Abstract:

This data set contains sample collection information, raw sequence data and Genbank accession numbers for DNA sequences of the ammonia monooxygenase genes (amoA) from ammonia-oxidizing archaea and bacteria samples collected in July 2016 from plots located five meters from the marsh edge at one oiled and one unoiled site within three regions: sites 1 (unoiled) and 2 (oiled) in Terrebonne Bay, LA (TB), sites 1 (unoiled) and 2 (oiled) western Barataria Bay, LA (WB), and sites 5 (unoiled) and 7 (oiled) in eastern Barataria Bay and Port Sulphur, LA (EB/PS).

Suggested Citation:

Bernhard, Anne E.. 2019. DNA sequences of ammonia monooxygenase genes from ammonia-oxidizing archaea and bacteria in Louisiana salt marshes six years after the Deepwater Horizon oil spill, July 2016. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-y6jj-fz88

Purpose:

This dataset was generated to determine if ammonia-oxidizing communities had changed since 2012 when the first set of sequences were generated (R1.x139.143:0066, R1.x139.143:0067).

Data Parameters and Units:

File AOA_AOB_Accession_Numbers_2016.xlsx, Worksheet- Betaproteobacterial amoA: Genbank accession numbers and Clone numbers for Betaproteobacterial sequences, Date: Month and year sample was collected in the field (Mon-YY), Depth (cm): Depth of the collected sediment, Site Name: User-defined identifier for collection site, Lat (decimal degrees): Latitude of the collection site in decimal degrees, Long (decimal degrees): Longitude of the collection site in decimal degrees. Worksheet- Archaeal amoA Genbank accession numbers and Clone numbers for Archaeal amoA sequences, Date: Month and year sample was collected in the field (Mon-YY), Depth (cm): Depth of the collected sediment, Site Name: User-defined identifier for collection site, Lat (decimal degrees): Latitude of the collection site in decimal degrees, Long (decimal degrees): Longitude of the collection site in decimal degrees. File AOA_AOB_Raw_Sequences_2016.txt: Raw sequence data for ammonia-oxidizing archaea and bacteria. Sequences are organized by user-defined identifiers that reference the collection site: TB1110 sequences are from TB-1 (unoiled), 29.29297, -90.604939; TB1114 sequences are from TB-2 (oiled), 29.2915, -90.602824; WB1126 sequences are from WB-1 (unoiled), 29.288949, -90.042667; WB1130 sequences are from WB-2 (oiled), 29.265837, -90.024864; EB1146 sequences are from EB/PS-5 (unoiled), 29.4508, -89.7500; EB1154 sequences are from EB/PS-7 (oiled), 29.4742, -89.8564.

Methods:

Clone libraries were generated from samples located 5 m from the marsh edge using primers Arc26F and Arc417R for archaeal amoA and primers amoA1F and amoA2R-TC for bacterial amoA. Sequences were obtained using T3 primers and Sanger sequencing conducted by Eurofins Genomics.

Error Analysis:

Specificity of each reaction was assessed by melt curve analysis and run in duplicate to control for pipetting errors. Standard curves were generated using a plasmid DNA containing a copy of the appropriate gene with concentrations ranging over five orders of magnitude.

Individual Files: