Jiasong Fang - Academia.edu (original) (raw)

Papers by Jiasong Fang

Research paper thumbnail of Complete genome sequence of a multiple-stress-tolerant bacterium Halomonas piezotolerans NBT06E8T isolated from a deep-sea sediment sample of the New Britain Trench

Research paper thumbnail of Additional file 5 of Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep

Additional file 5: Table S5. Deep metagenomic sequencing on the Challenger Deep sediment samples ... more Additional file 5: Table S5. Deep metagenomic sequencing on the Challenger Deep sediment samples and assembly.

Research paper thumbnail of Additional file 2 of Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep

Additional file 2: Table S2. Concentrations of nutrient ions NO3-, NO2-, PO4-, NH4+, and SO42- in... more Additional file 2: Table S2. Concentrations of nutrient ions NO3-, NO2-, PO4-, NH4+, and SO42- in porewater of the samples.

Research paper thumbnail of Additional file 1 of Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep

Additional file 1: Table S1. Geochemical characterization of the sediment samples from Challenger... more Additional file 1: Table S1. Geochemical characterization of the sediment samples from Challenger Deep.

Research paper thumbnail of Additional file 8 of Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep

Additional file 8: Table S8. The metabolic characteristics of the six major the Challenger Deep F... more Additional file 8: Table S8. The metabolic characteristics of the six major the Challenger Deep Fungi groups, and detailed information of the carbohydrate-active enzyme family (CAZymes) and peptidase family genes detected in major fungal groups.

Research paper thumbnail of Additional file 9 of Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep

Additional file 9: Table S9. List of host prediction for the Challenger Deep virome. For each pre... more Additional file 9: Table S9. List of host prediction for the Challenger Deep virome. For each prediction, the type of signal (blastn, CRISPR, tetranucleotide composition), the host sequence used for the prediction alongside its affiliation, and the strength of the prediction (length of the blastn match, number of mismatches in the CRISPR spacer, and distance between viral and host tetranucleotide frequencies vectors) are indicated.

Research paper thumbnail of Additional file 12 of Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep

Additional file 12: Table S12. The taxonomic assignment of the 1070 bacterial isolates. Their tax... more Additional file 12: Table S12. The taxonomic assignment of the 1070 bacterial isolates. Their taxonomy was assigned based on 16S rRNA gene sequences using NCBI rRNA/ITS databases.

Research paper thumbnail of Xiao et al., raw data about brGDGTs in Mariana Trench and global environmental settings

This supplemetnary table contain original data on branched glycerol dialkyl glycerol tetraethers ... more This supplemetnary table contain original data on branched glycerol dialkyl glycerol tetraethers (brGDGTs) in Mariana Trench, as welll as literature reported brGDGT data from soil, river, lake adn marine samples.

Research paper thumbnail of A Sediment Sample Transfer, Handing, Encapsulation and Analysis Subsystem Device in State of Fidelity

OCEANS 2019 - Marseille, 2019

The sediment pressure-holding transfer subsystem is mainly designed for 10,000-meter seabed sedim... more The sediment pressure-holding transfer subsystem is mainly designed for 10,000-meter seabed sediments. This set of equipment mainly uses high-pressure pumps and cooling circulation systems to keep the whole set of equipment in the seabed in-situ environment, including pressure and temperature. The sediment samples taken from the 10,000-meter sampler were transferred in the in-situ state of the seabed and transferred directly to the laboratory culture kettle for subsequent research. This paper mainly introduces the specific design, working process, calculation of key components and ANSYS analysis and maritime arrangement of the pressure-holding transfer subsystem.

Research paper thumbnail of Value-Added Site Monitoring and Infrastructure Maintenance for In-Situ Bioremediation Technology Development

: The original project was funded in FY '98 and designed to achieve three main objectives. Th... more : The original project was funded in FY '98 and designed to achieve three main objectives. These are: 1) The continued serial monitoring of contaminant, geochemical constituents, and indicators of bioremediation at two actual sites of fuel and/or solvent contamination during a BTEX-MTBE natural gradient tracer test conducted at the former Wurtsmith AFB near Oscoda, MI, 2) The improvement and maintenance of the existing historical database on the progress of intrinsic (i.e. natural) bioremediation at these sites which extends from the late 1980's, and 3) Statistical analyses of the impact of observed spatial and temporal variability in contaminant source mass distributions on the reliability of estimates of rates of net mass removal (i.e. the progress of bioremediation), and projected timeframes for site closure.

Research paper thumbnail of Response of secondary metabolites of hadal fungi to high hydrostatic pressure

Goldschmidt2021 abstracts, 2021

Research paper thumbnail of Probing the sedimentary DOM in the deepest sector of Earth’s surface

Goldschmidt2021 abstracts, 2021

Research paper thumbnail of Transitions in microbial communities along two sediment corescollected from the landward walls of the New Britain trench

Goldschmidt2021 abstracts, 2021

Research paper thumbnail of Design of A Deep-ocean Sampling Device for Microorganisms with In-situ Filtration and Preservation

OCEANS 2019 - Marseille, 2019

Microorganisms play an irreplaceable role in ocean ecological environment and material circulatio... more Microorganisms play an irreplaceable role in ocean ecological environment and material circulation due to their pervasiveness, abundance, and metabolic diversity [1] . With extreme conditions of low temperature, high pressure and high salinity, microorganisms in deep ocean usually have some unique characteristics. In recent years, more and more researchers have turned their attention to the sampling as well as analysis of deep-ocean microorganisms [2] . Study on the genetic material and information of deep-ocean microorganisms not only can help us understand the origin and evolution of deep-ocean life, but also has great significance for the development of biological enzymes and medicines.

Research paper thumbnail of Hanstruepera crassostreae He et al. 2018 is a later heterotypic synonym of Pseudobizionia ponticola Park et al. 2018

International Journal of Systematic and Evolutionary Microbiology, 2021

Hanstruepera crassostreae L53T was compared with Pseudobizionia ponticola MM-14T to examine the t... more Hanstruepera crassostreae L53T was compared with Pseudobizionia ponticola MM-14T to examine the taxonomic relationship between the two type strains. The 16S rRNA gene sequence of H. crassostreae L53T had complete similarity (100.0%) to that of P. ponticola MM-14T. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus Pseudobizionia . Draft genomic comparison between the two strains revealed an average nucleotide identity of 96.9 % and a digital DNA–DNA hybridization estimate of 75.3±2.8 %, strongly indicating that the two strains represented a single species. In addition, neither strain displayed any striking difference in metabolic, physiological or chemotaxonomic features. Therefore, we propose that Hanstruepera crassostreae is a later heterotypic synonym of Pseudobizionia ponticola .

Research paper thumbnail of Research on Pressure-Retaining Performance of Transfer Device for Abyssal Sediments

Marine Technology Society Journal, 2021

In order to retain the activity of microorganisms from abyssal sediment samples, this paper propo... more In order to retain the activity of microorganisms from abyssal sediment samples, this paper proposes the first device that can be used for the pressure-retaining transfer of seabed sediment samples. The device can transfer sediment from the sampler to the sample processing container and maintain the in-situ pressure of the sample, with the maximum pressure up to 100 MPa. The sample is stirred in the lower cavity of the transfer container and divided into the culture container by pressure difference control. In order to maintain the internal pressure of the device, a pressure stabilization system was designed, and a self-designed conical seal and right-angle combined seal were proposed. The high-pressure test is carried out through the experimental platform, the pressure is maintained for 1.5 h, and the pressure is actively reduced to verify the stability of the pressure stabilization system. The experimental results show that the pressure-retaining performance of the device can meet...

Research paper thumbnail of The Unseen Majority of Microorganisms in Hadal Trenche Sediments Revealed by Molecular and Biogeochemical Techniques

Goldschmidt Abstracts, 2020

Research paper thumbnail of Metabacillus sediminilitoris sp. nov., a marine bacterium isolated from a tidal sediment

International Journal of Systematic and Evolutionary Microbiology, 2020

A Gram-stain-positive, endospore-forming, motile and rod-shaped bacterium, designated as strain D... more A Gram-stain-positive, endospore-forming, motile and rod-shaped bacterium, designated as strain DSL-17T, was isolated from a tidal sediment of the East China Sea and characterized phylogenetically and phenotypically. The strain could grow at 16–47 °C (optimum 37 °C), at pH 6.0–10.0 (optimum 6.0) and with 1–7% (w/v) NaCl (optimum 3 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DSL-17T was related to members of the genus Metabacillus and shared the highest similarity with Metabacillus litoralis SW-211T (98.6 %), followed by Metabacillus halosaccharovorans E33T (97.9 %), Metabacillus crassostreae JSM 100118T (97.7 %), Metabacillus niabensis 4T19T (97.7 %) and Metabacillus malikii NCCP-662T (97.5 %). 16S rRNA gene sequence similarities between strain DSL-17T and other members of the genus Metabacillus were below 96.6 %. The sole respiratory quinone was MK-7. Strain DSL-17T had a cell-wall peptidoglycan based on meso-diaminopimelic acid. The polar lipids w...

Research paper thumbnail of Bulk and Active Sediment Prokaryotic Communities in the Mariana and Mussau Trenches

Frontiers in Microbiology, 2020

Surprisingly high rates of microbial respiration have recently been reported in hadal trench sedi... more Surprisingly high rates of microbial respiration have recently been reported in hadal trench sediment, yet the potentially active microorganisms and specific microbemicrobe relationships in trench sediment are largely unknown. We investigated the bulk and active prokaryotic communities and co-occurrence interactions of different lineages in vertically sectioned sediment cores taken from the deepest points of the Mariana and Mussau Trenches. Analysis on species novelty revealed for the first time the high rate of novel lineages in the microbial communities of the hadal trenches. Using 95, 97, and 99% similarity as thresholds, averagely 22.29, 32.3, and 64.1% of total OTUs retrieved from sediments of the two trenches were identified as the potentially novel lineages, respectively. The compositions of the potentially active communities, revealed via ribosomal RNA (rRNA), were significantly different from those of bulk communities (rDNA) in all samples from both trenches. The dominant taxa in bulk communities generally accounted for low proportions in the rRNA libraries, signifying that the abundance was not necessarily related to community functions in the hadal sediments. The potentially active communities showed high diversity and composed primarily of heterotrophic lineages, supporting their potential contributions in organic carbon consumption. Network analysis revealed high modularity and non-random cooccurrence of phylogenetically unrelated taxa, indicating highly specified micro-niches and close microbial interactions in the hadal sediments tested. Combined analysis of activity potentials and network keystone scores revealed significance of phyla Chloroflexi and Gemmatimonadetes, as well as several potentially alkane-degrading taxa in maintaining microbial interactions and functions of the trench communities. Overall, our results demonstrate that the hadal trenches harbor diverse, closely interacting, and active microorganisms, despite the extreme environmental conditions.

Research paper thumbnail of Georhizobium profundi gen. nov., sp. nov., a piezotolerant bacterium isolated from a deep-sea sediment sample of the New Britain Trench

International Journal of Systematic and Evolutionary Microbiology, 2019

A novel alphaproteobacterium, strain WS11T, was isolated from a deep-sea sediment sample collecte... more A novel alphaproteobacterium, strain WS11T, was isolated from a deep-sea sediment sample collected from the New Britain Trench. The full-length 16S rRNA gene of strain WS11T had the highest sequence similarity of 97.6 % to Rhizobium subbaraonis JC85T, followed by Mycoplana ramosa DSM 7292T (96.9 %) and Rhizobium azooxidifex Po 20/26T (96.8 %). Phylogenetic analysis of concatenated 16S rRNA, atpD and recA gene sequences showed that strain WS11T was deeply separated from the species within the family Rhizobiaceae. Phylogenomic analysis based on the whole-genome protein sequences showed that strain WS11T formed an independent monophyletic branch in the family Rhizobiaceae, paralleled with the species in the families Brucellaceae and Phyllobacteriaceae within the order Rhizobiales. Cells were Gram-stain-negative, oxidase- and catalase-positive, and aerobic short rods (1.5-2.4×0.9-1.0 µm). Growth was observed at salinities ranging from 0 to 5% (optimum, 1 %), from pH 6.5 to 9 (optimum, pH 7) and at temperatures between 20 and 30 °C (optimum, 28 °C). Strain WS11T was piezotolerant, growing optimally at 0.1 MPa (range 0.1-70 MPa). The main fatty acid was summed feature 8 (C18 : 1 ω7c/C18 : 1 ω 6c). The sole respiratory quinone was ubiquinone-10 (Q-10). The predominant polar lipids were phosphatidylcholine, two unidentified aminophospholipids and an unidentified phospholipid. The genome size was about 4.36 Mbp and the G+C content was 62.3 mol%. The combined genotypic and phenotypic data show that strain WS11T represents a novel species of a novel genus in the family Rhizobiaceae, for which the name Georhizobium profundi gen. nov., sp. nov. is proposed (type strain WS11T=MCCC 1K03498T=KCTC 62439T).

Research paper thumbnail of Complete genome sequence of a multiple-stress-tolerant bacterium Halomonas piezotolerans NBT06E8T isolated from a deep-sea sediment sample of the New Britain Trench

Research paper thumbnail of Additional file 5 of Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep

Additional file 5: Table S5. Deep metagenomic sequencing on the Challenger Deep sediment samples ... more Additional file 5: Table S5. Deep metagenomic sequencing on the Challenger Deep sediment samples and assembly.

Research paper thumbnail of Additional file 2 of Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep

Additional file 2: Table S2. Concentrations of nutrient ions NO3-, NO2-, PO4-, NH4+, and SO42- in... more Additional file 2: Table S2. Concentrations of nutrient ions NO3-, NO2-, PO4-, NH4+, and SO42- in porewater of the samples.

Research paper thumbnail of Additional file 1 of Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep

Additional file 1: Table S1. Geochemical characterization of the sediment samples from Challenger... more Additional file 1: Table S1. Geochemical characterization of the sediment samples from Challenger Deep.

Research paper thumbnail of Additional file 8 of Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep

Additional file 8: Table S8. The metabolic characteristics of the six major the Challenger Deep F... more Additional file 8: Table S8. The metabolic characteristics of the six major the Challenger Deep Fungi groups, and detailed information of the carbohydrate-active enzyme family (CAZymes) and peptidase family genes detected in major fungal groups.

Research paper thumbnail of Additional file 9 of Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep

Additional file 9: Table S9. List of host prediction for the Challenger Deep virome. For each pre... more Additional file 9: Table S9. List of host prediction for the Challenger Deep virome. For each prediction, the type of signal (blastn, CRISPR, tetranucleotide composition), the host sequence used for the prediction alongside its affiliation, and the strength of the prediction (length of the blastn match, number of mismatches in the CRISPR spacer, and distance between viral and host tetranucleotide frequencies vectors) are indicated.

Research paper thumbnail of Additional file 12 of Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep

Additional file 12: Table S12. The taxonomic assignment of the 1070 bacterial isolates. Their tax... more Additional file 12: Table S12. The taxonomic assignment of the 1070 bacterial isolates. Their taxonomy was assigned based on 16S rRNA gene sequences using NCBI rRNA/ITS databases.

Research paper thumbnail of Xiao et al., raw data about brGDGTs in Mariana Trench and global environmental settings

This supplemetnary table contain original data on branched glycerol dialkyl glycerol tetraethers ... more This supplemetnary table contain original data on branched glycerol dialkyl glycerol tetraethers (brGDGTs) in Mariana Trench, as welll as literature reported brGDGT data from soil, river, lake adn marine samples.

Research paper thumbnail of A Sediment Sample Transfer, Handing, Encapsulation and Analysis Subsystem Device in State of Fidelity

OCEANS 2019 - Marseille, 2019

The sediment pressure-holding transfer subsystem is mainly designed for 10,000-meter seabed sedim... more The sediment pressure-holding transfer subsystem is mainly designed for 10,000-meter seabed sediments. This set of equipment mainly uses high-pressure pumps and cooling circulation systems to keep the whole set of equipment in the seabed in-situ environment, including pressure and temperature. The sediment samples taken from the 10,000-meter sampler were transferred in the in-situ state of the seabed and transferred directly to the laboratory culture kettle for subsequent research. This paper mainly introduces the specific design, working process, calculation of key components and ANSYS analysis and maritime arrangement of the pressure-holding transfer subsystem.

Research paper thumbnail of Value-Added Site Monitoring and Infrastructure Maintenance for In-Situ Bioremediation Technology Development

: The original project was funded in FY '98 and designed to achieve three main objectives. Th... more : The original project was funded in FY '98 and designed to achieve three main objectives. These are: 1) The continued serial monitoring of contaminant, geochemical constituents, and indicators of bioremediation at two actual sites of fuel and/or solvent contamination during a BTEX-MTBE natural gradient tracer test conducted at the former Wurtsmith AFB near Oscoda, MI, 2) The improvement and maintenance of the existing historical database on the progress of intrinsic (i.e. natural) bioremediation at these sites which extends from the late 1980's, and 3) Statistical analyses of the impact of observed spatial and temporal variability in contaminant source mass distributions on the reliability of estimates of rates of net mass removal (i.e. the progress of bioremediation), and projected timeframes for site closure.

Research paper thumbnail of Response of secondary metabolites of hadal fungi to high hydrostatic pressure

Goldschmidt2021 abstracts, 2021

Research paper thumbnail of Probing the sedimentary DOM in the deepest sector of Earth’s surface

Goldschmidt2021 abstracts, 2021

Research paper thumbnail of Transitions in microbial communities along two sediment corescollected from the landward walls of the New Britain trench

Goldschmidt2021 abstracts, 2021

Research paper thumbnail of Design of A Deep-ocean Sampling Device for Microorganisms with In-situ Filtration and Preservation

OCEANS 2019 - Marseille, 2019

Microorganisms play an irreplaceable role in ocean ecological environment and material circulatio... more Microorganisms play an irreplaceable role in ocean ecological environment and material circulation due to their pervasiveness, abundance, and metabolic diversity [1] . With extreme conditions of low temperature, high pressure and high salinity, microorganisms in deep ocean usually have some unique characteristics. In recent years, more and more researchers have turned their attention to the sampling as well as analysis of deep-ocean microorganisms [2] . Study on the genetic material and information of deep-ocean microorganisms not only can help us understand the origin and evolution of deep-ocean life, but also has great significance for the development of biological enzymes and medicines.

Research paper thumbnail of Hanstruepera crassostreae He et al. 2018 is a later heterotypic synonym of Pseudobizionia ponticola Park et al. 2018

International Journal of Systematic and Evolutionary Microbiology, 2021

Hanstruepera crassostreae L53T was compared with Pseudobizionia ponticola MM-14T to examine the t... more Hanstruepera crassostreae L53T was compared with Pseudobizionia ponticola MM-14T to examine the taxonomic relationship between the two type strains. The 16S rRNA gene sequence of H. crassostreae L53T had complete similarity (100.0%) to that of P. ponticola MM-14T. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus Pseudobizionia . Draft genomic comparison between the two strains revealed an average nucleotide identity of 96.9 % and a digital DNA–DNA hybridization estimate of 75.3±2.8 %, strongly indicating that the two strains represented a single species. In addition, neither strain displayed any striking difference in metabolic, physiological or chemotaxonomic features. Therefore, we propose that Hanstruepera crassostreae is a later heterotypic synonym of Pseudobizionia ponticola .

Research paper thumbnail of Research on Pressure-Retaining Performance of Transfer Device for Abyssal Sediments

Marine Technology Society Journal, 2021

In order to retain the activity of microorganisms from abyssal sediment samples, this paper propo... more In order to retain the activity of microorganisms from abyssal sediment samples, this paper proposes the first device that can be used for the pressure-retaining transfer of seabed sediment samples. The device can transfer sediment from the sampler to the sample processing container and maintain the in-situ pressure of the sample, with the maximum pressure up to 100 MPa. The sample is stirred in the lower cavity of the transfer container and divided into the culture container by pressure difference control. In order to maintain the internal pressure of the device, a pressure stabilization system was designed, and a self-designed conical seal and right-angle combined seal were proposed. The high-pressure test is carried out through the experimental platform, the pressure is maintained for 1.5 h, and the pressure is actively reduced to verify the stability of the pressure stabilization system. The experimental results show that the pressure-retaining performance of the device can meet...

Research paper thumbnail of The Unseen Majority of Microorganisms in Hadal Trenche Sediments Revealed by Molecular and Biogeochemical Techniques

Goldschmidt Abstracts, 2020

Research paper thumbnail of Metabacillus sediminilitoris sp. nov., a marine bacterium isolated from a tidal sediment

International Journal of Systematic and Evolutionary Microbiology, 2020

A Gram-stain-positive, endospore-forming, motile and rod-shaped bacterium, designated as strain D... more A Gram-stain-positive, endospore-forming, motile and rod-shaped bacterium, designated as strain DSL-17T, was isolated from a tidal sediment of the East China Sea and characterized phylogenetically and phenotypically. The strain could grow at 16–47 °C (optimum 37 °C), at pH 6.0–10.0 (optimum 6.0) and with 1–7% (w/v) NaCl (optimum 3 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DSL-17T was related to members of the genus Metabacillus and shared the highest similarity with Metabacillus litoralis SW-211T (98.6 %), followed by Metabacillus halosaccharovorans E33T (97.9 %), Metabacillus crassostreae JSM 100118T (97.7 %), Metabacillus niabensis 4T19T (97.7 %) and Metabacillus malikii NCCP-662T (97.5 %). 16S rRNA gene sequence similarities between strain DSL-17T and other members of the genus Metabacillus were below 96.6 %. The sole respiratory quinone was MK-7. Strain DSL-17T had a cell-wall peptidoglycan based on meso-diaminopimelic acid. The polar lipids w...

Research paper thumbnail of Bulk and Active Sediment Prokaryotic Communities in the Mariana and Mussau Trenches

Frontiers in Microbiology, 2020

Surprisingly high rates of microbial respiration have recently been reported in hadal trench sedi... more Surprisingly high rates of microbial respiration have recently been reported in hadal trench sediment, yet the potentially active microorganisms and specific microbemicrobe relationships in trench sediment are largely unknown. We investigated the bulk and active prokaryotic communities and co-occurrence interactions of different lineages in vertically sectioned sediment cores taken from the deepest points of the Mariana and Mussau Trenches. Analysis on species novelty revealed for the first time the high rate of novel lineages in the microbial communities of the hadal trenches. Using 95, 97, and 99% similarity as thresholds, averagely 22.29, 32.3, and 64.1% of total OTUs retrieved from sediments of the two trenches were identified as the potentially novel lineages, respectively. The compositions of the potentially active communities, revealed via ribosomal RNA (rRNA), were significantly different from those of bulk communities (rDNA) in all samples from both trenches. The dominant taxa in bulk communities generally accounted for low proportions in the rRNA libraries, signifying that the abundance was not necessarily related to community functions in the hadal sediments. The potentially active communities showed high diversity and composed primarily of heterotrophic lineages, supporting their potential contributions in organic carbon consumption. Network analysis revealed high modularity and non-random cooccurrence of phylogenetically unrelated taxa, indicating highly specified micro-niches and close microbial interactions in the hadal sediments tested. Combined analysis of activity potentials and network keystone scores revealed significance of phyla Chloroflexi and Gemmatimonadetes, as well as several potentially alkane-degrading taxa in maintaining microbial interactions and functions of the trench communities. Overall, our results demonstrate that the hadal trenches harbor diverse, closely interacting, and active microorganisms, despite the extreme environmental conditions.

Research paper thumbnail of Georhizobium profundi gen. nov., sp. nov., a piezotolerant bacterium isolated from a deep-sea sediment sample of the New Britain Trench

International Journal of Systematic and Evolutionary Microbiology, 2019

A novel alphaproteobacterium, strain WS11T, was isolated from a deep-sea sediment sample collecte... more A novel alphaproteobacterium, strain WS11T, was isolated from a deep-sea sediment sample collected from the New Britain Trench. The full-length 16S rRNA gene of strain WS11T had the highest sequence similarity of 97.6 % to Rhizobium subbaraonis JC85T, followed by Mycoplana ramosa DSM 7292T (96.9 %) and Rhizobium azooxidifex Po 20/26T (96.8 %). Phylogenetic analysis of concatenated 16S rRNA, atpD and recA gene sequences showed that strain WS11T was deeply separated from the species within the family Rhizobiaceae. Phylogenomic analysis based on the whole-genome protein sequences showed that strain WS11T formed an independent monophyletic branch in the family Rhizobiaceae, paralleled with the species in the families Brucellaceae and Phyllobacteriaceae within the order Rhizobiales. Cells were Gram-stain-negative, oxidase- and catalase-positive, and aerobic short rods (1.5-2.4×0.9-1.0 µm). Growth was observed at salinities ranging from 0 to 5% (optimum, 1 %), from pH 6.5 to 9 (optimum, pH 7) and at temperatures between 20 and 30 °C (optimum, 28 °C). Strain WS11T was piezotolerant, growing optimally at 0.1 MPa (range 0.1-70 MPa). The main fatty acid was summed feature 8 (C18 : 1 ω7c/C18 : 1 ω 6c). The sole respiratory quinone was ubiquinone-10 (Q-10). The predominant polar lipids were phosphatidylcholine, two unidentified aminophospholipids and an unidentified phospholipid. The genome size was about 4.36 Mbp and the G+C content was 62.3 mol%. The combined genotypic and phenotypic data show that strain WS11T represents a novel species of a novel genus in the family Rhizobiaceae, for which the name Georhizobium profundi gen. nov., sp. nov. is proposed (type strain WS11T=MCCC 1K03498T=KCTC 62439T).