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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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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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3
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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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Bueno-Gonzalez V, Brady C, Denman S, Plummer S, Allainguillaume J, Arnold D. Pseudomonas daroniae sp. nov. and Pseudomonas dryadis sp. nov., isolated from pedunculate oak affected by acute oak decline in the UK. Int J Syst Evol Microbiol 2019; 69:3368-3376. [PMID: 31391144 DOI: 10.1099/ijsem.0.003615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Twenty-two cream-coloured bacterial strains were isolated from oak trees affected by acute oak decline (AOD) in Southern England. Isolates were Gram-negative, motile, slightly curved rods, aerobic, non-spore-forming, catalase positive and oxidase positive. 16S rRNA gene sequence analysis placed the strains in two separate phylogenetic clusters in the Pseudomonas straminea group, with Pseudomonas flavescens as the closest phylogenetic relative. Multilocus sequence analyses of the gyrB, rpoD and rpoB genes supported the delineation of the strains into two separate taxa, which could be differentiated phenotypically and chemotaxonomically from each other, and their closest relatives. Average nucleotide identity and in silico DNA-DNA hybridization values revealed percentages of genome similarity below the species threshold (95 and 70 %, respectively) between the two taxa and the closest relatives, confirming their novel species status. Therefore, on the basis of this polyphasic approach we propose two novel Pseudomonas species, Pseudomonasdaroniae sp. nov. (type strain FRB 228T=LMG 31087T=NCPPB 4672T) and Pseudomonasdryadis sp. nov. (type strain FRB 230T=LMG 31087T=NCPPB 4673T).
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Affiliation(s)
- Victoria Bueno-Gonzalez
- Centre for Research in Bioscience, Faculty of Health and Life Sciences, University of the West of England, Frenchay Campus, Bristol, UK
| | - Carrie Brady
- Centre for Research in Bioscience, Faculty of Health and Life Sciences, University of the West of England, Frenchay Campus, Bristol, UK
| | - Sandra Denman
- Forest Research, Centre for Ecosystems Society and Biosecurity, Alice Holt Lodge, Surrey, UK
| | - Sarah Plummer
- Forest Research, Centre for Ecosystems Society and Biosecurity, Alice Holt Lodge, Surrey, UK
| | - Joel Allainguillaume
- Centre for Research in Bioscience, Faculty of Health and Life Sciences, University of the West of England, Frenchay Campus, Bristol, UK
| | - Dawn Arnold
- Centre for Research in Bioscience, Faculty of Health and Life Sciences, University of the West of England, Frenchay Campus, Bristol, UK
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Samet M, Karray F, Mhiri N, Kamoun L, Sayadi S, Gargouri-Bouzid R. Effect of phosphogypsum addition in the composting process on the physico-chemical proprieties and the microbial diversity of the resulting compost tea. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:21404-21415. [PMID: 31124074 DOI: 10.1007/s11356-019-05327-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/30/2019] [Indexed: 06/09/2023]
Abstract
Phosphoric acid production and olive oil production are among the most important economical sectors in Tunisia. However, they generate huge amounts of wastes (phosphogypsum, olive mill waste water, and olive pomace). In a previous study, we used phosphogypsum (PG), in co-composting with organic wastes. Three composts were produced; their PG content was of 0 (AT), 10 (A10), and 30% (A30). In the present study, we focused on their derived compost teas. The physico-chemical characterization of the different compost teas showed that those from A10 and A30 composts presented higher P and Ca contents than that from control one (AT). The microbial characterization using DGGE showed a noticeable microbial diversity in the different compost teas and that the addition of 10% and 30% PG in the compost had different effects on the compost tea microbial diversity. The identification results showed that the addition of 10 and 30% of PG did not affect the presence of PGPR (plant growth-promoting rhizobacteria) and fungal soil antagonists in the compost teas. Two PGPRs were isolated from AT and A30 compost teas, and their effect on the growth of potato plants in vitro was evaluated.
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Affiliation(s)
- Mariem Samet
- Laboratoire d'Amélioration des Plantes et Valorisation des Agro-ressources, Ecole Nationale d'Ingénieurs de Sfax, Route Soukra Km 4, B.P 1173, 3038, Sfax, Tunisia.
| | - Fatma Karray
- Laboratoire des Bioprocédés Environnementaux, Centre de Biotechnologie de Sfax, Route Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia
| | - Najla Mhiri
- Laboratoire des Bioprocédés Environnementaux, Centre de Biotechnologie de Sfax, Route Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia
| | - Lotfi Kamoun
- Groupe Chimique Tunisien, Direction de la Recherche Scientifique, Route de Gabes km 3,5, 3000, Sfax, Tunisia
| | - Sami Sayadi
- Laboratoire des Bioprocédés Environnementaux, Centre de Biotechnologie de Sfax, Route Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia
| | - Radhia Gargouri-Bouzid
- Laboratoire d'Amélioration des Plantes et Valorisation des Agro-ressources, Ecole Nationale d'Ingénieurs de Sfax, Route Soukra Km 4, B.P 1173, 3038, Sfax, Tunisia
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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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He AL, Niu SQ, Zhao Q, Li YS, Gou JY, Gao HJ, Suo SZ, Zhang JL. Induced Salt Tolerance of Perennial Ryegrass by a Novel Bacterium Strain from the Rhizosphere of a Desert Shrub Haloxylon ammodendron. Int J Mol Sci 2018; 19:ijms19020469. [PMID: 29401742 PMCID: PMC5855691 DOI: 10.3390/ijms19020469] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 11/16/2022] Open
Abstract
Drought and soil salinity reduce agricultural output worldwide. Plant-growth-promoting rhizobacteria (PGPR) can enhance plant growth and augment plant tolerance to biotic and abiotic stresses. Haloxylon ammodendron, a C4 perennial succulent xerohalophyte shrub with excellent drought and salt tolerance, is naturally distributed in the desert area of northwest China. In our previous work, a bacterium strain numbered as M30-35 was isolated from the rhizosphere of H. ammodendron in Tengger desert, Gansu province, northwest China. In current work, the effects of M30-35 inoculation on salt tolerance of perennial ryegrass were evaluated and its genome was sequenced to identify genes associated with plant growth promotion. Results showed that M30-35 significantly enhanced growth and salt tolerance of perennial ryegrass by increasing shoot fresh and dry weights, chlorophyll content, root volume, root activity, leaf catalase activity, soluble sugar and proline contents that contributed to reduced osmotic potential, tissue K⁺ content and K⁺/Na⁺ ratio, while decreasing malondialdehyde (MDA) content and relative electric conductivity (REC), especially under higher salinity. The genome of M30-35 contains 4421 protein encoding genes, 12 rRNA, 63 tRNA-encoding genes and four rRNA operons. M30-35 was initially classified as a new species in Pseudomonas and named as Pseudomonas sp. M30-35. Thirty-four genes showing homology to genes associated with PGPR traits and abiotic stress tolerance were identified in Pseudomonas sp. M30-35 genome, including 12 related to insoluble phosphorus solubilization, four to auxin biosynthesis, four to other process of growth promotion, seven to oxidative stress alleviation, four to salt and drought tolerance and three to cold and heat tolerance. Further study is needed to clarify the correlation between these genes from M30-35 and the salt stress alleviation of inoculated plants under salt stress. Overall, our research indicated that desert shrubs appear rich in PGPRs that can help important crops tolerate abiotic stress.
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Affiliation(s)
- Ao-Lei He
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China.
| | - Shu-Qi Niu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China.
| | - Qi Zhao
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China.
| | - Yong-Sheng Li
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China.
| | - Jing-Yi Gou
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China.
| | - Hui-Juan Gao
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China.
| | - Sheng-Zhou Suo
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China.
| | - Jin-Lin Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China.
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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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9
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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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Korshunova TY, Mukhamatdyarova SR, Loginov ON. Molecular genetic and chemotaxonomic identification of the bacterium of the genus Ochrobactrum possessing oil-oxidizing and nitrogen-fixing activity. BIOL BULL+ 2017. [DOI: 10.1134/s1062359017050090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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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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12
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Draft Genome Sequence of the Plant Growth-Promoting Pseudomonas punonensis Strain D1-6 Isolated from the Desert Plant Erodium hirtum in Jordan. GENOME ANNOUNCEMENTS 2017; 5:5/2/e01437-16. [PMID: 28082490 PMCID: PMC5256217 DOI: 10.1128/genomea.01437-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pseudomonas punonensis strain D1-6 was isolated from roots of the desert plant Erodium hirtum, near the Dead Sea in Jordan. The genome of strain D1-6 reveals several key plant growth-promoting and herbicide-resistance genes, indicating a possible specialized role for this endophyte.
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13
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Korshunova TY, Ramírez-Bahena MH, Chetverikov SP, Igual JM, Peix Á, Loginov O. Pseudomonas turukhanskensis sp. nov., isolated from oil-contaminated soils. Int J Syst Evol Microbiol 2016; 66:4657-4664. [PMID: 27503709 DOI: 10.1099/ijsem.0.001406] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain named IB1.1T was isolated in a screening of hydrocarbon-degrading bacteria from oil-contaminated soils on the territory of the Turukhansk District of Krasnoyarsk Krai, East Siberia, Russia. The 16S rRNA gene sequence had 98.7 % identity with respect to the closest phylogenetic relative, Pseudomonas granadensis F-278,770T, and the next most closely related species with 98.6 % similarity was Pseudomonaspunonensis, suggesting that IB1.1T should be classified within the genus Pseudomonas. The analysis of housekeeping genes rpoB, rpoD and gyrB showed similarities lower than 90 % in all cases with respect to the closest relatives, confirming its phylogenetic affiliation. The strain showed a polar flagellum. The respiratory quinone was Q9. The major fatty acids were 16 : 1ω7c/16 : 1ω6c (summed feature 3), 18 : 1ω7c and 16 : 0. The strain was oxidase- and catalase-positive, but the arginine dihydrolase system was not present. Nitrate reduction, urease and β-galactosidase production, and aesculin hydrolysis were negative. The temperature range for growth was 4-34 °C, and the strain could grow at pH 11. The DNA G+C content was 58.5 mol%. DNA-DNA hybridization results showed values of less than 30 % relatedness with respect to the type strains of the eight most closely related species. Therefore, the dataset of genotypic, phenotypic and chemotaxonomic data support the classification of strain IB1.1T into a novel species of the genus Pseudomonas, for which the name Pseudomonasturukhanskensis sp. nov. is proposed. The type strain is IB1.1T (=VKM B-2935T=CECT 9091T).
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Affiliation(s)
- Tatiana Y Korshunova
- Laboratory of Biologically Active Agents, Ufa Institute of Biology of the Russian Academy of Sciences, Ufa, Russia
| | - 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
| | - Sergey P Chetverikov
- Laboratory of Biologically Active Agents, Ufa Institute of Biology of the Russian Academy of Sciences, Ufa, Russia
| | - Jose M 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
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA (CSIC), Salamanca, Spain.,Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
| | - Oleg Loginov
- Laboratory of Biologically Active Agents, Ufa Institute of Biology of the Russian Academy of Sciences, Ufa, Russia
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14
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Phylogenetic relationships of fluorescent pseudomonads deduced from the sequence analysis of 16S rRNA, Pseudomonas-specific and rpoD genes. 3 Biotech 2016; 6:80. [PMID: 28330150 PMCID: PMC4764612 DOI: 10.1007/s13205-016-0386-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 11/03/2015] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic relationship of 22 FLPs was
revealed on the basis of polymorphism in three genes namely 16S rDNA, Pseudomonas-specific and rpoD gene regions. The primers for 16S rDNA, Pseudomonas-specific region and rpoD gene region were amplifying a region of 1492, 990 and 760 bp, respectively, from all the isolates investigated. The RFLP analysis of the PCR products resulted in a classification of these fluorescent pseudomonads which was best answered by rpoD-based RFLP analysis. The 22 FLPs were placed in two major clusters and seven subclusters suggesting that these were genotypically heterogenous and might belong to several species within Pseudomonas sensu stricto. Sequence analysis of these three genes for three selected isolates AS5, AS7 and AS15 showed 16S rDNA and Pseudomonas-specific gene region phylogenies were generally similar, but rpoD gene phylogeny was somewhat different from these two genes. These results were also congruent with the results of RFLP of these three genes. rpoD provided comparable phylogenetic resolution to that of the 16S rRNA and Pseudomonas-specific genes at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution. This is particularly relevant in the context of a growing number of studies focusing on subspecies diversity, in which single-copy protein-encoding genes such as rpoD could complement and better justify the information provided by the 16S rRNA gene. Hence rpoD can be used further as an evolutionary chronometer for species-level identification.
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15
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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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16
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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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17
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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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18
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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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19
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Pseudomonas hunanensis sp. nov., Isolated from Soil Subjected to Long-Term Manganese Pollution. Curr Microbiol 2014; 69:19-24. [DOI: 10.1007/s00284-014-0545-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/04/2014] [Indexed: 10/25/2022]
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20
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Toro M, Ramírez-Bahena MH, Cuesta MJ, Velázquez E, Peix A. Pseudomonas guariconensis sp. nov., isolated from rhizospheric soil. Int J Syst Evol Microbiol 2013; 63:4413-4420. [PMID: 23847284 DOI: 10.1099/ijs.0.051193-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We isolated a bacterial strain designated PCAVU11(T) in the course of a study of phosphate-solubilizing bacteria occurring in rhizospheric soil of Vigna unguiculata (L.) Walp. in Guárico state, Venezuela. The 16S rRNA gene sequence had 99.2 % sequence similarity with respect to the most closely related species, Pseudomonas taiwanensis, and 99.1 % with respect to Pseudomonas entomophila, Pseudomonas plecoglossicida and Pseudomonas monteilii, on the basis of which PCAVU11(T) was classified as representing a member of the genus Pseudomonas. Analysis of the housekeeping genes rpoB, rpoD and gyrB confirmed the phylogenetic affiliation and showed sequence similarities lower than 95 % in all cases with respect to the above-mentioned closest relatives. Strain PCAVU11(T) showed two polar flagella. The respiratory quinone was Q9. The major fatty acids were 16 : 0 (25.7 %), 18 : 1ω7c (20.4 %), 17 : 0 cyclo (11.5 %) and 16 : 1ω7c/15 : 0 iso 2-OH in summed feature 3 (10.8 %). The strain was oxidase-, catalase- and urease-positive, the arginine dihydrolase system was present but nitrate reduction, β-galactosidase production and aesculin hydrolysis were negative. Strain PCAVU11(T) grew at 44 °C and at pH 10. The DNA G+C content was 61.5 mol%. DNA-DNA hybridization results showed values lower than 56 % relatedness with respect to the type strains of the four most closely related species. Therefore, the results of genotypic, phenotypic and chemotaxonomic analyses support the classification of strain PCAVU11(T) as representing a novel species of the genus Pseudomonas, which we propose to name Pseudomonas guariconensis sp. nov. The type strain is PCAVU11(T) ( = LMG 27394(T) = CECT 8262(T)).
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Affiliation(s)
- Marcia Toro
- Laboratorio de Estudios Ambientales, Instituto de Zoología Tropical, Facultad de Ciencias, Universidad Central de Venezuela, Caracas, Venezuela
| | - Martha-Helena Ramírez-Bahena
- Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA (CSIC), Spain.,Instituto de Recursos Naturales y Agrobiología. IRNASA-CSIC, Salamanca, Spain
| | - Maria José Cuesta
- Instituto de Recursos Naturales y Agrobiología. IRNASA-CSIC, Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Génetica, Universidad de Salamanca, Spain.,Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA (CSIC), Spain
| | - Alvaro Peix
- Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA (CSIC), Spain.,Instituto de Recursos Naturales y Agrobiología. IRNASA-CSIC, Salamanca, Spain
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