◽  
Ayako Kosaka ◽  
Satoru B. Ohkubo ◽  
...  
Keyword(s):  
Pore Water ◽  
Deep Sea ◽  
Hydrothermal Fluid ◽  
Okinawa Trough ◽  
Wide Spectrum ◽  
Hydrothermal Field ◽  
Sediment Pore Water ◽  
Southern Okinawa Trough ◽  
Chemical Conditions ◽  
Physical And Chemical

ABSTRACT A variety of archaeal lineages have been identified using culture-independent molecular phylogenetic surveys of microbial habitats occurring in deep-sea hydrothermal environments such as chimney structures, sediments, vent emissions, and chemosynthetic macrofauna. With the exception of a few taxa, most of these archaea have not yet been cultivated, and their physiological and metabolic traits remain unclear. In this study, phylogenetic diversity and distribution profiles of the archaeal genes encoding small subunit (SSU) rRNA, methyl coenzyme A (CoA) reductase subunit A, and the ammonia monooxygenase large subunit were characterized in hydrothermally influenced sediments at the Yonaguni Knoll IV hydrothermal field in the Southern Okinawa Trough. Sediment cores were collected at distances of 0.5, 2, or 5 m from a vent emission (90°C). A moderate temperature gradient extends both horizontally and vertically (5 to 69°C), indicating the existence of moderate mixing between the hydrothermal fluid and the ambient sediment pore water. The mixing of reductive hot hydrothermal fluid and cold ambient sediment pore water establishes a wide spectrum of physical and chemical conditions in the microbial habitats that were investigated. Under these different physico-chemical conditions, variability in archaeal phylotype composition was observed. The relationship between the physical and chemical parameters and the archaeal phylotype composition provides important insight into the ecophysiological requirements of uncultivated archaeal lineages in deep-sea hydrothermal vent environments, giving clues for approximating culture conditions to be used in future culturing efforts.

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