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Across large oceanic spatial scales, the mechanisms governing microbial community composition remain poorly understood, particularly regarding the influence of biotic factors. In this study, samples were collected over a 3772.55-km transect in the Western Pacific surface waters, with 16S and 18S ribosomal RNA gene sequencing employed to elucidate the assembly processes and drivers of microbial communities. Both eukaryotic (EM) and prokaryotic microbial (PM) communities exhibited a significant distance-decay relationship throughout the survey, although their assembly mechanisms differed. Biotic factors played a pivotal role in shaping the biogeographical patterns of both EM and PM communities, indicating that cross-domain microbial interactions significantly affect each other's distribution. Furthermore, the stability of the co-occurrence network was more strongly influenced by cross-domain microbial relationships than by keystone taxa. These findings advance our understanding of the mechanisms and biogeographical patterns sustaining microbial diversity across large oceanic spatial scales., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Upwelling along oceanic eastern boundaries has attracted significant attention due to its profound effects on ocean productivity and associated biological and socioeconomic implications. However, uncertainty persists regarding the evolution of coastal upwelling with climate change, particularly its impact on future biological production. Here, using a series of state-of-the-art climate models, we identify a significant seasonal advancement and prolonged duration of upwelling in major upwelling systems. Nevertheless, the upwelling intensity (total volume of upwelled water) exhibits complex changes in the future. In the North Pacific, the upwelling is expected to attenuate, albeit with a minor magnitude. Conversely, in other basins, coastal upwelling diminishes significantly in equatorward regions but displays a slight decline or even an enhancement at higher latitudes. The climate simulations also reveal a robust connection between changes in upwelling intensity and net primary production, highlighting the crucial impact of future coastal upwelling alterations on marine ecosystems., (© 2024. The Author(s).)

Bacillus cereus 2-6A, was isolated from the sediments in the hydrothermal area of the Pacific Ocean with a water depth of 2628 m. In this study, we report the whole genome sequence of strain 2-6A and analyze that to understand its metabolic capacities and biosynthesis potential of natural products. The genome of strain 2-6A consists of a circular chromosome of 5,191,018 bp with a GC content of 35.3 mol% and two plasmids of 234,719 bp and 411,441 bp, respectively. Genomic data mining reveals that strain 2-6A has several gene clusters involved in exopolysaccharides (EPSs) and polyhydroxyalkanoates (PHAs) production and complex polysaccharides degradation. It also possesses a variety of genes for allowing strain 2-6A to cope with osmotic stress, oxidative stress, heat shock, cold shock and heavy metal stress, which could play a vital role in the adaptability of the strain to hydrothermal environments. Gene clusters for secondary metabolite production, such as lasso peptide and siderophore, are also predicted. Therefore, genome sequencing and data mining provide insights into the molecular mechanisms of Bacillus in adapting to hydrothermal deep ocean environments and can facilitate further experimental exploration., Competing Interests: Declaration of Competing Interest The authors have no financial conflicts of interest to declare., (Copyright © 2023. Published by Elsevier B.V.)

The Mariana Trench is the deepest site on earth with diverse extreme conditions such as high hydrostatic pressure, low temperature and lack of light. Organisms surviving in this extreme environment and their life strategies have been largely uninvestigated. Here, we report the complete genome of Marinomonas profundi M1K-6 T , isolated from the Mariana Trench deep seawater. The assembled genome comprised 3,648,059 bp without any plasmid. Gene annotation showed that strain M1K-6 T possesses a series of genes encoding cold-shock proteins, DEAD box RNA helicase and enzymes for biosynthesis of unsaturated fatty acids, implying its high cold tolerance. Abundant genes responsible for transports of ion, branched-chain amino acids and organic compatible solutes were detected, which could maintain cellular osmotic balance disturbed by high hydrostatic pressure. In addition, detected genes (related to storage carbon, transport systems and two-component regulatory systems) could help strain M1K-6 T to improve its ecological fitness in the deep-sea microaerobic and nutrient-limiting environments. Genomic information on M. profundi M1K-6 T , provides insights into the adaptation strategies of Marinomonas spp. in the extreme deep-sea environment of the Mariana Trench., (Copyright © 2022. Published by Elsevier B.V.)

Diversity of microbial eukaryotes is estimated largely based on sequencing analysis of the hypervariable regions of 18S rRNA genes. But the use of different regions of 18S rRNA genes as molecular markers may generate bias in diversity estimation. Here, we compared the differences between the two most widely used markers, V4 and V9 regions of the 18S rRNA gene, in describing the diversity of epipelagic, bathypelagic, and hadal picoeukaryotes in the Challenger Deep of the Mariana Trench, which is a unique and little explored environment. Generally, the V9 region identified more OTUs in deeper waters than V4, while the V4 region provided greater Shannon diversity than V9. In the epipelagic zone, where Alveolata was the dominant group, picoeukaryotic community compositions identified by V4 and V9 markers are similar at different taxonomic levels. However, in the deep waters, the results of the two datasets show clear differences. These differences were mainly contributed by Retaria, Fungi, and Bicosoecida. The primer targeting the V9 region has an advantage in amplifying Bicosoecids in the bathypelagic and hadal zone of the Mariana Trench, and its high abundance in V9 dataset pointed out the possibility of Bicosoecids as a dominant group in this environment. Chrysophyceae, Fungi, MALV-I, and Retaria were identified as the dominant picoeukaryotes in the bathypelagic and hadal zone and potentially play important roles in deep-sea microbial food webs and biogeochemical cycling by their phagotrophic, saprotrophic, and parasitic life styles. Overall, the use of different markers of 18S rRNA gene allows a better assessment and understanding of the picoeukaryotic diversity in deep-sea environments., (© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Two novel Gram-stain-negative, facultative anaerobic, non-flagellated, rod-shaped bacterial strains, designated MT13 T and MT32, were isolated from sediment samples collected from the Mariana Trench at a depth of 8300 m. The two strains grew at -2-30 °C (optimum, 25 °C), at pH 5.5-10.0 (optimum, pH 7.5-8.0) and with 0-15 % (w/v) NaCl (optimum, 3-6 %). They did not reduce nitrate to nitrite nor hydrolyse Tweens 40 and 80, aesculin, casein, starch and DNA. The genomic G+C contents of draft genomes of strain MT13 T and MT32 were 52.2 and 54.1 m ol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains MT13 T and MT32 were affiliated with the genus Halomonas , with the highest similarity to the type strain of Halomonas olivaria . The values of average nucleotide identity and in silico DNA-DNA hybridization between strain MT13 T and MT32, and between strain MT13 T and five closely related type strains of Halomonas species indicated that strains MT13 T and MT32 belonged to the same species, but represented a novel species in the genus of Halomonas . The major cellular fatty acids of strains MT13 T and MT32 were C 16 : 0 , summed feature 3(C 16 : 1  ω 7 c / ω 6 c ) and summed feature 8 (C 18 : 1  ω 7 c ). Major polar lipids of strains MT13 ω 6 c and MT32 represent a novel species of the genus T and MT32 included phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Ubiquinone-9 was the predominant respiratory quinone. Based on data from the present polyphasic study, strains MT13 T and MT32 represent a novel species of the genus Halomonas , for which the name Halomonas profundi sp. nov. is proposed. The type strain is MT13 T (=MCCC 1K06389 T =KCTC 82923 T ).

Large amounts of anthropogenic East Asian (EA) particulate matters (PM), containing inorganic nutrients and organic matter, are deposited in the oligotrophic Northwest Pacific Ocean. However, the effects of such deposition on marine microbes remain unclear. In this study, the effect of EA PM deposition on marine bacteria was assessed by five on-board microcosm experiments, conducted in oligotrophic basins of the South China Sea. The addition of EA PM to the sampling water induced a clear shift in bacterial community composition from prevailing oligotrophs (i.e., SAR 11 clade, Prochlorococcus, AEGEAN-169 marine group) to less common copiotrophs (i.e., Alteromonas, Ruegeria, Flavobacteriaceae) and thus a slight increase in bacterial diversity. The shift to more active community composition, as well as stimulation of PM nutrients, resulted in a large increase in cell-specific and bulk bacterial production. In contrast, there were only minor changes in bacterial abundance, possibly due to increased top-down mortality. The EA PM also exhibited a stronge toxic effect on pico-cyanobacteria, leading to a significant decrease in their proportion. Moreover, the responses of bacterial metabolism and community composition exhibited significant relationships with the hydrographic condition of the locations. Stronger promotion effects of the EA PM on bacterial production and community shift from oligotrophs to copiotrophs was demonstrated at the more oligotrophic sites with lower chlorophyll a concentrations. These results suggest that PM deposition from polluted areas has the potential to alter the typical oligotrophic microbiomes and change the net metabolic balance of the bacterial community. These will then influence the dynamics of carbon flow in microbial food webs and biogeochemical cycles, especially with the trend of global warming and expansion of low-chlorophyll regions., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Picoeukaryotes are an essential component of microbial communities and play key roles in marine ecosystems. In this study, surface water picoeukaryotes were investigated at 32 stations along a latitudinal cross-section of the Western Pacific (WP) in 2015. Multivariate analyses demonstrated that there were clear spatial patterns in picoeukaryotic community structures which were consistent with the distributions of environmental variables. The spatial patterns of community structures and diversity indices were all significantly correlated with multiple environmental parameters, especially nutrients. Co-occurrence networks linked community variability to environmental heterogeneity. In summary, the construction of picoeukaryotic communities in the WP was significantly affected by numerous environmental variables, and certain variables were revealed as key forcing factors responsible for the main similarities between picoeukaryotic communities. This study details the relationships between the picoeukaryotes and environmental parameters in the WP, and provides insight for application of using picoeukaryotes as indicator in future bioassessment for open waters., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Microbial communities are a large component of abyssal and hadal benthic environments, especially in deep-sea areas like Yap Trench, they provide a continuous source of nutrients and energy in their unique ecosystems. However, due to sampling difficulties, these microbial communities are relatively understudied. In the summer of 2017, sediment samples were collected from 21 stations around Yap Trench in the Western Pacific Ocean (mostly in the West Caroline Basin), at depths ranging from 3156 to 7837 m. Sediment samples from deep water depths and shallow water depths differed in organic matter content, median grain size, silt-clay content, and biodiversity. The structure of the microbial communities in the surface sediments had distinct relationships with environmental factors and their co-occurrence networks exhibited a clear spatial pattern. In addition, for both prokaryotes or eukaryotes, a combination of variables including silt-clay content, organic matter content, median grain size, and depth had the greatest impact on community structure. It was notable that fungi played important roles in the co-occurrence networks of deep water depth sediment samples while bacteria dominated those of shallow water depth samples. The differences in structure and ecological niches in the different networks were due to differences in sediment texture and organic matter content. Since clay had a positive effect on the diversity of bacteria, it had an indirect positive effect on fungi, leading to differences in biodiversity among different groups. More organic matter meant more nutrients were available for the growth and reproduction of microbes, which led to fewer niche overlaps. This study conducted an extensive and systematic sequencing survey of surface sediments around Yap Trench in the Western Pacific Ocean, providing insight into microbial responses to environmental heterogeneity in deep-sea benthic ecosystems., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

A Gram-stain-negative, aerobic, ovoid-rod-shaped bacterium, designated strain SM1903 T , was isolated from surface seawater of the Mariana Trench. The strain grew at 15-37 °C (optimum, 35 °C) and with 1-15 % (optimum, 4 %) NaCl. It hydrolysed aesculin but did not reduce nitrate to nitrite and hydrolyse Tween 80. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SM1903 T formed a separate lineage within the family Rhodobacteraceae , sharing the highest 16S rRNA gene sequence similarity with type strains of Pseudooceanicola antarcticus (95.7 %) and Roseisalinus antarcticus (95.7 %). In phylogenetic trees based on single-copy OCs and whole proteins sequences, strain SM1903 T fell within a sub-cluster encompassed by Oceanicola granulosus , Roseisalinus antarcticus and Histidinibacterium lentulum and formed a branch adjacent to Oceanicola granulosus . The major cellular fatty acids were summed feature 8 (C 18 : 1  ω 7 c and/or C 18 : 1  ω 6 c ), C 16 : 0 . The polar lipids mainly comprised phosphatidylglycerol, phosphatidylcholine, one unidentified lipid, one unidentified aminolipid, and one unidentified glycolipid. The solo respiratory quinone was ubiquinone-10. The genomic DNA G+C content of strain SM1903 18 : 1 was 66.0 mol%. Based on the results of phenotypic, chemotaxonomic, and phylogenetic characterization for strain SM1903  ω , it is considered to represent a novel species of a novel genus in the family c . The polar lipids mainly comprised phosphatidylglycerol, phosphatidylcholine, one unidentified lipid, one unidentified aminolipid, and one unidentified glycolipid. The solo respiratory quinone was ubiquinone-10. The genomic DNA G+C content of strain SM1903 T was 66.0 mol%. Based on the results of phenotypic, chemotaxonomic, and phylogenetic characterization for strain SM1903 T , it is considered to represent a novel species of a novel genus in the family Rhodobacteraceae , for which the name Pelagovum pacificum gen. nov., sp. nov. is proposed. The type strain is SM1903 T (=MCCC 1K03608 T =KCTC 72046 T ).

A Gram-stain-negative, aerobic, polarly flagellated, straight or curved rod-shaped bacterium, designated strain M1K-6 T , was isolated from deep seawater samples collected from the Mariana Trench. The strain grew at -4 to 37 °C (optimum, 25-30 °C), at pH 5.5-10.0 (optimum, pH 7.0) and with 0.5-14.0  % (w/v) NaCl (optimum, 2.0 %). It did not reduce nitrate to nitrite nor hydrolyse gelatin or starch. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M1K-6 T was affiliated with the genus Marinomonas , sharing 93.1-97.0  % sequence similarity with the type strains of recognized Marinomonas species. The major cellular fatty acids were summed feature 3 (C 16 : 1 ω 6 c /C 16 : 1 ω 7 c ), summed feature 8 (C 18 : 1 ω 7 c /C 18 : 1 ω . The predominant respiratory quinone was ubiquinone-8. Polar lipids of strain M1K-6 c included phosphatidylethanolamine, phosphatidylglycerol and two unidentified lipids. The genomic G+C content of strain M1K-6 16 : 0 , C 10 : 0 3-OH and C 18 : 0 . The predominant respiratory quinone was ubiquinone-8. Polar lipids of strain M1K-6 T included phosphatidylethanolamine, phosphatidylglycerol and two unidentified lipids. The genomic G+C content of strain M1K-6 T was 46.0 mol%. Based on data from the present polyphasic study, strain M1K-6 T was considered to represent a novel species within the genus Marinomonas , for which the name Marinomonas profundi sp. nov. is proposed. The type strain is M1K-6 T (=KCTC 72501 T =MCCC 1K03890 T ).

A Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and non-flagellated marine bacterium strain, designated BOM4 T , was isolated from a mussel inhabiting the Tangyin hydrothermal field of the Okinawa Trough. The growth temperature was in the range of 16-40 °C, and the optimum temperature was 37 °C. Optimal growth occurred at pH 7.0 and in the presence of 1 % (w/v) NaCl. The predominant isoprenoid quinone of strain BOM4 T was identified as menaquinone-6 (MK-6). The predominant fatty acids (>10 %) were iso-C 15 : 0 (43.8 %) and iso-C 17 : 0 3-OH (17.5 %). The major polar lipids comprised one phosphatidylethanolamine, three unidentified aminolipids and two unidentified lipids. Based on 16S rRNA gene sequence analyses, strain BOM4 T was found to be most closely related to Gramella aestuarii JCM 17790 T (96.7 %), followed by Gramella flava JLT2011 T (96.1 %), Gramella sediminilitoris GHTF-27 T (95.6 %) and Gramella gaetbulicola RA5-111 T (95.5 %) and with lower sequence similarities (93.7- 95.4 %) to other species of the genus Gramella . Genome relatedness between strain BOM4 T and G. aestuarii JCM 17790 T was computed using both average nucleotide identity and DNA-DNA hybridization with values of 75.6 and 19.3±2.4 %, respectively. The DNA G+C content of strain BOM4 T was 41.4 mol%. On the basis of polyphasic analysis, strain BOM4 T was considered to represent a novel species of the genus Gramella , for which the name Gramella bathymodioli sp. nov. is proposed. The type strain is BOM4 T (=MCCC 1K03735 T =JCM 33424 T ).

Meiofauna particularly marine nematodes around the Caiwei Guyot in the northwest Pacific Ocean and a Polymetallic Nodule Field in the northeast Pacific Ocean were studied. Due to the geographic structure, the Caiwei Guyot and the Polymetallic Nodule Field had different environmental characteristics. Meiofaunal abundances around the Guyot area ranged from 9.18 to 25.59 ind./10 cm 2 , which were much lower than those in the Polymetallic Nodule Field. Marine nematode was the most dominant group. A total of 123 species, belonging to 74 genera and 29 families were found. Xyalidae (21.43%), Cyatholaimidae (9.82%), Linhomoeidae (8.03%) were the dominant families. The values of species number, Margalef's species richness and Shannon-Wiener diversity index ranged from 15 to 62, 4.75 to 12.84 and 2.58 to 3.93, respectively. The combination of water depth, silt-clay content and chlorophyll-a concentration can best explain the differences of nematode community. This study provides a baseline for deep-sea meiofauna distribution., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

A new cyanophage, S-B05, infecting a phycoerythrin-enriched (PE-type) Synechococcus strain was isolated by the liquid infection method, and its morphology and genetic features were examined. Phylogenetic analysis and morphological observation confirmed that S-B05 belongs to the family Myoviridae of the order Caudovirales. Its genome was fully sequenced, and found to be 208,857 bp in length with a G + C content of 39.9%. It contained 280 potential open reading frames and 123 conserved domains. Ninety-eight functional genes responsible for cyanophage structuring and packaging, DNA replication and regulation, and photosynthesis were identified, as well as genes encoding 172 hypothetical proteins. The genome of S-B05 is most similar to that of Prochlorococcus phage P-TIM68. Homologues of open reading frames of S-B05 can be found in various marine environments, as revealed by comparison of the S-B05 genome sequence to sequences in marine viral metagenomic databases. The presence of auxiliary metabolic genes (AMGs) related to photosynthesis, carbon metabolism, and phosphorus assimilation, as well as the phylogenetic relationships based on AMGs and the complete genome sequence, reflect the phage-host interaction mechanism or the specific adaptation strategy of the host to environmental conditions. The genome sequence information reported here will provide an important basis for further study of the adaptive evolution and ecological role of cyanophages and their hosts in the marine environment.

A Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterium, designated ZYF650 T , was isolated from the hadal seawater (9600 m) of the Mariana Trench. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that ZYF650 T formed a lineage within the family Alteromonadaceae that was distinct from the most closely related species Marinobacter mobilis and Marinobacter nitratireducens with 16S rRNA gene sequences similarities of 98.0 and 97.7 %, respectively. Strain ZYF650 T showed average nucleotide identity values of 75.7 % with Marinobacter hydrocarbonoclasticus , 73.3 % with Marinobacter mobilis and 79.3 % with Marinobacter nitratireducens , and DNA-DNAhybridization values of 21.5, 21.3 and 22.0 % with M. hydrocarbonoclasticus , M. mobilis and M. nitratireducens , respectively, which were lower than the threshold for species delineation. Strain ZYF650 T grew with 0-14 % (w/v) NaCl (optimum, 7-8 %) at a temperature range of 10-45 °C (optimum, 28 °C) and pH 6.0-9.5 (optimum, pH 7.0-8.0). The sole respiratory quinone was ubiquinone-9 (Q-9). The polar lipids in ZYF650 T comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, three unidentified polar lipids, two unidentified aminolipids and two phospholipids. The predominant fatty acids (more than 10 % of total fatty acids) were C 18 : 1  ω9 c (21.9 %), C 16 : 0 (21.7 %), C 12 : 0 3-OH (14.0 %), C 16 : 1  ω9 c (13.2 %) and C 12 : 0 (12.2 %). The DNA G+C content of strain ZYF650 T was 55.6 %. On the basis of polyphasic taxonomic analysis, strain ZY650 T is considered to represent a novel specie of the genus Marinobacter in the family Alteromonadaceae , for which the name Marinobacter salinexigens sp. nov. is proposed. The type strain is ZYF650 T (=JCM 33013 T =MCCC 1K03552 T ).

A Gram-stain-negative, obligately anaerobic, non-motile, non-spore-forming, long-rod-shaped and non-flagellated bacterial strain, designated T3-2 S1-C T , was isolated from a sediment sample collected at the Okinawa Trough. Phylogenetic analyses of 16S rRNA gene sequences and the whole genome revealed that strain T3-2 S1-C T was a member of the family Marinifilaceae and exhibited less than 95.1 % sequence similarities to the closely related type strains of the family Marinifilaceae . Optimal growth occurred at pH 7.0, 28 °C and in the presence of 3 % (w/v) NaCl. The isoprenoid quinone of strain T3-2 S1-C T was identified as menaquinone-7 (MK-7) and the predominant fatty acids (>10 %) were iso-C 15 : 0 (38.9 %) and anteiso-C 15 : 0 (11.6 %). The major polar lipids were one phosphatidylethanolamine, one phosphatidylmonomethylethanolamine, one aminolipids, two unidentified lipids and two unidentified phospholipids. The DNA G+C content of strain T3-2 S1-C T was 35.7 mol%. On the basis of the results of polyphasic analyses, strain T3-2 S1-C T is considered to represent a novel species of the genus Ancylomarina , for which the name Ancylomarina longa sp. nov. is proposed. The type strain is T3-2 S1-C T (=KCTC 15505 T =MCCC 1K01617 T ).

A Gram-stain-negative, strictly aerobic, non-motile, long, straight-rod and non-flagellated marine bacterium strain, designated SCR12 T , was isolated from the gill of a shrimp collected in the Tangyin hydrothermal field of the Okinawa Trough. The growth temperature was in the range of 16-40 °C and the optimum temperature was 37 °C. Optimal growth occurred at pH 6.5 and in the presence of 3 % (w/v) NaCl. The predominant isoprenoid quinone of strain SCR12 T was menaquinone-6 (MK-6). The predominant fatty acids (>10 %) were iso-C 15 : 0 (44.2 %), iso-C 15 : 1 G (19.0 %) and iso-C 17 : 0 3-OH (12.1 %). The major polar lipids comprised one phosphatidylethanolamine, three unidentified phospholipids, two unidentified aminolipids and three unidentified lipids. Based on the results of 16S rRNA gene sequence analysis, strain SCR12 T was found to be most closely related to Muricauda olearia CL-SS4 T (98.09 %), followed by Muricauda beolgyonensis BB-My12 T (97.65 %), Muricauda aquimarina SW-63 T (97.58 %) and Muricauda ruestringensis DSM 13258 T (97.31 %) and with lower sequence similarities (95.74-97.10 %) to other species of the genus Muricauda . Genome relatedness between strain SCR12 T and M. olearia CL-SS4 T was computed using both average nucleotide identity (ANI) and DNA-DNA hybridization (DDH) and resulted in values of 85.6 % and 29.3±2.3 %, respectively. The genomic DNA G+C content of strain SCR12 T was 42.3 mol%. On the basis of polyphasic analysis, the strain SCR12 T was considered to represent a novel species of the genus Muricauda, for which the name Muricauda alvinocaridis sp. nov. is proposed. The type strain is SCR12 T (=MCCC 1K03731 T =JCM 33425 T ).

A Gram-stain-negative, strictly aerobic, oval-shaped, non-motile bacterium with no flagella, designated strain SCR17 T , was isolated from a shrimp gill habitat in Tangyin hydrothermal field of Okinawa Trough. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SCR17 T formed a lineage within the family ' Rhodobacteraceae ', and shared 16S rRNA gene sequence similarity of 93.2-96.2 % to the related genera Aquicoccus and Roseivivax . Strain SCR17 T was able to grow with 0-14 % (w/v) NaCl (optimum, 9-10 %). The sole respiratory quinone was ubiquinone-10. The major polar lipids of strain SCR17 T comprised phosphatidylcholine (PC), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), an unidentified aminolipid (AL), an unidentified phospholipid (PL) and an unidentified lipid (L). The predominant fatty acids (more than 10 % of the total fatty acids) were C 18 : 1 ω7 c or/and C 18 : 1 ω6 c , anteiso-C 15 : 0 , C 16 : 0 and C 19 : 0 cyclo ω 8 c . The genomic DNA G+C content of strain SCR17 T was 67.7 mol%. Based on polyphasic taxonomic analyses, strain SCR17 T is considered to represent a novel species in a new genus of the family ' Rhodobacteraceae ', for which the name Carideicomes alvinocaridis gen. nov., sp. nov. is proposed. The type strain of Carideicomes alvinocaridis is SCR17 T (=JCM 33426 T =MCCC 1K03732 T ). The discovery of a novel host-associated bacterium in hydrothermal fields provides an opportunity for the study of host-bacterial symbiosis in extreme environments.

A Gram-stain-negative, strictly aerobic, rod-shaped bacterium, without flagellum and designated ZYF765 T , was isolated from seawater sampled at a depth of 4000 m in the Mariana Trench. Strain ZYF765 T grew with 1-15 % (w/v) NaCl (optimum, 4 %), at 16-37 °C (28 °C) and at pH 6.0-10.0 (pH 7.0-8.0). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain ZYF765 T formed a lineage within the family Hyphomonadaceae , and was distinct from the most closely related species Glycocaulis abyssi , Glycocaulis albus and Glycocaulis alkaliphilus with 16S rRNA gene sequences similarities ranging from 98.42 to 98.63 %. The major respiratory quinone was ubiquinone-10 (Q-10). The polar lipids comprised three unidentified glycolipids, one unidentified aminophospholipid, one unidentified phospholipid and one unidentified aminolipid. The predominant fatty acids (more than 10 % of total fatty acids) were C 18 : 1 ω7 c (46.2 %) and C 18 : 0 (14.1 %). The DNA G+C content was 67.7 mol%. On the basis of the results of polyphasic taxonomic analysis, strain ZYF765 T is considered to represent a novel species within the genus Glycocaulis , for which the name Glycocaulis profundi sp. nov. is proposed. The type strain is ZYF765 T (=JCM 33028 T =MCCC 1K03554 T ).

Fungi play an important role in cycling organic matter and nutrients in marine ecosystems. However, the distribution of fungal communities in the ocean, especially the vertical distribution along depth in the water column, remained poorly understood. Here, we assess the depth-related distribution pattern of fungal communities along the water column from epi- to abyssopelagic zones of the Western Pacific Ocean using internal transcribed spacer 2 (ITS2) metabarcoding. Majority of the assigned OTUs were affiliated to Ascomycota, followed by three other minor phyla (Basidiomycota, Chytridiomycota, and Mucoromycota). The epipelagic zone harbored a higher OTU richness with distinct fungal communities as compared with meso-, bathy-, and abyssopelagic zones. Across the whole water column, depth appears as a key parameter for both fungal α- and β-diversity. However, when the dataset was split into the upper (5-500 m) and deeper (below 500 m) layers, no significant correlation was observed between depth and community compositions. In the upper layer, temperature and dissolved oxygen were recognized as the primary environmental factors shaping fungal α- and β- diversity. By parsing fungal OTUs into ecological categories, multi-trophic mode of nutrition was found to be more prevalent with increasing depth, suggesting a potential adaptation to the extreme conditions of the deep sea. This study provides new and meaningful information on the depth-stratified fungal diversity, community structure, and putative ecological roles in the open sea.

A novel Gram-stain-negative, strictly aerobic, rod-shaped motile bacterium with a single flagellum, designated strain WRAS1 T , was isolated from deep seawater of the Okinawa Trough. Growth occurred in the presence of 0.0-9.0 % NaCl (w/v; optimum, 3.0-4.0 %), at 4-45 °C (optimum, 28-37 °C) and pH 7.0-10.0 (optimum, pH 7.0-8.0). The major fatty acid (>10 % of total fatty acids) was summed feature 8, comprising C18:1ω6c and/or C18:1ω7c. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and three unidentified lipids. The major respiratory quinone was ubiquinone-10. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WRAS1 T was in the genus Thalassococcus and showed the highest 16S rRNA gene sequence similarity of 97.5 % to Thalassococcus halodurans JCM13833 T . Genome relatedness between strain WRAS1 T and T. halodurans JCM13833 T was computed using both average nucleotide identity and DNA-DNA hybridization with values of 74.11 % and 22.70±2.3 %, respectively. The genomic DNA G+C content calculated from the genome sequence of strain WRAS1 T was 65.6 %. On the basis of polyphasic analyses, strain WRAS1 T is considered to represent a novel species in the genus Thalassococcus, for which the name Thalassococcusprofundi sp. nov. is proposed. The type strain is WRAS1 T (=CGMCC 1.16123 T =MCCC 1K03253 T =KCTC 52696 T ).

A Gram-stain-negative, rod-shaped, non-motile, strictly aerobic strain, designated as MTEO17 T , was isolated from a 1000 m deep seawater sample of the Mariana Trench. Growth was observed at 10-45 °C (optimum, 37 °C), in the presence of 0.0-12.0 % NaCl (w/v; optimum, 3.0 %) and at pH 6.0-10.0 (optimum, pH 7.0-8.0). Phylogenetic analysis, based on the 16S rRNA gene sequence, revealed that strain MTEO17 T belonged to the genus Alcanivorax and showed the highest sequence similarity of 97.9 % to Alcanivorax nanhaiticus MCCC 1A05629 T . The estimated average nucleotide identity and DNA-DNA hybridization values between strain MTEO17 T and A. nanhaiticus MCCC 1A05629 T were 78.98 and 23.80 %, respectively. The significant dominant fatty acids were C16 : 0, summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The polar lipids comprised two phosphatidylethanolamines, one phosphatidylglycerol, one unidentified phospholipid and four unidentified polar lipids. The DNA G+C content of strain MTEO17 T was 57.5 %. On the basis of the polyphasic evidence, strain MTEO17 T is proposed to represent a novel species of the genus Alcanivorax, for which the name Alcanivorax profundi sp. nov. is proposed. The type strain is MTEO17 T (=KCTC 52694 T =MCCC 1K03252 T ).

A Gram-stain-positive, endospore-forming, rod-shaped, motile and strictly aerobic strain, designated T3-209 T , was isolated from sediment sampled at a water depth of 1206 m of the southern Okinawa Trough at station T1 (25.07° N, 122.58° E) near the Tangyin hydrothermal vent during an expedition on the R/V Kexue in May 2014. The strain was able to grow at a temperature range of 10-42 °C (optimum 28 °C). Growth was observed at NaCl concentrations (w/v) of 0-6 % (optimum 0 %). The pH range for growth was 7.0-9.0 (optimum 8.0). The 16S rRNA gene sequence analysis indicated that strain T3-209 T belonged to the genus Bacillus within the family Bacillaceae and was most closely related to Bacillus drentensis LMG 21831 T and Bacillus bataviensis LMG 21833 T , with the same sequence similarity (97.0 %), but shared relatively low levels of similarity (92.6-96.9 %) to the type strains of other Bacillus species. The peptidoglycan type of strain T3-209 T was meso-diaminopimelic acid. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and alcohol-C16 : 1ω7c. The respiratory quinone was menaquinone-7. The polar lipids of strain T3-209 T comprised phosphatidylglycerol, two unidentified phospholipids and one unidentified aminolipid. The DNA G+C content was 41.8 mol%. Combining results of phylogenetic analysis, phenotypic characterization and chemotaxonomic studies, strain T3-209 T represents a novel species of the genus Bacillus, for which the name Bacillus alkalitolerans sp. nov. is proposed. The type strain is T3-209 T (=KCTC 33631 T =DSM 29135 T =MCCC 1K00503 T ).

A Gram-stain-positive, strictly aerobic, coccus-shaped, non-motile, yellow-pigmented bacterium, designated strain XH208(T), was isolated from a deep subseafloor sediment sample collected from the South Pacific Gyre (41° 58' S 163° 11' W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XH208(T) belonged to the genus Luteococcus and showed the highest 16S rRNA gene sequence similarities with Luteococcus peritonei CCUG 38120(T) (96.9%), Luteococcus japonicus DSM 10546(T) (95.4%) and Luteococcus sanguinis CCUG 33897(T) (95.2%). The DNA G+C content of strain XH208(T) was 66.9 mol%. The cell wall of strain XH208(T) possessed a type A3γ peptidoglycan (ll-diaminopimelic acid-glycine), and ribose, glucose and galactose as the major whole-cell sugars. The major fatty acids were C(17 : 1)ω8c, C(17 : 1)ω6c, and C(16 : 1)ω6c and/or C(16 : 1)ω7c (summed feature 3). The major respiratory quinone was menaquinone MK-9(H4). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol. On the basis of data from the polyphasic analysis, strain XH208(T) is considered to represent a novel species in the genus Luteococcus, for which the name Luteococcus sediminum sp. nov. is proposed. The type strain is XH208(T) ( = DSM 27277(T) = JCM 19259(T))., (© 2014 IUMS.)

A moderately halophilic bacterial strain, designated XH204(T), was isolated from deep-sea sediment core (45° 58' S 163° 11' W) of the South Pacific Gyre during the Integrated Ocean Drilling Program Expedition 329. The strain was Gram-stain-positive, rod-shaped, motile by peritrichous flagella and produced ellipsoidal endospores subterminally positioned within swollen sporangia. Growth of strain XH204(T) occurred at 15-42 °C (optimum 37 °C), in the presence of 0-14 % (w/v) NaCl (optimum 4 %) and at pH 7.0-10.0 (optimum pH 8.0). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XH204(T) belonged to the genus Oceanobacillus and showed the highest sequence similarity to Oceanobacillus profundus CL-MP28(T) (95.6 %); strain XH204(T) exhibited 93.4 % 16S rRNA gene sequence similarity to the type strain of the type species of the genus Oceanobacillus, Oceanobacillus iheyensis HTE831(T). The dominant fatty acids of strain XH204(T) were anteiso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The cell wall of strain XH204(T) contained meso-diaminopimelic acid as the diagnostic diamino acid, and ribose, glucose and galactose as the major whole-cell sugars. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. Menaquinone-7 (MK-7) was the only isoprenoid quinone and the DNA G+C content was 38.8 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic analysis, strain XH204(T) represents a novel species of the genus Oceanobacillus, for which the name Oceanobacillus pacificus sp. nov. is proposed. The type strain is XH204(T) ( = DSM 25873(T) = JCM 18381(T)).

A novel Gram-stain-negative, rod-shaped, non-flagellated, strictly aerobic strain with gliding motility, designated SW024(T), was isolated from surface seawater of the South Pacific Gyre (26° 29' S 137° 56' W) during the Integrated Ocean Drilling Program Expedition 329. Phylogenetic analyses based on 16S rRNA gene sequences showed that the novel strain was related most closely to Aquimarina muelleri KMM 6020(T), Aquimarina macrocephali JAMB N27(T), Aquimarina addita JC2680(T), Aquimarina mytili PSC33(T), Aquimarina intermedia KMM 6258(T), Aquimarina latercula ATCC 23177(T), Aquimarina spongiae A6(T), Aquimarina agarilytica ZC1(T) and Aquimarina brevivitae SMK-19(T) (96.1, 95.5, 95.0, 94.4, 94.3, 94.0, 93.4, 93.3 and 93.2 % similarities, respectively), demonstrating that the novel strain belonged to the genus Aquimarina. The DNA G+C content of strain SW024(T) was 30.8 mol%. The major respiratory quinone of strain SW024(T) was MK-6. The dominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G, C16 : 0 10-methyl and/or iso-C17 : 1ω9c, and iso-C15 : 0 3-OH. The polar lipids of strain SW024(T) were phosphatidylethanolamine, three unknown aminolipids and five unknown polar lipids. On the basis of combined phenotypic and phylogenetic analyses, strain SW024(T) represents a novel species of the genus Aquimarina, for which the name Aquimarina longa sp. nov. is proposed. The type strain is SW024(T) ( = CGMCC 1.11007(T) = JCM 17859(T)). An emended description of A. muelleri is also proposed.

Surface seawater in the South Pacific Gyre (SPG) is one of the cleanest oceanic environments on earth, and the photosynthetic primary production is extremely low. Despite the ecological significance of the largest aquatic desert on our planet, microbial community composition in the ultra-oligotrophic seawater remain largely unknown. In this study, we collected surface seawater along a southern transect of the SPG during the Integrated Ocean Drilling Program (IODP) Expedition 329. Samples from four distinct sites (Sites U1368, U1369, U1370 and U1371) were examined, representing ~5400 kilometers of transect line from the gyre heart to the edge area. Real-time PCR analysis showed 16S rRNA gene abundance in the gyre seawater, ranging from 5.96×10(5) to 2.55×10(6) copies ml(-1) for Bacteria and 1.17×10(3) to 1.90×10(4) copies ml(-1) for Archaea. The results obtained by statistic analyses of 16S rRNA gene clone libraries revealed the community composition in the southern SPG area: diversity richness estimators in the gyre center (Sites U1368 & U1369) are generally lower than those at sites in the gyre edge (Sites U1370 & U1371) and their community structures are clearly distinguishable. Phylogenetic analysis showed the predominance of Proteobacteria (especially Alphaproteobacteria) and Cyanobacteria in bacterial 16S rRNA gene clone libraries, whereas phylotypes of Betaproteobacteria were only detected in the central gyre. Archaeal 16S rRNA genes in the clone libraries were predominated by the sequences of Marine Group II within the Euryarchaeota, and the Crenarchaeota sequences were rarely detected, which is consistent with the real-time PCR data (only 9.9 to 22.1 copies ml(-1)). We also performed cultivation of heterotrophic microbes onboard, resulting in 18.9% of phylogenetically distinct bacterial isolates at least at the species level. Our results suggest that the distribution and diversity of microbial communities in the SPG surface seawater are closely related to the ultra-oligotrophic oceanographic features in the Pacific Ocean.