Olmsted Thesis Chapter 2 Supplementary Tables

SUPPLEMENTARY TABLE LEGENDS <strong>Supplementary Table 1.</strong> Lake-wide information. This table includes lake characteristics, lake-wide EET protein values and METABOLIC protein values and standard deviations when available. <strong>Supplementary Table 2.</strong> Abbreviations and descriptions. In addition to abbreviations, this table lists the names of proteins for which HMMs were used in METABOLIC for each category. <strong>Supplementary Table 3.</strong> Information unique to each metagenome assembled genome (MAG). This includes to what lake, sample, and mOTU each MAG belongs, its GTDB-tk taxonomy, genetic characteristics, and FEET and METBOLIC proteins. <strong>Supplementary Table 4.</strong> Bit scores for FeGenie Hidden Markov Models and observed redox association. This table also includes additional conditionals for whether each HMM was considered as promising evidence of EET capability. <strong>Supplementary Table 5. </strong>Unique taxa characteristics and references. This table includes average EET protein values for each unique taxa. It also contains our designation of the quality of evidence that each unique taxa contains members suspected capable of EET. These designations occur under the header “EET Evidence Quality” with following category keywords “obviously” (some members contain several promising EET genes as defined in Supplementary Table 2), “likely” (highest suspect members contain one or two promising EET genes), “possibly” (highest suspect members contain two or three DFE variants or FoxABCYZ proteins but no other more promising EET genes), and “unknown” (contains just one of such “possible” EET genes). This table also contains whether each unique taxa has been found in a previous study to have or likely have EET capabilities under the header “Previous EET evidence” with the following keyword meanings: “yes” (we found studies that show EET in organisms in the genus or species), “no” (we did not find studies including genus or species doing EET; or taxonomic level is not defined enough to know), and “related”(organisms in the same order or family but not the particular genus or species were found in a previous study with EET). <strong>Supplementary Table 6. </strong>Novel cluster information. This table includes each unique novel cluster sequence, its percent identity to the reference sequence, and its number of heme motifs. Also included is which open reading frame the sequence represents, and what taxa it was found in. <strong>Supplementary Table 7. </strong>Expression values for EET genes and METABOLIC oxidoreductases from Trout Bog Lake MAG metatranscriptomics dataset, averaged per timepoint (in hours) and integrated sampling layer. Timepoint zero is at 5:00 am CST, July 19th 2016. “NormAveTPM” is the TPM of the transcripts that mapped to the listed open reading frame normalized by the average of all open reading frames’ TPM values of the given MAG. “NormRefTPM” is normalized by the reference gene TPM value for the given MAG.