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Jin CZ, Wu XW, Zhuo Y, Yang Y, Li T, Jin FJ, Lee HG, Jin L. Genomic insights into a free-living, nitrogen-fixing but non nodulating novel species of Bradyrhizobium sediminis from freshwater sediment: Three isolates with the smallest genome within the genus Bradyrhizobium. Syst Appl Microbiol 2022; 45:126353. [PMID: 36030678 DOI: 10.1016/j.syapm.2022.126353] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/01/2022] [Accepted: 08/09/2022] [Indexed: 11/29/2022]
Abstract
Three bacterial strains isolated from a sediment sample collected at a water depth of 4 m from the Huaihe River in China were characterized. Phylogenetic investigation of the 16S rRNA gene and concatenated housekeeping gene sequences assigned the three novel strains in a highly supported lineage distinct from the published Bradyrhizobium species. The sequence similarities of the concatenated housekeeping genes of the three novel strains support their distinctiveness with the type strains of named species. Average nucleotide identity values of the genome sequences (79.9-82.5%) were below the threshold value of 95-96% for bacterial species circumscription. Close relatives to the novel strains are Bradyrhizobium erythrophlei, Bradyrhizobium jicamae, Bradyrhizobium lablabi, Bradyrhizobium mercantei, Bradyrhizobium elkanii and Bradyrhizobium japonicum. The complete genomes of strains S2-20-1T, S2-11-2 and S2-11-4 consist of single chromosomes of size 5.55, 5.45 and 5.47 Mb, respectively. These strains lack a symbiosis island, key nodulation and photosystem genes. Based on the data presented here, the three strains represent a novel species for which the name Bradyrhizobium sediminis sp. nov. is proposed for S2-20-1T as the type strain. Those three strains are proposed as novel species in free-living Bradyrhizobium isolates with the smallest genomes so far within the genus Bradyrhizobium. A number of functional differences between the three isolates and other published genomes indicate that the genus Bradyrhizobium is extremely heterogeneous and has roles within the community including non-symbiotic nitrogen fixation.
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Affiliation(s)
- Chun-Zhi Jin
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China; Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Xue-Wen Wu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China
| | - Ye Zhuo
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China
| | - Yizi Yang
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 210-037, China
| | - Taihua Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China
| | - Feng-Jie Jin
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China
| | - Hyung-Gwan Lee
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Long Jin
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China.
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León-Barrios M, Flores-Félix JD, Pérez-Yépez J, Ramirez-Bahena MH, Pulido-Suárez L, Igual JM, Velázquez E, Peix Á. Definition of the novel symbiovar canariense within Mesorhizobium neociceri sp. nov., a new species of genus Mesorhizobium nodulating Cicer canariense in the "Caldera de Taburiente" National Park (La Palma, Canary Islands). Syst Appl Microbiol 2021; 44:126237. [PMID: 34332368 DOI: 10.1016/j.syapm.2021.126237] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 11/26/2022]
Abstract
Cicer canariense is a highly promiscuous wild chickpea nodulated by Mesorhizobium strains in La Palma Island located at Canary archipelago. Four of these strains, CCANP34, CCANP35T, CCANP38 and CCANP95 belong to a group phylogenetically close to Mesorhizobium caraganae with 100% similarity values in the 16S rRNA gene. However, the genomes of the strains CCANP35T and M. caraganae LMG 24397T obtained in this work showed ANIb and dDDH values of 90.02% and 44.1%, respectively. These values are lower than those currently accepted for different bacterial species showing that the Canarian strains do not belong to the species M. caraganae. The Canarian strains also differ from M. caraganae in the amounts of several fatty acids and in several phenotypic traits. Based on the obtained results the Canarian strains belong to a novel species for which we propose the name Mesorhizobium neociceri sp. nov. and whose type strain is CCANP35T. The results of the phylogenetic analyses of nodC and nifH symbiotic genes showed that the Canarian strains represent a novel symbiovar within genus Mesorhizobium phylogenetically divergent to that encompassing M. caraganae. We propose the names canariense and caraganae for the symbiovars encompassing the strains of M. neociceri and M. caraganae, respectively.
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Affiliation(s)
- Milagros León-Barrios
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, Tenerife, Spain
| | | | - Juan Pérez-Yépez
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, Tenerife, Spain
| | | | - Laura Pulido-Suárez
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, Tenerife, Spain
| | - José M Igual
- IRNASA-CSIC, Salamanca, Spain; Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA-CSIC, Salamanca, 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; Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca, Spain
| | - Álvaro Peix
- IRNASA-CSIC, Salamanca, Spain; Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
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Ramoneda J, Roux JJL, Frossard E, Frey B, Gamper HA. Geographical patterns of root nodule bacterial diversity in cultivated and wild populations of a woody legume crop. FEMS Microbiol Ecol 2021; 96:5874250. [PMID: 32691840 DOI: 10.1093/femsec/fiaa145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 07/20/2020] [Indexed: 12/23/2022] Open
Abstract
There is interest in understanding how cultivation, plant genotype, climate and soil conditions influence the biogeography of root nodule bacterial communities of legumes. For crops from regions with relict wild populations, this is of even greater interest because the effects of cultivation on symbiont communities can be revealed, which is of particular interest for bacteria such as rhizobia. Here, we determined the structure of root nodule bacterial communities of rooibos (Aspalathus linearis), a leguminous shrub endemic to South Africa. We related the community dissimilarities of the root nodule bacteria of 18 paired cultivated and wild rooibos populations to pairwise geographical distances, plant ecophysiological characteristics and soil physicochemical parameters. Using next-generation sequencing data, we identified region-, cultivation- and farm-specific operational taxonomic units for four distinct classes of root nodule bacterial communities, dominated by members of the genus Mesorhizobium. We found that while bacterial richness was locally increased by organic cultivation, strong biogeographical differentiation in the bacterial communities of wild rooibos disappeared with cultivation of one single cultivar across its entire cultivation range. This implies that expanding rooibos farming has the potential to endanger wild rooibos populations through the homogenisation of root nodule bacterial diversity.
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Affiliation(s)
- Josep Ramoneda
- Department of Environmental Systems Science, ETH Zurich, Eschikon 33, 8315 Lindau, Zurich, Switzerland
| | - Johannes J Le Roux
- Department of Biological Sciences, Macquarie University, Balaclava Rd, Macquarie Park NSW 2109, Sydney, Australia
| | - Emmanuel Frossard
- Department of Environmental Systems Science, ETH Zurich, Eschikon 33, 8315 Lindau, Zurich, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Hannes Andres Gamper
- Department of Environmental Systems Science, ETH Zurich, Eschikon 33, 8315 Lindau, Zurich, Switzerland.,Faculty of Science and Technology, Free University of Bolzen-Bolzano, Piazza Università, 1, 39100 Bolzano BZ, Italy
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Menéndez E, Pérez-Yépez J, Hernández M, Rodríguez-Pérez A, Velázquez E, León-Barrios M. Plant Growth Promotion Abilities of Phylogenetically Diverse Mesorhizobium Strains: Effect in the Root Colonization and Development of Tomato Seedlings. Microorganisms 2020; 8:microorganisms8030412. [PMID: 32183288 PMCID: PMC7144016 DOI: 10.3390/microorganisms8030412] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 11/21/2022] Open
Abstract
Mesorhizobium contains species widely known as nitrogen-fixing bacteria with legumes, but their ability to promote the growth of non-legumes has been poorly studied. Here, we analyzed the production of indole acetic acid (IAA), siderophores and the solubilization of phosphate and potassium in a collection of 24 strains belonging to different Mesorhizobium species. All these strains produce IAA, 46% solubilized potassium, 33% solubilize phosphate and 17% produce siderophores. The highest production of IAA was found in the strains Mesorhizobiumciceri CCANP14 and Mesorhizobiumtamadayense CCANP122, which were also able to solubilize potassium. Moreover, the strain CCANP14 showed the maximum phosphate solubilization index, and the strain CCANP122 was able to produce siderophores. These two strains were able to produce cellulases and cellulose and to originate biofilms in abiotic surfaces and tomato root surface. Tomato seedlings responded positively to the inoculation with these two strains, showing significantly higher plant growth traits than uninoculated seedlings. This is the first report about the potential of different Mesorhizobium species to promote the growth of a vegetable. Considering their use as safe for humans, animals and plants, they are an environmentally friendly alternative to chemical fertilizers for non-legume crops in the framework of sustainable agriculture.
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Affiliation(s)
- Esther Menéndez
- Mediterranean Institute for Agriculture, Environment and Development (MED), Instituto de Investigação e Formação Avançada, Universidade de Évora, 7006-554 Évora, Portugal;
| | - Juan Pérez-Yépez
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, 38200 Tenerife, Canary Islands, Spain; (J.P.-Y.); (A.R.-P.); (M.L.-B.)
| | - Mercedes Hernández
- Instituto de Productos Naturales y Agrobiología-CSIC, La Laguna, 38206 Tenerife, Canary Islands, Spain;
| | - Ana Rodríguez-Pérez
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, 38200 Tenerife, Canary Islands, Spain; (J.P.-Y.); (A.R.-P.); (M.L.-B.)
| | - Encarna Velázquez
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, 37007 Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA-CSIC), 37007 Salamanca, Spain
- Correspondence: ; Tel.: +34-923-294-532
| | - Milagros León-Barrios
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, 38200 Tenerife, Canary Islands, Spain; (J.P.-Y.); (A.R.-P.); (M.L.-B.)
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Estrella MJ, Fontana MF, Cumpa Velásquez LM, Torres Tejerizo GA, Diambra L, Hansen LH, Pistorio M, Sannazzaro AI. Mesorhizobium intechi sp. nov. isolated from nodules of Lotus tenuis in soils of the Flooding Pampa, Argentina. Syst Appl Microbiol 2020; 43:126044. [DOI: 10.1016/j.syapm.2019.126044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/21/2019] [Accepted: 11/04/2019] [Indexed: 01/16/2023]
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Deciphering the Factors for Nodulation and Symbiosis of Mesorhizobium Associated with Cicer arietinum in Northwest India. SUSTAINABILITY 2019. [DOI: 10.3390/su11247216] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The compatibility between rhizobia and legumes for nitrogen-fixing nodules and the stages of root hair curling, formation of infection thread, and nodulation initiation have been vitally studied, but the factors for the sustainable root surface colonization and efficient symbiosis within chickpea and rhizobia have been poorly investigated. Hence, we aimed to analyze phenotypic properties and phylogenetic relationships of root-nodule bacteria associated with chickpea (Cicer arietinum) in the north-west Indo Gangetic Plains (NW-IGP) region of Uttar Pradesh, India. In this study, 54 isolates were recovered from five agricultural locations. Strains exhibited high exopolysaccharide production and were capable of survival at 15–42 °C. Assays for phosphate solubilization, catalase, oxidase, Indole acetic acid (IAA) production, and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity revealed that all the tested isolates possessed plant growth-promoting potential. Metabolic profiling using Biolog plates indicated that patterns of substrate utilization differed considerably among isolates. A biofilm formation assay showed that isolates displayed a nearly four-fold range in their capacity for biofilm development. Inoculation experiments indicated that all isolates formed nodules on chickpea, but they exhibited more than a two-fold range in symbiotic efficiency. No nodules were observed on four other legumes (Phaseolus vulgaris, Pisum sativum, Lens culinaris, and Vigna mungo). Concatenated sequences from six loci (gap, edD, glnD, gnD, rpoB, and nodC) supported the assignment of all isolates to the species Mesorhizobium ciceri, with strain M. ciceri Ca181 as their closest relative.
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Liu Q, Liu HC, Zhou YG, Xin YH. Genetic diversity of glacier-inhabiting Cryobacterium bacteria in China and description of Cryobacterium zongtaii sp. nov. and Arthrobacter glacialis sp. nov. Syst Appl Microbiol 2019; 42:168-177. [DOI: 10.1016/j.syapm.2018.10.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 09/20/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
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8
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Sannazzaro AI, Torres Tejerizo G, Fontana MF, Cumpa Velásquez LM, Hansen LH, Pistorio M, Estrella MJ. Mesorhizobium sanjuanii sp. nov., isolated from nodules of Lotus tenuis in the saline-alkaline lowlands of Flooding Pampa, Argentina. Int J Syst Evol Microbiol 2018; 68:2936-2942. [DOI: 10.1099/ijsem.0.002924] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- A. I. Sannazzaro
- 1IIB-INTECH (Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico Chascomús), CCT-La Plata, CONICET – Universidad Nacional de San Martín – Avenida Intendente Marino, Km 8.2, (7130) Chascomús, Argentina
| | - G. Torres Tejerizo
- 2IBBM (Instituto de Biotecnología y Biología Molecular), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - M. F. Fontana
- 1IIB-INTECH (Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico Chascomús), CCT-La Plata, CONICET – Universidad Nacional de San Martín – Avenida Intendente Marino, Km 8.2, (7130) Chascomús, Argentina
| | - L. M. Cumpa Velásquez
- 1IIB-INTECH (Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico Chascomús), CCT-La Plata, CONICET – Universidad Nacional de San Martín – Avenida Intendente Marino, Km 8.2, (7130) Chascomús, Argentina
| | - L. H. Hansen
- 3Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark
| | - M. Pistorio
- 2IBBM (Instituto de Biotecnología y Biología Molecular), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - M. J. Estrella
- 1IIB-INTECH (Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico Chascomús), CCT-La Plata, CONICET – Universidad Nacional de San Martín – Avenida Intendente Marino, Km 8.2, (7130) Chascomús, Argentina
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Tong W, Li X, Huo Y, Zhang L, Cao Y, Wang E, Chen W, Tao S, Wei G. Genomic insight into the taxonomy of Rhizobium genospecies that nodulate Phaseolus vulgaris. Syst Appl Microbiol 2018; 41:300-310. [PMID: 29576402 DOI: 10.1016/j.syapm.2018.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 10/17/2022]
Abstract
Due to the wide cultivation of bean (Phaseolus vulgaris L.), rhizobia associated with this plant have been isolated from many different geographical regions. In order to investigate the species diversity of bean rhizobia, comparative genome sequence analysis was performed in the present study for 69 Rhizobium strains mainly isolated from root nodules of bean and clover (Trifolium spp.). Based on genome average nucleotide identity, digital DNA:DNA hybridization, and phylogenetic analysis of 1,458 single-copy core genes, these strains were classified into 28 clusters, consistent with their species definition based on multilocus sequence analysis (MLSA) of atpD, glnII, and recA. The bean rhizobia were found in 16 defined species and nine putative novel species; in addition, 35 strains previously described as Rhizobium etli, Rhizobium phaseoli, Rhizobium vallis, Rhizobium gallicum, Rhizobium leguminosarum and Rhizobium spp. should be renamed. The phylogenetic patterns of symbiotic genes nodC and nifH were highly host-specific and inconsistent with the genomic phylogeny. Multiple symbiovars (sv.) within the Rhizobium species were found as a common feature: sv. phaseoli, sv. trifolii and sv. viciae in Rhizobium anhuiense; sv. phaseoli and sv. mimosae in Rhizobium sophoriradicis/R. etli/Rhizobium sp. III; sv. phaseoli and sv. trifolii in Rhizobium hidalgonense/Rhizobium acidisoli; sv. phaseoli and sv. viciae in R. leguminosarum/Rhizobium sp. IX; sv. trifolii and sv. viciae in Rhizobium laguerreae. Thus, genomic comparison revealed great species diversity in bean rhizobia, corrected the species definition of some previously misnamed strains, and demonstrated the MLSA a valuable and simple method for defining Rhizobium species.
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Affiliation(s)
- Wenjun Tong
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiangchen Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yunyun Huo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lu Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ying Cao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México D.F., Mexico
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Shiheng Tao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Molecular phylogeny of Bradyrhizobium bacteria isolated from root nodules of tribe Genisteae plants growing in southeast Poland. Syst Appl Microbiol 2017; 40:482-491. [DOI: 10.1016/j.syapm.2017.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/24/2017] [Accepted: 09/20/2017] [Indexed: 01/27/2023]
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11
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Carro L, Nouioui I. Taxonomy and systematics of plant probiotic bacteria in the genomic era. AIMS Microbiol 2017; 3:383-412. [PMID: 31294168 PMCID: PMC6604993 DOI: 10.3934/microbiol.2017.3.383] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022] Open
Abstract
Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.
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Affiliation(s)
- Lorena Carro
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Imen Nouioui
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
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Mohamad R, Willems A, Le Quéré A, Maynaud G, Pervent M, Bonabaud M, Dubois E, Cleyet-Marel JC, Brunel B. Mesorhizobium delmotii and Mesorhizobium prunaredense are two new species containing rhizobial strains within the symbiovar anthyllidis. Syst Appl Microbiol 2017; 40:135-143. [DOI: 10.1016/j.syapm.2017.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/18/2017] [Accepted: 01/27/2017] [Indexed: 11/28/2022]
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13
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León-Barrios M, Pérez-Yépez J, Dorta P, Garrido A, Jiménez C. Alkalinity of Lanzarote soils is a factor shaping rhizobial populations with Sinorhizobium meliloti being the predominant microsymbiont of Lotus lancerottensis. Syst Appl Microbiol 2017; 40:171-178. [PMID: 28216096 DOI: 10.1016/j.syapm.2016.12.005] [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] [Received: 10/27/2016] [Revised: 12/15/2016] [Accepted: 12/18/2016] [Indexed: 10/20/2022]
Abstract
Lotus lancerottensis is an endemic species that grows widely throughout Lanzarote Island (Canary Is.). Characterization of 48 strains isolated from root nodules of plants growing in soils from eleven locations on the island showed that 38 isolates (79.1%) belonged to the species Sinorhizobium meliloti, whereas only six belonged to Mesorhizobium sp., the more common microsymbionts for the Lotus. Other genotypes containing only one isolate were classified as Pararhizobium sp., Sinorhizobium sp., Phyllobacterium sp. and Bradyrhizobium-like. Strains of S. meliloti were distributed along the island and, in most of the localities they were exclusive or major microsymbionts of L. lancerottensis. Phylogeny of the nodulation nodC gene placed the S. meliloti strains within symbiovar lancerottense and the mesorhizobial strains with the symbiovar loti. Although strains from both symbiovars produced effective N2-fixing nodules, S. meliloti symbiovar lancerottense was clearly the predominant microsymbiont of L. lancerottensis. This fact correlated with the better adaptation of strains of this species to the alkaline soils of Lanzarote, as in vitro characterization showed that while the mesorhizobial strains were inhibited by alkaline pH, S. meliloti strains grew well at pH 9.
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Affiliation(s)
- Milagros León-Barrios
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, 38200 La Laguna, Tenerife, Canary Islands, Spain.
| | - Juan Pérez-Yépez
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, 38200 La Laguna, Tenerife, Canary Islands, Spain
| | - Paola Dorta
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, 38200 La Laguna, Tenerife, Canary Islands, Spain
| | - Ana Garrido
- Granja Agrícola Experimental, Área de Agricultura y Ganadería, Cabildo de Lanzarote, Canary Islands, Spain
| | - Concepción Jiménez
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, 38200 La Laguna, Tenerife, Canary Islands, Spain
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Davis II EW, Weisberg AJ, Tabima JF, Grunwald NJ, Chang JH. Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria. PeerJ 2016; 4:e2222. [PMID: 27547538 PMCID: PMC4958008 DOI: 10.7717/peerj.2222] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/15/2016] [Indexed: 11/20/2022] Open
Abstract
Understanding the population structure and genetic diversity of plant pathogens, as well as the effect of agricultural practices on pathogen evolution, is important for disease management. Developments in molecular methods have contributed to increase the resolution for accurate pathogen identification, but those based on analysis of DNA sequences can be less straightforward to use. To address this, we developed Gall-ID, a web-based platform that uses DNA sequence information from 16S rDNA, multilocus sequence analysis and whole genome sequences to group disease-associated bacteria to their taxonomic units. Gall-ID was developed with a particular focus on gall-forming bacteria belonging to Agrobacterium, Pseudomonas savastanoi, Pantoea agglomerans, and Rhodococcus. Members of these groups of bacteria cause growth deformation of plants, and some are capable of infecting many species of field, orchard, and nursery crops. Gall-ID also enables the use of high-throughput sequencing reads to search for evidence for homologs of characterized virulence genes, and provides downloadable software pipelines for automating multilocus sequence analysis, analyzing genome sequences for average nucleotide identity, and constructing core genome phylogenies. Lastly, additional databases were included in Gall-ID to help determine the identity of other plant pathogenic bacteria that may be in microbial communities associated with galls or causative agents in other diseased tissues of plants. The URL for Gall-ID is http://gall-id.cgrb.oregonstate.edu/.
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Affiliation(s)
- Edward W. Davis II
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR, United States
| | - Alexandra J. Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Javier F. Tabima
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Niklaus J. Grunwald
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR, United States
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, United States
- Horticultural Crops Research Laboratory, USDA-ARS, Corvallis, OR, United States
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR, United States
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, United States
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Gnat S, Małek W, Oleńska E, Wdowiak-Wróbel S, Kalita M, Rogalski J, Wójcik M. Multilocus sequence analysis supports the taxonomic position of Astragalus glycyphyllos symbionts based on DNA–DNA hybridization. Int J Syst Evol Microbiol 2016; 66:1906-1912. [DOI: 10.1099/ijsem.0.000862] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Sebastian Gnat
- Department of Veterinary Microbiology, University of Life Sciences, 13 Akademicka st., 20-950 Lublin, Poland
| | - Wanda Małek
- Department of Genetics and Microbiology, University of Maria Curie-Sklodowska, 19 Akademicka st., 20-033 Lublin, Poland
| | - Ewa Oleńska
- Department of Genetics and Evolution, University of Bialystok, 1J Ciolkowskiego st., 15-245 Bialystok, Poland
| | - Sylwia Wdowiak-Wróbel
- Department of Genetics and Microbiology, University of Maria Curie-Sklodowska, 19 Akademicka st., 20-033 Lublin, Poland
| | - Michał Kalita
- Department of Genetics and Microbiology, University of Maria Curie-Sklodowska, 19 Akademicka st., 20-033 Lublin, Poland
| | - Jerzy Rogalski
- Department of Biochemistry, University of Maria Curie-Sklodowska, 19 Akademicka st., 20-033 Lublin, Poland
| | - Magdalena Wójcik
- Department of Genetics and Microbiology, University of Maria Curie-Sklodowska, 19 Akademicka st., 20-033 Lublin, Poland
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16S-gyrB-rpoB multilocus sequence analysis for species identification in the genus Microbispora. Antonie van Leeuwenhoek 2016; 109:801-15. [DOI: 10.1007/s10482-016-0680-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
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Udaondo Z, Molina L, Segura A, Duque E, Ramos JL. Analysis of the core genome and pangenome ofPseudomonas putida. Environ Microbiol 2015; 18:3268-3283. [DOI: 10.1111/1462-2920.13015] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/04/2015] [Accepted: 08/06/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Zulema Udaondo
- Biotechnology Technological Area; Abengoa Research; Calle Energía Solar 1, Building E, Campus Palmas Altas 41014 Sevilla Spain
| | - Lázaro Molina
- Department of Environmental Protection; Estación Experimental del Zaidín; Consejo Superior de Investigaciones Científicas. C/ Profesor Albareda 1 18008 Granada Spain
| | - Ana Segura
- Biotechnology Technological Area; Abengoa Research; Calle Energía Solar 1, Building E, Campus Palmas Altas 41014 Sevilla Spain
| | - Estrella Duque
- Biotechnology Technological Area; Abengoa Research; Calle Energía Solar 1, Building E, Campus Palmas Altas 41014 Sevilla Spain
| | - Juan L. Ramos
- Biotechnology Technological Area; Abengoa Research; Calle Energía Solar 1, Building E, Campus Palmas Altas 41014 Sevilla Spain
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