deletions | additions       diff --git a/Introduction.tex b/Introduction.tex  index 43db2c5..50bc185 100644  --- a/Introduction.tex  +++ b/Introduction.tex 
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% Fakesubsubsection:A temporal cascade occurs in natural microbial  This study aimed to observe labile C versus polymeric C assimilation dynamics  in the soil microbial community. We addeda  mixture of nutrients and C substrates to soil microcosms that simulated the composition of plant  biomass. We All microcosms received the same C substrate mixture where the only  difference between treatments was the identity of the isotopically  labeled substrate. Specifically, we  set up a series of microcosms with  three microcosm series: treatments:  in one series treatment  xylose was substituted for its $^{13}$C-equivalent, in another cellulose was substituted for its $^{13}$C-equivalent, and in the third series treatment  all substrates in the mixture were unlabeled. We harvested microcosms at days 1, 3, 7, 14 and 30 except day  1 where only $^{13}$C-xylose treated microcosms were harvested. We  used labeled xylose and cellulose to contrast labile C and polymeric C decomposition, respectively and we sequenced 16S rRNA genes from SIP density fractions with high throughput DNA sequencing technology. Our experimental design allowed us to observe the soil microbial community members that assimilated xylose-C and cellulose-C over time. diff --git a/Results.tex b/Results.tex  index fa74c66..e65a434 100644  --- a/Results.tex  +++ b/Results.tex 
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\section{Results}  % Fakesubsubsection:We observed C use dynamics by the soil microbial  We Our experimental design allowed us to track the flow of xylose and cellulose  C through the soil microbial community (Figure~\ref{fig:setup}).  %We  observed C use dynamics in an agricultural %agricultural  soil microbial community by conducting a nucleic acid SIP experiment %experiment  wherein xylose or cellulose carried the isotopic label. We set up three %three  soil microcosm series (Figure~XX). Each  microcosm was (Figure~\ref{fig:setup}). We  amended with each microcosm  %with  a C substrate mixture that included cellulose and xylose. The C substrate mixture %mixture  approximated the C composition of fresh plant biomass. The same mixture was %was  added to all microcosms, however, for each microcosm  series except the control, %control,  xylose or cellulose was substituted for its $^{13}$C counterpart. 5.3 mg C substrate mixture per gram of soil was added to each  microcosm representing 18\% of the soil C. The mixture included 0.42 mg  xylose-C and 0.88 mg cellulose-C per gram soil.  Microcosms were harvested at  days 1, 3, 7, 14 and 30 during a 30 day incubation. $^{13}$C-xylose  assimilation peaked immediately and tapered over the 30 day incubation whereas  $^{13}$C-cellulose assimilation peaked two weeks after amendment additions  (Figure~\ref{fig:ord}, Figure~\ref{fig:rspndr_count}). See Supplemental~Note~XX  for sequencing and density fractionation statistics. Microcosm treatments (see  Methods)  are identified in figures by the following code: ``13CXPS'' refers to the amendment with $^{13}$C-xylose ($^{13}$\textbf{C}  \textbf{X}ylose \textbf{P}lant \textbf{S}imulant), ``13CCPS'' refers to the  $^{13}$C-cellulose amendment and ``12CCPS'' refers to the amendment that only  contained $^{12}$C (i.e. control).5.3 mg C substrate mixture per gram of soil  was added to each microcosm representing 18\% of the soil C. The mixture  included 0.42 mg xylose-C and 0.88 mg cellulose-C per gram soil. Microcosms  were harvested at days 1, 3, 7, 14 and 30 during a 30 day incubation.  $^{13}$C-xylose assimilation peaked immediately and tapered over the 30 day  incubation whereas $^{13}$C-cellulose assimilation peaked two weeks after  amendment additions (Figure~\ref{fig:ord}, Figure~\ref{fig:rspndr_count}). See  Supplemental~Note~XX for sequencing and density fractionation statistics.  \subsection{Soil microcosm microbial community changes with time}  % Fakesubsubsection:Changes in the soil microcosm microbial community structure 
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Twenty-nine OTUs significantly changed in relative abundance with time (``BH''  adjusted p-value $<$0.10, \citep{YBenjamini1995}) and of these 29 OTUs, 14 were  found to incorporate $^{13}$C from labeled substrates into biomass  (Figure~\ref{fig:time}). Four taxonomic  classes significantly (adjusted P-value < 0.10) changed in abundance: \textit{Bacilli} (decreased), \textit{Flavobacteria} (decreased), \textit{Gammaproteobacteria} (decreased) and \textit{Herpetosiphonales} (increased) (Figure~\ref{fig:time_class}). Abundances grouped at by  phylumlevel  for OTUs that incorporated $^{13}$C from cellulose increased with time whereas abundances grouped at the by  phylumlevel  of OTUs that incorporated $^{13}$C from xylose decreased over time although \textit{Proteobacteria} abundance spiked at day 14 (Figure~\ref{fig:babund}).  \subsection{OTUs that assimilated $^{13}$C into DNA} \label{responders} 
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% Fakesubsubsection:Isotope incorporation by an OTU  We refer to OTUs that putatively incorporated $^{13}$C into DNA originally from  an isotopically labeled substrate as substrate ``responders'' (see  Supplemental~Note~XX for operational ``response'' criteria). There were X, X,  X, X, 19, 19,  15, 6,  and X 1  $^{13}$C-xylose responders at days 1, 3, 7, 14, 30, respectively (Figure~\ref{fig:rspndr_count}).  %At day 1, 84\% of $^{13}$C-xylose responsive OTUs belonged to  %\textit{Firmicutes}, 11\% to \textit{Proteobacteria} and 5\% to 
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were found at days 1, 3, 7 but peaked at day 7 (Figure~\ref{fig:xyl_count}).   % Fakesubsubsection:Only 2 and 5 OTUs were found to  Only 2 and 5 OTUs had incorporated $^{13}$C from responded  $^{13}$C-cellulose at days 3 and 7, respectively. At days 14 and 30, 42 and 39 OTUs incorporated $^{13}$C from $^{13}$C-cellulose into  biomass responded to $^{13}$C-cellulose.  (Figure~\ref{fig:rspndr_count}). %A \textit{Cellvibrio} and \textit{Sandaracinaceae} OTU assimilated $^{13}$C  %from $^{13}$C-cellulose at day 3. Day 7 $^{13}$C-cellulose responders included  %the same \textit{Cellvibrio} responder as day 3, a \textit{Verrucomicrobia} OTU 
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\textit{Proteobacteria}, \textit{Verrucomicrobia}, and \textit{Chloroflexi} had  relatively high numbers of responders with strong response across multiple time  points (Figure~\ref{fig:l2fc}). \textit{Verrucomicrobia} $^{13}$C-cellulose  responders were XX\% 70\%  \textit{Spartobacteria}. \textit{Cloroflexi} \textit{Chloroflexi}  responders were annotated belonging to the \textit{Herpetosiphonales} and XX.  \textit{Cellvibrio} \textit{Anaerolineae} (Figure~\ref{fig:tiledtrees}). \textit{Cellvibrio},  a canonical soil cellulose degrader degrader,  was found to respond strongly in the microcosms to $^{13}$C-cellulose. See Supplemental~Note~XX for further analysis counts  of $^{13}$C-responsive OTUs at greater taxonomic resolution. \subsection{Ecological strategies of $^{13}$C responders}  % Fakesubsubsection:$^{13}$C-xylose responders are generally more abundant members based 
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abundant OTUs in bulk samples.  % Fakesubsubsection:Cellulose responders exhibited a greater shift in BD  Cellulose responders exhibited a greater shift in responder  buoyant density (BD) shifted further along the density  gradient  than xylose responders responder BD  in response to isotope $^{13}$C  incorporation (Figure~\ref{fig:c1}, Figure~\ref{fig:shift}, p-value 1.8610x$^{-06}$, Wilcoxon Rank Sum test). $^{13}$C-cellulose responders responder BD  shifted on average 0.0163 g mL$^{-1}$ (sd 0.0094) whereas xylose responders responder BD  shifted on average 0.0097 g mL$^{-1}$ (sd 0.0094). For reference, 100\% $^{13}$C DNA BD is 0.04  g mL$^{-1}$ greater than the BD of its $^{12}$C counterpart. DNA BD increases  as its ratio of $^{13}$C to $^{12}$C increases. An organism that only  assimilates C into DNA from a $^{13}$C isotopically labeled source, will have  a greater $^{13}$C:$^{12}$C $^{13}$C to $^{12}$C  ratio in its DNA than an organism utilizing a mixture of isotopically labeled and unlabeled C sources (see  Supplemental~Note~XX). We predicted the \textit{rrn} gene copy number for each  OTU as described previously CITE. $^{13}$C-xylose responder \citep{Kembel_2012}. The  estimated \textit{rrn} gene copy number for $^{13}$C-xylose responders  was inversely related to  time point  of the  first response per OTU  (p-value 2.02x10$^{-15}$, Figure~\ref{fig:copy}). OTUs that first did not  respond at later time points have day  1 respond but did respond at day 3 and/or day 7 had  fewer estimated \textit{rrn} copy number than OTUs that first respond earlier responded at day 1  (Figure~\ref{fig:copy}). %Fakesubsubsection:  We assessed phylogenetic clustering of $^{13}$C-responsive OTUs with the  Nearest Taxon Index (NTI) and the Net Relatedness Index (NRI). Briefly,  positive NRI and NTI with corresponding low P-values indicates deep  phylogenetic clustering whereas negative NRI with high P-values indicates taxa  are overdispersed against compared to  the null model CITE. \citep{Evans2014a}.  NRI and P-values for substrate responder groups suggest $^{13}$C-xylose responders are overdispersed (NRI: -1.33, P: 0.90) while cellulose $^{13}$C-cellulose  responders are clustered (NRI: 4.49, P: 0.001). Nearest taxon indices (NTI) NTI values  show that both $^{13}$C-cellulose and $^{13}$C-xylose responders are clustered near the tips of the tree (NTI: 1.43 (P: 0.072), 2.69 (P: 0.001), respectively).