1
|
Hakim S, Imran A, Hussain MS, Mirza MS. RNA-Seq analysis of mung bean (Vigna radiata L.) roots shows differential gene expression and predicts regulatory pathways responding to taxonomically different rhizobia. Microbiol Res 2023; 275:127451. [PMID: 37478540 DOI: 10.1016/j.micres.2023.127451] [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: 05/16/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/23/2023]
Abstract
Symbiotic interaction among legume and rhizobia is a complex phenomenon which results in the formation of nitrogen-fixing nodules. Mung bean is promiscuous host however expression profile of this important legume plant in response to rhizobial infection was particularly lacking and urgently needed. We have demonstrated the pattern of gene expression of mung bean roots inoculated with two symbionts Bradyrhizobium yuanmingense Vr50 and Sinorhizobium (Ensifer) aridi Vr33 and non-inoculated control (CK). The RNA-Seq data analyzed at two growth stages i.e., 1-3 h and 10-16 days post inoculation revealed significantly higher number of differentially expressed genes (DEGs) at nodulation stage. The DEGs encoding receptor kinases identified at early stage might be involved in perception of Nod factors produced by different rhizobia. At nodulation stage important genes involved in plant hormone signal transduction, nitrogen and sulfur metabolism were identified. KEGG pathway enrichment analysis showed that metabolic pathways were most prominent in both groups (Group 1: Vr33 vs CK; Group 2: Vr50 vs CK), followed by biosynthesis of secondary metabolites, plant hormone signal transduction and biosynthesis of amino acids. Furthermore, DEGs involved in cell communication and plant hormone signal transduction were found to be different among two symbiotic systems while DEGs involved in carbon, nitrogen and sulfur metabolism were similar but their expression varied in response to two rhizobial strains. This study provides the first insight into the mechanisms underlying interactions of mung bean host with two taxonomically different symbionts (Bradyrhizobium and Sinorhizobium) and the candidate genes for better understanding the mechanisms of symbiotic host-specificity.
Collapse
Affiliation(s)
- Sughra Hakim
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Asma Imran
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan
| | | | - M Sajjad Mirza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan.
| |
Collapse
|
2
|
Hakim S, Imran A, Mirza MS. Phylogenetic diversity analysis reveals Bradyrhizobium yuanmingense and Ensifer aridi as major symbionts of mung bean (Vigna radiata L.) in Pakistan. Braz J Microbiol 2021; 52:311-324. [PMID: 33141350 PMCID: PMC7966693 DOI: 10.1007/s42770-020-00397-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/27/2020] [Indexed: 11/26/2022] Open
Abstract
The present study was carried out to evaluate the diversity of rhizobia associated with nodules of mung bean in Pakistan, because this information is necessary for inoculum development. Based on sequence analysis of 16S rRNA gene of thirty-one bacteria, 11 were assigned to genus Bradyrhizobium, 17 to Ensifer, and 3 to Rhizobium. Phylogenetic analyses on the basis of 16S-23S ITS region, atpD, recA, nifH, and nodA of representative strains revealed that B. yuanmingense is the predominant species distributed throughout different mung bean-growing areas. Among the fast-growing rhizobia, Ensifer aridi was predominant in Faisalabad, Layyah, and Rawalpindi, while E. meliloti in Thal desert. Sequence variations and phylogeny of nifH and nodA genes suggested that these genes might have been co-evolved with the housekeeping genes and maintained by vertical gene transfer in rhizobia detected in the present study. Host infectivity assay revealed the successful nodulation of host by rhizobia related to genera Bradyrhizobium, Ensifer and Rhizobium. Among all, Bradyrhizobium and Ensifer spp. inoculation exhibited a significantly higher number of nodules (11-34 nodules plant-1) and nitrogenase activity (nodule ARA 60-110 μmol g-1 h-1). Contrary to the previous studies, our data reveal that B. yuanmingense and E. aridi are predominant species forming effective nodules in mung bean in Pakistan. Furthermore, to the best of our knowledge, this is the first report showing the effective symbiosis of E. aridi, E. meliloti, and Rhizobium pusense with mung bean. The diversity of rhizobia in different habitats revealed in the present study will contribute towards designing site-specific inocula for mung bean.
Collapse
Affiliation(s)
- Sughra Hakim
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Asma Imran
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan
| | - M Sajjad Mirza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan.
| |
Collapse
|
3
|
Jung YJ, Kim HJ, Hur M. Mesorhizobium terrae sp. nov., a novel species isolated from soil in Jangsu, Korea. Antonie van Leeuwenhoek 2020; 113:1279-1287. [PMID: 32564274 DOI: 10.1007/s10482-020-01435-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/09/2020] [Indexed: 10/24/2022]
Abstract
A gram-negative, white-pigmented, aerobic, rod-shaped bacterium, designated as strain NIBRBAC000500504T, was isolated from soil in Jangsu, Korea. Optimal growth of this strain was observed at 25 °C, pH 7.0, and in the presence of 0% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NIBRBAC000500504T belonged to the genus Mesorhizobium and was closely related to Mesorhizobium shangrilense LMG 24762T (98.3% sequence similarity), Mesorhizobium australicum LMG 24608T (98.2%), Mesorhizobium qingshengii LMG 26793T (98.1%), Mesorhizobium ciceri ATCC 51585T (98.0%), Mesorhizobium loti DSM 2626T (98.0%), Mesorhizobium sophorae LMG 28223T (97.9%), Mesorhizobium waitakense LMG 28227T (97.8%), and Mesorhizobium cantuariense LMG 28225T (97.8%). Next-generation sequencing analysis indicated that the genome of strain NIBRBAC000500504T comprised a circular chromosome (5,731,152 bp, G+C content: 63.26%) and a plasmid (293,638 bp, G+C content: 61.39%) with 5672 coding sequences, 50 tRNAs, and 6 rRNAs. The major respiratory isoprenoid quinone was Q10; the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine; the major fatty acids were summed feature 8 (comprising C18:1 ω7c/C18:1 ω6c), C19:0 cyclo ω8c, C16:0, and C18:1 ω7c 11-methyl; and the G+C content of the genomic DNA was 62.9 mol%. The DNA-DNA relatedness values between NIBRBAC000500504T and its closest type strains were low. On the basis of these polyphasic taxonomic data, it is proposed that strain NIBRBAC000500504T represents a novel species of the genus Mesorhizobium, with the type strain being NIBRBAC000500504T (= KCTC 72278T = JCM 33432T).
Collapse
Affiliation(s)
- You-Jung Jung
- Biological Resources Utilization Department, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Hyun-Joong Kim
- Department of Food Engineering, Mokpo National University, Muan, 58554, Republic of Korea
| | - Moonsuk Hur
- Biological Resources Utilization Department, National Institute of Biological Resources, Incheon, 22689, Republic of Korea.
| |
Collapse
|
4
|
Favero VO, Carvalho RH, Motta VM, Leite ABC, Coelho MRR, Xavier GR, Rumjanek NG, Urquiaga S. Bradyrhizobium as the Only Rhizobial Inhabitant of Mung Bean ( Vigna radiata) Nodules in Tropical Soils: A Strategy Based on Microbiome for Improving Biological Nitrogen Fixation Using Bio-Products. FRONTIERS IN PLANT SCIENCE 2020; 11:602645. [PMID: 33510747 PMCID: PMC7835340 DOI: 10.3389/fpls.2020.602645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/14/2020] [Indexed: 05/07/2023]
Abstract
The mung bean has a great potential under tropical conditions given its high content of grain protein. Additionally, its ability to benefit from biological nitrogen fixation (BNF) through association with native rhizobia inhabiting nodule microbiome provides most of the nitrogen independence on fertilizers. Soil microbial communities which are influenced by biogeographical factors and soil properties, represent a source of rhizobacteria capable of stimulating plant growth. The objective of this study is to support selection of beneficial bacteria that form positive interactions with mung bean plants cultivated in tropical soils, as part of a seed inoculation program for increasing grain yield based on the BNF and other mechanisms. Two mung bean genotypes (Camaleão and Esmeralda) were cultivated in 10 soil samples. Nodule microbiome was characterized by next-generation sequencing using Illumina MiSeq 16S rRNA. More than 99% of nodule sequences showed similarity with Bradyrhizobium genus, the only rhizobial present in nodules in our study. Higher bacterial diversity of soil samples collected in agribusiness areas (MW_MT-I, II or III) was associated with Esmeralda genotype, while an organic agroecosystem soil sample (SE_RJ-V) showed the highest bacterial diversity independent of genotype. Furthermore, OTUs close to Bradyrhizobium elkanii have dominated in all soil samples, except in the sample from the organic agroecosystem, where just B. japonicum was present. Bacterial community of mung bean nodules is mainly influenced by soil pH, K, Ca, and P. Besides a difference on nodule colonization by OTU sequences close to the Pseudomonas genus regarding the two genotypes was detected too. Although representing a small rate, around 0.1% of the total, Pseudomonas OTUs were only retrieved from nodules of Esmeralda genotype, suggesting a different trait regarding specificity between macro- and micro-symbionts. The microbiome analysis will guide the next steps in the development of an inoculant for mung bean aiming to promote plant growth and grain yield, composed either by an efficient Bradyrhizobium strain on its own or co-inoculated with a Pseudomonas strain. Considering the results achieved, the assessment of microbial ecology parameters is a potent coadjuvant capable to accelerate the inoculant development process and to improve the benefits to the crop by soil microorganisms.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Norma Gouvêa Rumjanek
- Embrapa Agrobiology, Seropédica, Rio de Janeiro, Brazil
- *Correspondence: Norma Gouvêa Rumjanek,
| | | |
Collapse
|
5
|
Hakim S, Mirza BS, Imran A, Zaheer A, Yasmin S, Mubeen F, Mclean JE, Mirza MS. Illumina sequencing of 16S rRNA tag shows disparity in rhizobial and non-rhizobial diversity associated with root nodules of mung bean (Vigna radiata L.) growing in different habitats in Pakistan. Microbiol Res 2019; 231:126356. [PMID: 31722286 DOI: 10.1016/j.micres.2019.126356] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/11/2019] [Accepted: 10/18/2019] [Indexed: 10/25/2022]
Abstract
In Rhizobium-legume symbiosis, the nodule is the most frequently studied compartment, where the endophytic/symbiotic microbiota demands critical investigation for development of specific inocula. We identified the bacterial diversity within root nodules of mung bean from different growing areas of Pakistan using Illumina sequencing of 16S rRNA gene. We observed specific OTUs related to specific site where Bradyrhizobium was found to be the dominant genus comprising of 82-94% of total rhizobia in nodules with very minor fraction of sequences from other rhizobia at three sites. In contrast, Ensifer (Sinorhizobium) was single dominant genus comprising 99.9% of total rhizobial sequences at site four. Among non-rhizobial sequences, the genus Acinetobacter was abundant (7-18% of total sequences), particularly in Bradyrhizobium-dominated nodule samples. Rhizobia and non-rhizobial PGPR isolated from nodule samples include Ensifer, Bradyrhizobium, Acinetobacter, Microbacterium and Pseudomonas strains. Co-inoculation of multi-trait PGPR Acinetobacter sp. VrB1 with either of the two rhizobia in field exhibited more positive effect on nodulation and plant growth than single-strain inoculation which favors the use of Acinetobacter as an essential component for development of mung bean inoculum. Furthermore, site-specific dominance of rhizobia and non-rhizobia revealed in this study may contribute towards decision making for development and application of specific inocula in different habitats.
Collapse
Affiliation(s)
- Sughra Hakim
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Babur S Mirza
- Missouri State University, Biology Department, Springfield, MO 65897, USA
| | - Asma Imran
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan
| | - Ahmad Zaheer
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan; Institute of Molecular Biology and Biotechnology, The University of Lahore, Pakistan
| | - Sumera Yasmin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan
| | - Fathia Mubeen
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan
| | - Joan E Mclean
- Utah Water Research Laboratory, Utah State University, Logan, Utah, USA
| | - M Sajjad Mirza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan.
| |
Collapse
|
6
|
Rejili M, Msaddak A, Filali I, Benabderrahim MA, Mars M, Marín M. New chromosomal lineages within Microvirga and Bradyrhizobium genera nodulate Lupinus angustifolius growing on different Tunisian soils. FEMS Microbiol Ecol 2019; 95:5537381. [DOI: 10.1093/femsec/fiz118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/17/2019] [Indexed: 11/13/2022] Open
Abstract
ABSTRACTThirty-one rhizobial isolates nodulating native Lupinus angustifolius (blue lupine) plants growing in Northern Tunisian soils were isolated and analysed using different chromosomal and symbiotic gene markers. Phylogenetic analyses based on recA partial sequences grouped them into at least five groups: four of them within the genus Bradyrhizobium (26 isolates) and one into the genus Microvirga (5 isolates). Representative strains were analysed by multilocus sequence analysis of three housekeeping genes rrs-recA-glnII and rrs-gyrB-dnaK for Bradyrhizobium and Microvirga isolates, respectively. Based on this analysis, eight isolates clustered with the previously described strains Bradyrhizobium lupini USDA3051 and Bradyrhizobium canariense BTA-1. However, five of the isolates clustered separately and may constitute a new species within the Bradyrhizobium genus. The remaining five isolates were closely related to the strain Microvirga sp. LmiM8 and may constitute a new Microvirga species. The analysis of the nodC gene showed that all Bradyrhizobium strains nodulating blue lupine belong to the symbiovar genistearum, whereas the Microvirga isolates are associated with the symbiovar mediterranense. The results of this study support that the L. angustifolius root nodule symbionts isolated in Northern Tunisia belong mostly to the B. canariense/B. lupini lineages. However, new clades of Bradyrhizobium and Microvirga have been identified as L. angustifolius endosymbionts.
Collapse
Affiliation(s)
- M Rejili
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources (BVBAA) – Faculty of Sciences of Gabes, University of Gabes, Erriadh, Zrig 6072, Gabes, Tunisia
| | - A Msaddak
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources (BVBAA) – Faculty of Sciences of Gabes, University of Gabes, Erriadh, Zrig 6072, Gabes, Tunisia
| | - I Filali
- College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University, Riyadh PO Box 84428, Saudi Arabia
| | - M A Benabderrahim
- Arid and Oases Cropping Laboratory, Arid Area Institute, Gabes 6051, Tunisia
| | - M Mars
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources (BVBAA) – Faculty of Sciences of Gabes, University of Gabes, Erriadh, Zrig 6072, Gabes, Tunisia
| | - M Marín
- Institute of Genetics, Ludwig Maximilians University of Munich (LMU), Grosshaderner Str. 2–4, D-82152 Martinsried, Germany
| |
Collapse
|
7
|
Hakim S, Mirza BS, Zaheer A, Mclean JE, Imran A, Yasmin S, Sajjad Mirza M. Retrieved 16S rRNA and nifH sequences reveal co-dominance of Bradyrhizobium and Ensifer (Sinorhizobium) strains in field-collected root nodules of the promiscuous host Vigna radiata (L.) R. Wilczek. Appl Microbiol Biotechnol 2017; 102:485-497. [PMID: 29110071 DOI: 10.1007/s00253-017-8609-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 10/11/2017] [Accepted: 10/13/2017] [Indexed: 11/27/2022]
Abstract
In the present study, the relative distribution of endophytic rhizobia in field-collected root nodules of the promiscuous host mung bean was investigated by sequencing of 16S ribosomal RNA (rRNA) and nifH genes, amplified directly from the nodule DNA. Co-dominance of the genera Bradyrhizobium and Ensifer was indicated by 32.05 and 35.84% of the total retrieved 16S rRNA sequences, respectively, and the sequences of genera Mesorhizobium and Rhizobium comprised only 0.06 and 2.06% of the recovered sequences, respectively. Sequences amplified from rhizosphere soil DNA indicated that only a minor fraction originated from Bradyrhizobium and Ensifer strains, comprising about 0.46 and 0.67% of the total retrieved sequences, respectively. 16S rRNA gene sequencing has also identified the presence of several non-rhizobial endophytes from phyla Proteobacteria, Actinobacteria, Bacteroides, and Firmicutes. The nifH sequences obtained from nodules also confirmed the co-dominance of Bradyrhizobium (39.21%) and Ensifer (59.23%) strains. The nifH sequences of the genus Rhizobium were absent, and those of genus Mesorhizobium comprised only a minor fraction of the sequences recovered from the nodules and rhizosphere soil samples. Two bacterial isolates, identified by 16S rRNA gene sequence analysis as Bradyrhizobium strain Vr51 and Ensifer strain Vr38, successfully nodulated the original host (mung bean) plants. Co-dominance of Bradyrhizobium and Ensifer strains in the nodules of mung bean indicates the potential role of the host plant in selecting specific endophytic rhizobial populations. Furthermore, successful nodulation of mung bean by the isolates showed that strains of both the genera Bradyrhizobium and Ensifer can be used for production of inoculum.
Collapse
Affiliation(s)
- Sughra Hakim
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Babur S Mirza
- Biology Department, Missouri State University, Springfield, MO, 65897, USA
| | - Ahmad Zaheer
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Joan E Mclean
- Utah Water Research Laboratory, Utah State University, Logan, UT, USA
| | - Asma Imran
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Sumera Yasmin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - M Sajjad Mirza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan. .,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan.
| |
Collapse
|
8
|
Carro L, Nouioui I. Taxonomy and systematics of plant probiotic bacteria in the genomic era. AIMS Microbiol 2017; 3:383-412. [PMID: 31294168 PMCID: PMC6604993 DOI: 10.3934/microbiol.2017.3.383] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022] Open
Abstract
Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.
Collapse
Affiliation(s)
- Lorena Carro
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Imen Nouioui
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| |
Collapse
|
9
|
Ji ZJ, Yan H, Cui QG, Wang ET, Chen WF, Chen WX. Competition between rhizobia under different environmental conditions affects the nodulation of a legume. Syst Appl Microbiol 2017; 40:114-119. [DOI: 10.1016/j.syapm.2016.12.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/13/2016] [Accepted: 12/15/2016] [Indexed: 11/26/2022]
|
10
|
Shamseldin A, Abdelkhalek A, Sadowsky MJ. Recent changes to the classification of symbiotic, nitrogen-fixing, legume-associating bacteria: a review. Symbiosis 2016. [DOI: 10.1007/s13199-016-0462-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
11
|
Zhu YJ, Lu JK, Chen YL, Wang SK, Sui XH, Kang LH. Mesorhizobium acaciae sp. nov., isolated from root nodules of Acacia melanoxylon R. Br. Int J Syst Evol Microbiol 2016; 65:3558-3563. [PMID: 26296667 DOI: 10.1099/ijsem.0.000455] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three novel strains, RITF741T, RITF1220 and RITF909, isolated from root nodules of Acacia melanoxylon in Guangdong Province of China, have been previously identified as members of the genus Mesorhizobium, displaying the same 16S rRNA gene RFLP pattern. Phylogenetic analysis of 16S rRNA gene sequences indicated that the three strains belong to the genus Mesorhizobium and had highest similarity (100.0 %) to Mesorhizobium plurifarium LMG 11892T. Phylogenetic analyses of housekeeping genes recA, atpD and glnII revealed that these strains represented a distinct evolutionary lineage within the genus Mesorhizobium. Strain RITF741T showed >73 % DNA–DNA relatedness with strains RITF1220 and RITF909, but < 60 % DNA–DNA relatedness with the closest type strains of recognized species of the genus Mesorhizobium. They differed from each other and from their closest phylogenetic neighbours by presence/absence of several fatty acids, or by large differences in the relative amounts of particular fatty acids. While showing distinctive features, they were generally able to utilize a wide range of substrates as sole carbon sources based on API 50CH and API 20NE tests. The three strains were able to form nodules with the original host Acacia melanoxylon and other woody legumes such as Acacia aneura, Albizia falcataria and Leucaena leucocephala. In conclusion, these strains represent a novel species belonging to the genus Mesorhizobium based on the data obtained in the present and previous studies, for which the name Mesorhizobium acaciae sp. nov. is proposed. The type strain is RITF741T ( = CCBAU 101090T = JCM 30534T), the DNA G+C content of which is 64.1 mol% (T m).
Collapse
Affiliation(s)
- Ya Jie Zhu
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China
| | - Jun Kun Lu
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China
| | - Ying Long Chen
- Institute of Soil and Water Conservation, Chinese Academy of Sciences, and Northwest A&F University, Yangling 712100, PR China
- School of Earth and Environment, and UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
| | - Sheng Kun Wang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China
| | - Xin Hua Sui
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| | - Li Hua Kang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China
| |
Collapse
|
12
|
Diouf F, Diouf D, Klonowska A, Le Queré A, Bakhoum N, Fall D, Neyra M, Parrinello H, Diouf M, Ndoye I, Moulin L. Genetic and genomic diversity studies of Acacia symbionts in Senegal reveal new species of Mesorhizobium with a putative geographical pattern. PLoS One 2015; 10:e0117667. [PMID: 25658650 PMCID: PMC4319832 DOI: 10.1371/journal.pone.0117667] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 12/29/2014] [Indexed: 11/29/2022] Open
Abstract
Acacia senegal (L) Willd. and Acacia seyal Del. are highly nitrogen-fixing and moderately salt tolerant species. In this study we focused on the genetic and genomic diversity of Acacia mesorhizobia symbionts from diverse origins in Senegal and investigated possible correlations between the genetic diversity of the strains, their soil of origin, and their tolerance to salinity. We first performed a multi-locus sequence analysis on five markers gene fragments on a collection of 47 mesorhizobia strains of A. senegal and A. seyal from 8 localities. Most of the strains (60%) clustered with the M. plurifarium type strain ORS 1032T, while the others form four new clades (MSP1 to MSP4). We sequenced and assembled seven draft genomes: four in the M. plurifarium clade (ORS3356, ORS3365, STM8773 and ORS1032T), one in MSP1 (STM8789), MSP2 (ORS3359) and MSP3 (ORS3324). The average nucleotide identities between these genomes together with the MLSA analysis reveal three new species of Mesorhizobium. A great variability of salt tolerance was found among the strains with a lack of correlation between the genetic diversity of mesorhizobia, their salt tolerance and the soils samples characteristics. A putative geographical pattern of A. senegal symbionts between the dryland north part and the center of Senegal was found, reflecting adaptations to specific local conditions such as the water regime. However, the presence of salt does not seem to be an important structuring factor of Mesorhizobium species.
Collapse
Affiliation(s)
- Fatou Diouf
- Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Centre de Recherche de Bel Air, Dakar, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Dakar, Senegal
- IRD-Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet, Montpellier, France
| | - Diegane Diouf
- Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Centre de Recherche de Bel Air, Dakar, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Dakar, Senegal
| | - Agnieszka Klonowska
- IRD-Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet, Montpellier, France
| | - Antoine Le Queré
- Laboratoire Mixte International Biotechnologie Microbienne et Végétale (LBMV), Rabat, Morocco
| | - Niokhor Bakhoum
- Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Centre de Recherche de Bel Air, Dakar, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Dakar, Senegal
| | - Dioumacor Fall
- Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Centre de Recherche de Bel Air, Dakar, Senegal
- Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
| | - Marc Neyra
- Irstea, UR MALY, centre de Lyon-Villeurbanne, Villeurbanne, France
| | - Hugues Parrinello
- MGX-Montpellier GenomiX, Institut de Génomique Fonctionnelle, Montpellier, France
| | - Mayecor Diouf
- Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
| | - Ibrahima Ndoye
- Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Centre de Recherche de Bel Air, Dakar, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Dakar, Senegal
| | - Lionel Moulin
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Dakar, Senegal
- IRD-Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet, Montpellier, France
| |
Collapse
|
13
|
Pérez-Yépez J, Armas-Capote N, Velázquez E, Pérez-Galdona R, Rivas R, León-Barrios M. Evaluation of seven housekeeping genes for multilocus sequence analysis of the genus Mesorhizobium: Resolving the taxonomic affiliation of the Cicer canariense rhizobia. Syst Appl Microbiol 2014; 37:553-9. [DOI: 10.1016/j.syapm.2014.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 10/02/2014] [Accepted: 10/08/2014] [Indexed: 10/24/2022]
|
14
|
Armas-Capote N, Pérez-Yépez J, Martínez-Hidalgo P, Garzón-Machado V, del Arco-Aguilar M, Velázquez E, León-Barrios M. Core and symbiotic genes reveal nine Mesorhizobium genospecies and three symbiotic lineages among the rhizobia nodulating Cicer canariense in its natural habitat (La Palma, Canary Islands). Syst Appl Microbiol 2014; 37:140-8. [DOI: 10.1016/j.syapm.2013.08.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 07/30/2013] [Accepted: 08/03/2013] [Indexed: 11/16/2022]
|
15
|
Laranjo M, Alexandre A, Oliveira S. Legume growth-promoting rhizobia: An overview on the Mesorhizobium genus. Microbiol Res 2014; 169:2-17. [DOI: 10.1016/j.micres.2013.09.012] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/16/2013] [Accepted: 09/21/2013] [Indexed: 11/24/2022]
|
16
|
Zhou S, Li Q, Jiang H, Lindström K, Zhang X. Mesorhizobium
sangaii sp. nov., isolated from the root nodules of Astragalus luteolus and Astragalus ernestii. Int J Syst Evol Microbiol 2013; 63:2794-2799. [DOI: 10.1099/ijs.0.044685-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Our previous published data indicated that the two rhizobial strains SCAU7T and SCAU27, which were isolated from the root nodules of Astragalus luteolus and Astragalus ernestii respectively, in Sichuan Province, China, might be novel species of the genus
Mesorhizobium
. Their exact taxonomic position was determined in the present study by using polyphasic approaches. Comparative analysis of nearly full-length 16S rRNA gene sequences showed that these strains belonged to the genus
Mesorhizobium
, with
Mesorhizobium ciceri
USDA 3383T,
Mesorhizobium loti
NZP 2213T,
Mesorhizobium shangrilense
CCBAU 65327T and
Mesorhizobium australicum
WSM2073T as the closest neighbours (>99 % 16S rRNA gene sequence similarity). Phylogenies of the housekeeping genes atpD and recA confirmed their distinct position, showing low similarity with respect to those of
M. loti
LMG 6125T (96.5 % and 92.3 % similarity respectively),
M. ciceri
USDA 3383T (96.8 % and 93.3 % similarity, respectively),
M. shangrilense
CCBAU 65327T (96.5 % and 92.7 % similarity, respectively) and
M. australicum
WSM2073T (95.4 % and 90.6 % similarity, respectively). The DNA–DNA relatedness values between strain SCAU7T and strain SCAU27 were 83.0 %, showing that they belong to the same species. The DNA–DNA relatedness values of SCAU7T with
M. loti
NZP 2213T,
M. ciceri
USDA 3383T and
M. shangrilense
CCBAU 65327T were 41.1 %, 48.8 % and 23.4 %, respectively, clearly indicating that strain SCAU7T represents a novel species. A series of phenotypic and genotypic tests and comparison of cellular fatty acids indicated that the novel group of isolates was distinct from previously described species. Therefore, we propose that strains SCAU7T and SCAU27 represent a novel species of the genus
Mesorhizobium
,
Mesorhizobium
sangaii sp. nov., with strain SCAU7T ( = HAMBI 3318T = ACCC 13218T) as the type strain.
Collapse
Affiliation(s)
- Shen Zhou
- Department of Resources and Environment, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Qiongfang Li
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, Sichuan, PR China
| | - Huaming Jiang
- Department of Resources and Environment, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Kristina Lindström
- Department of Applied Chemistry and Microbiology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Xiaoping Zhang
- Department of Resources and Environment, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| |
Collapse
|
17
|
Ramírez-Bahena MH, Hernández M, Peix Á, Velázquez E, León-Barrios M. Mesorhizobial strains nodulating Anagyris latifolia and Lotus berthelotii in Tamadaya ravine (Tenerife, Canary Islands) are two symbiovars of the same species, Mesorhizobium tamadayense sp. nov. Syst Appl Microbiol 2012; 35:334-41. [DOI: 10.1016/j.syapm.2012.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 04/25/2012] [Accepted: 05/06/2012] [Indexed: 10/28/2022]
|
18
|
Li M, Li Y, Chen WF, Sui XH, Li Y, Li Y, Wang ET, Chen WX. Genetic diversity, community structure and distribution of rhizobia in the root nodules of Caragana spp. from arid and semi-arid alkaline deserts, in the north of China. Syst Appl Microbiol 2012; 35:239-45. [DOI: 10.1016/j.syapm.2012.02.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 02/08/2012] [Accepted: 02/13/2012] [Indexed: 11/28/2022]
|
19
|
Risal CP, Djedidi S, Dhakal D, Ohkama-Ohtsu N, Sekimoto H, Yokoyama T. Phylogenetic diversity and symbiotic functioning in mungbean (Vigna radiata L. Wilczek) bradyrhizobia from contrast agro-ecological regions of Nepal. Syst Appl Microbiol 2011; 35:45-53. [PMID: 22178390 DOI: 10.1016/j.syapm.2011.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 06/13/2011] [Accepted: 06/15/2011] [Indexed: 11/16/2022]
Abstract
Nepal consists wide range of climatic and topographical variations. Here, we explored the phylogeny of native mungbean bradyrhizobia isolated from different agro-ecological regions of Nepal and accessed their nodulation and nitrogen fixation characteristics. Soil samples were collected from three agro-ecological regions with contrasting climate and topography. A local mungbean cultivar, Kalyan, was used as a trap plant. We characterized isolates based on the full nucleotide sequence of the 16S rRNA, ITS region, and nodA genes; and partial sequences of nodD1 and nifD genes. We found 50% of isolates phylogenetically related to B. yuanmingense, 13% to B. japonicum, 8% to B. elkanii, and 29% to novel phylogenetic origin. Results of the inoculation test suggested that expression of different symbiotic genes in isolates resulted in different degrees of symbiotic functioning. Our results indicate B. yuanmingense and novel strains are more efficient symbiotic partners than B. elkanii for the local mungbean cv. Kalyan. We also found most mungbean rhizobial genotypes were conserved across agro-ecological regions. All the strains from tropical Terai region belonged to B. yuanmingense or a novel lineage of B. yuanmingense, and dominance of B. japonicum related strains was observed in the Hill region. Higher genetic diversity of Bradyrhizobium strains was observed in temperate and sub-tropical region than in the tropical region.
Collapse
Affiliation(s)
- Chandra Prasad Risal
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 183-8509, Japan
| | | | | | | | | | | |
Collapse
|
20
|
Lorite MJ, Donate-Correa J, del Arco-Aguilar M, Pérez Galdona R, Sanjuán J, León-Barrios M. Lotus endemic to the Canary Islands are nodulated by diverse and novel rhizobial species and symbiotypes. Syst Appl Microbiol 2010; 33:282-90. [PMID: 20447791 DOI: 10.1016/j.syapm.2010.03.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 03/09/2010] [Accepted: 03/11/2010] [Indexed: 10/19/2022]
Abstract
Genetic and symbiotic characterization of 34 isolates from several Lotus species endemic to the Canary Islands showed extraordinary diversity, with bacteria belonging to different species of the genera Mesorhizobium (17 isolates), Sinorhizobium (12 isolates) and Rhizobium/Agrobacterium (5 isolates). In a previous report, we showed that the Sinorhizobium isolates mostly belonged to S. meliloti. Here, we focused on the remaining isolates. The Lotus mesorhizobial strains were distributed in the rrs tree within six poorly resolved branches. Partial sequences from atpD and recA genes produced much better resolved phylogenies that were, with some exceptions, congruent with the ribosomal phylogeny. Thus, up to six different mesorhizobial species were detected, which matched with or were sister species of M. ciceri, M. alhagi, M. plurifarium or M. caraganae, and two represented new lineages that did not correspond to any of the currently recognized species. Neither M. loti nor Bradyrhizobium sp. (Lotus), recognized as the typical Lotus-symbionts, were identified among the Canarian Lotus isolates, although their nodulation genes were closely related to M. loti. However, several subbranches of mesorhizobia nodulating Lotus spp. could be differentiated in a nodC tree, with the isolates from the islands distributed in two of them (A1 and A3). Subbranch A1 included reference strains of M. loti and a group of isolates with a host range compatible with biovar loti, whereas A3 represented a more divergent exclusive subbranch of isolates with a host range almost restricted to endemic Lotus and it could represent a new biovar among the Lotus rhizobia.
Collapse
Affiliation(s)
- Ma José Lorite
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | | | | | | | | | | |
Collapse
|