Banana farming is a major economic activity in Kenya. However, the current production trends by the smallholder farmers who form 85% of the banana producers in Kenya do not meet the market demand (Okumu et al., 2011). This is because there are various factors directly affecting production such as soil health as well as pests and diseases (Köberl et al., 2017).

There has been increasing interest in soil health, specifically microbial diversity in soil habitat. This is because soil microbial communities are considered as essential in improving soil health and quality. A wide range of microorganisms are essential in soil function since microbial communities are key contributors to sustainable agriculture. Microbes are known to act as mediators in many processes that are involved in agricultural production (Lupwayi et al., 1998; Rondon et al., 2000 and Gupta et al., 2018).

It has been observed that farm practices such as conservation tillage and legume-based crop rotation supports soil microbial communities and may have direct positive effects on agricultural ecosystems (Nguyen et al., 2018). The culturing techniques of studying microorganisms are not efficient in their study since majority of the microbes are unculturable (Goel et al., 2018)). Advances in molecular application in determining microbial diversity in nature shows that there is a lot of information that was not previously accessible (Gupta et al., 2018). Therefore, understanding the factors that influence microbial communities can assist greatly in the innovation of new agricultural tools for sustainable environment (Gupta et al., 2018).

There are numerous soil borne diseases that act as limiting factors in banana production all over the world (Köberl et al., 2017). Most farmers use conventional methods in their control that mainly target pathogens using antibacterial agents, pesticides and fungicides and this has the potential of reducing the soil microbial community (Dita et al., 2018). Therefore, studying microbial communities can aid in creating tools to mitigate problems affecting essential microbial communities (Chaparro et al., 2012).

Recent reports indicate that stressors that affect soil biodiversity such as human activities, the decline in soil organic matter and degradation of land has led to the loss of aboveground and below ground biodiversity (Orgiazzi et al., 2016). The decline in soil health and fertility including biological degradation (organic matter) is a worrying trend and has the potential to lower productivity significantly. Constant monitoring of soil health status is an essential factor in processes of development of land management systems that ensure the sustainability of soil resources (Tilhou et al., 2021). In order to reclaim the damage to soil and ensure global agricultural sustainability, the identification of these stressors as well as development of sustainable methods such as bioremediation is important (Tahat et al., 2020).

The soil microbial communities in agroecosystems play a crucial role in plant growth and health. Recent studies have been focusing on microbial communities in continuous cropping systems and their roles. Understanding their roles as well as environmental factors that affect the communities is important in improving banana production (Berg et al., 2017 and Gómez-Lama et al., 2021). Studying soil microbial diversity in relation to other soil physicochemical parameters is essential. This aids greatly in identifying factors affecting beneficial microbial communities, thus highlighting the need for adoption and development of tools for sustainable agricultural practices (Gómez-Lama et al., 2021). The current study was aimed at determining microbial diversity and abundance in banana rhizospheric soil from banana producing regions in Kenya and the influence of soil physicochemical parameters on the distribution of fungal and bacterial communities.

Soil health plays a critical role in ensuring the stability of microbial communities. Soil organic carbon levels are a good indicator of the health status of soil and positively correlate to the yield of crops (Bennett et al., 2010). Highly acidic conditions were detected in the majority of soil samples collected from Embu and Nyamira which is worrying. Delgado and Gómez (2016) has reported that a pH of below 5.5 is harmful to agroecosystems since it negatively influences plant and environment interaction, indicating that the soil pH in Embu County poses a great danger to agroecosystems.

It has been reported that rhizospheric soil that is closest to the root system and is essential in studying microbial communities (Berendsen et al., 2012). Sui et al. (2019) and Chaudhary et al. (2021) Zhu et al. (2018), reported that Actinobacteria are among the most identified rhizospheric bacteria phyla in banana plants. The abundance of Proteobacteria and Actinobacteria has been previously linked to long periods of production (Pang et al., 2021). However, Actinobacteria have been reported to produce antibiotics as well as having an important role in organic matter decomposition (Zhang et al., 2017). Berendsen et al. (2012) reported that microbial community composition in rhizosperic soil are linked to soil quality as well as the health of the crop grown. Microbiota associated with soil has great influence on how plants are able to adapt and respond to changes in the environments such as emergence of stressors such as salinity and drought (Zhang et al., 2017). High abundance were noted in the phyla Basidiomycota and Ascomycota similar to results by Sommermann et al. (2018) and Gómez-Lama et al. (2021).

Rossmann et al. (2012) reported the presence of potential plant, human and insect pathogens similar to the results obtained in this study. Gu et al. (2016) utilized high-throughput gene expression to visualize hierarchal classification and species richness, similar to this study. Plant beneficial bacteria genera diversity such as Rhizobium and Azotobacter differed with that of probable plant pathogenic bacteria genera such as Ralstonia in all the soil samples similar to results reported by Kepler et al (Kepler et al., 2020). The presence of Rhizoctonia, Colletotrichium and Verticillium was an indicator of disease causing fungal pathogens in some of the soil samples similar to results by Sommermann et al. (2018).

Investigation of abundance of plant beneficial fungi such as those used as biocontrol agents in agroecosystems is a field that has not been extensively studied (Harman et al., 2004). The variations in bacterial genera indicate differences in land use strategies resulting in changes in microbial community structure and diversity (Lynn et al., 2017). Fan et al. (2020) reported variations in bacterial and fungal communities in relation to soil parameters. It has been reported that many soil variables such as soil organic matter, salinity and pH have a lot of impact on soil microbial populations (Gans et al., 2005). Additionally, these microbial communities cannot recover to their natural state even after many years (Pellegrino et al., 2014). Based on previous studies pH impacts soil microbial communities therefore defines taxonomic composition of microbial communities (Delgado and Gómez, 2016).

It has been established that soil composition and function are associated with plant soil borne disease outbreaks in which healthy fields have different microbial communities from the infected ones (Zhang et al., 2017). Frac et al. (2018) reported that the diversity and fungi activity is regulated by biotic and abiotic factors such as soil pH, structure and some nutrients.

Based on the results obtained from this study, there were variations in soil composition and microbial populations in the different regions. The soil physicochemical properties played a significant role in the rhizosphere soil microbial communities. It has been established that plants modify the rhizosphere through various modes such as changes in microbiome composition and function. Studying the interaction between plants, microorganisms and soil physicochemical conditions enables one to understand how each plays a role in ecosystem balance and well as productivity in agroecosystems. The results show that studying soil microbiome in monocropping systems is a great tool in determining ideal microbial community structures for the crops. In addition, application of metagenomics techniques in studying microbial communities in agroecosystems will aid in designing banana production systems as well as targeted approaches in disease management.

The data presented in the study are deposited on Figshare (https://doi.org/10.6084/m9.figshare.21939977).

JM, OO, EN, and JK conceived and designed the research and data collection tools and participated in drafting the manuscript. CW collected the data, participated in the data analyses, and wrote the manuscript. MM was involved in molecular work and data analyses. All authors contributed to the article and approved the submitted version.