ABSTRACT
Ice-free areas are increasing worldwide due to the dramatic glacier shrinkage and are undergoing rapid colonization by multiple lifeforms, thus representing key environments to study ecosystem development. Soils have a complex vertical structure. However, we know little about how microbial and animal communities differ across soil depths and development stages during the colonization of deglaciated terrains, how these differences evolve through time, and whether patterns are consistent among different taxonomic groups. Here, we used environmental DNA metabarcoding to describe how community diversity and composition of six groups (Eukaryota, Bacteria, Mycota, Collembola, Insecta, Oligochaeta) differ between surface (0-5 cm) and relatively deep (7.5-20 cm) soils at different stages of development across five Alpine glaciers. Taxonomic diversity increased with time since glacier retreat and with soil evolution; the pattern was consistent across different groups and soil depths. For Eukaryota, and particularly Mycota, alpha-diversity was generally the highest in soils close to the surface. Time since glacier retreat was a more important driver of community composition compared to soil depth; for nearly all the taxa, differences in community composition between surface and deep soils decreased with time since glacier retreat, suggesting that the development of soil and/or of vegetation tends to homogenize the first 20 cm of soil through time. Within both Bacteria and Mycota, several molecular operational taxonomic units were significant indicators of specific depths and/or soil development stages, confirming the strong functional variation of microbial communities through time and depth. The complexity of community patterns highlights the importance of integrating information from multiple taxonomic groups to unravel community variation in response to ongoing global changes.
KEYWORDS : environmental DNA, glacier retreat, Hill’s number, beta-diversity, soil depth, springtails, earthworms, insects, fungi
The worldwide shrinkage of glaciers is causing a fast increase in ice-free areas on all continents, thus habitats multiple organisms (Ficetola et al., 2021). After ice loss, organisms with high dispersal abilities can colonize the newly exposed terrains relatively quickly (Gobbi et al., 2017; Hågvar et al., 2020; Kaufmann, 2001; Rosero et al., 2021). Both micro- and macro-organisms (e.g. bacteria, fungi and soil fauna) influence soil development being involved in many biogeochemical processes such as soil nutrient cycling (Bardgett 2005; Bardgett & Van Der Putten, 2014), and can interact with each other in determining ecosystem functioning (Ingham, Trofymow, Ingham, & Coleman, 1985). Assessing community variation in this biodiversity compartment and across multiple glacier forelands is important to understand how these ecosystems develop after the retreat of glaciers, and is a key topic of global change biology (Cauvy-Fraunié & Dangles, 2019).
To date, most of our knowledge about soil ecology focuses on the top 10 cm of soil and on microbial communities (Bahram et al., 2015). However, soil characteristics vary vertically (Khokon, Schneider, Daniel, & Polle, 2021). In particular, physical features (e.g., pH, soil moisture, micro-climatic characteristics) typically change through space, and the availability of nutrients (e.g., organic carbon, total nitrogen), together with the enzyme activities of the associated microorganisms, decrease from the topsoil to deeper soil layers (Herold et al., 2014; Moradi et al., 2020). Such variation of habitat conditions can strongly influence the community structure of inhabiting taxa (Carteron, Beigas, Joly, Turner, & Laliberté, 2021; Franzetti et al., 2020; Orwin, Kirschbaum, John, & Dickie, 2011; Rime et al., 2015) because different organisms can be associated with different soil conditions (Khokon, Schneider, Daniel, & Polle, 2021; Mundra et al., 2021). Several studies showed differences in microbial communities across soil depths in several terrestrial habitats including grasslands, forests, high elevation, post-mining and reforested-soils, and agreed that depth significantly affects the abundance, composition and diversity of bacteria and fungi, with the richest communities often associated to surface layers (e.g. Zhao, Zheng, Zhang, Gao, & Fan, 2021; Carteron et al., 2021; Chu et al., 2016; Moradi et al., 2020; Chen, Jiao, Li, & Du, 2020). These differences can be attributable to the decrease in nutrients content at increasing depths (Chu et al., 2016), or to differences in microclimatic conditions and water availability. However, the spatial structuring and micro-habitats conditions of soil communities are yet poorly known, and most studies only focused on very few limited taxonomic groups (Doblas-Miranda, Sánchez-Piñero, & González-Megías, 2009; Moradi et al., 2020; Sadaka & Ponge, 2003), making it difficult to compare the responses of functionally different taxa.
During soil formation after the retreat of glaciers, many features of the substrate change through time, with modifications of physical properties and nutrients content, and a progressive vertical stratification of developed soils (Schaetzl & Anderson, 2005; Mavris, Egli, Plotze, Blum, Mirabella and Giaccai, 2010; Khedim et al., 2021; Wietrzyk-Pełka, Rola, Szymański, & Węgrzyn, 2020). Despite many studies investigating the biotic colonization after glacier retreat, the majority of them focused on organisms living above or just below the surface (reviewed in Ficetola et al. 2021), while limited information is available about the vertical distribution of different topsoil organisms across stages of soil development. Assessing the vertical as well as the horizontal composition and distribution of topsoil colonizers along the glacier forelands is pivotal to infer the key ecological processes under the primary succession that occurs since the early years after glacier retreat. Rime et al. (2015) performed a rare attempt of integrating soil depth into the study of Alpine primary successions (see also Bajerski & Wagner, 2013; Schütte et al., 2009). They assessed the structure of microbial communities along one glacier foreland, and found that soil depth and development stage interact in shaping the biodiversity of bacteria and fungi. Differences between communities from surface and deep layers were particularly strong immediately after glacier retreat, while decreased at older soil development stages, with a homogenization through time. However, Rime et al. (2015) only focused on microorganisms and considered just one glacier foreland. As different topsoil organisms can have very different responses (Cauvy-Fraunié & Dangles, 2019; Donald et al., 2021; Ficetola et al., 2021; Rosero et al., 2021), the study of multiple taxa is needed for a better understanding of the ecological processing governing community development after glacier retreat.
Approaches based on the metabarcoding of environmental DNA (eDNA; Taberlet, Bonin, Zinger, & Coissac, 2018) help overcoming several limitations of conventional sampling and are increasingly used because of their relatively fast and cost-efficient data production. Environmental DNA metabarcoding allows the monitoring of communities of micro- and macro-organisms in a wide range of natural systems (Bohmann et al., 2014). With appropriate technical precautions (Guerrieri et al., 2020), soil communities can be sampled and studied via metabarcoding over broad geographic scales and from remote areas (e.g. Zinger, Taberlet, et al., 2019), and data can be related to environmental characteristics in order to infer ecological processes. The combination of multiple metabarcodes makes eDNA particularly powerful tool for estimating the multi-taxa soil diversity (Donald et al., 2021). Here, we used metabarcoding data from soil eDNA in order to study the vertical distribution of microbes and animals within the top 20 cm of soil, where most microbial diversity has been retrieved (Fierer, Schimel, & Holden, 2003) and where most soil invertebrates spend their life cycle (Menta, 2012). First, we tested whether and how the overall taxonomic diversity of multiple taxa changes with soil depth and time since glacier retreat. We expected that the alpha-diversity of communities increases through time and decreases with depth, especially in the youngest soils. Moreover, we tested whether the changes in alpha-diversity through time are consistent between surface and deep layers. Second, we evaluated the differences in community composition between different depths and tested for potential taxa characteristic of the different depths or stages of soil development. Rime et al (2015) observed that differences between surface and deep soil decrease at older soil development stages, with a homogenization of communities through time, but these conclusions were only based on microorganisms from one single glacier foreland. We analyzed the beta-diversity between surface and deep layers for six taxonomic groups representing a large proportion of biodiversity. If the Rime’s homogenization hypothesis applies to the whole biota, we expect that beta-diversity between surface and deep layers decreases from recent to more developed terrains, with a consistent pattern across taxa.