Dataset: Sediment bacteria in MN lakes

Site description 

For this study, we selected twenty lakes within Minnesota’s Sentinel Lakes in a Changing Environment (SLICE) program. SLICE is a collaborative research initiative providing long-term data on a representative sub-sampling of Minnesota’s lakes that span the diverse geographic, land-use, and climatic gradients present in Minnesota (Fig 1 in Sauer et al., 2022). The lakes span four of the seven Environmental Protection Agency/Commission for Environmental Cooperation’s (level III) ecological regions. These regions can be characterized by their underlying geology, soils, vegetation, and land use (S1 Table in Sauer et al., 2022). This is the first comprehensive sediment bacterial survey of these lakes.

 

Water Sample Collection & Analysis

From each site we collected water profile measures for temperature, pH, conductivity, turbidity, and dissolved oxygen using a YSI XO2 multi-parameter sonde (YSI, Inc.). We also collected an integrated (0-2m) epilimnetic water sample, and a hypolimnetic (maximum lake depth–1m) water sample when thermal stratification was present. All samples were stored on ice in the field and at 4°C or -20°C in the laboratory, depending on methodology, until processed. Samples for soluble reactive phosphorus (SRP), dissolved organic carbon (DOC), and dissolved inorganic carbon (DIC) were filtered, processed, and analyzed within 36 hours of sampling using standard methods for SRP (4500-P) on a SmartChem 170 (Unity Scientific, Inc.) and DIC/DOC Method 5310-C using a Torch Combustion TOC Analyzer (Teledyne Tekmar, Inc.)(American Public Health Association; 2012). Samples for total nitrogen (TN) and total phosphorus were frozen and analyzed using standard methods for TN (4500-N), and TP (4500-P). Samples for ammonia (NH3) and nitrate (NO3) were filtered and frozen prior to analysis following methods NH3 (4500-NH3) and NO3 (4500-NO3). All TP, TN, NH3, NO3 samples were analyzed within six months of sampling on a SmartChem 170 (Unity Scientific, Inc.) discrete analyzer (APHA 2012). Additionally, we filtered, froze, and analyzed samples for chlorophyll-a concentrations via fluorometry following the EPA method 445.0 (Arar et al., 1997). We provided a complete summary of aqueous chemistry results, including sampling dates, in the S2 Table (Table S2 in Sauer et al., 2022).

Sediment Sample Collection & DNA Isolation 

We collected sediment cores from July 2018 through June 2019 using a rod-driven piston corer with a 7cm diameter polycarbonate tube (Wright 1997). We determined coring locations (i.e., flat areas near the deepest basin) using publicly available bathymetric maps (https://www.dnr.state.mn.us/lakefind/index.html), avoiding steep-sided “holes” where sediment-focusing may be high. After sediment core retrieval, we stabilized core tops in the field using a gelling agent (e.g., Zorbitrol) and returned intact cores to the laboratory where we stored them vertically at 4°C for no more than seven days until processing. In cases where the upper sediments were extremely flocculent, we immediately sectioned the upper most sections (~0–30 cm) in the field to prevent mixing during transport.

We vertically extruded the cores in the lab in 1 to 2 cm intervals, depending on lake productivity, and took subsamples from two intervals for DNA analysis. The subsamples collected were from the 0-2cm (hereafter referred to as shallow) and either the 3-4cm or 4-6cm interval (hereafter referred to as deep). Subsamples were frozen under nitrogen for up to three months before DNA was extracted (S3 Table in Sauer et al., 2022). We extracted DNA from 0.25g of wet sediment from each subsample using a PowerSoil DNA Isolation Kit (Qiagen, Inc.) following the manufacturer’s protocols. We performed negative controls by carrying out extractions on blanks, using only reagents without sample. We determined final bulk DNA concentrations using a Qubit™ dsDNA HS Assay kit (Molecular Probes, Eugene, OR, USA) and Qubit™Fluorometer (Invitrogen, Carlsbad, CA, USA). The detection limit for the Qubit™ dsDNA HS Assay Kit is 10 pg/μL. All samples that yielded detectable amounts of DNA were sent for sequencing (S3 Table in Sauer et al., 2022). Despite not detecting DNA in our negative controls, these were submitted for sequencing where they failed to pass quality control performed by the University of Minnesota Genomic Center (UMGC) and no sequencing information was obtained.

Temporal bounds within the dataset

The date range associated with this dataset represents the sediment core collection dates. 

Data Availability in SRA

All relevant data are in Sauer et al., 2022. All 16S rRNA amplicon data are available from the SRA database at BioProject PRJNA763898.