Abstract Description

No root system in nature exists without a microbial community; and include both free-living and symbiotic species. Plant roots host a diverse range of microorganisms, and a well-functioning soil microbiome is crucial for soil health and quality. Soil microbes drive essential processes such as nutrient cycling, supporting plant health and productivity. Moreover, microbial diversity is central to sustaining ecosystem functions and provides resilience against physical and chemical disturbances. Excessive chemical inputs and intensive agricultural practices have led to serious environmental impacts and biodiversity loss. Such disruption reduces microbial diversity and weakens ecosystem functioning, ultimately compromising soil fertility and resilience to environmental stress. The integration of cover crops has been shown to improve soil health indicators, particularly physico-chemical properties, positioning them as potential tools to engineer the soil microbiome for better soil health management. However, a critical knowledge gap remains in using microbial dynamics as measurable indicators of soil health. This study aims to identify the influence of cover crops on the core microbiomes associated with citrus trees. To address this, DNA was isolated from the rhizosphere soil of the citrus trees, enabling the characterisation of resident bacterial and fungal ribosomal DNA (rDNA)-based fractions. Next Generation Sequencing (NGS; Oxford Nanopore) was used with targeted amplicon sequencing (16S and ITS), to gain insight into the microbial community composition and diversity. Soil enzyme activities were also assessed, as they provide early indicators of changes in soil health and are valuable for assessing microbial activity and soil productivity. Preliminary findings suggest that the use of cover crops in general, have a positive effect on both microbial diversity and function. These findings shed light on the role of cover crops in shaping soil microbial composition and function and provide a foundation for soil management practices aimed at restoring ecosystem processes in agricultural soils.