Electronic Journal of Polish Agricultural Universities (EJPAU) founded by all Polish Agriculture Universities presents original papers and review articles relevant to all aspects of agricultural sciences. It is target for persons working both in science and industry,regulatory agencies or teaching in agricultural sector. Covered by IFIS Publishing (Food Science and Technology Abstracts), ELSEVIER Science - Food Science and Technology Program, CAS USA (Chemical Abstracts), CABI Publishing UK and ALPSP (Association of Learned and Professional Society Publisher - full membership). Presented in the Master List of Thomson ISI.
Volume 22
Issue 4
DOI:10.30825/5.ejpau.180.2019.22.4, EJPAU 22(4), #03.
Available Online: http://www.ejpau.media.pl/volume22/issue4/art-03.html


Andre L. Bongo, Stanisław J. Pietr
Laboratory of Agricultural Microbiology, Department of Plant Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland



Among Fabaceae cowpea (Vigna unguiculata (L.) Walp.), common bean (Phaseolus vulgaris L.), and soybean (Glycine max L. Merry) are the major pulse crops grown in Sub-Saharan Africa (SSA), however, the yield remains very low due to the low efficacy of biological nitrogen fixation (BNF) process. Improvement of the yields is possible only in the presence of an efficient BNF rhizobia strains that can be either native or exogenous introduced as a seed inoculants capable to establish effective symbiotic interactions with their legume crops. There are very few studies targeting the phenotypic and genetic characterization of effective indigenous symbiotic rhizobia of Fabaceae plants in Sub-Saharan Africa ecozones. This review describes nearly 100 BNF rhizobia out of about 4000 indigenous strains isolated from soils and root nodules of pulses from different SSA ecozones. Most of these isolates outperformed reference strains and most of the commercial inoculants. The majority of the described indigenous isolates effectively nodulating common bean roots were identified as Rhizobium etli, R. leguminosarum, R. leguminosarum sv. phaseoli and R. tropici, whereas potent diazotrophs symbionts of soybean and cowpea were identified as Bradyrhizobium elkanii and B. japonicum. In addition, some strains of B. yuamingense were found to be beneficial as inoculates for cowpea along with several unidentified isolates effective as seed inoculants of common bean, soybean, and cowpea. Overall, this review provides a first comprehensive assessment of biodiversity of indigenous symbiotic rhizobia in legume plants grown in SSA and discusses their potential agricultural applications.

Key words: biodiversity, rhizobia, Sub-Saharan Africa, Fabaceae crops.


Fabaceae (Lindl. ) family with around 19, 000 species is one of the largest families of plants worldwide and among them soybean (Glycine max L. Merry), peanut (Arachis hypogaea L. ), and common bean (Phaseolus vulgaris L.) are three the most important crops world wide. However, in Sub-Saharan Africa (SSA) the cowpea (Vigna unguiculata (L.) Walp.), the native african pulse crop, is the most frequently cultivated beinggrown on about 8 million hectares annually mainly in Nigeria and Niger [14]. The common beanand soybean, non-native pulse crops, are the second and third most important in SSA beingcultivated on about 4 million hectares and on above 2 million hectares annually, respectively [14]. Kenya is considered the major producer of common bean and South Africa, Nigeria as well as Zambia are the leading soybean producers in SSA in recent years [14]. Additionally, among more than 30 species described in the genus Phaseolus beside common bean, only scarlet runner bean (P. coccineus L.), tepary bean (P. acutifolius A. Gray), lima bean (P. lunatus L.) and year bean (P. polyanthus Greenman) are cultivated in tropical, subtropical and temperate regions [30, 31]. Fabaceae family plants establish a mutualistic relationship with bacteria, collectively known as rhizobia, inducing root nodules where biological nitrogen fixation (BNF) takes place [22]. According to Lindström et al. [29], Fabaceae-rhizobia symbioses are one of the main stabilizers of the nitrogen cycle in the tropics and subtropics. Currently, one of the major goals is the evaluation of biodiversity of indigenous symbiotic diazotrophs which will support development of effective inoculants suitable for low input cropping system through the cultivation of Fabaceae for being cheaper for farmers and furthermore for being friendly to the environmental system [2]. The inoculation technology using specific indigenous rhizobia have shown positive results and is successful and widespread practice in Australia, Europe, North and South America [32, 58] but in Africa, the inoculation technology is rarely used and this practice is relatively new for most SSA countries. The first reports of indigenous symbiotic diazotrophs nodulating Fabaceae trees, pastures, and grain in SSA was published in 1935 by McDonald [33] who described the phenomenon of cross-inoculation with indigenous rhizobia in important legume crops. Later studies from Kenya described by Bumpus [8] and Souza [51] shown that only indigenous Fabaceae species like Crotalaria incana (L.), Dolichos lablab (L.), and Trifolium semipilosum (Fres.) formed effective natural nodules in those areas where these species are normally cultivated or occur in wilderness and inoculation did not benefit its growth. Souza [51] observed as well, effective natural nodulation on perennial soybean (Glycine javanica L.). Mwenda et al. [38] noted that while these early studies laid important groundwork, they did not quantify the activity of BNF, the abundance and biodiversity of indigenous rhizobia in soils of SSA ecozones and the overarching effects on crop yield.

This review describes studies examining both biodiversity of indigenous BNF rhizobia in different SSA ecozones. Such studies are rare in comparison with the plethora of investigations reported from both North and South America, Asia, and Europe. The aim of this review was to summarize the study of the abundance and diversity of rhizobia in soils of SSA ecozones. For this purpose, we analyzed, articles that provide the results of studies that focus on the mentioned above aims and we organized it considering the SSA ecozone as was described by Plant Taxonomic Database Standards No. 2 [19] and were illustrated on https://en. wikipedia. org/wiki/Tropical_Africa (2019).


Comprehensive studies of biodiversity in the last two decades have identified several effective indigenous strains of rhizobia as well as have reported surprising benefits of the use of rhizobia for Fabaceae crops in SSA countries. A comprehensive summary of these investigations presented 107 BNF rhizobia, out of more than 4000 indigenous strains isolated from the SSA ecozones, which were found to be able to establish effective symbiotic relationships and improve the growth and yield of major Fabaceae pulse crops (Tab. 1).

Biodiversity of rhizobia in Northeast, West, and East Tropical Africa ecozone
Most studies of native rhizobia in Northeast Tropical ecozone have been reported from Ethiopia. Wolde-Meskel et al. [57] described the study of 16S rRNA gene sequences of 195 indigenous rhizobia isolated from eight native and six introduced legumes tree, as well as three introduced grain legumes in Southern Ethiopia. They found that 49, 40, 20, and 78 isolates were closely related to Rhizobium (R. etli, R. leguminosarum, R. mongolense, R. giardinii and R. huautlense, and possibly four novel species), to Bradyrhizobium (B. elkanii, B. japonicum, B. liaoningense, B. yuanmingense and several of unrecognized yet taxa), to Mesorhizobium (M. chacoense, M. plurifarium, and possibly one novel species), and to Ensifer (E. fredii, E. meliloti, E. medicae, E. saheli, E. adhaerens) genus, respectively (Tab. 1). They also pointed out that many of possible novel species of rhizobia were isolated from previously uninvestigated indigenous woody legumes. Aserse et al. [5] using MLSA, observed that rhizobia nodulating common bean in soils of Ethiopia were closely related to R. phaseoli, R. etli and the novel group of Rhizobium sp. While few strains were considered sporadic symbionts for common bean and were closely related to R. leucaenae and R. giardinii. Therefore, they observed that several strains in the concatenated tree showed 99–100% partial 16S rRNA sequences similarity to R. etli CFN 42T as major species in the R. leguminosarum complex. Authors noted that most of the isolated rhizobia nodulating common bean had very similar nifH gene sequences. Study of Aserse et al. [5] gave support to conclusions of Segovia et al. [50] who reported that species R. phaseoli, also known as R. leguminosarum sv phaseoli, first identified in Europe, might have arisen from the addition by horizontal transfer of the symbiotic plasmid from Rhizobium sp. type I to R. leguminosarum chromosome. Common bean in West, East and South Tropical Africa, according to Diouf et al. [11] is naturally nodulated by the same species of rhizobia as those nodulating common bean at its site of origin. Therefore, authors supposed that common bean symbiotic rhizobia are cosmopolitan, and was co-introduced with common bean seeds. This hypothesis was also supported by Aserse et al. [5] who believe that Ethiopian soils were also colonized by R. phaseoli (R. leguminosarum sv phaseoli) after introduction of common bean into agriculture practice. Therefore, these native rhizobia may have acquired molecular characteristics of R. phaseoli from the introduced R. etli sv. phaseoli. Discrepancy argument with Diouf et al. [11] and Aserse et al. [5] was reported by Beyene et al. [6]. According to Beyene et al. [6] based on MLEE and 16S rDNA sequences similarities, rhizobia nodulating common bean in Ethiopia were related to R. leguminosarum or R. etli. Therefore, they concluded that it is unlikely that rhizobia nodulating common bean in Americas or Europe colonized soils of Ethiopia, because they did not identify R. tropici, R. gallicum, and R. giardinii that occur very often in soils of these continents. According to Beyene et al. [6], it is not completely clear how R. leguminosarum in Ethiopian soils acquired the determinants for nodulation of common bean, nor it is apparent how R. leguminosarum gained the 16S rRNA gene sequence characteristic of R. etli. Other studies from this ecozone had also demonstrated that indigenous strains isolated from cowpea (Vigna unguiculata (L.) Walp.), broad bean (Vicia faba L.) and lentil (Lens culinaris Medik.) were mostly identified as B. japonicum, B. yuanmingense, R. leguminosarum or R. etli [53, 57].

Most of reports describing native rhizobia in East Tropical Africa ecozone were based on studies of Kenyan soils. Anyango et al. [3] observed that indigenous rhizobia nodulating common bean in acid soil (pH ≤4. 5) were predominantly close to R. tropici, while species from the majority of soils with acidity above pH ≥6. 8 showed phenotypically similarity to R. etli. However, a relevant research in Kenya concerning the genetic diversity and symbiotic status of 41 indigenous bacteria isolated from root nodules of 13 trap host tree and herbaceous Fabaceae plants done by Odee et al. [44] shown that BNF bacteria were identified with 99–100% similarities as B. elkanii, B. japonicum, Mesorhizobium sp., R. leguminosarum, R. tropici IIBand Sinorhizobium sp. Otherwise, in discrepancy with Anyango et al. [3] findings, Odee et al. [44] observed that indigenous rhizobia related to R. tropici were isolated from soils characterized by wide range soil acidity including alkaline condition. Examination of 185 isolates from common bean conducted by Mwenda [37] indicated that 65% of isolates effectively nodulating common bean were putative novel taxa where others 45% isolates were identified as R. etli. R. leucaenae, R. paranaense, R. phaseoli and R. sophoriradicis. The putative novel taxa had recA sequences with less than 96. 6% identity to known Rhizobium strains. Also, later studies of biodiversity of rhizobia that nodulate common bean in Kenyan soils described by Mwenda et al. [39] which were genotyped stepwise by the analysis of genomic DNA fingerprints, PCR-RFLP and 16S rRNA, atpD, recA, and nodC gene sequences revealed at least six Rhizobium genospecies with most of the isolates belonging to Rhizobium phaseoli and a possibly novel Rhizobium species. Similarly like in Ethiopia [5] as well as like in earlier studies from Kenya [37] Mwenda et al. [39] sporadically identified R. leucaenae. Moreover, they [39] confirmed earlier reported about infrequent occurrence in Kenyan soils of R. paranaense and R. sophoriradicis as well as identified among isolates R. aegyptiacum. Also, Wekesa et al. [56] identified, among 24 isolates from nodules of common bean cultivated in western Kenya, but three strains only were closely related to Rhizobium sp. Aforementioned, papers have revealed that in Kenyan soils harbour site specific native rhizobia nodulating common bean. The diversity of BNF rhizobia in soils in East Tropical Africa ecozone was described by Onyango et al. [45] who identified BNF symbionts isolated from bambara groundnut (Vigna subterranea (L.) Verdc.). They described thirteen 16S rRNA sequences closely related to B. japonicum, R. leguminosarum, R. tropici, R. phaseoli, Burkholderia tuberum and Burkholderia phymatum (Tab. 1). The effect of land-use type on the diversity of indigenous rhizobia in Kenyan soils was evaluated by Mwangi et al. [36] with siratro (Macroptilium atropurpureum (DC.) Urb.) as a trap plant and the highest richness of five genera was found in indigenous forest soils (Bradyrhizobium sp., Rhizobium sp., Sinorhizobium sp., Agrobacterium sp., Herbaspirillum sp. ).

The diversity of BNF of cowpea in West Tropical Africa ecozone were described in Ghana soils by Pule-Meulenberg et al. [61] and in Senegal soils by Krasova-Wade et al. [25]. They used several cultivars of cowpea as a trap plant. They found that all bacteria nodulating cowpea belonged to the genus Bradyrhizobium as well as they suggested the occurrence of a new Bradyrhizobium species unique for this region. Krasova-Wade et al. [25] clustered selected isolates with B. japonicum, B. liaoningense, B. elkanii, and Bradyrhizobium sp. genospecies but Pule-Meulenberg et al. [61] clustered isolates with B. yuanmingense and with Bradyrhizobium sp. genospecies, only. Additionally, several strains isolated from cowpea nodules in Senegal by Krasova-Wade et al. [61] were very closely related to indigenous species isolated from nodules of Faidherbia albida ( (Delile) A. Chev.) collected in Senegal [13].

Biodiversity of rhizobia in South Tropical and Southern Africa ecozones
The majority of recent studies on the diversity of rhizobia in these ecozones mainly focused on the biodiversity of diazotrophic symbiotic bacteria of soybean. Studies reported by Bothaet al. [7] and by Naamala et al. [40] in South Africa as well as by Chibeba et al. [9] and by Gyogluu et al. [17] in Mozambique showed that most of the isolated rhizobia were related to B. elkanii and some to B. japonicum (Table 1). In addition to the species mentioned above Naamala et al. [40] based on phylogenetic analysis of 16S rDNA, nifH, atpD, gyrB, and glnII genes, identified isolated strains with 97. 3 to 100% of similarities to Bradyrhizobium genospecies. However, several isolates described by aforementioned researchers with low relatedness to known type species of Bradyrhizobium are probably novel species nodulating promiscuous soybean cultivars in this region (Table 1).

Table 1. Identified indigenous BNF strains nodulating Fabaceae plants from different SSA ecozones and their efficacy as seed inoculants of major cultivated legume plants under field or greenhouse conditions
Host plant Country Strain, Original signature Efficacy * Closest reference species Ref.
Phaseolus vulgaris L. Angola 43 2-1 + Rhizobium sp. 15
South Africa KM5 N. T R. leguminosarum 28
KJ3 N. T R. etli
KB1 N. T R. tropici
KM17 N. T R. leguminosarum bv phaseoli
KB5 N. T Rhizobium sp.
HBR9, HBR10, HBR11 + R. phaseoli ATCC 14482 5
HBR3, HBR7, HBR23 +++ N. R **
HBR4, HBR24 + R. etli CFN 42
HBR22, HBR42 + R. leguminosarum USDA2370
HBR21 + R. giardinii
HBR12 + R. leucaenae CFN 299
Gi7, DZ6-9, DZ6-14 N. T R. etli CFN 42 6
AC73d N. T R. huautlense 57
AC70c N. T B. liaoningense
Gambia ISRA582, ISRA350 N. T R. tropici CIAT 899 11
Senegal ISRA30 N. T R. etli CFN42
Kenya NAK458 ++ R. etli CFN42 37
NAK239 +++ R. phaseoli
NAK104 ++ R. leucaenae USDA9039T
NAK349 ++ R. paranaense
NAK220 ++ R. gallicum
NAK266 ++ R. anhuiense
NAK287 +++ R. laguerreae
NAK387 ++ R. saphoriradicis
ELM3, ELM4, ELM5, ELM8 +++ N. R 24
KSM001, KSM003, KSM005, MMUST005 +++ N. R 23
KIGALI 3II +++ N. R 35
Rwanda 4906 +++ N. R 26
1402, 6701, HRw11, HRw12, HRw41, 4405, RGB2, HRw46 ++ N. R
Tanzania NR12, NR13 +++ N. R 41
Glycine max L. South Africa TUTL14. 10. 9 N. T B. japonicum USDA6 40
TUTMP11. 7 N. T B. elkanii USDA 76
TUTMP2. 9 N. T B. yuanmingense CCBAU
TUTGP10 N. T B. diazoefficiens USDA 110
TUTL12. 20. 7, TUTMP19. 10, TUTMP18. 6 N. T Bradyrhizobium sp.
B3d, B6d ++ B. japonicum USDA 6 7
B2d, B3b ++ B. elkanii CB 1809
B4b ++ B. elkanii USDA 31
Mozambique Moz 4, Moz 19, Moz 22, Moz 39, Moz 17 +++ B. elkanii USDA 76T 9
Moz 27, Mo z61 +++ B. japonicum USDA 6T
D. R. Congo NAC10, NAC22, NAC40, NAC75 +++ N. R 43
Vigna unguiculata L. Angola 50 5-2 + Rhizobium sp. 15
Namibia 21 1-1 + B. yuanmingense
Ethiopia AC64a N. T B. yuanmingense 57
AC62a N. T B. japonicum
AC56b N. T R. etli
Botswana R3 N. T B. yuanmingense CCBAU10071T 52
R5 N. T B. elkanii USDA 76T
Mozambique TUTVU33, TUTVU67 N. T Neorhizobium galegae 10
TUTVU50, TUTVU31 N. T R. tropici
TUTVU40 N. T R. pusense
TUTVU44, TUTVU13 N. T B. yuanmingense
TUTVU21, TUTVU22 N. T B. pachyrhizi
TUTVU5 N. T B. arachidis
Vigna subterranea L. Namibia 55 1-1 + B. daqingense 15
37 1-1 + B. yuanmingense
South Africa TUTAHSA67 N. T B. guangdongense 20
TUTAHSA4 N. T B. japonicum
TUTAHSA27 N. T B. pachyrhizi
TUTAHSA87 N. T R. tropici
Kenya BAMKbay8 +++ Burkholderia sp. 45
BAMKis1 ++ R. tropici CIAT899
BAMsp3 +++ Burkholderia tuberum STM4287
BAMKis4 +++ Burkholderia phymatum
BAMKis12 +++ Bradyrhizobium sp.
BAMKis8 +++ Bradyrhizobium sp.
Vicia faba L. Ethiopia NSFBR-36, NSFBR-12, NSFBR. 30 +++ N. R 4
Lens culinaris Medik Ethiopia Lt29, Lt5 +++ R. etli USDA9032T 53
Lt87, Lt136 ++ R. leguminosarum USDA2372T

BNF indigenous rhizobia isolated from root nodules of common beanand runner bean cultivated in South Africa was assessed by Lindeque [28] who demonstrated that the majority of 18 isolates from common bean were similar to R. leguminosarum, R. tropici and others were identified as R. etli, R. leguminosarum bv phaseoli or R. lusitanum. The author observed that 50% of isolated strains from nodules of runner bean were similar to Burkholderia unamae and others were identified as B. tropicalis, R. leguminosarum and R. tropici while the remaining isolates was not able to be assigned to a specific genus or species.

Biodiversity of BNF rhizobia in soils of Southern Africa ecozone (Botswana and South Africa) nodulating cowpea and/or peanut were described by Law et al. [27], Pule-Meulenberg et al. [47], and Steenkamp et al. [52]. All mentioned above later reports [27, 47, 52] noted that nitrogen-fixing rhizobia effectively nodulation cowpea belonged to the genus Bradyrhizobium. Although, earlier report of Mpepereki et al. [34] claim to have isolated both bradyrhizobia (slow-growing) and rhizobia (fast-growing) from root nodules of cowpea South Tropical ecozone soils (Zimbabwe). Studies of bradyrhizobia biodiversity isolated from cowpea and peanut in Botswana and South Africa using the combined sequences for the core genome genes shown that the majority of the isolates was separated into unique lineages that most likely represent novel Bradyrhizobium species [27, 47, 52]. Mentioned above researchers found that several isolated genotypes from cowpea were also conspecific with B. yuanmingense, with B. elkanii and with Bradyrhizobium sp. genospecies like in Senegal and Ghana but isolates grouped with B. japonicum were described by Law et al. [27] only. The study of Law et al. [27] and Pule-Meulenberg et al. [47] suggested that isolated indigenous genotypes represented a novel Bradyrhizobium species are site-specific and underscoring the greater Bradyrhizobium biodiversity in for Southern Africa ecozone soils in comparison with others SSA ecozones.

Studies of biodiversity of symbiotic diazotrophs in South Tropical ecozone are rarely available. Grönemeyeret al. [15] isolated rhizobia from nodules of local varieties of the pulses cowpea, Bambara groundnut, peanut, hyacinth bean (Lablab purpureus (L.) Sweet) and common bean in the Okavango river basin in the area of Angola and Namibia and among 91 isolates 56 were found to be BNF rhizobia. They reported a striking geographical distribution. B. pachyrhizi dominated at sampling sites in Angola which were characterized by acid soils and a semi-humid climate but isolates from the semi-arid sampling sites in Namibia were more diverse with most of them being related to B. yuanmingense and B. daqingense. In addition, several isolates were related to B. jicamae, B. lablabi and B. iriomotense, while only one isolate was phylogenetically close to B. elkanii. Later survey done in Mozambique, based on isolated ninety-nine rhizobia nodulating cowpea showed alignment with Rhizobium and Bradyrhizobium genus [10]. Authors revealed a group of highly diverse and adapted cowpea nodulating microsymbionts which included Bradyrhizobium pachyrhizi, Bradyrhizobium arachidis, B. yuanmingense and one novel sequence Bradyrhizobium sp., as well as some isolates were similar to Rhizobium tropici, Rhizobium pusense and Neorhizobium galegae. It is noticeable that none of the isolates from the indigenous pulses described by the aforementioned reports, were grouped with B. canariense, or excluding the isolates from South Africa, with B. japonicum.


Summarizing aforementioned studies it is noticeable that rhizobia and bradyrhizobia diversity in SSA ecozones is affected by different factors such as soil acidity, land use system, geographic region as well as by the occurrence of native legume plants [eg. 15, 18, 38, 46, 47, 64]. Several species of BNF microsymbionts nodulating Fabaceae crops found in of SSA soils were also isolated from root nodule of the same pulse crops cultivated on others continents [e. g. 1, 21, 54]. The rhizobia nodulating cowpea, the native african pulse crop, were mostly identified as B. yuanmingense, B. liaoningense, B. elkanii, R. tropici or as R. pusence and rarely as a B. japonicum but several isolates probably represent novel Bradyrhizobium species were also isolated [e. g. 10, 25, 40, 47, 52] (Tab. 1) like B. kavangense, B. namibiense, B. subterraneum, B. vignae and "B. shewense" recently listed by Grönemeyer and Reinhold-Hurek [16].

Rhizobia nodulating effectively common bean were mostly identified as Rhizobium etli, R. leguminosarum, R. phaseoli or similar to R. tropici and infrequently as R. paranaense, R. leucaenae, R. sophoriradicis or R. aegyptiacum as well as it is also noticeable that soils of SSA harbouring native rhizobia differed by site, which formed phylogenetic clusters distinct from known lineages [e. g. 3, 5, 6, 11, 37, 39, 44, 50, 56] (Table 1) . Moreover, occurrence of isolates nodulating common bean closely related to R. giardinii, R. tropici, and R. gallicum, which aretypical for Americas and Europe in SSA soils is questionable [6].

The most commonly isolated species effectively nodulating soybean were B. japonicum and B. elkanii as well as several effective isolates nodulating promiscuous soybean cultivars are probably novel species of Bradyrhizobium in SSA ecozones [e. g. 7, 9, 13, 17, 40] (Table 1). It was noticeable that several researchers have isolated a number of unidentified and putative new species, mainly related to the genus Bradyrhizobium and Rhizobium, nodulating pulse crops in SSA which were highly diverse and grouped into separate clusters geographically specific and able to nodulate in association with common bean [5, 24, 26, 28, 35, 37, 42], cowpea [10, 25, 40, 47, 52], soybean [7, 9, 11, 40], and runner bean [28]. It is important to note that most of the unidentified rhizobia that nodulate Fabaceae crops do not bel1ong to “classic” rhizobia and the number of such isolates has considerably increased in the last years. Moreover, recently Chidebe et al. [10] described isolate representative the new genera Neorhizobium nodulating cowpea in Mozambique. Based on presented papers in this review which described a wide phylogenetic diversity of rhizobia isolated from a small number of Fabaceae in SSA [e. g. 44, 45, 57] as well as taking into account that among Fabaceae roughly hundreds of species are considered native in Southern Africa [55] we could assume that extensive studies will reveal the occurrence of new rhizobia genera and species in Sub-Saharan Africa ecozones as well we can expect a significant variety of effective BNF microsymbions for all SSA ecozones not only in Southern Africa ecozone as was suggested by Pule-Meulenberg [48]. The recent review of diversity of bradyrhizobia in SSA presented by Grönemeyer and Reinhold-Hurek [16] notes that most of described species originates from South America and other regions, including large number from China, but only five species from SSA have been published. Fact that some genera as well as species of rhizobia and bradyrhizobia have not been yet isolated in SSA ecozones could be explained by a lack of comprehensive studies of Fabaceae plants in most of SSA ecozones as well as by the fact that new genera and new rhizobia are recognized recently and were not taken into consideration in earlier studies.

The studies presented in this review allow us to extend hypothesis regarding the origin of the symbiotic BNF rhizobia of common bean presented by Mwenda [37] also for others introduced grain Fabaceae crops like soybean and peanut in SSA soils. We strongly corroborate Mwenda’s [37] argument that rhizobia and bradyrhizobia were transferred with crops from the regions of their origin and production and/or were introduced after the crop as seed inoculants. This thesis is supported by the fact that species nodulating common bean (e. g. R. etli, R. phaseoli, R. tropici, R. paranaense) , soybean (e. g. B. japonicum, B. elkanii), broad bean (e. g. R. etli, R. leguminosarum) and groundnut (e. g. B. yuanmingense, B. elkanii) were closely related to speciesreported from the regions of their origin and major production (Asia, North and South Americas) [5, 31, 49]. The fact that numerous indigenous isolated rhizobia from virgin soils of SSA ecozones without a history of grain legume cultivation were not identified also give strong support to the hypothesis of Mwenda et al. [38] that such strains harbor symbiotic genes corresponding to symbiovars known to nodulate not only common bean likewise others grain legume crops. Moreover, several native Bradyrhizobium species isolated in SSA nodulating mainly cowpea and native legume plants may produce highly differentiated nodulation factors, which potentially represent an important adaptation enabling nodulation of a great variety of legumes inhabiting the African continent [52].


Our review found that the majority of studies in SSA ecozones were performed in Kenya, Ethiopia and South Africa and reported the noticeable biodiversity of BNF rhizobia species nodulating main legume crops (G. max, P. vulgaris, V. unguiculata) in SSA ecozones. Moreover, it is also noticeable that many of the rhizobia isolated from a wide range of previously uninvestigated indigenous legumes for which SSA being the center of origin had novel 16S rRNA gene sequences and were phylogenetically diverse. Aforementioned, studies of screening and identification of indigenous symbiotic diazotrophs revealed the occurrence of noticeable site specific biodiversity of BNF bradyrhizobia and rhizobia nodulating effectively Fabaceae crops. These studies shows that the characterization of symbionts of unexplored legumes growing in previously unexplored biogeographical areas will reveal additional diversity. Furthermore, a survey of the diversity of nodulating BNF bacteria from SSA ecozones indicates a huge potential for selection of rhizobia strains establishing effective relationships with Fabaceae plants specific for each agro-environmental ecozone in SSA region. We could predict a significant increase in new rhizobia, which could be isolated and identified from soils of SSA ecozones. However, the real biodiversity and tolerance to major environmental factors of rhizobia nodulating Fabiaceae crops in different SSA ecozones is difficult to assess due to the fact that few studies focus on this problem. The selection and identification of strains, especially tolerant to soil acidity, with efficient symbiotic performance may be a strategy to improve Rhizobium-legume symbiosis and crop yield in SSA ecozones. This review showed that more and profound studies are necessary to expand our knowledge of abundance, the biodiversity of indigenous rhizobia in soils of SSA ecozones as well as the level of knowledge of symbiotic effectiveness of pulses in SSA for creating a valuable biological resource for supporting the development of sustainable agriculture in Sub-Saharan Africa.


This work was supported by Scholarship of the Ignacego Łukasiewicza Foundation of NAWA (National Agency for Academic Exchange of Poland) for Andre L. Bongo.


  1. Amarger N., Macheret V., Laguerre G., 1997. Rhizobium gallicum sp. nov. and Rhizobium giardinii sp. nov., from Phaseolus vulgaris Nodules. International Journal of Systematic Bacteriology, 47, 4, 996–1006.
  2. Anglade J., Billen G., Garnier J., 2015. Relationships for estimating N2 fixation in legumes: incidence for N balance of legume-based cropping systems in Europe. Ecosphere, 6, 3, 1–37. DOI: 10. 1890/ES14-00353. 1
  3. Anyango B., Wilson K. J., Beynon J. L., Giller K., 1995. Diversity of rhizobia nodulating Phaseolus vulgaris L. in two Kenyan soils with contrasting pHs. Applied and Environmental Microbiology, 61, 11, 4016–4021.
  4. Argaw A., 2012. Characterization of Symbiotic Effectiveness of Rhizobia Nodulating Faba bean (Vicia faba L.) Isolated from Central Ethiopia. Research Journal of Microbiology, 7, 6, 280–296. DOI: 10. 3923/JM. 2012. 280. 296
  5. Aserse A. A., Räsänen L. A., Assefa F., Hailemariam A., Lindström K., 2012. Phylogeny and genetic diversity of native rhizobia nodulating common bean (Phaseolus vulgaris L.) in Ethiopia. Systematic and Applied Microbiology, 35, 2, 120–131. DOI: 10. 1016/J. SYAPM. 2011. 11. 005
  6. Beyene D., Kassa S., Ampy F., Asseffa A., Gebremedhin T., van Berku P., 2004. Ethiopian soils harbor natural populations of rhizobia that form symbioses with common bean (Phaseolus vulgaris L.). Archives of Microbiology 181, 2, 129–136. DOI: 10. 1007/s00203-003-0636-2
  7. Botha W. J., Jaftha J. B., Bloem J. F., Habig J. H., Law I. J., 2004. Effect of soil Bradyrhizobia on the success of soybean inoculant strain CB 1809. Microbiological Research 159, 3, 219–231. DOI 10. 1016/J. MICRES. 2004. 04. 004
  8. Bumpus E. D., 1957, Legume nodulation in Kenya. East African Agricultural and Forestry Journal, 23, 2, 91–99.
  9. Chibeba A. M., Kyei-Boahen S., Guimarăes M. F., Nogueira M. A., Hungria M., 2017. Isolation, characterization, and selection of indigenous Bradyrhizobium strains with outstanding symbiotic performance to increase soybean yields in Mozambique. Agriculture, Ecosystems and Environment Journal, 246, 291–305. DOI: 10. 1016/J. AGEE. 2017. 06. 017
  10. Chidebe I. N., Jaiswal S. K., Dakora F. D., 2017. Distribution and phylogeny of microsymbionts associated with cowpea (Vigna unguiculata) nodulation in three agro-ecological regions of Mozambique. Applied and Environmental Microbiology, 84, 2e01712-17. DOI: 10. 1128/AEM. 01712-17
  11. Diouf A., Lajudie P., Neyra M., Kersters K., Gillis M., Martinez-Romero E., Gueye M., 2000. Polyphasic characterization of rhizobia that nodulate Phaseolus vulgaris in West Africa (Senegal and Gambia). International Journal of Systematic and Evolutionary Microbiology, 50, 159–170. DOI: 10. 1099/00207713-50-1-159
  12. Diouf D., Samba-Mbaye R., Lesueur D., de Lajudie P., 2007. Genetic diversity of Acacia seyal Del. indigenous to Senegalese soils in relation to the sampling. Microbial Ecology, 54, 3, 553–566. DOI: 10. 1007/S00248-007-9243-0
  13. Dupuy N. C., Dreyfus B. L., 1992. Bradyrhizobium population occur in deep soil under the leguminous tree Acacia albida. Applied Environmental Microbiology, 58, 2415–2419.
  14. FAO 2008. FAOSTAT Food and Agriculture Organization atwww. fao. org (07. 05. 2018).
  15. Grönemeyer J. L., Kulkarni A., Berkelmann D., Hurek T., Reinhold-Hurek B., 2014. Identification and characterization of rhizobia indigenous to the Okavango region in Sub-Saharan Africa. Applied and Environmental Microbiology, 80, 23, 7244–7257. DOI: 10. 1128/AEM. 02417-14
  16. Grönemeyer J. L., Reinhold-Hurek B., 2018. Diversity of Bradyrhizobia in Subsahara Africa: A Rich Resource. Frontiers in Microbiology, 9:2194. DOI: 10. 3389/FMICB. 2018. 02194
  17. Gyogluu C., Jaiswal S. K., Kyei-Boahen S., Dakora F. D., 2018, Identification and distribution of microsymbionts associated withs soybean nodulation in Mozambican soils. Systematic and Applied Microbiology, 41, 506–515. DOI: 10. 1016/J. SYAPM. 2018. 05. 003
  18. Hirsch P. R. 1996, Population dynamics of indigenous and genetically modified Rhizobia in the field. New Phytologist, 133, 159–171.
  19. Hollis S., Brummitt R. K., 1992, World Geographical Scheme for Recording Plant Distributions. International Working Group on Taxonomic Databases for Plant Sciences, No. 2. Hunt Institute for Botanical Documentation. Pittsburgh.
  20. Jaiswal S. K., Msimbira L. A., Dakora F. D., 2017. Phylogenetically diverse group of native bacterial symbionts isolated from root nodules of groundnut (Arachis hypogaea L.) in South Africa. Systematic and Applied Microbiology, 40, 4, 215–226. DOI: 10. 1016/J. SYAPM. 2017. 02. 002
  21. Jiao Y. S., Yan H., Ji Z. J., Liu Y. H., Sui H. S., Wang E. T., Guo B. L., Chen W. X., Chen W. F., 2015. Rhizobium sophorae sp. nov. and Rhizobium sophoriradicis sp. nov., nitrogen-fixing rhizobial symbionts of the medicinal legume Sophora flavescens. International Journal of Systematic and Evolutionary Microbiology, 65, 497-503. DOI: 10. 1099/IJS. 0. 068916-0
  22. Kapembwa Z. R., Mweetwa A. M., Ngulube M., Yengwe J., 2016. Morphological and biochemical characterization of soybean nodulating rhizobia indigenous to Zambia. Sustainable Agriculture Research, 5, 3, 84-92. DOI: 10. 5539/SAR. V5N3P84
  23. Kawaka F., Dida M. M., Opala P. A., Ombori O., Osoro N., Muthini M., Amoding A., Mukaminega D., Muoma J., 2014. Symbiotic efficiency of native rhizobia nodulating common bean (Phaseolus vulgaris L. ) in soils of western Kenya. International Scholarly Research Notices, 258497, 1–8. DOI: 10. 1155/2014/258497
  24. Koskey G., Mburu S. W., Njeru E. M., Kimiti J. M., Ombori O., Maingi J. M., 2017. Potential of native rhizobia in enhancing nitrogen fixation and yields of climbing beans (Phaseolus vulgaris L.) in contrasting environments of eastern Kenya. Frontiers in Plant Science, 8, 443, 1–12. DOI: 10. 3389/FPLS. 2017. 00443
  25. Krasova-Wade T., Ndoye I., Braconnier S., Sarr B., de Lajudie P., Neyra M., 2003, Diversity of indigenous bradyrhizobia associated with 3 cowpea cultivars (Vigna unguiculata (L.) Walp.) grow under limited and favorable water conditions in Senegal (West Africa). African Journal of Biotechnology, 21, 13–22. DOI: 10. 5897/ajb2003. 000-1003
  26. Lalande R., Bigwaneza P. C., Antoun H., 1990. Symbiotic effectiveness of strains of Rhizobium leguminosarum biovar phaseoli isolated from soils of Rwanda. Plant and Soil, 121, 1, 41–46.
  27. Law I. J., Botha W. F., Majaule U. C., Phalane F. L., 2017. Symbiotic and genomic diversity of ‘cowpea’ bradyrhizobia from soils in Botswana and South Africa. Biology and Fertility of Soils, 43, 653–663. DOI: 10. 1007/S00374-006-0145-Y
  28. Lindeque M. I., 2006. Diversity of root nodule bacteria associated with Phaseolus coccineus and Phaseolus vulgaris species in South Africa. Dissertation University of Pretoria, 138.
  29. Lindström K., Murwira M., Willems A., Altier N., 2010. The biodiversity of beneficial microbe-host mutualism: The case of rhizobia. Research in Microbiology, 161, 6, 453–463. DOI: 10. 1016/J. RESMIC. 2010. 05. 005
  30. Mackie W. W., 1943. Origin, and variability of lima bean (Phaseolus lunatus L.). California Agricultural Experiment Station, Journal of Agricultural Science, 15, 1, 1–31.
  31. Martínez-Romero E., 2003. Diversity of Rhizobium-Phaseolus vulgaris symbiosis: overview and perspectives. Plant and Soil, 252, 1, 11–22. DOI: 10. 1023/A:102419901
  32. Martins L. M. V., Xavier G. R., Rangel F. W., Ribeiro J. R. A., Neves M. C. P., Morgado L. B., 2003. Contribution of biological nitrogen fixation to cowpea; a strategy for improving grain yield in the semi-arid region of Brazil. Biology and Fertility of Soils, 38, 6, 333–339. DOI: 10. 1007/S00374-003-0668-4
  33. McDonald J., 1935. The inoculation of leguminous crops. East African Agricultural and Forestry Journal, 1, 4, 8–13.
  34. Mpepereki S., Wollum A. G,, Makonese F., 1996. Diversity in symbiotic specificity of cowpea rhizobia indigenous to Zimbabwean soil. Plant and Soil, 186, 167–171. DOI: 10. 1007/BF00035071
  35. Muthini M., Maingi J. M., Muoma J. O., Amoding A., Mukaminega D., Osoro N., Mugutu A., Ombori O., 2014. Morphological Assessment and Effectiveness of Indigenous Rhizobia Isolates that Nodulate P. vulgaris in Water Hyacinth Compost Testing Field in Lake Victoria Basin. British Journal of Applied Science and Technology, 4, 5, 718–738. DOI: 10. 9734/BJAST/2014/5757
  36. Mwangi S. N., Karanja N. K., Boga H., Kahindi J. H. P., Muigai A., Odee D., Mwenda G. M., 2011. Genetic diversity and symbiotic efficiency of legume nodulating bacteria from different land use systems in Taita Taveta, Kenya. Tropical and Subtropical Agroecosystems 13, 109–118.
  37. Mwenda G., 2017. Characterization of nitrogen-fixing bacteria from Phaseolus vulgaris L. in Kenya. Dissertation. Murdoch University, 196.
  38. Mwenda G. M., Karanja N. K., Boga H., Kahindi J. H. P., Muigai A., Odee D., 2011. Abundance and diversity of legume nodulating rhizobia in soils of Embu District, Kenya. Tropical and Subtropical Agroecosystems, 13, 1–10.
  39. Mwenda G. M., O’Hara G. W., de Meyer S. E., Howieson J. G., Terpolilli J. J., 2018. Genetic diversity and symbiotic effectiveness of Phaseolus vulgaris - nodulating rhizobia in Kenya. Systematic and Applied Microbiology, 41, 4, 291–299. DOI: 10. 1016/J. SYAPM. 2018. 02. 001
  40. Naamala J., Jaiswal S. K., Dakora F. D., 2016. Microsymbiont diversity and phylogeny of native bradyrhizobia associated with soybean (Glycine max L. Merr.) nodulation in South African soils. Systematic and Applied Microbiology, 39, 5, 336–344. DOI: 10. 1016/J. SYAPM. 2016. 05. 009
  41. Namkeleja Y., 2017. Isolation, authentication, and evaluation of symbiotic effectiveness of elite indigenous rhizobia nodulating Phaseolus vulgaris L. in hai district northern Tanzania. Dissertation. Nelson Mandela African Institution of Science and Technology, 77.
  42. Namkeleja Y., Mtei K., Ndakidemi P. A., 2016. Isolation and molecular characterization of elite indigenous rhizobia nodulating phaseolus bean (Phaseolus vulgaris L.). American Journal of Plant Sciences, 7, 14, 1905–1920. DOI: 10. 4236/AJPS. 2016. 714175
  43. Ndusha B. N., 2011. Effectiveness of rhizobia strains isolated from South Kivu soils on growth of soybeans (Glycine max L. ). Dissertation. The University of Nairobi, 98.
  44. Odee D. W., Haukka K., McInroy S. G., Sprent J. I., Sutherland J. M., Young J. P. W., 2002. Genetic and symbiotic characterization of rhizobia isolated from tree and herbaceous legumes grown in soils from ecologically diverse sites in Kenya. Soil Biology and Biochemistry, 34, 6, 801–811. DOI: 10. 1016/S0038-0717 (02) 00009-3
  45. Onyango B., Beatrice A., Regin N., Koech P. K., Skilton R., Francesca S., 2015. Morphological, genetic and symbiotic characterization of root nodule bacteria isolated from Bambara groundnuts (Vigna subterranea L. Verdc) from soils of Lake Victoria basin, western Kenya. Journal of Applied Biology and Biotechnology, 3, 01, 001–010. DOI: 10. 7324/JABB. 2015. 3101
  46. Palmer K. M., Young J. P. W., 2000. Higher diversity of Rhizobium leguminosarum biovar viciae in arable soils than in grass soils. Applied and Environmental Microbiology, 66, 2445–2450. DOI: 10. 1128/AEM. 66. 6. 2445-2450. 2000
  47. Pule-Meulenberg F., Belane A. K., Krasova-Wade T., Dakora F. D., 2010. Symbiotic functioning and bradyrhizobial biodiversity of cowpea (Vigna unguiculata L. Walp.) in Africa. BMC Microbiology, 10, 89, 1–12. DOI: 10. 1186/1471-2180-10-89
  48. Pule-Meulenberg F., 2014. Root-nodule bacteria of legumes growing in semi-arid African soils and other areas of the world [in:] Bacterial Diversity in Sustainable Agriculture, (Ed D. K. Meheshwari), Heidelberg-New York-Dordrecht-London: Springer, 101–130.
  49. Sawada H., Kuykendall L. D., Young J. M., 2003. Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts. Journal of General and Applied Microbiology, 49, 3, 155–179. DOI: 10. 2323/JGAM. 49. 155
  50. Segovia L. Young, J. P. W., Martínez-Romero E., 1993, Reclassification of American Rhizobium leguminosarum biovar phaseoli Type I Strains as Rhizobium etli sp. nov. International Journal of Systematic bacteriology, 43, 2, 374-377.
  51. Souza de D. I. A., 1969. Legume nodulation and nitrogen fixation studies in Kenya. East African Agricultural and Forestry Journal, 34, 3, 299-305.
  52. Steenkamp E. T., Stępkowski T., Przymusiak A., Botha W. J., Law I. J., 2008, Cowpea and peanut in southern Africa are nodulated by diverse Bradyrhizobium strains harboring nodulation genes that belong to the large pantropical clade common in Africa. Molecular Phylogenetics and Evolution 48, 3, 1131–1144. DOI: 10. 1016/J. YMPEV. 2008. 04. 032
  53. Tena W., Wolde-Meskel E., Degefu T., Walley F., 2017. Lentil (Lens culinaris Medik.) nodulates with genotypically and phenotypically diverse rhizobia in Ethiopian soils. Systematic and Applied Microbiology, 40, 1, 22–33. DOI: 10. 1016/J. SYAPM. 2016. 11. 001
  54. Thompson J. A., Bhromsiri A., Shutsrirung A., Lillakan S. 1991, Native root-nodule bacteria of traditional soybean-growing areas of northern Thailand. Plant and Soil, 135, 53-65.
  55. Trytsman M., Westfall R. H., Breytenbach P. J. J., Calitz F. J., van Wyk A. E., 2016. Diversity and biogeographical patterns of legumes (Leguminosae) indigenous to southern Africa. Phytokeys, 70, 53–96. DOI: 10. 3897/PHYTOKEYS. 70. 9147
  56. Wekesa C., Muoma J., Ombori O., Maingi J., Okun D., Juma K., Okoth P., Wamalwa E., Kollenberg M., Maut E., 2017. Genetic characterization of rhizosphere bacteria that inhabit common bean nodules in Western Kenya soils. Applied Microbiology, 3, 1, 128. DOI: 10. 4172/2471-9315. 1000128
  57. Wolde-meskel E., Terefework Z., Frostega A., Lindstrom K., 2005, Genetic diversity and phylogeny of rhizobia isolated from agroforestry legume species in southern Ethiopia. International Journal of Systematic and Evolutionary Microbiology, 55, 4, 1439–1452. DOI: 10. 1099/IJS. 0. 63534-0
  58. Yates J. R., Howieson G. J., Nandasena G. K., O’Hara W. G., 2004, Root–nodule bacteria from indigenous legumes in the north-west of Western Australia and their interactions with exotic legumes. Soil Biology and Biochemistry, 36, 8, 1319–1329. DOI: 10. 1016/J. SOILBIO. 2004. 04. 013

Received: 13.09.2019
Reviewed: 19.12.2019
Accepted: 19.12.2019

Andre L. Bongo
Laboratory of Agricultural Microbiology, Department of Plant Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
phone/fax: +48 71 320 6521
Grunwaldzka 53
50-375 Wrocław
email: andre.bongo@upwr.edu.pl

Stanisław J. Pietr
Laboratory of Agricultural Microbiology, Department of Plant Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
phone/fax: +48 71 320 6521
Grunwaldzka 53
50-375 Wrocław
email: stanislaw.pietr@upwr.edu.pl

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