Influence of Maize Residues in Shaping Soil Microbiota and Fusarium spp. Communities.

Fusarium head blight (FHB) is a devastating fungal disease of small grain cereals including wheat. Causal fungal agents colonize various components of the field during their life cycle including previous crop residues, soil, and grains. Although soil and residues constitute the main inoculum source, these components have received much less attention than grains. This study aimed at disentangling the role of previous crop residues in shaping soil microbiota, including Fusarium spp. communities, in fields under wheat-maize rotation. Such knowledge may contribute to better understand the complex interactions between Fusarium spp. and soil microbiota. Dynamics of bacterial and fungal communities, with a special focus on Fusarium spp., were monitored in soils at 3 time points: during wheat cultivation (April 2015 and 2017) and after maize harvest (November 2016) and in maize residues taken from fields after harvest. Shifts in microbiota were also evaluated under mesocosm experiments using soils amended with maize residues. Fusarium graminearum and F. avenaceum were predominant on maize residues but did not remain in soils during wheat cultivation. Differences in soil bacterial diversity and compositions among years were much lower than variation between fields, suggesting that bacterial communities are field-specific and more conserved over time. In contrast, soil fungal diversity and compositions were more influenced by sampling time. Maize residues, left after harvest, led to a soil enrichment with several fungal genera, including Epicoccum, Fusarium, Vishniacozyma, Papiliotrema, Sarocladium, Xenobotryosphaeria, Ramularia, Cladosporium, Cryptococcus, and Bullera, but not with bacterial genera. Likewise, under mesocosm conditions, the addition of maize residues had a stronger influence on fungal communities than on bacterial communities. In particular, addition of maize significantly increased soil fungal richness, while bacteria were much less prone to changes. Based on co-occurrence networks, OTUs negatively correlated to Fusarium spp. were identified, such as those assigned to Epicoccum and Vishniacozyma. Altogether, our results allowed to gain a deeper insight into the complex microbiota interactions in soils, with bacteria and fungi responding differently to environmental disturbances.

Water Microbiota in Greenhouses With Soilless Cultures of Tomato by Metabarcoding and Culture-Dependent Approaches.

Water supply, in hydroponic greenhouses, can originate from groundwater, surface water or rainwater stored in open tanks. To limit contamination of water supply, several methods have been used including active and passive methods such as slow filtration techniques which consist in passing the nutrient solutions slowly through filters. The purpose of this study was to describe the microbiota associated with water sampled before entering greenhouses and in recirculating nutrient solutions, either before or after running through a biofiltration system. Metabarcoding analysis revealed that water ecosystems were unique niches for diverse bacterial and fungal communities. Microbial composition varied greatly across storage conditions (groundwater vs. rainwater) and among greenhouses, suggesting that water microbiota is site- and storage-condition-specific. Nonetheless, we found that microbiota structure in open-stored water (either coming from ground or rain) shared a higher degree of similarity than with water directly pumped out of the ground. Open-stored waters were characterized by predominant taxa, notably those involved in aerobic chemoheterotrophy, such as the Sphingomonadaceae and Hyphomicrobiaceae families. Water directly collected from the ground showed the lowest levels of fungal and bacterial richness while also characterized by a significantly higher level of bacterial equitability and an enrichment in taxa involved in N-cycling. Slow filtration allowed reducing cultivable bacterial loads as well Pythium spp. and Fusarium oxysporum propagules, based on culture-dependent results, without compromising microbiota richness and diversity. Although compositional structure was similar following biofiltration, significant differences in bacterial (but not fungal) taxa abundance were reported, with primarily an enrichment of Chelativorans, Mycobacterium, and Gemmata as well as a depletion of Rhodobacter, Aminobacter, and Ellin329. The exact mechanisms by which such taxa would be favored at the expense of other remained unknown. Besides the accurate description of microbiota found in water at both taxonomical and predicted functional levels, our study allowed comparing the water microbiota between various storage system and following biofiltration. Although preliminary, our results provide a first insight into the potential microbial diversity, which can increase ecosystem functionality.

Co-occurrence analysis reveal that biotic and abiotic factors influence soil fungistasis against Fusarium graminearum.

The current study determined the levels of soil fungistasis against a soil-borne pathogen inoculum, Fusarium graminearum (Fg, a major causal agent of Fusarium Head Blight (FHB)), in 31 wheat fields by quantifying Fg growth after a 15-day incubation period using qPCR in autoclaved versus non-autoclaved soils. The results were used to define the six most Fg-resistant and the six most Fg-conducive soils. By using a metabarcoding approach, the diversity of the bacterial communities was significantly higher in Fg-resistant soils than in Fg-conducive soils. Microbial taxa potentially contributing to Fg-fungistasis of soil were selected if they were significantly more prevalent and/or abundant in Fg-resistant soils than in Fg-conducive soils. Some of these candidate indicators, e.g. Pseudomonas spp. and Bacillus spp., have been reported previously as effective biocontrol agents against plant pathogens. Correlation-based network analysis further showed that the members of the bacterial communities in Fg-resistant soils were more connected than in Fg-conducive soils. Moreover, network modules was found significantly correlated with certain edaphic abiotics factors (such as the soil manganese and nitrogen content) and Fg-fungistasis. Such observations may suggest and emphasize, although conceptual, the importance of synergistic rather than individual effects of network members, and the nutrient use efficiency in contributing to Fg-resistance of soils in wheat fields in France.