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Luo K, Chen L, Zhao Y, Peng G, Chen Z, Chen Q. Transcriptomics uncover the response of an aerobic denitrifying bacteria to zinc oxide nanoparticles exposure. ENVIRONMENTAL TECHNOLOGY 2023; 44:3685-3697. [PMID: 35466863 DOI: 10.1080/09593330.2022.2069517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
Zinc oxide nanoparticles (ZnO NPs) show adverse impacts on aerobic denitrifying bacteria, little is known about the response of these bacteria to ZnO NPs exposure at cellular level. This study assessed the multiple responses of Pseudomonas aeruginosa PCN-2 under ZnO NPs exposure. We demonstrated that ZnO NPs exposure could inhibit the intracellular metabolism and stimulate the antioxidant defence capability of PCN-2. At lower exposure concentration (5 mg/L), exogenous ROS generated and resulted in the inhibition of pyruvate metabolism and citrate cycle, which caused deficient energy for aerobic denitrification. At higher concentrations (50 mg/L), endogenous ROS additionally generated and triggered to stronger down-regulation of oxidative phosphorylation, which caused suppressed electron transfers for aerobic denitrification. Meanwhile, ZnO NPs exposure promoted EPS production and biofilm formation, and antioxidases was especially particularly stimulated at higher concentration. Our findings are significant for understanding of microbial bacterial susceptibility, tolerance and resistance under the exposure of ZnO NPs.
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Affiliation(s)
- Kongyan Luo
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, PR People's Republic of China
- State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing, People's Republic of China
- College of Environment and Resources, Dalian Minzu University, Dalian, PR People's Republic of China
| | - Long Chen
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, PR People's Republic of China
- State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing, People's Republic of China
| | - Yuanyi Zhao
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, PR People's Republic of China
- State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing, People's Republic of China
| | - Guyu Peng
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, PR People's Republic of China
- State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing, People's Republic of China
| | - Zhaobo Chen
- College of Environment and Resources, Dalian Minzu University, Dalian, PR People's Republic of China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, PR People's Republic of China
- State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing, People's Republic of China
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2
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Thakur P, Gauba P. Identification and examination of nitrogen metabolic genes in Lelliottia amnigena PTJIIT1005 for their ability to perform nitrate remediation. BMC Genomics 2023; 24:104. [PMID: 36894890 PMCID: PMC9999607 DOI: 10.1186/s12864-023-09207-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 02/23/2023] [Indexed: 03/11/2023] Open
Abstract
Lelliottia amnigena PTJIIT1005 is a bacterium that utilizes nitrate as the sole nitrogen source and can remediate nitrate from media. The annotation was done related to nitrogen metabolic genes using the PATRIC, RAST tools, and PGAP from the genome sequence of this bacterium. Multiple sequence alignments and phylogenetic analysis of respiratory nitrate reductase, assimilatory nitrate reductase, nitrite reductase, glutamine synthetase, hydroxylamine reductase, nitric oxide reductase genes from PTJIIT1005 were done to find out sequence identities with the most similar species. The identification of operon arrangement in bacteria was also identified. The PATRIC KEGG feature mapped the N-metabolic pathway to identify the chemical process, and the 3D structure of representative enzymes was also elucidated. The putative protein 3D structure was analyzed using I-TASSER software. It gave good quality protein models of all nitrogen metabolism genes and showed good sequence identity with reference templates, approximately 81-99%, except for two genes; assimilatory nitrate reductase and nitrite reductase. This study suggested that PTJIIT1005 can remove N-nitrate from water because of having N-assimilation and denitrification genes.
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Affiliation(s)
- Preeti Thakur
- Department of Biotechnology, Jaypee Institute of Information & Technology, Noida, 201307, India
| | - Pammi Gauba
- Dean & Head of Biotechnology Department, Jaypee Institute of Information & Technology, Noida, Uttar Pradesh, 201307, India.
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3
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Xue HP, Fu ZY, He W, Wang L, Li WJ, Zhang AH, Huang JK, Zhang DF, Zhao Z. Paracoccus marinaquae sp. nov., isolated from coastal water of the Yellow Sea. Arch Microbiol 2023; 205:58. [PMID: 36622427 DOI: 10.1007/s00203-023-03402-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/31/2022] [Accepted: 01/02/2023] [Indexed: 01/10/2023]
Abstract
A Gram-stain-negative, non-motile and coccoid bacterial strain, designated XHP0099T, was isolated from the coastal water of the Yellow Sea, China. Growth occurred at 20-37 ℃ (optimum, 28 ℃), pH 5.0-9.0 (optimum, pH 7.0-8.0), and with 0-7.0% NaCl (optimum, 2.0-3.0%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain XHP0099T was related to members of the genus Paracoccus and shared the highest sequence similarity with "P. siganidrum" M26 (98.2%), followed by P. alkanivorans 4-2 T (97.6%) and P. alkenifer DSM 11593 T (97.4%). The average nucleotide identity, amino acid identity, and digital DNA-DNA hybridization values of strain XHP0099T against related members in the genus Paracoccus were below the cut-off points proposed for the delineation of a novel species. The major cellular fatty acids (> 10%) were summed feature 8 (C18:1 ω7c/C18:1 ω6c), and C18:0. The major isoprenoid quinone was Q-10 and the polar lipids contained diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), aminolipid (AL) and unidentified polar lipids (L). The G + C content of the genomic DNA of strain XHP0099T was 66.0%. Genomic analysis suggested that strain XHP0099T harbored gene clusters for formaldehyde and the XoxF-type methanol oxidation and type 1 Calvin cycle, which could confer the methylotrophy pathway. Based on the phenotypic, phylogenetic, biochemical and chemotaxonomic analysis, strain XHP0099T represents a novel species of the genus Paracoccus, for which the name Paracoccus marinaquae sp. nov. is proposed. The type strain is XHP0099T (= JCM 34661 T = GDMCC 1.2414 T = MCCC 1K05846T).
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Affiliation(s)
- Hua-Peng Xue
- Institute of Marine Biotechnology and Bio-Resource Utilization, College of Oceanography, Hohai University, Nanjing, People's Republic of China
| | - Zi-Yue Fu
- Institute of Marine Biotechnology and Bio-Resource Utilization, College of Oceanography, Hohai University, Nanjing, People's Republic of China
| | - Wei He
- Institute of Marine Biotechnology and Bio-Resource Utilization, College of Oceanography, Hohai University, Nanjing, People's Republic of China
| | - Lei Wang
- MOA Key Laboratory of Soil Microbiology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Wen-Jun Li
- Institute of Marine Biotechnology and Bio-Resource Utilization, College of Oceanography, Hohai University, Nanjing, People's Republic of China.,State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China.,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, People's Republic of China
| | - Ai Hua Zhang
- Institute of Marine Biotechnology and Bio-Resource Utilization, College of Oceanography, Hohai University, Nanjing, People's Republic of China
| | - Jian-Ke Huang
- Institute of Marine Biotechnology and Bio-Resource Utilization, College of Oceanography, Hohai University, Nanjing, People's Republic of China
| | - Dao-Feng Zhang
- Institute of Marine Biotechnology and Bio-Resource Utilization, College of Oceanography, Hohai University, Nanjing, People's Republic of China.
| | - Zhe Zhao
- Institute of Marine Biotechnology and Bio-Resource Utilization, College of Oceanography, Hohai University, Nanjing, People's Republic of China.
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4
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Cicala F, Cisterna-Céliz JA, Paolinelli M, Moore JD, Sevigny J, Rocha-Olivares A. The Role of Diversity in Mediating Microbiota Structural and Functional Differences in Two Sympatric Species of Abalone Under Stressed Withering Syndrome Conditions. MICROBIAL ECOLOGY 2023; 85:277-287. [PMID: 35064808 DOI: 10.1007/s00248-022-01970-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Withering syndrome (WS) is a gastro-intestinal (GI) infectious disease likely affecting all abalone species worldwide. Structural and functional changes in abalone GI microbiotas under WS-stressed conditions remain poorly investigated. It is unclear if interspecific microbiota differences, such as the presence of certain microbes, their abundance, and functional capabilities, may be involved in the occurrence of this disease. Bacterial microbiotas of healthy Haliotis fulgens and Haliotis corrugata are mainly composed by Tenericutes, Proteobacteria, Fusobacteria, and Spirochaetes. We previously reported species-specific structural and functional profiles of those communities and suggested that they are of consequence to the different susceptibility of each species to WS. Here, we address this question by comparing the structure and function of healthy and dysbiotic microbiota through 454 pyrosequencing and PICRUSt 2, respectively. Our findings suggest that the extent to which WS-stressed conditions may explain structural and functional differences in GI microbiota is contingent on the microbiota diversity itself. Indeed, microbiota differences between stressed and healthy abalone were marginal in the more complex bacterial communities of H. corrugata, in which no significant structural or functional changes were detected. Conversely, significant structural changes were observed in the less complex bacterial microbiota of H. fulgens. Moreover, structural alterations led to a significant downregulation of some metabolic activities conducted by GI bacteria. Accordingly, results suggest that gastro-intestinal bacterial diversity appears to be related with both the health of abalone and the etiology of WS.
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Affiliation(s)
- Francesco Cicala
- Department of Biological Oceanography, CICESE, Carretera Tijuana-Ensenada km 3918, 22860, Ensenada, Baja CA, Mexico
- Department of Biomedical Innovation, CICESE, Carretera Tijuana-Ensenada km 3918, 22860, Ensenada, Baja CA, Mexico
| | | | - Marcos Paolinelli
- National Council of Scientific and Technical Research (CONICET), Av. Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina
- National Institute of Agricultural Technology INTA EEA Mendoza, San Martin 3853, Luján de Cuyo, 5507, Mendoza, Argentina
| | - James D Moore
- Bodega Marine Laboratory, University of California at Davis, P.O. Box 247, Bodega Bay, CA, USA
| | - Joseph Sevigny
- Hubbard Center for Genome Studies, University of New Hampshire, 35 Colovos Rd, Durham, NH, 03824, USA
| | - Axayácatl Rocha-Olivares
- Department of Biological Oceanography, CICESE, Carretera Tijuana-Ensenada km 3918, 22860, Ensenada, Baja CA, Mexico.
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5
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Cui X, Liu Y, Xu Y, Chen T, Zhang S, Wang J, Yang R, Liu G, Zhang W, Zhang G. Paracoccus everestensis sp. nov., a novel bacterium with great antioxidant capacity isolated from the north slope of Mount Everest. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated S8-55T, was isolated from moraine samples collected from the north slope of Mount Everest at an altitude of 5 500 m above sea level. The purpose of this study was to describe a novel species and its characteristics, through genome sequencing and analysis of the relationship between the members of the genus
Paracoccus
, and explore the antioxidant capacity of strain S8-55T. The polyphasic study confirmed the affiliation of strain S8-55T with the genus
Paracoccus
. Strain S8-55T was aerobic, Gram-negative and oxidase- and catalase positive. Cells were orange-pigmented, ellipsoid and had no spore formation, no flagella and no motility. Strain S8-55T grow at 10–37 °C, pH 7–11 and without NaCl. Ubiquinone 10 was its predominant respiratory menaquinone. The polar lipids of strain S8-55T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified phospholipid, an unidentified aminolipid and three unidentified lipids. Its major fatty acids were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c). The G+C content was 64.3 mol%. The phylogenetic analysis based on the 16S rRNA sequence showed that strain S8-55T was closely related to
Paracoccus angustae
E6T (97.9 %),
Paracoccus aerius
011410T (97.9 %) and
Paracoccus hibisci
THG-T2.8T (97.8 %). The average nucleotide identity values among strain S8-55T and
P. angustae
CCTCC AB 2015056T,
P. aerius
KCTC 42845T and
P. hibisci
CCTCC AB 2016181T were 84.1, 84.5 and 76.3 %, respectively. The genome of strain S8-55T contained antioxidant genes such as oxyR, recD, katE, recD and rpoH. Based on its morphological, physiological and chemical taxonomic characteristics, strain S8-55T (=JCM 35 227T=GDMCC 1.3026T) should be classified as a novel species of the genus
Paracoccus
with the proposed name Paracoccus everestensis sp. nov.
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Affiliation(s)
- Xiaowen Cui
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
- College of Geography and Environment Science, Northwest Normal University, Lanzhou 730070, Gansu Province, PR China
| | - Yang Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu Province, PR China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
| | - Yajie Xu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu Province, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
| | - Songlin Zhang
- College of Geography and Environment Science, Northwest Normal University, Lanzhou 730070, Gansu Province, PR China
| | - Jinxiu Wang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu Province, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
| | - Ruiqi Yang
- College of Urban Environment, Lanzhou City University, Lanzhou 730070, Gansu Province, PR China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu Province, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
| | - Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu Province, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu Province, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
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6
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Gao L, Fang BZ, Liu YH, Huang Y, Wang S, Jiang HC, Li WJ. Paracoccus salsus sp. nov., a novel slightly halophilic bacterium isolated from saline lake sediment. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, slightly halophilic and non-endospore-forming alphaproteobacterium, designated strain EGI L200073T, was isolated from saline lake sediment sampled in Xinjiang Uygur Autonomous Region, China. The taxonomic position of the isolate was determined using the polyphasic taxonomic analysis and phylogenomic analysis. Phylogenetic analysis based on 16S rRNA gene sequence similarities indicated that strain EGI L200073T formed a distinct clade with
Paracoccus seriniphilus
DSM 14827T and shared sequence identity of 98.56 %. The novel isolate could be distinguished from other species of the genus
Paracoccus
by its distinct phenotypic, physiological and genotypic characteristics. Optimal growth of strain EGI L200073T occurred on marine agar 2216 at pH 8.0 and 30 °C. The major respiratory quinone was Q-10, while the major fatty acids (>10%) were summed feature 8 (C17 : 1
ω6c and/or C17 : 1
ω7c) and C18 : 0. The detected polar lipids included diphosphatidylglycerol, phosphatidylcholine and phosphatidylglycerol. Based on the genome sequence of strain EGI L200073T, the G+C content of the novel isolate was 65.7 mol%. The average nucleotide identity, amino acid identity and digital DNA–DNA hybridization values of strain EGI L200073T against related members in the genus
Paracoccus
were below the cut-off points proposed for delineation of a novel species. According our polyphasic taxonomic data, strain EGI L200073T represents a new species of the genus
Paracoccus
, for which the name Paracoccus salsus sp. nov. is proposed. The type strain of the proposed novel isolate is EGI L200073T (=KCTC 92045T=CGMCC 1.19242T).
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Affiliation(s)
- Lei Gao
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China
| | - Bao-Zhu Fang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China
| | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China
| | - Yin Huang
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China
| | - Shuang Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Hong-Chen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China
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7
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Ramirez-Delgado D, Cicala F, Gonzalez-Sanchez RA, Avalos-Tellez R, Solana-Arellano E, Licea-Navarro A. Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México. PeerJ 2022; 10:e13235. [PMID: 35833012 PMCID: PMC9272818 DOI: 10.7717/peerj.13235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/17/2022] [Indexed: 01/13/2023] Open
Abstract
Background The gastrointestinal (GI) bacterial communities of sea lions described to date have occasionally revealed large intraspecific variability, which may originate from several factors including different methodological approaches. Indeed, GI bacterial community surveys commonly rely on the use of a single hypervariable region (HR) of 16S rRNA, which may result in misleading structural interpretations and limit comparisons among studies. Here, we considered a multi-locus analysis by targeting six HRs of 16S rRNA with the aims of (i) comprehensively assessing the GI bacterial consortium in rectal samples from Zalophus californianus pups and (ii) elucidating structural variations among the tested HRs. In addition, we evaluated which HRs may be most suitable for identifying intrinsic, structurally related microbiome characteristics, such as geographic variations or functional capabilities. Methods We employed a Short MUltiple Regions Framework (SMURF) approach using the Ion 16S™ Metagenomic Kit. This kit provides different proprietary primers designed to target six HRs of the 16S rRNA gene. To date, the only analytical pipeline available for this kit is the Ion Reporter™ Software of Thermo Fisher Scientific. Therefore, we propose an in-house pipeline to use with open-access tools, such as QIIME2 and PICRUSt 2, in downstream bioinformatic analyses. Results As hypothesized, distinctive bacterial community profiles were observed for each analyzed HR. A higher number of bacterial taxa were detected with the V3 and V6-V7 regions. Conversely, the V8 and V9 regions were less informative, as we detected a lower number of taxa. The synergistic information of these HRs suggests that the GI microbiota of Zalophus californianus pups is predominated by five bacterial phyla: Proteobacteria (~50%), Bacteroidetes (~20%), Firmicutes (~18%), Fusobacteria (~7%), and Epsilonbacteraeota (~4%). Notably, our results differ at times from previously reported abundance profiles, which may promote re-evaluations of the GI bacterial compositions in sea lions and other pinniped species that have been reported to date. Moreover, consistent geographic differences were observed only with the V3, V4, and V6-V7 regions. In addition, these HRs also presented higher numbers of predicted molecular pathways, although no significant functional changes were apparent. Together, our results suggests that multi-locus analysis should be encouraged in GI microbial surveys, as single-locus approaches may result in misleading structural results that hamper the identification of structurally related microbiome features.
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Affiliation(s)
| | - Francesco Cicala
- Biomedical Innovation Department, CICESE, Ensenada, Baja California, México
| | | | - Rosalia Avalos-Tellez
- Comisión Nacional de Areas Naturales Protegidas, Secretaría de Medio Ambiente y Recursos Naturales, Bahia de los Angeles, Baja California, México
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8
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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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9
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Liang KYH, Orata FD, Boucher YF, Case RJ. Roseobacters in a Sea of Poly- and Paraphyly: Whole Genome-Based Taxonomy of the Family Rhodobacteraceae and the Proposal for the Split of the "Roseobacter Clade" Into a Novel Family, Roseobacteraceae fam. nov. Front Microbiol 2021; 12:683109. [PMID: 34248901 PMCID: PMC8267831 DOI: 10.3389/fmicb.2021.683109] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
The family Rhodobacteraceae consists of alphaproteobacteria that are metabolically, phenotypically, and ecologically diverse. It includes the roseobacter clade, an informal designation, representing one of the most abundant groups of marine bacteria. The rapid pace of discovery of novel roseobacters in the last three decades meant that the best practice for taxonomic classification, a polyphasic approach utilizing phenotypic, genotypic, and phylogenetic characteristics, was not always followed. Early efforts for classification relied heavily on 16S rRNA gene sequence similarity and resulted in numerous taxonomic inconsistencies, with several poly- and paraphyletic genera within this family. Next-generation sequencing technologies have allowed whole-genome sequences to be obtained for most type strains, making a revision of their taxonomy possible. In this study, we performed whole-genome phylogenetic and genotypic analyses combined with a meta-analysis of phenotypic data to review taxonomic classifications of 331 type strains (under 119 genera) within the Rhodobacteraceae family. Representatives of the roseobacter clade not only have different environmental adaptions from other Rhodobacteraceae isolates but were also found to be distinct based on genomic, phylogenetic, and in silico-predicted phenotypic data. As such, we propose to move this group of bacteria into a new family, Roseobacteraceae fam. nov. In total, reclassifications resulted to 327 species and 128 genera, suggesting that misidentification is more problematic at the genus than species level. By resolving taxonomic inconsistencies of type strains within this family, we have established a set of coherent criteria based on whole-genome-based analyses that will help guide future taxonomic efforts and prevent the propagation of errors.
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Affiliation(s)
- Kevin Y H Liang
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Fabini D Orata
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Yann F Boucher
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University Singapore, Singapore, Singapore
| | - Rebecca J Case
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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10
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Wang F, Gong XF, Meng D, Liu YL, Gu PF, Fan XY, Huang ZS, Du ZJ, Li Q. Paracoccus binzhouensis sp. nov., isolated from activated sludge. Arch Microbiol 2021; 203:3007-3013. [PMID: 33774710 DOI: 10.1007/s00203-021-02286-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/23/2021] [Accepted: 03/16/2021] [Indexed: 11/29/2022]
Abstract
A gram-stain-negative, non-motile and rod-shaped strain, designated wg1T, was isolated from activated sludge obtained from wastewater treatment plant in Binzhou (Shandong province, PR China). Growth of strain wg1T occurred at 25-45 °C (optimum, 37 °C), at pH 7.0-9.0 (optimum growth at pH 8.0) and at a salinity range of 0-4% (optimum, 1%). The chemotaxonomic, phenotypic and genomic traits were investigated. The 16S rRNA gene sequence analysis showed that strain wg1T belonged to the genus Paracoccus. The species with highest similarity to strain wg1T was Paracoccus communis VKM B-2787T (98.27%), followed by Paracoccus kondratievae VKM B-2222T (98.25%). The isoprenoid quinone was Q-10. Major cellular fatty acids were summed feature 8, C16:0 and C18:0. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), aminoglycolipid (AGL), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), one unidentified lipid (L) and one unidentified phospholipid (PL). The genome size was 4,834,448 bp with a G+C content of 67.67 mol%. The prediction result of secondary metabolites based on genome has shown that the strain wg1T contained 12 clusters, and the gene involved in primary metabolism showed differences in the comparison between wg1T and reference strains. The dDDH values of strain wg1T with P. communis VKM B-2787T, P. kondratievae VKM B-2222T and P. denitrificans DSM 413T were 45.30, 30.60 and 39.50%, respectively. Based on its physiological properties, chemotaxonomic characteristics and low ANI and dDDH results, strain wg1T is considered to represent a novel species for which the name Paracoccus binzhouensis sp. nov., is proposed. The type strain is wg1T (= KCTC 72861T = CCTCC AB 2019400T).
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Affiliation(s)
- Fang Wang
- School of Biological Science and Technology, University of Jinan, 250022, Jinan, PR China
| | - Xiao-Fan Gong
- School of Biological Science and Technology, University of Jinan, 250022, Jinan, PR China
| | - Dong Meng
- School of Biological Science and Technology, University of Jinan, 250022, Jinan, PR China
| | - Yu-Ling Liu
- School of Biological Science and Technology, University of Jinan, 250022, Jinan, PR China
| | - Peng-Fei Gu
- School of Biological Science and Technology, University of Jinan, 250022, Jinan, PR China
| | - Xiang-Yu Fan
- School of Biological Science and Technology, University of Jinan, 250022, Jinan, PR China
| | - Zhao-Song Huang
- School of Biological Science and Technology, University of Jinan, 250022, Jinan, PR China
| | - Zong-Jun Du
- College of Marine Science, Shandong University, 264209, Weihai, PR China
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, 250022, Jinan, PR China.
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11
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Yang J, Feng L, Pi S, Cui D, Ma F, Zhao HP, Li A. A critical review of aerobic denitrification: Insights into the intracellular electron transfer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 731:139080. [PMID: 32417477 DOI: 10.1016/j.scitotenv.2020.139080] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/04/2020] [Accepted: 04/26/2020] [Indexed: 05/23/2023]
Abstract
Aerobic denitrification is a novel biological nitrogen removal technology, which has been widely investigated as an alternative to the conventional denitrification and for its unique advantages. To fully comprehend aerobic denitrification, it is essential to clarify the regulatory mechanisms of intracellular electron transfer during aerobic denitrification. However, reports on intracellular electron transfer during aerobic denitrification are rather limited. Thus, the purpose of this review is to discuss the molecular mechanism of aerobic denitrification from the perspective of electron transfer, by summarizing the advancements in current research on electron transfer based on conventional denitrification. Firstly, the implication of aerobic denitrification is briefly discussed, and the status of current research on aerobic denitrification is summarized. Then, the occurring foundation and significance of aerobic denitrification are discussed based on a brief review of the key components involved in the electron transfer of denitrifying enzymes. Moreover, a strategy for enhancing the efficiency of aerobic denitrification is proposed on the basis of the regulatory mechanisms of denitrification enzymes. Finally, scientific outlooks are given for further investigation on aerobic denitrification in the future. This review could help clarify the mechanism of aerobic denitrification from the perspective of electron transfer.
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Affiliation(s)
- Jixian Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Liang Feng
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Shanshan Pi
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Di Cui
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China; Engineering Research Center for Medicine, College of Pharmacy, Harbin University of Commerce, Harbin 150076, People's Republic of China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - He-Ping Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Ang Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China.
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12
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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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13
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Zhang YX, Li X, Li FL, Ma SC, Zheng GD, Chen WF, Li WJ, Wang L. Paracoccus alkanivorans sp. nov., isolated from a deep well with oil reservoir water. Int J Syst Evol Microbiol 2020; 70:2312-2317. [DOI: 10.1099/ijsem.0.004036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A Gram-stain-negative, non-motile and ovoid bacterial strain, designated 4-2T, was isolated from oil-contaminated water which was collected from Xinjiang Province, north-west PR China. The 16S rRNA gene sequence analysis showed that strain 4-2T belonged to the genus
Paracoccus
. The species with highest similarity to strain 4-2T was
Paracoccus saliphilus
YIM 90738T (97.83 %), followed by ‘
Paracoccus siganidrum
’ M26 (97.83 %) and
Paracoccus endophyticus
SYSUP0003T (97.25 %). The average nucleotide identity values between 4-2T and three type strains were 84.69, 77.88 and 74.07 %, respectively. The genomic DNA G+C content of strain 4-2T was 61.4 mol%. Chemotaxonomical characteristic results showed that the respiratory quinone was ubiquinone Q-10 and the major fatty acids were summed feature 8 (C18 : 1
ω7c or C18 : 1
ω6c) and C19 : 0 cyclo ω8c. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, unidentified phospholipids, an unidentified aminolipid and an unidentified polar lipid. The predominant polyamines were putrescine, cadaverine and spermidine. On the basis of phenotypic, chemotaxonomic and phylogenetic inferences, strain 4-2T represents a novel species of the genus
Paracoccus
, for which the name Paracoccus alkanivorans sp. nov. is proposed. The type strain is 4-2T (=CGMCC 1.13669T=LMG 30882T).
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Affiliation(s)
- Ya-Xi Zhang
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xin Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Fang-Ling Li
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Su-Chen Ma
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Guo-Di Zheng
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wen-Feng Chen
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Lei Wang
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
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14
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Li S, Zhang Z, Gu X, Lin X. Complete genome sequence of Paracoccus sp. Arc7-R13, a silver nanoparticles synthesizing bacterium isolated from Arctic Ocean sediments. Mar Genomics 2020. [DOI: 10.1016/j.margen.2019.100694] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Li J, Lu S, Jin D, Yang J, Lai XH, Huang Y, Tian Z, Dong K, Zhang S, Lei W, Pu J, Zhang G, Wu X, Huang Y, Ren Z, Wang S, Xu J. Paracoccus liaowanqingii sp. nov., isolated from Tibetan antelope ( Pantholops hodgsonii). Int J Syst Evol Microbiol 2020; 70:744-750. [PMID: 31674893 DOI: 10.1099/ijsem.0.003807] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains, designated 2251T and 3058, that were aerobic, Gram-stain-negative, non-motile, coccoid or short rod-shaped bacilli, have recently been isolated from Tibetan antelopes on the Qinghai-Tibet Plateau. The results of phylogenetic analyses of 16S rRNA gene sequences indicated that strains 2251T and 3058 represent a new species within the genus Paracoccus and are most similar to 'Paracoccus gahaiensis' CUG00006T (98.9 and 99.3 %), Paracoccus nototheniae I-41R45T (98.3 and 98.7 %) and Paracoccus hibiscisoli THG-T2.31T (97.6 and 97.8 %). Results of genomic sequence-based phylogenomic analysis agreed with those from 16S rRNA gene sequence analysis. Optimal growth was achieved at pH 7.0-7.5 and 28 °C with marine medium. Cells contained C18 : 1 ω7c as the major cellular fatty acid and ubiquinone-10 as the predominant menaquinone. The polar lipids comprised phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phospholipid, glycolipid and an unidentified lipid. The cell-wall peptidoglycan amino acids were meso-2,6-diaminopimelic acid, alanine and glutamic acid; the major cell-wall sugar was galactose. The G+C content of strain 2251T was 66.5 mol%. Both strains (2251T and 3058) had DNA-DNA relatedness values less than 50 % with all available genomes of the genus Paracoccus in the ncbi database. Differential genotypic inferences, together with phenotypic and biochemical characteristics, demonstrated that strains 2251T and 3058 should be classified as a novel species of the genus Paracoccus, for which the name Paracoccus liaowanqingii sp. nov. is suggested. The type strain is 2251T (=CGMCC 1.16490T=DSM 106269T).
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Affiliation(s)
- Junqin Li
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shan Lu
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Dong Jin
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jing Yang
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xin-He Lai
- School of Biology and Food Sciences, Shangqiu Normal University, Henan province, 475000, PR China
| | - Yuyuan Huang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Collaborative Innovation Center for Biomedicine, School of Public Health, Guangxi Medical University, Nanning 530021, Guangxi, PR China
| | - Zhi Tian
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Kui Dong
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Sihui Zhang
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Wenjing Lei
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Gui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xiaomin Wu
- Shaanxi Institute of Zoology, Xi'an, Shaanxi Province, 710032, PR China
| | - Ying Huang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Zhihong Ren
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Suping Wang
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Jianguo Xu
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China.,Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
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16
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Complete Genome Sequence and Annotation of the Paracoccus pantotrophus Type Strain DSM 2944. Microbiol Resour Announc 2020; 9:9/1/e01290-19. [PMID: 31896641 PMCID: PMC6940293 DOI: 10.1128/mra.01290-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Paracoccus spp. are metabolically versatile alphaproteobacteria able to perform heterotrophic and chemoautotrophic growth. This study describes the whole-genome sequence of the Paracoccus pantotrophus type strain DSM 2944 (ATCC 35512, LMD 82.5, GB17). The genome sequence revealed the presence of a complete phaZ phaC phaP phaR gene cluster related to polyhydroxyalkanoate metabolism. Paracoccus spp. are metabolically versatile alphaproteobacteria able to perform heterotrophic and chemoautotrophic growth. This study describes the whole-genome sequence of the Paracoccus pantotrophus type strain DSM 2944 (ATCC 35512, LMD 82.5, GB17). The genome sequence revealed the presence of a complete phaZ phaC phaP phaR gene cluster related to polyhydroxyalkanoate metabolism.
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17
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Ming H, Cheng LJ, Ding CL, Niu MM, Zhao ZL, Ji WL, Zhang LY, Zhang YM, Meng XL, Nie GX. Paracoccus luteus sp. nov., isolated from the intestine of grass carp. Int J Syst Evol Microbiol 2020; 70:543-549. [DOI: 10.1099/ijsem.0.003790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Hong Ming
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, PR China
| | - Li-Jiao Cheng
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Chen-Long Ding
- Suqian Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Suqian, 223800, PR China
| | - Ming-Ming Niu
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Zhuo-Li Zhao
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Wei-Li Ji
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, PR China
| | - Ling-Yu Zhang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Yan-min Zhang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Xiao-Lin Meng
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Guo-Xing Nie
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
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18
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Yoon J, Maharjan S, Choi H. Polyphasic taxonomic analysis of Paracoccus ravus sp. nov., an alphaproteobacterium isolated from marine sediment. FEMS Microbiol Lett 2019; 366:5565046. [DOI: 10.1093/femsle/fnz184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/04/2019] [Indexed: 01/20/2023] Open
Abstract
ABSTRACTPolyphasic taxonomic analysis was performed on a novel marine bacterium, designated as strain YJ057T, isolated from marine sediment collected in the Republic of Korea. The strain was Gram-negative, beige-colored, facultatively anaerobic, coccoid or ovoid-shaped and nonmotile. Preliminary 16S rRNA gene sequence-based phylogenetic analysis indicated that this novel marine isolate belongs to the family Rhodobacteraceae of the class Alphaproteobacteria, and has the greatest (96.2%) sequence similarity to Paracoccus aestuariivivens GHD-30T. Major (>10%) fatty acids of strain YJ057T were C16:0 and C18:1 ω7c, G+C content in the genomic DNA of the strain was 63.6 mol% and the sole respiratory quinone was ubiquinone Q-10. It had phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and some unidentified components (three aminolipids, a glycolipid, a phospholipid and two lipids). As per the distinct phylogenetic position and combination of phenotypic and genotypic traits, the strain is considered a novel species of the genus Paracoccus, and the name Paracoccus ravus sp. nov. is proposed.
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Affiliation(s)
- Jaewoo Yoon
- College of Pharmacy, Keimyung University, 1095 Dalgubeoldaero, Dalseo-Gu, Daegu 42601, Republic of Korea
| | - Sailesh Maharjan
- College of Pharmacy, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongbuk 42601, Republic of Korea
| | - Hyukjae Choi
- College of Pharmacy, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongbuk 42601, Republic of Korea
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19
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Paracoccus subflavus sp. nov., isolated from Pacific Ocean sediment. Int J Syst Evol Microbiol 2019; 69:1472-1476. [DOI: 10.1099/ijsem.0.003344] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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20
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Heo J, Cho HY, Kim JS, Hong SB, Kwon SW, Kim SJ. Paracoccus suum sp. nov., isolated from a pig farm dust collector. Int J Syst Evol Microbiol 2019; 69:970-974. [DOI: 10.1099/ijsem.0.003226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic, non-motile, non-spore-forming, coccoid- or short rod-shaped bacterial strain, designated SC2-6T, was isolated from a dust collector of a pig farm located in Wanju-gun, Jeollabuk-do, Republic of Korea. Strain SC2-6T grew within the ranges of 10–37 °C (28–30 °C, optimally), pH 6.0–10.0 (pH 7.0–8.0, optimally) and 0–3% NaCl (w/v). The 16S rRNA gene sequence similarity of strain SC2-6T showed the highest values to
Paracoccus kondratievae
GBT (96.3%),
Paracoccus denitrificans
DSM 413T (96.3%) and
Paracoccus sanguinis
5503T (96.1%). The phylogenetic tree based on the 16S rRNA gene sequences revealed that strain SC2-6T belonged to the genus
Paracoccus
and clustered with
Paracoccus pacificus
F14T. The phylogenetic tree based on the rpoD gene sequences also demonstrated that strain SC2-6T fell into the clade of the genus
Paracoccus
. The DNA G+C content was 66.9 mol%. The major respiratory quinone was ubiquinone-10 and the major fatty acids (> 10% of the total fatty acids) were summed feature 8 (comprising C18 : 1 ω6c and/or C18 : 1 ω7c). The polar lipids were composed of diphosphatidylglycerol, phosphatidylcholine, an unidentified glycolipid, two unidentified aminolipids and two unidentified lipids. On the basis of phenotypic, phylogenetic and genomic data, strain SC2-6T was classified in the genus
Paracoccus
as a member of a novel species, for which the name Paracoccus suum sp. nov. is proposed. The type strain is SC2-6T (=KACC 19328T=NBRC 113110T).
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Affiliation(s)
- Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Ha-Young Cho
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Jeong-Seon Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Seung-Beom Hong
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
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21
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Si YY, Xu KH, Yu XY, Wang MF, Chen XH. Complete genome sequence of Paracoccus denitrificans ATCC 19367 and its denitrification characteristics. Can J Microbiol 2019; 65:486-495. [PMID: 30897350 DOI: 10.1139/cjm-2019-0037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Studies show that Paracoccus denitrificans can denitrify nitrogen sources under aerobic conditions. However, the lack of data on its genome sequence has restricted molecular studies and practical applications. In this study, the complete genome of P. denitrificans ATCC 19367 was sequenced and its nitrogen metabolism properties were characterized. The size of the whole genome is 5 242 327 bp, with two chromosomes and one plasmid. The average G + C content is 66.8%, and it contains 5308 protein-coding genes, 54 tRNA genes, and nine rRNA operons. Among the protein-coding genes, 71.35% could be assigned to the Gene Ontology (GO) pathway, 86.66% to the Clusters of Orthologous Groups (COG) pathway, and 50.57% to the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Comparative genome analysis between P. denitrificans ATCC 19367 and P. denitrificans PD1222 revealed that there are 428 genes specific to ATCC 19367 and 4738 core genes. Furthermore, the expression of genes related to denitrification, biofilm formation, and nitrogen metabolism (nar, nir, and nor) by P. denitrificans ATCC 19367 under aerobic conditions was affected by incubation time and shaking speed. This study elucidates the genomic background of P. denitrificans ATCC 19367 and suggests the possibility of controlling nitrogen pollution in the environment by using this bacterium.
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Affiliation(s)
- Yuan-Yuan Si
- a College of Fisheries, Guangdong Ocean University, Zhanjiang, 524025, People's Republic of China.,b Key Laboratory for Marine Estuary Fishery Resources Protection of Yangjiang, Department of Food and Environmental Engineering, Yangjiang Polytechnic, Yangjiang, 529566, People's Republic of China
| | - Kai-Hang Xu
- a College of Fisheries, Guangdong Ocean University, Zhanjiang, 524025, People's Republic of China
| | - Xiang-Yong Yu
- a College of Fisheries, Guangdong Ocean University, Zhanjiang, 524025, People's Republic of China
| | - Mei-Fang Wang
- a College of Fisheries, Guangdong Ocean University, Zhanjiang, 524025, People's Republic of China
| | - Xing-Han Chen
- b Key Laboratory for Marine Estuary Fishery Resources Protection of Yangjiang, Department of Food and Environmental Engineering, Yangjiang Polytechnic, Yangjiang, 529566, People's Republic of China
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Bacterial diversity obtained by culturable approaches in the gut of Glossina pallidipes population from a non sleeping sickness focus in Tanzania: preliminary results. BMC Microbiol 2018; 18:164. [PMID: 30470192 PMCID: PMC6251091 DOI: 10.1186/s12866-018-1288-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Glossina pallidipes is a haematophagous insect that serves as a cyclic transmitter of trypanosomes causing African Trypanosomiasis (AT). To fully assess the role of G. pallidipes in the epidemiology of AT, especially the human form of the disease (HAT), it is essential to know the microbial diversity inhabiting the gut of natural fly populations. This study aimed to examine the diversity of G. pallidipes fly gut bacteria by culture-dependent approaches. RESULTS 113 bacterial isolates were obtained from aerobic and anaerobic microorganisms originating from the gut of G. pallidipes. 16S rDNA of each isolate was PCR amplified and sequenced. The overall majority of identified bacteria belonged in descending order to the Firmicutes (86.6%), Actinobacteria (7.6%), Proteobacteria (5.5%)and Bacteroidetes (0.3%). Diversity of Firmicutes was found higher when enrichments and isolation were performed under anaerobic conditions than aerobic ones. Experiments conducted in the absence of oxygen (anaerobiosis) led to the isolation of bacteria pertaining to four phyla (83% Firmicutes, 15% Actinobacteria, 1% Proteobacteria and 0.5% Bacteroidetes, whereas those conducted in the presence of oxygen (aerobiosis) led to the isolation of bacteria affiliated to two phyla only (90% Firmicutes and 10% Proteobacteria). Phylogenetic analyses placed these isolates into 11 genera namely Bacillus, Acinetobacter, Mesorhizobium, Paracoccus, Microbacterium, Micrococcus, Arthrobacter, Corynobacterium, Curtobacterium, Vagococcus and Dietzia spp.which are known to be either facultative anaerobes, aerobes, or even microaerobes. CONCLUSION This study shows that G. pallidipes fly gut is an environmental reservoir for a vast number of bacterial species, which are likely to be important for ecological microbial well being of the fly and possibly on differing vectorial competence and refractoriness against AT epidemiology.
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Cicala F, Cisterna-Céliz JA, Moore JD, Rocha-Olivares A. Structure, dynamics and predicted functional role of the gut microbiota of the blue ( Haliotis fulgens) and yellow ( H. corrugata) abalone from Baja California Sur, Mexico. PeerJ 2018; 6:e5830. [PMID: 30405968 PMCID: PMC6216945 DOI: 10.7717/peerj.5830] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 09/25/2018] [Indexed: 12/21/2022] Open
Abstract
The GI microbiota of abalone contains a highly complex bacterial assemblage playing an essential role in the overall health of these gastropods. The gut bacterial communities of abalone species characterized so far reveal considerable interspecific variability, likely resulting from bacterial interactions and constrained by the ecology of their abalone host species; however, they remain poorly investigated. Additionally, the extent to which structural changes in the microbiota entail functional shifts in metabolic pathways of bacterial communities remains unexplored. In order to address these questions, we characterized the gut microbiota of the northeast Pacific blue (Haliotis fulgens or HF) and yellow (Haliotis corrugata or HC) abalone by 16S rRNA gene pyrosequencing to shed light on: (i) their gut microbiota structure; (ii) how bacteria may interact among them; and (iii) predicted shifts in bacterial metabolic functions associated with the observed structural changes. Our findings revealed that Mycoplasma dominated the GI microbiome in both species. However, the structure of the bacterial communities differed significantly in spite of considerable intraspecific variation. This resulted from changes in predominant species composition in each GI microbiota, suggesting host-specific adaptation of bacterial lineages to these sympatric abalone. We hypothesize that the presence of exclusive OTUs in each microbiota may relate to host-specific differences in competitive pressure. Significant differences in bacterial diversity were found between species for the explored metabolic pathways despite their functional overlap. A more diverse array of bacteria contributed to each function in HC, whereas a single or much fewer OTUs were generally observed in HF. The structural and functional analyses allowed us to describe a significant taxonomic split and functional overlap between the microbiota of HF and HC abalone.
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Affiliation(s)
- Francesco Cicala
- Molecular Ecology Laboratory, Department of Biological Oceanography, CICESE, Ensenada, Baja California, Mexico
| | | | - James D Moore
- Bodega Marine Laboratory, University of California, Davis, Bodega Bay, CA, United States of America
| | - Axayácatl Rocha-Olivares
- Molecular Ecology Laboratory, Department of Biological Oceanography, CICESE, Ensenada, Baja California, Mexico
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Salt mine microorganisms used for the biotransformation of chlorolactones. PLoS One 2018; 13:e0197384. [PMID: 29771957 PMCID: PMC5957361 DOI: 10.1371/journal.pone.0197384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 05/01/2018] [Indexed: 11/26/2022] Open
Abstract
The aim of the project was to find new catalysts capable of chlorolactone biotransformation. Three bicyclic chlorolactones with structures possessing one or two methyl groups in their cyclohexane ring were subjected to screening biotransformation using seven bacterial strains and one fungal strain from a salt mine. Three strains of bacteria (Micrococcus luteus Pb10, Micrococcus luteus WSP45, Gordonia alkanivorans Pd25) and one fungal strain (Aspergillus sydowii KGJ10) were able to catalyse hydrolytic dehalogenation of one substrate. The classification of the strains that were effective biocatalysts was confirmed by 16S rDNA analysis. The best result (76%) was obtained using Aspergillus sydowii KGJ10. All strains catalysed hydrolytic dehalogenation without changing the conformation. The equatorial position of the chlorine atom in the substrate turned out to be warrant of the positive result of the biotransformation process.
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Sheu SY, Hsieh TY, Young CC, Chen WM. Paracoccus fontiphilus sp. nov., isolated from a freshwater spring. Int J Syst Evol Microbiol 2018; 68:2054-2060. [PMID: 29722645 DOI: 10.1099/ijsem.0.002793] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain MVW-1T, isolated from a freshwater spring in Taiwan, was characterized by using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain MVW-1T belongs to the genus Paracoccus and has the highest levels of sequence similarity to Paracoccus caeni MJ17T (97.6 %), Paracoccus sediminis CMB17T (97.4 %), Paracoccus angustae E6T (97.3 %) and Paracoccus acridae SCU-M53T (97.1 %). Cells were Gram-stain-negative, aerobic, poly-β-hydroxybutyrate-accumulating, non-motile, rod-shaped and formed light orange-coloured colonies. Optimal growth occurred at 20-25 °C, pH 6-7, and in the presence of 0-3 % NaCl. The major fatty acid of strain MVW-1T was C18 : 1ω7c. The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, an unidentified glycolipid, an unidentified aminolipid and three unidentified phospholipids. The predominant polyamines were spermidine, putrescine and cadaverine. The only isoprenoid quinone was Q-10. The genomic DNA G+C content of strain MVW-1T was 63.4 mol%. Strain MVW-1T exhibited less than 35 % DNA-DNA relatedness to P. caeni MJ17T, P. angustae E6T, P. sediminis CMB17T and P. acridae SCU-M53T. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain MVW-1T should be classified in a novel species of the genus Paracoccus, for which the name Paracoccus fontiphilus sp. nov. is proposed. The type strain is MVW-1T (=BCRC 80974T=LMG 29554T=KCTC 52239T).
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Affiliation(s)
- Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Tsai-Ying Hsieh
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Chiu-Chung Young
- College of Agriculture and Natural Resources, Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
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26
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Cicala F, Moore JD, Cáceres-Martínez J, Del Río-Portilla MA, Hernández-Rodríguez M, Vásquez-Yeomans R, Rocha-Olivares A. Monomorphic pathogens: The case of Candidatus Xenohaliotis californiensis from abalone in California, USA and Baja California, Mexico. J Invertebr Pathol 2018; 154:19-23. [PMID: 29577877 DOI: 10.1016/j.jip.2018.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 03/15/2018] [Accepted: 03/21/2018] [Indexed: 10/17/2022]
Abstract
Withering syndrome (WS) is a chronic wasting disease affecting abalone species attributed to the pathogen Candidatus Xenohaliotis californiensis (CXc). Wild populations of blue (Haliotis fulgens) and yellow (H. corrugata) abalone have experienced unusual mortality rates since 2009 off the peninsula of Baja California and WS has been hypothesized as a possible cause. Currently, little information is available about the genetic diversity of CXc and particularly the possible existence of strains differing in pathogenicity. In a recent phylogenetic analysis, we characterized five coding genes from this rickettsial pathogen. Here, we analyze those genes and two additional intergenic non-coding regions following multi-locus sequence typing (MLST) and multi-spacer typing (MST) approaches to assess the genetic variability of CXc and its relationship with blue, yellow and red (H. rufescens) abalone. Moreover, we used 16S rRNA pyrosequencing reads from gut microbiomes of blue and yellow abalone to complete the genetic characterization of this prokaryote. The presence of CXc was investigated in more than 150 abalone of the three species; furthermore, a total of 385 DNA sequences and 7117 16S rRNA reads from Candidatus Xenohaliotis californiensis were used to evaluate its population genetic structure. Our findings suggest the absence of polymorphism in the DNA sequences of analyzed loci and the presence of a single lineage of CXc infecting abalone from California (USA) and Baja California (Mexico). We posit that the absence of genetic variably in this marine rickettsia may be the result of evolutionary and ecological processes.
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Affiliation(s)
- Francesco Cicala
- Molecular Ecology Laboratory, Department of Biological Oceanography, CICESE, Carretera Tijuana-Ensenada km 3918, Ensenada, Baja California 22860, Mexico
| | - James D Moore
- Bodega Marine Laboratory, University of California at Davis, P.O. Box 247, Bodega Bay, CA, USA
| | - Jorge Cáceres-Martínez
- Department of Aquaculture, CICESE, Carretera Tijuana-Ensenada km 3918, Ensenada Baja California 22860, Mexico
| | - Miguel A Del Río-Portilla
- Department of Aquaculture, CICESE, Carretera Tijuana-Ensenada km 3918, Ensenada Baja California 22860, Mexico
| | - Mónica Hernández-Rodríguez
- Department of Aquaculture, CICESE, Carretera Tijuana-Ensenada km 3918, Ensenada Baja California 22860, Mexico
| | - Rebeca Vásquez-Yeomans
- Department of Aquaculture, CICESE, Carretera Tijuana-Ensenada km 3918, Ensenada Baja California 22860, Mexico
| | - Axayácatl Rocha-Olivares
- Molecular Ecology Laboratory, Department of Biological Oceanography, CICESE, Carretera Tijuana-Ensenada km 3918, Ensenada, Baja California 22860, Mexico.
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Cabral DJ, Wurster JI, Flokas ME, Alevizakos M, Zabat M, Korry BJ, Rowan AD, Sano WH, Andreatos N, Ducharme RB, Chan PA, Mylonakis E, Fuchs BB, Belenky P. The salivary microbiome is consistent between subjects and resistant to impacts of short-term hospitalization. Sci Rep 2017; 7:11040. [PMID: 28887570 PMCID: PMC5591268 DOI: 10.1038/s41598-017-11427-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/24/2017] [Indexed: 01/20/2023] Open
Abstract
In recent years, a growing amount of research has begun to focus on the oral microbiome due to its links with health and systemic disease. The oral microbiome has numerous advantages that make it particularly useful for clinical studies, including non-invasive collection, temporal stability, and lower complexity relative to other niches, such as the gut. Despite recent discoveries made in this area, it is unknown how the oral microbiome responds to short-term hospitalization. Previous studies have demonstrated that the gut microbiome is extremely sensitive to short-term hospitalization and that these changes are associated with significant morbidity and mortality. Here, we present a comprehensive pipeline for reliable bedside collection, sequencing, and analysis of the human salivary microbiome. We also develop a novel oral-specific mock community for pipeline validation. Using our methodology, we analyzed the salivary microbiomes of patients before and during hospitalization or azithromycin treatment to profile impacts on this community. Our findings indicate that azithromycin alters the diversity and taxonomic composition of the salivary microbiome; however, we also found that short-term hospitalization does not impact the richness or structure of this community, suggesting that the oral cavity may be less susceptible to dysbiosis during short-term hospitalization.
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Affiliation(s)
- Damien J Cabral
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI, 02912, USA
| | - Jenna I Wurster
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI, 02912, USA
| | - Myrto E Flokas
- Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School and Brown University, Providence, RI, 02903, USA
| | - Michail Alevizakos
- Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School and Brown University, Providence, RI, 02903, USA
| | - Michelle Zabat
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI, 02912, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI, 02912, USA
| | - Aislinn D Rowan
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI, 02912, USA
| | - William H Sano
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI, 02912, USA
| | - Nikolaos Andreatos
- Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School and Brown University, Providence, RI, 02903, USA
| | - R Bobby Ducharme
- Department of Medicine, Brown University, Providence, RI, 02903, USA
| | - Philip A Chan
- Department of Medicine, Brown University, Providence, RI, 02903, USA
| | - Eleftherios Mylonakis
- Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School and Brown University, Providence, RI, 02903, USA
| | - Beth Burgwyn Fuchs
- Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School and Brown University, Providence, RI, 02903, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, RI, 02912, USA.
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Chen WM, Li YS, Young CC, Sheu SY. Paracoccus mangrovi sp. nov., isolated from a mangrove. Int J Syst Evol Microbiol 2017; 67:2689-2695. [PMID: 28809137 DOI: 10.1099/ijsem.0.001993] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated gyp-1T, was isolated from a mangrove in Taiwan and characterized using the polyphasic taxonomic approach. Cells of gyp-1T were Gram-staining-negative, aerobic, poly-β-hydroxybutyrate-accumulating, non-motile, coccoid or short-rod-shaped and formed cream-coloured colonies. Growth occurred at 15-37 °C (optimum, 25-30 °C), at pH 5.5-7.0 (optimum, pH 6.0) and with 0-4 % NaCl (optimum, 1-2 %). Phylogenetic analyses based on 16S rRNA gene sequences indicated that gyp-1T represented a member of the genus Paracoccus and showed the highest levels of sequence similarity with respect to Paracoccus lutimaris HDM-25T (97.8 %) and Paracoccus aminovorans DM-82T (97.7 %). The major fatty acids (>10 %) of gyp-1T were C18 : 1ω7c and C16 : 0. The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, an unidentified glycolipid and two unidentified phospholipids. The major isoprenoid quinone was Q-10. The DNA G+C content was 64.6 mol%. The DNA-DNA hybridization value for gyp-1T with P. lutimaris HDM-25T and P. aminovorans DM-82T was less than 50 %. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that gyp-1T should be classified as representing a novel species of the genus Paracoccus, for which the name Paracoccus mangrovi sp. nov. is presented. The type strain is gyp-1T (=BCRC 80920T=LMG 29172T=KCTC 42899T).
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Affiliation(s)
- Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd., Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Yi-Shu Li
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd., Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Chiu-Chung Young
- College of Agriculture and Natural Resources, Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd., Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
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29
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Xue H, Piao CG, Guo MW, Wang LF, Li Y. Paracoccus aerius sp. nov., isolated from air. Int J Syst Evol Microbiol 2017; 67:2586-2591. [PMID: 28758621 DOI: 10.1099/ijsem.0.001976] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain 011410T, isolated from air at the foot of Xiangshan Mountain, Beijing, China, was Gram-reaction-negative, facultatively anaerobic, oval-shaped, motile with two flagella and catalase- and oxidase-positive. Growth of strain 011410T was observed at 4-41 °C (optimum, 30 °C), at pH 4.5-10.0 (optimum, pH 8.0) and at salinities of 0-10 % (w/v) NaCl (optimum, 0-2 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 011410T was a member of the genus Paracoccus and was related most closely to Paracoccus aestuarii B7T (96.62 % similarity) and Paracoccus sediminis CMB17T (96.48 % similarity). The major fatty acid was identified as C18 : 1ω7c, with smaller amounts of C18 : 0, C10 : 0 3-OH and summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I). The predominant respiratory quinone was ubiquinone-10 (Q-10), with Q-9 as a minor component. Polar lipid analysis indicated the presence of diphosphatidylglycerol, phosphatidylglycerol, one unknown phosphoglycolipid, five unknown phospholipids, one unknown aminolipid, one unknown glycolipid and two unknown polar lipids. The DNA G+C content of the strain was 63.5 mol%. On the basis of the data from this polyphasic characterization, strain 011410T represents a novel species, for which the name Paracoccus aerius sp. nov. is proposed. The type strain is 011410T (=CFCC 14285T=KCTC 42845T).
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Affiliation(s)
- Han Xue
- Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Dong xiao-fu NO. 1, Haidian District, Beijing 100091, PR China
| | - Chun-Gen Piao
- Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Dong xiao-fu NO. 1, Haidian District, Beijing 100091, PR China
| | - Min-Wei Guo
- Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Dong xiao-fu NO. 1, Haidian District, Beijing 100091, PR China
| | - Lai-Fa Wang
- Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Dong xiao-fu NO. 1, Haidian District, Beijing 100091, PR China
| | - Yong Li
- Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Dong xiao-fu NO. 1, Haidian District, Beijing 100091, PR China
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Martínez-Porchas M, Vargas-Albores F. An efficient strategy using k-mers to analyse 16S rRNA sequences. Heliyon 2017; 3:e00370. [PMID: 28795166 PMCID: PMC5537200 DOI: 10.1016/j.heliyon.2017.e00370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/11/2017] [Accepted: 07/21/2017] [Indexed: 11/28/2022] Open
Abstract
The use of k-mers has been a successful strategy for improving metagenomics studies, including taxonomic classifications, or de novo assemblies, and can be used to obtain sequences of interest from the available databases. The aim of this manuscript was to propose a simple but efficient strategy to generate k-mers and to use them to obtain and analyse in silico 16S rRNA sequence fragments. A total of 513,309 bacterial sequences contained in the SILVA database were considered for the study, and homemade PHP scripts were used to search for specific nucleotide chains, recover fragments of bacterial sequences, make calculations and organize information. Consensus sequences matching conserved regions were constructed by aligning most of the primers used in the literature. Sequences of k nucleotides (9- to 15-mers) were extracted from the generated primer contigs. Frequency analysis revealed that k-mer size was inversely proportional to the occurrence of k-mers in the different conserved regions, suggesting a stringency relationship; high numbers of duplicate reactions were observed with short k-mers, and a lower proportion of sequences were obtained with large ones, with the best results obtained using 12-mers. Using 12-mers with the proposed method to obtain and study sequences was found to be a reliable approach for the analysis of 16S rRNA sequences and this strategy may probably be extended to other biomarkers. Furthermore, additional applications such as evaluating the degree of conservation and designing primers and other calculations are proposed as examples.
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Affiliation(s)
| | - Francisco Vargas-Albores
- Centro de Investigación en Alimentación y Desarrollo, A. C. Km 0.6 Carretera a La Victoria. Hermosillo, Sonora, México
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31
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Lin P, Yan ZF, Won KH, Yang JE, Li CT, Kook M, Wang QJ, Yi TH. Paracoccus hibiscisoli sp. nov., isolated from the rhizosphere of Mugunghwa (Hibiscus syriacus). Int J Syst Evol Microbiol 2017; 67:2452-2458. [DOI: 10.1099/ijsem.0.001990] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Pei Lin
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Zheng-Fei Yan
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Kyung-Hwa Won
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Jung-Eun Yang
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Chang-Tian Li
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, PR China
| | - MooChang Kook
- Department of Food Nutrition, Baewha Women's University, Seoul 03039, Republic of Korea
| | - Qi-Jun Wang
- College of Food Science and Engineering, South China University of Technology, Guangzhou 510641, PR China
| | - Tae-Hoo Yi
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
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Ramadhani A, Kawada-Matsuo M, Komatsuzawa H, Oho T. Recombinant Sox Enzymes from Paracoccus pantotrophus Degrade Hydrogen Sulfide, a Major Component of Oral Malodor. Microbes Environ 2017; 32:54-60. [PMID: 28260736 PMCID: PMC5371076 DOI: 10.1264/jsme2.me16140] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Hydrogen sulfide (H2S) is emitted from industrial activities, and several chemotrophs possessing Sox enzymes are used for its removal. Oral malodor is a common issue in the dental field and major malodorous components are volatile sulfur compounds (VSCs), including H2S and methyl mercaptan. Paracoccus pantotrophus is an aerobic, neutrophilic facultatively autotrophic bacterium that possesses sulfur-oxidizing (Sox) enzymes in order to use sulfur compounds as an energy source. In the present study, we cloned the Sox enzymes of P. pantotrophus GB17 and evaluated their VSC-degrading activities for the prevention of oral malodor. Six genes, soxX, soxY, soxZ, soxA, soxB, and soxCD, were amplified from P. pantotrophus GB17. Each fragment was cloned into a vector for the expression of 6×His-tagged fusion proteins in Escherichia coli. Recombinant Sox (rSox) proteins were purified from whole-cell extracts of E. coli using nickel affinity chromatography. The enzyme mixture was investigated for the degradation of VSCs using gas chromatography. Each of the rSox enzymes was purified to apparent homogeneity, as confirmed by SDS-PAGE. The rSox enzyme mixture degraded H2S in dose- and time-dependent manners. All rSox enzymes were necessary for degrading H2S. The H2S-degrading activities of rSox enzymes were stable at 25–80°C, and the optimum pH was 7.0. The amount of H2S produced by periodontopathic bacteria or oral bacteria collected from human subjects decreased after an incubation with rSox enzymes. These results suggest that the combination of rSox enzymes from P. pantotrophus GB17 is useful for the prevention of oral malodor.
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Affiliation(s)
- Atik Ramadhani
- Department of Preventive Dentistry, Kagoshima University Graduate School of Medical and Dental Sciences
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Martinez-Porchas M, Villalpando-Canchola E, Ortiz Suarez LE, Vargas-Albores F. How conserved are the conserved 16S-rRNA regions? PeerJ 2017; 5:e3036. [PMID: 28265511 PMCID: PMC5333541 DOI: 10.7717/peerj.3036] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/26/2017] [Indexed: 12/20/2022] Open
Abstract
The 16S rRNA gene has been used as master key for studying prokaryotic diversity in almost every environment. Despite the claim of several researchers to have the best universal primers, the reality is that no primer has been demonstrated to be truly universal. This suggests that conserved regions of the gene may not be as conserved as expected. The aim of this study was to evaluate the conservation degree of the so-called conserved regions flanking the hypervariable regions of the 16S rRNA gene. Data contained in SILVA database (release 123) were used for the study. Primers reported as matches of each conserved region were assembled to form contigs; sequences sizing 12 nucleotides (12-mers) were extracted from these contigs and searched into the entire set of SILVA sequences. Frequency analysis shown that extreme regions, 1 and 10, registered the lowest frequencies. 12-mer frequencies revealed segments of contigs that were not as conserved as expected (≤90%). Fragments corresponding to the primer contigs 3, 4, 5b and 6a were recovered from all sequences in SILVA database. Nucleotide frequency analysis in each consensus demonstrated that only a small fraction of these so-called conserved regions is truly conserved in non-redundant sequences. It could be concluded that conserved regions of the 16S rRNA gene exhibit considerable variation that has to be considered when using this gene as biomarker.
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Dominguez-Moñino I, Jurado V, Hermosin B, Saiz-Jimenez C. Paracoccus cavernae sp. nov., isolated from a show cave. Int J Syst Evol Microbiol 2016; 66:2265-2270. [DOI: 10.1099/ijsem.0.001018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Irene Dominguez-Moñino
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Av. Reina Mercedes 10, 41012 Sevilla, Spain
| | - Valme Jurado
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Av. Reina Mercedes 10, 41012 Sevilla, Spain
| | - Bernardo Hermosin
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Av. Reina Mercedes 10, 41012 Sevilla, Spain
| | - Cesareo Saiz-Jimenez
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Av. Reina Mercedes 10, 41012 Sevilla, Spain
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Qu Z, Bakken LR, Molstad L, Frostegård Å, Bergaust LL. Transcriptional and metabolic regulation of denitrification in Paracoccus denitrificans allows low but significant activity of nitrous oxide reductase under oxic conditions. Environ Microbiol 2016; 18:2951-63. [PMID: 26568281 DOI: 10.1111/1462-2920.13128] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/02/2015] [Accepted: 11/08/2015] [Indexed: 11/27/2022]
Abstract
Oxygen is known to repress denitrification at the transcriptional and metabolic levels. It has been a common notion that nitrous oxide reductase (N2 OR) is the most sensitive enzyme among the four N-oxide reductases involved in denitrification, potentially leading to increased N2 O production under suboxic or fluctuating oxygen conditions. We present detailed gas kinetics and transcription patterns from batch culture experiments with Paracoccus denitrificans, allowing in vivo estimation of e(-) -flow to O2 and N2 O under various O2 regimes. Transcription of nosZ took place concomitantly with that of narG under suboxic conditions, whereas transcription of nirS and norB was inhibited until O2 levels approached 0 μM in the liquid. Catalytically functional N2 OR was synthesized and active in aerobically raised cells transferred to vials with 7 vol% O2 in headspace, but N2 O reduction rates were 10 times higher when anaerobic pre-cultures were subjected to the same conditions. Upon oxygen exposure, there was an incomplete and transient inactivation of N2 OR that could be ascribed to its lower ability to compete for electrons compared with terminal oxidases. The demonstrated reduction of N2 O at high O2 partial pressure and low N2 O concentrations by a bacterium not known as a typical aerobic denitrifier may provide one clue to the understanding of why some soils appear to act as sinks rather than sources for atmospheric N2 O.
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Affiliation(s)
- Zhi Qu
- Department of Environmental Sciences, Norwegian University of Life Sciences, PO Box 5003, N-1432, Ås, Norway
| | - Lars R Bakken
- Department of Environmental Sciences, Norwegian University of Life Sciences, PO Box 5003, N-1432, Ås, Norway
| | - Lars Molstad
- Department of Environmental Sciences, Norwegian University of Life Sciences, PO Box 5003, N-1432, Ås, Norway
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, N-1432, Ås, Norway
| | - Linda L Bergaust
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, N-1432, Ås, Norway.
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Zhong ZP, Liu Y, Wang F, Zhou YG, Liu HC, Liu ZP. Lacimonas salitolerans gen. nov., sp. nov., isolated from surface water of a saline lake. Int J Syst Evol Microbiol 2015; 65:4550-4556. [DOI: 10.1099/ijsem.0.000611] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative bacterium, strain TS-T30T, was isolated from a saline lake (Lake Tuosu) in Qaidam basin, Qinghai province, China, and its taxonomic position was determined by using a polyphasic approach. Cells were non-spore-forming rods, non-motile, 0.8–1.4 μm wide and 1.9–4.0 μm long. Strain TS-T30T was strictly heterotrophic and aerobic. Catalase- and oxidase-positive. Growth was observed in the presence of 0.5–11.0 % (w/v) NaCl (optimum 3.0 %), and at 10–35 °C (optimum 25 °C) and pH 6.5–10.0 (optimum pH 8.5). Strain TS-T30T contained C18 : 1ω7c as the only predominant fatty acid. The major respiratory quinone was Q-10. The DNA G+C content was 62 mol% (T
m). Phylogenetic trees based on 16S rRNA gene sequences showed that strain TS-T30T formed a distinct lineage that was independent of other most closely related genera: Lutimaribacter (95.2–95.9 % 16S rRNA gene sequence similarities), Poseidonocella (95.4 %), Ruegeria (92.8–94.9 %), Marivita (93.6–94.9 %), Seohaeicola (94.7 %), Sediminimonas (94.7 %), Shimia (93.9–94.7 %), Oceanicola (92.6–94.5 %) and Roseicyclus (94.5 %). The major polar lipids were phosphatidylglycerol, one unidentified phospholipid and an unknown aminolipid; phosphatidylcholine was not detected. These data demonstrated that strain TS-T30T represents a novel species of a new genus in the family Rhodobacteraceae, for which the name Lacimonas salitolerans gen. nov., sp. nov. is proposed. The type strain of the type species is TS-T30T ( = CGMCC 1.12477T = NBRC 110969T).
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Affiliation(s)
- Zhi-Ping Zhong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Fang Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100089, PR China
| | - Yu-Guang Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Characteristics of a novel thermophilic heterotrophic bacterium, Anoxybacillus contaminans HA, for nitrification–aerobic denitrification. Appl Microbiol Biotechnol 2015; 99:10695-702. [DOI: 10.1007/s00253-015-6870-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 07/20/2015] [Accepted: 07/22/2015] [Indexed: 10/23/2022]
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Nakamura A. Paracoccus laeviglucosivorans sp. nov., an l-glucose-utilizing bacterium isolated from soil. Int J Syst Evol Microbiol 2015; 65:3878-3884. [PMID: 26243274 DOI: 10.1099/ijsem.0.000508] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain 43PT was isolated as an l-glucose-utilizing bacterium from soil in Japan. Cells of the strain were Gram-stain-negative, aerobic and non-motile cocci. The 16S rRNA gene sequence of the strain showed high similarity to that of Paracoccus limosus (98.5 %). Phylogenetic analyses based on 16S rRNA gene sequences revealed that this strain belongs to the genus Paracoccus. Strain 43PT contained Q-10 as the sole isoprenoid quinone. The major cellular fatty acids were C18: 1ω7c or C18: 1ω6c and C16: 0, and C18: 0, C18: 1ω9c, C10: 0 3-OH and summed feature 2 were detected as minor components. The DNA G+C content of strain 43PT was 64.1 mol%. Strain 43PT contained the major polar lipids phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminolipid and two unknown glycolipids. The DNA-DNA relatedness between strain 43PT and the six related type strains of the genus Paracoccus, including P. limosus, was below 23 %. Based on the chemotaxonomic and physiological data and the values of DNA-DNA relatedness, especially the ability to assimilate l-glucose, this strain should be classified as a representative of a novel species of the genus Paracoccus, for which the name Paracoccus laeviglucosivorans sp. nov. (type strain 43PT = JCM 30587T = DSM 100094T) is proposed.
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Affiliation(s)
- Akira Nakamura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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Feng Y, Kumar R, Ravcheev DA, Zhang H. Paracoccus denitrificans possesses two BioR homologs having a role in regulation of biotin metabolism. Microbiologyopen 2015; 4:644-59. [PMID: 26037461 PMCID: PMC4554459 DOI: 10.1002/mbo3.270] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/04/2015] [Accepted: 05/12/2015] [Indexed: 11/05/2022] Open
Abstract
Recently, we determined that BioR, the GntR family of transcription factor, acts as a repressor for biotin metabolism exclusively distributed in certain species of α-proteobacteria, including the zoonotic agent Brucella melitensis and the plant pathogen Agrobacterium tumefaciens. However, the scenario is unusual in Paracoccus denitrificans, another closely related member of the same phylum α-proteobacteria featuring with denitrification. Not only does it encode two BioR homologs Pden_1431 and Pden_2922 (designated as BioR1 and BioR2, respectively), but also has six predictive BioR-recognizable sites (the two bioR homolog each has one site, whereas the two bio operons (bioBFDAGC and bioYB) each contains two tandem BioR boxes). It raised the possibility that unexpected complexity is present in BioR-mediated biotin regulation. Here we report that this is the case. The identity of the purified BioR proteins (BioR1 and BioR2) was confirmed with LC-QToF-MS. Phylogenetic analyses combined with GC percentage raised a possibility that the bioR2 gene might be acquired by horizontal gene transfer. Gel shift assays revealed that the predicted BioR-binding sites are functional for the two BioR homologs, in much similarity to the scenario seen with the BioR site of A. tumefaciens bioBFDAZ. Using the A. tumefaciens reporter system carrying a plasmid-borne LacZ fusion, we revealed that the two homologs of P. denitrificans BioR are functional repressors for biotin metabolism. As anticipated, not only does the addition of exogenous biotin stimulate efficiently the expression of bioYB operon encoding biotin transport/uptake system BioY, but also inhibits the transcription of the bioBFDAGC operon resembling the de novo biotin synthetic pathway. EMSA-based screening failed to demonstrate that the biotin-related metabolite is involved in BioR-DNA interplay, which is consistent with our former observation with Brucella BioR. Our finding defined a complex regulatory network for biotin metabolism in P. denitrificans by two BioR proteins.
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Affiliation(s)
- Youjun Feng
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
| | - Ritesh Kumar
- Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas, 77030
| | - Dmitry A Ravcheev
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 2, avenue de l'Université, L-4365, Esch-sur-Alzette, Luxembourg
| | - Huimin Zhang
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
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Hansel CM, Lentini CJ, Tang Y, Johnston DT, Wankel SD, Jardine PM. Dominance of sulfur-fueled iron oxide reduction in low-sulfate freshwater sediments. ISME JOURNAL 2015; 9:2400-12. [PMID: 25871933 DOI: 10.1038/ismej.2015.50] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 02/24/2015] [Accepted: 03/02/2015] [Indexed: 02/01/2023]
Abstract
A central tenant in microbial biogeochemistry is that microbial metabolisms follow a predictable sequence of terminal electron acceptors based on the energetic yield for the reaction. It is thereby oftentimes assumed that microbial respiration of ferric iron outcompetes sulfate in all but high-sulfate systems, and thus sulfide has little influence on freshwater or terrestrial iron cycling. Observations of sulfate reduction in low-sulfate environments have been attributed to the presumed presence of highly crystalline iron oxides allowing sulfate reduction to be more energetically favored. Here we identified the iron-reducing processes under low-sulfate conditions within columns containing freshwater sediments amended with structurally diverse iron oxides and fermentation products that fuel anaerobic respiration. We show that despite low sulfate concentrations and regardless of iron oxide substrate (ferrihydrite, Al-ferrihydrite, goethite, hematite), sulfidization was a dominant pathway in iron reduction. This process was mediated by (re)cycling of sulfur upon reaction of sulfide and iron oxides to support continued sulfur-based respiration--a cryptic sulfur cycle involving generation and consumption of sulfur intermediates. Although canonical iron respiration was not observed in the sediments amended with the more crystalline iron oxides, iron respiration did become dominant in the presence of ferrihydrite once sulfate was consumed. Thus, despite more favorable energetics, ferrihydrite reduction did not precede sulfate reduction and instead an inverse redox zonation was observed. These findings indicate that sulfur (re)cycling is a dominant force in iron cycling even in low-sulfate systems and in a manner difficult to predict using the classical thermodynamic ladder.
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Affiliation(s)
- Colleen M Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Chris J Lentini
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Yuanzhi Tang
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - David T Johnston
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA
| | - Scott D Wankel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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Nguyen NL, Kim YJ, Hoang VA, Tran BT, Pham HS, Yang DC. Paracoccus panacisoli sp. nov., isolated from a forest soil cultivated with Vietnamese ginseng. Int J Syst Evol Microbiol 2015; 65:1491-1497. [PMID: 25701850 DOI: 10.1099/ijs.0.000125] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, designated DCY94(T), was isolated from forest soil cultivated with ginseng in Vietnam. The strain was Gram-reaction-negative, facultatively anaerobic, non-motile, rod-shaped and catalase- and oxidase-positive. 16S rRNA gene sequence analysis demonstrated that strain DCY94(T) was closely related to Paracoccus sphaerophysae Zy-3(T) (97.5% 16S rRNA gene sequence similarity) and Paracoccus caeni MJ17(T) (96.9%). The fatty acid profile of strain DCY94(T) contained a predominant amount of summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 88.4%) and moderate to small quantities of C8 : 0 3-OH (1.0%), C10 : 0 3-OH (2.8%) and C18 : 0 (5.2%). Phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and one unidentified glycolipid were major polar lipids; one unidentified aminolipid, one unidentified aminophospholipid, one unidentified phospholipid and four unidentified polar lipids were minor components. The polyamine pattern comprised the major compounds putrescine and spermidine and minor amounts of sym-homospermidine and spermine. The ubiquinone of the strain was Q-10 and the G+C content of its genomic DNA was 68.3 mol%. All these results support the placement of strain DCY94(T) within the genus Paracoccus . Levels of DNA-DNA relatedness between strain DCY94(T) and P. sphaerophysae HAMBI 3106(T) and P. caeni KCTC 22480(T) were 52 and 50%, respectively. The results of phylogenetic analysis, phenotypic tests, chemotaxonomic characterization and DNA-DNA relatedness studies distinguished strain DCY94(T) from the closest recognized species of the genus Paracoccus , suggesting that this strain represents a novel species, for which the name Paracoccus panacisoli sp. nov. is proposed. The type strain is DCY94(T) ( = KCTC 42086(T) =JCM 30337(T)).
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Affiliation(s)
- Ngoc-Lan Nguyen
- Department of Oriental Medicinal Biotechnology, Kyung-Hee University, Seocheon-dong, Giheung-gu, Yongin-si, Gyeonggi-do 446-701, Republic of Korea
| | - Yeon-Ju Kim
- Department of Oriental Medicinal Biotechnology, Kyung-Hee University, Seocheon-dong, Giheung-gu, Yongin-si, Gyeonggi-do 446-701, Republic of Korea
| | - Van-An Hoang
- Department of Oriental Medicinal Biotechnology, Kyung-Hee University, Seocheon-dong, Giheung-gu, Yongin-si, Gyeonggi-do 446-701, Republic of Korea
| | - Bao-Tram Tran
- Center for Experimental Biology, National Center for Technological Progress, Ministry of Science and Technology, C6 Thanh Xuan Bac, Hanoi, Vietnam
| | - Huong-Son Pham
- Center for Experimental Biology, National Center for Technological Progress, Ministry of Science and Technology, C6 Thanh Xuan Bac, Hanoi, Vietnam
| | - Deok-Chun Yang
- Graduate School of Biotechnology and Ginseng Bank, Kyung-Hee University, Seocheon-dong, Giheung-gu, Yongin-si, Gyeonggi-do 446-701, Republic of Korea.,Department of Oriental Medicinal Biotechnology, Kyung-Hee University, Seocheon-dong, Giheung-gu, Yongin-si, Gyeonggi-do 446-701, Republic of Korea
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43
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Wan C, Lee DJ, Yang X, Wang Y, Wang X, Liu X. Calcium precipitate induced aerobic granulation. BIORESOURCE TECHNOLOGY 2015; 176:32-37. [PMID: 25460981 DOI: 10.1016/j.biortech.2014.11.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/01/2014] [Accepted: 11/04/2014] [Indexed: 06/04/2023]
Abstract
Aerobic granulation is a novel biotechnology for wastewater treatment. This study refined existing aerobic granulation mechanisms as a sequencing process including formation of calcium precipitate under alkaline pH to form inorganic cores, followed by bacterial attachment and growth on these cores to form the exopolysaccharide matrix. Mature granules comprised an inner core and a matrix layer and a rim layer with enriched microbial strains. The inorganic core was a mix of different crystals of calcium and phosphates. Functional strains including Sphingomonas sp., Paracoccus sp. Sinorhizobium americanum strain and Flavobacterium sp. attached onto the cores. These functional strains promote c-di-GMP production and the expression by Psl and Alg genes for exopolysaccharide production to enhance formation of mature granules.
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Affiliation(s)
- Chunli Wan
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Duu-Jong Lee
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China; Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan; Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan.
| | - Xue Yang
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xingzu Wang
- Key Laboratory of Reservoir Aquatic Environment, Chinese Academy of Sciences, Chongqing 400714, China
| | - Xiang Liu
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
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Paracoccus pacificus sp. nov., isolated from the Western Pacific Ocean. Antonie van Leeuwenhoek 2014; 106:725-31. [DOI: 10.1007/s10482-014-0242-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/21/2014] [Indexed: 10/24/2022]
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Isolation and characterization of a novel heterotrophic nitrifying and aerobic denitrifying bacterium Pseudomonas stutzeri KTB for bioremediation of wastewater. BIOTECHNOL BIOPROC E 2014. [DOI: 10.1007/s12257-013-0580-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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46
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Paracoccus siganidrum sp. nov., isolated from fish gastrointestinal tract. Antonie van Leeuwenhoek 2013; 103:1133-9. [DOI: 10.1007/s10482-013-9894-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 02/02/2013] [Indexed: 10/27/2022]
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Kappler U, Maher MJ. The bacterial SoxAX cytochromes. Cell Mol Life Sci 2013; 70:977-92. [PMID: 22907414 PMCID: PMC11113948 DOI: 10.1007/s00018-012-1098-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Revised: 07/09/2012] [Accepted: 07/17/2012] [Indexed: 10/28/2022]
Abstract
SoxAX cytochromes are heme-thiolate proteins that play a key role in bacterial thiosulfate oxidation, where they initiate the reaction cycle of a multi-enzyme complex by catalyzing the attachment of sulfur substrates such as thiosulfate to a conserved cysteine present in a carrier protein. SoxAX proteins have a wide phylogenetic distribution and form a family with at least three distinct types of SoxAX protein. The types of SoxAX cytochromes differ in terms of the number of heme groups present in the proteins (there are diheme and triheme versions) as well as in their subunit structure. While two of the SoxAX protein types are heterodimers, the third group contains an additional subunit, SoxK, that stabilizes the complex of the SoxA and SoxX proteins. Crystal structures are available for representatives of the two heterodimeric SoxAX protein types and both of these have shown that the cysteine ligand to the SoxA active site heme carries a modification to a cysteine persulfide that implicates this ligand in catalysis. EPR studies of SoxAX proteins have also revealed a high complexity of heme dependent signals associated with this active site heme; however, the exact mechanism of catalysis is still unclear at present, as is the exact number and types of redox centres involved in the reaction.
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Affiliation(s)
- Ulrike Kappler
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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Sun LN, Zhang J, Kwon SW, He J, Zhou SG, Li SP. Paracoccus huijuniae sp. nov., an amide pesticide-degrading bacterium isolated from activated sludge of a wastewater biotreatment system. Int J Syst Evol Microbiol 2013; 63:1132-1137. [DOI: 10.1099/ijs.0.044180-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A facultatively anaerobic, non-spore-forming, non-motile, catalase- and oxidase-positive, Gram-reaction-negative, coccoid to short rod-shaped strain, designated FLN-7T, was isolated from activated sludge of a wastewater biotreatment facility. The strain was able to hydrolyse amide pesticides (e.g. diflubenzuron, propanil, chlorpropham and dimethoate) through amide bond cleavage. Strain FLN-7T grew at 4–42 °C (optimum 28 °C), at pH 5.0–8.0 (optimum pH 7.0) and with 0–5.0 % (w/v) NaCl (optimum 1.0 %). The major respiratory quinone was ubiquinone-10. The major cellular fatty acid was C18 : 1ω7c. The genomic DNA G+C content of strain FLN-7T was 66.4±0.5 mol%. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine and an unidentified glycolipid. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain FLN-7T was a member of the genus
Paracoccus
and showed highest 16S rRNA gene sequence similarities with
Paracoccus aminovorans
JCM 7685T (99.2 %),
P. denitrificans
DSM 413T (97.8 %),
P. yeei
CDC G1212T (97.3 %) and
P. thiocyanatus
THI 011T (97.1 %). Strain FLN-7T showed low DNA–DNA relatedness with
P. aminovorans
KACC 12261T (36.5±3.4 %),
P. denitrificans
KACC 12251T (30.5±2.6 %),
P. yeei
CCUG 46822T (26.2±2.4 %) and
P. thiocyanatus
KACC 13901T (15.5±0.9 %). Based on the phylogenetic analysis, DNA–DNA hybridization, whole-cell fatty acid composition and biochemical characteristics, strain FLN-7T was clearly distinguished from all recognized species of the genus
Paracoccus
and should be classified in a novel species, for which the name Paracoccus huijuniae sp. nov. is proposed. The type strain is FLN-7T ( = KACC 16242T = ACCC 05690T).
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Affiliation(s)
- Li-Na Sun
- Key Laboratory for Microbiological Engineering of Agricultural Environment of Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jun Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
- Key Laboratory for Microbiological Engineering of Agricultural Environment of Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Soon-Wo Kwon
- Korean Agricultural Culture Collection (KACC), National Agrobiodiversity Center, National Academy of Agricultural Science, RDA, Suwon 441-707, Republic of Korea
| | - Jian He
- Key Laboratory for Microbiological Engineering of Agricultural Environment of Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Shun-Gui Zhou
- Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, PR China
| | - Shun-Peng Li
- Key Laboratory for Microbiological Engineering of Agricultural Environment of Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China
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Mao DP, Zhou Q, Chen CY, Quan ZX. Coverage evaluation of universal bacterial primers using the metagenomic datasets. BMC Microbiol 2012; 12:66. [PMID: 22554309 PMCID: PMC3445835 DOI: 10.1186/1471-2180-12-66] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 05/03/2012] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The coverage of universal primers for the bacterial 16S rRNA gene plays a crucial role in the correct understanding of microbial community structure. However, existing studies on primer coverage are limited by the lack of appropriate databases and are restricted to the domain level. Additionally, most studies do not account for the positional effect of single primer-template mismatches. In this study, we used 7 metagenomic datasets as well as the Ribosomal Database Project (RDP) to assess the coverage of 8 widely used bacterial primers. RESULTS The coverage rates for bacterial primers were found to be overestimated by previous studies that only investigated the RDP because of PCR amplification bias in the sequence composition of the dataset. In the RDP, the non-coverage rates for all primers except 27F were ≪6%, while in the metagenomic datasets, most were ≫10%. If one considers that a single mismatch near the 3' end of the primer might greatly reduce PCR efficiency, then some phylum non-coverage rates would change by more than 20%. Primer binding-site sequence variants that could not pair with their corresponding primers are discussed. CONCLUSIONS Our study revealed the potential bias introduced by the use of universal bacterial primers in the assessment of microbial communities. With the development of high-throughput, next-generation sequencing techniques, it will become feasible to sequence more of the hypervariable regions of the bacterial 16S rRNA gene. This, in turn, will lead to the more frequent use of the primers discussed here.
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Affiliation(s)
- Dan-Ping Mao
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
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50
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Kämpfer P, Lai WA, Arun AB, Young CC, Rekha PD, Martin K, Busse HJ, Chen WM. Paracoccus rhizosphaerae sp. nov., isolated from the rhizosphere of the plant Crossostephium chinense (L.) Makino (Seremban). Int J Syst Evol Microbiol 2012; 62:2750-2756. [PMID: 22286908 DOI: 10.1099/ijs.0.039057-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, coccoid-shaped bacterium, strain CC-CCM15-8(T), was isolated from a rhizosphere soil sample of the plant Crossostephium chinense (L.) Makino (Seremban) from Budai Township, Chiayi County, Taiwan. 16S rRNA gene sequence analysis clearly allocated strain CC-CCM15-8(T) to the Paracoccus cluster, showing highest similarities to the type strains of 'Paracoccus beibuensis' (98.8%), Paracoccus homiensis (97.6%), Paracoccus aestuarii (97.7%) and Paracoccus zeaxanthinifaciens (97.7%). The fatty acid profile, comprising C(18:1)ω7c as the major component and C(10:0) 3-OH as the characteristic hydroxylated fatty acid, supported the placement of strain CC-CCM15-8(T) within the genus Paracoccus. The polyamine pattern consisted of putrescine and spermidine as major components. Ubiqinone Q-10 was the major quinone type (95%); ubiquinone Q-9 was also detected (5%). The complex polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, and unidentified phospholipids, lipids and glycolipids. Levels of DNA-DNA relatedness between strain CC-CCM15-8(T) and 'P. beibuensis' LMG 25871(T), P. aestuarii DSM 19484(T), P. zeaxanthinifaciens LMG 21993(T) and P. homiensis KACC 11518(T) were 24.9% (34.8%, reciprocal analysis), 15.7% (17.5%), 17.7% (23.4%) and 16.0% (25.4%), respectively. Physiological and biochemical test results allowed the phenotypic differentiation of strain CC-CCM15-8(T) from its closest relatives in the genus Paracoccus. Based on the data presented, it is concluded that strain CC-CCM15-8(T) represents a novel species of the genus Paracoccus, for which the name Paracoccus rhizosphaerae sp. nov. is proposed. The type strain is CC-CCM15-8(T) (=LMG 26205(T)=CCM 7904(T)).
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Affiliation(s)
- P Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Wei-An Lai
- College of Agriculture and Natural Resources, Department of Soil & Environmental Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| | - A B Arun
- Yenepoya Research Centre, Yenepoya University, University Road, Deralakatee, Mangalore, Karnataka, India
| | - Chiu-Chung Young
- College of Agriculture and Natural Resources, Department of Soil & Environmental Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| | - P D Rekha
- Yenepoya Research Centre, Yenepoya University, University Road, Deralakatee, Mangalore, Karnataka, India
| | - K Martin
- Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie eV, Hans-Knöll-Institut, D-07745 Jena, Germany
| | - H-J Busse
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, Kaohsiung, Taiwan, ROC
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