deletions | additions       diff --git a/Methods.tex b/Methods.tex  index d636ccd..b779f2b 100644  --- a/Methods.tex  +++ b/Methods.tex 
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values (using corresponding standard errors). The user-defined null  hypothesis for the Wald test was that LFC was less than one standard  deviation above the mean of all LFC values. P-values were corrected for  multiple comparisons by using the Benjamini and Hochberg method CITE. \citep{benjamini1995}.  Independent filtering was performed on the basis of sparsity prior to correcting P-values for multiple comparisons. The sparsity value that yielded the most P-values less than 0.10 was selected for independent filtering by sparsity. Briefly, OTUs were eliminated if they failed to appear in at least 45\% of high density gradient fractions for a given $^{13}$C/control treatment pair, these OTUs are unlikely to have sufficient data to allow for the determination of statistical significance. diff --git a/Results.tex b/Results.tex  index 404363f..0d89996 100644  --- a/Results.tex  +++ b/Results.tex 
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total C in the soil. The cellulose-C (0.88 mg C g$^{-1}$ soil d.w.) and  xylose-C (0.42 mg C g$^{-1}$ soil d.w.) in the amendment comprised 6\% and 3\%  of the total C in the soil, respectively. The soil microbial community respired  65\% of the xylose within one day(Figure~\ref{fig:13C})  and 29\% of the added xylose remained in the soil at day 30 (Figure~\ref{fig:setup}). (Figure~\ref{fig:13C}).  In contrast, cellulose-C declined at a constant rate of approximately 18 $\mu$g  C d $^{-1}$ g $^{-1}$ soil d.w. and 40\% of added cellulose-C remained in the  soil at day~30 (Figure~\ref{fig:setup}). (Figure~\ref{fig:13C}).  \subsection{$^{13}$C-labeling of OTUs changed with time and substrate}  % Fakesubsubsection:Changes in the soil microcosm microbial community structure 
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$^{13}$C-labeled substrates for unlabeled equivalents could not be shown to  alter community composition. Twenty-nine OTUs exhibited sufficient statistical  evidence (adjusted P-value $<$ 0.10) to conclude they changed in relative  abundance over the course of the experiment. experiment (Figure~\ref{fig:time}).  When SSU rRNA gene abundances were combined at the taxonomic rank of "class", the classes that changed in abundance (P-value $<$ 0.10) were the \textit{Bacilli} (decreased), \textit{Flavobacteria} (decreased), \textit{Gammaproteobacteria} (decreased), and \textit{Herpetosiphonales} (increased) (Figure~\ref{fig:time_class}). Of the 29 OTUs that changed in relative abundance over time, 14 putatively incorporated $^{13}$C into DNA (Figure~\ref{fig:time}). OTUs that likely assimilated $^{13}$C from $^{13}$C-cellulose into DNA tended to increase in relative abundance with time whereas OTUs that assimilated $^{13}$C from $^{13}$C-xylose tended to decrease. decrease(Figure~\ref{fig:babund}).  Those OTUs that responded to both substrates did not exhibit a consistent relative abundance response over time as a group (Figure~\ref{fig:time}~and~\ref{fig:babund}). \subsection{OTUs that assimilated $^{13}$C into DNA} \label{responders}  % Fakesubsubsection:If an OTU exhibited  If an OTU exhibited strong evidence for assimilating $^{13}$C into DNA, we refer to that OTU as a "responder" (see Supplemental Note 1.7.4 Supplemental Methods  for our operational definition of "responder"). The SSU rRNA gene sequences produced in this study could be distributed into 5,940 OTUs and we assessed the evidence of $^{13}$C incorporation into DNA from $^{13}$C-cellulose and $^{13}$C-xylose for each OTU. Forty-one OTUs responded to $^{13}$C-xylose,  55 $^{13}$C-xylose,~55  OTUs responded to $^{13}$C-cellulose, and 8 OTUs responded to both xylose and cellulose (Figure~\ref{fig:l2fc}, Tables~{tab:cell}~and~\ref{tab:xyl}). Figure~\ref{fig:genspec}, Figure~\ref{fig:tiledtree},  Table~\ref{tab:cell},~and~Table~\ref{tab:xyl}).  The number of xylose responders peaked at days 1 and 3 and declined with time. In contrast, the number of  cellulose responders increased with time peaking at days 14 and 30  (Figure~\ref{fig:rspndr_count}).  
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day~3 (Figure~\ref{fig:example}). Finally, on day~7, \textit{Actinobacteria}  OTUs represented 53\% of the xylose responders and these OTUs were closely  related to cultured representatives of \textit{Micrococcales}  (Table~\ref{tab:xyl}). (Table~\ref{tab:xyl}, Figure~\ref{fig:tiledtree}).  For example, ``OTU.4'', annotated as \textit{Agromyces}, had signal of $^{13}$C labeling in the $^{13}$C-xylose treatment on days 1, 3 and 7 with the strongest evidence of $^{13}$C labeling at day~7 and did not  appear $^{13}$C labeled at days~14 and~30. ``OTU.4'' relative abundance in  non-fractionated DNA increased until day~3 and then declined until  day~30 (Figure\ref{fig:example}). \textit{Proteobacteria} were also common  among xylose responders at day~7 where they comprised 40\% of xylose responder  OTUs. Notably, \textit{Proteobacteria} represented the majority (6 of 8) of  OTUs that responded to both cellulose and xylose. xylose (Figure~\ref{fig:genspec}).  %Fakesubsubsection:Cellulose responders were  The phylogenetic composition of cellulose responders did not change with time 
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\textit{Proteobacteria} shared $<$ 97\% SSU rRNA gene sequence identity to  bacteria cultured in isolation. For example, most (70\%) of the  \textit{Verrucomicrobia} cellulose responders fell within unidentified  \textit{Spartobacteria} clades, clades (Figure~\ref{tiledtree}),  and these shared $<$ 85\% SSU rRNA gene sequence identity to any characterized isolate. The \textit{Spartobacteria} OTU ``OTU.2192'' exemplified many cellulose responders (Figure~\ref{:fig:example}). (Figure~\ref{:fig:example}, Table\ref{tab:cell}).  ``OTU.2192'' increased in non-fractionated DNA relative abundance with time and evidence for $^{13}$C labeling of ``OTU.2192'' in the $^{13}$C-cellulose treatment increased over time with the strongest evidence at days~14 and~30 (Figure\ref{fig:example}). Most \textit{Choloflexi} cellulose responders belonged to an unidentified clade within the \textit{Herpetosiphonales} and they shared $<$ 89\% SSU rRNA gene sequence identity to any characterized isolate. Characteristic of \textit{Chloroflexi} cellulose responders, "OTU.64" increased in relative abundance over 30 days and evidence for $^{13}$C labeling of ``OTU.64'' in the $^{13}$C-cellulose treatment peaked days 14 and~30 (Figure~\ref{fig:example}). Cellulose responders found within the \textit{Bacteroidetes} fell within the \textit{Cytophagales} contrasting with \textit{Bacteroidetes} xylose responders  that fell instead within the \textit{Flavobacteria} or  \textit{Sphingobacteriales}. \textit{Sphingobacteriales} (Figure~\ref{tiledtree}).  \textit{Bacteroidetes} cellulose responders included one OTU that shared 100\% SSU rRNA gene sequence identity to species of \textit{Sporocytophaga}, a genus that includes known cellulose degraders. \subsection{Characteristics of cellulose and xylose responders}  % Fakesubsubsection:Cellulose responders tended  Cellulose responders, relative to xylose responders, tended to have lower  relative abundance in non-fractionated DNA, demonstrated signal consistent with  higher atom \% $^{13}$C in labeled DNA, and had lower estimated \textit{rrn}  copy number. number (Figure~\ref{fig:shift}).  In the non-fractionated DNA, cellulose responders had lower relative abundance (7e$^{-4}$ (s.d. 2e$^{-3}$)) than xylose responders (2e$^{-3}$ (s.d. 4e$^{-3}$)) (Figure~\ref{fig:xyl_count}, P-value $=$ 0.00028, Wilcoxon Rank Sum test). Six of the ten most common OTUs observed in the non-fractionated DNA responded to xylose, and, eight of the ten most abundant responders to xylose or cellulose in the non-fractionated DNA were xylose responders. % Fakesubsubsection:DNA buoyant density increases as the amount  DNA buoyant density (BD) increases in proportion to the atom \% $^{13}$C of the 
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(Figures~\ref{fig:shift} and \ref{fig:copy}; P = 1.878e$^{-9}$). Furthermore,  the estimated \textit{rrn} gene copy number for xylose responders was inversely  related to the day of first response (P = 2.02e$^{-15}$,  Figure~\ref{fig:copy}). Figure~\ref{fig:copy},Figure~\ref{fig:shift}).  % Fakesubsubsection:We assessed phylogenetic  We assessed phylogenetic clustering of $^{13}$C-responsive OTUs with the  diff --git a/bibliography/biblio.bib b/bibliography/biblio.bib  index 0e9327a..b31b8ef 100644  --- a/bibliography/biblio.bib  +++ b/bibliography/biblio.bib 
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@article{benjamini1995,  title = {Controlling the false discovery rate: {A} practical and powerful approach to multiple testing},  volume = {57},  rights = {Copyright © 1995 Royal Statistical Society},  issn = {0035-9246},  shorttitle = {Controlling the False Discovery Rate},  timestamp = {2015-07-06 19:19:39},  eprinttype = {jstor},  eprint = {2346101},  number = {1},  journaltitle = {Journal of the Royal Statistical Society. Series B (Methodological)},  journal = {Journal of the Royal Statistical Society. Series B (Methodological)},  author = {Benjamini, Yoav and Hochberg, Yosef},  date = {1995-01-01},  date = {1995},  pages = {289--300},  }  @article{derito2005,  eprinttype = {pmid},  eprint = {16332760},