Bacterial-fungal interactions in soil ecosystems: From biocontrol and niche partitioning to biogeochemical impacts

Soil ecosystems are highly dynamic environments where complex interactions between bacteria and fungi significantly influence biogeochemical processes, plant health, and ecosystem stability. This review provides a comprehensive overview of the current understanding of bacterial-fungal interactions (BFIs) in the rhizosphere and bulk soil, focusing on their roles in biocontrol, niche differentiation, and nutrient cycling. We discuss the molecular mechanisms driving these interactions, including signaling molecules, extracellular enzymes, and secondary metabolites, which mediate both competitive and cooperative relationships between bacteria and fungi. The review also highlights the cascading effects of BFIs on carbon, nitrogen, and phosphorus cycles, emphasizing the distinct functional roles of bacteria and fungi in decomposition, mineralization, and nutrient mobilization processes. Furthermore, we explore the impact of environmental disturbances, such as climate change, agricultural practices, and pollution, on the stability and functionality of BFIs, highlighting the need for sustainable management strategies. The application of "omics" technologies, including metagenomics, metatranscriptomics, and metabolomics, is discussed as a powerful tool for unraveling the genetic, physiological, and metabolic processes underpinning BFIs. We highlight the potential of harnessing beneficial BFIs for sustainable agriculture, ecosystem restoration, and biotechnological applications. Finally, we identify knowledge gaps and propose future research directions, emphasizing the importance of integrating novel methodological approaches and expanding experimental data to develop models for microbial manipulation and sustainable agricultural practices.