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Kumar P, Verma A, Yadav P, Das J, Kumar L, Krishnamurthi S. Phylogenomic evaluation of Mangrovimicrobium sediminis gen. nov. sp. nov., the first nitrogen fixing member of the family Halieaceae adapted to mangrove habitat and reclassification of Halioglobus pacificus to Pseudohaliglobus pacificus comb. nov. Sci Total Environ 2024; 933:172995. [PMID: 38719044 DOI: 10.1016/j.scitotenv.2024.172995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 04/20/2024] [Accepted: 05/02/2024] [Indexed: 05/19/2024]
Abstract
The taxonomic position and genomic characteristics of a nitrogen fixing and polymer degrading marine bacterium, strain SAOS 164 isolated from a mangrove sediment sample was investigated. Sequence analysis based on 16S rRNA gene identified it as a member of family Halieaceae with closest similarity to Haliea salexigens DSM 19537T (96.3 %), H. alexandrii LZ-16-2T (96.2 %) and Parahaliea maris HSLHS9T (96.0 %) but was distantly related to the genera Haliea, Parahaliea and Halioglobus in phylogenetic trees. In order to ascertain the exact taxonomic position, phylogeny based on RpoBC proteins, whole genome, core and orthologous genes, and comparative analysis of metabolic potential retrieved the strain in an independent lineage clustering along with the genera Halioglobus, Pseudohalioglobus and Seongchinamella. Further, various genome based delimitation parameters represented by mol % GC content, percentage of conserved proteins (POCP), and amino acid identity (AAI) along with chemotaxonomic markers (i.e. fatty acids and polar lipids) supported the inferences of genome based phylogeny and indicated that the strain SAOS 164 belongs to a novel genus. The genome was mapped to 4.8 Mb in size with 65.1 % DNA mol% G + C content. In-silico genomic investigation and phenotyping revealed diverse metabolite genes/pathways related to polymer hydrolysis, nitrogen fixation, light induced growth, carbohydrate, sulfur, phosphorus and amino acid metabolism, virulence factors, defense mechanism, and stress-responsive elements facilitating survival in the mangrove habitat. Based on polyphasic taxonomic approach including genome analyses, a novel genus Mangrovimicrobium sediminis gen. nov. sp. nov. (=SAOS 164T = MTCC 12907T = KCTC 52755T = JCM 32136T) is proposed. Additionally, the reclassification of Halioglobus pacificus (=DSM 27932T = KCTC 23430T = S1-72T) to Pseudhalioglobus pacificus comb. nov. is also proposed.
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Affiliation(s)
- Pravin Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Ashish Verma
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India; Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden; Umeå Marine Sciences Centre, Hörnefors, Sweden
| | - Pooja Yadav
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Joyasree Das
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Lalit Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India.
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Shiroudi A, Czub J, Altarawneh M. Chemical Investigation on the Mechanism and Kinetics of the Atmospheric Degradation Reaction of Trichlorofluoroethene by OH⋅ and Its Subsequent Fate in the Presence of O 2 /NOx. Chemphyschem 2024; 25:e202300665. [PMID: 37983906 DOI: 10.1002/cphc.202300665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 11/22/2023]
Abstract
The M06-2X/6-311++G(d,p) level of theory was used to examine the degradation of Trichlorofluoroethene (TCFE) initiated by OH⋅ radicals. Additionally, the coupled-cluster single-double with triple perturbative [CCSD(T)] method was employed to refine the single-point energies using the complete basis set extrapolation approach. The results indicated that OH-addition is the dominant pathway. OH⋅ adds to both the C1 and C2 carbons, resulting in the formation of the C(OH)Cl2 -⋅CClF and ⋅CCl2 -C(OH)ClF species. The associated barrier heights were determined to be 1.11 and -0.99 kcal mol-1 , respectively. Furthermore, the energetic and thermodynamic parameters show that pathway 1 exhibits greater exothermicity and exergonicity compared to pathway 2, with differences of 8.11 and 8.21 kcal mol-1 , correspondingly. The primary pathway involves OH addition to the C2 position, with a rate constant of 6.2×10-13 cm3 molecule-1 sec-1 at 298 K. This analysis served to estimate the atmospheric lifetime, along with the photochemical ozone creation potential (POCP) and ozone depletion potential (ODP). It yielded an atmospheric lifetime of 8.49 days, an ODP of 4.8×10-4 , and a POCP value of 2.99, respectively. Radiative forcing efficiencies were also estimated at the M06-2X/6-311++G(d,p) level. Global warming potentials (GWPs) were calculated for 20, 100, and 500 years, resulting in values of 9.61, 2.61, and 0.74, respectively. TCFE is not expected to make a significant contribution to the radiative forcing of climate change. The results obtained from the time-dependent density functional theory (TDDFT) indicated that TCFE and its energized adducts are unable to photolysis under sunlight in the UV and visible spectrum. Secondary reactions involve the [TCFE-OH-O2 ]⋅ peroxy radical, leading subsequently to the [TCFE-OH-O]⋅ alkoxy radical. It was found that the alkoxy radical resulting from the peroxy radical can lead to the formation of phosgene (COCl2 ) and carbonyl chloride fluoride (CClFO), with phosgene being the primary product.
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Affiliation(s)
- Abolfazl Shiroudi
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk, 80-233, Poland
- BioTechMed Center, Gdańsk University of Technology, Gdańsk, 80-233, Poland
| | - Jacek Czub
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk, 80-233, Poland
- BioTechMed Center, Gdańsk University of Technology, Gdańsk, 80-233, Poland
| | - Mohammednoor Altarawneh
- United Arab Emirates University, Department of Chemical and Petroleum Engineering, Sheikh Khalifa bin Zayed Street, Al-Ain, 15551, United Arab Emirates
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Chen JW, Shih CJ, Wu LW, Wu YC, Chiang WF, Chen YL, Wu JH. Phocaeicola oris sp. nov., an anaerobic bacterium isolated from the saliva of a patient with oral squamous cell carcinoma. Int J Syst Evol Microbiol 2023; 73. [PMID: 36749694 DOI: 10.1099/ijsem.0.005703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
A Gram-stain-negative or -positive, strictly anaerobic, non-spore-forming and pleomorphic bacterium (designated 14-104T) was isolated from the saliva sample of a patient with oral squamous cell carcinoma. It was an acid-tolerant neutralophilic mesophile, growing at between 20 and 40 °C (with optimum growth at 30 °C) and pH between pH 3.0 and 7.0 (with optimum growth at pH 6.0-7.0). It contained anteiso-C15 : 0 and C15 : 0 as the major fatty acids. The genome size of strain 14-104T was 2.98 Mbp, and the G+C content was 39.6 mol%. It shared <87 % 16S rRNA sequence similarity, <71 % orthologous average nucleotide identity, <76 % average amino acid identity and <68 %% of conserved proteins with its closest relative, Phocaeicola abscessus CCUG 55929T. Reconstruction of phylogenetic and phylogenomic trees revealed that strain 14-104T and P. abscessus CCUG 55929T were clustered as a distinct clade without any other terminal node. The phylogenetic and phylogenomic analyses along with physiological and chemotaxonomic data indicated that strain 14-104T represents a novel species in the genus Phocaeicola, for which the name Phocaeicola oris sp. nov. is proposed. The type strain is 14-104T (=BCRC 81305T= NBRC 115041T).
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Affiliation(s)
- Jiung-Wen Chen
- Department of Environmental Engineering, National Cheng Kung University, Tainan, Taiwan, ROC.,Present address: Department of Biology, The University of Alabama at Birmingham, 1300 University Blvd, AL 35294, Birmingham, USA
| | - Chao-Jen Shih
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Li-Wha Wu
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC.,Department of Laboratory Science and Technology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, ROC
| | - Yen-Chi Wu
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Wei-Fan Chiang
- Department of Oral & Maxillofacial Surgery, Chi-Mei Medical Center, Liouying, Taiwan, ROC
| | - Yuh-Ling Chen
- Institute of Oral Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Jer-Horng Wu
- Department of Environmental Engineering, National Cheng Kung University, Tainan, Taiwan, ROC
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Gtari M. Taxogenomic status of phylogenetically distant Frankia clusters warrants their elevation to the rank of genus: A description of Protofrankia gen. nov., Parafrankia gen. nov., and Pseudofrankia gen. nov. as three novel genera within the family Frankiaceae. Front Microbiol 2022; 13:1041425. [PMID: 36425027 PMCID: PMC9680954 DOI: 10.3389/fmicb.2022.1041425] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
The genus Frankia is at present the sole genus in the family Frankiaceae and encompasses filamentous, sporangia-forming actinomycetes principally isolated from root nodules of taxonomically disparate dicotyledonous hosts named actinorhizal plants. Multiple independent phylogenetic analyses agree with the division of the genus Frankia into four well-supported clusters. Within these clusters, Frankia strains are well defined based on host infectivity range, mode of infection, morphology, and their behaviour in culture. In this study, phylogenomics, overall genome related indices (OGRI), together with available data sets for phenotypic and host-plant ranges available for the type strains of Frankia species, were considered. The robustness and the deep radiation observed in Frankia at the subgeneric level, fulfilling the primary principle of phylogenetic systematics, were strengthened by establishing genome criteria for new genus demarcation boundaries. Therefore, the taxonomic elevation of the Frankia clusters to the rank of the genus is proposed. The genus Frankia should be revised to encompass cluster 1 species only and three novel genera, Protofrankia gen. nov., Parafrankia gen. nov., and Pseudofrankia gen. nov., are proposed to accommodate clusters 2, 3, and 4 species, respectively. New combinations for validly named species are also provided.
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Affiliation(s)
- Maher Gtari
- USCR Bactériologie Moléculaire & Génomique, Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Tunis, Tunisia
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Ullmann L, Wibberg D, Busche T, Rückert C, Müsgens A, Kalinowski J, Blank LM. Seventeen Ustilaginaceae High-Quality Genome Sequences Allow Phylogenomic Analysis and Provide Insights into Secondary Metabolite Synthesis. J Fungi (Basel) 2022; 8. [PMID: 35330271 DOI: 10.3390/jof8030269] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 02/04/2023] Open
Abstract
The family of Ustilaginaceae belongs to the order of Basidiomycetes. Despite their plant pathogenicity causing, e.g., corn smut disease, they are also known as natural producers of value-added chemicals such as extracellular glycolipids, organic acids, and polyols. Here, we present 17 high-quality draft genome sequences (N50 > 1 Mb) combining third-generation nanopore and second-generation Illumina sequencing. The data were analyzed with taxonomical genome-based bioinformatics methods such as Percentage of Conserved Proteins (POCP), Average Nucleotide Identity (ANI), and Average Amino Acid Identity (AAI) analyses indicating that a reclassification of the Ustilaginaceae family might be required. Further, conserved core genes were determined to calculate a phylogenomic core genome tree of the Ustilaginaceae that also supported the results of the other phylogenomic analysis. In addition, to genomic comparisons, secondary metabolite clusters (e.g., itaconic acid, mannosylerythritol lipids, and ustilagic acid) of biotechnological interest were analyzed, whereas the sheer number of clusters did not differ much between species.
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Holtomo O, Ngue'zeo H, Nsangou M, Motapon O. Theoretical investigation of the atmospheric implication for the reaction of •OH radical with CF 2C(CH 3)-CX 3, X = H, F. J Mol Graph Model 2021; 106:107905. [PMID: 33984816 DOI: 10.1016/j.jmgm.2021.107905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/05/2021] [Accepted: 03/16/2021] [Indexed: 11/23/2022]
Abstract
The atmospheric implication of the hydrofluoroolefines (HFO) CF2C(CH3)-CX3, X=(H,F), through the reactions with •OH radical were assessed using the M06-2X/6-311++G(df,p)//6-31+G(df,p) method. The rate coefficient was calculated over the temperature range 200-500 K, and was accurately expressed in non-Arrhenius form exp(a+bT-1+cT-2) cm3molecule-1s-1, where a, b, and c are real constants. This served to estimate the atmospheric lifetime along with the photochemical ozone creation potential (POCP), which yielded lifetimes of 0.39 and 3.53 days and POCPs of 51.00 and 3.57 for X = H and F, respectively. The radiative forcing efficiencies (RFEs) were also estimated at G96LYP/6-311G(df,p) along with the global warming potentials (GWPs). The results showed negligible impact towards global warming for the HFOs.
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Quereda JJ, Leclercq A, Moura A, Vales G, Gómez-Martín Á, García-Muñoz Á, Thouvenot P, Tessaud-Rita N, Bracq-Dieye H, Lecuit M. Listeria valentina sp. nov., isolated from a water trough and the faeces of healthy sheep. Int J Syst Evol Microbiol 2020; 70:5868-5879. [PMID: 33016862 DOI: 10.1099/ijsem.0.004494] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In the context of a study on the occurrence of Listeria species in an animal farm environment in Valencia, Spain, six Listeria-like isolates could not be assigned to any known species. Phylogenetic analysis based on the 16S rRNA gene and on 231 Listeria core genes grouped these isolates in a monophyletic clade within the genus Listeria, with highest similarity to Listeria thailandensis. Whole-genome sequence analyses based on in silico DNA-DNA hybridization, the average nucleotide blast and the pairwise amino acid identities against all currently known Listeria species confirmed that these isolates constituted a new taxon within the genus Listeria. Phenotypically, these isolates differed from other Listeria species mainly by the production of acid from inositol, the absence of acidification in presence of methyl α-d-glucoside, and the absence of α-mannosidase and nitrate reductase activities. The name Listeria valentina sp. nov. is proposed for this novel species, and the type strain is CLIP 2019/00642T (=CIP 111799T=DSM 110544T).
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Affiliation(s)
- Juan J Quereda
- Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Alexandre Leclercq
- Institut Pasteur, Biology of Infection Unit, Paris, France.,Institut Pasteur, National Reference Centre, WHO Collaborating Centre for Listeria, Paris, France
| | - Alexandra Moura
- Institut Pasteur, Biology of Infection Unit, Paris, France.,Institut Pasteur, National Reference Centre, WHO Collaborating Centre for Listeria, Paris, France.,Inserm U1117, Paris, France
| | - Guillaume Vales
- Institut Pasteur, Biology of Infection Unit, Paris, France.,Institut Pasteur, National Reference Centre, WHO Collaborating Centre for Listeria, Paris, France
| | - Ángel Gómez-Martín
- Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Ángel García-Muñoz
- Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Pierre Thouvenot
- Institut Pasteur, Biology of Infection Unit, Paris, France.,Institut Pasteur, National Reference Centre, WHO Collaborating Centre for Listeria, Paris, France
| | - Nathalie Tessaud-Rita
- Institut Pasteur, Biology of Infection Unit, Paris, France.,Institut Pasteur, National Reference Centre, WHO Collaborating Centre for Listeria, Paris, France
| | - Hélène Bracq-Dieye
- Institut Pasteur, Biology of Infection Unit, Paris, France.,Institut Pasteur, National Reference Centre, WHO Collaborating Centre for Listeria, Paris, France
| | - Marc Lecuit
- Institut Pasteur, National Reference Centre, WHO Collaborating Centre for Listeria, Paris, France.,Institut Pasteur, Biology of Infection Unit, Paris, France.,Inserm U1117, Paris, France.,Université de Paris, Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, Institut Imagine, APHP, Paris, France
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Kim MJ, Seo YK, Kim JH, Baek SO. Impact of industrial activities on atmospheric volatile organic compounds in Sihwa-Banwol, the largest industrial area in South Korea. Environ Sci Pollut Res Int 2020; 27:28912-28930. [PMID: 32418108 DOI: 10.1007/s11356-020-09217-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
The impact of industrial activities on atmospheric volatile organic compounds (VOCs) in the Sihwa-Banwol complexes, i.e., the largest industrial area in Korea, was investigated. More than 60 VOCs were determined from 850 samples collected from four sites in and around the complexes through a 2-year monitoring campaign from 2005 to 2007. The VOCs of particular concern found in the area were benzene, toluene, ethylbenzene, xylenes, trichloroethylene, and formaldehyde, given their toxicity, concentration, and detection frequency. Toluene was the most abundant one. The VOC concentration rankings were consistent with their emission rankings. Most VOCs had higher concentrations at the industrial sites than at residential sites, indicating a significant impact of industrial emissions. The ambient levels of benzene and formaldehyde were additionally affected by vehicular emissions and secondary formation, respectively. Overall, the VOC levels increased in winter and at night, because of the local weather conditions. In contrast, the formaldehyde concentration increased in summer, owing to its secondary formation in the atmosphere. The ambient VOC levels in Sihwa-Banwol were higher than those in other parts of Korea. Additionally, the cumulative cancer risks posed by the toxic VOCs exceeded a tolerable risk level of 1 × 10-4 in not only the industrial areas but also the residential areas. The sum of the non-cancer risks in both areas significantly exceeded the threshold criterion of 1. The large amounts of aromatic compounds emitted from the industrial complexes are believed to play a crucial role in the elevated levels of surface ozone in the Seoul metropolitan area during the summer season. Therefore, comprehensive measures for controlling the VOC emissions in the Sihwa-Banwol area need to be prioritized to reduce the health risks for residents of not only this area but also the capital Seoul and its surrounding areas.
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Affiliation(s)
- Min-Ji Kim
- Department of Environmental Engineering, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Young-Kyo Seo
- National Institute of Environmental Research, Incheon, 22689, Republic of Korea
| | - Jong-Ho Kim
- Department of Infra System, Hanseo University, Seosan, 31962, Republic of Korea
| | - Sung-Ok Baek
- Department of Environmental Engineering, Yeungnam University, Gyeongsan, 38541, Republic of Korea.
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Abstract
A novel aerobic, Gram-stain-negative, non-motile and rod-shaped bacterium, designated strain U0301T, was isolated from a marine sediment sample in Weihai, China. This strain grew optimally at 33 °C, pH 7.5 and in the presence of 2.0-3.0 % (w/v) NaCl. Strain U0301T shared pairwise 16S rRNA gene sequence similarities of 95.5, 95.4, 95.2 and 95.0 % to Parahaliea aestuarii S2-26T, Halioglobus pacificus KCTC 23430T, Halioglobus lutimaris HF004T and Halioglobus japonicus KCTC 23429T, respectively. Phylogenetic analysis based on the 16S rRNA gene sequences demonstrated that U0301T formed a tight phylogenetic lineage with type strains of H. pacificus and H. japonicus. The percentage of conserved protein values of strain U0301T as compared with H. japonicus KCTC 23429Tand Parahalieamediterranea 7SM29T were 62.5 and 58.0 %, respectively. The ANI values of strain U0301T with H. japonicus KCTC 23429T and P. mediterranea 7SM29T were 78.2 and 75.3 %, respectively. Both metrics of genome comparison suggested that strain U0301T showed higher homology with the genus Halioglobus than the genus Parahaliea. The strain contained ubiquinone 8 as the sole respiratory quinone. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C17 : 1ω8c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 61.7 mol%. Considering the phenotypic characteristics, chemotaxonomic data and phylogenetic analysis comprehensively, strain U0301T should represent a novel species of the genus Halioglobus, for which the name of Halioglobus sediminis sp. nov. is proposed. The type strain is U0301T (=KCTC 62082T=MCCC 1H00234T).
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Affiliation(s)
- Ji-Ru Han
- 1College of Marine Science, Shandong University, Weihai 264209, PR China.,2The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Meng-Qi Ye
- 1College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Chong Wang
- 1College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Zong-Jun Du
- 1College of Marine Science, Shandong University, Weihai 264209, PR China
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Abstract
A novel strain, U0105T, was isolated from marine sediment of the coast of Weihai, China. The bacterium was aerobic, Gram-stain-negative, oxidase-positive, catalase-positive, rod-shaped and motile. Growth was observed at salinities of 1.0-6.0 % (w/v) NaCl (optimum with 2.0-3.0 %), temperatures of 20-40 °C (optimum at 37 °C) and pH of 6.5-9.5 (optimum at pH 7.0-7.5). The isolate could not reduce nitrate to nitrite. It could hydrolyse starch and Tweens 20, 40 and 60, but not casein or cellulose. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain U0105T belonged to the genus Alteromonas, with highest sequence similarity to Alteromonas aestuariivivens KCTC 52655T (97.1 %). The average nucleotide identity value and the digital DNA-DNA hybridization value between strain U0105T and A. aestuariivivens KCTC 52655T were 69.2 % and 21.2 %, respectively. Strain U0105T was found to contain Q-8 as the sole menaquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as the major fatty acids. The major polar lipids were identified as phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the chromosomal DNA was 45.3 mol%. The combined genotypic and phenotypic data show that strain U0105T represents a novel species of the genus Alteromonas, for which the name Alteromonas sediminis sp. nov. is proposed. The type strain is U0105T (=KCTC 62080T=MCCC 1H00299T).
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Affiliation(s)
- Meng-Qi Ye
- 1College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Ji-Ru Han
- 1College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Chong Wang
- 1College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Zong-Jun Du
- 2State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.,1College of Marine Science, Shandong University, Weihai 264209, PR China
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Chan K, See‐Too W, Chua K, Peix Á, Goh KM, Hong K, Yin W, Lee L. Aquella oligotrophica gen. nov. sp. nov.: A new member of the family Neisseriaceae isolated from laboratory tap water. Microbiologyopen 2019; 8:e00793. [PMID: 30656855 PMCID: PMC6612550 DOI: 10.1002/mbo3.793] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/06/2018] [Accepted: 12/08/2018] [Indexed: 01/24/2023] Open
Abstract
A bacterial strain designated as P08T was isolated from laboratory tap water during a water quality assessment in University of Malaya, Malaysia. The strain was a Gram-negative, rod-shaped, nonmotile, and aerobic bacterium. Complete genome of P08T comprised of a 2,820,660 bp chromosome with a G + C content of 36.43%. Both 16S rRNA phylogeny and phylogenetic tree inferred from the core gene matrix demonstrated that P08T formed a hitherto unknown subline within the family Neisseriaceae. Ortho average nucleotide identity (OrthoANI) values and the percentage of conserved proteins (POCP) calculated from complete genome sequence indicated low relatedness between P08T and its phylogenetic neighbors. Respiratory quinone analysis revealed Q-8 as the only detectable quinone. The predominant cellular fatty acids were identified as C14:0 , iso-C15:0 , and summed feature 3 (C16:1 ω7c/C16:1 ω6c). The polar lipids consisted of uncharacterized aminolipid, phosphatidylglycerol, and phosphatidylethanolamine. All aspects of phenotypic and phylogenetic data suggested that strain P08T represents a novel genus within family Neisseriaceae, for which the name Aquella gen. nov. is proposed. The type species of the genus is Aquella oligotrophica sp. nov., and the type strain is P08T (=LMG 29629T =DSM 100970T ).
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Affiliation(s)
- Kok‐Gan Chan
- International Genome CentreJiangsu UniversityZhenjiangChina,Faculty of Science, Institute of Biological SciencesUniversity of MalayaKuala LumpurMalaysia
| | - Wah‐Seng See‐Too
- Faculty of Science, Institute of Biological SciencesUniversity of MalayaKuala LumpurMalaysia
| | - Kah‐Ooi Chua
- Faculty of Science, Institute of Biological SciencesUniversity of MalayaKuala LumpurMalaysia
| | - Álvaro Peix
- Instituto de Recursos Naturales y AgrobiologíaIRNASA‐CSICSalamancaSpain
| | - Kian Mau Goh
- Faculty of SciencesUniversiti Teknologi MalaysiaSkudaiMalaysia
| | - Kar‐Wai Hong
- Faculty of Science, Institute of Biological SciencesUniversity of MalayaKuala LumpurMalaysia
| | - Wai‐Fong Yin
- Faculty of Science, Institute of Biological SciencesUniversity of MalayaKuala LumpurMalaysia
| | - Li‐Sin Lee
- Faculty of Science, Institute of Biological SciencesUniversity of MalayaKuala LumpurMalaysia
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12
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Abstract
During a screening of Listeria species in food samples in Thailand, a Listeria-like bacterium was recovered from fried chicken and could not be assigned to any known species. Phylogenetic analysis based on the 16S rRNA gene and on 243 Listeria core genes placed the novel taxon within the Listeria aquatica, Listeria floridensis, Listeria fleishmannii and Listeria costaricensis clade (Listeria sensu lato), with highest similarity to L. floridensis (98.9 %) and L. costaricensis (98.8 %). Whole-genome sequence analyses based on the average nucleotide blast identity (ANI<86 %), the pairwise amino acid identity (AAI>64 %) and on the percentage of conserved proteins (POCP>77 %) with currently known Listeria species confirmed that the strain constituted a new taxon within the genus Listeria. At the phenotypical level, it differs from other Listeria species by the production of acid from d-tagatose and inositol. The name Listeria thailandensis sp. nov. is proposed for the novel species, and is represented by the type strain CLIP 2015/00305T (=CIP 111635T=DSM 107638T).
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Affiliation(s)
- Alexandre Leclercq
- 3Inserm U1117, Paris, France.,1Institut Pasteur, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France.,2Biology of Infection Unit, Institut Pasteur, Paris, France
| | - Alexandra Moura
- 1Institut Pasteur, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France.,3Inserm U1117, Paris, France.,2Biology of Infection Unit, Institut Pasteur, Paris, France
| | - Guillaume Vales
- 1Institut Pasteur, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France.,2Biology of Infection Unit, Institut Pasteur, Paris, France
| | - Nathalie Tessaud-Rita
- 1Institut Pasteur, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France.,2Biology of Infection Unit, Institut Pasteur, Paris, France
| | | | - Marc Lecuit
- 5Division of Infectious Diseases and Tropical Medicine, Paris Descartes University, Sorbonne Paris Cité, Institut Imagine, Necker-Enfants Malades University Hospital, APHP, Paris, France.,2Biology of Infection Unit, Institut Pasteur, Paris, France.,3Inserm U1117, Paris, France.,1Institut Pasteur, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France
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13
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Abstract
A bacterial strain isolated from a food processing drainage system in Costa Rica fulfilled the criteria as belonging to the genus Listeria, but could not be assigned to any of the known species. Phylogenetic analysis based on the 16S rRNA gene revealed highest sequence similarity with the type strain of Listeria floridensis (98.7 %). Phylogenetic analysis based on Listeria core genomes placed the novel taxon within the Listeria fleishmannii, L. floridensis and Listeria aquatica clade (Listeria sensu lato). Whole-genome sequence analyses based on the average nucleotide blast identity (ANI<80 %) indicated that this isolate belonged to a novel species. Results of pairwise amino acid identity (AAI>70 %) and percentage of conserved proteins (POCP>68 %) with currently known Listeria species, as well as of biochemical characterization, confirmed that the strain constituted a novel species within the genus Listeria. The name Listeria costaricensis sp. nov. is proposed for the novel species, and is represented by the type strain CLIP 2016/00682T (=CIP 111400T=DSM 105474T).
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Affiliation(s)
- Kattia Núñez-Montero
- Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
| | - Alexandre Leclercq
- Institut Pasteur, Biology of Infection Unit, Paris, France.,Inserm U1117, Paris, France.,Institut Pasteur, National Reference Center and WHO Collaborating Center for Listeria, Paris, France
| | - Alexandra Moura
- Institut Pasteur, National Reference Center and WHO Collaborating Center for Listeria, Paris, France.,Institut Pasteur, Biology of Infection Unit, Paris, France.,Inserm U1117, Paris, France
| | - Guillaume Vales
- Institut Pasteur, National Reference Center and WHO Collaborating Center for Listeria, Paris, France.,Institut Pasteur, Biology of Infection Unit, Paris, France.,Inserm U1117, Paris, France
| | - Johnny Peraza
- Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
| | - Javier Pizarro-Cerdá
- INRA USC2020, Paris, France.,Present address: Institut Pasteur, Yersinia Research Unit, Paris, France.,Inserm U604, Paris, France.,Institut Pasteur, Bacteria-Cell Interactions Unit, Paris, France
| | - Marc Lecuit
- Paris Descartes University, Sorbonne Paris Cité, Division of Infectious Diseases and Tropical Medicine, Institut Imagine, Necker-Enfants Malades University Hospital, APHP, Paris, France.,Inserm U1117, Paris, France.,Institut Pasteur, National Reference Center and WHO Collaborating Center for Listeria, Paris, France.,Institut Pasteur, Biology of Infection Unit, Paris, France
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