Abstract:

This dataset contains fungal amplicon sequencing data from rhizosphere soil associated with Spartina alterniflora plants using ITS1 markers, respectively. The dataset was in support of the study assessing the influence of S. alterniflora plant traits on associated soil microbial communities, which was conducted along Bay Jimmy, Louisiana in 2013. The table is the raw (non-rarified) fungal OTU abundances table generated from the soil surrounding each plant. Fungal response variables are the abundance, diversity and composition in rhizosphere soil using culture-independent sequencing of ITS region for taxonomy; and high throughput sequencing for community analyses. Environmental parameters including location, residual oil, individual GPS points etc. measured from the individual plant as well as biotic parameters such as plant provenance are also included.

Suggested Citation:

Candice Y. Lumibao, Michael J. Blum. 2020. Fungal amplicon sequencing data from rhizosphere soil associated with Spartina alterniflora collected in Bay Jimmy, Louisiana from 2013-01-19 to 2013-06-26. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/A59VQEW2

Purpose:

The dataset was in support of the study assessing the influence of S. alterniflora plant traits on associated soil microbial communities, which was conducted along Bay Jimmy, Louisiana in 2013.

Data Parameters and Units:

SampleID (sample identification), report_folder_name (additional info on sample identification), field_sample_number (additional info on sample identification), date_collected (date of collection), site (site of each plant provenance collected), plant_community (type of ecosystem - saltmarsh), month (month of collection), season (season during sample collection), provenance (plant provenance where rhizosphere soil was collected and profiled), zone (zone or plot where plant provenance were planted and collected), Plot (zone or plot where plant provenance were planted and collected), Total.C1.C3.Chrysenes (sum of all C1 and C3-chrysenes, u/ug), Total.C1.C4.naphthalenes (sum of all C1 and C3-naphthalenes, u/ug), Total.C1.C4.phenanthrenes (sum of all C1 and C3-phenanthrenes, u/ug), Total.C1.C3.dibenzothiophenes (sum of all C1 and C3-dibenzothiophenes, u/ug), Total.relevant.PAHs (the sum of C compounds, u/ug), naphthalene.weathering.ratio (weathering ratios of alkylated 3-ring naphthalene (PWR) relative to recalcitrant 4-ring chrysenes, u/ug), phenanthrene.weathering.ratio (weathering ratios of alkylated 3-ring phenanthrenes (PWR) relative to recalcitrant 4-ring chrysenes u/ug), dibenzothiophene.weathering.ratio (weathering ratios of alkylated 3-ring dibenzothiophenes (DWR) relative to recalcitrant 4-ring chrysenes, u/ug), Latitude (UTM coordinates of each plant provenance), Longitude (UTM coordinates of each plant provenance), Position (arbitrary location of each plant provenance), Description (type of microbiome - rhizosphere soil), and SH…. (and henceforth, specific bacteria OTUs and corresponding abundance).

Methods:

Fungal sequences were obtained via amplicon-based sequencing of 16S rRNA in Illumina. Rhizospheric porewater was sampled using a clean syringe from the soil below each plant and analyzed for conductivity, total dissolved solids (parts per thousand) and pH using a multimeter (Myron L, Carlsbad, USA). Approximately 10 g of soil were used for extraction and measurement of crude oil components. Polycyclic aromatic hydrocarbon (PAH) analysis was performed using 6890N gas chromatograph (Agilent Technologies, Santa Clara, USA) equipped with 5973N mass selective detector.

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