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

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\textbf{Differential taxa C utilization.} Individual OTUs that assimilated \textsuperscript{13}C-substrates were identified by using the DESeq framework \cite{Anders_Huber_2010} to analyze differential representation in heavy fractions (\href{https://www.authorea.com/users/3537/articles/3612/master/file/figures/l2fc_fig1/l2fc_fig.pdf}{Fig. 2}). There were 43 and 35 unique OTUs that significantly (\textit{p}-value < 0.10) assimilated \textsuperscript{13}C-xylose and \textsuperscript{13}C-cellulose, respectively; herein called 'responders' ((\href{https://www.authorea.com/users/3537/articles/8459/master/file/figures/OTU_screening_schematic/OTU_screening_schematic.pdf}{Fig. (\href{https://www.authorea.com/users/3537/articles/8459/master/file/figures/OTU_screening_schematic/OTU_screening_schematic.pdf}{Fig.  S2}, \href{https://www.authorea.com/users/3537/articles/8459/master/file/figures/l2fc_fig_pVal/l2fc_fig_pVal.png}{Fig. S3}).For OTUs passing a conservative threshold of \textit{p}-value = <0.10 for log\textsubscript{2} fold change (FigSx), we measured the density shift in the experimental treatment compared to the control (Fig Sx). Those OTUs with a center of mass shift greater than zero were considered 'responders'.  For the \textsuperscript{13}C-xylose treatment at day 1 OTUs within Firmicutes demonstrate the strongest response. 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}. Additionally, Proteobacteria, Bacteroidetes, and Actinobacteria contain responder OTUs at day 1. 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.  

Furthermore, this demonstrates the sensitivity of this technique by being able to detect \textsuperscript{13}C-label incorporation in samples with low C additions (2.18mgC g\textsuperscript{-1} soil).   temporal changes in microbial community composition are consistent with C decomposition being accompanied by a microbial community succession. The dynamics of \textsuperscript{13}C-cellulose and \textsuperscript{13}C-xylose assimilation varied dramatically for different microorganisms.  For OTUs passing a conservative threshold of \textit{p}-value = <0.10 for log\textsubscript{2} fold change (FigSx), we measured the density shift in the experimental treatment compared to the control (Fig Sx). Those OTUs with a center of mass shift greater than zero were considered 'responders'.