Microbial symbioses deal with the symbiotic interactions between a given microorganism and another host. The most widely known and investigated microbial symbiosis is the association between leguminous plants and nitrogen-fixing rhizobia. It is one of the best-studied plant–microbe interactions that occur in the soil rhizosphere and one of the oldest plant–microbe interactions extensively studied for the past several decades globally. Until recently, it used to be a common understanding among scientists in the field of rhizobia and microbial ecology that the root nodules of thousands of leguminous species only contain nitrogen-fixing symbiotic rhizobia. With the advancement of molecular microbiology and the coming into being of state-of-the-art biotechnology innovations, including next-generation sequencing, it has now been revealed that rhizobia living in the root nodules of legumes are not alone. Microbiome studies such as metagenomics of the root nodule microbial community showed that, in addition to symbiotic rhizobia, other bacteria referred to as non-rhizobial endophytes (NREs) exist in the nodules. This review provides an insight into the occurrence of non-rhizobial endophytes in the root nodules of several legume species and the beneficial roles of the tripartite interactions between the legumes, the rhizobia and the non-rhizobial endophytes (NREs).

Prolonged inoculation of soya bean (Glycine max L.) farms with exotic strains of Bradyrhizobium species starting in the 1960s resulted in the establishment of populations of Bradyrhizobium strains in the soils of several soya bean farms in South Africa. With the increasing number of new soya bean genotypes in the country, it is challenging to determine which genotypes are highly compatible with a given rhizobium strain. In this study, we investigated the symbiotic compatibility of native rhizobial isolates and the strains from the South African Rhizobium Culture Collection (SARCC) on ten selected locally available soya bean genotypes. A glasshouse soil trap experiment using soil samples collected from Lothair, Bothaville, and Standerton was performed on five cultivars. The trapped rhizobial strains were further screened in the glasshouse to authenticate their nodulation compatibility with the different soya bean cultivars. The rhizobial strains showed significant nodulation compatibility with the selected cultivars. These strains were also tested for beneficial traits in vitro and characterized using DNA sequencing methods to elucidate their taxonomic identity. Some of the most nodulation-compatible strains characterized as Bradyrhizobium and Sinorhizobium species exhibited significant symbiotic performance in terms of plant biomass, nodule number, and nodule dry weight. The study generated valuable data that provide information on the extent of symbiotic compatibility of some of the existing cultivars used in South Africa with native rhizobia and whether inoculation of soya bean with commercial products is vital on some soya bean farms.

Leguminous crops contribute approximately 40–60 million tonnes of biologically fixed nitrogen annually to agricultural soils through symbiotic associations with rhizobia, underpinning the sustainability of diverse cropping systems. However, rising herbicide use, driven by the adoption of herbicide-tolerant crops and intensifying weed resistance, poses significant threats to the integrity of the legume–rhizobia symbiosis, depending on the herbicide type, exposure level, soil conditions, and microbial variability. This review synthesizes possible herbicide-induced disruptions of symbiotic nitrogen fixation, including herbicide impairment of symbiosis through multiple interconnected pathways, such as cytotoxicity to rhizobia and soil microbial communities, inhibition of nod-gene-inducing flavonoid biosynthesis by the host plant, suppression of Nod factor production and signalling by rhizobial disruption of cytoskeletal functioning that enhances the progression of infection thread formation, oxidative stress induction, alterations of auxin–cytokinin homeostasis, and modification of soil physicochemical parameters that can affect rhizobial survival and competitiveness. Though still unclear, laboratory (in vitro), field and glasshouse studies suggest that symbiotic impairment is dose- and time-dependent, species-specific, and strongly influenced by the rhizobial strain and probably the host plant species variety. Mitigation strategies, such as the use of herbicide-tolerant rhizobial strains, organic soil amendments, optimized herbicide application, and integrated weed management frameworks, have shown considerable promise. However, many research gaps exist regarding tropical legume systems and the long-term consequences of herbicide use on the legume–rhizobia symbiosis. Little is known about the direct effects of herbicides on the bacterial symbionts and host plants, as well as how soil type, climate and management/agronomic practices influence herbicide exposure and the effect of herbicide degradation products on rhizobial survival, competitiveness, and symbiotic N₂-fixation. The existence of herbicide-tolerant soybean suggests that not all herbicides are lethally phytotoxic, an aspect that can be exploited for sustainable agriculture.