Data from: Differentiation of the foliar microbiomes from co-occurring grass species reflects their recency of invasion

Published by Agricultural Research Service | Department of Agriculture | Metadata Last Checked: February 12, 2026 | Last Modified: 2026-01-16

These microbiome data and analyses are part of a DNA amplicon sequencing project performed by USDA-ARS scientists at the Foreign-Disease Weed Science Research Unit in Frederick, Maryland. The data characterize foliar endophytic microbiomes from two invasive grass species that co-occur in the same Mid-Atlantic forest environments. One is a recently introduced invasive weed (Oplismenus undulatifolius), and the other a species that has been established for over 100 years (Microstegium vimineum).The data contained here are derived from individual plant leaves collected at two locations in Maryland, USA in September 2023. The sampling locations were 90 km apart but both fell within riparian, deciduous hardwood forests. Replicated observational plots (4 or 5) at each site were separated by 10m. These sampling plots were 1m2 and arranged to capture overlapping Oplismenus and Microstegium infestations. In all plots, each invasive grass provided approximately 50% groundcover and other plant species accounted for <1% groundcover. The uppermost leaf from 10 randomly selected individuals of each grass species were collected using sterile tools and transported to a laboratory. Leaves were rinsed in sterile water, surface disinfested with diluted bleach, and triple rinsed in sterile water. Leaves were then air dried and split lengthwise. Metagenomic DNA extracts were purified from half leaves using the Zymo Quick-DNA Fungal/Bacterial Kit. A randomly selected subset of seven extracts from each plot and species were ultimately selected for sequencing (n = 63 extracts per grass host). Library preparation and Illumina sequencing were performed at the University of Minnesota Genomics Center. Amplicons of the fungal internal transcribed spacer region of ribosomal DNA (ITS 2 primers: 5.8SR TCGATGAAGAACGCAGCG and ITS4 TCCTCCGCTTATTGATATGC) and of the bacterial 16S ribosomal DNA (16S V4 primers: 515F GTGCCAGCMGCCGCGGTAA and 806R GGACTACHVGGGTWTCTAAT) were sequenced on an Illumina HiSeq 2000 outputting 2x300 bp reads. The resulting DNA sequencing data were deposited with NCBI GenBank (BioProject PRJNA1245354, Samples SAMN47750341-SAMN47750466). Raw sequencing data were processed using QIIME2 v2024.2 (see qiime_procedures.txt), to produce the secondary data files and analysis results contained here. Additional analyses of microbial community diversity and composition were performed using R statistical software. In brief, microbial sequences were contrasted between plant species to compare inferred fungal and bacterial richness, diversity, community dissimilarity and dispersion, and spatial autocorellation (see foliar_eco-evo_analysis.r file for full details). The interpretation of this data set is constrained by a narrow temporal and spatial timeframe, which limits conclusions to the specific environmental conditions and locations observed. See README.txt for additional information about individual file contents.

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@type	dcat:Dataset
accessLevel	public
bureauCode	[ "005:18" ]
contactPoint	{ "fn": "Fulcher, Michael, R", "hasEmail": "mailto:michael.fulcher@usda.gov" }
description	<p dir="ltr">These microbiome data and analyses are part of a DNA amplicon sequencing project performed by USDA-ARS scientists at the Foreign-Disease Weed Science Research Unit in Frederick, Maryland. The data characterize foliar endophytic microbiomes from two invasive grass species that co-occur in the same Mid-Atlantic forest environments. One is a recently introduced invasive weed (<i>Oplismenus undulatifolius</i>), and the other a species that has been established for over 100 years (<i>Microstegium vimineum</i>).</p><p dir="ltr">The data contained here are derived from individual plant leaves collected at two locations in Maryland, USA in September 2023. The sampling locations were 90 km apart but both fell within riparian, deciduous hardwood forests. Replicated observational plots (4 or 5) at each site were separated by 10m. These sampling plots were 1m<sup>2</sup> and arranged to capture overlapping <i>Oplismenus</i> and <i>Microstegium</i> infestations. In all plots, each invasive grass provided approximately 50% groundcover and other plant species accounted for <1% groundcover. The uppermost leaf from 10 randomly selected individuals of each grass species were collected using sterile tools and transported to a laboratory. Leaves were rinsed in sterile water, surface disinfested with diluted bleach, and triple rinsed in sterile water. Leaves were then air dried and split lengthwise. Metagenomic DNA extracts were purified from half leaves using the Zymo Quick-DNA Fungal/Bacterial Kit. A randomly selected subset of seven extracts from each plot and species were ultimately selected for sequencing (n = 63 extracts per grass host). Library preparation and Illumina sequencing were performed at the University of Minnesota Genomics Center. Amplicons of the fungal internal transcribed spacer region of ribosomal DNA (ITS 2 primers: 5.8SR TCGATGAAGAACGCAGCG and ITS4 TCCTCCGCTTATTGATATGC) and of the bacterial 16S ribosomal DNA (16S V4 primers: 515F GTGCCAGCMGCCGCGGTAA and 806R GGACTACHVGGGTWTCTAAT) were sequenced on an Illumina HiSeq 2000 outputting 2x300 bp reads. The resulting DNA sequencing data were deposited with NCBI GenBank (BioProject PRJNA1245354, Samples SAMN47750341-SAMN47750466). </p><p dir="ltr">Raw sequencing data were processed using QIIME2 v2024.2 (see qiime_procedures.txt), to produce the secondary data files and analysis results contained here. Additional analyses of microbial community diversity and composition were performed using R statistical software. In brief, microbial sequences were contrasted between plant species to compare inferred fungal and bacterial richness, diversity, community dissimilarity and dispersion, and spatial autocorellation (see foliar_eco-evo_analysis.r file for full details). The interpretation of this data set is constrained by a narrow temporal and spatial timeframe, which limits conclusions to the specific environmental conditions and locations observed. See README.txt for additional information about individual file contents.</p>
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identifier	10.15482/USDA.ADC/31061641.v1
keyword	[ "Basketgrass", "Invasive plants", "Microbiome", "Stiltgrass", "Weeds", "foliar endophytes", "source code" ]
license	https://creativecommons.org/publicdomain/zero/1.0/
modified	2026-01-16
programCode	[ "005:040" ]
publisher	{ "name": "Agricultural Research Service", "@type": "org:Organization" }
temporal	2023-09-01/2023-09-30
title	Data from: Differentiation of the foliar microbiomes from co-occurring grass species reflects their recency of invasion