1
|
Cao S, Duan M, Zhang X, Yang Z, Zhuo R. Bacterial community structure analysis of sludge from Taozi lake and isolation of an efficient 17β-Estradiol (E2) degrading strain Sphingobacterium sp. GEMB-CSS-01. Chemosphere 2024; 355:141806. [PMID: 38548087 DOI: 10.1016/j.chemosphere.2024.141806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 01/28/2024] [Accepted: 03/24/2024] [Indexed: 04/08/2024]
Abstract
Environmental challenges arising from organic pollutants pose a significant problem for modern societies. Efficient microbial resources for the degradation of these pollutants are highly valuable. In this study, the bacterial community structure of sludge samples from Taozi Lake (polluted by urban sewage) was studied using 16S rRNA sequencing. The bacterial phyla Proteobacteria, Bacteroidetes, and Chloroflexi, which are potentially important in organic matter degradation by previous studies, were identified as the predominant phyla in our samples, with relative abundances of 48.5%, 8.3%, and 6.6%, respectively. Additionally, the FAPROTAX and co-occurrence network analysis suggested that the core microbial populations in the samples may be closely associated with organic matter metabolism. Subsequently, sludge samples from Taozi Lake were subjected to enrichment cultivation to isolate organic pollutant-degrading microorganisms. The strain Sphingobacterium sp. GEMB-CSS-01, tolerant to sulfanilamide, was successfully isolated. Subsequent investigations demonstrated that Sphingobacterium sp. GEMB-CSS-01 efficiently degraded the endocrine-disrupting compound 17β-Estradiol (E2). It achieved degradation efficiencies of 80.0% and 53.5% for E2 concentrations of 10 mg/L and 20 mg/L, respectively, within 10 days. Notably, despite a reduction in degradation efficiency, Sphingobacterium sp. GEMB-CSS-01 retained its ability to degrade E2 even in the presence of sulfanilamide concentrations ranging from 50 to 200 mg/L. The findings of this research identify potential microbial resources for environmental bioremediation, and concurrently provide valuable information about the microbial community structure and patterns within Taozi Lake.
Collapse
Affiliation(s)
- Shanshan Cao
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, PR China; Hunan Provincial Certified Enterprise Technology Center, Hunan Xiangjiao Liquor Industry Co., Ltd., Shaoyang, 422000, PR China
| | - Mifang Duan
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, PR China
| | - Xuan Zhang
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, 410004, PR China
| | - Zhilong Yang
- Hunan Provincial Certified Enterprise Technology Center, Hunan Xiangjiao Liquor Industry Co., Ltd., Shaoyang, 422000, PR China
| | - Rui Zhuo
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, PR China; Hunan Provincial Certified Enterprise Technology Center, Hunan Xiangjiao Liquor Industry Co., Ltd., Shaoyang, 422000, PR China.
| |
Collapse
|
2
|
Zhang S, Liu Y, Mohisn A, Zhang G, Wang Z, Wu S. Biodegradation of penicillin G sodium by Sphingobacterium sp. SQW1: Performance, degradation mechanism, and key enzymes. J Hazard Mater 2024; 468:133485. [PMID: 38377898 DOI: 10.1016/j.jhazmat.2024.133485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 02/22/2024]
Abstract
Biodegradation is an efficient and cost-effective approach to remove residual penicillin G sodium (PGNa) from the environment. In this study, the effective PGNa-degrading strain SQW1 (Sphingobacterium sp.) was screened from contaminated soil using enrichment technique. The effects of critical operational parameters on PGNa degradation by strain SQW1 were systematically investigated, and these parameters were optimized by response surface methodology to maximize PGNa degradation. Comparative experiments found the extracellular enzyme to completely degrade PGNa within 60 min. Combined with whole genome sequencing of strain SQW1 and LC-MS analysis of degradation products, penicillin acylase and β-lactamase were identified as critical enzymes for PGNa biodegradation. Moreover, three degradation pathways were postulated, including β-lactam hydrolysis, penicillin acylase hydrolysis, decarboxylation, desulfurization, demethylation, oxidative dehydrogenation, hydroxyl reduction, and demethylation reactions. The toxicity of PGNa biodegradation intermediates was assessed using paper diffusion method, ECOSAR, and TEST software, which showed that the biodegradation products had low toxicity. This study is the first to describe PGNa-degrading bacteria and detailed degradation mechanisms, which will provide new insights into the PGNa biodegradation.
Collapse
Affiliation(s)
- Sinan Zhang
- Engineering Research Center of Resource Utilization of Carbon-containing Waste with Carbon Neutrality, Ministry of Education, East China University of Science and Technology, Shanghai 200237, China; Department of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - YuXuan Liu
- Engineering Research Center of Resource Utilization of Carbon-containing Waste with Carbon Neutrality, Ministry of Education, East China University of Science and Technology, Shanghai 200237, China
| | - Ali Mohisn
- Department of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Guohui Zhang
- Engineering Research Center of Resource Utilization of Carbon-containing Waste with Carbon Neutrality, Ministry of Education, East China University of Science and Technology, Shanghai 200237, China
| | - Zejian Wang
- Department of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Shiyong Wu
- Engineering Research Center of Resource Utilization of Carbon-containing Waste with Carbon Neutrality, Ministry of Education, East China University of Science and Technology, Shanghai 200237, China.
| |
Collapse
|
3
|
Li Y, Guo X, Qiu Y, Fang C, Liu D, Liu Q, Dai X, Zhang L. Characterization of a novel multidrug-resistant genomic island in Sphingobacterium spp. strains recovered from pleural fluid of lung cancer patients. J Glob Antimicrob Resist 2023; 32:18-20. [PMID: 36521646 DOI: 10.1016/j.jgar.2022.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/02/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022] Open
Affiliation(s)
- Ying Li
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, China
| | - Xiyuan Guo
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, China; Biomedical Sciences Program, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Yichuan Qiu
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, China
| | - Chengju Fang
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, China
| | - Dan Liu
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Qian Liu
- Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Sichuan, China
| | - Xiaoyi Dai
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, China.
| | - Luhua Zhang
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, China.
| |
Collapse
|
4
|
Tan Z, Chen J, Liu Y, Chen L, Xu Y, Zou Y, Li Y, Gong B. The survival and removal mechanism of Sphingobacterium changzhouense TC931 under tetracycline stress and its' ecological safety after application. Bioresour Technol 2021; 333:125067. [PMID: 33878498 DOI: 10.1016/j.biortech.2021.125067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Sphingobacterium changzhouense TC931 was isolated as a novel TC (tetracycline) removal bacterium through adsorption on extracellular polymerase substances (EPS) and cellular surface and biodegradation. TC biodegradation efficiency by strain TC931 was affected by solution initial pH and carbon source. Polysaccharides and hydrocarbons in EPS and cellular surface were responsible for TC biosorption. Eight possible biodegradation products were identified and the biodegradation pathway was proposed. Strain TC931 was rich in antibiotic resistance genes, and tetX-TC931 and antibiotics resistance genome island (GI) may be acquired via horizontal gene transfer in early evolutionary history. The GI was incomplete and may stable in strain TC931, but it could develop into an intact and transferability GI with help of other mobile genetic elements. This work offers a theoretical basis for understanding the survival and biodegradation mechanisms of S. changzhouense TC931 under TC stress, and offers an ecological safety assessment for its application in environmental bioremediation.
Collapse
Affiliation(s)
- Zewen Tan
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Jiacheng Chen
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Yiling Liu
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Lian Chen
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Yuqing Xu
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Yixuan Zou
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Yongtao Li
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Beini Gong
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China.
| |
Collapse
|
5
|
Satti SM, Castro-Aguirre E, Shah AA, Marsh TL, Auras R. Genome Annotation of Poly(lactic acid) Degrading Pseudomonas aeruginosa, Sphingobacterium sp. and Geobacillus sp. Int J Mol Sci 2021; 22:ijms22147385. [PMID: 34299026 PMCID: PMC8305213 DOI: 10.3390/ijms22147385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/27/2021] [Accepted: 06/28/2021] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas aeruginosa and Sphingobacterium sp. are well known for their ability to decontaminate many environmental pollutants while Geobacillus sp. have been exploited for their thermostable enzymes. This study reports the annotation of genomes of P. aeruginosa S3, Sphingobacterium S2 and Geobacillus EC-3 that were isolated from compost, based on their ability to degrade poly(lactic acid), PLA. Draft genomes of the strains were assembled from Illumina reads, annotated and viewed with the aim of gaining insight into the genetic elements involved in degradation of PLA. The draft genome of Sphinogobacterium strain S2 (435 contigs) was estimated at 5,604,691 bp and the draft genome of P. aeruginosa strain S3 (303 contigs) was estimated at 6,631,638 bp. The draft genome of the thermophile Geobacillus strain EC-3 (111 contigs) was estimated at 3,397,712 bp. A total of 5385 (60% with annotation), 6437 (80% with annotation) and 3790 (74% with annotation) protein-coding genes were predicted for strains S2, S3 and EC-3, respectively. Catabolic genes for the biodegradation of xenobiotics, aromatic compounds and lactic acid as well as the genes attributable to the establishment and regulation of biofilm were identified in all three draft genomes. Our results reveal essential genetic elements that facilitate PLA metabolism at mesophilic and thermophilic temperatures in these three isolates.
Collapse
Affiliation(s)
- Sadia Mehmood Satti
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (S.M.S.); (A.A.S.)
- School of Packaging, Michigan State University, East Lansing, MI 48824-1223, USA;
- University Institute of Biochemistry and Biotechnology, PMAS Arid Agriculture University, Shamasabad, Muree Road, Rawalpindi 46300, Pakistan
| | - Edgar Castro-Aguirre
- School of Packaging, Michigan State University, East Lansing, MI 48824-1223, USA;
- Kraft Heinz Company, Glenview, IL 60025-4312, USA
| | - Aamer Ali Shah
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (S.M.S.); (A.A.S.)
| | - Terence L. Marsh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824-1223, USA
- Correspondence: (T.L.M.); (R.A.)
| | - Rafael Auras
- School of Packaging, Michigan State University, East Lansing, MI 48824-1223, USA;
- Correspondence: (T.L.M.); (R.A.)
| |
Collapse
|
6
|
Kakumanu ML, Marayati BF, Wada-Katsumata A, Wasserberg G, Schal C, Apperson CS, Ponnusamy L. Sphingobacterium phlebotomi sp. nov., a new member of family Sphingobacteriaceae isolated from sand fly rearing substrate. Int J Syst Evol Microbiol 2021; 71:004809. [PMID: 33956595 PMCID: PMC8289205 DOI: 10.1099/ijsem.0.004809] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 04/14/2021] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, non-motile, non-spore-forming, aerobic bacterium, designated type strain SSI9T, was isolated from sand fly (Phlebotomus papatasi Scopoli; Diptera: Psychodidae) rearing substrate and subjected to polyphasic taxonomic analysis. Strain SSI9T contained phosphatidylethanolamine as a major polar lipid, MK-7 as the predominant quinone, and C16 : 1ω6c/C16 : 1ω7c, iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 0 as the major cellular fatty acids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that SSI9T represents a member of the genus Sphingobacterium, of the family Sphingobacteriaceae sharing 96.5-88.0 % sequence similarity with other species of the genus Sphingobacterium. The results of multilocus sequence analysis using the concatenated sequences of the housekeeping genes recA, rplC and groL indicated that SSI9T formed a separate branch in the genus Sphingobacterium. The genome of SSI9T is 5 197 142 bp with a DNA G+C content of 41.8 mol% and encodes 4395 predicted coding sequences, 49 tRNAs, and three complete rRNAs and two partial rRNAs. SSI9T could be distinguished from other species of the genus Sphingobacterium with validly published names by several phenotypic, chemotaxonomic and genomic characteristics. On the basis of the results of this polyphasic taxonomic analysis, the bacterial isolate represents a novel species within the genus Sphingobacterium, for which the name Sphingobacterium phlebotomi sp. nov. is proposed. The type strain is SSI9T (=ATCC TSD-210T=LMG 31664T=NRRL B-65603T).
Collapse
Affiliation(s)
- Madhavi L. Kakumanu
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Bahjat Fadi Marayati
- Department of Biology, University of North Carolina Greensboro, 235 Eberhart Bldg., Greensboro, North Carolina, USA
| | - Ayako Wada-Katsumata
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Gideon Wasserberg
- Department of Biology, University of North Carolina Greensboro, 235 Eberhart Bldg., Greensboro, North Carolina, USA
| | - Coby Schal
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
| | - Charles S. Apperson
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
| | - Loganathan Ponnusamy
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
| |
Collapse
|
7
|
Sant' Anna D, Sampaio JLM, Sommaggio LRD, Mazzeo DEC, Marin-Morales MA, Marson FAL, Levy CE. The applicability of gene sequencing and MALDI-TOF to identify less common gram-negative rods (Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium) from environmental isolates. Antonie Van Leeuwenhoek 2019; 113:233-252. [PMID: 31560092 DOI: 10.1007/s10482-019-01333-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 09/13/2019] [Indexed: 11/26/2022]
Abstract
Our aim was to identify less common non-fermenting gram-negative rods during the bioremediation process. Five genera were found: Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium, for a total of 15 isolates. Therefore, we evaluated the applicability of four methods currently available for bacteria identification: (1) conventional biochemical methods, (2) the VITEK®-2 system, (3) MALDI-TOF mass spectrometry and (4) 16S rRNA gene sequencing. The biochemical methods and the VITEK®-2 system were reliable only for the Sphingobacterium isolate and solely at the genus level. Both MALDI-TOF mass spectrometry platforms (Bruker and VITEK® MS) did not achieve reliable identification results for any of these genera. 16S rRNA gene sequencing identified eight isolates to the species level but not to the subspecies level, when applicable. The remaining seven isolates were reliably identified through 16S rRNA gene sequencing to the genus level only. Our findings suggest that the detection and identification of less common genera (and species) that appeared at certain moments during the bioremediation process can be a challenge to microbiologists considering the most used techniques. In addition, more studies are required to confirm our results.
Collapse
Affiliation(s)
- Débora Sant' Anna
- Microbiology Laboratory, Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Villela, 1331, Barretos, São Paulo, Brazil.
| | - Jorge Luiz Mello Sampaio
- Microbiology Section, Fleury-Centers for Diagnostic Medicine, Av. General Waldomiro de Lima 508, São Paulo, 04344-070, Brazil
- Clinical Analysis and Toxicology Department, School of Pharmacy, University of São Paulo, Av. Professor Lineu Prestes, 580, Butantã, São Paulo, 05508-000, Brazil
| | - Lais Roberta Deroldo Sommaggio
- Department of Biology, Institute of Biosciences, São Paulo State University - Rio Claro, Av. 24 A, 1515, Bela Vista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Dânia Elisa Christofoletti Mazzeo
- Department of Analytical Chemistry, Institute of Chemistry, São Paulo State University - Araraquara, Rua Professor Francisco Degni, 55, Araraquara, São Paulo, 14800-060, Brazil
| | - Maria Aparecida Marin-Morales
- Department of Biology, Institute of Biosciences, São Paulo State University - Rio Claro, Av. 24 A, 1515, Bela Vista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Fernando Augusto Lima Marson
- Department of Pediatrics, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Laboratory of Pulmonary Physiology, Center for Pediatrics Investigation, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Department of Medical Genetics and Genomic Medicine, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Post-Graduate Program in Health Science, São Francisco University, Avenida São Francisco de Assis, 218, Cidade Universitária, Bragança Paulista, São Paulo, 12916-400, Brazil.
| | - Carlos Emílio Levy
- Microbiology Laboratory, Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Department of Pediatrics, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
| |
Collapse
|
8
|
Liu L, Hui N, Liang LX, Zhang XX, Li LB, Sun QW. Sphingobacterium haloxyli sp. nov., an endophytic bacterium isolated from Haloxylon ammodendron stems in Kumtag desert. Int J Syst Evol Microbiol 2018; 68:3279-3284. [PMID: 30156529 DOI: 10.1099/ijsem.0.002982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, aerobic, non-spore-forming, rod-shaped, bacterial strain, designated 5JN-11T, was isolated from Haloxylonammodendron stems in Kumtag desert, Xinjiang province, China. Strain 5JN-11T grew at salinities of 0-6 % (w/v; optimum 0-2 %), a pH of 7.0-9.0 (pH 7.0-8.0) and temperatures of 20-42 °C (28-30 °C). Based on 16S rRNA gene sequences, the strain was designated a member of the genus Sphingobacterium and the phylogenetic analysis showed that strain 5JN-11T shared the highest similarity to Sphingobacterium gobiense H7T, followed by Sphingobacterium chuzhouense DH-5T and Sphingobacterium arenae H-12T. The unfinished draft genome of strain 5JN-11T was 4.69 Mb. The G+C content of strain 5JN-11T was 42.8 mol%. The average nucleotide identity to S. gobiense H7T was 90.5 %. The respiratory quinone was MK-7, and the major polar lipids were phosphatidylethanolamine and phosphoglycolipid. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH. On the basis of phenotypic, genotypic and phylogenetic evidence, strain 5JN-11T represents a novel species in the genus Sphingobacterium, for which the name Sphingobacteriumhaloxyli sp. nov. is proposed. The type strain is 5JN-11T (=ACCC 60072T=KCTC 62457T).
Collapse
Affiliation(s)
- Lei Liu
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Nan Hui
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Li-Xiong Liang
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Xiao-Xia Zhang
- 2Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Lu-Bin Li
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Qi-Wu Sun
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| |
Collapse
|
9
|
Zhou XK, Li QQ, Mo MH, Zhang YG, Dong LM, Xiao M, Li WJ, Duan YQ. Sphingobacterium tabacisoli sp. nov., isolated from a tobacco field soil sample. Int J Syst Evol Microbiol 2017; 67:4808-4813. [PMID: 28984223 DOI: 10.1099/ijsem.0.002381] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, non-motile and rod-shaped bacterium, designated strain h337T, was isolated from an arable soil sample of a tobacco field in Kunming, south-west China. The cells showed oxidase-positive and catalase-positive reactions. Growth was observed at 10-35 °C, at pH 6.0-9.0 and in the presence of up to 3 % (w/v) NaCl, with optimal growth at 30 °C, pH 7.0 and with 1-2 % (w/v) NaCl. The predominant isoprenoid quinone was MK-7. The major fatty acids were identified as iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The cellular polar lipids contained phosphatidylethanolamine, sphingophospholipid, four unidentified phospholipids, five unidentified lipids and three unidentified aminophospholipids. The genomic DNA G+C content was 41.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain h337T should be assigned to the genus Sphingobacterium. 16S rRNA gene sequence similarity analysis showed that strain h337T was most closely related to 'Sphingobacteriumyamdrokense' 3-0-1 (98.8 %) and Sphingobacteriumyanglingense CCNWSP36-1T (98.5 %) and shared less than 97 % similarity with other species of the genus Sphingobacterium. DNA-DNA hybridization data indicated that the isolate represented a novel genomic species belonging to the genus Sphingobacterium. The characteristics determined in this polyphasic taxonomic study indicated that strain h337T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium tabacisoli sp. nov. (type strain h337T=KCTC 52298T=CCTCC AB 2017155T) is proposed.
Collapse
Affiliation(s)
- Xing-Kui Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China
| | - Qing-Qing Li
- Life Science College, Southwest Forestry University, Kunming 650224, PR China
- Kunming Xianghao Technology Co. Ltd., Kunming 650204, PR China
| | - Ming-He Mo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China
| | - Yong-Guang Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
| | - Li-Min Dong
- China Tobacco Yunnan Industrial Co. Ltd., Kunming 650231, PR China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China
| | - Yan-Qing Duan
- China Tobacco Yunnan Industrial Co. Ltd., Kunming 650231, PR China
| |
Collapse
|
10
|
Li S, Liu J, Sun M, Ling W, Zhu X. Isolation, Characterization, and Degradation Performance of the 17β-Estradiol-Degrading Bacterium Novosphingobium sp. E2S. Int J Environ Res Public Health 2017; 14:E115. [PMID: 28125060 PMCID: PMC5334669 DOI: 10.3390/ijerph14020115] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 01/16/2017] [Accepted: 01/16/2017] [Indexed: 11/17/2022]
Abstract
A 17β-estradiol (E2)-degrading bacterium E2S was isolated from the activated sludge in a sewage treatment plant (STP). The morphology, biological characteristics, and 16S ribosomal RNA (rRNA) gene sequence of strain E2S indicated that it belonged to the genus Novosphingobium. The optimal degrading conditions were 30 °C and pH 7.0. The ideal inoculum volume was 5% (v/v), and a 20-mL degradation system was sufficient to support the removal ability of strain E2S. The addition of extra NaCl to the system did not benefit the E2 degradation in batch culture by this strain. Strain E2S exhibited high degradation efficiency with initial substrate concentrations of 10-50 mg·L-1. For example, in mineral salt medium containing 50 mg·L-1 of E2, the degradation efficiency was 63.29% after seven days. In cow manure samples supplemented with 50 mg·L-1 of E2, strain E2S exhibited 66.40% degradation efficiency after seven days. The finding of the E2-degrading strain E2S provided a promising method for removing E2 from livestock manure in order to reduce the potential environmental risks of E2.
Collapse
Affiliation(s)
- Shunyao Li
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Juan Liu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Minxia Sun
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xuezhu Zhu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
11
|
Wang J, Chen J, Zhu W, Ma J, Rong Y, Cai Z. Isolation of the Novel Chiral Insecticide Paichongding (IPP) Degrading Strains and Biodegradation Pathways of RR/SS-IPP and SR/RS-IPP in an Aqueous System. J Agric Food Chem 2016; 64:7431-7437. [PMID: 27617492 DOI: 10.1021/acs.jafc.6b02862] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Chiral insecticide paichongding (IPP) is a member of cis-nitromethylene neonicotinoid insecticides used in China. IPP was the promising replacement for imidacloprid as a result of its higher activity against imidacloprid-resistant insects. Two pairs of enantiomers, RR/SS-IPP and SR/RS-IPP, were separated by preparative high-performance liquid chromatography and employed in an aqueous system to investigate their biodegradation process. In this study, the strains G1-13/G1-14 and G2-19 with effective IPP degrading capability were isolated from agricultural soils. G1-14 was mutated from G1-13 by ultraviolet light exposure. Sequence alignment of 16S rRNA proved that these three strains belonged to the genus of Sphingobacterium. The degradation rate of RR/SS-IPP by Sphingobacterium sp. G1-13 and G1-14 reached 13 and 30% within 6 and 4 days, respectively. The degradation rate of SR/RS-IPP by Sphingobacterium sp. G2-19 could reach 35% within 5 days. Degradation intermediates (I1-I6) of enantiomers were detected, and two possible biodegradation pathways were proposed on the basis of the identification of metabolites.
Collapse
Affiliation(s)
- Jing Wang
- Laboratory of Applied Microbiology and Biotechnology, School of Pharmaceutical Engineering & Life Science, Changzhou University , Changzhou, Jiangsu 213164, People's Republic of China
| | - Jie Chen
- Laboratory of Applied Microbiology and Biotechnology, School of Pharmaceutical Engineering & Life Science, Changzhou University , Changzhou, Jiangsu 213164, People's Republic of China
| | - Wenjuan Zhu
- Laboratory of Applied Microbiology and Biotechnology, School of Pharmaceutical Engineering & Life Science, Changzhou University , Changzhou, Jiangsu 213164, People's Republic of China
| | - Jiangtao Ma
- Laboratory of Applied Microbiology and Biotechnology, School of Pharmaceutical Engineering & Life Science, Changzhou University , Changzhou, Jiangsu 213164, People's Republic of China
| | - Yan Rong
- Laboratory of Applied Microbiology and Biotechnology, School of Pharmaceutical Engineering & Life Science, Changzhou University , Changzhou, Jiangsu 213164, People's Republic of China
| | - Zhiqiang Cai
- Laboratory of Applied Microbiology and Biotechnology, School of Pharmaceutical Engineering & Life Science, Changzhou University , Changzhou, Jiangsu 213164, People's Republic of China
| |
Collapse
|
12
|
Siddiqi MZ, Muhammad Shafi S, Choi KD, Im WT, Aslam Z. Sphingobacterium jejuense sp. nov., with ginsenoside-converting activity, isolated from compost. Int J Syst Evol Microbiol 2016; 66:4433-4439. [PMID: 27498829 DOI: 10.1099/ijsem.0.001370] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic, non-motile, light yellow, short-rod bacterium (designated GJ30-7T) isolated from compost, was characterized using a polyphasic approach, in order to clarify its taxonomic position. Strain GJ30-7T was observed to grow optimally at 30 °C and at pH 7.0 on R2A agar medium. Strain Gsoil GJ30-7T possessed β-glucosidase activity, which was responsible for its ability to transform ginsenosides Rb1 and Rc (the two main active components of ginseng) to ginsenoside F2. Phylogenetic analysis, based on 16S rRNA gene sequence similarities, indicated that GJ30-7T belongs to the genus Sphingobacterium of the family Sphingobacteriaceae and was most closely related to Sphingobacterium yanglingense JCM 30166T (92.6 %), Sphingobacterium psychroaquaticum KACC 18188T (92.6 %), and Sphingobacterium thermophilum KCTC 23708T (92.0 %). The DNA G+C content was 43 mol% and MK-7 was the major isoprenoid quinone. The main polar lipids were phosphatidylethanolamine, one unidentified phospolipid and one unknown polar lipid. In contrast to standard and reference strains, unidentified sphingolipid was also present. The predominant fatty acids of strain GJ30-7T were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3) and iso-C17 : 1ω9c and/or C16 : 0 10-methyl (summed feature 9), supporting the affiliation of strain GJ30-7T to the genus Sphingobacterium. However, strain GJ30-7T could be distinguished genotypically and phenotypically from species of the genus Sphingobacterium with validly published names. The novel isolate therefore represents a novel species, for which the name Sphingobacterium jejuense sp. nov. is proposed, with the type strain GJ30-7T (=KACC 18625T=JCM 30948T).
Collapse
Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
| | | | - Kang Duk Choi
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
| | - Wan-Taek Im
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
| | - Zubair Aslam
- Department of Agronomy, Faculty of Agriculture, University of Agriculture, Faisalabad-38040, Pakistan
| |
Collapse
|
13
|
Zangi-Kotler M, Ben-Dov E, Tiehm A, Kushmaro A. Microbial community structure and dynamics in a membrane bioreactor supplemented with the flame retardant dibromoneopentyl glycol. Environ Sci Pollut Res Int 2015; 22:17615-17624. [PMID: 26146373 DOI: 10.1007/s11356-015-4975-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/29/2015] [Indexed: 06/04/2023]
Abstract
Brominated flame retardants (BFRs) are a group of widely used compounds that, due to their limited biodegradability, exhibit excessive persistence in the environment. The persistence and high toxicity of these compounds to the natural biota causes great environmental concern. We investigated the biodegradation of the BFR dibromoneopentyl glycol (DBNPG) under continuous culture conditions using a miniature membrane bioreactor (mMBR) to assess its feasibility as a bioremediation approach. This system demonstrated long-term, stable biodegradation of DBNPG (>90 days), with an average removal rate of about 50%. Pyrosequencing of the 16S rRNA gene of the microorganisms involved in this process revealed the dominance of reads affiliated with the genus Brevundimonas of the Alphaproteobacteria class during the different mMBR operational stages. The bacterial community was also dominated by reads affiliated with the Sinorhizobium and Sphingopyxis genera within the Alphaproteobacteria class and the Sediminibacterium genus of the Sphingobacteria class. Real-time PCR used to analyze possible changes in the population dynamics of these four dominant groups revealed their consistent presence throughout the long-term mMBR biodegradation activity. Two genera, Brevundimonas and Sphingopyxis, were found to increase in abundance during the acclimation period and then remained relatively stable, forming the main parts of the consortium over the prolonged active stage.
Collapse
Affiliation(s)
- Moran Zangi-Kotler
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, 8410501, Beer-Sheva, Israel
| | - Eitan Ben-Dov
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, 8410501, Beer-Sheva, Israel
- Achva Academic College, 7980400, M.P. Shikmim, Israel
| | - Andreas Tiehm
- DVGW-Technologiezentrum Wasser (TZW), Karlsruher Straße 84, 76139, Karlsruhe, Germany
| | - Ariel Kushmaro
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, 8410501, Beer-Sheva, Israel.
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore.
| |
Collapse
|
14
|
Cai Z, Zhang W, Li S, Ma J, Wang J, Zhao X. Microbial Degradation Mechanism and Pathway of the Novel Insecticide Paichongding by a Newly Isolated Sphingobacterium sp. P1-3 from Soil. J Agric Food Chem 2015; 63:3823-3829. [PMID: 25815695 DOI: 10.1021/acs.jafc.5b00706] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Using 1-((6-chloropydidin-3-yl)methyl)-7-methyl-8-nitro-5propoxy-1,2,3,5,6,7-hexahydroimidazo[1,2-α-]-pyridine (IPP) as the sole carbon source, we isolated a strain with a higher activity of IPP-degrading bacterium Sphingobacterium sp. P1-3 from soil. At 30 °C, pH 7.0 ,and 10 mg L(-1) IPP content, the degradation rate of IPP by Sphingobacterium sp. P1-3 could reach 57.75 and 62.47% in 20 and 30 days, respectively. The value of DT50 of IPP was 27 d at the level of 30 mg L(-1) IPP, while DT50 in the blank test was 151 d. During the IPP biodegradation process, five intermediates (M1-M5) were monitored and identified. On the basis of the identified metabolites and their biodegradation courses, a possible biodegradation pathway was proposed. IPP biodegradation mainly occurred on the tetrahydropyridine ring. IPP was transformed to five different metabolites by strain P1-3 through the oxidation and elimination of methyl, propyl, and nitro groups. Moreover, a new pathway involving M2 (1-((6-chloropydidin-3-yl)methyl)-7-methyl-8-hydroxy-5-propoxy-1,2,3,5,6,7-hexahydroimidazo [1,2-α-]-pyridine), M3 (1-((6-chloropydidin-3-yl)methyl)-7-methyl-5-carbonyl-1,2,3,5,6,7-hexahydroimidazo[1,2-α-]-pyridine), and M5 (8-amino-1,2,3,5,6,7-hexahydroimidazo[1,2-α-]-pyridine) was first monitored and identified.
Collapse
|
15
|
Gao C, Jin X, Ren J, Fang H, Yu Y. Bioaugmentation of DDT-contaminated soil by dissemination of the catabolic plasmid pDOD. J Environ Sci (China) 2015; 27:42-50. [PMID: 25597661 DOI: 10.1016/j.jes.2014.05.045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 05/12/2014] [Accepted: 05/27/2014] [Indexed: 06/04/2023]
Abstract
A plasmid transfer-mediated bioaugmentation method for the enhancement of dichlorodiphenyltrichloroethane (DDT) degradation in soil was developed using the catabolic plasmid pDOD from Sphingobacterium sp. D-6. The pDOD plasmid could be transferred to soil bacteria, such as members of Cellulomonas, to form DDT degraders and thus accelerate DDT degradation. The transfer efficiency of pDOD was affected by the donor, temperature, moisture, and soil type. Approximately 50.7% of the DDT in the contaminated field was removed 210 days after the application of Escherichia coli TG I (pDOD-gfp). The results suggested that seeding pDOD into soil is an effective bioaugmentation method for enhancing the degradation of DDT.
Collapse
Affiliation(s)
- Chunming Gao
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiangxiang Jin
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jingbei Ren
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hua Fang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Yunlong Yu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
16
|
Peng S, Hong DD, Xin YB, Jun LM, Hong WG. Sphingobacterium yanglingense sp. nov., isolated from the nodule surface of soybean. Int J Syst Evol Microbiol 2014; 64:3862-3866. [PMID: 25168614 DOI: 10.1099/ijs.0.068254-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
A Gram-staining-negative, non-motile, catalase- and oxidase-positive strain, designated CCNWSP36-1(T), was isolated from the nodule surface of soybean [Glycine max (L.) Merrill] cultivar Zhonghuang 13. The 16S rRNA gene sequence analysis clearly showed that the isolate represented a member of the genus Sphingobacterium. On the basis of pairwise comparisons of 16S rRNA gene sequences, strain CCNWSP36-1(T) showed 96.8% similarity to Sphingobacterium nematocida CCTCC AB 2010390(T) and less than 95.2% similarity to other members of the genus Sphingobacterium. Growth of strain CCNWSP36-1(T) occurred at 10-40 °C and at pH 5.0-9.0. The NaCl range (w/v) for growth was 0-4%. The predominant isoprenoid quinone was MK-7. The polar lipids were phosphatidylethanolamine and several unidentified polar lipids. Sphingolipid was present. The major fatty acids were iso-C(15:0) and summed feature 3 (comprising C(16:1)ω6c and/or C(16:1)ω7c). The G+C content of the genomic DNA was 41.1 mol%. As the physiological and biochemical characteristics of strain CCNWSP36-1(T) and the type strains of its closest phylogenetic neighbours showed clear differences, a novel species, Sphingobacterium yanglingense, is proposed. The type strain is CCNWSP36-1(T) ( =ACCC 19328(T) =JCM 30166(T)).
Collapse
Affiliation(s)
- Shi Peng
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Dong Dan Hong
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yang Bing Xin
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Li Ming Jun
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Wei Ge Hong
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| |
Collapse
|
17
|
Cong Y, Xu Q, Feng H, Shen D. Efficient electrochemically active biofilm denitrification and bacteria consortium analysis. Bioresour Technol 2013; 132:24-27. [PMID: 23395754 DOI: 10.1016/j.biortech.2013.01.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 12/30/2012] [Accepted: 01/02/2013] [Indexed: 06/01/2023]
Abstract
The electrochemically active biofilms have been successfully developed for nitrate removal from the wastewater. The electrochemically "selected" bacteria showed higher activity than the control bacteria. Electron exchange occurred between the electrochemically active bacteria and cathode was identified. Direct electron transfer between the "selected" bacteria and cathodes may be involved in efficient denitrification besides hydrogen transfer, and would contribute to improve denitrification efficiency. The gene analysis of 16S rDNA demonstrated that there was a pronounced enrichment in bacteria of the β-Proteobacteria with 41.93%, Uncultured bacterium clone Dok04 with 25.11% and Sphingobacteria with 6.36% of the sequences from the bacteria consortium with current acclimation. The engineering-oriented multispecies bacteria were favorable to form conductive biofilms and showed high potential for nitrate treatment.
Collapse
Affiliation(s)
- Yanqing Cong
- College of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, People's Republic of China.
| | | | | | | |
Collapse
|
18
|
|
19
|
Liu J, Yang LL, Xu CK, Xi JQ, Yang FX, Zhou F, Zhou Y, Mo MH, Li WJ. Sphingobacterium nematocida sp. nov., a nematicidal endophytic bacterium isolated from tobacco. Int J Syst Evol Microbiol 2012; 62:1809-1813. [PMID: 21984669 DOI: 10.1099/ijs.0.033670-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-negative strain, designated M-SX103(T), was isolated from a fresh leaf of Nicotiana tabacum Linn. collected at Yuxi City, Yunnan province, China, and subjected to a polyphasic taxonomic study. Growth occurred at 10-40 °C, at pH 6.0-9.0 and with 0-3% (w/v) NaCl. The predominant isoprenoid quinone was MK-7. The major cellular fatty acids of strain M-SX103(T) were iso-C(15:0), iso-C(17:0) 3-OH and summed feature 3 (C(16:1)ω7c and/or C(16:1)ω6c). The G+C content of the genomic DNA was 40.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belongs to the genus Sphingobacterium, sharing 95.4-89.7% sequence similarity with type strains of members of the genus Sphingobacterium; it was most closely related to Sphingobacterium composti T5-12(T). On the basis of the taxonomic evidence, a novel species, Sphingobacterium nematocida sp. nov., is proposed. The type strain is M-SX103(T) ( = JCM 17339(T) = CCTCC AB 2010390(T)).
Collapse
Affiliation(s)
- Jie Liu
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Ling-Ling Yang
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Chuan-Kun Xu
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Jia-Qin Xi
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, PR China
| | - Fa-Xiang Yang
- Yunnan Yunye Fertilizer Co. Ltd, Kunming 650217, PR China
| | - Feng Zhou
- Shandong TaiFengYuan Biotechnology Co. Ltd, Jinan 250014, PR China
| | - Yu Zhou
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Ming-He Mo
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Wen-Jun Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, PR China
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, PR China
| |
Collapse
|
20
|
Szabó I, Szoboszlay S, Kriszt B, Háhn J, Harkai P, Baka E, Táncsics A, Kaszab E, Privler Z, Kukolya J. Olivibacter oleidegradans sp. nov., a hydrocarbon-degrading bacterium isolated from a biofilter clean-up facility on a hydrocarbon-contaminated site. Int J Syst Evol Microbiol 2011; 61:2861-2865. [PMID: 21257685 DOI: 10.1099/ijs.0.026641-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel hydrocarbon-degrading, Gram-negative, obligately aerobic, non-motile, non-sporulating, rod-shaped bacterium, designated strain TBF2/20.2(T), was isolated from a biofilter clean-up facility set up on a hydrocarbon-contaminated site in Hungary. It was characterized by using a polyphasic approach to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate is affiliated with the genus Olivibacter in the family Sphingobacteriaceae. It was found to be related most closely to Olivibacter ginsengisoli Gsoil 060(T) (93.3% 16S rRNA gene sequence similarity). Strain TBF2/20.2(T) grew at pH 6-9 (optimally at pH 6.5-7.0) and at 15-42 °C (optimally at 30-37 °C). The major fatty acids were iso-C(15:0) (39.4%), summed feature 3 (iso-C(15:0) 2-OH and/or C(16:1)ω7c; 26.0%), iso-C(17:0) 3-OH (14.5%) and C(16:0) (4.5%). The major menaquinone was MK-7 and the predominant polar lipid was phosphatidylethanolamine. The DNA G+C content of strain TBF2/20.2(T) was 41.2 mol%. Physiological and chemotaxonomic data further confirmed the distinctiveness of strain TBF2/20.2(T) from recognized members of the genus Olivibacter. Thus, strain TBF2/20.2(T) is considered to represent a novel species of the genus Olivibacter, for which the name Olivibacter oleidegradans sp. nov. is proposed. The type strain is TBF2/20.2(T) (=NCAIM B 02393(T) =CCM 7765(T)).
Collapse
Affiliation(s)
- István Szabó
- Department of Environmental Protection and Environmental Safety, Szent István University, Páter K. u. 1., 2103 Gödöllő, Hungary
| | - Sándor Szoboszlay
- Department of Environmental Protection and Environmental Safety, Szent István University, Páter K. u. 1., 2103 Gödöllő, Hungary
| | - Balázs Kriszt
- Department of Environmental Protection and Environmental Safety, Szent István University, Páter K. u. 1., 2103 Gödöllő, Hungary
| | - Judit Háhn
- Regional University Center of Excellence, Szent István University, Gödöllő, Hungary
| | - Péter Harkai
- Regional University Center of Excellence, Szent István University, Gödöllő, Hungary
| | - Erzsébet Baka
- Regional University Center of Excellence, Szent István University, Gödöllő, Hungary
| | - András Táncsics
- Regional University Center of Excellence, Szent István University, Gödöllő, Hungary
| | - Edit Kaszab
- Department of Environmental Protection and Environmental Safety, Szent István University, Páter K. u. 1., 2103 Gödöllő, Hungary
| | | | | |
Collapse
|
21
|
Duan XQ, Zheng JW, Zhang J, Hang BJ, He J, Li SP. [Characteristics of a 3-phenoxybenzoic acid degrading-bacterium and the construction of a engineering bacterium]. Huan Jing Ke Xue 2011; 32:240-246. [PMID: 21404693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A bacterium capable of utilizing 3-phenoxybenzoic acid (3-PBA) as sole carbon source was isolated from petroleum-contaminated soil. This bacterium, designated as BA3, was identified as Sphingobium sp. according to its physiological & biochemical characteristic and the similarity analysis of its 16S rDNA sequence. Strain BA3 was able to degrade 99% of 100 mg x L(-1) 3-phenoxybenzoic acid within 60 h. The optimal pH and temperature for the degradation were 7.0 and 30 degrees C, respectively. The degradation efficiency was related positively to initial inoculum size. The pyrethroid hydrolase gene (pytH) gene was amplified from the genomic DNA of Sphingobium sp. JZ-2 by PCR. Recombinant plasmids pPYTH was constructed by ligating pytH gene into the broad host vector pBBRMCS- 5. Under the help of plasmid RK600, pPYTH was transferred into Sphingobium sp. BA3 to construct engineering strain BA3-pytH; Fenpropathrin degradation experiments showed that strain JZ-2 was able to degrade only 60% of 50 mg x L(-1) fenpropathrin in 48 h while engineering strain BA3-pytH was able to degrade over 95% of 50 mg x L(-1) fenpropathrin under the same conditions. Even more, BA3-pytH could rapidly degrade 3-PBA, metabolic products of pyrethroid insecticides, eliminating the inhibition of 3-PBA to pyrethroid hydrolase. Therefore, in contrast to strain JZ-2, engineering strain BA3-pytH had more advantages in bioremediation of pyrethroid insecticides contaminated environment.
Collapse
Affiliation(s)
- Xiao-Qin Duan
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | | | | | | | | | | |
Collapse
|
22
|
Tamboli DP, Kagalkar AN, Jadhav MU, Jadhav JP, Govindwar SP. Production of polyhydroxyhexadecanoic acid by using waste biomass of Sphingobacterium sp. ATM generated after degradation of textile dye Direct Red 5B. Bioresour Technol 2010; 101:2421-2427. [PMID: 20031399 DOI: 10.1016/j.biortech.2009.11.094] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Revised: 11/24/2009] [Accepted: 11/25/2009] [Indexed: 05/28/2023]
Abstract
The degradation of textile effluent using microorganisms has been studied extensively, but disposal of generated biomass after dye degradation is a serious problem. The isolated Sphingobacterium sp. ATM was found to decolorize dye Direct Red 5B (DR5B) and simultaneously it produced polyhydroxyhexadecanoic acid (PHD). The organism decolorized DR5B at 500mgl(-1) concentration within 24h of dye addition and gave optimum production of PHD. The medium contains carbon source as a molasses which was found to be more significant within all carbon sources used. The Nuclear Magnetic Resonance spectroscopy (NMR), Fourier Transform Infrared spectroscopy (FTIR) and Gas Chromatography-Mass Spectroscopy (GC-MS) characterization of polyhydroxyalkanoates obtained revealed the compound as a polyhydroxyhexadecanoic acid. The activity of PHA synthase was found more at 24h after dye addition. The enzymes responsible for dye degradation include veratrol oxidase, laccase, DCIP (2,6-dichlorophenol-indophenol) reductase, riboflavin reductase and azo reductase was found to be induced during decolorization process. The FTIR analysis of samples before and after decolorization of dye confirmed the biotransformation of DR5B. The GC-MS analysis of product obtained led to the identification of two metabolites after biotransformation of dye as p-amino benzenesulfonic acid and naphthalene-1-ol.
Collapse
Affiliation(s)
- Dhawal P Tamboli
- Department of Biotechnology, Shivaji University, Kolhapur 416 004, India
| | | | | | | | | |
Collapse
|
23
|
Tang Y, Wang Y, Ji S, Zhang K, Dai J, Zhang L, Peng F, Fang C. Pedobacter xinjiangensis sp. nov., from desert, Xinjiang. J Microbiol Biotechnol 2010; 20:397-402. [PMID: 20208447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A Gram-negative, rod-shaped, gliding, aerobic bacterium, designated 12157(T), was isolated from the desert of Xinjiang, China and subjected to a polyphasic taxonomic study. The strain 12157(T) grew optimally at pH 7.0 and 30 degrees Celsius. MK-7 was the predominant respiratory menaquinone. The DNA G+C content was 42.0 mol%. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the isolate was mostly related to the members of the genus Pedobacter, with similarities ranging from 90.0 % to 93.7 %. Phylogenetic evidence and the results of phenotypic, genotypic and chemotaxonomic analysis support the establishment of a novel species, Pedobacter xinjiangensis sp. nov., with strain 12157(T) (=CCTCC AB 208092(T)=NRRL B-51338(T)) as the type strain.
Collapse
Affiliation(s)
- Yali Tang
- College of Life Sciences, Wuhan University, Wuhan 430072, P. R. China
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Zhang K, Wang Y, Tang Y, Dai J, Zhang L, An H, Luo G, Rahman E, Fang C. Niastella populi sp. nov., isolated from soil of Euphrates poplar (Populus euphratica) forest, and emended description of the genus Niastella. Int J Syst Evol Microbiol 2009; 60:542-545. [PMID: 19654358 DOI: 10.1099/ijs.0.012112-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, designated THYL-44(T), was isolated from the soil of a Euphrates poplar (Populus euphratica) forest in Xinjiang, China. The cells were strictly aerobic, Gram-staining-negative, non-flagellated, non-motile and filamentous. Growth occurred at 17-37 degrees C (optimum 30 degrees C), at pH 5.0-8.0 (optimum pH 7.0) and with 0-1 % NaCl (w/v; optimum 0 %). Flexirubin pigments were not produced. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain THYL-44(T) was closely related to Niastella koreensis KACC 11465(T) (95.5 % sequence similarity). The major respiratory quinone was MK-7 and the predominant cellular fatty acids were iso-C(15 : 0) (28.6 %), iso-C(17 : 0) 3-OH (23.9 %) and iso-C(15 : 1) G (17.4 %). The DNA G+C content was 45.2 mol%. Therefore, the phylogenetic, physiological and chemotaxonomic data demonstrated that strain THYL-44(T) represents a novel species of the genus Niastella , for which the name Niastella populi sp. nov. is proposed. The type strain is THYL-44(T) (=CCTCC AB 208238(T)=KCTC 22560(T)). On the basis of new data, an emended description of the genus Niastella is also proposed.
Collapse
Affiliation(s)
- Kundi Zhang
- College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Yang Wang
- College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Yali Tang
- College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Jun Dai
- College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Lei Zhang
- College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Hongli An
- College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Guangchao Luo
- College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Erkin Rahman
- College of Life Science and Technology, Xinjiang University, Urumchi 830046, PR China
| | - Chengxiang Fang
- College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| |
Collapse
|
25
|
Hantsis-Zacharov E, Halpern M. Culturable psychrotrophic bacterial communities in raw milk and their proteolytic and lipolytic traits. Appl Environ Microbiol 2007; 73:7162-8. [PMID: 17890340 PMCID: PMC2168224 DOI: 10.1128/aem.00866-07] [Citation(s) in RCA: 196] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 08/10/2007] [Indexed: 11/20/2022] Open
Abstract
During cold storage after milk collection, psychrotrophic bacterial populations dominate the microflora, and their extracellular enzymes, mainly proteases and lipases, contribute to the spoilage of dairy products. The diversity, dynamics, and enzymatic traits of culturable psychrotrophs in raw milk from four farms were investigated over a 10-month period. About 20% of the isolates were found to be novel species, indicating that there is still much to be learned about culturable psychrotrophs in raw milk. The psychrotrophic isolates were identified and classified in seven classes. Three classes were predominant, with high species richness (18 to 21 species per class) in different seasons of the year: Gammaproteobacteria in spring and winter, Bacilli in summer, and Actinobacteria in autumn. The four minor classes were Alphaproteobacteria, Betaproteobacteria, Flavobacteria, and Sphingobacteria. The dominant classes were found in all four dairies, although every dairy had its own unique "bacterial profile." Most but not all bacterial isolates had either lipolytic or both lipolytic and proteolytic activities. Only a few isolates showed proteolytic activity alone. The dominant genera, Pseudomonas and Acinetobacter (Gammaproteobacteria), showed mainly lipolytic activity, Microbacterium (Actinobacteria) was highly lipolytic and proteolytic, and the lactic acid bacteria (Lactococcus and Leuconostoc) displayed very minor enzymatic ability. Hence, the composition of psychrotrophic bacterial flora in raw milk has an important role in the determination of milk quality. Monitoring the dominant psychrotrophic species responsible for the production of heat-stable proteolytic and lipolytic enzymes offers a sensitive and efficient tool for maintaining better milk quality in the milk industry.
Collapse
Affiliation(s)
- Elionora Hantsis-Zacharov
- Department of Evolutionary and Environmental Biology, Faculty of Science and Science Education, University of Haifa, Mount Carmel, Haifa 31905, Israel
| | | |
Collapse
|
26
|
Abstract
A free-living Gram-negative bacterial strain CR11(T) was isolated from corn roots. Polyphasic taxonomy was performed, including API20 NE and API50 CH bacterial identification kits, Biolog analysis, lipids and fatty acid analysis, DNA-DNA hybridization, 16S rRNA and cpn60 gene sequence analyses. 16S rRNA gene sequence analysis indicated that strain CR11(T) belonged to the genus Sphingobacterium and was closely related to Sphingobacterium multivorum IFO 14947(T) (98% similarity) and Sphingobacterium. thalpophilum ATCC 43320(T) (97% similarity). DNA-DNA hybridization showed 11% and 13% DNA re-association with S. multivorum LMG 8342(T) and S. thalpophilum LMG 11520(T), respectively. Major fatty acids (16:0, 15:0 iso and 17:0 iso 3-OH) and the G+C content of the DNA (40.5 mol%), were also similar to those of the genus Sphingobacterium. The predominant respiratory quinone was MK-7. In all analyses, including phenotypic characterization, this isolate was found to be different from the closely related species, S. multivorum and S. thalpophilum. On the basis of these results, this strain represents a new species within the genus Sphingobacterium. The name Sphingobacterium canadense sp. nov. is suggested and the type strain is CR11(T) (=NCCB 100125(T)=LMG 23727(T)).
Collapse
MESH Headings
- Bacterial Typing Techniques
- Base Composition
- Chaperonin 60/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Genes, rRNA
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phospholipids/analysis
- Phylogeny
- Plant Roots/microbiology
- Quinones/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sphingobacterium/chemistry
- Sphingobacterium/classification
- Sphingobacterium/genetics
- Sphingobacterium/isolation & purification
- Zea mays/microbiology
Collapse
Affiliation(s)
- Samina Mehnaz
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | | | | |
Collapse
|
27
|
Yoo SH, Weon HY, Jang HB, Kim BY, Kwon SW, Go SJ, Stackebrandt E. Sphingobacterium composti sp. nov., isolated from cotton-waste composts. Int J Syst Evol Microbiol 2007; 57:1590-1593. [PMID: 17625199 DOI: 10.1099/ijs.0.64948-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, strictly aerobic, short rod-shaped, non-motile bacterial strain designated 4M24Twas isolated from cotton-waste compost. Analysis of the 16S rRNA gene sequence of strain 4M24Trevealed that it is a member of the genusSphingobacterium, sharing 88.5–94.5 % sequence similarity with type strains of the genusSphingobacteriumand being most closely related toSphingobacterium daejeonenseTR6-04T(94.5 % sequence similarity) andSphingobacterium mizutaiiATCC 33299T(92.2 % similarity). The major fatty acids of strain 4M24Tgrown on trypticase soy agar medium were summed feature 3 (iso-C15 : 02-OH and/or C16 : 1ω7c; 37.5 %), iso-C15 : 0(29.5 %) and iso-C17 : 03-OH (19.7 %). The G+C content of the genomic DNA was 42.3 mol%. On the basis of phenotypic and genotypic characteristics, strain 4M24Trepresents a novel species of the genusSphingobacterium, for which the nameSphingobacterium compostisp. nov. is proposed. The type strain is 4M24T(=KACC 11313T=DSM 18850T).
Collapse
MESH Headings
- Aerobiosis
- Bacterial Typing Techniques
- Base Composition
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Genes, rRNA
- Gossypium/microbiology
- Korea
- Locomotion
- Molecular Sequence Data
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil
- Soil Microbiology
- Sphingobacterium/chemistry
- Sphingobacterium/classification
- Sphingobacterium/genetics
- Sphingobacterium/isolation & purification
Collapse
Affiliation(s)
- Seung-Hee Yoo
- Korean Agricultural Culture Collection (KACC), Microbial Genetics Division, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Hang-Yeon Weon
- Applied Microbiology Division, National Institute of Agricultural Science and Technology, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Han-Byul Jang
- Korean Agricultural Culture Collection (KACC), Microbial Genetics Division, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Byung-Yong Kim
- Korean Agricultural Culture Collection (KACC), Microbial Genetics Division, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Soon-Wo Kwon
- Korean Agricultural Culture Collection (KACC), Microbial Genetics Division, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Seung-Joo Go
- Korean Agricultural Culture Collection (KACC), Microbial Genetics Division, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Erko Stackebrandt
- Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| |
Collapse
|
28
|
Kwon SW, Kim BY, Lee KH, Jang KY, Seok SJ, Kwon JS, Kim WG, Weon HY. Pedobacter suwonensis sp. nov., isolated from the rhizosphere of Chinese cabbage (Brassica campestris). Int J Syst Evol Microbiol 2007; 57:480-484. [PMID: 17329772 DOI: 10.1099/ijs.0.64196-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A mesophilic bacterium, strain 15-52T, was isolated from the rhizosphere of Chinese cabbage (Brassica campestris). On the basis of phenotypic and genotypic characteristics, the bacterium was identified as representing a novel species belonging to the genus Pedobacter. The strain is non-flagellated, non-spore-forming and grows at temperatures in the range 1–37 °C. Physiological tests of the strain showed the presence of oxidase, catalase, protease (gelatin and casein hydrolysis), β-glucosidase and β-galactosidase activities. The highest levels of 16S rRNA gene sequence similarity were found with respect to Pedobacter roseus CL-GP80T (97.3 %) and Pedobacter sandarakinus DS-27T (97.2 %). A phylogenetic analysis based on 16S rRNA gene sequence data indicated that strain 15-52T is a member of the genus Pedobacter. DNA–DNA hybridization analysis revealed low levels of relatedness (<42.3 %) between the isolate and two phylogenetically related type strains, P. roseus KCCM 42272T and P. sandarakinus KCTC 12559T. The DNA G+C content is 44.2 mol% and the predominant fatty acids are iso-C15 : 0 (35.4 %), iso-C15 : 0 2-OH and/or C16 : 1
ω7c (27.8 %) and iso-C17 : 0 3-OH (15.8 %). On the basis of these data, strain 15-52T represents a novel species of the genus Pedobacter, for which the name Pedobacter suwonensis sp. nov. is proposed. The type strain is 15-52T (=KACC 11317T=DSM 18130T).
Collapse
Affiliation(s)
- Soon-Wo Kwon
- Korean Agricultural Culture Collection (KACC), Genetic Resources Division, National Institute of Agricultural Biotechnology, Rural Development Administration (RDA), Suwon 441-707, Korea
| | - Byung-Yong Kim
- Korean Agricultural Culture Collection (KACC), Genetic Resources Division, National Institute of Agricultural Biotechnology, Rural Development Administration (RDA), Suwon 441-707, Korea
| | - Kang-Hyo Lee
- Applied Microbiology Division, National Institute of Agricultural Science and Technology, RDA, Suwon 441-707, Korea
| | - Kab-Yeul Jang
- Applied Microbiology Division, National Institute of Agricultural Science and Technology, RDA, Suwon 441-707, Korea
| | - Soon-Ja Seok
- Applied Microbiology Division, National Institute of Agricultural Science and Technology, RDA, Suwon 441-707, Korea
| | - Jang-Sik Kwon
- Applied Microbiology Division, National Institute of Agricultural Science and Technology, RDA, Suwon 441-707, Korea
| | - Wan-Gyu Kim
- Applied Microbiology Division, National Institute of Agricultural Science and Technology, RDA, Suwon 441-707, Korea
| | - Hang-Yeon Weon
- Applied Microbiology Division, National Institute of Agricultural Science and Technology, RDA, Suwon 441-707, Korea
| |
Collapse
|
29
|
Takahashi M, Suzuki KI, Nakagawa Y. Emendation of the genus Flammeovirga and Flammeovirga aprica with the proposal of Flammeovirga arenaria nom. rev., comb. nov. and Flammeovirga yaeyamensis sp. nov. Int J Syst Evol Microbiol 2006; 56:2095-2100. [PMID: 16957105 DOI: 10.1099/ijs.0.64324-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic positions of five bacterial strains isolated from the Yaeyama Islands of Japan and ‘Microscilla arenaria’ NBRC 15982 were determined using a polyphasic taxonomic approach. 16S rRNA gene sequence analyses placed all of the strains close to the genus Flammeovirga. DNA–DNA hybridization studies, biochemical and physiological characterizations and chemotaxonomic analyses suggested that ‘M. arenaria’ NBRC 15982 and the five novel isolates represented two separate species of the genus Flammeovirga. Emendation of the genus Flammeovirga Nakagawa et al. 1997 and the species Flammeovirga aprica (Reichenbach 1989) Nakagawa et al. 1997 is proposed. In addition, ‘Microscilla arenaria’ Lewin 1969 is proposed as Flammeovirga arenaria nom. rev., comb. nov. (with the type strain NBRC 15982T=CIP 109101T) and the novel isolates are proposed as Flammeovirga yaeyamensis sp. nov. (type strain IR25-3T=NBRC 100898T=CIP 109099T).
Collapse
Affiliation(s)
- Mai Takahashi
- Biological Resource Center (NBRC), Department of Biotechnology, National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Ken-Ichiro Suzuki
- Biological Resource Center (NBRC), Department of Biotechnology, National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Yasuyoshi Nakagawa
- Biological Resource Center (NBRC), Department of Biotechnology, National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| |
Collapse
|
30
|
Abstract
A Gram-negative, strictly aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated TR6-04T, was isolated from compost and characterized taxonomically by using a polyphasic approach. The organism grew optimally at 30 °C and at pH 6.5–7.0. The isolate was positive for catalase and oxidase tests but negative for gelatinase, indole and H2S production. Comparative 16S rRNA gene sequence analysis showed that strain TR6-04T fell within the radiation of the cluster comprising Sphingobacterium species and clustered with Sphingobacterium mizutaii ATCC 33299T (96.7 % sequence similarity); the similarity to sequences of other species within the family Sphingobacteriaceae was less than 92.0 %. The G+C content of the genomic DNA was 38.7 mol%. The predominant respiratory quinone was MK-7. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1
ω7c). These chemotaxonomic data supported the affiliation of strain TR6-04T to the genus Sphingobacterium. However, on the basis of its phenotypic properties and phylogenetic distinctiveness, strain TR6-04T (=KCTC 12579T=LMG 23402T=CCUG 52468T) should be classified as the type strain of a novel species, for which the name Sphingobacterium daejeonense sp. nov. is proposed.
Collapse
Affiliation(s)
- Kyoung-Ho Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Leonid N Ten
- National University of Uzbekistan, Students town, Tashkent, 700-174, Uzbekistan
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Qing-Mei Liu
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Wan-Taek Im
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Sung-Taik Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
| |
Collapse
|
31
|
Cérémonie H, Boubakri H, Mavingui P, Simonet P, Vogel TM. Plasmid-encoded gamma-hexachlorocyclohexane degradation genes and insertion sequences in Sphingobium francense (ex-Sphingomonas paucimobilis Sp+). FEMS Microbiol Lett 2006; 257:243-52. [PMID: 16553860 DOI: 10.1111/j.1574-6968.2006.00188.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The lin genes encode the gamma-hexachlorocyclohexane (gamma-HCH or lindane) catabolic pathway in lindane-degrading strains. The location and stability of these genes have been explored in the lindane-degrading Sphingobium francense strain Sp+, and in two non-lindane-degrading mutants (Sp1- and Sp2-). The lin genes, linA, linB, linE and linX were localized by hybridization on three of the six plasmids of the S. francense strain Sp+ showing dispersal within the genome. The linC gene was detected by PCR, but was not detected by hybridization on any of the plasmids. The hybridization of the linA and linX genes was negative with the two non-lindane-degrading mutants S. francense strains, Sp1- and Sp2-. The dynamic of this genome associated with gene loss and acquisition, and plasmid rearrangement was explored by a search for associated insertion sequences. A new insertion sequence, ISSppa4, belonging to the IS21 family was detected and compared with IS6100 and ISsp1. Insertion sequence localization was explored on different hybridization patterns (plasmid, total genome) with the lindane-degrading Sp+ strain and the two non-degrading derivatives (Sp1-, Sp2-). Insertion sequence movement and plasmid rearrangement could explain the emergence of the non-lindane-degrading mutants.
Collapse
Affiliation(s)
- Hélène Cérémonie
- Ecologie Microbienne UMR-CNRS 5557, Université Claude Bernard Lyon 1, Villeurbanne Cedex, France
| | | | | | | | | |
Collapse
|
32
|
Abstract
A Gram-negative, non-motile, rod-shaped bacterial strain, designated DS-27T, was isolated from a soil sample, and its taxonomic position was investigated by using a polyphasic approach. The organism grew optimally at 30 °C and in the presence of 0–0.5 % (w/v) NaCl. Strain DS-27T contained MK-7 as the predominant menaquinone and iso-C15 : 0, C16 : 1
ω7c and/or iso-C15 : 0 2-OH and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 39.7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DS-27T is most closely related to the genus Pedobacter of the family Sphingobacteriaceae. Similarity values between the 16S rRNA gene sequences of strain DS-27T and the type strains of recognized Pedobacter species ranged from 90.6 to 95.5 %. Differential phenotypic properties, together with the phylogenetic distinctiveness, were sufficient to categorize strain DS-27T as representing a species that is separate from recognized Pedobacter species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DS-27T (=KCTC 12559T=CIP 108922T) was classified in the genus Pedobacter as a member of a novel species, for which the name Pedobacter sandarakinus sp. nov. is proposed.
Collapse
Affiliation(s)
- Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Mi-Hwa Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - So-Jung Kang
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Soo-Yeon Park
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| |
Collapse
|
33
|
Kämpfer P, Engelhart S, Rolke M, Sennekamp J. Extrinsic allergic alveolitis (hypersensitivity pneumonitis) caused by Sphingobacterium spiritivorum from the water reservoir of a steam iron. J Clin Microbiol 2005; 43:4908-10. [PMID: 16145174 PMCID: PMC1234114 DOI: 10.1128/jcm.43.9.4908-4910.2005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A case of extrinsic allergic alveolitis (EAA) caused by Sphingobacterium spiritivorum is described. The symptoms were associated with the use of a steam iron. The water reservoir was heavily contaminated with S. spiritivorum (10(6) CFU ml(-1)). This is the first report of S. spiritivorum as a causative agent of EAA.
Collapse
Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig Universität Giessen, Germany.
| | | | | | | |
Collapse
|
34
|
Ye YF, Min H, Du YF. Characterization of a strain of Sphingobacterium sp. and its degradation to herbicide mefenacet. J Environ Sci (China) 2004; 16:343-347. [PMID: 15137667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A bacterium (designated strain Y1) degrading acetanilide herbicide mefenacet was isolated from aerobic sludge. Based on the analyses of partial 16S rRNA gene, cellular fatty acid and BIOLOG-GN, and general physiological and biochemical characteristics, strain Y1 was identified as Sphingobacterium multivolum. Strain Y1 was able to degrade mefenacet used as sources of carbon and energy. Degradation of mefenacet was accompanied by producing the metabolites N-methylaniline and an unidentified compound with molecular weight 205, indicating a metabolic pathway of mefenacet initiated by hydrolysis of amido bond.
Collapse
Affiliation(s)
- Yang-fang Ye
- College of Life Science, Zhejiang University, Hangzhou 310029, China
| | | | | |
Collapse
|
35
|
Gao N, Cheng X, Yang J, Zhang S. [Production of a novel heparinase from Sphingobacterium sp]. Wei Sheng Wu Xue Bao 2003; 43:813-6. [PMID: 16276908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The novel heparinase-producing bacterial strain Sphingobacterium sp. was isolated and screened from soil. The optimum medium composition is (g/L): Soytone 20, NaCl 1, K2HPO4 2.5, MgSO4 0.5, Heparin 2, Sucrose 15, pH 7.5. The optimum temperature for growth and enzyme production was 32 degrees C. When cultured at a rotating shaker at 30 degrees C for 36 hours, 200 r/min, 50 mL medium in 500 mL flask, the production of heparinase reached 4000 U/L.
Collapse
Affiliation(s)
- Ningguo Gao
- Institute of Microbiology, Chinese academy of Sciences, Beijing 100080, China
| | | | | | | |
Collapse
|