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

frontiers in microbiology

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