Chuck Pepe-Ranney edited Results_and_Discussion.tex  over 9 years ago

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In this study, we couple nucleic acid SIP with next generation sequencing (SIP-NGS) to observe C use dynamics by the soil microbial community. A series of parallel soil microcosms amended with an identical C substrate mixture, in which the only difference is the identity of the $^{13}$C-labeled substrate, were incubated for 30 days. The C substrate mixture was designed to approximate freshly degrading plant biomass and either xylose or cellulose were isotopically labeled to examine the dynamics of C assimilation for labile, soluble C and insoluble, polymeric C. A 5.3 mg total mass of C substrate mixture per gram soil (including 0.42 mg xylose-C and 0.88 mg cellulose-C g soil$^{-1}$) was added to each microcosm, representing 18\% of the total C present in the soils. Microcosms were harvested at several time points during the incubation period and $^{13}$C assimilation by the microbial community was observed by sequencing 16S rRNA gene amplicons from bulk soil DNA and CsCl gradient fractions (\href{https://www.authorea.com/users/3537/articles/8459/master/file/figures/20140708_ConceptualFig2/20140708_ConceptualFig2.pdf}{Fig. S1}). Xylose degradation was observed immediately, while cellulose degradation was observed after two weeks.  \subsection{Xylose C is assimilated before cellulose C and by different microbial community members in soil microcosms}  Ordination of CsCl gradient fractions by fraction  16S rRNA gene OTU profiles demonstrates four characteristics of this DNA-SIP experiment: 1) Bouyant density accounts for significant variance in gradient fraction microbial membership/structure, OTU profiles  2) $^{13}$C assimilation into community DNA causes heavy  fractions from labeled and control gradients to diverge at the heavy end of the CsCl gradient, diverge,  3) $^{13}$C from cellulose was assimilated after $^{13}$C from xylose, and, 4) phylogenetically different  microbes that assimilate $^{13}$C from celluloseare generally different phylogenetic types  thanthose that assimilate  $^{13}$C from xylose. Buoyant density represents XX\% of variance in gradient fraction membership in control gradient fractions (Adonis test with weighted Unifrac distances, p-value X.XX).The categorical grouping of heavy (greater than X.XX g/mL) fractions by $^{13}$C label represents  XX\% of fraction membership heavy fraction OTU profile  variance is explained by gradient type ($^{13}$C-labeled or control)  (Adonis test with weighted Unifrac distancs, p-value X.XX). Different microbial community members are responsible for the consumption of xylose versus cellulose; xylose is consumed quickly, whereas, cellulose decomposition takes longer. A pattern of microbial community transition accompanies 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 have been observed \cite{Hu_1997} to take longer to respond with less than 42\% of cellulose metabolized over the first 5 days of incubation.