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Gupta G, Chauhan PS, Jha PN, Verma RK, Singh S, Yadav VK, Sahoo DK, Patel A. Secretory molecules from secretion systems fine-tune the host-beneficial bacteria (PGPRs) interaction. Front Microbiol 2024; 15:1355750. [PMID: 38468848 PMCID: PMC10925705 DOI: 10.3389/fmicb.2024.1355750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/05/2024] [Indexed: 03/13/2024] Open
Abstract
Numerous bacterial species associate with plants through commensal, mutualistic, or parasitic association, affecting host physiology and health. The mechanism for such association is intricate and involves the secretion of multiple biochemical substances through dedicated protein systems called secretion systems SS. Eleven SS pathways deliver protein factors and enzymes in their immediate environment or host cells, as well as in competing microbial cells in a contact-dependent or independent fashion. These SS are instrumental in competition, initiation of infection, colonization, and establishment of association (positive or negative) with host organisms. The role of SS in infection and pathogenesis has been demonstrated for several phytopathogens, including Agrobacterium, Xanthomonas, Ralstonia, and Pseudomonas. Since there is overlap in mechanisms of establishing association with host plants, several studies have investigated the role of SSs in the interaction of plant and beneficial bacteria, including symbiotic rhizobia and plant growth bacteria (PGPB). Therefore, the present review updates the role of different SSs required for the colonization of beneficial bacteria such as rhizobia, Burkholderia, Pseudomonas, Herbaspirillum, etc., on or inside plants, which can lead to a long-term association. Most SS like T3SS, T4SS, T5SS, and T6SS are required for the antagonistic activity needed to prevent competing microbes, including phytopathogens, ameliorate biotic stress in plants, and produce substances for successful colonization. Others are required for chemotaxis, adherence, niche formation, and suppression of immune response to establish mutualistic association with host plants.
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Affiliation(s)
- Garima Gupta
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, India
- Microbial Technologies Group, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Puneet Singh Chauhan
- Microbial Technologies Group, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Prabhat Nath Jha
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Rakesh Kumar Verma
- Department of Biosciences, SLAS Mody University of Science and Technology, Sikar, Rajasthan, India
| | - Sachidanand Singh
- Department of Biotechnology, School of Energy Technology, Pandit Deendayal Energy University, Gandhinagar, Gujarat, India
| | - Virendra Kumar Yadav
- Department of Lifesciences, Hemchandracharya North Gujarat University, Patan, Gujarat, India
| | - Dipak Kumar Sahoo
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Ashish Patel
- Department of Lifesciences, Hemchandracharya North Gujarat University, Patan, Gujarat, India
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Mao HC, Sun Y, Tao C, Deng X, Xu X, Shen Z, Zhang L, Zheng Z, Huang Y, Hao Y, Zhou G, Liu S, Li R, Guo K, Tian Z, Shen Q. Rhizosphere Microbiota Promotes the Growth of Soybeans in a Saline-Alkali Environment under Plastic Film Mulching. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091889. [PMID: 37176946 PMCID: PMC10180738 DOI: 10.3390/plants12091889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023]
Abstract
The rhizosphere microbiota plays a critical and crucial role in plant health and growth, assisting plants in resisting adverse stresses, including soil salinity. Plastic film mulching is an important method to adjust soil properties and improve crop yield, especially in saline-alkali soil. However, it remains unclear whether and to what extent the association between these improvements and rhizosphere microbiota exists. Here, from a field survey and a greenhouse mesocosm experiment, we found that mulching plastic films on saline-alkali soil can promote the growth of soybeans in the field. Results of the greenhouse experiment showed that soybeans grew better in unsterilized saline-alkali soil than in sterilized saline-alkali soil under plastic film mulching. By detecting the variations in soil properties and analyzing the high-throughput sequencing data, we found that with the effect of film mulching, soil moisture content was effectively maintained, soil salinity was obviously reduced, and rhizosphere bacterial and fungal communities were significantly changed. Ulteriorly, correlation analysis methods were applied. The optimization of soil properties ameliorated the survival conditions of soil microbes and promoted the increase in relative abundance of potential beneficial microorganisms, contributing to the growth of soybeans. Furthermore, the classification of potential key rhizosphere microbial OTUs were identified. In summary, our study suggests the important influence of soil properties as drivers on the alteration of rhizosphere microbial communities and indicates the important role of rhizosphere microbiota in promoting plant performance in saline-alkali soil under plastic film mulching.
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Affiliation(s)
- Han-Cheng Mao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Bio-Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Yifei Sun
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Bio-Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Chengyuan Tao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Bio-Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuhui Deng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Bio-Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Xu Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Bio-Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenquan Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Bio-Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Laijie Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Bio-Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Zehui Zheng
- Institute of Environment and Ecology, Shandong Normal University, No. 88, Wenhuadong Road, Lixia District, Ji'nan 250014, China
| | - Yanhua Huang
- Institute of Environment and Ecology, Shandong Normal University, No. 88, Wenhuadong Road, Lixia District, Ji'nan 250014, China
| | - Yongren Hao
- Institute of Environment and Ecology, Shandong Normal University, No. 88, Wenhuadong Road, Lixia District, Ji'nan 250014, China
| | - Guoan Zhou
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shulin Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Bio-Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Kai Guo
- Institute of Environment and Ecology, Shandong Normal University, No. 88, Wenhuadong Road, Lixia District, Ji'nan 250014, China
| | - Zhixi Tian
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Bio-Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
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3
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Lindström K, Mousavi SA. Effectiveness of nitrogen fixation in rhizobia. Microb Biotechnol 2020; 13:1314-1335. [PMID: 31797528 PMCID: PMC7415380 DOI: 10.1111/1751-7915.13517] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 12/01/2022] Open
Abstract
Biological nitrogen fixation in rhizobia occurs primarily in root or stem nodules and is induced by the bacteria present in legume plants. This symbiotic process has fascinated researchers for over a century, and the positive effects of legumes on soils and their food and feed value have been recognized for thousands of years. Symbiotic nitrogen fixation uses solar energy to reduce the inert N2 gas to ammonia at normal temperature and pressure, and is thus today, especially, important for sustainable food production. Increased productivity through improved effectiveness of the process is seen as a major research and development goal. The interaction between rhizobia and their legume hosts has thus been dissected at agronomic, plant physiological, microbiological and molecular levels to produce ample information about processes involved, but identification of major bottlenecks regarding efficiency of nitrogen fixation has proven to be complex. We review processes and results that contributed to the current understanding of this fascinating system, with focus on effectiveness of nitrogen fixation in rhizobia.
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Affiliation(s)
- Kristina Lindström
- Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science (HELSUS)University of HelsinkiFI‐00014HelsinkiFinland
| | - Seyed Abdollah Mousavi
- Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science (HELSUS)University of HelsinkiFI‐00014HelsinkiFinland
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Bromfield ESP, Cloutier S, Robidas C, Tran Thi TV, Darbyshire SJ. Invasive Galega officinalis (Goat's rue) plants in Canada form a symbiotic association with strains of Neorhizobium galegae sv. officinalis originating from the Old World. Ecol Evol 2019; 9:6999-7004. [PMID: 31380028 PMCID: PMC6662265 DOI: 10.1002/ece3.5266] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/23/2019] [Accepted: 04/29/2019] [Indexed: 11/09/2022] Open
Abstract
The toxic legume plant, Galega officinalis, is native to the Eastern Mediterranean and Black Sea regions. This legume is considered to be a noxious weed, and its establishment in Canada may have resulted from ornamental planting and/or field trials. In its native range, a highly specific nitrogen-fixing symbiosis with the bacterium, Neorhizobium galegae symbiovar (sv.) officinalis, is required for normal growth. In North America, nothing is known about the bacterial symbionts of G. officinalis. Our purpose was to determine the species and symbiovar identity of symbiotic bacteria associated with invasive plants of G. officinalis at five sites in the province of Ontario, Canada. Sequence analysis of four housekeeping (16S rRNA, atpD, glnII, and recA) and two symbiosis (nodC and nifH) genes showed that all 50 bacterial isolates from root nodules of G. officinalis at the five Canadian sites were identical to strains of N. galegae sv. officinalis originating either from Europe or the Caucasus. Plant tests indicated that soils collected from four Canadian sites without a history of agriculture or presence of G. officinalis were deficient in symbiotic bacteria capable of eliciting nodules on this plant. Collectively our data support the hypothesis of anthropogenic co-introduction of G. officinalis and its specific symbiotic bacterium into Canada from the Old World. Factors that may limit the spread of G. officinalis in new environments are discussed.
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Affiliation(s)
- Eden S. P. Bromfield
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaOntarioCanada
| | - Sylvie Cloutier
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaOntarioCanada
| | - Catherine Robidas
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaOntarioCanada
| | - Thu Van Tran Thi
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaOntarioCanada
| | - Stephen J. Darbyshire
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaOntarioCanada
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Saad MM, Michalet S, Fossou R, Putnik-Delić M, Crèvecoeur M, Meyer J, de Malézieux C, Hopfgartner G, Maksimović I, Perret X. Loss of NifQ Leads to Accumulation of Porphyrins and Altered Metal-Homeostasis in Nitrogen-Fixing Symbioses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:208-216. [PMID: 30070615 DOI: 10.1094/mpmi-07-18-0188-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Symbiotic nitrogen fixation between legumes and rhizobia involves a coordinated expression of many plant and bacterial genes as well as finely tuned metabolic activities of micro- and macrosymbionts. In spite of such complex interactions, symbiotic proficiency remains a resilient process, with host plants apparently capable of compensating for some deficiencies in rhizobia. What controls nodule homeostasis is still poorly understood and probably varies between plant species. In this respect, the promiscuous Sinorhizobium (Ensifer) fredii strain NGR234 has become a model to assess the relative contribution of single gene products to many symbioses. Here, we describe how a deletion in nifQ of NGR234 (strain NGRΔnifQ) makes nodules of Vigna unguiculata, V. radiata, and Macroptilium atropurpureum but not of the mimisoid tree Leucaena leucocephala, purple-red. This peculiar dark-nodule phenotype did not necessarily correlate with a decreased proficiency of NGRΔnifQ but coincided with a 20-fold or more accumulation of coproporphyrin III and uroporphyrin III in V. unguiculata nodules. Porphyrin accumulation was not restricted to plant cells infected with bacteroids but also extended to the nodule cortex. Nodule metal-homeostasis was altered but not sufficiently to prevent assembly and functioning of nitrogenase. Although the role of NifQ in donating molybdenum during assembly of nitrogenase cofactor FeMo-co makes it essential in free-living diazotrophs, our results highlight the dispensability of NifQ in many legume species.
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Affiliation(s)
- Maged M Saad
- 1 University of Geneva, Sciences III, Department of Botany and Plant Biology, Microbiology Unit, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
- 2 King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal 6900-2355, Kingdom of Saudi Arabia
| | - Sophie Michalet
- 3 University of Geneva, Mass Spectrometry Core Facility (MZ 2.0), Faculty of Sciences, Bd d'Yvoy 11, CH-1211 Geneva 4, Switzerland
| | - Romain Fossou
- 1 University of Geneva, Sciences III, Department of Botany and Plant Biology, Microbiology Unit, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | | | - Michèle Crèvecoeur
- 1 University of Geneva, Sciences III, Department of Botany and Plant Biology, Microbiology Unit, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Julien Meyer
- 3 University of Geneva, Mass Spectrometry Core Facility (MZ 2.0), Faculty of Sciences, Bd d'Yvoy 11, CH-1211 Geneva 4, Switzerland
| | - Chloé de Malézieux
- 1 University of Geneva, Sciences III, Department of Botany and Plant Biology, Microbiology Unit, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Gérard Hopfgartner
- 5 University of Geneva, Department of Inorganic and Analytical Chemistry, Faculty of Sciences, 26 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Ivana Maksimović
- 4 University of Novi Sad, Faculty of Agriculture, Novi Sad, Serbia; and
| | - Xavier Perret
- 1 University of Geneva, Sciences III, Department of Botany and Plant Biology, Microbiology Unit, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
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6
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Soenens A, Gomila M, Imperial J. Neorhizobium tomejilense sp. nov., first non-symbiotic Neorhizobium species isolated from a dryland agricultural soil in southern Spain. Syst Appl Microbiol 2018; 42:128-134. [PMID: 30268635 DOI: 10.1016/j.syapm.2018.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/30/2018] [Accepted: 09/10/2018] [Indexed: 01/05/2023]
Abstract
We describe for the first time a non-symbiotic species of the recently described genus Neorhizobium, lacking nodulation or nitrogen fixation genes. The strains were isolated from a dryland agricultural soil in southern Spain where no record of legume cultivation is available, thus we propose the name Neorhizobium tomejilense sp. nov. (type strain T17_20T, LMG 30623T and CECT 9621T). N. tomejilense exhibit a clear distinct lineage from the other Neorhizobium species, Neorhizobium galegae, Neorhizobium alkalisoli and Neorhizobium huautlense, based on polyphasic evidence. Phylogenetic marker analysis of 16S rDNA, atpD, glnII, recA, rpoB and thrC genes and genomic identity data derived from the draft genomic sequences showed that N. tomejilense strains clearly separated from the other Neorhizobium species and that N. galegae represents the closest species, with Average Nucleotide Identities (ANIb) ranging from 90% (for type strain HAMBI 540T) to just under 95.0% (for two N. galegae sv. officinalis strains). Genomes from N. galegae and N. tomejilense, however, clearly differed in important traits, such as the number of rRNA operon copies or the number of tRNAs. Phenotypic characterisation of N. tomejilense also displayed differences with the other Neorhizobium species. Whole-cell matrix-assisted laser-desorption time-of-flight mass spectrometry (WC MALDI-TOF-MS) fingerprint analysis and the dendrogram derived from the fingerprint profiles, showed a clearly distinct group formed by the three N. tomejilense isolates (T17_20T, T20_22 and T11_12) from the other Neorhizobium especies.
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Affiliation(s)
- Amalia Soenens
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
| | - Juan Imperial
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28223 Pozuelo de Alarcón, Madrid, Spain; Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain.
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7
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Yan H, Xie JB, Ji ZJ, Yuan N, Tian CF, Ji SK, Wu ZY, Zhong L, Chen WX, Du ZL, Wang ET, Chen WF. Evolutionarily Conserved nodE, nodO, T1SS, and Hydrogenase System in Rhizobia of Astragalus membranaceus and Caragana intermedia. Front Microbiol 2017; 8:2282. [PMID: 29209294 PMCID: PMC5702008 DOI: 10.3389/fmicb.2017.02282] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/06/2017] [Indexed: 02/01/2023] Open
Abstract
Mesorhizobium species are the main microsymbionts associated with the medicinal or sand-fixation plants Astragalus membranaceus and Caragana intermedia (AC) in temperate regions of China, while all the Mesorhizobium strains isolated from each of these plants could nodulate both of them. However, Rhizobium yanglingense strain CCBAU01603 could nodulate AC plants and it's a high efficiency symbiotic and competitive strain with Caragana. Therefore, the common features shared by these symbiotic rhizobia in genera of Mesorhizobium and Rhizobium still remained undiscovered. In order to study the genomic background influencing the host preference of these AC symbiotic strains, the whole genomes of two (M. silamurunense CCBAU01550, M. silamurunense CCBAU45272) and five representative strains (M. septentrionale CCBAU01583, M. amorphae CCBAU01570, M. caraganae CCBAU01502, M. temperatum CCBAU01399, and R. yanglingense CCBAU01603) originally isolated from AC plants were sequenced, respectively. As results, type III secretion systems (T3SS) of AC rhizobia evolved in an irregular pattern, while an evolutionarily specific region including nodE, nodO, T1SS, and a hydrogenase system was detected to be conserved in all these AC rhizobia. Moreover, nodO was verified to be prevalently distributed in other AC rhizobia and was presumed as a factor affecting the nodule formation process. In conclusion, this research interpreted the multifactorial features of the AC rhizobia that may be associated with their host specificity at cross-nodulation group, including nodE, nodZ, T1SS as the possible main determinants; and nodO, hydrogenase system, and T3SS as factors regulating the bacteroid formation or nitrogen fixation efficiency.
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Affiliation(s)
- Hui Yan
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, China.,State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian Bo Xie
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhao Jun Ji
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Na Yuan
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Chang Fu Tian
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Shou Kun Ji
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhong Yu Wu
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Liang Zhong
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Wen Xin Chen
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Zheng Lin Du
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico, Mexico
| | - Wen Feng Chen
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, China
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8
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Marek-Kozaczuk M, Wdowiak-Wróbel S, Kalita M, Chernetskyy M, Deryło K, Tchórzewski M, Skorupska A. Host-dependent symbiotic efficiency of Rhizobium leguminosarum bv. trifolii strains isolated from nodules of Trifolium rubens. Antonie van Leeuwenhoek 2017; 110:1729-1744. [PMID: 28791535 PMCID: PMC5676844 DOI: 10.1007/s10482-017-0922-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/29/2017] [Indexed: 11/28/2022]
Abstract
Trifolium rubens L., commonly known as the red feather clover, is capable of symbiotic interactions with rhizobia. Up to now, no specific symbionts of T. rubens and their symbiotic compatibility with Trifolium spp. have been described. We characterized the genomic diversity of T. rubens symbionts by analyses of plasmid profiles and BOX-PCR. The phylogeny of T. rubens isolates was inferred based on the nucleotide sequences of 16S rRNA and two core genes (atpD, recA). The nodC phylogeny allowed classification of rhizobia nodulating T. rubens as Rhizobium leguminosarum symbiovar trifolii (Rlt). The symbiotic efficiency of the Rlt isolates was determined on four clover species: T. rubens, T. pratense, T. repens and T. resupinatum. We determined that Rlt strains formed mostly inefficient symbiosis with their native host plant T. rubens and weakly effective (sub-optimal) symbiosis with T. repens and T. pratense. The same Rlt strains were fully compatible in the symbiosis with T. resupinatum. T. rubens did not exhibit strict selectivity in regard to the symbionts and rhizobia closely related to Rhizobium grahamii, Rhizobium galegae and Agrobacterium radiobacter, which did not nodulate Trifolium spp., were found amongst T. rubens nodule isolates.
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Affiliation(s)
- Monika Marek-Kozaczuk
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland.
| | - Sylwia Wdowiak-Wróbel
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Michał Kalita
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Mykhaylo Chernetskyy
- The Botanic Garden of Maria Curie-Skłodowska University, Sławinkowska 3, 20-810, Lublin, Poland
| | - Kamil Deryło
- Department of Molecular Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Marek Tchórzewski
- Department of Molecular Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Anna Skorupska
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
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Grover S, Gupta P, Kahlon PS, Goyal S, Grover A, Dalal K, Sabeeha, Ehtesham NZ, Hasnain SE. Analyses of methyltransferases across the pathogenicity spectrum of different mycobacterial species point to an extremophile connection. MOLECULAR BIOSYSTEMS 2016; 12:1615-25. [PMID: 26983646 DOI: 10.1039/c5mb00810g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuberculosis is a devastating disease, taking one human life every 20 seconds globally. We hypothesize that professional pathogens such as M.tb have acquired specific features that might assist in causing infection, persistence and transmissible pathology in their host. We have identified 121 methyltransferases (MTases) in the M.tb proteome, which use a variety of substrates - DNA, RNA, protein, intermediates of mycolic acid biosynthesis and other fatty acids - that are involved in cellular maintenance within the host. A comparative analysis of the proteome of the virulent strain H37Rv and the avirulent strain H37Ra identified 3 MTases, which displayed significant variations in terms of N-terminal extension/deletion and point mutations, possibly impacting various physicochemical properties. The cross-proteomic comparison of MTases of M.tb H37Rv with 15 different Mycobacterium species revealed the acquisition of novel MTases in a MTB complex as a function of evolution. Phylogenetic analysis revealed that these newly acquired MTases showed common roots with certain extremophiles such as halophilic and acidophilic organisms. Our results establish an evolutionary relationship of M.tb with halotolerant organisms and also the role of MTases of M.tb in withstanding the host osmotic stress, thereby pointing to their likely role in pathogenesis, virulence and niche adaptation.
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Affiliation(s)
- Sonam Grover
- Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India.
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Parkinson JE, Baumgarten S, Michell CT, Baums IB, LaJeunesse TC, Voolstra CR. Gene Expression Variation Resolves Species and Individual Strains among Coral-Associated Dinoflagellates within the Genus Symbiodinium. Genome Biol Evol 2016; 8:665-80. [PMID: 26868597 PMCID: PMC4824173 DOI: 10.1093/gbe/evw019] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Reef-building corals depend on symbiotic mutualisms with photosynthetic dinoflagellates in the genus Symbiodinium. This large microalgal group comprises many highly divergent lineages (“Clades A–I”) and hundreds of undescribed species. Given their ecological importance, efforts have turned to genomic approaches to characterize the functional ecology of Symbiodinium. To date, investigators have only compared gene expression between representatives from separate clades—the equivalent of contrasting genera or families in other dinoflagellate groups—making it impossible to distinguish between clade-level and species-level functional differences. Here, we examined the transcriptomes of four species within one Symbiodinium clade (Clade B) at ∼20,000 orthologous genes, as well as multiple isoclonal cell lines within species (i.e., cultured strains). These species span two major adaptive radiations within Clade B, each encompassing both host-specialized and ecologically cryptic taxa. Species-specific expression differences were consistently enriched for photosynthesis-related genes, likely reflecting selection pressures driving niche diversification. Transcriptional variation among strains involved fatty acid metabolism and biosynthesis pathways. Such differences among individuals are potentially a major source of physiological variation, contributing to the functional diversity of coral holobionts composed of unique host–symbiont genotype pairings. Our findings expand the genomic resources available for this important symbiont group and emphasize the power of comparative transcriptomics as a method for studying speciation processes and interindividual variation in nonmodel organisms.
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Affiliation(s)
| | - Sebastian Baumgarten
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Craig T Michell
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | | | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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