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. S2}, \href{https://www.authorea.com/users/3537/articles/8459/master/file/figures/l2fc_fig_pVal/l2fc_fig_pVal.png}{Fig. S3}). Overall, we found xylose responders were from higher rank abundances than cellulose responders, however, cellulose responders exhibited a greater change in buoyant density than xylose responders in response to isotope incorporation (Figure 3).   Kernel The kernel  density estimates estimate  (KDE) of buoyant density shifts resulting from \textsuperscript{13}C-assimilation reveal that cellulose responders exhibit a significantly (wolcox: (wilcox:  p<...) greater buoyant density shift than xylose responders (Figure 3A). First, a density profile for each responder is generated for the experimental and control treatment at each of the sampling time points using relative abundances from sequence libraries (Fig Sx). Then, for a responder OTU at a single time point Then  the center of mass is measured for the density profile of a responder in  the control and the density profile of the respective  experimental treatment. treatment for a single time point.  A density shift is then calculated by substracting the center of mass for the control from the experimental. Finally, this is repeated for all responder OTUs times points  and all time points responders  for both the \textsuperscript{13}-cellulose and \textsuperscript{13}C-xylose treatments. Each  KDE curve  represents the collection of density shifts calculated for all responders and time points within a treatment (Figure 3A). In a pure culture An organism with 100\% \textsuperscript{13}C-labeling of DNA would exhibit a density shift of 0.04gmL\textsuperscript{-1}. Xylose utilizers have a smaller density shift (<0.02 gmL\textsuperscript{-1}) than cellulose utilizers (0.005-0.03 gmL\textsuperscript{-1}), with few exceptions. This suggests a greater substrate specificity among cellulose degraders than xylose degraders. Partial \textsuperscript{13}C-labeling (<0.04gmL\textsuperscript{-1} density shift) could be a result of various lifestyles ('trophic strategy' better word choice?) such as (1) assimilation of C from multiple substrates (both \textsuperscript{12}C and \textsuperscript{13}C in this instance) or (2) \textsuperscript{13}C-label dilution as it cascades through trophic levels via consumption of \textsuperscript{13}C-labeled organisms or waste products from organisms that are metabolizing the \textsuperscript{13}C-substrate. Most xylose responders are found at higher rank abundances than cellulose responders which fall among the rare taxa in the tail of the RA curve (Fig 3B). This demonstrates that many taxa important to C-cycling are present in the rare biosphere and may be difficult or unable to detect in bulk community sequencing efforts. Responders of xylose or cellulose are wide spread across 7 phyla (Fig 4). There are very few OTUs that utilize both cellulose and xylose (should put in a number of how many OTUs utilize both over how many responders total there were), however, at the phyla level many phylum had responders for both xylose and cellulose.