US Long-Term Ecological Research Network

Microbial Observatory at North Temperate Lakes LTER High-resolution temporal and spatial dynamics of microbial community structure in freshwater bog lakes 2005 - 2009 original format

The North Temperate Lakes - Microbial Observatory seeks to study freshwater microbes over long time scales (10+ years). Observing microbial communities over multiple years using DNA sequencing allows in-depth assessment of diversity, variability, gene content, and seasonal/annual drivers of community composition. Combining information obtained from DNA sequencing with additional experiments, such as investigating the biochemical properties of specific compounds, gene expression, or nutrient concentrations, provides insight into the functions of microbial taxa. Our 16S rRNA gene amplicon datasets were collected from bog lakes in Vilas County, WI, and from Lake Mendota in Madison, WI. Ribosomal RNA gene amplicon sequencing of freshwater environmental DNA was performed on samples from Crystal Bog, North Sparkling Bog, West Sparkling Bog, Trout Bog, South Sparkling Bog, Hell’s Kitchen, and Mary Lake. These microbial time series are valuable both for microbial ecologists seeking to understand the properties of microbial communities and for ecologists seeking to better understand how microbes contribute to ecosystem functioning in freshwater.
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Protocol available in methods section of:
Prior to collection, water temperature and dissolved oxygen concentrations are measured using a YSI 550a. The ranges of the epilimnion and hypolimnion are determined based on the location of the thermocline (where temperature/oxygen is changing the fastest). The two layers are collected separately in 1 meter increments using an integrated water column sampler. Water samples are taken back to the lab, shaken thoroughly, and filtered via peristaltic pump through 0.22 micron filters (Pall Supor). Filters are temporarily stored at -20C after collection and then transferred to -80C after transport on dry ice from Trout Lake Station to UW-Madison. Nutrient samples are collected bi-weekly following standard LTER protocols. DNA is extracted from filters using a FASTDNA SpinKit for Soil with minor modifications. (In cases of low yield or specialized sequencing methods, a phenol-chloroform extraction is used instead). The protocol for sequencing and analysis of data varies by year and by sub-project.
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