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Morando-Grijalva CA, Ramos-Díaz A, Cabrera-Ramirez AH, Cuevas-Bernardino JC, Pech-Cohuo SC, Kú-González AF, Cano-Sosa J, Herrera-Pool IE, Valdivia-Rivera S, Ayora-Talavera T, Pacheco N. Isolation, Identification and Screening of Plastic-Degrading Microorganisms: Qualitative and Structural Effects on Poly(Butylene Succinate) (PBS) Films. Polymers (Basel) 2025; 17:1128. [PMID: 40284393 PMCID: PMC12031546 DOI: 10.3390/polym17081128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2025] [Revised: 03/25/2025] [Accepted: 04/12/2025] [Indexed: 04/29/2025] Open
Abstract
(1) Background: Plastic contamination is on the rise, despite ongoing research focused on alternatives such as bioplastics. However, most bioplastics require specific conditions to biodegrade. A promising alternative involves using microorganisms isolated from landfill soils that have demonstrated the ability to degrade plastic materials. (2) Methods: Soil samples were collected, and bacteria were isolated, characterized, and molecularly identified. Their degradative capacity was evaluated using the zone of clearing method, while their qualitative and structural degradative activity was assessed in a liquid medium on poly(butylene succinate) (PBS) films prepared by the cast method. (3) Results: Three strains-Bacillus cereus CHU4R, Acinetobacter baumannii YUCAN, and Pseudomonas otitidis YUC44-were selected. These strains exhibited the ability to cause severe damage to the microscopic surface of the films, attack the ester bonds within the PBS structure, and degrade lower-weight PBS molecules during the process. (4) Conclusions: this study represents the first report of strains isolated in Yucatán with plastic degradation activity. The microorganisms demonstrated the capacity to degrade PBS films by causing surface and structural damage at the molecular level. These findings suggest that the strains could be applied as an alternative in plastic biodegradation.
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Affiliation(s)
- Cristina América Morando-Grijalva
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Parque Científico Tecnológico de Yucatán, Km 5.5 Carretera, Sierra Papacal-Chuburna, Chuburna, Merida 97302, Yucatan, Mexico; (C.A.M.-G.); (A.R.-D.); (A.H.C.-R.); (J.C.-S.); (I.E.H.-P.); (T.A.-T.)
| | - Ana Ramos-Díaz
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Parque Científico Tecnológico de Yucatán, Km 5.5 Carretera, Sierra Papacal-Chuburna, Chuburna, Merida 97302, Yucatan, Mexico; (C.A.M.-G.); (A.R.-D.); (A.H.C.-R.); (J.C.-S.); (I.E.H.-P.); (T.A.-T.)
| | - Angel H. Cabrera-Ramirez
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Parque Científico Tecnológico de Yucatán, Km 5.5 Carretera, Sierra Papacal-Chuburna, Chuburna, Merida 97302, Yucatan, Mexico; (C.A.M.-G.); (A.R.-D.); (A.H.C.-R.); (J.C.-S.); (I.E.H.-P.); (T.A.-T.)
| | - Juan Carlos Cuevas-Bernardino
- SECIHTI-Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Parque Científico Tecnológico de Yucatán, Km 5.5 Carretera, Sierra Papacal-Chuburna, Chuburna, Merida 97302, Yucatan, Mexico; (J.C.C.-B.); (S.V.-R.)
| | - Soledad Cecilia Pech-Cohuo
- Departamento de Ingeniería en Robótica Computacional, Universidad Politécnica de Yucatán, Tablaje Catastral 7193, Carretera, Merida-Tetiz Km 4.5, Merida 97357, Yucatan, Mexico;
| | | | - Julia Cano-Sosa
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Parque Científico Tecnológico de Yucatán, Km 5.5 Carretera, Sierra Papacal-Chuburna, Chuburna, Merida 97302, Yucatan, Mexico; (C.A.M.-G.); (A.R.-D.); (A.H.C.-R.); (J.C.-S.); (I.E.H.-P.); (T.A.-T.)
| | - Iván Emanuel Herrera-Pool
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Parque Científico Tecnológico de Yucatán, Km 5.5 Carretera, Sierra Papacal-Chuburna, Chuburna, Merida 97302, Yucatan, Mexico; (C.A.M.-G.); (A.R.-D.); (A.H.C.-R.); (J.C.-S.); (I.E.H.-P.); (T.A.-T.)
| | - Sergio Valdivia-Rivera
- SECIHTI-Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Parque Científico Tecnológico de Yucatán, Km 5.5 Carretera, Sierra Papacal-Chuburna, Chuburna, Merida 97302, Yucatan, Mexico; (J.C.C.-B.); (S.V.-R.)
| | - Teresa Ayora-Talavera
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Parque Científico Tecnológico de Yucatán, Km 5.5 Carretera, Sierra Papacal-Chuburna, Chuburna, Merida 97302, Yucatan, Mexico; (C.A.M.-G.); (A.R.-D.); (A.H.C.-R.); (J.C.-S.); (I.E.H.-P.); (T.A.-T.)
| | - Neith Pacheco
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Parque Científico Tecnológico de Yucatán, Km 5.5 Carretera, Sierra Papacal-Chuburna, Chuburna, Merida 97302, Yucatan, Mexico; (C.A.M.-G.); (A.R.-D.); (A.H.C.-R.); (J.C.-S.); (I.E.H.-P.); (T.A.-T.)
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Selami N, Zitouni-Haouar FEH, Zerouki C, Aibeche C, Draou N, Khelil O, Choubane S, Maatallah M, Madani I, Ouenzar K, Zemmour A, Kerkoud M, Mnasri B, Moumen B, Vriet C, Djabeur A. Pseudomonas retamae sp. nov., a novel endophytic bacterium with plant growth-promoting potential, isolated from root nodules of Retama monosperma in Northwestern Algeria. Int J Syst Evol Microbiol 2025; 75. [PMID: 39812647 DOI: 10.1099/ijsem.0.006646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2025] Open
Abstract
A thorough polyphasic taxonomic study, integrating genome-based taxonomic approaches, was carried out to characterize the RB5T strain isolated from root nodules of Retama monosperma growing on the coastal dunes of Bousfer Beach (Oran, Algeria). The 16S rRNA gene sequence analysis revealed that strain RB5T had the highest similarity to Pseudomonas granadensis LMG27940T (98.94%) and Pseudomonas gozinkensis IzPS32dT (98.73%). Phylogenetic studies, including both 16S rRNA gene sequence and multilocus sequence analysis using 16S rRNA, gyrB and rpoD housekeeping genes, positioned RB5T in a distinct branch alongside its closest relative, P. granadensis LMG27940T. Phylogenomic analysis using the Bac120 marker set and Type (Strain) Genome Server confirmed the unique position of RB5T and its close relationship with P. granadensis LMG27940T. Similarly, genomic comparisons using average nucleotide identity based on blast (ANIb) and digital DNA-DNA hybridization (dDDH) revealed values of 92.85 and 59.3%, respectively, when compared with its closest relative, P. granadensis LMG27940T. Both values fall below the established species delimitation thresholds of 95-96% for ANIb and 70% for dDDH, providing strong genomic evidence that strain RB5T represents a novel species. Further average nucleotide identity comparisons with unclassified Pseudomonas spp. (384 genomes) and metagenomic-derived genomes from the Genome Taxonomy Database (GTDB) showed values between 84.27 and 89.2%, indicating that strain RB5T belongs to a unique evolutionary line. The genome of RB5T, with a size of 6 311 310 bp and a G+C content of 60%, harbours several key genes associated with plant growth-promoting traits, making it a promising candidate for sustainable agriculture. Phenotypically, RB5T strain is an aerobic, rod-shaped, Gram-negative, non-spore-forming bacterium that is motile with a single polar flagellum. It grows under a wide range of temperature (4-42 °C) and pH (5-10) conditions and tolerates up to 6% (w/v) NaCl. The main cellular fatty acid composition of RB5T includes C16:0, C17:0 cyclo and the summed features 3 consisting of C16:1 ω7c/C16:1 ω6c. Based on the phylogenetic, phenotypic, chemotaxonomic and genome comparison analyses, strain RB5T was identified as a novel species of the genus Pseudomonas, for which the name Pseudomonas retamae sp. nov. is proposed. The type strain is RB5T (=DSM 117471T=LMG 33633T=CIP 112482T).
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Affiliation(s)
- Nawel Selami
- Dpartement de Biotechnologie, Laboratoire des Productions, Valorisations Vgtales et Microbiennes (LP2VM), Facult des Sciences de la Nature et de la Vie, B.P. 1505, El-Mnaour, Universit des Sciences et de la Technologie dOran Mohamed Boudiaf USTO-MB, Oran 31000, Algeria
| | - Fatima El-Houaria Zitouni-Haouar
- Laboratory of Biology of Microorganisms and Biotechnology, Department of Biotechnology, Faculty of Natural and Life Sciences, Oran 1 Ahmed Ben Bella University, Oran 31000, Algeria
| | - Chahira Zerouki
- School of Forest Sciences, University of Eastern Finland, Yliopistokatu 7, 80101, Joensuu, Finland
| | - Chahrazed Aibeche
- Dpartement de Biotechnologie, Laboratoire des Productions, Valorisations Vgtales et Microbiennes (LP2VM), Facult des Sciences de la Nature et de la Vie, B.P. 1505, El-Mnaour, Universit des Sciences et de la Technologie dOran Mohamed Boudiaf USTO-MB, Oran 31000, Algeria
| | - Nassima Draou
- Dpartement de Biotechnologie, Laboratoire des Productions, Valorisations Vgtales et Microbiennes (LP2VM), Facult des Sciences de la Nature et de la Vie, B.P. 1505, El-Mnaour, Universit des Sciences et de la Technologie dOran Mohamed Boudiaf USTO-MB, Oran 31000, Algeria
| | - Omar Khelil
- Laboratoire dAquaculture et de Bioremdiation (AQUABIOR), Universit d'Oran 1 Ahmed Ben Bella, B.P 1524, El M'Naouer, 31000, Oran, Algeria
- Ecole Suprieure en Sciences Biologiques d'Oran (ESSBO), BP 1042 Saim Mohamed, Cit Emir Abdelkader (EX-INESSMO) 31000, Oran, Algeria
| | - Slimane Choubane
- Laboratoire dAquaculture et de Bioremdiation (AQUABIOR), Universit d'Oran 1 Ahmed Ben Bella, B.P 1524, El M'Naouer, 31000, Oran, Algeria
- Ecole Suprieure en Sciences Biologiques d'Oran (ESSBO), BP 1042 Saim Mohamed, Cit Emir Abdelkader (EX-INESSMO) 31000, Oran, Algeria
| | - Makaoui Maatallah
- Facult de pharmacie de Monastir, Laboratoire dAnalyse, Traitement et Valorisation des Polluants de lEnvironnement et des Produits (LATVPEP : LR 01 ES 16), Universit de Monastir, Monastir, Tunisia
| | - Ikram Madani
- Dpartement de Biotechnologie, Laboratoire des Productions, Valorisations Vgtales et Microbiennes (LP2VM), Facult des Sciences de la Nature et de la Vie, B.P. 1505, El-Mnaour, Universit des Sciences et de la Technologie dOran Mohamed Boudiaf USTO-MB, Oran 31000, Algeria
| | - Khadidja Ouenzar
- Dpartement de Biotechnologie, Laboratoire des Productions, Valorisations Vgtales et Microbiennes (LP2VM), Facult des Sciences de la Nature et de la Vie, B.P. 1505, El-Mnaour, Universit des Sciences et de la Technologie dOran Mohamed Boudiaf USTO-MB, Oran 31000, Algeria
| | - Assia Zemmour
- Dpartement de Biotechnologie, Laboratoire des Productions, Valorisations Vgtales et Microbiennes (LP2VM), Facult des Sciences de la Nature et de la Vie, B.P. 1505, El-Mnaour, Universit des Sciences et de la Technologie dOran Mohamed Boudiaf USTO-MB, Oran 31000, Algeria
| | | | - Bacem Mnasri
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cdria, BP 901, Hammam-lif 2050, Tunisia
| | - Bouziane Moumen
- Laboratoire Ecologie et Biologie des Interactions (EBI), UMR CNRS 7267, Universit de Poitiers, Poitiers, France
| | - Cécile Vriet
- Laboratoire Ecologie et Biologie des Interactions (EBI), UMR CNRS 7267, Universit de Poitiers, Poitiers, France
| | - Abderrezak Djabeur
- Dpartement de Biotechnologie, Laboratoire des Productions, Valorisations Vgtales et Microbiennes (LP2VM), Facult des Sciences de la Nature et de la Vie, B.P. 1505, El-Mnaour, Universit des Sciences et de la Technologie dOran Mohamed Boudiaf USTO-MB, Oran 31000, Algeria
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Yoon Y, Aziz AA, Chang IS, Kim B. Prevalence of Escherichia coli in electrogenic biofilm on activated carbon in microbial fuel cell. Appl Microbiol Biotechnol 2024; 108:52. [PMID: 38183478 DOI: 10.1007/s00253-023-12829-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 10/11/2023] [Accepted: 11/04/2023] [Indexed: 01/08/2024]
Abstract
For a better understanding of the distribution of depth-dependent electrochemically active bacteria at in the anode zone, a customized system in a microbial fuel cell (MFC) packed with granular activated carbon (GAC) was developed and subsequently optimized via electrochemical tests. The constructed MFC system was sequentially operated using two types of matrice solutions: artificially controlled compositions (i.e., artificial wastewater, AW) and solutions obtained directly from actual sewage-treating municipal plants (i.e., municipal wastewater, MW). Notably, significant difference(s) of system efficiencies between AW or MW matrices were observed via performance tests, in that the electricity production capacity under MW matrices is < 25% that of the AW matrices. Interestingly, species of Escherichia coli (E. coli) sampled from the GAC bed (P1: deeper region in GAC bed, P2: shallow region of GAC near electrolytes) exhibited an average relative abundance of 75 to 90% in AW and a relative abundance of approximately 10% in MW, while a lower relative abundance of E. coli was found in both the AW and MW anolyte samples (L). Moreover, similar bacterial communities were identified in samples P1 and P2 for both the AW and MW solutions, indicating a comparable distribution of bacterial communities over the anode area. These results provide new insights into E. coli contribution in power production for the GAC-packed MFC systems (i.e., despite the low contents of Geobacter (> 8%) and Shewanella (> 1%)) for future applications in sustainable energy research. KEY POINTS: • A microbial community analysis for depth-dependence in biofilm was developed. • The system was operated with two matrices; electrochemical performance was assessed. • E. coli spp. was distinctly found in anode zone layers composed of activated carbon.
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Affiliation(s)
- Younggun Yoon
- SELS Center, Division of Biotechnology, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan, Jeonbuk, 54596, South Korea
| | - Azilah Abd Aziz
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-Ro, Buk-Gu, Gwangju, 61005, South Korea
| | - In Seop Chang
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-Ro, Buk-Gu, Gwangju, 61005, South Korea.
| | - Bongkyu Kim
- SELS Center, Division of Biotechnology, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan, Jeonbuk, 54596, South Korea.
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Rudra B, Gupta RS. Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera. Front Microbiol 2024; 14:1273665. [PMID: 38249459 PMCID: PMC10797017 DOI: 10.3389/fmicb.2023.1273665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/17/2023] [Indexed: 01/23/2024] Open
Abstract
Genus Pseudomonas is a large assemblage of diverse microorganisms, not sharing a common evolutionary history. To clarify their evolutionary relationships and classification, we have conducted comprehensive phylogenomic and comparative analyses on 388 Pseudomonadaceae genomes. In phylogenomic trees, Pseudomonas species formed 12 main clusters, apart from the "Aeruginosa clade" containing its type species, P. aeruginosa. In parallel, our detailed analyses on protein sequences from Pseudomonadaceae genomes have identified 98 novel conserved signature indels (CSIs), which are uniquely shared by the species from different observed clades/groups. Six CSIs, which are exclusively shared by species from the "Aeruginosa clade," provide reliable demarcation of this clade corresponding to the genus Pseudomonas sensu stricto in molecular terms. The remaining 92 identified CSIs are specific for nine other Pseudomonas species clades and the genera Azomonas and Azotobacter which branch in between them. The identified CSIs provide strong independent evidence of the genetic cohesiveness of these species clades and offer reliable means for their demarcation/circumscription. Based on the robust phylogenetic and molecular evidence presented here supporting the distinctness of the observed Pseudomonas species clades, we are proposing the transfer of species from the following clades into the indicated novel genera: Alcaligenes clade - Aquipseudomonas gen. nov.; Fluvialis clade - Caenipseudomonas gen. nov.; Linyingensis clade - Geopseudomonas gen. nov.; Oleovorans clade - Ectopseudomonas gen. nov.; Resinovorans clade - Metapseudomonas gen. nov.; Straminea clade - Phytopseudomonas gen. nov.; and Thermotolerans clade - Zestomonas gen. nov. In addition, descriptions of the genera Azomonas, Azotobacter, Chryseomonas, Serpens, and Stutzerimonas are emended to include information for the CSIs specific for them. The results presented here should aid in the development of a more reliable classification scheme for Pseudomonas species.
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Affiliation(s)
| | - Radhey S. Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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Kim HS, Suh MK, Kim JS, Do HE, Eom MK, Jin JS, Lee JS. Pseudomonas aestuarii sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 38047902 DOI: 10.1099/ijsem.0.006190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
Two novel Pseudomonas strains, SA3-5T and SA3-6, were isolated from a tidal flat (getbol) in the Republic of Korea. Strains SA3-5T and SA3-6 were subjected to polyphasic characterization to determine their taxonomic affiliations. Cells were Gram-stain-negative, aerobic, rod-shaped and motile by using peritrichous flagella. Based on their 16S rRNA gene sequences, strains SA3-5T and SA3-6 exhibited a high degree of similarity (100 %) and were classified within the genus Pseudomonas. Furthermore, the closest related species to SA3-5T and SA3-6 were Pseudomonas taeanensis MS-3T (98.3 %). The ranges of average nucleotide identity and digital DNA-DNA hybridization values between SA3-5T and closely related species were 75.9-89.1% and 21.3-38.7%, respectively, both of which being below the thresholds for delineating novel strains. Strain SA3-5T and SA3-6 contained C16 : 1 ω6с and/or C16 : 1 ω7с (summed feature 3), C16 : 0 and C18 : 1 ω6с and/or C18 : 1 ω7с (summed feature 8) as the major fatty acids. The predominant respiratory quinone was Q-9. The DNA G+C content of strain SA3-5T was 62.5 mol%. Based on their combined phenotypic, chemotaxonomic and phylogenetic characterisitics, strains SA3-5T and SA3-6 represent a novel species of the genus Pseudomonas for which the name Pseudomonas aestuarii sp. nov. is proposed. The type strain is SA3-5T (=KCTC 92395T=JCM 35697T).
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Affiliation(s)
- Han Sol Kim
- Korean Collection for Type CulturesKorea Research Institute of Bioscience and Biotechnology(KRIBB), Jeongeup-si, 181 Ipsin-gil, Jeollabuk-do 56212, Republic of Korea
- Department of Lifestyle Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do 54596, Republic of Korea
| | - Min Kuk Suh
- Korean Collection for Type CulturesKorea Research Institute of Bioscience and Biotechnology(KRIBB), Jeongeup-si, 181 Ipsin-gil, Jeollabuk-do 56212, Republic of Korea
- Department of Lifestyle Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do 54596, Republic of Korea
| | - Ji-Sun Kim
- Korean Collection for Type CulturesKorea Research Institute of Bioscience and Biotechnology(KRIBB), Jeongeup-si, 181 Ipsin-gil, Jeollabuk-do 56212, Republic of Korea
| | - Hyo Eun Do
- Korean Collection for Type CulturesKorea Research Institute of Bioscience and Biotechnology(KRIBB), Jeongeup-si, 181 Ipsin-gil, Jeollabuk-do 56212, Republic of Korea
- Department of Oriental Medicine Resources, Jeonbuk National University, 79 Gobong-ro, Iksan-si54596,Jeollabuk-do, Republic of Korea
| | - Mi Kyung Eom
- Korean Collection for Type CulturesKorea Research Institute of Bioscience and Biotechnology(KRIBB), Jeongeup-si, 181 Ipsin-gil, Jeollabuk-do 56212, Republic of Korea
| | - Jong-Sik Jin
- Department of Oriental Medicine Resources, Jeonbuk National University, 79 Gobong-ro, Iksan-si54596,Jeollabuk-do, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type CulturesKorea Research Institute of Bioscience and Biotechnology(KRIBB), Jeongeup-si, 181 Ipsin-gil, Jeollabuk-do 56212, Republic of Korea
- University of Science and Technology(UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
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Pseudomonas oryzagri sp. nov., isolated from a rice field soil. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A Gram-stain-negative, aerobic, rod-shaped and non-motile novel bacterial strain, designated MAHUQ-58T, was isolated from soil sample of a rice field. The colonies were observed to be light pink-coloured, smooth, spherical and 0.6–1.0 mm in diameter when grown on nutrient agar (NA) medium for 2 days. Strain MAHUQ-58T was found to be able to grow at 15–40 °C, at pH 5.5–10.0 and with 0–1.0 % NaCl (w/v). Cell growth occurred on tryptone soya agar, Luria–Bertani agar, NA, MacConkey agar and Reasoner's 2A agar. The strain was found to be positive for both oxidase and catalase tests. The strain was positive for hydrolysis of Tween 20 and l-tyrosine. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus
Pseudomonas
and to be closely related to
Pseudomonas oryzae
WM-3T (98.9 % similarity),
Pseudomonas linyingensis
LYBRD3-7T (97.7 %),
Pseudomonas sagittaria
JCM 18195 T (97.6 %) and
Pseudomonas guangdongensis
SgZ-6T (97.2 %). The novel strain MAHUQ-58T has a draft genome size of 4 536 129 bp (46 contigs), annotated with 4064 protein-coding genes, 60 tRNA genes and four rRNA genes. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain MAHUQ-58T and four closely related type strains were in the range of 85.5–89.5 % and 29.5–38.0 %, respectively. The genomic DNA G+C content was determined to be 67.0 mol%. The predominant isoprenoid quinone was ubiquinone 9. The major fatty acids were identified as C16:0, summed feature 3 (C16 : 1
ω6c and/or C16 : 1
ω7c) and summed feature 8 (C18 : 1
ω6c and/or C18 : 1
ω7c). On the basis of dDDH and ANI values, genotypic results, and chemotaxonomic and physiological data, strain MAHUQ-58T represents a novel species within the genus
Pseudomonas
, for which the name Pseudomonas oryzagri sp. nov. is proposed, with MAHUQ-58T (=KACC 22005T=CGMCC 1.18518T) as the type strain.
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Yoshimi T, Fujii S, Oki H, Igawa T, Adams HR, Ueda K, Kawahara K, Ohkubo T, Hough MA, Sambongi Y. Crystal structure of thermally stable homodimeric cytochrome c'-β from Thermus thermophilus. Acta Crystallogr F Struct Biol Commun 2022; 78:217-225. [PMID: 35647678 PMCID: PMC9158659 DOI: 10.1107/s2053230x22005088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/11/2022] [Indexed: 11/10/2022] Open
Abstract
Cytochrome c'-β is a heme protein that belongs to the cytochrome P460 family and consists of homodimeric subunits with a predominantly antiparallel β-sheet fold. Here, the crystal structure of cytochrome c'-β from the thermophilic Thermus thermophilus (TTCP-β) is reported at 1.74 Å resolution. TTCP-β has a typical antiparallel β-sheet fold similar to that of cytochrome c'-β from the moderately thermophilic Methylococcus capsulatus (MCCP-β). The phenylalanine cap structure around the distal side of the heme is also similar in TTCP-β and MCCP-β, indicating that both proteins similarly bind nitric oxide and carbon monoxide, as observed spectroscopically. Notably, TTCP-β exhibits a denaturation temperature of 117°C, which is higher than that of MCCP-β. Mutational analysis reveals that the increased homodimeric interface area of TTCP-β contributes to its high thermal stability. Furthermore, 14 proline residues, which are mostly located in the TTCP-β loop regions, possibly contribute to the rigid loop structure compared with MCCP-β, which has only six proline residues. These findings, together with those from phylogenetic analysis, suggest that the structures of Thermus cytochromes c'-β, including TTCP-β, are optimized for function under the high-temperature conditions in which the source organisms live.
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Affiliation(s)
- Taisuke Yoshimi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Sotaro Fujii
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Hiroya Oki
- Research Institute for Microbial Diseases, Osaka University, Yamadaoka, Suita, Osaka, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka, Suita, Osaka, Japan
| | - Takeshi Igawa
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Division of Bioresource Science, Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hannah R. Adams
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, United Kingdom
| | - Kengo Ueda
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka, Suita, Osaka, Japan
| | - Kazuki Kawahara
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka, Suita, Osaka, Japan
| | - Tadayasu Ohkubo
- Division of Bioresource Science, Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Japan
| | - Michael A. Hough
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, United Kingdom
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, United Kingdom
| | - Yoshihiro Sambongi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
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Zhang C, Liu S, Hussain S, Li L, Baiome BA, Xiao S, Cao H. Fe(II) Addition Drives Soil Bacterial Co-Ocurrence Patterns and Functions Mediated by Anaerobic and Chemoautotrophic Taxa. Microorganisms 2022; 10:microorganisms10030547. [PMID: 35336122 PMCID: PMC8950066 DOI: 10.3390/microorganisms10030547] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 12/10/2022] Open
Abstract
Iron is among the most abundant elements in the soil of paddy fields, and its valence state and partitioning can be transformed by flooding and drainage alternations. However, little is known about the function of soil microbes that interact with Fe(II). In this study, sandy and loamy soils originating from rice fields were treated with Fe(II) at low and high concentrations. The findings demonstrate that additional Fe(II) has various effects on the soil’s microbial community structure and metabolic pathways. We conclude that Fe(II) at high concentrations reduced bacterial abundance and diversity in two textured paddy soils, yet the abundance in loamy soils was higher than it was in sandy soil. Additionally, in environments with high Fe(II) levels, the relative abundance of both anaerobic and chemoautotrophic bacteria increased. The Fe(II) concentration was positively correlated with total reduced substances but negatively correlated with redox potential and pH. Co-occurrence networks revealed that Fe(II) significantly promoted interactions with the most anaerobic and chemoautotrophic bacteria. In addition, adding Fe(II) greatly increased the number of more complex bacterial networks, and an increase in the number of mutually beneficial taxa occurred. We found that Fe(II) promoted the methane pathway, the Calvin cycle, and nitrate reduction to small but significant extents. These pathways involve the growth and interrelation of autotrophic and anaerobic bacteria. These results suggest that changes in the bacterial community structure occur in many dry–wet alternating environments.
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Affiliation(s)
- Chenyang Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, College of Life Sciences, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, China; (C.Z.); (S.L.); (S.H.); (L.L.); (B.A.B.)
| | - Senlin Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, College of Life Sciences, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, China; (C.Z.); (S.L.); (S.H.); (L.L.); (B.A.B.)
- Wellington Research Group, School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Sarfraz Hussain
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, College of Life Sciences, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, China; (C.Z.); (S.L.); (S.H.); (L.L.); (B.A.B.)
| | - Lifeng Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, College of Life Sciences, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, China; (C.Z.); (S.L.); (S.H.); (L.L.); (B.A.B.)
| | - Baiome Abdelmaguid Baiome
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, College of Life Sciences, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, China; (C.Z.); (S.L.); (S.H.); (L.L.); (B.A.B.)
| | - Shuiqing Xiao
- School of Intercultural Studies, Jiangxi Normal University, Nanchang 330022, China;
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, College of Life Sciences, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, China; (C.Z.); (S.L.); (S.H.); (L.L.); (B.A.B.)
- Correspondence: ; Tel./Fax: +86-025-8439-6753
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9
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Lalucat J, Gomila M, Mulet M, Zaruma A, García-Valdés E. Past, present and future of the boundaries of the Pseudomonas genus: Proposal of Stutzerimonas gen. Nov. Syst Appl Microbiol 2021; 45:126289. [PMID: 34920232 DOI: 10.1016/j.syapm.2021.126289] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/10/2021] [Accepted: 11/24/2021] [Indexed: 11/25/2022]
Abstract
Pseudomonas is one the best studied bacterial genera, and it is the genus with the highest number of species among the gram-negative bacteria. Pseudomonas spp. are widely distributed and play relevant ecological roles; several species are commensal or pathogenic to humans, animals and plants. The main aim of the present minireview is the discussion of how the Pseudomonas taxonomy has evolved with the development of bacterial taxonomy since the first description of the genus in 1894. We discuss how the successive implementation of novel methodologies has influenced the taxonomy of the genus and, vice versa, how the taxonomic studies developed in Pseudomonas have introduced novel tools and concepts to bacterial taxonomy. Current phylogenomic analyses of the family Pseudomonadaceae demonstrate that a considerable number of named Pseudomonas spp. are not monophyletic with P. aeruginosa, the type species of the genus, and that a reorganization of several genera can be foreseen. Phylogenomics of Pseudomonas, Azomonas and Azotobacter within the Pseudomonadaceae is presented as a case study. Five new genus names are delineated to accommodate five well-defined phylogenetic branches that are supported by the shared genes in each group, and two of them can be differentiated by physiological and ecological properties: the recently described genus Halopseudomonas and the genus Stutzerimonas proposed in the present study. Five former Pseudomonas species are transferred to Halopseudomonas and 10 species to Stutzerimonas.
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Affiliation(s)
- Jorge Lalucat
- Microbiologia, Departament Biologia, Universitat de les Illes Balears, Spain; Institut Mediterrani d'Estudis Avançats, IMEDEA (CSIC-UIB), Spain.
| | - Margarita Gomila
- Microbiologia, Departament Biologia, Universitat de les Illes Balears, Spain
| | - Magdalena Mulet
- Microbiologia, Departament Biologia, Universitat de les Illes Balears, Spain
| | - Anderson Zaruma
- Microbiologia, Departament Biologia, Universitat de les Illes Balears, Spain
| | - Elena García-Valdés
- Microbiologia, Departament Biologia, Universitat de les Illes Balears, Spain; Institut Mediterrani d'Estudis Avançats, IMEDEA (CSIC-UIB), Spain
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10
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Martínez-Ruiz EB, Cooper M, Barrero-Canosa J, Haryono MAS, Bessarab I, Williams RBH, Szewzyk U. Genome analysis of Pseudomonas sp. OF001 and Rubrivivax sp. A210 suggests multicopper oxidases catalyze manganese oxidation required for cylindrospermopsin transformation. BMC Genomics 2021; 22:464. [PMID: 34157973 PMCID: PMC8218464 DOI: 10.1186/s12864-021-07766-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 06/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cylindrospermopsin is a highly persistent cyanobacterial secondary metabolite toxic to humans and other living organisms. Strain OF001 and A210 are manganese-oxidizing bacteria (MOB) able to transform cylindrospermopsin during the oxidation of Mn2+. So far, the enzymes involved in manganese oxidation in strain OF001 and A210 are unknown. Therefore, we analyze the genomes of two cylindrospermopsin-transforming MOB, Pseudomonas sp. OF001 and Rubrivivax sp. A210, to identify enzymes that could catalyze the oxidation of Mn2+. We also investigated specific metabolic features related to pollutant degradation and explored the metabolic potential of these two MOB with respect to the role they may play in biotechnological applications and/or in the environment. RESULTS Strain OF001 encodes two multicopper oxidases and one haem peroxidase potentially involved in Mn2+ oxidation, with a high similarity to manganese-oxidizing enzymes described for Pseudomonas putida GB-1 (80, 83 and 42% respectively). Strain A210 encodes one multicopper oxidase potentially involved in Mn2+ oxidation, with a high similarity (59%) to the manganese-oxidizing multicopper oxidase in Leptothrix discophora SS-1. Strain OF001 and A210 have genes that might confer them the ability to remove aromatic compounds via the catechol meta- and ortho-cleavage pathway, respectively. Based on the genomic content, both strains may grow over a wide range of O2 concentrations, including microaerophilic conditions, fix nitrogen, and reduce nitrate and sulfate in an assimilatory fashion. Moreover, the strain A210 encodes genes which may convey the ability to reduce nitrate in a dissimilatory manner, and fix carbon via the Calvin cycle. Both MOB encode CRISPR-Cas systems, several predicted genomic islands, and phage proteins, which likely contribute to their genome plasticity. CONCLUSIONS The genomes of Pseudomonas sp. OF001 and Rubrivivax sp. A210 encode sequences with high similarity to already described MCOs which may catalyze manganese oxidation required for cylindrospermopsin transformation. Furthermore, the analysis of the general metabolism of two MOB strains may contribute to a better understanding of the niches of cylindrospermopsin-removing MOB in natural habitats and their implementation in biotechnological applications to treat water.
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Affiliation(s)
- Erika Berenice Martínez-Ruiz
- Chair of Environmental Microbiology, Technische Universität Berlin, Institute of Environmental Technology, Straße des 17. Juni 135, 10623, Berlin, Germany.
| | - Myriel Cooper
- Chair of Environmental Microbiology, Technische Universität Berlin, Institute of Environmental Technology, Straße des 17. Juni 135, 10623, Berlin, Germany.
| | - Jimena Barrero-Canosa
- Chair of Environmental Microbiology, Technische Universität Berlin, Institute of Environmental Technology, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Mindia A S Haryono
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 119077, Singapore
| | - Irina Bessarab
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 119077, Singapore
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 119077, Singapore
| | - Ulrich Szewzyk
- Chair of Environmental Microbiology, Technische Universität Berlin, Institute of Environmental Technology, Straße des 17. Juni 135, 10623, Berlin, Germany
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11
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Guo L, Wang G, Sheng Y, Sun X, Shi Z, Xu Q, Mu W. Temperature governs the distribution of hot spring microbial community in three hydrothermal fields, Eastern Tibetan Plateau Geothermal Belt, Western China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 720:137574. [PMID: 32145630 DOI: 10.1016/j.scitotenv.2020.137574] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 06/10/2023]
Abstract
The eastern Tibetan Plateau geothermal belt in the southwest of China hosts a number of hot springs with a wide range of temperature and hydrogeochemical conditions, which may harbor different niches for the distribution of microbial communities. In this study, we investigated hydrochemical characteristics and microbial community composition in 16 hot springs with a temperature range of 34.6 to 88.2 °C within and across three typical hydrothermal fields (Kangding, Litang, and Batang). According to aquifer lithologic and tectonic differences, the hydrochemical compositions of hot springs displayed an apparent regional-specific pattern with distinct distributions of major and trace elements (e.g., Ca2+, Mg2+, F-/B) and were primarily formed by water-rock interaction across the three hydrothermal fields. Nonetheless, microbial communities significantly assembled with the temperature rather than the geographic locations with distinct hydrogeological features. Low temperature (<45 °C), moderate temperature (55-70 °C) and high temperature (>70 °C) groups were identified based on their community compositions. Proteobacteria and Nitrospirae were the predominant phyla in low-temperature hot springs, while in moderate to high-temperature springs they were mainly composed of Aquificae, Deinococcus-Thermus, Thermodesulfobacteria, Thermotogae and Cyanobacteria. Variation partition analysis suggested a higher explanation of temperature (29.6%) than spatial variable (1.8%) and other geochemical variables (2.5%) on the microbial distribution. Microbial co-occurrence network showed >80% negative associations hinting a low co-existence pattern and highlighted the driving force of temperature as well as F- or total organic carbon (TOC) for microbial interactions. Microbial dissimilarity displayed significant linear correlations with environmental (temperature) and geographic distance in Batang but only with temperature in Kangding area, which might be attributed to the regional-specific hydrogeochemistry. This study may help us to better understand the distribution of the microbial community in hot spring across different hydrothermal fields.
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Affiliation(s)
- Liang Guo
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Guangcai Wang
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China.
| | - Yizhi Sheng
- School of Environment, Tsinghua University, Beijing 100084, China; Department of Geology and Environmental Earth Science, Miami University, Oxford, OH 45056, USA.
| | - Xiaoyi Sun
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Zheming Shi
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Qingyu Xu
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Wenqing Mu
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
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12
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Pavlov MS, Lira F, Martinez JL, Olivares-Pacheco J, Marshall SH. Pseudomonas fildesensis sp. nov., a psychrotolerant bacterium isolated from Antarctic soil of King George Island, South Shetland Islands. Int J Syst Evol Microbiol 2020; 70:3255-3263. [PMID: 32375985 DOI: 10.1099/ijsem.0.004165] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The strain KG01T was isolated from a soil sample from King George Island, Antarctica. Cells of KG01T are rod-shaped and motile by means of multiple polar flagella. The absence of arginine dihydrolase activity could be a key feature to readily distinguish KG01T from its closest phylogenetic relative species. The main fatty acids of the strain include summed feature 3 (C16 : 1 ω7c and/or C15 : 0 iso 2-OH), C16 : 0 and C18 : 1 ω7c. Phylogenetic analysis based on the 16S rRNA gene sequence and on a multilocus sequence analysis (MLSA) using housekeeping genes (16S rRNA, rpoB, rpoD, gyrB) were carried out. These analyses allowed us to include the strain within the Pseudomonas fluorescens group, presenting the highest similarity of multilocus sequence with Pseudomonas veronii LMG 17761T (96.67 %). The genome of KG01T was sequenced and in silico compared with genomes of the most closely related species of the P. fluorescens group. The average nucleotide identity (ANIb) and average amino acid identity (AAI) values of the species phylogenetically closest to KG01T were less than 95-96 %, threshold currently accepted to define strain as belonging to a bacterial species, the highest scores being those to Pseudomonas veronii LMG 17761T (87.98 %) and Pseudomonas marginalis ICMP 3553T (91.90 %). Therefore, the phenotypic and genotypic analyses results, allow us to propose that KG01T represents a member of a novel species of the genus Pseudomonas, for which the name Pseudomonas fildesensis is proposed, and KG01T (=CECT 9084T;=DSM 102036T) is established as the type strain .
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Affiliation(s)
- Maria S Pavlov
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Valparaíso, Chile
| | - Felipe Lira
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - José Luis Martinez
- Centro Nacional de Biotecnología, CNB, CSIC, Darwin 3, Campus de Cantoblanco, Madrid, Spain
| | - Jorge Olivares-Pacheco
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R). Santiago, Chile.,Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Valparaíso, Chile
| | - Sergio H Marshall
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Valparaíso, Chile
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13
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Yan Z, Li M, Wang J, Pan J. Genome Analysis Revealing the Potential Mechanisms for the Heavy Metal Resistance of Pseudomonas sp. P11, Isolated from Industrial Wastewater Sediment. Curr Microbiol 2019; 76:1361-1368. [PMID: 31471685 DOI: 10.1007/s00284-019-01728-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 06/25/2019] [Indexed: 11/29/2022]
Abstract
Pseudomonas sp. P11 was isolated from the industrial wastewater sediment nearby the Daye Non-ferrous Metals Company, China. This strain possesses the ability to resist various heavy metals and efficiently precipitate arsenic. We here present a summary classification and a set of features of Pseudomonas sp. P11, together with the description of the genomic sequencing and annotation. The genomic sequence is 6,644,817 bp with a G+C content of 62.20% and contains 6143 protein-coding genes, 250 pseudo genes, and 76 tRNAs/rRNAs genes. Operons and gene clusters responsible for multiple heavy metal tolerance or detoxification were identified and accounted for the observed resistance phenotypes. Phylogenetic analysis revealed that the paralogous arsenic resistant genes possess different evolutionary paths. This study provides important insights to illuminate the versatility and adaptation of this strain to the heavy metal-contaminated environment.
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Affiliation(s)
- Zhenjun Yan
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization & College of Life Sciences, Hubei Normal University, Huangshi, 435002, Hubei, People's Republic of China
| | - Minglan Li
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization & College of Life Sciences, Hubei Normal University, Huangshi, 435002, Hubei, People's Republic of China
| | - Jingsong Wang
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization & College of Life Sciences, Hubei Normal University, Huangshi, 435002, Hubei, People's Republic of China
| | - Jicheng Pan
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization & College of Life Sciences, Hubei Normal University, Huangshi, 435002, Hubei, People's Republic of China.
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14
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Yu XY, Zhai JY, Wu C, Zhang CY, Shi JY, Ding LX, Wu M. Pseudomonas pharmafabricae sp. nov., Isolated From Pharmaceutical Wastewater. Curr Microbiol 2018; 75:1119-1125. [PMID: 29725767 DOI: 10.1007/s00284-018-1495-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/17/2018] [Indexed: 11/25/2022]
Abstract
A Gram-stain-negative, aerobic, rod-shaped bacterial strain, designated ZYSR67-ZT, was isolated from a pharmaceutical wastewater sample collected from a chemical factory in Zhejiang, China. The strain was motile by a single polar flagellum and grew at 4-42 °C (optimum, 35 °C), pH 5.0-9.0 (optimum, 6.0) and 0-5.0% (w/v) NaCl (optimum, 2.0%). Based on multilocus sequence analysis using 16S rRNA, gyrB, rpoB and rpoD, the strain ZYSR67-ZT formed a distinct phylogenetic group in the genus Pseudomonas. The average nucleotide identity values between strain ZYSR67-ZT and the closely related 10 type strains of the Pseudomonas species were 75.8-78.6%. The in silico DNA-DNA hybridization values indicated that strain ZYSR67-ZT and the type strains of the Pseudomonas shared 21.4-23.1% DNA relatedness. The predominant isoprenoid quinone system was ubiquinone-9 while ubiquinone-8 was present in trace amounts. The major fatty acids (> 10%) identified were C12:0, C16:0, C18:1 ω7c and summed features 3 (C16:1 ω7c and/or iso-C15:0 2OH). The major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content was 62.6 mol%. On the basis of morphological, physiological and chemotaxonomic characteristics, together with the results of phylogenetic analysis, strain ZYSR67-ZT was proposed to represent a novel species of the genus Pseudomonas, named Pseudomonas pharmafabricae sp. nov.. The type strain is ZYSR67-ZT (= CGMCC 1.15498T = JCM 31306T).
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Affiliation(s)
- Xiao-Yun Yu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Jing-Yu Zhai
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, People's Republic of China
| | - Chen Wu
- Zhejiang University of Water Resources and Electric Power, Hangzhou, 310018, People's Republic of China
| | - Chong-Ya Zhang
- Ocean College, Zhejiang University, Zhoushan, 316000, People's Republic of China
| | - Jie-Ying Shi
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, People's Republic of China
| | - Lin-Xian Ding
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, People's Republic of China.
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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15
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The current status on the taxonomy of Pseudomonas revisited: An update. INFECTION GENETICS AND EVOLUTION 2017; 57:106-116. [PMID: 29104095 DOI: 10.1016/j.meegid.2017.10.026] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 10/28/2017] [Accepted: 10/30/2017] [Indexed: 12/20/2022]
Abstract
The genus Pseudomonas described in 1894 is one of the most diverse and ubiquitous bacterial genera which encompass species isolated worldwide. In the last years more than 70 new species have been described, which were isolated from different environments, including soil, water, sediments, air, animals, plants, fungi, algae, compost, human and animal related sources. Some of these species have been isolated in extreme environments, such as Antarctica or Atacama desert, and from contaminated water or soil. Also, some species recently described are plant or animal pathogens. In this review, we revised the current status of the taxonomy of genus Pseudomonas and the methodologies currently used for the description of novel species which includes, in addition to the classic ones, new methodologies such as MALDI-TOF MS, MLSA and genome analyses. The novel Pseudomonas species described in the last years are listed, together with the available genome sequences of the type strains of Pseudomonas species present in different databases.
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16
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Paiva MC, Reis MP, Costa PS, Dias MF, Bleicher L, Scholte LLS, Nardi RMD, Nascimento AMA. Identification of new bacteria harboring qnrS and aac(6')-Ib/cr and mutations possibly involved in fluoroquinolone resistance in raw sewage and activated sludge samples from a full-scale WWTP. WATER RESEARCH 2017; 110:27-37. [PMID: 27984803 DOI: 10.1016/j.watres.2016.11.056] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 06/06/2023]
Abstract
Wastewater treatment plants (WWTPs) harbor bacteria and antimicrobial resistance genes, favoring gene exchange events and resistance dissemination. Here, a culture-based and metagenomic survey of qnrA, qnrB, qnrS, and aac(6')-Ib genes from raw sewage (RS) and activated sludge (AS) of a full-scale municipal WWTP was performed. A total of 96 bacterial isolates were recovered from nalidixic acid-enrichment cultures. Bacteria harboring the aac(6')-Ib gene predominated in RS, whereas qnrS-positive isolates were specific to AS. Novel qnrS- and aac(6')-Ib-cr positive species were identified: Morganella morganii, Providencia rettgeri, and Pseudomonas guangdongensis (qnrS), and Alcaligenes faecalis and P. rettgeri (aac(6')-Ib-cr). Analysis of qnrS and aac(6')-Ib sequences from isolates and clone libraries suggested that the diversity of qnrS is wider than that of aac(6')-Ib. A large number of amino acid mutations were observed in the QnrS and AAC(6')-Ib proteins at previously undetected positions, whose structural implications are not clear. An accumulation of mutations at the C72, Q73, L74, A75 and M76 positions of QnrS, and D181 of AAC(6')-Ib might be important for resistance. These findings add significant information on bacteria harboring qnrS and aac(6')-Ib genes, and the presence of novel mutations that may eventually emerge in clinical isolates.
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Affiliation(s)
- Magna C Paiva
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Campus Dona Lindu, Universidade Federal de São João del Rei, Divinópolis, Minas Gerais, Brazil
| | - Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Patrícia S Costa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marcela F Dias
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lucas Bleicher
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Larissa L S Scholte
- Centro de Pesquisas René Rachou - FIOCRUZ, Belo Horizonte, Minas Gerais, Brazil
| | - Regina M D Nardi
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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17
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Azhar EI, Papadioti A, Bibi F, Ashshi AM, Raoult D, Angelakis E. ' Pseudomonas saudimassiliensis' sp. nov. a new bacterial species isolated from air samples in the urban environment of Makkah, Saudi Arabia. New Microbes New Infect 2017; 16:43-44. [PMID: 28179986 PMCID: PMC5288317 DOI: 10.1016/j.nmni.2016.12.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 12/27/2016] [Accepted: 12/27/2016] [Indexed: 11/26/2022] Open
Abstract
We report here the main characteristics of ‘Pseudomonas saudimassiliensis’ strain 12M76_airT (CSUR P1220), a new species of the Pseudomonas genus that was isolated from air samples in the city environment of Makkah, Saudi Arabia, during the pilgrim period of Hajj 2012.
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Affiliation(s)
- E I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - A Papadioti
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE CNRS-IRD 198 UMR 6236, Aix Marseille Université, Faculté de Médecine, Marseille, France
| | - F Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - A M Ashshi
- Department of Laboratory Medicine, Faculty of Applied Medical Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - D Raoult
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia; Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE CNRS-IRD 198 UMR 6236, Aix Marseille Université, Faculté de Médecine, Marseille, France
| | - E Angelakis
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE CNRS-IRD 198 UMR 6236, Aix Marseille Université, Faculté de Médecine, Marseille, France
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Azhar EI, Papadioti A, Bibi F, Ashshi AM, Raoult D, Angelakis E. 'Pseudomonas saudiphocaensis' sp. nov., a new bacterial species isolated from currency notes collected during the Hajj pilgrimage in 2012 at Makkah, Saudi Arabia. New Microbes New Infect 2016; 15:131-133. [PMID: 28070338 PMCID: PMC5219595 DOI: 10.1016/j.nmni.2016.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 11/22/2016] [Accepted: 12/01/2016] [Indexed: 11/15/2022] Open
Abstract
We report here the main characteristics of ‘Pseudomonas saudiphocaensis’ strain 20_BNT (CSUR P1224), a new species of the Pseudomonas genus that was isolated from currency notes collected during the Hajj pilgrimage in 2012 at Makkah, Saudi Arabia.
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Affiliation(s)
- E I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, Jeddah, Saudi Arabia; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - A Papadioti
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, URMITE CNRS-IRD 198 UMR 6236, Aix Marseille Université, Faculté de Médecine, Marseille, France
| | - F Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, Jeddah, Saudi Arabia
| | - A M Ashshi
- Department of Laboratory Medicine, Faculty of Applied Medical Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - D Raoult
- Special Infectious Agents Unit, King Fahd Medical Research Center, Jeddah, Saudi Arabia; Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, URMITE CNRS-IRD 198 UMR 6236, Aix Marseille Université, Faculté de Médecine, Marseille, France
| | - E Angelakis
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, URMITE CNRS-IRD 198 UMR 6236, Aix Marseille Université, Faculté de Médecine, Marseille, France
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Zhong ZP, Liu Y, Hou TT, Liu HC, Zhou YG, Wang F, Liu ZP. Pseudomonas salina sp. nov., isolated from a salt lake. Int J Syst Evol Microbiol 2015; 65:2846-2851. [DOI: 10.1099/ijs.0.000341] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, facultatively aerobic bacterium, strain XCD-X85T, was isolated from Xiaochaidan Lake, a salt lake (salinity 9.9 %, w/v) in Qaidam basin, Qinghai province, China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain XCD-X85T were non-endospore-forming rods, 0.4–0.6 μm wide and 1.0–1.6 μm long, and motile by means of a single polar flagellum. Strain XCD-X85T was catalase- and oxidase-positive. Growth was observed in the presence of 0–12.0 % (w/v) NaCl (optimum, 1.0–2.0 %) and at 4–35 °C (optimum, 25–30 °C) and pH 6.5–10.5 (optimum, pH 8.0–8.5). Strain XCD-X85T contained (>10 %) summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C12 : 0, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the predominant fatty acids. The major respiratory quinone was ubiquinone 9 (Q-9). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 57.4 mol%. Phylogenetic trees based on 16S rRNA gene sequences showed that strain XCD-X85T was associated with the genus Pseudomonas, and showed highest 16S rRNA gene sequence similarities to Pseudomonas pelagia CL-AP6T (99.0 %) and Pseudomonas bauzanensis BZ93T (96.8 %). DNA–DNA relatedness of strain XCD-X85T to P. pelagia JCM 15562T was 19 ± 1 %. On the basis of the data presented above, it is concluded that strain XCD-X85T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas salina sp. nov. is proposed. The type strain is XCD-X85T ( = CGMCC 1.12482T = JCM 19469T).
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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
| | - Ting-Ting Hou
- 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
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center, 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
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Zhang L, Pan Y, Wang K, Zhang X, Zhang C, Zhang S, Fu X, Jiang J. Pseudomonas zhaodongensis sp. nov., isolated from saline and alkaline soils. Int J Syst Evol Microbiol 2015; 65:1022-1030. [PMID: 25574037 DOI: 10.1099/ijs.0.000057] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain NEAU-ST5-21(T) was isolated from saline and alkaline soils in Zhaodong City, Heilongjiang Province, China. It was aerobic, Gram-stain-negative, rod-shaped and motile with a polar flagellum. It produced yellow-orange colonies with a smooth surface, and grew in the presence of 0-5 % (w/v) NaCl (optimum 0 %, w/v), at temperatures of 20-40 °C (optimum 28 °C) and at pH 7-11 (optimum pH 7). Phylogenetic analyses based on the separate 16S rRNA gene sequences and concatenated 16S rRNA, gyrB and rpoD gene sequences indicated that strain NEAU-ST5-21(T) belongs to the genus Pseudomonas in the class Gammaproteobacteria. The most closely related species is Pseudomonas xanthomarina, whose type strain (KMM 1447(T)) showed gene sequence similarities of 99.0 % for 16S rRNA, 81.8 % for gyrB and 85.0 % for rpoD with strain NEAU-ST5-21(T). DNA-DNA hybridization values between strain NEAU-ST5-21(T) and P. xanthomarina DSM 18231(T), Pseudomonas kunmingensis CGMCC 1.12273(T), Pseudomonas stutzeri DSM 5190(T), Pseudomonas oleovorans subsp. lubricantis DSM 21016(T), Pseudomomas chengduensis CGMCC 2318(T), Pseudomonas alcaliphila DSM 17744(T) and Pseudomonas toyotomiensis DSM 26169(T) were 52±0 % to 25±2 %. The DNA G+C content of strain NEAU-ST5-21(T) was 65 mol%. The major fatty acids (>10 %) were C18 : 1ω7c and/or C18 : 1ω6c, C16 : 1ω7c and/or C16 : 1ω6c and C16 : 0, the predominant respiratory quinone was ubiquinone 9, and polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, one unknown phospholipid, phosphatidylglycerol, one unknown aminolipid, one unknown lipid and a glycolipid. The proposed name is Pseudomonas zhaodongensis sp. nov., NEAU-ST5-21(T) ( = ACCC 06362(T) = DSM 27559(T)) being the type strain.
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Affiliation(s)
- Lei Zhang
- Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, 150030, PR China
| | - Yuanyuan Pan
- Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, 150030, PR China
| | - Kaibiao Wang
- Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, 150030, PR China
| | - Xiaoxia Zhang
- Agricultural Cultural Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Cheng Zhang
- Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, 150030, PR China
| | - Shuang Zhang
- Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, 150030, PR China
| | - Xiaowei Fu
- Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, 150030, PR China
| | - Juquan Jiang
- Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, 150030, PR China
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Pascual J, García-López M, Bills GF, Genilloud O. Pseudomonas granadensis sp. nov., a new bacterial species isolated from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain. Int J Syst Evol Microbiol 2014; 65:625-632. [PMID: 25410940 DOI: 10.1099/ijs.0.069260-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
During the course of screening bacterial isolates as sources of as-yet unknown bioactive compounds with pharmaceutical applications, a chemo-organotrophic, Gram-negative bacterium was isolated from a soil sample taken from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain. Strain F-278,770(T) was oxidase- and catalase-positive, aerobic, with a respiratory type of metabolism with oxygen as the terminal electron acceptor, non-spore-forming and motile by one polar flagellum, although some cells had two polar flagella. Phylogenetic analysis of the 16S rRNA, gyrB, rpoB and rpoD genes revealed that strain F-278,770(T) belongs to the Pseudomonas koreensis subgroup (Pseudomonas fluorescens lineage), with Pseudomonas moraviensis, P. koreensis, P. baetica and P. helmanticensis as its closest relatives. Chemotaxonomic traits such as polar lipid and fatty acid compositions and G+C content of genomic DNA corroborated the placement of strain F-278,770(T) in the genus Pseudomonas. DNA-DNA hybridization assays and phenotypic traits confirmed that this strain represents a novel species of the genus Pseudomonas, for which the name Pseudomonas granadensis sp. nov. is proposed. The type strain is F-278,770(T) ( = DSM 28040(T) = LMG 27940(T)).
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Affiliation(s)
- Javier Pascual
- Fundación MEDINA, Avenida del Conocimiento, 3. Health Sciences Technology Park, 18016 Granada, Spain
| | - Marina García-López
- Fundación MEDINA, Avenida del Conocimiento, 3. Health Sciences Technology Park, 18016 Granada, Spain
| | - Gerald F Bills
- Fundación MEDINA, Avenida del Conocimiento, 3. Health Sciences Technology Park, 18016 Granada, Spain
| | - Olga Genilloud
- Fundación MEDINA, Avenida del Conocimiento, 3. Health Sciences Technology Park, 18016 Granada, Spain
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