Sampling and molecular work
Soil samples were collected in September, 2012, in Kinabalu and Crocker Range Parks of Sabah, Borneo; in May, 2011 and 2013, in Jujuy, Salta and Tucumán provinces of Argentina; and in June, 2016, in Bocas del Toro, Chiriquí, Colón and Panamá provinces of Panama. The sampling sites represent the entire elevation range of various types of forests in the respective regions. Forest type, elevation, geographic coordinates, and localities are shown in Table S1 and on maps corresponding to the three regions (Figs. S1-3).
In Argentina and Borneo, 40 soil cores, 2 cm in diameter and ca. 20 cm deep, were taken at each sampling site (ca. 10 × 25 m). Cores were collected ca. 2 m from each other to minimize the probability of sampling the same genet repeatedly. In Panama, 10 soil cores of the above dimensions were collected in each site (ca. 4 × 5 m). Soil cores taken at a given site were pooled, resulting in a composite soil sample for each site. With respect to the samples collected in Argentina and Panama, ca. 20 g of each sample was kept frozen until lyophilization ca. 2 weeks later. In Borneo, because of the more remote location, soil samples were dried immediately at 30-35 °C. Because of these differences, we handled the data separately for each region for the analyses that are the focus of this paper. We did use the combined dataset to provide the first characterization of the putative ‘core’ pantropical mycobiome of montane and lowland forests, i.e., fungi shared among the Neotropical and Paleotropical regions and characteristic of the different elevation zones.
Genomic DNA was extracted from 0.5 ml of dry soil from each sample with the NucleoSpin® soil kit (Macherey-Nagel Gmbh & Co., Düren, Germany) according to manufacturer’s protocol. For each sample, two independent DNA extractions were carried out and the extracts were pooled. The ITS2 region (ca. 250 bp) of the nuclear ribosomal DNA repeat was amplified via PCR with primers fITS7 (Ihrmark et al. 2012) and ITS4 (White et al. 1990). The ITS4 primer was labelled with sample-specific Multiplex Identification DNA-tags (MIDs). The amplicon library was sequenced at Naturalis Biodiversity Center (Naturalis) with an Ion 318TM Chip and an Ion Torrent Personal Genome Machine (Life Technologies, Guilford, CT, U.S.A.). Chemical analyses of soil samples from Argentina and Borneo were carried out as described in Geml et al. (2014) and Geml et al. (2017), respectively. The samples from Panama were analysed by the Instituto de Investigación Agropecuaria de Panamá (IDIAP). Climate data were obtained from the WorldClim database (www.worldclim.org) based on the geographic coordinates of the sampling sites.