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Description of Novosphingopyxis iocasae sp. nov., isolated from deep sea sediment from the Mariana Trench, and emended description of the genus Novosphingopyxis.
Zhou, HZ, Zhang, J, Sun, QL
International journal of systematic and evolutionary microbiology. 2021;(7)
Abstract
In this study, we reported a Gram-stain-negative, orange-coloured, rod-shaped, motile and faculatively anaerobic bacterium named strain PB63T, which was isolated from the deep-sea sediment from the Mariana Trench. Growth of PB63T occurred at 10-35 °C (optimum, 28 °C), pH 5.0-8.0 (optimum, 5.0-6.0) and with 0-7 % (w/v) NaCl (optimum, 2-3 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that PB63T represented a member of the genus Novosphingopyxis and was closely related to Novosphingopyxis baekryungensis DSM 16222T (97.9 % sequence similarity). PB63T showed tolerance to a variety of heavy metals, including Co2+, Zn2+, Mn2+ and Cu2+. The complete genome of PB63T was obtained, and many genes involved in heavy metal resistance were found. The genomic DNA G+C content of PB63T was 62.8 mol%. The predominant respiratory quinone of PB63T was ubiquinone-10 (Q-10). The polar lipids of PB63T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, glycolipid, phosphatidylcholines and three unidentified lipids. The major fatty acids of PB63T included summed feature 8 (C18 : 1ω7c or/and C18 : 1ω6c), C14 : 0 2-OH, 11-methyl C18 : 1ω7c, C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C17 : 1ω6c. The results of phylogenetic, physiological, biochemical and morphological analyses indicated that strain PB63T represents a novel species of the genus Novosphingopyxis, and the name Novosphingopyxis iocasae sp. nov. is proposed with the type species PB63T (=CCTCC AB 2019195T=JCM 34178T).
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2.
Psychrosphaera ytuae sp. nov., isolated from the deep-sea cold seep sediment of South China Sea.
Xu, XD, Zhang, J, Sun, QL, Sun, YY, Tang, YZ
International journal of systematic and evolutionary microbiology. 2021;(8)
Abstract
In this study, we report a Gram-stain-negative, rod-shaped, non-pigmented, motile and aerobic bacterium named strain MTZ26T, which was isolated from deep-sea sediment sampled at a cold seep in the South China Sea. Growth of strain MTZ26T occurred at 4-40 °C (optimum, 25-30 °C), pH 6.0-10.0 (optimum, 7.0-8.0) and with 1.0-11.0 % (w/v) NaCl (optimum, 6.0-8.0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MTZ26T belonged to the genus Psychrosphaera and was closely related to Psychrosphaera aestuarii PSC101T (97.5 % sequence similarity) and Psychrosphaera haliotis KDW4T (97.5 %). Genomic analysis indicated that strain MTZ26T contains a circular chromosome of 3 331 814 bp with G+C content of 42.2 mol%. The predominant respiratory quinone of MTZ26T was ubiquinone-8. The polar lipids of MTZ26T contained phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminophospholipid and one unidentified phospholipid. The major fatty acids of strain MTZ26T contained C15:0, C16:0, C17:0, C17 : 1 ω8c, C10 : 0 3-OH, C11 : 0 3-OH, C15 : 1 ω8c and summed feature 8 (C18 : 1 ω7c or/and C18 : 1 ω6c). Results of phylogenetic, physiological, biochemical and morphological analyses suggested that strain MTZ26T represents a novel species of the genus Psychrosphaera, and the name Psychrosphaera ytuae sp. nov. is proposed with the type strain MTZ26T (=MCCC 1K05568T=JCM 34321T).
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3.
Fictibacillus iocasae sp. nov., isolated from the deep-sea sediment in Pacmanus, Manus Basin.
Wang, HL, Zhang, J, Sun, L
Archives of microbiology. 2018;(7):1123-1128
Abstract
A novel bacterium, designed strain S38T, was isolated from the deep-sea sediment of Pacmanus hydrothermal field in Manus Basin. The isolate was gram-positive, aerobic, motile, and was defined by endospore-forming rods. Strain S38T grew at 16-38 °C, pH 6-8, and in the presence of 0-7% (w/v) NaCl. Based on 16S rRNA gene sequence, S38T was grouped into the genus Fictibacillus and was most closely related to Fictibacillus phosphorivorans CCM 8426T (97.8%), Fictibacillus nanhaiensis DSM 23009T (97.8%), Fictibacillus halophilus DSM 100124T (97.7%), and Fictibacillus barbaricus DSM 14730T (97.5%). The diagnostic diamino acid of the cell wall was meso-diaminopimelic acid. The major fatty acids were iso-C15:0 and anteiso-C15:0. MK-7 was the predominant respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine were the major polar lipids. The genomic DNA G + C content was 46.8 mol%. Phylogenetic analysis, DNA-DNA relatedness, and phenotypic characteristics supported that strain S38T represents a novel species within the genus Fictibacillus, for which the name Fictibacillus iocasae sp. nov. was proposed. The type strain is S38T (= KCTC 33865T = DSM 104298T = CGMCC 1.16031T).
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4.
A comparative study revealed first insights into the diversity and metabolisms of the microbial communities in the sediments of Pacmanus and Desmos hydrothermal fields.
Wang, HL, Zhang, J, Sun, QL, Lian, C, Sun, L
PloS one. 2017;(7):e0181048
Abstract
Currently, little is known about the microbial diversity in the sediments of Pacmanus and Desmos hydrothermal fields in Manus Basin. In this study, Illumina-based sequencing of 16S rRNA gene amplicons and metagenomic analysis were conducted to investigate the microbial populations and metabolic profiles in the sediments from four different regions in Pacmanus and Desmos hydrothermal fields. It was found that Gammaproteobacteria and Thaumarchaeota were the most abundant bacterial and archaeal populations, respectively. The autotrophic prokaryotes in the four communities probably fixed CO2 via four major pathways, i.e. Calvin-Benson-Bassham cycle, reductive acetyl-CoA cycle, rTCA cycle, and 3-hydroxypropionate/4-hydroxybutyrate cycle. Ammonia-oxidizing Thaumarchaeota, nitrifiers, denitrifiers, and sulfur oxidizers belonging to the subgroups of Proteobacteria (e.g., alpha, beta, gamma, and epsilon), Nitrospira, and Nitrospina, and sulfate-reducing Desulfobacterales likely played critical roles in nitrogen and sulfur cycling, in which ammonia, sulfur compounds, and hydrogen could be utilized as potential energy sources. These findings revealed new insights into the operational mechanism of the microbial communities associated with Pacmanus and Desmos hydrothermal fields.
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5.
Microbial diversity in the deep-sea sediments of Iheya North and Iheya Ridge, Okinawa Trough.
Zhang, J, Sun, QL, Zeng, ZG, Chen, S, Sun, L
Microbiological research. 2015;:43-52
Abstract
In this study, we analyzed the bacterial and archaeal diversities of the deep-sea sediments in Iheya North and Iheya Ridge, Okinawa Trough, using the high-throughput sequencing technology of Illumina MiSeq 2500 platform. Four samples (IN1, IN2, IR1 and IR2) were used in this study, of which IN1 and IN2 were located at regions close to and distant, respectively, from the active hydrothermal vents in Iheya North, while IR1 and IR2 were located at regions close to and distant, respectively, from the active hydrothermal vents in Iheya Ridge. The four samples were rich in different metal elements. Sequence analysis based on the V3-V4 regions of 16S rDNA gene obtained 170,363 taxon tags, including 122,920 bacterial tags and 47,433 archaeal tags, which cover 31 phyla, 50 classes, 59 orders, 87 families, and 138 genera. Overall, the microbial communities in all samples were dominated by bacteria, in which Proteobacteria was the largest phylum, followed by Chloroflexi, Firmicutes, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Nitrospirae, which together accounted for 64.6% of the total taxon tags. In contrast to the high bacterial diversities, the archaeal diversity was low and dominated by Thaumarchaeota, which accounted for 22.9% of the total taxon tags. Comparative analysis showed that (i) IN2 and IR2 exhibited more microbial richness than IN1 and IR1, (ii) IR1 and IR2 exhibited higher microbial diversities than IN1 and IN2, (iii) samples from Iheya Ridge and Iheya North fell into two groups based on principle component analysis. Furthermore, microbes potentially involved in sulfur, nitrogen, and metal metabolism and cycling were detected in all samples. These results provide for the first time a comparative picture of the microbial diversities in the sediments of Iheya North and Iheya Ridge and indicate that geological features and distance from active hydrothermal vents likely play important roles in the shaping of microbial community structure.