In this dataset, we used a controlled flow-through reactor (FTR) experiment to test the role of nitrate as an electron acceptor, and its effect on organic matter decomposition and the associated microbial community in salt marsh sediments. Organic matter decomposition significantly increased in response to nitrate, even at sediment depths typically considered resistant to decomposition. The use of isotope tracers suggests this pattern was largely driven by stimulated denitrification. Nitrate addition also significantly altered the microbial community and decreased alpha diversity, selecting for taxa belonging to groups known to reduce nitrate and oxidize more complex forms of organic matter. Fourier Transform-Infrared Spectroscopy further supported these results, suggesting that nitrate facilitated decomposition of complex organic matter compounds into more bioavailable forms. Taken together, these results suggest the existence of organic matter pools that only become accessible with nitrate and would otherwise remain stabilized in the sediment. The existence of such pools could have important implications for carbon storage, since greater decomposition rates as N loading increases may result in less overall burial of organic-rich sediment. Given the extent of nitrogen loading along our coastlines, it is imperative that we better understand the resilience of salt marsh systems to nutrient enrichment, especially if we hope to rely on salt marshes, and other blue carbon systems, for long-term carbon storage.
The FTR experimental design is a modified version of a system described in Pallud & Van Cappellen (2006). We collected sediment cores (n=3; 5 cm diameter and 30 cm deep) from tall Spartina alterniflora approximately 1 meter from the creek bank edge, in West Creek (42.759N, 70.891 W). We sectioned each core into shallow (0-5 cm), mid (10-15 cm), and deep (20-25 cm) sediments and homogenized sections under anoxic conditions, and split each depth section into two treatments -- nitrate (+500 uM labeled potassium nitrate in 0.2um filtered seawater) and unamended (0.2 um filtered seawater only). These sediments were loaded into the FTRs, with an approximate volume of 31.81 cm^3. The reactors received constant flow of one of the two treatments mentioned above using peristaltic pumps flowing at ~0.08 mL/min, under anoxic conditions. We collected outflow samples to assess biogeochemical parameters, and collected sediment at the beginning and end of the experiment to assess the microbial community and sediment carbon parameters. More information regarding the experimental design can be found in Bulseco et al. 2019.
We measured the following biogeochemical parameters using the associated methods: dissolved inorganic carbon using an Apollo SciTech AS-C3 DIC Analyzer (Dickson & Goyet 1994); nitrate + nitrite using chemiluminescence on a Teledyne T200 NOx analyzer (Cox 1980); ammonium on a Shimadzu 1601 spectrophotometer (Solorzano 1969); sulfide on a Shimadzu 1601 spectrophotometer (Gilboa-Garber 1971); denitrification and DNRA by measuring production of 28, 29, and 30N2 on a membrane inlet mass spectrometer (Kana et al. 1994; Yin et al. 2014); %C and %N on a Perkin Elmer 2400 Series Elemental Analyzer; %sulfur on a LECO S635S sulfur analyzer; sediment functional groups on a Fourier Transform-Infrared Spectrometer (Margenot et al. 2015).
We performed molecular work using the following procedures. We extracted DNA using the MoBio PowerSoil DNA Isolation Kit; amplified the V4 region of the 16S rRNA gene using the general bacterial primer pair 515F/806R (Caporaso et al. 2011) on an Illumia MiSeq (Caporaso et al. 2012) using a 300-cycle kit and V2 chemistry. Sequence analysis was conducted in QIIME2, version 2017.12) and statistical analyses were completed using R (R Core Team 2013). Microbial genomic sequence data from this study is available in the Sequence Read Archive under accession number PRJNA505917.
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