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Cover crop-driven shifts in soil microbial communities could modulate early tomato biomass via plant-soil feedbacks

  • Mariotte, P. et al. Plant–soil feedback: Bridging natural and agricultural sciences. Trends Ecol. Evol. 33, 129–142 (2018).

    PubMed 
    Article 

    Google Scholar 

  • Daryanto, S., Fu, B., Wang, L., Jacinthe, P. A. & Zhao, W. Quantitative synthesis on the ecosystem services of cover crops. Earth-Sci. Rev. 185, 357–373 (2018).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • Shackelford, G. E., Kelsey, R. & Dicks, L. V. Effects of cover crops on multiple ecosystem services: Ten meta-analyses of data from arable farmland in California and the Mediterranean. Land Use Policy 88, 104204 (2019).

    Article 

    Google Scholar 

  • 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 (2014).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Wittwer, R. A., Dorn, B., Jossi, W. & van der Heijden, M. G. A. A. Cover crops support ecological intensification of arable cropping systems. Sci. Rep. 7, 41911 (2017).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Chahal, I. & Van Eerd, L. L. Cover crops increase tomato productivity and reduce nitrogen losses in a temperate humid climate. Nutr. Cycl. Agroecosyst. 119, 195–211 (2021).

    CAS 
    Article 

    Google Scholar 

  • Belfry, K. D., Trueman, C., Vyn, R. J., Loewen, S. A. & Van Eerd, L. L. Winter cover crops on processing tomato yield, quality, pest pressure, nitrogen availability, and profit margins. PLoS ONE 12, 1–17 (2017).

    Article 
    CAS 

    Google Scholar 

  • Wall, L. G. et al. Changes of paradigms in agriculture soil microbiology and new challenges in microbial ecology. Acta Oecologica 95, 68–73 (2019).

    ADS 
    Article 

    Google Scholar 

  • Schmidt, R., Gravuer, K., Bossange, A. V., Mitchell, J. & Scow, K. Long-term use of cover crops and no-till shift soil microbial community life strategies in agricultural soil. PLoS ONE 13, 1–19 (2018).

    Google Scholar 

  • Schmidt, R., Mitchell, J. & Scow, K. Cover cropping and no-till increase diversity and symbiotroph:saprotroph ratios of soil fungal communities. Soil Biol. Biochem. 129, 99–109 (2019).

    CAS 
    Article 

    Google Scholar 

  • Ali, A. et al. Hiseq base molecular characterization of soil microbial community, diversity structure, and predictive functional profiling in continuous cucumber planted soil affected by diverse cropping systems in an intensive greenhouse region of Northern China. Int. J. Mol. Sci. 20, 2619 (2019).

    CAS 
    PubMed Central 
    Article 

    Google Scholar 

  • Kim, N., Zabaloy, M. C., Guan, K. & Villamil, M. B. Do cover crops benefit soil microbiome? A meta-analysis of current research. Soil Biol. Biochem. 142, 107701 (2020).

    CAS 
    Article 

    Google Scholar 

  • Vukicevich, E., Lowery, T., Bowen, P., Úrbez-Torres, J. R. & Hart, M. Cover crops to increase soil microbial diversity and mitigate decline in perennial agriculture. A review. Agron. Sustain. Dev. 36, 1–14 (2016).

    CAS 
    Article 

    Google Scholar 

  • Nevins, C. J., Nakatsu, C. & Armstrong, S. Characterization of microbial community response to cover crop residue decomposition. Soil Biol. Biochem. 127, 39–49 (2018).

    CAS 
    Article 

    Google Scholar 

  • Peralta, A. L., Sun, Y., McDaniel, M. D. & Lennon, J. T. Crop rotational diversity increases disease suppressive capacity of soil microbiomes. Ecosphere 9, e02235 (2018).

    Article 

    Google Scholar 

  • Cloutier, M. L. et al. Fungal community shifts in soils with varied cover crop treatments and edaphic properties. Sci. Rep. 10, 1–15 (2020).

    Article 
    CAS 

    Google Scholar 

  • 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 (2017).

    Article 

    Google Scholar 

  • Calderón, F. J., Nielsen, D., Acosta-Martínez, V., Vigil, M. F. & Lyon, D. Cover crop and irrigation effects on soil microbial communities and enzymes in semiarid agroecosystems of the central great plains of North America. Pedosphere 26, 192–205 (2016).

    Article 
    CAS 

    Google Scholar 

  • Romdhane, S. et al. Cover crop management practices rather than composition of cover crop mixtures affect bacterial communities in no-till agroecosystems. Front. Microbiol. 10, 1–11 (2019).

    Article 

    Google Scholar 

  • Blanco-Canqui, H. & Lal, R. Crop residue removal impacts on soil productivity and environmental quality. CRC. Crit. Rev. Plant Sci. 28, 139–163 (2009).

    CAS 
    Article 

    Google Scholar 

  • Turmel, M. S., Speratti, A., Baudron, F., Verhulst, N. & Govaerts, B. Crop residue management and soil health: A systems analysis. Agric. Syst. 134, 6–16 (2015).

    Article 

    Google Scholar 

  • Yang, Q., Wang, X. & Shen, Y. Comparison of soil microbial community catabolic diversity between rhizosphere and bulk soil induced by tillage or residue retention. J. Soil Sci. Plant Nutr. https://doi.org/10.4067/S0718-95162013005000017 (2013).

    Article 

    Google Scholar 

  • Tang, H. et al. Tillage and crop residue incorporation effects on soil bacterial diversity in the double-cropping paddy field of southern China. Arch. Agron. Soil Sci. 67, 435–446 (2021).

    CAS 
    Article 

    Google Scholar 

  • Zhang, Y. et al. Long-term harvest residue retention could decrease soil bacterial diversities probably due to favouring oligotrophic lineages. Microb. Ecol. 76, 771–781 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Zhang, C. et al. Straw retention efficiently improves fungal communities and functions in the fallow ecosystem. BMC Microbiol. 21, 52 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Chahal, I. & Van Eerd, L. L. Cover crop and crop residue removal effects on temporal dynamics of soil carbon and nitrogen in a temperate, humid climate. PLoS ONE 15, e0235665 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Chahal, I. & Van Eerd, L. L. Evaluation of commercial soil health tests using a medium-term cover crop experiment in a humid, temperate climate. Plant Soil 427, 351–367 (2018).

    CAS 
    Article 

    Google Scholar 

  • Ruis, S. J. & Blanco-Canqui, H. Cover crops could offset crop residue removal effects on soil carbon and other properties: A review. Agron. J. 109, 1785–1805 (2017).

    CAS 
    Article 

    Google Scholar 

  • Zhao, M. et al. Intercropping affects genetic potential for inorganic nitrogen cycling by root-associated microorganisms in Medicago sativa and Dactylis glomerata. Appl. Soil Ecol. 119, 260–266 (2017).

    ADS 
    Article 

    Google Scholar 

  • Wardle, D. A. et al. Ecological linkages between aboveground and belowground biota. Science (80-). 304, 1629–1633 (2004).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • Xiong, C. et al. Host selection shapes crop microbiome assembly and network complexity. New Phytol. 229, 1091–1104 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • McDaniel, M. D., Grandy, A. S., Tiemann, L. K. & Weintraub, M. N. Eleven years of crop diversification alters decomposition dynamics of litter mixtures incubated with soil. Ecosphere 7, e01426 (2016).

    Article 

    Google Scholar 

  • Buyer, J. S., Teasdale, J. R., Roberts, D. P., Zasada, I. A. & Maul, J. E. Factors affecting soil microbial community structure in tomato cropping systems. Soil Biol. Biochem. 42, 831–841 (2010).

    CAS 
    Article 

    Google Scholar 

  • Fernandez-Gnecco, G. et al. Microbial community analysis of soils under different soybean cropping regimes in the Argentinean south-eastern Humid Pampas. FEMS Microbiol. Ecol. 97, 1–14 (2021).

    Article 
    CAS 

    Google Scholar 

  • Semenov, M. V., Krasnov, G. S., Semenov, V. M. & van Bruggen, A. H. C. Long-term fertilization rather than plant species shapes rhizosphere and bulk soil prokaryotic communities in agroecosystems. Appl. Soil Ecol. 154, 103641 (2020).

    Article 

    Google Scholar 

  • White, C. M. & Weil, R. R. Forage radish cover crops increase soil test phosphorus surrounding radish taproot holes. Soil Sci. Soc. Am. J. 75, 121–130 (2011).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • Schulz, M., Marocco, A., Tabaglio, V., Macias, F. A. & Molinillo, J. M. G. Benzoxazinoids in rye allelopathy—From discovery to application in sustainable weed control and organic farming. J. Chem. Ecol. 39, 154–174 (2013).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Cheng, F. & Cheng, Z. Research progress on the use of plant allelopathy in agriculture and the physiological and ecological mechanisms of allelopathy. Front. Plant Sci. 6, 1020 (2015).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Thapa, V. R., Ghimire, R., Acosta-Martínez, V., Marsalis, M. A. & Schipanski, M. E. Cover crop biomass and species composition affect soil microbial community structure and enzyme activities in semiarid cropping systems. Appl. Soil Ecol. 157, 103735 (2021).

    Article 

    Google Scholar 

  • Drost, S. M., Rutgers, M., Wouterse, M., de Boer, W. & Bodelier, P. L. E. Decomposition of mixtures of cover crop residues increases microbial functional diversity. Geoderma 361, 114060 (2020).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • Di Rauso Simeone, G., Müller, M., Felgentreu, C. & Glaser, B. Soil microbial biomass and community composition as affected by cover crop diversity in a short-term field experiment on a podzolized Stagnosol-Cambisol. J. Plant Nutr. Soil Sci. 183, 539–549 (2020).

    Article 
    CAS 

    Google Scholar 

  • Maul, J. E. et al. Microbial community structure and abundance in the rhizosphere and bulk soil of a tomato cropping system that includes cover crops. Appl. Soil Ecol. 77, 42–50 (2014).

    Article 

    Google Scholar 

  • Huang, J. et al. Allocation and turnover of rhizodeposited carbon in different soil microbial groups. Soil Biol. Biochem. 150, 107973 (2020).

    CAS 
    Article 

    Google Scholar 

  • Strickland, M. S. & Rousk, J. Considering fungal:bacterial dominance in soils—Methods, controls, and ecosystem implications. Soil Biol. Biochem. 42, 1385–1395 (2010).

    CAS 
    Article 

    Google Scholar 

  • Leff, J. W. et al. Predicting the structure of soil communities from plant community taxonomy, phylogeny, and traits. ISME J. 12, 1794–1805 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Milcu, A. et al. Functionally and phylogenetically diverse plant communities key to soil biota. Ecology 94, 1878–1885 (2013).

    PubMed 
    Article 

    Google Scholar 

  • Lozupone, C. A., Hamady, M., Kelley, S. T. & Knight, R. Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities. Appl. Environ. Microbiol. 73, 1576–1585 (2007).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Lay, C.-Y., Hamel, C. & St-Arnaud, M. Taxonomy and pathogenicity of Olpidium brassicae and its allied species. Fungal Biol. 122, 837–846 (2018).

    PubMed 
    Article 

    Google Scholar 

  • Liu, L., Zhu, K., Wurzburger, N. & Zhang, J. Relationships between plant diversity and soil microbial diversity vary across taxonomic groups and spatial scales. Ecosphere 11, e02999 (2020).

    Google Scholar 

  • Hartwright, L. M., Hunter, P. J. & Walsh, J. A. A comparison of Olpidium isolates from a range of host plants using internal transcribed spacer sequence analysis and host range studies. Fungal Biol. 114, 26–33 (2010).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Barel, J. M. et al. Winter cover crop legacy effects on litter decomposition act through litter quality and microbial community changes. J. Appl. Ecol. 56, 132–143 (2019).

    CAS 
    Article 

    Google Scholar 

  • Austin, E. E., Wickings, K., McDaniel, M. D., Robertson, G. P. & Grandy, A. S. Cover crop root contributions to soil carbon in a no-till corn bioenergy cropping system. GCB Bioenergy 9, 1252–1263 (2017).

    CAS 
    Article 

    Google Scholar 

  • Bai, Z., Liang, C., Bodé, S., Huygens, D. & Boeckx, P. Phospholipid 13C stable isotopic probing during decomposition of wheat residues. Appl. Soil Ecol. 98, 65–74 (2016).

    Article 

    Google Scholar 

  • Põlme, S. et al. FungalTraits: A user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Divers. 105, 1–16 (2020).

    Article 

    Google Scholar 

  • Pepe, A., Giovannetti, M. & Sbrana, C. Lifespan and functionality of mycorrhizal fungal mycelium are uncoupled from host plant lifespan. Sci. Rep. 8, 1–10 (2018).

    Google Scholar 

  • Frey, S. D. Mycorrhizal fungi as mediators of soil organic matter dynamics. Annu. Rev. Ecol. Evol. Syst. 50, 237–259 (2019).

    Article 

    Google Scholar 

  • Saleem, M., Hu, J. & Jousset, A. More than the sum of its parts: Microbiome biodiversity as a driver of plant growth and soil health. Annu. Rev. Ecol. Evol. Syst. 50, 145–168 (2019).

    Article 

    Google Scholar 

  • Wei, Z. et al. Initial soil microbiome composition and functioning predetermine future plant health. Sci. Adv. 5, 1–12 (2019).

    Google Scholar 

  • Ozimek, E. & Hanaka, A. Mortierella species as the plant growth-promoting fungi present in the agricultural soils. Agriculture 11, 7 (2020).

    Article 
    CAS 

    Google Scholar 

  • Li, F. et al. Mortierella elongata’s roles in organic agriculture and crop growth promotion in a mineral soil. L. Degrad. Dev. 29, 1642–1651 (2018).

    Article 

    Google Scholar 

  • Sansinenea, E. Bacillus spp.: As plant growth-promoting bacteria. in Secondary Metabolites of Plant Growth Promoting Rhizomicroorganisms: Discovery and Applications 225–237 (Springer, 2019). https://doi.org/10.1007/978-981-13-5862-3_11.

  • Palaniyandi, S. A., Yang, S. H., Zhang, L. & Suh, J.-W. Effects of actinobacteria on plant disease suppression and growth promotion. Appl. Microbiol. Biotechnol. 97, 9621–9636 (2013).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Jung, M.-Y. et al. Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities. ISME J. 16, 272–283 (2022).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Zhong, Y. et al. Microbial community assembly and metabolic function during wheat straw decomposition under different nitrogen fertilization treatments. Biol. Fertil. Soils 56, 697–710 (2020).

    CAS 
    Article 

    Google Scholar 

  • Liu, X. et al. Decomposing cover crops modify root-associated microbiome composition and disease tolerance of cash crop seedlings. Soil Biol. Biochem. 160, 108343 (2021).

    CAS 
    Article 

    Google Scholar 

  • Larkin, R. P., Griffin, T. S. & Honeycutt, C. W. Rotation and cover crop effects on soilborne potato diseases, tuber yield, and soil microbial communities. Plant Dis. 94, 1491–1502 (2010).

    PubMed 
    Article 

    Google Scholar 

  • van der Putten, W. H., Bradford, M. A., Brinkman, E. P., van de Voorde, T. F. J. & Veen, G. F. Where, when and how plant–soil feedback matters in a changing world. Funct. Ecol. 30, 1109–1121 (2016).

    Article 

    Google Scholar 

  • Menalled, U. D., Seipel, T. & Menalled, F. D. Farming system effects on biologically mediated plant–soil feedbacks. Renew. Agric. Food Syst. 36, 1–7 (2021).

    Article 

    Google Scholar 

  • Fierer, N. & Jackson, J. Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Appl. Environ. Microbiol. 71, 4117 (2005).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Vainio, E. J. & Hantula, J. Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNA. Mycol. Res. 104, 927–936 (2000).

    CAS 
    Article 

    Google Scholar 

  • Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. 108, 4516–4522 (2011).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 

  • White, T. J., Bruns, T., Lee, S. & Taylor, J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR Protocols: A Guide to Methods and Applications (eds Innis, M. A. et al.) 315–322 (Academic Press, 1990).

    Google Scholar 

  • Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Rivers, A. R., Weber, K. C., Gardner, T. G., Liu, S. & Armstrong, S. D. ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis. F1000Research 7, 1418 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—Approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Bokulich, N. A. et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome 6, 90 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Abarenkov, K. et al. UNITE QIIME release for Fungi. https://doi.org/10.15156/bio/786385 (2020).

  • R Core Team. R: A Language and Environment for Statistical Computing. (2020).

  • Oksanen, J. et al. vegan: Community Ecology Package. (2020).

  • Anderson, M. J., Gorley, R. N. & Clarke, K. R. PERMANOVA+ for PRIMER: Guide to Software and Statistical Methods. (PRIMER-E, 2008).

  • Anderson, M. J. & Willis, T. J. Canonical analysis of principal coordinates: A useful method of constrained ordination for ecology. Ecology 84, 511–525 (2003).

    Article 

    Google Scholar 

  • Cáceres, M. D. & Legendre, P. Associations between species and groups of sites: Indices and statistical inference. Ecology 90, 3566–3574 (2009).

    PubMed 
    Article 

    Google Scholar 

  • Fernandes, A. D. et al. Unifying the analysis of high-throughput sequencing datasets: Characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis. Microbiome 2, 15 (2014).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 


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