Abstract:

This data was generated from a a mesocosm project to examine the effect of oil exposure on denitrifier functional abundance within sediments associated with genotypically diverse plant species. Sediments samples were collected from control and oil-amended mesocosms set up at Dauphin Island Sea Lab that consisted of Avicennia germinans (black mangrove) co-occurring with mono- or polycultures of Spartina alterniflora (smooth cord grass). Data were collected in triplicates from control and amended mesocosms at three time points, before treatment in September 2015, 6 months after treatment in April 2016, and 11 months after treatment in September 2016. Additional data from this mesocosm study can be found in GRIIDC datasets R4.x262.000:0021, R4.x262.000:0026, and R4.x262.000:0034.

Suggested Citation:

Patrice Crawford, Nikaela Flournoy. 2019. Quantifying denitrifier functional marker gene abundance from sediments associated with genotypically diverse plant types: A mesocosms study in April and September 2016. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/VGZXJT9F

Purpose:

The purpose of this study was to enumerate genes involved in denitrification from mesocosm sediment samples associated with mono- and polycultures of Spartina alterniflora co-occuring with Avicennia germinans that either were or weren’t exposed to oiling.

Data Parameters and Units:

Sample date: Date when sampled was collected, mesocosm number: internal use, bucket number: internal use, oiling: Yes indicates sample was exposed to oil; No indicates samples was not exposed to oil, Plant Genotype: vegetation treatment (Avicennia germinans and either mono or polycultures of Spartina alterniflora), 16S rRNA: copies per gram wet sediment, nirS: copies per gram wet sediment, nosZ: copies per gram wet sediment.

Methods:

Oiled was Macon surrogate obtained through GOMRI, weathered and emulsified (350 ml of weathered oil, 350 ml of seawater) and applied to the buckets (0.17 m2 surface area). Quantitative PCR (qPCR) was performed on April and September 2016 samples to assess the abundance of two genes in the denitrification pathway: nirS (nitrite reductase) and norB (nitric oxide reductase). Quantification of a novel group of nitrate-reducing bacteria in the environment by real-time PCR. J Microbiol Meth 57: 399-407. Smith, C. J., D.B. Nedwell, L.F. Dong, and A.M. Osborn. 2007. Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments. App. Environ. Microbiol. 73: 3612-3622. Throbäck IN, Enwall K, Jarvis A, Hallin S. 2004. Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiology Ecology 49:401-417.

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