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Accounting for environmental variation in co‐occurrence modelling reveals the importance of positive interactions in root‐associated fungal communities

Citation

Abrego, Nerea et al. (2020), Accounting for environmental variation in co‐occurrence modelling reveals the importance of positive interactions in root‐associated fungal communities, Dryad, Dataset, https://doi.org/10.5061/dryad.9kd51c5dp

Abstract

Understanding the role of interspecific interactions in shaping ecological communities is one of the central goals in community ecology. In fungal communities, measuring interspecific interactions directly is challenging because these communities are composed of large numbers of species, many of which are unculturable. An indirect way of assessing the role of interspecific interactions in determining community structure is to identify the species co-occurrences that are not constrained by the environmental conditions. In this study, we investigated co-occurrences among root-associated fungi, asking whether fungi co-occur more or less strongly than expected based on the environmental conditions and the host plant species examined. For this purpose, we generated molecular data on root-associated fungi of five plant species evenly sampled along an elevational gradient at a high Arctic site. We analysed the data using a joint species distribution modelling approach that allowed us to identify those co-occurrences that could be explained by the environmental conditions and the host plant species, as well as those co-occurrences that remained unexplained and thus more likely reflect interactive associations. Our results indicate that positive interactions play an important role in shaping microbial communities in arctic plant roots. In particular, we found that mycorrhizal fungi are especially prone to positively co-occur with other fungal species. Our results bring new understanding to the structure of arctic interaction networks by suggesting that interactions among root-associated fungi are predominantly positive.

Methods

These data consist of molecularly identified root-associated fungal communities of five plant species occurring along an arctic elevational gradient. The original sequence data based on the ITS region are published in Abarenkov et al (2019 https://doi.org/10.5061/dryad.9dr6j0c), and the data published here consist of the postprocessed and taxonomically assigned using the Protax-fungi approach. The data further contains information about the functional group of each taxonomical unit (mycorrhizal, endophytic or unclassified), and data on the environmental covariates used in the analyses. The data are accompained by the R-scripts for carrying out the analyses presented in Abrego et al (2020, Molecular Ecology) about raw vs. environmentally constrained co-occurrences using the R-package Hmsc-R.

Usage Notes

The data are given in the format of R-files which can be used as shown in the uploaded R-scripts. You may need to add ".rdata" file extension to the 

Funding

Academy of Finland, Award: 308651

Ella and Georg Ehrnrooth Foundation

Academy of Finland, Award: 276909

Academy of Finland, Award: 285803

Vetenskapsrådet, Award: 2015‐03993

Academy of Finland, Award: 1273253

Academy of Finland, Award: 250444

Norges Forskningsråd, Award: 223257

Ella ja Georg Ehrnroothin Säätiö

Ella and Georg Ehrnrooth Foundation