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 i...