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Liu Y, Wang Y, Wang H. Effects of ciprofloxacin and levofloxacin on initial colonization of intestinal microbiota in Bufo gargarizans at embryonic stages. CHEMOSPHERE 2024; 361:142587. [PMID: 38871193 DOI: 10.1016/j.chemosphere.2024.142587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024]
Abstract
Ciprofloxacin (CIP) and levofloxacin (LEV) are broad-spectrum antibiotics with potent antibacterial activity. Although many studies have shown that antibiotics can lead to gut microbiota disruption, the effects of CIP and LEV on gut microbial colonization at the embryonic stage remain poorly characterized. Here, we evaluated the response of Bufo gargarizans embryos in terms of gut microbiota colonization, growth and developmental stages to CIP and LEV exposure. Embryos treated with 100 μg/L CIP and LEV exhibited significantly reduced diversity and richness of the gut microbiota, as well as altered community structure. Both CIP and LEV treatments resulted in an increase in the pathogenic bacteria Bosea and Aeromonas, and they appeared to be more resistant to CIP than LEV. Additionally, CIP exposure caused reduced total length and delayed the development in B. gargarizans embryos, while LEV increased the total length and promoted embryonic development. The present study revealed the adverse effects of CIP and LEV exposure on host gut microbiota, growth and development during the embryonic stage, and contributed new perspectives to the evaluation of early aquatic ecological risk under CIP and LEV exposure.
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Affiliation(s)
- Ying Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Yaxi Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Hongyuan Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
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2
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Stoll DA, Grimmler C, Hetzer B, Masoura A, Kulling SE, Huch M. Bosea rubneri sp. nov. Isolated from Organically Grown Allium cepa. Curr Microbiol 2024; 81:212. [PMID: 38839619 PMCID: PMC11153308 DOI: 10.1007/s00284-024-03717-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/25/2024] [Indexed: 06/07/2024]
Abstract
Strain ZW T0_25T was isolated from an onion sample (Allium cepa var. Hytech F1) within a storage trial and proofed to be a novel, aerobic, Gram-stain negative, rod-shaped bacterial strain. Analyses of the 16S rRNA gene sequence and of the whole draft genome sequences, i.e., digital DNA-DNA hybridization (dDDH), Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) showed that this strain represents a new species of the genus Bosea. The genome size of strain ZW T0_25T is 6.19 Mbp, and the GC content is 66.9%. As whole cell sugars, rhamnose, ribose and glucose were identified. Ubiquinone Q-10 is the major respiratory quinone with 97.8%. Polar lipids in strain ZW T0_25T are composed of one phosphatidylethanolamine, one phosphatidylglycerol, one aminophospholipid, two aminolipids, one glycolipid and two phospholipids whereas the fatty acid profile predominantly consists of C18:1 w7c (63.3%), C16:1 w7c (19.5%) and C16:0 (7.1%). Phenotypic traits were tested in the wet lab as well as predicted in silico from genome data. Therefore, according to this polyphasic approach, the new name Bosea rubneri sp. nov. with the type strain ZW T0_25T (= DSM 116094 T = LMG 33093 T) is proposed.
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Affiliation(s)
- Dominic A Stoll
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany
| | - Christina Grimmler
- Department of Safety and Quality of Meat, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, E.-C.-Baumann-Straße 20, 95326, Kulmbach, Germany
| | - Birgit Hetzer
- Department of Food Technology and Bioprocess Engineering, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany
| | - Alexandra Masoura
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany
| | - Sabine E Kulling
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany
| | - Melanie Huch
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany.
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3
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Guo XY, Zhang QM, Fu JC, Qiu LH. Terrirubrum flagellatum gen. nov., sp. nov. of Terrirubraceae fam. nov. and Lichenibacterium dinghuense sp. nov. from forest soil and proposal of Rhodoblastaceae fam. nov. Int J Syst Evol Microbiol 2024; 74. [PMID: 38652005 DOI: 10.1099/ijsem.0.006348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
Two Gram-negative, aerobic, rod-shaped bacterial strains, 7MK25T and 6Y81T, were isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Based on the results of 16S rRNA gene sequence analysis, strain 7MK25T showed the highest similarity (93.6 %) to Methyloferula stellata AR4T, followed by Bosea thiooxidans DSM 9653T (93.3 %). Strain 6Y81T had the highest similarity of 97.9 % to Lichenibacterium minor RmlP026T, followed by Lichenibacterium ramalinae RmlP001T (97.2 %). Phylogenomic analysis using the UBCG and PhyloPhlAn methods consistently showed that strain 7MK25T formed a sister clade to Boseaceae, while strain 6Y81T formed an independent clade within the genus Lichenibacterium, both in the order Hyphomicrobiales. The digital DNA-DNA hybridization and average nucleotide identity values between strains 7MK25T, 6Y81T and their close relatives were in the ranges of 19.1-29.9 % and 72.5-85.5 %, respectively. The major fatty acids of 7MK25T were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), C19 : 0 cyclo ω8c, C16 : 0 and C17 : 0 cyclo, while those of 6Y81T were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), C16 : 0 and C16 : 0 3-OH. Strains 7MK25T and 6Y81T took diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine as their dominant polar lipids, and Q-10 as their major respiratory quinone. On the basis of phenotypic and phylogenetic data, strain 7MK25T is proposed to represent a novel species of a novel genus with name Terrirubrum flagellatum gen. nov., sp. nov., within a novel family Terrirubraceae fam. nov., with 7MK25T (=KCTC 62738T=GDMCC 1.1452T) as its type strain. Strain 6Y81T represents a novel species in the genus Lichenibacterium, for which the name Lichenibacterium dinghuense sp. nov. (type strain 6Y81T=KACC 21 727T=GDMCC 1.2176T) is proposed. Rhodoblastaceae fam. nov. with Rhodoblastus as the type genus is also proposed to solve the non-monophylectic problem of the family Roseiarcaceae.
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Affiliation(s)
- Xiu-Yin Guo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Qiu-Mei Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jia-Cheng Fu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Li-Hong Qiu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
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D'Incau E, Ouvrard S, Devers-Lamrani M, Jeandel C, Mohamed CE, Henry S. Biodegradation of a complex hydrocarbon mixture and biosurfactant production by Burkholderia thailandensis E264 and an adapted microbial consortium. Biodegradation 2024:10.1007/s10532-024-10073-6. [PMID: 38517619 DOI: 10.1007/s10532-024-10073-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 02/12/2024] [Indexed: 03/24/2024]
Abstract
Bioremediation is considered to be an effective treatment for hydrocarbon removal from polluted soils. However, the effectiveness of this treatment is often limited by the low availability of targeted contaminants. Biosurfactants produced by some microorganisms can increase organic compound solubility and might then overcome this limitation. Two different inocula producers of biosurfactants (Burkholderia thailandensis E264 and SHEMS1 microbial consortium isolated from a hydrocarbon-contaminated soil) were incubated in Bushnell-Haas medium supplemented with hydrocarbons to investigate their biodegradation potential. Experimental results showed their ability to degrade 9.1 and 6.1% of hydrocarbons respectively after 65 days of incubation with an initial total hydrocarbon concentration of 16 g L-1. The biodegradation was more effective for the light and medium fractions (C10 to C36). B. thailandensis and SHEMS1 consortium produced surfactants after 14 days of culture during the stationary phase with hydrocarbons as the sole carbon and energy source. However, biosurfactant production did not appear to directly increase hydrocarbon degradation efficiency. The complexity and recalcitrance of hydrocarbon mixture used in this study appeared to continue to limit its biodegradation even in the presence of biosurfactants. In conclusion, B. thailandensis and SHEMS1 consortium can degrade recalcitrant hydrocarbon compounds and are therefore good candidates for the bioremediation of environments polluted by total hydrocarbons.
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Affiliation(s)
| | | | - Marion Devers-Lamrani
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | | | | | - Sonia Henry
- Université de Lorraine, INRAE, LSE, 54000, Nancy, France
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Gu HY, Hao SY, Sun ZB, Xu JL, Ren Q, Pan HX. Bosea beijingensis sp. nov., Telluria beijingensis sp. nov. and Agrococcus beijingensis sp. nov., isolated from baijiu mash. Int J Syst Evol Microbiol 2024; 74. [PMID: 38530339 DOI: 10.1099/ijsem.0.006304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Abstract
The baijiu fermentation environment hosts a variety of micro-organisms, some of which still remain uncultured and uncharacterized. In this study, the isolation, cultivation and characterization of three novel aerobic bacterial strains are described. The cells of strain REN20T were Gram-negative, strictly aerobic, motile and grew at 26-37 °C, at pH 6.0-9.0 and in the presence of 0-5.0 % (w/v) NaCl. The cells of strain REN29T were Gram-negative, strictly aerobic, motile and grew at 15-30 °C, at pH 6.0-9.0 and in the presence of 0-10.0 % (w/v) NaCl. The cells of strain REN33T were Gram-positive, strictly aerobic, motile and grew at 15-37 °C, at pH 5.0-10.0 and in the presence of 0-7.0 % (w/v) NaCl. The digital DNA-DNA hybridization and average nucleotide identity by orthology values between type strains in related genera and REN20T (20.3-36.8 % and 79.8-89.9 %), REN29T (20.3-36.8 % and 74.5-88.5 %) and REN33T (22.6-48.6 % and 75.8-84.2 %) were below the standard cut-off criteria for the delineation of bacterial species, respectively. Based on polyphasic taxonomy analysis, we propose three new species, Bosea beijingensis sp. nov. (=REN20T=GDMCC 1.2894T=JCM 35118T), Telluria beijingensis sp. nov. (=REN29T=GDMCC 1.2896T=JCM 35119T) and Agrococcus beijingensis sp. nov. (=REN33T=GDMCC 1.2898T=JCM 35164T), which were recovered during cultivation and isolation from baijiu mash.
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Affiliation(s)
- Hao-Yue Gu
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, PR China
| | - Shu-Yue Hao
- Guizhou Guotai Liquor Group Co. Ltd., Guizhou, PR China
| | - Zhan-Bin Sun
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, PR China
| | - Jia-Liang Xu
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, PR China
| | - Qing Ren
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, PR China
| | - Han-Xu Pan
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, PR China
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Chaudhary S, Sindhu SS, Dhanker R, Kumari A. Microbes-mediated sulphur cycling in soil: Impact on soil fertility, crop production and environmental sustainability. Microbiol Res 2023; 271:127340. [PMID: 36889205 DOI: 10.1016/j.micres.2023.127340] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/06/2023] [Accepted: 02/18/2023] [Indexed: 03/08/2023]
Abstract
Reduction in soil fertility and depletion of natural resources due to current intensive agricultural practices along with climate changes are the major constraints for crop productivity and global food security. Diverse microbial populations' inhabiting the soil and rhizosphere participate in biogeochemical cycling of nutrients and thereby, improve soil fertility and plant health, and reduce the adverse impact of synthetic fertilizers on the environment. Sulphur is 4th most common crucial macronutrient required by all organisms including plants, animals, humans and microorganisms. Effective strategies are required to enhance sulphur content in crops for minimizing adverse effects of sulphur deficiency on plants and humans. Various microorganisms are involved in sulphur cycling in soil through oxidation, reduction, mineralization, and immobilization, and volatalization processes of diverse sulphur compounds. Some microorganisms possess the unique ability to oxidize sulphur compounds into plant utilizable sulphate (SO42-) form. Considering the importance of sulphur as a nutrient for crops, many bacteria and fungi involved in sulphur cycling have been characterized from soil and rhizosphere. Some of these microbes have been found to positively affect plant growth and crop yield through multiple mechanisms including the enhanced mobilization of nutrients in soils (i.e., sulphate, phosphorus and nitrogen), production of growth-promoting hormones, inhibition of phytopathogens, protection against oxidative damage and mitigation of abiotic stresses. Application of these beneficial microbes as biofertilizers may reduce the conventional fertilizer application in soils. However, large-scale, well-designed, and long-term field trials are necessary to recommend the use of these microbes for increasing nutrient availability for growth and yield of crop plants. This review discusses the current knowledge regarding sulphur deficiency symptoms in plants, biogeochemical cycling of sulphur and inoculation effects of sulphur oxidizing microbes in improving plant biomass and crop yield in different crops.
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Affiliation(s)
- Suman Chaudhary
- Research Associate, EBL Laboratory, ICAR-Central Institute of Research on Buffaloes, Hisar 125001, Haryana, India.
| | - Satyavir Singh Sindhu
- Department of Microbiology, CCS Haryana Agricultural University, Hisar 125004, Haryana, India.
| | - Rinku Dhanker
- International Institute of Veterinary, Education & Research, Bahuakbarpur, Rohtak 124001, Haryana, India.
| | - Anju Kumari
- Center of Food Science and Technology, CCS Haryana Agricultural University, Hisar 125004, Haryana, India.
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Endophytic Bosea spartocytisi sp. nov. Coexists with rhizobia in root nodules of Spartocytisus supranubius growing in soils of Teide National Park (Canary Islands). Syst Appl Microbiol 2022; 45:126374. [DOI: 10.1016/j.syapm.2022.126374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/10/2022] [Accepted: 10/15/2022] [Indexed: 11/06/2022]
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8
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Wu Y, Xiang L, Wang H, Ma L, Qiu X, Liu D, Feng L, Lu X. Transcriptome analysis of an arsenite-/antimonite-oxidizer, Bosea sp. AS-1 reveals the importance of the type 4 secretion system in antimony resistance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:154168. [PMID: 35231521 DOI: 10.1016/j.scitotenv.2022.154168] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Bosea sp. AS-1 is an arsenite [As(III)] and antimonite [Sb(III)] oxidizer previously isolated by our group from the Xikuangshan Antimony (Sb) Mine area. Our previous study showed that Bosea sp. AS-1 had a preference for oxidizing As(III) or Sb(III) with different carbon sources, which suggested that different metabolic mechanisms may be utilized by the bacteria to survive in As(III)- or Sb(III)-contaminated environments. Here, we conducted whole-genome and transcriptome sequencing to reveal the molecular mechanisms utilized by Bosea sp. AS-1 to resist As(III) or Sb(III). We discovered that AS-1 acquired various As- and Sb-resistant genes in its genome and might resist As(III) or Sb(III) through the regulation of multiple pathways, such as As and Sb metabolism, the bacterial secretion system, oxidative phosphorylation, the TCA cycle and bacterial flagellar motility. Interestingly, we discovered that genes of the type IV secretion system (T4SS) were activated in response to Sb(III), and inhibiting T4SS activity in AS-1 dramatically reduced its oxidation efficiency and tolerance to Sb(III). To our knowledge, this is the first study showing the activation of T4SS genes by Sb and a direct involvement of T4SS in bacterial Sb resistance. Our findings establish the T4SS as an important Sb resistance factor in bacteria and may help us understand the spread of Sb resistance genes in the environment.
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Affiliation(s)
- Yanmei Wu
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Li Xiang
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Hongmei Wang
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China; State Key Laboratory of Biogeology and Environmental Geology, China University of China (Wuhan), Wuhan 430074, China
| | - Liyuan Ma
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Xuan Qiu
- State Key Laboratory of Biogeology and Environmental Geology, China University of China (Wuhan), Wuhan 430074, China
| | - Deng Liu
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Liang Feng
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Xiaolu Lu
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China.
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Srinivasan R, Krishnan SR, Ragunath KS, Ponni KK, Balaji G, Prabhakaran N, Chelliappan B, Narayanan RL, Gracy M, Latha K. Prospects of utilizing a multifarious yeast (MSD1), isolated from South Indian coast as an Agricultural input. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2021.102232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Jeon H, Choi E, Hwang J. Identification and characterization of VapBC toxin-antitoxin system in Bosea sp. PAMC 26642 isolated from Arctic lichens. RNA (NEW YORK, N.Y.) 2021; 27:1374-1389. [PMID: 34429367 PMCID: PMC8522696 DOI: 10.1261/rna.078786.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Toxin-antitoxin (TA) systems are genetic modules composed of a toxin interfering with cellular processes and its cognate antitoxin, which counteracts the activity of the toxin. TA modules are widespread in bacterial and archaeal genomes. It has been suggested that TA modules participate in the adaptation of prokaryotes to unfavorable conditions. The Bosea sp. PAMC 26642 used in this study was isolated from the Arctic lichen Stereocaulon sp. There are 12 putative type II TA loci in the genome of Bosea sp. PAMC 26642. Of these, nine functional TA systems have been shown to be toxic in Escherichia coli The toxin inhibits growth, but this inhibition is reversed when the cognate antitoxin genes are coexpressed, indicating that these putative TA loci were bona fide TA modules. Only the BoVapC1 (AXW83_01405) toxin, a homolog of VapC, showed growth inhibition specific to low temperatures, which was recovered by the coexpression of BoVapB1 (AXW83_01400). Microscopic observation and growth monitoring revealed that the BoVapC1 toxin had bacteriostatic effects on the growth of E. coli and induced morphological changes. Quantitative real time polymerase chain reaction and northern blotting analyses showed that the BoVapC1 toxin had a ribonuclease activity on the initiator tRNAfMet, implying that degradation of tRNAfMet might trigger growth arrest in E. coli Furthermore, the BoVapBC1 system was found to contribute to survival against prolonged exposure at 4°C. This is the first study to identify the function of TA systems in cold adaptation.
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Affiliation(s)
- Hyerin Jeon
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea
| | - Eunsil Choi
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea
- Microbiological Resource Research Institute, Pusan National University, Busan 46241, Republic of Korea
| | - Jihwan Hwang
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea
- Microbiological Resource Research Institute, Pusan National University, Busan 46241, Republic of Korea
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Effects of Mineral-Solubilizing Microorganisms on Root Growth, Soil Nutrient Content, and Enzyme Activities in the Rhizosphere Soil of Robinia pseudoacacia. FORESTS 2021. [DOI: 10.3390/f12010060] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background: Abandoned mining sites are becoming increasingly common due to anthropogenic activities. Consequently, external-soil spray seeding technology has attracted increasing attention as a strategy to remediate them. However, significant challenges remain that greatly inhibit the efficacy of such technologies, such as insufficient nutrients available for plants. Methods: For this study, we designed an experiment, which involved the addition of mineral-solubilizing microorganisms and R. pseudoacacia seedlings to the external-soil spray seeding (ESSS) substrate, and measured the soil nutrients, enzyme activities, and root growth of R. pseudoacacia. Results: First, the combination of certain mineral-solubilizing microorganisms with ESSS advanced its efficiency by increasing the availability of soil nutrients and soil enzymatic activities in association with R. pseudoacacia. Furthermore, the improvement of root growth of R. pseudoacacia was intimately related to soil nutrients, particularly for soil total nitrogen (TN) and total sulfur (TS). In general, the effects of the J2 (combined Bacillus thuringiensis and Gongronella butleri) treatment for soil nutrients, enzyme activities, and plant growth were the strongest. Conclusion: In summary, the results of our experiment revealed that these mineral-solubilizing microorganisms conveyed a promotional effect on R. pseudoacacia seedlings by increasing the soil nutrient content. These results provide basic data and microbial resources for the development and applications of mineral-solubilizing microorganisms for abandoned mine remediation.
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12
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Zhang Y, Sun K, Li Z, Chai X, Fu X, Kholodkevich S, Kuznetsova T, Chen C, Ren N. Effescts of acute diclofenac exposure on intestinal histology, antioxidant defense, and microbiota in freshwater crayfish (Procambarus clarkii). CHEMOSPHERE 2021; 263:128130. [PMID: 33297118 DOI: 10.1016/j.chemosphere.2020.128130] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/14/2020] [Accepted: 08/24/2020] [Indexed: 06/12/2023]
Abstract
In the present study, we exposed Procambarus clarkii to different doses (0, 1, and 10 mg/L) of diclofenac (DCF). Meanwhile, we investigated the effects of exposure to DCF on intestinal histology, antioxidant defense, and microbial communities in P. clarkii. The results showed DCF caused histological changes in the intestines. Additionally, DCF induced significant changes in the expression of antioxidant genes including Mn-sod, cat, gst, and gpx. High-throughput sequencing of 16 S rRNA gene revealed DCF changed the diversity, richness, and composition of intestinal microbial communities. The relative abundances of the predominant phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria showed significant changes at the phylum level after treatment with DCF. At the genus level, the most predominant genera with marked differences in abundance were Lucibacterium, Shewanella, Bacteroides, Anaerorhabdus, Aeromonas, Acinetobacter, Clostridium XlVb, Arcobacter, Bosea, and so on. To conclude, treatment with DCF could cause intestinal histological damage, induce significant changes of the expression of intestinal antioxidant genes, and impact the composition of intestinal microbiota in P. clarkii. This research will provide novel insights into the toxic effects of DCF on aquatic crustaceans.
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Affiliation(s)
- Yu Zhang
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Kai Sun
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Zheyu Li
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Xiaoxing Chai
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Xiangyu Fu
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Sergey Kholodkevich
- Saint-Petersburg Scientific Research Center for Ecological Safety, Russian Academy of Sciences, Saint-Petersburg, 197110, Russia
| | - Tatiana Kuznetsova
- Saint-Petersburg Scientific Research Center for Ecological Safety, Russian Academy of Sciences, Saint-Petersburg, 197110, Russia
| | - Chuan Chen
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Nanqi Ren
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
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Zheng J, Wang S, Zhou A, Zhao B, Dong J, Zhao X, Li P, Yue X. Efficient elimination of sulfadiazine in an anaerobic denitrifying circumstance: Biodegradation characteristics, biotoxicity removal and microbial community analysis. CHEMOSPHERE 2020; 252:126472. [PMID: 32200179 DOI: 10.1016/j.chemosphere.2020.126472] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 06/10/2023]
Abstract
Sulfadiazine (SDZ) is widely used in clinical treatment, livestock husbandry and aquaculture as an antibacterial agent, resulting in environmental risks. In this work, batch experiments were conducted to investigate the characteristics of SDZ biodegradation and reaction mechanisms in a nitrate anaerobic denitrifying system for the first time. The results showed that 98.52% of the SDZ, which had an initial concentration of 50 mg L-1, was degraded after 70 h, indicating that the removal efficiency of SDZ in anaerobic denitrifying system was 55.27% higher than that in anaerobic system. Furthermore, LC-MS-MS analysis confirmed that SDZ could be degraded into 16 byproducts via 3 main degradation pathways that contained 6 different reactions. After analyzing the microbial communities of the reactor, the denitrifying bacteria and desulfurizing bacteria Desulforhabdus, Ignavibacterium, SBR1031_norank, Nocardioides, etc. were highly associated with the removal of SDZ in the system. The biological toxicity test of the effluent indicated that the remaining organic matter and inorganic matter of the effluent could provide nutrients for E. coli and promote its growth. In other words, anaerobic denitrifying systems are highly efficient, simple and environmentally friendly, and have an impressive prospect in the biodegradation of sulfonamide antibiotics.
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Affiliation(s)
- Jierong Zheng
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, PR China
| | - Sufang Wang
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, PR China.
| | - Aijuan Zhou
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, PR China
| | - Bowei Zhao
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, PR China
| | - Jing Dong
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, PR China
| | - Xiaochan Zhao
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, PR China
| | - Peirui Li
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, PR China
| | - Xiuping Yue
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, PR China.
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14
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Deb S, Das L, Das SK. Composition and functional characterization of the gut microbiome of freshwater pufferfish (Tetraodon cutcutia). Arch Microbiol 2020; 202:2761-2770. [PMID: 32737543 DOI: 10.1007/s00203-020-01997-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/10/2020] [Accepted: 07/22/2020] [Indexed: 11/26/2022]
Abstract
This study describes the community composition and functions of the gut microbiome of the freshwater omnivorous pufferfish based on metagenomic approach. Metagenome sequence data showed a dominance of the class Gammaproteobacteria followed by Fusobacteria, Actinobacteria, Anerolineae, Betaproteobacteria, Deinococci, Clostridia and Deltaproteobacteria. At the order level, the most abundant groups were Aeromonadales, Fusobacteriales, Enterobacterales, Synechococcales. The genus Aeromonas was the most predominant followed by Plesiomonas and Cetobacterium. Additionally, within the domain Archaea, class Methanomicrobia was most abundant followed by Hadesarchaea, Thermoplasmata, Candidatus Altiarchaeales, Candidatus Bathyarchaeota and Thermoprotei. The metabolic profile of the bacterial community exhibited a high prevalence of genes associated with core housekeeping functions, such as synthesis of cofactors, vitamins, prosthetic groups, pigments, amino acids and its derivatives, carbohydrate and protein metabolism. Comparative analysis with other fish gut microbiome showing similarity in protein metabolism with carnivorous Salmon and carbohydrate metabolism with herbivorous grass carp respectively. This study describes the bacterial community compositions are influenced by the trophic level.
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Affiliation(s)
- Sushanta Deb
- Department of Biotechnology, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, India
| | - Lipika Das
- Department of Biotechnology, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, India
| | - Subrata K Das
- Department of Biotechnology, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, India.
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15
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Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 2020; 11:468. [PMID: 32373076 PMCID: PMC7179689 DOI: 10.3389/fmicb.2020.00468] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
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Affiliation(s)
- Anton Hördt
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marina García López
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marcel Schleuning
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Lisa-Maria Weinhold
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Markus Göker
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
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16
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Zhang Y, Li Z, Kholodkevich S, Sharov A, Feng Y, Ren N, Sun K. Microcystin-LR-induced changes of hepatopancreatic transcriptome, intestinal microbiota, and histopathology of freshwater crayfish (Procambarus clarkii). THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 711:134549. [PMID: 31810700 DOI: 10.1016/j.scitotenv.2019.134549] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/19/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
As a hepatotoxin, microcystin-LR (MC-LR) poses a great threat to aquatic organisms. In this research, the hepatopancreatic transcriptome, intestinal microbiota, and histopathology of Procambarus clarkii (P. clarkii) in response to acute MC-LR exposure were studied. RNA-seq analysis of hepatopancreas identified 372 and 781 differentially expressed genes (DEGs) after treatment with 10 and 40 μg/L MC-LR, respectively. Among the DEGs, 23 genes were immune-related and 21 genes were redox-related. GO functional enrichment analysis revealed that MC-LR could impact nuclear-transcribed mRNA catabolic process, cobalamin- and heme-related processes, and sirohydrochlorin cobaltochelatase activity of P. clarkii. In addition, the only significantly enriched KEGG pathway induced by MC-LR was galactose metabolism pathway. Meanwhile, sequencing of the bacterial 16S rRNA gene demonstrated that MC-LR decreased bacterial richness and diversity, and altered the intestinal microbiota composition. At the phylum level, after 96 h, the abundance of Verrucomicrobia decreased after treatment with 10 and 40 μg/L MC-LR, while Firmicutes increased in the 40 μg/L MC-LR-treated group. At the genus level, the abundances of 15 genera were significantly altered after exposure to MC-LR. Our research demonstrated that MC-LR exposure caused histological alterations such as structural damage of hepatopancreas and intestines. This research provides an insight into the mechanisms associated with MC-LR toxicity in aquatic crustaceans.
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Affiliation(s)
- Yu Zhang
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Zheyu Li
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Sergey Kholodkevich
- Institute of Earth Sciences, Saint-Petersburg State University, Saint-Petersburg 199034, Russia; Saint-Petersburg Scientific Research Center for Ecological Safety, Russian Academy of Sciences, Saint-Petersburg 197110, Russia
| | - Andrey Sharov
- Saint-Petersburg Scientific Research Center for Ecological Safety, Russian Academy of Sciences, Saint-Petersburg 197110, Russia; Papanin Institute for Biology of the Inland Waters, Russian Academy of Sciences, Borok 152742, Russia
| | - Yujie Feng
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nanqi Ren
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Kai Sun
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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17
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Ming YZ, Liu L, Xian WD, Jiao JY, Liu ZT, Li MM, Xiao M, Li WJ. Rhabdaerophilum calidifontis gen. nov., sp. nov., a novel bacterium isolated from a hot spring, and proposal of Rhabdaerophilaceae fam. nov. Int J Syst Evol Microbiol 2020; 70:2298-2304. [PMID: 32043955 DOI: 10.1099/ijsem.0.004035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel thermotolerant bacterial strain was isolated from a hot spring in a Tibetan geothermal field. Phylogenetic analysis of the 16S rRNA gene sequence of the novel strain showed that it belongs to a distinct lineage far from any known taxa. The new isolate shared the highest pairwise sequence identity with Phreatobacter cathodiphilus S-12T (92.8 % similarity) according to the 16S rRNA gene sequences. Cells were Gram-stain-negative, aerobic, rod-shaped and formed white round colonies. The strain grew at the ranges of 28-45 °C (optimum, 37 °C), pH 5.0-7.0 (optimum, pH 6.0) and 0-2 % NaCl. The strain was positive for catalase and oxidase. The major respiratory quinone was ubiquinone Q-10. Polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The major fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The DNA G+C content was 68.3 mol%. Based on these distinguishing properties, this strain is proposed to represent a new species of a new genus Rhabdaerophilum calidifontis gen. nov., sp. nov., within a new family Rhabdaerophilaceae fam. nov. The type strain of the type species of Rhabdaerophilum calidifontis is SYSU G02060T (=KCTC 72351T=CGMCC 1.17070T).
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Affiliation(s)
- Yu-Zhen Ming
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Lan Liu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Ze-Tao Liu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong 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 Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China.,CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Urumqi 830011, PR China
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18
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Zhao Y, Zhao Z, Song X, Jiang X, Wang Y, Cao X, Si Z, Pan F. Effects of nZVI dosing on the improvement in the contaminant removal performance of constructed wetlands under the dye stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 703:134789. [PMID: 31715467 DOI: 10.1016/j.scitotenv.2019.134789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 09/28/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
In this study, different dosages of nanoscale zero-valent iron (nZVI) were used to improve the nitrogen removal efficiency in CWs under different C/N ratios and dye stress conditions. The addition of nZVI enhanced the dye and nitrogen removal efficiencies in constructed wetlands (CWs) through chemical reduction and biological denitrification processes. However, total nitrogen (TN) and dye removal efficiencies firstly increased and then decreased with the increases of the nZVI dosage and influent COD/N (C/N) ratio. Under the influent C/N ratio of 5, the higher TN removal efficiencies (80.2%, 55.1%, and 69.14% under 25 mg/L, 50 mg/L, and 75 mg/L dye concentration, respectively) and higher COD removal efficiencies (48.3%, 74.95%, and 30.76% under 25 mg/L, 50 mg/L, and 75 mg/L dye concentration, respectively) were obtained in CWs by adding the optimal nZVI dosage (0.1 g/L). The dye removal efficiencies in CWs with nZVI at C/N = 1 (75%-91%) and at C/N = 5 (81%-97%) were all significantly higher than that in CWs without nZVI (60%-82%). Moreover, the functional bacteria for nitrogen removal in denitrification and the dye degradation (Zoogloea and Acinetobacter) were enriched in CWs with 0.1 g/L nZVI.
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Affiliation(s)
- Yufeng Zhao
- State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, PR China
| | - Zhimiao Zhao
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, PR China; Engineering Research Center for Water Environment Ecology in Shanghai, Shanghai 201306, PR China
| | - Xinshan Song
- State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, PR China
| | - Xingyi Jiang
- State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, PR China
| | - Yuhui Wang
- State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, PR China
| | - Xin Cao
- State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, PR China
| | - Zhihao Si
- State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, PR China
| | - Fanfeng Pan
- China New Energy (shanghai) Limited Company, Shanghai 201620, PR China.
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19
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Glutamicibacter mishrai sp. nov., isolated from the coral Favia veroni from Andaman Sea. Arch Microbiol 2019; 202:733-745. [PMID: 31796989 DOI: 10.1007/s00203-019-01783-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/21/2019] [Accepted: 11/25/2019] [Indexed: 10/25/2022]
Abstract
A novel aerobic marine actinobacterium (strain S5-52T) belonging to the genus Glutamicibacter was isolated from the coral Favia veroni sampled from the Andaman Sea, India. Cells are Gram stain positive and rod shaped. The DNA G+C content was 58.7 mol%. The major quinones were MK-8 and MK-9. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, glycolipid, trimannosyldiacylglycerol, phospholipid and dimannosylglyceride. The peptidoglycan type was A4α. Strain S5-52T showed a maximum 16S rRNA similarity of 99.36% with Glutamicibacter halophytocola DSM 101718T. The genome of strain S5-52T was 3.57 Mb that contains 3274 protein coding sequences (CDS). DNA-DNA similarity and ANI values between S5-52T and the reference strains were below 70% and 95-96%, respectively. Analysis of genomic reduction events in the evolutionary path from the LUCA (last universal common ancestor) to G. mishrai LMG 29155T and G. halophytocola DSM 101718T exhibit a number of genes involved in amino acid metabolism, cell wall biogenesis and replication, recombination and repair mechanism that reduced in both the species. Based on phenotypic, chemotaxonomic properties and comparative genomic studies, the strain S5-52T is considered a novel species of the genus Glutamicibacter, for which the name Glutamicibacter mishrai sp. nov. is proposed. The type strain is S5-52T (= KCTC 39846T = LMG 29155T).
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20
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Skipper C, Ferrieri P, Cavert W. Bacteremia and central line infection caused by Bosea thiooxidans. IDCases 2019; 19:e00676. [PMID: 31890589 PMCID: PMC6926286 DOI: 10.1016/j.idcr.2019.e00676] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 11/26/2022] Open
Abstract
We describe a case of central venous catheter infection and bacteremia caused by Bosea thiooxidans, which has not been previously described in the literature. Bosea spp. is a gram-negative bacterium that has been isolated from hospital water supplies and may become an important cause of nosocomial infections.
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Affiliation(s)
- Caleb Skipper
- Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Patricia Ferrieri
- Departments of Medicine and Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Winston Cavert
- Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota, USA
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21
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Sazanova AL, Safronova VI, Kuznetsova IG, Karlov DS, Belimov AA, Andronov EE, Chirak ER, Popova JP, Verkhozina AV, Willems A, Tikhonovich IA. Bosea caraganae sp. nov. a new species of slow-growing bacteria isolated from root nodules of the relict species Caragana jubata (Pall.) Poir. originating from Mongolia. Int J Syst Evol Microbiol 2019; 69:2687-2695. [DOI: 10.1099/ijsem.0.003509] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Anna L. Sazanova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, Sh. Podbelskogo 3, St. Petersburg, Russian Federation
| | - Vera I. Safronova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, Sh. Podbelskogo 3, St. Petersburg, Russian Federation
| | - Irina G. Kuznetsova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, Sh. Podbelskogo 3, St. Petersburg, Russian Federation
| | - Denis S. Karlov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, Sh. Podbelskogo 3, St. Petersburg, Russian Federation
| | - Andrey A. Belimov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, Sh. Podbelskogo 3, St. Petersburg, Russian Federation
- Kazan Institute of Biochemistry and Biophysics of the Russian Academy of Sciences (KIBB of RAS), 420111, Lobachevsky Str. 2/31, Kazan, Russian Federation
| | - Evgeny E. Andronov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, Sh. Podbelskogo 3, St. Petersburg, Russian Federation
| | - Elizaveta R. Chirak
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, Sh. Podbelskogo 3, St. Petersburg, Russian Federation
| | - Janna P. Popova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, Sh. Podbelskogo 3, St. Petersburg, Russian Federation
| | - Alla V. Verkhozina
- Siberian Institute of Plant Physiology and Biochemistry (SIPPB), 664033, Lermontova Str. 132, Irkutsk, Russian Federation
| | - Anne Willems
- Ghent University, Department of Biochemistry and Microbiology, Faculty of Sciences, 9000, K.L. Ledeganckstraat 35, Ghent, Belgium
| | - Igor A. Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, Sh. Podbelskogo 3, St. Petersburg, Russian Federation
- Saint Petersburg State University, Department of Genetics and Biotechnology, 199034, Universitetskaya Emb. 7/9, St. Petersburg, Russian Federation
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22
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Albert RA, McGuine M, Pavlons SC, Roecker J, Bruess J, Mossman S, Sun S, King M, Hong S, Farrance CE, Danner J, Joung Y, Shapiro N, Whitman WB, Busse HJ. Bosea psychrotolerans sp. nov., a psychrotrophic alphaproteobacterium isolated from Lake Michigan water. Int J Syst Evol Microbiol 2019; 69:1376-1383. [PMID: 30882299 DOI: 10.1099/ijsem.0.003319] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three strains of a Gram-stain negative bacterium were isolated from Lake Michigan water. 16S rRNA gene sequence analysis revealed that strain 1131 had sequence similarities to Bosea vaviloviae LMG 28367T, Bosea lathyri LMG 26379T, Bosea lupini LMG 26383T, Bosea eneae CCUG 43111T, Bosea vestrisii CCUG 43114T and Boseamassiliensis CCUG 43117T of 99.8, 99.1, 98.4, 98.4, 98.4 and 98.2 %, respectively. The average nucleotide identity value between strain 1131T and Bosea vaviloviae Vaf-18T was 93.4 % and the DNA relatedness was 38 %. The primary cellular fatty acids of strain 1131T were C16 : 1ω7c and C18 : 1ω7c. The primary polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The major compound in the quinone system was ubiquinone Q-10 and in the polyamine pattern sym-homospermidine was predominant. Additional phenotypic characteristics included growth at 5-35 °C, pH values of pH 5.5-8.0, a salt tolerance range of 0.0-1.2 % (w/v), and production of an unknown water soluble brown pigment. After phenotypic, chemotaxonomic and genomic analyses, this isolate was identified as a novel species for which the name Bosea psychrotolerans is proposed. The type strain is 1131T (NRRL B-65405=LMG 30034).
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Affiliation(s)
- Richard A Albert
- 1Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA.,2Water Quality Center, Marquette University, Civil and Environmental Engineering, P.O. Box 1881 Milwaukee, WI, USA
| | - Molly McGuine
- 1Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Shawn C Pavlons
- 1Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Jon Roecker
- 1Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Jennifer Bruess
- 1Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Shane Mossman
- 1Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Sona Sun
- 3Microbial Discovery Group, Franklin, WI, USA
| | - Mike King
- 3Microbial Discovery Group, Franklin, WI, USA
| | - Sunhee Hong
- 4Charles River Laboratories, Microbial Solutions, Newark, DE, USA
| | | | - Joseph Danner
- 4Charles River Laboratories, Microbial Solutions, Newark, DE, USA
| | - Yochan Joung
- 5Department of Biological Sciences, College of Natural Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Nicole Shapiro
- 6DOE Joint Genomics Institute, Walnut Creek, CA 94598, USA
| | - William B Whitman
- 7Microbiology Department, Univeristy of Georgia, Athens, GA 30602, USA
| | - Hans-Jürgen Busse
- 8Institute of Microbiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
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23
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24
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Walczak AB, Yee N, Young LY. Draft genome sequence of Bosea sp. WAO an arsenite and sulfide oxidizer isolated from a pyrite rock outcrop in New Jersey. Stand Genomic Sci 2018; 13:6. [PMID: 29682167 PMCID: PMC5894208 DOI: 10.1186/s40793-018-0312-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 03/21/2018] [Indexed: 11/30/2022] Open
Abstract
This genome report describes the draft genome and physiological characteristics of Bosea sp. WAO (=DSM 102914), a novel strain of the genus Bosea in the family Bradyrhizobiaceae. Bosea sp. WAO was isolated from pulverized pyritic shale containing elevated levels of arsenic. This aerobic, gram negative microorganism is capable of facultative chemolithoautotrophic growth under aerobic conditions by oxidizing the electron donors arsenite, elemental sulfur, thiosulfate, polysulfide, and amorphous sulfur. The draft genome is of a single circular chromosome 6,125,776 bp long consisting of 21 scaffolds with a G + C content of 66.84%. A total 5727 genes were predicted of which 5665 or 98.92% are protein-coding genes and 62 RNA genes. We identified the genes aioA and aioB, which encode the large and small subunits of the arsenic oxidase respectively. We also identified the genes for the complete sulfur oxidation pathway sox which is used to oxidize thiosulfate to sulfate.
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Affiliation(s)
- Alexandra B Walczak
- 1Division of Life Sciences, Rutgers University, The State University of New Jersey, Piscataway, New Jersey USA
| | - Nathan Yee
- 2Department of Environmental Sciences, Rutgers University, The State University of New Jersey, New Brunswick, New Jersey USA
| | - Lily Y Young
- 2Department of Environmental Sciences, Rutgers University, The State University of New Jersey, New Brunswick, New Jersey USA
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Abstract
PURPOSE To report an unusual case of postcataract endophthalmitis secondary to Bosea thiooxidans. METHODS Case report. RESULTS An 86-year-old man presented with postoperative endophthalmitis 3 weeks after uncomplicated cataract surgery. He complained of a headache and blurry vision but denied having eye pain. Slit-lamp examination demonstrated leukocytes with a fibrinous membrane in the anterior segment and vitritis. A diagnosis of acute postoperative endophthalmitis was made, and the patient was treated with intravitreal antibiotics. Culture of vitreous tap revealed Bosea thiooxidans, a gram-negative rod found in soil and water systems. CONCLUSION To our knowledge, this report is the first to describe Bosea thiooxidans endophthalmitis and one of a few reports of human infection with this microbial agent.
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26
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Jadhav K, Jadhav I. Sulfur oxidation by Achromobacter xylosoxidans strain wsp05 reveals ecological widening over which thiotrophs are distributed. World J Microbiol Biotechnol 2017; 33:192. [PMID: 28975472 DOI: 10.1007/s11274-017-2359-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/26/2017] [Indexed: 10/18/2022]
Abstract
Achromobacter xylosoxidans is a versatile bacterium known for its ability to degrade aromatic compounds. However, its ability to oxidize sulfur compounds for electron and energy source is not reported much. In the present work, the Gram-negative bacterium Achromobacter xylosoxidans strain wsp05 isolated from a waste stabilization ponds (WSPs) system was studied for its ability to oxidize reduced sulfur compounds. The strain was able to oxidize thiosulfate and sodium sulfite. To observe the effect of physicochemical parameters on the rate of sulfur oxidation, strain wsp05 was grown in thiosulfate (20 mM) containing minimal salt medium at varied pH, temperature and ammonium and phosphate ions concentration. Maximum thiosulfate oxidation was observed at 30 °C with initial pH of 7-7.2. The strain was characterized using universal 16S rRNA gene primers revealing high similarity (> 99%) with Achromobacter xylosoxidans NBRC 15126T belonging to β-proteobacteria. In the present study, we investigated the sulfur oxidation properties of the Achromobacter xylosoxidans strain wsp05, which revealed an ecological and phylogenetic widening over which the thiotrophs are distributed.
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Affiliation(s)
- Kapilesh Jadhav
- School of Studies in Botany, Vikram University Ujjain, Ujjain, 456010, India. .,School of Life Sciences, Jaipur National University, Jaipur, 302017, India.
| | - Indrani Jadhav
- School of Studies in Botany, Vikram University Ujjain, Ujjain, 456010, India.,School of Life Sciences, Jaipur National University, Jaipur, 302017, India
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Limnobacter humi sp. nov., a thiosulfate-oxidizing, heterotrophic bacterium isolated from humus soil, and emended description of the genus Limnobacter Spring et al. 2001. J Microbiol 2017; 55:508-513. [PMID: 28664518 DOI: 10.1007/s12275-017-6645-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/06/2017] [Accepted: 04/07/2017] [Indexed: 10/19/2022]
Abstract
Three Gram-negative, strictly aerobic, chemolithoheterotrophic bacterial strains, designated UCM-30, UCM-33, and UCM-39T, were isolated in South Korea. Based on their 16S rRNA gene sequences, the three isolated strains were found to be similar to Limnobacter thiooxidans CS-K2T (97.41-97.68%), Limnobacter litoralis KP1-19T (95.55-95.76%), and various genera belonging to the class Betaproteobacteria (90.34-93.34%). DNA-DNA hybridization showed 79.3-83.9% similarity between the genomic DNA of UCM-39T, UCM-30, and UCM-33, while the sequence similarity between UCM-39T and L. thiooxidans KACC 13837T or L. litoralis LMG 24869T was 23.7% and 18.6%, respectively. The DNA G+C content of UCM 39T was 59.7 mol%, the major ubiquinone was Q-8, and the optimal oxidation rate was observed at 10 mM thiosulfate. The major fatty acids (≥ 10%) were summed features 3 (C16:1 ω7c and/or C16:1 ω6c) and 8 (C18:1 ω7c and/or C18:1 ω6c), and C16:0. The major polar lipids (diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol) were found in all members of genus Limnobacter. Based on phenotypic, physiological, and phylogenetic analyses, the UCM-39T strain was found to be significantly distinct to represent a novel species affiliated to the genus Limnobacter. We propose to name it Limnobacter humi sp. nov. with the type strain UCM-39T (=KACC 18574T =NBRC 111650T).
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28
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Kang S, Han SR, Oh TJ, Park H. Complete genome sequence of thiosulfate-oxidizing Bosea sp. strain PAMC26642 isolated from an Arctic lichen. J Biotechnol 2016; 223:38-9. [PMID: 26924237 DOI: 10.1016/j.jbiotec.2016.02.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 02/24/2016] [Indexed: 10/22/2022]
Abstract
Thiosulfate-oxidizing Bosea sp. strain PAMC26642 was isolated from the Arctic lichen Stereocaulon sp. Complete genome sequencing of Bosea sp. PAMC26642 revealed several genes involved in thiosulfate oxidation. An analysis of the Bosea sp. PAMC26642 genome will provide novel insight into the genetic basis of its physiology and enable further analysis of key genes in the thiosulfate oxidation pathway.
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Affiliation(s)
- Seunghyun Kang
- Korea Polar Research Institute (KOPRI), 213-3, Songdo-dong, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - So-Ra Han
- Department of BT-convergent Pharmaceutical Engineering, SunMoon University, #100, Kalsan-ri, Tangjeong-myeon, Asansi, Chungnam 31460, Republic of Korea
| | - Tae-Jin Oh
- Department of BT-convergent Pharmaceutical Engineering, SunMoon University, #100, Kalsan-ri, Tangjeong-myeon, Asansi, Chungnam 31460, Republic of Korea.
| | - Hyun Park
- Korea Polar Research Institute (KOPRI), 213-3, Songdo-dong, Yeonsu-gu, Incheon 21990, Republic of Korea.
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Sanyal SK, Mou TJ, Chakrabarty RP, Hoque S, Hossain MA, Sultana M. Diversity of arsenite oxidase gene and arsenotrophic bacteria in arsenic affected Bangladesh soils. AMB Express 2016; 6:21. [PMID: 26980601 PMCID: PMC4792827 DOI: 10.1186/s13568-016-0193-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/08/2016] [Indexed: 11/10/2022] Open
Abstract
Arsenic (As) contaminated soils are enriched with arsenotrophic bacteria. The present study analyzes the microbiome and arsenotrophic genes-from As affected soil samples of Bhanga, Charvadrason and Sadarpur of Faridpur district in Bangladesh in summer (SFDSL1, 2, 3) and in winter (WFDSL1, 2, 3). Total As content of the soils was within the range of 3.24-17.8 mg/kg as per atomic absorption spectroscopy. The aioA gene, conferring arsenite [As (III)] oxidation, was retrieved from the soil sample, WFDSL-2, reported with As concentration of 4.9 mg/kg. Phylogenetic analysis revealed that the aioA genes of soil WFDSL-2 were distributed among four major phylogenetic lineages comprised of α, β, γ Proteobacteria and Archaea with a dominance of β Proteobacteria (56.67 %). An attempt to enrich As (III) metabolizing bacteria resulted 53 isolates. ARDRA (amplified ribosomal DNA restriction analysis) followed by 16S rRNA gene sequencing of the 53 soil isolates revealed that they belong to six genera; Pseudomonas spp., Bacillus spp., Brevibacillus spp., Delftia spp., Wohlfahrtiimonas spp. and Dietzia spp. From five different genera, isolates Delftia sp. A2i, Pseudomonas sp. A3i, W. chitiniclastica H3f, Dietzia sp. H2f, Bacillus sp. H2k contained arsB gene and showed arsenite tolerance up-to 27 mM. Phenotypic As (III) oxidation potential was also confirmed with the isolates of each genus and isolate Brevibacillus sp. A1a showed significant As (III) transforming potential of 0.2425 mM per hour. The genetic information of bacterial arsenotrophy and arsenite oxidation added scientific information about the possible bioremediation potential of the soil isolates in Bangladesh.
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Zhang L, Zhou QX, Song M, Chen XL, Xu XH, Chen K, Li SP, Jiang JD. Qingshengfania soli gen. nov., sp. nov., a member of the order Rhizobiales isolated from the soil of a pesticide factory. Int J Syst Evol Microbiol 2015; 65:4608-4614. [PMID: 26382584 DOI: 10.1099/ijsem.0.000620] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain negative, coccoid to oval-shaped, non-spore-forming bacteria (LR4T and LR4-1), isolated from the soil of a pesticide factory in Nanjing, China, were investigated for their taxonomic allocation by using a polyphasic approach. Both strains grew optimally at pH 7.0, 30 °C and in the absence of NaCl. Both strains were positive for catalase and oxidase activities. Q-10 was the predominant respiratory ubiquinone. The major polar lipids were phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and two unknown aminolipids. The major fatty acids (>10 % of the total fatty acids) were C18:1ω7c/C18:1ω6c (summed feature 8) and C17:1 iso I/C17:1 anteiso B (summed feature 4). Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the two isolates formed a distinct line within a clade containing the genera Chelatococcus, Bosea, Camelimonas, Salinarimonas, Psychroglaciecola, Microvirga, Methylobacterium, Albibacter, Hansschlegelia and Methylopila in the order Rhizobiales, with the highest 16S rRNA gene sequence similarity to Chelatococcus asaccharovorans TE2T (94.12 %), followed by Bosea thiooxidans DSM 9653T (93.25 %). Strains LR4T and LR4-1 were closely related on the basis of DNA-DNA reassociation and therefore represent a single novel species. Based on phenotypic, chemotaxonomic and phylogenetic data, strains LR4T and LR4-1 represent a novel species of a new genus in the order Rhizobiales, for which the name Qingshengfania soli gen. nov., sp. nov. is proposed. The type strain of the type species is LR4T ( = CCTCC AB 2015036T = KCTC 42463T).
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Affiliation(s)
- Long Zhang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Qing-Xin Zhou
- Institute of Agro-Food Science & Technology, Shandong Academy of Agricultural Sciences, 250100, Jinan, PR China
| | - Man Song
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Xiao-Long Chen
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Xi-Hui Xu
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Kai Chen
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Shun-Peng Li
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Jian-Dong Jiang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, PR China
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Bosea vaviloviae sp. nov., a new species of slow-growing rhizobia isolated from nodules of the relict species Vavilovia formosa (Stev.) Fed. Antonie van Leeuwenhoek 2015; 107:911-20. [PMID: 25603982 DOI: 10.1007/s10482-015-0383-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 01/12/2015] [Indexed: 10/24/2022]
Abstract
The Gram-negative, rod-shaped slow-growing strains Vaf-17, Vaf-18(T) and Vaf-43 were isolated from the nodules of Vavilovia formosa plants growing in the hard-to-reach mountainous region of the North Ossetian State Natural Reserve (north Caucasus, Russian Federation). The sequencing of 16S rDNA (rrs), ITS region and five housekeeping genes (atpD, dnaK, recA, gyrB and rpoB) showed that the isolated strains were most closely related to the species Bosea lathyri (class Alphaproteobacteria, family Bradyrhizobiaceae) which was described for isolates from root nodules of Lathyrus latifolius. However the sequence similarity between the isolated strains and the type strain B. lathyri LMG 26379(T) for the ITS region was 90 % and for the housekeeping genes it was ranged from 92 to 95 %. All phylogenetic trees, except for the rrs-dendrogram showed that the isolates from V. formosa formed well-separated clusters within the Bosea group. Differences in phenotypic properties of the B. lathyri type strain and the isolates from V. formosa were studied using the microassay system GENIII MicroPlate BioLog. Whole-cell fatty acid analysis showed that the strains Vaf-17, Vaf-18(T) and Vaf-43 had notable amounts of C16:0 (4.8-6.0 %), C16:0 3-OH (6.4-6.6 %), C16:1 ω5c (8.8-9.0 %), C17:0 cyclo (13.5-13.9 %), C18:1 ω7c (43.4-45.4 %), C19:0 cyclo ω8c (10.5-12.6 %) and Summed Feature (SF) 3 (6.4-8.0 %). The DNA-DNA relatedness between the strains Vaf-18(T) and B. lathyri LMG 26379(T) was 24.0 %. On the basis of genotypic and phenotypic analysis a new species Bosea vaviloviae sp. nov. (type strain RCAM 02129(T) = LMG 28367(T) = Vaf-18(T)) is proposed.
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Kämpfer P, Glaeser SP, Gräber M, Rabenstein A, Kuever J, Busse HJ. Pseudochelatococcus lubricantis gen. nov., sp. nov. and Pseudochelatococcus contaminans sp. nov. from coolant lubricants. Int J Syst Evol Microbiol 2015; 65:147-153. [DOI: 10.1099/ijs.0.067652-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-negative, rod-shaped, non-spore-forming bacteria, isolated from metal working fluids were investigated to determine their taxonomic positions. On the basis of 16S rRNA gene sequence phylogeny, both strains (MPA 1113T and MPA 1105T) formed a distinct cluster with 97.7 % sequence similarity between them, which was in the vicinity of members of the genera
Methylobacterium
,
Camelimonas
,
Chelatococcus
,
Bosea
,
Salinarimonas
and
Microvirga
to which they showed low sequence similarities (below 94 %). The predominant compounds in the polyamine pattern and in the quinone system of the two strains were spermidine and ubiquinone Q-10, respectively. The polar lipid profiles were composed of the major compounds: phosphatidylmonomethylethanolamine, phosphatidylglycerol, phosphatidylcholine, major or moderate amounts of diphosphatidylglycerol, two unidentified glycolipids and three unidentified aminolipids. Several minor lipids were also detected. The major fatty acids were either C19 : 0 cyclo ω8c or C18 : 1ω7c. The results of fatty acid analysis and physiological and biochemical tests allowed both, the genotypic and phenotypic differentiation of the isolates from each other, while the chemotaxonomic traits allowed them to be differentiated from the most closely related genera. In summary, low 16S rRNA gene sequence similarities and marked differences in polar lipid profiles, as well as in polyamine patterns, is suggestive of a novel genus for which the name Pseudochelatococcus gen. nov. is proposed. MPA 1113T ( = CCM 8528T = LMG 28286T = CIP 110802T) and MPA 1105T ( = CCM 8527T = LMG 28285T) are proposed to be the type strains representing two novel species within the novel genus, Pseudochelatococcus gen. nov., for which the names Pseudochelatococcus lubricantis sp. nov. and Pseudochelatococcus contaminans sp. nov. are suggested, respectively.
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Stefanie P. Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Marco Gräber
- Bremen Institute for Materials Testing, Department of Microbiology, Bremen, Germany
| | - Andreas Rabenstein
- Bremen Institute for Materials Testing, Department of Microbiology, Bremen, Germany
| | - Jan Kuever
- Bremen Institute for Materials Testing, Department of Microbiology, Bremen, Germany
| | - Hans-Jürgen Busse
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, A-1210 Wien, Austria
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Paisie TK, Miller TE, Mason OU. Effects of a ciliate protozoa predator on microbial communities in pitcher plant (Sarracenia purpurea) leaves. PLoS One 2014; 9:e113384. [PMID: 25423622 PMCID: PMC4244144 DOI: 10.1371/journal.pone.0113384] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/24/2014] [Indexed: 11/18/2022] Open
Abstract
The aquatic communities found within the water filled leaves of the pitcher plant, Sarracenia purpurea, have a simple trophic structure providing an ideal system to study microscale interactions between protozoan predators and their bacterial prey. In this study, replicate communities were maintained with and without the presence of the bactivorous protozoan, Colpoda steinii, to determine the effects of grazing on microbial communities. Changes in microbial (Archaea and Bacteria) community structure were assessed using iTag sequencing of 16S rRNA genes. The microbial communities were similar with and without the protozoan predator, with>1000 species. Of these species, Archaea were negligible, with Bacteria comprising 99.99% of the microbial community. The Proteobacteria and Bacteroidetes were the most dominant phyla. The addition of a protozoan predator did not have a significant effect on microbial evenness nor richness. However, the presence of the protozoan did cause a significant shift in the relative abundances of a number of bacterial species. This suggested that bactivorous protozoan may target specific bacterial species and/or that certain bacterial species have innate mechanisms by which they evade predators. These findings help to elucidate the effect that trophic structure perturbations have on predator prey interactions in microbial systems.
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Affiliation(s)
- Taylor K Paisie
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, United States of America
| | - Thomas E Miller
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Olivia U Mason
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, United States of America
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Ghosh PK, Ganguly J, Maji P, Maiti TK. Production and Composition of Extracellular Polysaccharide Synthesized by Rhizobium undicola Isolated from Aquatic Legume, Neptunia oleracea Lour. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s40011-014-0368-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Deep K, Poddar A, Das SK. Photobacterium panuliri sp. nov., an alkalitolerant marine bacterium isolated from eggs of spiny lobster, Panulirus penicillatus from Andaman Sea. Curr Microbiol 2014; 69:660-8. [PMID: 24962598 DOI: 10.1007/s00284-014-0638-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 05/07/2014] [Indexed: 10/25/2022]
Abstract
A facultative anaerobe, alkalitolerant, gram-negative marine bacterium strain LBS5(T), was isolated from eggs carried on the pleopods of female spiny lobster (Panulirus penicillatus) in Andaman Sea from a depth of 3.5 m. Heterotrophic growth was observed at 15-38 °C and pH 5.5-11. Optimum growth occurred at 28 °C and pH 7.5. It can grow in the presence of 0.5-7 % NaCl (w/v), and the optimal NaCl required for growth was 2-4 %. 16S rRNA gene sequence analysis revealed the strain LBS5(T) belongs to the genus Photobacterium and showed 99.6 % similarity with P. aquae AE6(T), 98.2 % with P. aphoticum M46(T), 97 % with P. rosenbergii CC1(T), 96.9 % with P. lutimaris DF-42(T), and 96.6 % with P. halotolerans MACL01(T). The DNA-DNA similarities between strains LBS5(T) with other closely related strains were well below 70 %. The DNA G + C content was 50.52 (±0.9) mol%. The major fatty acids were C16:1w7c/w6c, C18:1w6c/w7c, C16:0, C15:0 iso, C16:0 10-methyl/17:1 iso w9c, C17:0 iso. Polar lipids included a phosphatidylglycerol, a diphosphatidylglycerol, a phosphatidylethanolamine, and one unidentified lipid. Based on the polyphasic evidences, strain LBS5(T) represents a novel species of the genus Photobacterium for which Photobacterium panuliri sp. nov. is proposed. The type strain is LBS5(T) (=DSM 27646(T) = LMG 27617(T) = JCM 19199(T)).
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Affiliation(s)
- Kamal Deep
- Department of Biotechnology, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751 023, India
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Kim KK, Lee KC, Eom MK, Kim JS, Kim DS, Ko SH, Kim BH, Lee JS. Variibacter gotjawalensis gen. nov., sp. nov., isolated from soil of a lava forest. Antonie van Leeuwenhoek 2014; 105:915-24. [PMID: 24599521 DOI: 10.1007/s10482-014-0146-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 02/25/2014] [Indexed: 11/28/2022]
Abstract
A novel bacterial strain designated GJW-30(T) was isolated from soil of the lava forest, Gotjawal, located in Aewol, Jeju, Korea. Strain GJW-30(T) was found to be strictly aerobic, Gram-negative and to form pleomorphic, non-motile rods and white colonies on R2A agar. The major fatty acids were identified as C18:1ω7c, C16:0 and C17:0, the predominant isoprenoid quinone as Q-10, the polar lipids as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified aminolipid and an unidentified lipid. The cell-wall sugar pattern of strain GJW-30(T) was found to be composed of glucose, ribose and rhamnose and meso-DAP as the diagnostic diamino acid in the cell-wall peptidoglycan. The DNA G+C content of strain GJW-30(T) is 62.2 mol%. Phylogenetic analysis, based on 16S rRNA gene sequence similarities, showed that strain GJW-30(T) forms a deep branch within the order Rhizobiales, sharing the highest level of sequence homology with Bradyrhizobium oligotrophicum LMG 10732(T) (93.6 %). On the basis of the phenotypic, chemotaxonomic and phylogenetic characteristics, strain GJW-30(T) is considered to represent a novel genus and species, for which the name Variibacter gotjawalensis gen. nov., sp. nov. (the type strain is GJW-30(T) = KCTC 32391(T) = CECT 8514(T) = LMG 28093(T)) is proposed.
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Affiliation(s)
- Kwang Kyu Kim
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 305-806, Republic of Korea
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Deep K, Poddar A, Das SK. Anoxybacillus suryakundensis sp. nov, a moderately thermophilic, alkalitolerant bacterium isolated from hot spring at Jharkhand, India. PLoS One 2013; 8:e85493. [PMID: 24376881 PMCID: PMC3869905 DOI: 10.1371/journal.pone.0085493] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 12/05/2013] [Indexed: 12/03/2022] Open
Abstract
Four closely related facultative anaerobe, moderately thermophilic, Gram positive rods (JS1(T), JS5, JS11, and JS15) were isolated from sediment samples from a hot spring at Suryakund, Jharkhand, India. Colonies were pale yellow, rough surface with uneven edges on TSA after 72 h incubation. Heterotrophic growth was observed at 40-60°C and pH 5.5-11.5; optimum growth occurred at 55°C and pH 7.5. 16S rRNA gene sequence analysis revealed the strains belong to genus Anoxybacillus. DNA-DNA homology values among strains were above 70% and showed distinct ERIC and REP PCR profile. On the basis of morphology and biochemical characteristics, strain JS1(T) was studied further. Strain JS1(T) showed 99.30% sequence similarity with A. flavithermus subsp. yunnanensis, 99.23% with A. mongoliensis, 99.16% with A. eryuanensis, 98.74% with A. flavithermus subsp. flavithermus, 98.54% with A. tengchongensis, 98.51% with A. pushchinoensis, 97.91% with A. thermarum, 97.82% with A. kaynarcensis, 97.77% with A. ayderensis and A. kamchatkensis, 97.63% with A. salavatliensis, 97.55% with A. kestanbolensis, 97.48% with A. contaminans, 97.27% with A. gonensis and 97.17% with A. voinovskiensis. In 16S rRNA secondary structure based phylogenetic comparison, strain JS1(T) was clustered with Anoxybacillus eryuanensis, A. mongoliensis, and A. flavithermus subsp. yunnanensis and showed 15 species specific base substitutions with maximum variability in helix 6. Moreover, DNA-DNA relatedness between JS1(T) and the closely related type strains were well below 70%. The DNA G+C content was 42.1 mol%. The major fatty acids were C(15:0 iso), C(16:0 iso) and C(17:0iso). The polar lipids were a phosphatidylgylycerol, a diphosphatidylglycerol, a phosphatidylethnolamine, a phosphatidylcholine, a phosphatidyl monomethylethanolamine and four unknown lipids. Based on polyphasic approach, strain JS1(T) represent a novel species of the genus Anoxybacillus for which Anoxybacillus suryakundensis sp. nov. is proposed. The type strain is JS1(T) (= DSM 27374(T) = LMG 27616(T) =JCM19211(T)).
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Affiliation(s)
- Kamal Deep
- Institute of Life Sciences, Department of Biotechnology, Bhubaneswar, India
| | - Abhijit Poddar
- Institute of Life Sciences, Department of Biotechnology, Bhubaneswar, India
| | - Subrata K. Das
- Institute of Life Sciences, Department of Biotechnology, Bhubaneswar, India
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Tóth EM, Vengring A, Homonnay ZG, Kéki Z, Spröer C, Borsodi AK, Márialigeti K, Schumann P. Phreatobacter oligotrophus gen. nov., sp. nov., an alphaproteobacterium isolated from ultrapure water of the water purification system of a power plant. Int J Syst Evol Microbiol 2013; 64:839-845. [PMID: 24277862 DOI: 10.1099/ijs.0.053843-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strains of a novel alphaproteobacterium were isolated from ultrapure water of a Hungarian power plant on a newly developed medium. Phylogenetic analysis of the 16S rRNA gene sequences of the novel strains showed that these bacteria belong to a distinct lineage far from any known taxa. Based on the 16S rRNA gene sequences, strains PI_31, PI_25 and PI_21(T) exhibited the highest sequence similarity to Bosea minatitlanensis AMX51(T) (93.43 %) and Bosea thiooxidans DSM 9653(T) (93.36 %); similarity to all other taxa was less than 93.23 %. Fatty acid profiles, matrix-assisted laser-desorption/ionization time-of-flight mass spectra of cell extracts as well as physiological and biochemical characteristics indicated that our strains represent a novel genus and species within the class Alphaproteobacteria. The major isoprenoid quinone of the strains was Q-10, the major cellular fatty acids were C18 : 1ω7c and 11-methyl C18 : 1ω7c and the polar lipid profiles of the strains contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and several unknown phospholipids and other lipids. The characteristic diamino acid in their cell wall was meso-diaminopimelic acid. The G+C content of DNA of the proposed type strain PI_21(T) was 68.9 mol%. A new genus and species, Phreatobacter oligotrophus gen. nov., sp. nov., is proposed to accommodate the strains. Strain PI_21(T) ( = DSM 25521(T) = NCAIM B 02510(T)) is the type strain of Phreatobacter oligotrophus.
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Affiliation(s)
- E M Tóth
- Eötvös Loránd University, Faculty of Science, Department of Microbiology, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - A Vengring
- Eötvös Loránd University, Faculty of Science, Department of Microbiology, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Z G Homonnay
- Eötvös Loránd University, Faculty of Science, Department of Microbiology, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Zs Kéki
- Eötvös Loránd University, Faculty of Science, Department of Microbiology, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - C Spröer
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
| | - A K Borsodi
- Eötvös Loránd University, Faculty of Science, Department of Microbiology, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - K Márialigeti
- Eötvös Loránd University, Faculty of Science, Department of Microbiology, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - P Schumann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
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39
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Poddar A, Lepcha RT, Das SK. Taxonomic study of the genus Tepidiphilus: transfer of Petrobacter succinatimandens to the genus Tepidiphilus as Tepidiphilus succinatimandens comb. nov., emended description of the genus Tepidiphilus and description of Tepidiphilus thermophilus sp. nov., isolated from a terrestrial hot spring. Int J Syst Evol Microbiol 2013; 64:228-235. [PMID: 24048864 DOI: 10.1099/ijs.0.056424-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Comparative phenotypic, chemotaxonomic and genetic analysis revealed significant similarities among strains of the genera Tepidiphilus and Petrobacter. Analysis of 16S rRNA gene sequences and DNA-DNA relatedness of the type strains Tepidiphilus margaritifer N2-214(T) and Petrobacter succinatimandens 4BON(T) showed sequence similarity of 98.9 % and less than 40 % relatedness, indicating that these strains represent different species of same genus. Both strains had phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and diphosphatidylglycerol as major polar lipids. Their fatty acid profiles were almost identical, with the predominant fatty acids C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c. In view of this, we propose to transfer the member of the genus Petrobacter to the genus Tepidiphilus as Tepidiphilus succinatimandens comb. nov. and to emend the description of the genus Tepidiphilus. Further, a novel bacterium, strain JHK30(T), was isolated from a terrestrial hot spring located at Jharkhand, India, and was identified following a polyphasic approach. Cells were non-sporulating, aerobic, Gram-stain-negative rods and motile by a single polar flagellum. Optimum temperature for growth was 50-55 °C at pH 6.5-7.0. 16S rRNA gene sequence analysis revealed 99.71 % similarity with P. succinatimandens 4BON(T) ( = DSM 15512(T)) and 98.71 % with T. margaritifer N2-214(T) ( = DSM 15129(T)). However, DNA-DNA relatedness of strain JHK30(T) with these two type strains was well below 70 %. The DNA G+C base composition was 66.1 mol%. Strain JHK30(T) represents a novel species of the genus Tepidiphilus for which the name Tepidiphilus thermophilus sp. nov. is proposed. The type strain is JHK30(T) ( = JCM 19170(T) = LMG 27587(T)= DSM 27220(T)).
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Affiliation(s)
- Abhijit Poddar
- Institute of Life Sciences, Department of Biotechnology, Nalco Square, Bhubaneswar-751 023, India
| | - Rinchen T Lepcha
- Institute of Life Sciences, Department of Biotechnology, Nalco Square, Bhubaneswar-751 023, India
| | - Subrata K Das
- Institute of Life Sciences, Department of Biotechnology, Nalco Square, Bhubaneswar-751 023, India
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40
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De Meyer SE, Willems A. Multilocus sequence analysis of
Bosea
species and description of Bosea lupini sp. nov., Bosea lathyri sp. nov. and Bosea robiniae sp. nov., isolated from legumes. Int J Syst Evol Microbiol 2012; 62:2505-2510. [DOI: 10.1099/ijs.0.035477-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gram-negative, rod-shaped bacteria were isolated from root nodules of Lupinus polyphyllus, Lathyrus latifolius and Robinia pseudoacacia. Based on the 16S rRNA gene phylogeny, they were closely related to
Bosea
species (100–97 % similarity), belonging to the class
Alphaproteobacteria
, family
Bradyrhizobiaceae
. The closest relatives of LMG 26383T, LMG 26379T and LMG 26381T were respectively the type strains of
Bosea thiooxidans
(99.6 %),
B. eneae
(98.3 %) and
B. minatitlanensis
(99.0 %). Chemotaxonomic data, including major fatty acid profiles, supported the assignment of our strains to the genus
Bosea
. Analysis of the concatenated sequences of five housekeeping genes (atpD, dnaK, gyrB, recA and rpoB) and the results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of our strains from each other and from the five
Bosea
species with validly published names. No nodA or nodC genes could be amplified, while nifH PCR gave non-specific products. On the basis of genotypic and phenotypic data, three novel species, Bosea lupini sp. nov. (type strain LMG 26383T = CCUG 61248T = R-45681T), Bosea lathyri sp. nov. (type strain LMG 26379T = CCUG 61247T = R-46060T) and Bosea robiniae sp. nov. (type strain LMG 26381T = CCUG 61249T = R-46070T), are proposed.
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Affiliation(s)
- Sofie E. De Meyer
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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Rhizobium pusense sp. nov., isolated from the rhizosphere of chickpea (Cicer arietinum L.). Int J Syst Evol Microbiol 2011; 61:2632-2639. [DOI: 10.1099/ijs.0.028407-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, designated NRCPB10T, was isolated from rhizosphere soil of chickpea (Cicer arietinum L.) in Pusa, New Delhi, India. The 16S rRNA gene sequence of strain NRCPB10T showed highest similarity (98.9 %) to that of Rhizobium radiobacter NCPPB 2437T, followed by Rhizobium larrymoorei AF3-10T (97.7 %) and Rhizobium rubi IFO 13261T (97.4 %). Phylogenetic analysis of strain NRCPB10T based on the housekeeping genes recA and atpD confirmed its position as distinct from recognized Rhizobium species. Levels of DNA–DNA relatedness between strain NRCPB10T and R. radiobacter ICMP 5785T, R. larrymoorei LMG 21410T and R. rubi ICMP 6428T were 51.0, 32.6 and 27.3 %, respectively. Cellular fatty acids of strain NRCPB10T were C18 : 1ω7c (58.9 %), C16 : 0 (15.5 %), C19 : 0 cyclo ω8c (11.5 %), iso-C16 : 1 (5.8 %), C16 : 0 3-OH (4.5 %), C16 : 1ω7c (2.1 %) and C18 : 0 (1.3 %). The G+C content of the genomic DNA of strain NRCPB10T was 59.0 mol%. Strain NRCPB10T did not nodulate chickpea plants or induce tumours in tobacco plants. Phenotypic and physiological properties along with SDS-PAGE of whole-cell soluble proteins differentiated strain NRCPB10T from its closest phylogenetic neighbours. On the basis of data from the present polyphasic taxonomic study, strain NRCPB10T is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium pusense sp. nov. is proposed. The type strain is NRCPB10T ( = LMG 25623T = JCM 16209T = NCIMB 14639T).
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42
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Zhang J, Wang J, Song F, Fang C, Xin Y, Zhang Y. Bacillus nanhaiisediminis sp. nov., an alkalitolerant member of Bacillus rRNA group 6. Int J Syst Evol Microbiol 2011; 61:1078-1083. [DOI: 10.1099/ijs.0.023671-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, rod-shaped bacterium, designated strain NH3T, was isolated from a sediment sample from the South China Sea and was subjected to a polyphasic taxonomic study. The isolate grew optimally at 37 °C and pH 9. Strain NH3T had cell-wall peptidoglycan based on meso-diaminopimelic acid and MK-7 as the predominant menaquinone. The cellular fatty acid profile included significant amounts of iso-C15 : 0 and iso-C14 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content of strain NH3T was 40.3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain NH3T was a member of rRNA group 6 of the genus Bacillus, which includes alkalitolerant, alkaliphilic and halotolerant species. The closest phylogenetic relatives were Bacillus akibai 1139T (96.82 % 16S rRNA gene sequence similarity), B. pseudofirmus DSM 8715T (96.76 %), B. okhensis Kh10-101T (96.76 %) and B. alkalidiazotrophicus MS 6T (96.47 %). Strain NH3T could be distinguished from these phylogenetically close neighbours based on a number of phenotypic properties. On the basis of phenotypic and chemotaxonomic characteristics and phylogenetic data, we conclude that strain NH3T ( = CGMCC 1.10116T = JCM 16507T) merits classification as the type strain of a novel species, for which the name Bacillus nanhaiisediminis sp. nov. is proposed.
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Affiliation(s)
- Jianli Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Jiewei Wang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Fei Song
- School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Caiyuan Fang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Yuhua Xin
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yabo Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
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43
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Falk S, Liu B, Braker G. Isolation, genetic and functional characterization of novel soil nirK-type denitrifiers. Syst Appl Microbiol 2010; 33:337-47. [DOI: 10.1016/j.syapm.2010.06.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 06/03/2010] [Accepted: 06/08/2010] [Indexed: 10/19/2022]
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44
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Nisola GM, Tuuguu E, Farnazo DMD, Han M, Kim Y, Cho E, Chung WJ. Hydrogen sulfide degradation characteristics of Bordetella sp. Sulf-8 in a biotrickling filter. Bioprocess Biosyst Eng 2010; 33:1131-8. [PMID: 20535619 DOI: 10.1007/s00449-010-0440-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Accepted: 05/26/2010] [Indexed: 11/26/2022]
Abstract
The applicability of Bordetella sp. Sulf-8 to degrade Hydrogen Sulfide (H(2)S) gas in a biotrickling system was investigated. The isolate is a heterotrophic gram-negative, catalase- and oxidase-positive, rod-shaped bacterium which can metabolize thiosulfate or sulfide into sulfate. The mesophilic Bordetella sp. Sulf-8 can grow within a wide pH range using yeast as carbon source, with or without the presence of sulfur. In batch experiments, kinetic constants such as maximum specific growth rate (μ (max) = 0.12 1/h), saturation constant (K (S) = 0.017 g/L), and specific sulfur removal rate (88 mg S/g cells h) were obtained. In biotrickling experiments removal efficiencies were satisfactory, but the system performance was observed to be more influenced by empty bed residence time than by H(2)S feed gas concentration. Critical and maximum elimination capacities were 78.0 and 94.5 g H(2)S/m(3) day, respectively. Macrokinetic analysis of the biotrickling system revealed maximum H(2)S removal rate V (max) = 15.97 g S/kg media-day and half saturation constant K (S') = 12.45 ppm(v).
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Affiliation(s)
- Grace M Nisola
- Department of Environmental Engineering and Biotechnology, Energy and Environment Fusion Technology Center (E2FTC), Myongji University, San 38-2 Namdong, Cheoingu, Yongin City, Gyeonggi Province, South Korea
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45
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Jyoti V, Narayan KD, Das SK. Gulbenkiania indica sp. nov., isolated from a sulfur spring. Int J Syst Evol Microbiol 2010; 60:1052-1055. [DOI: 10.1099/ijs.0.014035-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium, designated strain HT27T, was isolated from a sulfur spring sample collected from Athamallik, Orissa, India, and was characterized by using a polyphasic approach. Cells were Gram-negative, strictly aerobic, rod-shaped and motile by means of a single polar flagellum. Strain HT27T was oxidase- and catalase-positive. Growth was observed at pH 5.0–11.0 and at 15–45 °C; the highest growth yield was observed at pH 7.5–8.0 and 30–37 °C. The G+C content of the genomic DNA of strain HT27T was 63 mol%. The major cellular fatty acids were C16 : 1
ω7c (44.24 %), C16 : 0 (27.65 %), C18 : 1
ω7c (13.98 %), C12 : 0 (2.60 %) and C12 : 0 3-OH (2.22 %). 16S rRNA gene sequence analysis indicated that strain HT27T clustered with the genus Gulbenkiania and showed 99.0 % similarity to Gulbenkiania mobilis E4FC31T. However, the level of DNA–DNA relatedness between strain HT27T and G. mobilis E4FC31T was 30 %. On the basis of phenotypic and chemotaxonomic characteristics, 16S rRNA gene sequence analysis and DNA–DNA hybridization data, strain HT27T is considered to represent a novel species of the genus Gulbenkiania, for which the name Gulbenkiania indica sp. nov. is proposed. The type strain is HT27T (=DSM 17901T =JCM 15969T).
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Affiliation(s)
- V. Jyoti
- Institute of Life Sciences, Department of Biotechnology, Nalco Square, Bhubaneswar 751 023, India
| | - Kunwar Digvijay Narayan
- Institute of Life Sciences, Department of Biotechnology, Nalco Square, Bhubaneswar 751 023, India
| | - Subrata K. Das
- Institute of Life Sciences, Department of Biotechnology, Nalco Square, Bhubaneswar 751 023, India
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Chelatococcus sambhunathii sp. nov., a moderately thermophilic alphaproteobacterium isolated from hot spring sediment. Int J Syst Evol Microbiol 2010; 60:861-865. [DOI: 10.1099/ijs.0.013466-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A moderately thermophilic bacterial strain (HT4T) isolated from a hot spring sediment was characterized phenotypically and phylogenetically. Cells were Gram-negative, aerobic, non-sporulating, rod-shaped and motile by means of a single polar flagellum. Both oxidase and catalase activities were positive. Heterotrophic growth was observed at pH 6.0–8.5 and at 20–50 °C; optimum growth occurred at pH 7.5–8.0 and 37–42 °C. The major cellular fatty acids were C14 : 0 3-OH, C18 : 0 3-OH, C18 : 1 2-OH, C18 : 1
ω7c and C19 : 0 cyclo ω8c. The DNA G+C content of strain HT4T was 67.8 mol%.16S rRNA gene sequence analysis indicated that strain HT4T clustered within the radiation of the genus Chelatococcus and showed 99.0 % similarity with Chelatococcus daeguensis CCUG 54519T and 96 % similarity with Chelatococcus asaccharovorans DSM 6462T. However, levels of DNA–DNA relatedness between strain HT4T and Chelatococcus daeguensis CCUG 54519T and Chelatococcus asaccharovorans DSM 6462T were 52 and 20 %, respectively. On the basis of the phenotypic, physiological and chemotaxonomic data, 16S rRNA gene sequence analysis and DNA–DNA hybridization results, strain HT4T is considered to represent a novel species of the genus Chelatococcus, for which the name Chelatococcus sambhunathii sp. nov. is proposed. The type strain is HT4T (=DSM 18167T=JCM 14988T).
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47
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Narayan KD, Pandey SK, Das SK. Characterization of Comamonas thiooxidans sp. nov., and comparison of thiosulfate oxidation with Comamonas testosteroni and Comamonas composti. Curr Microbiol 2010; 61:248-53. [PMID: 20148250 DOI: 10.1007/s00284-010-9602-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2009] [Accepted: 01/26/2010] [Indexed: 01/27/2023]
Abstract
Comamonas thiooxidans (strain S23(T)) capable of oxidizing thiosulfate under a mixotrophic growth condition was isolated from a sulfur spring. DNA-DNA homology study showed 55% similarity with Comamonas testosteroni KCTC2990(T) and 52% with Comamonas composti LMG24008(T), the nearest phylogenetic relative (16S rRNA sequence similarity <97%). Comparative genomic fingerprinting by using ERIC and Rep-PCR further delineated species identity of the strain S23(T) for which Comamonas thiooxidans sp. nov. is proposed. In addition, thiosulfate oxidation potential of the strain S23(T) was compared with Comamonas testosteroni and Comamonas composti.
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Affiliation(s)
- Kunwar Digvijay Narayan
- Department of Biotechnology, Institute of Life Sciences, Nalco Square, Bhubaneswar 751 023, India
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48
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Liu JH, Wang YX, Zhang XX, Wang ZG, Chen YG, Wen ML, Xu LH, Peng Q, Cui XL. Salinarimonas rosea gen. nov., sp. nov., a new member of the α-2 subgroup of the Proteobacteria. Int J Syst Evol Microbiol 2010; 60:55-60. [DOI: 10.1099/ijs.0.006981-0] [Citation(s) in RCA: 27] [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-negative, rod-shaped, facultatively anaerobic, halotolerant bacterial strain, designated YIM YD3T, was isolated from a salt mine in Yunnan, south-west China. The taxonomy of strain YIM YD3T was investigated by a polyphasic approach. Strain YIM YD3T was motile, formed pink colonies and was positive for catalase and oxidase activities. Q-10 was the predominant respiratory ubiquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine and two unknown phospholipids. The major fatty acids (>10 % of total fatty acids) were C18 : 1
ω7c, C18 : 1
ω9c, C16 : 0 and C19 : 0 cyclo ω8c. The DNA G+C content was 71.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the isolate formed a distinct line within a clade containing the genera Balneimonas, Bosea, Chelatococcus and Microvirga in the order Rhizobiales, with highest levels of 16S RNA gene sequence similarity to the type strain of Balneimonas flocculans (93.5 %). On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain YIM YD3T represents a novel species in a new genus, for which the name Salinarimonas rosea gen. nov., sp. nov. is proposed, with strain YIM YD3T (=KCTC 22346T=CCTCC AA208038T) as the type strain.
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Affiliation(s)
- Ji-Hui Liu
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Yong-Xia Wang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Xiao-Xia Zhang
- Agricultural Cultural Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100080, PR China
| | - Zhi-Gang Wang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Yi-Guang Chen
- College of Bio-resources and Environmental Science, Jishou University, Jishou, Hunan 416000, PR China
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Meng-Liang Wen
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Li-Hua Xu
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Qian Peng
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Xiao-Long Cui
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
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49
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Abstract
Despite using modern microbiological diagnostic approaches, the aetiological agents of pneumonia remain unidentified in about 50% of cases. Some bacteria that grow poorly or not at all in axenic media used in routine clinical bacteriology laboratory but which can develop inside amoebae may be the agents of these lower respiratory tract infections (RTIs) of unexplained aetiology. Such amoebae-resisting bacteria, which coevolved with amoebae to resist their microbicidal machinery, may have developed virulence traits that help them survive within human macrophages, i.e. the first line of innate immune defence in the lung. We review here the current evidence for the emerging pathogenic role of various amoebae-resisting microorganisms as agents of RTIs in humans. Specifically, we discuss the emerging pathogenic roles of Legionella-like amoebal pathogens, novel Chlamydiae (Parachlamydia acanthamoebae, Simkania negevensis), waterborne mycobacteria and Bradyrhizobiaceae (Bosea and Afipia spp.).
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Affiliation(s)
- Frédéric Lamoth
- Infectious Diseases Service, University of Lausanne, Lausanne, Switzerland
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Satoh H, Odagiri M, Ito T, Okabe S. Microbial community structures and in situ sulfate-reducing and sulfur-oxidizing activities in biofilms developed on mortar specimens in a corroded sewer system. WATER RESEARCH 2009; 43:4729-39. [PMID: 19709714 DOI: 10.1016/j.watres.2009.07.035] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Revised: 07/24/2009] [Accepted: 07/31/2009] [Indexed: 05/10/2023]
Abstract
Microbially induced concrete corrosion (MICC) caused by sulfuric acid attack in sewer systems has been a serious problem for a long time. A better understanding of microbial community structures of sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) and their in situ activities is essential for the efficient control of MICC. In this study, the microbial community structures and the in situ hydrogen sulfide production and consumption rates within biofilms and corroded materials developed on mortar specimens placed in a corroded manhole was investigated by culture-independent 16S rRNA gene-based molecular techniques and microsensors for hydrogen sulfide, oxygen, pH and the oxidation-reduction potential. The dark-gray gel-like biofilm was developed in the bottom (from the bottom to 4 cm) and the middle (4-20 cm from the bottom of the manhole) parts of the mortar specimens. White filamentous biofilms covered the gel-like biofilm in the middle part. The mortar specimens placed in the upper part (30 cm above the bottom of the manhole) were corroded. The 16S rRNA gene-cloning analysis revealed that one clone retrieved from the bottom biofilm sample was related to an SRB, 12 clones and 6 clones retrieved from the middle biofilm and the corroded material samples, respectively, were related to SOB. In situ hybridization results showed that the SRB were detected throughout the bottom biofilm and filamentous SOB cells were mainly detected in the upper oxic layer of the middle biofilm. Microsensor measurements demonstrated that hydrogen sulfide was produced in and diffused out of the bottom biofilms. In contrast, in the middle biofilm the hydrogen sulfide produced in the deeper parts of the biofilm was oxidized in the upper filamentous biofilm. pH was around 3 in the corroded materials developed in the upper part of the mortar specimens. Therefore, it can be concluded that hydrogen sulfide provided from the bottom biofilms and the sludge settling tank was emitted to the sewer atmosphere, then oxidized to corrosive compounds in the upper and middle parts of the manhole, and only the upper part of the mortar specimens were corroded, because in the middle part of the manhole the generated corrosive compounds (e.g., sulfuric acid) was reduced in the deeper parts of the biofilm.
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Affiliation(s)
- Hisashi Satoh
- Division of Field Engineering for Environment, Graduate School of Engineering, Hokkaido University, Sapporo, Japan
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