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Selvakumar S, Singh S, Swaminathan P. Detection and evaluation of susceptibility to antibiotics in non-hydrogen sulfide-producing antibiotic-resistant soil microbe: Pseudomonas guariconensis. Int Microbiol 2024:10.1007/s10123-024-00537-3. [PMID: 38767682 DOI: 10.1007/s10123-024-00537-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/07/2024] [Accepted: 05/15/2024] [Indexed: 05/22/2024]
Abstract
Antimicrobial resistance in bacteria is a global threat that can make antibacterial treatments ineffective. One well-known method of antibiotic resistance and a common defensive mechanism in many harmful bacteria is the synthesis of endogenous hydrogen sulfide (H2S) in bacteria. In this study, soil bacteria were screened using the lead acetate agar test and the triple sugar iron test to determine that they were non-endogenous H2S producers. This was further validated by full genome analysis of the identified organism against the gene sequences of H2S-producing genes. Antibacterial resistance of the bacteria was phenotypically analyzed using the Kirby-Bauer disk diffusion method. Then, the effect of exogenous H2S on the antibiotic-resistant bacteria was checked in sodium sulfide, leading to antibiotic re-sensitization.
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Affiliation(s)
- Sahithya Selvakumar
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, 603203, Kattankulathur, India
| | - Shubhi Singh
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, 603203, Kattankulathur, India
| | - Priya Swaminathan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, 603203, Kattankulathur, India.
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2
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Yoon C, Lee Y. Emerging of multidrug-resistant Pseudomonas guariconensis with bla VIM-2 in an asymptomatic bacteriuria patient: A rare clinical presentation. Diagn Microbiol Infect Dis 2024; 108:116182. [PMID: 38215518 DOI: 10.1016/j.diagmicrobio.2024.116182] [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] [Received: 12/09/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/14/2024]
Abstract
This case presents the clinical and genomic aspects of a rare and multidrug-resistant Pseudomonas guariconensis isolate carrying blaVIM-2 and highlights the need for heightened awareness in healthcare facilities. A 63-year-old woman underwent surgery for the diagnosis of a paraspinal abscess and infectious spondylitis. During hospitalization, the patient was diagnosed with heart failure exacerbation. The patient had no symptoms of urinary tract infection and met the criteria for asymptomatic bacteriuria. In urine culture, colonies of the organism grew >105 CFU/mL on blood agar and on MacConkey agar. The Bruker Biotyper mass spectrometry showed P. guariconensis. Based on the 16S rRNA gene sequence showed that a 99.79 % match with as P. guariconensis LMG 27394T. The average nucleotide identity with P. guariconensis LMG 27394T was 91.53 %. Antimicrobial susceptibility testing showed that the isolate was not susceptible to most of the antibiotics. Antimicrobial resistance genes identified were aph(6)-Id, aph(3″)-Ib, aac(6')-Ib3, aac(3)-If, gyrA mutation (T83I) and blaVIM-2.
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Affiliation(s)
- Choseok Yoon
- Department of Internal Medicine, Hanyang University Seoul Hospital, Hanyang University of College of Medicine, 222 Wangsimni-ro, Seongdong-gu, Seoul 04763, South Korea
| | - Yangsoon Lee
- Department of Laboratory medicine, Hanyang University of College of Medicine, South Korea.
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3
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Moseley EJ, Zhang JC, Williams OM. Pseudomonas guariconensis Necrotizing Fasciitis, United Kingdom. Emerg Infect Dis 2024; 30:185-187. [PMID: 38147508 PMCID: PMC10756353 DOI: 10.3201/eid3001.231192] [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: 12/28/2023] Open
Abstract
We describe a case of necrotizing fasciitis in the United Kingdom in which Pseudomonas guariconensis was isolated from multiple blood culture and tissue samples. The organism carried a Verona integron-encoded metallo-β-lactamase gene and evidence of decreased susceptibility to β-lactam antimicrobial agents. Clinicians should use caution when treating infection caused by this rare pathogen.
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Heroes AS, Okitale P, Ndalingosu N, Vandekerckhove P, Lunguya O, Jacobs J. Presence of Gram-negative bacteria and Staphylococcus aureus on the skin of blood donors in the Democratic Republic of the Congo. Transfusion 2023; 63:360-372. [PMID: 36478388 DOI: 10.1111/trf.17196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Skin bacteria may contaminate blood products but few data are available on sub-Saharan Africa (sSA). We assessed the presence of Gram-negative bacteria and Staphylococcus aureus on blood donor skin and evaluated skin antisepsis in the Democratic Republic of the Congo (DRC). STUDY DESIGN AND METHODS Among blood donors at the National Blood Transfusion Center (NBTC) and at a rural hospital, the antecubital fossa skin of the non-disinfected arm (not used for blood collection) was swabbed (25cm2 surface) and cultured for total and Gram-negative bacterial counts. Bacteria were identified with MALDI-TOF and tested for antibiotic susceptibility by disk diffusion. For evaluation of the NBTC antisepsis procedure (i.e., ethanol 70%), the culture results of the disinfected arm (used for blood collection) were compared with those of the non-disinfected arm. RESULTS Median total bacterial counts on 161 studied non-disinfected arms were 1065 Colony-Forming Units (CFU) per 25 cm2 , with 43.8% (70/160) of blood donors growing Gram-negative bacteria and 3.8% (6/159) Staphylococcus aureus (2/6 methicillin-resistant). Non-fermentative Gram-negative rods predominated (74/93 isolates, majority Pseudomonas spp., Acinetobacter spp.). Enterobacterales comprised 19/93 isolates (mostly Pantoea spp. and Enterobacter spp.), 5/19 were multidrug-resistant. In only two cases (1.9%, 2/108) the NBTC antisepsis procedure met the acceptance criterion of ≤2 CFU/25 cm2 . CONCLUSION Skin bacterial counts and species among blood donors in DRC were similar to previously studied Caucasian populations, including cold-tolerating species and bacteria previously described in transfusion reactions. Prevention of contamination (e.g., antisepsis) needs further evaluation and customization to sSA.
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Affiliation(s)
- Anne-Sophie Heroes
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Patient Okitale
- Department of Microbiology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo.,Department of Clinical Biology, Cliniques Universitaires, Kinshasa, Democratic Republic of the Congo
| | - Natacha Ndalingosu
- Hemovigilance Department, Centre National de Transfusion Sanguine, Kinshasa, Democratic Republic of the Congo
| | - Philippe Vandekerckhove
- Belgian Red Cross-Flanders, Mechelen, Belgium.,Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium.,Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Octavie Lunguya
- Department of Microbiology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo.,Department of Clinical Biology, Cliniques Universitaires, Kinshasa, Democratic Republic of the Congo
| | - Jan Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
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He Z, Dong L, Zhang K, Zhang D, Pan X. Lactic acid bacteria induce phosphate recrystallization for the in situ remediation of uranium-contaminated topsoil: Principle and application. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 314:120277. [PMID: 36167164 DOI: 10.1016/j.envpol.2022.120277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/10/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Uranium (U) contamination often occurs in the topsoil (arable layer), and is a serious threat to crop growth. However, conventional microbial reduction methods are sensitive to oxygen and cannot be used to treat aerobic topsoils. In this study, phosphate-solubilizing microorganisms (PSM) were isolated from U-contaminated topsoil and used for soil remediation. Microbial metabolites and products were analyzed, and the pathways and mechanisms of PSM immobilization were revealed. The results showed that strain PSM8 had the highest phosphate-solubilizing capacity (dissolved P was 208 ± 5 mg/L) and the highest U removal rate (97.3 ± 0.1%). Multi-technical analyses indicated that bacterial surface functional groups adsorbed (UO2)2+ ions on the cell surface, glycolysis produced 3-10 mg/L of lactic acid (pH 4.7-6.0), and lactic acid solubilized Ca3(PO4)2 to form stable chernikovite (a type of uranyl phosphate) on the cell surface. The coupled application of Ca3(PO4)2 and strain PSM8 significantly reduced the bioavailability of soil U (62 ± 11%), converting U from the exchangeable to the residual phase and P from the steady to the available form. In addition, pot experiments showed that soil remediation promoted crop growth and significantly reduced U uptake and toxicity to photosynthetic systems. These findings demonstrate that PSM and Ca3(PO4)2 are good coupled fertilizers for U-contaminated agricultural soil.
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Affiliation(s)
- Zhanfei He
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Lingfeng Dong
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Keqing Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Daoyong Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China; Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China.
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China; Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
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Occurrence of Antibiotic-Resistant Genes and Bacteria in Household Greywater Treated in Constructed Wetlands. WATER 2022. [DOI: 10.3390/w14050758] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
There is a growing body of knowledge on the persistence of antibiotic-resistant genes (ARGs) and antibiotic-resistant bacteria (ARB) in greywater and greywater treatment systems such as constructed wetlands (CWs). Our research quantified ARGs (sul1, qnrS, and blaCTXM32), class one integron (intI1), and bacterial marker (16S) in four recirculating vertical flow CWs in a small community in the Negev desert, Israel, using quantitative polymerase chain reaction (qPCR). The greywater microbial community was characterized using 16S rRNA amplicon sequencing. Results show that CWs can reduce ARG in greywater by 1–3 log, depending on the gene and the quality of the raw greywater. Community sequencing results showed that the bacterial community composition was not significantly altered after treatment and that Proteobacteria, Epsilonbacteraeota, and Bacteroidetes were the most dominant phyla before and after treatment. Pseudomonas, Citrobacter, Enterobacter, and Aeromonas were the most commonly identified genera of the extended spectrum beta lactamase (ESBL) colonies. Some of the ESBL bacteria identified have been linked to clinical infections (Acinetobacter nosocomialis, Pseudomonas fulva, Pseudomonas putida, Pseudomonas monteilii, and Roseomonas cervicalis). It is important to monitor intI1 for the potential transfer of ARGs to pathogenic bacteria.
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Yadav AN, Kour D, Kaur T, Devi R, Yadav A, Dikilitas M, Abdel-Azeem AM, Ahluwalia AS, Saxena AK. Biodiversity, and biotechnological contribution of beneficial soil microbiomes for nutrient cycling, plant growth improvement and nutrient uptake. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102009] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Biosurfactant based formulation of Pseudomonas guariconensis LE3 with multifarious plant growth promoting traits controls charcoal rot disease in Helianthus annus. World J Microbiol Biotechnol 2021; 37:55. [PMID: 33615389 DOI: 10.1007/s11274-021-03015-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 01/28/2021] [Indexed: 10/22/2022]
Abstract
Biosurfactants are environment compatible surface-active biomolecules with multifunctional properties which can be utilized in various industries. In this study a biosurfactant producing novel plant growth promoting isolate Pseudomonas guariconensis LE3 from the rhizosphere of Lycopersicon esculentum is presented as biostimulant and biocontrol agent. Biosurfactant extracted from culture was characterized to be mixture of various mono- and di-rhamnolipids with antagonistic activity against Macrophomina phaseolina, causal agent of charcoal rot in diverse crops. Fourier transform infrared spectroscopy (FTIR) and proton nuclear magnetic resonance (1H NMR) analysis confirmed the rhamnolipid nature of biosurfactant. PCR analysis established the presence of genes involved in synthesis of antibiotics diacetylphloroglucinol, phenazine 1-carboxylic acid and pyocyanin, and lytic enzymes chitinase and endoglucanase suggesting biocontrol potential of the isolate. Plant growth promoting activities shown by LE3 were phosphate solubilization and production of siderophores, indole acetic acid (IAA), ammonia and 1-aminocyclopropane-1-carboxylate deaminase (ACCD). To assemble all the characteristics of LE3 various bioformuations were developed. Amendment of biosurfactant in bioformulation of LE3 cells improved the shelf life. Biosurfactant amended formulation of LE3 cells was most effective in biocontrol of charcoal rot disease of sunflower and growth promotion in field conditions. The root adhered soil mass of plantlets inoculated with LE3 plus biosurfactant was significantly higher over control. Biosurfactant amended formulation of LE3 cells caused maximum yield enhancement (80.80%) and biocontrol activity (75.45%), indicating that addition of biosurfactant improves the plant-bacterial interaction and soil properties leading to better control of disease and overall improvement of plant health and yield.
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Peral-Aranega E, Saati-Santamaría Z, Kolařik M, Rivas R, García-Fraile P. Bacteria Belonging to Pseudomonas typographi sp. nov. from the Bark Beetle Ips typographus Have Genomic Potential to Aid in the Host Ecology. INSECTS 2020; 11:insects11090593. [PMID: 32899185 PMCID: PMC7564387 DOI: 10.3390/insects11090593] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/23/2020] [Accepted: 09/01/2020] [Indexed: 11/16/2022]
Abstract
Simple Summary European Bark Beetle (Ips typographus) is a pest that affects dead and weakened spruce trees. Under certain environmental conditions, it has massive outbreaks, resulting in attacks of healthy trees, becoming a forest pest. It has been proposed that the bark beetle’s microbiome plays a key role in the insect’s ecology, providing nutrients, inhibiting pathogens, and degrading tree defense compounds, among other probable traits. During a study of bacterial associates from I. typographus, we isolated three strains identified as Pseudomonas from different beetle life stages. In this work, we aimed to reveal the taxonomic status of these bacterial strains and to sequence and annotate their genomes to mine possible traits related to a role within the bark beetle holobiont. Our study indicates that these bacteria constitute a new species for which the name of Pseudomonas typographi sp. nov. is proposed. Moreover, their genome analysis suggests different metabolic pathways possibly related to the beetle’s ecology. Finally, in vitro tests conclude the capability of these bacteria to inhibit beetle’s fungal pathogens. Altogether, these results suggest that P. typographi aids I. typographi nutrition and resistance to fungal pathogens. These findings might be of interest in the development of integrated methods for pest control. Abstract European Bark Beetle Ips typographus is a secondary pest that affects dead and weakened spruce trees (Picea genus). Under certain environmental conditions, it has massive outbreaks, resulting in the attacks of healthy trees, becoming a forest pest. It has been proposed that the bark beetle’s microbiome plays a key role in the insect’s ecology, providing nutrients, inhibiting pathogens, and degrading tree defense compounds, among other probable traits yet to be discovered. During a study of bacterial associates from I. typographus, we isolated three strains identified as Pseudomonas from different beetle life stages. A polyphasic taxonomical approach showed that they belong to a new species for which the name Pseudomonas typographi sp nov. is proposed. Genome sequences show their potential to hydrolyze wood compounds and synthesize several vitamins; screening for enzymes production was verified using PNP substrates. Assays in Petri dishes confirmed cellulose and xylan hydrolysis. Moreover, the genomes harbor genes encoding chitinases and gene clusters involved in the synthesis of secondary metabolites with antimicrobial potential. In vitro tests confirmed the capability of the three P. typographi strains to inhibit several Ips beetles’ pathogenic fungi. Altogether, these results suggest that P. typographi aids I. typographi nutrition and resistance to fungal pathogens.
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Affiliation(s)
- Ezequiel Peral-Aranega
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (Z.S.-S.); (R.R.)
- Spanish-Portuguese Institute for Agricultural Research (CIALE), 37185 Salamanca, Spain
| | - Zaki Saati-Santamaría
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (Z.S.-S.); (R.R.)
- Spanish-Portuguese Institute for Agricultural Research (CIALE), 37185 Salamanca, Spain
| | - Miroslav Kolařik
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01 Prague, Czech Republic;
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic
| | - Raúl Rivas
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (Z.S.-S.); (R.R.)
- Spanish-Portuguese Institute for Agricultural Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
| | - Paula García-Fraile
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (Z.S.-S.); (R.R.)
- Spanish-Portuguese Institute for Agricultural Research (CIALE), 37185 Salamanca, Spain
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
- Correspondence:
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Guerrieri MC, Fanfoni E, Fiorini A, Trevisan M, Puglisi E. Isolation and Screening of Extracellular PGPR from the Rhizosphere of Tomato Plants after Long-Term Reduced Tillage and Cover Crops. PLANTS 2020; 9:plants9050668. [PMID: 32466288 PMCID: PMC7285081 DOI: 10.3390/plants9050668] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 02/04/2023]
Abstract
Plant growth promoting rhizobacteria provide an innovative solution to address challenges in sustainable agro-ecosystems, improving plant growth as well as acting as agents of biocontrol. In this study autochthonous bacteria were isolated from the rhizosphere of processing tomato plants (Solanum lycopersicum L.) cultivated with conservation agriculture practices (i.e., reduced tillage and cover crops), and evaluated for both growth-promoting activities (PGPAs), and antagonistic potential against the phytopathogenic pest Sclerotinia sclerotiorum. Considering the several activities of PGPR, we decided to structure the screening with a hierarchic approach, starting from testing the capability of fixing nitrogen. The obtained bacteria were processed through the molecular typing technique rep-PCR (Repetitive Extragenic Palindromic) in order to discriminate microbial strains with the same profiles, and identified via 16S rDNA sequencing. Thirty-eight selected isolates were screened in vitro for different activities related to plant nutrition and plant growth regulation as well as for antifungal traits. Isolated bacteria were found to exhibit different efficiencies in indoleacetic acid production and siderophore production, phosphate solubilization and biocontrol activity against the widespread soil-borne plant pathogen S. sclerotiorum. All the 38 bacterial isolates showed at least one property tested. With a view to detect the suitable candidates to be developed as biofertilizers, the selected isolates were ranked by their potential ability to function as PGPR. Thus, consortium of native PGPR bacteria inoculants may represent a suitable solution to address the challenges in sustainable agriculture, to ensure crop yield and quality, lowering the application of chemicals input.
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Affiliation(s)
- Maria Chiara Guerrieri
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (M.C.G.); (E.F.); (E.P.)
| | - Elisabetta Fanfoni
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (M.C.G.); (E.F.); (E.P.)
| | - Andrea Fiorini
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy;
| | - Marco Trevisan
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (M.C.G.); (E.F.); (E.P.)
- Correspondence: ; Tel.: +39-0523-599152
| | - Edoardo Puglisi
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (M.C.G.); (E.F.); (E.P.)
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Li J, Hu M, Xue Y, Chen X, Lu G, Zhang L, Zhou J. Screening, Identification and Efficacy Evaluation of Antagonistic Bacteria for Biocontrol of Soft Rot Disease Caused by Dickeya zeae. Microorganisms 2020; 8:microorganisms8050697. [PMID: 32397545 PMCID: PMC7285164 DOI: 10.3390/microorganisms8050697] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/04/2020] [Accepted: 05/07/2020] [Indexed: 12/23/2022] Open
Abstract
Dickeya zeae is the causal agent of bacterial soft rot disease, with a wide range of hosts all over the world. At present, chemical agents, especially agricultural antibiotics, are commonly used in the prevention and control of bacterial soft rot, causing the emergence of resistant pathogens and therefore increasing the difficulty of disease prevention and control. This study aims to provide a safer and more effective biocontrol method for soft rot disease caused by D. zeae. The spot-on-lawn assay was used to screen antagonistic bacteria, and three strains including SC3, SC11 and 3-10 revealed strong antagonistic effects and were identified as Pseudomonas fluorescens, P. parafulva and Bacillus velezensis, respectively, using multi-locus sequence analysis (MLSA) based on the sequences of 16S rRNA and other housekeeping genes. In vitro antimicrobial activity showed that two Pseudomonas strains SC3 and SC11 were only antagonistic to some pathogenic bacteria, while strain 3-10 had broad-spectrum antimicrobial activity on both pathogenic bacteria and fungi. Evaluation of control efficacy in greenhouse trials showed that they all restrained the occurrence and development of soft rot disease caused by D. zeae MS2 or EC1. Among them, strain SC3 had the most impressive biocontrol efficacy on alleviating the soft rot symptoms on both monocotyledonous and dicotyledonous hosts, and strain 3-10 additionally reduced the occurrence of banana wilt disease caused by Fusarium oxysporum f. sp. cubensis. This is the first report of P. fluorescens, P. parafulva and B. velezensis as potential bio-reagents on controlling soft rot disease caused by D. zeae.
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Affiliation(s)
- Jieling Li
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; (J.L.); (M.H.); (Y.X.); (X.C.); (L.Z.)
| | - Ming Hu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; (J.L.); (M.H.); (Y.X.); (X.C.); (L.Z.)
| | - Yang Xue
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; (J.L.); (M.H.); (Y.X.); (X.C.); (L.Z.)
| | - Xia Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; (J.L.); (M.H.); (Y.X.); (X.C.); (L.Z.)
| | - Guangtao Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China;
| | - Lianhui Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; (J.L.); (M.H.); (Y.X.); (X.C.); (L.Z.)
| | - Jianuan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; (J.L.); (M.H.); (Y.X.); (X.C.); (L.Z.)
- Correspondence:
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Devi R, Madhavan Nampoothiri K, Sukumaran RK, Sindhu R, Arumugam M. Lipase of Pseudomonas guariconesis
as an additive in laundry detergents and transesterification biocatalysts. J Basic Microbiol 2019; 60:112-125. [DOI: 10.1002/jobm.201900326] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 09/03/2019] [Accepted: 09/22/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Rajan Devi
- Microbial Processes and Technology Division; CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST); Thiruvananthapuram Kerala India
| | - Kesavan Madhavan Nampoothiri
- Microbial Processes and Technology Division; CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST); Thiruvananthapuram Kerala India
| | - Rajeev Kumar Sukumaran
- Microbial Processes and Technology Division; CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST); Thiruvananthapuram Kerala India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division; CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST); Thiruvananthapuram Kerala India
| | - Muthu Arumugam
- Microbial Processes and Technology Division; CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST); Thiruvananthapuram Kerala India
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Rao Q, Liu Y, Chen C, Lin Q, Ren L, Huang M, Tu J, Luo T. Pseudomonas ovata sp. nov., Isolated from the Skin of the Tail of Farmed Murray cod (Maccullochella peelii peelii) with a Profound Ulceration. Curr Microbiol 2019; 76:1168-1174. [PMID: 31263923 DOI: 10.1007/s00284-019-01729-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 06/25/2019] [Indexed: 12/30/2022]
Abstract
A Gram-negative, strictly aerobic, motile, rod-shaped bacterium with monopolar flagellum, designated as F51T, was isolated from the skin ulcer of farmed Murray cod sampled from Zhejiang Province, China. Strain F51T grew at 4-37 °C (optimal temperature, 28 °C), pH 5.0-8.5 (optimal pH, 7.5) and NaCl concentration of 0-6.0% (w/v) (optimal concentration, 2.0%). Phylogenetic analysis based on average nucleotide identity (76.2-78.4%) and in silico DNA-DNA hybridization (22.3-23.2%) values revealed that strain F51T forms a distinct lineage in the clade of genus Pseudomonas with less than 98.9% 16S rRNA gene sequence similarity to type strains of the genus and represents a novel species related most closely to Pseudomonas floridensis LMG 30013T. Three housekeeping genes (rpoB, rpoD and gyrB) of strain F51T were analysed to further confirm that the isolate is distinctly delineated from related Pseudomonas species. Chemotaxonomic analysis indicated that the sole respiratory quinone of strain F51T is Q-9; its predominant cellular fatty acids are C16:0, summed feature 3 (iso-C15:0 2-OH and/or C16:1ω7c), summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C10:0 3-OH; and its major polar lipids consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified glycolipids, three unidentified phospholipids and an unidentified aminophosphoglycolipid. This composition is typical of the chemotaxonomic attributes of Pseudomonas. Based on its phenotypic, chemotaxonomic and phylogenetic features, strain F51T is considered to represent a novel species for which the name Pseudomonas ovata sp. nov. is proposed. The type strain is F51T (= KCTC 62133T = MCCC 1K03458T).
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Affiliation(s)
- Qiuhua Rao
- Institute of Quality Standards and Testing Technology for Agro-Products, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, People's Republic of China
| | - Yang Liu
- Institute of Quality Standards and Testing Technology for Agro-Products, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, People's Republic of China.,College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, People's Republic of China
| | - Can Chen
- Ocean College, Zhejiang University, Zhoushan, 316000, People's Republic of China
| | - Qiu Lin
- Institute of Quality Standards and Testing Technology for Agro-Products, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, People's Republic of China
| | - Lihua Ren
- Institute of Quality Standards and Testing Technology for Agro-Products, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, People's Republic of China
| | - Minmin Huang
- Institute of Quality Standards and Testing Technology for Agro-Products, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, People's Republic of China
| | - Jiefeng Tu
- Institute of Quality Standards and Testing Technology for Agro-Products, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, People's Republic of China
| | - Tuyan Luo
- Institute of Quality Standards and Testing Technology for Agro-Products, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, People's Republic of China.
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Keshavarz-Tohid V, Vacheron J, Dubost A, Prigent-Combaret C, Taheri P, Tarighi S, Taghavi SM, Moënne-Loccoz Y, Muller D. Genomic, phylogenetic and catabolic re-assessment of the Pseudomonas putida clade supports the delineation of Pseudomonas alloputida sp. nov., Pseudomonas inefficax sp. nov., Pseudomonas persica sp. nov., and Pseudomonas shirazica sp. nov. Syst Appl Microbiol 2019; 42:468-480. [DOI: 10.1016/j.syapm.2019.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/15/2019] [Accepted: 04/21/2019] [Indexed: 12/21/2022]
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15
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Adelowo OO, Vollmers J, Mäusezahl I, Kaster AK, Müller JA. Detection of the carbapenemase gene bla VIM-5 in members of the Pseudomonas putida group isolated from polluted Nigerian wetlands. Sci Rep 2018; 8:15116. [PMID: 30310126 PMCID: PMC6181998 DOI: 10.1038/s41598-018-33535-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/28/2018] [Indexed: 12/27/2022] Open
Abstract
There are increasing concerns about possible dissemination of clinically relevant antibiotic resistance genes, including genes encoding for carbapenemases in the environment. However, little is known about environmental distribution of antibiotic resistance in Africa. In this study, four polluted urban wetlands in Nigeria were investigated as potential reservoirs of carbapenem-resistant bacteria (CRB). CRB were isolated from the wetlands, characterized by Blue-Carba test, MIC determinations and whole genome sequencing (WGS). Nine of 65 bacterial isolates identified as members of the Pseudomonas putida group (P. plecoglossicida and P. guariconensis, respectively) harboured the metallo-beta-lactamase gene blaVIM-5. WGS revealed the blaVIM-5 in three novel Tn402-like class 1 integron structures containing the cassette arrays aadB|blaVIM-5|blaPSE-1, aadB|blaVIM-5|aadB|blaPSE-1, and blaVIM-5|aadB|tnpA|blaPSE-1|smr2|tnpA, respectively. Strains carrying the aadB|blaVIM-5|blaPSE-1 cassette also carried an identical integron without blaVIM-5. In addition, the strains harboured another Tn402-like class 1 integron carrying bcr2, several multidrug resistance efflux pumps, and at least one of ampC, aph(3”)-lb, aph(6)-ld, tetB, tetC, tetG, floR, and macAB. This is the first report of a carbapenemase gene in bacteria from environmental sources in Nigeria and the first report of blaVIM-5 in environmental bacteria isolates. This result underscores the role of the Nigerian environment as reservoir of bacteria carrying clinically relevant antibiotic resistance genes.
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Affiliation(s)
- Olawale O Adelowo
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany. .,Environmental Microbiology and Biotechnology Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Nigeria.
| | - John Vollmers
- Institute for Biological Interfaces (IBG5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Ines Mäusezahl
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IBG5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Jochen A Müller
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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16
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Behera P, Mahapatra M, Seuylemezian A, Vaishampayan P, Ramana VV, Joseph N, Joshi A, Shouche Y, Suar M, Pattnaik AK, Rastogi G. Taxonomic description and draft genome of Pseudomonas sediminis sp. nov., isolated from the rhizospheric sediment of Phragmites karka. J Microbiol 2018; 56:458-466. [DOI: 10.1007/s12275-018-7549-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 10/14/2022]
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17
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Saati-Santamaría Z, López-Mondéjar R, Jiménez-Gómez A, Díez-Méndez A, Větrovský T, Igual JM, Velázquez E, Kolarik M, Rivas R, García-Fraile P. Discovery of Phloeophagus Beetles as a Source of Pseudomonas Strains That Produce Potentially New Bioactive Substances and Description of Pseudomonas bohemica sp. nov. Front Microbiol 2018; 9:913. [PMID: 29867824 PMCID: PMC5953339 DOI: 10.3389/fmicb.2018.00913] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/20/2018] [Indexed: 12/21/2022] Open
Abstract
Antimicrobial resistance is a worldwide problem that threatens the effectiveness of treatments for microbial infection. Consequently, it is essential to study unexplored niches that can serve for the isolation of new microbial strains able to produce antimicrobial compounds to develop new drugs. Bark beetles live in phloem of host trees and establish symbioses with microorganisms that provide them with nutrients. In addition, some of their associated bacteria play a role in the beetle protection by producing substances that inhibit antagonists. In this study the capacity of several bacterial strains, isolated from the bark beetles Ips acuminatus, Pityophthorus pityographus Cryphalus piceae, and Pityogenes bidentatus, to produce antimicrobial compounds was analyzed. Several isolates exhibited the capacity to inhibit Gram-positive and Gram-negative bacteria, as well as fungi. The genome sequence analysis of three Pseudomonas isolates predicted the presence of several gene clusters implicated in the production of already described antimicrobials and moreover, the low similarity of some of these clusters with those previously described, suggests that they encode new undescribed substances, which may be useful for developing new antimicrobial agents. Moreover, these bacteria appear to have genetic machinery for producing antitumoral and antiviral substances. Finally, the strain IA19T showed to represent a new species of the genus Pseudomonas. The 16S rRNA gene sequence analysis showed that its most closely related species include Pseudomonas lutea, Pseudomonas graminis, Pseudomonas abietaniphila and Pseudomonas alkylphenolica, with 98.6, 98.5 98.4, and 98.4% identity, respectively. MLSA of the housekeeping genes gyrB, rpoB, and rpoD confirmed that strain IA19T clearly separates from its closest related species. Average nucleotide identity between strains IA19T and P. abietaniphila ATCC 700689T, P. graminis DSM 11363T, P. alkylphenolica KL28T and P. lutea DSM 17257T were 85.3, 80.2, 79.0, and 72.1%, respectively. Growth occurs at 4-37°C and pH 6.5-8. Optimal growth occurs at 28°C, pH 7-8 and up to 2.5% NaCl. Respiratory ubiquinones are Q9 (97%) and Q8 (3%). C16:0 and in summed feature 3 are the main fatty acids. Based on genotypic, phenotypic and chemotaxonomic characteristics, the description of Pseudomonas bohemica sp. nov. has been proposed. The type strain is IA19T (=CECT 9403T = LMG 30182T).
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Affiliation(s)
- Zaki Saati-Santamaría
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain.,Spanish-Portuguese Institute for Agricultural Research (CIALE), Salamanca, Spain
| | | | - Alejandro Jiménez-Gómez
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain.,Spanish-Portuguese Institute for Agricultural Research (CIALE), Salamanca, Spain
| | - Alexandra Díez-Méndez
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain.,Spanish-Portuguese Institute for Agricultural Research (CIALE), Salamanca, Spain
| | - Tomáš Větrovský
- Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czechia
| | - José M Igual
- Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Salamanca, Spain.,Associated R&D Unit, USAL-CSIC (IRNASA), Salamanca, Spain
| | - Encarna Velázquez
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain.,Spanish-Portuguese Institute for Agricultural Research (CIALE), Salamanca, Spain.,Associated R&D Unit, USAL-CSIC (IRNASA), Salamanca, Spain
| | - Miroslav Kolarik
- Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czechia
| | - Raúl Rivas
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain.,Spanish-Portuguese Institute for Agricultural Research (CIALE), Salamanca, Spain.,Associated R&D Unit, USAL-CSIC (IRNASA), Salamanca, Spain
| | - Paula García-Fraile
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain.,Spanish-Portuguese Institute for Agricultural Research (CIALE), Salamanca, Spain.,Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czechia
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18
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Kimura N, Watanabe T, Suenaga H, Fujihara H, Futagami T, Goto M, Hanada S, Hirose J. Pseudomonas furukawaii sp. nov., a polychlorinated biphenyl-degrading bacterium isolated from biphenyl-contaminated soil in Japan. Int J Syst Evol Microbiol 2018; 68:1429-1435. [PMID: 29595413 DOI: 10.1099/ijsem.0.002670] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain KF707T was isolated from a biphenyl-contaminated site in Kitakyushu, Japan. Analysis of 16S rRNA gene sequences, retrieved from the whole-genome sequence, revealed that the isolate was closely related to members of the genus Pseudomonas, sharing the highest sequence similarities with Pseudomonas balearica strain SP1402T (DSM 6083) (97.8 %). The DNA G+C chromosome and plasmid content of strain KF707T were 65.5 and 60.5 mol%. The major cellular fatty acids were iso-C15 : 0 and C16 : 1ω7c/C16 : 1ω6c. Polyphasic analysis indicated that strain KF707T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas furukawaii sp. nov. is proposed. The type strain is KF707T (=DSM 10086T=NBRC 110670T).
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Affiliation(s)
- Nobutada Kimura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Takahito Watanabe
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Japan
| | - Hikaru Suenaga
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | | | - Taiki Futagami
- Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima, Japan
| | - Masatoshi Goto
- Department of Applied Biochemistry and Food Science, Saga University, Saga, Japan
| | - Satoshi Hanada
- Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji, Japan
| | - Jun Hirose
- Department of Applied Chemistry, Faculty of Engineering, University of Miyazaki, Miyazaki, Japan
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19
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Mitsutomi S, Sekimizu K, Kaito C. Isolation of antibiotic-producing Pseudomonas species with low-temperature cultivation of temperate soil. Drug Discov Ther 2017; 11:267-275. [PMID: 29081439 DOI: 10.5582/ddt.2017.01053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We performed low-temperature cultivation of soil samples in Tokyo, Japan, and isolated 30 bacterial strains that formed colonies at 4°C. All the culture supernatants of these bacteria exhibited antibacterial activity against Escherichia coli. The 16S rDNA sequences of 29 strains showed similarity to that of the Pseudomonas genus, whereas the 16S rDNA sequence of one strain showed similarity to that of the Janthinobacterium genus. We classified the 29 strains into 10 groups according to the 16S rDNA sequence similarities, and performed two phylogenetic analyses using the 16S rDNA and rpoD gene sequences. Four groups formed a unique branch within Pseudomonas species in both phylogenetic analyses. Four other groups were closely related to the Pseudomonas species, but the most closely related species differed between the two phylogenic tree analyses. These results suggest that low-temperature cultivation of temperate soil is effective for isolating new bacterial sources for producing antibiotics.
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Affiliation(s)
- Shuhei Mitsutomi
- Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo
| | | | - Chikara Kaito
- Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo
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20
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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: 129] [Impact Index Per Article: 18.4] [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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21
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Liu S, Lin N, Chen Y, Liang Z, Liao L, Lv M, Chen Y, Tang Y, He F, Chen S, Zhou J, Zhang L. Biocontrol of Sugarcane Smut Disease by Interference of Fungal Sexual Mating and Hyphal Growth Using a Bacterial Isolate. Front Microbiol 2017; 8:778. [PMID: 28536557 PMCID: PMC5422470 DOI: 10.3389/fmicb.2017.00778] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 04/18/2017] [Indexed: 12/03/2022] Open
Abstract
Sugarcane smut is a fungal disease caused by Sporisorium scitamineum, which can cause severe economic losses in sugarcane industry. The infection depends on the mating of bipolar sporida to form a dikaryon and develops into hyphae to penetrate the meristematic tissue of sugarcane. In this study, we set to isolate bacterial strains capable of blocking the fungal mating and evaluate their potential in control of sugarcane smut disease. A bacterial isolate ST4 from rhizosphere displayed potent inhibitory activity against the mating of S. scitamineum bipolar sporida and was selected for further study. Phylogenetic analyses and biochemical characterization showed that the isolate was most similar to Pseudomonas guariconensis. Methanol extracts from minimum and potato dextrose agar (PDA) agar medium, on which strain ST4 has grown, showed strong inhibitory activity on the sexual mating of S. scitamineum sporida, without killing the haploid cells MAT-1 or MAT-2. Further analysis showed that only glucose, but not sucrose, maltose, and fructose, could support strain ST4 to produce antagonistic chemicals. Consistent with the above findings, greenhouse trials showed that addition of 2% glucose to the bacterial inoculum significantly increased the strain ST4 biocontrol efficiency against sugarcane smut disease by 77% than the inoculum without glucose. The results from this study depict a new strategy to screen for biocontrol agents for control and prevention of the sugarcane smut disease.
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Affiliation(s)
- Shiyin Liu
- Integrative Microbiology Research Centre, South China Agricultural UniversityGuangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural UniversityGuangzhou, China
| | - Nuoqiao Lin
- Integrative Microbiology Research Centre, South China Agricultural UniversityGuangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural UniversityGuangzhou, China
| | - Yumei Chen
- Integrative Microbiology Research Centre, South China Agricultural UniversityGuangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural UniversityGuangzhou, China
| | - Zhibin Liang
- Integrative Microbiology Research Centre, South China Agricultural UniversityGuangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural UniversityGuangzhou, China
| | - Lisheng Liao
- Integrative Microbiology Research Centre, South China Agricultural UniversityGuangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural UniversityGuangzhou, China
| | - Mingfa Lv
- Integrative Microbiology Research Centre, South China Agricultural UniversityGuangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural UniversityGuangzhou, China
| | - Yufan Chen
- Integrative Microbiology Research Centre, South China Agricultural UniversityGuangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural UniversityGuangzhou, China
| | - Yingxin Tang
- Integrative Microbiology Research Centre, South China Agricultural UniversityGuangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural UniversityGuangzhou, China
| | - Fei He
- Integrative Microbiology Research Centre, South China Agricultural UniversityGuangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural UniversityGuangzhou, China
| | - Shaohua Chen
- Integrative Microbiology Research Centre, South China Agricultural UniversityGuangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural UniversityGuangzhou, China
| | - Jianuan Zhou
- Integrative Microbiology Research Centre, South China Agricultural UniversityGuangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural UniversityGuangzhou, China
| | - Lianhui Zhang
- Integrative Microbiology Research Centre, South China Agricultural UniversityGuangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural UniversityGuangzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangzhou, China
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22
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Uncommonly isolated clinical Pseudomonas: identification and phylogenetic assignation. Eur J Clin Microbiol Infect Dis 2016; 36:351-359. [DOI: 10.1007/s10096-016-2808-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/02/2016] [Indexed: 10/20/2022]
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23
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Wang MQ, Sun L. Pseudomonas oceani sp. nov., isolated from deep seawater. Int J Syst Evol Microbiol 2016; 66:4250-4255. [PMID: 27468709 DOI: 10.1099/ijsem.0.001343] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, we identified a novel Gram-stain-negative, aerobic, motile, and rod-shaped bacterium, strain KX 20T, isolated from the deep seawater in Okinawa Trough, northwestern Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain KX 20T was related to members of the genus Pseudomonas and shares the highest sequence identities with Pseudomonas aestusnigri CECT 8317T (99.4 %) and Pseudomonas pachastrellae JCM 12285T (98.5 %). The 16S rRNA gene sequence identities between strain KX 20T and other members of the genus Pseudomonaswere below 96.6 %. The gyrB and rpoD genes of strain KX 20T shared 82.0 to 89.3 % sequence identity with the gyrB and rpoD genes of the closest phylogenetic neighbours of KX 20T. The predominant cellular fatty acids of strain KX 20T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) (29.2 %), C16 : 0 (24.5 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (21.5 %) and C12 : 0 (8.2 %). The major polar lipids of strain KX 20T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unknown phospholipids. The genomic DNA G+C content of strain KX 20T was 62.9 mol%. On the basis of phylogenetic analysis and phenotypic characteristics, a novel species, Pseudomonas oceani sp. nov. is proposed. The type strain is KX 20T (=CGMCC 1.15195T=DSM 100277T).
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Affiliation(s)
- Ming-Qing Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China.,Function Laboratory for Marine Biology and Biotechnology, Qingdao National Oceanography Laboratory, Qingdao, PR China
| | - Li Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China.,Function Laboratory for Marine Biology and Biotechnology, Qingdao National Oceanography Laboratory, Qingdao, PR China
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24
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Bahena MHR, Salazar S, Velázquez E, Laguerre G, Peix A. Characterization of phosphate solubilizing rhizobacteria associated with pea (Pisum sativum L.) isolated from two agricultural soils. Symbiosis 2016. [DOI: 10.1007/s13199-015-0375-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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25
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Ramírez-Bahena MH, Cuesta MJ, Tejedor C, Igual JM, Fernández-Pascual M, Peix Á. Pseudomonas endophytica sp. nov., isolated from stem tissue of Solanum tuberosum L. in Spain. Int J Syst Evol Microbiol 2015; 65:2110-2117. [DOI: 10.1099/ijs.0.000230] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain named BSTT44T was isolated in the course of a study of endophytic bacteria occurring in stems and roots of potato growing in a soil from Salamanca, Spain. The 16S rRNA gene sequence had 99.7 % identity with respect to that of its closest relative, Pseudomonas psychrophila E-3T, and the next most closely related type strains were those of Pseudomonas fragi, with 99.6 % similarity, Pseudomonas deceptionensis, with 99.2 % similarity, and Pseudomonas lundensis, with 99.0 % similarity; these results indicate that BSTT44T should be classified within the genus Pseudomonas. Analysis of the housekeeping genes rpoB, rpoD and gyrB confirmed its phylogenetic affiliation and showed identities lower than 92 % in all cases with respect to the above-mentioned closest relatives. Cells of the strain bore one polar–subpolar flagellum. The respiratory quinone was Q-9.The major fatty acids were C16:0, C18:1ω7c and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The strain was oxidase-, catalase- and urease-positive and the arginine dihydrolase system was present, but tests for nitrate reduction, β-galactosidase production and aesculin hydrolysis were negative. It could grow at 35 °C and at pH 5–9.The DNA G+C content was 60.2 mol%. DNA–DNA hybridization results showed less than 48 % relatedness with respect to the type strains of the four most closely related species. Therefore, the combined results of genotypic, phenotypic and chemotaxonomic analyses support the classification of strain BSTT44 into a novel species of the genus Pseudomonas, for which the name Pseudomonas endophytica sp. nov. is proposed. The type strain is BSTT44T ( = LMG 28456T = CECT 8691T).
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Affiliation(s)
- Martha-Helena Ramírez-Bahena
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA (CSIC), Salamanca, Spain
| | - Maria José Cuesta
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
| | - Carmen Tejedor
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - José Mariano Igual
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA (CSIC), Salamanca, Spain
| | | | - Álvaro Peix
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA (CSIC), Salamanca, Spain
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Arnau VG, Sánchez LA, Delgado OD. Pseudomonas yamanorum sp. nov., a psychrotolerant bacterium isolated from a subantarctic environment. Int J Syst Evol Microbiol 2015; 65:424-431. [DOI: 10.1099/ijs.0.065201-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A psychrotolerant strain, 8H1T, was isolated from soil samples collected in Isla de los Estados, Ushuaia, Argentina. Cells were Gram-negative, aerobic, straight rods, occurring singly or in pairs, non-spore-forming and motile by means of two polar flagella. The isolate was able to grow in the range 4–35 °C, with optimum growth at 28 °C. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The polar lipid pattern of strain 8H1T comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid. Ubiquinone 9 (Q-9) was the predominant lipoquinone. The DNA G+C content was 59.8 mol%. 16S rRNA gene sequence-based phylogeny suggested the affiliation of strain 8H1T to the ‘Pseudomonas fluorescens group’, displaying ≥98.5 % sequence similarity to 29 type strains. A multilocus sequence analysis (MLSA) study performed by concatenating 16S rRNA, gyrB, rpoD and rpoB gene sequences showed that isolate 8H1T could be discriminated from closely related species of the genus
Pseudomonas
and placed in the ‘Pseudomonas gessardii subgroup’, including the species with the highest MLSA sequence similarities:
Pseudomonas brenneri
(96.2 %),
P. gessardii
(96.1 %),
P. proteolytica
(96.0 %),
P. meridiana
(96.0 %) and
P. mucidolens
(95.4 %). DNA–DNA hybridization analysis between 8H1T and the type strains of these closely related species revealed relatedness values of 27.0, 8.8, 41.2, 39.7 and 46.1 %, respectively. These results, together with differences in several phenotypic features, support the classification of a novel species, for which the name Pseudomonas yamanorum sp. nov. is proposed. The type strain is 8H1T ( = DSM 26522T = CCUG 63249T = LMG 27247T).
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Affiliation(s)
| | | | - Osvaldo Daniel Delgado
- Centro de Investigación y Transferencia Catamarca (CITCa), Universidad Nacional de Catamarca, CONICET, Av. Belgrano 300 (K4700AAP), San Fernando del Valle de Catamarca, Catamarca, Argentina
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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: 2.6] [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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Pseudomonas donghuensis sp. nov., exhibiting high-yields of siderophore. Antonie van Leeuwenhoek 2014; 107:83-94. [DOI: 10.1007/s10482-014-0306-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
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Amoozegar MA, Shahinpei A, Sepahy AA, Makhdoumi-Kakhki A, Seyedmahdi SS, Schumann P, Ventosa A. Pseudomonas salegens sp. nov., a halophilic member of the genus Pseudomonas isolated from a wetland. Int J Syst Evol Microbiol 2014; 64:3565-3570. [PMID: 25062699 DOI: 10.1099/ijs.0.062935-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic, non-endospore-forming, non-pigmented, rod-shaped, slightly halophilic bacterium, designated GBPy5(T), was isolated from aquatic plants of the Gomishan wetland, Iran. Cells of strain GBPy5(T) were motile. Growth occurred with between 1 and 10% (w/v) NaCl and the isolate grew optimally with 3% (w/v) NaCl. The optimum pH and temperature for growth of the strain were pH 8.0 and 30 °C, respectively, while it was able to grow over a pH range of 6.5-9.0 and a temperature range of 4-35 °C. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain GBPy5(T) is a member of the genus Pseudomonas forming a monophyletic branch. The novel strain exhibited 16S rRNA gene sequence similarity of 95.4% with type strains of Pseudomonas guariconensis PCAVU11(T) and Pseudomonas sabulinigri J64(T), respectively. The major cellular fatty acids of the isolate were C18:1ω7c (37.8%), C16:0 (14.9%), C16:1ω7c (12.9%), C12:0 3-OH (7.1%) and C12:0 (7.0%). The polar lipid pattern of strain GBPy5(T) comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and one phospholipid. Ubiquinone 9 (Q-9) was the predominant lipoquinone. The G+C content of the genomic DNA of strain GBPy5(T) was 59.2 mol%. On the basis of the phenotypic and phylogenetic data, strain GBPY5(T) represents a novel species of the genus Pseudomonas, for which the name Pseudomonas salegens sp. nov. is proposed. The type strain is GBPy5(T) ( = IBRC-M 10762(T) = CECT 8338(T)).
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Affiliation(s)
- Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Azadeh Shahinpei
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran, Iran
| | - Abbas Akhavan Sepahy
- Department of Microbiology, Faculty of Biological Sciences, Islamic Azad University North Tehran Branch, Tehran, Iran.,Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran, Iran
| | - Ali Makhdoumi-Kakhki
- Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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Ramírez-Bahena MH, Cuesta MJ, Flores-Félix JD, Mulas R, Rivas R, Castro-Pinto J, Brañas J, Mulas D, González-Andrés F, Velázquez E, Peix Á. Pseudomonas helmanticensis sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2014; 64:2338-2345. [DOI: 10.1099/ijs.0.063560-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, OHA11T, was isolated during the course of a study of phosphate-solubilizing bacteria occurring in a forest soil from Salamanca, Spain. The 16S rRNA gene sequence of strain OHA11T shared 99.1 % similarity with respect to
Pseudomonas baetica
a390T, and 98.9 % similarity with the type strains of
Pseudomonas jessenii
,
Pseudomonas moorei
,
Pseudomonas umsongensis
,
Pseudomonas mohnii
and
Pseudomonas koreensis
. The analysis of housekeeping genes rpoB, rpoD and gyrB confirmed its phylogenetic affiliation to the genus
Pseudomonas
and showed similarities lower than 95 % in almost all cases with respect to the above species. Cells possessed two polar flagella. The respiratory quinone was Q9. The major fatty acids were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH). The strain was oxidase-, catalase- and urease-positive, positive for arginine dihydrolase but negative for nitrate reduction, β-galactosidase production and aesculin hydrolysis. It was able to grow at 31 °C and at pH 11. The DNA G+C content was 58.1 mol%. DNA–DNA hybridization results showed values lower than 49 % relatedness with respect to the type strains of the seven closest related species. Therefore, the combined genotypic, phenotypic and chemotaxonomic data support the classification of strain OHA11T to a novel species of the genus
Pseudomonas
, for which the name Pseudomonas helmanticensis sp. nov. is proposed. The type strain is OHA11T ( = LMG 28168T = CECT 8548T).
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Affiliation(s)
- Martha-Helena Ramírez-Bahena
- Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA (CSIC), Salamanca, Spain
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
| | - Maria José Cuesta
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
| | | | - Rebeca Mulas
- Instituto de Medio Ambiente, Recursos Naturales y Biodiversidad, Universidad de León, León, Spain
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA (CSIC), Salamanca, Spain
| | | | | | | | - Fernando González-Andrés
- Instituto de Medio Ambiente, Recursos Naturales y Biodiversidad, Universidad de León, León, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA (CSIC), Salamanca, Spain
| | - Álvaro Peix
- Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA (CSIC), Salamanca, Spain
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
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