Metagenomic-Based Biocontrol: Future Role of Rhizosphere Fungi in Suppressing Downy Mildew in Maize

Abstract

Downy mildew is one of the major diseases affecting maize (Zea mays L.), caused by obligate Oomycetes of the species Peronosclerospora spp. The infection can lead to severe yield losses sometimes reaching 100%. Overdependence on chemical fungicides has led to issues such as the development of resistant pathogen, environmental contamination, and health risks, emphasizing the need for safer, and more sustainable control strategies. Rhizosphere fungi have attracted considerable inteterst as biological control agents. However, many of these beneficial microorganisms in the rhizosphere remain unculturable and poorly characterized. This review aims to synthesize current findings on rhizosphere fungi and explore how metagenomic can be applied to streghten their role in sustainable management of downy mildew on maize. Fugal communities in rhizosphere contribute to protecting plants through multiple mechanisms, including direct antagonism, competition for nutrients and space, secretion of lytic enzymes, induction of systemic resistance, and the production of secondary metabolites and antibiotics. The advancement of multi-omic technology, especially the combination of metagenomics, next-generation sequencing (NGS), and ITS rRNA profiling—has opened opportunities to uncover unculturable fungi, identify gene related to biocontrol, microbial diversity, nutrient cycling, and stress tolerance. This review summarizes recent progress, outlines research gaps, and provides insight in to future integration of rhizosphere fungi and metagenomic tools as environtmental friendly alternatives to conventional fungicides. Such integration could enhance the resilience and sustainability of maize production systems. Keywords: Plant protection, diversity of microorganisms, multi-omics, oomycetes.

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