Abstract:
This data set contains gene abundance data for six microbial genes (archaeal amoA, betaproteobacterial amoA, comammox amoA, nirS, pmoA, and bacterial 16S rRNA) collected from salt marsh sediment in four areas on the eastern coast of the United States (Barn Island Wildlife Management Area, Connecticut; Cottrell Marsh, Connecticut; Plum Island Estuary, Massachusetts; Great Sippewissett Marsh, Massachusetts) between 2001 to 2017. Potential nitrification rates are provided for Barn Island and Plum Island, while various sediment chemistries are provided for all four locations (see Methods for details).
Suggested Citation:
Bernhard, A.E.. 2020. Gene abundance of nitrifiers, denitrifiers, methane-oxidizers and total bacteria, nitrification rates, and sediment chemistry in four marshes on the East Coast of the United States, 2001-04-24 to 2017-06-28. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-mjpn-eq50
Purpose:
A synthesis examination of the impacts of restoration, drought, salinity, and long-term fertilization on salt marsh microbial communities, as well as the characterization of nitrifiers.
Data Parameters and Units:
Worksheet Barn Island: Date: Date sample was collected (DD-MMM-YYYY); Site: Site identifier where sample was collected (HQ=Headquarters marsh, WE=Wequetequock marsh, IP1=impoundment 1, IP2=impoundment 2, IP3=impoundment 3, IP4=impoundment 4); LAT (dec degrees): Latitude of sampling site in decimal degrees; LONG (dec degrees): Longitude of sampling site in decimal degrees; Sample #: Unique sample identifier; Habitat: Type of dominant vegetation or unvegetated (TSA=tall Spartina alterniflora, SSA=short S. alterniflora, SP=S. patens, FO=forbes, JG=Juncus gerardii, MAT=microbial mat or unvegetated); Depth (cm): Sediment depth in centimeters; AOA: ammonia oxidizing archaea measured by archaeal amoA (ammonia monooxygenase) gene abundance (gene copies/gr dry wt sediment); AOB: ammonia-oxidizing bacteria measured by betaproteobacterial amoA gene abundance (gene copies/gr dr wt sediment); COM: comammox bacteria measured by comammox amoA gene abundance (gene copies/gr dry wt sediment); Bac16S: bacterial 16S rRNA gene abundance (gene copies/gr dry wt sediment); MOB: methane-oxidizing bacteria measured by particulate methane monooxygenase (pmoA) gene abundance (gene copies/gr dry wt sediment); DNB: denitrifying bacteria measured by nitrite reductase (nirS) gene abundance (gene copies/gr dry wt sediment); Rates: potential nitrification rates (µM NO3--N/gr dr wt sediment/day); Salinity: Porewater salinity in psu; pH: Porewater pH; Soil moisture (% water); percent water in the soil; pwNH4 (µM-NH4+-N): porewater ammonium;
Worksheet Cottrell Marsh: Date: Date sample was collected; Site: Site identifier where sample was collected (CO1, CO2, CO3); LAT (dec degrees): Latitude of sampling site in decimal degrees; LONG (decimal degrees): Longitude of sampling site in decimal degrees; Sample #: Unique sample identifier; Habitat: Type of dominant vegetation or unvegetated (TSA=tall Spartina alterniflora, SP=S. patens); Depth (cm): Sediment depth in centimeters; Soil moisture (% water); percent water in the soil; Salinity: Porewater salinity in psu; pH: Porewater pH; AOA: ammonia oxidizing archaea measured by archaeal amoA (ammonia monooxygenase) gene abundance (gene copies/gr dry wt sediment); AOB: ammonia-oxidizing bacteria measured by betaproteobacterial amoA gene abundance (gene copies/gr dr wt sediment); COM: comammox bacteria measured by comammox amoA gene abundance (gene copies/gr dry wt sediment); Bac16S: bacterial 16S rRNA gene abundance (gene copies/gr dry wt sediment); MOB: methane-oxidizing bacteria measured by particulate methane monooxygenase (pmoA) gene abundance (gene copies/gr dry wt sediment); DNB: denitrifying bacteria measured by nitrite reductase (nirS) gene abundance (gene copies/gr dry wt sediment);
Worksheet Plum Island Estuary: Date: Date sample was collected; Site: Site identifier where sample was collected (P14=Parker River, mid estuarine station, 14 km from Plum Island Sound; P22= Parker River, upper estuarine station, 22 km from Plum Island Sound; R8C= Rowley River, Laws Point, 8 km from Plum Island Sound; R8M= Rowley River, Laws Point, 8 km from Plum Island Sound); LAT (dec degrees): Latitude of sampling site in decimal degrees; LONG (dec degrees): Longitude of sampling site in decimal degrees; Sample #: Unique sample identifier; Habitat: Type of dominant vegetation or unvegetated (TSA=tall Spartina alterniflora, creekbottom); Depth (cm): Sediment depth in centimeters; AOA: ammonia oxidizing archaea measured by archaeal amoA (ammonia monooxygenase) gene abundance (gene copies/gr dry wt sediment); AOB: ammonia-oxidizing bacteria measured by betaproteobacterial amoA gene abundance (gene copies/gr dr wt sediment); COM: comammox bacteria measured by comammox amoA gene abundance (gene copies/gr dry wt sediment); Bac16S: bacterial 16S rRNA gene abundance (gene copies/gr dry wt sediment); MOB: methane-oxidizing bacteria measured by particulate methane monooxygenase (pmoA) gene abundance (gene copies/gr dry wt sediment); DNB: denitrifying bacteria measured by nitrite reductase (nirS) gene abundance (gene copies/gr dry wt sediment); Rates: potential nitrification rates (µM NO3--N/gr dr wt sediment/day); Soil moisture (% water): percent water in the soil; Salinity: Porewater salinity in psu;
Worksheet Sippewissett: Date: Date sample was collected; Site: Site identifier where sample was collected (control, control-high, HF, LF, XF, XF-High); LAT (dec degrees): Latitude of sampling site in decimal degrees; LONG (dec degrees): Longitude of sampling site in decimal degrees; Sample #: Unique sample identifier; Habitat: Type of dominant vegetation or unvegetated (TSA=tall Spartina alterniflora, SP=S. patens, mixed=mixed vegetation, DS=Distichlis spicata); Depth (cm): Sediment depth in centimeters; AOA: ammonia oxidizing archaea measured by archaeal amoA (ammonia monooxygenase) gene abundance (gene copies/gr dry wt sediment); AOB: ammonia-oxidizing bacteria measured by betaproteobacterial amoA gene abundance (gene copies/gr dr wt sediment); COM: comammox bacteria measured by comammox amoA gene abundance (gene copies/gr dry wt sediment); Bac16S: bacterial 16S rRNA gene abundance (gene copies/gr dry wt sediment); MOB: methane-oxidizing bacteria measured by particulate methane monooxygenase (pmoA) gene abundance (gene copies/gr dry wt sediment); DNB: denitrifying bacteria measured by nitrite reductase (nirS) gene abundance (gene copies/gr dry wt sediment); Salinity: Porewater salinity in psu; pwNH4 (µM-NH4+-N): porewater ammonium; Soil moisture (% water): percent water in the soil.
Methods:
Barn Island: Sediment samples were collected on 9 different sampling trips in Oct 2005, Mar, Apr, Jun, Jul, and Oct 2006, and late June or early July in 2014, 2016, and 2017 and from different vegetation zones. Samples were collected for a variety of different studies, including characterization of nitrifiers in different salt marsh vegetation zones, impacts of restoration on salt marsh microbial communities, and impacts of drought on microbial communities in the marsh. Gene abundances were generated by QPCR using published primers and protocols. Salinity (measured by handheld refractometer), pH (measured with a pH meter or pH paper), soil moisture (measured by the difference in weight loss after drying), and porewater ammonium concentrations (measured with the phenol-hypochlorite method) were also obtained. Potential nitrification rates were measured by measuring the generation of nitrate over 72 hours using the enzymatic reduction of nitrate to nitrite method. Cottrell Marsh: Sediment samples were collected on 2 different sampling trips in July and Oct 2006 from different vegetation zones. Samples were collected for a study of the impacts of restoration on salt marsh microbial communities. Gene abundances were generated by QPCR using published primers and protocols. Salinity (measured by handheld refractometer), pH (measured with a pH meter or pH paper), soil moisture (measured by the difference in weight loss after drying) were also obtained. Plum Island: Sediment samples were collected on 6 different sampling trips from April 2001 to Sept 2003 from vegetated marsh and unvegetated creek bottom. Gene abundances were generated by QPCR using published primers and protocols. Salinity (measured by handheld refractometer), soil moisture (measured by the difference in weight loss after drying) were also obtained. Potential nitrification rates were measured by measuring the generation of nitrate over 72 hours using the enzymatic reduction of nitrate to nitrite method. Great Sippewissett Marsh: Sediment samples were collected in July 2009 from different vegetation areas. Gene abundances were generated by QPCR using published primers and protocols. Salinity (measured by handheld refractometer), pH (measured with a pH meter or pH paper), soil moisture (measured by the difference in weight loss after drying), and porewater ammonium concentrations (measured with the phenol-hypochlorite method) were also obtained. Key to Site Codes: control=fertilizer added in the low marsh habitat, LF=low fertilizer concentration added (8.4 g/m2/wk), HF=High fertilizer concentration added (25 g/m2/wk), XF= extra high fertilizer concentration added (75 g/m2/wk) in the low marsh habitat, control-high=no fertilizer added in the high marsh habitat, XF=extra high fertilizer concentration added (75 g/m2/wk) in the high marsh habitat.
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