Smallholder agroecosystems play a key role in the world's food security providing more than 50% of the food produced globally. These unique agroecosystems face a myriad of challenges and remain largely unsupported, yet they are thought to be a critical resource for feeding the projected increasing human population in the coming years. The new challenge to increase food production through agricultural intensification in shrinking per capita arable lands, dwindling world economies, and unpredictable climate change, has led to over-dependence on agrochemical inputs that are often costly and hazardous to both human and animal health and the environment. To ensure healthy crop production approaches, the search for alternative ecofriendly strategies that best fit to the smallholder systems have been proposed. The most common and widely accepted solution that has gained a lot of interest among researchers and smallholder farmers is the use of biological agents; mainly plant growth promoting microorganisms (PGPMs) that provide essential agroecosystem services within a holistic vision of enhancing farm productivity and environmental protection. PGPMs play critical roles in agroecological cycles fundamental for soil nutrient amelioration, crop nutrient improvement, plant tolerance to biotic and abiotic stresses, biocontrol of pests and diseases, and water uptake. This review explores different research strategies involving the use of beneficial microorganisms, within the unique context of smallholder agroecosystems, to promote sustainable maintenance of plant and soil health and enhance agroecosystem resilience against unpredictable climatic perturbations.

Climbing bean (Phaseolus vulgaris L.) production in Kenya is greatly undermined by low soil fertility, especially in agriculturally prolific areas. The use of effective native rhizobia inoculants to promote nitrogen fixation could be beneficial in climbing bean production. In this study, we carried out greenhouse and field experiments to evaluate symbiotic efficiency, compare the effect of native rhizobia and commercial inoculant on nodulation, growth and yield parameters of mid-altitude climbing bean (MAC 13 and MAC 64) varieties. The greenhouse experiment included nine native rhizobia isolates, a consortium of native isolates, commercial inoculant Biofix, a mixture of native isolates + Biofix, nitrogen treated control and a non-inoculated control. In the field experiments, the treatments included the best effective native rhizobia isolate ELM3, a consortium of native isolates, a commercial inoculant Biofix, a mixture of native isolates + Biofix, and a non-inoculated control. Remarkably, four native rhizobia isolates ELM3, ELM4, ELM5 and ELM8 showed higher symbiotic efficiencies compared to the Biofix. Interestingly, there was no significant difference in symbiotic efficiency between the two climbing bean varieties. Field results demonstrated a significant improvement in nodule dry weight and seed yields of MAC 13 and MAC 64 climbing bean varieties upon rhizobia inoculation when compared to the non-inoculated controls. Inoculation with ELM3 isolate resulted to the highest seed yield of 4,397.75 kg ha-1, indicating 89 % increase over non-inoculated control (2,334.81 kg ha-1) and 30 % increase over Biofix (3,698.79 kg ha-1). Farm site significantly influenced nodule dry weight and seed yields. This study, therefore, revealed the potential of native rhizobia isolates to enhance delivery of agroecosystem services including nitrogen fixation and bean production. Further characterization and mapping of the native isolates will be imperative in development of effective and affordable commercial inoculants.

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

Globally, there is great concern about expanding agricultural activities due to their impact in the conservation of agrobiodiversity. African continent is known for its richness in biodiversity. In Kenya, there is a continuous unabated expansion of agriculture into natural habitats due to demographic and economic pressures posing a significant threat to biodiversity. Therefore, there is a need to study biodiversity loss and its regain through practices in agricultural landscapes. In this study, we assessed the status of agrobiodiversity and its contribution to food security in four agroecological zones of Eastern Kenya. Sixty households were sampled from two selected agroecological zones (upper and lower midland zones) in Embu and Tharaka-Nithi counties. Structured questionnaires and checklists were used to collect the data. Thirty-nine crop species were identified dominated by vegetables, fruits, legumes and cereals with relative densities of 28.8, 20.5, 18.3 and 8.3 %, respectively. Embu Lower Midland and Tharaka-Nithi Lower Midland zones had relatively higher crop species richness of 243 and 240, respectively, and Shannon–Wiener diversity indices (H′) of 3.403 and 3.377, respectively, compared with Embu Upper Midland and Tharaka-Nithi Upper Midland zones with species richness of 229 and 207, respectively, and H′ of 3.298 and 3.204, respectively. Households from lower midland zones with high crop diversity and richness were more food secure compared with those from the Upper Midland zones with low crop diversity and richness. These findings suggest that farm production systems with high agrobiodiversity contributed more toward food security among smallholder farmers in the selected sites.

Relay intercropping is considered a valuable agroecological practice to increase and stabilize crop yields while ensuring the provision of several ecosystem services as well as sustainability and resilience to changing climatic conditions. However, farmers are still reluctant in the use of intercropping practices since there is a huge knowledge gap regarding the time of sowing, sowing ratio, crop stand density, and cultivar choice. In this study, we carried out a 3-year field experiment in Central Italy to assess the effect of relay intercropping on the agronomic performance and competitiveness of winter durum wheat (Triticum durum Desf. cv. Minosse) and spring lentil (Lens culinaris Medik. cv. Elsa) under a low-input management system, comparing different crop stand types (monocrop vs. intercrop) and target plant densities (350 plants m²—full dose vs. 116 plants m²—1/3 dose). The results revealed that intercropping increased grain yield compared to monocropping: significantly (p < 0.0001) against both monocrops in 2021 and non-significantly against durum wheat in 2019 and 2020. Yield advantage in both intercropping systems ranged between 164 and 648%. Durum wheat competitiveness was stronger in 2019 and 2021, while lentil was the most competitive component in 2020. Intercropping favored P accumulation in durum wheat shoots. There was no difference in grain yield of both crops between the highly- and lowly-dense system in 2020 and 2021. Both intercropping strategies were as effective as mechanical hoeing in controlling weeds and proved beneficial in stabilizing lentil productivity. Further economic analysis capturing the additional costs incurred in intercropping and mechanical weeding would highlight the magnitude of profitability of these systems.

Purpose: Commercial production and the use of liquid vermicompost extract (LVE) is gaining attention as a technique that supports integrated soil-microbial-crop management for sustainable agriculture. However, the interaction effects of LVE, arbuscular mycorrhizal fungi (AMF), and host plants on the delivery of agroecosystem services in alkaline soil have been less studied. Methods: We carried out a 3-year field experiment in Central Italy, to investigate the short-term effect of LVE on soil mycorrhizal inoculum potential (MIP), AMF root colonization, and productivity of berseem clover, lentil, and sunflower. LVE produced in different years were screened for microbial properties using Illumina Miseq sequencing. LVE was applied at seeding, crop stem elongation and flowering stages. Control crops received water as a placebo. Results: LVE bacterial communities were more diverse and showed a higher turnover between 2019 and 2020 than fungal communities. Diverse microbial groups, the majority of which belonged to phyla Proteobacteria, Bacteroidetes, Firmicutes, and Mucoromycota, were detected, including N-fixers (Flavobacterium, Malikia, and Citrobacter), P-solubilizers (Pseudomonas), and C-degraders (Tolumonas, Arcobacter, and Mucor). Notably, LVE treatment enhanced soil MIP and AMF root colonization in most crops, but selectively improved shoot biomass of berseem clover (+ 32%) and sunflower (+ 34%), and grain yield (+ 37%) and oil concentration (+ 5%) in sunflower, compared to the corresponding non-treated controls. Conclusions: LVE had diverse groups of bacteria and a few fungal taxa, and its application enhanced mycorrhizal properties and selected growth- and yield-related variables in lentil, berseem clover, and sunflower. This could be due to LVE’s biostimulating effect arising from the vermicompost-associated microbiome and biomolecules.