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Wang W, Sheng Y. Interactions between Microcystis and its associated bacterial community on electron transfer and transcriptomic processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175372. [PMID: 39117231 DOI: 10.1016/j.scitotenv.2024.175372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 07/31/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024]
Abstract
Microcystis and bacteria always live together in the mucilage of Microcystis colonies. Extracellular electrons between Microcystis and bacteria can be translated from bioenergy to electric energy. Here, photosynthetic microbial fuel cells (PMFCs) were constructed to make clear the electron transfer mechanism between Microcystis and bacteria. A remarkable enhancement of current density with 2.5-fold change was detected in the coculture of Microcystis and bacteria than pure culture of Microcystis. Transcriptome analyses showed that photosynthesis efficiency of Microcystis was upregulated and may release more electron to improve extracellular electron transfer rate. Significant increase on oxidative phosphorylation of bacterial community was observed according to meta-transcriptome. Bacterial electrons were transferred out of cell membranes by enhancing VgrG and IcmF copies though the type II bacterial secretion system. Not only Microcystis and bacteria attached with each other tightly by filamentous, but also more gene copies relating to pilin and riboflavin production were detected from Microcystis culture. A confirmatory experiment found that riboflavin can upregulate the electron transfer and current density by adding riboflavin into cocultures. Thus, the direct contact and indirect interspecies electron transfer processes between Microcystis and bacteria were observed. Results enlarge knowledge for activities of Microcystis colonies in cyanobacterial blooms, and provide a better understanding for energy transformation.
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Affiliation(s)
- Wenjing Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Shandong Key Laboratory of Coastal Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266061, China
| | - Yanqing Sheng
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Shandong Key Laboratory of Coastal Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China; Key Laboratory of Land and Sea Ecological Governance and Systematic Regulation, Shandong Academy for Environmental Planning, Jinan 250101, China.
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Liu WJ, Zhang Y, Cao K, Li JX, Wen YQ, Sun C, Xu L. Aurantiacibacter hainanensis sp. nov. and Qipengyuania zhejiangensis sp. nov., two novel Erythrobacteraceae species isolated from tidal flat sediments. Int J Syst Evol Microbiol 2024; 74. [PMID: 39052323 DOI: 10.1099/ijsem.0.006469] [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: 07/27/2024] Open
Abstract
Two Gram-stain-negative, rod-shaped, non-motile, aerobic and carotenoid-producing strains, belonging to the family Erythrobacteraceae, designated as H149T and Z2T, were isolated from tidal flat sediment samples collected in Hainan and Zhejiang, PR China, respectively. Growth of strain H149T occurred at 15-42 °C, 0-10.0 % (w/v) NaCl, and pH 6.0-8.5, with the optima at 35-37 °C, 3.0-3.5 % (w/v) NaCl and pH 7.0. Strain Z2T grew at 15-37 °C, 0-6.0 % (w/v) NaCl, and pH 6.0-9.5, with the optima at 25-30 °C, 0.5-1.0 % (w/v) NaCl and pH 6.0-6.5. Ubiquinone-10 was the sole ubiquinone in two strains. The predominant cellular fatty acids of strain H149T were C16 : 0, summed feature 3 and summed feature 8, while those of strain Z2T were C17 : 1 ω6c, summed feature 3 and summed feature 8. Strains H149T and Z2T shared diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid as major polar lipids. The 16S rRNA gene sequence identity analysis indicated that strain H149T had the highest sequence identity of 98.4 % with Aurantiacibacter odishensis KCTC 23981T, and strain Z2T had that of 98.2 % with Qipengyuania pacifica NZ-96T. Phylogenetic trees based on 16S rRNA gene and core-genome sequences revealed that strains H149T and Z2T formed two independent clades in the genera Aurantiacibacter and Qipengyuania, respectively. Strain H149T had average nucleotide identity values of 74.0-81.3 % and in silico DNA-DNA hybridization values of 18.5-23.1 % with Aurantiacibacter type strains, while strain Z2T had values of 73.3-78.7 % and 14.5-33.3 % with Qipengyuania type strains. The genomic DNA G+C contents of strains H149T and Z2T were 64.3 and 61.8 %, respectively. Based on the genetic, genomic, phylogenetic, physiological and chemotaxonomic results, strains H149T (=KCTC 8397T=MCCC 1K08920T) and Z2T (=KCTC 8396T=MCCC 1K08946T) are concluded to represent two novel Erythrobacteraceae species for which the names Aurantiacibacter hainanensis sp. nov. and Qipengyuania zhejiangensis sp. nov. are proposed, respectively.
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Affiliation(s)
- Wen-Jia Liu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
- Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd., Zhejiang Engineering Research Center for the Development Technology of Medicinal and Edible Homologous Health Food, Shaoxing 312075, PR China
| | - Yu Zhang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
- Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd., Zhejiang Engineering Research Center for the Development Technology of Medicinal and Edible Homologous Health Food, Shaoxing 312075, PR China
| | - Ke Cao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Jia-Xi Li
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Yu-Qiao Wen
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Cong Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
- Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd., Zhejiang Engineering Research Center for the Development Technology of Medicinal and Edible Homologous Health Food, Shaoxing 312075, PR China
| | - Lin Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
- Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd., Zhejiang Engineering Research Center for the Development Technology of Medicinal and Edible Homologous Health Food, Shaoxing 312075, PR China
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Wang Y, You H, Bu YX, Zhou P, Xu L, Fu GY, Xu XW. Qipengyuania benthica sp. nov. and Qipengyuania profundimaris sp. nov., two novel Erythrobacteraceae members isolated from deep-sea environments. Int J Syst Evol Microbiol 2024; 74. [PMID: 38546450 DOI: 10.1099/ijsem.0.006313] [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: 04/04/2024] Open
Abstract
Two Gram-stain-negative, rod-shaped and non-motile strains, designated as DY56-A-20T and G39T, were isolated from deep-sea sediment of the Pacific Ocean and deep-sea seawater of the Indian Ocean, respectively. Strain DY56-A-20T was found to grow at 15-37 °C (optimum, 28 °C), at pH 6.0-10.0 (optimum, pH 6.5-7.0) and in 0.5-6.0 % (w/v) NaCl (optimum, 1.0-2.0 %), while strain G39T was found to grow at 10-42 °C (optimum, 35-40 °C), at pH 5.5-10.0 (optimum, pH 6.5-7.0) and in 0-12.0 % (w/v) NaCl (optimum, 1.0-2.0 %). The 16S rRNA gene sequence identity analysis indicated that strain DY56-A-20T had the highest sequence identity with Qipengyuania marisflavi KEM-5T (97.6 %), while strain G39T displayed the highest sequence identity with Qipengyuania citrea H150T (98.8 %). The phylogenomic reconstruction indicated that both strains formed independent clades within the genus Qipengyuania. The digital DNA-DNA hybridization and average nucleotide identity values between strains DY56-A-20T/G39T and Qipengyuania/Erythrobacter type strains were 17.8-23.8 % and 70.7-81.1 %, respectively, which are below species delineation thresholds. The genome DNA G+C contents were 65.0 and 63.5 mol% for strains DY56-A-20T and G39T, respectively. The predominant cellular fatty acids (>10 %) of strain DY56-A-20T were C17 : 1 ω6c, summed feature 8 and summed feature 3, and the major cellular fatty acids of strain G39T were C17 : 1 ω6c and summed feature 8. The major polar lipids in both strains were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and an unidentified polar lipid. The only respiratory quinone present in both strains was ubiquinone-10. Based on those genotypic and phenotypic results, the two strains represent two novel species belonging to the genus Qipengyuania, for which the names Qipengyuania benthica sp. nov. and Qipengyuania profundimaris sp. nov. are proposed. The type strain of Q. benthica is DY56-A-20T (=MCCC M27941T=KCTC 92309T), and the type strain of Q. profundimaris is G39T (=MCCC M30353T=KCTC 8208T).
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Affiliation(s)
- Yuan Wang
- Ocean College, Zhejiang University, Zhoushan 316021, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Hao You
- Ocean College, Zhejiang University, Zhoushan 316021, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Yu-Xin Bu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Peng Zhou
- Ocean College, Zhejiang University, Zhoushan 316021, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Lin Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
- Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd, Zhejiang Engineering Research Center for the Development Technology of Medicinal and Edible Homologous Health Food, Shaoxing 312075, PR China
| | - Ge-Yi Fu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
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Ko SR, Le VV, Srivastava A, Kang M, Oh HM, Ahn CY. Algicidal activity of a novel bacterium, Qipengyuania sp. 3-20A1M, against harmful Margalefidinium polykrikoides: Effects of its active compound. MARINE POLLUTION BULLETIN 2023; 186:114397. [PMID: 36493515 DOI: 10.1016/j.marpolbul.2022.114397] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 11/14/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Margalefidinium polykrikoides causes significant economic losses in the aquaculture industry by red tide formation. Algicidal bacteria have attracted research interests as a potential bloom control approach without secondary pollution. Qipengyuania sp. 3-20A1M, isolated from surface seawater, exerted an algicidal effect on M. polykrikoides. However, it exhibited a significantly lower algicidal activity toward other microalgae. It reduced photosynthetic efficiency of M. polykrikoides and induced lipid peroxidation and cell disruption. The growth inhibition of M. polykrikoides reached 64.9 % after 24 h of co-culturing, and expression of photosynthesis-related genes was suppressed. It killed M. polykrikoides indirectly by secreting algicidal compounds. The algicide was purified and identified as pyrrole-2-carboxylic acid. After 24 h of treatment with pyrrole-2-carboxylic acid (20 μg/mL), 60.8 % of the M. polykrikoides cells were destroyed. Overall, our results demonstrated the potential utility of Qipengyuania sp. 3-20A1M and its algicidal compound in controlling M. polykrikoides blooms in the marine ecosystem.
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Affiliation(s)
- So-Ra Ko
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Ve Van Le
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Ankita Srivastava
- Department of Botany, Siddharth University, Kapilvastu, Siddharth Nagar, 272202, Uttar Pradesh, India
| | - Mingyeong Kang
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.
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Comparative Genomics Reveals Genetic Diversity and Metabolic Potentials of the Genus Qipengyuania and Suggests Fifteen Novel Species. Microbiol Spectr 2022; 10:e0126421. [PMID: 35446150 PMCID: PMC9241875 DOI: 10.1128/spectrum.01264-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Members of the genus Qipengyuania are heterotrophic bacteria frequently isolated from marine environments with great application potential in areas such as carotenoid production. However, the genomic diversity, metabolic function, and adaption of this genus remain largely unclear. Here, 16 isolates related to the genus Qipengyuania were recovered from coastal samples and their genomes were sequenced. The phylogenetic inference of these isolates and reference type strains of this genus indicated that the 16S rRNA gene was insufficient to distinguish them at the species level; instead, the phylogenomic reconstruction could provide the reliable phylogenetic relationships and confirm 15 new well-supported branches, representing 15 putative novel genospecies corroborated by the digital DNA-DNA hybridization and average nucleotide identity analyses. Comparative genomics revealed that the genus Qipengyuania had an open pangenome and possessed multiple conserved genes and pathways related to metabolic functions and environmental adaptation, despite the presence of divergent genomic features and specific metabolic potential. Genetic analysis and pigment detection showed that the members of this genus were identified as carotenoid producers, while some proved to be potentially aerobic anoxygenic photoheterotrophs. Collectively, the first insight into the genetic diversity and metabolic potentials of the genus Qipengyuania will contribute to better understanding of the speciation and adaptive evolution in natural environments. IMPORTANCE The deciphering of the phylogenetic diversity and metabolic features of the abundant bacterial taxa is critical for exploring their ecological importance and application potential. Qipengyuania is a genus of frequently isolated heterotrophic microorganisms with great industrial application potential. Numerous strains related to the genus Qipengyuania have been isolated from diverse environments, but their genomic diversity and metabolic functions remain unclear. Our study revealed a high degree of genetic diversity, metabolic versatility, and environmental adaptation of the genus Qipengyuania using comparative genomics. Fifteen novel species of this genus have been established using a polyphasic taxonomic approach, expanding the number of described species to almost double. This study provided an overall view of the genus Qipengyuania at the genomic level and will enable us to better uncover its ecological roles and evolutionary history.
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Yoon J, Lee EY, Nam SJ. Erythrobacter rubeus sp. nov., a carotenoid-producing alphaproteobacterium isolated from coastal seawater. Arch Microbiol 2022; 204:125. [PMID: 34997854 DOI: 10.1007/s00203-021-02736-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/02/2021] [Accepted: 12/17/2021] [Indexed: 11/26/2022]
Abstract
A study based on a polyphasic taxonomic approach was carried out to identify and classify a novel marine alphaproteobacterium, designated as KMU-140T, isolated from coastal seawater collected at Jeju Island, Republic of Korea. Cells of strain KMU-140T were spherical, Gram-stain-negative, reddish-orange colored, strictly aerobic, catalase- and oxidase-positive, non-motile, and chemoorganoheterotrophic. The novel isolate was able to grow at NaCl concentrations of 0-5%, pH 6.0-9.5, and 10-45 °C. A phylogenetic analysis based on the 16S rRNA gene sequence showed that strain KMU-140T belongs to the family Erythrobacteraceae and was most closely related to Erythrobacter longus OCh101T (98.7%). Strain KMU-140T contained ubiquinone-10 (Q-10) as the only respiratory quinone and C18:1 ω7c, iso-C18:0, and C16:0 as the main (> 10%) cellular fatty acids. Strain KMU-140T produced carotenoid compounds that rendered the cell biomass a reddish-orange color. The assembled draft genome size of strain KMU-140T was 3.04 Mbp with G + C content of 60.6 mol%. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values of KMU-140T and the species of the genus Erythrobacter were found to be 76.6-78.4%, 14.0-18.7%, and 69.6-77.8%, respectively. Phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, and two unidentified lipids were identified as major polar lipids. On the basis of the polyphasic taxonomic features presented, the strain is considered to represent a novel species of the genus Erythrobacter for which the name Erythrobacter rubeus sp. nov. is proposed. The type strain of E. rubeus sp. nov. is KMU-140T (= KCCM 90479T = NBRC 115159T).
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Affiliation(s)
- Jaewoo Yoon
- College of Pharmacy, Keimyung University, 1095 Dalgubeoldaero, Dalseo-gu, Daegu, 42601, Republic of Korea.
| | - Eun-Young Lee
- Department of Chemistry and Nanoscience, Ewha Womans University, 11-1 Daehyun-dong, Seodaemun-gu, Seoul, 03760, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, 11-1 Daehyun-dong, Seodaemun-gu, Seoul, 03760, Republic of Korea.
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Liu Y, Pei T, Deng MR, Zhu H. Qipengyuania soli sp. nov., Isolated from Mangrove Soil. Curr Microbiol 2021; 78:2806-2814. [PMID: 34047831 DOI: 10.1007/s00284-021-02538-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/05/2021] [Indexed: 11/26/2022]
Abstract
A novel Gram-stain-negative, non-motile, and rod-shaped bacterial strain, designated as 6D36T, was isolated from mangrove soil and characterized by using a polyphasic taxonomic approach. Strain 6D36T was found to grow at 10-37 °C (optimum, 28 °C), at pH 6.0-9.0 (optimum, 7.0) and in 0-8% (w/v) NaCl (optimum, 3%). The predominant cellular fatty acids of strain 6D36T were summed feature 8 (C19:1 ω7c and/or C18:1 ω6c) and C17:1 ω6c; the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, and sphingoglycolipid; the sole respiratory quinone was Q-10. The phylogenetic analysis based on 16S rRNA gene sequences showed that strain 6D36T fell into the genus Qipengyuania and was closely related to "Erythrobacter mangrovi" MCCC 1K03690T (98.5%), Qipengyuania citrea CGMCC 1.8703T (97.6%), and Qipengyuania pelagi JCM 17468T (97.4%). The phylogenomic analysis indicated that strain 6D36T formed an independent branch distinct from reference-type strains of species within this genus. The digital DNA-DNA hybridization and average nucleotide identity values between strain 6D36T and the three type strains above were, respectively, 20.2-21.3% and 79.5-81.5%, of which were far below their respective threshold for species definition, implying that the strain represents a novel genospecies. The genomic DNA G + C content was 63.3%. Based on phenotypic and genotypic characteristics, strain 6D36T is concluded to represent a novel species of the genus Qipengyuania, for which the name Qipengyuania soli sp. nov., is proposed. The type strain of the species is 6D36T (= GDMCC 1.1977T = KCTC 82333T).
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Affiliation(s)
- Yang Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Tao Pei
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Ming-Rong Deng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Honghui Zhu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China.
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Xu L, Sun C, Fang C, Oren A, Xu XW. Genomic-based taxonomic classification of the family Erythrobacteraceae. Int J Syst Evol Microbiol 2020; 70:4470-4495. [PMID: 32726199 PMCID: PMC7660246 DOI: 10.1099/ijsem.0.004293] [Citation(s) in RCA: 290] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 06/01/2020] [Indexed: 12/22/2022] Open
Abstract
The family Erythrobacteraceae, belonging to the order Sphingomonadales, class Alphaproteobacteria, is globally distributed in various environments. Currently, this family consist of seven genera: Altererythrobacter, Croceibacterium, Croceicoccus, Erythrobacter, Erythromicrobium, Porphyrobacter and Qipengyuania. As more species are identified, the taxonomic status of the family Erythrobacteraceae should be revised at the genomic level because of its polyphyletic nature evident from 16S rRNA gene sequence analysis. Phylogenomic reconstruction based on 288 single-copy orthologous clusters led to the identification of three separate clades. Pairwise comparisons of average nucleotide identity, average amino acid identity (AAI), percentage of conserved protein and evolutionary distance indicated that AAI and evolutionary distance had the highest correlation. Thresholds for genera boundaries were proposed as 70 % and 0.4 for AAI and evolutionary distance, respectively. Based on the phylo-genomic and genomic similarity analysis, the three clades were classified into 16 genera, including 11 novel ones, for which the names Alteraurantiacibacter, Altericroceibacterium, Alteriqipengyuania, Alteripontixanthobacter, Aurantiacibacter, Paraurantiacibacter, Parerythrobacter, Parapontixanthobacter, Pelagerythrobacter, Tsuneonella and Pontixanthobacter are proposed. We reclassified all species of Erythromicrobium and Porphyrobacter as species of Erythrobacter. This study is the first genomic-based study of the family Erythrobacteraceae, and will contribute to further insights into the evolution of this family.
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Affiliation(s)
- Lin Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Cong Sun
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Chen Fang
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- College of Oceanography, Hohai University, Nanjing 210000, PR China
| | - Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, PR China
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Xu L, Wu YH, Zhou P, Cheng H, Liu Q, Xu XW. Investigation of the thermophilic mechanism in the genus Porphyrobacter by comparative genomic analysis. BMC Genomics 2018; 19:385. [PMID: 29792177 PMCID: PMC5966882 DOI: 10.1186/s12864-018-4789-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 05/14/2018] [Indexed: 11/10/2022] Open
Abstract
Background Type strains of the genus Porphyrobacter belonging to the family Erythrobacteraceae and the class Alphaproteobacteria have been isolated from various environments, such as swimming pools, lake water and hot springs. P. cryptus DSM 12079T and P. tepidarius DSM 10594T out of all Erythrobacteraceae type strains, are two type strains that have been isolated from geothermal environments. Next-generation sequencing (NGS) technology offers a convenient approach for detecting situational types based on protein sequence differences between thermophiles and mesophiles; amino acid substitutions can lead to protein structural changes, improving the thermal stabilities of proteins. Comparative genomic studies have revealed that different thermal types exist in different taxa, and few studies have been focused on the class Alphaproteobacteria, especially the family Erythrobacteraceae. In this study, eight genomes of Porphyrobacter strains were compared to elucidate how Porphyrobacter thermophiles developed mechanisms to adapt to thermal environments. Results P. cryptus DSM 12079T grew optimally at 50 °C, which was higher than the optimal growth temperature of other Porphyrobacter type strains. Phylogenomic analysis of the genus Porphyrobacter revealed that P. cryptus DSM 12079T formed a distinct and independent clade. Comparative genomic studies uncovered that 1405 single-copy genes were shared by Porphyrobacter type strains. Alignments of single-copy proteins showed that various types of amino acid substitutions existed between P. cryptus DSM 12079T and the other Porphyrobacter strains. The primary substitution types were changes from glycine/serine to alanine. Conclusions P. cryptus DSM 12079T was the sole thermophile within the genus Porphyrobacter. Phylogenomic analysis and amino acid frequencies indicated that amino acid substitutions might play an important role in the thermophily of P. cryptus DSM 12079T. Bioinformatic analysis revealed that major amino acid substitutional types, such as changes from glycine/serine to alanine, increase the frequency of α-helices in proteins, promoting protein thermostability in P. cryptus DSM 12079T. Hence, comparative genomic analysis broadens our understanding of thermophilic mechanisms in the genus Porphyrobacter and may provide a useful insight in the design of thermophilic enzymes for agricultural, industrial and medical applications. Electronic supplementary material The online version of this article (10.1186/s12864-018-4789-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lin Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, 310012, Hangzhou, People's Republic of China.,College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, People's Republic of China
| | - Yue-Hong Wu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, 310012, Hangzhou, People's Republic of China
| | - Peng Zhou
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, 310012, Hangzhou, People's Republic of China
| | - Hong Cheng
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, 310012, Hangzhou, People's Republic of China
| | - Qian Liu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, 310012, Hangzhou, People's Republic of China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, 310012, Hangzhou, People's Republic of China. .,Ocean College, Zhejiang University, 316021, Zhoushan, People's Republic of China.
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