DOI: 10.5061/dryad.hmgqnk9c8
title: Effects of past and present-day landscape structure on forest soil microorganisms

description: Principles of landscape ecology have been built on birds and plant species
 distribution, but the number of clues is now growing on below-ground
 organisms, whose dispersal may also be affected by above-ground landscape
 structure. For communities of microorganisms, the question remains if and
 how they answer to landscape structure, with or without time lag, and if
 some groups of microorganisms may react more than others. Here, we
 investigated if fungi or bacteria diversity is driven by the amount of
 forest cover in the current or the past landscape. We tested the Habitat
 Amount Hypothesis (HAH) on ancient forests of Cevennes national park, that
 were particularly fragmented 150 years ago, and are today surrounded by
 recent forests. As ancient forests are often more diverse in plant
 species, we hypothesized that the higher quantity of ancient forests in
 the landscape, the richer fungal and bacterial communities would be
 locally. More precisely, we expected that ectomycorrhizal fungi, and
 pathotrophic fungi, often indicators of mature forests, would be also more
 sensitive to forest history and therefore to the quantity of ancient
 forests than bacteria and saprotrophic fungi. We sampled 40 soil cores per
 0.5 ha, pooled in 8 composite samples per plot in 27 landscapes and
 sequenced ITS and 16S marker by Illumina-Mi seq. To identify functional
 groups of fungi, we relied on their taxonomy and the use of public
 databases. Our results partly follow the HAH, as fungi richness was
 positively related with the quantity of ancient forests in the landscape
 and not by the focal patch size. Ectomycorrhizal and pathotrophic fungi
 were positively affected by the ancient forest cover, and so were
 saprotrophic ones, but not bacteria. Local factors also shaped the
 communities such as soil composition and elevation, confirming classical
 patterns in soil ecology. Interestingly, past landscape structure better
 explained fungi communities richness than contemporary landscape,
 suggesting a time lag in the response of communities to landscape
 modification and a potential extinction debt. Our results invite to
 consider below-ground communities in landscape studies and historical
 ecology, as their structure and functions might be intimately linked with
 soil and landscape history.
description: Soil samples were collected on April 2017 (average temperature 4.4 °C, average precipitation 17.6 mm from www infoclimat.fr). In each study site, soil cores were collected along two 60 m transect, spaced from 20 m : every 20 m a soil core was collected, and pooled with four soil cores collected at 3.5 m from the focal point in each cardinal direction. As a result, 40 soil cores pooled in 8 composite samples were collected per plot. The composite samples were then opened back to the lab the same day, and 15 g of soil was isolated in a clean tea-bag and dried with 50 g of silicagel (eventually more if the sample was not dry the day after). Soil DNA was extracted less than one month later with Macherey Nagel NucleoSpin® Soil kit (Ref 740780.250). Amplifications targeted ITS1 nuclear rDNA primers for fungi (Fwd: ITS5 GGAAGTAAAAGTCGTAACAAGG from Epp et al. 2012 and a modified version of Rev: 5.8S_Fungi CAAGAGATCCGTTGTTGAAAGTK, Taberlet et al. 2018), and 16S rDNA (V5-V6) for bacteria (Bact01 primers - Fwd: GGATTAGATACCCTGGTAGT and Rev: CACGACACGAGCTGACG (Fliegerova et al. 2014)). Each PCR was performed with a unique set of primers, characterized by a unique set of 8 nucleotide tags added to the universal primers, allowing to distinguish samples later in the analysis (as described in Taberlet et al. 2018). Negative controls without any PCR reactants were integrated (10% of our reactions) and all PCR reactions were replicated twice. PCR conditions followed Nagati et al. (2018). All PCR reactions were pooled to prepare Illumina-Miseq libraries, which were sent to GenoToul Core Facility platform for sequencing.