Multi-targeted metagenetic analysis of the influence of climate and environmental parameters on soil microbial communities along an elevational gradient

Abstract

Mountain elevation gradients are invaluable sites for understanding the effects of climate change on ecosystem function, community structure and distribution. However, relatively little is known about the impact on soil microbial communities, in spite of their importance for the functioning of the soil ecosystem. Previous studies of microbial diversity along elevational gradients were often limited by confounding variables such as vegetation, pH, and nutrients. Here, we utilised a transect in the Pyrenees established to minimise variation in such parameters, to examine prokaryotic, fungal, protist and metazoan communities throughout three consecutive years. We aimed to determine the influences of climate and environmental parameters on soil microbial community structure; as well as on the relationships between those microbial communities. Further, functional diversity of heterotrophic bacteria was determined using Biolog. Prokaryotic and fungal community structure, but not alpha-diversity, correlated significantly with elevation. However, carbon-to-nitrogen ratio and pH appeared to affect prokaryotic and protist communities more strongly. Both community structure and physicochemical parameters varied considerably between years, illustrating the value of long-term monitoring of the dynamic processes controlling the soil ecosystem. Our study also illustrates both the challenges and strengths of using microbial communities as indicators of potential impacts of climate change.

Figure 1. Annual mean of daily minimum, median and maximum soil temperatures (2013–2014), and predicted days under snow coverage, along the studied gradient.

Figure 2. Identified correlations between alpha-diversity estimates and physicochemical parameters.

Figure 3. Non-metric multidimensional scaling (NMDS) based on Bray-Curtis dissimilarities of microbial community composition.

Composition was based on Hellinger-transformed relative OTU abundances from prokaryotic 16S, eukaryotic 18S and fungal ITS amplicon data. 18S data was also divided into organism groups. Sites are labelled according to legend and red vectors indicate fitted environmental parameters significantly correlated to NMDS coordinates. Where parameter measurements were only available for a subset of samples, this is indicated in parenthesis (samples/total), whereas thick lines indicate that measurements were available for the complete dataset. Black bidirectional arrows illustrate Mantel tests for similarity between community dissimilarity matrices.

Figure 4. Distribution of most abundant taxa across samples.

Relative abundances of taxa at order level are presented as bar-charts for each individual sample, grouped by elevation (in 100 m) for the three specific amplicon library types prepared. Total 18S amplicon results are divided by organism type into fungi, “protists” and metazoa. Typically parasitic taxa are marked with asterisks.

Figure 5. Non-metric multidimensional scaling (NMDS) based on Bray-Curtis dissimilarities of plant community composition.

Sites are labelled with elevation in metres and red vectors indicate fitted environmental parameters significantly correlated to NMDS coordinates.