Rhizobia Indigenous to the Okavango Region in Sub-Saharan Africa: Diversity, Adaptations, and Host Specificity

Comparative genomics analysis reveals genetic characteristics and nitrogen fixation profile of Bradyrhizobium

Bradyrhizobium is a genus of nitrogen-fixing bacteria, with some species producing nodules in leguminous plants. Investigations into Bradyrhizobium have recently revealed its substantial genetic resources and agricultural benefits, but a comprehensive survey of its genetic diversity and functional properties is lacking. Using a panel of various strains (N = 278), this study performed a comparative genomics analysis to anticipate genes linked with symbiotic nitrogen fixation. Bradyrhizobium's pan-genome consisted of 84,078 gene families, containing 824 core genes and 42,409 accessory genes. Core genes were mainly involved in crucial cell processes, while accessory genes served diverse functions, including nitrogen fixation and nodulation. Three distinct genetic profiles were identified based on the presence/absence of gene clusters related to nodulation, nitrogen fixation, and secretion systems. Most Bradyrhizobium strains from soil and non-leguminous plants lacked major nif/nod genes and were evolutionarily more closely related. These findings shed light on Bradyrhizobium's genetic features for symbiotic nitrogen fixation.

Towards inoculant development for Bambara groundnut (Vigna subterranean (L.) Verdc) pulse crop production in Namibia

Introduction

The globally expanding population, together with climate change, poses a risk to the availability of food for humankind. Bambara groundnut (BGN) (Vigna subterranea (L.) Verdc) is a neglected, relatively drought-tolerant native legume of Sub-Saharan Africa that has the potential to become a successful food crop because of its nutritional quality and climate-smart features. Nitrogen fixation from root nodule symbiosis with climate-adapted rhizobial symbionts can contribute nitrogen and organic material in nutrient-poor soil and improve yields. However, high soil temperature and drought often reduce the abundance of native rhizobia in such soil. Therefore, the formulation of climate-smart biofertilizers has the potential to improve the farming of BGN at a low cost in a sustainable manner.

Method

The effect of seven Bradyrhizobium spp. strains native to Namibia, including B. vignae and B. subterraneum, were tested on three Namibian BGN varieties (red, brown, cream) in greenhouse pot experiments in Namibia, using soil from the target region of Kavango. Each variety was treated with a mixed inoculant consisting of seven preselected strains ("MK") as well as with one promising single inoculant strain.

Results

The results revealed that in all three varieties, the two inoculants (mixed or single) outperformed the non-inoculated cultivars in terms of shoot dry weight by up to 70%; the mixed inoculant treatment performed significantly better (p < 0.05) in all cases compared to the single inoculant used. To test whether the inoculant strains were established in root nodules, they were identified by sequence analysis. In many cases, the indigenous strains of Kavango soil outcompeted the inoculant strains of the mix for nodule occupancy, depending on the BGN variety. As a further preselection, each of the individual strains of the mix was used to inoculate the three varieties under sterile conditions in a phytotron. The agronomic trait and root nodulation response of the host plant inoculations strongly differed with the BGN variety. Even competitiveness in nodule occupancy without involving any indigenous strains from soil differed and depended strictly on the variety.

Discussion

Severe differences in symbiont-plant interactions appear to occur in BGN depending on the plant variety, demanding for coupling of breeding efforts with selecting efficient inoculant strains.

Impact of nitrogen-fixation bacteria on nitrogen-fixation efficiency of Bambara groundnut [Vigna subterranea (L) Verdc] genotypes

Nitrogen fixation by bacteria is essential for sustaining the growth, development, and yield of legumes. Pot experiments were carried out at the International Institute of Tropical Agriculture (IITA) in the glasshouse between August to December 2018/2019 cropping season in Ibadan, Nigeria. Field studies were also performed in two different agroecological zones, "Ibadan and Ikenne" between August and December of 2019/2020 cropping season. The studies were set up to determine the potential of nitrogen-fixation bacteria strain inoculation on the nitrogen-fixation potential of 10 Bambara groundnut (BGN) genotypes, namely, TVSu-378, TVSu-506, TVSu-787, TVSu-1,606, TVSu-1,698, TVSu-1739, TVSu-710, TVSu-365, TVSu-475, and TVSu-305. The strains were inoculated as a broth to seedlings of each BGN genotype in the pot experiment. While six seeds from each BGN genotype were coated with each of the following nitrogen-fixation bacteria (Bradyrhizobium japonicum strains), FA3, USDA110, IRJ2180A, and RACA6, nitrogen fertilizer (urea, 20 kg/ha) was applied as a check to the nitrogen-fixation bacteria to seedlings of BGN genotypes 2 weeks after planting in both glasshouses and fields. Uninoculated plants served as controls (zero inoculation and zero fertilization). The field experiments were arranged in Randomized Complete Block Design (RCBD), while the glasshouse experiments were arranged in Complete Randomized Design (CRD) in triplicate. The result gotten showed that higher nodule numbers and weight were recorded in TVSu-1739 and TVSu-475 in both locations and seasons compared to other genotypes; the highest nitrogen fixed values were recorded among BGN genotypes TVSu-1739, TVSu-1,698, TVSu-787, TVSu-365, TVSu-305, TVSu-710, and TVSu-1,606, with a range of (62-67 kg ha-1), and were mostly enhanced by RACA6 and USDA110 strains compared to other strains that were used.

Characterization of rhizobia for beneficial traits that promote nodulation in legumes under abiotically stressed conditions

The growing interest in using rhizobia as inoculants in sustainable agricultural systems has prompted the screening of rhizobia species for beneficial traits that enhance nodulation and nitrogen fixation under abiotic stressed conditions. This study reports phenotypic and phylogenetic characterization of rhizobia strains previously isolated from the root nodules of several indigenous and exotic legumes growing in South Africa and other countries. The Rhizobia strains were screened for their ability to tolerate various abiotic stresses (temperature 16, 28, and 36 °C; acidity/alkalinity pH 5, 7, and 9; heavy metals 50, 100, and 150 mM AlCl3.6H2O; and salinity 50, 100, and 150 mM NaCl). Phylogenetic characterization of the isolates was determined using multilocus sequence analysis of the 16S rRNA, recA, acdS, exoR, nodA, and nodC genes. The analysis indicated that the isolates are phylogenetically related to Sinorhizobium, Bradyrhizobium, Rhizobium, Mesorhizobium, and Aminobacter genera and exhibited significant variations in their tolerance to abiotic stresses. Amid the increasing threats of the global stresses, these current results provide baseline information in the selection of rhizobia for use as inoculants under extreme temperatures, acidity/alkalinity, and salinity stress conditions in South Africa.

Exploring the benefits of inoculated cowpeas under different climatic conditions in Namibia

Cowpeas (Vigna uniculata L. Walp) are grown by many smallholder farmers in sub-Saharan Africa for food and their ability to fix nitrogen even under stress. Their performance depends on the indigenous rhizobial strains that live in symbiotic association with the roots; it can be enhanced if the seeds are inoculated with more effective ones. Data of the effectiveness of the technique under a variety of climatic conditions is rare. Here, we thus use a model to upscale two field experiments conducted in Namibia to include different climate change scenarios. The simulations show that non-inoculated cowpeas have mean yields of 0.5 t/ha and inoculated cowpeas 1 t/ha. If climatic conditions are favorable (cool and wet), estimated yield differences increase to over 1 t/ha. In dry years (< 200 mm), the average yield difference is only 0.1 t/ha. In the far future (2080-2100), instances of dry and hot years will increase. Using inoculated cowpea seeds instead of non-inoculated ones thus does not benefit farmers as much then as in the near future (2030-2050). In conclusion, using cowpea seeds inoculated with an efficient rhizobial strain can significantly increase yields under varying climatic conditions, but yield advantages decrease markedly in very dry and hot years.

Distribution, Characterization and the Commercialization of Elite Rhizobia Strains in Africa

Grain legumes play a significant role in smallholder farming systems in Africa because of their contribution to nutrition and income security and their role in fixing nitrogen. Biological Nitrogen Fixation (BNF) serves a critical role in improving soil fertility for legumes. Although much research has been conducted on rhizobia in nitrogen fixation and their contribution to soil fertility, much less is known about the distribution and diversity of the bacteria strains in different areas of the world and which of the strains achieve optimal benefits for the host plants under specific soil and environmental conditions. This paper reviews the distribution, characterization, and commercialization of elite rhizobia strains in Africa.

Phylogenetically diverse Bradyrhizobium genospecies nodulate Bambara groundnut (Vigna subterranea L. Verdc) and soybean (Glycine max L. Merril) in the northern savanna zones of Ghana

A total of 102 bacterial strains isolated from nodules of three Bambara groundnut and one soybean cultivars grown in nineteen soil samples collected from northern Ghana were characterized using multilocus gene sequence analysis. Based on a concatenated sequence analysis (glnII-rpoB-recA-gyrB-atpD-dnaK), 54 representative strains were distributed in 12 distinct lineages, many of which were placed mainly in the Bradyrhizobium japonicum and Bradyrhizobium elkanii supergroups. Twenty-four of the 54 representative strains belonged to seven putative novel species, while 30 were conspecific with four recognized Bradyrhizobium species. The nodA phylogeny placed all the representative strains in the cosmopolitan nodA clade III. The strains were further separated in seven nodA subclusters with reference strains mainly of African origin. The nifH phylogeny was somewhat congruent with the nodA phylogeny, but both symbiotic genes were mostly incongruent with the core housekeeping gene phylogeny indicating that the strains acquired their symbiotic genes horizontally from distantly related Bradyrhizobium species. Using redundancy analysis, the distribution of genospecies was found to be influenced by the edaphic factors of the respective sampling sites. In general, these results mainly underscore the high genetic diversity of Bambara groundnut-nodulating bradyrhizobia in Ghanaian soils and suggest a possible vast resource of adapted inoculant strains.

Ecological adaptation and phylogenetic analysis of microsymbionts nodulating Polhillia, Wiborgia and Wiborgiella species in the Cape fynbos, South Africa

Polhillia, Wiborgia and Wiborgiella species are shrub legumes endemic to the Cape fynbos of South Africa. They have the ability to fix atmospheric N₂ when in symbiosis with soil bacteria called ‘rhizobia’. The aim of this study was to assess the morpho-physiological and phylogenetic characteristics of rhizobia associated with the nodulation of Polhillia, Wiborgia and Wiborgiella species growing in the Cape fynbos. The bacterial isolates from root nodules consisted of a mixture of fast and intermediate growers that differed in colony shape and size. The isolates exhibited tolerance to salinity (0.5–3% NaCl) and pH (pH 5–10) and different antibiotic concentrations, and could produce 0.51 to 51.23 µg mL⁻¹ of indole-3-acetic acid (IAA), as well as solubilize tri-calcium phosphate. The ERIC-PCR results showed high genomic diversity in the rhizobial population and grouped them into two major clusters. Phylogenetic analysis based on 16S rRNA, atpD, glnII, gyrB, nifH and nodC gene sequences revealed distinct and novel evolutionary lineages related to the genus Rhizobium and Mesorhizobium, with some of them being very close to Mesorhizobium australicum. However, the phylogenetic analysis of glnII and nifH genes of some isolates showed incongruency.

Studies of Phylogeny, Symbiotic Functioning and Ecological Traits of Indigenous Microsymbionts Nodulating Bambara Groundnut (Vigna subterranea L. Verdc) in Eswatini

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 N₂-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 N₂ 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.

Functional and genetic diversity of native rhizobial isolates nodulating cowpea (Vigna unguiculata L. Walp.) in Mozambican soils

Identification and symbiotic characterization of indigenous rhizobial isolates are the basis for inoculant formulations needed for sustainable grain legume production. This study screened for morpho-genetic diversity of indigenous cowpea nodulating rhizobia in farmers' fields across two contrasting agroecological zones of Northern Mozambique. The photosynthetic function induced by the isolates in their homologous cowpea was assessed. The results showed high genetic variability among the isolates based on morphology and ERIC-PCR fingerprinting. The trap cowpea genotype did not influence the diversity of isolates collected from the two different agroecologies, suggesting that the cowpea-rhizobia compatibility may be conserved at species level. Phylogenetic analysis of the 16S rRNA gene assigned representative rhizobial isolates to species in the Bradyrhizobium and Rhizobium genera, with some isolates showing high divergence from the known reference type strains. The isolates from both agroecologies highly varied in the number and biomass of nodules induced in the homologous cowpea, resulting in variable plant growth and photosynthetic activities. A total of 72% and 83% of the isolates collected from the agroecological zones 7 and 8 were respectively classified as highly effective candidates with > 80% relative effectiveness compared to plants fertilized with nitrate, indicating that elite native strains populated the studied soils. Moreover, the top 25% of high N₂-fixing isolates from the two agroecologies recorded relative effectiveness ranging from 115 to 154%, values higher than the effectiveness induced by the commercial Bradyrhizobium sp. strain CB756. These strains are considered as having potential for use in inoculant formulations. However, future studies should be done to assess the ecologically adaptive traits and symbiotic performance under field conditions.

Root Nodule Rhizobia From Undomesticated Shrubs of the Dry Woodlands of Southern Africa Can Nodulate Angolan Teak Pterocarpus angolensis, an Important Source of Timber

Pterocarpus angolensis, a leguminous tree native to the dry woodlands of Southern Africa, provides valuable timber, but is threatened by land conversion and overharvesting while showing limited natural regeneration. Nitrogen-fixing root nodule symbionts that could improve establishment of young seedlings have not yet been described. Therefore, we investigated the ability of P. angolensis to form nodules with a diverse range of rhizobia. In drought-prone areas under climate change with higher temperatures, inoculants that are heat-tolerant and adapted to these conditions are likely to be of advantage. Sources of bacterial isolates were roots of P. angolensis from nurseries in the Kavango region, other shrubs from this area growing near Pterocarpus such as Indigofera rautanenii, Desmodium barbatum, Chamaecrista sp., or shrubs from drought-prone areas in Namaqualand (Wiborgia monoptera, Leobordea digitata) or Kalahari (Indigofera alternans). Only slight protrusions were observed on P. angolensis roots, from which a non-nodulating Microbacterium sp. was isolated. Rhizobia that were isolated from nodules of other shrubs were affiliated to Bradyrhizobium ripae WR4T, Bradyrhizobium spp. (WR23/WR74/WR93/WR96), or Ensifer/Mesorhizobium (WR41/WR52). As many plant growth-promoting rhizobacteria (PGPR), nodule isolates produced siderophores and solubilized phosphate. Among them, only the Bradyrhizobium strains nodulated P. angolensis under controlled conditions in the laboratory. Isolates were further characterized by multilocus sequence analysis and were found to be distant from known Bradyrhizobium species. Among additional reference species tested for nodulation on P. angolensis, Bradyrhizobium vignae 7-2T and Bradyrhizobium namibiense 5-10T from the Kavango region of Namibia as well as Bradyrhizobium elkanii LMG6234T and Bradyrhizobium yuanmingense LMG21728T induced nitrogen-fixing nodules, while Bradyrhizobium diazoefficiens USDA110T and Bradyrhizobium tropiciagri SEMIA6148T did not. This suggests a broad microsymbiont range from Bradyrhizobium japonicum and B. elkanii lineages. Phylogenetic analysis of nodC genes indicated that nodulating bradyrhizobia did not belong to a specific symbiovar. Also, for I. rautanenii and Wiborgia, nodule isolates B. ripae WR4T or Mesorhizobium sp. WR52, respectively, were authenticated. Characterization of symbionts inducing effective root nodules in P. angolensis and other shrubs from Subsahara Africa (SSA) give insights in their symbiotic partners for the first time and might help in future to develop bioinoculants for young seedlings in nurseries, and for reforestation efforts in Southern Africa.

Phylogenetic evidence of allopatric speciation of bradyrhizobia nodulating cowpea (Vigna unguiculata L. walp) in South African and Mozambican soils

The legume host and soil environment play a major role in establishing effective symbiosis with diverse rhizobia for plant growth promotion and nodule formation. The aim of this study was to assess the morpho-physiology, distribution and phylogenetic position of rhizobia nodulating cowpea from South Africa and Mozambique. The results showed that the isolates were highly diverse in their appearance on yeast mannitol agar plates. The isolates tested also showed an ability to produce IAA at concentrations ranging from 0.64 to 56.46 μg.ml⁻¹ and to solubilise phosphorus at levels from 0 to 3.55 index. Canonical correspondence analysis showed that soil pH and mineral nutrients significantly influenced bradyrhizobial distribution. Analysis of BOX-PCR placed the isolates in eight major clusters with 0.01 to 1.00 similarity coefficient which resulted in 45 unique BOX-types. Phylogenetic analyses based on 16S rRNA, atpD, glnII, gyrB and recA gene sequences showed distinct novel evolutionary lineages within the genus Bradyrhizobium, with some of them being closely related to Bradyrhizobium kavangense, B. subterraneum and B. pachyrhizi. Furthermore, symbiotic gene phylogenies suggested that the isolates’ sym loci probably relates to the isolates’ geographical origin. The results indicated that geographical origin did affect the isolates’ phylogenetic placement and could be the basis for allopatric speciation

Bradyrhizobium ivorense sp. nov. as a potential local bioinoculant for Cajanus cajan cultures in Côte d'Ivoire

For many smallholder farmers of Sub-Saharan Africa, pigeonpea (Cajanus cajan) is an important crop to make ends meet. To ascertain the taxonomic status of pigeonpea isolates of Côte d’Ivoire previously identified as bradyrhizobia, a polyphasic approach was applied to strains CI-1B^T, CI-14A, CI-19D and CI-41S. Phylogeny of 16S ribosomal RNA (rRNA) genes placed these nodule isolates in a separate lineage from current species of the B. elkanii super clade. In phylogenetic analyses of single and concatenated partial dnaK, glnII, gyrB, recA and rpoB sequences, the C. cajan isolates again formed a separate lineage, with strain CI-1B^T sharing the highest sequence similarity (95.2 %) with B. tropiciagri SEMIA 6148^T. Comparative genomic analyses corroborated the novel species status, with 86 % ANIb and 89 % ANIm as the highest average nucleotide identity (ANI) values with B. elkanii USDA 76^T. Although CI-1B^T, CI-14A, CI-19D and CI-41S shared similar phenotypic and metabolic properties, growth of CI-41S was slower in/on various media. Symbiotic efficacy varied significantly between isolates, with CI-1B^T and CI-41S scoring on the C. cajan ‘Light-Brown’ landrace as the most and least proficient bacteria, respectively. Also proficient on Vigna radiata (mung bean), Vigna unguiculata (cowpea, niébé) and additional C. cajan cultivars, CI-1B^T represents a potential bioinoculant adapted to local soil conditions and capable of fostering the growth of diverse legume crops in Côte d'Ivoire. Given the data presented here, we propose the 19 C. cajan isolates to belong to a novel species called Bradyrhizobium ivorense sp. nov., with CI-1B^T (=CCOS 1862^T=CCMM B1296^T) as a type strain.

The role of legumes in the sustainable intensification of African smallholder agriculture: Lessons learnt and challenges for the future

Grain legumes play a key role in smallholder farming systems in sub-Saharan Africa (SSA), in relation to food and nutrition security and income generation. Moreover, because of their N2-fixation capacity, such legumes can also have a positive influence on soil fertility. Notwithstanding many decades of research on the agronomy of grain legumes, their N2-fixation capacity, and their contribution to overall system productivity, several issues remain to be resolved to realize fully the benefits of grain legumes. In this paper we highlight major lessons learnt and expose key knowledge gaps in relation to grain legumes and their contributions to farming system productivity. The symbiosis between legumes and rhizobia forms the basis for its benefits and biological N2-fixation (BNF) relies as much on the legume genotype as on the rhizobial strains. As such, breeding grain legumes for BNF deserves considerably more attention. Even promiscuous varieties usually respond to inoculation, and as African soils contain a huge pool of unexploited biodiversity with potential to contribute elite rhizobial strains, strain selection should go hand-in-hand with legume breeding for N2-fixation. Although inoculated strains can outcompete indigenous strains, our understanding of what constitutes a good competitor is rudimentary, as well as which factors affect the persistence of inoculated rhizobia, which in its turn determines whether a farmer needs to re-inoculate each and every season. Although it is commonly assumed that indigenous rhizobia are better adapted to local conditions than elite strains used in inoculants, there is little evidence that this is the case. The problems of delivering inoculants to smallholders through poorly-developed supply chains in Africa necessitates inoculants based on sterile carriers with long shelf life. Other factors critical for a well-functioning symbiosis are also central to the overall productivity of grain legumes. Good agronomic practices, including the use of phosphorus (P)-containing fertilizer, improve legume yields though responses to inputs are usually very variable. In some situations, a considerable proportion of soils show no response of legumes to applied inputs, often referred to as non-responsive soils. Understanding the causes underlying this phenomenon is limited and hinders the uptake of legume agronomy practices. Grain legumes also contribute to the productivity of farming systems, although such effects are commonly greater in rotational than in intercropping systems. While most cropping systems allow for the integration of legumes, intercropped legumes provide only marginal benefits to associated crops. Important rotational benefits have been shown for most grain legumes though those with the highest N accumulation and lowest N harvest index appear to demonstrate higher residual benefits. N balance estimates often results in contradictory observations, mostly caused by the lack of understanding of belowground contributions of legumes to the N balance. Lastly, the ultimate condition for increased uptake of grain legumes by smallholder farmers lies in the understanding of how legume technologies and management practices can be tailored to the enormous diversity of agroecologies, farming systems, and smallholder farms in SSA. In conclusion, while research on grain legumes has revealed a number of important insights that will guide realization of the full potential of such legumes to the sustainable intensification of smallholder farming systems in SSA, many research challenges remain to be addressed to realize the full potential of BNF in these systems.

Symbiotic effectiveness and ecologically adaptive traits of native rhizobial symbionts of Bambara groundnut (Vigna subterranea L. Verdc.) in Africa and their relationship with phylogeny

Bambara groundnut (Vigna subterranea L. Verdc.) is an indigenous, drought-tolerant, underutilized African food legume, with the ability to fix atmospheric N₂ in symbiosis with soil bacteria called rhizobia. The aim of this study was to assess the morpho-physiological, symbiotic and phylogenetic characteristics of rhizobia nodulating Bambara groundnut in Ghana, Mali and South Africa. The morpho-physiologically diverse isolates tested were also found to exhibit differences in functional efficiency and phylogenetic positions. Based on Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR banding patterns, the isolates were grouped into eight major clusters. The concentrations of Ca, Na and K in soils had a significant (p ≤ 0.01) effect on the distribution of rhizobia. Though many isolates were symbiotically very effective, the effectiveness index varied markedly (p ≤ 0.05) among them. Moreover, the isolates also exhibited tolerance to a wide range of NaCl (0.5–7%), streptomycin (50–500 µg.ml⁻¹), and kanamycin (25–150 µg.ml⁻¹) concentrations. Additionally, these isolates could produce 0.02 to 69.71 µg.ml⁻¹ of indole-3-acetic acid (IAA) in tryptophan-supplemented medium, as well as solubilize tri-calcium phosphate. Phylogenetic analysis of these rhizobial isolates using 16S rRNA, atpD, glnII, gyrB, recA and symbiotic (nifH and nodC) gene sequences revealed distinct and novel evolutionary lineages related to the genus Bradyrhizobium, with some of them being very close to Bradyrhizobium vignae, B. kavangense, B. subterraneum, B. elkanii and B. pachyrhizi.

Bradyrhizobium nanningense sp. nov., Bradyrhizobium guangzhouense sp. nov. and Bradyrhizobium zhanjiangense sp. nov., isolated from effective nodules of peanut in Southeast China

Nine slow-growing rhizobia isolated from effective nodules on peanut (Arachis hypogaea) were characterized to clarify the taxonomic status using a polyphasic approach. They were assigned to the genus Bradyrhizobium on the basis of 16S rRNA sequences. MLSA of concatenated glnII-recA-dnaK genes classified them into three species represented by CCBAU 53390^T, CCBAU 51670^T and CCBAU 51778^T, which presented the closest similarity to B. guangxiense CCBAU 53363^T, B. guangdongense CCBAU 51649^T and B. manausense BR 3351^T, B. vignae 7-2^T and B. forestalis INPA 54B^T, respectively. The dDDH (digital DNA-DNA hybridization) and ANI (Average Nucleotide Identity) between the genomes of the three representative strains and type strains for the closest Bradyrhizobium species were less than 42.1% and 91.98%, respectively, below the threshold of species circumscription. Effective nodules could be induced on peanut and Lablab purpureus by all representative strains, while Vigna radiata formed effective nodules only with CCBAU 53390^T and CCBAU 51778^T. Phenotypic characteristics including sole carbon sources and growth features supported the phylogenetic results. Based on the genotypic and phenotypic features, strains CCBAU 53390^T, CCBAU 51670^T and CCBAU 51778^T are designated the type strains of three novel species, for which the names Bradyrhizobium nanningense sp. nov., Bradyrhizobium guangzhouense sp. nov. and Bradyrhizobium zhanjiangense sp. nov. are proposed, respectively.

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

Kersting's 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 N₂ 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, aspects that are much needed for its conservation and improvement. This study explored the morphogenetic diversity, phylogenetic relationships, and N₂-fixing efficiency of Kersting's groundnut rhizobial isolates from contrasting environments in Ghana, South Africa, and Mozambique. BOX-PCR fingerprinting revealed high diversity among the rhizobial populations, which was influenced by geographic origin. Of the 164 isolates evaluated, 130 BOX-PCR types were identified at a 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 genes and multilocus sequence analysis of protein-coding genes (atpD, glnII, gyrB, and rpoB) and symbiotic genes (nifH and nodC) showed that Kersting's groundnut is primarily nodulated by members of the genus Bradyrhizobium, which are closely related to Bradyrhizobium vignae 7-2^T, Bradyrhizobium kavangense 14-3^T, Bradyrhizobium subterraneum 58-2-1^T, Bradyrhizobium pachyrhizi PAC48^T, the type strain of Bradyrhizobium elkanii, and novel groups of Bradyrhizobium species. The bradyrhizobial populations identified exhibited high N₂ fixation and induced greater nodulation, leaf chlorophyll concentration, and photosynthetic rates in their homologous host than did the 5 mM KNO₃-fed plants and/or the commercial Bradyrhizobium sp. 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 Kersting's groundnut, a neglected orphan legume. The results revealed the presence of different bradyrhizobial populations with high N₂-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 Kersting's 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.

Phylogeny and distribution of Bradyrhizobium symbionts nodulating cowpea (Vigna unguiculata L. Walp) and their association with the physicochemical properties of acidic African soils

In the N2-fixing symbiosis, the choice of a symbiotic partner is largely influenced by the host plant, the rhizobial symbiont, as well as soil factors. Understanding the soil environment conducive for the survival and multiplication of root-nodule bacteria is critical for microbial ecology. In this study, we collected cowpea-nodules from acidic soils in Ghana and South Africa, and nodule DNA isolates were characterized using 16S-23S rRNA-RFLP, phylogenetic analysis of housekeeping and symbiotic genes, and bradyrhizobial community structure through canonical correspondence analysis (CCA). The CCA ordination plot results showed that arrow of soil pH was overlapping on CCA2 axis and was the most important to the ordination. The test nodule DNA isolates from Ghana were positively influenced by soil Zn, Na and K while nodule DNA isolates from South Africa were influenced by P. The amplified 16S-23S rRNA region yielded single polymorphic bands of varying lengths (573-1298bp) that were grouped into 28 ITS types. The constructed ITS-dendrogram placed all the nodule DNA isolates in five major clusters at low cut-off of approx. 0.1 Jaccard's similarity coefficient. The phylogenetic analysis of 16S rRNA and housekeeping genes (glnII, gyrB, and atpD) formed distinct Bradyrhizobium groups in the phylogenetic trees. It revealed the presence of highly diverse bradyrhizobia (i.e. Bradyrhizobium vignae, Bradyrhizobium elkanii, Bradyrhizobium iriomotense, Bradyrhizobium pachyrhizi, and Bradyrhizobium yuanmingense) together with novel/unidentified bradyrhizobia in the acidic soils from Ghana and South Africa. Discrepancies noted in the phylogenies of some nodule DNA isolates could be attributed to horizontal gene transfer or recombination.

Widespread Distribution of Highly Adapted Bradyrhizobium Species Nodulating Diverse Legumes in Africa

Bradyrhizobium is one of the most cosmopolitan and diverse bacterial group nodulating a variety of host legumes in Africa, however, the diversity and distribution of bradyrhizobial symbionts nodulating indigenous African legumes are not well understood, though needed for increased food legume production. In this review, we have shown that many African food legumes are nodulated by bradyrhizobia, with greater diversity in Southern Africa compared to other parts of Africa. From a few studies done in Africa, the known bradyrhizobia (i.e., Bradyrhizobium elkanii, B. yuanmingense) along with many novel Bradyrhizobium species are the most dominant in African soils. This could be attributed to the unique edapho-climatic conditions of the contrasting environments in the continent. More studies are needed to identify the many novel bradyrhizobia resident in African soils in order to better understand the biogeography of bradyrhizobia and their potential for inoculant production.

Classification of the inoculant strain of cowpea UFLA03-84 and of other strains from soils of the Amazon region as Bradyrhizobium viridifuturi (symbiovar tropici)

Cowpea (Vigna unguiculata L.) is a legume species that considerably benefits from inoculation with nitrogen fixing bacteria of the genus Bradyrhizobium. One of the strains recommended for inoculation in cowpea in Brazil is UFLA03-84 (Bradyrhizobium sp.). The aim of our study was to define the taxonomic position of the UFLA03-84 strain and of two other strains of Bradyrhizobium (UFLA03-144 and INPA237B), all belonging to the same phylogenetic group and isolated from soils of the Brazilian Amazon. Multilocus sequence analysis (MLSA) of the housekeeping genes atpD, gyrB, recA, and rpoB grouped (with similarity higher than 99%) the three strains with Bradyrhizobium viridifuturi SEMIA 690^T. The analyses of average nucleotide identity and digital DNA-DNA hybridization supported classification of the group as Bradyrhizobium viridifuturi. The three strains exhibited similar behavior in relation to the most of the phenotypic characteristics evaluated. However, some characteristics exhibited variation, indicating phenotypic diversity within the species. Phylogenetic analysis of the nodC and nifH genes showed that the three strains are members of the same symbiovar (tropici) that contains type strains of Bradyrhizobium species coming from tropical soils (SEMIA 690^TB. viridifuturi, CNPSo 1112^TB. tropiciagri, CNPSo 2833^TB. embrapense, and B. brasilense UFLA03-321^T).

Distribution and correlation between phylogeny and functional traits of cowpea (Vigna unguiculata L. Walp.)-nodulating microsymbionts from Ghana and South Africa

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.

Genetic diversity of symbiotic bacteria nodulating common bean (Phaseolus vulgaris) in western Kenya

Biological nitrogen fixation (BNF) in legumes plays a critical role in improving soil fertility. Despite this vital role, there is limited information on the genetic diversity and BNF of bacteria nodulating common bean (Phaseolus vulgaris L.). This study evaluated the genetic diversity and symbiotic nitrogen fixation of bacteria nodulating common bean in soils of Western Kenya. The genetic diversity was determined using 16S rRNA gene partial sequences while BNF was estimated in a greenhouse experiment. The sequences of the native isolates were closely affiliated with members from the genera Pantoea, Klebsiella, Rhizobium, Enterobacter and Bacillus. These results show that apart from rhizobia, there are non-rhizobial strains in the nodules of common bean. The symbiotic efficiency (SE) of native isolates varied and exhibited comparable or superior BNF compared to the local commercial inoculants (CIAT 899 and Strain 446). Isolates (MMUST 003 [KP027691], MMUST 004 [KP027687], MMUST 005 [KP027688], KSM 001 [KP027682], KSM 002 [KP027680], KSM 003 [KP027683] and KSM 005 [KP027685]) recorded equal or significantly higher SE (p < 0.05) compared to N supplemented treatments. The results demonstrate the presence of genetic diversity of native bacteria nodulating bean that are effective in N fixation. These elite bacterial strains should be exploited as candidates for the development of Phaseolus vulgaris inoculants.

Diversity of Bradyrhizobia in Subsahara Africa: A Rich Resource

Making use of biological nitrogen fixation (BNF) with pulses and green manure legumes can help to alleviate nitrogen deficiencies and increase soil fertility, problems faced particularly in smallholder agriculture in Subsahara Africa (SSA). The isolation of indigenous rhizobia provides a basis for the formulation of rhizobial inoculants. Moreover, their identification and characterization contribute to the general understanding of species distribution and ecology. Here we discuss global species discovery of Bradyrhizobium spp. Although recently the number of validly published Bradyrhizobium species is rapidly increasing, their diversity in SSA is not well-represented. We summarize the recent knowledge on species diversity in the Bradyrhizobium yuanmingense lineage to which most SSA isolates belong, and their biogeographic distribution and adaptations. Most indigenous rhizobia appear to differ from species found on other continents. We stress that an as yet hidden diversity may be a rich resource for inoculant development in future. As some species are exceptionally temperature tolerant, they may be potential biofertilizer candidates for global warming scenarios.

Phenotypic, genetic and symbiotic characterization of Erythrina velutina rhizobia from Caatinga dry forest

Erythrina velutina ("mulungu") is a legume tree from Caatinga that associates with rhizobia but the diversity and symbiotic ability of "mulungu" rhizobia are poorly understood. The aim of this study was to characterize "mulungu" rhizobia from Caatinga. Bacteria were obteined from Serra Talhada and Caruaru in Caatinga under natural regeneration. The bacteria were evaluated to the amplification of nifH and nodC and to metabolic characteristics. Ten selected bacteria identified by 16S rRNA sequences. They were tested in vitro to NaCl and temperature tolerance, auxin production and calcium phosphate solubilization. The symbiotic ability were assessed in an greenhouse experiment. A total of 32 bacteria were obtained and 17 amplified both symbiotic genes. The bacteria showed a high variable metabolic profile. Bradyrhizobium (6), Rhizobium (3) and Paraburkholderia (1) were identified, differing from their geographic origin. The isolates grew up to 45°C to 0.51molL-1 of NaCl. Bacteria which produced more auxin in the medium with l-tryptophan and two Rhizobium and one Bradyrhizobium were phosphate solubilizers. All bacteria nodulated and ESA 90 (Rhizobium sp.) plus ESA 96 (Paraburkholderia sp.) were more efficient symbiotically. Diverse and efficient rhizobia inhabit the soils of Caatinga dry forests, with the bacterial differentiation by the sampling sites.

Feasibility of transference of inoculation-related technologies: A case study of evaluation of soybean rhizobial strains under the agro-climatic conditions of Brazil and Mozambique

The soybean-Bradyrhizobium symbiosis can be very effective in fixing nitrogen and supply nearly all plant's demand on this nutrient, obviating the need for N-fertilizers. Brazil has been investing in research and use of inoculants for soybean for decades and with the expansion of the crop in African countries, the feasibility of transference of biological nitrogen fixation (BNF) technologies between the continents should be investigated. We evaluated the performance of five strains (four Brazilian and one North American) in the 2013/2014 and 2014/2015 crop seasons in Brazil (four sites) and Mozambique (five sites). The experimental areas were located in relatively similar agro-climatic regions and had soybean nodulating rhizobial population ranging from ≪ 10 to 2 × 105 cells g-1 soil. The treatments were: (1) NI, non-inoculated control with no N-fertilizer; (2) NI + N, non-inoculated control with 200 kg of N ha-1; and inoculated with (3) Bradyrhizobium japonicum SEMIA 5079; (4) B. diazoefficiens SEMIA 5080; (5) B. elkanii SEMIA 587; (6) B. elkanii SEMIA 5019; (7) B. diazoefficiens USDA 110; (8) SEMIA 5079 + 5080 (only tested in Brazil). The best inoculation treatments across locations and crop seasons in Brazil were SEMIA 5079 + 5080, SEMIA 5079 and USDA 110, with average grain yield gains of 4-5% in relation to the non-inoculated treatment. SEMIA 5079, SEMIA 5080, SEMIA 5019 and USDA 110 were the best strains in Mozambique, with average 20-29% grain yield gains over the non-inoculated treatment. Moreover, the four best performing strains in Mozambique resulted in similar or better yields than the non-inoculated + N treatment, confirming the BNF as an alternative to N-fertilizers. The results also confirm the feasibility to transfer soybean inoculation technologies between countries, speeding up the establishment of sustainable cropping systems.

Cowpea (Vigna unguiculata L. Walp) hosts several widespread bradyrhizobial root nodule symbionts across contrasting agro-ecological production areas in Kenya

Cowpea (Vigna unguiculata L. Walp.) is an important African food legume suitable for dry regions. It is the main legume in two contrasting agro-ecological regions of Kenya as an important component of crop rotations because of its relative tolerance to unpredictable drought events. This study was carried out in an effort to establish a collection of bacterial root nodule symbionts and determine their relationship to physicochemical soil parameters as well as any geographical distributional patterns. Bradyrhizobium spp. were found to be widespread in this study and several different types could be identified at each site. Unique but rare symbionts were recovered from the nodules of plants sampled in a drier in-land region, where there were also overall more different bradyrhizobia found. Plants raised in soil from uncultivated sites with a natural vegetation cover tended to also associate with more different bradyrizobia. The occurrence and abundance of different bradyrhizobia correlated with differences in soil texture and pH, but did neither with the agro-ecological origin, nor the origin from cultivated (n = 15) or uncultivated (n = 5) sites. The analytical method, protein profiling of isolated strains by Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS), provided higher resolution than 16S rRNA gene sequencing and was applied in this study for the first time to isolates recovered directly from field-collected cowpea root nodules. The method thus seems suitable for screening isolate collections on the presence of different groups, which, provided an appropriate reference database, can also be assigned to known species.

Genetic Characterization and Diversity of Rhizobium Isolated From Root Nodules of Mid-Altitude Climbing Bean (Phaseolus vulgaris L.) Varieties

The increasing interest in the use of rhizobia as biofertilizers in smallholder agricultural farming systems of the Sub-Saharan Africa has prompted the identification of a large number of tropical rhizobia strains and led to studies on their diversity. Inoculants containing diverse strains of rhizobia have been developed for use as biofertilizers to promote soil fertility and symbiotic nitrogen fixation in legumes. In spite of this success, there is paucity of data on rhizobia diversity and genetic variation associated with the newly released and improved mid-altitude climbing (MAC) bean lines (Phaseolus vulgaris L.). In this study, 41 rhizobia isolates were obtained from the root nodules of MAC 13 and MAC 64 climbing beans grown in upper and lower midland agro-ecological zones of Eastern Kenya. Eastern Kenya was chosen because of its high production potential of diverse common bean cultivars. The rhizobia isolates were characterized phenotypically on the basis of colony morphology, growth and biochemical features. Rhizobia diversity from the different regions of Eastern Kenya was determined based on the amplified ribosomal DNA restriction analysis (ARDRA) of PCR amplified 16S rRNA genes using Msp I, EcoR I, and Hae III restriction enzymes. Notably, native rhizobia isolates were morphologically diverse and grouped into nine different morphotypes. Correspondingly, the analysis of molecular variance based on restriction digestion of 16S rRNA genes showed that the largest proportion of significant (p < 0.05) genetic variation was distributed within the rhizobia population (97.5%) than among rhizobia populations (1.5%) in the four agro-ecological zones. The high degree of morphological and genotypic diversity of rhizobia within Eastern Kenya shows that the region harbors novel rhizobia strains worth exploiting to obtain strains efficient in biological nitrogen fixation with P. vulgaris L. Genetic sequence analysis of the isolates and testing for their symbiotic properties should be carried out to ascertain their identity and functionality in diverse environments.

Distribution and Phylogeny of Microsymbionts Associated with Cowpea (Vigna unguiculata) Nodulation in Three Agroecological Regions of Mozambique

Cowpea derives most of its N nutrition from biological nitrogen fixation (BNF) via symbiotic bacteroids in root nodules. In Sub-Saharan Africa, the diversity and biogeographic distribution of bacterial microsymbionts nodulating cowpea and other indigenous legumes are not well understood, though needed for increased legume production. The aim of this study was to describe the distribution and phylogenies of rhizobia at different agroecological regions of Mozambique using PCR of the BOX element (BOX-PCR), restriction fragment length polymorphism of the internal transcribed spacer (ITS-RFLP), and sequence analysis of ribosomal, symbiotic, and housekeeping genes. A total of 122 microsymbionts isolated from two cowpea varieties (IT-1263 and IT-18) grouped into 17 clades within the BOX-PCR dendrogram. The PCR-ITS analysis yielded 17 ITS types for the bacterial isolates, while ITS-RFLP analysis placed all test isolates in six distinct clusters (I to VI). BLAST_n sequence analysis of 16S rRNA and four housekeeping genes (glnII, gyrB, recA, and rpoB) showed their alignment with Rhizobium and Bradyrhizobium species. The results revealed a group of highly diverse and adapted cowpea-nodulating microsymbionts which included Bradyrhizobium pachyrhizi, Bradyrhizobium arachidis, Bradyrhizobium yuanmingense, and a novel Bradyrhizobium sp., as well as Rhizobium tropici, Rhizobium pusense, and Neorhizobium galegae in Mozambican soils. Discordances observed in single-gene phylogenies could be attributed to horizontal gene transfer and/or subsequent recombinations of the genes. Natural deletion of 60 bp of the gyrB region was observed in isolate TUTVU7; however, this deletion effect on DNA gyrase function still needs to be confirmed. The inconsistency of nifH with core gene phylogenies suggested differences in the evolutionary history of both chromosomal and symbiotic genes.

IMPORTANCE A diverse group of both Bradyrhizobium and Rhizobium species responsible for cowpea nodulation in Mozambique was found in this study. Future studies could prove useful in evaluating these bacterial isolates for symbiotic efficiency and strain competitiveness in Mozambican soils.

African origin of Bradyrhizobium populations nodulating Bambara groundnut (Vigna subterranea L. Verdc) in Ghanaian and South African soils

Flavonoids secreted by legumes play a major role as signal molecules for attracting compatible rhizobia. The aim of this study was to assess and understand the diversity of microsymbionts nodulating Bambara groundnut (Vigna subterranea L. Verdc.) landraces of different seedcoat colours using restriction fragment length polymorphism and phylogenetic analysis. Seedcoat pigmentation of landraces had effect on the diversity of microsymbionts of Bambara groundnut. Even when planted together in one hole, nodulating bradyrhizobia clustered differently. For example, 16S rDNA-RFLP typing of rhizobial samples TUTVSBLM.I, TUTVSCRM.I and TUTVSRDM.I originating respectively from Black, Cream and Red landraces that were co-planted in the same hole at Manga in the Sudano-sahelian savanna, as well as TUTVSCRK.I and TUTVSRDK.I respectively from Cream and Red landraces co-planted at Kpalisogu in the Guinea savanna, revealed different 16S rDNA- RFLP types. Phylogenetic analysis of 16S rDNA, glnII, recA and atpD sequences showed that Vigna subterranea was nodulated specifically by a diverse group of Bradyrhizobium species (e.g. Bradyrhizobium vignae, and a novel group of Bradyrhizobium spp.) in soils from Ghana and South Africa. The recA gene phylogeny showed incongruency with the other housekeeping genes, indicating the possibility of lateral gene transfer and/or recombination events. The grouping of isolates according to symbiotic gene (nifH and nodD) phylogenies revealed inter- and intra-specific symbiotic plasmid transfer and different evolutionary history. The results also showed that a cropping history and physico-chemical environment of soils increased bradyrhizobial diversity in Ghana and South Africa.

Isolation, characterization and selection of indigenous Bradyrhizobium strains with outstanding symbiotic performance to increase soybean yields in Mozambique

Soybean inoculation with effective rhizobial strains makes unnecessary the use of N-fertilizers in the tropics. A frequently reported problem is the failure of the inoculant strains to overcome the competition imposed by indigenous rhizobial populations. The screening of indigenous rhizobia, already adapted to local conditions, searching for highly effective strains for use as inoculants represents a promising strategy in overcoming inoculation failure. The objective of this study was to isolate and characterize indigenous rhizobia and to identify strains that hold potential to be included in inoculant formulations for soybean production, with both promiscuous and non-promiscuous soybean cultivars, in Mozambican agro-climatic conditions. A total of 105 isolates obtained from nodules of promiscuous soybean grown at 15 sites were screened for N2-fixation effectiveness in the greenhouse along with five commercial strains. Eighty-seven isolates confirmed the ability to form effective nodules on soybean and were used for genetic characterization by rep-PCR (BOX) and sequencing of the 16S rRNA gene, and also for symbiotic effectiveness. BOX-PCR fingerprinting revealed remarkable genetic diversity, with 41 clusters formed, considering a similarity level of 65%. The 16S rRNA analysis assigned the isolates to the genera Bradyrhizobium (75%) and Agrobacterium/Rhizobium (25%). Great variability in symbiotic effectiveness was detected among the indigenous rhizobia from Mozambique, with ten isolates performing better than the commercial strain B. diazoefficiens USDA 110, the best reference strain, and 51 isolates with lower performance than all reference strains. Thirteen of the best isolates from the first greenhouse trial were evaluated, along with the five commercial strains, in two promiscuous (TGx 1963-3F and TGx 1835-10E) and one non-promiscuous (BRS 284) soybean cultivars in a second greenhouse trial. In general the promiscous soybeans responded better to inoculation. The 13 isolates were also characterized for tolerance to acidity and alkalinity (pH 3.5 and 9.0, respectively), salinity (0.1, 0.3 and 0.5 mol L-1 of NaCl) and high temperatures (35, 40 and 45 °C) in vitro. Five isolates, three (Moz 4, Moz 19 and Moz 22) belonging to the superclade B. elkanii and two (Moz 27 and Moz 61) assigned to the superclade B. japonicum, consistently showed high symbiotic effectiveness, suggesting that the inoculation with indigenous rhizobia adapted to local conditions represents a possible strategy for increasing soybean yields in Mozambique. Phylogenetic position of the five elite isolates was confirmed by the MLSA with four protein-coding housekeeping genes, dnaK, glnII, gyrB and recA.

Specificity in Legume-Rhizobia Symbioses

Most species in the Leguminosae (legume family) can fix atmospheric nitrogen (N₂) via symbiotic bacteria (rhizobia) in root nodules. Here, the literature on legume-rhizobia symbioses in field soils was reviewed and genotypically characterised rhizobia related to the taxonomy of the legumes from which they were isolated. The Leguminosae was divided into three sub-families, the Caesalpinioideae, Mimosoideae and Papilionoideae. Bradyrhizobium spp. were the exclusive rhizobial symbionts of species in the Caesalpinioideae, but data are limited. Generally, a range of rhizobia genera nodulated legume species across the two Mimosoideae tribes Ingeae and Mimoseae, but Mimosa spp. show specificity towards Burkholderia in central and southern Brazil, Rhizobium/Ensifer in central Mexico and Cupriavidus in southern Uruguay. These specific symbioses are likely to be at least in part related to the relative occurrence of the potential symbionts in soils of the different regions. Generally, Papilionoideae species were promiscuous in relation to rhizobial symbionts, but specificity for rhizobial genus appears to hold at the tribe level for the Fabeae (Rhizobium), the genus level for Cytisus (Bradyrhizobium), Lupinus (Bradyrhizobium) and the New Zealand native Sophora spp. (Mesorhizobium) and species level for Cicer arietinum (Mesorhizobium), Listia bainesii (Methylobacterium) and Listia angolensis (Microvirga). Specificity for rhizobial species/symbiovar appears to hold for Galega officinalis (Neorhizobium galegeae sv. officinalis), Galega orientalis (Neorhizobium galegeae sv. orientalis), Hedysarum coronarium (Rhizobium sullae), Medicago laciniata (Ensifer meliloti sv. medicaginis), Medicago rigiduloides (Ensifer meliloti sv. rigiduloides) and Trifolium ambiguum (Rhizobium leguminosarum sv. trifolii). Lateral gene transfer of specific symbiosis genes within rhizobial genera is an important mechanism allowing legumes to form symbioses with rhizobia adapted to particular soils. Strain-specific legume rhizobia symbioses can develop in particular habitats.

Isolation and characterization of culturable seed-associated bacterial endophytes from gnotobiotically grown Marama bean seedlings

Marama bean (Tylosema esculentum) is an indigenous non-nodulating legume to the arid agro-ecological parts of Southern Africa. It is a staple food for the Khoisan and Bantu people from these areas. It is intriguing how it is able to synthesize the high-protein content in the seeds since its natural habitat is nitrogen deficient. The aim of the study was to determine the presence of seed transmittable bacterial endophytes that may have growth promoting effects, which may be particularly important for the harsh conditions. Marama bean seeds were surface sterilized and gnotobiotically grown to 2 weeks old seedlings. From surface-sterilized shoots and roots, 123 distinct bacterial isolates were cultured using three media, and identified by BOX-PCR fingerprinting and sequence analyses of the 16S rRNA and nifH genes. Phylogenetic analyses of 73 putative endophytes assigned them to bacterial species from 14 genera including Proteobacteria (Rhizobium, Massilia, Kosakonia, Pseudorhodoferax, Caulobacter, Pantoea, Sphingomonas, Burkholderia, Methylobacterium), Firmicutes (Bacillus), Actinobacteria (Curtobacterium, Microbacterium) and Bacteroidetes (Mucilaginibacter, Chitinophaga). Screening for plant growth-promoting activities revealed that the isolates showed production of IAA, ACC deaminase, siderophores, endoglucanase, protease, AHLs and capacities to solubilize phosphate and fix nitrogen. This is the first report that marama bean seeds may harbor endophytes that can be cultivated from seedlings; in this community of bacteria, physiological characteristics that are potentially plant growth promoting are widespread.

Bradyrhizobium kavangense sp. nov., a symbiotic nitrogen-fixing bacterium from root nodules of traditional Namibian pulses

Eight strains of symbiotic bacteria from root nodules of local races of cowpea (Vigna unguiculata) and Bambara groundnut (Vigna subterranea) grown on subsistence farmers’ fields in the Kavango region, Namibia, were previously characterized and identified as a novel group within the genus Bradyrhizobium. To clarify their taxonomic status, these strains were further characterized using a polyphasic approach. In phylogenetic analysis of the 16S rRNA gene sequence the novel group was most closely related to Bradyrhizobium iriomotense EK05T and Bradyrhizobium ingae BR 10250T, and to ‘Bradyrhizobium arachidis’ CCBAU 051107 in the ITS sequence analysis. Phylogenetic analysis of concatenated glnII-recA-rpoB-dnaK sequences placed the strains in a lineage distinct from named species of the genus Bradyrhizobium. The species status was validated by results of DNA–DNA hybridization. Phylogenetic analysis of nifH and nodC genes placed the novel strains in a group with ’B. arachidis’ CCBAU 051107. The combination of phenotypic characteristics from several tests including carbon source utilization and antibiotic resistance could be used to differentiate representative strains from recognized species of the genus Bradyrhizobium. Novel strain 14-3T induces effective nodules on Vigna subterranea, Vigna unguiculata, Arachis hypogaea and Lablab purpureus. Based on the data presented, it is concluded that the strains represent a novel species of the genus Bradyrhizobium, for which the name Bradyrhizobium kavangense sp. nov. is proposed. The type strain is 14-3T [ = DSM 100299T = LMG 28790T = NTCCM 0012T (Windhoek)]. The DNA G+C content of strain 14-3T is 63.8 mol% (T m ).

Bradyrhizobium subterraneum sp. nov., a symbiotic nitrogen-fixing bacterium from root nodules of groundnuts

Seven strains of symbiotic bacteria from root nodules of local races of Bambara groundnut (Vigna subterranea) and peanuts (Arachis hypogaea) grown on subsistence farmers' fields in the Kavango region, Namibia, were previously characterized and identified as a novel group within the genus Bradyrhizobium. To corroborate their taxonomic status, these strains were further characterized using a polyphasic approach. All strains possessed identical 16S rRNA gene sequences with Bradyrhizobium yuanmingense CCBAU 10071T being the most closely related type strain in the 16S rRNA gene phylogenetic analysis, and Bradyrhizobium daqingense CCBAU 15774T in the ITS sequence analysis. Phylogenetic analysis of concatenated glnII-recA-rpoB-dnaK placed the strains in a highly supported lineage distinct from named species of the genus Bradyrhizobium, most closely related to Bradyrhizobium yuanmingense CCBAU 10071T. The species status was validated by results of DNA–DNA hybridization. Phylogenetic analysis of nifH genes placed the novel strains in a group with nifH of ‘Bradyrhizobium arachidis’ CCBAU 051107 that also nodulates peanuts. The combination of phenotypic characteristics from several tests including carbon source utilization and antibiotic resistance could be used to differentiate representative strains from recognized species of the genus Bradyrhizobium. Novel strain 58 2-1T induced effective nodules on V. subterranea, Vigna unguiculata and A. hypogaea, and some strains on Lablab purpureus. Based on the data presented, we conclude that our strains represent a novel species for which the name Bradyrhizobium subterraneum sp. nov. is proposed, with 58 2-1T [ = DSM 100298T = LMG 28792T = NTCCM0016T (Windhoek)] as the type strain. The DNA G+C content of strain 58 2-1T was 64.7 mol% (T m).