Dataset: Diversity and distribution of sediment bacteria across an ecological and trophic gradient from 2018 to 2019 (Cyanos Great Lakes project)

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 that provides long-term data on a representative sub-sampling of Minnesota’s lakes spanning 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 (Level III) ecological regions. These regions are characterized by differences in underlying geology, soils, vegetation, and land use (Table S1 in Sauer et al., 2022). This is the first comprehensive sediment bacterial survey of these lakes.

 

Water Sample Collection & Analysis

At each site, we collected water profile measurements of temperature, pH, conductivity, turbidity, and dissolved oxygen using a YSI EXO2 multi-parameter sonde (YSI, Inc.). We also collected an integrated epilimnetic water sample (0–2 m) and a hypolimnetic water sample (maximum lake depth – 1 m) when thermal stratification was present. All samples were stored on ice in the field and at either 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 for 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 (TP) 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 4500-NH₃ and 4500-NO₃. All TP, TN, NH₃, and NO₃ samples were analyzed within six months of sampling on a SmartChem 170 (Unity Scientific, Inc.) discrete analyzer (APHA, 2012).

Additionally, samples for chlorophyll-a were filtered, frozen, and analyzed via fluorometry following EPA Method 445.0 (Arar et al., 1997). A complete summary of aqueous chemistry results, including sampling dates, is provided in Table S2 (Sauer et al., 2022).

Sediment Sample Collection & DNA Isolation 

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

Cores were vertically extruded in the laboratory at 1–2 cm intervals, depending on lake productivity, and subsamples from two intervals were collected for DNA analysis. Subsamples were collected from the 0–2 cm interval (hereafter referred to as shallow) and from either the 3–4 cm or 4–6 cm interval (hereafter referred to as deep). Subsamples were frozen under nitrogen for up to three months prior to DNA extraction (Table S3 in Sauer et al., 2022).

DNA was extracted from 0.25 g of wet sediment from each subsample using a PowerSoil DNA Isolation Kit (Qiagen, Inc.) following the manufacturer’s protocols. Negative controls were performed by carrying out extractions on blanks containing only reagents and no sample. Final bulk DNA concentrations were determined using a Qubit™ dsDNA HS Assay Kit (Molecular Probes, Eugene, OR, USA) and a Qubit™ Fluorometer (Invitrogen, Carlsbad, CA, USA). The detection limit of the Qubit™ dsDNA HS Assay Kit is 10 pg μL⁻¹. All samples that yielded detectable amounts of DNA were submitted for sequencing (Table S3 in Sauer et al., 2022). Although DNA was not detected in negative controls, these samples were submitted for sequencing; they failed quality control performed by the University of Minnesota Genomics Center (UMGC), and no sequencing data were obtained.

Nucleic acid preparation, amplification, and sequencing

DNA samples were submitted to the University of Minnesota Genomics Center (UMGC), where library preparation for Illumina high-throughput sequencing was performed using a Nextera XT workflow with 2 × 300 bp chemistry. This workflow utilizes transposome-based shearing, which fragments DNA and adds adapter sequences in a single step. DNA was amplified and dual-indexed with adapter sequences through PCR using primers 515F (5′-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTGCCAGCMGCCGCGGTAA-3′) and 806R (5′-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGGACTACHVGGGTWTCTAAT-3′), targeting the V4 hypervariable region of the bacterial 16S SSU rRNA gene.

The amplicon library preparation methods developed and employed by the UMGC have been shown to be more quantitatively accurate and qualitatively complete, detecting taxonomic groups that often go undetected with existing methods (Gohl et al., 2016). Indexed samples were sequenced once using an Illumina MiSeq at the UMGC. A total of 3.29 million (3,290,170) raw reads were obtained from 40 samples.

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 reported in the results paper, Sauer et al. (2022). All 16S rRNA amplicon data are available from the Sequence Read Archive (SRA) under BioProject accession PRJNA763898.