Olmsted Thesis Chapter 2 Supplementary Tables

SUPPLEMENTARY TABLE LEGENDS Supplementary Table 1. Lake-wide information. This table includes lake characteristics, lake-wide EET protein values and METABOLIC protein values and standard deviations when available. Supplementary Table 2. Abbreviations and descriptions. In addition to abbreviations, this table lists the names of proteins for which HMMs were used in METABOLIC for each category. Supplementary Table 3. 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. Supplementary Table 4. 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. Supplementary Table 5. 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). Supplementary Table 6. 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. Supplementary Table 7. 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.补充表图例 补充表1：全湖概况信息。本表涵盖湖泊特征、全湖范围的胞外电子传递（Extracellular Electron Transfer, EET）蛋白质数值、METABOLIC蛋白质数值，以及可获取情况下的标准差。 补充表2：缩写与说明。本表除缩写术语外，还列出了METABOLIC分析中各分类所使用的隐马尔可夫模型（Hidden Markov Model, HMM）对应的蛋白质名称。 补充表3：每份宏基因组组装基因组（Metagenome Assembled Genome, MAG）的专属信息。本表包含每份MAG所属的湖泊、样本及多分类操作单元（multi-taxonomic operational unit, mOTU）、基于GTDB-tk的分类学注释、基因组特征，以及FEET和METABOLIC相关蛋白质。 补充表4：FeGenie隐马尔可夫模型的比特分值及观测到的氧化还原关联信息。本表还包含各HMM是否被认定为胞外电子传递能力潜在证据的附加判定条件。 补充表5：独特类群特征与参考文献。本表包含每类独特类群的平均EET蛋白质数值，同时标注了各类群成员具备胞外电子传递能力的证据质量等级，该等级位于“EET证据质量”表头下，分为以下类别关键词：“明显”（部分成员含有补充表2中定义的多个潜在EET基因）、“大概率”（嫌疑最高的成员含有1~2个潜在EET基因）、“疑似”（嫌疑最高的成员含有2~3个DFE变异体或FoxABCYZ蛋白质，但无其他更具潜力的EET基因）、“未知”（仅含有1个此类“疑似”EET基因）。本表还在“既往EET证据”表头下列出每类独特类群是否在既往研究中被报道具备或大概率具备EET能力，各关键词含义如下：“是”（本研究已找到属或种水平生物具有EET能力的相关研究）、“否”（未检索到包含该属或种生物进行EET的研究；或分类学层级不足以明确判定）、“相关”（同目或同科但非该属或种的生物在既往研究中被发现具有EET能力）。 补充表6：新型簇类信息。本表包含每类独特的新型簇序列、该序列与参考序列的同源相似度百分比，以及血红素基序数量。本表还涵盖该序列所属的开放阅读框（Open Reading Frame, ORF）信息，以及其被发现的类群来源。 补充表7：来自特劳特博格湖（Trout Bog Lake）MAG宏转录组数据集的EET基因与METABOLIC氧化还原酶的表达量数值，按时间点（以小时为单位）及整合采样层进行平均计算。时间零点为2016年7月19日中部夏令时（CST）上午5:00。“NormAveTPM”指比对至指定开放阅读框的转录本的每百万转录本（Transcripts Per Million, TPM）值，经对应MAG所有开放阅读框的TPM平均值归一化后所得结果。“NormRefTPM”指经对应MAG的参考基因TPM值归一化后的结果。