Ashley Campbell edited Results & Discussion.tex  over 9 years ago

Commit id: 56102858105507d2b3b8dcb4233bd0486af73338

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  For the \textsuperscript{13}C-xylose treatment at day 1, 57\% of responsive OTUs belong to the Firmicutes (\href{https://www.authorea.com/users/3537/articles/3612/master/file/figures/l2fc_fig1/l2fc_fig.pdf}{Fig. 2}), belonging to one of three families - Paenibacillaceae, Planococcaceae, or Bacillaceae. These families are among the 12 families in the order of Bacillales, known for their endospore forming capabilities (Bergeys). The average rRNA operon copy number for the order of Bacillales is 9 according to representative taxa in the rrnDB (v. 3.1.227, \cite{18948294, 11125085})  This is not surprising as it has been demonstrated that Firmicutes maintain a metabolically-ready state \cite{Jenkins_2010,Griffiths_1998,Brookes_1987,De_Nobili_2001}. The remaining 43\% of responders at day 1 were comprised of 19\% Bacteroidetes, 14\% Proteobacteria, and 10\% Actinobacteria. Genomic analysis of fast growing bacteria, specifically Proteobacteria and Firmicutes, have a higher number of total transporters enabling them to import or export a broad range of compounds \cite{Barabote_2005}. The low affinity of these transporters facilitates fast growth in times of high nutrient conditions \cite{Trivedi_2013}. Day 3 exhibits a strong increase in Bacteroidetes response and the onset of Verrucomicrobia reponders. Notably, this pronounced response by Bacteroidetes is not captured by the bulk community abundances. Day 7 demonstrates an increased response from Proteo- and Actinobacterial OTUs. While there is a slight increase in their abundances in the bulk community analysis at day 7, it would be difficult to differentiate that change from natural variation or methodological noise. All OTUs have a decreasing log\textsubscript{2} fold change by days 14 and 30, with only a single Firmicutes OTU passing the 'responder' criteria. For the \textsuperscript{13}C-cellulose treatment only one Proteobacteria passes the 'responder' criteria at day 3 and two OTUs (Proteobacteria and Chloroflexi) at day 7. It is likely that the slow degradation of cellulose can be attributed to the energy-taxing process of synthesizing cellulolytic enzymes and exporting them, as cellulose is most often broken down externally (Schimel & Schaeffer 2012, Lynd et al 2002). As a result, microorganisms responsible for the synthesis of cellulases preferentially shuttle energy towards enzyme synthesis rather than biomass until cellulose hydrolysis begins (Schimel & Schaeffer 2012). This accounts for the delay in growth and ultimately the slow decomposition of cellulose (Perez et al 2002,Schimel & Schaeffer 2012).