DOI: 10.5061/dryad.c866t1gfz
title: Achieving bio-protection in New Zealand ecosystems mesocosm fungal pathogen OTU table

description: We established 80 experimental ecosystems (mesocosms), manipulated
 interactions between plants and soil biota in a fully factorial design.
 Each mesocosm was grown in a 125 L pot (575 mm diameter), and comprised
 one of 20 unique, eight-species plant communities varying orthogonally in
 the proportion of exotic and woody shrub/tree species (0-100% and 0-63%,
 respectively). These plants were taken from a pool of 20 exotic and 19
 native/endemic New Zealand plant species. Soil biota were manipulated
 using a modified plant-soil feedback approach, where each plant species
 was grown in monoculture in 10 L pots containing field-collected soil for
 9-10 months, allowing the conditioning of typical associated soil biota
 for each of the plant species. We created ‘home’ soils by taking the
 conditioned soil from each of the eight representative species in a
 mesocosm and mixing it together to create a single inoculum. Each ‘home’
 soil mixture was also used as an ‘away soil’ in a different mesocosm that
 did not contain any of the representative plants in that inoculum. These
 soils were intended to increase the relative biomass in inocula of
 specialized and preferred interaction partners of the resident (or
 non-resident) plant species. After approximately one year of growth, we
 harvested all plants from each mesocosm, took root samples from each
 individual plant (n=491), extracted DNA and sequenced the fungi in the
 roots. Fungal sequences were paired and clustered into operational
 taxonomic units (OTUs) at 97% similarity. We assigned functional
 attributes to fungal OTUs using the FUNGUILD database and retained only
 the taxa assigned as “probable” or “highly probable” plant pathogens.
description: DNA was extracted from a total of 491 root samples harvested from
 individual plants from all 80 mesocosms at the end of the experiment,
 using MoBio PowerSoil (QIAGEN) extraction kits. Root samples were taken
 from each individual plant using a sterile razor blade, cutting
 approximately 10-15 fine-root fragments from random places on the washed
 root ball, then bundling the roots together and slicing a 0.5-1.0 cm cross
 section piece from the bundle. Root samples were immediately placed into a
 96 well plate from the extraction kit and frozen at
 -80<sup>o</sup>C as soon as a plate was full. We characterized
 the fungal communities by amplifying the internal transcribed spacer (ITS)
 of the ribosomal RNA (rRNA) operon using polymerase chain reaction (PCR)
 with the barcoded primers fITS7/ITS4.  PCR was run on
 each sample and controls using the following thermal cycler conditions:
 one cycle of initial denaturation at 94°C for 5 mins; 35 cycles of
 denaturation at 94°C for 30 secs; annealing at 57°C for 30 secs; extension
 at 72°C for 30 secs; final extension at 72°C for 7 min. PCR products were
 checked for adequate intensity single bands on a 1% agarose gel with
 RedSafe. PCR reactions were carried out in duplicates for each sample and
 pooled prior to library preparation using the 96 well SequalPrep
 Normalization Kit (Invitrogen). Once PCR products were cleaned and
 normalized with the SequalPrep Kit, all samples were pooled and sent to
 Massey Genome Services, (Palmerston North, New Zealand) to be
 sequenced. Amplicons were sequenced on an Illumina MiSeq analyzer using
 the 600-cycle Reagent Kit V3, delivering 2 X 300 base pair reads/sequence
 (Illumina, San Diego, California, USA). Sequences were
 paired, putative chimeras removed, and clustered into operational
 taxonomic units (OTUs) at 97% sequence similarity using Vsearch. Quality
 and barcode filtering resulted in 6,093,371 reads with a median length of
 225 bases. We assigned functional attributes to OTUs
 using the FUNGuild database and retained only the taxa assigned as
 “probable” or “highly probable” plant pathogens for subsequent analyses.
 We restricted our inclusion of taxa to those that receive most of their
 nutrients by harming host cells (defined as “pathotrophs” by FUNGuild) and
 excluded taxa with mixed strategies from our analyses (i.e.
 “pathotroph-saprotroph”), as many of these taxa are primarily saprotrophs
 and only occasionally pathogens. We acknowledge that by limiting our
 pathogen assignment in this way we have likely excluded many taxa that may
 be pathogens in some environments, so our results represent a conservative
 analysis of the pathogen communities hosted by our plants. Moreover, the
 taxa listed here are putative pathogens (hereafter referred to simply as
 ”pathogens”), as we rely on commonly accepted life history descriptions
 rather than performing real-time functional assays for each plant-fungal
 interaction.
description: # Achieving Bio-Protection in New Zealand Ecosystems mesocosm fungal
 pathogen OTU table
 [https://doi.org/10.5061/dryad.c866t1gfz](https://doi.org/10.5061/dryad.c866t1gfz) This dataset contains the OTU table describing the fungal pathogens sequenced in roots from 491 unique species grown in mesocosm communities. The aim of this work was to understand the extent to which exotic plants share generalist pathogens with native plants and whether this "pathogen spillover" from exotic to native plants impacts exotic plant success in mixed communities. ## Description of the data and file structure This dataset contains a list of all of the plant species grown in the experiment, and from which DNA was extracted and sequenced. Each plant is labeled with a unique ID, provenance (native or exotic), the mesocosm community in which it grew, and the number of sequences from each potential operational taxonomic units (OTUs). Each OTU represents a putative fungal pathogen, as listed in the FUNGUILD data base.