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Yan N, Xia H, Hou W, Wang H, Wang H, Zhou M. Biological Characterization of Pseudomonas fluorescens Phage Pf17397_F_PD1 and Its Application in Food Preservation. J Food Prot 2023; 86:100125. [PMID: 37406883 DOI: 10.1016/j.jfp.2023.100125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023]
Abstract
In order to explore the application prospects of phages for controlling bacterial contamination, a lytic phage Pf17397_F_PD1 (Later abbreviated as PD1) was isolated from fish guts using Pseudomonas fluorescens ATCC 17397 as the host bacterium. The phage displayed short latency (18 min), long lysis period (212 min), and high lysis volume (1.47 × 102 PFU/each cell). It displayed wide temperature (30-70°C) and pH (4-11) tolerance. Genomic comparison revealed a maximum sequence identity of 48.65% between phage PD1 and other identified phages, indicating that PD1 was a new phage. The phage PD1 significantly inhibited the growth of P. fluorescens in milk and grass carp at 4°C and 25°C. Compared to the negative control, bacterial levels in milk stored at 25°C for 48 h were reduced by 2.71 log CFU/mL and 2.84 log CFU/mL at the multiplicity of infection (MOI) of 100 and 1,000, respectively. In contrast, when grass carp were stored at 25°C for 24 h, the bacterial load was reduced by 1.28 log CFU/g and 2.64 log CFU/g compared to the control (MOI of 100 and 1,000). When the phage was applied for preservation of grass carp blocks, total volatile salt nitrogen (TVB-N) values of phage-treated samples increased by 6.8 mg/100 g and 7.5 mg/100 g at MOI of 100 and 1,000, respectively, after 7 days of storage, which was significantly lower than that of the control group (15.83 mg/100 g). This study showed that phage PD1 was a good natural biological antimicrobial agent against P. fluorescens ATCC 17397.
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Affiliation(s)
- Na Yan
- School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430000, China
| | - Hai Xia
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430000, China
| | - Wenfu Hou
- School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430000, China
| | - Huajuan Wang
- School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430000, China
| | - Hongxun Wang
- School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430000, China.
| | - Min Zhou
- School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430000, China.
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2
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Atanasov KE, Galbis DM, Cornadó D, Serpico A, Sánchez G, Bosch M, Ferrer A, Altabella T. Pseudomonas fitomaticsae sp. nov., isolated at Marimurtra Botanical Garden in Blanes, Catalonia, Spain. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
In the framework of the research project called fitomatics, we have isolated and characterized a bacterial plant-endophyte from the rhizomes of Iris germanica, hereafter referred to as strain FIT81T. The bacterium is Gram negative, rod-shaped with lophotrichous flagella, and catalase- and oxidase-positive. The optimal growth temperature of strain FIT81T is 28 °C, although it can grow within a temperature range of 4–32 °C. The pH growth tolerance ranges between pH 5 and 10, and it tolerates 4% (w/v) NaCl. A 16S rRNA phylogenetic analysis positioned strain FIT81T within the genus
Pseudomonas
, and multilocus sequence analysis revealed that
Pseudomonas gozinkensis
IzPS32dT,
Pseudomonas glycinae
MS586T,
Pseudomonas allokribbensis
IzPS23T, 'Pseudomonas kribbensis' 46–2 and
Pseudomonas koreensis
PS9-14T are the top five most closely related species, which were selected for further genome-to-genome comparisons, as well as for physiological and chemotaxonomic characterization. The genome size of strain FIT81T is 6 492 796 base-pairs long, with 60.6 mol% of G+C content. Average nucleotide identity and digital DNA–DNA hybridization analyses yielded values of 93.6 and 56.1%, respectively, when the FIT81T genome was compared to that of the closest type strain
P. gozinkensis
IzPS32dT. Taken together, the obtained genomic, physiologic and chemotaxonomic data indicate that strain FIT81T is different from its closest relative species, which lead us to suggest that it is a novel species to be included in the list of type strains with the name Pseudomonas fitomaticsae sp. nov. (FIT81T=CECT 30374T=DSM 112699T).
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Affiliation(s)
- Kostadin Evgeniev Atanasov
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
- Department of Biology, Healthcare and the Environment, Plant Physiology Section, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
| | - David Miñana Galbis
- Department of Biology, Healthcare and the Environment, Microbiology Section, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
| | - Deborah Cornadó
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Annabel Serpico
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Guiomar Sánchez
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Montserrat Bosch
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Albert Ferrer
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
| | - Teresa Altabella
- Department of Biology, Healthcare and the Environment, Plant Physiology Section, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
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3
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Atanasov KE, Galbis DM, Gallego J, Serpico A, Bosch M, Altabella T, Ferrer A. Pseudomonas germanica sp. nov., isolated from Iris germanica rhizomes. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005268] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Through bacterial plant–endophyte extraction from rhizomes of Iris germanica plant, a Gram-stain-negative, aerobic, catalase- and oxidase-positive gammaproteobacterial strain, referred to as FIT28T, was isolated. FIT28T shows vigorous growth on nutrient rich media within the temperature range of 4–35 °C, with optimal growth at 28 °C, a wide pH tolerance from pH 5 to 11, and salt tolerance up to 6 % (w/v) NaCl. Colonies are white-yellow and quickly become mucoid. The results of analysis of the 16S rRNA gene sequence placed the strain within the genus
Pseudomonas
, and multilocus sequence analysis (MLSA) using 16S rRNA, rpoB, gyrB and rpoD concatenated sequences revealed that the closest relatives of FIT28T are
Pseudomonas zeae
OE48.2T, '
Pseudomonas crudilactis
' UCMA 17988,
Pseudomonas tensinigenes
ZA5.3T,
Pseudomonas helmanticensis
OHA11T,
Pseudomonas baetica
a390T,
Pseudomonas iridis
P42T,
Pseudomonas atagonensis
PS14T and
Pseudomonas koreensis
Ps 9-14T, within the
Pseudomonas koreensis
subgroup of the
Pseudomonas fluorescens
lineage. The genome size of FIT28T is about 6.7 Mb with 59.09 mol% DNA G+C content. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values calculated from the genomic sequences of FIT28T, and the closely related
P. zeae
OE48.2T are 95.23 and 63.4 %, respectively. Biochemical, metabolic and chemotaxonomic studies further support our proposal that Pseudomonas germanica sp. nov., should be considered a novel species of the genus
Pseudomonas
. Hence, the type strain FIT28T (=LMG 32353T=DSM 112698T) has been deposited in public cell-type culture centres.
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Affiliation(s)
- Kostadin Evgeniev Atanasov
- Department of Biology, Healthcare and the Environment, Plant Physiology Section, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
| | - David Miñana Galbis
- Department of Biology, Healthcare and the Environment, Microbiology Section, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Julia Gallego
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Annabel Serpico
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Montserrat Bosch
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Teresa Altabella
- Department of Biology, Healthcare and the Environment, Plant Physiology Section, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
| | - Albert Ferrer
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
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4
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Rodríguez-Castrejón UE, Serafin-Muñoz AH, Alvarez-Vargas A, Cruz-Jímenez G, Noriega-Luna B. Isolation and molecular identification of native As-resistant bacteria: As(III) and As(V) removal capacity and possible mechanism of detoxification. Arch Microbiol 2022; 204:191. [PMID: 35194697 DOI: 10.1007/s00203-022-02794-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 11/26/2022]
Abstract
The study of arsenic (As)-resistant microorganisms with high As removal capacity is fundamental for the development of economically sustainable technologies used for the treatment of water contaminated with metalloid. In the current study, four bacterial strains were isolated from As-contaminated water samples of the Xichu region, Mexico. Based on 16S rRNA gene sequencing and phylogenetic analysis of the isolated strains, Rhodococcus gordoniae, Microbacterium hydrocarbonoxydans, Exiguobacterium indicum, and Pseudomonas kribbensis were identified as potential As removal strains. R. gordoniae shows the highest growth capacity in both As(III) and As(V). R. gordoniae, M. hydrocarbonoxydans, and E. indicum removed approximately 81.6, 79.9, and 61.7% of As(III), as well as 77.2, 68.9, and 74.8% of As(V), respectively. P. kribbensis removed only about 80.2% of As(V). This study contributes to the possible detoxification mechanisms employed by these bacteria. Such insight could be crucial in the successful implementation of in situ bioremediation programs using these little-known bacteria.
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Affiliation(s)
- U E Rodríguez-Castrejón
- Division of Engineering, Guanajuato Campus of the University of Guanajuato, Guanajuato, Mexico
| | - A H Serafin-Muñoz
- Division of Engineering, Guanajuato Campus of the University of Guanajuato, Guanajuato, Mexico.
| | - A Alvarez-Vargas
- Division of Natural and Exact Sciences, Guanajuato Campus of the University of Guanajuato, Guanajuato, Mexico
| | - G Cruz-Jímenez
- Division of Natural and Exact Sciences, Guanajuato Campus of the University of Guanajuato, Guanajuato, Mexico
| | - B Noriega-Luna
- Division of Engineering, Guanajuato Campus of the University of Guanajuato, Guanajuato, Mexico
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5
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Morimoto Y, Lu YJ, Zuo H, Aibibula Z, Tohya M, Kirikae T, Hiramatsu K, Daida H, Baba T. Pseudomonas allokribbensis sp. nov. and Pseudomonas gozinkensis sp. nov., Two New Species Isolated from a Volcanic Island, Izu Oshima, Japan. Curr Microbiol 2021; 78:1670-1677. [PMID: 33660045 DOI: 10.1007/s00284-021-02409-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/10/2021] [Indexed: 12/22/2022]
Abstract
The genomes of two Pseudomonas strains, IzPS23T and IzPS32dT isolated from soil samples of Izu Oshima were compared to Pseudomonas type strains. Whole-genome sequence analysis revealed both belong to the Pseudomonas fluorescens lineage. The average nucleotide identity values of the whole-genome sequences of IzPS23T and IzPS32dT compared with other type strains showed high correlations with Pseudomonas kribbensis (93.1%) and Pseudomonas glycinae (93.5%), respectively. Genome-to-genome distances between the whole-genome sequences of IzPS23T and IzPS32dT showed correlations with Pseudomonas kribbensis (51.0%) and Pseudomonas glycinae (53.2%), respectively. Genotypic and phenotypic analysis indicated the two strains were novel species, and were named Pseudomonas allokribbensis (IzPS23T = CECT 9961T, = LMG 31525T) and Pseudomonas gozinkensis (IzPS32dT = CECT 9962T, = LMG 31526T), respectively.
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Affiliation(s)
- Yuh Morimoto
- Department of Microbiology, Faculty of Medicine, Juntendo University, Tokyo, Japan.,Faculty of Health Science, Juntendo University, Tokyo, Japan
| | - Yu Jie Lu
- Center of Excellence for Infection Control Science, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Hui Zuo
- Department of Microbiology, Faculty of Medicine, Juntendo University, Tokyo, Japan.,Atopy (Allergy) Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Zulipiya Aibibula
- Atopy (Allergy) Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Mari Tohya
- Department of Microbiology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Teruo Kirikae
- Department of Microbiology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Keiichi Hiramatsu
- Department of Microbiology, Faculty of Medicine, Juntendo University, Tokyo, Japan.,Center of Excellence for Infection Control Science, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Hiroyuki Daida
- Faculty of Health Science, Juntendo University, Tokyo, Japan
| | - Tadashi Baba
- Department of Microbiology, Faculty of Medicine, Juntendo University, Tokyo, Japan. .,Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
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6
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Park JK, Chang DH, Rhee MS, Jeong H, Song J, Ku BJ, Kim SB, Lee M, Kim BC. Heminiphilus faecis gen. nov., sp. nov., a member of the family Muribaculaceae, isolated from mouse faeces and emended description of the genus Muribaculum. Antonie van Leeuwenhoek 2021; 114:275-286. [PMID: 33566238 DOI: 10.1007/s10482-021-01521-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 01/19/2021] [Indexed: 11/26/2022]
Abstract
The novel strain AM35T was isolated from the faeces of C57BL/6 mice. These cells are strictly anaerobic, gram negative, oxidase negative, catalase positive, rod-shaped and non-motile. The strain produced creamy yellowish colonies on brain heart infusion (BHI) agar with hemin. Growth was investigated at 30-41 °C in the presence of 0.5-1.5% (w/v) NaCl at pH 6.5-8.5. Taxonomic analysis based on 16S rRNA gene sequencing revealed that strain AM35T is affiliated with the family Muribaculaceae and closely related to the genus Muribaculum. The genomic DNA G + C content of strain AM35T was 47.8 mol%. We detected the whole-cell sugars ribose and galactose; meso-2,6-diaminopimelic acid was absent. The major fatty acids (> 10%) were anteiso-C15:0 and iso-C15:0; the major polar lipid was phosphatidylethanolamine. The major respiratory quinones were MK-10 and MK-11. Based on our phylogenetic, phenotypic and chemotaxonomic analyses, strain AM35T represents a novel genus within the family Muribaculaceae, for which we propose the name Heminiphilus faecis gen. nov., sp. nov. The type strain of Heminiphilus faecis gen. nov., sp. nov. is AM35T (= KCTC 15907 T = DSM 110151 T).
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Affiliation(s)
- Jun Kyu Park
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- 114 Bioventure Center, HealthBiome, Inc, Daejeon, South Korea
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Dong-Ho Chang
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Moon-Soo Rhee
- Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Haeyoung Jeong
- Infectious Disease Research Center, KRIBB, Daejeon, South Korea
- Gwanggyo R&D Center, Medytox Inc, 114 Central town-ro, Yeongtong-gu, Suwon, Gyeonggi-do, 16506, Republic of Korea
| | - Jinhoi Song
- 114 Bioventure Center, HealthBiome, Inc, Daejeon, South Korea
| | - Bon Jeong Ku
- Department of Internal Medicine, Chungnam National University School of Medicine, 282 Munhwa-ro, Jung-gu, Daejeon, 35015, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Mina Lee
- Department of Obstetrics and Gynecology, Chungnam National University College of Medicine, Daejeon, South Korea.
| | - Byoung-Chan Kim
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- 114 Bioventure Center, HealthBiome, Inc, Daejeon, South Korea.
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, UST, Daejeon, Republic of Korea.
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7
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Jia J, Wang X, Deng P, Ma L, Baird SM, Li X, Lu S. Pseudomonas glycinae sp. nov. isolated from the soybean rhizosphere. Microbiologyopen 2020; 9:e1101. [PMID: 32657018 PMCID: PMC7520993 DOI: 10.1002/mbo3.1101] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/31/2020] [Accepted: 06/20/2020] [Indexed: 01/26/2023] Open
Abstract
Strains MS586T and MS82, which are aerobic, Gram-negative, rod-shaped, and polar-flagellated bacteria, were isolated from the soybean rhizosphere in Mississippi. Taxonomic positions of MS586T and MS82 were determined using a polyphasic approach. 16S rRNA gene sequence analyses of the two strains showed high pairwise sequence similarities (>98%) to some Pseudomonas species. Analysis of the concatenated 16S rRNA, rpoB, rpoD, and gyrB gene sequences indicated that the strains belonging to the Pseudomonas koreensis subgroup (SG) shared the highest similarity with Pseudomonas kribbensis strain 46-2T . Analyses of average nucleotide identity (ANI), genome-to-genome distance, delineated MS586T and MS82 from other species within the genus Pseudomonas. The predominant quinone system of the strain was ubiquinone 9 (Q-9), and the DNA G+C content was 60.48 mol%. The major fatty acids were C16:0 , C17:0 cyclo, and the summed features 3 and 8 consisting of C16:1 ω7c/C16:1 ω6c and C18:1 ω7c/C18:1 ω6c, respectively. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. Based on these data, it is proposed that strains MS586T and MS82 represent a novel species within the genus Pseudomonas. The proposed name for the new species is Pseudomonas glycinae, and the type strain is MS586T (accession NRRL B-65441 = accession LMG 30275).
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Affiliation(s)
- Jiayuan Jia
- Department of Biochemistry, Molecular Biology, Entomology and Plant PathologyMississippi State UniversityMississippi StateMSUSA
| | - Xiaoqiang Wang
- Department of Biochemistry, Molecular Biology, Entomology and Plant PathologyMississippi State UniversityMississippi StateMSUSA
- Tobacco Research InstituteChinese Academy of Agricultural SciencesQingdaoChina
| | - Peng Deng
- Department of Biochemistry, Molecular Biology, Entomology and Plant PathologyMississippi State UniversityMississippi StateMSUSA
| | - Lin Ma
- Department of Biochemistry, Molecular Biology, Entomology and Plant PathologyMississippi State UniversityMississippi StateMSUSA
- Institute of Vegetable CropsJiangsu Academy of Agricultural SciencesNanjingChina
| | - Sonya M. Baird
- Department of Biochemistry, Molecular Biology, Entomology and Plant PathologyMississippi State UniversityMississippi StateMSUSA
| | - Xiangdong Li
- Department of Plant PathologyShandong Agricultural UniversityTaianChina
| | - Shi‐En Lu
- Department of Biochemistry, Molecular Biology, Entomology and Plant PathologyMississippi State UniversityMississippi StateMSUSA
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8
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Complete Genome Sequence of the Soil Bacterium Pseudomonas kribbensis Strain 46-2 T. Microbiol Resour Announc 2018; 7:MRA01161-18. [PMID: 30533839 PMCID: PMC6284727 DOI: 10.1128/mra.01161-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 11/08/2018] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas kribbensis is a novel species belonging to the Pseudomonas fluorescens intrageneric group of the genus Pseudomonas. Herein, we report the complete genome sequence of strain 46-2T, isolated from garden soil in Daejeon, South Korea. Pseudomonas kribbensis is a novel species belonging to the Pseudomonas fluorescens intrageneric group of the genus Pseudomonas. Herein, we report the complete genome sequence of strain 46-2T, isolated from garden soil in Daejeon, South Korea. The 6.32-Mb chromosome contains 5,626 coding sequences with a G+C content of 60.55%.
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9
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Tchagang CF, Xu R, Overy D, Blackwell B, Chabot D, Hubbard K, Doumbou CL, Bromfield ESP, Tambong JT. Diversity of bacteria associated with corn roots inoculated with Canadian woodland soils, and description of Pseudomonas aylmerense sp. nov. Heliyon 2018; 4:e00761. [PMID: 30186983 PMCID: PMC6120581 DOI: 10.1016/j.heliyon.2018.e00761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/24/2018] [Accepted: 08/24/2018] [Indexed: 11/15/2022] Open
Abstract
Bacteria associated with corn roots inoculated with soils collected from the Canadian woodlands were isolated and characterized. Genus-level identification based on 16S rRNA sequence analysis classified the 161 isolates in 19 genera. The majority (64%) of the isolates were affiliated with the genus Pseudomonas. Further analysis of the Pseudomonas isolates based on BLASTn and rpoD-rpoB-gyrB concatenated gene phylogeny revealed three unique clusters that could not be assigned to known species. This study reports the taxonomic description of one of the distinct lineages represented by two strains (S1E40T and S1E44) with P. lurida LMG 21995T, P. costantinii LMG 22119T, P. palleroniana LMG 23076T, P. simiae CCUG 50988T and P. extremorientalis LMG 19695T as the closest taxa. Both strains showed low ANIm (<90%) and genome-based DNA-DNA hybridization (<50%) values, which unequivocally delineated the new strains from the closest relatives. These findings were supported by multilocus sequence analysis (MLSA) and DNA fingerprinting. In addition, growth characteristics and biochemical tests revealed patterns that differed from the related species. Strains S1E40T and S1E44 are Gram-negative, aerobic, rod-shaped and motile by at least one flagellum; and grew optimally at 30 °C. The predominant polar lipid is phosphatidylethanolamine while the major respiratory quinone is ubiquinone-9. Based on phenotypic and genotypic data presented here, strains S1E40T and S1E44 represent a novel species for which the name Pseudomonas aylmerense sp. nov. is proposed. The type strain is S1E40T (= LMG 30784T = DOAB 703T = HAMI 3696T) with a G + C content of 61.6%.
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Affiliation(s)
- Caetanie F Tchagang
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada.,Institut des sciences de la santé et de la vie, Collège La Cité, 801 Aviation Parkway, Ottawa, Ontario, Canada
| | - Renlin Xu
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - David Overy
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Barbara Blackwell
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Denise Chabot
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Keith Hubbard
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Cyr Lézin Doumbou
- Institut des sciences de la santé et de la vie, Collège La Cité, 801 Aviation Parkway, Ottawa, Ontario, Canada
| | - Eden S P Bromfield
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - James T Tambong
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
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10
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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: 131] [Impact Index Per Article: 18.7] [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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