Title

Amplicon ITS and 16S RNA seq of soil metagenome: Quantifying plant-soil feedback effects in classic diversity-productivity experiments

Description

Two-way interactions between plants and soil microbiota, also known as plant-soil feedbacks, have major effects on the productivity of plant species. This project tested the role of plant-soil feedbacks in plant community productivity across two sites, one at Cedar Creek Ecosystem Science Reserve in East Bethel, Minnesota, USA, and the other at the Jena Experiment in Jena, Thuringia, Germany. Soil metagenomic analyses were undertaken to help identify the specific microbes that drive feedbacks.

OCLC

1236212650

Document Type

Dataset

DCMI Type

Dataset

File Format

.xlsx, .gz, .txt

Viewing Instructions

QIIME2 is recommended for processing the fastq data.

Publication Date

12-7-2020

Funder

NSF, Division of Environmental Biology DEB

Publisher

NCBI BioProject

Award Number

NSF, Division of Environmental Biology DEB 1354129

Award Title

Quantifying plant-soil feedback effects in classic diversity-productivity experiments

Methodology

Cedar Creek Plant-Soil Feedback Experiment: A 1750 m2 fallow area adjacent to a large, long-term biodiversity experiment at Cedar Creek was sprayed with glyphosate and disked to thoroughly remove vegetation and homogenize soils in the top 15 cm. 0.75 mm thick HDPE root barrier was inserted to 35 cm deep between each plot. 2,720 0.75 by 0.35 m PSF plots were established. In spring 2015, all plots were seeded with 10 g pure live seed per m2. During the first year, plots were watered weekly to ensure germination. To establish the phase 1 treatment, each of the 16 target species were planted as monocultures and grown from 2015 to 2016. Non-target species were removed by hand-weeding. In 2016, fall PSF plots were sprayed with glyphosate and hand-tilled using a garden claw. Plots with exceptionally thick roots were tilled using a rototiller. In spring 2017, any living plants were sprayed again with glyphosate. 2,608 plots realized growth in phase I. Plots were replanted with either the same (“self” treatment) or a different (“other” treatment) species. Plots that did not realize growth were replanted randomly as a control soil treatment. Yearly growth was recorded as ocular estimate of percent cover prior to soil sampling for metagenomic analyses.

Cedar Creek Bulk Soil Metagenomic Sampling: On 7/20/2015, 7/15/2016, 10/30/2017, and 10/7/2018, a 15cm x 4cm core consisting of approximately 200 g of soil was taken from the center of three randomly-selected “self” plots and stored on ice. Soil corers were cleaned with 90% ethanol between samples. Samples were immediately transported to the University of Minnesota campus and stored at -80° C until DNA could be extracted. Soils were sieved and DNA was extracted using a MoBio Power Soil DNA kit. “Self” plots were re-sampled whenever growth on such plots was above zero, however, failed growth in some plots necessitated changes in plots being sampled in 2016, 2017, and 2018.

Cedar Creek Rhizosphere Soil Metagenomic Sampling: On 10/7/2018, three individuals from the bulk soil plots sampled in 2018 were removed from the plot and stored on ice. Trowels used to remove individuals were cleaned with 90% ethanol between samples. Samples were immediately transported to the University of Minnesota campus and stored at -80° C until DNA could be extracted. Soils were dusted from the roots of the stored individuals and DNA was extracted using a MoBio Power Soil DNA kit.

Jena Plant-Soil Feedback Experiment: A 730 m2 area in a fallowed field was sprayed with glyphosate to remove existing vegetation. 0.75 mm thick HDPE root barrier was inserted to 35 cm deep between each plot. 1251 0.75 by 0.35 m PSF plots were established in the area. In spring 2015, all plots were seeded with 2000 pure live seeds per m2. During the first year, plots received water twice weekly to ensure germination. To establish the phase 1 treatment, each of the nine target species were planted as monocultures and grown from 2015 to 2016. Non-target species were removed by hand-weeding. In 2016, fall PSF plots were sprayed with glyphosate and hand-tilled using a garden claw. To prevent regrowth roots of phase 1 species were removed. Plots were replanted with 2000 pure live seeds per square meter with either the same (“self” treatment) or a different (“other” treatment) species. Yearly growth was recorded as ocular estimate of percent cover prior to soil sampling for metagenomic analyses.

Jena Bulk Soil Metagenomic Sampling: On 9/1/2015, 1/1/2017, 10/1/2017, and 9/1/2018, a 15cm x 4cm core consisting of approximately 200 g of soil was taken from the center of nine randomly-selected “self” plots and stored on ice. Soil corers were cleaned with 90% ethanol between samples. Samples were transported to the Friedrich-Schiller-Universität Jena campus and stored at -80 ° C until DNA could be extracted. Soils for three “self” plots were pooled and sieved through a 2mm sieve to create three pooled samples from three plots for each species. DNA was extracted using a MoBio Power Soil DNA kit.

Jena Rhizosphere Soil Metagenomic Sampling: On 9/1/2018, a minimum of three individuals from the bulk soil plots sampled in 2018 were removed from the plot and stored on ice. Trowels used to remove individuals were cleaned with 90% ethanol between samples. Samples were transported to the Friedrich-Schiller-Universität Jena campus and stored at -80° C until DNA could be extracted. Soils were dusted from the roots of the stored individuals and pooled to create three pooled samples from three plots for each species. DNA was extracted using a MoBio Power Soil DNA kit.

Metagenomic Processing: DNA concentrations were checked using PicoGreen assay on a Modulus Microplate reader. Purified DNA was diluted to a maximum concentration of 6.0 ng/ul for bulk samples and 50.0 ng/ul for rhizosphere samples and stored at -80 °C until sequencing. Fungal ITS and bacterial 16S rRNA genes in the rhizosphere and bulk soil samples were amplified by Argonne National Laboratory using the primer sets ITS1f-ITS2 (ITS) and 515F-806R (bacterial). The amplified genes were subsequently sequenced by Argonne National Laboratory on the Illumina MiSeq platform (Novogene Corporation, Beijing China) using the Earth Microbiome Protocol.

Start Date

5-2015

End Date

11-2018

Location

Cedar Creek Field Site: 45.403290, -93.187411 Jena Field Site: 50.951951, 11.623832

Language

eng

Code Lists

See the README.txt file

Comments

Description of files:

MIMARKS.survey.soil.5.0.xlsx Description of MIMARKS.survey.soil.5.0.xlsx: This file broadly describes the collection dates, elevations, environmental contexts, and agricultural additives for the microbial data collected.

SRA_metadata.xlsx Description of SRA_metadata_vers2.xlsx: This file broadly describes the library strategy, library source, library selection, library layout, platform, instrument, and design description for the microbial data collected.

Each of the BioSamples consists of four files:

###_fungal_forward_001.fastq.gz Description of ###_fungal_forward_001.fastq.gz: This file includes the forward reads for the ITS fungal amplicons.

###_fungal_reverse_001.fastq.gz Description of ###_fungal_reverse_001.fastq.gz: This file includes the reverse reads for the ITS fungal amplicons.

###_bacterial_reverse_001.fastq.gz Description of ###_bacterial_reverse_001.fastq.gz: This file includes the reverse reads for the 16S bacterial amplicons.

###_bacterial_forward_001.fastq.gz Description of ###_bacterial_forward_001.fastq.gz: This file includes the forward reads for the 16S bacterial amplicons.

Disciplines

Ecology and Evolutionary Biology | Plant Sciences | Soil Science

License

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.

Identifier

https://www.ncbi.nlm.nih.gov/bioproject/683074

Additional Files

README.txt (8 kB)
MD5: 1bc62cb3d83ec08d76fc54f26b5e3da4

Share

 
COinS