The fungal community changes over time in developing wheat heads

Hertz, Morten; Jensen, Iben Ravnborg; Jensen, Laura Østergaard; Thomsen, Søren Nøhr; Winde, Jacob; Dueholm, Morten Simonsen; Sørensen, Lydia Henriette; Wollenberg, Rasmus Dam; Sørensen, Hans Otto; Søndergaard, Teis Esben; Sørensen, Jens Laurids

doi:10.1016/j.ijfoodmicro.2016.01.018

Cited by 42 publications

(41 citation statements)

References 44 publications

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“…In fact, the microbial biodiversity in wheat roots shifted mostly in accordance with the crop age: Fusarium/Gibberella , Lewia , Alternaria , Stenotrophomonas , and unclassified Dothideomycetes dominated the first weeks, while Sphingomonas , unclassified Herpotrichiellaceae, Exophiala , and Pedobacter were highly abundant in the roots at later stages of wheat crop. Although it had been previously reported that fungal communities could change over time in wheat heads (Hertz et al , ) and wheat roots (Shi et al , ), this study shows those changes in microbial communities are not random, following instead a pattern (succession of distinct genera and OTUs). This pattern was independent of the plants being grown in the field or in the greenhouse and also of the soil types employed.…”

Section: Discussioncontrasting

confidence: 62%

Analogous wheat root rhizosphere microbial successions in field and greenhouse trials in the presence of biocontrol agents Paenibacillus peoriae SP9 and Streptomyces fulvissimus FU14

Araújo

Dunlap

Franco

2020

Molecular Plant Pathology

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Two Pythium‐infested soils were used to compare the wheat root and rhizosphere soil microbial communities from plants grown in the field or in greenhouse trials and their stability in the presence of biocontrol agents. Bacteria showed the highest diversity at early stages of wheat growth in both field and greenhouse trials, while fungal diversity increased later on, at 12 weeks of the crop cycle. The microbial communities were stable in roots and rhizosphere samples across both soil types used in this study. Such stability was also observed irrespective of the cultivation system (field or greenhouse) or addition of biocontrol coatings to wheat seeds to control Pythium disease (in this study soil infected with Pythium sp. clade F was tested). In greenhouse plant roots, Archaeorhizomyces, Debaryomyces, Delftia, and unclassified Pseudeurotiaceae were significantly reduced when compared to plant roots obtained from the field trials. Some operational taxonomic units (OTUs) represented genetic determinants clearly transmitted vertically by seed endophytes (specific OTUs were found in plant roots) and the plant microbiota was enriched over time by OTUs from the rhizosphere soil. This study provided key information regarding the microbial communities associated with wheat roots and rhizosphere soils at different stages of plant growth and the role that Paenibacillus and Streptomyces strains play as biocontrol agents in supporting plant growth in infested soils.

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Section: Discussioncontrasting

confidence: 62%

Analogous wheat root rhizosphere microbial successions in field and greenhouse trials in the presence of biocontrol agents Paenibacillus peoriae SP9 and Streptomyces fulvissimus FU14

Araújo

Dunlap

Franco

2020

Molecular Plant Pathology

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“…Using HTS of the ITS region, Alternaria and an OTU including F. graminearum and closely related species were the two most abundant fungal OTUs recovered from wheat kernels in Denmark (Nicolaisen et al, 2014). It has also been reported that Fusarium fungi only constitute a minor part of the fungal community of wheat heads (Hertz et al, 2016).…”

Section: Discussionmentioning

confidence: 94%

Agricultural factors affecting Fusarium communities in wheat kernels

Karlsson

Friberg

Kolseth

et al. 2017

International Journal of Food Microbiology

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Fusarium head blight (FHB) is a devastating disease of cereals caused by Fusarium fungi. The disease is of great economic importance especially owing to reduced grain quality due to contamination by a range of mycotoxins produced by Fusarium. Disease control and prediction is difficult because of the many Fusarium species associated with FHB. Different species may respond differently to control methods and can have both competitive and synergistic interactions. Therefore, it is important to understand how agricultural practices affect Fusarium at the community level.Lower levels of Fusarium mycotoxin contamination of organically produced cereals compared with conventionally produced have been reported, but the causes of these differences are not well understood. The aim of our study was to investigate the effect of agricultural factors on Fusarium abundance and community composition in different cropping systems. Winter wheat kernels were collected from 18 organically and conventionally cultivated fields in Sweden, paired based on their geographical distance and the wheat cultivar grown. We characterised the Fusarium community in harvested wheat kernels using 454 sequencing of translation elongation factor 1-a amplicons. In addition, we quantified Fusarium spp. using real-time PCR to reveal differences in biomass between fields.We identified 12 Fusarium operational taxonomic units (OTUs) with a median of 4.5 OTUs per field. Fusarium graminearum was the most abundant species, while F. avenaceum had the highest occurrence. The abundance of Fusarium spp. ranged two orders of magnitude between fields. Two pairs of Fusarium species co-occurred between fields: F. poae with F. tricinctum and F. culmorum with F. sporotrichoides. We could not detect any difference in Fusarium communities between the organic and conventional systems. However, agricultural intensity, measured as the number of pesticide applications and the amount of nitrogen fertiliser applied, had an impact on Fusarium communities, specifically increasing the abundance of F. tricinctum. There were geographical differences in the Fusarium community composition where F. graminearum was more abundant in the western part of Sweden. The application of amplicon sequencing provided a comprehensive view of the Fusarium community in cereals. This gives us better opportunities to understand the ecology of Fusarium spp., which is important in order to limit FHB and mycotoxin contamination in cereals.

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“…S5. Among these genera, some are known to be associated with plants, such as Alternaria, Acremonium [14, 47, 48], Cryptococcus [49], Sarocladium [50] and Cladosporium [13, 47–50].…”

Section: Resultsmentioning

confidence: 99%

“…A key point to be taken into account is that the trophic status of many species known to be principally pathogenic or non-pathogenic is not definitive [65]. For instance, Alternaria infectoria is sometimes described as a pathogen of wheat [13, 66], sometimes as an endophyte [67], and has even been tested as a potential biocontrol agent against Fusarium pseudograminearum on wheat [68]. Crop residues, half-plant/half-soil, should be the focus of future studies aiming to disentangle the succession of microbial species with different lifestyles and to characterise their relative impacts on the development of currently minor, but potentially threatening diseases.…”

Section: Discussionmentioning

confidence: 99%

“…Many studies have investigated the structure of the microbial communities present during the life cycle of the plant [e.g. 13–15], but few have investigated the microbiota associated with plant residues. Several ecological studies have investigated the impact of the residue compartment on the structure of soil microbial communities [2, 16–19], but not the impact of the soil compartment on structure of the residue communities.…”

Section: Introductionmentioning

confidence: 99%

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Crop residues in wheat-oilseed rape rotation system: a pivotal, shifting platform for microbial meetings

Kerdraon

Balesdent

Barret

et al. 2018

Preprint

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Crop residues are a crucial ecological niche with a major biological impact on agricultural ecosystems. In this study we used a combined diachronic and synchronic field experiment based on wheat-oilseed rape rotations to test the hypothesis that plant is a structuring factor of microbial communities in crop residues, and that this effect decreases over time with their likely progressive degradation and colonization by other microorganisms. We characterized an entire fungal and bacterial community associated with 150 wheat and oilseed rape residue samples at a plurennial scale by metabarcoding. The impact of plant species on the residue microbiota decreased over time and our data revealed turnover, with the replacement of oligotrophs, often plant-specific genera (such as pathogens) by copiotrophs, belonging to more generalist genera. Within a single cropping season, the plant-specific genera and species were gradually replaced by taxa that are likely to originate from the soil. These changes occurred more rapidly for bacteria than for fungi, known to degrade complex compounds. Overall, our findings suggest that crop residues constitute a key fully-fledged microbial ecosystem. Taking into account this ecosystem, that has been neglected for too long, is essential, not only to improve the quantitative management of residues, the presence of which can be detrimental to crop health, but also to identify groups of beneficial micro-organisms. Our findings are of particular importance, because the wheat-oilseed rape rotation, in which no-till practices are frequent, is particularly widespread in the European arable cropping systems.

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The fungal community changes over time in developing wheat heads

Cited by 42 publications

References 44 publications

Analogous wheat root rhizosphere microbial successions in field and greenhouse trials in the presence of biocontrol agents Paenibacillus peoriae SP9 and Streptomyces fulvissimus FU14

Analogous wheat root rhizosphere microbial successions in field and greenhouse trials in the presence of biocontrol agents Paenibacillus peoriae SP9 and Streptomyces fulvissimus FU14

Agricultural factors affecting Fusarium communities in wheat kernels

Crop residues in wheat-oilseed rape rotation system: a pivotal, shifting platform for microbial meetings

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