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

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.

理解种间相互作用在塑造生态群落中的作用，是群落生态学的核心研究目标之一。在真菌群落中，直接测定种间相互作用颇具挑战——这类群落包含大量物种，其中多数无法人工培养。评估种间相互作用对群落结构调控作用的间接途径，是识别不受环境条件约束的物种共现模式。本研究聚焦根系相关真菌的共现模式，旨在探究相较于基于环境条件与所调查宿主植物物种的预期结果，真菌间的共现强度是否更强或更弱。为此，我们在高北极样点沿海拔梯度均匀采样了5种植物的根系相关真菌，并生成了对应的分子数据。我们采用联合物种分布模型（Joint Species Distribution Modelling）对数据进行分析，该方法可区分两类共现模式：一类可通过环境条件与宿主植物物种解释，另一类则无法被上述因素解释，因而更可能反映真菌间的相互作用关联。研究结果表明，正相互作用在北极植物根系的微生物群落塑造过程中发挥着重要作用。尤其值得注意的是，我们发现菌根真菌更倾向于与其他真菌物种形成正共现关系。本研究提出根系相关真菌间的相互作用以正相互作用为主，为北极相互作用网络的结构研究提供了新的认知。

方法
本数据集包含沿北极海拔梯度分布的5种植物的根系相关真菌群落的分子鉴定结果。基于内转录间隔区（ITS）的原始序列数据已发表于Abarenkov等人（2019，https://doi.org/10.5061/dryad.9dr6j0c），本次发布的数据为经后处理并通过Protax-fungi方法完成分类学注释的数据集。数据集还包含各分类单元的功能群信息（菌根真菌、内生真菌或未分类），以及分析中使用的环境协变量数据。此外，本数据集配套了用于复现Abrego等人（2020，《分子生态学》）研究中基于Hmsc-R包开展的原始共现与受环境约束的共现分析的R脚本。