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

  • Rykiel EJ. Towards a definition of ecological disturbance. Austral Ecology. 1985;10:361–5.

    Google Scholar 

  • Glasby TM, Underwood AJ. Sampling to differentiate between pulse and press perturbations. Environ Monit. Assess. 1996;42:241–52.

    CAS 
    PubMed 

    Google Scholar 

  • Sullivan TP, Sullivan DS. Vegetation management and ecosystem disturbance: impact of glyphosate herbicide on plant and animal diversity in terrestrial systems. Environ Rev. 2003;11:37–59.

    CAS 

    Google Scholar 

  • Landers TF, Cohen B, Wittum TE, Larson EL. A review of antibiotic use in food animals: perspective, policy, and potential. Public Health Rep. 2012;127:4–22.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Shade A, Peter H, Allison SD, Baho DL, Berga M, Bürgmann H, et al. Fundamentals of microbial community resistance and resilience. Front Microbiol. 2012;3:417.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Hahn M. The rising threat of fungicide resistance in plant pathogenic fungi: Botrytis as a case study. J Chem Biol. 2014;7:133–41.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Schaeffer RN, Vannette RL, Brittain C, Williams NM, Fukami T. Non-target effects of fungicides on nectar-inhabiting fungi of almond flowers. Environ. Microbiol. Rep. 2017;9:79–84.

    PubMed 

    Google Scholar 

  • Zubrod JP, Bundschuh M, Arts G, Brühl CA, Imfeld G, Knäbel A, et al. Fungicides: An Overlooked Pesticide Class? Environ Sci Technol. 2019;53:3347–65.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Delmas CEL, Dussert Y, Delière L, Couture C, Mazet ID, Richart Cervera S, et al. Soft selective sweeps in fungicide resistance evolution: recurrent mutations without fitness costs in grapevine downy mildew. Mol. Ecol. 2017;26:1936–51.

    CAS 
    PubMed 

    Google Scholar 

  • McDonald MC, Renkin M, Spackman M, Orchard B, Croll D, Solomon PS, et al. Rapid parallel evolution of azole fungicide resistance in Australian populations of the wheat pathogen Zymoseptoria tritici. Appl Environ Microbiol. 2019;85:e01908–e01918.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Riat A, Plojoux J, Gindro K, Schrenzel J, Sanglard D. Azole Resistance of environmental and clinical Aspergillus fumigatus isolates from Switzerland. Antimicrob Agents Chemother. 2018;62:e02088–e02017.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Verweij PE, Snelders E, Kema GHJ, Mellado E, Melchers WJG. Azole resistance in Aspergillus fumigatus: a side-effect of environmental fungicide use? Lancet Infect Dis. 2009;9:789–95.

    CAS 
    PubMed 

    Google Scholar 

  • Wise K, Mueller D Are fungicides no longer just for fungi? An analysis of foliar fungicide use in corn. APSnet Features doi 2011; 10.

  • Kandel YR, Hunt C, Ames K, Arneson N, Bradley CA, Byamukama E, et al. Meta-Analysis of Soybean Yield Response to Foliar Fungicides Evaluated from 2005 to 2018 in the United States and Canada. Plant Dis. 2021;105:1382–9.

    PubMed 

    Google Scholar 

  • Imfeld G, Vuilleumier S. Measuring the effects of pesticides on bacterial communities in soil: A critical review. Eur J Soil Biol. 2012;49:22–30.

    CAS 

    Google Scholar 

  • Fournier B, Dos Santos SP, Gustavsen JA, Imfeld G, Lamy F, Mitchell EAD, et al. Impact of a synthetic fungicide (fosetyl-Al and propamocarb-hydrochloride) and a biopesticide (Clonostachys rosea) on soil bacterial, fungal, and protist communities. Sci Total Environ. 2020;738:139635.

    CAS 
    PubMed 

    Google Scholar 

  • Morton V, Staub T A Short History of Fungicides. APSnet Feature Articles. 2008.

  • Brent KJ, Hollomon DW Fungicide resistance in crop pathogens: how can it be managed? 2007. FRAC Monogr. No. 1, Global Prot. Fed.

  • Perazzolli M, Antonielli L, Storari M, Puopolo G, Pancher M, Giovannini O, et al. Resilience of the natural phyllosphere microbiota of the grapevine to chemical and biological pesticides. Appl Environ Microbiol. 2014;80:3585–96.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Knorr K, Jørgensen LN, Nicolaisen M. Fungicides have complex effects on the wheat phyllosphere mycobiome. PLoS One. 2019;14:e0213176.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Sapkota R, Knorr K, Jørgensen LN, O’Hanlon KA, Nicolaisen M. Host genotype is an important determinant of the cereal phyllosphere mycobiome. New Phytol. 2015;207:1134–44.

    CAS 
    PubMed 

    Google Scholar 

  • Southwell RJ, Brown JF, Welsby SM. Microbial interactions on the phylloplane of wheat and barley after applications of mancozeb and triadimefon. Australasian Plant Pathol. 1999;28:139.

    Google Scholar 

  • Dickinson CH, Wallace B. Effects of late applications of foliar fungicides on activity of micro-organisms on winter wheat flag leaves. Trans Br Mycological Soc. 1976;67:103–12.

    Google Scholar 

  • Freimoser FM, Rueda-Mejia MP, Tilocca B, Migheli Q. Biocontrol yeasts: mechanisms and applications. World J Microbiol Biotechnol. 2019;35:154.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Fonseca Á, Inácio J Phylloplane Yeasts. In: Péter G, Rosa C (eds). Biodiversity and Ecophysiology of Yeasts. 2006. Springer Berlin Heidelberg, Berlin, Heidelberg, pp. 263–301.

  • Cobban A, Edgcomb VP, Burgaud G, Repeta D, Leadbetter ER. Revisiting the pink-red pigmented basidiomycete mirror yeast of the phyllosphere. Microbiologyopen. 2016;5:846–55.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cadez N, Zupan J, Raspor P. The effect of fungicides on yeast communities associated with grape berries. FEMS Yeast Res. 2010;10:619–30.

    CAS 
    PubMed 

    Google Scholar 

  • Schaeffer RN, Mei YZ, Andicoechea J, Manson JS, Irwin RE. Consequences of a nectar yeast for pollinator preference and performance. Funct Ecol. 2017;31:613–21.

    Google Scholar 

  • Agler MT, Ruhe J, Kroll S, Morhenn C, Kim S-T, Weigel D, et al. Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation. PLoS Biol. 2016;14:e1002352.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Tilman D. The ecological consequences of changes in biodiversity: a search for general principles. Ecology. 1999;80:1455.

    Google Scholar 

  • Ripple WJ, Beschta RL. Linking wolves and plants: aldo leopold on trophic cascades. BioScience. 2005;55:613.

    Google Scholar 

  • Sahasrabudhe S, Motter AE. Rescuing ecosystems from extinction cascades through compensatory perturbations. Nat Commun. 2011;2:170.

    PubMed 

    Google Scholar 

  • Zhou J, Deng Y, Luo F, He Z, Tu Q, Zhi X. Functional molecular ecological networks. mBio. 2010;1:e00169–e00210.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Wagg C, Schlaeppi K, Banerjee S, Kuramae EE, van der Heijden MGA. Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning. Nat Commun. 2019;10:4841.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Claassen R, Bowman M, McFadden J, Smith D, Wallander S. Tillage intensity and conservation cropping in the United States. US Dep Agric Bull Econ Rese Ser. 2018;197:1–21.

    Google Scholar 

  • Gdanetz K, Trail F. The wheat microbiome under four management strategies, and potential for endophytes in disease protection. Phytobiomes J. 2017;1:158–68.

    Google Scholar 

  • Longley R, Noel ZA, Benucci GMN, Chilvers MI, Trail F, Bonito G. Crop management impacts the soybean microbiome. Front Microbiol. 2020;11:1116.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Sułowicz S, Cycoń M, Piotrowska-Seget Z. Non-target impact of fungicide tetraconazole on microbial communities in soils with different agricultural management. Ecotoxicology. 2016;25:1047–60.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Karlsson I, Friberg H, Steinberg C, Persson P. Fungicide effects on fungal community composition in the wheat phyllosphere. PLoS One. 2014;9:e111786.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Robertson GP, Hamilton SK Long-term ecological research at the Kellogg Biological Station LTER site. The ecology of agricultural landscapes: Long-term research on the path to sustainability 2015; 1–32.

  • Fehr WR, Caviness CE, Burmood DT, Pennington JS. Stage of development descriptions for soybeans, Glycine max (L.) Merrill 1. Crop Sci. 1971;11:929–31.

    Google Scholar 

  • Gdanetz K, Noel Z, Trail F. Influence of plant host and organ, management strategy, and spore traits on microbiome composition. Phytobiomes J. 2021;5:202–19.

    Google Scholar 

  • Lundberg DS, Yourstone S, Mieczkowski P, Jones CD, Dangl JL. Practical innovations for high-throughput amplicon sequencing. Nat Methods. 2013;10:999–1002.

    CAS 
    PubMed 

    Google Scholar 

  • Bowsher AW, Benucci GMN, Bonito G, Shade A. Seasonal Dynamics of Core Fungi in the Switchgrass Phyllosphere, and Co-Occurrence with Leaf Bacteria. Phytobiomes J. 2021;5:60–68.

    Google Scholar 

  • Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: Community Ecology Package v. 2.5-7. 2020

  • Anderson MJ, Willis TJ. Canonical analysis of principle coordinates: a useful method of constrained ordination for ecology. Ecology. 2003;84:511–25.

    Google Scholar 

  • Mandal S, Van Treuren W, White RA, Eggesbø M, Knight R, Peddada SD. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb Ecol Health Dis. 2015;26:27663.

    PubMed 

    Google Scholar 

  • Shade A, Stopnisek N. Abundance-occupancy distributions to prioritize plant core microbiome membership. Curr Opin Microbiol. 2019;49:50–58.

    PubMed 

    Google Scholar 

  • Liaw A, Wiener M. Classification and regression by randomForest. R News. 2002;2:18–22.

    Google Scholar 

  • Kursa MB, Rudnicki WR. Feature selection with the Boruta package. J Stat Softw. 2010;36:1–13.

    Google Scholar 

  • Kurtz ZD, Müller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA. Sparse and compositionally robust inference of microbial ecological networks. PLoS Comput Biol. 2015;11:e1004226.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Lindow SE, Brandl MT. Microbiology of the phyllosphere. Appl Environ Microbiol. 2003;69:1875–83.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wang K, Sipilä TP, Overmyer K. The isolation and characterization of resident yeasts from the phylloplane of Arabidopsis thaliana. Sci Rep. 2016;6:39403.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Sun PF, Fang WT, Shin LY, Wei JY, Fu SF, Chou JY. Indole-3-acetic acid-producing yeasts in the phyllosphere of the carnivorous plant Drosera indica L. PLoS One. 2014;9:e114196.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Yurkov AM, Kurtzman CP. Three new species of Tremellomycetes isolated from maize and northern wild rice. FEMS Yeast Res. 2019;19:foz004.

    CAS 
    PubMed 

    Google Scholar 

  • Sommermann L, Geistlinger J, Wibberg D, Deubel A, Zwanzig J, Babin D, et al. Fungal community profiles in agricultural soils of a long-term field trial under different tillage, fertilization and crop rotation conditions analyzed by high-throughput ITS-amplicon sequencing. PLOS ONE. 2018;13:e0195345.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Li A-H, Yuan F-X, Groenewald M, Bensch K, Yurkov AM, Li K, et al. Diversity and phylogeny of basidiomycetous yeasts from plant leaves and soil: proposal of two new orders, three new families, eight new genera and one hundred and seven new species. Stud Mycol. 2020;96:17–140.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Gilbert DG. Dispersal of yeasts and bacteria by Drosophila in a temperate forest. Oecologia. 1980;46:135–7.

    PubMed 

    Google Scholar 

  • Starmer WT, Peris F, Fontdevila A. The transmission of yeasts by Drosophila buzzatii during courtship and mating. Animal Behaviour. 1988;36:1691–5.

    Google Scholar 

  • Murrell EG. Can agricultural practices that mitigate or improve crop resilience to climate change also manage crop pests? Curr Opin Insect Sci. 2017;23:81–88.

    PubMed 

    Google Scholar 

  • Latin R A Practical Guide to Turfgrass Fungicides. 2017.

  • Banerjee S, Walder F, Büchi L, Meyer M, Held AY, Gattinger A, et al. Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots. ISME J. 2019;13:1722–36.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Schmidt JE, Kent AD, Brisson VL, Gaudin ACM. Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling. Microbiome. 2019;7:146.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Brockhurst MA, Buckling A, Gardner A. Cooperation peaks at intermediate disturbance. Curr Biol. 2007;17:761–5.

    CAS 
    PubMed 

    Google Scholar 

  • Brockhurst MA, Habets MGJL, Libberton B, Buckling A, Gardner A. Ecological drivers of the evolution of public-goods cooperation in bacteria. Ecology. 2010;91:334–40.

    PubMed 

    Google Scholar 

  • Kwak M-J, Jeong H, Madhaiyan M, Lee Y, Sa T-M, Oh TK, et al. Genome information of Methylobacterium oryzae, a plant-probiotic methylotroph in the phyllosphere. PLoS One. 2014;9:e106704.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Yoshida S, Hiradate S, Koitabashi M, Kamo T, Tsushima S. Phyllosphere Methylobacterium bacteria contain UVA-absorbing compounds. J Photochem Photobiol B. 2017;167:168–75.

    CAS 
    PubMed 

    Google Scholar 

  • Grady KL, Sorensen JW, Stopnisek N, Guittar J, Shade A. Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops. Nat Commun. 2019;10:4135.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, et al. Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci USA. 2009;106:16428–33.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 


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