Sample collection and dataset information
Details on soil sampling, vegetation survey, measurement of soil
properties, sequencing and bioinformatics were described in our previous
study (Yang et al. 2017; Shi et al. 2019). Briefly, in the
growing season of 2011, 180 soil samples were collected across the
north-eastern and central Tibetan Plateau.
Within each of the sites, three of the ten small plots - each 1×1m in
size - were randomly chosen on the diagonals of the 1-ha site at least
40 m apart (Fig S1). In each 1×1m plot, seven randomly located soil
cores of the top 5 cm of topsoil (under any litter layer) were collected
and homogenized as a composite soil sample. All vascular plant species
and the number of individuals of each were recorded, at each of the 180
plots, and summarized at the site level (60 sites), and plant species
richness was calculated.
All soil properties, including pH, soil moisture (SM), total carbon,
total nitrogen, soil total phosphorus (STP), soil organic carbon (SOC),
were measured at the individual plot level following (Jing et al.2015), and then averaged at the site level. As three small plots were
merged from each site, this gave 60 sites samples in total.
Soil DNA from each plot was extracted and amplified in the Illumina
MiSeq platform PE250 (Illumina Inc., San Diego, CA, USA). The primers
ITS3 (50-GCATCGATGAAGAACGCAGC)/ITS4 (50-TCCTCCGCTTATTGATATGC) were used
to target the fungal internal transcribed spacer 2 (ITS2) region. The
bioinformatic pipeline on ITS2 sequencing data was identical to the
description of Teng et al (Yang et al. 2017). The primer set of
F515: 5’-GTGCCAGCMGCCGCGG, R907: 5’-CCGTCAATTCMTTTRAGTTT (Lane et
al. 1985) were used to amplify the V4-V5 hyper-variable regions of
bacterial 16S rRNA gene. The high-throughput sequencing process and
analysis of soil fungi and bacteria has been described already by Teng
et al (Yang et al. 2017) and Shi et al (Shi et al. 2019).
In order to be compatible with plant and soil data, we merged the OTU
table at the site level. Finally, 11,576,489 fungal sequences
(min=123,753 sequences per site) and 1,031,092 bacterial sequences
(min=9,037 sequences per site) were obtained in the 60 sites. In order
to analyze the microbial data at the same sequencing depth, the OTU
matrices were rarefied to 123,753 sequences per sample for fungi. But
for bacteria, most sites were rarefied to 12850 sequences, only two
sites far less than 12850 sequences were rarefied to 9037 reads, to keep
as many reads as possible without compromising the bacterial alpha
diversity. The richness of bacteria and fungi species were then
calculated by “countif” function in Excel.