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.