DOI: 10.5061/dryad.5tb2rbp33
title: Light availability and light demand of plants shape the arbuscular fungal communities in their roots

description: Plants involved in the arbuscular mycorrhizal (AM) symbiosis trade
 photosynthetically derived carbon for fungal-provided soil nutrients.
 However, little is known about how plant light demand and ambient light
 conditions influence root-associating AM fungal communities. We conducted
 a manipulative field experiment to test whether plants’ shade tolerance
 influences their root AM fungal communities in open and shaded grassland
 sites. We found similar light-dependent shifts shifts in AM
 fungal community structure for experimental bait plant roots and the
 surrounding soil. Yet, deviation from the sorrounding soil towards lower
 AM fungal beta-diversity in the roots of shade-intolerant plants in shade
 suggested preferential carbon allocation to specific AM fungi in
 conditions where plant-assimilated carbon available to fungi was limited.
 We conclude that favourable environmental conditions widen the plant
 biotic niche, as demonstrated here with optimal light availability
 reducing plants' selectivity for specific AM fungi, and promote
 compatibility with a larger number of AM fungal taxa. The deposited
 dataset contains the raw fungal sequence table for each sample and
 information on the characteristics of the sample (light treatment, sample
 type, sampling point in time etc).
description: Lines from the method section of the related paper (accepted in
 Ecology Letters) <em>Experimental
 site: </em> We conducted a field experiment in a
 species rich wooded meadow situated on the west coast of Estonia (Laelatu,
 58.5835001 N and 23.5677568 E) and covering an area of 153 ha. The meadow
 has been under continuous, extensive management for centuries; notably
 mowing for hay and cutting shrubs and trees for fuel. The wooded meadow is
 a mosaic of open, well illuminated sites and shaded sites containing
 shrubs (Corylus avellana L.) and some trees such as Quercus robur L. and
 Betula pendula Roth (Semchenko & Zobel 2007). Shaded sites are
 characterized by lower plant diversity and cover of herbaceous species
 compared with open sites. <em>Sampling
 design: </em> We chose 40 perennial plant species
 native to the wooded meadow and with contrasting plant shade tolerance as
 experimental species. Plant species shade-tolerance was estimated based on
 their Ellenberg indicator value for light (Ellenberg et al. 1992); species
 with a light indicator value ≥ 5 were categorised as shade-intolerant, and
 species with lower light indicator values were categorised as
 shade-tolerant. We grouped the seeds into 10 unique
 seed mixtures each containing seeds of two shade-intolerant and two
 shade-tolerant species, with some exceptions due to differences in seed
 availability. In October 2011, we established the experiment at four sites
 (10 x 10 m) within the continuously managed part of Laelatu wooded meadow:
 two sites in open and two sites in shaded parts. We created a grid of 1 m2
 plots in each of the four experimental sites, and each seed mixture was
 assigned to five randomly selected plots in a site. In each of the plots,
 50 seeds per seed mixture were sown into a metal ring of 15cm diameter
 (experimental unit) positioned in the centre of the plot. Altogether, we
 created 200 experimental units (10 seed mixtures x 5 replicates x 4
 sites). <em>Data collection:</em>
 One year after seeding we conducted the first sampling campaign
 (October 2012), collecting 3-5 seedlings of all bait plant species that
 germinated within the first year (10 out of 40 species; Table 1) from each
 experimental unit. Seedlings from each experimental unit were cleaned from
 soil and dried for 24 h at 50 ˚C; the roots of each plant species were
 separated from the shoots and stored dry for further molecular analysis of
 root colonizing AM fungi. We repeated the same procedure in July 2013 for
 the bait plant species that had not germinated in the first year (7 out of
 40 species; Table 1). For the second census, we sampled all the previously
 sampled plant species – i.e., all those that had germinated in October
 2012 or July 2013 – again in June 2014. While the interval between censues
 varied, we interpret sampling census as an indicator of AM fungal
 community maturity, with young, potentially dynamic composition in the
 first census, and mature, potentially stable composition in the second
 census. The final set of species inlcuded into the analyses (and those
 present in the uploaded dataset) comprised eight shade-tolerant and nine
 shade-intolerant species.  During selection of
 experimental plant species, we took care to limit phylogenetic differences
 between shade-tolerant and -intolerant species, thus froming pairs of two
 species from the same genus or familiy with contrasting shade tolerance
 (where possible). This balance remained evident also in the final set of
 data. After the final sampling campaign (October 2014),
 we collected 10 cm3 soil cores from five random locations per site (n = 20
 , hereafter `background samples´) to characterise the AM fungal
 communities in plant roots (across all plant species present in the
 community) and in soil surrounding the experimental units. Background
 samples provided local context to AM fungal community shifts observed in
 bait root samples. From background samples, we separated plant roots from
 soil, dried them for 24 h at 50 ˚C and stored them dry for further
 molecular analysis. To homogenize root composition within samples, we
 crushed the roots in each sample with liquid nitrogen and thoroughly mixed
 them as described by Garcia de Leon et al. (2016). We collected 10g of
 soil from each background sample, dried it with silica gel and stored it
 airtight at room temperature for further molecular analysis.
 <em>Molecular Analyses and
 Bioinformatics:</em> AM fungal communities in
 bait plant roots were analysed for each bait plant species and
 experimental unit separately. We extracted DNA from 70 mg (dry weight) of
 roots from bait plants (1-3 individuals per experimental unit) and mixed
 root samples using the Power Soil® DNA Isolation Kit (MO BIO Laboratories,
 Inc., Carlsbad, CA, USA) following Saks et al. (2014). For soil samples,
 we extracted DNA from 5 g of dried soil using the Power Max Soil® DNA
 Isolation Kit (MO BIO Laboratories, Inc., Carlsbad, CA, USA) according to
 Gazol et al. (2016). We amplified Glomeromycotina SSU rRNA gene sequences
 with the primers NS31 and AML2 (Simon et al. 1992; Lee et al. 2008) and
 identified them using 454-sequencing on a Genome Sequencer FLX System with
 Titanium Series reagents (Roche Applied Science, Mannheim, Germany) at
 GATC Biotech (Konstanz, Germany) as described in Davison et al. (2012) and
 Öpik et al. (2013). We assigned taxonomic information
 to quality-filtered reads using the MaarjAM database (status May 2020)
 that classifies the central part of published Glomeromycotina SSU rRNA
 gene sequences into phylogenetically delimited sequence clusters – virtual
 taxa (VT, cf. Öpik et al. 2010, 2014). Taxonomic identification and
 quality filtering followed the same approach as described in Neuenkamp et
 al. 2018 (see Appendix S3 for a more detailed description). The final data
 matrix consisted of 198 samples, 265 375 reads and 142 VT for AM fungi in
 bait plants root samples, and 36 samples, 56 755 reads and 86 VT for AM
 fungi in background samples (mixed roots, soil) (Appendix S4). We excluded
 singletons (VT represented by a single read in the whole dataset; 22 VT in
 total) from the dataset. For bait plants root samples, the minimum number
 of reads per sample was 9 and the median number of reads per sample was
 1055; for background samples, the respective numbers were 195 and 1969. A
 set of representative sequence reads was deposited in the EMBL nucleotide
 collection (accession numbers: LR890754-LR897751).  
description: The dataset of fungal sequences is uploaded and contains a
 "Glossary" sheet where terms if necessary are
 explained.  The dataset is organised so that each row
 is a sample and then sample information is provided in colums. 
 Read counts on arbuscular mycorrhizal (AM) fungi are presented as
 quality-filerted but raw reads. So no rarefaction has been applied to
 them, but is encouraged before analysis. Reads were
 assigned to virtual fungal taxa (VT) based on their similarity to the
 taxonomy established in the MaarjAM database (see methods above;
 https://maarjam.botany.ut.ee/).