1
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Hollensteiner J, Schneider D, Poehlein A, Brinkhoff T, Daniel R. Pan-genome analysis of six Paracoccus type strain genomes reveal lifestyle traits. PLoS One 2023; 18:e0287947. [PMID: 38117845 PMCID: PMC10732464 DOI: 10.1371/journal.pone.0287947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 11/15/2023] [Indexed: 12/22/2023] Open
Abstract
The genus Paracoccus capable of inhabiting a variety of different ecological niches both, marine and terrestrial, is globally distributed. In addition, Paracoccus is taxonomically, metabolically and regarding lifestyle highly diverse. Until now, little is known on how Paracoccus can adapt to such a range of different ecological niches and lifestyles. In the present study, the genus Paracoccus was phylogenomically analyzed (n = 160) and revisited, allowing species level classification of 16 so far unclassified Paracoccus sp. strains and detection of five misclassifications. Moreover, we performed pan-genome analysis of Paracoccus-type strains, isolated from a variety of ecological niches, including different soils, tidal flat sediment, host association such as the bluespotted cornetfish, Bugula plumosa, and the reef-building coral Stylophora pistillata to elucidate either i) the importance of lifestyle and adaptation potential, and ii) the role of the genomic equipment and niche adaptation potential. Six complete genomes were de novo hybrid assembled using a combination of short and long-read technologies. These Paracoccus genomes increase the number of completely closed high-quality genomes of type strains from 15 to 21. Pan-genome analysis revealed an open pan-genome composed of 13,819 genes with a minimal chromosomal core (8.84%) highlighting the genomic adaptation potential and the huge impact of extra-chromosomal elements. All genomes are shaped by the acquisition of various mobile genetic elements including genomic islands, prophages, transposases, and insertion sequences emphasizing their genomic plasticity. In terms of lifestyle, each mobile genetic elements should be evaluated separately with respect to the ecological context. Free-living genomes, in contrast to host-associated, tend to comprise (1) larger genomes, or the highest number of extra-chromosomal elements, (2) higher number of genomic islands and insertion sequence elements, and (3) a lower number of intact prophage regions. Regarding lifestyle adaptations, free-living genomes share genes linked to genetic exchange via T4SS, especially relevant for Paracoccus, known for their numerous extrachromosomal elements, enabling adaptation to dynamic environments. Conversely, host-associated genomes feature diverse genes involved in molecule transport, cell wall modification, attachment, stress protection, DNA repair, carbon, and nitrogen metabolism. Due to the vast number of adaptive genes, Paracoccus can quickly adapt to changing environmental conditions.
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Affiliation(s)
- Jacqueline Hollensteiner
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
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2
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Xu SS, Lai QL, Liu ZZ, Xu Y. Paracoccus onchidii sp. nov., a moderately halophilic bacterium isolated from a marine invertebrate from the South China Sea. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01848-7. [PMID: 37231142 DOI: 10.1007/s10482-023-01848-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
A novel moderately halophilic bacterial strain, designated Z330T, was isolated from the egg of a marine invertebrate of the genus Onchidium collected in the South China Sea. The 16S rRNA gene sequence of strain Z330T exhibited the highest similarity value to that of the type strain Paracoccus fistulariae KCTC 22803T (97.6%), Paracoccus seriniphilus NBRC 100798T (97.6%) and Paracoccus aestuarii DSM 19484T (97.6%). Phylogenomic and 16S rRNA phylogenetic analysis showed that strain Z330T was most closely related to P. seriniphilus NBRC 100798T and P. fistulariae KCTC 22803T. Strain Z330T grew optimally at 28-30 °C, pH 7.0-8.0 with the presence of 5.0-7.0% (w/v) NaCl. In addition, growth of strain Z330T occurred at 0.5-16% NaCl, indicated strain Z330T was a moderately halophilic and halotolerant bacterium of genus Paracoccus. The predominant respiratory quinone in strain Z330T was identified as ubiquinone-10. The major polar lipids of strain Z330T were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, glycolipid and six unidentified polar lipids. The major fatty acids of strain Z330T was summed feature 8 (C18:1 ω6c and/or C18:1 ω7c). The draft genome sequence of strain Z330T includes 4,084,570 bp in total (N50 = 174,985 bp) with a medium read coverage of 463.6 × and 83 scaffolds. The DNA G + C content of strain Z330T was 60.5%. In silico DNA-DNA hybridization with the four type strains showed 20.5, 22.3, 20.1 and 20.1% relatedness to Paracoccus fistulariae KCTC 22803T, Paracoccus seriniphilus NBRC 100798T, Paracoccus aestuarii DSM 19484T and Paracoccus denitrificans 1A10901T, respectively. And the average nucleotide identity (ANIb) values between strain Z330T and these four type strains were 76.2, 80.0, 75.8 and 73.8%, respectively, lower than the 95-96% threshold value for dividing prokaryotic species. On the basis of the phenotypic, phylogenetic, phylogenomic and chemotaxonomic properties, a novel species of the genus Paracoccus, Paracoccus onchidii sp. nov. is proposed with the type strain Z330T (= KCTC 92727T = MCCC 1K08325T).
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Affiliation(s)
- Shan-Shan Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, People's Republic of China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Qi-Liang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, People's Republic of China
| | - Zeng-Zhi Liu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, People's Republic of China.
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China.
| | - Ying Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, People's Republic of China
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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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Puri A, Bajaj A, Singh Y, Lal R. Harnessing taxonomically diverse and metabolically versatile genus Paracoccus for bioplastic synthesis and xenobiotic biodegradation. J Appl Microbiol 2022; 132:4208-4224. [PMID: 35294092 DOI: 10.1111/jam.15530] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 03/11/2022] [Accepted: 03/12/2022] [Indexed: 11/26/2022]
Abstract
The genus Paracoccus represents a taxonomically diverse group comprising more than 80 novel species isolated from various pristine and polluted environments. The species are characterized as coccoid shaped Gram-negative bacteria with versatile metabolic attributes and classified as autotrophs, heterotrophs and/or methylotrophs. Present study highlights the up-to-date global taxonomic diversity and critically discusses the significance of genome analysis for identifying the genomic determinants related to functional attributes mainly bioplastic synthesis and biodegradation potential that makes these isolates commercially viable. The analysis accentuates polyphasic and genomic attributes of Paracoccus spp. which could be harnessed for commercial applications and emphasizes the need of integrating genome based computational analysis for evolutionary species and functional diversification. The work reflects on the underexplored genetic potential for bioplastic synthesis which can be harnessed using advanced genomic methods. It also underlines the degradation potential and possible use of naturally-occurring pollutant-degrading Paracoccus isolates for development of biodegradation system and efficient removal of contaminants. The work contemplates plausible use of such potent isolates to establish the plant-microbe interaction, contributing towards contaminated land reclamation. Overall; the work signifies need and application of genome analysis to identify and explore prospective potential of Paracoccus spp. for environmental application towards achieving sustainability.
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Affiliation(s)
- Akshita Puri
- Department of Zoology, University of Delhi, Delhi, India.,Present addresses: P.G.T.D, Zoology, R.T.M Nagpur University, Nagpur, 440033, India
| | - Abhay Bajaj
- Department of Zoology, University of Delhi, Delhi, India.,Present addresses: CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020, India
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, India
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, India.,Present addresses: NASI Senior Scientist Platinum Jubilee Fellow, The Energy and Resources Institute Darbari Seth Block, IHC Complex, Lodhi Road New Delhi-110003, India
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5
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Gutierrez-Patricio S, Gonzalez-Pimentel JL, Miller AZ, Hermosin B, Saiz-Jimenez C, Jurado V. Paracoccus onubensis sp. nov., a novel alphaproteobacterium isolated from the wall of a show cave. Int J Syst Evol Microbiol 2021; 71. [PMID: 34388083 PMCID: PMC8513619 DOI: 10.1099/ijsem.0.004942] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A novel facultatively anaerobic, non-motile, Gram-stain-negative, non-endospore-forming alphaproteobacterium, strain 1011MAR3C25T, was isolated from a white biofilm colonizing the walls of the Andalusian show cave Gruta de las Maravillas (Huelva, Spain). Strain 1011MAR3C25T grew at 8–42 °C (optimum, 20–30 °C), at pH 5.0–9.0 (optimum, pH 5.0–6.0) and in the presence of 0–12 % (w/v) NaCl (optimum 3–5 %). Cells were catalase- and oxidase-positive. The strain grew heterotrophically with various carbon sources and chemoautotrophically with thiosulfate under aerobic conditions. Results of phylogenetic analysis showed that strain 1011MAR3C25T was related to Paracoccus saliphilus DSM 18447T and Paracoccus alkanivorans LMG 30882T (97.90 % and 97.32 % 16S rRNA sequence identity values, respectively). The major respiratory quinone was ubiquinone Q-10 and the predominant fatty acid was C18 : 1 ω7c. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid, an unidentified glycolipid and an unidentified polar lipid. The DNA G+C content was 60.3 mol%. Based on a polyphasic taxonomic study it is proposed that strain 1011MAR3C25T (=CECT 9092T=LMG 29414T) represents a novel species of the genus Paracoccus, for which the name Paracoccus onubensis sp. nov. is proposed.
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Affiliation(s)
- Sara Gutierrez-Patricio
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain
| | | | - Ana Zelia Miller
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain.,HERCULES Laboratory, Evora University, Largo Marquês de Marialva 8, 7000-809, Évora, Portugal
| | - Bernardo Hermosin
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain
| | - Cesareo Saiz-Jimenez
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain
| | - Valme Jurado
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain
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6
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Salam N, Xian WD, Asem MD, Xiao M, Li WJ. From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:132-147. [PMID: 37073336 PMCID: PMC10077289 DOI: 10.1007/s42995-020-00064-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/22/2020] [Indexed: 05/03/2023]
Abstract
Earth is dominated by a myriad of microbial communities, but the majority fails to grow under in situ laboratory conditions. The basic cause of unculturability is that bacteria dominantly occur as biofilms in natural environments. Earlier improvements in the culture techniques are mostly done by optimizing media components. However, with technological advancement particularly in the field of genome sequencing and cell imagining techniques, new tools have become available to understand the ecophysiology of microbial communities. Hence, it becomes easier to mimic environmental conditions in the culture plate. Other methods include co-culturing, emendation of growth factors, and cultivation after physical cell sorting. Most recently, techniques have been proposed for bacterial cultivation by employing genomic data to understand either microbial interactions (network-directed targeted bacterial isolation) or ecosystem engineering (reverse genomics). Hopefully, these techniques may be applied to almost all environmental samples, and help fill the gaps between the cultured and uncultured microbial communities.
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Affiliation(s)
- Nimaichand Salam
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Mipeshwaree Devi Asem
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Min Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 China
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7
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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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8
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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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9
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Doronina NV, Shmareva MN, Kaparullina EN, Vasilenko OV, Tarlachkov SV, Trotsenko YA. Reclassification of Methylarcula marina Doronina et al. 2000 as Paracoccus methylarcula nom. nov. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720020034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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10
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Meng XL, Ming H, Huang JR, Zhang LY, Cheng LJ, Zhao ZL, Ji WL, Li WJ, Nie GX. Paracoccus halotolerans sp. nov., isolated from a salt lake. Int J Syst Evol Microbiol 2019; 69:523-528. [DOI: 10.1099/ijsem.0.003190] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Xiao-Lin Meng
- 1College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Hong Ming
- 2Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, PR China
| | - Jian-Rong Huang
- 1College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Ling-Yu Zhang
- 1College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Li-Jiao Cheng
- 1College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Zhuo-Li Zhao
- 1College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Wei-Li Ji
- 2Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, PR China
| | - Wen-Jun Li
- 3State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Guo-Xing Nie
- 1College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
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11
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Navarro RR, Hori T, Inaba T, Matsuo K, Habe H, Ogata A. High-resolution phylogenetic analysis of residual bacterial species of fouled membranes after NaOCl cleaning. WATER RESEARCH 2016; 94:166-175. [PMID: 26945453 DOI: 10.1016/j.watres.2016.02.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/17/2016] [Accepted: 02/18/2016] [Indexed: 06/05/2023]
Abstract
Biofouling is one of the major problems during wastewater treatment using membrane bioreactors (MBRs). In this regard, sodium hypochlorite (NaOCl) has been widely used to wash fouled membranes for maintenance and recovery purposes. Advanced chemical and biological characterization was conducted in this work to evaluate the performance of aqueous NaOCl solutions during washing of polyacrylonitrile membranes. Fouled membranes from MBR operations supplemented with artificial wastewater were washed with 0.1% and 0.5% aqueous NaOCl solutions for 5, 10 and 30 min. The changes in organics composition on the membrane surface were directly monitored by an attenuated total reflection Fourier transform infrared (ATR-FT-IR) spectrometer. In addition, high-throughput Illumina sequencing of 16S rRNA genes was applied to detect any residual microorganisms. Results from ATR-FT-IR analysis indicated the complete disappearance of functional groups representing different fouling compounds after at least 30 min of treatment with 0.1% NaOCl. However, the biomolecular survey revealed the presence of residual bacteria even after 30 min of treatment with 0.5% NaOCl solution. Evaluation of microbial diversity of treated samples using Chao1, Shannon and Simpson reciprocal indices showed an increase in evenness while no significant decline in richness was observed. These implied that only the population of dominant species was mainly affected. The high-resolution phylogenetic analysis revealed the presence of numerous operational taxonomic units (OTUs) whose close relatives exhibit halotolerance. Some OTUs related to thermophilic and acid-resistant strains were also identified. Finally, the taxonomic analysis of recycled membranes that were previously washed with NaOCl also showed the presence of numerous halotolerant-related OTUs in the early stage of fouling. This further suggested the possible contribution of such chemical tolerance on their survival against NaOCl washing, which in turn affected their re-fouling potential.
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Affiliation(s)
- Ronald R Navarro
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan.
| | - Tomohiro Inaba
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Kazuyuki Matsuo
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Hiroshi Habe
- Research Institute for Sustainable Chemistry, AIST, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Atsushi Ogata
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
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12
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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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13
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Brown BP, Brown SR, Senko JM. Microbial communities associated with wet flue gas desulfurization systems. Front Microbiol 2012; 3:412. [PMID: 23226147 PMCID: PMC3510643 DOI: 10.3389/fmicb.2012.00412] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 11/14/2012] [Indexed: 02/01/2023] Open
Abstract
Flue gas desulfurization (FGD) systems are employed to remove SO(x) gasses that are produced by the combustion of coal for electric power generation, and consequently limit acid rain associated with these activities. Wet FGDs represent a physicochemically extreme environment due to the high operating temperatures and total dissolved solids (TDS) of fluids in the interior of the FGD units. Despite the potential importance of microbial activities in the performance and operation of FGD systems, the microbial communities associated with them have not been evaluated. Microbial communities associated with distinct process points of FGD systems at several coal-fired electricity generation facilities were evaluated using culture-dependent and -independent approaches. Due to the high solute concentrations and temperatures in the FGD absorber units, culturable halothermophilic/tolerant bacteria were more abundant in samples collected from within the absorber units than in samples collected from the makeup waters that are used to replenish fluids inside the absorber units. Evaluation of bacterial 16S rRNA genes recovered from scale deposits on the walls of absorber units revealed that the microbial communities associated with these deposits are primarily composed of thermophilic bacterial lineages. These findings suggest that unique microbial communities develop in FGD systems in response to physicochemical characteristics of the different process points within the systems. The activities of the thermophilic microbial communities that develop within scale deposits could play a role in the corrosion of steel structures in FGD systems.
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Affiliation(s)
- Bryan P Brown
- Department of Biology, The University of Akron, Akron OH, USA
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14
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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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Fu Y, Li Q, Liu K, Xu Y, Wang Y, Jiao N. Paracoccus oceanense sp. nov., Isolated from the West Pacific. Curr Microbiol 2011; 63:561-7. [DOI: 10.1007/s00284-011-0015-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 09/12/2011] [Indexed: 10/17/2022]
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16
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Lee M, Woo SG, Park G, Kim MK. Paracoccus caeni sp. nov., isolated from sludge. Int J Syst Evol Microbiol 2011; 61:1968-1972. [DOI: 10.1099/ijs.0.017897-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, non-motile bacterium, designated MJ17T, was isolated from sludge at the Daejeon sewage disposal plant in South Korea. Comparative 16S rRNA gene sequence analysis showed that strain MJ17T belonged to the genus Paracoccus in the family Rhodobacteraceae of the class Alphaproteobacteria. 16S rRNA gene sequence similarities between strain MJ17T and type strains of species of the genus Paracoccus were 94.1–97.4 %. The highest similarities were between strain MJ17T and Paracoccus homiensis DD-R11T, Paracoccus zeaxanthinifaciens ATCC 21588T and Paracoccus alcaliphilus JCM 7364T (97.4, 97.2 and 96.3 %, respectively). Strain MJ17T exhibited <22 % DNA–DNA relatedness with P. homiensis KACC 11518T and P. zeaxanthinifaciens JCM 21774T. The G+C content of the genomic DNA was 58.7 mol%. Strain MJ17T contained ubiquinone Q-10. The major fatty acids were C18 : 0 (11.3 %), C16 : 0 (10.2 %) and summed feature 7 (containing one or more of C18 : 1ω7c, C18 : 1ω9c and C18 : 1ω12t; 54.3 %). Poly-β-hydroxybutyrate granules are formed. On the basis of phenotypic and genotypic properties and phylogenetic distinctiveness, strain MJ17T should be classified in a novel species of the genus Paracoccus, for which the name Paracoccus caeni sp. nov. is proposed. The type strain is MJ17T ( = KCTC 22480T = JCM 16385T = KEMB 9004-001T).
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Affiliation(s)
- Myungjin Lee
- Research and Development Division, H-Plus Eco Ltd, BVC #301, KRIBB, Eoeun-dong, Yuseong-gu, Daejeon 305-333, Republic of Korea
| | - Song-Geun Woo
- School of Civil and Environmental Engineering, Yonsei University, Seoul 120-749, Republic of Korea
- Research and Development Division, H-Plus Eco Ltd, BVC #301, KRIBB, Eoeun-dong, Yuseong-gu, Daejeon 305-333, Republic of Korea
| | - Giho Park
- Daewoo Institute of Construction Technology, 60 Songjuk-dong, Jangan-gu, Suwon-si, Gyeonggi-do 440-210, Republic of Korea
| | - Myung Kyum Kim
- Department of Bio & Environmental Technology, Division of Environmental & Life Science, College of Natural Science, Seoul Women’s University, 623 Hwarangno, Nowon-gu, Seoul 139-774, Republic of Korea
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Paracoccus beibuensis sp. nov., isolated from the South China Sea. Curr Microbiol 2010; 62:710-4. [PMID: 20936472 DOI: 10.1007/s00284-010-9768-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 09/14/2010] [Indexed: 10/19/2022]
Abstract
A Gram-negative, non-motile, short rod-shaped or spherical bacterial strain that accumulates poly-β-hydroxybutyrate (PHB) granules was isolated from the Beibu Gulf in the South China Sea. Cells have no polar or subpolar flagella, dividing by binary fission. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Paracoccus, family Rhodobacteraceae, order Rhodobacterales, class Alphaproteobacteria. The closest neighbours were Paracoccus aestuarii strain B7(T) (97.2% similarity), Paracoccus zeaxanthinifaciens ATCC 21588(T) (97.1% similarity) and Paracoccus homiensis DD-R11(T) (96.8%). The predominant fatty acids were C(18:1) ω7c (82.1%), and significant amounts of C(18:0) (5.6%), C(10:0) 3-OH (2.3%) and C(16:0) (1.5%) were present. The predominant respiratory ubiquinone of strain JLT1284(T) was Q-10 and the DNA G+C content of strain JLT1284(T) was 67.0 mol%. The isolate was also distinguishable from members of the genus Paracoccus on the basis of phenotypic and biochemical characteristics. It is evident from the genotypic, chemotaxonomic and phenotypic data, therefore, that strain JLT1284(T) represents a novel species of the genus Paracoccus, for which the name Paracoccus beibuensis sp. nov. is proposed. The type strain is JLT1284(T)=LMG 24871(T)=CGMCC 1.7295(T)).
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18
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Dastager SG, Deepa CK, Li WJ, Tang SK, Pandey A. Paracoccus niistensis sp. nov., isolated from forest soil, India. Antonie van Leeuwenhoek 2010; 99:501-6. [DOI: 10.1007/s10482-010-9515-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 09/17/2010] [Indexed: 10/19/2022]
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Catellibacterium aquatile sp. nov., isolated from fresh water, and emended description of the genus Catellibacterium Tanaka et al. 2004. Int J Syst Evol Microbiol 2010; 60:2027-2031. [DOI: 10.1099/ijs.0.017632-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, rod-shaped, non-pigmented, non-spore-forming bacterial strain that was motile by a single polar flagellum, designated A1-9T, was isolated from Daqing reservoir in north-east China and its taxonomic position was studied using a polyphasic approach. Strain A1-9Twas non-halophilic, strictly aerobic and heterotrophic and lacked carotenoids, internal membranes and genes for photosynthesis (pufgenes). Strain A1-9Tgrew at 10–40 °C (optimum, 25–30 °C) and pH 5.5–9.0 (optimum, pH 6.0–6.5) and tolerated up to 1.0 % NaCl (w/v). Neither phototrophic nor fermentative growth was observed. The predominant ubiquinone was Q-10 and the major fatty acid was C18 : 1ω7c(70 %). The DNA G+C content was 64.4 mol% (Tm). Phylogenetic analyses based on the 16S rRNA gene sequence revealed that strain A1-9T, together withCatellibacterium nectariphilumAST4T, formed a deep line within the ‘Rhodobacterclade’ of the familyRhodobacteraceaeand strain A1-9Tshowed 94.2 % 16S rRNA gene sequence similarity toC. nectariphilumAST4T. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain A1-9Tis considered to represent a novel species of the genusCatellibacterium, for which the nameCatellibacterium aquatilesp. nov. is proposed. The type strain is A1-9T(=CGMCC 1.7029T=NBRC 104254T).
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Bioprospecting microbial natural product libraries from the marine environment for drug discovery. J Antibiot (Tokyo) 2010; 63:415-22. [PMID: 20606699 DOI: 10.1038/ja.2010.56] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Marine microorganisms are fascinating resources due to their production of novel natural products with antimicrobial activities. Increases in both the number of new chemical entities found and the substantiation of indigenous marine actinobacteria present a fundamental difficulty in the future discovery of novel antimicrobials, namely dereplication of those compounds already discovered. This review will share our experience on the taxonomic-based construction of a highly diversified and low redundant marine microbial natural product library for high-throughput antibiotic screening. We anticipate that libraries such as these can drive the drug discovery process now and in the future.
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