Abstract:

This data set contains terminal restriction fragment polymorphism (TRFLP) profiles of ammonia-oxidizing archaea from four New England salt marshes: Barn Island Wildlife Management Area and Cottrell Marsh in southeastern Connecticut, the Great Sippewissett Marsh on Cape Cod, Massachusetts, and the Plum Island Estuary in northeastern Massachusetts. TRFLP profiles based on the archaeal amoA gene were generated from sediment samples collected from the top 2 or 4 cm. Gene abundance data, potential nitrification rates and various sediment chemistries for samples collected at the same sites can be found in GRIIDC under Unique Dataset Identifier (UDI) R6.x808.000:0014 (DOI: 10.7266/n7-mjpn-eq50).

Suggested Citation:

Bernhard, A.E.. 2020. DNA fingerprints (TRFLP) of ammonia-oxidizing archaea in New England salt marshes 2001-04-01 to 2017-06-28. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-4fss-ek19

Purpose:

Impacts of restoration, characterization of nitrifiers, impacts of drought on salt marsh microbial communities, regional comparisons.

Data Parameters and Units:

Sample #: Unique sample identifier; Date: Date sample was collected (DD-MM-YY); Marsh: General marsh location descriptor where samples were collected (BI=Barn Island, CO=Cottrell, PIE=Plum Island Estuary, SIP=Sippewissett); Site: Site identifier where samples were collected (CO1=Cottrell site 1, CO2=Cottrell site 2, CO3=Cottrell site 3, Control=no fertilization site, Control-high=no fertilization in high marsh, HF=high fertilization site, HQ=Headquarters marsh, IP1=impoundment 1, IP2=impoundment 2, IP3=impoundment 3, IP4=impoundment 4, LF=low fertilization site, P22=Parker River site 22, P14=Parker River site 14, R8C=Rowley Creek site 8, R8M=Rowley Marsh site 8, WE=Wequetequock marsh, XF=extra high fertilization site, XF-high=extra high fertilization site in high marsh); LAT (dec degrees): Latitude of sampling site in decimal degrees; LONG (dec degrees): Longitude of sampling site in decimal degrees; 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, UNV=unvegetated creek bottom, DS=Distichlis spicata, mixed=mixed vegetation); Sed. Depth (cm): Sediment depth in centimeters; AOA73 (relative abundance of terminal restriction fragment of 73 base pairs) AOA83 (relative abundance of terminal restriction fragment of 83 base pairs) AOA119 (relative abundance of terminal restriction fragment of 119 base pairs) AOA170 (relative abundance of terminal restriction fragment of 170 base pairs) AOA208 (relative abundance of terminal restriction fragment of 208 base pairs) AOA283 (relative abundance of terminal restriction fragment of 283 base pairs) AOA296 (relative abundance of terminal restriction fragment of 296 base pairs) AOA316 (relative abundance of terminal restriction fragment of 316 base pairs) AOA414 (relative abundance of terminal restriction fragment of 414 base pairs)

Methods:

In Barn Island, samples were collected in October 2005, April, June and July 2006, June 2014, July 2016, and June 2017. In Cottrell Marsh, samples were collected in July 2006. Plum Island samples were collected in April and August 2001, April and September 2002, and September 2003. Sippewissett samples were collected in July 2009. 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 nitrifying communities, and impacts of drought on nitrifiers in the marsh.

Instruments:

TRFLP profiles of archaeal amoA genes were generated by amplifying the amoA genes with fluorescently labeled forward primer (Arch26F-FAM) and a reverse primer (Arch417R). PCR products were analyzed by capillary eletrohoresis (ABI 3700) at the Cornell University Life Sciences Core Laboratories Center using an Applied Biosystems 3730XL DNA Analyzer. Data were analyzed using GeneMarker v.1.4 (Soft Genetics).

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