Abstract:

This dataset contains abundances of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), methane-oxidizing bacteria (MOB), denitrifying bacteria (DNB), and total bacteria collected in June 2015 from marsh sediments at the Louisiana Universities Marine Consortium (LUMCON) in Chauvin, Louisiana, representing six different marsh habitats: Spartina-dominated, Juncus-dominated, marsh edge, tidal creek, marsh depression, and tidal pool. Each sample was analyzed by quantitative PCR for the abundance of AOB (betaproteobacterial amoA genes), AOA (archaeal amoA genes), MOB (pmoA genes), DNB (nirS genes), and total bacteria (16S rRNA genes).

Suggested Citation:

Bernhard, Anne E.. 2019. Abundance of nitrogen and carbon cycling bacterial and archaeal populations from six habitat types in a south Louisiana salt marsh, June 2015. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-jsaz-by45

Purpose:

To measure microbial community abundances in different marsh habitats in Louisiana, to compare to abundances in other marshes, and gain a better understanding of nutrient cycling processes in different marsh habitats.

Data Parameters and Units:

Sample #: Unique sample identifier for each sediment sample; Site: Indicates the site (LUM1, LUM2, LUM3) and an abbreviation for the habitat (S=Spartina-dominated, D=marsh Depression, J=Juncus-dominated, E=marsh Edge, C=tidal Creek bottom, P=tidal Pool); Date Collected (Month-Year): Month and Year the soil sample was collected; Latitude (Decimal Degrees): Indicates the latitude for the site in decimal degrees; Longitude (Decimal Degrees): Indicates the longitude for the site in decimal degrees; Habitat: Describes the type of habitat where sediment was collected (Spartina, Depression, Juncus, Subtidal Edge, Creek Bottom, or Pond); AOA (copies/gdw): Ammonia-oxidizing archaea, number of archaeal ammonia monooxygenase (amoA) given in gene copies per gram of dry weight (gdw); AOB (copies/gdw): Ammonia-oxidizing bacteria, number of betaproteobacterial ammonia monooxygenase (amoA) given in gene copies per gram of dry weight (gdw); MOB (copies/gdw): Methane-oxidizing bacteria, number of particulate methane monooxygenase (pmoA) given in gene copies per gram of dry weight (gdw); DNB (copies/gdw): Denitrifying bacteria, number of dissimilatory nitrite reductase (nirS) given in gene copies per gram of dry weight (gdw); Bac 16S (copies/gdw): Total bacteria, number of 16S rRNA given in gene copies per gram of dry weight (gdw).

Methods:

Archaeal amoA genes were amplified by QPCR with the primers Arch26F/417R. Bacterial AmoA genes were amplified by QPCR using primers amoA1f/amoA2r-TC. pmoA genes were amplified with pmo189F and mb661R. nirS genes were amplified with nirS-1F and nirs-3R. 5-cm sediment cores were collected using a 6.7cm diameter acrylic corer with beveled edges. Soils were stored in Whirl-Paks and placed on ice until they were returned to the laboratory; processing began within 24 hours. Sediments for DNA extraction were stored at -80°C until they were shipped on dry ice to Connecticut College where they were stored at -80°C until processed. DNA was extracted with the MoBio PowerSoil DNA extraction kit. The sequences of the primers are published in the accompanying publications- Arch26F/Arch417R: Park, et al (2008); amoA1F: Rotthauwe et al(1997); amoA2R-TC: Nicolaisen and Ramsing (2002); pmo189F/mb661R: Tavormina et al (2008); nirS-1F/nirS-3R: Braker et al (1998).

Instruments:

All QPCRs were run on either an iCycler (Bio-Rad) or a CFX Connect (Bio-Rad).

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 5 orders of magnitude.

Provenance and Historical References:

Braker, G., Fesefeldt, A., & Witzel, K. P. (1998). Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Appl. Environ. Microbiol., 64(10), 3769-3775. Park, S.-J., Park, B.-J., & Rhee, S.-K. (2008). Comparative analysis of archaeal 16S rRNA and amoA genes to estimate the abundance and diversity of ammonia-oxidizing archaea in marine sediments. Extremophiles, 12(4), 605–615. doi:10.1007/s00792-008-0165-7 Nicolaisen, M. H., & Ramsing, N. B. (2002). Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteria. Journal of Microbiological Methods, 50(2), 189–203. doi:10.1016/s0167-7012(02)00026-x Rotthauwe, J. H., Witzel, K. P., & Liesack, W. (1997). The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ. Microbiol., 63(12), 4704-4712. Tavormina, P. L., Ussler, W., & Orphan, V. J. (2008). Planktonic and Sediment-Associated Aerobic Methanotrophs in Two Seep Systems along the North American Margin. Applied and Environmental Microbiology, 74(13), 3985–3995. doi:10.1128/aem.00069-08

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