Combined Metabarcoding and Co-occurrence Network Analysis to Profile the Bacterial, Fungal and Communities and Their Interactions in Maize Stalks.

Fusarium Head Blight (FHB) is one of the most devastating diseases of cereals worldwide, threatening both crop production by affecting cereal grain development, and human and animal health by contaminating grains with mycotoxins. Despite that maize residues constitute the primary source of inoculum for pathogenic species, the structure and diversity of spp. and microbial communities in maize residues have received much less attention than in grains. In this study, a metabarcoding approach was used to study the bacterial, fungal and communities encountered in maize stalks collected from 8 fields in Brittany, France, after maize harvest during fall 2015. Some predominant genera found in maize residues were cereal or maize pathogens, such as the fungal , , and genera, and the bacterial and genera. Furthermore, a high predominance of genera with previously reported biocontrol activity was found, including the bacterial , , , and genera; and the fungal , , , and genera. Among spp., and were dominant. We also found that the maize cultivar and previous crop could influence the structure of microbial communities. Using SparCC co-occurrence network analysis, significant negative correlations were obtained between spp. responsible for FHB (including and ) and bacterial OTUs classified as and fungal OTUs classified as and . Considering that isolates belonging to these taxa have already been associated with antagonist effect against different spp. and/or other pathogenic microorganisms and due to their predominance and negative associations with spp., they may be good candidates as biocontrol agents. Combining the use of -specific primers with universal primers for bacteria and fungi allowed us to study the microbial communities, but also to track correlations between spp. and other bacterial and fungal genera, using co-occurrence network analysis. Such approach could be a useful tool as part of a screening strategy for novel antagonist candidates against toxigenic spp., allowing the selection of taxa of interest.