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Belowground fungi, soil, and root chemistry in tropical landuse systems

Cite this dataset

Polle, Andrea; Ballauff, Johannes (2021). Belowground fungi, soil, and root chemistry in tropical landuse systems [Dataset]. Dryad.


The data were collected in the humid tropical climate on Sumatra (Indonesia) in rain forests, in jungle rubber (rubber planted into forests), in rubber, and oil palm plantations. A total of 44 plots were sampled. The data set consists of two tables. The table Environmental_data contains plot information, geographic coordinates of the plots, and data on soil properties (pH, nitrogen, carbon, C/N, potassium, calcium, magnesium, manganese, iron, phosporous, soil resource index, soil PC1, soil PC2) and on root traits (biomass, nitrogen, carbon, C/N, potassium, calcium, magnesium, manganese, iron, phosporous, root resource index, root PC1, soil PC, root vitality). Table 2 contain abundance data (OTU counts) for fungi associated with roots or with soil and their phylogenetic and functional assignments.


Sampling: Root and soil were collected in 44 plots in different landuse systems on Sumatra. In each plot three replicates were sampled and analysed individually. Environmental_data are means of n = 3 per plot. Fungal_data contain the sum of the OTU counts of three plots.

Environmental_data: Soil and root tissue were dried and milled. Carbon and nitrogen were determined in a C/N analyzer (Vario MICRO analyzer, Elementar, Langensbold, Germany). Other elements were extracted  in 65% HNO3 in a digestion microwave (Ethos Start, Milestone, Sorisole, Italy) for 30 min at 210 ℃ and measured using inductively coupled plasma mass spectrometry (ICP-OES, iCap 7000, Thermo Fisher Scientific, Waltham, USA). pH was determined in 0.1 M KCl. Root tips were inspected under a microscope and classified as vital or dead.

Fungal_data: DNA was extracted from freeze-dried, milled soil and root samples using kits (uPREP Plant DNA kits Analytik Jena AG, Jena, Germany, DNeasy PowerSoil Kit Qiagen, Venlo, Netherlands). For amplication of the fungal ITS1 marker region, the ITS1f-KYO2 and ITS2 primer pair with specific overhang adapters for Illumina sequencing were used. Amplicon sequencing and amplicon sequence variants (ASV) assembly were conducted on the MiSeq platform using the MiSeq Reagent Kit v3 (Illumina Inc., San Diego, USA). OTU clustering occurred at a 97% similarity threshold. Reads were mapped to the library and used to generate a count table. The count table was rarefied. OTUs were taxonomically classified using the BLAST algorithm against the UNITE v.7.2 public database. OTUs were functionally annotated as symbiotroph, pathotroph, and saprotroph using the FUNGuild public database.

Usage notes

Abbreviations: H = harapan landscape; B = bukit landscape; F = forest; J = jungle-rubber; R = rubber plantation; O = oil palm plantation; c = core plot (well drained soil); r = riparian site.

Units: Elements are indicated in the units: mg g-1 dry mass of soil or dry mass of roots. Root biomass (g m-2 to a depth of 0.15 m), Vitality (% of vital root tips per total root tips).

Table Environmental_data: Landscape, land-use type and coordinates of all research plots as well as all measured soil chemical properties and root community traits. RI = Resource Index (sum of standardized calcium, magnesium, potassium, iron and manganese concentrations), PC = principle component axis scores from the principle component analysis for soil and roots.

Table Fungal_data: Read counts of fungal operational taxonomic units (OTU; clustered at 97 % similarity threshold) in soil and root samples of each plot (columns 1 – 89) as well as taxonomic (columns 90 – 92) and functional (column 93 – 98) classification;



Deutsche Forschungsgemeinschaft, Award: CRC990, project B07