deletions | additions       diff --git a/Discussion.tex b/Discussion.tex  index 28fa0b1..b513a2b 100644  --- a/Discussion.tex  +++ b/Discussion.tex 
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$^{13}$C from xylose and/or cellulose into biomass over time. With this  information we can build a conceptual model for the soil food web with respect  to xylose and cellulose in our microcosms. We propose xylose and  cellulose C cellulose-C  added to soil microcosms took the following path through the microbial food web (Figure~\ref{fig:foodweb}): fast-growing \textit{Firmicutes}  spore formers first assimilated xylose C within 24 hours. Over the next  6 days, biomass from early-responding \textit{Firmicutes} and the remaining 
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\subsection{Ecological strategies of soil microorganisms participating in the  decomposition of organic matter}  % Fakesubsubsection:Models of soil C cycling rely on  Models of soil C cycling rely on functional niches defined by ecologists and soil  microbiologists. In these models  ecological strategies such as growth rate and substrate specificity are parameters for functional niche behaviorin soil C models  \citep{Kaiser2014a}. Functional niches are commonly discovered by observing how community structure changes with changing conditions \cite{Fierer2007}. In this experiment, DNA-SIP revealed functional niche membership. We also used DNA-SIP data to quantify substrate specificity which is related to the magnitude of DNA BD shift upon $^{13}$C labeling (see Results). Moreover, we assessed growth rate of functional niche members by estimating niche member \textit{rrn} gene copy number, a genomic feature reliably extrapolated from phylogeny that is indicative of how fast a microorganism grows \citep{11125085,Kembel_2012}. We found that $^{13}$C-cellulose responsive OTUs are likely  slow growing substrate specialists relative to $^{13}$C-xylose responders (Figure~\ref{fig:shift},  Figure~\ref{fig:copy}). We also found that $^{13}$C-xylose responsive OTUs that  incorporated $^{13}$C into biomass at day one grow faster than OTUs that 
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directly assimilating labile C and has implications for modelling trophic  niches. We also note that $^{13}$C-cellulose responders are generally lower  abundance members of the bulk community than $^{13}$C-xylose responsive OTUs  (Figure~\ref{fig:shift}), however, High high  \textit{rrn} gene copy number may inflate $^{13}$C-xylose-responder abundance.  % Fakesubsubsection:NRI values have been used to assess 
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labeled as a result of primary xylose assimilation (see below), and therefore  it's not clear if $^{13}$C-xylose responsive OTUs in this experiment constitute  a single ecologically meaningful group or multiple ecological groups.  Temporally defined $^{13}$C-xylose responder groups, however, are were  phylogenetically coherent (Figure~\ref{fig:tiledtree},  Figure~\ref{fig:xyl_count}). For example, most day  1 $^{13}$C-xylose responders are members of the \textit{Paenibacillus} (see 
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assessed by functionally screening isolates and/or genomes. Xylose use in soil,  for instance, may be less a function of catabolic pathway distribution across  genomes and more a function of lifestyle. Phenomena such as seasonal change  \citep{Schmidt2007}, and rainfall \citep{Placella2012} pulse deliver nutrients cause nutrient  and resources resource concentrations in soil  to soil. fluctuate.  Therefore, fast growth and/or rapid resuscitation upon wet up \citep{Placella2012} allow microorganisms to favorably compete for labile C resources. Life history ecological strategies tied to phylogeny like growth rate \cite{Fierer2007} may constrain the diversity of labile C assimilators even though the ability to use labile C is phylogenetically dispersed. DNA-SIP is useful for establishing \textit{in situ} phylogenetic clustering and diversity of functional guilds because DNA-SIP can account for life history strategies by targeting \textit{active} microorganisms. Additionally, snapshot estimates of community composition commonly inform soil  structure-function-relationship soil-structure-function-relationship  studies \citep{Fierer2007} but labile C decomposition might not be linked to snapshot community structure. Alternatively labile C decomposition might be linked specifically to community  structure \textit{dynamics}. That is, fast growing spore formers would not need  to maintain high abundance to significantly mediate cycling of pulse delivered 
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biogeochemical processes that are the sum of many subprocesses involve a broad  array of taxa and are assumed to be less influenced by community change than  narrow processes that involve a single, specific chemical transformation by  a smaller narrow  suite of microbial participants \citep{Schimel_1995,McGuire2010}. Within an aggregate process such as C decomposition, subprocesses can be  further classified as broad or narrow \citep{McGuire2010}. In theory, ``broad'' and ``narrow'' functional guilds decompose labile and recalcitrant C, respectively \citep{McGuire2010}. However, the diversity of active labile C and recalcitrant C decomposers in soil has not been directly quantified. Notably, we found more OTUs responded to $^{13}$C-cellulose, 63, than $^{13}$C-xylose, 49. Also, it is possible that many $^{13}$C-xylose responders are predatory bacteria or saprophytes as opposed to primary labile C degraders (see below). Cellulose and xylose decomposer functional guilds were non-overlapping in membership -- of 104 $^{13}$C-responders only 8 responded to both cellulose and xylose -- and  represented a small fraction of total soil community diversity  (Figure~\ref{fig:genspec}). While xylose use is undoubtedly more widely 
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Figure~\ref{fig:babund}). Considering \textit{Agromyces} and  \textit{Bacteroidetes} phylotypes are likely soil predators, one parsimonious  hypothesis for $^{13}$C-labelling of \textit{Bacteroidetes} and  \textit{Actinobacteria} with a corresponding decrease in  $^{13}$C-labeled \textit{Firmicutes} abundance is that \textit{Bacteroidetes} and  \textit{Actinobacteria} fed on $^{13}$C-labeled \textit{Firmicutes}. Besides  predation, mother cell lysis, the last step in sporulation, would release 
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composition could affect C dynamics and fate. Genomic evidence shows cellulose  degradation is a phylogenetically conserved trait \citep{Berlemont2013}. Our  study evaluates the phylogenetic conservation of soil cellulose degradation in  active microorganisms via DNA-SIP andgenomic evidence concurs with  our results. results concur with genomic  evidence.  A decrease in cellulose degrader abundance would diminish cellulose decomposition process rates as few soil microorganisms can fill the phylogenetically conserved cellulose degradation niche. Dispersed cellulose  decomposers could renew ecosystem function, however. For labile  C decomposition, the absence of fast growing spore formers would allow other  microbes to assimilate labile C provided dispersal does not enable rapid  recolonization. Primary labile C degraders in this study grow fast, and form spores and these distinct ecological strategies might indicate distinct C use dynamics and/or resource allocation. New labile C degraders may metabolize and allocate labile C differently thus changing labile C dynamics and fate. Further, labile C degrader substitution could affect biomass C turnover by predatory bacteria or saprophytes that feed on fast growing, spore forming labile C decomposers. On the other hand, spore formation enables dispersal \citep{Nicholson2000} which would allow fast growing spore formers to continuously occupy the labile C decomposition niche. One proposed mechanism  for similar decomposition rates of labile C across soils varying in community  composition is that labile C is decomposed by a diverse suite of soil  diff --git a/Introduction.tex b/Introduction.tex  index 3c2a4f9..eb6c964 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. Io To  soil microcosms we added a mixture of nutrients and C substrates that simulated the composition of plant biomass. All  microcosms received the same C substrate mixture where the only difference  between treatments was the identity of the isotopically labeled substrate.  diff --git a/Results.tex b/Results.tex  index 83e7d5f..01468cc 100644  --- a/Results.tex  +++ b/Results.tex 
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Supplemental~Note~XX). We predicted the \textit{rrn} gene copy number for each  OTU as described previously \citep{Kembel_2012}. The estimated  \textit{rrn} gene copy number for $^{13}$C-xylose responders was inversely  related to the  timepoint  ofthe  first response for each OTU (P-value 2.02x10$^{-15}$, Figure~\ref{fig:copy}). OTUs that did not respond at day  1respond  but did respond at day 3 and/or day 7 had fewer estimated \textit{rrn} copy number than OTUs that responded at day 1  (Figure~\ref{fig:copy}).   %Fakesubsubsection:  We assessed phylogenetic clustering of $^{13}$C-responsive OTUs with the  Nearest Taxon Index (NTI), the Net Relatedness Index (NRI), (NRI)  \citep{Webb2000},  and the consenTRAIT metric \citep{Martiny2013}. 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 compared to the null model \citep{Evans2014a}. NRI and P-values for substrate responder groups suggest $^{13}$C-xylose responders are overdispersed (NRI: -1.33, P: 0.90) while $^{13}$C-cellulose responders are clustered (NRI: 4.49, P: 0.001). 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). The consenTRAIT clade depth for $^{13}$C-xylose and $^{13}$C-cellulose responders was 0.012 and 0.028 16S rRNA sequence  dissimilarity, respectively.