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Felix D. Dakora - One of the best experts on this subject based on the ideXlab platform.

  • adaptability to local conditions and phylogenetic differentiation of Microsymbionts of tgx soybean genotypes in the semi arid environments of ghana and south africa
    Systematic and Applied Microbiology, 2021
    Co-Authors: Sanjay K. Jaiswal, Mustapha Mohammed, Jalilatu Ayuba, Nicholas N Denwar, Felix D. Dakora
    Abstract:

    Abstract The study of the nitrogen fixation and phylogenetic diversity of nodule Microsymbionts of grain legumes in many parts of the globe is often carried out in order to identify legume-rhizobia combinations for agricultural sustainability. Several reports have therefore found that rhizobial species diversity is shaped by edapho-climatic conditions that characterize different geographic locations, suggesting that rhizobial communities often possess traits that aid their adaptation to their habitat. In this study, the soybean-nodulating rhizobia from semi-arid savannahs of Ghana and South Africa were evaluated. The authenticated rhizobial isolates were highly diverse based on their colony characteristics, as well as their BOX-PCR profiles and gene sequences. In the 16S rRNA phylogeny, the isolates were placed in the different clades Bradyrhizobium iriomotense and B. jicamae together with two superclades B. japonicum and B. elkanii. The multilocus (atpD, glnII, gyrB, recA) phylogenetic analyses indicated the dominancy of B. diazoefficiens and putative new Bradyrhizobium species in the semi-arid Ghanaian region. The phylogenetic analyses based on the symbiotic genes (nifH and nodC) clustered the test isolates into different symbiovars (sv. glycinearum, sv. retame and sv. sojae). Principal component analysis (PCA) showed that soil factors played a significant role in favoring the local conditions for the soybean-nodulating Microsymbionts. The results suggested that isolates had marked local adaptation conditions in semi-arid regions but further studies are needed to confirm new Bradyrhizobium species.

  • Studies of Phylogeny, Symbiotic Functioning and Ecological Traits of Indigenous Microsymbionts Nodulating Bambara Groundnut (Vigna subterranea L. Verdc) in Eswatini 
    Microbial Ecology, 2021
    Co-Authors: Sibusiso T. Dlamini, Sanjay K. Jaiswal, Mustapha Mohammed, Felix D. Dakora
    Abstract:

    Rhizobial Microsymbionts of grain legumes are ubiquitous in soils and exhibit a wide range of diversity with respect to colony morphology, genetic variability, biochemical characteristics, and phylogenetic relationships. This study assessed the phylogenetic positions of rhizobial Microsymbionts of Bambara groundnut from Eswatini exhibiting variations in morpho-physiology, adaptive characteristics, and N_2-fixing efficiency. The isolates’ ERIC-PCR profiles revealed the presence of high genetic variation among them. These test isolates also exhibited differences in pH tolerance and IAA production. Multilocus sequence analysis based on the 16S rRNA, atpD , glnII , gyrB , and recA gene sequences of representative test isolates closely aligned them to the type strains of  Bradyrhizobium arachidis , B. manausense , B. guangdongense , B. elkanii , and B. pachyrhizi. However, some isolates showed a high divergence from the known reference type strains, indicating that they may represent species yet to be properly characterized and described. Functional characterization in the glasshouse revealed that most of the isolates from the contrasting Agro-ecologies of Eswatini were efficient in N_2 fixation, and therefore elicited greater stomatal conductance and photosynthetic rates in the homologous Bambara groundnut. Of the 75 isolates tested, 51% were more effective than the commercial Bradyrhizobium sp. strain CB756, with relative symbiotic effectiveness ranging from 138 to 308%. The findings of this study indicated that the analysis of housekeeping genes and functional traits of Bambara-nodulating Microsymbionts can provide a clear view for understanding and predicting rhizobial community structure across environmental gradients.

  • insights into the phylogeny nodule function and biogeographic distribution of Microsymbionts nodulating the orphan kersting s groundnut macrotyloma geocarpum harms marechal baudet in african soils
    Applied and Environmental Microbiology, 2019
    Co-Authors: Mustapha Mohammed, Sanjay K. Jaiswal, Felix D. Dakora
    Abstract:

    Kersting9s groundnut [ Macrotyloma geocarpum (Harms) Marechal & Baudet] is a neglected indigenous African legume adapted to growth in N-deficient soils due to its ability to fix atmospheric N 2 via symbiosis with rhizobia. Despite its nutritional and medicinal uses, to date, there is little information on the phylogeny and functional traits of its Microsymbionts, an aspect much needed for its conservation and improvement. This study explored the morpho-genetic diversity, phylogenetic relationships and N 2 -fixing efficiency of Kersting9s groundnut rhizobial isolates from contrasting environments in Ghana, South Africa and Mozambique. Box-PCR fingerprinting revealed high diversity among rhizobial populations which was influenced by geographic origin. Of the 164 isolates evaluated, 130 Box-PCR types were identified at 70% similarity coefficient, indicating that they were not clones. Soil pH and mineral concentrations were found to influence the distribution of bradyrhizobial populations in African soils. Phylogenetic analysis of 16S rRNA gene and multilocus sequence analysis of protein-coding genes ( atp D, gln II, gyr B and rpo B) and symbiotic genes ( nif H and nod C) showed that, Kersting9s groundnut is primarily nodulated by members of genus Bradyrhizobium, which are closely related to B. vignae 7-2 T , B. kavangense 14-3 T , B. subterraneum 58-2-1 T , B. pachyrhizi PAC48 T , B. elkanii T and novel groups of Bradyrhizobium species. The bradyrhizobial populations identified exhibited high N 2 fixation, and induced greater nodulation, leaf chlorophyll concentration and photosynthetic rates on their homologous host when compared to the 5 mM KNO 3 -fed plants and/or the commercial Bradyrhizobium strain CB756, suggesting that they could be good candidates for inoculant formulations upon field testing. IMPORTANCE Rhizobia play important roles in agroecosystems where they contribute to improving overall soil health through their symbiotic relationship with legumes. This study explored the Microsymbionts nodulating Kersting9s groundnut, a neglected orphan legume. The results revealed the presence of different bradyrhizobial populations with high N 2 -fixing efficiencies as the dominant symbionts of this legume across diverse agroecologies in Africa. Our findings represent a useful contribution to the literature in terms of the community of Microsymbionts nodulating a neglected cultivated legume, and its potential for elevation as a major food crop. The presence of potentially novel bradyrhizobial symbionts of Kersting9s groundnut found in this study offers an opportunity for future studies to properly describe, characterize and delineate these isolates functionally and phylogenetically for use in inoculant production to enhance food/nutritional security.

  • distribution and correlation between phylogeny and functional traits of cowpea vigna unguiculata l walp nodulating Microsymbionts from ghana and south africa
    Scientific Reports, 2018
    Co-Authors: Mustapha Mohammed, Sanjay K. Jaiswal, Felix D. Dakora
    Abstract:

    Cowpea (Vigna unguiculata L. Walp.) is indigenous to Africa, and highly valued for its N2-fixing trait and the nutritional attributes of its grain and leaves. The species’ ability to establish effective symbiosis with diverse rhizobial populations gives it survival and growth advantage in N-limited environments. To explore the functional diversity and phylogenetic positions of rhizobia nodulating cowpea in Africa, nodules were collected from various cowpea varieties grown in soils from the Guinea savanna and Sudano-sahelian agroecologies of Northern Ghana, and from the lowveld and middleveld areas of Mpumalanga Province in South Africa. Box-PCR profiling and multilocus sequence analysis revealed the presence of diverse Microsymbionts responsible for cowpea nodulation across the study sites. BOX-PCR amplifications yielded variable band sizes, ranging from 618 bp to 5354 bp, which placed the isolates in six major clusters (Cluster A–F). Phylogenetic analysis based on 16S rRNA, atpD, glnII, gyrB, rpoB, nifH and nodC genes revealed the presence of diverse Bradyrhizobium sp. closely related to Bradyrhizobium daqingense, Bradyrhizobium subterraneum, Bradyrhizobium yuanmingense, Bradyrhizobium embrapense, Bradyrhizobium pachyrhizi, Bradyrhizobium elkanii and novel Bradyrhizobium species in the soils studied, a finding that could be attributed to the unique edapho-climatic conditions of the contrasting environments. The test isolates exhibited distinct symbiotic efficiencies, and also induced variable (p ≤ 0.001) photosynthetic rates, leaf transpiration, total chlorophyll and shoot biomass accumulation on cowpea (their homologous host). Canonical correspondence analysis showed that the distribution of these Microsymbionts was influenced by the concentrations of macro- and micronutrients in soils. The pairwise genetic distances derived from phylogenies and nodule functioning showed significant (p < 0.05) correlation, which suggests that local environmental factors played a major role in the cowpea-Bradyrhizobium symbiosis.

  • identification and distribution of Microsymbionts associated with soybean nodulation in mozambican soils
    Systematic and Applied Microbiology, 2018
    Co-Authors: Cynthia Gyogluu, Sanjay K. Jaiswal, Stephen Kyeiboahen, Felix D. Dakora
    Abstract:

    Abstract Indigenous soybean rhizobial strains were isolated from root nodules sampled from farmers’ fields in Mozambique to determine their identity, distribution and symbiotic relationships. Plant infection assays revealed variable nodulation and symbiotic effectiveness among the 43 bacterial isolates tested. Strains from Ruace generally promoted greater whole-plant growth than the others. 16S rRNA-RFLP analysis of genomic DNA extracted from the rhizobial isolates produced different banding patterns, a clear indication of high bacterial diversity. However, the multilocus sequence analysis (MLSA) data showed alignment of the isolates with B. elkanii species. The 16S rRNA sequences of representative soybean isolates selected from each 16S rRNA-RFLP cluster showed their relatedness to B. elkanii, as well as to other Bradyrhizobium species. But a concatenated phylogeny of two housekeeping genes (glnII and gyrB) identified the soybean nodulating isolates as Bradyrhizobium, with very close relatedness to B. elkanii. The nifH and nodC sequences also showed that the majority of the test soybean isolates were closely related to B. elkanii, albeit the inconsistency with some isolates. Taken together, these findings suggest that the B. elkanii group are the preferred dominant microsymbiont of soybean grown in Mozambican soils. Furthermore, the distribution of soybean rhizobia in the agricultural soils of Mozambique was found to be markedly influenced by soil pH, followed by the concentrations of plant-available P and Mn. This study suggested that the identified isolates TUTMJM5, TUTMIITA5A and TUTLBC2B can be used as inoculants for increased soybean production in Mozambique.

Sanjay K. Jaiswal - One of the best experts on this subject based on the ideXlab platform.

  • adaptability to local conditions and phylogenetic differentiation of Microsymbionts of tgx soybean genotypes in the semi arid environments of ghana and south africa
    Systematic and Applied Microbiology, 2021
    Co-Authors: Sanjay K. Jaiswal, Mustapha Mohammed, Jalilatu Ayuba, Nicholas N Denwar, Felix D. Dakora
    Abstract:

    Abstract The study of the nitrogen fixation and phylogenetic diversity of nodule Microsymbionts of grain legumes in many parts of the globe is often carried out in order to identify legume-rhizobia combinations for agricultural sustainability. Several reports have therefore found that rhizobial species diversity is shaped by edapho-climatic conditions that characterize different geographic locations, suggesting that rhizobial communities often possess traits that aid their adaptation to their habitat. In this study, the soybean-nodulating rhizobia from semi-arid savannahs of Ghana and South Africa were evaluated. The authenticated rhizobial isolates were highly diverse based on their colony characteristics, as well as their BOX-PCR profiles and gene sequences. In the 16S rRNA phylogeny, the isolates were placed in the different clades Bradyrhizobium iriomotense and B. jicamae together with two superclades B. japonicum and B. elkanii. The multilocus (atpD, glnII, gyrB, recA) phylogenetic analyses indicated the dominancy of B. diazoefficiens and putative new Bradyrhizobium species in the semi-arid Ghanaian region. The phylogenetic analyses based on the symbiotic genes (nifH and nodC) clustered the test isolates into different symbiovars (sv. glycinearum, sv. retame and sv. sojae). Principal component analysis (PCA) showed that soil factors played a significant role in favoring the local conditions for the soybean-nodulating Microsymbionts. The results suggested that isolates had marked local adaptation conditions in semi-arid regions but further studies are needed to confirm new Bradyrhizobium species.

  • Studies of Phylogeny, Symbiotic Functioning and Ecological Traits of Indigenous Microsymbionts Nodulating Bambara Groundnut (Vigna subterranea L. Verdc) in Eswatini 
    Microbial Ecology, 2021
    Co-Authors: Sibusiso T. Dlamini, Sanjay K. Jaiswal, Mustapha Mohammed, Felix D. Dakora
    Abstract:

    Rhizobial Microsymbionts of grain legumes are ubiquitous in soils and exhibit a wide range of diversity with respect to colony morphology, genetic variability, biochemical characteristics, and phylogenetic relationships. This study assessed the phylogenetic positions of rhizobial Microsymbionts of Bambara groundnut from Eswatini exhibiting variations in morpho-physiology, adaptive characteristics, and N_2-fixing efficiency. The isolates’ ERIC-PCR profiles revealed the presence of high genetic variation among them. These test isolates also exhibited differences in pH tolerance and IAA production. Multilocus sequence analysis based on the 16S rRNA, atpD , glnII , gyrB , and recA gene sequences of representative test isolates closely aligned them to the type strains of  Bradyrhizobium arachidis , B. manausense , B. guangdongense , B. elkanii , and B. pachyrhizi. However, some isolates showed a high divergence from the known reference type strains, indicating that they may represent species yet to be properly characterized and described. Functional characterization in the glasshouse revealed that most of the isolates from the contrasting Agro-ecologies of Eswatini were efficient in N_2 fixation, and therefore elicited greater stomatal conductance and photosynthetic rates in the homologous Bambara groundnut. Of the 75 isolates tested, 51% were more effective than the commercial Bradyrhizobium sp. strain CB756, with relative symbiotic effectiveness ranging from 138 to 308%. The findings of this study indicated that the analysis of housekeeping genes and functional traits of Bambara-nodulating Microsymbionts can provide a clear view for understanding and predicting rhizobial community structure across environmental gradients.

  • insights into the phylogeny nodule function and biogeographic distribution of Microsymbionts nodulating the orphan kersting s groundnut macrotyloma geocarpum harms marechal baudet in african soils
    Applied and Environmental Microbiology, 2019
    Co-Authors: Mustapha Mohammed, Sanjay K. Jaiswal, Felix D. Dakora
    Abstract:

    Kersting9s groundnut [ Macrotyloma geocarpum (Harms) Marechal & Baudet] is a neglected indigenous African legume adapted to growth in N-deficient soils due to its ability to fix atmospheric N 2 via symbiosis with rhizobia. Despite its nutritional and medicinal uses, to date, there is little information on the phylogeny and functional traits of its Microsymbionts, an aspect much needed for its conservation and improvement. This study explored the morpho-genetic diversity, phylogenetic relationships and N 2 -fixing efficiency of Kersting9s groundnut rhizobial isolates from contrasting environments in Ghana, South Africa and Mozambique. Box-PCR fingerprinting revealed high diversity among rhizobial populations which was influenced by geographic origin. Of the 164 isolates evaluated, 130 Box-PCR types were identified at 70% similarity coefficient, indicating that they were not clones. Soil pH and mineral concentrations were found to influence the distribution of bradyrhizobial populations in African soils. Phylogenetic analysis of 16S rRNA gene and multilocus sequence analysis of protein-coding genes ( atp D, gln II, gyr B and rpo B) and symbiotic genes ( nif H and nod C) showed that, Kersting9s groundnut is primarily nodulated by members of genus Bradyrhizobium, which are closely related to B. vignae 7-2 T , B. kavangense 14-3 T , B. subterraneum 58-2-1 T , B. pachyrhizi PAC48 T , B. elkanii T and novel groups of Bradyrhizobium species. The bradyrhizobial populations identified exhibited high N 2 fixation, and induced greater nodulation, leaf chlorophyll concentration and photosynthetic rates on their homologous host when compared to the 5 mM KNO 3 -fed plants and/or the commercial Bradyrhizobium strain CB756, suggesting that they could be good candidates for inoculant formulations upon field testing. IMPORTANCE Rhizobia play important roles in agroecosystems where they contribute to improving overall soil health through their symbiotic relationship with legumes. This study explored the Microsymbionts nodulating Kersting9s groundnut, a neglected orphan legume. The results revealed the presence of different bradyrhizobial populations with high N 2 -fixing efficiencies as the dominant symbionts of this legume across diverse agroecologies in Africa. Our findings represent a useful contribution to the literature in terms of the community of Microsymbionts nodulating a neglected cultivated legume, and its potential for elevation as a major food crop. The presence of potentially novel bradyrhizobial symbionts of Kersting9s groundnut found in this study offers an opportunity for future studies to properly describe, characterize and delineate these isolates functionally and phylogenetically for use in inoculant production to enhance food/nutritional security.

  • distribution and correlation between phylogeny and functional traits of cowpea vigna unguiculata l walp nodulating Microsymbionts from ghana and south africa
    Scientific Reports, 2018
    Co-Authors: Mustapha Mohammed, Sanjay K. Jaiswal, Felix D. Dakora
    Abstract:

    Cowpea (Vigna unguiculata L. Walp.) is indigenous to Africa, and highly valued for its N2-fixing trait and the nutritional attributes of its grain and leaves. The species’ ability to establish effective symbiosis with diverse rhizobial populations gives it survival and growth advantage in N-limited environments. To explore the functional diversity and phylogenetic positions of rhizobia nodulating cowpea in Africa, nodules were collected from various cowpea varieties grown in soils from the Guinea savanna and Sudano-sahelian agroecologies of Northern Ghana, and from the lowveld and middleveld areas of Mpumalanga Province in South Africa. Box-PCR profiling and multilocus sequence analysis revealed the presence of diverse Microsymbionts responsible for cowpea nodulation across the study sites. BOX-PCR amplifications yielded variable band sizes, ranging from 618 bp to 5354 bp, which placed the isolates in six major clusters (Cluster A–F). Phylogenetic analysis based on 16S rRNA, atpD, glnII, gyrB, rpoB, nifH and nodC genes revealed the presence of diverse Bradyrhizobium sp. closely related to Bradyrhizobium daqingense, Bradyrhizobium subterraneum, Bradyrhizobium yuanmingense, Bradyrhizobium embrapense, Bradyrhizobium pachyrhizi, Bradyrhizobium elkanii and novel Bradyrhizobium species in the soils studied, a finding that could be attributed to the unique edapho-climatic conditions of the contrasting environments. The test isolates exhibited distinct symbiotic efficiencies, and also induced variable (p ≤ 0.001) photosynthetic rates, leaf transpiration, total chlorophyll and shoot biomass accumulation on cowpea (their homologous host). Canonical correspondence analysis showed that the distribution of these Microsymbionts was influenced by the concentrations of macro- and micronutrients in soils. The pairwise genetic distances derived from phylogenies and nodule functioning showed significant (p < 0.05) correlation, which suggests that local environmental factors played a major role in the cowpea-Bradyrhizobium symbiosis.

  • identification and distribution of Microsymbionts associated with soybean nodulation in mozambican soils
    Systematic and Applied Microbiology, 2018
    Co-Authors: Cynthia Gyogluu, Sanjay K. Jaiswal, Stephen Kyeiboahen, Felix D. Dakora
    Abstract:

    Abstract Indigenous soybean rhizobial strains were isolated from root nodules sampled from farmers’ fields in Mozambique to determine their identity, distribution and symbiotic relationships. Plant infection assays revealed variable nodulation and symbiotic effectiveness among the 43 bacterial isolates tested. Strains from Ruace generally promoted greater whole-plant growth than the others. 16S rRNA-RFLP analysis of genomic DNA extracted from the rhizobial isolates produced different banding patterns, a clear indication of high bacterial diversity. However, the multilocus sequence analysis (MLSA) data showed alignment of the isolates with B. elkanii species. The 16S rRNA sequences of representative soybean isolates selected from each 16S rRNA-RFLP cluster showed their relatedness to B. elkanii, as well as to other Bradyrhizobium species. But a concatenated phylogeny of two housekeeping genes (glnII and gyrB) identified the soybean nodulating isolates as Bradyrhizobium, with very close relatedness to B. elkanii. The nifH and nodC sequences also showed that the majority of the test soybean isolates were closely related to B. elkanii, albeit the inconsistency with some isolates. Taken together, these findings suggest that the B. elkanii group are the preferred dominant microsymbiont of soybean grown in Mozambican soils. Furthermore, the distribution of soybean rhizobia in the agricultural soils of Mozambique was found to be markedly influenced by soil pH, followed by the concentrations of plant-available P and Mn. This study suggested that the identified isolates TUTMJM5, TUTMIITA5A and TUTLBC2B can be used as inoculants for increased soybean production in Mozambique.

Wayne Reeve - One of the best experts on this subject based on the ideXlab platform.

  • complete genome sequence of mesorhizobium ciceri bv biserrulae wsm1497 an efficient nitrogen fixing microsymbiont of the forage legume biserrula pelecinus
    Genome Announcements, 2016
    Co-Authors: Timothy L Haskett, J.g. Howieson, Joshua P Ramsay, Wayne Reeve, G W Ohara, Penghao Wang, Jason Terpolilli
    Abstract:

    We report the complete genome sequence of Mesorhizobium ciceri bv. biserrulae strain WSM1284, a nitrogen-fixing microsymbiont of the pasture legume Biserrula pelecinus. The genome consists of 6.88 Mb distributed between a single chromosome (6.33 Mb) and a single plasmid (0.55 Mb).

  • Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325, an effective microsymbiont of annual Mediterranean clovers
    Standards in Genomic Sciences, 2010
    Co-Authors: Wayne Reeve, Patrick Chain, Lambert Bräu, Kemanthi Nandesena, Julie Ardley, Ravi Tiwari, Graham O’hara, Alex Copeland, Matt Nolan, Thomas Brettin
    Abstract:

    Rhizobium leguminosarum bv trifolii is a soil-inhabiting bacterium that has the capacity to be an effective nitrogen fixing microsymbiont of a diverse range of annual Trifolium (clover) species. Strain WSM1325 is an aerobic, motile, non-spore forming, Gram-negative rod isolated from root nodules collected in 1993 from the Greek Island of Serifos. WSM1325 is produced commercially in Australia as an inoculant for a broad range of annual clovers of Mediterranean origin due to its superior attributes of saprophytic competence, nitrogen fixation and acid-tolerance. Here we describe the basic features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence for a microsymbiont of annual clovers. We reveal that its genome size is 7,418,122 bp encoding 7,232 protein-coding genes and 61 RNA-only encoding genes. This multipartite genome contains 6 distinct replicons; a chromosome of size 4,767,043 bp and 5 plasmids of size 828,924 bp, 660,973 bp, 516,088 bp, 350,312 bp and 294,782 bp.

  • complete genome sequence of the medicago microsymbiont ensifer sinorhizobium medicae strain wsm419
    Standards in Genomic Sciences, 2010
    Co-Authors: Wayne Reeve, Lambert Bräu, Kemanthi Nandesena, Julie Ardley, G W Ohara, Stephanie Malfatti, Patrick S G Chain, R P Tiwari
    Abstract:

    Ensifer (Sinorhizobium) medicae is an effective nitrogen fixing microsymbiont of a diverse range of annual Medicago (medic) species. Strain WSM419 is an aerobic, motile, non-spore forming, Gram-negative rod isolated from a M. murex root nodule collected in Sardinia, Italy in 1981. WSM419 was manufactured commercially in Australia as an inoculant for annual medics during 1985 to 1993 due to its nitrogen fixation, saprophytic competence and acid tolerance properties. Here we describe the basic features of this organism, together with the complete genome sequence, and annotation. This is the first report of a complete genome sequence for a microsymbiont of the group of annual medic species adapted to acid soils. We reveal that its genome size is 6,817,576 bp encoding 6,518 protein-coding genes and 81 RNA only encoding genes. The genome contains a chromosome of size 3,781,904 bp and 3 plasmids of size 1,570,951 bp, 1,245,408 bp and 219,313 bp. The smallest plasmid is a feature unique to this medic microsymbiont.

  • Complete genome sequence of Rhizobium leguminosarum bv trifolii strain WSM2304, an effective microsymbiont of the South American clover Trifolium polymorphum
    Standards in Genomic Sciences, 2010
    Co-Authors: Wayne Reeve, Patrick Chain, Lambert Bräu, Kemanthi Nandesena, Hajnalka Kiss, Julie Ardley, Ravi Tiwari, Graham O’hara, Stephanie Malfatti, Alla Lapidus
    Abstract:

    Rhizobium leguminosarum bv trifolii is the effective nitrogen fixing microsymbiont of a diverse range of annual and perennial Trifolium (clover) species. Strain WSM2304 is an aerobic, motile, non-spore forming, Gram-negative rod, isolated from Trifolium polymorphum in Uruguay in 1998. This microsymbiont predominated in the perennial grasslands of Glencoe Research Station, in Uruguay, to competitively nodulate its host, and fix atmospheric nitrogen. Here we describe the basic features of WSM2304, together with the complete genome sequence, and annotation. This is the first completed genome sequence for a nitrogen fixing microsymbiont of a clover species from the American center of origin. We reveal that its genome size is 6,872,702 bp encoding 6,643 protein-coding genes and 62 RNA only encoding genes. This multipartite genome was found to contain 5 distinct replicons; a chromosome of size 4,537,948 bp and four circular plasmids of size 1,266,105 bp, 501,946 bp, 308,747 bp and 257,956 bp.

  • host strain mediated selection for an effective nitrogen fixing symbiosis between trifolium spp and rhizobium leguminosarum biovar trifolii
    Soil Biology & Biochemistry, 2008
    Co-Authors: R J Yates, J.g. Howieson, Lambert Bräu, Wayne Reeve, J Speijers, K G Nandasena, Daniel Real, E Sezmis, G W Ohara
    Abstract:

    We have previously reported significant strain–host incompatibility between the microsymbiont Rhizobium leguminosarum biovar trifolii and Trifolium spp. related to geographic and phenological barriers. Additionally, we have shown that an effective symbiosis between strains of R. l. trifolii and clover was established despite the soil harbouring ineffective R. l. trifolii capable of nodulating the host. We termed this “selection” for effective symbiosis. This paper reports glasshouse-based experiments to validate and further explore this in situ selection phenomenon. The effect of cell density and strain ratio at the time of inoculation, as well as soil pH, were investigated on two hosts (Trifolium purpureum and Trifolium polymorphum) that were each exposed to one microsymbiont capable and one incapable of N2 fixation. In co-inoculation experiments at a cell density of 104 cells/mL, each host nodulated solely with its effective strain, even when this strain was outnumbered 100-fold by the ineffective strain. However, the selection process ceased when the effective strain was outnumbered 1000-fold. At higher basal cell concentrations of 105–108 cells/mL, selection for WSM1325 to form effective nodulation on T. purpureum was evident, but was significantly reduced as the ratio of ineffective cells in the inoculum increased above 4-fold. The results indicate that the selection mechanism is highly dependent on the basal rhizobial cell density. Soil pH did not significantly alter the process, and both strains grew at similar rates and formed nodules at similar rates. A preliminary investigation into the genetic backgrounds of WSM1325 and WSM2304 revealed that although their 16S rRNA sequences were identical, they have considerable differences in their symbiotic and chromosomal replicons through examination of atpD, GSII and nodD sequences.

Mustapha Mohammed - One of the best experts on this subject based on the ideXlab platform.

  • adaptability to local conditions and phylogenetic differentiation of Microsymbionts of tgx soybean genotypes in the semi arid environments of ghana and south africa
    Systematic and Applied Microbiology, 2021
    Co-Authors: Sanjay K. Jaiswal, Mustapha Mohammed, Jalilatu Ayuba, Nicholas N Denwar, Felix D. Dakora
    Abstract:

    Abstract The study of the nitrogen fixation and phylogenetic diversity of nodule Microsymbionts of grain legumes in many parts of the globe is often carried out in order to identify legume-rhizobia combinations for agricultural sustainability. Several reports have therefore found that rhizobial species diversity is shaped by edapho-climatic conditions that characterize different geographic locations, suggesting that rhizobial communities often possess traits that aid their adaptation to their habitat. In this study, the soybean-nodulating rhizobia from semi-arid savannahs of Ghana and South Africa were evaluated. The authenticated rhizobial isolates were highly diverse based on their colony characteristics, as well as their BOX-PCR profiles and gene sequences. In the 16S rRNA phylogeny, the isolates were placed in the different clades Bradyrhizobium iriomotense and B. jicamae together with two superclades B. japonicum and B. elkanii. The multilocus (atpD, glnII, gyrB, recA) phylogenetic analyses indicated the dominancy of B. diazoefficiens and putative new Bradyrhizobium species in the semi-arid Ghanaian region. The phylogenetic analyses based on the symbiotic genes (nifH and nodC) clustered the test isolates into different symbiovars (sv. glycinearum, sv. retame and sv. sojae). Principal component analysis (PCA) showed that soil factors played a significant role in favoring the local conditions for the soybean-nodulating Microsymbionts. The results suggested that isolates had marked local adaptation conditions in semi-arid regions but further studies are needed to confirm new Bradyrhizobium species.

  • Studies of Phylogeny, Symbiotic Functioning and Ecological Traits of Indigenous Microsymbionts Nodulating Bambara Groundnut (Vigna subterranea L. Verdc) in Eswatini 
    Microbial Ecology, 2021
    Co-Authors: Sibusiso T. Dlamini, Sanjay K. Jaiswal, Mustapha Mohammed, Felix D. Dakora
    Abstract:

    Rhizobial Microsymbionts of grain legumes are ubiquitous in soils and exhibit a wide range of diversity with respect to colony morphology, genetic variability, biochemical characteristics, and phylogenetic relationships. This study assessed the phylogenetic positions of rhizobial Microsymbionts of Bambara groundnut from Eswatini exhibiting variations in morpho-physiology, adaptive characteristics, and N_2-fixing efficiency. The isolates’ ERIC-PCR profiles revealed the presence of high genetic variation among them. These test isolates also exhibited differences in pH tolerance and IAA production. Multilocus sequence analysis based on the 16S rRNA, atpD , glnII , gyrB , and recA gene sequences of representative test isolates closely aligned them to the type strains of  Bradyrhizobium arachidis , B. manausense , B. guangdongense , B. elkanii , and B. pachyrhizi. However, some isolates showed a high divergence from the known reference type strains, indicating that they may represent species yet to be properly characterized and described. Functional characterization in the glasshouse revealed that most of the isolates from the contrasting Agro-ecologies of Eswatini were efficient in N_2 fixation, and therefore elicited greater stomatal conductance and photosynthetic rates in the homologous Bambara groundnut. Of the 75 isolates tested, 51% were more effective than the commercial Bradyrhizobium sp. strain CB756, with relative symbiotic effectiveness ranging from 138 to 308%. The findings of this study indicated that the analysis of housekeeping genes and functional traits of Bambara-nodulating Microsymbionts can provide a clear view for understanding and predicting rhizobial community structure across environmental gradients.

  • insights into the phylogeny nodule function and biogeographic distribution of Microsymbionts nodulating the orphan kersting s groundnut macrotyloma geocarpum harms marechal baudet in african soils
    Applied and Environmental Microbiology, 2019
    Co-Authors: Mustapha Mohammed, Sanjay K. Jaiswal, Felix D. Dakora
    Abstract:

    Kersting9s groundnut [ Macrotyloma geocarpum (Harms) Marechal & Baudet] is a neglected indigenous African legume adapted to growth in N-deficient soils due to its ability to fix atmospheric N 2 via symbiosis with rhizobia. Despite its nutritional and medicinal uses, to date, there is little information on the phylogeny and functional traits of its Microsymbionts, an aspect much needed for its conservation and improvement. This study explored the morpho-genetic diversity, phylogenetic relationships and N 2 -fixing efficiency of Kersting9s groundnut rhizobial isolates from contrasting environments in Ghana, South Africa and Mozambique. Box-PCR fingerprinting revealed high diversity among rhizobial populations which was influenced by geographic origin. Of the 164 isolates evaluated, 130 Box-PCR types were identified at 70% similarity coefficient, indicating that they were not clones. Soil pH and mineral concentrations were found to influence the distribution of bradyrhizobial populations in African soils. Phylogenetic analysis of 16S rRNA gene and multilocus sequence analysis of protein-coding genes ( atp D, gln II, gyr B and rpo B) and symbiotic genes ( nif H and nod C) showed that, Kersting9s groundnut is primarily nodulated by members of genus Bradyrhizobium, which are closely related to B. vignae 7-2 T , B. kavangense 14-3 T , B. subterraneum 58-2-1 T , B. pachyrhizi PAC48 T , B. elkanii T and novel groups of Bradyrhizobium species. The bradyrhizobial populations identified exhibited high N 2 fixation, and induced greater nodulation, leaf chlorophyll concentration and photosynthetic rates on their homologous host when compared to the 5 mM KNO 3 -fed plants and/or the commercial Bradyrhizobium strain CB756, suggesting that they could be good candidates for inoculant formulations upon field testing. IMPORTANCE Rhizobia play important roles in agroecosystems where they contribute to improving overall soil health through their symbiotic relationship with legumes. This study explored the Microsymbionts nodulating Kersting9s groundnut, a neglected orphan legume. The results revealed the presence of different bradyrhizobial populations with high N 2 -fixing efficiencies as the dominant symbionts of this legume across diverse agroecologies in Africa. Our findings represent a useful contribution to the literature in terms of the community of Microsymbionts nodulating a neglected cultivated legume, and its potential for elevation as a major food crop. The presence of potentially novel bradyrhizobial symbionts of Kersting9s groundnut found in this study offers an opportunity for future studies to properly describe, characterize and delineate these isolates functionally and phylogenetically for use in inoculant production to enhance food/nutritional security.

  • distribution and correlation between phylogeny and functional traits of cowpea vigna unguiculata l walp nodulating Microsymbionts from ghana and south africa
    Scientific Reports, 2018
    Co-Authors: Mustapha Mohammed, Sanjay K. Jaiswal, Felix D. Dakora
    Abstract:

    Cowpea (Vigna unguiculata L. Walp.) is indigenous to Africa, and highly valued for its N2-fixing trait and the nutritional attributes of its grain and leaves. The species’ ability to establish effective symbiosis with diverse rhizobial populations gives it survival and growth advantage in N-limited environments. To explore the functional diversity and phylogenetic positions of rhizobia nodulating cowpea in Africa, nodules were collected from various cowpea varieties grown in soils from the Guinea savanna and Sudano-sahelian agroecologies of Northern Ghana, and from the lowveld and middleveld areas of Mpumalanga Province in South Africa. Box-PCR profiling and multilocus sequence analysis revealed the presence of diverse Microsymbionts responsible for cowpea nodulation across the study sites. BOX-PCR amplifications yielded variable band sizes, ranging from 618 bp to 5354 bp, which placed the isolates in six major clusters (Cluster A–F). Phylogenetic analysis based on 16S rRNA, atpD, glnII, gyrB, rpoB, nifH and nodC genes revealed the presence of diverse Bradyrhizobium sp. closely related to Bradyrhizobium daqingense, Bradyrhizobium subterraneum, Bradyrhizobium yuanmingense, Bradyrhizobium embrapense, Bradyrhizobium pachyrhizi, Bradyrhizobium elkanii and novel Bradyrhizobium species in the soils studied, a finding that could be attributed to the unique edapho-climatic conditions of the contrasting environments. The test isolates exhibited distinct symbiotic efficiencies, and also induced variable (p ≤ 0.001) photosynthetic rates, leaf transpiration, total chlorophyll and shoot biomass accumulation on cowpea (their homologous host). Canonical correspondence analysis showed that the distribution of these Microsymbionts was influenced by the concentrations of macro- and micronutrients in soils. The pairwise genetic distances derived from phylogenies and nodule functioning showed significant (p < 0.05) correlation, which suggests that local environmental factors played a major role in the cowpea-Bradyrhizobium symbiosis.

  • Distribution and correlation between phylogeny and functional traits of cowpea (Vigna unguiculata L. Walp.)-nodulating Microsymbionts from Ghana and South Africa
    Nature Publishing Group, 2018
    Co-Authors: Mustapha Mohammed, Sanjay K. Jaiswal, Felix D. Dakora
    Abstract:

    Abstract Cowpea (Vigna unguiculata L. Walp.) is indigenous to Africa, and highly valued for its N2-fixing trait and the nutritional attributes of its grain and leaves. The species’ ability to establish effective symbiosis with diverse rhizobial populations gives it survival and growth advantage in N-limited environments. To explore the functional diversity and phylogenetic positions of rhizobia nodulating cowpea in Africa, nodules were collected from various cowpea varieties grown in soils from the Guinea savanna and Sudano-sahelian agroecologies of Northern Ghana, and from the lowveld and middleveld areas of Mpumalanga Province in South Africa. Box-PCR profiling and multilocus sequence analysis revealed the presence of diverse Microsymbionts responsible for cowpea nodulation across the study sites. BOX-PCR amplifications yielded variable band sizes, ranging from 618 bp to 5354 bp, which placed the isolates in six major clusters (Cluster A–F). Phylogenetic analysis based on 16S rRNA, atp D, gln II, gyr B, rpo B, nifH and nodC genes revealed the presence of diverse Bradyrhizobium sp. closely related to Bradyrhizobium daqingense, Bradyrhizobium subterraneum, Bradyrhizobium yuanmingense, Bradyrhizobium embrapense, Bradyrhizobium pachyrhizi, Bradyrhizobium elkanii and novel Bradyrhizobium species in the soils studied, a finding that could be attributed to the unique edapho-climatic conditions of the contrasting environments. The test isolates exhibited distinct symbiotic efficiencies, and also induced variable (p ≤ 0.001) photosynthetic rates, leaf transpiration, total chlorophyll and shoot biomass accumulation on cowpea (their homologous host). Canonical correspondence analysis showed that the distribution of these Microsymbionts was influenced by the concentrations of macro- and micronutrients in soils. The pairwise genetic distances derived from phylogenies and nodule functioning showed significant (p 

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  • Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325, an effective microsymbiont of annual Mediterranean clovers
    Standards in Genomic Sciences, 2010
    Co-Authors: Wayne Reeve, Patrick Chain, Lambert Bräu, Kemanthi Nandesena, Julie Ardley, Ravi Tiwari, Graham O’hara, Alex Copeland, Matt Nolan, Thomas Brettin
    Abstract:

    Rhizobium leguminosarum bv trifolii is a soil-inhabiting bacterium that has the capacity to be an effective nitrogen fixing microsymbiont of a diverse range of annual Trifolium (clover) species. Strain WSM1325 is an aerobic, motile, non-spore forming, Gram-negative rod isolated from root nodules collected in 1993 from the Greek Island of Serifos. WSM1325 is produced commercially in Australia as an inoculant for a broad range of annual clovers of Mediterranean origin due to its superior attributes of saprophytic competence, nitrogen fixation and acid-tolerance. Here we describe the basic features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence for a microsymbiont of annual clovers. We reveal that its genome size is 7,418,122 bp encoding 7,232 protein-coding genes and 61 RNA-only encoding genes. This multipartite genome contains 6 distinct replicons; a chromosome of size 4,767,043 bp and 5 plasmids of size 828,924 bp, 660,973 bp, 516,088 bp, 350,312 bp and 294,782 bp.

  • complete genome sequence of the medicago microsymbiont ensifer sinorhizobium medicae strain wsm419
    Standards in Genomic Sciences, 2010
    Co-Authors: Wayne Reeve, Lambert Bräu, Kemanthi Nandesena, Julie Ardley, G W Ohara, Stephanie Malfatti, Patrick S G Chain, R P Tiwari
    Abstract:

    Ensifer (Sinorhizobium) medicae is an effective nitrogen fixing microsymbiont of a diverse range of annual Medicago (medic) species. Strain WSM419 is an aerobic, motile, non-spore forming, Gram-negative rod isolated from a M. murex root nodule collected in Sardinia, Italy in 1981. WSM419 was manufactured commercially in Australia as an inoculant for annual medics during 1985 to 1993 due to its nitrogen fixation, saprophytic competence and acid tolerance properties. Here we describe the basic features of this organism, together with the complete genome sequence, and annotation. This is the first report of a complete genome sequence for a microsymbiont of the group of annual medic species adapted to acid soils. We reveal that its genome size is 6,817,576 bp encoding 6,518 protein-coding genes and 81 RNA only encoding genes. The genome contains a chromosome of size 3,781,904 bp and 3 plasmids of size 1,570,951 bp, 1,245,408 bp and 219,313 bp. The smallest plasmid is a feature unique to this medic microsymbiont.

  • Complete genome sequence of Rhizobium leguminosarum bv trifolii strain WSM2304, an effective microsymbiont of the South American clover Trifolium polymorphum
    Standards in Genomic Sciences, 2010
    Co-Authors: Wayne Reeve, Patrick Chain, Lambert Bräu, Kemanthi Nandesena, Hajnalka Kiss, Julie Ardley, Ravi Tiwari, Graham O’hara, Stephanie Malfatti, Alla Lapidus
    Abstract:

    Rhizobium leguminosarum bv trifolii is the effective nitrogen fixing microsymbiont of a diverse range of annual and perennial Trifolium (clover) species. Strain WSM2304 is an aerobic, motile, non-spore forming, Gram-negative rod, isolated from Trifolium polymorphum in Uruguay in 1998. This microsymbiont predominated in the perennial grasslands of Glencoe Research Station, in Uruguay, to competitively nodulate its host, and fix atmospheric nitrogen. Here we describe the basic features of WSM2304, together with the complete genome sequence, and annotation. This is the first completed genome sequence for a nitrogen fixing microsymbiont of a clover species from the American center of origin. We reveal that its genome size is 6,872,702 bp encoding 6,643 protein-coding genes and 62 RNA only encoding genes. This multipartite genome was found to contain 5 distinct replicons; a chromosome of size 4,537,948 bp and four circular plasmids of size 1,266,105 bp, 501,946 bp, 308,747 bp and 257,956 bp.

  • host strain mediated selection for an effective nitrogen fixing symbiosis between trifolium spp and rhizobium leguminosarum biovar trifolii
    Soil Biology & Biochemistry, 2008
    Co-Authors: R J Yates, J.g. Howieson, Lambert Bräu, Wayne Reeve, J Speijers, K G Nandasena, Daniel Real, E Sezmis, G W Ohara
    Abstract:

    We have previously reported significant strain–host incompatibility between the microsymbiont Rhizobium leguminosarum biovar trifolii and Trifolium spp. related to geographic and phenological barriers. Additionally, we have shown that an effective symbiosis between strains of R. l. trifolii and clover was established despite the soil harbouring ineffective R. l. trifolii capable of nodulating the host. We termed this “selection” for effective symbiosis. This paper reports glasshouse-based experiments to validate and further explore this in situ selection phenomenon. The effect of cell density and strain ratio at the time of inoculation, as well as soil pH, were investigated on two hosts (Trifolium purpureum and Trifolium polymorphum) that were each exposed to one microsymbiont capable and one incapable of N2 fixation. In co-inoculation experiments at a cell density of 104 cells/mL, each host nodulated solely with its effective strain, even when this strain was outnumbered 100-fold by the ineffective strain. However, the selection process ceased when the effective strain was outnumbered 1000-fold. At higher basal cell concentrations of 105–108 cells/mL, selection for WSM1325 to form effective nodulation on T. purpureum was evident, but was significantly reduced as the ratio of ineffective cells in the inoculum increased above 4-fold. The results indicate that the selection mechanism is highly dependent on the basal rhizobial cell density. Soil pH did not significantly alter the process, and both strains grew at similar rates and formed nodules at similar rates. A preliminary investigation into the genetic backgrounds of WSM1325 and WSM2304 revealed that although their 16S rRNA sequences were identical, they have considerable differences in their symbiotic and chromosomal replicons through examination of atpD, GSII and nodD sequences.