scholarly journals Rhizobial microsymbionts of the narrowly endemic Oxytropis species growing in Kamchatka possess a set of genes that are associated with T3SS and T6SS secretion systems and can affect the development of symbiosis

2020 ◽  
Author(s):  
P. Guro ◽  
V. Safronova ◽  
A. Sazanova ◽  
I. Kuznetsova ◽  
A. Belimov ◽  
...  
Keyword(s):  
Host Specificity ◽  
Root Nodules ◽  
Kamchatka Peninsula ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Symbiotic Genes ◽  
Secretion Systems ◽  
Legume Symbiosis ◽  
Microbe Interactions ◽  
Different Strains

A collection of rhizobial strains isolated from root nodules of the narrowly endemic legume species Oxytropis erecta, O. anadyrensis, O. kamtschatica and O. pumilio growing on the Kamchatka Peninsula (Russian Federation) was obtained. Analysis of the 16S rRNA gene sequence showed a significant diversity of isolates belonging to the families Rhizobiaceae (Rhizobium), Phyllobacteriaceae (Mesorhizobium, Phyllobacterium) and Bradyrhizobiaceae (Bosea, Tardiphaga). Pairs of taxonomically different strains in various combinations were isolated from some nodules of Oxytropis plants. Plant nodulation assays showed that only strains belonging to the genus Mesorhizobium (M. jarvisii, M. loti and M. huakuii) could form nitrogen-fixing nodules. The nitrogen-fixing activity of the strains was more associated with the host plant than with the species of strains. The whole genome sequences analysis showed that the strains M. loti 582 and M. huakuii 583 possessed symbiotic genes necessary for the formation of effective symbiosis and grouped into Sym-clusters. In contrast, the strain T. robiniae 581 had only a reduced number of fix genes, while the strains Phyllobacterium sp. 628 and R. lusitanum 629 possesed only individual symbiotic genes, which obviously did not participate in the formation of nodules. It was also stated that the strains M. loti 582 and M. huakuii 583 had a significantly larger set of genes related to the secretion systems T3SS and T6SS that can affect the host specificity of strains, compared with 6 commercial strains used as reference. These two strains formed nodules of two types (typical elongated and atypical rounded) on Oxytropis plants. We suggest that a possible cause of the observed phenomenon is the availability of different nodulation strategies in these strains (dependent and independent of Nod-factors). Thus, as a result of studying the collection of strains isolated from the narrow endemic species of Kamchatka Oxytropis, interesting objects were selected to study the functions of the T3SS and T6SS genes, and their role in the development of rhizobia-legume symbiosis. The prospects of using strains with gene systems for both symbiotic and non-symbiotic nodulation to enhance the efficiency of plant-microbe interactions by expanding the host specificity and increasing the efficiency of nodulation are discussed.

scholarly journals Rhizobial Microsymbionts of Kamchatka Oxytropis Species Possess Genes of the Type III and VI Secretion Systems, Which Can Affect the Development of Symbiosis

2020 ◽  
Vol 33 (10) ◽  
pp. 1232-1241
Author(s):  
Vera I. Safronova ◽  
Polina V. Guro ◽  
Anna L. Sazanova ◽  
Irina G. Kuznetsova ◽  
Andrey A. Belimov ◽  
...  
Keyword(s):  
Host Specificity ◽  
Ribosomal Rna ◽  
Root Nodules ◽  
Kamchatka Peninsula ◽  
Secretion Systems ◽  
Nod Factor ◽  
Type Iii ◽  
Type Vi Secretion ◽  
Legume Symbiosis ◽  
Microbe Interactions

A collection of rhizobial strains isolated from root nodules of the narrowly endemic legume species Oxytropis erecta, O. anadyrensis, O. kamtschatica, and O. pumilio originating from the Kamchatka Peninsula (Russian Federation) was obtained. Analysis of the 16S ribosomal RNA gene sequence showed a significant diversity of isolates belonging to families Rhizobiaceae (genus Rhizobium), Phyllobacteriaceae (genera Mesorhizobium, Phyllobacterium), and Bradyrhizobiaceae (genera Bosea, Tardiphaga). A plant nodulation assay showed that only strains belonging to genus Mesorhizobium could form nitrogen-fixing nodules on Oxytropis plants. The strains M. loti 582 and M. huakuii 583, in addition to symbiotic clusters, possessed genes of the type III and type VI secretion systems (T3SS and T6SS, respectively), which can influence the host specificity of strains. These strains formed nodules of two types (elongated and rounded) on O. kamtschatica roots. We suggest this phenomenon may result from Nod factor–dependent and –independent nodulation strategies. The obtained strains are of interest for further study of the T3SS and T6SS gene function and their role in the development of rhizobium-legume symbiosis. The prospects of using rhizobia having both gene systems related to symbiotic and nonsymbiotic nodulation strategies to enhance the efficiency of plant-microbe interactions by expanding the host specificity and increasing nodulation efficiency are discussed.

scholarly journals Taxonomically Different Co-Microsymbionts of a Relict Legume, Oxytropis popoviana, Have Complementary Sets of Symbiotic Genes and Together Increase the Efficiency of Plant Nodulation

2018 ◽  
Vol 31 (8) ◽  
pp. 833-841 ◽  
Author(s):  
Vera I. Safronova ◽  
Andrey A. Belimov ◽  
Anna L. Sazanova ◽  
Elizaveta R. Chirak ◽  
Alla V. Verkhozina ◽  
...  
Keyword(s):  
Root Nodules ◽  
Housekeeping Genes ◽  
Nodule Formation ◽  
Symbiotic Genes ◽  
Internal Transcribed Spacer Region ◽  
Bradyrhizobium Sp ◽  
The Common ◽  
Different Strains ◽  
Slow Growing ◽  
Fix Genes

Ten rhizobial strains were isolated from root nodules of a relict legume Oxytropis popoviana Peschkova. For identification of the isolates, sequencing of rrs, the internal transcribed spacer region, and housekeeping genes recA, glnII, and rpoB was used. Nine fast-growing isolates were Mesorhizobium-related; eight strains were identified as M. japonicum and one isolate belonged to M. kowhaii. The only slow-growing isolate was identified as a Bradyrhizobium sp. Two strains, M. japonicum Opo-242 and Bradyrhizobium sp. strain Opo-243, were isolated from the same nodule. Symbiotic genes of these isolates were searched throughout the whole-genome sequences. The common nodABC genes and other symbiotic genes required for plant nodulation and nitrogen fixation were present in the isolate Opo-242. Strain Opo-243 did not contain the principal nod, nif, and fix genes; however, five genes (nodP, nodQ, nifL, nolK, and noeL) affecting the specificity of plant-rhizobia interactions but absent in isolate Opo-242 were detected. Strain Opo-243 could not induce nodules but significantly accelerated the root nodule formation after coinoculation with isolate Opo-242. Thus, we demonstrated that taxonomically different strains of the archaic symbiotic system can be co-microsymbionts infecting the same nodule and promoting the nodulation process due to complementary sets of symbiotic genes.

Plant-microbe-microbe interactions influenced the faba bean nodule colonization by diverse endophytic bacteria

2021 ◽  
Author(s):  
Sameh H Youseif ◽  
Fayrouz H Abd El-Megeed ◽  
Ali S Abdelaal ◽  
Amr Ageez ◽  
Esperanza Martínez-Romero
Keyword(s):  
Faba Bean ◽  
Root Nodules ◽  
N Uptake ◽  
Nifh Gene ◽  
Housekeeping Genes ◽  
Soil Conditions ◽  
Pgp Traits ◽  
Plant Growth Promoting ◽  
Legume Symbiosis ◽  
Microbe Interactions

Abstract Legume root nodules harbor rhizobia and other non-nodulating endophytes known as nodule-associated bacteria (NAB) whose role in the legume symbiosis is still unknown. We analyzed the genetic diversity of thirty-four NAB isolates obtained from the root nodules of faba bean grown under various soil conditions in Egypt using 16S rRNA and concatenated sequences of three housekeeping genes. All isolates were identified as members of the family Enterobacteriaceae belonging to the genera Klebsiella, Enterobacter, and Raoultella. We identified nine enterobacterial genospecies, most of which have not been previously reported as NAB. All isolated strains harbored nifH gene sequences and most of them possessed plant growth-promoting (PGP) traits. Upon co-inoculation with an N2 fixing rhizobium (Rlv NGB-FR128), two strains (E. sichanensis NGB-FR97 and K. variicola NGB-FR116) significantly increased nodulation, growth, and N-uptake of faba bean plants over the single treatments or the uninoculated control. The presence of these enterobacteria in nodules was significantly affected by the host plant genotype, symbiotic rhizobium genotype, and endophyte genotype, indicating that the nodule colonization process is regulated by plant-microbe-microbe interactions. This study emphasizes the importance of nodule-associated enterobacteria and suggests their potential role in improving the effectiveness of rhizobial inoculants.

scholarly journals Methylobacterium nodulans sp. nov., for a group of aerobic, facultatively methylotrophic, legume root-nodule-forming and nitrogen-fixing bacteria

2004 ◽  
Vol 54 (6) ◽  
pp. 2269-2273 ◽  
Author(s):  
Philippe Jourand ◽  
Eric Giraud ◽  
Gilles Béna ◽  
Abdoulaye Sy ◽  
Anne Willems ◽  
...  
Keyword(s):  
Carbon Source ◽  
16S Rrna ◽  
Root Nodule ◽  
Root Nodules ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Bacterial Strains ◽  
Protein Patterns ◽  
Gene Encoding

Data on 72 non-pigmented bacterial strains that specifically induce nitrogen-fixing root nodules on the legume species Crotalaria glaucoides, Crotalaria perrottetii and Crotalaria podocarpa are reviewed. By SDS-PAGE analysis of total protein patterns and by 16S rRNA PCR-RFLP, these strains form a homogeneous group that is separate from other legume root-nodule-forming bacteria. The 16S rRNA gene-based phylogeny indicates that these bacteria belong to the genus Methylobacterium. They can grow on C1 compounds such as methanol, formate and formaldehyde but not methylamine as sole carbon source, and carry an mxaF gene, encoding methanol dehydrogenase, which supports their methylotrophic metabolism. Presence of a nodA nodulation gene, and ability to nodulate plants of Crotalaria species and to fix nitrogen are features that separate the strains currently included in this group from other members of the genus Methylobacterium. The present study includes additional genotypic and phenotypic characterization of this novel Methylobacterium species, i.e. nifH gene sequence, morphology, physiology, enzymic and carbon source assimilation tests and antibiotic resistance. The name Methylobacterium nodulans sp. nov. (type strain, ORS 2060T=CNCM I 2342T=LMG 21967T) is proposed for this group of root-nodule-forming bacteria.

scholarly journals Divulging diazotrophic bacterial community structure in Kuwait desert ecosystems and their N2-fixation potential

2019 ◽  
Author(s):  
M. K. Suleiman ◽  
A. M. Quoreshi ◽  
N. R. Bhat ◽  
A. J. Manuvel ◽  
M. T. Sivadasan
Keyword(s):  
Plant Species ◽  
Root Nodules ◽  
Rrna Gene ◽  
Limited Information ◽  
Native Plant ◽  
Rhizospheric Soil ◽  
Nitrogen Fixing ◽  
Free Living ◽  
Nitrogen Fixers ◽  
Haloxylon Salicornicum

AbstractKuwait is a semi-arid region with harsh climatic conditions with poor available soil nutrient essential for the growth of plants. Kuwait’s ecosystem is relatively N-poor ecosystem when compared to the other ecosystems. Biological nitrogen fixation (BNF) is a spontaneous process in which diazotrophic bacteria fixes the atmospheric nitrogen directly in to the bionetwork. At present, there is limited information on free-living and root associated nitrogen-fixing bacteria, their potential to fix nitrogen to aid natural plant communities in the desert of Kuwait. In this study, free-living N2-fixing bacteria were enriched and isolated from the rhizospheric soil of three keystone native plant species of Kuwait; such as Rhanterium epapposum, Farsetia aegyptia, and Haloxylon salicornicum. Root associated bacteria were directly isolated from the root nodules of Vachellia pachyceras. In this study, a number of free-living and root associated dizotrophs were isolated from various rhizospheric soils of three native shrubs and root nodules from one tree species. The screened isolates were assessed for nitrogen-fixing ability and identified using Acetylene Reduction Assay (ARA) and 16s rRNA gene sequencing, respectively. Our study successfully identified all the 50 nitrogen-fixers isolated initially and out of that, 78% were confirmed as nitrogen-fixers using ARA. Among the identified nitrogen fixers, the genus Rhizobium is dominant in rhizospheric soil of Rhanterium epapposum, whereas Pseudomonas and Rhizobium are dominant in the rhizospheric soil of Farsetia aegyptia, and Haloxylon salicornicum respectively. The species Agrobacterium tumefaciens is found dominant in the root nodules of V. pachyceras. The current results indicate that plant species and their rhizospheric effects are important drivers for specificity of microbial diversity in arid soils. To our knowledge, this study is the first investigation of culture-based isolation, molecular identification, and evaluation of N2-fixing ability of diazotrophs from Kuwait desert environment.

scholarly journals Genetic characterization of root-nodule bacteria associated with Acacia salicina and A. stenophylla (Mimosaceae) across south-eastern Australia

2011 ◽  
Vol 61 (2) ◽  
pp. 299-309 ◽  
Author(s):  
Mohammad S. Hoque ◽  
Linda M. Broadhurst ◽  
Peter H. Thrall
Keyword(s):  
Root Nodule ◽  
Root Nodules ◽  
Disease Suppression ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Symbiotic Relationships ◽  
South Eastern ◽  
Eastern Australia ◽  
Microbe Interactions ◽  
Ecological Importance

Symbiotic relationships between legumes and nitrogen-fixing soil micro-organisms are of ecological importance in plant communities worldwide. For example, nutrient-poor Australian soils are often dominated by shrubby legumes (e.g. species of Acacia). However, relatively few studies have quantified patterns of diversity, host-specificity and effectiveness of these ecologically important plant–microbe interactions. In this study, 16S rRNA gene sequence and PCR-RFLP analyses were used to examine bacterial strains isolated from the root nodules of two widespread south-eastern Australian legumes, Acacia salicina and Acacia stenophylla, across nearly 60 sites. The results showed that there was extensive genetic diversity in microbial populations, including a broad range of novel genomic species. While previous studies have suggested that most native Australian legumes nodulate primarily with species of the genus Bradyrhizobium, our results indicate significant associations with members of other root-nodule-forming bacterial genera, including Rhizobium, Ensifer, Mesorhizobium, Burkholderia, Phyllobacterium and Devosia. Genetic analyses also revealed a diverse suite of non-nodulating bacterial endophytes, only a subset of which have been previously recorded. Although the ecological roles of these endosymbionts are not well understood, they may play both direct and indirect roles in promoting plant growth, nodulation and disease suppression.

scholarly journals From roots to leaves: the capacity of Micromonospora to colonize different legume tissues

2021 ◽  
Author(s):  
Patricia Benito ◽  
Lorena Carro ◽  
Rodrigo Bacigalupe ◽  
Maite Ortuzar ◽  
Martha E. Trujillo
Keyword(s):  
16S Rrna ◽  
Pisum Sativum ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Root Nodules ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Rrna Gene Sequence ◽  
Plant Model ◽  
Plant Polymer

An important number of Micromonospora strains have been reported from nitrogen fixing root nodules of legume and actinorhizal plants. However, the question of whether this bacterium can also be found in other parts of these plants remains unanswered. Over 150 strains were recovered from different Lupinus angustifolius and Pisum sativum tissues including leaves, stems, roots, and nodules. Ninety-seven percent of the isolates were identified by 16S rRNA gene sequence in the target genus and were associated with 27 different Micromonospora species. Plant-polymer degrading enzymes are suspected to play a role in the colonization of plants. To this end, bacterial enzymatic activity assays for amylases, cellulases, chitinases, pectinases and xylanases were determined. All strains produced xylanases and pectinases, while 98.6%, 98%, and 94.6% of them produced amylases, cellulases, and chitinases, respectively. The most productive strains included seven isolates from P. sativum and one from L. angustifolius. Strain Micromonospora lupini ML01-gfp was used to determine its capacity to reach and colonize different plant organs using P. sativum as the plant model. Stem and leaf samples were monitored by optical and fluorescence microscopy to locate the tagged strain. These results strongly suggest that Micromonospora is able, not only to infect nitrogen-fixing nodules, but also of reaching other parts of the host plant, especially the leaves.

Diversity of Indigenous Symbiotic Nitrogen Fixing Bacteria from Blackgram [Vigna mungo (L.) Hepper] Cultivated in Rice Fallows

2020 ◽  
Author(s):  
T. Satyanandam ◽  
K. Babu ◽  
B. Yellamanda ◽  
K. Vijaya Kumar ◽  
G. Rosaiah ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Root Nodules ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Nitrogen Fixing Bacteria ◽  
High Genetic Diversity ◽  
Microbiological Methods

Background: Legume nodulating bacteria (LNB), also known as rhizobia produce root nodules on leguminous plants where in nitrogen fixation takes place. In agriculture, this symbiotic relationship is significant as it provides nitrogenous fertilizers to the leguminous crops. Traditionally rhizobia were exclusively members of the Rhizobiaceae family in the Alphaproteobacteria class of bacteria. Several reports revealed that large number of diazotrophs have the ability to nodulate and fix atmospheric N2 in legumes in addition to rhizobia which are outside the Alphaproteobacteria class. Relatively less information is available on the genetic diversity of indigenous rhizobia nodulating blackgram cultivated in rice fallows. Hence the present study was carried out to know the diversity of symbiotic native nitrogen fixing bacteria isolated from the root nodules of blackgram grown in rice fallows using partial 16S rRNA sequencing.Methods: Nitrogen fixing microsymbionts (Rhizobium strains) from root nodules of blackgram were isolated on yeast extract mannitol agar (YEMA) medium. The pure cultures were maintained at 28±2°C for 48 h. Identification of Rhizobium isolates was done by using various tests and Morphological characterization of isolates was also done by using standard microbiological methods. The PCR amplification and sequencing of 16S rRNA gene of isolates were carried out to identify the isolates.Result: In the present study four strains of Rhizobium designated as VM-2, VM-8, VM-9 and VM-15 were isolated. Morphologically colonies of all strains are round, transparent, entire, convex and smooth. They are Gram-ve and rod shaped. Mucilage production is noticed in VM-2, VM-8 and VM-9. The 16S rRNA gene sequences revealed that the strain VM-2 showed a close relation with Rhizobium, VM-8 and VM-9 with Bradyrhizobium where as VM-15 with Achromobater. It was concluded that the symbiotic nitrogen fixing bacteria isolated from the root nodules of blackgram cultivated in rice fallows exhibited high genetic diversity. 

scholarly journals Biochemical and Molecular Phylogenetic Study of Agriculturally Useful Association of a Nitrogen-Fixing Cyanobacterium and NoduleSinorhizobiumwithMedicago sativaL.

2015 ◽  
Vol 2015 ◽  
pp. 1-16 ◽  
Author(s):  
E. V. Karaushu ◽  
I. V. Lazebnaya ◽  
T. R. Kravzova ◽  
N. A. Vorobey ◽  
O. E. Lazebny ◽  
...  
Keyword(s):  
Sinorhizobium Meliloti ◽  
Root Nodules ◽  
Bacterial Consortium ◽  
Biochemical Properties ◽  
Nostoc Muscorum ◽  
Phylogenetic Study ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Molecular Phylogenetic Study ◽  
Molecular Phylogenetic

Seed inoculation with bacterial consortium was found to increase legume yield, providing a higher growth than the standard nitrogen treatment methods. Alfalfa plants were inoculated by mono- and binary compositions of nitrogen-fixing microorganisms. Their physiological and biochemical properties were estimated. Inoculation by microbial consortium ofSinorhizobium melilotiT17 together with a new cyanobacterial isolateNostocPTV was more efficient than the single-rhizobium strain inoculation. This treatment provides an intensification of the processes of biological nitrogen fixation by rhizobia bacteria in the root nodules and an intensification of plant photosynthesis. Inoculation by bacterial consortium stimulates growth of plant mass and rhizogenesis and leads to increased productivity of alfalfa and to improving the amino acid composition of plant leaves. The full nucleotide sequence of the rRNA gene cluster and partial sequence of the dinitrogenase reductase (nifH) gene ofNostocPTV were deposited to GenBank (JQ259185.1, JQ259186.1). Comparison of these gene sequences ofNostocPTV with all sequences present at the GenBank shows that this cyanobacterial strain does not have 100% identity with any organisms investigated previously. Phylogenetic analysis showed that this cyanobacterium clustered with high credibility values withNostoc muscorum.

Low genetic diversity amongFrankiaspp. strains nodulating sympatric populations of actinorhizal species of Rosaceae,Ceanothus(Rhamnaceae) andDatisca glomerata(Datiscaceae) west of the Sierra Nevada (California)

2004 ◽  
Vol 50 (12) ◽  
pp. 989-1000 ◽  
Author(s):  
Brian D Vanden Heuvel ◽  
David R Benson ◽  
Esteban Bortiri ◽  
Daniel Potter
Keyword(s):  
Host Specificity ◽  
Sierra Nevada ◽  
Root Nodules ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Internal Transcribed Spacer Region ◽  
Strain Diversity ◽  
Environmental Selection ◽  
Group 1

Frankia spp. strains typically induce N2-fixing root nodules on actinorhizal plants. The majority of host plant taxa associated with the uncultured Group 1 Frankia strains, i.e., Ceanothus of the Rhamnaceae, Datisca glomerata (Datiscaceae), and all actinorhizal members of the Rosaceae except Dryas, are found in California. A study was conducted to determine the distribution of Frankia strains among root nodules collected from both sympatric and solitary stands of hosts. Three DNA regions were examined, the 5' end of the 16S rRNA gene, the internal transcribed spacer region between the 16S and 23S rRNA genes, and a portion of the glutamine synthetase gene (glnA). The results suggest that a narrow range of Group 1 Frankia spp. strains dominate in root nodules collected over a large area of California west of the Sierra Nevada crest with no apparent host-specificity. Comparisons with Group 2 Frankia strain diversity from Alnus and Myrica within the study range suggest that the observed low diversity is peculiar to Group 1 Frankia strains only. Factors that may account for the observed lack of genetic variability and host specificity include strain dominance over a large geographical area, current environmental selection, and (or) a past evolutionary bottleneck.Key words: actinorhizal Rosaceae, Ceanothus, Frankia, Datisca, strain diversity.

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