Non-target impacts of fungicide disturbance on phyllosphere yeasts in conventional and no-till management

Noel, Zachary A; Longley, Reid; Benucci, Gian Maria Niccolò; Trail, Frances; Chilvers, Martin I.; Bonito, Gregory

doi:10.1038/s43705-022-00103-w

Cited by 23 publications

(19 citation statements)

References 64 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…One the other hand, repeated MS fumigation decreased Basidiomycota , represented by Tremellomycetes yeasts, such as Solicocozyma , Tausonia , Papiliotrema , and Vishniacozyma . This suggests that these soil yeasts are sensitive to MS or the active compound MITC as documented in previous research with other pesticides [ 107 – 109 ]. However, how fumigation affects soil yeast communities remains understudied.…”

Section: Discussionsupporting

confidence: 65%

Legacy effects of fumigation on soil bacterial and fungal communities and their response to metam sodium application

Skillman

Dung

et al. 2022

Environmental Microbiome

View full text Add to dashboard Cite

Background Soil microorganisms are integral to maintaining soil health and crop productivity, but fumigation used to suppress soilborne diseases may affect soil microbiota. Currently, little is known about the legacy effects of soil fumigation on soil microbial communities and their response to fumigation at the production scale. Here, 16S rRNA gene and internal transcribed spacer amplicon sequencing was used to characterize the bacterial and fungal communities in soils from intensively managed crop fields with and without previous exposure to metam sodium (MS) fumigation. The effect of fumigation history, soil series, and rotation crop diversity on microbial community variation was estimated and the response of the soil microbiome to MS application in an open microcosm system was documented. Results We found that previous MS fumigation reduced soil bacterial diversity but did not affect microbial richness and fungal diversity. Fumigation history, soil series, and rotation crop diversity were the main contributors to the variation in microbial β-diversity. Between fumigated and non-fumigated soils, predominant bacterial and fungal taxa were similar; however, their relative abundance varied with fumigation history. In particular, the abundance of Basidiomycete yeasts was decreased in fumigated soils. MS fumigation also altered soil bacterial and fungal co-occurrence network structure and associations. In microcosms, application of MS reduced soil microbial richness and bacterial diversity. Soil microbial β-diversity was also affected but microbial communities of the microcosm soils were always similar to that of the field soils used to establish the microcosms. MS application also induced changes in relative abundance of several predominant bacterial and fungal genera based on a soil’s previous fumigation exposure. Conclusions The legacy effects of MS fumigation are more pronounced on soil bacterial diversity, β-diversity and networks. Repeated fumigant applications shift soil microbial compositions and may contribute to differential MS sensitivity among soil microorganisms. Following MS application, microbial richness and bacterial diversity decreases, but microbial β-diversity was similar to that of the field soils used to establish the microcosms in the short-term (< 6 weeks). The responses of soil microbiome to MS fumigation are context dependent and rely on abiotic, biotic, and agricultural management practices.

show abstract

Section: Discussionsupporting

confidence: 65%

Legacy effects of fumigation on soil bacterial and fungal communities and their response to metam sodium application

Skillman

Dung

et al. 2022

Environmental Microbiome

View full text Add to dashboard Cite

show abstract

“…While fungal diversity was not altered in this study, fungal OTUs were identified as hubs, potentially demonstrating meaningful interactions with in a spermosphere soil. Of most interest was the yeast Hannella since these fungi are commonly found in soils, the phyllosphere, and as part of the core seed and phyllosphere microbiome (Noel et al 2022; Simonin et al 2022; Yurkov 2018). Dioszegia , in the same family as Hannaella , was identified as a network hub in the phyllosphere (Agler et al 2016), and the closely related yeast Bullera has been a network hub of the soybean phyllosphere (Longley et al 2020).…”

Section: Discussionmentioning

confidence: 99%

“…Cleaned amplicon pools were verified by gel electrophoresis, quantified using a Qubit fluorometer (Thermo Fisher, USA), and sequenced on an Illumina MiSeq 2x300 bp using the v3 600 cycles kit at SeqCenter LLC (Pittsburgh, PA). Primers and cycling parameters to construct libraries were the same as in Noel (2022).…”

Section: Methodsmentioning

confidence: 99%

Soybean and cotton spermosphere soil microbiome shows dominance of soil-borne copiotrophs

Olofintila

Noel

2023

Preprint

Self Cite

View full text Add to dashboard Cite

The spermosphere is the transient, immediate zone of soil around imbibing and germinating seeds, rich in microbial activity. It represents a habitat where there is contact between seed-associated microbes and soil microbes, but is studied less compared to other plant habitats. Previous studies on spermosphere microbiology were primarily culture-based or did not sample the spermosphere soil as initially defined in space and time. Thus, the objectives of this study were to develop an efficient strategy to collect spermosphere soils around imbibing soybean and cotton in non-sterile soil and investigate factors contributing to changes in microbial communities. The method employed sufficiently collected spermosphere soil as initially defined in space (3-10 mm soil around a seed) by constraining the soil sampled with an cork borer and confining the soil to a 12-well microtiter plate. Spermosphere prokaryote composition changed over time and depended on the crop within six hours after seeds were sown. By 12 to 18 hours, crops had unique microbial communities in spermosphere soils. Prokaryote evenness dropped following seed imbibition and the proliferation of copiotroph soil bacteria in the phyla Proteobacteria and Firmicutes. Due to their long history of plant growth promotion, prokaryote OTUs in Bacillus, Paenibacillus, Burkholderia, Massilia, Azospirillum, and Pseudomonas were notable genera enriched in the cotton and soybean spermosphere. There was no consistent evidence that fungal communities changed like prokaryotes. However, fungi and prokaryotes were hub taxa in cotton and soybean spermosphere networks. Additionally, the enriched taxa were not hubs in networks, suggesting other taxa besides the copiotrophic may be important for spermosphere communities. Overall, this study advances knowledge in the assembly of the plant microbiome early in a plant's life, which may have plant health implications in more mature plant growth stages.

show abstract

“…Extensive studies have shown that the composition of the phyllosphere microbiome can be affected by multiple factors. Although the tissue compartment and host genotype are the most dominant factors [27,28], environmental conditions, stress [23,29], foliar spray [30,31], and fertilizer application [32] may also alter the microbial abundance and composition. Among these factors, data on foliar spray impacts on the phyllosphere microbiome are limited.…”

Section: Introductionmentioning

confidence: 99%

Effects of synthetic and environmentally friendly fungicides on powdery mildew management and the phyllosphere microbiome of cucumber

Chang

Shen

2023

PLoS ONE

View full text Add to dashboard Cite

Modern agricultural practices rely on synthetic fungicides to control plant disease, but the application of these fungicides has raised concerns regarding human and environmental health for many years. As a substitute, environmentally friendly fungicides have been increasingly introduced as alternatives to synthetic fungicides. However, the impact of these environmentally friendly fungicides on plant microbiomes has received limited attention. In this study, we used amplicon sequencing to compare the bacterial and fungal microbiomes in the leaves of powdery mildew-infected cucumber after the application of two environmentally friendly fungicides (neutralized phosphorous acid (NPA) and sulfur) and one synthetic fungicide (tebuconazole). The phyllosphere α-diversity of both the bacterial and fungal microbiomes showed no significant differences among the three fungicides. For phyllosphere β-diversity, the bacterial composition exhibited no significant differences among the three fungicides, but fungal composition was altered by the synthetic fungicide tebuconazole. While all three fungicides significantly reduced disease severity and the incidence of powdery mildew, NPA and sulfur had minimal impacts on the phyllosphere fungal microbiome relative to the untreated control. Tebuconazole altered the phyllosphere fungal microbiome by reducing the abundance of fungal OTUs such as Dothideomycetes and Sordariomycetes, which included potentially beneficial endophytic fungi. These results indicated that treatments with the environmentally friendly fungicides NPA and sulfur have fewer impacts on the phyllosphere fungal microbiome while maintaining the same control efficacy as the synthetic fungicide tebuconazole.

show abstract

Non-target impacts of fungicide disturbance on phyllosphere yeasts in conventional and no-till management

Cited by 23 publications

References 64 publications

Legacy effects of fumigation on soil bacterial and fungal communities and their response to metam sodium application

Legacy effects of fumigation on soil bacterial and fungal communities and their response to metam sodium application

Soybean and cotton spermosphere soil microbiome shows dominance of soil-borne copiotrophs

Effects of synthetic and environmentally friendly fungicides on powdery mildew management and the phyllosphere microbiome of cucumber

Contact Info

Product

Resources

About