Abstract:

Updated calculations of relative abundance and new calculations for absolute abundance from Illumina MiSeq data for surfactant-associated bacteria in samples collected during the LASER 2016 cruise (November 4, 2015 to February 12, 2016). The equation for calculating relative abundance was updated in order to take into account the efficiencies of the PCR reactions, since they were not exactly 100%. Absolute abundance results of surfactant-associated bacteria were obtained via sequencing (Illumina MiSeq) from Argonne National Lab and analysis was performed using QIIME.

Suggested Citation:

Alexander Soloviev, Cayla Dean, John Kluge, Brian Haus. 2017. Updated and new abundance calculations for LASER 2016 Microlayer bacteria data. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N75T3HZ4

Publications:

Parks, G., Dean, C. W., Kluge, J. A., Soloviev, A. V., Shivji, M., Tartar, A., … Schuler, P. (2020). Analysis of surfactant-associated bacteria in the sea surface microlayer using deoxyribonucleic acid sequencing and synthetic aperture radar. International Journal of Remote Sensing, 41(10), 3886–3901. doi:10.1080/01431161.2019.1708508

Purpose:

To determine the bacterial microlayer composition off the Louisiana coast.

Data Parameters and Units:

Bacterial relative abundance (ratio) and absolute abundance (average counts per site) results and calculations. Date (MM/DD/YYYY); Site number; Sample ID; Average-average relative abundance, Standard deviation; T-student's distribution coefficient; N-number of samples; Min-minimum confidence interval (50%); Max-maximum confidence interval (50%); Type (SML-microlayer, SSW-subsurface water, NE-non-exposed controls); Location; Time (HH:MM); Slick; Sample condition; Wind speed (knots); Wind speed (m/s); Wave height (ft); SAR overpass time (HH:MM); Comments; Cycle threshold - CT; Slope-slope value generated by LightCycler 96 software; Efficiency-calculated efficiency of the qPCR reaction; Delta CT target; Delta CT ref; Pffafl-relative abundance using Pffafl method; average OTU hits per site for several well-known surfactant-associated bacterial genera. In location column empty cell inherits the lat/lon from the cell above it.

Methods:

The Pffafl (2001) method was used to calculate relative abundance and a Student's distribution coefficient was used to calculate confidence intervals at 50%. For absolute abundance, confidence intervals were calculated at 95% using Poisson distribution.

Provenance and Historical References:

Pfaffle, M.W. (2001). A new mathematical model for relative quantification in real-time RT–PCR. Nucleic Acids Research 29(9): e45. doi:10.1093/nar/29.9.e45

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