Rarefaction analysis of soil AMF samples from Järvselja forest reserve.

<p>Mean VT richness is estimated in relation to the number of reads analysed for subsets of the data representing soil samples collected in different months and from different plots.</p

Variation in the AMF communities present in soil at Järvselja forest reserve.

<p>The results of PERMANOVA analysis are shown. The seasonal model describes variation between sampling month (May, June, July and September) and sample location (SampleID) in Plot A; the spatial model describes variation between Plots A, B and C in September. In the seasonal model, the significance of explanatory variables was not sensitive to their order in the model.</p

Change in soil AMF community similarity as a function of spatial and temporal distance.

<p>A) spatial - soil samples from 10×10 m plots in September and; B) temporal - soil samples from plot A in May, June, July and September. The data points show pairwise similarity estimates between all samples; the bold red line shows the relationship between similarity and distance in the real data; the faint black lines show the same relationship in 1000 randomised data matrices. Note that the x axis does not represent direction in space or time; thus greater values denote the greatest distance between samples – e.g. between May and September – and not the timing or location of samples <i>per se</i>. The slope of the real model was steeper than the randomised set for the spatial model (P<0.01) but not the temporal model (P = 0.57).</p

Sampling design used to study soil AMF communities in Järvselja forest reserve.

<p>Nine soil samples (SampleID 1–9) were collected in each of three 10×10 m plots (A, B and C). See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041938#pone-0041938-t001" target="_blank">Table 1</a> for further details of the sampling design.</p

Figure 3. Two-dimensional non-metric multi-dimensional scaling (NMDS) plots of variation in soil AMF community composition.

<p>A) in three spatially distinct 10×10 m plots (A–C) in September; and B) in plot A in May, June, July and September.</p

Site by OTU matrix

This file contains the relative abundance matrix of OTU detected in the study by each sample. Metadata is included

Hiiesalu_etal._datapackage

Hiiesalu_etal._datapackag

DataSheet_1_Metabarcoding of soil environmental DNA to estimate plant diversity globally.pdf

IntroductionTraditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods.MethodsWe sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data.ResultsLarge-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region.DiscussioneDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region.</p