Insights into the Biodiversity of Native Rhizobia from Africa: Documented Novel Species, Valorization Status and Perspectives—A Review

Abstract

Rhizobia are a polyphyletic group of Proteobacteria comprising approximately 700 different species. Despite significant advancements in their taxonomy, evolutionary history, and ecological importance, substantial knowledge gaps remain regarding a detailed understanding of rhizobial biodiversity in a geographical context and the interest in studying and valorizing native rhizobial strains. This bibliometric study used data from the last four decades (1985–2025) to review the taxonomic and functional diversity of the documented novel taxa of rhizobia described from African ecosystems, as well as their valorization status as biofertilizers. It aims to discuss the interest in knowing, preserving, and valorizing native rhizobial resources in the global context of climate change and biodiversity erosion. The study revealed that the first African indigenous novel species of rhizobia was published in 1988, although research on rhizobia dates back to the 1950s in Africa. To date, ~63 species (approximately 9% of the total in the world) and two genera of rhizobia have been described using native isolates from 11 African countries, with substantial discoveries from the Succulent Karoo hotspot of biodiversity in South Africa. Approximately 51% of species are affiliated with Bradyrhizobium and Mesorhizobium, with Vachellia karroo and Senegalia spp. (formerly Acacia spp.) as their primary hosts. Most species-type strains (~89%) were found to be infective on legumes and are good candidates for biofertilizer development. However, there is a limited level of commercial valorization of indigenous isolates as inoculants, mainly because the production of biological intrants is still at the experimental stage in Africa. Interestingly, important breaking point discoveries have been made using native rhizobial strains from Africa, including the pioneering demonstration in 2001 that Burkholderia (beta-rhizobia) is a symbiotic genus with legumes. It also includes the discovery of stem-nodulating rhizobia and Nod factor-independent symbiotic processes in some rhizobia. Together, this review highlights the importance of native African rhizobial strains. This underscores the need to accelerate their agronomic valorization to better support the transition to more resilient and sustainable legume-based farming systems in African countries.

1. Introduction

Rhizobia are Proteobacteria that induce nodule formation on the roots and/or stems of legumes (and exceptionally non-legume lineage Parasponia Miq. (syn. Trema Lour.; Cannabaceae [1])), where they reduce atmospheric dinitrogen gas (N₂) to ammonia (NH₃) using the nitrogenase enzyme [2]. It is estimated that 50–60 × 10⁶ tons of nitrogen (N) is fixed annually worldwide by 250 million hectares of pulse and oilseed legumes and 220 million hectares of managed pastures containing legumes [3]. The amount of N fixed by rhizobium–legume symbiosis is a major input of N into natural and agricultural ecosystems, and it contributes to the reduction in the need for chemical N fertilizers [2,4]. Thus, rhizobia-based symbioses play a pivotal role in the transformation of conventional agricultural systems into more resilient and sustainable agrifood systems [3,5]. Legume–rhizobia symbiosis further contributes to achieving the 2030 Agenda for Sustainable Development Goals (SDGs), including global targets related to the end of poverty (SDG 1), zero hunger (SDG 2), good health (SDG 3), sustainable consumption and production (SDG 12), and climate change (SDG 13) [6]. The efficacy of biological nitrogen fixation (BNF) by legumes depends on multiple parameters, including plant genotype and mineral nutrient balance [7]. BNF can also be improved through rhizobial inoculation technology with biofertilizers [8]. Rhizobia-based biofertilizers represent a widespread and eco-friendly solution for increasing N-inputs in cropping systems [9,10]. In many countries in South America, pulse legumes such as soybeans have reached high yields with no N-fertilizer once inoculated with highly effective inoculant strains adapted to local farming conditions [8]. In Africa, rhizobia-based biofertilizers have been promoted through multiple projects as a sustainable alternative to synthetic N-fertilizers. The different projects aim to support smallholder farmers who have limited access to fertilizers while facing low yields and food insecurity problems [9,10]. For example, the “putting nitrogen fixation to work for smallholder farmers in Africa,” also known as the N₂Africa project (https://www.n2africa.org/home; accessed on 15 December 2025), was funded by the Bill and Melinda Gates foundation to support the production and use of rhizobia inoculants in 11 African countries [9]. It has reached several thousand smallholder farmers with improved technologies for grain legume production.

Owing to the multiple benefits of legume–rhizobia symbiosis for sustaining agricultural production, research on the genetic diversity, taxonomy, and functional traits of rhizobia has increased worldwide over the past 25 years [2,11]. The exploration of rhizobial biodiversity has led to several results and applications, including the selection of candidate effective strains for the development and commercialization of biofertilizers. Simultaneously, several new species and genera of rhizobia have been formally described using the guidelines established by the Subcommittee on Taxonomy of Rhizobia and Agrobacteria of the International Committee on Systematics of Prokaryotes (ICSP) [2,11]. To date, approximately 21 genera of rhizobia have been officially described, including both alpha- and beta-rhizobia. The most popular genera include Bradyrhizobium, Mesorhizobium, Rhizobium, Sinorhizobium (alpha-rhizobia), Cuprivadus, Paraburkholderia (beta-rhizobia), etc. [2,11]. Rhizobium [12] represents the first genus of rhizobia described to science and has the highest number of described species [13] (https://lpsn.dsmz.de/genus/rhizobium; accessed on 15 December 2025), while Bradyrhizobium [14] is likely the ancestor of all rhizobia [15,16]. Many countries, including Australia, Brazil, China, Germany, Mexico, South Africa, Spain, and the United Kingdom, have made substantial contributions to the taxonomic description of new taxa of rhizobia [17,18]. They also have several validly published names of bacteria per year (https://lpsn.dsmz.de/statistics/figure/10; accessed on 15 December 2025). Moreover, countries with the most successful histories of legume inoculation with biofertilizers include Brazil and Argentina in America [19,20] and Australia and New Zealand in Oceania [3,21]. For example, Australia has approximately 100 years of legume inoculation history and has a specialized center for Rhizobium studies, currently known as Legume Rhizobium Sciences [22].

In Africa, applied fundamental research on rhizobia and their application as biofertilizers dates back to the 1950s [23]. It probably started in Southern Africa, in Rhodesia (now Zimbabwe) or South Africa [23]. Over the last four decades, many studies have explored African rhizobial biodiversity from different ecosystems using both phenotypic and molecular techniques. To complement the traditional morphological and biochemical characterization of isolates, several molecular markers have been used to describe the genetic diversity of rhizobia at the genus and/or species levels. The sequencing of the 16S rRNA gene, analysis of the intergenic space between 16S and 23S rDNA (ITS), and multilocus sequence analysis (MLSA) of housekeeping genes are frequently used to elucidate rhizobial diversity and taxonomy in Africa [24,25]. Moreover, the use of a whole genome’s overall genome-related indices (OGRIs) [26], such as the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) metrics, has gained prominence among African researchers for describing both alpha- and beta-rhizobia [25,27]. Pioneering and current research efforts have led to the description of rhizobial diversity in many African regions and/or hotspots of biodiversity, including the Okavango region [28,29], Guinean forest in West Africa [30,31], Succulent Karoo and Cape floristic Regions in Southern Africa [27,32], and Mediterranean basin [33,34]. Despite these achievements, comprehensive reviews on legume nodulation by rhizobia in Africa are rather sparse in terms of the diversity of legumes studied and the types of rhizobial symbionts found to nodulate legume species in African soils [35]. Moreover, the extent to which African indigenous rhizobia are taxonomically diversified and potentially useful for inoculant production remains elusive. We hypothesized that African soils harbor a highly diverse, largely underexplored, and ecologically important pool of indigenous rhizobial species, including numerous novel taxa with a high symbiotic efficiency. Moreover, their potential for development as locally adapted biofertilizer inoculants remains underexploited, mainly due to a lack of research infrastructure linked to commercial inoculant development, limited geographic coverage of existing investigations, and insufficient integration of biodiversity insights into practical agricultural applications. Here, we provide an in-depth synthesis of the growing body of knowledge on the taxonomy, functional diversity, and potential use as biofertilizers of native rhizobial species isolated from African soils. This review aims to (i) synthesize the taxonomic diversity of new taxa of rhizobia described over the past four decades from African regions, (ii) assess the symbiotic effectiveness and potential use of indigenous rhizobia for local biofertilizer development, (iii) highlight the breaking point discoveries made using native rhizobia strains from Africa, and (iv) discuss the potential of emerging taxonomic rules, such as the Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode), to facilitate a description of African rhizobial biodiversity.

2. Ecological and Economic Values of Rhizobia and Their Legume Hosts

The symbiosis between rhizobia and legumes provides multiple benefits in line with sustainability principles. The benefits include legume-based cropping systems, soil fertility, food and fuel production, and food security [4,36]. A clear link has been established between the promotion of symbiosis between soil bacteria and legumes and the achievement of the Sustainable Development Goals (SDGs) related to food security and nutrition [6]. Both symbiotic partners contribute to SDG 1, linking to the end of poverty in all its forms everywhere; SDG 2, related to zero hunger; SDG 3 (good health and well-being); SDG 12 (sustainable consumption and production); and SDG 13, which aims to take urgent action to combat climate change and its impacts [6]. The celebration of World Pulses Day (WPD) by the United Nations on February 10th every year helps to recognize the potential of pulses to further achieve the 2030 Agenda for Sustainable Development (https://www.fao.org/world-pulses-day/en; accessed on 15 December 2025). This celebration highlights the fundamental role played by pulse legumes and associated symbiotic rhizobia for better production, nutrition, environment, and life [5,6].

The potential of legume–rhizobia symbiosis to ensure sustainable agrifood systems is maximized through the deliberate inoculation of legumes with rhizobial biofertilizers. The surface area under legume cultivation has steadily increased over the years owing to rhizobia inoculation in many regions [19]. To date, commercial rhizobial inoculants cover approximately 100 cultivated legume species [3,21]. Soybean (Glycine max (L.) Merr., Papilionoideae) is the most successful example of a legume crop that benefits from the application of rhizobia as inoculants [37,38]. In 2025, it was grown on 137 million hectares [39]. Performant inoculants are also available for other major legume crops, such as chickpea (Cicer arietinum L., Papilionoideae), common bean (Phaseolus vulgaris L., Papilionoideae), pigeonpea (Cajanus cajan (L.) Huth, Papilionoideae), etc. Many types of biofertilizer products are commercialized worldwide. Interestingly, the percentage of the nitrogen-fixing biofertilizer market represents the largest part of the global biofertilizer market (Figure 1). Nitrogen-fixing biofertilizers are formulated with efficient rhizobial isolates belonging mainly to the Bradyrhizobium and Rhizobium genera [38,40]. The annual cost for farmers worldwide to replace the N fixed by legumes with fertilizer N is estimated to be $50–60 billion, highlighting the remarkable economic value of symbiotic rhizobia [3,6].

Several agrotechnological measures can be used to improve the efficiency of biological N₂ fixation in agricultural systems. For example, the use of effective inocula of rhizobia and plant growth-promoting bacteria has been shown to enhance nodulation efficiency and nitrogenase activity, thereby increasing the efficiency of biological N input. This enables the use of less inorganic nitrogen fertilizers without any deleterious effects on yields [42,43]. The efficiency of inoculation can be further improved through an adequate NPK and micronutrient supply (e.g., Fe and Mo), as these are required for the synthesis of the nitrogenase enzyme [44]. In Africa, the application of phosphate-based fertilizers is often required prior to or alongside rhizobial inoculation to ensure successful nitrogen fixation, because many African soils are P-deficient [45,46]. Many African soils are characterized by a low inherent fertility, low organic carbon, and acidity, particularly in humid zones [47]. In addition, the use of legume-based rotations and intercropping systems is an effective measure for improving soil fertility and biological N inputs, thereby creating an environment conducive to N₂ fixation efficiency over time. However, it is equally important to avoid high rates of inorganic nitrogen fertilizer application, as high rates of N availability in the soil reduce the efficiency of symbiotic N₂ fixation and biological nitrogen inputs [42,48].

3. Guidelines for the Description of New Genera and Species of Rhizobia and Their Evolutions

Rhizobia have been discovered and described for more than 135 years [12]. However, the first formal guideline for describing a new taxon of rhizobia (and agrobacteria) was published later in 1991, after a century of legume–rhizobia studies [49]. At that time (i.e., 1991), only four rhizobial genera were described, namely Rhizobium, Bradyrhizobium, Azorhizobium, and Ensifer (syn. Sinorhizobium), along with nine other species [11,49]. The general approach proposed by Graham et al. [49] for the determination of species boundaries within rhizobial isolates was a polyphasic approach that involved the analysis of a range of phenotypic and genotypic characters, including 16S rRNA gene sequences and DNA-DNA hybridization (DDH) values [11,49]. In the 2010s, the limitations of these taxonomic practices became clear to the community, while advances in DNA sequencing showed that genome-based measures of similarity could provide the primary evidence for microbial species affiliation [11]. Therefore, since 2020, new minimal standards for the description of new genera and species of rhizobia have been proposed, recommending genome-based metrics for the comparison of isolates [11]. These genome-based metrics, collectively known as the overall general relatedness index (OGRI) [26], include digital DDH (dDDH), average nucleotide identity (ANI), and average amino acid identity [50]. The new guidelines have been validated by the members of the Subcommittee on Taxonomy of Rhizobia and Agrobacteria of the International Committee on Systematics of Prokaryotes, recommending genome-based metrics for the comparison of isolates [11]. They require eight different points to describe a new species of rhizobia, including (1) a genome sequence of at least the proposed type strain and (2) evidence for the differentiation of the proposed species from other species based on genome comparisons. It is also recommended to (3) demonstrate that several strains of the new species differ substantially from each other using sequence data (e.g., ITS, recA, rpoB) and (4) describe phenotypic data and their variation between a set of representative strains. It also encourages (5) the analysis of the ability of strains to nodulate with relevant symbiotic gene sequences (e.g., nifH and nodC). Data from selected symbiotic gene analyses (e.g., nodC and nifH) could be used to assess the influence of lateral gene transfer on the symbiotic genes and/or to define symbiotic variants (symbiovars) [51,52]. A cut-off value of 92.5% was applied to distinguish symbiovars [53]. In addition to rules 1–5, it requires (6) a name for the new species that conforms to the International Code of Nomenclature of Prokaryotes (ICNP), and (7) validation of the name by publishing in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) or indirectly in a validation list when published elsewhere in other scientific journals (e.g., Diversity (MDPI)). Finally, a pure culture of the proposed type of strain for a novel species must be deposited in at least two international culture collections located in separate countries and made available upon request without restrictions (8).

Under the International Code of Nomenclature of Prokaryotes (ICNP) for rhizobia, new microbial names are not valid as long as the distribution of type strains is restricted [11,32]. Unfortunately, this requirement is not applicable under some national regulations due to the restrictions imposed by the Nagoya Protocol for the access and sharing of indigenous biological material [32,54]. Since 2022, an alternative system that seems to facilitate the naming of prokaryotes has been introduced [55]. It is known as the Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode), and broadly uses the same naming rules as the ICNP, except for the nature of type material. Indeed, it recommends genome sequences as nomenclature types (type sequences, TS) [55]. SeqCode has the potential to accelerate the naming and taxonomic description of both cultivated and non-culturable microbial biodiversity [55]. However, the validity of naming under SeqCode rules is still debated [18,56,57]. For example, the ICNP subcommittee for rhizobia recently reported that it could not recognize the naming of seven novel Mesorhizobium species from South Africa proposed under SeqCode [18]. Although this first attempt to publish novel taxa of rhizobia under the seqCode system is not considered valid [18], SeqCode is gaining prominence among African microbiologists for describing novel species of rhizobia [58,59]. Both validly and not-validly published names of bacteria are regularly added to the List of Prokaryotic Names with Standing in Nomenclature (LPSN), also known as bacterio.net (http://www.bacterio.net/index.html; accessed on 15 December 2025) [60,61]. Thus, the LPSN database provides comprehensive and updated information on the nomenclature and taxonomy of prokaryotes (https://lpsn.dsmz.de/statistics/figure/110; accessed on 15 December 2025), including rhizobia.

4. Taxonomy of Rhizobia Across the Globe—A Brief Overview

Taxonomically, rhizobia belong to the class Alphaproteobacteria (alpha-rhizobia) in the order Hyphomicrobiales and the class Betaproteobacteria (beta-rhizobia) in the order Burkholderiales. Some works have also reported the existence of rhizobia within the orders Enterobacteriales (e.g., genera Escherichia, Leclercia, Pantoea and Enterobacter), Pseudomonadales (genus Pseudomonas) [62] and Sphingomonadales (genus Sphingomonas) [63], but these claims remain controversial as they generally do not fulfill Koch’s postulates and have not been validated by the scientific community [64,65]. Thus, to date, all bona fide rhizobia belong to the orders Hyphomicrobiales (formerly Rhizobiales) and Burkholderiales [65]. They are distributed across eight families of bacteria (https://sites.google.com/view/taxonomyagrorhizo/home/species-with-standing-in-nomenclature) [2]. The families consist of Brucellaceae (genus Ochrobactrum), Devosiaceae (Devosia), Methylobacteriaceae (Methylobacterium, Microvirga), Nitrobacteraceae (formerly known as Bradyrhizobiaceae) (Bradyrhizobium), Phyllobacteriaceae (Aminobacter, Mesorhizobium, Phyllobacterium), Rhizobiaceae (Allorhizobium, Ferranicluibacter, Georhizobium, Ensifer/Sinorhizobium, Neorhizobium, Onobrychidicola, Pararhizobium, Rhizobium and Shinella), Xanthobacteraceae (Azorhizobium) and Burkholderiaceae (Cupriavidus, Paraburkholderia, and Trinickia), the last three genera belonging to the class of Betaproteobacteria. To date, the diversity of rhizobia described in science is estimated to comprise 21 genera and 701 species (

Table 1. Alpha- and Betaproteobacteria genera harboring rhizobial species and their corresponding relevant characteristics (adapted from Gnangui et al. [66]).

Genus	Number of Species 3	Symbiotic Species (Nod+/Fix+) 4	Genus Type Species	Genome Accession	Symbiotic Capacity of the Genus Type Species
Allorhizobium	10	1	Allorhizobium undicola ORS 992T	NZ_JHXQ01000045	Nod+/Fix+ [67]
Aminobacter	6	1	Aminobacter aminovorans DSM 7048T	NZ_SLZO01000023	Not described [68]
Azorhizobium	3	2	Azorhizobium caulinodans ORS 571T	AP009384	Nod+/Fix+ [69]
Bradyrhizobium	94	84	Bradyrhizobium japonicum USDA 6T	NC_017249	Nod+/Fix+ [14]
Cupriavidus  1	23	3	Cupriavidus necator  N-1T 5	CNE_1c16970	Nod− [70] 5
Devosia	46	1	Devosia riboflavina IFO13584T	NZ_JQGC01000043	nod/fix genes not detected [71]
Ensifer	24	17	Ensifer adhaerens Casida AT	NZ_CP015880	Nod−, nod genes not detected [72]
Ferranicluibacter	1	0	Ferranicluibacter rubi CRRU44T	JAANCM000000000	nod/fix genes not found in genome [73]
Georhizobium	1	0	Georhizobium profundi WS11T	CP032509	symbiotic status not described [74]
Mesorhizobium	78	57	Mesorhizobium loti DSM 2626T	NZ_QGGH01000001	Nod+/Fix+ [75,76]
Methylobacterium	64	1	Methylobacterium organophilum NBRC 15689T	NZ_BPQV01000023	Not described [77]
Microvirga	38	9	Microvirga subterranea DSM 14364T	NZ_QQBB01000028	Not described [78]
Neorhizobium	14	4	Neorhizobium galegae HAMBI 540T	HG938353	Nod+/Fix+ [79,80]
Onobrychidicola	1	0	Onobrychidicola muellerharveyae TH2T	CP062231	Nod− on its original host plant [81]
Ochrobactrum 2	21	2	Ochrobactrum anthropi ATCC 49188T	NC_009667	Non-symbiotic bacterium [82,83]
Paraburkholderia  1	113	24	Paraburkholderia graminis LMG 18924T	CADIK010000048	Not described [84,85]
Pararhizobium	9	2	Pararhizobium giardinii H152T	NZ_KB902704	Nod+/Fix+ [86,87]
Phyllobacterium	18	3	Phyllobacterium myrsinacearum DSM 5892T	NZ_SHLH01000013	Nod− [88]
Rhizobium	114	60	Rhizobium leguminosarum USDA 2370T	GCA_003058385	Nod+/Fix+ [12]
Shinella	12	1	Shinella granuli DSM 18401T	NZ_SLVX01000061	Not described [89]
Trinickia  1	11	1	Trinickia symbiotica  JPY-345T	NZ_PTIR01000049	Nod+/Fix+ [70]
Total number	701	273 (~39%)	About 39% of the 701 species of rhizobia described to this date can nodulate and/or fix N2 in symbiosis with legume plants

¹ The genera shown in bold are beta-rhizobia; they belong to the class of Betaproteobacteria. ² Brucella anthropi [82,90] is now proposed as comb. nov. of Ochrobactrum anthropi. The type species of Brucella is B. melitensis 16M^T [90,91]. ³ Number of species with a validly published and correct name (LPSN website (https://lpsn.dsmz.de/) accessed on 4 January 2026). ⁴ The capacity of each type species to form nodules (Nod⁺) and/or fix N₂ (Fix⁺) with legumes was assessed in a previous study [66], using original publications describing the novel taxa of rhizobia accessible directly via the LPSN website and additional relevant references on rhizobia [17,92,93] (Appendix A.2). ⁵ The type strain does not have nodulation capacity, but other strains have this feature [70,94].

; Appendix A.1). Type strains of 273 of the 701 species (~39%) are reported to be capable of nodulation (Nod⁺) and/or N₂ fixation (Fix⁺) with legume hosts. Moreover, the type species of nine (09) genera out of 21 genera of rhizobia were unambiguously reported as Nod⁺ and/or Fix⁺ (Table 1; Appendix A.2). Nodulation ability varies greatly within rhizobial species and among different genera. For example, less than 2% of all species of Methylobacterium can nodulate, while, for Bradyrhizobium, the nodulation ability is positive for approximately 90% of species. These results are consistent with those of previous studies [66].

Of the 21 genera of documented rhizobia worldwide, ten genera accounted for approximately 88% of all species, all of which were dominated by Rhizobium (n = 114 species; 16.3%), Paraburkholderia (n = 113 species; 16.1%), Bradyrhizobium (n = 94 species;13.4%), and Mesorhizobium (n = 78 species; 11.1%) (Figure 2). Each of the four dominant genera exhibited at least 10% of the total number of species. The growth rate of new species discoveries has increased markedly over the past few decades. During the past five years (2021–2025), the highest growth rate of discovery was observed for Bradyrhizobium (+37 novel species) and Paraburkholderia (+40 novel species) (Figure 2), representing on average ca. eight species described per year for each of the two aforementioned genera.

5. Biodiversity of Rhizobia in Africa and Its Main Features

The first novel taxon of rhizobia described using native rhizobial isolates from Africa was published in 1988, according to a literature survey (Appendix A.1). It consists of Azorhizobium caulinodans gen. nov., sp. nov. [69]. Hence, articles from 1988 to 2025 (~four decades) were selected as the main object for analysis (

Table 2. Novel genera and species of rhizobia discovered and described using isolates native to African ecosystems (1985–2025).

Country of Origin	Species Name	Type Strain (T) or Type Sequence (Ts)	Legume Host	Symbiotic Capacity	Potential Use as Biofertilizer	Year of Description	Main References
Algeria	Bradyrhizobium algeriense	RST89T (=LMG 27618T and CECT 8363T)	Retama sphaerocarpa	Nod+/Fix+ on Retama raetam, Lupinus spp. and Genista numidica; Nod+/Fix− on V. unguiculata & Nod− on G. max	Not specified in the main publication	2018	[95]
Côte d’Ivoire	Bradyrhizobium ivorense	CI-1BT (=CCOS 1862T = CCMM B1296T)	Cajanus cajan (Pigeonpea)	Fix N2 with C. cajan, Vigna radiata, and V. unguiculata, but not with Glycine max & Leucaena leucocephala	Yes	2020	[31]
Egypt	Rhizobium aegyptiacum	1010T (=USDA 7124T = LMG 29296T = CECT 9098T)	Trifolium alexandrinum	Forms effective nodules on the original host	Yes	2016	[96]
Ethiopia	Bradyrhizobium shewense	ERR11T (HAMBI 3532T = LMG 30162T)	Erythrina brucei	Forms effective nodules on the original host	Yes	2017	[97]
Ethiopia	Mesorhizobium abyssinicae	AC98cT (=LMG 26967T = HAMBI 3306T)	Acacia tortilis & A. abyssinica	Effective N2 fixation in symbiosis with A. abyssinica and A. tortilis	Yes	2013	[98]
Ethiopia	Mesorhizobium hawassense	AC99bT (=LMG 26968T = HAMBI 3301T	Sesbania sesban	Forms effective nitrogen-fixing nodules with Sesbania sesban	Yes	2013	[98]
Ethiopia	Mesorhizobium shonense	AC39aT (=LMG 26966T = HAMBI 3295T)	Acacia abyssinica	Forms effective nitrogen-fixing nodules with Acacia abyssinica	Yes	2013	[98]
Ethiopia	Rhizobium aethiopicum	HBR26T (=HAMBI 3550T = LMG 29711T)	Phaseolus vulgaris (common bean)	Fix N2 on P. vulgaris; no symbiosis with Vicia faba (faba bean), Pisum sativum and Lens culinaris (lentil)	Yes	2017	[99]
Morocco	Bradyrhizobium cytisi	CTAW11T (=LMG 25866T = CECT 7749T)	Cytisus villosus	Nodulates Cytisus but not Glycine max	Not specified	2011	[100]
Morocco	Bradyrhizobium retamae	Ro19T (LMG 27393T = CECT 8261T)	Retama monosperma	Nodulates Retama species but not Glycine max (soybean)	Not specified	2013	[101]
Morocco	Bradyrhizobium rifense	CTAW71T (=LMG 26781T = CECT 8066T)	Cytisus villosus	Nitrogen-fixing nodules on Cytisus villosus	Not specified	2012	[102]
Morocco	Ensifer aridi	LMR001T (=LMG 31426T = HAMBI 3707T)	Phaseolus fliform	Fix N2 with P. fliform, P. vulgaris; Nod- with M. pudica, M. sativa, C. arietinum, Erythrina americana, etc.	Not specified	2020	[103,104]
Namibia	Bradyrhizobium kavangense	14-3T (=DSM 100299T = LMG 28790T)	Vigna unguiculata (Cowpea)	Forms effective nodules on Vigna unguiculata, V. subterranean, Arachis hypogaea, Lablab purpureus	Yes	2015	[105]
Namibia	Bradyrhizobium namibiense	5-10T (=LMG 28789 T = DSM 100300T)	Lablab purpureus	Forms effective nodules on Lablab purpureus, Vigna subterranea, V. unguiculata and Arachis hypogaea	Yes	2017	[106]
Namibia	Bradyrhizobium ripae	WR4T (=LMG 30283T = DSM 105795T)	Indigofera rautanenii	Forms effective nodules on Indigofera rautanenii and V. unguiculata	Yes	2018	[107]
Namibia	Bradyrhizobium subterraneum	58 2-1T (=DSM 100298T = LMG 28792T)	Vigna subterranea	Forms effective nitrogen-fixing nodules on Vigna subterranea, V. unguiculata and Arachis hypogaea	Yes	2015	[108]
Namibia	Bradyrhizobium vignae	7-2T (=LMG 28791T = DSMZ 100297T)	Vigna unguiculata (Cowpea)	Forms effective nodules on V. unguiculata, V. subterranea, Arachis hypogaea & Lablab purpureus	Yes	2016	[109]
Senegal	Allorhizobium undicola (Description also of Allorhizobium gen. nov.)	ORS 992T (LMG 11875T)	Neptunia natans	Type strain is Nod- (but some strains fix N2 on their original host and are Nod+/Fix- with Acacia spp.)	No	1998	[67]
Senegal	Azorhizobium caulinodans (Description also of Azorhizobium gen. nov.)	ORS 571T (=LMG 6465T)	Sesbania rostrata	Forms root and stem nodules on Sesbania rostrata	Yes	1988	[69]
Senegal	Mesorhizobium plurifarium	ORS 1032T (=HAMBI 208T= LMG 11892T)	Acacia senegal	Forms root nodules with Acacia senegal, A. tortilis, A. nilotica, A. seya, and L. leucocephala	Not specified	1998	[110]
Senegal	Methylobacterium nodulans	ORS 2060T (CNCM I 2342T = LMG 21967T)	Crotalaria podocarpa	Forms nitrogen-fixing nodules with C rotalaria podocarpa, C. perrottetii and C. glaucoides	Yes	2004	[111]
Senegal	Sinorhizobium (Ensifer) saheli	ORS 609T (=LMG 7837T)	Sesbania cannabina	Forms root nodules with Sesbania cannabina	Yes	1994	[30]
Senegal	Sinorhizobium (Ensifer) terangae	ORS 1009T (=LMG 7834T)	Acacia laeta	Forms root nodules with Acacia laeta	Yes	1994	[30]
South Africa	Bradyrhizobium acaciae	10BBT (SARCC 730T = LMG 31409T)	Acacia dealbata	Forms effective nodules on Vigna unguiculata and M. atropurpureum	Yes	2022	[112]
South Africa	Bradyrhizobium altum	Pear77T (SARCC 754T = LMG 31407T)	Pearsonia obovata	Forms effective nodules on Vigna unguiculata and M. atropurpureum	Yes	2022	[112]
South Africa	Bradyrhizobium australafricanum	WSM 4400T (=CNPSo 4015T = LMG 31648T)	Glycine sp.	Forms effective N2-fixing nodules in Macroptilium atropurpureum and less effective in Glycine max	Yes	2022	[53]
South Africa	Bradyrhizobium oropedii	Pear76T (SARCC 731T = LMG 31408T)	Pearsonia obovata	Forms effective nodules on Vigna unguiculata and M. atropurpureum	Yes	2022	[112]
South Africa	Bradyrhizobium xenonodulans	14ABT (=LMG 31415T = SARCC-753T)	Acacia dealbata	Forms nodules on Acacia dealbata and Acacia mearnsii	Not specified	2023	[113]
South Africa	Burkholderia aspalathi	VG1CT (DSM 27239T = LMG 27731T)	Aspalathus abietina Thunb	No nodulation with Cyclopia genistoides & Psoralea pinnata (seeds of the original host were unavailable)	No	2014	[114]
South Africa	Burkholderia dilworthii	WSM3556T (=HAMBI 3353T = LMG 27173T)	Lebeckia ambigua	Forms nitrogen-fixing symbiosis with Lebeckia ambigua and L. sepiaria	Yes	2014	[115]
South Africa	Burkholderia kirstenboschensis	Kb15T (=LMG 28727T = SARC 695T)	Virgilia oroboides	Fix nitrogen with M. atropurpureum and V. unguiculata	Yes	2015	[116]
South Africa	Burkholderia rhynchosiae	WSM3937T (LMG 27174T= HAMBI 3354T)	Rhynchosia ferulifolia	Nitrogen fixation with R. ferulifolia	Yes	2013	[117]
South Africa	Burkholderia sprentiae	WSM5005T (=LMG 27175T= HAMBI 3357T)	Lebeckia ambigua	Forms nitrogen-fixing symbiosis with Lebeckia ambigua & L. sepiaria	Yes	2013	[118]
South Africa	Burkholderia tuberum	STM678T (=LMG 21444T = CCUG 47178T)	Aspalathus carnosa	Forms nitrogen-fixing symbiosis with M. atropurpureum	Not specified	2002	[119]
South Africa	Paraburkholderia fynbosensis	WSM4178T (LMG 27177T= HAMBI 3356T)	Lebeckia ambigua	The type strain is Nod-, but some strains from the species do it	No	2018	[93]
South Africa	Paraburkholderia steynii	HC1.1baT (=LMG 28730T = SARCC696T)	Hypocalyptus sophoroides ( rhizosphere)	Forms nitrogen-fixing symbiosis with M. atropurpureum	Yes	2019	[120]
South Africa	Paraburkholderia strydomiana	WK1.1fT (=LMG 28731T = SARCC1213T)	Hypocalyptus sophoroides (rhizosphere)	Forms nitrogen-fixing symbiosis with Macroptilium atropurpureum	Yes	2019	[120]
South Africa	Mesorhizobium album	VK24DTs	Vachellia karroo	Forms effective symbiosis with Vachellia karroo	Not specified	2024	[32]
South Africa	Mesorhizobium argentiipisi	Cs1330R2N1Ts	Calobta cericea	Forms root nodules with Calobta cericea	Not specified	2025	[58]
South Africa	Mesorhizobium australafricanum	VK9DTs	Vachellia karroo	Forms effective symbiosis with Vachellia karroo	Not specified	2024	[32]
South Africa	Mesorhizobium captivum	VK22ETs	Vachellia karroo	Forms effective symbiosis with Vachellia karroo	Not specified	2024	[32]
South Africa	Mesorhizobium dulcispinae	VK23DTs	Vachellia karroo	Forms effective symbiosis with Vachellia karroo	Not specified	2024	[32]
South Africa	Mesorhizobium humile	VK2BTs	Vachellia karroo	Forms effective symbiosis with Vachellia karroo	Not specified	2024	[32]
South Africa	Mesorhizobium montanum	MSK 1335Ts	Vachellia karroo	Forms effective symbiosis with Vachellia karroo	Not specified	2024	[32]
South Africa	Mesorhizobium salmacidum	Ld1326N3Ts	Lessertia diffusa	Forms root nodules with Lessertia diffusa	Not specified	2025	[58]
South Africa	Mesorhizobium vachelliae	VK25ATs	Vachellia karroo	Forms effective symbiosis with Vachellia karroo	Not specified	2024	[32]
Sudan	Sinorhizobium (Ensifer) arboris	TTR 38T (=HAMBI 1552T = LMG 14919T)	Prosopis chilensis	Strain can nodulate Acacia senegal and Prosopis chilensis	Yes	1999	[121]
Sudan	Sinorhizobium (Ensifer) kostiense	TTR 15T (=HAMBI 1489T = LMG 15613T)	Acacia senegal	Strain can nodulate Acacia senegal and Prosopis chilensis	Yes	1999	[121]
Tunisia	Bradyrhizobium hipponense	aSej3T (=DSM 108913T = LMG 31020T)	Lupinus angustifolius	Nodulate L. angustifolius plants under axenic conditions	Yes	2020	[33]
Tunisia	Bradyrhizobium tunisiense	1AS2LT (=LMG 33170T = DSM 114401T)	Acacia saligna	Forms effective nodules on A. saligna, A. salicina, A. tortilis and L. leucocephala; ineffective on P. vulgaris; no nodulation with G. max	Not specified	2025	[33]
Tunisia	Ensifer garamanticus	ORS 1400T (=LMG 24692T = CIP 109916T)	Argyrolobium uniflorum	Forms effective nodules on A. uniflorum and Medicago sativa	Yes	2010	[122]
Tunisia	Ensifer numidicus	ORS 1407T (=LMG 24690T = CIP 109850T)	Argyrolobium uniflorum	Forms effective nodules on Argyrolobium uniflorum	Yes	2010	[122]
Tunisia	Mesorhizobium retamae	IRAMC:0171T (=DSM 112841T = CECT 30767T	Retama raetam	The type strain is Nod−	No	2024	[123]
Tunisia	Microvirga tunisiensis	LmiM8T (CECT 9163T, LMG 29689T)	Lupinus micranthus	Fix N2 with L. micranthus, L. luteus, L. angustifolius & M. atropurpureum but not with Vigna	Yes	2019	[124]
Tunisia	Neorhizobium tunisiense	RAMC 0178T (=HAMBI 3839T = CGMCC 1.65424T = DSM 119302T)	Retama raetam	The type strain is Nod−	No	2025	[125]
Tunisia	Phyllobacterium ifriqiyense	STM 370T (=LMG 22831T = CFBP 6742T)	Lathyrus numidicus	Non-nodulating (Nod−)	Not specified	2006	[126]
Tunisia	Phyllobacterium leguminum	ORS 1419T (=LMG 22833T = CFBP 6745T)	Astragalus algerianus	Non-nodulating (Nod−)	Not specified	2006	[126]
Tunisia	Rhizobium acaciae	1AS11T (=DSM 113913T = ACCC 62388T)	Acacia saligna	Nodulate A. saligna, A. salicina, L. leucocephala, but not G.max, P. vulgaris or Retama raetam	Not specified	2023	[127]
Tunisia	Rhizobium aouanii	1AS14IT (=DSM 113914T = LMG 33206T )	Acacia saligna	Nodulate A. saligna, A. salicina, L. leucocephala, but not G.max, P. vulgaris or Retama raetam	Not specified	2024	[128]
Tunisia	Rhizobium azibense	23C2T (=CCBAU 101087T = HAMBI3541T)	P. vulgaris (Common bean)	Nitrogen-fixing P. vulgaris	Yes	2014	[129]
Tunisia	Rhizobium laguerreae	FB206T (=LMG 27434T = CECT 8280T)	Vicia faba	Fix N2 on V. faba (faba bean) & Lens culinaris (lentil)	Yes, tested on field trial	2013	[130]
Zambia	Microvirga lotononidis	WSM3557T (LMG 26455T = HAMBI 3237T)	Listia angolensis	Fix N2 with the host plant; Nod+/Fix− on Phaseolus vulgaris	Yes	2012	[131]
Zambia	Microvirga zambiensis	WSM3693T (LMG 26454T = HAMBI 3238T)	Listia angolensis	Fix N2 with the host plant; Nod+/Fix− on Phaseolus vulgaris, Acacia saligna and Vigna unguiculata	Yes	2012	[131]
Key findings 1: The novel species of rhizobia have been discovered in 11 African countries.	A total of 60 novel species of rhizobia have been described in Africa. They are scattered into 11 genera of rhizobia out of the ca. 21 genera validly published.	The type strains of the novel species are deposited mainly in LMG culture collection in Gent/Belgium (n = 48), followed by HAMBI in Finland (n = 17) and by DSMZ in Germany (n = 12).	The type strains were isolated from 41 legume species, all of which were dominated by Vachellia karroo and Senegalia spp.	Only seven (07) type strains of the native African rhizobial species (out of 63) did not form nodules on their original hosts and related legume species tested so far. The other 56 (~89%) species were effective and/or infective on legumes.	The potential use as biofertilizers was suggested and/or reported for 36 infective type strains.	The 1st novel species of rhizobia from Africa was described in Senegal in 1988.	All the 63 native species of rhizobia from Africa were described by 32 different first authors.

¹ The main findings of Table 2 are further discussed in Section 5.

).

We observed that the pace of species discovery in Africa was very low until the 2010s (Figure 3). Only 13 species were described from 1988 to 2010, that is, over 23 years (~0.6 species/year). In contrast, 50 of the 63 novel species (~80%) have been published within a short period of 15 years (2011–2025), representing an average of 4.2 species per year. The year 2024 has the highest growth rate of discovery, with nine (09) species, of which seven (07) have been published in a single paper under SeqCode rules [32]. In addition to the 63 novel species of rhizobia, two genera of rhizobia native to African soils have also been described, namely Allorhizobium gen. nov. [67] and Azorhizobium gen. nov. [69]. Both genera have type strains isolated from Senegal in West Africa (Table 2).

5.1. About 9% of Rhizobia Species Are Native from Africa

Our study revealed that 65 novel taxa of rhizobia native to African soils, including two (02) genera and 63 species, have been discovered over the last four decades (Table 2). The 63 novel species of rhizobia described from Africa to date represent 9% of all species of rhizobia described worldwide. South Africa dominates all African countries in terms of the total number of new species described per country, with 23 species (36.5% of the African total) (Figure 4). Regarding authorship, all 63 novel species were published by 32 different first authors (Table 2), including both African and non-African scientists. Scientists such as Dr. Sophie E. de Meyer (formerly at Murdoch University, Australia) and Dr. Jann Lasse Grönemeyer (a former PhD student at the University of Bremen, Germany) have made substantial contributions over the last 10 years, with first authorship reported for four different species for each of the aforementioned scientists (Table 2). African taxonomists who have recently focused on the description of novel species of rhizobia native to Africa include Mr Jihed Hsouna (Center of Biotechnology of Borj-Cédria, Tunisia). He is the first author of three taxonomic publications related to the description of three novel species of rhizobia native to Tunisian soils in 2023 [127], 2024 [128] and 2025 [34], respectively. Moreover, the highest number of new species described in a single paper was recently published in 2024 from South Africa under SeqCode rules, consisting of seven novel species of Mesorhizobium [32]. Van Lill et al. [32] contributed to an increase in the total number of species described in South Africa, which ranks first in terms of the highest number of new species described per country (23 species) (Figure 4). While writing this manuscript (September 2025), four additional novel species were published from South Africa under SeqCode rules [58,59]. Thus, SeqCode has the potential to accelerate the pace of rhizobial species discovery in South Africa.

5.2. Geographical Origin of the New Taxa of Rhizobia Native from African Soils Showed a Domination of South Africa

The 63 novel species of rhizobia native to Africa were discovered in 11 African countries, dominated by South Africa, with 23 species described to date (4 January 2026) (Table 2; Figure 4). Tunisia is the second most represented country, with 13 novel rhizobial species. The two countries accounted for approximately 57% of the total number of novel species of rhizobia described on the continent. Most African geographical regions are represented, including countries from the North (Algeria, Egypt, Morocco, and Tunisia), East (Ethiopia and Sudan), West (Côte d’Ivoire and Senegal), and South (Namibia, South Africa, and Zambia) (Figure 5). These countries are located in major hotspots of biodiversity in Africa, such as the Guinean forest in West Africa, the Succulent Karoo and Cape Floristic Region in Southern Africa, and the Mediterranean Basin in North Africa, Eastern Afromontane, and the Horn of Africa [132]. It also includes the Okavango region, which is a putative rich reservoir of Bradyrhizobium in Sub-Saharan Africa [28,29].

The unequal distribution of novel species observed among African countries can be explained by several factors.

(i) 

There is a lack of DNA sequencing platforms and bioinformatic pipelines. Most African countries lack DNA sequencing capacity and local expertise in bioinformatics analyses [133]. This situation limits their ability to describe native rhizobial biodiversity. In some cases, strong expertise in microbial taxonomy is lacking. Thus, international collaborations and academic journeys outside of the African country have been required to perform the batch of phenotypic and molecular analyses required to fulfill the minimal standards for a novel species described, except for a few cases (e.g., South Africa). North and South African countries usually collaborate with laboratories from Spain and Australia, respectively, while West African countries, such as Senegal and Côte d’Ivoire, usually interact with French-speaking countries in Europe (e.g., France and Switzerland) for the taxonomic description of native rhizobial species. Laboratories from Finland and Germany also substantially contributed to the description of native rhizobia from East and Central African countries, such as Ethiopia and Namibia (Table 2).

(ii) 

In recent years, there has been an intensive exploration of rich microbial niches in some African countries. This has opened the door for the description of several novel rhizobial species. For example, an exploratory study conducted in 2014 on a few legumes growing in the Okavango Delta in Namibia [28] described at least five Bradyrhizobium species, most of which were described by Dr. J. L. Grönemeyer (a former PhD student at the University of Bremen, Germany) (Table 2).

(iii) 

There is a growing interest in studying “orphan” legumes in many African countries. Many orphan legumes and their symbiotic bacteria have been explored in the few past years, including pigeonpea (Cajanus cajan (L.) Huth, Papilionoideae) [31], Bambara or Voandzou pea (Vigna subterranea (L.) Verdc., Papilionoideae) [108], Kersting’s groundnut (Macrotyloma geocarpum (Harms) Maréchal & Baudet, Papilionoideae) [134], etc. For example, from an exploratory study on pigeon pea published in 2016 [24], one novel species of Bradyrhizobium, B. ivorense, has been published from Côte d’Ivoire. Moreover, approximately three additional putative novel species of rhizobia have been identified in the symbionts of local C. cajan genotypes growing in Ivorian soils [135].

5.3. Bradyrhizobium and Mesorhizobium Cover About 51% of the Novel Species of Rhizobia Described from African Soils

The 63 species of rhizobia described from Africa are scattered in 11 genera of rhizobia (Figure 6) out of the 21 genera of rhizobia published to date. Bradyrhizobium (n = 18 species) and Mesorhizobium (n = 14 species) dominated in terms of species frequency. These two genera account for 50.8% of the total number of indigenous species found in African ecosystems. While new species of Bradyrhizobium were shown to be ubiquitous (with presence detected in 7 countries out of the list of 11 countries), the majority of species belonging to Mesorhizobium (2nd largest genus) were found in South Africa and Ethiopia. Both countries hosted 12 of the 14 species of Mesorhizobium described in Africa. These findings are not congruent with those of a previous study that reported a ubiquitous distribution of Mesorhizobium [66]. Gnangui et al. [66] used a metagenomic approach in the savannah zones of Northern Côte d’ Ivoire, however.

5.4. Legume Hosts of Native Rhizobia Species from Africa

Comprehensive reports on legume nodulation by rhizobia in Africa are sparse, notably in terms of the diversity of legumes studied so far and the taxonomy of their symbiotic rhizobia [35]. We help fill this knowledge gap by providing a summary of the growing body of knowledge on native rhizobial species from Africa and their legume hosts (Table 2). All the novel species of rhizobia native to Africa were isolated from 41 different hosts, of which Vachellia karroo (Hayne) Banfi & Galasso, Caesalpinioideae (Figure 7) provided the highest number of rhizobial species described (n = 7). Both alpha- and beta-rhizobia form nodules with V. karroo in Africa [136]. In terms of frequency of species isolation per host, V. karoo is followed by different species of Senegalia spp. (formerly Acacia spp.) [137]. Vachellia was split from the Acacia genus according to recent taxonomic revisions [138], but both are genera of the mimosoid clade in the recircumscribed Caesalpinioideae subfamily [139]. Until 2005, V. karroo was known as Acacia karroo, but according to an in-depth taxonomic analysis the Acacia genus was shown to be polyphyletic [137]. Therefore, the Acacia genus was split into five monophyletic genera, with all African Acacia now falling under Vachellia and Senegalia [138]. Ten (10) different species of rhizobia belonging to Bradyrhizobium, Ensifer, Mesorhizobium and Rhizobium genera have been isolated from five (05) species of Acacia (currently Senegalia), namely Acacia abyssinica (two species of rhizobia), A. dealbata (two species), A. saligna (three species), A. senegal (two species) and A. laeta (one species) (Table 2). Vachelia karroo and Senegalia/Acacia spp. are widespread in Africa and represent useful trees, including usages for soil fertility and restoration [138] (Figure 7).

Most of the legume hosts identified in this study were wild plants, including V. karroo (Figure 7). Only a few hosts are cultivated legumes that serve as grain legumes in African countries. They consist of common bean (Phaseolus vulgaris L., Papilionoideae), cowpea (Vigna unguiculata (L.) Walp., Papilionoideae), pigeonpea (Cajanus cajan (L.) Huth, Papilionoideae), and soybean (Glycine max (L.) Merr., Papilionoideae). Both wild and cultivated legumes contribute to soil fertility through N₂ fixation in symbiosis with native rhizobia. Among the 63 novel species isolated from the root systems of these two categories of legumes, we found that only seven (07) type strains were not capable of forming nodules on legume species tested so far. These type strains consist of Allorhizobium undicola ORS 992^T, Burkholderia aspalathi VG1C^T, Mesorhizobium retamae IRAMC:0171^T, Neorhizobium tunisiense RAMC 0178^T, Paraburkholderia fynbosensis WSM4178^T, Phyllobacterium ifriqiyense STM 370^T, and Phyllobacterium leguminum ORS 1419^T (Table 2). The other 56 type strains were effective for N₂ fixation. The potential use of the novel species as good candidates for developing biofertilizers was suggested and/or reported for the majority (64%) of the 56 nitrogen-fixing type strains. The symbiotic effectiveness of these type strains has been assessed in greenhouse and/or field trials (Table 2). Although some encouraging results have been obtained with these native rhizobial strains from Africa in terms of valorization, most of the bioinoculants commercialized in African countries are made with exotic strains [23,25]. Several technical issues could explain this [140,141].

6. Valorization Status of Native Rhizobia from Africa as Biofertilizers

Many initiatives have been launched in Africa to explore local rhizobial biodiversity and promote biofertilizer production in different countries [23,25]. Country-scale initiatives to promote biofertilizers are usually supported by local funds, while research programs covering several African countries are usually sponsored by international agencies such as the Food and Agricultural Organization (FAO), the International Atomic Energy Agency (IAEA), the International Institute of Tropical Agriculture (IITA), and the United Nations Educational, Scientific and Cultural Organization (UNESCO) [23,140]. In the 1980s, the United Nations Educational Scientific and Cultural Organization (UNESCO) and the Nitrogen Fixation in Tropical Agriculture (NifTAL) established a joint initiative under the Microbiological Resource Centers (MIRCENs) to support the research, development, and technological capability of biofertilizers in African regions [23,140]. To our knowledge, the latest large-scale, science-based “research-in-development” project established to support the production and use of rhizobia inoculants in different African countries was founded by the Bill and Melinda Gates Foundation (https://www.n2africa.org/home; accessed on 15 December 2025). The N₂Africa project was active from 2013 to 2019. They selected legume genotypes with good potential and identified their best-matching rhizobial strains to optimize grain legume production in fields. Despite decades of existence of the inoculation technology and sponsored research programs on legume–rhizobia in Africa, the production and use of inoculants in Africa is still at the pilot stage [23,140]. To date, few countries in Africa have progressed towards the commercialization of elite rhizobial strains [25]. Biofertilizer adoption and production are effective in a limited number of African countries. Only Kenya, Malawi, South Africa, and Zimbabwe have a satisfactory level of inoculant production and usage [23,25]. The main African biofertilizer-producing country is South Africa, with a world market value of USD 0.0293 billion in 2017 [41]. There is a limited level of valorization of indigenous elite strains into biological intrants. A review by Wekesa et al. [25] showed that rhizobia-based inoculants in Africa are usually developed with rhizobia isolated outside Africa. For example, most commercial soybean inoculants available on the market in African countries, such as Kenya, Uganda, and Zimbabwe, contain cells of Bradyrhizobium diazoefficiens strain USDA 110, originally obtained from the University of Hawaii NifTAL Project [140]. B. diazoefficiens USDA 110 (formerly known as B. japonicum USDA 110) [142,143] or B. japonicum strain MAR1491 [140] is commercialized as a legume biofertilizer on African markets under various commercial names (e.g., “Biofix”, “BIO-NFIX”, “MakBiofixer” [23,25,144]. In recent years, the feasibility of transferring Brazilian elite strains and inoculation technologies to African countries has been investigated. In this context, Bradyrhizobium japonicum SEMIA 5079, B. diazoefficiens SEMIA 5080, B. elkanii SEMIA 587, and B. elkanii SEMIA 5019 have been tested in Mozambique, together with B. diazoefficiens USDA 110 as a reference strain [145]. These initiatives are of great interest. However, the efficacy of the introduced bioinoculants is sometimes impaired in Africa and does not allow a substantial increase in yields after inoculation [146]. Several factors could lead to contrasting results, including the competitiveness of resident rhizobia that are better adapted to local conditions and are more competitive [144,147]. Local ecological factors, such as temperature, pH, and salinity, also influence the results of inoculation. Several studies have suggested that native rhizobial strains have evolved in African soils to better suit their environment, increasing their survival and competitiveness [29]. In this context, the development of indigenous performant isolates into bioinoculants must be a priority.

Our study revealed that the potential use as bioinoculants was reported for the majority of the type strains of all the rhizobial species described from Africa so far (Table 2). However, these elite rhizobial strains native to Africa are not well valorized. They are not yet commercially available as biofertilizers. There are only a few exceptions of native rhizobia used as commercial inoculants, including Bradyrhizobium strains CB756 and IRAT FA3. CB756 (host of origin = Macrotyloma africanum from Zimbabwe) is one of the most promiscuous strains, being effective against 19 genera and several legume species [40,148]. In Africa, it is used as a commercial inoculant for cowpea (Vigna unguiculata (L.) Walp., Papilionoideae), Bambara groundnut (Vigna subterranea (L.) Verdc., Papilionoideae) and Kersting’s groundnut (Macrotyloma geocarpum (Harms) Maréchal & Baudet, Papilionoideae) [149]. It has also been successfully used as a commercial inoculant for Cajanus cajan in Australia, although it showed a moderate competitiveness and poor capacity to survive in the soil and rhizosphere [148]. IRAT FA3 was isolated from soil in Cameroon. Subsequently, it was characterized at the Institut de Recherches Agronomiques Tropicales (IRAT) (Montpellier, France), and was henceforth known as Bradyrhizobium japonicum IRAT FA3 [150]. IRAT FA3 was further selected by the Nitrogen Fixation in Tropical Agricultural Legumes (NifTAL) project under the Microbial Resource Center Rhizobium (MIRCENs). It is used to inoculate strict, nodulating soybean varieties adapted to tropical agricultural zones in Africa and Latin America [151]. Recent studies have demonstrated that highly effective native Bradyrhizobium strains from Côte d’Ivoire outcompete IRAT FA3 in soybean varieties [146]. For comparative tests between IRAT FA3 and other indigenous Bradyrhizobium strains, soybean seeds were inoculated with approximately 10⁷ to 10⁸ freshly grown bacteria per seed or plantlet before planting [146,151]. In addition to soybean native biofertilizers, native performant strains have been selected for cowpea varieties, especially in Nigeria, where inoculant use for legumes was initiated in the 1970s [152]. Cowpea inoculants were prepared by incorporating three native Bradyrhizobium strains: Ife CR9, Ife CR15, and a B. japonicum strain. The local inoculants increased cowpea yield by 72%, 54%, and 10%, respectively, relative to uninoculated plants, whereas an imported peat-based commercial inoculant increased the yield by only 25% [152,153]. Taken together, these examples confirm that Bradyrhizobium-performing isolates for inoculation can be found in native soils in Africa. These native rhizobia deserve better valorization and utilization as biofertilizers in sustainable agriculture. The development of biofertilizers requires a strong collaboration between researchers, managers, and funding agencies, which could lead to more impactful actions [23,25].

In the rest of the world, native rhizobia are extensively studied and used as commercial inoculants for sustainable agriculture [154]. Non-African regions generally have detailed scientific knowledge of the diversity, taxonomy, and genomic features of their native rhizobia [40,155]. They also have important microbial genetic resources that support rhizobial research and inoculant development [154,156]. For example, the International Legume Inoculant Genebank (ILIG) established at Murdoch University (Australia) provides a centralized strain storage facility that includes 11,558 strains representing 96 bacterial species from 778 legume species. Strains were collected from >1200 locations across 100 countries over several years [154] (http://ilig.murdoch.edu.au). Moreover, many countries in non-African regions have developed advanced technology and/or commercial inoculant manufacturing industries to enable the agronomic and commercial application of rhizobial strains as biofertilizers [154,157,158]. Thus, the interest in knowing and valorizing native rhizobia is very effective in many regions of the world, while in Africa substantial technical and commercial efforts are needed.

7. Breaking Point Discoveries Using Native Rhizobia Strains from Africa

Many native rhizobial isolates from Africa have been used in pioneering demonstrations that Burkholderia (Beta-rhizobia) is a symbiotic genus with legumes. Historically, Moulin et al. [159] were the first to reveal the occurrence of legume nodulation by members of the β-subclass of Proteobacteria, commonly known as beta-rhizobia [160]. The study revealed that the strain STM678, originally isolated from the nodule of South African Aspalathus carnosa P.J. Bergius, Papilionoideae, was taxonomically very distant from known rhizobia, together with the strain STM815 isolated from Machaerium lunatum (L.f.) Ducke, Papilionoideae, French Guinea [159]. Before this discovery, the strain STM678 and other strains isolated from Aspalathus spp. (L.) are thought to belong to Bradyrhizobium sp. (alpha-rhizobia) [161]. Further taxonomic refinement led to the description of one of the first beta-rhizobial species of nodulating legumes, Burkholderia tuberum sp. nov. (Type strain STM678^T) [119]. To date, approximately 10 species of Burkholderia/Paraburkholderia have been described as native rhizobial isolates from Africa (Table 2). Moreover, two genera of rhizobia have been described using native rhizobial isolates from Africa, including Allorhizobium gen. nov. [67] and Azorhizobium gen. nov. [69]. The type strains of both genera were isolated from Senegal, highlighting the richness of microbial resources in West African ecosystems. Allorhizobium undicola gen. nov., sp. nov. ORS 992^T is an efficient nitrogen-fixing bacteria isolated from Neptunia natans (L.f.) Druce, Caesalpinioideae. Azorhizobium caulinodans gen. nov., sp. nov. ORS 571^T is a stem-nodulating nitrogen-fixing bacterium isolated from Sesbania rostrata Bremek & Oberm, Papilionoideae [69] (Figure 8).

Tropical legume species belonging to the genera Neptunia Lour., Aeschynomene L., and Sesbania Adans can form stem nodules and/or both root and stem nodules [69,162]. These peculiar symbiotic legume species commonly grow in wetlands. In Africa, they are commonly found in countries such as Senegal and Madagascar [69,162]. Interestingly, the long-term characterization of several rhizobia isolated from these legume genera has led to some breaking point discoveries. This includes the discovery of photosynthetic Bradyrhizobium isolates from Aeschynomene, including strains ORS285 (Senegal) and ORS278 (Senegal). The complete genome sequencing of photosynthetic Bradyrhizobium strains ORS278 and BTAi1 (USA) revealed, for the first time, that canonical nodABC genes and typical lipochito-oligosaccharidic Nod factors (NF) are not required to establish symbiosis with some legumes [163]. Moreover, nodulation (nod) gene-containing photosynthetic rhizobia, such as strain ORS285, can use both NF-dependent and NF-independent symbiotic processes, depending on the host plant [164,165]. These findings related to stem-nodulating rhizobia and the use of an alternative pathway by photosynthetic Bradyrhizobium to initiate symbiosis in NF-independent symbiotic strains extend our knowledge of legume–rhizobia symbiosis [162,163]. They also highlight the importance of studying native rhizobia and their symbiotic legumes in Africa.

8. Challenges and Future in Description of Novel Species of Rhizobia in Africa

Several technical issues represent real challenges that impede rapid progress in the description of novel species in Africa. Some of these are presented below.

(i)

Technical issues: An insufficient or limited access to DNA sequencing platforms and bioinformatic pipelines: Regional or hub bioinformatic platform developments have been proposed as possible solutions to address this limitation [133]. Capacity building is also required for African scientists lacking experience in using molecular techniques to explore microbial biodiversity. In general, molecular techniques complemented by traditional morpho-cultural analysis are used to characterize rhizobial strains [25]. Genome sequencing-based analysis supported by strong phylogenetic reconstructions (multiple gene (s) phylogeny, genome phylogeny, etc.) is also used to cluster new isolates with their closely related species. It is also used to identify putative new taxa that require further taxonomic description. Cut-off values of approximately 97% and 95–96% were used for species differentiation based on housekeeping genes (e.g., recA, glnII) and the average nucleotide identity (ANI) of genome sequences, respectively [53]. Moreover, metagenomic methods are currently used to decipher the composition of the African soil rhizobial microbiome [66]. Regional bioinformatic workshops promoted by the International Society of Microbial Ecology in Africa (ISME-Africa) and other microbial scientific societies could help train a new generation of African microbiologists [133].

(ii)

Legal issues: Several reports on rhizobia native to Africa have revealed several putative novel taxa waiting to be confirmed and/or published [35]. However, the slow pace at which new rhizobial taxa are described in some African countries is linked to their current restrictive national regulations [32]. Indeed, for a valid publication, the International Code of Nomenclature of Prokaryotes (ICNP) requires that an axenic culture of the proposed type strain for a novel species be deposited in two international culture collections and made available upon request without restrictions. Unfortunately, the application of this rule is not possible under several African countries’ national restrictive regulations related to access to biological resources in line with the Nagoya Protocol [32]. Under the ICNP, if deposits outside a country and the distribution of type strains are restricted, new microbial taxon names are not validly published [11,32]. In contrast, the rules of the recently published Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode) recognize genome data as nomenclature-type material [55]. Therefore, it represents a good alternative to ICNP rules and has the potential to facilitate the naming of new microbial taxa [55]. The seqCode is gaining interest among African countries for describing new rhizobial species, including in South Africa [32,58,59]. However, the validity of rhizobial naming under SeqCode rules is still debated. For example, a recent statement about the pioneering work of Van Lill et al. [32] under SeqCode by the ICNP subcommittee for rhizobia was formulated as follows: “Our Subcommittee found this article interesting as an example of the need for genome- based classifications (…) However, as a Subcommittee of the International Committee on Systematics of Prokaryotes, we cannot recognize the names proposed under SeqCode” [18]. Although the first cases of novel species described under SeqCode rules are not yet recognized, we believe that they represent more flexible rules for naming indigenous biological material in the African context. This could foster rapid progress in research on microbial biodiversity in Africa [32].

9. Summary and Conclusions

Comprehensive reports on legume nodulation by rhizobia in Africa are scarce in terms of the diversity of legumes studied and the taxonomy of their symbiotic bacteria. This study contributes to filling the knowledge gap by providing key data on the biodiversity and functional characteristics of rhizobia isolated from different ecosystems in Africa. The analysis revealed that the first novel species native to African soils was published in 1988, although research on rhizobia in Africa dates back to the 1950s. Interestingly, important breakthroughs have been made using native rhizobial strains from Africa, including the pioneering demonstration that Burkholderia (beta-rhizobia) is a symbiotic genus with legumes. In the last four decades, 63 novel species of rhizobia belonging to 11 different genera have been described from 11 African countries, suggesting a low rate of species discovery in general (~1.7 species/year). Approximately 80% of all species have been published within a short period of 15 years (2011–2025), representing an average of 4.2 species described per year. A peak was observed in 2024 with the publication of nine (09) novel species, the majority of which were described under the SeqCode rules. Thus, SeqCode has the potential to accelerate the taxonomic description of new taxa of rhizobia native to African countries.

Taken together, the review revealed that there is a growing body of research on the biodiversity of native rhizobia in Africa. Many strains have been isolated from different countries and further described as new species. However, their application as commercial biofertilizers is limited. We suggest different strategies for increasing the current outputs. They include the need to (i) facilitate access to sequencing capability and research infrastructure; (ii) integrate emerging taxonomic rules such as the SeqCode on microbial research in Africa; (iii) establish regional strain storage facilities to support collaborative rhizobial research and inoculant development; and (iv) develop an inoculant manufacturing industry to produce commercial biofertilizers. Such pillars are crucial for accelerating the description and valorization of native rhizobia from Africa.