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

Abstract

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 <i>Fusarium</i> pathogenic species, the structure and diversity of <i>Fusarium</i> 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 <i>Fusarium</i> 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 <i>Fusarium</i>, <i>Acremonium</i>, and <i>Phoma</i> genera, and the bacterial <i>Pseudomonas</i> and <i>Erwinia</i> genera. Furthermore, a high predominance of genera with previously reported biocontrol activity was found, including the bacterial <i>Sphingomonas</i>, <i>Pedobacter</i>, <i>Flavobacterium, Pseudomonas</i>, and <i>Janthinobacterium</i> genera; and the fungal <i>Epicoccum</i>, <i>Articulospora</i>, <i>Exophiala</i>, and <i>Sarocladium</i> genera. Among <i>Fusarium</i> spp., <i>F. graminearum</i> and <i>F. avenaceum</i> 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 <i>Fusarium</i> spp. responsible for FHB (including <i>F. graminearum</i> and <i>F. avenaceum</i>) and bacterial OTUs classified as <i>Sphingomonas</i> and fungal OTUs classified as <i>Sarocladium</i> and <i>Epicoccum</i>. Considering that isolates belonging to these taxa have already been associated with antagonist effect against different <i>Fusarium</i> spp. and/or other pathogenic microorganisms and due to their predominance and negative associations with <i>Fusarium</i> spp., they may be good candidates as biocontrol agents. Combining the use of <i>Fusarium</i>-specific primers with universal primers for bacteria and fungi allowed us to study the microbial communities, but also to track correlations between <i>Fusarium</i> 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 <i>Fusarium</i> spp., allowing the selection of taxa of interest.