deletions | additions       diff --git a/Results & Discussion.tex b/Results & Discussion.tex  index e28e8c8..b42882f 100644  --- a/Results & Discussion.tex  +++ b/Results & Discussion.tex 
...
\section{Results and Discussion}  \textbf{Temporal microbial and C-cycling dynamics.} With the rapid advancement and declining costs of high throughput sequencing, it has become increasingly easy to investigate microbial communities. In this study, we couple stable-isotope probing with 454 pyrosequencing in order to better understand organic matter decomposition dynamics as a function of soil microbial community C utilization. A series of soil microcosms amendeded with a complex C mixture containing either \textsuperscript{13}C-xylose, \textsuperscript{13}C-cellulose, or no isotope were incubated in parallel for 30 days. Microcosms were harvested at discrete time points during the incubation period and the temporal and isotope assimilation dynamics of the microbial community were measured by sequencing 16S rRNA in the bulk microbial community and fractions from CsCl gradient fractionation (\href{https://www.authorea.com/users/3537/articles/8459/master/file/figures/20140708_ConceptualFig2/20140708_ConceptualFig2.pdf}{Fig. S1}). Our approach provided the sensitivity necessary to detect xylose and cellulose degradation amidst a low dose complex C amendment (5.3mgC g\textsuperscript{-1} soil) with each representing 20 and 38 percent, respectively, of the total C added. Xylose degradation was observed immediately within the first 7 days, while cellulose degradation is observed after 14 days. \textbf{Temporal microbial and C-cycling dynamics.}  The dynamics of \textsuperscript{13}C-cellulose and \textsuperscript{13}C-xylose assimilation varied dramatically for different microorganisms. Isotope incorporation into DNA was revealed by analyzing variation in 16S rRNA amplicons across gradient fractions (n = 20) from control samples in relation to identical experimental samples that differed by a single substitution of \textsuperscript{12}C-cellulose or \textsuperscript{12}C-xylose with their \textsuperscript{13}C equivalents (\href{https://www.authorea.com/users/3537/articles/8459/master/file/figures/20140708_ConceptualFig2/20140708_ConceptualFig2.pdf}{Fig. S1}). Isotope incorporation changes amplicon composition relative to control in the gradient fractions and this effect can be visualized in ordination by divergence of experimental samples from corresponding control points (\href{https://www.authorea.com/users/3537/articles/3612/master/file/figures/ordination_all1/ordination_all1.png}{Fig. 1}). Primary variation of amplicon composition in gradient fractions along axis 1 is attributed to varying bouyant densities of genomes due to G+C content (\href{https://www.authorea.com/users/3537/articles/3612/master/file/figures/ordination_all1/ordination_all1.png}{Fig. 1}). Divergence due to isotope incorporation can be seen in high-buoyant density fractions that partition along axis 2 in Figure 1. The differential divergence of high density fractions in the \textsuperscript{13}C-xylose treatment compared to the \textsuperscript{13}C-cellulose treatment is indicative of a difference in the \textsuperscript{13}C-assimilating OTUs for each of the substrates (\href{https://www.authorea.com/users/3537/articles/3612/master/file/figures/ordination_all1/ordination_all1.png}{Fig. 1A}). Had the isotope incorportation from \textsuperscript{13}C-xylose and \textsuperscript{13}C-cellulose occured in the same community members, the divergence of the high-buoyant density fractions of these two treatments relative to control would have coincided in the ordination space.   The \textsuperscript{13}C-incorporation reveals temporal dynamics of C degradation demonstrated by \textsuperscript{13}C-xylose incorporation at days 1, 3, and 7 and \textsuperscript{13}C-cellulose incorporation at days 14 and 30 (\href{https://www.authorea.com/users/3537/articles/3612/master/file/figures/ordination_all1/ordination_all1.png}{Fig. 1B}). In support of this, the bulk community sequencing demonstrates significant (pval) microbial community changes over time. Although within a single time point, the bulk community failed to capture the subtlety between treatments. The temporal dynamics reveal the composition of \textsuperscript{13}C-xylose assimilating amplicons are different for each of the days the label is detected based on their separate distributions for each of the time points (\href{https://www.authorea.com/users/3537/articles/3612/master/file/figures/ordination_all1/ordination_all1.png}{Fig. 1B}). The disappearance of the \textsuperscript{13}C-xylose incorporation signature (relative to control) for days 14 and 30 result from loss of \textsuperscript{13}C-label in DNA over time. This occurs by dilution of \textsuperscript{13}C-label out of the DNA when a switch from \textsuperscript{13}C to \textsuperscript{12}C substrate utilization takes place during biomass turnover and/or predation. \textsuperscript{13}C-cellulose incorporation isn't detected until day 14 and amplicon composition is consistent for both days 14 and 30 (\href{https://www.authorea.com/users/3537/articles/3612/master/file/figures/ordination_all1/ordination_all1.png}{Fig. 1B}). The consistency of amplicon composition for cellulose degradation over time compared to xylose suggests a wider array of microorganisms utilize xylose, whereas, cellulose utilization occurs in a select few. This is consistent with long standing notions that more microorganisms are capable of utilizing simple carbohydrates than complex C substrates. Overall patterns of C degradation observed in this study demonstrate different microbial community members are responsible for the consumption of these two substrates; xylose is consumed quickly, whereas, cellulose decomposition takes longer. This suggests a pattern of microbial community transition accompanying the decomposition process. This is consistent with \cite{Engelking_2007} who observed as much as 75\% of labile C respired or converted into microbial biomass in the first 5 days of decomposition, whereas, cellulose degraders take longer to respond \cite{Hu_1997} with less than 42\% of cellulose metabolized over the first 5 days of incubation \cite{Engelking_2007}.