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Abstract
Chickens are in constant interaction with their environment, e.g., bedding and litter, and their microbiota. However, how litter microbiota develops over time and whether bedding and litter microbiota may affect the cecal microbiota is not clear. We addressed these questions using sequencing of V3/V4 variable region of 16S rRNA genes of cecal, bedding, and litter samples from broiler breeder chicken flocks for 4 months of production. Cecal, bedding, and litter samples were populated by microbiota of distinct composition. The microbiota in the bedding material did not expand in the litter. Similarly, major species from litter microbiota did not expand in the cecum. Only cecal microbiota was found in the litter forming approximately 20% of total litter microbiota. A time-dependent development of litter microbiota was observed. Escherichia coli, Staphylococcus saprophyticus, and Weissella jogaejeotgali were characteristic of fresh litter during the first month of production. Corynebacterium casei, Lactobacillus gasseri, and Lactobacillus salivarius dominated in a 2-month-old litter, Brevibacterium, Brachybacterium, and Sphingobacterium were characteristic for 3-month-old litter, and Salinococcus, Dietzia, Yaniella, and Staphylococcus lentus were common in a 4-month-old litter. Although the development was likely determined by physicochemical conditions in the litter, it might be interesting to test some of these species for active modification of litter to improve the chicken environment and welfare. IMPORTANCE Despite intimate contact, the composition of bedding, litter, and cecal microbiota differs considerably. Species characteristic for litter microbiota at different time points of chicken production were identified thus opening the possibility for active manipulation of litter microbiota.
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iChip increases the success of cultivation of TBT-resistant and TBT-degrading bacteria from estuarine sediment. World J Microbiol Biotechnol 2022; 38:180. [PMID: 35948836 PMCID: PMC9365728 DOI: 10.1007/s11274-022-03297-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/27/2022] [Indexed: 12/03/2022]
Abstract
Standard methods of microbial cultivation only enable the isolation of a fraction of the total environmental bacteria. Numerous techniques have been developed to increase the success of isolation and cultivation in the laboratory, some of which derive from diffusion chambers. In a diffusion chamber, environmental bacteria in agar medium are put back in the environment to grow as close to their natural conditions as possible, only separated from the environment by semi-permeable membranes. In this study, the iChip, a device that possesses hundreds of mini diffusion chambers, was used to isolate tributyltin (TBT) resistant and degrading bacteria. IChip was shown to be efficient at increasing the number of cultivable bacteria compared to standard methods. TBT-resistant strains belonging to Oceanisphaera sp., Pseudomonas sp., Bacillus sp. and Shewanella sp. were identified from Liverpool Dock sediment. Among the isolates in the present study, only members of Pseudomonas sp. were able to use TBT as a sole carbon source. It is the first time that members of the genus Oceanisphaera have been shown to be TBT-resistant. Although iChip has been used in the search for molecules of biomedical interest here we demonstrate its promising application in bioremediation.
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Uddin MR, Roy P, Mandal S. Production of extracellular lipase from psychrotrophic bacterium Oceanisphaera sp. RSAP17 isolated from arctic soil. Antonie van Leeuwenhoek 2021; 114:2175-2188. [PMID: 34665377 DOI: 10.1007/s10482-021-01671-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/03/2021] [Indexed: 01/08/2023]
Abstract
Cold-active extracellular lipases produced by different psychrotrophs are important for various industrial applications. We have isolated a Gram-negative, rod-shaped, aerobe, non-pigment producing psychrotrophic bacterial strain RSAP17 (MTCC 12991, MCC 4275) from the unexplored Arctic soil sample of NyAlesund, Svalbard, Norway (78° 55″ N, 11° 54″ E). The detailed morphological, biochemical, and molecular characteristics were investigated to characterize the isolate RSAP17. Analyses of the 16S rDNA sequence of strain RSAP17 (Accession no. MK391379) shows the closest match with Oceanisphaera marina YM319T (99.45%) and Oceanisphaera sediminis TW92 JCM 17329T (97.40%). The isolate is capable of producing extracellular lipase but not amylase, cellulase or urease. The optimal parameters for lipase production have been found in tributyrin based (10 mL/L) agar media supplemented with 3% (w/v) NaCl after 2-3 days of incubation at 20-22 °C temperature and pH 9 at shaking condition. We have purified the extracellular lipase from the RSAP17 grown culture supernatant through 75% ammonium sulfate precipitation followed by dialysis and DEAE cellulose column chromatography. The invitro lipolytic activity of the purified lipase enzymes has been done through zymogram analysis. The molecular weight found for the lipase is 103.8 kD. The optimal activity of the purified lipase has been found at 25 °C and pH 9. MALDI-TOF-MS study of the purified lipase showed the highest match with the sequence of prolipoprotein diacylglyceryl transferase with 44% sequence coverage. Further study on large-scale production, substrate utilization and enzymatic kinetics of this lipase could unravel its possibility in future biotechnological applications.
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Affiliation(s)
- Md Raihan Uddin
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Pranab Roy
- Department of Molecular Biology, Institute of Child Health, 11, Dr. Biresh Guha Street, Kolkata, West Bengal, 700017, India
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
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Huang SP, Chen TY, Chen JS, Wang LT, Huang L, Lin ST, Wei CL, Lin S, Wang PL, Chen YM, Shieh WY. Dongshaea marina gen. nov., sp. nov., a facultatively anaerobic marine bacterium that ferments glucose with gas production. Int J Syst Evol Microbiol 2018; 69:3318-3325. [PMID: 30422104 DOI: 10.1099/ijsem.0.003080] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two isolates of heterotrophic, facultatively anaerobic, marine bacteria, designated DM1 and DM2T, were recovered from a lagoon sediment sample of Dongsha Island, Taiwan. Cells were Gram-reaction-negative rods. Nearly all of the cells were non-motile and non-flagellated during the late exponential to early stationary phase of growth, while a few of the cells exhibited motility with monotrichous flagellation. The two isolates required NaCl for growth and grew optimally at about 30 °C, 2-3 % NaCl and pH 7-8. They grew aerobically and could achieve anaerobic growth by fermenting d-glucose or other carbohydrates with production of acids and the gases, including CO2 and H2. Ubiquinone Q-8 was the only respiratory quinone. Cellular fatty acids were predominated by C16 : 0, C18 : 1ω7c and C16 : 1ω7c. The major polar lipid was phosphatidylethanolamine. Strains DM1 and DM2T had DNA G+C contents of 52.0 and 51.8 mol%, respectively, as determined by HPLC analysis. Phylogenetic analyses based on 16S rRNA gene sequences clearly indicated that the two isolates formed a distinct genus-level lineage in the family Aeromonadaceae of the class Gammaproteobacteria and was an outgroup with respect to a stable supragenic clade comprising species of the genera Oceanimonas, Oceanisphaera and Zobellella. The phylogenetic data and those from chemotaxonomic, physiological and morphological characterizations support the establishment of a novel species and genus inside the family Aeromonadaceae, for which the name Dongshaea marina gen. nov., sp. nov. is proposed. The type strain is DM2T (=BCRC 81069T=JCM 32096T).
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Affiliation(s)
- Ssu-Po Huang
- Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan, ROC
| | - Tzu-Yin Chen
- Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan, ROC
| | - Jwo-Sheng Chen
- College of Health Care, China Medical University, No. 91, Shyue-Shyh Rd, Taichung, Taiwan, ROC
| | - Li-Ting Wang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 30099, Taiwan, ROC
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 30099, Taiwan, ROC
| | - Shih-Ting Lin
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 30099, Taiwan, ROC
| | - Chih-Lin Wei
- Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan, ROC
| | - Saulwood Lin
- Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan, ROC
| | - Pei-Ling Wang
- Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan, ROC
| | - Yi-Min Chen
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, University Road, Tainan City 701, Taiwan, ROC
| | - Wung Yang Shieh
- Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan, ROC
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Oceanisphaera avium sp. nov., isolated from the gut of the cinereous vulture, Aegypius monachus. Int J Syst Evol Microbiol 2018; 68:2068-2073. [DOI: 10.1099/ijsem.0.002797] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Dong WW, Kong DL, Zhang Q, Zhu J, Wang YW, Song JL, Zhou YQ, Jiang X, Zhang W, Zhao SM, Ruan ZY. Chitinophaga salinisoli sp. nov., isolated from saline soil. Antonie van Leeuwenhoek 2017; 111:265-273. [PMID: 28980087 DOI: 10.1007/s10482-017-0947-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 09/19/2017] [Indexed: 11/26/2022]
Abstract
A novel aerobic bacterium, designated strain LAM9153T, was isolated from a saline soil sample collected from Lingxian County, Shandong Province, China. Cells of strain LAM9153T were observed to be Gram-stain negative, non-motile, non-spore-forming and rod-shaped. The new isolate grew optimally at 30-35 °C, pH 7.0 and 0.5% of NaCl concentration (w/v). According to the phylogenetic analysis based on the 16S rRNA gene sequence, strain LAM9153T shares high similarity with Chitinophaga terrae Gsoil 238T (96.9%) and Chitinophaga niabensis JS 13-10T (95.9%), forming a subcluster with C. terrae Gsoil 238T, Chitinophaga cymbidii R156-2T, C. niabensis JS 13-10T and Chitinophaga soli Gsoil 219T in the phylogenetic tree. The major cellular fatty acids (> 10%) were identified as iso-C15:0, iso-C17:0 3-OH and summed features 3 (C16:1 ω6c and/or C16:1 ω7c). The predominant respiratory quinone was identified as menaquinone MK-7. The polar lipids consisted of phosphatidylethanolamine, aminophospholipid, three unidentified aminolipids and five unidentified lipids. The genomic DNA G+C content was determined to be 53.2 ± 1.6 mol%. On the basis of phylogenetic, chemotaxonomic and phenotypic data, strain LAM9153T is concluded to represent a novel species of the genus Chitinophaga, for which the name Chitinophaga salinisoli sp. nov. is proposed. The type strain is LAM9153T (= ACCC 19960T = JCM 30847T).
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Affiliation(s)
- Wei-Wei Dong
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China
| | - De-Long Kong
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China
| | - Qi Zhang
- College of Life Science, Xinjiang Normal University, Urumqi, 830046, XinJiang, China
| | - Jie Zhu
- College of Life Science, Xinjiang Normal University, Urumqi, 830046, XinJiang, China
| | - Yan-Wei Wang
- Key Laboratory of Development and Application of Rural Renewable Energy (MOA, China), Biogas Institute of Ministry of Agriculture, Chengdu, 610041, China
| | - Jin-Long Song
- Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Yi-Qing Zhou
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China
| | - Xu Jiang
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China
| | - Wei Zhang
- College of Life Science, Xinjiang Normal University, Urumqi, 830046, XinJiang, China
| | - Shu-Miao Zhao
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Zhi-Yong Ruan
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China.
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Liu J, Sun YW, Zhang DD, Li SN, Zhang DC. Oceanisphaera marina sp. nov., isolated from a deep-sea seamount. Int J Syst Evol Microbiol 2017. [DOI: 10.1099/ijsem.0.001906] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jie Liu
- Department of Bioengineering, College of Marine Sciences and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Ya-Wen Sun
- Department of Bioengineering, College of Marine Sciences and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Dan-Dan Zhang
- Department of Bioengineering, College of Marine Sciences and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Sheng-Nan Li
- Department of Bioengineering, College of Marine Sciences and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - De-Chao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
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Kong D, Guo X, Zhou S, Wang H, Wang Y, Zhu J, Dong W, Li Y, He M, Hu G, Zhao B, Ruan Z. Frigoribacterium salinisoli sp. nov., isolated from saline soil, transfer of Frigoribacterium mesophilum to Parafrigoribacterium gen. nov. as Parafrigoribacterium mesophilum comb. nov. Int J Syst Evol Microbiol 2016; 66:5252-5259. [PMID: 27654623 DOI: 10.1099/ijsem.0.001504] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, short-rod, aerobic bacterium, designated as strain LAM9155T, was isolated from saline soil sample collected from Lingxian County, Shandong Province, PR China. The strain grew optimally at 25-30 °C, pH 7.0 and 0.5 % (w/v) NaCl. The 16S rRNA gene sequence analysis revealed that strain LAM9155T belonged to the genus Frigoribacterium and was closely related to Frigoribacteriumendophyticum EGI 6500707T (99.4 %), Frigoribacteriumfaeni 801T (98.6 %) and Frigoribacteriummesophilum MSL-08T (96.2 %). The DNA-DNA hybridization values between strain LAM9155T and F. endophyticum JCM 30093T and between strain LAM9155T and F. faeni DSM 10309T were 40.2±2.1 and 32.8±1.6 %, respectively. The major fatty acids of LAM9155T were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The cell-wall analysis showed the B-type peptidoglycan containing alanine, glutamate, glycine, serine and lysine and that the cell wall contained the sugars galactose and ribose. The genomic DNA G+C content of strain LAM9155T was 68.2 mol%. The predominant menaquinone was MK-9. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, one unknown glycolipid and four unknown lipids. Based on the DNA-DNA hybridization and phenotypic, phylogenetic and chemotaxonomic properties, strain LAM9155T could be distinguished from the recognized species of the genus Frigoribacterium and was suggested to represent a novel species, for which the name Frigoribacterium salinisoli sp. nov. is proposed. The type strain is LAM9155T (=ACCC 19902T=JCM 30848T). Moreover, the transfer of F. mesophilum Dastager et al. 2008 to Parafrigoribacterium gen. nov. as Parafrigoribacterium mesophilum comb. nov. (type strain MSL-08T=DSM 19442T=KCTC 19311T) is also proposed.
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Affiliation(s)
- Delong Kong
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Xiang Guo
- Key Laboratory of Development and Application of Rural Renewable Energy (MOA, China), Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Shan Zhou
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Huimin Wang
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Yanwei Wang
- Key Laboratory of Development and Application of Rural Renewable Energy (MOA, China), Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Jie Zhu
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Weiwei Dong
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Yanting Li
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Mingxiong He
- Key Laboratory of Development and Application of Rural Renewable Energy (MOA, China), Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Guoquan Hu
- Key Laboratory of Development and Application of Rural Renewable Energy (MOA, China), Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Bingqiang Zhao
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Zhiyong Ruan
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
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Zhou S, Guo X, Wang H, Kong D, Wang Y, Zhu J, Dong W, He M, Hu G, Zhao B, Zhao B, Ruan Z. Chromobacterium rhizoryzae sp. nov., isolated from rice roots. Int J Syst Evol Microbiol 2016; 66:3890-3896. [PMID: 27393690 DOI: 10.1099/ijsem.0.001284] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel facultatively anaerobic, rod-shaped bacterium, designated LAM1188T, was isolated from the roots of rice (Oryzasativa) in Hubei Province. Cells of LAM1188T were Gram-stain-negative and motile. The temperature and pH ranges for growth were 15-40 °C (optimum: 30 °C) and pH 5-10 (optimum: pH 7), respectively. The strain did not require NaCl for growth but tolerated up to 3.5 % NaCl (w/v). Analysis of the 16S rRNA gene sequence indicated that the isolate represented a member of the genus Chromobacterium, and was most closely related to Chromobacterium haemolyticum MDA0585T and Chromobacterium aquaticum CC-SEYA-1T with 98.7 % and 97.3 % sequence similarity, respectively. The values of DNA-DNA hybridization between LAM1188T and C. haemolyticum JCM 14163T and C. aquaticum CCUG 55175T were 54.0±2.1 % and 44.0±1.2 %, respectively. The major cellular fatty acids were C16 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, four unidentified aminolipids and four unidentified lipids. The respiratory quinone was ubiquinone Q-8. The DNA G+C content was 64.1 mol% as determined by the Tm method. On the basis of its phenotypic, chemotaxonomic and phylogenetic characteristics, strain LAM1188T is suggested to represent a novel species of the genus Chromobacterium, for which the name Chromobacte riumrhizoryzae sp. nov. is proposed. The type strain is LAM1188T (=ACCC 19900T=JCM 31180T).
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Affiliation(s)
- Shan Zhou
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China.,State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xiang Guo
- Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Huimin Wang
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Delong Kong
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Yanwei Wang
- Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Jie Zhu
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Weiwei Dong
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Mingxiong He
- Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Guoquan Hu
- Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Bingqiang Zhao
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Bin Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Zhiyong Ruan
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
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Wang H, Zhou S, Wang Y, Kong D, Guo X, Zhu J, Dong W, Ruan Z. Advenella alkanexedens sp. nov., an alkane-degrading bacterium isolated from biogas slurry samples. Int J Syst Evol Microbiol 2015; 66:906-911. [PMID: 26620977 DOI: 10.1099/ijsem.0.000811] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel aerobic bacterium, designated strain LAM0050T, was isolated from a biogas slurry sample, which had been enriched with diesel oil for 30 days. Cells of strain LAM0050T were gram-stain-negative, non-motile, non-spore-forming and coccoid-shaped. The optimal temperature and pH for growth were 30-35 °C and 8.5, respectively. The strain did not require NaCl for growth, but tolerated up to 5.3 % (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain LAM0050T was a member of the genus Advenella, and was most closely related to Advenella faeciporci KCTC 23732T, Advenella incenata CCUG 45225T, Advenella kashmirensis DSM 17095T and Advenella mimigardefordensis DSM 17166T, with 98.1, 96.6, 96.6 and 96.3 % sequence similarity, respectively. The DNA-DNA hybridization relatedness between strain LAM0050T and A. faeciporci KCTC 23732T was 41.7 ± 2.4 %. The genomic DNA G+C content was 51.2 mol%, as determined by the Tm method. The major fatty acids of strain LAM0050T were C16 : 0, C17 : 0 cyclo, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The predominant ubiquinone was Q-8. The main polar lipids were diphosphatidyglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine and four unidentified phospholipids. Based on the phenotypic and genotypic properties, strain LAM0050T is suggested to represent a novel species of the genus Advenella, for which the name Advenella alkanexedens sp. nov., is proposed, the type strain is LAM0050T ( = ACCC 06485T = JCM 30465T).
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Affiliation(s)
- Huimin Wang
- Key Laboratory of Microbial Resources (Ministry of Agriculture, PR China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China.,Key Laboratory of Development and Application of Rural Renewable Energy (MOA, PR China), Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Shan Zhou
- Key Laboratory of Microbial Resources (Ministry of Agriculture, PR China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Yanwei Wang
- Key Laboratory of Development and Application of Rural Renewable Energy (MOA, PR China), Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Delong Kong
- Key Laboratory of Microbial Resources (Ministry of Agriculture, PR China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Xiang Guo
- Key Laboratory of Microbial Resources (Ministry of Agriculture, PR China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Jie Zhu
- Key Laboratory of Microbial Resources (Ministry of Agriculture, PR China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Weiwei Dong
- Key Laboratory of Microbial Resources (Ministry of Agriculture, PR China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Zhiyong Ruan
- Key Laboratory of Microbial Resources (Ministry of Agriculture, PR China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
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Zhou S, Wang H, Wang Y, Ma K, He M, Chen X, Kong D, Guo X, Ruan Z, Zhao B. Oceanisphaera psychrotolerans sp. nov., isolated from coastal sediment samples. Int J Syst Evol Microbiol 2015; 65:2797-2802. [PMID: 25991663 DOI: 10.1099/ijs.0.000331] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel aerobic, Gram-staining-negative bacterium, designated strain LAM-WHM-ZC(T), was isolated from coastal sediment samples from the Bohai Sea, near Yantai, China. Cells of LAM-WHM-ZC(T) were non-motile, short-rod- or coccoid-shaped. The temperature and pH ranges for growth were 4-40 °C (optimum: 20-33 °C) and pH 5-9 (optimum: pH 7.5). The strain did not require NaCl for growth but tolerated up to 10% NaCl (w/v). The major fatty acids of strain LAM-WHM-ZC(T) were summed feature 3, C12 : 0, C16 : 0, summed feature 2 and summed feature 8. The predominant respiratory quinone was ubiquinone Q-8. The main polar lipids were diphosphatidyglycerol, phosphatigylethanolamine, phosphatidyglycerol, one phospholipid and four unidentified glycolipids. The DNA G+C content was 59.3 mol% as determined by the melting temperature (Tm) method. Analysis of the 16S rRNA gene sequence indicated that the isolate represented a member of the genus Oceanisphaera and was closely related to Oceanisphaera arctica KCTC 23013(T), Oceanisphaera litoralis DSM 15406(T), Oceanisphaera sediminis KACC 15117(T) and Oceanisphaera donghaensis KCTC 12522(T) with 97.7%, 97.1%, 96.6% and 96.6% sequence similarity, respectively. The DNA-DNA hybridization values between strain LAM-WHM-ZC(T) and the four reference strains were 47.4 ± 2.8%, 33.5 ± 2.2%, 28.4 ± 1.8% and 13.7 ± 0.8%, respectively. Based on its phenotypic and genotypic properties, strain LAM-WHM-ZC(T) is suggested to represent a novel species of the genus Oceanisphaera, for which the name Oceanisphaera psychrotolerans sp. nov. is proposed. The type strain is LAM-WHM-ZC(T) ( = ACCC 06516(T) = JCM 30466(T)).
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Affiliation(s)
- Shan Zhou
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Huimin Wang
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Yanwei Wang
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Kedong Ma
- College of Environmental and Chemical Engineering, Dalian University, Dalian 116622, PR China
| | - Mingxiong He
- Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Xiaorong Chen
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Delong Kong
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Xiang Guo
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Zhiyong Ruan
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Bin Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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12
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Kunihiro T, Veuger B, Vasquez-Cardenas D, Pozzato L, Le Guitton M, Moriya K, Kuwae M, Omori K, Boschker HTS, van Oevelen D. Phospholipid-derived fatty acids and quinones as markers for bacterial biomass and community structure in marine sediments. PLoS One 2014; 9:e96219. [PMID: 24769853 PMCID: PMC4000199 DOI: 10.1371/journal.pone.0096219] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 04/04/2014] [Indexed: 11/18/2022] Open
Abstract
Phospholipid-derived fatty acids (PLFA) and respiratory quinones (RQ) are microbial compounds that have been utilized as biomarkers to quantify bacterial biomass and to characterize microbial community structure in sediments, waters, and soils. While PLFAs have been widely used as quantitative bacterial biomarkers in marine sediments, applications of quinone analysis in marine sediments are very limited. In this study, we investigated the relation between both groups of bacterial biomarkers in a broad range of marine sediments from the intertidal zone to the deep sea. We found a good log-log correlation between concentrations of bacterial PLFA and RQ over several orders of magnitude. This relationship is probably due to metabolic variation in quinone concentrations in bacterial cells in different environments, whereas PLFA concentrations are relatively stable under different conditions. We also found a good agreement in the community structure classifications based on the bacterial PLFAs and RQs. These results strengthen the application of both compounds as quantitative bacterial biomarkers. Moreover, the bacterial PLFA- and RQ profiles revealed a comparable dissimilarity pattern of the sampled sediments, but with a higher level of dissimilarity for the RQs. This means that the quinone method has a higher resolution for resolving differences in bacterial community composition. Combining PLFA and quinone analysis as a complementary method is a good strategy to yield higher resolving power in bacterial community structure.
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Affiliation(s)
- Tadao Kunihiro
- Department of Ecosystem Studies, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
- Department of Marine Microbiology, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
- * E-mail:
| | - Bart Veuger
- Department of Ecosystem Studies, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
| | - Diana Vasquez-Cardenas
- Department of Ecosystem Studies, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
- Department of Marine Microbiology, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
| | - Lara Pozzato
- Department of Ecosystem Studies, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
| | - Marie Le Guitton
- Department of Ecosystem Studies, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
| | - Kazuyoshi Moriya
- School of Natural Science & Technology, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Michinobu Kuwae
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Ehime, Japan
| | - Koji Omori
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Ehime, Japan
| | - Henricus T. S. Boschker
- Department of Marine Microbiology, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
| | - Dick van Oevelen
- Department of Ecosystem Studies, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
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13
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Xu Z, Zhang XY, Su HN, Yu ZC, Liu C, Li H, Chen XL, Song XY, Xie BB, Qin QL, Zhou BC, Shi M, Huang Y, Zhang YZ. Oceanisphaera profunda sp. nov., a marine bacterium isolated from deep-sea sediment, and emended description of the genus Oceanisphaera. Int J Syst Evol Microbiol 2014; 64:1252-1256. [DOI: 10.1099/ijs.0.058115-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, oxidase- and catalase-positive, flagellated, rod-shaped bacterial strain, designated SM1222T, was isolated from the deep-sea sediment of the South China Sea. The strain grew at 4–35 °C and with 0.5–8 % NaCl (w/v). Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SM1222T was affiliated with the genus
Oceanisphaera
in the class
Gammaproteobacteria
. It shared the highest sequence similarity with the type strain of
Oceanisphaera ostreae
(96.8 %) and 95.4–96.6 % sequence similarities with type strains of other species of the genus
Oceanisphaera
with validly published names. Strain SM1222T contained summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C18 : 1ω7c, C16 : 0, C12 : 0 and summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I) as the major fatty acids and ubiquinone Q-8 as the predominant respiratory quinone. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content of strain SM1222T was 51.5 mol%. On the basis of the evidence presented in this study, strain SM1222T represents a novel species of the genus
Oceanisphaera
, for which the name Oceanisphaera profunda sp. nov. is proposed. The type strain of Oceanisphaera profunda is SM1222T ( = CCTCC AB 2013241T = KCTC 32510T). An emended description of the genus
Oceanisphaera
Romanenko et al. 2003 emend. Choi et al. 2011 is also proposed.
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Affiliation(s)
- Zhong Xu
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- School of Life Science, Liaocheng University, Liaocheng 252059, PR China
| | - Xi-Ying Zhang
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Hai-Nan Su
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Zi-Chao Yu
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Chang Liu
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Hai Li
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Xiu-Lan Chen
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Xiao-Yan Song
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Bin-Bin Xie
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Qi-Long Qin
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Bai-Cheng Zhou
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Mei Shi
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Yong Huang
- School of Life Science, Liaocheng University, Liaocheng 252059, PR China
| | - Yu-Zhong Zhang
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
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