scholarly journals Abundance and Distribution of Dimethylsulfoniopropionate Degradation Genes and the Corresponding Bacterial Community Structure at Dimethyl Sulfide Hot Spots in the Tropical and Subtropical Pacific Ocean

2015 ◽  
Vol 81 (12) ◽  
pp. 4184-4194 ◽  
Author(s):  
Yingshun Cui ◽  
Shotaro Suzuki ◽  
Yuko Omori ◽  
Shu-Kuan Wong ◽  
Minoru Ijichi ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
Marine Bacteria ◽  
Dimethyl Sulfide ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Surface Seawater ◽  
Content Type ◽  
The Pacific ◽  
The Pacific Ocean ◽  
Abundance And Distribution

ABSTRACTDimethylsulfoniopropionate (DMSP) is mainly produced by marine phytoplankton but is released into the microbial food web and degraded by marine bacteria to dimethyl sulfide (DMS) and other products. To reveal the abundance and distribution of bacterial DMSP degradation genes and the corresponding bacterial communities in relation to DMS and DMSP concentrations in seawater, we collected surface seawater samples from DMS hot spot sites during a cruise across the Pacific Ocean. We analyzed the genes encoding DMSP lyase (dddP) and DMSP demethylase (dmdA), which are responsible for the transformation of DMSP to DMS and DMSP assimilation, respectively. The averaged abundance (±standard deviation) of these DMSP degradation genes relative to that of the 16S rRNA genes was 33% ± 12%. The abundances of these genes showed large spatial variations.dddPgenes showed more variation in abundances thandmdAgenes. Multidimensional analysis based on the abundances of DMSP degradation genes and environmental factors revealed that the distribution pattern of these genes was influenced by chlorophyllaconcentrations and temperatures.dddPgenes,dmdAsubclade C/2 genes, anddmdAsubclade D genes exhibited significant correlations with the marineRoseobacterclade, SAR11 subgroup Ib, and SAR11 subgroup Ia, respectively. SAR11 subgroups Ia and Ib, which possesseddmdAgenes, were suggested to be the main potential DMSP consumers. TheRoseobacterclade members possessingdddPgenes in oligotrophic subtropical regions were possible DMS producers. These results suggest that DMSP degradation genes are abundant and widely distributed in the surface seawater and that the marine bacteria possessing these genes influence the degradation of DMSP and regulate the emissions of DMS in subtropical gyres of the Pacific Ocean.

scholarly journals Solimonas marina sp. nov., isolated from deep seawater of the Pacific Ocean

2021 ◽  
Vol 71 (1) ◽  
Author(s):  
Xiupian Liu ◽  
Qiliang Lai ◽  
Fengqin Sun ◽  
Yaping Du ◽  
Yingbao Gai ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Deep Seawater ◽  
Content Type ◽  
Link Type ◽  
The Pacific ◽  
The Pacific Ocean

A taxonomic study was carried out on strain C16B3T, which was isolated from deep seawater of the Pacific Ocean. The bacterium was Gram-stain-negative, oxidase- and catalase- positive and rod-shaped. Growth was observed at salinities of 0–8.0 % and at temperatures of 10–45 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C16B3T belonged to the genus Solimonas , with the highest sequence similarity to Solimonas terrae KIS83-12T (97.2 %), followed by Solimonas variicoloris MN28T (97.0 %) and the other four species of the genus Solimonas (94.5 –96.8 %). The average nucleotide identity and estimated DNA–DNA hybridization values between strain C16B3T and the type strains of the genus Solimonas were 74.05−79.48 % and 19.5–22.5 %, respectively. The principal fatty acids (>5 %) were summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c; 20.9 %), iso-C16 : 0 (14.6 %), C16 : 1  ω5c (9.4 %), iso-C12 : 0 (8.4 %), summed feature 2 (C14 : 0 3-OH/iso I-C16 : 1 and C12 : 0 aldehyde; 6.8 %) and C16 : 0 (5.5 %). The G+C content of the chromosomal DNA was 65.37 mol%. The respiratory quinone was determined to be Q-8 (100 %). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, four unidentified aminolipids, six unidentified phospholipids and one unidentified polar lipid. The combined genotypic and phenotypic data show that strain C16B3T represents a novel species within the genus Solimonas , for which the name Solimonas marina sp. nov. is proposed, with the type strain C16B3T (=MCCC 1A04678T=KCTC 52314T).

Prospects for agriculture in 2017

2016 ◽  
Keyword(s):  
Pacific Ocean ◽  
El Nino ◽  
Extreme Weather ◽  
Extreme Weather Events ◽  
Content Type ◽  
Weather Events ◽  
The Pacific ◽  
Weather Phenomenon ◽  
Global Agriculture ◽  
The Pacific Ocean

Subject Prospects for agriculture in 2017. Significance The El Nino weather phenomenon, the heating of the Pacific Ocean, experienced through 2015 and 2016 was one of the strongest recorded, causing extreme weather events and decreasing global agriculture production. Next year promises a departure.

scholarly journals Paracoccus sediminis sp. nov., isolated from Pacific Ocean marine sediment

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2512-2516 ◽  
Author(s):  
Jie Pan ◽  
Cong Sun ◽  
Xin-Qi Zhang ◽  
Ying-Yi Huo ◽  
Xu-Fen Zhu ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
Marine Sediment ◽  
Type Species ◽  
Optimal Growth ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Pacific ◽  
The Pacific Ocean

Strain CMB17T was a short rod-shaped bacterium isolated from marine sediment of the Pacific Ocean. Cells were Gram-stain-negative and non-motile. Optimal growth occurred at 25–30 °C, pH 6.5–7 and 0.5–1 % (w/v) NaCl. The major fatty acid was C18 : 1ω7c (87.59 %), and ubiquinone-10 was detected as the only isoprenoid quinone. The DNA G+C content of the genomic DNA was 62.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CMB17T is most closely related to Paracoccus stylophorae KTW-16T (96.7 %), P. solventivorans DSM 6637T (96.4 %) and P. saliphilus YIM 90738T (96.4 %). Based on phenotypic, genotypic and phylogenetic characteristics, strain CMB17T is proposed to represent a novel species, denominated Paracoccus sediminis sp. nov. (type strain CMB17T = JCM 18467T = DSM 26170T = CGMCC 1.12681T).

scholarly journals Genome Sequence of Geothermobacter sp. Strain HR-1, an Iron Reducer from the Lō‘ihi Seamount, Hawai’i

2018 ◽  
Vol 6 (21) ◽  
Author(s):  
Hillary Smith ◽  
Karla Abuyen ◽  
Jason Tremblay ◽  
Pratixaben Savalia ◽  
Ileana Pérez-Rodríguez ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
Genome Sequence ◽  
Content Type ◽  
The Pacific ◽  
The Pacific Ocean

ABSTRACT Geothermobacter sp. strain HR-1 was isolated from the Lō‘ihi Seamount vent system in the Pacific Ocean at a depth of 1,000 m. Reported here is its 3.84-Mb genome sequence.

scholarly journals Abundance and Genetic Diversity of Aerobic Anoxygenic Phototrophic Bacteria of Coastal Regions of the Pacific Ocean

2012 ◽  
Vol 78 (8) ◽  
pp. 2858-2866 ◽  
Author(s):  
Anna E. Ritchie ◽  
Zackary I. Johnson
Keyword(s):  
Genetic Diversity ◽  
Pacific Ocean ◽  
Environmental Variables ◽  
Anoxygenic Phototrophic Bacteria ◽  
Bacterial Populations ◽  
Content Type ◽  
The Pacific ◽  
Near Shore ◽  
The Pacific Ocean ◽  
Abundance And Diversity

ABSTRACTAerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophic microbes that are found in a broad range of aquatic environments. Although potentially significant to the microbial ecology and biogeochemistry of marine ecosystems, their abundance and genetic diversity and the environmental variables that regulate these properties are poorly understood. Using samples along nearshore/offshore transects from five disparate islands in the Pacific Ocean (Oahu, Molokai, Futuna, Aniwa, and Lord Howe) and off California, we show that AAP bacteria, as quantified by thepufMgene biomarker, are most abundant near shore and in areas with high chlorophyll orSynechococcusabundance. These AAP bacterial populations are genetically diverse, with most members belonging to the alpha- or gammaproteobacterial groups and with subclades that are associated with specific environmental variables. The genetic diversity of AAP bacteria is structured along the nearshore/offshore transects in relation to environmental variables, and unculturedpufMgene libraries suggest that nearshore communities are distinct from those offshore. AAP bacterial communities are also genetically distinct between islands, such that the stations that are most distantly separated are the most genetically distinct. Together, these results demonstrate that environmental variables regulate both the abundance and diversity of AAP bacteria but that endemism may also be a contributing factor in structuring these communities.

scholarly journals Phylogeny of hydrothermal vent Iphionidae, with the description of a new species (Aphroditiformia, Annelida)

ZooKeys ◽  
2018 ◽  
Vol 779 ◽  
pp. 89-107
Author(s):  
Marina F. McCowin ◽  
Greg W. Rouse
Keyword(s):  
Pacific Ocean ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
East Pacific Rise ◽  
Rrna Genes ◽  
28S Rrna ◽  
West Pacific ◽  
East Pacific ◽  
The Pacific ◽  
The Pacific Ocean

The scale-worm family Iphionidae consists of four genera. Of these, Thermiphione has two accepted species, both native to hydrothermal vents in the Pacific Ocean; T.fijiensis Miura, 1994 (West Pacific) and T.tufari Hartmann-Schröder, 1992 (East Pacific Rise). Iphionella is also known from the Pacific, and has two recognized species; Iphionellarisensis Pettibone, 1986 (East Pacific Rise, hydrothermal vents) and I.philippinensis Pettibone, 1986 (West Pacific, deep sea). In this study, phylogenetic analyses of Iphionidae from various hydrothermal vent systems of the Pacific Ocean were conducted utilizing morphology and mitochondrial (COI and 16S rRNA) and nuclear (18S and 28S rRNA) genes. The results revealed a new iphionid species, described here as Thermiphionerapanuisp. n. The analyses also demonstrated the paraphyly of Thermiphione, requiring Iphionellarisensis to be referred to the genus, as Thermiphionerisensis (Pettibone, 1986).

scholarly journals Pusillimonas maritima sp. nov., isolated from surface seawater

2020 ◽  
Vol 70 (5) ◽  
pp. 3483-3490 ◽  
Author(s):  
Jianyang Li ◽  
Mingming Qi ◽  
Qiliang Lai ◽  
Chunming Dong ◽  
Xiupian Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Surface Seawater ◽  
Content Type ◽  
Link Type ◽  
Gene Similarity

Two Gram-stain-negative, short rod-shaped and non-flagellated strains, designated 17-4AT and L52-1-41, were isolated from the surface seawater of the Indian Ocean and South China Sea, respectively. The 16S rRNA genes of the two strains shared sequence similarity of 99.45 %. Strain 17-4AT shared the highest 16S rRNA gene similarity of 98.02 % with Pusillimonas caeni EBR-8-1T, followed by Pusillimonas noertemannii BN9T (97.47 %), Pusillimonas soli MJ07T (96.93 %), Parapusillimonas granuli Ch07T (96.68 %), Pusillimonas ginsengisoli DCY25T (96.65 %), Eoetvoesia caeni PB3-7BT (96.63 %), Paracandidimonas caeni 24T (96.34 %), Castellaniella defragrans 54PinT (96.28 %) and Pusillimonas harenae B201T (96.05 %). L52-1-41 shared the highest 16S rRNA gene similarity of 97.74 % with Pusillimonas caeni EBR-8-1T, followed by Pusillimonas noertemannii BN9T (97.47 %), Pusillimonas soli MJ07T (96.65 %), Parapusillimonas granuli Ch07T (96.41 %), Pusillimonas ginsengisoli DCY25T (96.37 %), Eoetvoesia caeni PB3-7BT (96.35 %), Pusillimonas harenae B201T (96.28 %), and Paracandidimonas caeni 24T (96.06 %). The results of phylogenetic analyses indicated that 17-4AT and L52-1-41 formed a stable, distinct and highly supported lineage affiliated to the genus Pusillimonas . The results of the digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses indicated that they represented a single species. They featured similar genomic DNA G+C contents of 53.2–53.4 mol%. Activities of catalase and oxidase were negative for both strains. The fatty acids patterns of 17-4AT and L52-1-41 were most similar, mostly comprised of C16 : 0, C17 : 0cyclo, C18 : 0, C18 : 1ω9c and summed feature 8 (C18 : 1ω7c and/or C18 : 1  ω6c). The major polar lipids of the two strains were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unidentified aminolipids. The respiratory quinone of the two strains was Q-8. Hence, on the basis of the phenotypic, chemotaxonomic and genotypic data presented in this study, we proposed the classification of both strains as representatives of a novel species named Pusillimonas maritima sp. nov., with the type strain 17-4AT (=MCCC 1A12670T=KCTC 62121T=NBRC 113794T), and another strain L52-1-41 (=MCCC 1A05046=KCTC 52313).

scholarly journals Distribution of plutonium in the Pacific Ocean and implications for tracing of ocean circulation

2021 ◽  
Author(s):  
Junwen Wu ◽  
Jisheng Chen ◽  
Cui Wang ◽  
Zhaoyong Zheng ◽  
Liang Wang
Keyword(s):  
Pacific Ocean ◽  
Ocean Circulation ◽  
Ocean Surface ◽  
North Equatorial Current ◽  
Great Promise ◽  
Depth Range ◽  
Surface Seawater ◽  
Transport Pathway ◽  
The Pacific ◽  
The Pacific Ocean

Abstract This study examined plutonium (Pu) sources and distribution in the Pacific Ocean based on extensive field datasets over the past 50 years. The basin wide 240Pu/239Pu atom ratios in surface and deep seawater ranged from 0.192 to 0.279 averaging 0.235 ± 0.019, a value consistently higher than that of global fallout at ~ 0.180. The distribution of 240Pu/239Pu atom ratios exhibited a decreasing trend along the North Equatorial Current-Kuroshio to their extension areas. The activity levels of 239+240Pu in Pacific Ocean surface seawater ranged widely from 0.2 to 43.5 mBq m− 3, and increased with latitude. We determined the Pu sourced from the Pacific Proving Grounds (PPG) and global nuclear fallout in the Pacific Ocean based on the Pu isotopic composition. Using a mixing model, we found that the PPG made the dominant Pu contribution (average = 69.6 ± 14.4%) to Pacific Ocean surface seawater. The depth range of maximal 239+240Pu activity in the Pacific Ocean was well defined, averaging 608 ± 137 m. The vertical distribution of the 239+240Pu inventory showed most of Pu retained in the upper 3000 m, namely, the contributions of 239+240Pu inventories at 0-1000 m and 0-3000 m depths accounted for 43.5 ± 9.0% and 75.1 ± 12.0% of the total, respectively. We identified the transport pathway of Pu-PPG in the Pacific Ocean and demonstrated that Pu isotopes hold great promise as tracers of ocean circulation. Finally, via this extensive compilation of Pu isotopic compositions in the Pacific Ocean water, we established a Pu baseline in the region.

scholarly journals Pseudooceanicola pacificus sp. nov., isolated from deep-sea sediment of the Pacific Ocean

2020 ◽  
Vol 70 (7) ◽  
pp. 4372-4377 ◽  
Author(s):  
Lina Lyu ◽  
Qiliang Lai ◽  
Jianyang Li ◽  
Zongze Shao ◽  
Zhiqiang Yu
Keyword(s):  
Pacific Ocean ◽  
Deep Sea ◽  
Type Species ◽  
Aerobic Bacterium ◽  
Content Type ◽  
Deep Sea Sediment ◽  
Link Type ◽  
The Pacific ◽  
The Pacific Ocean ◽  
Gene Similarity

A Gram-strain-negative, rod-shaped, aerobic bacterium, designated 216_PA32_1T, was isolated from deep-sea sediment of the Pacific Ocean. Cells of strain 216_PA32_1T were non-motile, oxidase-positive and catalase-negative. The strain could grow at temperatures of 10–45 °C (optimum, 32–35 °C), at pH 5.0–10.0 (optimum, 6.0–7.0) and at salinities of 0–10% (optimum, 2–8%). The principal fatty acid (>10 %) was summed feature 8 (C18:1 ω6c/ω7c). The sole respiratory quinone was Q10 (100 %). The polar lipids included phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, two unidentified phospholipids and five unidentified aminolipids. The G+C content of the chromosomal DNA was 66.3 mol%. According to the 16S rRNA gene similarity, strain 216_PA32_1T showed the highest sequence similarity to Pseudooceanicola nitratireducens JLT 1210T (97.3 %), followed by Pseudooceanicola nanhaiensis SS011B1-20T (97.1 %). Phylogenetic trees indicated that strain 216_PA32_1T clustered with strain P. nanhaiensis SS011B1-20T. The average nucleotide identity and the DNA–DNA hybridization values between strain 216_PA32_1T and all species of the genus Pseudooceanicola were below 79.5 and 20.6%, respectively. A combination of the phylogenetic, phenotypic, chemotaxonomic and genomic evidence demonstrated that strain 216_PA32_1T represents a novel species of the genus Pseudooceanicola , for which the name Pseudooceanicola pacificus sp. nov. is proposed. The type strain is 216_PA32_1T (=MCCC 1A14128T=KCTC 72688T).

scholarly journals The Unique 16S rRNA Genes of Piezophiles Reflect both Phylogeny and Adaptation

2006 ◽  
Vol 73 (3) ◽  
pp. 838-845 ◽  
Author(s):  
Federico M. Lauro ◽  
Roger A. Chastain ◽  
Lesley E. Blankenship ◽  
A. Aristides Yayanos ◽  
Douglas H. Bartlett
Keyword(s):  
16S Rrna ◽  
Deep Ocean ◽  
Elevated Pressure ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Deep Trench ◽  
The Pacific ◽  
Geographic Origins ◽  
Physiological Adaptations ◽  
The Pacific Ocean

ABSTRACT In the ocean's most extreme depths, pressures of 70 to 110 megapascals prevent the growth of all but the most hyperpiezophilic (pressure-loving) organisms. The physiological adaptations required for growth under these conditions are considered to be substantial. Efforts to determine specific adaptations permitting growth at extreme pressures have thus far focused on relatively few γ-proteobacteria, in part due to the technical difficulties of obtaining piezophilic bacteria in pure culture. Here, we present the molecular phylogenies of several new piezophiles of widely differing geographic origins. Included are results from an analysis of the first deep-trench bacterial isolates recovered from the southern hemisphere (9.9-km depth) and of the first gram-positive piezophilic strains. These new data allowed both phylogenetic and structural 16S rRNA comparisons among deep-ocean trench piezophiles and closely related strains not adapted to high pressure. Our results suggest that (i) the Circumpolar Deep Water acts as repository for hyperpiezophiles and drives their dissemination to deep trenches in the Pacific Ocean and (ii) the occurrence of elongated helices in the 16S rRNA genes increases with the extent of adaptation to growth at elevated pressure. These helix changes are believed to improve ribosome function under deep-sea conditions.

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