Abstract:

These data are from a manipulative field experiment designed to test the effects of restoration treatments on the marsh ecology. The data were collected from remediation treatment plots that included three levels of planting: planted with Spartina, planted with Juncus, and not planted. Each planting level also included a fertilized and unfertilized treatment, so there were a total of six treatments. Each treatment was replicated in the marsh 5 times. For the soil microbial community study, DNA was isolated from soil samples and sequenced with Illumina MiSeq, then processed using QIIME.

Suggested Citation:

A Hou, G Cagle. 2017. Soil microbial community in oiled sites, Juncus and Spartina planted treatments with and without fertilizer, and reference sites, northern Barataria Bay, 2014-2016. Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7MP51NQ

Publications:

Cagle, G., Lin, Q., Graham, S. A., Mendelssohn, I., Fleeger, J. W., Deis, D., … Hou, A. (2020). Planting Spartina alterniflora in a salt marsh denuded of vegetation by an oil spill induces a rapid response in the soil microbial community. Ecological Engineering, 151, 105815. doi:10.1016/j.ecoleng.2020.105815

Purpose:

The purpose of this study is to determine how alterations in microbial community structure and function recover as a function of initial oiling intensity and remediation treatment. In order to capture the effects of each aspect of remediation treatment on the soil microbial community, the treatments include a combination of fertilization, planting, and control plots.

Data Parameters and Units:

replant-2015-otu-w-tax.xlsx: sample ID (internal sample ID), treatment (N- = no fertilizer and not planted, N+ = fertilizer and not planted, J- = no fertilizer and planted with Juncus, J+ = fertilizer and planted with Juncus, S+ = fertilizer and planted with Spartina, S- = no fertilizer and planted with Spartina), Site (block number and treatment), Block (replicate number), plant (n = not planted, j = Juncus roemerianus, s = Spartina alterniflora), fert (f = not fertilized, t = fertilized), Year, Month, Season, operational taxonomic units (OTUs) = counts (Kingdom, Phylum, Class, Order, Family, Genus, Species. The data are observations of OTUs (operational taxonomic units) in each sample. The data are count data of each OTU recorded in each sample. R2.x211.000-0008-SraRunTable.txt - AvgSpotLen, BioSample (NCBI Biosample Accession), Experiment (NCBI Experiment Accession), Library_Name, LoadDate (MM/DD/YYYY) date data submitted to NCBI, MBases (megabases), MBytes (megabytes), Planting treatment (not planted, Juncus roemerianus, Spartina alterniflora), ReceivedFertilization (True, False), Run, SRA_Sample (NCBI SRA Sample Accession), Sample_Name, Site_s (block number and treatment), treatment ((N- = no fertilizer and not planted, N+ = fertilizer and not planted, J- = no fertilizer and planted with Juncus, J+ = fertilizer and planted with Juncus, S+ = fertilizer and planted with Spartina, S- = no fertilizer and planted with Spartina), agrochem_addition (None, Slow release fertilizer), collection_date (YYYY-MM) (date sample collected from block), Assay_type, Bioproject (NCBI Bioproject Accession), BioSampleModel, Consent, InsertSize, Instrument, LibraryLayout, LibrarySelection, LibrarySource, Organism, Platform, ReleaseDate (MM,DD, YYYY) (date data released to public), SRA_Study (NCBI SRA Study Accession), depth (m), elevation (meters), env_biome, env_feature, env_material, geo_loc_name (geographic location name), lat_lon (latitude, decimal degrees, longitude decimal degrees)

Methods:

Sampling sites in this study are 2.1 meter square treatment plots that are directly adjacent to one another other. Fertilized treatment received Slow-release fertilizer (Osmocote Plus with 15% N, 8% P2O5 and 11% K2O) was applied twice a year (April and September) in fertilizing plots at a rate of 326 kg N/ha/yr, 76 kg P/ha/yr and 198 kg K/ha/yr. Fertilizer was inserted 10 cm beneath the soil. The top 10 cm of soil was collected from within each treatment plot. The soil was transported to the lab on ice and stored at -80°C. DNA was extracted from each soil sample, checked for purity,and amplified by PCR of the V4 barcode region, 16S rDNA for prokaryotes. Sequencing of PCR amplicons was conducted with Illumina MiSeq. DNA processing was done in QIIME v. 1.9.1 with default settings except for a Phred score of 25. Please contact the authors for further information.

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