Ashley Campbell edited Results & Discussion.tex  over 9 years ago

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\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. 1}). 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 Engelking \textit{et al.}\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 with less than 42\% of cellulose metabolized over the first 5 days of incubation \cite{Hu_1997}.   \textbf{Differential C utilization by taxa.} Individual OTUs that assimilated \textsuperscript{13}C-substrates were identified 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 \textless 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 (i.e. assimilated more \textsuperscript{13}C) than xylose responders in response to isotope incorporation (\href{https://authorea.com/users/3537/articles/3612/master/file/figures/shift_and_rabund2/shift_and_rabund2.png}{Fig. 3}).  \textit{Xylose}. Within the first 7 days of incubation an average 63\% of \textsuperscript{13}C-xylose was respired and only an additional 6\% more was respired between days 7 and 30. Of the 60 total xylose responders 53 were responsive within the first 7 days and only 7 responders detected for days 14 and 30 (supplemental table). At day 1, 57\% of responsive OTUs belong to Firmicutes (Paenibacillaceae, Planococcaceae, and Bacillaceae) and the remaining 43\% of responders were comprised of 19\% Bacteroidetes (Flavobacteriaceae), 14\% Proteobacteria (Enterobacteriaceae, Comamonadaceae, and uncultured Gammaproteobacteria), and 10\% Actinobacteria (Micrococcaceae and Microbacteriaceae) (\href{https://www.authorea.com/users/3537/articles/3612/master/file/figures/l2fc_fig1/l2fc_fig.pdf}{Fig. 2}). At any given time soils harbor microorganisms at varying degrees of dormancy depending on nutrient availability \cite{Jones_2010}. The sudden addition of our complex C mixture would most certainly prompt dormant and non-dormant microbes back into metabolic activity, with those exhibiting higher rRNA operon copy numbers responding the fastest. The responders identified at day 1 for xylose utilization have all been noted for exhibiting some form of dormancy strategy \cite{Jones_2010, Mulyukin_2009, Darcy_2011, Sachidanandham_2008, Finkel_2006, Rittershaus_2013, Tada_2013, Lay_2013} as well as 6-14 rRNA operon copies with the exception of the Betaproteobacteria Comamonadaceae and the Actinobacterial OTUs which exhibit 1-2 copies according to representative taxa in the rrnDB v. 3.1.227 \cite{18948294,11125085}.  

Between both the xylose and cellulose treatments there were 6 shared responders of all responders (n = 72); Stenotrophomonas, Planctomyces, Rhizobiaceae, Comamonadaceae, Cellvibrio. Of these, Stenotrophomonas and Comamonadaceae are the only taxa that are among the top ten responders in both treatments. On the other hand, the only shared responder that is not among the top ten responders for either the cellulose or xylose treatment is Rhizobiaceae. Two of the shared responders corresponded in time between the two treatments (supplemental table); Cellvibrio (day 3) and Planctomyces (day 14).   \textit{Responder Characteristics}. Overall, we found xylose responders were from higher rank abundances than cellulose responders, however, cellulose responders exhibited a greater change in buoyant density (i.e. assimilated more \textsuperscript{13}C) than xylose responders in response to isotope incorporation (\href{https://authorea.com/users/3537/articles/3612/master/file/figures/shift_and_rabund2/shift_and_rabund2.png}{Fig. 3}).  The kernel density estimate (KDE) of buoyant density shifts resulting from \textsuperscript{13}C-assimilation reveal that cellulose responders exhibit a significantly (wilcox rank sum; p\textless...) 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 the center of mass is measured for the density profile of a responder in the control and respective experimental treatment for a single time point. A density shift is then calculated by differentially calculating the center of mass for the control from the experimental. Finally, this is repeated for all responders at each time point for both the \textsuperscript{13}C-cellulose and \textsuperscript{13}C-xylose treatments. Each KDE curve represents the collection of density shifts calculated for all responders at each time point within a treatment (Figure 3A). The ‘difference in center of mass’ is a function of both the density shift for individual DNA molecules and the heterogeneity of labeling for the population of cells within that OTU. As such, we would not expect to observe the maximum density shift (0.04gmL\textsuperscript{-1}) measured in pure cultures with 100\% \textsuperscript{13}C-labeling of DNA (cite). We observe xylose utilizers having a smaller density shift (\textless0.02 gmL\textsuperscript{-1}) than cellulose utilizers (0.005-0.03 gmL\textsuperscript{-1}), with few exceptions. This suggests greater substrate specificity among cellulose degraders than xylose degraders. Partial \textsuperscript{13}C-labeling (\textless 0.04gmL\textsuperscript{-1} density shift) could be a result of various trophic strategies 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 rarer taxa in the tail of the RA curve (Fig 3B). This demonstrates that many taxa important to C-cycling are present in the rarer fraction of the overall microbial community and may be difficult or unable to detect in bulk community sequencing efforts. The shift in cellulose responders is more readily observable in the bulk community abundances than discerned with xylose responders (Fig Sx and Sy). This is likely due to the initial low abundance of these phyla, where changes in bulk community abundance are more pronounced and easier to detect. Comparatively, phyla of consistently high abundance (as with xylose responders) mask response changes unless they present changes of grand proportions. For example, the increase in Bacteroidetes in the xylose treatment at day 3 is not captured by the bulk community abundances. In another instance, the increased response from Proteo- and Actinobacterial OTUs at day 7 is also observed in the bulk community analysis as a marginal increase, yet it would be difficult to differentiate that change from natural variation or methodological noise.