Abstract:

This dataset provides information about spatial and temporal heterogeneity of environmental gradients (e.g. bacterial community composition of sediment and water, sediment properties, water quality, and atmospheric physicochemistry) on an exposed sandy beach intensively sampled over diurnal tidal cycles. Twenty parallel intertidal beach transects, perpendicular to the shoreline, were marked and excavated over five days. Field measurements and observations include water quality (temperature, pH, conductivity, dissolved oxygen concentration) recorded at each sampling time using meters; atmospheric physicochemistry (solar radiation, temperature, wind speed, barometric pressure, etc.) at each sampling time and transect location; tide height, water level and wave frequency; and other observations made at the time of collection of sediment and water sample collection. Filtered water samples were used for DNA isolation. Bacterial community composition for beach surface sediment and water are provided at the phylum and Proteobacteria class levels for four of the twenty transects (Day 1).

Suggested Citation:

Engel, Annette S., Paterson, Audrey T.. 2016. Changes in Microbial Diversity Over Tidal Cycles (Analog Site, Dauphin Island Beach). Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7HT2M7P

Purpose:

To examine the bacterial community composition and sediment properties of samples collected on the south beach of Dauphin Island, AL.

Data Parameters and Units:

Worksheet: Sample names & tides Parameter Descriptions: ND= no data available; Latitude; Longitude; Sample #; Event type (LT= low tide, L-H= transition from low to high tide approx. half way, HT= high tide, H-L= transition from high to low tide approx. half way); Event date (MM/DD/YYYY); Event time (HH:MM); Wave frequency (/min); Water depth (cm); Type of sample (Sterivex filters or sediment); Comments Worksheet: Field Data Parameter Descriptions: ND= no data available; Sample #; Event type (LT= low tide, L-H= transition from low to high tide approx. half way, HT= high tide, H-L= transition from high to low tide approx. half way); Event date (MM/DD/YY); Event time (HH:MM); Water measurements: YSI: Dissolved Oxygen (DO1, % Local, corrected); Dissolved Oxygen (DO2, mg/L); Conductivity (Con 1, mS); Specific Conductivity (Sp Cond, mS); Salinity (ppt); Temperature (Temp, oC); Accumet #1: pH; Temperature (Temp, oC); Accumet #2: Conductivity (Con, mS); Salinity (ppt); Temperature (Temp, oC); Calculated Alkalinity (replicated) (mg/L); Weather Kestral: Wind direction (deg); Maximum wind speed (Max. wind, mph); Average wind speed (Avg Wind, mpg); Relative humidity (RH, %); Air temperature (Air temp, oC); Chill temperature (Chill temp, oC); Heat index temperature (HI temp, oC); Dewpoint temperature (DP temp, oC); Bulb temperature (oC); Barometric pressure (Hg); Quantum: Photosynthetically Active Radiation (PAR Sun, mM); Solar radiation (Solar Rad, W/m^2); Ultraviolet A&B radiation (UV A&B, mM); Comments Worksheet: Bacteria Phyla Parameter Descriptions: Sequence Sample ID; Field sample ID; Total classified amplicons; Bacteria phyla identified per sample Worksheet: Proteobacteria Class Parameter Descriptions: Sequence Sample ID; Field sample ID; Total classified amplicons; Proteobacteria classes identified per sample

Methods:

Bacterial community composition: Total nucleic acids were extracted in triplicate. Three to six grams of beach sediment were subjected to DNA isolation methods that incorporated sucrose lysis buffer with lysozyme (1 mg/ml) and a solution of 5X proteinase K/CTAB/SDS; incubation at 55 degrees C while shaking at 40-120 rpm; nucleic acids precipitation in isopropanol at -20 degrees C; and ethanol washing. Amplification and pyrosequencing of the V1-V3 region of 16S rRNA genes were done using a 454 GS FLX Titanium (Roche, 454 Life Sciences, Branford, CT, USA) by the Molecular Research LP (Sweetwater, TX). Raw 16S rRNA gene sequences were processed using the microbial ecology community software Mothur (http://www.mothur.org/wiki/Download_mothur) . Amplicons were trimmed for length (200-500bp) and quality (average quality score of 35 over a sliding window of 50bp), aligned and classified using the SILVA reference database (https://www.arb-silva.de/silva-license-information), screened and filtered, and removed of chimera detected by UCHIME (http://drive5.com/uchime). Inventories of processed reads classified at the phylum level and Proteobacterial classes are provided for each sediment sample.

Instruments:

Field Instruments: Fisher Scientific accumet AP115 portable pH/ORP meter; YSI Inc. 85 (conductivity, salinity, dissolved oxygen and temperature) or Fisher Scientific™ accumet™ AP75 (conductivity; total dissolved solids, temperature); Kestrel 3500 weather meter (wind speed, temperature, wind chill, relative humidity, heat stress, dew point, wet bulb temperature, barometric pressure, pressure trend, altitude); Spectrum Technologies, Inc. Field Scout Light Sensor Reader with UV Sensor (UV A&B intensity); Spectrum Technologies, Inc. Field Scout Light Sensor Reader with Quantum Light Sensor (PAR SUN).

Individual Files: