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Lin SY, Lin TY, Hameed A, Tang YS, Young CC. Neopusillimonas aromaticivorans sp. nov. isolated from poultry manure. Int J Syst Evol Microbiol 2023; 73. [PMID: 37962187 DOI: 10.1099/ijsem.0.006146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023] Open
Abstract
A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-YST667T, isolated from poultry manure sampled in Taiwan. The cells were observed to be aerobic, motile and non-spore-forming rods, displaying positive reactions for oxidase. Optimal growth of CC-YST667T was observed at 25 °C, pH 8.0 and with 1 % (w/v) NaCl. The polar lipid profile consisted of phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and multiple unidentified polar lipids. The major polyamine was spermidine. The major cellular fatty acids (>5 %) included C16 : 0, C17 : 0cyclo, C19 : 0cyclo ω8c and C14 : 0 3OH/iso-C16 : 1 I. On the basis of the results of analysis of 16S rRNA gene sequences, this isolate showed the closest phylogenetic relationship with 'Neopusillimonas minor' (with 98.2 % similarity) and Paralcaligenes ureilyticus (with 97.3 % similarity) of the family Alcaligenaceae. The draft genome, (3.3 Mb) with a DNA G+C content of 57.2 mol%, harboured various genes involved in the biodegradation of aromatic hydrocarbons. CC-YST667T shared highest orthologous average nucleotide identity (OrthoANI) with the type strains of species of of the genera Neopusillimonas (72.4‒77.9 %, n=2), Pusillimonas (72.8‒73.0 %, n=2) and Pollutimonas (71.7‒73.0 %, n=5). On the basis of its distinct phylogenetic, phenotypic and chemotaxonomic traits together with the results of comparative 16S rRNA gene sequencing, OrthoANI, digital DNA-DNA hybridization (DDH) and the phylogenomic placement, strain CC-YST667T is considered to represent a novel species of the genus Neopusillimonas, for which the name Neopusillimonas aromaticivorans sp. nov. is proposed. The type strain is CC-YST667T (=BCRC 81321T =JCM 34761T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung, 40227, Taiwan, ROC
| | - Tzu-Yu Lin
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte 575018, Mangalore, Karnataka, India
| | - Yu-Shan Tang
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung, 40227, Taiwan, ROC
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung, 40227, Taiwan, ROC
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, 145, XingDa Rd., Taichung, 40227, Taiwan, ROC
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Babich TL, Grouzdev DS, Sokolova DS, Tourova TP, Poltaraus AB, Nazina TN. Genome analysis of Pollutimonas subterranea gen. nov., sp. nov. and Pollutimonas nitritireducens sp. nov., isolated from nitrate- and radionuclide-contaminated groundwater, and transfer of several Pusillimonas species into three new genera Allopusillimonas, Neopusillimonas, and Mesopusillimonas. Antonie Van Leeuwenhoek 2023; 116:109-127. [PMID: 36244039 DOI: 10.1007/s10482-022-01781-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/28/2022] [Indexed: 02/01/2023]
Abstract
Two facultatively anaerobic, chemoorganoheterotrophic bacterial strains, designated JR1/69-2-13T and JR1/69-3-13T, were isolated from nitrate- and radionuclide-contaminated groundwater (Ozyorsk town, South Urals, Russia). Both strains were found to be motile, Gram-stain negative rod-shaped neutrophilic, psychrotolerant bacteria that grow within the temperature range from 5-10 to 33 °C at 0-3 (0-5)% NaCl (w/v). The major cellular fatty acids were identified as C16:0, C16:1 ω7c, C18:1 ω7c and C17:0 cyclo. The major polar lipids were found to consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol and unidentified aminophospholipids. The genomic G + C content of strains JR1/69-2-13T and JR1/69-3-13T was determined to be 57.2 and 57.9%, respectively. The 16S rRNA gene sequences of the strains showed high similarity between each other (98.6%) and to members of the genera Pusillimonas (96.8-98.4%) and Candidimonas (97.1-98.0%). The average nucleotide identity and digital DNA-DNA hybridization (dDDH) values among genomes of the new isolates and Pusillimonas and Candidimonas genomes were below 84.5 and 28.8%, respectively, i.e., below the thresholds for species delineation. Based on the phylogenomic, phenotypic and chemotaxonomic characterisation, we propose assignment of strains JR1/69-3-13T (= VKM B-3223T = KCTC 62615T) and JR1/69-2-13T (= VKM B-3222T = KCTC 62614T) to a new genus Pollutimonas as the type strains of two new species, Pollutimonas subterranea gen. nov., sp. nov. and Pollutimonas nitritireducens sp. nov., respectively. As a result of the taxonomic revision of the genus Pusillimonas, three novel genera, Allopusillimonas, Neopusillimonas, and Mesopusillimonas are also proposed; and Candidimonas bauzanensis is reclassified as Pollutimonas bauzanensis comb. nov. Genome analysis of the new isolates suggested molecular mechanisms of their adaptation to an environment highly polluted with nitrate and radionuclides.
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Affiliation(s)
- Tamara L Babich
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow, Russia, 119071
| | - Denis S Grouzdev
- SciBear OU, Tartu mnt 67/1-13b, Kesklinna linnaosa, 10115, Tallinn, Estonia
| | - Diyana S Sokolova
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow, Russia, 119071
| | - Tatyana P Tourova
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow, Russia, 119071
| | - Andrey B Poltaraus
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32, bld. 1 Vavilova, Moscow, Russia, 119991
| | - Tamara N Nazina
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow, Russia, 119071.
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Absence of oxygen effect on microbial structure and methane production during drying and rewetting events. Sci Rep 2022; 12:16570. [PMID: 36195651 PMCID: PMC9532411 DOI: 10.1038/s41598-022-20448-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/13/2022] [Indexed: 11/15/2022] Open
Abstract
Natural environments with frequent drainage experience drying and rewetting events that impose fluctuations in water availability and oxygen exposure. These relatively dramatic cycles profoundly impact microbial activity in the environment and subsequent emissions of methane and carbon dioxide. In this study, we mimicked drying and rewetting events by submitting methanogenic communities from strictly anaerobic environments (anaerobic digestors) with different phylogenetic structures to consecutive desiccation events under aerobic (air) and anaerobic (nitrogen) conditions followed by rewetting. We showed that methane production quickly recovered after each rewetting, and surprisingly, no significant difference was observed between the effects of the aerobic or anaerobic desiccation events. There was a slight change in the microbial community structure and a decrease in methane production rates after consecutive drying and rewetting, which can be attributed to a depletion of the pool of available organic matter or the inhibition of the methanogenic communities. These observations indicate that in comparison to the drying and rewetting events or oxygen exposure, the initial phylogenetic structure and the organic matter quantity and quality exhibited a stronger influence on the methanogenic communities and overall microbial community responses. These results change the current paradigm of the sensitivity of strict anaerobic microorganisms to oxygen exposure.
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Lin SY, Hameed A, Tsai CF, Tang YS, Young CC. Pusillimonas faecipullorum sp. nov., isolated from the poultry manure. Arch Microbiol 2022; 204:256. [PMID: 35414138 DOI: 10.1007/s00203-022-02859-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 11/02/2022]
Abstract
A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-YST705T, isolated from poultry manure sampled in Taiwan. Cells of strain CC-YST705T were aerobic, Gram-stain-negative, non-motile, non-spore-forming rods, displaying positive reactions for catalase, oxidase and β-glucosidase. Optimal growth occurred at 30 °C and pH 8. Strain CC-YST705T shared the highest (> 96.0%) pair-wise 16S rRNA gene sequence similarity with Pusillimonas noertemannii (96.7%), followed by Pusillimonas caeni (96.6%), Eoetvoesia caeni (96.1%) and Paracandidimonas soli (96.0%), and formed a distinct phyletic lineage associate with the clade that accommodated Pusillimonas species. The draft genome (3.1 Mb) having 57.4 mol % G + C content contained genes involved in the catabolism of aromatic hydrocarbons. The orthologous average nucleotide identity (OrthoANI) values were 62.8-73.1% (n = 8), 72.6 (n = 1), 71.5% (n = 1) compared within the type strains of the genera Pusillimonas, Eoetvoesia and Paracandidimonas, respectively. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminolipid, two unidentified phospholipids and five unidentified lipids. The major polyamine was spermidine. The dominating cellular fatty acids (> 5%) included C12:0, C16:0, C17:0 cyclo, C19:0 cyclo ω8c and 2 C14:0 3OH/iso-C16:1 I. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, OrthoANI, digital DDH, and the phylogenomic placement, strain CC-YST705T is considered to represent a novel species of the genus Pusillimonas, for which the name Pusillimonas faecipullorum sp. nov. is proposed. The type strain is CC-YST705T (= BCRC 81285 T = JCM 34168 T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung, 40227, Taiwan
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore, Karnataka, India
| | - Chia-Fang Tsai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung, 40227, Taiwan
| | - Yu-Shan Tang
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung, 40227, Taiwan
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung, 40227, Taiwan. .,Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan.
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Yao L, Jia Y, Lai YH, Xue F, Wang JL. Pusillimonas minor sp. nov., a novel member of the genus Pusillimonas isolated from activated sludge. Int J Syst Evol Microbiol 2022; 72. [PMID: 35451948 DOI: 10.1099/ijsem.0.005323] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel pale white-pigmented bacterial strain designated YC-7-48T was isolated from activated sludge in China. Cells of the strain, which grew at 15-37 °C (optimum at 30 °C) and pH 6.0-9.0 (optimum at 7.0), were Gram-stain-negative, rod-shaped and motile. Strain YC-7-48T had 97.4-97.1% 16S rRNA gene sequence similarity to type strains of eight species in the genera Pusillimonas, Eoetvoesia, Paralcaligenes, Parapusillimonas and Paracandidimonas of the family Alcaligenaceae. Phylogenetic analysis based on 16S rRNA gene sequencing placed the strain on a separate branch in the genus Pusillimonas and showed that it exhibited 97.4, 97.3 and 96.6% similarity to Pusillimonas caeni EBR-8-1T, Pusillimonas noertemannii BN9T and Pusillimonas maritima 17-4AT, respectively. The genome size of strain YC-7-48T was 3202438 bp, with 54.3 mol% G+C content. According to the genome analysis, YC-7-48T encodes several heavy metal resistance proteins and enzymes related to the metabolism of nicotine and aromatic compounds. The results of digital DNA-DNA hybridization and average nucleotide identity analyses based on whole genome sequences between strain YC-7-48T and the closely related strains indicated that the strain represented a new species of the genus Pusillimonas. The chemotaxonomic results identified Q-8 as the predominant respiratory quinone, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol and two unidentified aminolipids as the major polar lipids, and C16:0 (27.4 %), C17:0 cyclo (22.0 %), C18:0 (11.7 %) and C19:0 cyclo ω8c (9.5 %) as the major fatty acids. Thus, based on morphological, chemotaxonomic and phylogenetic characterization and genomic data, we proposed that the isolate is a representative of a novel species named Pusillimonas minor sp. nov., with the type strain YC-7-48T (=CGMCC 1.17466T=KACC 21349T).
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Affiliation(s)
- Li Yao
- College of Marine and Bio-Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224000, PR China
| | - Yan Jia
- College of Marine and Bio-Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224000, PR China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 210000, PR China
| | - Yu-Han Lai
- College of Marine and Bio-Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224000, PR China
| | - Fei Xue
- College of Marine and Bio-Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224000, PR China
| | - Jia-Lian Wang
- College of Marine and Bio-Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224000, PR China
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6
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Li J, Qi M, Lai Q, Dong C, Liu X, Wang G, Shao Z. Pusillimonas maritima sp. nov., isolated from surface seawater. Int J Syst Evol Microbiol 2020; 70:3483-3490. [PMID: 32369004 DOI: 10.1099/ijsem.0.004202] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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).
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Affiliation(s)
- Jianyang Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China.,School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, PR China
| | - Mingming Qi
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Xiupian Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Guangyi Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
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The effect of the microalgae-bacteria microbiome on wastewater treatment and biomass production. Appl Microbiol Biotechnol 2019; 104:893-905. [PMID: 31828407 DOI: 10.1007/s00253-019-10246-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 10/13/2019] [Accepted: 11/05/2019] [Indexed: 10/25/2022]
Abstract
The use of microalgae for wastewater treatment has been proposed as a cost-effective method to produce biofuels while remediating waste streams. This study examined the microalgae biomass production rate, wastewater treatment efficiency, and prokaryotic organism microbiome associated with microalgae Chlorella sorokiniana cultivated on anaerobic digestate effluent. Final microalgae biomass concentrations from nine photobioreactors were highly variable and had values that ranged between 0.14 g/L and 0.90 g/L. Nutrient removal efficiencies for TN (total nitrogen), N-NH4 (ammonium nitrogen), and COD (chemical oxygen demand) ranged from 34% to 67%, 65% to 97%, and-60% to 14%, respectively. Analysis of individual OTUs (operational taxonomic units) from the microbial community revealed that microalgae biomass concentrations were significantly correlated with the relative abundance of OTUs in the genus Pusillimonas. Predictive metagenomic analyses identified additional correlations associated with biomass production and nutrient removal. These results suggest that the microbial community present during microalgae cultivation on wastewater can impact the performance of the system for biomass production and wastewater treatment.
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Koh HW, Song MS, Do KT, Kim H, Park SJ. Pusillimonas thiosulfatoxidans sp. nov., a thiosulfate oxidizer isolated from activated sludge. Int J Syst Evol Microbiol 2019; 69:1041-1046. [DOI: 10.1099/ijsem.0.003266] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, motile bacterium, designated strain YE3T, was isolated from activated sludge obtained from a municipal wastewater treatment plant in Daejeon Metropolitan City, Republic of Korea. The cells were oxidase- and catalase-positive, and grew under aerobic conditions at 10–40 °C (optimum, 30 °C), with 1.0–8.0 % (w/v) NaCl (1.0 %) and at pH 5.5–9.0 (pH 7.0). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YE3T was most closely related to
Pusillimonas
harenae
KACC 14927T (98.2 % sequence similarity) and
Pusillimonas
ginsengisoli
KCTC 22046T (98.0 %). DNA–DNA relatedness values for strain YE3T and
P. harenae
KACC 14927T,
P. ginsengisoli
KCTC 22046T and
P. soli
KCTC 22455T were 28.7±2.27 %, 21.3±1.16 %, and 14.0±0.67 %, respectively. The genomic G+C content of the type strain YE3T was 59.3 mol%, as determined by whole-genome sequencing. The dominant fatty acids were C16 : 0 (39.2 %) and C17 : 0cyclo (37.5 %). The major polar lipids of strain YE3T were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Two aminophospholipids and four unidentified lipids were also detected. Furthermore, strain YE3T was able to oxidize thiosulfate under heterotrophic conditions. Based on the phenotypic, genotypic, chemotaxonomic and phylogenetic analyses, strain YE3T represents a novel species of the genus
Pusillimonas
, for which the name Pusillimonas thiosulfatoxidans sp. nov. is proposed. The type strain is YE3T (=KCTC 62737T=NBRC 113113T).
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Affiliation(s)
- Hyeon-Woo Koh
- R&D Division, VITABIO, Inc., Daejeon 34025, Republic of Korea
| | - Myeong-Sub Song
- R&D Division, VITABIO, Inc., Daejeon 34025, Republic of Korea
| | - Kyoung-Tag Do
- Department of Animal Biotechnology, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, Republic of Korea
| | - Hongik Kim
- R&D Division, VITABIO, Inc., Daejeon 34025, Republic of Korea
| | - Soo-Je Park
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, Republic of Korea
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Cui Y, Chun SJ, Cho AR, Wong SK, Lee HG, Oh HM, Ahn CY. Nevskia lacus sp. nov., a gammaproteobacterium isolated from a eutrophic lake. Antonie van Leeuwenhoek 2018; 112:723-729. [PMID: 30506271 DOI: 10.1007/s10482-018-1206-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 11/23/2018] [Indexed: 11/26/2022]
Abstract
A novel Gram-stain negative, rod-shaped and motile bacterial strain, designated strain Seoho-38T, was isolated from a eutrophic lake in South Korea. Polyphasic taxonomic studies were performed to investigate the taxonomic position of the new isolate. The phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain Seoho-38T formed a distinct cluster with Nevskia ramosa Soe1T, Nevskia persephonica G6M-30T, Nevskia soli GR15-1T, Nevskia terrae KIS13-15T and Nevskia aquatilis F2-63T with bootstrap resampling value of 100%. Of those Nevskia strains, the new isolate shows high sequence similarity with N. ramosa Soe1T (98.7%) and N. persephonica G6M-30T (97.2%), and values lower than 96.5% with the other type strains. The new isolate was observed to grow aerobically in 0-1.5% (w/v) NaCl (optimum 0%), at pH 7.0-9.0 (optimum pH 7.0) and temperature 15-36 °C (optimum 20-30 °C) on R2A medium. DNA-DNA relatedness values between strain Seoho-38T and the type strains of reference species in the genus Nevskia were < 24%. The genomic DNA G + C content was determined to be 67.4 mol%. Ubiquinone-8 (Q-8) (95%) and ubiquinone-7 (Q-7) (5%) were identified as the respiratory quinones. The cellular polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phosphoaminolipid, two glycolipids, an aminolipid and four unidentified lipids. The major fatty acid components were found to include summed feature 3 (C16:1ω7c and/or C16:1ω6c), summed feature 8 (C18:0ω7c and/or C18:0ω6c), C16:0 and C14:0. Based on the above polyphasic evidence, strain Seoho-38T (= KCTC 52221T = JCM 31888T) represents a new species of the genus Nevskia, for which the name Nevskia lacus sp. nov. is proposed.
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Affiliation(s)
- Yingshun Cui
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Seong-Jun Chun
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - A-Ra Cho
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Shu Kuan Wong
- Marine Microbiology, Department of Marine Ecosystem Dynamics, Atmosphere and Ocean Research Institute, University of Tokyo, Kashiwa, Japan
| | - Hyung-Gwan Lee
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
- University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
| | - Chi-Yong Ahn
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
- University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
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Yao L, Lai Y, Xue F, Sun L, Wang J. Paracandidimonas caeni sp. nov., isolated from sludge. Int J Syst Evol Microbiol 2018; 69:3332-3337. [PMID: 30465641 DOI: 10.1099/ijsem.0.003131] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A beige-pigmented, Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, named 24T, was isolated from sludge of a pesticide manufacturing factory in Nantong, Jiangsu Province, China. 16S rRNA gene sequence analysis revealed that strain 24T shared highest similarity with Parapusillimonas granuli Ch07T (98.20 %), followed by Candidimonas nitroreducens SC-089T (98.07 %) and Paracandidimonas soli IMT-305T (98.03 %). Phylogenetic trees showed that strain 24T formed a distinct clade with Paracandidimonas soli IMT-305T. The results of DNA-DNA hybridization tests showed that reassociation values were less than 45 % with respect to these closely related type strains. Strain 24T contained Q-8 and putrescine as the major respiratory quinone and polyamine, respectively. The main cellular fatty acids were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), summed feature 2 (iso-C16 : 1 I/C14 0 3-OH/C12 : 0 aldehyde), summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) and C12 : 0. The polar lipid profile included phosphatidylmethylethanolamin, phosphatidylethanolamine, phosphatidylglycerol, one unidentified phospholipid and one unidentified aminolipid. The G+C content was 56.83 mol%. Combined data from phenotypic, phylogenetic and DNA-DNA relatedness studies demonstrated that strain 24T represents a novel species of the genus Paracandidimonas, for which the name Paracandidimonas caeni sp. nov. is proposed. The type strain is 24T (=CCTCC AB 2018057T=KACC 19692T).
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Affiliation(s)
- Li Yao
- College of Marine and Bio-Engineering, Yancheng Teachers University, Yancheng, Jiangsu 210095, PR China
| | - Yuhan Lai
- College of Marine and Bio-Engineering, Yancheng Teachers University, Yancheng, Jiangsu 210095, PR China
| | - Fei Xue
- College of Marine and Bio-Engineering, Yancheng Teachers University, Yancheng, Jiangsu 210095, PR China
| | - Lina Sun
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, PR China
| | - Jialian Wang
- College of Marine and Bio-Engineering, Yancheng Teachers University, Yancheng, Jiangsu 210095, PR China
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Grouzdev DS, Tourova TP, Babich TL, Shevchenko MA, Sokolova DS, Abdullin RR, Poltaraus AB, Toshchakov SV, Nazina TN. Whole-genome sequence data and analysis of type strains ' Pusillimonas nitritireducens' and ' Pusillimonas subterraneus' isolated from nitrate- and radionuclide-contaminated groundwater in Russia. Data Brief 2018; 21:882-887. [PMID: 30426040 PMCID: PMC6222257 DOI: 10.1016/j.dib.2018.10.060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 10/11/2018] [Accepted: 10/17/2018] [Indexed: 12/01/2022] Open
Abstract
Two strains, 'Pusillimonas nitritireducens' JR1/69-2-13T and 'Pusillimonas subterraneus' JR1/69-3-13T, of aerobic, motile, Gram-negative, non-spore-forming, organotrophic, psychrotolerant bacteria were isolated from a sample of nitrate- and radionuclide-contaminated groundwater in Russia. Here we describe the draft genomes of these strains. The sequenced and annotated genome of the strain JR1/69-2-13T contained 4.3 Mbp with 4108 protein-coding genes. The genome of the strain JR1/69-3-13T contained 4.5 Mbp with 4260 protein-coding genes. Genome analysis of both strains provides an insight into the genomic basis of their resistance to nitrate, heavy metals and metalloids. The draft genome sequences of strains 'Pusillimonas nitritireducens' JR1/69-2-13T and 'Pusillimonas subterraneus' JR1/69-3-13T are available at DDBJ/EMBL/GenBank under the accession nos. https://www.ncbi.nlm.nih.gov/nuccore/PDNV00000000 and https://www.ncbi.nlm.nih.gov/nuccore/PDNW00000000, respectively.
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Affiliation(s)
- Denis S Grouzdev
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Tatiyana P Tourova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Tamara L Babich
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Diyana S Sokolova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Ruslan R Abdullin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Andrey B Poltaraus
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Tamara N Nazina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russian Federation.,V.I. Vernadsky Institute of Geochemistry and Analytical Chemistry of Russian Academу of Sciences, Moscow, Russian Federation
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Chun SJ, Cui Y, Ko SR, Lee HG, Oh HM, Ahn CY. Silanimonas algicola sp. nov., isolated from laboratory culture of a bloom-forming cyanobacterium, Microcystis. Int J Syst Evol Microbiol 2017; 67:3274-3278. [DOI: 10.1099/ijsem.0.002102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Seong-Jun Chun
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Yingshun Cui
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - So-Ra Ko
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
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13
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Cui Y, Chun SJ, Ko SR, Lee HG, Srivastava A, Oh HM, Ahn CY. Reyranella aquatilis sp. nov., an alphaproteobacterium isolated from a eutrophic lake. Int J Syst Evol Microbiol 2017; 67:3496-3500. [DOI: 10.1099/ijsem.0.002151] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yingshun Cui
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Seong-Jun Chun
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - So-Ra Ko
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Ankita Srivastava
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Chi-Yong Ahn
- University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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Acidovorax lacteus sp. nov., isolated from a culture of a bloom-forming cyanobacterium (Microcystis sp.). Antonie van Leeuwenhoek 2017; 110:1199-1205. [DOI: 10.1007/s10482-017-0892-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 05/22/2017] [Indexed: 11/26/2022]
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2017; 67:529-531. [DOI: 10.1099/ijsem.0.001845] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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