Metadata file AUTHORS: Aaron S. David, Eric W. Seabloom, Georgiana May" PROJECT DESCRIPTION: Datasets for beachgrass experiments conducted in the field and growth chamber. The overall goals of the experiments to understand the ecological factors underlying community assembly of fungal endophytes found in beachgrass roots, and to understand the drivers behind beachgrass invasion. METHODS: Field Study: Study considers endophytes associated with three species of beachgrass (Elymus mollis, Ammophila arenaria, and Ammophila breviligulata), and the growth of these plants. Study lasted 11 weeks during summer 2012 in three sites of coastal Oregon. This study was conducted at three sites in Oregon: Pacific City (Bob Straub State Park, Pacific City, OR, USA, 45 deg 10' N, 123 deg 58' W), Sand Lake (Sand Lake Recreation Area, Cloverdale, OR, USA, 45 deg 17' N, 123 deg 57' W), and Cape Meares (Bayocean Peninsula County Park, Tillamook, OR, USA, 45 deg 30' N, 123 deg 57' W). Plant traits were measured pre- and post-treatment. Endophytes were sampled using both a culture-based approach and a next-generation sequencing (NGS) approach with Illumina MiSeq. For the culture-based approach, individual plants were sampled pre- and post-experiment. These are differentiated by the project - prjJ is pre-treatment and prjS is post-treatment. Because there was mortality during the experiment (167 of 216 individuals survived), there are more samples from prjJ. We only recorded data for those individuals of prjJ that survived until the end of the experiment and could be resampled in prjS. Data was not recorded for prjJ samples from those individuals that died, those these samples are still saved. Note that the combination of 'site', 'species','source',and 'plant.number' gives the unique plant identifier for linking prjJ with prjS. Following surface-sterilization, tissue segments were plated in individual 2ml microcentrifuge tubes (with caps) with 2% malt extract agar. We sampled 20 surface-sterilized plant segments from the main section of the root. The notation is {project name}+{unique individual identifier}+{letter indicating unique within individual sample}. For instance, sample J132F refers to prjJ (pre-treatment sampling), unique plant 132, and tissue segment F. We attempted to sequence all emergent fungi and classify them into operational taxonomic units (OTUs). Taxonomy was assigned using the MOTHUR naive Bayes classifier. For the NGS approach, roots of individual plants were sampled post-treatment only. We surface-sterilized root tissue, and stored tissue at -20C until processing. We ground 10mg of frozen root tissue and extracted DNA with the Extract N Amp kit (Sigma-Aldrich), and amplified the ITS1 region. The run was sequenced using Illumina Miseq. Included in the run are two negative controls (blank DNA extractions) and 20 additional samples which were randomly selected to be amplified with a proofreading Qiagen HotStart Taq for comparison with the non-proofreading Extract 'N Amp taq. Sequences were quality-controlled, and clustered into OTUs at 97% using USEARCH. Taxonomy was assigned using the MOTHUR naive Bayes classifier. Growth Chamber Study: Study considers endophytes associated with two species of beachgrass (Ammophila arenaria and Ammophila breviligulata) grown in a growth chamber in Saint Paul, MN with three different microbial filtrate inoculation. The Control treatment was de-ionized water, the Foredune treatment was a microbial wash from the foredune of Pacific City, OR, and the Backdune treatment was a microbial wash from the backdune of Pacific City, OR. To make the microbial washes, we allowed 18.2kg of soil with 5L of DI water, and poured off the liquid filtrate. Study lasted 4 months in summer/fall 2012. Culture-based sampling of root endophytes found in experimental plants of the growth_chamber study. Individual plants were sampled pre- and post-experiment. These are differentiated by the project - prjN is pre-treatment and prjU is post-treatment. Because there was one mortality during the experiment (71 of 72 individuals survived), there are more samples from prjN. Following surface-sterilization, tissue segments were plated in individual 2ml microcentrifuge tubes (with caps) with 2% malt extract agar. We sampled 20 surface-sterilized plant segments from the main section of the root. The notation is {project name}+{unique individual identifier}+{letter indicating unique within individual sample}. For instance, sample U132F refers to prjU (pre-treatment sampling), unique plant 132, and tissue segment F. We attempted to sequence all emergent fungi and classify them into operational taxonomic units (OTUs). Taxonomy was assigned using the MOTHUR naive Bayes classifier. CONTACT: Aaron S. David, Email - david250@umn.edu, Phone - (612) 624-6713, Fax - (612) 624-6777 Datasets FILE plant-level.csv This file contains data for each individual plant that survived the experiment. It contains plant traits (pre- and post-treatment), microscopy measurements (occurrences of arbuscular mycorrhizal fungi, dark septate endophytes, microsclerotia, and total fields of view checked), community dataset of culture-based OTUS (pre- and post-treatment), and community dataset of the NGS OTUS. S.id Identification for each plant at the conclusion of the experiment (post-treatment) J.id Identification for each plant at the beginning of the experiment (pre-treatment) site site that individual plant was transplanted to. Note that all individuals were collected at site PC, and so prjJ data reflects initial endophyte communities of these individuals taken from site PC. SL = Sand Lake, OR, PC = Pacific City, OR, CM = Cape Meares, OR. block.id block where each pair of plots was located. Each block contained 4 plots, of which one pair was in the foredune and one pair in the backdune. pair.id Plots were paired together within blocks. Within pairs, one plot was disturbed and the other was undisturbed. Each pair of plots in the experiment received a unique 'pair.id' identifier. plot.id Unique plot identifier position habitat that individual plants were transplanted to. F = foredune habitat, B = backdune habitat comp competition treatment that individual plants were assigned to. Ctrl = competition remained intact and undisturbed, CompRed = competition was removed and the soil was disturbed species host species, AMBR = Ammophila breviligulata, AMAR = Ammophila arenaria, ELMO = Elymus mollis source source of the individual plant at PC site, b = backdune source, f = foredune source ngs.data.available 0 = no data is available, 1 = data is available. Note that roots from some samples were sequenced but should not be used in analyses because they were old roots ngs These are the samples for which we have reliable sequencing of the endophyte communities of new roots. 0 = no data or data should not be used in analysis, 1 = data to use in analyses. pres.x presence of endophyte recorded in pre-treatment (prj J)(0 or 1), if isolated deemed a contaminant, this was recorded as 0 pres.y presence of endophyte recorded in post-treatment (prj S)(0 or 1), if isolated deemed a contaminant, this was recorded as 0 J.ht height of plant (cm) pre-treatment (prjJ) J.rhilen length of rhizome (cm) of plant pre-treatment (prjJ) J.roots number of roots of each plant pre-treatment (prjJ) J.mass wet weight(g) of each plant pre-treatment (prjJ) S.ht height of plant (cm) post-treatment (prjS) S.rhilen length of rhizome (cm) of plant post-treatment (prjS) S.roots number of roots of each plant post-treatment (prjS) S.nodes number of nodes on rhizome post-treatment (prjS) S.tillers.live number of live tillers post-treatment (prjS) S.tillers.dead number of dead tillers post-treatment (prjS) S.mass.abv.dead dry weight (g) of dead aboveground tissue post-treatment (prjS) S.mass.abv.live dry weight (g) of live aboveground tissue post-treatment (prjS) S.mass.bel dry weight (g) of belowground tissue post-treatment (prjS) S.mass.abv dry weight (g) of live and dead aboveground tissue post-treatment (prjS) S.mass.tot dry weight (g) of all live and dead tissue post-treatment (prjS) tot.fields total microscope fields of view (typically 40) measured for roots of each plant amf total microscope fields of views with arbuscular mycorrhizal fungi dse total microscope fields of views with dark septate endophytes microsclerotia total microscope fields of views with microsclerotia J.culture.effort number of surface-sterilized root segments plated on nutrient media to sample for cultured endophytes in the pre-treatment samples (typically 20) Je.OTU... columns that begin with this format are cultured OTUs, and the number indicates the number of isolations of that OTU in the pre-treatment samples (typically 0-20) S.culture.effort number of surface-sterilized root segments plated on nutrient media to sample for cultured endophytes in the post-treatment samples (typically 20) Se.OTU... columns that begin with this format are cultured OTUs, and the number indicates the number of isolations of that OTU in the post-treatment samples (typically 0-20) newOTU columns that begin with this format are number of non-rarefied sequences reads for each OTU in the NGS dataset FILE cultured-otus.lookup.csv This file gives taxonomic information for all OTUs in the culture-based datasets of both the Field Study and the Growth Chamber Study. Note that the OTU names can refer to OTUs found in either pre- or post-treatment samples otu name of OTU taxonomy taxonomy string assigned via the MOTHUR naive Bayes classifer and the combined UNITE and Emerencia database Phylum Phylum that OTU belongs to Class Class that OTU belongs to Order Order that OTU belongs to Family Family that OTU belongs to Genus Genus that OTU belongs to subphylum subphylum that OTU belongs to. This was added manually. FILE NGS-otus.lookup.csv This file gives taxonomic information for all OTUs in the NGS dataset (post-treatment samples) otu name of OTU columns beginning with "S" or "X" These columns refer to post-treatment samples, and the number of non-rarefied sequence reads are given. Columns beginning with "X" refer to those samples which were sequenced with the proof-reading Taq, and can be compared to the sample without the "X". For example, "XS113" is comparable to "S113". taxonomy taxonomy string assigned via the MOTHUR naive Bayes classifer and the combined UNITE and Emerencia database Kingdom Kingdom that OTU belongs to (all are fungi) Phylum Phylum that OTU belongs to Class Class that OTU belongs to Order Order that OTU belongs to Family Family that OTU belongs to Genus Genus that OTU belongs to subphylum subphylum that OTU belongs to. This was added manually. counts total number of sequences for that OTU in the Illumina Miseq run. This is simply a sum across the row. FILE soil.csv This file contains data for soil properties. Samples were taken within each 'pair.id'. pair.id Plots were paired together within blocks. Within pairs, one plot was disturbed and the other was undisturbed. Each pair of plots in the experiment received a unique 'pair.id' identifier. Organic Matter percent organic matter of each sample Cation.Exchange.Capacity cation exchange capacity of each sample pH pH of each sample Potassium concentration in part per million Calcium concentration in part per million Magnesium concentration in part per million Sulfur concentration in part per million Sodium concentration in part per million Zinc concentration in part per million Manganese concentration in part per million Iron concentration in part per million C Percent carbon N Percent Nitrogen block.id block where each pair of plots was located. Each block contained 4 plots, of which one pair was in the foredune and one pair in the backdune. site site that individual plant was transplanted to. Note that all individuals were collected at site PC, and so prjJ data reflects initial endophyte communities of these individuals taken from site PC. SL = Sand Lake, OR, PC = Pacific City, OR, CM = Cape Meares, OR. position habitat that individual plants were transplanted to. F = foredune habitat, B = backdune habitat FILE background-plant-communities.csv This file contains data for the pre-treatment, naturally-occurring plant communities found in the undisturbed plots in the Field Study. Note that vegetation was removed from all disturbed plots. site site that individual plant was transplanted to. SL = Sand Lake, OR, PC = Pacific City, OR, CM = Cape Meares, OR. block.id block where each pair of plots was located. Each block contained 4 plots, of which one pair was in the foredune and one pair in the backdune. position habitat that individual plants were transplanted to. F = foredune habitat, B = backdune habitat Bare.ground percentage of undisturbed plot with bare ground columns beginning with "cover." percent cover of each species in the undisturbed plots. Note that cover can sum to more than 1 rich plant species richness of each control plot FILE cultured-isolates.csv This file contains data on each cultured isolate in the Field Study plant.id refers to either the J.id (if isolated from pre-treatment sample) or S.id (post-treatment sample). These map onto the 'plant-level.csv' file ID unique identifier for an individual culture. The first 4 characters are the same as the 'plant.id'. otu OTU assigned based on 97% clustering of ITS1 region Accession GenBank accession number for each isolate FILE growth-chamber-data.csv This file contains plant measurements, microscopy data, and culturing data for the growth-chamber experiment plant.id unique identifier for each individual plant in the experiment, numbers range from 101 to 172 NID unique identifier for pre-treatment data UID unique identifier for post-treatment data species grass species, AB = Ammophila breviligulata, AA = Ammophila arenaria, EM = Elmyus mollis source source of the individual plant at PC site, b = backdune source, f = foredune source block block that individual plant was assigned to, 1 or 2. Blocks were placed until different adjacent lights. treatment microbial filtrate treatment. 1 = control (DI water), 2 = foredune filtrate, 3 = backdune filtrate pre.height height of plant (cm) pre-treatment pre.rhizome.len length of rhizome (cm) of plant pre-treatment pre.roots number of roots of each plant pre-treatment pre.biomass.wet wet weight(g) of each plant pre-treatment post.height height of plant (cm) post-treatment post.rhizome.len length of rhizome (cm) of plant post-treatment nodes number of nodes on rhizome post-treatment live.tillers number of live tillers post-treatment dead.tillers number of dead tillers post-treatment biomass.ab dry weight (g) of live aboveground tissue post-treatment biomass.rhizome dry weight (g) of rhizome tissue post-treatment biomass.root dry weight (g) of root tissue post-treatment biomass.dead dry weight (g) of dead aboveground tissue post-treatment biomass.ab.total dry weight (g) of live and dead aboveground tissue post-treatment biomass.below.total dry weight (g) of belowground tissue (rhizome and roots biomasses) post-treatment root.shoot.tot ratio of total aboveground biomass (live and dead) to total belowground biomass (rhizomes and roots) post-treatment biomass.total aboveground biomass (live and dead) and belowground biomass (rhizomes and roots) post-treatment tot.fields total microscope fields of view (typically 40) measured for roots of each plant amf total microscope fields of views with arbuscular mycorrhizal fungi dse total microscope fields of views with dark septate endophytes microsclerotia total microscope fields of views with microsclerotia pres.x presence of endophyte recorded in pre-treatment 0 or 1), if isolated deemed a contaminant, this was recorded as 0 count.x number of surface-sterilized root segments plated on nutrient media to sample for cultured endophytes in the pre-treatment samples (typically 20) pres.y presence of endophyte recorded in post-treatment 0 or 1), if isolated deemed a contaminant, this was recorded as 0 count.y number of surface-sterilized root segments plated on nutrient media to sample for cultured endophytes in the post-treatment samples (typically 20) N.OTU... columns that begin with this format are cultured OTUs, and the number indicates the number of isolations of that OTU in the pre-treatment samples (typically 0-20) U.OTU... columns that begin with this format are cultured OTUs, and the number indicates the number of isolations of that OTU in the post-treatment samples (typically 0-20) FILE growth-chamber-isolates.csv This file contains data on each cultured isolate in the Growth Chamber Study plant.id unique plant identifier ID unique identifier for an individual culture. otu OTU assigned based on 97% clustering of ITS1 region Accession GenBank accession number for each isolate