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Kuzmina LY, Gilvanova EA, Galimzyanova NF, Arkhipova TN, Ryabova AS, Aktuganov GE, Sidorova LV, Kudoyarova GR, Melent’ev AI. Characterization of the Novel Plant Growth-Stimulating Strain Advenella kashmirensis IB-K1 and Evaluation of Its Efficiency in Saline Soil. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722020072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Wang Y, Mairinger W, Raj SJ, Yakubu H, Siesel C, Green J, Durry S, Joseph G, Rahman M, Amin N, Hassan MZ, Wicken J, Dourng D, Larbi E, Adomako LAB, Senayah AK, Doe B, Buamah R, Tetteh-Nortey JNN, Kang G, Karthikeyan A, Roy S, Brown J, Muneme B, Sene SO, Tuffuor B, Mugambe RK, Bateganya NL, Surridge T, Ndashe GM, Ndashe K, Ban R, Schrecongost A, Moe CL. Quantitative assessment of exposure to fecal contamination in urban environment across nine cities in low-income and lower-middle-income countries and a city in the United States. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 763:143007. [PMID: 34718001 DOI: 10.1016/j.scitotenv.2020.143007] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 10/08/2020] [Accepted: 10/08/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND During 2014 to 2019, the SaniPath Exposure Assessment Tool, a standardized set of methods to evaluate risk of exposure to fecal contamination in the urban environment through multiple exposure pathways, was deployed in 45 neighborhoods in ten cities, including Accra and Kumasi, Ghana; Vellore, India; Maputo, Mozambique; Siem Reap, Cambodia; Atlanta, United States; Dhaka, Bangladesh; Lusaka, Zambia; Kampala, Uganda; Dakar, Senegal. OBJECTIVE Assess and compare risk of exposure to fecal contamination via multiple pathways in ten cities. METHODS In total, 4053 environmental samples, 4586 household surveys, 128 community surveys, and 124 school surveys were collected. E. coli concentrations were measured in environmental samples as an indicator of fecal contamination magnitude. Bayesian methods were used to estimate the distributions of fecal contamination concentration and contact frequency. Exposure to fecal contamination was estimated by the Monte Carlo method. The contamination levels of ten environmental compartments, frequency of contact with those compartments for adults and children, and estimated exposure to fecal contamination through any of the surveyed environmental pathways were compared across cities and neighborhoods. RESULTS Distribution of fecal contamination in the environment and human contact behavior varied by city. Universally, food pathways were the most common dominant route of exposure to fecal contamination across cities in low-income and lower-middle-income countries. Risks of fecal exposure via water pathways, such as open drains, flood water, and municipal drinking water, were site-specific and often limited to smaller geographic areas (i.e., neighborhoods) instead of larger areas (i.e., cities). CONCLUSIONS Knowledge of the relative contribution to fecal exposure from multiple pathways, and the environmental contamination level and frequency of contact for those "dominant pathways" could provide guidance for Water, Sanitation, and Hygiene (WASH) programming and investments and enable local governments and municipalities to improve intervention strategies to reduce the risk of exposure to fecal contamination.
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Affiliation(s)
- Yuke Wang
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
| | - Wolfgang Mairinger
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Suraja J Raj
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Habib Yakubu
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Casey Siesel
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jamie Green
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Sarah Durry
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - George Joseph
- Water Global Practice, The World Bank, Washington, DC, USA
| | - Mahbubur Rahman
- Environmental Interventions Unit, Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Nuhu Amin
- Environmental Interventions Unit, Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | | | | | | | - Eugene Larbi
- Training Research and Networking for Development (TREND), Accra, Ghana
| | | | | | - Benjamin Doe
- Training Research and Networking for Development (TREND), Accra, Ghana
| | - Richard Buamah
- Department of Civil Engineering, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Gagandeep Kang
- Wellcome Research Laboratory, Christian Medical College, Vellore, India
| | - Arun Karthikeyan
- Wellcome Research Laboratory, Christian Medical College, Vellore, India
| | - Sheela Roy
- Wellcome Research Laboratory, Christian Medical College, Vellore, India
| | - Joe Brown
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Bacelar Muneme
- Water Supply and Mapping, WE Consult, Maputo, Mozambique
| | - Seydina O Sene
- Initiative Prospective Agricole et Rurale (IPAR), Dakar, Senegal
| | - Benedict Tuffuor
- Training Research and Networking for Development (TREND), Accra, Ghana
| | - Richard K Mugambe
- Department of Disease Control and Environmental Health, Makerere University School of Public Health, Kampala, Uganda
| | - Najib Lukooya Bateganya
- Department of Environment and Public Health, Kampala Capital City Authority, Kampala, Uganda
| | - Trevor Surridge
- Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ) GmbH, Lusaka, Zambia
| | | | - Kunda Ndashe
- Department of Environmental Health, Faculty of Health Science, Lusaka Apex Medical University, Lusaka, Zambia
| | - Radu Ban
- Bill & Melinda Gates Foundation, Seattle, WA, USA
| | | | - Christine L Moe
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
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Advenella mandrilli sp. nov., a bacterium isolated from the faeces of Mandrillus sphinx. Antonie van Leeuwenhoek 2022; 115:271-280. [PMID: 35031912 DOI: 10.1007/s10482-021-01695-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 11/26/2021] [Indexed: 10/19/2022]
Abstract
A novel Gram-negative strain WQ 585T, isolated from the faeces of mandrills (Mandrillus sphinx) collected at Yunnan Wild Animal Park, Yunnan province, China, was subjected to a polyphasic taxonomic study. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belongs to the genus Advenella, sharing 98.5% and 98.2% sequence similarity with the type strain Advenella alkanexedens LAM0050T and Advenella faeciporci M-07T, respectively. The predominant ubiquinone was Q-8. The major cellular fatty acids (> 10%) were C16:0, C17:0 cyclo and Summed Feature 2. The G + C content of the genomic DNA of strain WQ 585T was 49.0%. The whole genome average nucleotide identity (gANI) values of strain WQ 585T with strain A. alkanexedens LAM0050T and A. faeciporci M-07T were 86.7% and 86.7%, and the digital DNA-DNA hybridization values of strain WQ 585T with strain A. alkanexedens LAM0050T and A. faeciporci M-07T were 64.5% and 62.5%, respectively. Growth occurred at 10-45 °C (optimally at 20-30 °C), pH 6.0-9.0 (optimally at pH 7.0), and 0-5% (w/v) NaCl (optimally at 0.5-2.0%). On the basis of the taxonomic evidence, a novel species, Advenella mandrilli sp. nov., is proposed. The type strain is WQ 585T (= KCTC 82396 T = CCTCC AA 2020028 T).
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Raabis SM, Quick AE, Skarlupka JH, Suen G, Ollivett TL. The nasopharyngeal microbiota of preweaned dairy calves with and without ultrasonographic lung lesions. J Dairy Sci 2021; 104:3386-3402. [PMID: 33455760 DOI: 10.3168/jds.2020-19096] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/17/2020] [Indexed: 12/18/2022]
Abstract
The primary objective of this cross-sectional study was to identify associations between the diversity and composition of the nasopharyngeal (NP) microbiota and pneumonia status, as diagnosed by ultrasonography (US), in preweaned dairy calves. Characteristics of the NP microbiota were compared between calves with and without pneumonia, as diagnosed by US. Secondary objectives were to compare the composition of the NP microbiota between calves by age, clinical respiratory score (CRS), and previous antibiotic therapy. Holstein heifer calves (n = 50) from a southern Wisconsin dairy were enrolled at either 3 or 6 wk of age; 4 calves were sampled at both time points. Antibiotic treatment history was also collected for the 30 d before enrollment. For the purpose of this study, pneumonia was defined as having lobar pneumonia, as diagnosed by US, in at least 1 lung lobe. Following examination by CRS and US, a deep nasopharyngeal swab was obtained for 16S rRNA amplicon sequencing. Alpha diversity was reduced in calves that were CRS positive, and beta diversity tended to be different in calves previously treated with antibiotics and in calves that were CRS positive. Microbial diversity was not different between calves with and without pneumonia. The most dominant genus identified was Mycoplasma spp.; however, there was no association between relative abundance (RA) and pneumonia status. The median RA of Mycoplasma spp. was increased by 25 (95% confidence interval, CI: 3, 40) in calves at 3 wk of age compared with 6 wk of age. The median RA of Pasteurella spp. was increased by 1.5 (95% CI: 0.1, 3) in calves with pneumonia, as diagnosed by US, compared with calves without pneumonia. Additionally, Pasteurella spp. was increased by 2.3 (95% CI: 0, 9) in CRS-positive calves compared with CRS-negative calves. The median RA of Psychrobacter spp. was increased by 2 (95% CI: 0, 12) and median RA of Chryseobacterium spp. was increased by 0.15 (95% CI: 0, 2) in calves that were not treated previously with antibiotics compared with calves previously treated with antibiotics.
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Affiliation(s)
- S M Raabis
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison 53706
| | - A E Quick
- Department of Animal and Dairy Science, University of Wisconsin, Madison 53706
| | - J H Skarlupka
- Department of Bacteriology, University of Wisconsin, Madison 53706
| | - G Suen
- Department of Bacteriology, University of Wisconsin, Madison 53706
| | - T L Ollivett
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison 53706.
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Pyne P, Alam M, Rameez MJ, Mandal S, Sar A, Mondal N, Debnath U, Mathew B, Misra AK, Mandal AK, Ghosh W. Homologs from sulfur oxidation (Sox) and methanol dehydrogenation (Xox) enzyme systems collaborate to give rise to a novel pathway of chemolithotrophic tetrathionate oxidation. Mol Microbiol 2018; 109:169-191. [DOI: 10.1111/mmi.13972] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Prosenjit Pyne
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Masrure Alam
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Moidu Jameela Rameez
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Subhrangshu Mandal
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Abhijit Sar
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Nibendu Mondal
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Utsab Debnath
- Division of Molecular Medicine; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Boby Mathew
- Clinical Proteomics Unit, Division of Molecular Medicine; St. John's Research Institute St. John's National Academy of Health Sciences, 100ft Road; Koramangala 560034 Bangalore India
| | - Anup Kumar Misra
- Division of Molecular Medicine; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Amit Kumar Mandal
- Clinical Proteomics Unit, Division of Molecular Medicine; St. John's Research Institute St. John's National Academy of Health Sciences, 100ft Road; Koramangala 560034 Bangalore India
| | - Wriddhiman Ghosh
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
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Schmitz-Esser S, Dzieciol M, Nischler E, Schornsteiner E, Bereuter O, Mann E, Wagner M. Abundance and potential contribution of Gram-negative cheese rind bacteria from Austrian artisanal hard cheeses. Int J Food Microbiol 2017; 266:95-103. [PMID: 29190534 DOI: 10.1016/j.ijfoodmicro.2017.11.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/23/2017] [Accepted: 11/18/2017] [Indexed: 11/19/2022]
Abstract
Many different Gram-negative bacteria have been shown to be present on cheese rinds. Their contribution to cheese ripening is however, only partially understood until now. Here, cheese rind samples were taken from Vorarlberger Bergkäse (VB), an artisanal hard washed-rind cheese from Austria. Ripening cellars of two cheese production facilities in Austria were sampled at the day of production and after 14, 30, 90 and 160days of ripening. To obtain insights into the possible contribution of Advenella, Psychrobacter, and Psychroflexus to cheese ripening, we sequenced and analyzed the genomes of one strain of each genus isolated from VB cheese rinds. Additionally, quantitative PCRs (qPCRs) were performed to follow the abundance of Advenella, Psychrobacter, and Psychroflexus on VB rinds during ripening in both facilities. qPCR results showed that Psychrobacter was most abundant on cheese rinds and the abundance of Advenella decreased throughout the first month of ripening and increased significantly after 30days of ripening (p<0.01). Psychrobacter and Psychroflexus increased significantly during the first 30 ripening days (p<0.01), and decreased to their initial abundance during the rest of the ripening time (p<0.05). Genome sequencing resulted in 17 to 27 contigs with assembly sizes of 2.7 Mbp for Psychroflexus, 3 Mbp for Psychrobacter, and 4.3 Mbp for Advenella. Our results reveal that each genome harbors enzymes shown to be important for cheese ripening in other bacteria such as: Cystathionine/Methionine beta or gamma-lyases, many proteases and peptidases (including proline iminopeptidases), aminotransferases, and lipases. Thus, all three isolates have the potential to contribute positively to cheese ripening. In conclusion, the three species quantified were stable community members throughout the ripening process and their abundance on cheese rinds together with the results from genome sequencing suggest an important contribution of these bacteria to cheese ripening.
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Affiliation(s)
- Stephan Schmitz-Esser
- Institute for Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria.
| | - Monika Dzieciol
- Institute for Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Eva Nischler
- Institute for Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Elisa Schornsteiner
- Institute for Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria
| | | | - Evelyne Mann
- Institute for Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Martin Wagner
- Institute for Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria
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Dhotre DP, Rajabal V, Sharma A, Kulkarni GJ, Prakash O, Vemuluri VR, Joseph N, Rahi P, Shouche YS. Reclassification of Phycicola gilvus (Lee et al. 2008) and Leifsonia pindariensis (Reddy et al. 2008) as Microterricola gilva comb. nov. and Microterricola pindariensis comb. nov. and emended description of the genus Microterricola. Int J Syst Evol Microbiol 2017; 67:2766-2772. [PMID: 28857730 DOI: 10.1099/ijsem.0.002019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic positions of Microterricola viridarii JCM 15926T, Phycicola gilvus DSM 18319T and Leifsonia pindariensis JCM 15132T were re-examined. Phylogenetic analysis and 16S rRNA gene sequence similarities revealed that all three strains are closely related with each other and form a monophyletic cluster with high sequence similarity (99.2 -99.9 %). A dendrogram constructed based on the protein spectra generated by matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy also displayed close clustering of these three strains. The fatty acid profiles of three strains were very similar to each other and contained branched fatty acids (anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0) as the predominant cellular fatty acids. The polar lipid profiles of the three stains were similar and consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine as major polar lipids and an unknown lipid. Comparisons of morphological, chemotaxonomic and physiological data of Microterricola viridarii JCM 15926T, Leifsonia pindariensis JCM 15132T and Phycicola gilvus DSM 18319T are in agreement with the features of a common genus. DNA-DNA hybridization data generated during this study showed less than 70 % reassociation value with each other indicating that they are different at species level. Based on the present study, we conclude that Phycicola gilvus DSM 18319T and Leifsonia pindariensis JCM 15132T should be reclassified under the genus Microterricola, since this genus has the nomenclatural priority, and reclassified as Microterricolagilva comb. nov. (type strain SSWW-21T=DSM 18319T=KCTC 19185T=JCM 30550T) and Microterricolapindariensis comb. nov. (type strain PON10T=LMG 24222T=JCM 15132T=MTCC9128T). An emended description of the genus Microterricola is also presented.
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Affiliation(s)
- Dhiraj Prakash Dhotre
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Vaheesan Rajabal
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Avinash Sharma
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Girish J Kulkarni
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Om Prakash
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Venkata Ramana Vemuluri
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Neetha Joseph
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Praveen Rahi
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Yogesh S Shouche
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
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Dobrovol’skaya TG, Khusnetdinova KA, Manucharova NA, Golovchenko AV. Structure of epiphytic bacterial communities of weeds. Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717020072] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Meinert C, Brandt U, Heine V, Beyert J, Schmidl S, Wübbeler JH, Voigt B, Riedel K, Steinbüchel A. Proteomic analysis of organic sulfur compound utilisation in Advenella mimigardefordensis strain DPN7T. PLoS One 2017; 12:e0174256. [PMID: 28358882 PMCID: PMC5373536 DOI: 10.1371/journal.pone.0174256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/06/2017] [Indexed: 01/07/2023] Open
Abstract
2-Mercaptosuccinate (MS) and 3,3´-ditiodipropionate (DTDP) were discussed as precursor substance for production of polythioesters (PTE). Therefore, degradation of MS and DTDP was investigated in Advenella mimigardefordensis strain DPN7T, applying differential proteomic analysis, gene deletion and enzyme assays. Protein extracts of cells cultivated with MS, DTDP or 3-sulfinopropionic acid (SP) were compared with those cultivated with propionate (P) and/or succinate (S). The chaperone DnaK (ratio DTDP/P 9.2, 3SP/P 4.0, MS/S 6.1, DTDP/S 6.2) and a Do-like serine protease (DegP) were increased during utilization of all organic sulfur compounds. Furthermore, a putative bacterioferritin (locus tag MIM_c12960) showed high abundance (ratio DTDP/P 5.3, 3SP/P 3.2, MS/S 4.8, DTDP/S 3.9) and is probably involved in a thiol-specific stress response. The deletion of two genes encoding transcriptional regulators (LysR (MIM_c31370) and Xre (MIM_c31360)) in the close proximity of the relevant genes of DTDP catabolism (acdA, mdo and the genes encoding the enzymes of the methylcitric acid cycle; prpC,acnD, prpF and prpB) showed that these two regulators are essential for growth of A. mimigardefordensis strain DPN7T with DTDP and that they most probably regulate transcription of genes mandatory for this catabolic pathway. Furthermore, proteome analysis revealed a high abundance (ratio MS/S 10.9) of a hypothetical cupin-2-domain containing protein (MIM_c37420). This protein shows an amino acid sequence similarity of 60% to a newly identified MS dioxygenase from Variovorax paradoxus strain B4. Deletion of the gene and the adjacently located transcriptional regulator LysR, as well as heterologous expression of MIM_c37420, the putative mercaptosuccinate dioxygenase (Msdo) from A. mimigardefordensis, showed that this protein is the key enzyme of MS degradation in A. mimigardefordensis strain DPN7T (KM 0.2 mM, specific activity 17.1 μmol mg-1 min-1) and is controlled by LysR (MIM_c37410).
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Affiliation(s)
- Christina Meinert
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Ulrike Brandt
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Viktoria Heine
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Jessica Beyert
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Sina Schmidl
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Jan Hendrik Wübbeler
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Birgit Voigt
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Katharina Riedel
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
- Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail:
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Shmareva MN, Agafonova NV, Kaparullina EN, Doronina NV, Trotsenko YA. Emended Descriptions of Advenella kashmirensis subsp. kashmirensis subsp. nov., Advenella kashmirensis subsp. methylica subsp. nov., and Methylopila turkiensis sp. nov. Microbiology (Reading) 2016. [DOI: 10.1134/s0026261716050155] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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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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Poroshina MN, Doronina NV, Kaparullina EN, Trotsenko YA. Advenella kashmirensis subsp. methylica PK1, a facultative methylotroph from carex rhizosphere. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715010117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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13
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Cultivation-independent analysis of microbial communities on Austrian raw milk hard cheese rinds. Int J Food Microbiol 2014; 180:88-97. [DOI: 10.1016/j.ijfoodmicro.2014.04.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 03/24/2014] [Accepted: 04/06/2014] [Indexed: 01/18/2023]
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14
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Wübbeler JH, Hiessl S, Schuldes J, Thürmer A, Daniel R, Steinbüchel A. Unravelling the complete genome sequence of Advenella mimigardefordensis strain DPN7T and novel insights in the catabolism of the xenobiotic polythioester precursor 3,3'-dithiodipropionate. MICROBIOLOGY-SGM 2014; 160:1401-1416. [PMID: 24739217 DOI: 10.1099/mic.0.078279-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Advenella mimigardefordensis strain DPN7(T) is a remarkable betaproteobacterium because of its extraordinary ability to use the synthetic disulfide 3,3'-dithiodipropionic acid (DTDP) as the sole carbon source and electron donor for aerobic growth. One application of DTDP is as a precursor substrate for biotechnically synthesized polythioesters (PTEs), which are interesting non-degradable biopolymers applicable for plastics materials. Metabolic engineering for optimization of PTE production requires an understanding of DTDP conversion. The genome of A. mimigardefordensis strain DPN7(T) was sequenced and annotated. The circular chromosome was found to be composed of 4,740,516 bp and 4112 predicted ORFs, whereas the circular plasmid consisted of 23,610 bp and 24 predicted ORFs. The genes participating in DTDP catabolism had been characterized in detail previously, but knowing the complete genome sequence and with support of Tn5: :mob-induced mutants, putatively involved transporter proteins and a transcriptional regulator were also identified. Most probably, DTDP is transported into the cell by a specific tripartite tricarboxylate transport system and is then cleaved by the disulfide reductase LpdA, sulfoxygenated by the 3-mercaptopropionate dioxygenase Mdo, activated by the CoA ligase SucCD and desulfinated by the acyl-CoA dehydrogenase-like desulfinase AcdA. Regulation of this pathway is presumably performed by a transcriptional regulator of the xenobiotic response element family. The excessive sulfate that is inevitably produced is secreted by the cells by a unique sulfate exporter of the CPA (cation : proton antiporter) superfamily.
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Affiliation(s)
- Jan Hendrik Wübbeler
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Sebastian Hiessl
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Jörg Schuldes
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Andrea Thürmer
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Alexander Steinbüchel
- Faculty of Biology, King Abdulaziz University, Jeddah, Saudi Arabia.,Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
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15
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Prakash O, Munot H, Nimonkar Y, Sharma M, Kumbhare S, Shouche YS. Description of Pelistega indica sp. nov., isolated from human gut. Int J Syst Evol Microbiol 2014; 64:1389-1394. [DOI: 10.1099/ijs.0.059782-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, motile, non-spore-forming, coccoid bacterium was isolated from a stool sample of a healthy human subject and formed cream colour colonies on tryptic soy agar. Almost full-length (1500 bp) small subunit rRNA (16S rRNA) gene sequences were generated and a similarity search was conducted by blast. The results of the similarity search indicated that the bacterium belongs to the class
Betaproteobacteria
, family
Alcaligenaceae
. It showed maximum sequence similarity (96.5 %) with
Pelistega europaea
CCUG 39967T followed by
Advenella mimigardefordensis
DSM 17166T (96.1 %) and
Taylorella asinigenitalis
LMG 19572T (95.3 %). The DNA G+C content of strain HM-7T was 42 mol%. Strain HM-7T contained C14 : 0, C16 : 0, C16 : 0 3-OH and C18 : 0 as the dominant fatty acids. Morphological, physiological and biochemical data also indicated that strain HM-7T represents a member of the genus
Pelistega
, but at the same time distinguished it from
Pelistega europaea
CCUG 39967T, the only species of the genus with a validly published name. Based on polyphasic characterization we conclude that the bacterium represents a novel species of the genus
Pelistega
and propose the name Pelistega indica sp. nov., with strain HM-7T ( = MCC 2185T = DSM 27484T) as the type strain of the species.
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Affiliation(s)
- Om Prakash
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharastra 411007, India
| | - Hitendra Munot
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharastra 411007, India
| | - Yogesh Nimonkar
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharastra 411007, India
| | - Madhu Sharma
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharastra 411007, India
| | - Shreyas Kumbhare
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharastra 411007, India
| | - Yogesh S. Shouche
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharastra 411007, India
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16
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Genome implosion elicits host-confinement in Alcaligenaceae: evidence from the comparative genomics of Tetrathiobacter kashmirensis, a pathogen in the making. PLoS One 2013; 8:e64856. [PMID: 23741407 PMCID: PMC3669393 DOI: 10.1371/journal.pone.0064856] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 04/19/2013] [Indexed: 11/24/2022] Open
Abstract
This study elucidates the genomic basis of the evolution of pathogens alongside free-living organisms within the family Alcaligenaceae of Betaproteobacteria. Towards that end, the complete genome sequence of the sulfur-chemolithoautotroph Tetrathiobacter kashmirensis WT001T was determined and compared with the soil isolate Achromobacter xylosoxidans A8 and the two pathogens Bordetella bronchiseptica RB50 and Taylorella equigenitalis MCE9. All analyses comprehensively indicated that the RB50 and MCE9 genomes were almost the subsets of A8 and WT001T, respectively. In the immediate evolutionary past Achromobacter and Bordetella shared a common ancestor, which was distinct from the other contemporary stock that gave rise to Tetrathiobacter and Taylorella. The Achromobacter-Bordetella precursor, after diverging from the family ancestor, evolved through extensive genome inflation, subsequent to which the two genera separated via differential gene losses and acquisitions. Tetrathiobacter, meanwhile, retained the core characteristics of the family ancestor, and Taylorella underwent massive genome degeneration to reach an evolutionary dead-end. Interestingly, the WT001T genome, despite its conserved architecture, had only 85% coding density, besides which 578 out of its 4452 protein-coding sequences were found to be pseudogenized. Translational impairment of several DNA repair-recombination genes in the first place seemed to have ushered the rampant and indiscriminate frame-shift mutations across the WT001T genome. Presumably, this strain has just come out of a recent evolutionary bottleneck, representing a unique transition state where genome self-degeneration has started comprehensively but selective host-confinement has not yet set in. In the light of this evolutionary link, host-adaptation of Taylorella clearly appears to be the aftereffect of genome implosion in another member of the same bottleneck. Remarkably again, potent virulence factors were found widespread in Alcaligenaceae, corroborating which hemolytic and mammalian cell-adhering abilities were discovered in WT001T. So, while WT001T relatives/derivatives in nature could be going the Taylorella way, the lineage as such was well-prepared for imminent host-confinement.
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17
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Kinetic enrichment of 34S during proteobacterial thiosulfate oxidation and the conserved role of SoxB in S-S bond breaking. Appl Environ Microbiol 2013; 79:4455-64. [PMID: 23686269 DOI: 10.1128/aem.00956-13] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During chemolithoautotrophic thiosulfate oxidation, the phylogenetically diverged proteobacteria Paracoccus pantotrophus, Tetrathiobacter kashmirensis, and Thiomicrospira crunogena rendered steady enrichment of (34)S in the end product sulfate, with overall fractionation ranging between -4.6‰ and +5.8‰. The fractionation kinetics of T. crunogena was essentially similar to that of P. pantotrophus, albeit the former had a slightly higher magnitude and rate of (34)S enrichment. In the case of T. kashmirensis, the only significant departure of its fractionation curve from that of P. pantotrophus was observed during the first 36 h of thiosulfate-dependent growth, in the course of which tetrathionate intermediate formation is completed and sulfate production starts. The almost-identical (34)S enrichment rates observed during the peak sulfate-producing stage of all three processes indicated the potential involvement of identical S-S bond-breaking enzymes. Concurrent proteomic analyses detected the hydrolase SoxB (which is known to cleave terminal sulfone groups from SoxYZ-bound cysteine S-thiosulfonates, as well as cysteine S-sulfonates, in P. pantotrophus) in the actively sulfate-producing cells of all three species. The inducible expression of soxB during tetrathionate oxidation, as well as the second leg of thiosulfate oxidation, by T. kashmirensis is significant because the current Sox pathway does not accommodate tetrathionate as one of its substrates. Notably, however, no other Sox protein except SoxB could be detected upon matrix-assisted laser desorption ionization mass spectrometry analysis of all such T. kashmirensis proteins as appeared to be thiosulfate inducible in 2-dimensional gel electrophoresis. Instead, several other redox proteins were found to be at least 2-fold overexpressed during thiosulfate- or tetrathionate-dependent growth, thereby indicating that there is more to tetrathionate oxidation than SoxB alone.
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Employing a recombinant strain of Advenella mimigardefordensis for biotechnical production of Homopolythioesters from 3,3'-dithiodipropionic acid. Appl Environ Microbiol 2012; 78:3286-97. [PMID: 22344658 DOI: 10.1128/aem.00007-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Advenella mimigardefordensis strain DPN7(T) was genetically modified to produce poly(3-mercaptopropionic acid) (PMP) homopolymer by exploiting the recently unraveled process of 3,3'-dithiodipropionic acid (DTDP) catabolism. Production was achieved by systematically engineering the metabolism of this strain as follows: (i) deletion of its inherent 3MP dioxygenase-encoding gene (mdo), (ii) introduction of the buk-ptb operon (genes encoding the butyrate kinase, Buk, and the phosphotransbutyrylase, Ptb, from Clostridium acetobutylicum), and (iii) overexpression of its own polyhydroxyalkanoate synthase (phaC(Am)). These measures yielded the potent PMP production strain A. mimigardefordensis strain SHX22. The deletion of mdo was required for adequate synthesis of PMP due to the resulting accumulation of 3MP during utilization of DTDP. Overexpression of the plasmid-borne buk-ptb operon caused a severe growth repression. This effect was overcome by inserting this operon into the genome. Polyhydroxyalkanoate (PHA) synthases from different origins were compared. The native PHA synthase of A. mimigardefordensis (phaC(Am)) was obviously the best choice to establish homopolythioester production in this strain. In addition, the cultivation conditions, including an appropriate provision of the carbon source, were further optimized to enhance PMP production. The engineered strain accumulated PMP up to approximately 25% (wt/wt) of the cell dry weight when cultivated in mineral salts medium containing glycerol as the carbon source in addition to DTDP as the sulfur-providing precursor. According to our knowledge, this is the first report of PMP homopolymer production by a metabolically engineered bacterium using DTDP, which is nontoxic, as the precursor substrate.
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Matsuoka M, Park S, An SY, Miyahara M, Kim SW, Kamino K, Fushinobu S, Yokota A, Wakagi T, Shoun H. Advenella faeciporci sp. nov., a nitrite-denitrifying bacterium isolated from nitrifying-denitrifying activated sludge collected from a laboratory-scale bioreactor treating piggery wastewater. Int J Syst Evol Microbiol 2012; 62:2986-2990. [PMID: 22307513 DOI: 10.1099/ijs.0.037440-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain M-07(T) was isolated from nitrifying-denitrifying activated sludge treating piggery wastewater. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain M-07(T) belonged to the genus Advenella. 16S rRNA gene sequence similarity between M-07(T) and Advenella incenata CCUG 45225(T), Advenella mimigardefordensis DPN7(T) and Advenella kashmirensis WT001(T) was 96.5, 97.3 and 96.9%, respectively. The DNA G+C content of strain M-07(T) was 49.5 mol%, which was approximately 5 mol% lower than the range for the genus Advenella (53.5-58.0 mol%). The predominant cellular fatty acids of strain M-07(T) were C(16:0), summed feature 3 (comprising C(16:1)ω7c and/or iso-C(15:0) 2-OH), C(17:0) cyclo and summed feature 2 (comprising one or more of C(14:0) 3-OH, iso-C(16:1) I, an unidentified fatty acid with an equivalent chain-length of 10.928 and C(12:0) alde). The isoprenoid quinone was Q-8. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness, strain M-07(T) should be classified as a novel species of the genus Advenella, for which the name Advenella faeciporci sp. nov. is proposed. The type strain is M-07(T) ( = JCM 17746(T) = KCTC 23732(T)).
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Affiliation(s)
- Masaki Matsuoka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Sanghwa Park
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Sun-Young An
- Biotechnology Field, National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu-shi, Chiba 292-0818, Japan
| | - Morio Miyahara
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Sang-Wan Kim
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kei Kamino
- Biotechnology Field, National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu-shi, Chiba 292-0818, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akira Yokota
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takayoshi Wakagi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hirofumi Shoun
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Abstract
Two unusual, Gram-negative, catalase- and oxidase-positive rods, designated C2T and C5, were isolated from compost samples. Comparative 16S rRNA gene sequencing studies demonstrated that both isolates were members of the genus Pseudomonas and belonged to the Pseudomonas aeruginosa group. Strain C2T was most closely related to Pseudomonas cuatrocienegasensis 1NT and Pseudomonas borbori R-20821T (97.9 and 97.8 % 16S rRNA gene sequence similarity, respectively). However, phylogenetic analysis based on rpoD gene sequences revealed that both isolates could be discriminated from members of the P. aeruginosa group that exhibited >97 % 16S rRNA gene sequence similarity. The DNA G+C content of strain C2T was 61.5 mol%. The major fatty acids of strain C2T were a summed feature (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C18 : 1ω7c/12t/9t, C16 : 0 and C12 : 0, which supported the isolates’ affiliation with the genus Pseudomonas. Moreover, strain C2T could be distinguished from its closest phylogenetic neighbours of the genus Pseudomonas by DNA–DNA hybridization studies and biochemical tests. On the basis of both phenotypic and phylogenetic findings, it is proposed that the isolates be classified as a novel species, with the name Pseudomonas composti sp. nov. The type strain is C2T ( = CECT 7516T = CCUG 59231T).
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21
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Whole-genome shotgun sequencing of the sulfur-oxidizing chemoautotroph Tetrathiobacter kashmirensis. J Bacteriol 2011; 193:5553-4. [PMID: 21914874 DOI: 10.1128/jb.05781-11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The chemolithoautotrophic betaproteobacterium Tetrathiobacter kashmirensis belongs to the family Alcaligenaceae and is phylogenetically closely related to pathogens such as Taylorella and Bordetella species. While a complete inorganic sulfur oxidation gene cluster, soxCDYZAXWB, is present in its genome, pathogenicity islands or genes associated with virulence, disease, cellular invasion, and/or intracellular resistance are completely absent.
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Novel reaction of succinyl coenzyme A (Succinyl-CoA) synthetase: activation of 3-sulfinopropionate to 3-sulfinopropionyl-CoA in Advenella mimigardefordensis strain DPN7T during degradation of 3,3'-dithiodipropionic acid. J Bacteriol 2011; 193:3078-89. [PMID: 21515777 DOI: 10.1128/jb.00049-11] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The sucCD gene of Advenella mimigardefordensis strain DPN7(T) encodes a succinyl coenzyme A (succinyl-CoA) synthetase homologue (EC 6.2.1.4 or EC 6.2.1.5) that recognizes, in addition to succinate, the structural analogues 3-sulfinopropionate (3SP) and itaconate as substrates. Accumulation of 3SP during 3,3'-dithiodipropionic acid (DTDP) degradation was observed in Tn5::mob-induced mutants of A. mimigardefordensis strain DPN7(T) disrupted in sucCD and in the defined deletion mutant A. mimigardefordensis ΔsucCD. These mutants were impaired in growth with DTDP and 3SP as the sole carbon source. Hence, it was proposed that the succinyl-CoA synthetase homologue in A. mimigardefordensis strain DPN7(T) activates 3SP to the corresponding CoA-thioester (3SP-CoA). The putative genes coding for A. mimigardefordensis succinyl-CoA synthetase (SucCD(Am)) were cloned and heterologously expressed in Escherichia coli BL21(DE3)/pLysS. Purification and characterization of the enzyme confirmed its involvement during degradation of DTDP. 3SP, the cleavage product of DTDP, was converted into 3SP-CoA by the purified enzyme, as demonstrated by in vitro enzyme assays. The structure of 3SP-CoA was verified by using liquid chromatography-electrospray ionization-mass spectrometry. SucCD(Am) is Mg²⁺ or Mn²⁺ dependent and unspecific regarding ATP or GTP. In kinetic studies the enzyme showed highest enzyme activity and substrate affinity with succinate (V(max) = 9.85 ± 0.14 μmol min⁻¹ mg⁻¹, K(m) = 0.143 ± 0.001 mM). In comparison to succinate, activity with 3SP was only ca. 1.2% (V(max) = 0.12 ± 0.01 μmol min⁻¹ mg⁻¹) and the affinity was 6-fold lower (K(m) = 0.818 ± 0.046 mM). Based on the present results, we conclude that SucCD(Am) is physiologically associated with the citric acid cycle but is mandatory for the catabolic pathway of DTDP and its degradation intermediate 3SP.
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23
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Dam B. A type Ib plasmid segregation machinery of the Advenella kashmirensis plasmid pBTK445. Plasmid 2010; 65:185-91. [PMID: 21192970 DOI: 10.1016/j.plasmid.2010.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 12/17/2010] [Accepted: 12/21/2010] [Indexed: 10/18/2022]
Abstract
pBTK445 is a newly described large (∼60Kb), low-copy number, conjugative plasmid indigenous to the sulfur-chemolithoautotroph Advenella kashmirensis. Based on its minimal replication region, a shuttle vector, pBTKS was constructed which can be used for diverse Alcaligenaceae members. The construct was found to be stably maintained both in the native host as well as in Escherichia coli in the absence of selective pressure which indicated that pBTKS harbors the stabilizing system of pBTK445, that are commonly coded by low-copy-number plasmids. Deletion analyzes of pBTKS confirmed the essentiality of parA (encoding a Walker-type ATPase of 214 amino acids) and the downstream located small parB (encoding an 85 amino acid protein having no sequence homolog in the database) in the faithful partitioning of pBTK445. A 1075bp PCR product, containing parA, parB and an upstream sequence having nine 11bp direct repeats (parS site) was found to comprise the partition functions of pBTK445, stabilizing both low-copy or high-copy number homologous and heterologous replicons in diverse hosts. The incompatibility determinant and the par promoter, P(par) were both found to be present within a 191bp iterated sequence present upstream of parA. ParB was found to regulate the expression of the Par proteins from P(par). The presence of a typical Walker-type ATPase motif in ParA, a short phylogenetically unrelated ParB, that acts as a repressor of P(par), and location of the iterated parS site upstream of parA, confirm that the active partition system of pBTK445 belongs to the type Ib.
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Affiliation(s)
- Bomba Dam
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl Von Frisch Strasse 10, D-35043 Marburg, Germany.
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Dihydrolipoamide dehydrogenases of Advenella mimigardefordensis and Ralstonia eutropha catalyze cleavage of 3,3'-dithiodipropionic acid into 3-mercaptopropionic acid. Appl Environ Microbiol 2010; 76:7023-8. [PMID: 20833784 DOI: 10.1128/aem.01706-10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The catabolism of the disulfide 3,3'-dithiodipropionic acid (DTDP) is initiated by the reduction of its disulfide bond. Three independent Tn5::mob-induced mutants of Advenella mimigardefordensis strain DPN7(T) were isolated that had lost the ability to utilize DTDP as the sole source of carbon and energy and that harbored the transposon insertions in three different sites of the same dihydrolipoamide dehydrogenase gene encoding the E3 subunit of the pyruvate dehydrogenase multi-enzyme complex of this bacterium (LpdA(Am)). LpdA(Am) was analyzed in silico and compared to homologous proteins, thereby revealing high similarities to the orthologue in Ralstonia eutropha H16 (PdhL(Re)). Both bacteria are able to cleave DTDP into two molecules of 3-mercaptopropionic acid (3MP). A. mimigardefordensis DPN7(T) converted 3MP to 3-sulfinopropionic acid, whereas R. eutropha H16 showed no growth with DTDP as the sole carbon source but was instead capable of synthesizing heteropolythioesters using the resulting cleavage product 3MP. Subsequently, the genes lpdA(Am) and pdhL(Re) were cloned, heterologously expressed in Escherichia coli applying the pET23a expression system, purified, and assayed by monitoring the oxidation of NADH. The physiological substrate lipoamide was reduced to dihydrolipoamide with specific activities of 1,833 mkat/kg of protein (LpdA(Am)) or 1,667 mkat/kg of protein (PdhL(Re)). Reduction of DTDP was also unequivocally detected with the purified enzymes, although the specific enzyme activities were much lower: 0.7 and 0.5 mkat/kg protein, respectively.
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Biodegradation of the xenobiotic organic disulphide 4,4′-dithiodibutyric acid by Rhodococcus erythropolis strain MI2 and comparison with the microbial utilization of 3,3′-dithiodipropionic acid and 3,3′-thiodipropionic acid. Microbiology (Reading) 2010; 156:1221-1233. [DOI: 10.1099/mic.0.036178-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Application of the non-toxic 3,3′-thiodipropionic acid (TDP) and 3,3′-dithiodipropionic acid (DTDP) as precursors for the microbial production of polythioesters (PTEs), a class of biologically persistent biopolymers containing sulphur in the backbone, was successfully established previously. However, synthesis of PTEs containing 4-mercaptobutyrate (4MB) as building blocks could not be achieved. The very harmful 4MB is not used as a PTE precursor or as the carbon source for growth by any known strain. As a promising alternative, the harmless oxidized disulfide of two molecules of 4MB, 4,4′-dithiodibutyric acid (DTDB), was employed for enrichments of bacterial strains capable of biodegradation. Investigation of novel precursor substrates for PTEs and comparison of respective strains growing on TDP, DTDP and DTDB as sole carbon source was accomplished. A broad variety of bacteria capable of using one of these organic sulphur compounds were isolated and compared. TDP and DTDP were degraded by several strains belonging to different genera, whereas all DTDB-utilizing strains were affiliated to the species Rhodococcus erythropolis. Transposon mutagenesis of R. erythropolis strain MI2 and screening of 7500 resulting mutants yielded three mutants exhibiting impaired growth on DTDB. Physiological studies revealed production of volatile hydrogen sulphide and accumulation of significant amounts of 4MB, 4-oxo-4-sulphanylbutanoic acid and succinic acid in the culture supernatants. Based on this knowledge, a putative pathway for degradation of DTDB was proposed: DTDB could be cleaved into two molecules of 4MB, followed by an oxidation yielding 4-oxo-4-sulphanylbutanoic acid. A putative desulphydrase probably catalyses the abstraction of sulphur, thereby generating succinic acid and hydrogen sulphide.
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Barra Caracciolo A, Fajardo C, Grenni P, Saccà ML, Amalfitano S, Ciccoli R, Martin M, Gibello A. The role of a groundwater bacterial community in the degradation ofâ the herbicide terbuthylazine. FEMS Microbiol Ecol 2010; 71:127-36. [DOI: 10.1111/j.1574-6941.2009.00787.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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