Symbiotic efficiency and genetic characterization of rhizobia and non rhizobial endophytes associated with cowpea grown in semi-arid tropics of Kenya

Unveiling remarkable bacterial diversity trapped by cowpea (Vigna unguiculata) nodules inoculated with soils from indigenous lands in Central-Western Brazil

Cowpea (Vigna unguiculata) is recognized as a promiscuous legume in its symbiotic relationships with rhizobia, capable of forming associations with a wide range of bacterial species. Our study focused on assessing the diversity of bacterial strains present in cowpea nodules when inoculated with soils from six indigenous lands of Mato Grosso do Sul state, Central-Western Brazil, comprising the Cerrado and the Pantanal biomes, which are known for their rich diversity. The DNA profiles (BOX-PCR) of 89 strains indicated great genetic diversity, with 20 groups and 23 strains occupying single positions, and all strains grouped at a final similarity level of only 25%. Further characterization using 16S rRNA gene sequencing revealed a diverse array of bacterial genera associated with the cowpea nodules. The strains (number in parenthesis) were classified into ten genera: Agrobacterium (47), Ancylobacter (2), Burkholderia (12), Ensifer (1), Enterobacter (1), Mesorhizobium (1), Microbacterium (1), Paraburkholderia (1), Rhizobium (22), and Stenotrophomonas (1), split into four different classes. Notably, only Ensifer, Mesorhizobium, Rhizobium, and Paraburkholderia are classified as rhizobia. Phylogenetic analysis was conducted based on the classes of the identified genera and the type strains of the closest species. Our integrated analyses, combining phenotypic, genotypic, and phylogenetic approaches, highlighted the significant promiscuity of cowpea in associating with a diverse array of bacteria within nodules, showcasing the Brazilian soils as a hotspot of bacterial diversity.

Non-Rhizobial Endophytes (NREs) of the Nodule Microbiome Have Synergistic Roles in Beneficial Tripartite Plant-Microbe Interactions

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).

Prevalence, diversity and applications potential of nodules endophytic bacteria: a systematic review

Legumes are renowned for their distinctive biological characteristic of forming symbiotic associations with soil bacteria, mostly belonging to the Rhizobiaceae familiy, leading to the establishment of symbiotic root nodules. Within these nodules, rhizobia play a pivotal role in converting atmospheric nitrogen into a plant-assimilable form. However, it has been discerned that root nodules of legumes are not exclusively inhabited by rhizobia; non-rhizobial endophytic bacteria also reside within them, yet their functions remain incompletely elucidated. This comprehensive review synthesizes available data, revealing that Bacillus and Pseudomonas are the most prevalent genera of nodule endophytic bacteria, succeeded by Paenibacillus, Enterobacter, Pantoea, Agrobacterium, and Microbacterium. To date, the bibliographic data available show that Glycine max followed by Vigna radiata, Phaseolus vulgaris and Lens culinaris are the main hosts for nodule endophytic bacteria. Clustering analysis consistently supports the prevalence of Bacillus and Pseudomonas as the most abundant nodule endophytic bacteria, alongside Paenibacillus, Agrobacterium, and Enterobacter. Although non-rhizobial populations within nodules do not induce nodule formation, their presence is associated with various plant growth-promoting properties (PGPs). These properties are known to mediate important mechanisms such as phytostimulation, biofertilization, biocontrol, and stress tolerance, emphasizing the multifaceted roles of nodule endophytes. Importantly, interactions between non-rhizobia and rhizobia within nodules may exert influence on their leguminous host plants. This is particularly shown by co-inoculation of legumes with both types of bacteria, in which synergistic effects on plant growth, yield, and nodulation are often measured. Moreover these effects are pronounced under both stress and non-stress conditions, surpassing the impact of single inoculations with rhizobia alone.

Food waste compost and digestate as novel fertilizers: Impacts on antibiotic resistome and potential risks in a soil-vegetable system

As a novel agricultural practice, the reuse of food waste compost and digestate as fertilizers leads to a circular economy, but inevitably introduces bio-contaminants such as antibiotic resistance genes (ARGs) into the agroecosystem. Moreover, heavy metal and antibiotic contamination in farmland soil may exert selective pressures on the evolution of ARGs, posing threats to human health. This study investigated the fate, influencing mechanisms and potential risks of ARGs in a soil-vegetable system under different food waste fertilization and remediation treatments and soil contamination conditions. Application of food waste fertilizers significantly promoted the pakchoi growth, but resulted in the spread of ARGs from fertilizers to pakchoi. A total of 56, 80, 84, 41, and 73 ARGs, mobile genetic elements (MGEs) and metal resistance genes (MRGs) were detected in the rhizosphere soil (RS), bulk soil (BS), control soil (CS), root endophytes (RE), and leaf endophytes (LE), respectively. Notably, 7 genes were shared in the above five subgroups, indicating a specific soil-root-endophytes transmission pathway. 36 genes were uniquely detected in the LE, which may originate from airborne ARGs. The combined application of biochar and fertilizers reduced the occurrence of ARGs and MGEs to some extent, showing the remediation effect of biochar. The average abundance of ARGs in the RS, BS and CS was 3.15 × 10-2, 1.31 × 10-2 and 2.35 × 10-1, respectively. Rhizosphere effects may reduce the abundance of ARGs in soil. The distribution pattern of ARGs was influenced by the types of soil, endophyte and contaminant. MGEs is the key driver shaping ARGs dynamics. Soil properties and pakchoi growth status may affect the bacterial composition, and consequently regulate ARGs fate, while endophytic ARGs were more impacted by biotic factors. Moreover, the average daily doses of ARGs from pakchoi consumption is 107-109 copies/d/kg, and its potential health risks should be emphasized.

Bacterial Endophytes from Legumes Native to Arid Environments Are Promising Tools to Improve Mesorhizobium-Chickpea Symbiosis under Salinity

Symbiotic nitrogen fixation is a major contributor of N in agricultural ecosystems, but the establishment of legume-rhizobium symbiosis is highly affected by soil salinity. Our interest is focused on the use of non-rhizobial endophytes to assist the symbiosis between chickpea and its microsymbiont under salinity to avoid loss of production and fertility. Our aims were (1) to investigate the impact of salinity on both symbiotic partners; including on early events of the Mesorhizobium-chickpea symbiosis, and (2) to evaluate the potential of four non-rhizobial endophytes isolated from legumes native to arid regions (Phyllobacterium salinisoli, P. ifriqiyense, Xanthomonas translucens, and Cupriavidus respiraculi) to promote chickpea growth and nodulation under salinity. Our results show a significant reduction in chickpea seed germination rate and in the microsymbiont Mesorhizobium ciceri LMS-1 growth under different levels of salinity. The composition of phenolic compounds in chickpea root exudates significantly changed when the plants were subjected to salinity, which in turn affected the nod genes expression in LMS-1. Furthermore, the LMS-1 response to root exudate stimuli was suppressed by the presence of salinity (250 mM NaCl). On the contrary, a significant upregulation of exoY and otsA genes, which are involved in exopolysaccharide and trehalose biosynthesis, respectively, was registered in salt-stressed LMS-1 cells. In addition, chickpea co-inoculation with LMS-1 along with the consortium containing two non-rhizobial bacterial endophytes, P. salinisoli and X. translucens, resulted in significant improvement of the chickpea growth and the symbiotic performance of LMS-1 under salinity. These results indicate that this non-rhizobial endophytic consortium may be an appropriate ecological and safe tool to improve chickpea growth and its adaptation to salt-degraded soils.

Phenotypic, molecular, and symbiotic characterization of the rhizobial symbionts isolated from Acacia saligna grown in different regions in Morocco: a multivariate approach

The introduced species Acacia saligna is a very promiscuous host as it can be efficiently nodulated with a wide range diversity of rhizobia taxa, including both fast and slow-growing strains. Fourteen nitrogen (N)-fixing bacteria were isolated from root nodules of wild Acacia saligna growing in distinct geographic locations in Morocco and were examined for their symbiotic efficiency and phenotypic properties. Multivariate tools, such as principal component analysis (PCA) and hierarchical clustering analysis (HCA), were used to study the correlation between phenotypic and symbiotic variables and discriminate and describe the similarities between different isolated bacteria with respect to all the phenotypic and symbiotic variables. Phenotypic characterization showed a variable response to extreme temperature, salinity and soil pH. At the plant level, the nodulation, nitrogen fixation, and the shoot and root dry weights were considered. The obtained results show that some of the tested isolates exhibit remarkable tolerances to the studied abiotic stresses while showing significant N2 fixation, indicating their usefulness as effective candidates for the inoculation of acacia trees. The PCA also allowed showing the isolates groups that present a similarity with evaluated phenotypic and symbiotic parameters. The genotypic identification of N2-fixing bacteria, carried out by the 16S rDNA approach, showed a variable genetic diversity among the 14 identified isolates, and their belonging to three different genera, namely Agrobacterium, Phyllobacterium and Rhizobium.

Contribution of Biofertilizers to Pulse Crops: From Single-Strain Inoculants to New Technologies Based on Microbiomes Strategies

Pulses provide distinct health benefits due to their low fat content and high protein and fiber contents. Their grain production reaches approximately 93,210 × 103 tons per year. Pulses benefit from the symbiosis with atmospheric N2-fixing bacteria, which increases productivity and reduces the need for N fertilizers, thus contributing to mitigation of environmental impact mitigation. Additionally, the root region harbors a rich microbial community with multiple traits related to plant growth promotion, such as nutrient increase and tolerance enhancement to abiotic or biotic stresses. We reviewed the eight most common pulses accounting for almost 90% of world production: common beans, chickpeas, peas, cowpeas, mung beans, lentils, broad beans, and pigeon peas. We focused on updated information considering both single-rhizobial inoculation and co-inoculation with plant growth-promoting rhizobacteria. We found approximately 80 microbial taxa with PGPR traits, mainly Bacillus sp., B. subtilis, Pseudomonas sp., P. fluorescens, and arbuscular mycorrhizal fungi, and that contributed to improve plant growth and yield under different conditions. In addition, new data on root, nodule, rhizosphere, and seed microbiomes point to strategies that can be used to design new generations of biofertilizers, highlighting the importance of microorganisms for productive pulse systems.

Molecular identification and characterization of phytobeneficial osmotolerant endophytic bacteria inhabiting root nodules of the Saharan tree Vachellia tortilis subsp. raddiana

Nodular endophytes of drought-tolerant legumes are understudied. For this reason, we have isolated and studied non-symbiotic endophytic bacteria from nodules of Vachellia tortilis subsp. raddiana, a leguminous tree adapted to the harsh arid climate of Southern Morocco. Rep-PCR analysis followed by 16S rDNA sequencing revealed two main genera, Pseudomonas and Bacillus. Isolates responded variably to salt and water stresses, and mostly produced exopolysaccharides. Differences concerned also plant growth-promoting activities: phosphate, potassium, and zinc solubilization; biological nitrogen fixation; auxin, siderophore, ammonia, and HCN production; and ACC deaminase activity. Some strains exhibited antagonistic activities against phytopathogenic fungi (Fusarium oxysporum and Botrytis cinerea) and showed at least two enzymatic activities (cellulase, protease, chitinase). Four selected strains inoculated to vachellia plants under controlled conditions have shown significant positive impacts on plant growth parameters. These strains are promising bio-inoculants for vachellia plants to be used in reforestation programs in arid areas increasingly threatened by desertification.

Non-rhizobia are the alternative sustainable solution for growth and development of the nonlegume plants

The major research focus for biological nitrogen fixation (BNF) has mostly been on typical rhizobia with legumes. But the newly identified non-rhizobial bacteria, both individually or in combination could also be an alternative for nitrogen supplementation in both legumes and nonlegume plants. Although about 90% of BNF is derived from a legume - rhizobia symbiosis, the non-legumes specially the cereals lack canonical nitrogen fixation system through root-nodule organogenesis. The non-rhizobia may colonize in the rhizosphere or present in endophytic/associative nature. The non-rhizobia are well known for facilitating plant growth through their potential to alleviate various stresses (salt, drought, and pathogens), acquisition of minerals (P, K, etc.), or by producing phytohormones. Bacterial symbiosis in non-legumes represents by the Gram-positive Frankia having a major contribution in overall fortification of usable nitrogenous material in soil where they are associated with their hosts. This review discusses the recent updates on the diversity and association of the non-rhizobial species and their impact on the growth and productivity of their host plants with particular emphasis on major economically important cereal plants. The future application possibilities of non-rhizobia for soil fertility and plant growth enhancement for sustainable agriculture have been discussed.

Treatment with atypical rhizobia, Pararhizobium giardinii and Ochrobactrum sp. modulate the rhizospheric bacterial community, and enhances Lens culinaris growth in fallow-soil

Diazotrophic nodule isolates are acknowledged promoters of plant growth and rhizospheric community. Consequently, in the lentil agroecosystem, inoculation of atypical rhizobial isolates could be a viable alternative to chemical fertilizers for fallow land usage optimization. The aim of this study is to evaluate and select the rhizobial isolates of lentil nodules with plant-growth-promoting (PGP) attributes and to elucidate their application in rice-fallow soil for determining the growth of lentils and its impact on the rhizospheric bacterial community. Lentil's nodule isolates were identified and screened for their PGP attributes, biofilm, exopolysaccharide (EPS) formation, and early plant growth promotion. The pot experiment with the selected atypical rhizobial isolates Pararhizobium giardinii (P1) and Ochrobactrum sp. (42S) significantly enhanced germination, vigour index, nodule formation (P1 60%, 42S 42% increase), nodule fresh weight, shoot length (65% P1 & 35% 42S), and chlorophyll content as compared to the uninoculated control treatment. The genes for nitrogen fixation nifH and nifK were detected in both isolates. Scanning Electron Microscopy (SEM) revealed successful root and nodule colonization by both isolates, while Transmission Electron Microscopy (TEM) displayed nitrogen-fixing zones within root nodules. Proteobacteria predominated in the lentil rhizosphere of all the treatments. Whereas, application of either P1 or 42S increased Rhizobium, Mesorhizobium, and Bradyrhizobium genra, thus positively modulating rhizospheric community structure. The correlation network analysis revealed an abundance of some interdependent bacterial genera with a possible role in overall plant growth. Functional genes for siderophore biosynthesis and ABC transporter were positively modulated by application of either P1 or 42S. This study showed the significant effect of P. giardinii P1 and Ochrobactrum sp. 42S of L. culinaris on lentil growth, improving fallowsoil health for optimum usage, and modulated rhizospheric community structure which strongly manifest prospects of low-cost, eco-friendly and sustainable biofertilizers.

Genetic control of earliness in cowpea (Vigna unguiculata (L) Walp)

Global climate change is expected to further intensify the already harsh conditions in the dry savannah ecological zones of sub-Saharan Africa, posing serious threats to food and income security of millions of smallholder farmers. Breeding cowpea for improved earliness could help minimize this risk, by ensuring that the crops complete their lifecycle before the cessation of rainfall. In this study, we crossed two sets of cowpea lines showing contrasting phenotypes for earliness in terms of days to 50% flowering (DFF). One set of the lines comprised three extra-early parents (viz.: Sanzi-Nya, Tobonaa and CB27, 30-35 DFF), and the other set consisted of three early-to-medium maturity lines (viz.: Kirkhouse-Benga, Wang-Kae and Padi-Tuya, 42-45 DFF). The derived crosses and their parents were evaluated for key earliness-related traits at Nyankpala and Manga sites of CSIR-Savanna Agricultural Research Institute (SARI), Ghana. To unravel the genetic control of measured traits, we compared the appropriateness of Chi-square goodness of fit tests using classical Mendelian ratios, and frequency distribution (histogram)-related statistics such as skewness and kurtosis. The Chi-square test suggested a single dominant gene mode of inheritance for earliness, whereas the quantitative methods implicated duplicate epistasis and complementary epistatic gene actions. Our results show that coercing segregating lines to fit into classical Mendelian ratios to determine the genetic control of earliness could be misleading, due to its subjectivity. Thus, the genetic control of earliness in cowpea is governed by complementary and duplicate epistasis. The most applicable breeding approach for traits influenced by duplicate epitasis is selection of desirable recombinants from segregating populations developed from bi-parental crosses. Complementary epitasis, as found in the Wang-Kae × CB27 cross, could be exploited in developing improved extra-early lines through backcrossing. Heritability and genetic advance estimates were high for days to first flower appearance (DFFA) and days to 95 % pod maturity (DNPM) in the Padi-Tuya × CB27 and Kirkhouse-Benga x CB27 crosses, indicating that breeding for extra-earliness is feasible. CB27 could be a good donor for introgression of earliness into medium to late maturing improved cowpea varieties, because crosses developed from it had high heritability and genetic advance estimates.

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

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

Genetic variability, heritability and correlation analysis among maturity and yield traits in Cowpea (Vigna unguiculata (L) Walp) in Northern Ghana

Experimental studies were conducted to evaluate 16 advanced breeding lines of cowpea (Vigna unguiculata (L) Walp) for genetic variability, heritability and correlation between maturity and yield related traits. The genotypes exhibited significant (P < 0.05) differences for the eight traits evaluated viz., number of days to 50 % flowering, number of days to 90 % pod maturity, plant height at maturity, number of pods per plant, number of seeds per pod, pod yield, grain yield and hundred seed weight. SARI-3-11-100, SARI-6-2-6, SARVX-09-004 and IT07K-299-6 had grain yields of 1.99 ± 0.30, 1.88 ± 0.20, 1.95 ± 0.30 and 1.91 ± 0.20 t/ha, respectively, which were significantly higher than the check (Songotra) (1.68 ± 0.01 t/ha). In addition, SARI-5-5-5 matured significantly earlier than the check but no significant difference was observed for grain yield. The higher value of phenotypic component compared to the corresponding genotypic component for all the traits suggest that there was an environmental influence on the performance of the genotypes. Hence, the need for multi-location evaluation of the promising lines for onward release if found stable. The information provided in this study, can be exploited in cowpea breeding program.