in

Fungal community shifts in soils with varied cover crop treatments and edaphic properties

  • 1.

    Allison, S. D. & Martiny, J. B. H. Resistance, resilience, and redundancy in microbial communities. P. Natl. Acad. Sci. 105, 11512–11519, https://doi.org/10.1073/pnas.0801925105 (2008).

  • 2.

    Chaparro, J. M., Sheflin, A. M., Manter, D. K. & Vivanco, J. M. Manipulating the soil microbiome to increase soil health and plant fertility. Biol. Fertil. Soils 48, 489–499, https://doi.org/10.1007/s00374-012-0691-4 (2012).

    • Article
    • Google Scholar
  • 3.

    Broeckling, C. D., Broz, A. K., Bergelson, J., Manter, D. K. & Vivanco, J. M. Root exudates regulate soil fungal community composition and diversity. Appl. Environ. Microbiol. 74, 738–744, https://doi.org/10.1128/AEM.02188-07 (2008).

  • 4.

    McDaniel, M. D., Tiemann, L. K. & Grandy, A. S. Does agricultural crop diversity enhance soil microbial biomass and organic matter dynamics? a meta-analysis. Ecol. Appl. 24, 560–570, https://doi.org/10.1890/13-0616.1 (2014).

  • 5.

    Zhou, Y., Zhu, H., Yao, Q. Improving soil fertility and soil functioning in cover cropped agroecosystems with symbiotic microbes. Agro-Environmental Sustainability. Springer, pp. 149–171. https://doi.org/10.1007/978-3-319-49724-2_8 (2017)

  • 6.

    Schipanski, M. E. et al. A framework for evaluating ecosystem services provided by cover crops in agroecosystems. Agric. Syst. 125, 12–22, https://doi.org/10.1016/j.agsy.2013.11.004 (2014).

    • Article
    • Google Scholar
  • 7.

    Finney, D. M. & Kaye, J. P. Functional diversity in cover crop polycultures increases multifunctionality of an agricultural system. J. Appl. Ecol. 54, 509–517, https://doi.org/10.1111/1365-2664.12765 (2017).

    • Article
    • Google Scholar
  • 8.

    Finney, D.M., et al. Ecosystem services and disservices are bundled in simple and diverse cover cropping systems. Agric. Environ. Lett. 2, https://doi.org/10.2134/ael2017.09.0033 (2017)

  • 9.

    Murrell, E. G. et al. Achieving diverse cover crop mixtures: effects of planting date and seeding rate. Agron. J. 109, 259–271, https://doi.org/10.2134/agronj2016.03.0174 (2017).

    • Article
    • Google Scholar
  • 10.

    Salon, P.R. Diverse cover crop mixes for good soil health. In: USDA-NRCS (Ed.), USDA-NRCS. (2012).

  • 11.

    Steinauer, K., Chatzinotas, A. & Eisenhauer, N. Root exudate cocktails: the link between plant diversity and soil microorganisms? Ecol. Evol. 6, 7387–7396, https://doi.org/10.1002/ece3.2454 (2016).

    • Article
    • Google Scholar
  • 12.

    Spatafora, J. W. et al. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia 108, 1028–1046, https://doi.org/10.3852/16-042 (2016).

  • 13.

    Carrera, L. M. et al. Effects of cover crops, compost, and manure amendments on soil microbial community structure in tomato production systems. Appl. Soil Ecol. 37, 247–255, https://doi.org/10.1016/j.apsoil.2007.08.003 (2007).

    • Article
    • Google Scholar
  • 14.

    Galvez, L. et al. An overwintering cover crop increases inoculum of VAM fungi in agricultural soil. Am. J. Alternative Agric. 10, 152–156, https://doi.org/10.1017/S0889189300006391 (1995).

    • Article
    • Google Scholar
  • 15.

    Kabir, Z. & Koide, R. T. Effect of autumn and winter mycorrhizal cover crops on soil properties, nutrient uptake and yield of sweet corn in Pennsylvania, USA. Plant Soil 238, 205–215, https://doi.org/10.1023/A:1014408723664 (2002).

  • 16.

    Lehman, R. M., Taheri, W. I., Osborne, S. L., Buyer, J. S. & Douds, D. D. Fall cover cropping can increase arbuscular mycorrhizae in soils supporting intensive agricultural production. Appl. Soil Ecol. 61, 300–304, https://doi.org/10.1016/j.apsoil.2011.11.008 (2012).

    • Article
    • Google Scholar
  • 17.

    Martínez-García, L. B., Korthals, G., Brussaard, L., Jørgensen, H. B. & De Deyn, G. B. Organic management and cover crop species steer soil microbial community structure and functionality along with soil organic matter properties. Agric. Ecosyst. Environ. 263, 7–17, https://doi.org/10.1016/j.agee.2018.04.018 (2018).

    • Article
    • Google Scholar
  • 18.

    Mbuthia, L. W. et al. Long term tillage, cover crop, and fertilization effects on microbial community structure, activity: implications for soil quality. Soil Biol. Biochem. 89, 24–34, https://doi.org/10.1016/j.soilbio.2015.06.016 (2015).

  • 19.

    Njeru, E. M. et al. Contrasting effects of cover crops on ‘hot spot’arbuscular mycorrhizal fungal communities in organic tomato. Biol. Fertil. Soils 51, 151–166, https://doi.org/10.1007/s00374-014-0958-z (2015).

    • Article
    • Google Scholar
  • 20.

    White, C. M. & Weil, R. R. Forage radish and cereal rye cover crop effects on mycorrhizal fungus colonization of maize roots. Plant Soil 328, 507–521, https://doi.org/10.1007/s11104-009-0131-x (2010).

  • 21.

    Benitez, M., Taheri, W. I. & Lehman, R. M. Selection of fungi by candidate cover crops. Appl. Soil Ecol. 103, 72–82, https://doi.org/10.1016/j.apsoil.2016.03.016 (2016).

    • Article
    • Google Scholar
  • 22.

    Higo, M. et al. Impact of a 5-year winter cover crop rotational system on the molecular diversity of arbuscular mycorrhizal fungi colonizing roots of subsequent soybean. Biol. Fertil. Soils 50, 913–926, https://doi.org/10.1007/s00374-014-0912-0 (2014).

    • Article
    • Google Scholar
  • 23.

    Higo, M. et al. Molecular diversity and distribution of indigenous arbuscular mycorrhizal communities colonizing roots of two different winter cover crops in response to their root proliferation. J. Microbiol. 54, 86–97, https://doi.org/10.1007/s12275-016-5379-2 (2016).

  • 24.

    Hontoria, C., García-González, I., Quemada, M., Roldán, A. & Alguacil, M. M. The cover crop determines the AMF community composition in soil and in roots of maize after a ten-year continuous crop rotation. Sci. Total Environ. 660, 913–922, https://doi.org/10.1016/j.scitotenv.2019.01.095 (2019).

  • 25.

    Turrini, A. et al. Changes in the composition of native root arbuscular mycorrhizal fungal communities during a short-term cover crop-maize succession. Biol. Fertil. Soils 52, 643–653, https://doi.org/10.1007/s00374-016-8 (2016).

    • Article
    • Google Scholar
  • 26.

    Higo, M. et al. Temporal variation of the molecular diversity of arbuscular mycorrhizal communities in three different winter cover crop rotational systems. Biol. Fertil. Soils 51, 21–32. https://doi.org/10.1007/s00374-014-0945-4 (2015)

    • Article
    • Google Scholar
  • 27.

    Shade, A. & Handelsman, J. Beyond the Venn diagram: the hunt for a core microbiome. Environ. Microbiol. 14, 4–12, https://doi.org/10.1111/j.1462-2920.2011.02585.x (2012).

  • 28.

    Hartman, K. et al. Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming. Microbiome 6, 14, https://doi.org/10.1186/s40168-017-0389-9 (2018).

  • 29.

    Mendes, R., Garbeva, P. & Raaijmakers, J. M. The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Micobiol. Rev. 37, 634–663, https://doi.org/10.1111/1574-6976.12028 (2013).

  • 30.

    Toju, H. et al. Core microbiomes for sustainable agroecosystems. Nat. Plants 4, 247–257, https://doi.org/10.1038/s41477-018-0139-4 (2018).

  • 31.

    Lennon, J. T. & Jones, S. E. Microbial seed banks: the ecological and evolutionary implications of dormancy. Nat. Rev. Microbiol. 9, 119, https://doi.org/10.1038/nrmicro2504 (2011).

  • 32.

    Lynch, M. D. J. & Neufeld, J. D. Ecology and exploration of the rare biosphere. Nat. Rev. Microbiol. 13, 217, https://doi.org/10.1038/nrmicro3400 (2015).

  • 33.

    Randhawa, P.K., Mullen, C., Barbercheck, M. Plant identity, but not diversity, and agroecosystem characteristics affect the occurrence of M. robertsii in an organic cropping system. Biol. Control 124, 18–29, 10.1016.j.biocontrol.2018.06.001 (2018)

  • 34.

    Dean, S. L. et al. A study of Glycine max (soybean) fungal communities under different agricultural practices. Plant Gene 11, 8–16, https://doi.org/10.1016/j.plgene.2016.11.003 (2017).

  • 35.

    Detheridge, A. P. et al. The legacy effect of cover crops on soil fungal populations in a cereal rotation. Agric. Ecosyst. Environ. 228, 49–61, https://doi.org/10.1016/j.agee.2016.04.022 (2016).

    • Article
    • Google Scholar
  • 36.

    Finney, D. M., Buyer, J. S. & Kaye, J. P. Living cover crops have immediate impacts on soil microbial community structure and function. J. Soil Water Conserv. 72, 361–373, https://doi.org/10.2489/jswc.72.4.361 (2017).

    • Article
    • Google Scholar
  • 37.

    Higo, M. et al. How are arbuscular mycorrhizal associations related to maize growth performance during short-term cover crop rotation? J. Sci. Food Agri. 98, 1388–1396, https://doi.org/10.1002/jsfa.8606 (2018).

  • 38.

    Alguacil, M. M., Torrecillas, E., García-Orenes, F. & Roldán, A. Changes in the composition and diversity of AMF communities mediated by management practices in a Mediterranean soil are related with increases in soil biological activity. Soil Biol. Biochem. 76, 34–44, https://doi.org/10.1016/j.soilbio.2014.05.002 (2014).

  • 39.

    Bowles, T. M., Acosta-Martinez, V., Calderon, F. & Jackson, L. E. Soil enzyme activities, microbial communities, and carbon and nitrogen availability in organic agroecosystems across an intensively-managed agricultural landscape. Soil Biol. Biochem. 68, 252–262, https://doi.org/10.1016/j.soilbiol.2013.10.004 (2014).

  • 40.

    Wang, Z., Chen, Q., Liu, L., Wen, X. & Liao, Y. Responses of soil fungi to 5-year conservation tillage treatments in the drylands of northern China. Appl. Soil Ecol. 101, 132–140, https://doi.org/10.1016/j.apsoil.2016.02.002 (2016).

    • Article
    • Google Scholar
  • 41.

    Neher, D. A., Weicht, T. R., Bates, S. T., Leff, J. W. & Fierer, N. Changes in bacterial and fungal communities across compost recipes, preparation methods, and composting times. PLoS One 8, e79512, https://doi.org/10.1371/journal.pone.0079512 (2013).

  • 42.

    Tuomela, M., Vikman, M., Hatakka, A. & Itävaara, M. Biodegradation of lignin in a compost environment: a review. Bioresour. Technol. 72, 169–183, https://doi.org/10.1016/S0960-8524(99)00104-2 (2000).

  • 43.

    Hartmann, M., Frey, B., Mayer, J., Mäder, P. & Widmer, F. Distinct soil microbial diversity under long-term organic and conventional farming. Int. Soc. Micobiol. Ecol. 9, 1177–1194, https://doi.org/10.1038/ismej.2014.210 (2015).

    • Article
    • Google Scholar
  • 44.

    Li, F. et al. Mortierella elongata’s roles in organic agriculture and crop growth promotion in a mineral soil. Land Degrad. Develop. 29, 1642–1651, https://doi.org/10.1002/ldr.2965 (2018).

    • Article
    • Google Scholar
  • 45.

    Osorio, N. W. & Habte, M. Synergistic effect of phosphate-solubilizing fungus and an arbuscular mycorrhizal fungus on Leucaena seedlings in an oxisol fertilized with rock phosphate. Botany 91, 274–281, https://doi.org/10.1139/cjb-2012-0226 (2013).

  • 46.

    Zhang, H.S., Qin, F.F., Qin, P., Pan, S.M. Evidence that arbuscular mycorrhizal and phosphate-solubilizing fungi alleviate NaCl stress in the halophyte Kosteletzkya virginica: nutrient uptake and ion distribution within root tissues. Mycorrhiza 24, 383–395, 10.007/s00572-013-0546-3 (2014)

  • 47.

    Priemé, A., et al. Coping with copper: legacy effect of copper on potential activity of soil bacteria following a century of exposure. FEMS Microbiol. Ecol. 92, https://doi.org/10.1093/femsec/fiw175 (2016)

  • 48.

    Wakelin, S. A. et al. Structural and functional response of soil microbiota to addition of plant substrate are moderated by soil Cu levels. Biol. Fertil. Soils 46, 333–342, https://doi.org/10.1007/s00374-009-0436-1 (2010).

  • 49.

    Fernández-Calviño, D. et al. Enzyme activities in vineyard soils long-term treated with copper-based fungicides. Soil Biol. Biochem. 42, 2119–2127, https://doi.org/10.1016/j.soilbio.2010.08.007 (2010).

  • 50.

    Schutter, M., Sandeno, J. & Dick, R. Seasonal, soil type, and alternative management influences on microbial communities of vegetable cropping systems. Biol. Fertil. Soils 34, 397–410, https://doi.org/10.1007/s00374-001-0423-7 (2001).

  • 51.

    Wakelin, S. A. et al. Habitat selective factors influencing the structural composition and functional capacity of microbial communities in agricultural soils. Soil Biol. Biochem. 40, 803–813, https://doi.org/10.1016/j.soilbio.2007.10.015 (2008).

  • 52.

    Keller, S., Kessler, P. & Schweizer, C. Distribution of insect pathogenic soil fungi in Switzerland with special reference to Beauveria brongniartii and Metarhizium anisopliae. BioControl 48, 07–319, https://doi.org/10.1023/A:1023646207455 (2003).

    • Article
    • Google Scholar
  • 53.

    Inyang, E. N., Butt, T. M., Doughty, K. J., Todd, A. D. & Archer, S. The effects of isothiocyanates on the growth of the entomopathogenic fungus Metarhizium anisopliae and its infection of the mustard beetle. Mycol. Res. 103, 974–980 (1999).

  • 54.

    Klingen, I., Hajek, A., Meadow, R. & Renwick, J. A. A. Effect of brassicaceous plants on the survival and infectivity of insect pathogenic fungi. BioControl 47, 411–425, https://doi.org/10.1023/A:1015653910648 (2002).

  • 55.

    Ekesi, S., Maniania, N. K., Onu, I. & Löhr, B. Pathogenicity of entomopathogenic fungi (Hyphomycetes) to the legume flower thrips, Megalurothrips sjostedti (Trybom)(Thysan., Thripidae). J.of Appl. Entomol. 122, 629–634, https://doi.org/10.1111/j.1439-0418.1998.tb01557.x (1998).

    • Article
    • Google Scholar
  • 56.

    Mishra, R. K. et al. Utilization of biopesticides as sustainable solutions for management of pests in legume crops: achievements and prospects. Egypt. J. Biol. Pest Co. 28, 3, https://doi.org/10.1186/s41938-017-0004-1 (2018).

    • Article
    • Google Scholar
  • 57.

    Higo, M. et al. Can phosphorus application and cover cropping alter arbuscular mycorrhizal fungal communities and soybean performance after a five-year phosphorus-unfertilized crop rotational system? PeerJ 6, e4606, https://doi.org/10.7717/peerj.4606 (2018).

  • 58.

    Higo, M., Tatewaki, Y., Gunji, K., Kaseda, A. & Isobe, K. Cover cropping can be a stronger determinant than host crop identity for arbuscular mycorrhizal fungal communities colonizing maize and soybean. PeerJ 7, e6403, https://doi.org/10.7717/peerj.6403 (2019).

  • 59.

    Morimoto, S., Uchida, T., Matsunami, H. & Kobayashi, H. Effect of winter wheat cover cropping with no-till cultivation on the community structure of arbuscular mycorrhizal fungi colonizing the subsequent soybean. Soil Sci. Plant Nutr. 64, 545–553, https://doi.org/10.1080/00380768.2018.1486171 (2018).

    • Article
    • Google Scholar
  • 60.

    Vierheilig, H., Bennett, R., Kiddle, G., Kaldorf, M. & Ludwig-MÜLler, J. Differences in glucosinolate patterns and arbuscular mycorrhizal status of glucosinolate-containing plant species. New Phytol. 146, 343–352, https://doi.org/10.1046/j.1469-8137.2000.00642.x (2000).

  • 61.

    Cosme, M., Fernandez, I., Van der Heijden, M. G. A. & Pieterse, C. M. J. Non-mycorrhizal plants: the exceptions that prove the rule. Trends Plant Sci. 23, 577–587, https://doi.org/10.1016/j.tplants.2018.04.004 (2018).

  • 62.

    de Souza, R. S. C. et al. Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome. Sci. Rep. 6, 28774, https://doi.org/10.1038/srep28774 (2016).

  • 63.

    Hamonts, K. et al. Field study reveals core plant microbiota and relative importance of their drivers. Environ. Microbiol. 20, 124–140, https://doi.org/10.1111/1462-2920.14031 (2018).

  • 64.

    Jiao, S., Xu, Y., Zhang, J., Hao, X. & Lu, Y. Core microbiota in agricultural soils and their potential associations with nutrient cycling. mSystems 4, e00313–18, https://doi.org/10.1128/mSystems.00313-18 (2010).

    • Article
    • Google Scholar
  • 65.

    Murrell, E.G., Ray, S., Lemmon, M.E., Luthe, D.S., Kaye, J.P. Cover crop species affect mycorrhizae-mediated nutrient uptake and pest resistance in maize. Renew. Agric. Food Syst. 1–8. https://doi.org/10.1017/S1742170519000061 (2019).

  • 66.

    Bever, J. D. Host-specificity of AM fungal population growth rates can generate feedback on plant growth. Plant Soil 244, 281–290, https://doi.org/10.1023/A:1020221609080 (2002).

  • 67.

    CTIC. 2016. Report of the 2015-2016 National Cover Crop Survey. West Lafayette, IN.

  • 68.

    Snapp, S. S. et al. Evaluating cover crops for benefits, costs and performance within cropping system niches. Agron. J. 97, 322–332, https://doi.org/10.2134/agronj2005.0322 (2005).

  • 69.

    Qiao, Y. J. et al. Effect of legume-cereal mixtures on the diversity of bacterial communities in the rhizosphere. Plant Soil Environ. 58, 174–180, https://doi.org/10.17221/351/2011-PSE (2012).

    • Article
    • Google Scholar
  • 70.

    Zak, D. R., Holmes, W. E., White, D. C., Peacock, A. D. & Tilman, D. Plant diverity, soil microbial communities, and ecosystem function: are there any links? Ecology 84, 2042–2050, https://doi.org/10.1890/02-0433 (2003).

    • Article
    • Google Scholar
  • 71.

    Gee, G.W., Bowder, J.W. Particle-size analysis, pp 383–411, In Methods of Soil Analysis. Part 1—Physical and Mineralogical Method—Agronomy Monograph No. 9, 2nd ed. A. Klute, ed., American Society of Agronomy, Madison, WI. (1986).

  • 72.

    Gardner, W.H. Early soil physics into the mid-20th century. Advances in Soil Sci. Springer, pp. 1–101, (1986).

  • 73.

    Hamblin, A. P. Filter-paper method for routine measurement of field water potential. J. Hydrol. 53, 355–360, https://doi.org/10.1016/0022-1694(81)90011-1 (1981).

  • 74.

    Weil, R. R., Islam, K. R., Stine, M. A., Gruver, J. B. & Samson-Liebig, S. E. Estimating active carbon for soil quality assessment: A simplified method for laboratory and field use. Am. J. Alternative Agric. 18, 3–17, https://doi.org/10.1079/AJAA200228 (2003).

    • Article
    • Google Scholar
  • 75.

    Culman, S. W. et al. Permanganate oxidizable carbon reflects a processed soil fraction that is sensitive to management. Soil Sci. Soc. Am. J. 76, 494–504, https://doi.org/10.2136/sssaj2011.0286 (2012).

  • 76.

    van der Linde, S., Alexander, I. & Anderson, I. C. A PCR-based method for detecting the mycelia of stipitate hydnoid fungi in soil. J. Microbiol. Methods 75, 40–46, https://doi.org/10.1016/j.mimet.2008.04.010 (2008).

  • 77.

    Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336, https://doi.org/10.1038/nmeth.f.303 (2010).

  • 78.

    Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461, https://doi.org/10.1093/bioinformatics/btq461 (2010).

  • 79.

    Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200, https://doi.org/10.1093/bioinformatics/btr381 (2011).

  • 80.

    R Core Development Team. R: a language and environment for statistical computing. R Foundation for Statistical Computing Vienna, Austria. (2015).

  • 81.

    Oksanen, J., et al. Vegan: community ecology package. (2016)

  • 82.

    Bates, D., Maechler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. of Statistical Softw. 67, 1–48, https://doi.org/10.18637/jss.v067.i01 (2015).

    • Article
    • Google Scholar
  • 83.

    Kuznetsova, A., Brockhoff, P. B. & Christensen, R. H. B. lmerTest package: tests in linear mixed effects models. J. of Statistical Softw. 82, 1–26, https://doi.org/10.18637/jss.v082.i13 (2017).

    • Article
    • Google Scholar
  • 84.

    Lenth, R. emmeans: estimated marginal means, aka least-squares means. CRAN.R-project.org/package=emmeans. (2019).

  • 85.

    Benjamin, Y., Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple hypothesis testing. J. Royal Statistical Society, https://doi.org/10.1111/j.2517-6161.1995.tb02031.x (1995)

  • 86.

    Hervé, M. RVAideMemoire: testing and plotting procedures for biostatistics. CRAN.R-project.org/package=RVAideMemoire. (2019).


  • Source: Ecology - nature.com

    Direct evidence of Neanderthal fibre technology and its cognitive and behavioral implications

    Reducing delays in wireless networks