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Taxonomic shifts in arbuscular mycorrhizal fungal communities with shade and soil nitrogen across conventionally managed and organic coffee agroecosystems

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Abstract

The composition of arbuscular mycorrhizal fungal (AMF) communities should reflect not only responses to host and soil environments, but also differences in functional roles and costs vs. benefits among arbuscular mycorrhizal fungi. The coffee agroecosystem allows exploration of the effects of both light and soil fertility on AMF communities, because of the variation in shade and soil nutrients farmers generate through field management. We used high-throughput ITS2 sequencing to characterize the AMF communities of coffee roots in 25 fields in Costa Rica that ranged from organic management with high shade and no chemical fertilizers to conventionally managed fields with minimal shade and high N fertilization, and examined relationships between AMF communities and soil and shade parameters with partial correlations, NMDS, PERMANOVA, and partial least squares analysis. Gigasporaceae and Acaulosporaceae dominated coffee AMF communities in terms of relative abundance and richness, respectively. Gigasporaceae richness was greatest in conventionally managed fields, while Glomeraceae richness was greatest in organic fields. While total AMF richness and root colonization did not differ between organic and conventionally managed fields, AMF community composition did; these differences were correlated with soil nitrate and shade. OTUs differing in relative abundance between conventionally managed and organic fields segregated into four groups: Gigasporaceae associated with high light and nitrate availability, Acaulosporaceae with high light and low nitrate availability, Acaulosporaceae and a single relative of Rhizophagus fasciculatus with shade and low nitrate availability, and Claroideoglomus/Glomus with conventionally managed fields but uncorrelated with shade and soil variables. The association of closely related taxa with similar shade and light availabilities is consistent with phylogenetic trait conservatism in AM fungi.

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Data availability

The ITS2 DNA sequences generated and analyzed during this study are publicly available as BioProject PRJNA531329, BioSamples SAMN11371063-87 and Sequence Read Archives SRR8868669-93 at the National Center for Biotechnology Information, USA. The environmental dataset for the 25 coffee fields is available through Dryad (https://doi.org/10.5061/dryad.q2bvq83g1).

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Acknowledgments

The authors acknowledge the many farmers who welcomed us onto their land and patiently answered our questions; Sydney Redmond for assistance in scoring root colonization; Ylva Lekberg for her invaluable logistical assistance; David Janos and two anonymous reviewers, whose suggestions greatly improved the manuscript; and the Minnesota Supercomputing Institute (MSI) at the University of Minnesota for providing resources that contributed to the research results reported in this paper (URL: http://www.msi.umn.edu).

Funding

This research was funded by the Office of Undergraduate Research, the Biology Department Fuglestad-Torstveit Fund, and NSF award DUE-0969568 to the Division of Science and Mathematics at Concordia College, and EPSCoR Track 1 Award OIA-1355466 to North Dakota State University. Any opinions, findings, conclusions, or recommendations expressed here are those of the authors and do not necessarily reflect the views of the National Science Foundation.

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Authors and Affiliations

  1. Department of Biological Sciences, North Dakota State University, Fargo, ND, USA

    Laura Aldrich-Wolfe

  2. Biology Department, Concordia College, Moorhead, MN, USA

    Katie L. Black, Eliza D. L. Hartmann, W. Gaya Shivega, Logan C. Schmaltz, Riley D. McGlynn, Peter G. Johnson & Rebecca J. Asheim Keller

  3. Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands

    Stefanie N. Vink

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  1. Laura Aldrich-Wolfe
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  2. Katie L. Black
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  3. Eliza D. L. Hartmann
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Contributions

LAW, RM, LS, EH, and PJ designed and executed the field study; RM, LS, EH, PJ, KB, WGS, and RA conducted the lab work; EH, PJ, RM, LS, KB, WGS, and RA contributed to data analysis; KB and SV conducted the bioinformatics; all authors contributed to the drafts of the manuscript; LAW wrote the final draft.

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Correspondence to Laura Aldrich-Wolfe.

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Aldrich-Wolfe, L., Black, K.L., Hartmann, E.D.L. et al. Taxonomic shifts in arbuscular mycorrhizal fungal communities with shade and soil nitrogen across conventionally managed and organic coffee agroecosystems. Mycorrhiza 30, 513–527 (2020). https://doi.org/10.1007/s00572-020-00967-7

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