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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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Yang ZZ, Xiong LS, Yuan Q, Zuo SY, Chen XM, Jiang MG, Tian XP, Jiang CL, Jiang Y. Marinimicrococcus flavescens gen. nov., sp. nov., a new member of the family Geminicoccaceae, isolated from a marine sediment of the South China Sea. Int J Syst Evol Microbiol 2024; 74. [PMID: 38240641 DOI: 10.1099/ijsem.0.006241] [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: 01/23/2024] Open
Abstract
A Gram-stain-negative, catalase-positive and oxidase-positive, nonmotile, aerobic, light yellow, spherical-shaped bacterial strain with no flagella, designated strain YIM 152171T, was isolated from sediment of the South China Sea. Colonies were smooth and convex, light yellow and circular, and 1.0-1.5×1.0-1.5 µm in cell diameter after 7 days of incubation at 28°C on YIM38 media supplemented with sea salt. Colonies could grow at 20-45°C (optimum 28-35°C) and pH 6.0-11.0 (optimum, pH 7.0-9.0), and they could proliferate in the salinity range of 0-6.0 % (w/v) NaCl. The major cellular fatty acids were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), C18 : 1 ω7c 11-methyl, C16 : 0, C16 : 1 ω11c, C16 : 1 ω5c, C17 : 1 ω6c and C18 : 1 ω5c. The respiratory quinone was ubiquinone 10, and the polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol mannoside, one unidentified phospholipid and one unidentified aminolipid. Phylogenetic analyses based on the 16S rRNA gene sequences placed strain YIM 152171T within the order Rhodospirillales in a distinct lineage that also included the genus Geminicoccus. The 16S rRNA gene sequence similarities of YIM 152171T to those of Arboricoccus pini, Geminicoccus roseus and Constrictibacter antarcticus were 92.17, 89.25 and 88.91 %, respectively. The assembled draft genome of strain YIM 152171T had 136 contigs with an N50 value of 134704 nt, a total length of 3 001 346 bp and a G+C content of 70.27 mol%. The phylogenetic, phenotypic and chemotaxonomic data showed that strain YIM 152171T (=MCCC 1K08488T=KCTC 92884T) represents a type of novel species and genus for which we propose the name Marinimicrococcus gen. nov., sp. nov.
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Affiliation(s)
- Zu-Zhen Yang
- The Lab for Research and Development of Actinomycete Resources, Yunnan Institute of Microbiology, Chenggong campus of Yunnan University, Kunming, 650500, PR China
| | - Lian-Shuang Xiong
- The Lab for Research and Development of Actinomycete Resources, Yunnan Institute of Microbiology, Chenggong campus of Yunnan University, Kunming, 650500, PR China
| | - Qing Yuan
- The Lab for Research and Development of Actinomycete Resources, Yunnan Institute of Microbiology, Chenggong campus of Yunnan University, Kunming, 650500, PR China
| | - Shu-Ya Zuo
- The Lab for Research and Development of Actinomycete Resources, Yunnan Institute of Microbiology, Chenggong campus of Yunnan University, Kunming, 650500, PR China
| | - Xue-Mei Chen
- The Lab for Research and Development of Actinomycete Resources, Yunnan Institute of Microbiology, Chenggong campus of Yunnan University, Kunming, 650500, PR China
| | - Ming-Guo Jiang
- School of Marine Science and Biotechnology, Guangxi Key Laboratory for Polysaccharide Materials and Modifications, Guangxi University for Nationalities, Nanning 530008, PR China
| | - Xin-Peng Tian
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Cheng-Lin Jiang
- The Lab for Research and Development of Actinomycete Resources, Yunnan Institute of Microbiology, Chenggong campus of Yunnan University, Kunming, 650500, PR China
| | - Yi Jiang
- The Lab for Research and Development of Actinomycete Resources, Yunnan Institute of Microbiology, Chenggong campus of Yunnan University, Kunming, 650500, PR China
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3
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Toumi M, Whitman WB, Kyrpides NC, Woyke T, Wolf J, Neumann-Schaal M, Abbaszade G, Károly B, Tóth E. Antiquaquibacter oligotrophicus gen. nov., sp. nov., a novel oligotrophic bacterium from groundwater. Int J Syst Evol Microbiol 2023; 73. [PMID: 38108591 DOI: 10.1099/ijsem.0.006205] [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: 12/19/2023] Open
Abstract
In this study, a Gram-stain-positive, non-motile, oxidase- and catalase-negative, rod-shaped, bacterial strain (SG_E_30_P1T) that formed light yellow colonies was isolated from a groundwater sample of Sztaravoda spring, Hungary. Based on 16S rRNA phylogenetic and phylogenomic analyses, the strain was found to form a distinct linage within the family Microbacteriaceae. Its closest relatives in terms of near full-length 16S rRNA gene sequences are Salinibacterium hongtaonis MH299814 (97.72 % sequence similarity) and Leifsonia psychrotolerans GQ406810 (97.57 %). The novel strain grows optimally at 20-28 °C, at neutral pH and in the presence of NaCl (1-2 w/v%). Strain SG_E_30_P1T contains MK-7 and B-type peptidoglycan with diaminobutyrate as the diagnostic amino acid. The major cellular fatty acids are anteiso-C15 : 0, iso-C16 : 0 and iso-C14 : 0, and the polar lipid profile is composed of diphosphatidylglycerol and phosphatidylglycerol, as well as an unidentified aminoglycolipid, aminophospholipid and some unidentified phospholipids. The assembled draft genome is a contig with a total length of 2 897 968 bp and a DNA G+C content of 65.5 mol%. Amino acid identity values with it closest relatives with sequenced genomes of <62.54 %, as well as other genome distance results, indicate that this bacterium represents a novel genus within the family Microbacteriaceae. We suggest that SG_E_30_P1T (=DSM 111415T=NCAIM B.02656T) represents the type strain of a novel genus and species for which the name Antiquaquibacter oligotrophicus gen. nov., sp. nov. is proposed.
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Affiliation(s)
- Marwene Toumi
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny, 1/C, H-1117 Budapest, Hungary
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Jacqueline Wolf
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124, Braunschweig, Germany
| | - Gorkhmaz Abbaszade
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny, 1/C, H-1117 Budapest, Hungary
| | - Bóka Károly
- Department of plant anatomy, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny, 1/C, H-1117 Budapest, Hungary
| | - Erika Tóth
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny, 1/C, H-1117 Budapest, Hungary
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Zhou Z, Ma W, Li F, Zhong D, Zhang W, Liu L, Zhang J, Zhu Y, Su P. Deciphering the distribution and microbial secretors of extracellular polymeric substances associated antibiotic resistance genes in tube wall biofilm. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163218. [PMID: 37004772 DOI: 10.1016/j.scitotenv.2023.163218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 06/01/2023]
Abstract
Antibiotics and disinfectants have both been proposed to exert selective pressures on the biofilm as well as affecting the emergence and spread of antibiotic resistance genes (ARGs). However, the transfer mechanism of ARGs in drinking water distribution system (DWDS) under the coupling effect of antibiotics and disinfectants has not been completely understood. In the current study, four lab-scale biological annular reactors (BARs) were constructed to evaluate the effects of sulfamethoxazole (SMX) and NaClO coupling in DWDS and reveal the related mechanisms of ARGs proliferation. TetM was abundant in both the liquid phase and the biofilm, and redundancy analysis showed that the total organic carbon (TOC) and temperature were significantly correlated with ARGs in the water phase. There was a significant correlation between the relative abundance of ARGs in the biofilm phase and extracellular polymeric substances (EPS). Additionally, the proliferation and spread of ARGs in water phase were related to microbial community structure. Partial least-squares path modeling showed that antibiotic concentration may influence ARGs by affecting MGEs. These findings help us to better understand the diffusion process of ARGs in drinking water and provide a theoretical support for technologies to control ARGs at the front of pipeline.
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Affiliation(s)
- Ziyi Zhou
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Wencheng Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Feiyu Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Dan Zhong
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Wenxuan Zhang
- Guangdong Yuehai Water Investment Co., Ltd., Shenzhen 518000, China
| | - Luming Liu
- Harbin Institute of Technology National Engineering Research Center of Urban Water Resources Co., Ltd., Harbin 150090, China
| | - Jingna Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yisong Zhu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Peng Su
- Changjiang Institute of Survey, Planning, Design and Research, Wuhan 430010, China
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5
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Hu D, Zeng J, Chen J, Lin W, Xiao X, Feng M, Yu X. Microbiological quality of roof tank water in an urban village in southeastern China. J Environ Sci (China) 2023; 125:148-159. [PMID: 36375901 DOI: 10.1016/j.jes.2022.01.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 06/16/2023]
Abstract
Urban villages are unique residential neighborhoods in urban areas in China. Roof tanks are their main form of water supply, and water quality deterioration might occur in this system because of poor hygienic conditions and maintenance. In this study, water samples were seasonally collected from an urban village to investigate the influence of roof tanks as an additional water storage device on the variation in the microbial community structure and pathogenic gene markers. Water stagnation in the roof tank induced significant decreases in chlorine (p < 0.05), residual chlorine was as low as 0.02 mg/L in spring. Propidium monoazide (PMA)-qPCR revealed a one-magnitude higher level of total viable bacterial concentration in roof tank water samples (2.14 ± 1.81 × 105 gene copies/mL) than that in input water samples (3.57 ± 2.90 × 104 gene copies/mL, p < 0.05), especially in spring and summer. In addition, pathogenic fungi, Mycobacterium spp., and Legionella spp. were frequently detected in the roof tanks. Terminal users might be exposed to higher microbial risk induced by high abundance of Legionella gene marker. Spearman's rank correlation and redundancy analysis showed that residual chlorine was the driving force that promoted bacterial colonization and shaped the microbial community. It is worth noted that the sediment in the pipe will be agitated when the water supply is restored after the water outages, which can trigger an increase in turbidity and bacterial biomass. Overall, the findings provide practical suggestions for controlling microbiological health risks in roof tanks in urban villages.
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Affiliation(s)
- Dong Hu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Zeng
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jing Chen
- Shitang Community Health Service Center, Xiamen 361026, China
| | - Wenfang Lin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xinyan Xiao
- College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Mingbao Feng
- College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Xin Yu
- College of the Environment and Ecology, Xiamen University, Xiamen 361005, China.
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Foysal MJ, Nguyen TTT, Sialumano M, Phiri S, Chaklader MR, Fotedar R, Gagnon MM, Tay A. Zeolite mediated processing of nitrogenous waste in the rearing environment influences gut and sediment microbial community in freshwater crayfish (Cherax cainii) culture. CHEMOSPHERE 2022; 298:134276. [PMID: 35278449 DOI: 10.1016/j.chemosphere.2022.134276] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Zeolite is known to uptake toxic metals and filter nitrogenous waste from aquaculture effluents. The present study aimed to investigate the impacts of zeolite in three different applications namely, dietary zeolite (DZ), suspended zeolite (SZ) in the water column, and a combination of both (DZSZ) relative to unexposed freshwater crayfish, marron (control). At the end of the 56-days trial, the impact was assessed in terms of characterization of microbial communities in the culture environment and the intestine of marron. Alongside the microbial communities, the innate immune response of marron was also evaluated. The 16S rRNA data showed that marrons exposed to the suspended zeolite had a significant increase of bacterial diversity in the gut, including the restoration of marron core operational taxonomic units (OTUs), relative to other forms of exposures (DZ, DZSZ) and the control. Suspended zeolite alone also increased the number of unshared OTUs and genera, and improved predicted metabolic functions for the biosynthesis and digestion of proteins, amino acids, fatty acids, and hormones. In the tank sediment, the shift of microbial communities was connected more strongly with the time of experiment than the type of zeolite exposure. In the second case, only control marron had a different microbial ordination in terms of rare taxa present in the community. Nevertheless, the modulation in the gut environment was found more prominent in DZ, relative to modulation in the tank sediments. The taxa-environment correlation identified Rhodoferax as the most potential bacteria in removing nitrogenous waste from the rearing environment. Further analysis showed that SZ resulted in the upregulation of genes associated with the innate immune response of marron. Overall results suggest that SZ can be used to enrich microbial communities in the gut and tank sediments and better immune performance of marron.
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Affiliation(s)
- Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh.
| | - Thi Thu Thuy Nguyen
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Experimental Biology, Research Institute for Aquaculture No. 2, Ho Chi Minh City, Viet Nam.
| | - Mavis Sialumano
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Veterinary Services, Ministry of Fisheries and Livestock, Zambia
| | - Simon Phiri
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Veterinary Services, Ministry of Fisheries and Livestock, Zambia
| | - Md Reaz Chaklader
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Primary Industries and Regional Development, Fleet Street, Fremantle, WA, Australia
| | - Ravi Fotedar
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | | | - Alfred Tay
- Marshall Centre for Infectious Disease Research and Training, University of Western Australia, WA, Australia
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Szabonella alba gen. nov., sp. nov., a motile alkaliphilic bacterium of the family Rhodobacteraceae isolated from a soda lake. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005219] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, oxidase- and catalase-positive, rod-shaped, creamy white coloured bacterial strain, DMG-N-6T, was isolated from a water sample of Lake Fertő/Neusiedler See (Hungary). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain forms a distinct linage within the family
Rhodobacteraceae
. Its closest relatives are
Tabrizicola alkalilacus
DJCT (96.76% similarity) and
Tabrizicola piscis
K13M18T (96.76%), followed by
Tabrizicola sediminis
DRYC-M-16T (96.69 %),
Rhodobacter sediminicola
JA983T (96.62 %),
Tabrizicola aquatica
RCRI19T (96.47 %) and
Cereibacter johrii
JA192T (96.18 %). The novel bacterial strain favours an alkaline environment (pH 8.0-12.0) and grows optimally at 18–28°C in the presence of 2–4 % (w/v) NaCl. Cells of DMG-N-6T were motile by a single subpolar flagellum. Bacteriochlorophyll a was not detected. The predominant respiratory quinone was ubiquinone Q-10. The major cellular fatty acid was C18:1
ω7c. The polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, phosphatidylcholine, an unidentified phospholipid and five unidentified lipids. The assembled draft genome of strain DMG-N-6T had 52 contigs with a total length of 4 219 778 bp and a G+C content of 64.3 mol%. Overall genome-related indices (ANI <77.8 %, AAI <69.0 %, dDDH <19.6 %) with respect to close relatives were all significantly below the corresponding threshold to demarcate bacterial genus and species. Strain DMG-N-6T (=DSM 108208T=NCAIM B.02645T) is strongly different from its closest relatives and is suggested as the type strain of a novel species of a new genus in the family
Rhodobacteraceae
, for which the name Szabonella alba gen. nov., sp. nov. is proposed.
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Miao X, Bai X. Characterization of the synergistic relationships between nitrification and microbial regrowth in the chloraminated drinking water supply system. ENVIRONMENTAL RESEARCH 2021; 199:111252. [PMID: 34015300 DOI: 10.1016/j.envres.2021.111252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
Deterioration of water quality is commonly found in secondary water supply systems (SWSSs), especially the growth of microbes. To explore the metabolic mechanism for rapid microbial regrowth in SWSSs, a regrowth potential assessment, flow cytometry, and quantitative PCR were conducted. Metagenomic and 16S rRNA gene sequencing were performed to better understand the microbial communities and metabolism. It was found that the increased biomass in the SWSS was significantly higher than that in the drinking water distribution system (DWDS). Statistical analysis revealed that ammonia oxidation was the dominant driver of increased biomass in the SWSS. The abundances of ammonia oxidation bacteria, concentration of nitrogen species, and related enzymes demonstrated that ammonia oxidation in the SWSS was more vigorous than that in the DWDS. In the SWSS, the metabolism of the ammonia oxidation cluster was more vigorous, and ammonia-oxidizing bacteria (AOB) were the dominant nitrifying bacteria. Incomplete nitrification products were involved in the metabolism of heterotrophic bacteria and promoted the growth of heterotrophic bacteria in the SWSS. More attention should be given to controlling incomplete nitrification to improve tap water quality.
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Affiliation(s)
- Xiaocao Miao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Xiaohui Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
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Jing Z, Lu Z, Mao T, Cao W, Wang W, Ke Y, Zhao Z, Wang X, Sun W. Microbial composition and diversity of drinking water: A full scale spatial-temporal investigation of a city in northern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 776:145986. [PMID: 33640542 DOI: 10.1016/j.scitotenv.2021.145986] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/15/2021] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
The microbiological water quality of drinking water distribution systems (DWDSs) is of primary importance for public health. The detachment of biofilm attached on the pipe wall attribution to water source switch and the occurrence of potentially pathogenic chlorine-resistant bacteria (CRB) under chlorine disinfection get lots of attention. Studies examining microbial communities after the water source switch, particularly in low-salinity water, have been scant. The UV‑chlorine combined disinfection applied in one of the investigated drinking water plants provided insight into the control of CRBs. We applied high-throughput sequencing of the 16S rRNA gene to characterize the bacterial communities of the DWDS in northern China over 1 year. A network comprising four different DWDSs was sampled at 48 sites every season (temperate continental monsoon climate), and the impact of key spatial-temporal and physicochemical parameters was investigated. Overall, the entire bacterial community was not significantly different among the four DWDSs (spatial parameter) but varied with seasons (temporal parameter). The switch in water sources might increase the relative abundance of potentially opportunistic pathogens in DWDSs. UV‑chlorine combined disinfection can decrease community diversity and is likely to control the growth of potential opportunistic pathogens in DWDSs.
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Affiliation(s)
- Zibo Jing
- School of Environment, Tsinghua University, Beijing 100084, China; Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zedong Lu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Ted Mao
- Research Institute for Environmental Innovation (Suzhou) Tsinghua, Suzhou 215163, China; MW Technologies, Inc., London, Ontario, Canada
| | - Wenfeng Cao
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Weibo Wang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Yanchu Ke
- School of Environment, Tsinghua University, Beijing 100084, China; State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Zhinan Zhao
- School of Environment, Tsinghua University, Beijing 100084, China; Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaohui Wang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Wenjun Sun
- School of Environment, Tsinghua University, Beijing 100084, China; Research Institute for Environmental Innovation (Suzhou) Tsinghua, Suzhou 215163, China.
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Calero Preciado C, Boxall J, Soria-Carrasco V, Martínez S, Douterelo I. Implications of Climate Change: How Does Increased Water Temperature Influence Biofilm and Water Quality of Chlorinated Drinking Water Distribution Systems? Front Microbiol 2021; 12:658927. [PMID: 34168627 PMCID: PMC8217620 DOI: 10.3389/fmicb.2021.658927] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/04/2021] [Indexed: 01/04/2023] Open
Abstract
Temperature variation can promote physico-chemical and microbial changes in the water transported through distribution systems and influence the dynamics of biofilms attached to pipes, thus contributing to the release of pathogens into the bulk drinking water. An experimental real-scale chlorinated DWDS was used to study the effect of increasing temperature from 16 to 24°C on specific pathogens, bacterial-fungal communities (biofilm and water samples) and determine the risk of material accumulation and mobilisation from the pipes into the bulk water. Biofilm was developed for 30 days at both temperatures in the pipe walls, and after this growth phase, a flushing was performed applying 4 gradual steps by increasing the shear stress. The fungal-bacterial community characterised by Illumina MiSeq sequencing, and specific pathogens were studied using qPCR: Mycobacterium spp., Mycobacterium avium complex, Acanthamoeba spp., Pseudomonas aeruginosa, Legionella pneumophilia, and Stenotrophomonas maltophilia. Sequencing data showed that temperature variation significantly modified the structure of biofilm microbial communities from the early stages of biofilm development. Regarding bacteria, Pseudomonas increased its relative abundance in biofilms developed at 24°C, while fungal communities showed loss of diversity and richness, and the increase in dominance of Fusarium genus. After the mobilisation phase, Pseudomonas continued being the most abundant genus at 24°C, followed by Sphingobium and Sphingomonas. For biofilm fungal communities after the mobilisation phase, Helotiales incertae sedis and Fusarium were the most abundant taxa. Results from qPCR showed a higher relative abundance of Mycobacterium spp. on day 30 and M. avium complex throughout the growth phase within the biofilms at higher temperatures. The temperature impacts were not only microbial, with physical mobilisation showing higher discolouration response and metals release due to the increased temperature. While material accumulation was accelerated by temperature, it was not preferentially to either stronger or weaker biofilm layers, as turbidity results during the flushing steps showed. This research yields new understanding on microbial challenges that chlorinated DWDS will undergo as global temperature rises, this information is needed in order to protect drinking water quality and safety while travelling through distribution systems.
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Affiliation(s)
- Carolina Calero Preciado
- Department of Civil and Structural Engineering, Sheffield Water Centre, The University of Sheffield, Sheffield, United Kingdom.,NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, The University of Sheffield, Sheffield, United Kingdom
| | - Joby Boxall
- Department of Civil and Structural Engineering, Sheffield Water Centre, The University of Sheffield, Sheffield, United Kingdom
| | - Víctor Soria-Carrasco
- Department of Animal and Plant Sciences, The University of Sheffield, Sheffield, United Kingdom
| | - Soledad Martínez
- Área de Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Isabel Douterelo
- Department of Civil and Structural Engineering, Sheffield Water Centre, The University of Sheffield, Sheffield, United Kingdom
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11
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Cao Y, Yu X, Ju F, Zhan H, Jiang B, Kang H, Xie Z. Airborne bacterial community diversity, source and function along the Antarctic Coast. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:142700. [PMID: 33069481 DOI: 10.1016/j.scitotenv.2020.142700] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/11/2020] [Accepted: 09/26/2020] [Indexed: 06/11/2023]
Abstract
Antarctica is an isolated and relatively simple ecosystem dominated by microorganisms, providing a rare opportunity to study the spread of airborne microbes and to predict future global climate change. However, little is known about on the diversity and potential sources of microorganisms in the marine atmosphere along the Antarctica coast. Here we explored the airborne bacterial community (i.e., bacteriome) diversity, sources and functional potential along the Antarctic coast based on 16S rRNA gene amplicon sequencing of 25 bioaerosol samples collected during the 33rd Xuelong Antarctic scientific expedition. The results showed that bacterial communities in the Antarctic bioaerosols i) were predominated by Proteobacteria (91.3%) including Sphingomonas, ii) showed relative low alpha-diversity but high spatiotemporal variabilities; and iii) were potentially immigrated with terrestrial, marine and Antarctic polar bacteria through long-range transport and sea-air exchange pathways. Moreover, canonical correspondence analysis of bacteriome composition showed that wind speed, temperature, and organic carbon had a significant effect on the bacterial community (P < 0.05), although bacterial richness (Richness index) and diversity (Simpson index and Shannon index) showed no statistically significant differences between rainy, cloudy and snowy weather conditions (Adjust P > 0.05, ANOVA, Tukey HSD test). iv) The functional profiles predicted by Tax4fun2 suggest high representation of function genes related to fatty acid biosynthesis and metabolism, amino acid metabolism, nucleotide metabolism, and carbohydrate metabolism, which is conducive to the formation of microlayers on the surface of the ocean and the survival and growth of bacteria.
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Affiliation(s)
- Yue Cao
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiawei Yu
- Anhui Key Laboratory of Polar Environment and Global Change & Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Feng Ju
- School of Engineering, Westlake University, Hangzhou 310024, China; Key Laboratory of Coastal Environment and Resource Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310024, China
| | - Haicong Zhan
- Anhui Key Laboratory of Polar Environment and Global Change & Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Bei Jiang
- Anhui Key Laboratory of Polar Environment and Global Change & Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Hui Kang
- Anhui Key Laboratory of Polar Environment and Global Change & Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhouqing Xie
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China; Anhui Key Laboratory of Polar Environment and Global Change & Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China; Center for Excellence in Urban Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China.
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12
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Szuróczki S, Abbaszade G, Buni D, Bóka K, Schumann P, Neumann-Schaal M, Vajna B, Tóth E. Fertoeibacter niger gen. nov., sp. nov. a novel alkaliphilic bacterium of the family Rhodobacteraceae. Int J Syst Evol Microbiol 2021; 71. [PMID: 33734953 DOI: 10.1099/ijsem.0.004762] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Three Gram-stain-negative, non-motile, oxidase- and catalase-positive, rod-shaped, black, facultative phototrophic bacterial strains, RG-N-1aT, DMA-N-7a and RA-N-9 were isolated from the water sample from Lake Fertő/Neusiedler See (Hungary). Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the strains form a distinct linage within the family Rhodobacteraceae and their closest relatives are Tabrizicola piscis K13M18T (96.32%) followed by Cypionkella psychrotolerans PAMC 27389T (96.25%). The novel bacterial strains prefer alkaline environments and grow optimally at 23-33 °C in the presence of NaCl (1-2 w/v%). Bacteriochlorophyll a was detected. Cells contained exclusively ubiquinone Q-10. The major cellular fatty acids were C18 : 1ω7c, C19 : 1iso ω5c, C18 : 0 3-OH and C18 : 1ω7c 11-methyl. The polar lipid profile contains diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified phospholipid and four unidentified lipids. The assembled draft genome of RG-N-1aT had 33 contigs with N50 values 315 027 nt, 96× genome coverage, total length of 4 326 551 bp and a DNA G+C content of 64.9%. Genome-based calculations (genome-to-genome distance and DNA G+C percentage) and pairwise amino acid identity (AAI <73.5%) indicate that RG-N-1aT represents a novel genus. RG-N-1aT (=DSM 108317T=NCAIM B.02647T) is suggested as the type strain of a novel genus and species in the family Rhodobacteraceae, for which the name Fertoeibacter niger gen. nov., sp. nov. is proposed.
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Affiliation(s)
- Sára Szuróczki
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
| | - Gorkhmaz Abbaszade
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
| | - Dominika Buni
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
| | - Károly Bóka
- Department of Plant Anatomy, Faculty of Science, Eötvös Loránd University, Budapest, Pázmány Péter stny. 1/C, H-1117, Hungary
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124, Braunschweig, Germany
| | - Balázs Vajna
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
| | - Erika Tóth
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
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13
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Straub TJ, Shaw WR, Marcenac P, Sawadogo SP, Dabiré RK, Diabaté A, Catteruccia F, Neafsey DE. The Anopheles coluzzii microbiome and its interaction with the intracellular parasite Wolbachia. Sci Rep 2020; 10:13847. [PMID: 32796890 PMCID: PMC7427791 DOI: 10.1038/s41598-020-70745-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/27/2020] [Indexed: 11/26/2022] Open
Abstract
Wolbachia, an endosymbiotic alpha-proteobacterium commonly found in insects, can inhibit the transmission of human pathogens by mosquitoes. Biocontrol programs are underway using Aedes aegypti mosquitoes trans-infected with a non-natural Wolbachia strain to reduce dengue virus transmission. Less is known about the impact of Wolbachia on the biology and vectorial capacity of Anopheles mosquitoes, the vectors of malaria parasites. A naturally occurring strain of Wolbachia, wAnga, infects populations of the major malaria vectors Anopheles gambiae and Anopheles coluzzii in Burkina Faso. Previous studies found wAnga infection was negatively correlated with Plasmodium infection in the mosquito and wAnga influenced mosquito egg-laying behavior. Here, we investigate wAnga in natural populations of An. coluzzii and its interactions with other resident microbiota using targeted 16S sequencing. Though we find no major differences in microbiota composition associated with wAnga infection, we do find several taxa that correlate with the presence or absence of wAnga in female mosquitoes following oviposition, with the caveat that we could not rule out batch effects due to the unanticipated impact of wAnga on oviposition timing. These data suggest wAnga may influence or interact with the Anopheles microbiota, which may contribute to the impact of wAnga on Anopheles biology and vectorial capacity.
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Affiliation(s)
- Timothy J Straub
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02144, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - W Robert Shaw
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Perrine Marcenac
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Simon P Sawadogo
- Institut de Recherche en Sciences de La Santé/Centre Muraz, O1 BP 390, Bobo-Dioulasso 01, Burkina Faso
| | - Roch K Dabiré
- Institut de Recherche en Sciences de La Santé/Centre Muraz, O1 BP 390, Bobo-Dioulasso 01, Burkina Faso
| | - Abdoulaye Diabaté
- Institut de Recherche en Sciences de La Santé/Centre Muraz, O1 BP 390, Bobo-Dioulasso 01, Burkina Faso
| | - Flaminia Catteruccia
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Daniel E Neafsey
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02144, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
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14
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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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15
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Szuróczki S, Abbaszade G, Szabó A, Bóka K, Schumann P, Tóth E. Phragmitibacter flavus gen. nov., sp. nov. a new member of the family Verrucomicrobiaceae. Int J Syst Evol Microbiol 2020; 70:2108-2114. [DOI: 10.1099/ijsem.0.004025] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Gram-stain-negative, aerobic, non-motile, oxidase- and catalase-positive, rod-shaped yellow-coloured bacterial strain MG-N-17T was isolated from a water sample of Lake Fertő/Neusiedler See (Hungary). Results of phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain forms a distinct linage within the family
Verrucomicrobiaceae
of the phylum
Verrucomicrobia
, and its closest relatives are
Verrucomicrobium spinosum
DSM 4136T (94.38 %) and
Roseimicrobium gellanilyticum
DC2a-G7T (91.55 %). The novel bacterial strain prefers a weak alkaline environment and grows optimally between 22–28 °C in the absence of NaCl. The major isoprenoid quinones are MK-10, MK-11, MK-12 and MK-9. The major cellular fatty acids are anteiso-C15 : 0, C16 : 0, C16 : 1ω5c and iso-C14 : 0. The polar lipid profile contains phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and four unidentified glycolipids. The assembled draft genome of strain MG-N-17T had 44 contigs with an N50 value 348255 nt, 56.5× genome coverage, total length of 5 910 933 bp and G+C content of 56.9 mol%. Strain MG-N-17T (=DSM 106674T=NCAIM B.02643T) is proposed as the type strain of a new genus and species in the family
Verrucomicrobiaceae
, for which the name Phragmitibacter flavus gen. nov., sp. nov. is proposed.
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Affiliation(s)
- Sára Szuróczki
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
| | - Gorkhmaz Abbaszade
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
| | - Attila Szabó
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
| | - Károly Bóka
- Department of Plant Anatomy, Faculty of Science, Eötvös Loránd University, Budapest, Pázmány Péter stny. 1/C, H-1117, Hungary
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124, Braunschweig, Germany
| | - Erika Tóth
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
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16
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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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17
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Complete Genome Sequence of Phreatobacter sp. Strain NMCR1094, a Formate-Utilizing Bacterium Isolated from a Freshwater Stream. Microbiol Resour Announc 2019; 8:8/37/e00860-19. [PMID: 31515346 PMCID: PMC6742797 DOI: 10.1128/mra.00860-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phreatobacter sp. strain NMCR1094 was isolated from a freshwater stream. In this study, we report the complete genome sequence of strain NMCR1094, which contains 4,974,952 bp with 65.8% G+C content and 4,701 predicted coding sequences. In particular, the Phreatobacter sp. NMCR1094 genome contains a formate dehydrogenase region. Phreatobacter sp. strain NMCR1094 was isolated from a freshwater stream. In this study, we report the complete genome sequence of strain NMCR1094, which contains 4,974,952 bp with 65.8% G+C content and 4,701 predicted coding sequences. In particular, the Phreatobacter sp. NMCR1094 genome contains a formate dehydrogenase region.
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18
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Szuróczki S, Khayer B, Spröer C, Toumi M, Szabó A, Felföldi T, Schumann P, Tóth E. Arundinibacter roseus gen. nov., sp. nov., a new member of the family Cytophagaceae. Int J Syst Evol Microbiol 2019; 69:2076-2081. [PMID: 31099731 DOI: 10.1099/ijsem.0.003436] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-stain-negative, aerobic, non-motile, oxidase- and catalase positive, rod-shaped, pink-coloured bacterial strains, DMA-K-7aT, DMA-K-1 and DMG-N-1, were isolated from water sampled at Lake Fertő/Neusiedler See (Hungary). Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the strains form a distinct linage within the family Cytophagaceae of the phylum Bacteroidetes, and their closest relatives are Rhabdobacter roseus R49T (95.66 %) and Dyadobacter sediminis Z12T (95.38 %). The assembled genome of strain DMA-K-7aT had a total length of 5.8 Mb and a DNA G+C content of 45.7 mol%. The major isoprenoid quinone was menaquinone-7 (MK-7). The major cellular fatty acids were C16 : 1 ω7c, iso-C15 : 0, C16 : 1 ω5c, C16 : 0 and iso-C17 : 0 3-OH. The polar lipid profile contained phosphatidylethanolamine, phosphatidylserine, an unknown aminolipid, an unknown glycolipid and five unknown lipids. Flexirubin-type pigments were absent. Strain DMA-K-7aT (=DSM 106737T=NCAIM B.02641T) is proposed as the type strain of a new genus and species in the family Cytophagaceae, for which the name Arundinibacter roseus gen. nov., sp. nov. is proposed.
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Affiliation(s)
- S Szuróczki
- 1Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny., 1/C, H-1117 Budapest, Hungary
| | - B Khayer
- 2Department of Water Hygiene, National Public Health Center, Albert Flórián út 2-6. H-1097 Budapest, Hungary
| | - C Spröer
- 3Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124, Braunschweig, Germany
| | - M Toumi
- 1Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny., 1/C, H-1117 Budapest, Hungary
| | - A Szabó
- 1Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny., 1/C, H-1117 Budapest, Hungary
| | - T Felföldi
- 1Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny., 1/C, H-1117 Budapest, Hungary
| | - P Schumann
- 3Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124, Braunschweig, Germany
| | - E Tóth
- 1Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny., 1/C, H-1117 Budapest, Hungary
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Felföldi T, Márton Z, Szabó A, Mentes A, Bóka K, Márialigeti K, Máthé I, Koncz M, Schumann P, Tóth E. Siculibacillus lacustris gen. nov., sp. nov., a new rosette-forming bacterium isolated from a freshwater crater lake (Lake St. Ana, Romania). Int J Syst Evol Microbiol 2019; 69:1731-1736. [PMID: 30950779 DOI: 10.1099/ijsem.0.003385] [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
A new aerobic alphaproteobacterium, strain SA-279T, was isolated from a water sample of a crater lake. The 16S rRNA gene sequence analysis revealed that strain SA-279T formed a distinct lineage within the family Ancalomicrobiaceae and shared the highest pairwise similarity values with Pinisolibacterravus E9T (96.4 %) and Ancalomicrobiumadetum NBRC 102456T (94.2 %). Cells of strain SA-279T were rod-shaped, motile, oxidase and catalase positive, and capable of forming rosettes. Its predominant fatty acids were C18 : 1ω7c (69.0 %) and C16 : 1ω7c (22.7 %), the major respiratory quinone was Q-10, and the main polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, an unidentified aminophospholipid and an unidentified lipid. The G+C content of the genomic DNA of strain SA-279T was 69.2 mol%. On the basis of the phenotypic, chemotaxonomic and molecular data, strain SA-279T is considered to represent a new genus and species within the family Ancalomicrobiaceae, for which the name Siculibacillus lacustris gen. nov., sp. nov. is proposed. The type strain is SA-279T (=DSM 29840T=JCM 31761T).
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Affiliation(s)
- Tamás Felföldi
- 2Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104 Miercurea Ciuc, Romania.,1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Zsuzsanna Márton
- 1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Attila Szabó
- 1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Anikó Mentes
- 1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Károly Bóka
- 3Department of Plant Anatomy, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Károly Márialigeti
- 1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - István Máthé
- 2Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104 Miercurea Ciuc, Romania
| | - Mihály Koncz
- 2Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104 Miercurea Ciuc, Romania.,†Present address: Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62, 6726 Szeged, Hungary
| | - Peter Schumann
- 4Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Erika Tóth
- 1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
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Perrin Y, Bouchon D, Delafont V, Moulin L, Héchard Y. Microbiome of drinking water: A full-scale spatio-temporal study to monitor water quality in the Paris distribution system. WATER RESEARCH 2019; 149:375-385. [PMID: 30471533 DOI: 10.1016/j.watres.2018.11.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/25/2018] [Accepted: 11/05/2018] [Indexed: 05/22/2023]
Abstract
The microbiological water quality of drinking water distribution system (DWDS) is of primary importance for human health. High-throughput sequencing has gained more and more attention in the last decade to describe this microbial diversity in water networks. However, there are few studies describing this approach on large drinking water distribution systems and for extended periods of time. To fill this gap and observe the potential subtle variation in microbiota of a water network through time and space, we aimed to apply high-throughput sequencing of the 16S rRNA gene approach to characterize bacterial communities of the Paris' DWDS over a one-year period. In this study, the Paris network, composed of four different DWDSs, was sampled at 31 sites, each month for one year. The sampling campaign was one of the largest described so far (n = 368) and the importance of key spatio-temporal and physico-chemical parameters was investigated. Overall, 1321 taxa were identified within the Paris network, although only fifteen of them were found in high relative abundance (>1%) in all samples. Two genera, Phreatobacter and Hyphomicrobium were dominant. The whole bacterial diversity was not significantly affected between the four DWDSs (spatial parameter) and by physico-chemical parameters. However, the bacterial diversity was slightly modified over the one-year period (temporal parameter) as we were able to observe DWDS microbiome perturbations, presumably linked to a preceding flood event. Comparison of high-throughput sequencing of the 16S rRNA gene amplicons vs. cultivation-based techniques showed that only 1.8% of bacterial diversity was recovered through cultivation. High throughput sequencing has made it possible to monitor DWDS more accurately than conventional methods by describing the whole diversity and detecting slight fluctuations in bacterial communities. This method would be further used to supervise drinking water networks, to follow any perturbations due to internals events (such as treatments) or external events (such as flooding).
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Affiliation(s)
- Yoann Perrin
- Laboratoire Ecologie et Biologie des Interactions, Equipes Microbiologie de l'Eau, et., Ecologie, Evolution, Symbiose, Université de Poitiers, UMR CNRS 7267, F-86073, Poitiers, France; Eau de Paris, Direction de la Recherche et du Développement pour la Qualité de l'Eau, R&D Biologie, 33, Avenue Jean Jaurès, F-94200, Ivry sur Seine, France
| | - Didier Bouchon
- Laboratoire Ecologie et Biologie des Interactions, Equipes Microbiologie de l'Eau, et., Ecologie, Evolution, Symbiose, Université de Poitiers, UMR CNRS 7267, F-86073, Poitiers, France
| | - Vincent Delafont
- Laboratoire Ecologie et Biologie des Interactions, Equipes Microbiologie de l'Eau, et., Ecologie, Evolution, Symbiose, Université de Poitiers, UMR CNRS 7267, F-86073, Poitiers, France
| | - Laurent Moulin
- Eau de Paris, Direction de la Recherche et du Développement pour la Qualité de l'Eau, R&D Biologie, 33, Avenue Jean Jaurès, F-94200, Ivry sur Seine, France.
| | - Yann Héchard
- Laboratoire Ecologie et Biologie des Interactions, Equipes Microbiologie de l'Eau, et., Ecologie, Evolution, Symbiose, Université de Poitiers, UMR CNRS 7267, F-86073, Poitiers, France.
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21
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Van Assche A, Crauwels S, De Brabanter J, Willems KA, Lievens B. Characterization of the bacterial community composition in water of drinking water production and distribution systems in Flanders, Belgium. Microbiologyopen 2018; 8:e00726. [PMID: 30318762 PMCID: PMC6528567 DOI: 10.1002/mbo3.726] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 08/09/2018] [Accepted: 08/09/2018] [Indexed: 12/25/2022] Open
Abstract
The quality of drinking water is influenced by its chemical and microbial composition which in turn may be affected by the source water and the different processes applied in drinking water purification systems. In this study, we investigated the bacterial diversity in different water samples from the production and distribution chain of thirteen drinking water production and distribution systems from Flanders (Belgium) that use surface water or groundwater as source water. Water samples were collected over two seasons from the source water, the processed drinking water within the production facility and out of the tap in houses along its distribution network. 454‐pyrosequencing of 16S ribosomal RNA gene sequences revealed a total of 1,570 species‐level bacterial operational taxonomic units. Strong differences in community composition were found between processed drinking water samples originating from companies that use surface water and other that use groundwater as source water. Proteobacteria was the most abundant phylum in all samples. Yet, several phyla including Actinobacteria were significantly more abundant in surface water while Cyanobacteria were more abundant in surface water and processed water originating from surface water. Gallionella, Acinetobacter, and Pseudomonas were the three most abundant genera detected. Members of the Acinetobacter genus were even found at a relative read abundance of up to 47.5% in processed water samples, indicating a general occurrence of Acinetobacter in drinking water (systems).
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Affiliation(s)
- Ado Van Assche
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME & BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Campus De Nayer, Sint-Katelijne-Waver, Belgium
| | - Sam Crauwels
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME & BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Campus De Nayer, Sint-Katelijne-Waver, Belgium
| | - Joseph De Brabanter
- Department of Electrical Engineering (ESAT - STADIUS), KU Leuven, Leuven, Belgium
| | - Kris A Willems
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME & BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Campus De Nayer, Sint-Katelijne-Waver, Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME & BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Campus De Nayer, Sint-Katelijne-Waver, Belgium
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Kim SJ, Ahn JH, Heo J, Cho H, Weon HY, Hong SB, Kim JS, Kwon SW. Phreatobacter cathodiphilus sp. nov., isolated from a cathode of a microbial fuel cell. Int J Syst Evol Microbiol 2018; 68:2855-2859. [PMID: 30016224 DOI: 10.1099/ijsem.0.002904] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, S-12T, of a member of the genus Phreatobacterwas isolated from a cathode of a microbial fuel cell from Suwon City, South Korea. Cells were Gram-staining-negative, aerobic, non-sporulating rods, motile by means of a polar flagellum, and formed white round colonies. The strain grew at the range of 10-40 °C (optimum, 28-30 °C), pH 6.0-10.0 (optimum 7.0-8.0) and 0-1 % NaCl. The 16S rRNA gene sequence analysis showed the relatedness of S-12T to Phreatobacter stygiusYC6-17T (98.2 %) and Phreatobacter oligotrophusPI_21T (98.1 %). The major respiratory quinone was ubiquinone Q-10. Polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and an unidentified lipid. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content was 69.3 mol%. On the basis of its differences from species of the genus Phreatobacter with validly published names, strain S-12T is identified as representing a novel species, for which the proposed name is Phreatobactercathodiphilus sp. nov., with S-12T as the type strain (=KACC 18497T=JCM 31612T).
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Affiliation(s)
- Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agriculural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Jae-Hyung Ahn
- Agricultural Microbiology Division, National Institute of Agriculural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Jun Heo
- Agricultural Microbiology Division, National Institute of Agriculural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Hayoung Cho
- Agricultural Microbiology Division, National Institute of Agriculural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agriculural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Seung-Beom Hong
- Agricultural Microbiology Division, National Institute of Agriculural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Jeong-Seon Kim
- Agricultural Microbiology Division, National Institute of Agriculural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agriculural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
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23
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Dahal RH, Chaudhary DK, Kim J. Pinisolibacter ravus gen. nov., sp. nov., isolated from pine forest soil and allocation of the genera Ancalomicrobium and Pinisolibacter to the family Ancalomicrobiaceae fam. nov., and emendation of the genus Ancalomicrobium Staley 1968. Int J Syst Evol Microbiol 2018; 68:1955-1962. [PMID: 29683414 DOI: 10.1099/ijsem.0.002772] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium, designated strain E9T, was isolated from pine forest soil of Kyonggi University (Suwon, Republic of Korea). Cells were facultatively anaerobic, Gram-staining-negative, catalase-negative, oxidase-positive, non-motile, non-spore-forming, rod-shaped and straw coloured. Prosthecae were absent. Glucose was fermented. The strain grew in the pH range of 5.0-10.0 (optimum, 6.5-8.5) and at 45 °C (optimum, 28-32 °C). E9T was sensitive to NaCl at low concentration and tolerated only 0.2 % NaCl (w/v). A phylogenetic analysis based on 16S rRNA gene sequences revealed that E9T formed a lineage within the phylum Proteobacteria that was distinct from various members of the order Rhizobiales, including Ancalomicrobium adetum DSM 4722T (94.76 % sequence similarity), 'Nitratireductor lucknowense' IITR-21 (92.72 %), Prosthecomicrobium hirschii 16T (92.66 %) and Kaistia soli DSM 19436T (92.53 %). The predominant isoprenoid quinone was Q-10. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidyl-N-methylethanolamine. Major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), and C16 : 0. The DNA G+C content of the type strain was 68.4 mol%. Polyphasic characterization indicated that strain E9T represented a novel species in a novel genus within a novel family, for which the name Pinisolibacter ravus gen. nov., sp. nov. is proposed. The type strain of Pinisolibacter ravus is E9T (=KEMB 9005-534T=KACC 19120T=NBRC 112686T). A formal allocation of the genus Ancalomicrobium to the family Ancalomicrobiaceae fam. nov. is also proposed.
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Affiliation(s)
- Ram Hari Dahal
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Dhiraj Kumar Chaudhary
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
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Kukolya J, Bata-Vidács I, Luzics S, Tóth E, Kéki Z, Schumann P, Táncsics A, Nagy I, Olasz F, Tóth Á. Xylanibacillus composti gen. nov., sp. nov., isolated from compost. Int J Syst Evol Microbiol 2018; 68:698-702. [PMID: 29458465 DOI: 10.1099/ijsem.0.002523] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive bacterial strain, designated as K13T, was isolated from compost and characterized using a polyphasic approach to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, the strain showed highest similarity (93.8 %) to Paenibacillus nanensis MX2-3T. Cells of strain K13T were aerobic, motile rods. The major fatty acids were anteiso C15 : 0 (34.4 %), iso C16 : 0 (17.3 %) and C16 : 0 (10.0 %). The major menaquinone was MK-7, the polar lipid profile included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine and an aminophospholipid. The DNA G+C content was 52.3 %. Based on phenotypic, including chemotaxonomic characteristics and analysis of the 16S rRNA gene sequences, it was concluded that strain K13T represents a novel genus, for which the name Xylanibacillus gen. nov., sp. nov. is proposed. The type species of the genus is Xylanibacillus composti, the type strain of which is strain K13T (=DSM 29793T=NCAIM B.02605T).
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Affiliation(s)
- József Kukolya
- Department of Environmental and Applied Microbiology, Agro-Environmental Research Institute, National Agricultural Research and Innovation Centre, H-1022 Budapest, Herman Ottó u. 15, Hungary
| | - Ildikó Bata-Vidács
- Department of Environmental and Applied Microbiology, Agro-Environmental Research Institute, National Agricultural Research and Innovation Centre, H-1022 Budapest, Herman Ottó u. 15, Hungary
| | - Szabina Luzics
- Department of Environmental and Applied Microbiology, Agro-Environmental Research Institute, National Agricultural Research and Innovation Centre, H-1022 Budapest, Herman Ottó u. 15, Hungary
| | - Erika Tóth
- Department of Microbiology, Eötvös Loránd University, H-1117 Budapest, Pázmány P. stny. 1/C, Hungary
| | - Zsuzsa Kéki
- Department of Microbiology, Eötvös Loránd University, H-1117 Budapest, Pázmány P. stny. 1/C, Hungary
| | - Peter Schumann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - András Táncsics
- Regional University Center of Excellence in Environmental Industry, Szent István University, H-2100 Gödöllő, Károly Róbert u. 1, Hungary
| | - István Nagy
- SeqOmics Biotechnology Ltd., H-6782 Mórahalom, Vállalkozók ú. 7, Hungary.,Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Temesvári krt. 62, Hungary
| | - Ferenc Olasz
- Department of Microbiology, National Agricultural Research and Innovation Centre Research, Agricultural Biotechnology Institute, H-2100 Gödölloő, Szent-Györgyi Albert u. 4, Hungary
| | - Ákos Tóth
- Department of Environmental and Applied Microbiology, Agro-Environmental Research Institute, National Agricultural Research and Innovation Centre, H-1022 Budapest, Herman Ottó u. 15, Hungary
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Untapped bacterial diversity and metabolic potential within Unkeshwar hot springs, India. Arch Microbiol 2018; 200:753-770. [PMID: 29396619 DOI: 10.1007/s00203-018-1484-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/23/2018] [Accepted: 01/24/2018] [Indexed: 01/04/2023]
Abstract
Hot springs support diverse and interesting groups of microorganisms adapted to extreme conditions and gaining attention in biotechnological applications. However, due to limitations of cultivation methods, a majority of such extremophiles remain uncultivated and unexplored. The advent of multiple cultivation conditions and specialized culture media could possibly aid to access the unexplored microbial portion of hot springs. In the present study, different media and isolation strategies were applied to isolate hitherto unexplored bacterial taxa in the water samples collected from Unkeshwar hot springs, India. Molecular, phylogenetic and predictive functional characterization of the isolated bacterial population was done using 16S rRNA sequencing coupled with Tax4Fun tools. Furthermore, representative isolates were screened for important enzymes (cellulase, xylanase, amylase, and protease) and heavy metal tolerance (chromium, arsenic) properties. A total of 454 bacterial isolates obtained were mapped into 57 unique bacterial genera and 4 different bacterial phyla. Interestingly, 37 genera not previously isolated from Indian hot springs, were isolated for the first time in the present study. However, most of these genera (23 out of 37) were reported only in metagenomics studies from Indian and global hot springs. Furthermore, around 14 genera not previously cultivated and not detected in metagenomics studies of hot springs are documented here. The metabolic potential was ascertained by determining the abundance of specific genes using in silico based Tax4Fun tool, which identified around 315 metabolic pathways for metabolism of carbohydrates, synthesis of secondary metabolites and degradation of xenobiotic compounds. Bioprospection study revealed that 33 and 25 bacterial genera were positive for enzyme production and resistance to the heavy metals, respectively. The present study revealed the advantages of cultivation methods using a comprehensive multiple isolation approach for exploring untapped and unique bacterial diversity, and also utilities for various biotechnological and environmental applications.
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Tóth E, Szuróczki S, Kéki Z, Bóka K, Szili-Kovács T, Schumann P. Gellertiella hungarica gen. nov., sp. nov., a novel bacterium of the family Rhizobiaceae isolated from a spa in Budapest. Int J Syst Evol Microbiol 2017; 67:4565-4571. [DOI: 10.1099/ijsem.0.002332] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Erika Tóth
- Department of Microbiology, Faculty of Science, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Sára Szuróczki
- Department of Microbiology, Faculty of Science, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Zsuzsa Kéki
- Department of Microbiology, Faculty of Science, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Károly Bóka
- Department of Plant Anatomy, Faculty of Science, Eötvös Loránd University, Budapest, Hungary
| | - Tibor Szili-Kovács
- Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Herman O. Str. 15, Hungary
| | - Peter Schumann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
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27
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Tóth Á, Baka E, Bata-Vidács I, Luzics S, Kosztik J, Tóth E, Kéki Z, Schumann P, Táncsics A, Nagy I, Sós E, Kukolya J. Micrococcoides hystricis gen. nov., sp. nov., a novel member of the family Micrococcaceae, phylum Actinobacteria. Int J Syst Evol Microbiol 2017; 67:2758-2765. [PMID: 28853684 DOI: 10.1099/ijsem.0.002018] [Citation(s) in RCA: 11] [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 bacterium, designated TSL3T, was isolated from faeces of a porcupine, Hystrix indica, from the Budapest Zoo and Botanical Garden, Hungary. On the basis of 16S rRNA gene sequence analysis, the strain is phylogenetically related to the family Micrococcaceae. The highest 16S rRNA gene sequence similarity was found with Micrococcus terreus V3M1T (96.50 %) followed by Arthrobacter humicola KV-653T (96.43 %). Cells of strain TSL3T were aerobic, non-motile and coccoid-shaped. The main fatty acids were anteiso-C15 : 0 (54.4 %), iso-C16 : 0 (18.2 %) and iso C15 : 0 (9.7 %). The major menaquinone was MK-7, and the polar lipid profile included phosphatidylglycerol, diphosphatidylglycerol, dimannosylglyceride, trimannosyldiacylglycerol, phosphatidylinositol, three unknown phospholipids and two unknown glycolipids. Strain TSL3T showed the peptidoglycan structure A4alpha l-Lys - Gly - l-Glu. The DNA G+C content of strain TSL3T was 58.4 mol%. Phenotypic and genotypic characterisation clearly showed that strain TSL3T could be differerentiated from the members of other genera in the family Micrococcaceae. According to these results, strain TSL3T represents a novel genus and species, for which the name Micrococcoides hystricis gen. nov., sp. nov. is proposed. The type strain is TSL3T (=DSM 29785T=NCAIM B. 02604T).
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Affiliation(s)
- Ákos Tóth
- Department of Applied and Environmental Microbiology, Agro-Environmental Research Institute, National Agricultural Research and Innovation Centre, H-1022 Budapest, Herman Ottó u. 15, Hungary
| | - Erzsébet Baka
- Department of Applied and Environmental Microbiology, Agro-Environmental Research Institute, National Agricultural Research and Innovation Centre, H-1022 Budapest, Herman Ottó u. 15, Hungary
| | - Ildikó Bata-Vidács
- Department of Applied and Environmental Microbiology, Agro-Environmental Research Institute, National Agricultural Research and Innovation Centre, H-1022 Budapest, Herman Ottó u. 15, Hungary
| | - Szabina Luzics
- Department of Applied and Environmental Microbiology, Agro-Environmental Research Institute, National Agricultural Research and Innovation Centre, H-1022 Budapest, Herman Ottó u. 15, Hungary
| | - Judit Kosztik
- Department of Applied and Environmental Microbiology, Agro-Environmental Research Institute, National Agricultural Research and Innovation Centre, H-1022 Budapest, Herman Ottó u. 15, Hungary
| | - Erika Tóth
- Department of Microbiology, Eötvös Loránd University, H-1117 Budapest, Pázmány P. stny. 1/C, Hungary
| | - Zsuzsa Kéki
- Department of Microbiology, Eötvös Loránd University, H-1117 Budapest, Pázmány P. stny. 1/C, Hungary
| | - Peter Schumann
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - András Táncsics
- Regional University Center of Excellence in Environmental Industry, Szent István University, H-2100 Gödöllő, Károly Róbert u. 1, Hungary
| | - István Nagy
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Temesvári krt. 62, Hungary.,SeqOmics Biotechnology Ltd, H-6782 Mórahalom, Vállalkozók útja 7, Hungary
| | - Endre Sós
- Budapest Zoo and Botanical Garden, H-1146 Budapest, Állatkerti krt. 6-12, Hungary
| | - József Kukolya
- Department of Applied and Environmental Microbiology, Agro-Environmental Research Institute, National Agricultural Research and Innovation Centre, H-1022 Budapest, Herman Ottó u. 15, Hungary
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28
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Lee SD, Joung Y, Cho JC. Phreatobacter stygius sp. nov., isolated from pieces of wood in a lava cave and emended description of the genus Phreatobacter. Int J Syst Evol Microbiol 2017; 67:3296-3300. [DOI: 10.1099/ijsem.0.002106] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Soon Dong Lee
- Faculty of Science Education, Jeju National University, Jeju 63243, Republic of Korea
| | - Yochan Joung
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
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29
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Yang C, Wang Q, Simon PN, Liu J, Liu L, Dai X, Zhang X, Kuang J, Igarashi Y, Pan X, Luo F. Distinct Network Interactions in Particle-Associated and Free-Living Bacterial Communities during a Microcystis aeruginosa Bloom in a Plateau Lake. Front Microbiol 2017; 8:1202. [PMID: 28713340 PMCID: PMC5492469 DOI: 10.3389/fmicb.2017.01202] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/13/2017] [Indexed: 12/23/2022] Open
Abstract
Particle-associated bacteria (PAB) and free-living bacteria (FLB) from aquatic environments during phytoplankton blooms differ in their physical distance from algae. Both the interactions within PAB and FLB community fractions and their relationship with the surrounding environmental properties are largely unknown. Here, by using high-throughput sequencing and network-based analyses, we compared the community and network characteristics of PAB and FLB from a plateau lake during a Microcystis aeruginosa bloom. Results showed that PAB and FLB differed significantly in diversity, structure and microbial connecting network. PAB communities were characterized by highly similar bacterial community structure in different sites, tighter network connections, important topological roles for the bloom-causing M. aeruginosa and Alphaproteobacteria, especially for the potentially nitrogen-fixing (Pleomorphomonas) and algicidal bacteria (Brevundimonas sp.). FLB communities were sensitive to the detected environmental factors and were characterized by significantly higher bacterial diversity, less connectivity, larger network size and marginal role of M. aeruginosa. In both networks, covariation among bacterial taxa was extensive (>88% positive connections), and bacteria potentially affiliated with biogeochemical cycling of nitrogen (i.e., denitrification, nitrogen-fixation and nitrite-oxidization) were important in occupying module hubs, such as Meganema, Pleomorphomonas, and Nitrospira. These findings highlight the importance of considering microbial network interactions for the understanding of blooms.
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Affiliation(s)
- Caiyun Yang
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Qi Wang
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Paulina N Simon
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Jinyu Liu
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Lincong Liu
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Xianzhu Dai
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Xiaohui Zhang
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Jialiang Kuang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen UniversityGuangzhou, China
| | - Yasuo Igarashi
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Xuejun Pan
- Faculty of Environmental Science and Engineering, Kunming University of Science and TechnologyKunming, China
| | - Feng Luo
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
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30
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Tóth E, Szuróczki S, Kéki Z, Kosztik J, Makk J, Bóka K, Spröer C, Márialigeti K, Schumann P. Brevundimonas balnearis sp. nov., isolated from the well water of a thermal bath. Int J Syst Evol Microbiol 2017; 67:1033-1038. [DOI: 10.1099/ijsem.0.001746] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- E. Tóth
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - S. Szuróczki
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Zs. Kéki
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - J. Kosztik
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - J. Makk
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - K. Bóka
- Department of Plant Anatomy, Faculty of Science, Eötvös Loránd University, Budapest, Hungary
| | - C. Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124, Braunschweig, Germany
| | - K. Márialigeti
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, 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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31
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Makk J, Homonnay ZG, Kéki Z, Nemes-Barnás K, Márialigeti K, Schumann P, Tóth EM. Arenimonas subflava sp. nov., isolated from a drinking water network, and emended description of the genus Arenimonas. Int J Syst Evol Microbiol 2015; 65:1915-1921. [PMID: 25795065 DOI: 10.1099/ijs.0.000201] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strain designated PYM3-14T was isolated from the drinking water network of Budapest (Hungary) and was studied by polyphasic taxonomic methods. The straight-rod-shaped cells stained Gram-negative, were aerobic and non-motile. Phylogenetic analysis of the 16S rRNA gene sequence of strain PYM3-14T revealed a clear affiliation with members of the family Xanthomonadaceae within the class Gammaproteobacteria. The 16S rRNA gene sequence of strain PYM3-14T showed the closest sequence similarities to Arenimonas daechungensis CH15-1T (96.2 %), Arenimonas oryziterrae YC6267T (95.2 %) and Lysobacter brunescens UASM DT (94.4 %). The DNA G+C content of strain PYM3-14T, measured by two different methods (52.0 mol% and 55.9 mol%, respectively), was much lower than that of any member of the genus Arenimonas. The predominant fatty acids (>8 %) were iso-C16:0, iso-C15:0, iso-C14:0, iso-C17:1ω9c and C16:1ω7c alcohol. Strain PYM3-14T contained Q-8 as the major ubiquinone and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylmonomethylethanolamine as the major polar lipids. According to phenotypic and genotypic data strain PYM3-14T represents a novel species of the genus Arenimonas, for which the name Arenimonas subflava sp. nov. is proposed. The type strain is PYM3-14T ( = NCAIM B 02508T = DSM 25526T). On the basis of new data obtained in this study, an emended description of the genus Arenimonas is also proposed.
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Affiliation(s)
- Judit Makk
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Zalán G Homonnay
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Zsuzsa Kéki
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Katalin Nemes-Barnás
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Károly Márialigeti
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Peter Schumann
- DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Erika M Tóth
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
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