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van Lill M, Venter SN, Muema EK, Palmer M, Chan WY, Beukes CW, Steenkamp ET. SeqCode facilitates naming of South African rhizobia left in limbo. Syst Appl Microbiol 2024; 47:126504. [PMID: 38593622 DOI: 10.1016/j.syapm.2024.126504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
South Africa is well-known for the diversity of its legumes and their nitrogen-fixing bacterial symbionts. However, in contrast to their plant partners, remarkably few of these microbes (collectively referred to as rhizobia) from South Africa have been characterised and formally described. This is because the rules of the International Code of Nomenclature of Prokaryotes (ICNP) are at odds with South Africa's National Environmental Management: Biodiversity Act and its associated regulations. The ICNP requires that a culture of the proposed type strain for a novel bacterial species be deposited in two international culture collections and be made available upon request without restrictions, which is not possible under South Africa's current national regulations. Here, we describe seven new Mesorhizobium species obtained from root nodules of Vachellia karroo, an iconic tree legume distributed across various biomes in southern Africa. For this purpose, 18 rhizobial isolates were delineated into putative species using genealogical concordance, after which their plausibility was explored with phenotypic characters and average genome relatedness. For naming these new species, we employed the rules of the recently published Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode), which utilizes genome sequences as nomenclatural types. The work presented in this study thus provides an illustrative example of how the SeqCode allows for a standardised approach for naming cultivated organisms for which the deposition of a type strain in international culture collections is currently problematic.
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Affiliation(s)
- Melandré van Lill
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Esther K Muema
- Department of Soil Science, Faculty of AgriSciences, Stellenbosch University, South Africa
| | - Marike Palmer
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Wai Y Chan
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | | | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
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2
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Martinez-Romero E, Peix A, Hungria M, Mousavi SA, Martinez-Romero J, Young P. Guidelines for the description of rhizobial symbiovars. Int J Syst Evol Microbiol 2024; 74:006373. [PMID: 38743471 PMCID: PMC11165908 DOI: 10.1099/ijsem.0.006373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/25/2024] [Indexed: 05/16/2024] Open
Abstract
Rhizobia are bacteria that form nitrogen-fixing nodules in legume plants. The sets of genes responsible for both nodulation and nitrogen fixation are carried in plasmids or genomic islands that are often mobile. Different strains within a species sometimes have different host specificities, while very similar symbiosis genes may be found in strains of different species. These specificity variants are known as symbiovars, and many of them have been given names, but there are no established guidelines for defining or naming them. Here, we discuss the requirements for guidelines to describe symbiovars, propose a set of guidelines, provide a list of all symbiovars for which descriptions have been published so far, and offer a mechanism to maintain a list in the future.
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Affiliation(s)
| | - Alvaro Peix
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
- Interacción Planta-Microorganismo, Universidad de Salamanca, Unidad Asociada al CSIC por el IRNASA, Salamanca, Spain
| | | | | | | | - Peter Young
- Department of Biology, University of York, York YO10 5DD, UK
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3
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Ren J, Lu H, Lu S, Huang Z. Impacts of sulfamethoxazole stress on vegetable growth and rhizosphere bacteria and the corresponding mitigation mechanism. Front Bioeng Biotechnol 2024; 12:1303670. [PMID: 38390364 PMCID: PMC10882545 DOI: 10.3389/fbioe.2024.1303670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/02/2024] [Indexed: 02/24/2024] Open
Abstract
Antibiotics are an important pharmaceutical class excessively used by humans. Its presence in the soil can impact plant growth and induce antibiotic resistance. This research studies the effect of sulfamethoxazole (SMX) on plant growth, rhizosphere bacteria composition, and resistance genes. Two sets of vegetables (basil, cilantro, and spinach) were treated separately with water and SMX solution. The plant growth data and soil samples were collected and analyzed. The results revealed that SMX increased spinach leaf length (34.0%) while having no significant impacts on basil and cilantro. On the other hand, SMX improved the bacterial diversity in all samples. The shifts in the abundance of plant growth-promoting bacteria could indirectly affect vegetable stem and leaf length. SMX also significantly increased the abundance of resistance genes Sul1 and Sul2. A further study into the correlation between bacteria highlights the importance of Shingomonas and Alfipia for inhibiting the spread of key resistance gene hosts, namely, Pseudomonas, Stenotrophomonas, and Agrobacterium. This research provides insight into SMX's impact on vegetable growth and microbial diversity. It also points out important microbial interactions that could potentially be utilized to mitigate ARG proliferation.
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Affiliation(s)
- Jiawei Ren
- State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing, China
- Lake Forest Academy, Lake Forest, IL, United States
| | - Hongbin Lu
- State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing, China
- State Key Laboratory of Coal Conversion, Institute of Coal Chemistry, Chinese Academy of Sciences, Taiyuan, China
| | - Shaoyong Lu
- State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Zhanggen Huang
- State Key Laboratory of Coal Conversion, Institute of Coal Chemistry, Chinese Academy of Sciences, Taiyuan, China
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Eren Eroğlu AE, Eroğlu V, Yaşa İ. Genomic Insights into the Symbiotic and Plant Growth-Promoting Traits of " Candidatus Phyllobacterium onerii" sp. nov. Isolated from Endemic Astragalus flavescens. Microorganisms 2024; 12:336. [PMID: 38399740 PMCID: PMC10891626 DOI: 10.3390/microorganisms12020336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
A novel strain of Gram-negative, rod-shaped aerobic bacteria, identified as IY22, was isolated from the root nodules of Astragalus flavescens. The analysis of the 16S rDNA and recA (recombinase A) gene sequences indicated that the strain belongs to the genus Phyllobacterium. During the phylogenetic analysis, it was found that strain IY22 is closely related to P. trifolii strain PETP02T and P. bourgognense strain STM 201T. The genome of IY22 was determined to be 6,010,116 base pairs long with a DNA G+C ratio of 56.37 mol%. The average nucleotide identity (ANI) values showed a range from 91.7% to 93.6% when compared to its close relatives. Moreover, IY22 and related strains had digital DNA-DNA hybridization (dDDH) values ranging from 16.9% to 54.70%. Multiple genes (including nodACDSNZ, nifH/frxC, nifUS, fixABCJ, and sufABCDES) associated with symbiotic nitrogen fixation have been detected in strain IY22. Furthermore, this strain features genes that contribute to improving plant growth in various demanding environments. This study reports the first evidence of an association between A. flavescens and a rhizobial species. Native high-altitude legumes are a potential source of new rhizobia, and we believe that they act as a form of insurance for biodiversity against the threats of desertification and drought.
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Affiliation(s)
- Asiye Esra Eren Eroğlu
- Basic and Industrial Microbiology Section, Biology Department, Faculty of Science, Ege University, 35100 Izmir, Türkiye;
| | - Volkan Eroğlu
- Botany Section, Biology Department, Faculty of Science, Ege University, 35100 Izmir, Türkiye;
| | - İhsan Yaşa
- Basic and Industrial Microbiology Section, Biology Department, Faculty of Science, Ege University, 35100 Izmir, Türkiye;
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Weisberg AJ, Wu Y, Chang JH, Lai EM, Kuo CH. Virulence and Ecology of Agrobacteria in the Context of Evolutionary Genomics. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:1-23. [PMID: 37164023 DOI: 10.1146/annurev-phyto-021622-125009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Among plant-associated bacteria, agrobacteria occupy a special place. These bacteria are feared in the field as agricultural pathogens. They cause abnormal growth deformations and significant economic damage to a broad range of plant species. However, these bacteria are revered in the laboratory as models and tools. They are studied to discover and understand basic biological phenomena and used in fundamental plant research and biotechnology. Agrobacterial pathogenicity and capability for transformation are one and the same and rely on functions encoded largely on their oncogenic plasmids. Here, we synthesize a substantial body of elegant work that elucidated agrobacterial virulence mechanisms and described their ecology. We review findings in the context of the natural diversity that has been recently unveiled for agrobacteria and emphasize their genomics and plasmids. We also identify areas of research that can capitalize on recent findings to further transform our understanding of agrobacterial virulence and ecology.
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Affiliation(s)
- Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
| | - Yu Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan;
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan;
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan;
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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Provorov NA, Andronov EE, Kimeklis AK, Onishchuk OP, Igolkina AA, Karasev ES. Microevolution, speciation and macroevolution in rhizobia: Genomic mechanisms and selective patterns. FRONTIERS IN PLANT SCIENCE 2022; 13:1026943. [PMID: 36388581 PMCID: PMC9640933 DOI: 10.3389/fpls.2022.1026943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Nodule bacteria (rhizobia), N2-fixing symbionts of leguminous plants, represent an excellent model to study the fundamental issues of evolutionary biology, including the tradeoff between microevolution, speciation, and macroevolution, which remains poorly understood for free-living organisms. Taxonomically, rhizobia are extremely diverse: they are represented by nearly a dozen families of α-proteobacteria (Rhizobiales) and by some β-proteobacteria. Their genomes are composed of core parts, including house-keeping genes (hkg), and of accessory parts, including symbiotically specialized (sym) genes. In multipartite genomes of evolutionary advanced fast-growing species (Rhizobiaceae), sym genes are clustered on extra-chromosomal replicons (megaplasmids, chromids), facilitating gene transfer in plant-associated microbial communities. In this review, we demonstrate that in rhizobia, microevolution and speciation involve different genomic and ecological mechanisms: the first one is based on the diversification of sym genes occurring under the impacts of host-induced natural selection (including its disruptive, frequency-dependent and group forms); the second one-on the diversification of hkgs under the impacts of unknown factors. By contrast, macroevolution represents the polyphyletic origin of super-species taxa, which are dependent on the transfer of sym genes from rhizobia to various soil-borne bacteria. Since the expression of newly acquired sym genes on foreign genomic backgrounds is usually restricted, conversion of resulted recombinants into the novel rhizobia species involves post-transfer genetic changes. They are presumably supported by host-induced selective processes resulting in the sequential derepression of nod genes responsible for nodulation and of nif/fix genes responsible for symbiotic N2 fixation.
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Affiliation(s)
- Nikolay A. Provorov
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia
| | - Evgeny E. Andronov
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia
- Laboratory of Soil Biology and Biochemistry, V.V. Dokuchaev Soil Science Institute, Moscow, Russia
| | - Anastasiia K. Kimeklis
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia
- Department of Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia
| | - Olga P. Onishchuk
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia
| | - Anna A. Igolkina
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Evgeny S. Karasev
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia
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Rajkumari J, Katiyar P, Dheeman S, Pandey P, Maheshwari DK. The changing paradigm of rhizobial taxonomy and its systematic growth upto postgenomic technologies. World J Microbiol Biotechnol 2022; 38:206. [PMID: 36008736 DOI: 10.1007/s11274-022-03370-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 07/28/2022] [Indexed: 11/29/2022]
Abstract
Rhizobia are a diazotrophic group of bacteria that are usually isolated form the nodules in roots, stem of leguminous plants and are able to form nodules in the host plant owing to the presence of symbiotic genes. The rhizobial community is highly diverse, and therefore, the taxonomy and genera-wise classification of rhizobia has been constantly changing since the last three decades. This is mainly due to technical advancements, and shifts in definitions, resulting in a changing paradigm of rhizobia taxonomy. Initially, the taxonomic definitions at the species and sub species level were based on phylogenetic analysis of 16S rRNA sequence, followed by polyphasic approach to have phenotypic, biochemical, and genetic analysis including multilocus sequence analysis. Rhizobia mainly belonging to α- and β-proteobacteria, and recently new additions from γ-proteobacteria had been classified. Nowadays rhizobial taxonomy has been replaced by genome-based taxonomy that allows gaining more insights of genomic characteristics. These omics-technologies provide genome specific information that considers nodulation and symbiotic genes, along with molecular markers as taxonomic traits. Taxonomy based on complete genome sequence (genotaxonomy), average nucleotide identity, is now being considered as primary approach, resulting in an ongoing paradigm shift in rhizobial taxonomy. Also, pairwise whole-genome comparisons, phylogenomic analyses offer correlations between DNA and DNA re-association values that have delineated biologically important species. This review elaborates the present classification and taxonomy of rhizobia, vis-a-vis development of technical advancements, parameters and controversies associated with it, and describe the updated information on evolutionary lineages of rhizobia.
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Affiliation(s)
- Jina Rajkumari
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India
| | - Prashant Katiyar
- Department of Botany and Microbiology, Gurukula Kangri Vishwavidyalaya, Haridwar, 249-404, India
| | - Shrivardhan Dheeman
- Department of Microbiology, Sardar Bhagwan Singh University, Dehra Dun, Uttarakhand, 248161, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India.
| | - Dinesh Kumar Maheshwari
- Department of Botany and Microbiology, Gurukula Kangri Vishwavidyalaya, Haridwar, 249-404, India.
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Tiwari M, Mishra AK, Chakrabarty D. Agrobacterium-mediated gene transfer: recent advancements and layered immunity in plants. PLANTA 2022; 256:37. [PMID: 35819629 PMCID: PMC9274631 DOI: 10.1007/s00425-022-03951-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/19/2022] [Indexed: 05/15/2023]
Abstract
Plant responds to Agrobacterium via three-layered immunity that determines its susceptibility or resistance to Agrobacterium infection. Agrobacterium tumefaciens is a soil-borne Gram-negative bacterium that causes crown gall disease in plants. The remarkable feat of interkingdom gene transfer has been extensively utilised in plant biotechnology to transform plant as well as non-host systems. In the past two decades, the molecular mode of the pathogenesis of A. tumefaciens has been extensively studied. Agrobacterium has also been utilised as a premier model to understand the defence response of plants during plant-Agrobacterium interaction. Nonetheless, the threat of Agrobacterium-mediated crown gall disease persists and is associated with a huge loss of plant vigour in agriculture. Understanding the molecular dialogues between these two interkingdom species might provide a cure for crown gall disease. Plants respond to A. tumefaciens by mounting a three-layered immune response, which is manipulated by Agrobacterium via its virulence effector proteins. Comparative studies on plant defence proteins versus the counter-defence of Agrobacterium have shed light on plant susceptibility and tolerance. It is possible to manipulate a plant's immune system to overcome the crown gall disease and increase its competence via A. tumefaciens-mediated transformation. This review summarises the recent advances in the molecular mode of Agrobacterium pathogenesis as well as the three-layered immune response of plants against Agrobacterium infection.
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Affiliation(s)
- Madhu Tiwari
- Biotechnology and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
| | - Arun Kumar Mishra
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
| | - Debasis Chakrabarty
- Biotechnology and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Kuzmanović N, Biondi E, Overmann J, Puławska J, Verbarg S, Smalla K, Lassalle F. Genomic analysis provides novel insights into diversification and taxonomy of Allorhizobium vitis (i.e. Agrobacterium vitis). BMC Genomics 2022; 23:462. [PMID: 35733110 PMCID: PMC9219206 DOI: 10.1186/s12864-022-08662-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 05/17/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Allorhizobium vitis (formerly named Agrobacterium vitis or Agrobacterium biovar 3) is the primary causative agent of crown gall disease of grapevine worldwide. We obtained and analyzed whole-genome sequences of diverse All. vitis strains to get insights into their diversification and taxonomy. RESULTS Pairwise genome comparisons and phylogenomic analysis of various All. vitis strains clearly indicated that All. vitis is not a single species, but represents a species complex composed of several genomic species. Thus, we emended the description of All. vitis, which now refers to a restricted group of strains within the All. vitis species complex (i.e. All. vitis sensu stricto) and proposed a description of a novel species, All. ampelinum sp. nov. The type strain of All. vitis sensu stricto remains the current type strain of All. vitis, K309T. The type strain of All. ampelinum sp. nov. is S4T. We also identified sets of gene clusters specific to the All. vitis species complex, All. vitis sensu stricto and All. ampelinum, respectively, for which we predicted the biological function and infer the role in ecological diversification of these clades, including some we could experimentally validate. All. vitis species complex-specific genes confer tolerance to different stresses, including exposure to aromatic compounds. Similarly, All. vitis sensu stricto-specific genes confer the ability to degrade 4-hydroxyphenylacetate and a putative compound related to gentisic acid. All. ampelinum-specific genes have putative functions related to polyamine metabolism and nickel assimilation. Congruently with the genome-based classification, All. vitis sensu stricto and All. ampelinum were clearly delineated by MALDI-TOF MS analysis. Moreover, our genome-based analysis indicated that Allorhizobium is clearly separated from other genera of the family Rhizobiaceae. CONCLUSIONS Comparative genomics and phylogenomic analysis provided novel insights into the diversification and taxonomy of Allorhizobium vitis species complex, supporting our redefinition of All. vitis sensu stricto and description of All. ampelinum. Our pan-genome analyses suggest that these species have differentiated ecologies, each relying on specialized nutrient consumption or toxic compound degradation to adapt to their respective niche.
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Affiliation(s)
- Nemanja Kuzmanović
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany.
- Present address, Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Horticulture and Forests, Messeweg 11-12, 38104, Braunschweig, Germany.
| | - Enrico Biondi
- Department of Agricultural and Food Sciences (DISTAL), Plant Pathology, Alma Mater Studiorum-University of Bologna, Viale G. Fanin, 42, 40127, Bologna, Italy
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124, Braunschweig, Germany
| | - Joanna Puławska
- The National Institute of Horticultural Research, ul. Konstytucji 3 Maja 1/3, 96-100, Skierniewice, Poland
| | - Susanne Verbarg
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124, Braunschweig, Germany
| | - Kornelia Smalla
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
| | - Florent Lassalle
- Department of Infectious Disease Epidemiology, Imperial College London, St-Mary's Hospital Campus, Praed Street, London, W2 1NY, UK.
- Imperial College London, St-Mary's Hospital Campus, MRC Centre for Global Infectious Disease Analysis, Praed Street, London, W2 1NY, UK.
- Wellcome Sanger Institute, Pathogens and Microbes Programme, Wellcome Genome Campus, Saffron Walden, Hinxton, CB10 1RQ, UK.
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Mohamad R, Willems A, Le Quéré A, Prevent M, Maynaud G, Bonabaud M, Dubois E, Cleyet-Marel JC, Brunel B. Mesorhizobium ventifaucium sp. nov. and Mesorhizobium escarrei sp. nov., two novel root-nodulating species isolated from Anthyllis vulneraria. Syst Appl Microbiol 2022; 45:126341. [DOI: 10.1016/j.syapm.2022.126341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/23/2022] [Accepted: 06/07/2022] [Indexed: 10/18/2022]
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Characterization of the Agrobacterium octopine-cucumopine catabolic plasmid pAtAg67. Plasmid 2022; 121:102629. [DOI: 10.1016/j.plasmid.2022.102629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/06/2022] [Accepted: 03/29/2022] [Indexed: 11/21/2022]
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Almeida BK, Cline E, Sklar F, Afkhami ME. Hydrology shapes microbial communities and microbiome‐mediated growth of an Everglades tree island species. Restor Ecol 2022. [DOI: 10.1111/rec.13677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brianna K. Almeida
- Department of Biology University of Miami Coral Gables Florida 33146 USA
| | - Eric Cline
- South Florida Water Management District West Palm Beach Florida 33406 USA
| | - Fred Sklar
- South Florida Water Management District West Palm Beach Florida 33406 USA
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Chou L, Lin YC, Haryono M, Santos MNM, Cho ST, Weisberg AJ, Wu CF, Chang JH, Lai EM, Kuo CH. Modular evolution of secretion systems and virulence plasmids in a bacterial species complex. BMC Biol 2022; 20:16. [PMID: 35022048 PMCID: PMC8756689 DOI: 10.1186/s12915-021-01221-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/23/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Many named species as defined in current bacterial taxonomy correspond to species complexes. Uncertainties regarding the organization of their genetic diversity challenge research efforts. We utilized the Agrobacterium tumefaciens species complex (a.k.a. Agrobacterium biovar 1), a taxon known for its phytopathogenicity and applications in transformation, as a study system and devised strategies for investigating genome diversity and evolution of species complexes. RESULTS We utilized 35 genome assemblies, including 14 newly generated ones, to achieve a phylogenetically balanced sampling of A. tumefaciens. Our genomic analysis suggested that the 10 genomospecies described previously are distinct biological species and supported a quantitative guideline for species delineation. Furthermore, our inference of gene content and core-genome phylogeny allowed for investigations of genes critical in fitness and ecology. For the type VI secretion system (T6SS) involved in interbacterial competition and thought to be conserved, we detected multiple losses and one horizontal gene transfer. For the tumor-inducing plasmids (pTi) and pTi-encoded type IV secretion system (T4SS) that are essential for agrobacterial phytopathogenicity, we uncovered novel diversity and hypothesized their involvement in shaping this species complex. Intriguingly, for both T6SS and T4SS, genes encoding structural components are highly conserved, whereas extensive diversity exists for genes encoding effectors and other proteins. CONCLUSIONS We demonstrate that the combination of a phylogeny-guided sampling scheme and an emphasis on high-quality assemblies provides a cost-effective approach for robust analysis in evolutionary genomics. We show that the T6SS VgrG proteins involved in specific effector binding and delivery can be classified into distinct types based on domain organization. The co-occurrence patterns of VgrG-associated domains and the neighboring genes that encode different chaperones/effectors can be used to infer possible interacting partners. Similarly, the associations between plant host preference and the pTi type among these strains can be used to infer phenotype-genotype correspondence. Our strategies for multi-level investigations at scales that range from whole genomes to intragenic domains and phylogenetic depths from between- to within-species are applicable to other bacteria. Furthermore, modularity observed in the molecular evolution of genes and domains is useful for inferring functional constraints and informing experimental works.
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Affiliation(s)
- Lin Chou
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Chen Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Mindia Haryono
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Mary Nia M Santos
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan.,Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Chih-Feng Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan.,Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan. .,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan. .,Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.
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14
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Shen L, Liu JJ, Liu PX, An MM, He XW, Zhao GZ. A non-symbiotic novel species, Rhizobium populisoli sp. nov., isolated from rhizosphere soil of Populus popularis. Arch Microbiol 2021; 204:50. [PMID: 34935074 DOI: 10.1007/s00203-021-02706-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 10/19/2022]
Abstract
Strain XQZ8T, isolated from the rhizosphere soil of a Populus popularis plant in China, was characterized using a polyphasic taxonomic approach. Cells were Gram-negative, aerobic, non-spore-forming, and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XQZ8T was related to members of the genus Rhizobium and had the highest 16S rRNA gene sequence similarity to Rhizobium smilacinae PTYR-5T (96.6%). The average nucleotide identity and digital DNA-DNA hybridization value between strain XQZ8T and R. smilacinae PTYR-5T were 77.5% and 21.4%, respectively. TYGS whole-genome-based taxonomic and multi-locus sequence analyses of three concatenated housekeeping genes (atpD-recA-glnII) further indicated that strain XQZ8T was a new member of the genus Rhizobium. The major cellular fatty acids included summed feature 8 (C18:1 ω7c/C18:1 ω6c), summed feature 2 (C12:0 aldehyde/unknown 10.928), C16:0, and C19:0 cyclo ω8c. The major respiratory quinones were Q-9 and Q-10. The polar lipids were phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, an unidentified glycophospholipid, and three unidentified lipids. The genomic DNA G + C content of the strain was 60.1 mol%. Based on the phylogenetic, phenotypic, and genotypic characteristics, strain XQZ8T represents a novel species of the genus Rhizobium, for which the name Rhizobium populisoli sp. nov. is proposed. The type strain is XQZ8T (= JCM 34442T = GDMCC 1.2201T).
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Affiliation(s)
- Lei Shen
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, People's Republic of China.,College of Life Sciences, Langfang Normal University, Langfang, 065000, People's Republic of China
| | - Jing-Ju Liu
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Peng-Xiao Liu
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Miao-Miao An
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Xiang-Wei He
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Guo-Zhu Zhao
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, People's Republic of China.
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15
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Matveeva T, Otten L. Opine biosynthesis in naturally transgenic plants: Genes and products. PHYTOCHEMISTRY 2021; 189:112813. [PMID: 34192603 DOI: 10.1016/j.phytochem.2021.112813] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/03/2021] [Accepted: 05/07/2021] [Indexed: 06/13/2023]
Abstract
The plant pathogen Agrobacterium transfers DNA into plant cells by a specific transfer mechanism. Expression of this transferred DNA or T-DNA leads to crown gall tumors or abnormal, hairy roots and the synthesis of specific compounds, called opines. Opines are produced from common plant metabolites like sugars, amino acids and α-keto acids, which are combined into different low molecular weight structures by T-DNA-encoded opine synthase enzymes. Opines can be converted back by Agrobacterium into the original metabolites and used for agrobacterial growth. Recently it has been discovered that about 7% of Angiosperms carry T-DNA-like sequences. These result from ancient Agrobacterium transformation events, followed by spontaneous regeneration of transformed cells into natural genetically transformed organisms (nGMOs). Nearly all nGMOs identified up to date carry opine synthesis genes, several of these are intact and potentially encode opine synthesis. So far, only tobacco and cuscuta have been demonstrated to contain opines. Whereas opines from crown gall and hairy root tissues have been studied for over 60 years, those from the nGMOs remain to be explored.
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Affiliation(s)
- Tatiana Matveeva
- St. Petersburg State University, University Emb., 7/9, Saint Petersburg, Russia.
| | - Léon Otten
- Institute of Plant Molecular Biology, C.N.R.S, 67084, Strasbourg, France.
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16
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de Lajudie P, Mousavi SA, Young JPW. International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the closed meeting by videoconference, 6 July 2020. Int J Syst Evol Microbiol 2021; 71. [PMID: 33956594 PMCID: PMC8289204 DOI: 10.1099/ijsem.0.004784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Philippe de Lajudie
- IRD, University of Montpellier, CIRAD, INRAE, SupAgro, LSTM, Montpellier, France
| | - Seyed Abdollah Mousavi
- Ecosystems and Environment Research Programme, University of Helsinki, Finland.,Department of Biology, University of Turku, Finland
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
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17
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Padilla R, Gaillard V, Le TN, Bellvert F, Chapulliot D, Nesme X, Dessaux Y, Vial L, Lavire C, Kerzaon I. Development and validation of a UHPLC-ESI-QTOF mass spectrometry method to analyze opines, plant biomarkers of crown gall or hairy root diseases. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1162:122458. [PMID: 33383499 DOI: 10.1016/j.jchromb.2020.122458] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 11/14/2020] [Accepted: 11/17/2020] [Indexed: 11/26/2022]
Abstract
Opines are low-molecular-weight metabolites specifically biosynthesized by agrobacteria-transformed plant cells when plants are struck by crown gall and hairy root diseases, which cause uncontrolled tissue overgrowth. Transferred DNA is sustainably incorporated into the genomes of the transformed plant cells, so that opines constitute a persistent biomarker of plant infection by pathogenic agrobacteria and can be targeted for crown gall/hairy root disease diagnosis. We developed a general, rapid, specific and sensitive analytical method for overall opine detection using ultra-high-performance liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-MS-QTOF), with easy preparation of samples. Based on MS, MS/MS and chromatography data, the detection selectivity of a wide range of standard opines was validated in pure solution and in different plant extracts. The method was successfully used to detect different structural types of opines, including opines for which standard compounds are unavailable, in tumors or hairy roots induced by pathogenic strains. As the method can detect a wide range of opines in a single run, it represents a powerful tool for plant gall analysis and crown gall/hairy root disease diagnosis. Using an appropriate dilution of plant extract and a matrix-based calibration curve, the quantification ability of the method was validated for three opines belonging to different families (nopaline, octopine, mannopine), which were accurately quantified in plant tissue extracts.
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Affiliation(s)
- Rosa Padilla
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Vincent Gaillard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Thao Nhi Le
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France; Université d'Orléans, CNRS, Institut de Chimie Organique et Analytique, F-45067 Orléans, France
| | - Floriant Bellvert
- Université de Toulouse, CNRS, INRAE, INSA, Laboratoire Ingénierie des Systèmes Biologiques et des Procédés, F-31077 Toulouse, France; MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, F-31077 Toulouse, France
| | - David Chapulliot
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Xavier Nesme
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Yves Dessaux
- Université Paris-Sud, Université Paris-Saclay, CNRS, CEA, Institut de Biologie Intégrative de la Cellule, F-91190 Gif-sur-Yvette, France
| | - Ludovic Vial
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Céline Lavire
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Isabelle Kerzaon
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France.
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18
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Phylogenomics reveals the basis of adaptation of Pseudorhizobium species to extreme environments and supports a taxonomic revision of the genus. Syst Appl Microbiol 2020; 44:126165. [PMID: 33360413 DOI: 10.1016/j.syapm.2020.126165] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 11/21/2022]
Abstract
The family Rhizobiaceae includes many genera of soil bacteria, often isolated for their association with plants. Herein, we investigate the genomic diversity of a group of Rhizobium species and unclassified strains isolated from atypical environments, including seawater, rock matrix or polluted soil. Based on whole-genome similarity and core genome phylogeny, we show that this group corresponds to the genus Pseudorhizobium. We thus reclassify Rhizobium halotolerans, R. marinum, R. flavum and R. endolithicum as P. halotolerans sp. nov., P. marinum comb. nov., P. flavum comb. nov. and P. endolithicum comb. nov., respectively, and show that P. pelagicum is a synonym of P. marinum. We also delineate a new chemolithoautotroph species, P. banfieldiae sp. nov., whose type strain is NT-26T (=DSM 106348T=CFBP 8663T). This genome-based classification was supported by a chemotaxonomic comparison, with increasing taxonomic resolution provided by fatty acid, protein and metabolic profiles. In addition, we used a phylogenetic approach to infer scenarios of duplication, horizontal transfer and loss for all genes in the Pseudorhizobium pangenome. We thus identify the key functions associated with the diversification of each species and higher clades, shedding light on the mechanisms of adaptation to their respective ecological niches. Respiratory proteins acquired at the origin of Pseudorhizobium were combined with clade-specific genes to enable different strategies for detoxification and nutrition in harsh, nutrient-poor environments.
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19
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Yang LL, Jiang Z, Li Y, Wang ET, Zhi XY. Plasmids Related to the Symbiotic Nitrogen Fixation Are Not Only Cooperated Functionally but Also May Have Evolved over a Time Span in Family Rhizobiaceae. Genome Biol Evol 2020; 12:2002-2014. [PMID: 32687170 PMCID: PMC7719263 DOI: 10.1093/gbe/evaa152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2020] [Indexed: 12/17/2022] Open
Abstract
Rhizobia are soil bacteria capable of forming symbiotic nitrogen-fixing nodules associated with leguminous plants. In fast-growing legume-nodulating rhizobia, such as the species in the family Rhizobiaceae, the symbiotic plasmid is the main genetic basis for nitrogen-fixing symbiosis, and is susceptible to horizontal gene transfer. To further understand the symbioses evolution in Rhizobiaceae, we analyzed the pan-genome of this family based on 92 genomes of type/reference strains and reconstructed its phylogeny using a phylogenomics approach. Intriguingly, although the genetic expansion that occurred in chromosomal regions was the main reason for the high proportion of low-frequency flexible gene families in the pan-genome, gene gain events associated with accessory plasmids introduced more genes into the genomes of nitrogen-fixing species. For symbiotic plasmids, although horizontal gene transfer frequently occurred, transfer may be impeded by, such as, the host’s physical isolation and soil conditions, even among phylogenetically close species. During coevolution with leguminous hosts, the plasmid system, including accessory and symbiotic plasmids, may have evolved over a time span, and provided rhizobial species with the ability to adapt to various environmental conditions and helped them achieve nitrogen fixation. These findings provide new insights into the phylogeny of Rhizobiaceae and advance our understanding of the evolution of symbiotic nitrogen fixation.
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Affiliation(s)
- Ling-Ling Yang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, PR China
| | - Zhao Jiang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, PR China
| | - Yan Li
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, PR China
| | - En-Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City D.F., México
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, PR China
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20
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Fagorzi C, Ilie A, Decorosi F, Cangioli L, Viti C, Mengoni A, diCenzo GC. Symbiotic and Nonsymbiotic Members of the Genus Ensifer (syn. Sinorhizobium) Are Separated into Two Clades Based on Comparative Genomics and High-Throughput Phenotyping. Genome Biol Evol 2020; 12:2521-2534. [PMID: 33283865 PMCID: PMC7719227 DOI: 10.1093/gbe/evaa221] [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] [Accepted: 10/12/2020] [Indexed: 01/03/2023] Open
Abstract
Rhizobium–legume symbioses serve as paradigmatic examples for the study of mutualism evolution. The genus Ensifer (syn. Sinorhizobium) contains diverse plant-associated bacteria, a subset of which can fix nitrogen in symbiosis with legumes. To gain insights into the evolution of symbiotic nitrogen fixation (SNF), and interkingdom mutualisms more generally, we performed extensive phenotypic, genomic, and phylogenetic analyses of the genus Ensifer. The data suggest that SNF likely emerged several times within the genus Ensifer through independent horizontal gene transfer events. Yet, the majority (105 of 106) of the Ensifer strains with the nodABC and nifHDK nodulation and nitrogen fixation genes were found within a single, monophyletic clade. Comparative genomics highlighted several differences between the “symbiotic” and “nonsymbiotic” clades, including divergences in their pangenome content. Additionally, strains of the symbiotic clade carried 325 fewer genes, on average, and appeared to have fewer rRNA operons than strains of the nonsymbiotic clade. Initial characterization of a subset of ten Ensifer strains identified several putative phenotypic differences between the clades. Tested strains of the nonsymbiotic clade could catabolize 25% more carbon sources, on average, than strains of the symbiotic clade, and they were better able to grow in LB medium and tolerate alkaline conditions. On the other hand, the tested strains of the symbiotic clade were better able to tolerate heat stress and acidic conditions. We suggest that these data support the division of the genus Ensifer into two main subgroups, as well as the hypothesis that pre-existing genetic features are required to facilitate the evolution of SNF in bacteria.
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Affiliation(s)
- Camilla Fagorzi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Alexandru Ilie
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Francesca Decorosi
- Genexpress Laboratory, Department of Agriculture, Food, Environment and Forestry, University of Florence, Sesto Fiorentino, Italy
| | - Lisa Cangioli
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Carlo Viti
- Genexpress Laboratory, Department of Agriculture, Food, Environment and Forestry, University of Florence, Sesto Fiorentino, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - George C diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.,Department of Biology, Queen's University, Kingston, Ontario, Canada
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21
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Cabral Michel D, Martins da Costa E, Azarias Guimarães A, Soares de Carvalho T, Santos de Castro Caputo P, Willems A, de Souza Moreira FM. Bradyrhizobium campsiandrae sp. nov., a nitrogen-fixing bacterial strain isolated from a native leguminous tree from the Amazon adapted to flooded conditions. Arch Microbiol 2020; 203:233-240. [PMID: 32857180 DOI: 10.1007/s00203-020-02022-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/23/2020] [Accepted: 08/13/2020] [Indexed: 01/05/2023]
Abstract
The nitrogen-fixing bacterial strain UFLA 01-1174T was isolated from nodules of Campsiandra laurilifolia Benth. originating from the Amazon region, Brazil. Its taxonomic position was defined using a polyphasic approach. Analysis of the 16S rRNA gene placed the strain in the Bradyrhizobium genus, the closest species being B. guangdongense CCBAU 51649T and B. guangzhouense CCBAU 51670T, both with 99.8% similarity. Multilocus sequence analysis (MLSA) of recA, gyrB, glnII, rpoB, atpD, and dnaK indicated that UFLA 01-1174T is a new species, most closely related to B. stylosanthis BR 446T (94.4%) and B. manausense BR 3351T (93.7%). Average nucleotide identity (ANI) differentiated UFLA 01-1174T from the closest species with values lower than 90%. The G + C content in the DNA of UFLA 01-1174T is 63.6 mol%. Based on this data, we conclude that the strain represents a new species. The name proposed is Bradyrhizobium campsiandrae, with UFLA 01-1174T (= INPA 394BT = LMG 10099T) as type strain.
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Affiliation(s)
- Daniele Cabral Michel
- Setor de Biologia, Microbiologia e Processos Biológicos Do Solo, Departamento de Ciência Do Solo, Universidade Federal de Lavras, Campus UFLA, Lavras, Minas Gerais, 37200-900, Brazil
| | - Elaine Martins da Costa
- Universidade Federal Do Piauí, Campus Professora Cinobelina Elvas, Bom Jesus, Piauí, 64900-000, Brazil
| | - Amanda Azarias Guimarães
- Setor de Biologia, Microbiologia e Processos Biológicos Do Solo, Departamento de Ciência Do Solo, Universidade Federal de Lavras, Campus UFLA, Lavras, Minas Gerais, 37200-900, Brazil
| | - Teotonio Soares de Carvalho
- Setor de Biologia, Microbiologia e Processos Biológicos Do Solo, Departamento de Ciência Do Solo, Universidade Federal de Lavras, Campus UFLA, Lavras, Minas Gerais, 37200-900, Brazil
| | - Polyane Santos de Castro Caputo
- Setor de Biologia, Microbiologia e Processos Biológicos Do Solo, Departamento de Ciência Do Solo, Universidade Federal de Lavras, Campus UFLA, Lavras, Minas Gerais, 37200-900, Brazil
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Fatima Maria de Souza Moreira
- Setor de Biologia, Microbiologia e Processos Biológicos Do Solo, Departamento de Ciência Do Solo, Universidade Federal de Lavras, Campus UFLA, Lavras, Minas Gerais, 37200-900, Brazil.
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22
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Delamuta JRM, Scherer AJ, Ribeiro RA, Hungria M. Genetic diversity of Agrobacterium species isolated from nodules of common bean and soybean in Brazil, Mexico, Ecuador and Mozambique, and description of the new species Agrobacterium fabacearum sp. nov. Int J Syst Evol Microbiol 2020; 70:4233-4244. [PMID: 32568030 DOI: 10.1099/ijsem.0.004278] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Agrobacterium strains are associated with soil, plants and animals, and known mainly by their pathogenicity. We studied 14 strains isolated from nodules of healthy soybean and common bean plants in Brazil, Mexico, Ecuador and Mozambique. Sequence analysis of the 16S rRNA gene positioned the strains as Agrobacterium, but with low phylogenetic resolution. Multilocus sequence analysis (MLSA) of three partial housekeeping genes (glnII, gyrB and recA) positioned the strains in four distinct clades, with Agrobacterium pusense, Agrobacterium deltaense, Agrobacterium radiobacter and Agrobacterium sp. genomospecies G1. Analysis by BOX-PCR revealed high intraspecies diversity. Genomic analysis of representative strains of the three clades indicated that they carry the protelomerase telA gene, and MLSA analysis with six complete housekeeping genes (atpD, glnII, gyrB, recA, rpoB and thrC), as well as average nucleotide identity (less than 90 % with closest species) and digital DNA-DNA hybridization (less than 41 % with closest species) revealed that strain CNPSo 675T and Agrobacterium sp. genomospecies G1 compose a new species. Other phenotypic and genotypic characteristics were determined for the new clade. Although not able to re-nodulate the host, we hypothesize that several strains of Agrobacterium are endophytes in legume nodules, where they might contribute to plant growth. Our data support the description of the CNPSo 675T and Agrobacterium sp. genomospecies G1 strains as a new species, for which the name Agrobacterium fabacearum is proposed. The type strain is CNPSo 675T (=UMR 1457T=LMG 31642T) and is also deposited in other culture collections.
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Affiliation(s)
- Jakeline Renata Marçon Delamuta
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C and D, Lago Sul, 71605-001, Brasília, Federal District, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
| | - Anderson José Scherer
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
| | - Renan Augusto Ribeiro
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C and D, Lago Sul, 71605-001, Brasília, Federal District, Brazil
| | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C and D, Lago Sul, 71605-001, Brasília, Federal District, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
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23
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Paudel D, Liu F, Wang L, Crook M, Maya S, Peng Z, Kelley K, Ané JM, Wang J. Isolation, Characterization, and Complete Genome Sequence of a Bradyrhizobium Strain Lb8 From Nodules of Peanut Utilizing Crack Entry Infection. Front Microbiol 2020; 11:93. [PMID: 32117123 PMCID: PMC7020250 DOI: 10.3389/fmicb.2020.00093] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/16/2020] [Indexed: 12/29/2022] Open
Abstract
In many legumes, the colonization of roots by rhizobia is via "root hair entry" and its molecular mechanisms have been extensively studied. However, the nodulation of peanuts (Arachis hypogaea L.) by Bradyrhizobium strains requires an intercellular colonization process called "crack entry," which is understudied. To understand the intercellular crack entry process, it is critical to develop the tools and resources related to the rhizobium in addition to focus on investigating the mechanisms of the plant host. In this study, we isolated a Bradyrhizobium sp. strain, Lb8 from peanut root nodules and sequenced it using PacBio long reads. The complete genome sequence was a circular chromosome of 8,718,147 base-pair (bp) with an average GC content of 63.14%. No plasmid sequence was detected in the sequenced DNA sample. A total of 8,433 potential protein-encoding genes, one rRNA cluster, and 51 tRNA genes were annotated. Fifty-eight percent of the predicted genes showed similarity to genes of known functions and were classified into 27 subsystems representing various biological processes. The genome shared 92% of the gene families with B. diazoefficens USDA 110T. A presumptive symbiosis island of 778 Kb was detected, which included two clusters of nif and nod genes. A total of 711 putative protein-encoding genes were in this region, among which 455 genes have potential functions related to symbiotic nitrogen fixation and DNA transmission. Of 21 genes annotated as transposase, 16 were located in the symbiosis island. Lb8 possessed both Type III and Type IV protein secretion systems, and our work elucidated the association of flagellar Type III secretion systems in bradyrhizobia. These observations suggested that complex rearrangement, such as horizontal transfer and insertion of different DNA elements, might be responsible for the plasticity of the Bradyrhizobium genome.
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Affiliation(s)
- Dev Paudel
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Fengxia Liu
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Liping Wang
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Matthew Crook
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - Stephanie Maya
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Ze Peng
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Karen Kelley
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
| | - Jean-Michel Ané
- Departments of Bacteriology and Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, United States.,Plant Molecular and Cellular Biology Program, Genetic Institute, University of Florida, Gainesville, FL, United States
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Modulation of Quorum Sensing as an Adaptation to Nodule Cell Infection during Experimental Evolution of Legume Symbionts. mBio 2020; 11:mBio.03129-19. [PMID: 31992622 PMCID: PMC6989110 DOI: 10.1128/mbio.03129-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Over millions of years, changes have occurred in regulatory circuitries in response to genome reorganization and/or persistent changes in environmental conditions. How bacteria optimize regulatory circuitries is crucial to understand bacterial adaptation. Here, we analyzed the experimental evolution of the plant pathogen Ralstonia solanacearum into legume symbionts after the transfer of a natural plasmid encoding the essential mutualistic genes. We showed that the Phc quorum sensing system required for the virulence of the ancestral bacterium was reconfigured to improve intracellular infection of root nodules induced by evolved Ralstonia A single mutation in either the PhcB autoinducer synthase or the PhcQ regulator of the sensory cascade tuned the kinetics of activation of the central regulator PhcA in response to cell density so that the minimal stimulatory concentration of autoinducers needed for a given response was increased. Yet, a change in the expression of a PhcA target gene was observed in infection threads progressing in root hairs, suggesting early programming for the late accommodation of bacteria in nodule cells. Moreover, this delayed switch to the quorum sensing mode decreased the pathogenicity of the ancestral strain, illustrating the functional plasticity of regulatory systems and showing how a small modulation in signal response can produce drastic changes in bacterial lifestyle.IMPORTANCE Rhizobia are soil bacteria from unrelated genera able to form a mutualistic relationship with legumes. Bacteria induce the formation of root nodules, invade nodule cells, and fix nitrogen to the benefit of the plant. Rhizobial lineages emerged from the horizontal transfer of essential symbiotic genes followed by genome remodeling to activate and/or optimize the acquired symbiotic potential. This evolutionary scenario was replayed in a laboratory evolution experiment in which the plant pathogen Ralstonia solanacearum successively evolved the capacities to nodulate Mimosa pudica and poorly invade, then massively invade, nodule cells. In some lines, the improvement of intracellular infection was achieved by mutations modulating a quorum sensing regulatory system of the ancestral strain. This modulation that affects the activity of a central regulator during the earliest stages of symbiosis has a huge impact on late stages of symbiosis. This work showed that regulatory rewiring is the main driver of this pathogeny-symbiosis transition.
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Flores-Félix JD, Menéndez E, Peix A, García-Fraile P, Velázquez E. History and current taxonomic status of genus Agrobacterium. Syst Appl Microbiol 2020; 43:126046. [DOI: 10.1016/j.syapm.2019.126046] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 11/15/2019] [Accepted: 11/22/2019] [Indexed: 10/25/2022]
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Casanova C, Lo Priore E, Egli A, Seth-Smith HMB, Räber L, Ott D, Pflüger V, Droz S, Marschall J, Sommerstein R. Agrobacterium spp. nosocomial outbreak assessment using rapid MALDI-TOF MS based typing, confirmed by whole genome sequencing. Antimicrob Resist Infect Control 2019; 8:171. [PMID: 31700617 PMCID: PMC6829841 DOI: 10.1186/s13756-019-0619-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/01/2019] [Indexed: 11/10/2022] Open
Abstract
Background A number of episodes of nosocomial Agrobacterium spp. bacteremia (two cases per year) were observed at Bern University Hospital, Switzerland, from 2015 to 2017. This triggered an outbreak investigation. Methods Cases of Agrobacterium spp. bacteremias that occurred between August 2011 and February 2017 were investigated employing line lists, environmental sampling, rapid protein- (MALDI-TOF MS), and genome-based typing (pulsed field gel electrophoresis and whole genome sequencing) of the clinical isolates. Results We describe a total of eight bacteremia episodes due to A. radiobacter (n = 2), Agrobacterium genomovar G3 (n = 5) and A. pusense (n = 1). Two tight clusters were observed by WGS typing, representing the two A. radiobacter isolates (cluster I, isolated in 2015) and four of the Agrobacterium genomovar G3 isolates (cluster II, isolated in 2016 and 2017), suggesting two different point sources. The epidemiological investigations revealed two computer tomography (CT) rooms as common patient locations, which correlated with the two outbreak clusters. MALDI-TOF MS permitted faster evaluation of strain relatedness than DNA-based methods. High resolution WGS-based typing confirmed the MALDI-TOF MS clustering. Conclusions We report clinical and epidemiological characteristics of two outbreak clusters with Agrobacterium. spp. bacteremia likely acquired during CT contrast medium injection and highlight the use of MALDI-TOF MS as a rapid tool to assess relatedness of rare gram-negative pathogens in an outbreak investigation.
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Affiliation(s)
- Carlo Casanova
- 1Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001 Bern, Switzerland
| | - Elia Lo Priore
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Freiburgstrasse, 3001 Bern, Switzerland
| | - Adrian Egli
- 3Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland.,4Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Helena M B Seth-Smith
- 3Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland.,4Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Lorenz Räber
- Department of Cardiology, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Daniel Ott
- Department of Radiology, Bern University Hospital, University of Bern, Bern, Switzerland
| | | | - Sara Droz
- 1Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001 Bern, Switzerland
| | - Jonas Marschall
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Freiburgstrasse, 3001 Bern, Switzerland
| | - Rami Sommerstein
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Freiburgstrasse, 3001 Bern, Switzerland
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Mafakheri H, Taghavi SM, Puławska J, de Lajudie P, Lassalle F, Osdaghi E. Two Novel Genomospecies in the Agrobacterium tumefaciens Species Complex Associated with Rose Crown Gall. PHYTOPATHOLOGY 2019; 109:1859-1868. [PMID: 31298994 DOI: 10.1094/phyto-05-19-0178-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this study, we explored the pathogenicity and phylogenetic position of Agrobacterium spp. strains isolated from crown gall tissues on annual, perennial, and ornamental plants in Iran. Of the 43 strains studied, 10 strains were identified as Allorhizobium vitis (formerly Agrobacterium vitis) using the species-specific primer pair PGF/PGR. Thirty-three remaining strains were studied using multilocus sequence analysis of four housekeeping genes (i.e., atpD, gyrB, recA, and rpoB), from which seven strains were identified as A. larrymoorei and one strain was identified as A. rubi (Rer); the remaining 25 strains were scattered within the A. tumefaciens species complex. Two strains were identified as genomospecies 1 (G1), seven strains were identified as A. radiobacter (G4), seven strains were identified as A. deltaense (G7), two strains were identified as A. nepotum (G14), and one strain was identified as "A. viscosum" (G15). The strains Rnr, Rnw, and Rew as well as the two strains OT33 and R13 all isolated from rose and the strain Ap1 isolated from apple were clustered in three atypical clades within the A. tumefaciens species complex. All but eight strains (i.e., Nec10, Ph38, Ph49, fic9, Fic72, R13, OT33, and Ap1) were pathogenic on tomato and sunflower seedlings in greenhouse conditions, whereas all but three strains (i.e., fic9, Fic72, and OT33) showed tumorigenicity on carrot root discs. The phylogenetic analysis and nucleotide diversity statistics suggested the existence of two novel genomospecies within the A. tumefaciens species complex, which we named "G19" and "G20." Hence, we propose the strains Rew, Rnw, and Rnr as the members of "G19" and the strains R13 and OT33 as the members of G20, whereas the phylogenetic status of the atypical strain Ap1 remains undetermined.
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Affiliation(s)
- Hamzeh Mafakheri
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Joanna Puławska
- Research Institute of Horticulture, 96-100 Skierniewice, Poland
| | - Philippe de Lajudie
- IRD (Institut de recherche pour le développement), Campus de Baillarguet TA A-82/J, Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398 Montpellier Cédex 5, France
| | - Florent Lassalle
- Department of Infectious Disease Epidemiology, St. Mary's Hospital Campus, Imperial College London, London W2 1NY, United Kingdom
| | - Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
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Zuniga-Soto E, Fitzpatrick DA, Doohan FM, Mullins E. Insights into the transcriptomic response of the plant engineering bacterium Ensifer adhaerens OV14 during transformation. Sci Rep 2019; 9:10344. [PMID: 31316079 PMCID: PMC6637203 DOI: 10.1038/s41598-019-44648-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 05/08/2019] [Indexed: 11/08/2022] Open
Abstract
The ability to engineer plant genomes has been primarily driven by the soil bacterium Agrobacterium tumefaciens but recently the potential of alternative rhizobia such as Rhizobium etli and Ensifer adhaerens OV14, the latter of which supports Ensifer Mediated Transformation (EMT) has been reported. Surprisingly, a knowledge deficit exists in regards to understanding the whole genome processes underway in plant transforming bacteria, irrespective of the species. To begin to address the issue, we undertook a temporal RNAseq-based profiling study of E. adhaerens OV14 in the presence/absence of Arabidopsis thaliana tissues. Following co-cultivation with root tissues, 2333 differentially expressed genes (DEGs) were noted. Meta-analysis of the RNAseq data sets identified a clear shift from plasmid-derived gene expression to chromosomal-based transcription within the early stages of bacterium-plant co-cultivation. During this time, the number of differentially expressed prokaryotic genes increased steadily out to 7 days co-cultivation, a time at which optimum rates of transformation were observed. Gene ontology evaluations indicated a role for both chromosomal and plasmid-based gene families linked specifically with quorum sensing, flagellin production and biofilm formation in the process of EMT. Transcriptional evaluation of vir genes, housed on the pCAMBIA 5105 plasmid in E. adhaerens OV14 confirmed the ability of E. adhaerens OV14 to perceive and activate its transcriptome in response to the presence of 200 µM of acetosyringone. Significantly, this is the first study to characterise the whole transcriptomic response of a plant engineering bacterium in the presence of plant tissues and provides a novel insight into prokaryotic genetic processes that support T-DNA transfer.
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Affiliation(s)
- Evelyn Zuniga-Soto
- Department of Crop Science, Teagasc Crops Research Centre, Oak Park, Carlow, Ireland
- School of Biology and Environmental Sciences, University College Dublin, Belfield, Dublin 4, Ireland
| | - David A Fitzpatrick
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland
| | - Fiona M Doohan
- School of Biology and Environmental Sciences, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ewen Mullins
- Department of Crop Science, Teagasc Crops Research Centre, Oak Park, Carlow, Ireland.
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Ormeño-Orrillo E, Martínez-Romero E. A Genomotaxonomy View of the Bradyrhizobium Genus. Front Microbiol 2019; 10:1334. [PMID: 31263459 PMCID: PMC6585233 DOI: 10.3389/fmicb.2019.01334] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/28/2019] [Indexed: 11/13/2022] Open
Abstract
Whole genome analysis of the Bradyrhizobium genus using average nucleotide identity (ANI) and phylogenomics showed the genus to be essentially monophyletic with seven robust groups within this taxon that includes nitrogen-fixing nodule forming bacteria as well as free living strains. Despite the wide genetic diversity of these bacteria no indication was found to suggest that the Bradyrhizobium genus have to split in different taxa. Bradyrhizobia have larger genomes than other genera of the Bradyrhizobiaceae family, probably reflecting their metabolic diversity and different lifestyles. Few plasmids in the sequenced strains were revealed from rep gene analysis and a relatively low proportion of the genome is devoted to mobile genetic elements. Sequence diversity of recA and glnII gene metadata was used to theoretically estimate the number of existing species and to predict how many would exist. There may be many more species than those presently described with predictions of around 800 species in nature. Different arguments are presented suggesting that nodulation might have arose in the ancestral genus Bradyrhizobium.
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Affiliation(s)
- Ernesto Ormeño-Orrillo
- Laboratorio de Ecología Microbiana y Biotecnología, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
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The Ecology of Agrobacterium vitis and Management of Crown Gall Disease in Vineyards. Curr Top Microbiol Immunol 2019; 418:15-53. [PMID: 29556824 DOI: 10.1007/82_2018_85] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Agrobacterium vitis is the primary causal agent of grapevine crown gall worldwide. Symptoms of grapevine crown gall disease include tumor formation on the aerial plant parts, whereas both tumorigenic and nontumorigenic strains of A. vitis cause root necrosis. Genetic and genomic analyses indicated that A. vitis is distinguishable from the members of the Agrobacterium genus and its transfer to the genus Allorhizobium was suggested. A. vitis is genetically diverse, with respect to both chromosomal and plasmid DNA. Its pathogenicity is mainly determined by a large conjugal tumor-inducing (Ti) plasmid characterized by a mosaic structure with conserved and variable regions. Traditionally, A. vitis Ti plasmids and host strains were differentiated into octopine/cucumopine, nopaline, and vitopine groups, based on opine markers. However, tumorigenic and nontumorigenic strains of A. vitis may carry other ecologically important plasmids, such as tartrate- and opine-catabolic plasmids. A. vitis colonizes vines endophytically. It is also able to survive epiphytically on grapevine plants and is detected in soil exclusively in association with grapevine plants. Because A. vitis persists systemically in symptomless grapevine plants, it can be efficiently disseminated to distant geographical areas via international trade of propagation material. The use of healthy planting material in areas with no history of the crown gall represents the crucial measure of disease management. Moreover, biological control and production of resistant grape varieties are encouraging as future control measures.
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International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the meeting by video conference, 11 July 2018. Int J Syst Evol Microbiol 2019; 69:1835-1840. [DOI: 10.1099/ijsem.0.003335] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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de Lajudie PM, Andrews M, Ardley J, Eardly B, Jumas-Bilak E, Kuzmanović N, Lassalle F, Lindström K, Mhamdi R, Martínez-Romero E, Moulin L, Mousavi SA, Nesme X, Peix A, Puławska J, Steenkamp E, Stępkowski T, Tian CF, Vinuesa P, Wei G, Willems A, Zilli J, Young P. Minimal standards for the description of new genera and species of rhizobia and agrobacteria. Int J Syst Evol Microbiol 2019; 69:1852-1863. [PMID: 31140963 DOI: 10.1099/ijsem.0.003426] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Herein the members of the Subcommittee on Taxonomy of Rhizobia and Agrobacteria of the International Committee on Systematics of Prokaryotes review recent developments in rhizobial and agrobacterial taxonomy and propose updated minimal standards for the description of new species (and genera) in these groups. The essential requirements (minimal standards) for description of a new species are (1) a genome sequence of at least the proposed type strain and (2) evidence for differentiation from other species based on genome sequence comparisons. It is also recommended that (3) genetic variation within the species is documented with sequence data from several clearly different strains and (4) phenotypic features are described, and their variation documented with data from a relevant set of representative strains. Furthermore, it is encouraged that information is provided on (5) nodulation or pathogenicity phenotypes, as appropriate, with relevant gene sequences. These guidelines supplement the current rules of general bacterial taxonomy, which require (6) a name that conforms to the International Code of Nomenclature of Prokaryotes, (7) validation of the name by publication either directly in the International Journal of Systematic and Evolutionary Microbiology or in a validation list when published elsewhere, and (8) deposition of the type strain in two international culture collections in separate countries.
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Affiliation(s)
| | - Mitchell Andrews
- 2Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Julie Ardley
- 3School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia
| | | | - Estelle Jumas-Bilak
- 5UMR 5569, Department of Microbiology, Faculty of Pharmacy, University of Montpellier, France
| | - Nemanja Kuzmanović
- 6Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
| | - Florent Lassalle
- 7Department of Infectious Disease Epidemiology - MRC Centre for Outbreak Analysis and Modelling, St Mary's Hospital, Praed Street, London W2 1NY, UK
| | - Kristina Lindström
- 8Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
| | - Ridha Mhamdi
- 9Centre of Biotechnology of Borj-Cedria, BP 901 Hammam-lif 2050, Tunisia
| | - Esperanza Martínez-Romero
- 10Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos, Mexico
| | - Lionel Moulin
- 11IRD, CIRAD, University of Montpellier, IPME, Montpellier, France
| | - Seyed Abdollah Mousavi
- 8Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
| | - Xavier Nesme
- 12LEM, UCBL, CNRS, INRA, Univ Lyon, Villeurbanne, France
| | - Alvaro Peix
- 13Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Joanna Puławska
- 14Department of Phytopathology, Research Institute of Horticulture, ul. Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | - Emma Steenkamp
- 15Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria 0002, South Africa
| | - Tomasz Stępkowski
- 16Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Chang-Fu Tian
- 17State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, College of Biological Sciences, China Agricultural University, 100193, Beijing, PR China
| | - Pablo Vinuesa
- 10Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos, Mexico
| | - Gehong Wei
- 18Northwest A&F University, Yangling, Shaanxi, PR China
| | - Anne Willems
- 19Department Biochemistry and Microbiology, Lab. Microbiology, Ghent University, Belgium
| | - Jerri Zilli
- 20Embrapa Agrobiologia, BR 465 km 07, Seropédica, Rio de Janeiro, Brazil, 23891-000, Brazil
| | - Peter Young
- 21Department of Biology, University of York, York YO10 5DD, UK
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González V, Santamaría RI, Bustos P, Pérez-Carrascal OM, Vinuesa P, Juárez S, Martínez-Flores I, Cevallos MÁ, Brom S, Martínez-Romero E, Romero D. Phylogenomic Rhizobium Species Are Structured by a Continuum of Diversity and Genomic Clusters. Front Microbiol 2019; 10:910. [PMID: 31114559 PMCID: PMC6503217 DOI: 10.3389/fmicb.2019.00910] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/10/2019] [Indexed: 01/07/2023] Open
Abstract
The bacterial genus Rhizobium comprises diverse symbiotic nitrogen-fixing species associated with the roots of plants in the Leguminosae family. Multiple genomic clusters defined by whole genome comparisons occur within Rhizobium, but their equivalence to species is controversial. In this study we investigated such genomic clusters to ascertain their significance in a species phylogeny context. Phylogenomic inferences based on complete sets of ribosomal proteins and stringent core genome markers revealed the main lineages of Rhizobium. The clades corresponding to R. etli and R. leguminosarum species show several genomic clusters with average genomic nucleotide identities (ANI > 95%), and a continuum of divergent strains, respectively. They were found to be inversely correlated with the genetic distance estimated from concatenated ribosomal proteins. We uncovered evidence of a Rhizobium pangenome that was greatly expanded, both in its chromosomes and plasmids. Despite the variability of extra-chromosomal elements, our genomic comparisons revealed only a few chromid and plasmid families. The presence/absence profile of genes in the complete Rhizobium genomes agreed with the phylogenomic pattern of species divergence. Symbiotic genes were distributed according to the principal phylogenomic Rhizobium clades but did not resolve genome clusters within the clades. We distinguished some types of symbiotic plasmids within Rhizobium that displayed different rates of synonymous nucleotide substitutions in comparison to chromosomal genes. Symbiotic plasmids may have been repeatedly transferred horizontally between strains and species, in the process displacing and substituting pre-existing symbiotic plasmids. In summary, the results indicate that Rhizobium genomic clusters, as defined by whole genomic identities, might be part of a continuous process of evolutionary divergence that includes the core and the extrachromosomal elements leading to species formation.
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Affiliation(s)
- Víctor González
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Rosa Isela Santamaría
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Patricia Bustos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Soledad Juárez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Irma Martínez-Flores
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Miguel Ángel Cevallos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Susana Brom
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - David Romero
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Ramírez-Puebla ST, Hernández MAR, Guerrero Ruiz G, Ormeño-Orrillo E, Martinez-Romero JC, Servín-Garcidueñas LE, Núñez-de la Mora A, Amescua-Villela G, Negrete-Yankelevich S, Martínez-Romero E. Nodule bacteria from the cultured legume Phaseolus dumosus (belonging to the Phaseolus vulgaris cross-inoculation group) with common tropici phenotypic characteristics and symbiovar but distinctive phylogenomic position and chromid. Syst Appl Microbiol 2018; 42:373-382. [PMID: 30612723 DOI: 10.1016/j.syapm.2018.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/15/2018] [Accepted: 12/16/2018] [Indexed: 10/27/2022]
Abstract
Phaseolus dumosus is an endemic species from mountain tops in Mexico that was found in traditional agriculture areas in Veracruz, Mexico. P. dumosus plants were identified by ITS sequences and their nodules were collected from agricultural fields or from trap plant experiments in the laboratory. Bacteria from P. dumosus nodules were identified as belonging to the phaseoli-etli-leguminosarum (PEL) or to the tropici group by 16S rRNA gene sequences. We obtained complete closed genomes from two P. dumosus isolates CCGE531 and CCGE532 that were phylogenetically placed within the tropici group but with a distinctive phylogenomic position and low average nucleotide identity (ANI). CCGE531 and CCGE532 had common phenotypic characteristics with tropici type B rhizobial symbionts. Genome synteny analysis and ANI showed that P. dumosus isolates had different chromids and our analysis suggests that chromids have independently evolved in different lineages of the Rhizobium genus. Finally, we considered that P. dumosus and Phaseolus vulgaris plants belong to the same cross-inoculation group since they have conserved symbiotic affinites for rhizobia.
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Affiliation(s)
| | | | | | - Ernesto Ormeño-Orrillo
- Laboratorio de Ecología Microbiana y Biotecnología, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
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Agrobacterium-mediated horizontal gene transfer: Mechanism, biotechnological application, potential risk and forestalling strategy. Biotechnol Adv 2018; 37:259-270. [PMID: 30579929 DOI: 10.1016/j.biotechadv.2018.12.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 11/20/2022]
Abstract
The extraordinary capacity of Agrobacterium to transfer its genetic material to host cell makes it evolve from phytopathogen to a powerful transgenic vector. Agrobacterium-mediated stable transformation is widely used as the preferred method to create transgenic plants for molecular plant biology research and crop breeding. Recent years, both mechanism and application of Agrobacterium-mediated horizontal gene transfer have made significant progresses, especially Agrobacterium-mediated transient transformation was developed for plant biotechnology industry to produce recombinant proteins. Agrobacterium strains are almost used and saved not only by each of microbiology and molecular plant labs, but also by many of plant biotechnology manufacturers. Agrobacterium is able to transfer its genetic material to a broad range of hosts, including plant and non-plant hosts. As a consequence, the concern of environmental risk associated with the accidental release of genetically modified Agrobacterium arises. In this article, we outline the recent progress in the molecular mechanism of Agrobacterium-meditated gene transfer, focus on the application of Agrobacterium-mediated horizontal gene transfer, and review the potential risk associated with Agrobacterium-meditated gene transfer. Based on the comparison between the infecting process of Agrobacterium as a pathogen and the transgenic process of Agrobacterium as a transgenic vector, we realize that chemotaxis is the distinct difference between these two biological processes and thus discuss the possible role of chemotaxis in forestalling the potential risk of Agrobacterium-meditated horizontal gene transfer to non-target plant species.
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Draft Genome Sequence of Rhizobium sp. Strain T2.30D-1.1, Isolated from 538.5 Meters Deep on the Subsurface of the Iberian Pyrite Belt. Microbiol Resour Announc 2018; 7:MRA01098-18. [PMID: 30533741 PMCID: PMC6256577 DOI: 10.1128/mra.01098-18] [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: 08/30/2018] [Accepted: 10/03/2018] [Indexed: 11/20/2022] Open
Abstract
Rhizobium sp. strain T2.30D-1.1 was isolated from the deep subsurface of the Iberian Pyrite Belt. We report its draft genome, consisting of 60 contigs with a chromosome of ≈4.6 Mb and a plasmid of 179 kb. The annotation revealed 4,526 coding DNA sequences, 45 tRNA genes, and 1 rRNA operon.
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37
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Haryono M, Tsai YM, Lin CT, Huang FC, Ye YC, Deng WL, Hwang HH, Kuo CH. Presence of an Agrobacterium-Type Tumor-Inducing Plasmid in Neorhizobium sp. NCHU2750 and the Link to Phytopathogenicity. Genome Biol Evol 2018; 10:3188-3195. [PMID: 30398651 PMCID: PMC6286910 DOI: 10.1093/gbe/evy249] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2018] [Indexed: 12/02/2022] Open
Abstract
The genus Agrobacterium contains a group of plant-pathogenic bacteria that have been developed into an important tool for genetic transformation of eukaryotes. To further improve this biotechnology application, a better understanding of the natural genetic variation is critical. During the process of isolation and characterization of wild-type strains, we found a novel strain (i.e., NCHU2750) that resembles Agrobacterium phenotypically but exhibits high sequence divergence in several marker genes. For more comprehensive characterization of this strain, we determined its complete genome sequence for comparative analysis and performed pathogenicity assays on plants. The results demonstrated that this strain is closely related to Neorhizobium in chromosomal organization, gene content, and molecular phylogeny. However, unlike the characterized species within Neorhizobium, which all form root nodules with legume hosts and are potentially nitrogen-fixing mutualists, NCHU2750 is a gall-forming pathogen capable of infecting plant hosts across multiple families. Intriguingly, this pathogenicity phenotype could be attributed to the presence of an Agrobacterium-type tumor-inducing plasmid in the genome of NCHU2750. These findings suggest that these different lineages within the family Rhizobiaceae are capable of transitioning between ecological niches by having novel combinations of replicons. In summary, this work expanded the genomic resources available within Rhizobiaceae and provided a strong foundation for future studies of this novel lineage. With an infectivity profile that is different from several representative Agrobacterium strains, this strain may be useful for comparative analysis to better investigate the genetic determinants of host range among these bacteria.
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Affiliation(s)
- Mindia Haryono
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Ming Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chien-Ting Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Fan-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
| | - Yan-Chen Ye
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Wen-Ling Deng
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Hau-Hsuan Hwang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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38
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Lassalle F, Planel R, Penel S, Chapulliot D, Barbe V, Dubost A, Calteau A, Vallenet D, Mornico D, Bigot T, Guéguen L, Vial L, Muller D, Daubin V, Nesme X. Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium. Genome Biol Evol 2018; 9:3413-3431. [PMID: 29220487 PMCID: PMC5739047 DOI: 10.1093/gbe/evx255] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2017] [Indexed: 12/12/2022] Open
Abstract
Horizontal gene transfer (HGT) is considered as a major source of innovation in bacteria, and as such is expected to drive adaptation to new ecological niches. However, among the many genes acquired through HGT along the diversification history of genomes, only a fraction may have actively contributed to sustained ecological adaptation. We used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial species. We identified clade-specific blocks of cotransferred genes encoding coherent biochemical pathways that may have contributed to the evolutionary success of key Agrobacterium clades. This pattern of gene coevolution rejects a neutral model of transfer, in which neighboring genes would be transferred independently of their function and rather suggests purifying selection on collectively coded acquired pathways. The acquisition of these synapomorphic blocks of cofunctioning genes probably drove the ecological diversification of Agrobacterium and defined features of ancestral ecological niches, which consistently hint at a strong selective role of host plant rhizospheres.
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Affiliation(s)
- Florent Lassalle
- Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, France.,Biométrie et Biologie Evolutive, CNRS, UCBL, Université de Lyon, Villeurbanne, France.,Ecole Normale Supérieure de Lyon, Lyon, France
| | - Rémi Planel
- Biométrie et Biologie Evolutive, CNRS, UCBL, Université de Lyon, Villeurbanne, France
| | - Simon Penel
- Biométrie et Biologie Evolutive, CNRS, UCBL, Université de Lyon, Villeurbanne, France
| | - David Chapulliot
- Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, France
| | - Valérie Barbe
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) Direction de la Recherche Fondamentale, Institut de Biologie Francois-Jacob (IBFJ), Genoscope, Evry, France
| | - Audrey Dubost
- Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, France
| | - Alexandra Calteau
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) Direction de la Recherche Fondamentale, Institut de Biologie Francois-Jacob (IBFJ), Genoscope, Evry, France.,Laboratoire d'Analyse Bioinformatiques pour la Génomique et le Métabolisme, CNRS, UMR 8030, Evry, France.,UEVE, Université d'Evry Val d'Essonne, France
| | - David Vallenet
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) Direction de la Recherche Fondamentale, Institut de Biologie Francois-Jacob (IBFJ), Genoscope, Evry, France.,Laboratoire d'Analyse Bioinformatiques pour la Génomique et le Métabolisme, CNRS, UMR 8030, Evry, France.,UEVE, Université d'Evry Val d'Essonne, France
| | - Damien Mornico
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) Direction de la Recherche Fondamentale, Institut de Biologie Francois-Jacob (IBFJ), Genoscope, Evry, France.,Laboratoire d'Analyse Bioinformatiques pour la Génomique et le Métabolisme, CNRS, UMR 8030, Evry, France.,UEVE, Université d'Evry Val d'Essonne, France
| | - Thomas Bigot
- Biométrie et Biologie Evolutive, CNRS, UCBL, Université de Lyon, Villeurbanne, France
| | - Laurent Guéguen
- Biométrie et Biologie Evolutive, CNRS, UCBL, Université de Lyon, Villeurbanne, France
| | - Ludovic Vial
- Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, France
| | - Daniel Muller
- Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, France
| | - Vincent Daubin
- Biométrie et Biologie Evolutive, CNRS, UCBL, Université de Lyon, Villeurbanne, France
| | - Xavier Nesme
- Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, France
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39
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An J, Sun M, van Velzen R, Ji C, Zheng Z, Limpens E, Bisseling T, Deng X, Xiao S, Pan Z. Comparative transcriptome analysis of Poncirus trifoliata identifies a core set of genes involved in arbuscular mycorrhizal symbiosis. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:5255-5264. [PMID: 30312435 PMCID: PMC6184448 DOI: 10.1093/jxb/ery283] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 07/24/2018] [Indexed: 05/20/2023]
Abstract
The perennial woody plants of citrus are one of the most important fruit crops in the world and largely depends on arbuscular mycorrhizal symbiosis (AMS) to obtain essential nutrients from soil. However, the molecular aspects of AMS in citrus and perennial woody plants in general have largely been understudied. We used RNA-sequencing to identify differentially expressed genes in roots of Poncirus trifoliata upon mycorrhization by the AM fungus Glomus versiforme and evaluated their conservation by comparative transcriptome analyses with four herbaceous model plants. We identified 282 differentially expressed genes in P. trifoliata, including orthologs of 21 genes with characterized roles in AMS and 83 genes that are considered to be conserved in AM-host plants. Comparative transcriptome analysis revealed a 'core set' of 156 genes from P. trifoliata whose orthologous genes from at least three of the five species also exhibited similar transcriptional changes during AMS. Functional analysis of one of these conserved AM-induced genes, a 3-keto-acyl-ACP reductase (FatG) involved in fatty acid biosynthesis, confirmed its involvement in AMS in Medicago truncatula. Our results identify a core transcriptional program for AMS that is largely conserved between P. trifoliata and other plants. The comparative transcriptomics approach adds to previous phylogenomics studies to identify conserved genes required for AMS.
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Affiliation(s)
- Jianyong An
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, P.R. China
| | - Mengqian Sun
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, P.R. China
| | - Robin van Velzen
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg, PB Wageningen, Netherlands
| | - Chuanya Ji
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, P.R. China
| | - Zijun Zheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, P.R. China
| | - Erik Limpens
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg, PB Wageningen, Netherlands
| | - Ton Bisseling
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg, PB Wageningen, Netherlands
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, P.R. China
| | - Shunyuan Xiao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, P.R. China
- Institute for Bioscience and Biotechnology Research & Department of Plant Sciences and Landscape Architecture, University of Maryland College Park, Rockville, MD, USA
| | - Zhiyong Pan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, P.R. China
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40
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Pathogenicity, Phylogenetic relationship and NGS based identification and assembly of tumorigenic Agrobacterium radiabacter plasmidic and chromosomic reads isolated from Prunus duclcis. Genomics 2018; 111:1423-1430. [PMID: 30287402 DOI: 10.1016/j.ygeno.2018.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/25/2018] [Indexed: 11/22/2022]
Abstract
Although many Agrobacterium radiobacter strains have already been identified, only a few genomes of strains belonging to genomovar G4 have been sequenced so far. In this study, we report the first virulent genome sequence of Agrobacterium radiobacter strain tun 183, which is highly virulent to almond specie. The genome size was estimated to be 5.53 Mb, with 57.9%GC content. In total, 6486 genes encoding proteins and 61 genes encoding RNAs were identified in this genome. Comparisons with the available sequenced genomes of genomovar G4 as well as with other A. sp. were conducted, revealing a hexapartite genome containing circular and linear chromosomes in addition to two accessory plasmids and a tumor inducing plasmid (pTi) in strain tun 183. The phylogenetic analysis of recA gene clearly showed the clustering of tun 183 strain within genomovar G4, supporting the monophyly within this genomovar.
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41
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Máthé I, Tóth E, Mentes A, Szabó A, Márialigeti K, Schumann P, Felföldi T. A new Rhizobium species isolated from the water of a crater lake, description of Rhizobium aquaticum sp. nov. Antonie van Leeuwenhoek 2018; 111:2175-2183. [DOI: 10.1007/s10482-018-1110-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 06/01/2018] [Indexed: 11/28/2022]
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42
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Palmer M, Steenkamp ET, Coetzee MPA, Blom J, Venter SN. Genome-Based Characterization of Biological Processes That Differentiate Closely Related Bacteria. Front Microbiol 2018; 9:113. [PMID: 29467735 PMCID: PMC5808187 DOI: 10.3389/fmicb.2018.00113] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/17/2018] [Indexed: 12/21/2022] Open
Abstract
Bacteriologists have strived toward attaining a natural classification system based on evolutionary relationships for nearly 100 years. In the early twentieth century it was accepted that a phylogeny-based system would be the most appropriate, but in the absence of molecular data, this approach proved exceedingly difficult. Subsequent technical advances and the increasing availability of genome sequencing have allowed for the generation of robust phylogenies at all taxonomic levels. In this study, we explored the possibility of linking biological characters to higher-level taxonomic groups in bacteria by making use of whole genome sequence information. For this purpose, we specifically targeted the genus Pantoea and its four main lineages. The shared gene sets were determined for Pantoea, the four lineages within the genus, as well as its sister-genus Tatumella. This was followed by functional characterization of the gene sets using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. In comparison to Tatumella, various traits involved in nutrient cycling were identified within Pantoea, providing evidence for increased efficacy in recycling of metabolites within the genus. Additionally, a number of traits associated with pathogenicity were identified within species often associated with opportunistic infections, with some support for adaptation toward overcoming host defenses. Some traits were also only conserved within specific lineages, potentially acquired in an ancestor to the lineage and subsequently maintained. It was also observed that the species isolated from the most diverse sources were generally the most versatile in their carbon metabolism. By investigating evolution, based on the more variable genomic regions, it may be possible to detect biologically relevant differences associated with the course of evolution and speciation.
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Affiliation(s)
- Marike Palmer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Emma T Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Martin P A Coetzee
- Department of Genetic, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Stephanus N Venter
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
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43
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Zahradník J, Nunvar J, Pařízková H, Kolářová L, Palyzová A, Marešová H, Grulich M, Kyslíková E, Kyslík P. Agrobacterium bohemicum sp. nov. isolated from poppy seed wastes in central Bohemia. Syst Appl Microbiol 2018; 41:184-190. [PMID: 29402492 DOI: 10.1016/j.syapm.2018.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 01/11/2018] [Accepted: 01/17/2018] [Indexed: 10/18/2022]
Abstract
Two non-pathogenic strains R89-1 and R90T isolated from poppy seed (Papaver somniferum L.) wastes were phenotypically and genotypically characterized. Multilocus sequence analysis (MLSA) was conducted with six genes (atpD, glnA, gyrB, recA, rpoB, 16S rRNA). The strains represented a new species which clustered with Agrobacterium rubi NBRC 13261T and Agrobacterium skierniewicense Ch11T type strains. MLSA was further accompanied by whole-genome phylogeny, in silico DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses for both strains. ANI and dDDH values were deep below the species delineation threshold. Phenotypic features of the novel strains unequivocally allowed their differentiation from all other Agrobacterium species. Unlike other agrobacteria, the strains were salt sensitive and were able to biotransform morphine alkaloids. The dominant cellular fatty acids are 18:1 w7c, 16:0 and 12:0 aldehyde/16:1 iso I/14:0 3OH summed in feature 2 and the major respiratory quinine is Q-10 (87%). The DNA G+C content is 56mol%. Microbial community analysis indicated probable association with P. somniferum plant material. Altogether, these characteristics showed that strains R90T and R89-1 represent a new species of the genus Agrobacterium which we propose to name Agrobacterium bohemicum. The type strain of A. bohemicum is R90T (=CCM 8736T=DSM 104667T).
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Affiliation(s)
- Jiří Zahradník
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic; Laboratory of Biomolecular Recognition, Institute of Biotechnology, v.v.i., BIOCEV, Průmyslová 595, CZ-252 42 Vestec, Czech Republic; Faculty of Science, Charles University Prague, Viničná 5, CZ-128 44 Prague 2, Czech Republic.
| | - Jaroslav Nunvar
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University Prague, V Uvalu 84, CZ-150 06 Prague 5, Czech Republic
| | - Hana Pařízková
- Laboratory of Biomolecular Recognition, Institute of Biotechnology, v.v.i., BIOCEV, Průmyslová 595, CZ-252 42 Vestec, Czech Republic
| | - Lucie Kolářová
- Laboratory of Biomolecular Recognition, Institute of Biotechnology, v.v.i., BIOCEV, Průmyslová 595, CZ-252 42 Vestec, Czech Republic
| | - Andrea Palyzová
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Helena Marešová
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Michal Grulich
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Eva Kyslíková
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Pavel Kyslík
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic.
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Coba de la Peña T, Fedorova E, Pueyo JJ, Lucas MM. The Symbiosome: Legume and Rhizobia Co-evolution toward a Nitrogen-Fixing Organelle? FRONTIERS IN PLANT SCIENCE 2018; 8:2229. [PMID: 29403508 PMCID: PMC5786577 DOI: 10.3389/fpls.2017.02229] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 12/19/2017] [Indexed: 05/21/2023]
Abstract
In legume nodules, symbiosomes containing endosymbiotic rhizobial bacteria act as temporary plant organelles that are responsible for nitrogen fixation, these bacteria develop mutual metabolic dependence with the host legume. In most legumes, the rhizobia infect post-mitotic cells that have lost their ability to divide, although in some nodules cells do maintain their mitotic capacity after infection. Here, we review what is currently known about legume symbiosomes from an evolutionary and developmental perspective, and in the context of the different interactions between diazotroph bacteria and eukaryotes. As a result, it can be concluded that the symbiosome possesses organelle-like characteristics due to its metabolic behavior, the composite origin and differentiation of its membrane, the retargeting of host cell proteins, the control of microsymbiont proliferation and differentiation by the host legume, and the cytoskeletal dynamics and symbiosome segregation during the division of rhizobia-infected cells. Different degrees of symbiosome evolution can be defined, specifically in relation to rhizobial infection and to the different types of nodule. Thus, our current understanding of the symbiosome suggests that it might be considered a nitrogen-fixing link in organelle evolution and that the distinct types of legume symbiosomes could represent different evolutionary stages toward the generation of a nitrogen-fixing organelle.
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Affiliation(s)
- Teodoro Coba de la Peña
- Instituto de Ciencias Agrarias ICA-CSIC, Madrid, Spain
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), La Serena, Chile
| | - Elena Fedorova
- Instituto de Ciencias Agrarias ICA-CSIC, Madrid, Spain
- K. A. Timiryazev Institute of Plant Physiology, Russian Academy of Science, Moscow, Russia
| | - José J Pueyo
- Instituto de Ciencias Agrarias ICA-CSIC, Madrid, Spain
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45
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Barton IS, Fuqua C, Platt TG. Ecological and evolutionary dynamics of a model facultative pathogen: Agrobacterium and crown gall disease of plants. Environ Microbiol 2018; 20:16-29. [PMID: 29105274 PMCID: PMC5764771 DOI: 10.1111/1462-2920.13976] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 10/20/2017] [Accepted: 10/25/2017] [Indexed: 01/09/2023]
Abstract
Many important pathogens maintain significant populations in highly disparate disease and non-disease environments. The consequences of this environmental heterogeneity in shaping the ecological and evolutionary dynamics of these facultative pathogens are incompletely understood. Agrobacterium tumefaciens, the causative agent for crown gall disease of plants has proven a productive model for many aspects of interactions between pathogens and their hosts and with other microbes. In this review, we highlight how this past work provides valuable context for the use of this system to examine how heterogeneity and transitions between disease and non-disease environments influence the ecology and evolution of facultative pathogens. We focus on several features common among facultative pathogens, such as the physiological remodelling required to colonize hosts from environmental reservoirs and the consequences of competition with host and non-host associated microbiota. In addition, we discuss how the life history of facultative pathogens likely often results in ecological tradeoffs associated with performance in disease and non-disease environments. These pathogens may therefore have different competitive dynamics in disease and non-disease environments and are subject to shifting selective pressures that can result in pathoadaptation or the within-host spread of avirulent phenotypes.
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Affiliation(s)
- Ian S. Barton
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Clay Fuqua
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Thomas G. Platt
- Division of Biology, Kansas State University, Manhattan, KS, USA
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46
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Abstract
This chapter presents a historical overview of the development and changes in scientific approaches to classifying members of the Agrobacterium genus. We also describe the changes in the inference of evolutionary relationships among Agrobacterium biovars and Agrobacterium strains from using the 16S rRNA marker to recA genes and to the use of multilocus sequence analysis (MLSA). Further, the impacts of the genomic era enabling low cost and rapid whole genome sequencing on Agrobacterium phylogeny are reviewed with a focus on the use of new and sophisticated bioinformatics approaches to refine phylogenetic inferences. An updated genome-based phylogeny of ninety-seven Agrobacterium tumefaciens complex isolates representing ten known genomic species is presented, providing additional support to the monophyly of the Agrobacterium clade. Additional taxon sampling within Agrobacterium genomovar G3 indicates potential exceptions to interpretation of the concept of bacterial genomics species as ecological species because the genomovar G3 genomic cluster, which initially includes clinical strains, now also includes plant-associated and cave isolates.
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Affiliation(s)
- Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.
| | - Michael A Savka
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA.
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47
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Cordeiro AB, Ribeiro RA, Helene LCF, Hungria M. Rhizobium esperanzae sp. nov., a N 2 -fixing root symbiont of Phaseolus vulgaris from Mexican soils. Int J Syst Evol Microbiol 2017; 67:3937-3945. [DOI: 10.1099/ijsem.0.002225] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Andrey Barbosa Cordeiro
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70040-020, Brasília, Distrito Federal, Brazil
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI I Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Distrito Federal, Brazil
| | - Luisa Caroline Ferraz Helene
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70040-020, Brasília, Distrito Federal, Brazil
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, C.P. 60001, 86051-990, Londrina, Paraná, Brazil
| | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, C.P. 60001, 86051-990, Londrina, Paraná, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI I Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Distrito Federal, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil
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48
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de Lajudie PM, Young JPW. International Committee on Systematics of Prokaryotes Subcommittee for the Taxonomy of Rhizobium and Agrobacterium Minutes of the meeting, Budapest, 25 August 2016. Int J Syst Evol Microbiol 2017; 67:2485-2494. [PMID: 28771120 DOI: 10.1099/ijsem.0.002144] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
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Toma MA, Soares de Carvalho T, Azarias Guimarães A, Martins da Costa E, Savana da Silva J, de Souza Moreira FM. Tripartite symbiosis of Sophora tomentosa, rhizobia and arbuscular mycorhizal fungi. Braz J Microbiol 2017; 48:680-688. [PMID: 28756029 PMCID: PMC5628302 DOI: 10.1016/j.bjm.2017.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 02/28/2017] [Accepted: 03/17/2017] [Indexed: 11/24/2022] Open
Abstract
Sophora tomentosa is a pantropical legume species with potential for recovery of areas degraded by salinization, and for stabilization of sand dunes. However, few studies on this species have been carried out, and none regarding its symbiotic relationship with beneficial soil microorganisms. Therefore, this study aimed to evaluate the diversity of nitrogen-fixing bacteria isolated from nodules of Sophora tomentosa, and to analyze the occurrence of colonization of arbuscular mycorrhizal fungi on the roots of this legume in seafront soil. Thus, seeds, root nodules, and soil from the rhizosphere of Sophora tomentosa were collected. From the soil samples, trap cultures with this species were established to extract spores and to evaluate arbuscular mycorhizal fungi colonization in legume roots, as well as to capture rhizobia. Rhizobia strains were isolated from nodules collected in the field or from the trap cultures. Representative isolates of the groups obtained in the similarity dendrogram, based on phenotypic characteristics, had their 16S rRNA genes sequenced. The legume species showed nodules with indeterminate growth, and reddish color, distributed throughout the root. Fifty-one strains of these nodules were isolated, of which 21 were classified in the genus Bacillus, Brevibacillus, Paenibacillus, Rhizobium and especially Sinorhizobium. Strains closely related to Sinorhizobium adhaerens were the predominant bacteria in nodules. The other genera found, with the exception of Rhizobium, are probably endophytic bacteria in the nodules. Arbuscular mycorrhizal fungi was observed colonizing the roots, but arbuscular mycorhizal fungi spores were not found in the trap cultures. Therefore Sophora tomentosa is associated with both arbuscular mycorhizal fungi and nodulating nitrogen-fixing bacteria.
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Affiliation(s)
- Maíra Akemi Toma
- Universidade Federal de Lavras (UFLA), Departamento de Ciência do Solo (DCS), Lavras, MG, Brazil
| | | | - Amanda Azarias Guimarães
- Universidade Federal de Lavras (UFLA), Departamento de Ciência do Solo (DCS), Lavras, MG, Brazil
| | - Elaine Martins da Costa
- Universidade Federal de Mato Grosso do Sul (UFMS) - Campus de Chapadão do Sul, Chapadão do Sul, MS, Brazil
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50
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Zeng Y, Wang Y, Yu Z, Huang Y. Hypersensitive Response of Plasmid-Encoded AHL Synthase Gene to Lifestyle and Nutrient by Ensifer adhaerens X097. Front Microbiol 2017; 8:1160. [PMID: 28702008 PMCID: PMC5487405 DOI: 10.3389/fmicb.2017.01160] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/07/2017] [Indexed: 11/16/2022] Open
Abstract
It is known that some bacteria, especially members of the family Rhizobiaceae, have multiple N-acyl homoserine lactones (AHL) synthase genes and produce multiple AHL signals. However, how bacteria selectively utilize these multiple genes and signals to cope with changing environments is poorly understood. Ensifer adhaerens is an important microorganism in terms of biotechnology, ecology and evolutionary. In this study, we investigated the AHL-based QS system of E. adhaerens X097 and its response to different lifestyles or nutrients. Draft genome sequence data indicated that X097 harbored three distinct AHL synthase genes (ensI1, 2, 3) and seven luxR homologs, which was different from other E. adhaerens strains. In vitro expression indicated that plasmid-encoded ensI1 and ensI2 directed production of multiple AHLs, while chromosome-encoded ensI3 only directed production of C14-HSL. Predicted three dimensional structure of EnsI3 was quite different from that of EnsI1 and EnsI2. X097 produced different AHL profiles in Luria-Bertani (LB) and NFB medium, under biofilm and planktonic lifestyle, respectively. Notably, expression of ensI1 and ensI2 but not ensI3 is hypersensitive to different lifestyles and nutrients. The hypersensitive response of plasmid-encoded AHL synthase genes to different culture conditions may shed a light on the phylogenetic development of AHL synthase genes in Rhizobiaceae family.
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Affiliation(s)
- Yanhua Zeng
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang UniversityHangzhou, China
| | - Yanli Wang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang UniversityHangzhou, China
| | - Zhiliang Yu
- College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China
| | - Yili Huang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang UniversityHangzhou, China
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