Spring Microbial Mat Community High-Abundance Proteins in the Octopus Identification and Distribution of

sp. RS-1, the major FAP in the mat, has not been shown tohave photoautotrophic activity, even though it contains the genesfor the 3-OHP pathway (10). Other extant taxa have not beenbrought into cultivation, but metagenomic and metatranscrip-tomicanalyseshaverevealedtheirfunctionalpotential(11–13).Incontrast to metatranscriptomics, which indicates the potential forproteinexpressionand,thus,functioninacomplexsample,meta-proteomics reveals the proteins present in the sample at any giventime. Since gene expression does not always correlate with proteincontent (reviewed in reference 7) and, to date, analysis of specificproteins in the OS microbial mat community has been limited toa targeted study of nitrogen fixation (16), the current study wasperformed to help understand the functions of individual OS matcommunity members and to predict how they contribute to theprocesses occurring in the mat. This report is the first metapro-teomics analysis of the OS microbial mat community.Microbial mat cores were taken from OS at an average temper-ature of 60°C under midday high-light conditions. Proteins wereextracted from mat samples, digested with trypsin, and then ana-lyzed by offline Mud-PIT liquid chromatography-tandem massspectrometry (LC-MS/MS) (see the supplemental material). Theresulting spectra were used by the Mascot search engine (MatrixScience,London,UnitedKingdom)toquerydatabasescomprisedof either protein sequences from NCBI associated with thermo-philes or the translated metagenome from OS and MS (11).Unique proteins (based on spectra) from each database searchwere merged into a final data set (see the supplemental material).Functions of identified proteins were determined using the KyotoEncyclopedia of Genes and Genomes (KEGG; see the supplemen-tal material).A total of 1,560 spectra, corresponding to 202 proteins (ap-proximately 1% of the known metagenome [12]), were identified(see the supplemental data set). Proteins associated with 12 bac-terial phyla were identified; however, 89% of the proteins wereassociated with three phyla,