US Long-Term Ecological Research Network
Microbial Observatory at North Temperate Lakes LTER Microbial Community Composition in Lakes - Taxonomic/Ecological characteristics of the sample at North Temperate Lakes LTER 2000 - 2007

Abstract

Microbial community composition is inferred by a combination of automated ribosomal intergenic spacer analysis (ARISA) and PCR-generated clone library analysis. Clone libraries include both the 16S rRNA gene and the 16S-23S ribosomal intergenic spacer fragment. Phylogenetic assignments for individual ARISA fragments are obtained by comparing the ARISA fragment length from each clone to all of the profiles stored in our database. We have analyzed over 3900 clones obtained from 41 lakes that represent the range of trophic types found in temperate landscapes. Querying by a combination of taxonomic and ecological characteristics of the sample allows the user to retrieve sample information [sample IDs, sample dates, lake information (region, type, size, depth) and physical/chemical data (water temperature, clarity, pH, DOC, SUVA, TN, TP, nitrates/nitrites)] and clone information [clone IDs, sequence data, and characteristics of the sequence (length, chimera status, accession number, taxonomic affiliation)]. The data can be filtered by ecological characteristics of the sample [lake name, sample date, lake information (region, type, size, depth)] and taxonomic characteristics of the community members [clone ID, ARISA fragment length (raw or binned), and/or taxonomic characteristics (Phylum and Phylum-Class)]. The output can include links to individual sample records, which contain links to the taxonomic composition of the sample inferred by dynamically matching clones to ARISA fragments in the individual sample. The output can also include links to clone records directly (though this creates a very large number of lines in the output and is not recommended). Project ID's 30 Lakes - Survey of 30 lakes in northern and southern Wisconsin. June, August and October, 2002. Lake Characteristics. CB0000 - Time series monitoring microbial community composition in Crystal Bog. 2000-2002. CBX_02 - Food web manipulation experiment in Crystal Bog. Summer, 2002.
Dataset ID
76

Data Citation Suggestion

Kent, A., K. McMahon, R. Newton, and A. Yannarell. 2021. Microbial Community Composition in Lakes - Taxonomic/Ecological characteristics of the sample at North Temperate Lakes LTER 2000 - 2007 ver 3. Environmental Data Initiative. https://doi.org/10.6073/pasta/f71d99dbcd233aeff6ae251f890d71f9. Accessed 2021-10-20.

Data Download

Microbial Community Composition - Taxonomic/Ecological characteristics of the sample