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

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Our study is consistent with carbon degradative succession that has previously been demonstrated \cite{Bastian_2009} (more refs). We demonstrate a rapid decrease in the labile carbon, xylose, confirmed by its \textsuperscript{13}C label incorporation into the microbial community DNA during the first 7 days of the experiment, after which, the label is not detectable in the DNA. Subsequently our data demonstrates a slow degradation of the more recalcitrant, polymeric carbon demonstrated by \textsuperscript{13}C-cellulose label incorporation into the microbial community DNA at 14 and 30 days. We did not observe the \textsuperscript{13}C-cellulose signal leave the DNA within the time limits, 30 days, of our experiment. This degradative succession is also confirmed by isotopic analysis of the soil from the microcosms (Table S1).   We did not observe consistent C utilization at the phylum level although both xylose and cellulose utilization were observed across 7 phyla each revealing a high diversity of bacteria able to utilize these substrates. The high taxonomic diversity may enable substrate metabolism under a broad range of environmental conditions \cite{Goldfarb_2011}. Other studies of microbial communities have observed a positive correlation with taxonomic or phylogenetic diversity and functional diversity \cite{Fierer_2012,Fierer_2013,Philippot_2010,Tringe_2005,Gilbert_2010,Bryant_2012}. The data presented here supports that specific functional attributes can be shared among diverse, yet distinct, taxa while closely related taxa may have very different physiologies \cite{Fierer_2012,Philippot_2010}. This information adds to the growing collection of data suggesting that community membership is important to biogeochemical processes. Furthermore, demonstrates a need to examine substrate utilization by discrete microbial taxa within a whole community context to better understand how specific community members function within the whole. The sensitivity of SIP-NGS provides a means to elucidate substrate utilization by discrete microbial taxa with the hope that we can begin to construct a belowground C food web.       Degradative succession refers to the temporal changes in species or functional guilds that occurs during the sequential degradation of constituents of a nutrient resource \cite{townsend2003essentials,Bastian_2009}. The decomposition of a nutrient source is hypothesized to promote succession of active community members as compounds are sequentially degraded \cite{Biddanda_1988}.   Analysis of the sequenced bulk community DNA demonstrates Proteobacteria (26-35\%), Actinobacteria (19-26\%), and Acidobacteria (12-21\%) as the most dominant phyla throughout the duration of the experiment. This is consistent with previous observations \cite{Goldfarb_2011,Fierer_2007,Rui_2009,Fierer_2012}. We found trends of Proteobacteria and Actinobacteria decreasing and Acidobacteria increasing as C availability declines (TableS1). This is congruent with findings in soils sampled from a wide range of ecosystems in the US \cite{Fierer_2007}. At days 1, 3, and 7 the bulk community was composed of $\sim$12-18\% Bacteriodetes and Firmicutes (combined). At days 14 and 30, these phyla declined to a combined 7-9\% of the whole community accompanied with an increase in Planctomycetes, Verrucomicrobia, and Chloroflexi (2-3\% at day 1 to 5-7\% at day 30). There has been conflicting evidence about the correlation of Bacteriodetes abundance with C availability \cite{Fierer_2007,Rui_2009,Sharp_2000,L_pez_Lozano_2013,Bastian_2009}. Our bulk data demonstrates a positive correlation between labile C availability and Bacteroidetes abundance. Additionally, the abundance of Planctomycetes, Verrucomicrobia, and Chloroflexi at later stages of decomposition are in accord with findings in wheat straw degradation \cite{Bastian_2009}. The rank abundance (RA) of the community depicts transitions we observe in high ranking phyla abundance beginning at day 7 (Fig S2A). Despite the fluctuations we observe at the phylum level, the biological variability observed over time is low (FigS2B) demonstrating community stability.  Furthermore, this demonstrates the sensitivity of this technique by being able to detect \textsuperscript{13}C-label incorporation in samples with low C additions (2.18mgC g\textsuperscript{-1} soil).   temporal changes in microbial community composition are consistent with C decomposition being accompanied by a microbial community succession. The dynamics of \textsuperscript{13}C-cellulose and \textsuperscript{13}C-xylose assimilation varied dramatically for different microorganisms.  For OTUs passing a conservative threshold of \textit{p}-value = <0.10 for log\textsubscript{2} fold change (FigSx), we measured the density shift in the experimental treatment compared to the control (Fig Sx). Those OTUs with a center of mass shift greater than zero were considered 'responders'.   As a result, microorganisms responsible for the synthesis of cellulases preferentially shuttle energy towards enzyme synthesis rather than biomass until cellulose hydrolysis begins (Schimel & Schaeffer 2012). This accounts for the delay in growth and ultimately the slow decomposition of cellulose (Perez et al 2002,Schimel & Schaeffer 2012).   Microbes that respire sugars have previousy been observed increasing in abundance dramatically during the initial decompostion stages \cite{GARRETT_1951,Alexander_1964}.