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Beneficial microorganisms – their potential to improve crop production under changing climate in Africa


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Beneficial microorganisms – their potential to improve crop production under changing climate in Africa


For smallholder farmers in the semi-arid regions of Kenya who are unable to afford vital inorganic fertilisers for their crops, there is an alternative: the microorganisms that increase nutrient uptake in crops. Ezekiel Mugendi Njeru is mapping biodiversity patterns of these microorganisms to optimise their introduction to crops and improve yield and drought tolerance. These findings will inform and promote the development of affordable and sustainable crop production strategies to improve the performance, quality, sustainability and resilience of crops cultivated by smallholders in Kenya and beyond.

Food security challenges in Kenya

Agriculture today faces the unprecedented combination of growing demand for sufficient and healthy food to match Africa’s growing population, limited resources and a changing climate. To increase agricultural sustainability and conserve agroecosystems, scientists and farmers are searching for alternatives to the current soil health management practices. These include using certain root-associated microorganisms (living organisms that are too small to be seen with a naked eye) better known for improving the nutritional uptake of crops and contributing to resistance to stress caused by living organisms and other forces. Since most smallholder farmers in the semi-arid tropics of Kenya cannot afford inorganic fertilisers, the implementation of low-cost and sustainable fertilisation strategies that promote productive and resilient cropping systems is imperative.

In Kenya today, about 3.2 million people lack adequate and healthy food; compounding this is damage to the economy by the global Covid-19 pandemic. Most smallholder farmers cannot afford to invest in high-cost chemical fertilisers, quality pesticides or soil testing procedures; this limitation is a barrier to achieving a food secure nation as articulated in the UN Sustainable Development Goals, particularly SDG2 (end hunger), SDG3 (ensure healthy lives) and SDG8 (inclusive and sustainable economic growth.) Given that agriculture is the largest sector of the Kenyan economy, there is a pressing need to establish affordable and sustainable agronomic management practices to combat food insecurity, soil fertility depletion and environmental pollution. Food insecure families live mostly in rural areas where they depend to a great degree on farming for income. Therefore, poor crop production impoverishes the widest population of farmers and families in the country.

Beneficial microorganisms

Beneficial soil microorganisms are essential to productivity in cropping systems where the use of external inputs (such as fertiliser) is often limited. The understanding and use of microorganisms of significant ecological value in Kenya, and all of Africa, is still limited. Such information is a prerequisite to the implementation of efficient cropping systems that capitalise on biological processes, a key step towards agricultural sustainability and food security. The identification and isolation of microorganisms that promote crop nutritional uptake and drought tolerance is imperative to enable smallholder farmers who cannot afford inorganic fertilisers and costly irrigation systems. Furthermore, there is rising demand for healthier, more nutritious food and growing public awareness and concern about the negative ecological and health consequences of excessive use of agrochemicals like fertilisers and pesticides.

Bioprospecting indigenous microbes to increase smallholder crop production  

This research was carried out in dry areas of Eastern Kenya including Kitui, Embu and Tharaka Nithi Counties. Microorganisms with high ecological value, including selected bacteria (phosphate solubilizing and nitrogen fixing bacteria) and mycorrhizal fungi (soil-borne fungi that form a non-disease producing association with plant roots) , were targeted. These are believed to have the greatest potential to sustainably improve crop production and drought tolerance at low cost in smallholder farming systems.

An extensive search for these microorganisms was performed in smallholder farms. Once found, they were isolated, purified and identified, and their potential to improve crop production under greenhouse and field conditions was determined.

Remarkably, the mycorrhizal fungiused in this study enhanced the yield of field-grown maize in drought prone areas by 19.1%, a significant increase. Mycorrhizal fungi increase the uptake of essential plant growth nutrients such as phosphorus. They also help the plants to defend themselves against pathogens and drought stress.

The bacteria identified were also isolated from smallholder farming systems and tested for their ability to improve cowpea and maize production. Three of the types obtained in this study demonstrated an ability to significantly improve plant growth compared to a phosphate-treated control under greenhouse conditions.  

Nitrogen is one of the most limited nutrients in the soil. Six rhizobia (nitrogen fixing bacteria that are found in the soil and in the root nodules of legume crops) isolates with significantly higher nitrogen fixing potential than commercial rhizobia isolates were identified under greenhouse conditions. A combination of three of the isolates improved cowpea grain yield under field conditions by 28.6%. Follow up after field trials showed comparably enhanced production of these crops, especially farm-grown maize.

Pests that are driven by climate change are a major impediment to crop production. Biocontrol is the best option for smallholder farmers since it is affordable and environment friendly. Four indigenous Trichoderma (free living fungi that are common in soil) isolates with higher biocontrol efficacy compared to the commercially available Trichoderma against common maize diseases such as leaf blight were identified.

The future of beneficial microorganism research in Africa

As demonstrated in this study, African soils have a rich biodiversity of unexploited indigenous microorganisms. These microorganisms have considerable potential to revitalise food production and contribute to economic growth in Kenya, and Africa at large. Most smallholder farmers and other stakeholders have limited knowledge of the use of beneficial microorganisms to boost crop production and agroecosystem resilience. Moreover, research and production of microbial inoculants for use by farmers is not well established in Africa, leaving African farmers with very few options to inorganic agrochemicals, which are both prohibitive and are major climate change drivers.

This work has led me to focus on identifying indigenous microbes with the greatest potential to improve crop production due to their adaptation to the local agro-environment. Going forward, extensive farmer training and involvement in the research process will be incorporated into the study design to ease technology uptake by farmers. Once the most effective organisms are identified, efforts will focus on reproducing the isolates, assuring quality and developing distribution channels to make uptake by farmers as effective and affordable as possible. 

About Ezekiel Mugendi Njeru

Ezekiel Mugendi Njeru is a Kenyan microbiologist and Senior Lecturer of Environmental and Agricultural Microbiology at Kenyatta University in Kenya. Njeru has conducted extensive research on the use of beneficial microorganisms to improve crop production and resilience in smallholder agroecosystems in Africa. He is a Fellow of the Future Leaders – African Independent Research (FLAIR) programme, which supports talented early-career African researchers who have the potential to become leaders in their field. FLAIR is implemented through the Alliance for Accelerating Excellence in Science in Africa (AESA), a funding, agenda-setting, programme management initiative of the African Academy of Sciences (AAS), the African Union Development Agency (AUDA-NEPAD), founding and funding global partners, and through a resolution of the African Union Heads of Governments. FLAIR is supported by the UK Royal Society through the Global Challenges Research Fund (GCRF).