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 Occurrence and recent long-distance dispersal of deep-sea hydrothermal vent shrimps

2005 ◽  
Vol 2 (2) ◽  
pp. 257-260 ◽  
Author(s):  
Gaku Tokuda ◽  
Akinori Yamada ◽  
Kazuma Nakano ◽  
Nao Arita ◽  
Hideo Yamasaki
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
Okinawa Trough ◽  
Rrna Gene ◽  
Cold Seeps ◽  
Long Distance Dispersal ◽  
High Concentration ◽  
Long Distance ◽  
The Okinawa Trough

Deep-sea hydrothermal vents and methane seeps are extreme environments that have a high concentration of hydrogen sulphide. However, abundant unique invertebrates including shrimps of the family Bresiliidae have been found in such environments. The bresiliid shrimps are believed to have radiated in the Miocene (less than 20 Myr); however, the period when and the mechanisms by which they dispersed across the hydrothermal vents and cold seeps in oceans worldwide have not been clarified. In the present study, we collected the deep-sea blind shrimp Alvinocaris longirostris from the hydrothermal vent site in the Okinawa Trough and carried out the first investigation of the 18S rRNA gene of a bresiliid shrimp. The phylogenetic analysis revealed that the bresiliid shrimp is situated at an intermediate lineage within the infraorder Caridea and shows monophyly with palaemonid shrimps, which live in shallow sea and freshwater. Furthermore, the mitochondrial cytochrome oxidase I ( COI ) gene sequences were analysed to determine the phylogenetic relationship with known bresiliid shrimps. A. longirostris of the Okinawa Trough had two haplotypes of the COI gene, one of which was identical to the Alvinocaris sp. of the cold seeps in Sagami Bay. These results indicate that a long-distance dispersal of A. longirostris occurred possibly within the last 100 000 years.

EXPRESS: A Piecewise Model for In Situ Raman Measurement of the Chlorinity of Deep-Sea High-Temperature Hydrothermal Fluids

2021 ◽  
pp. 000370282199911
Author(s):  
meng ge ◽  
Lianfu Li ◽  
Xin Zhang ◽  
Zhendong Luan ◽  
Zengfeng Du ◽  
...  
Keyword(s):  
High Temperature ◽  
Deep Sea ◽  
Okinawa Trough ◽  
Peak Position ◽  
Hydrothermal Fluids ◽  
Calibration Model ◽  
The Okinawa Trough ◽  
Temperature Ranges ◽  
Piecewise Model ◽  
C 50

The chlorinity of deep-sea hydrothermal fluids, representing one of the crucial deep-sea hydrothermal indicators, indicates the degree of deep phase separation of hydrothermal fluids and water/rock reactions. However, accurately measuring the chlorinity of high-temperature hydrothermal fluids is still a significant challenge. In this paper, a piecewise chlorinity model to measure the chlorinity of high-temperature hydrothermal fluids was developed based on the OH stretching band of water, exhibiting an accuracy of 96.20%. The peak position, peak area ratio and F value were selected to establish the chlorinity piecewise calibration model within the temperature ranges of 0-50°C, 50-200°C and 200-300°C. Compared with that of the chlorinity calibration model built based on a single parameter, the accuracy of this piecewise model increased by approximately 4.83-12.33%. This chlorinity calibration model was applied to determine the concentrations of Cl for high-temperature hydrothermal fluids in the Okinawa Trough hydrothermal field.

scholarly journals Population connectivity of the crab Gandalfus yunohana (Takeda, Hashimoto & Ohta, 2000) (Decapoda: Brachyura: Bythograeidae) from deep-sea hydrothermal vents in the northwestern Pacific

2020 ◽  
Vol 40 (5) ◽  
pp. 556-562
Author(s):  
Hiromi K Watanabe ◽  
Chong Chen ◽  
Shigeaki Kojima ◽  
Shogo Kato ◽  
Hiroyuki Yamamoto
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vents ◽  
Okinawa Trough ◽  
Coi Gene ◽  
Genetic Connectivity ◽  
Reverse Direction ◽  
Northwestern Pacific ◽  
Brachyuran Crab ◽  
The Okinawa Trough ◽  
Mariana Arc

Abstract Genetic connectivity provides a basis for evaluating the resilience of animal communities by elucidating gene flow and serves as a proxy for realized dispersal through planktonic larval dispersal, settlement, and reproductive success. Gandalfus yunohana (Takeda, Hashimoto & Ohta, 2000) is a brachyuran crab endemic to deep-sea hydrothermal vents in the northwestern Pacific. Although an iconic and often dominant species, the connectivity among its populations is yet to be examined. We obtained barcoding sequences of the mitochondrial COI gene of G. yunohana from four vent fields including two on the Izu Arc, one on the northern Mariana Arc, and one in the Okinawa Trough. Genetic diversity of populations on the Izu and northern Mariana arcs were similar and shared the dominant haplotypes, showing no genetic subdivision regardless of the habitat depth. The Okinawa Trough population, for which only one specimen was available, was not genetically different from specimens from the Izu/Mariana arc populations. Estimation of the number of immigrants among populations suggests that the migration from north to south is higher than in the reverse direction. Our results resonate with previous laboratory-culture experiments, suggesting a high dispersal capability for G. yunohana. Visual observations and sampling, however, suggest that G. yunohana is exceedingly rare in the Okinawa Trough. This perhaps results from a lack of sufficient larval supply from the Izu-Bonin-Mariana Arc vents, and there may not be a reproductive population in the Okinawa Trough.

New ways for research and development using a deep-sea hydrothermal vent system in the Okinawa Trough

2015 ◽  
Author(s):  
Tomokazu Saruhashi ◽  
Masanori Kyo ◽  
Ikuo Sawada ◽  
Takahiro Yokoyama ◽  
Noriaki Sakurai ◽  
...  
Keyword(s):  
Research And Development ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Okinawa Trough ◽  
The Okinawa Trough

scholarly journals Draft Genome Sequence of Exiguobacterium sp. HVEsp1, a Thermophilic Bacterium Isolated from a Deep-Sea Hydrothermal Vent in the Okinawa Trough

2017 ◽  
Vol 5 (17) ◽  
Author(s):  
Chen Chen ◽  
Li Sun
Keyword(s):  
Genome Sequence ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
Sequence Data ◽  
Okinawa Trough ◽  
Draft Genome ◽  
Thermophilic Bacterium ◽  
Draft Genome Sequence ◽  
The Okinawa Trough

ABSTRACT We report here the draft genome sequence of Exiguobacterium sp. HVEsp1, a thermophilic bacterium isolated from a deep-sea hydrothermal vent. The estimated genome size of this strain is 2,838,499 bp with a G+C content of 48.2%. The genome sequence data provide valuable information that will facilitate studies on the adaptation mechanisms of bacteria living in deep-sea hydrothermal vents.

scholarly journals Ancient DNA complements microfossil record in deep-sea subsurface sediments

2013 ◽  
Vol 9 (4) ◽  
pp. 20130283 ◽  
Author(s):  
Franck Lejzerowicz ◽  
Philippe Esling ◽  
Wojciech Majewski ◽  
Witold Szczuciński ◽  
Johan Decelle ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Deep Sea ◽  
Environmental Dna ◽  
Small Subunit ◽  
Marine Biodiversity ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Core Sediment ◽  
Subsurface Sediments ◽  
Sediment Layers

Deep-sea subsurface sediments are the most important archives of marine biodiversity. Until now, these archives were studied mainly using the microfossil record, disregarding large amounts of DNA accumulated on the deep-sea floor. Accessing ancient DNA (aDNA) molecules preserved down-core would offer unique insights into the history of marine biodiversity, including both fossilized and non-fossilized taxa. Here, we recover aDNA of eukaryotic origin across four cores collected at abyssal depths in the South Atlantic, in up to 32.5 thousand-year-old sediment layers. Our study focuses on Foraminifera and Radiolaria, two major groups of marine microfossils also comprising diverse non-fossilized taxa. We describe their assemblages in down-core sediment layers applying both micropalaeontological and environmental DNA sequencing approaches. Short fragments of the foraminiferal and radiolarian small subunit rRNA gene recovered from sedimentary DNA extracts provide evidence that eukaryotic aDNA is preserved in deep-sea sediments encompassing the last glacial maximum. Most aDNA were assigned to non-fossilized taxa that also dominate in molecular studies of modern environments. Our study reveals the potential of aDNA to better document the evolution of past marine ecosystems and opens new horizons for the development of deep-sea palaeogenomics.

scholarly journals Psychrobium conchae gen. nov., sp. nov., a psychrophilic marine bacterium isolated from the Iheya North hydrothermal field

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3668-3675 ◽  
Author(s):  
Yuichi Nogi ◽  
Mariko Abe ◽  
Shinsuke Kawagucci ◽  
Hisako Hirayama
Keyword(s):  
Type Species ◽  
Okinawa Trough ◽  
Hydrothermal Field ◽  
Rrna Gene ◽  
The Novel ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Okinawa Trough ◽  
Major Respiratory Quinone

A novel psychrophilic, marine, bacterial strain designated BJ-1T was isolated from the Iheya North hydrothermal field in the Okinawa Trough off Japan. Cells were Gram-negative, rod-shaped, non-spore-forming, aerobic chemo-organotrophs and motile by means of a single polar flagellum. Growth occurred at temperatures below 16 °C, with the optimum between 9 and 12 °C. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the closest relatives of strain BJ-1T were Shewanella denitrificans OS-217T (93.5 % similarity), Shewanella profunda DSM 15900T (92.9 %), Shewanella gaetbuli TF-27T (92.9 %), Paraferrimonas sedimenticola Mok-106T (92.1 %) and Ferrimonas kyonanensis Asr22-7T (91.7 %). The major respiratory quinone was Q-8. The predominant fatty acids were C16 : 1ω7c and C16 : 0. The G+C content of the novel strain was 40.5 mol%. Based on phylogenetic, phenotypic and chemotaxonomic evidence, it is proposed that strain BJ-1T represents a novel species in a new genus, for which the name Psychrobium conchae gen. nov., sp. nov. is proposed. The type strain of Psychrobium conchae is BJ-1T ( = JCM 30103T = DSM 28701T).

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).

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