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

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\section{Results and Discussion}  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 all amended with a C substrate mixture--the substrate mixture was identical for each bottle except in one series of bottles the cellulose was $^{13}$C-labeled in another the xylose was $^{13}$C-labeld and in the last no sustrattes were labeled--were incubated for 30 days. The C substrate mixture was designed to approximate freshly degrading plant biomass and xylose biomass. Xylose  or cellulosewere chosen  to carry carried  the isotopic labeled to label so we could  examinedynamics of  C assimilation dynamics  for labile, soluble C and versus  insoluble, polymeric C. 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, microcosm  representing 18\% of the total C present in the soils. soil C.  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{$^{13}$C from cellulose assimilated by canonical cellulose-degrading and uncharacterized microbial lineages in many phyla including \textit{Chloroflexi} and \textit{Verrucomicrobia}}  Only 2 and 5 OTUs were found to have incorporated $^{13}$C from labeled cellulose at days 3 and 7, respectively. At days 14 and 30, however, 42 and 39 OTUs were found to incorporate $^{13}$C from cellulose into biomass. An average 16\% of the $^{13}$C-cellulose added was respired within the first 7 days, 38\% by day 14, and 60\% by day 30. A \textit{Cellvibrio} and \textit{Sandaracinaceae} OTU assimilated $^{13}$C from cellulose at day 3. Day 7 responders included the same \textit{Cellvirio} responder at day 3, a \texit{Verrucomicrobia} OTU and three \textit{Chloroflexi} OTUs. 50\% of Day 14 responders belong to Proteobacteria (66\% Alpha-, 19\% Gamma-, and 14\% Beta-) followed by 17\% \textit{Planctomycetes}, 14\% \textit{Verrucomicrobia}, 10\% \textit{Chloroflexi}, 7\% \textit{Actinobacteria} and 2\% \textit{Cyanobacteria}. \textit{Bacteroidetes} OTUs begin to incoporate $^{13}$C from cellulose at dat 30 (13\% of day 30 responders). Other day 30 responding phyla include \textit{Proteobacteria} (30\% of day 30 responders; 42\% Alpha-, 42\% Delta, 8\% Gamma-, and 8\% Beta-), \textit{Planctomycetes} (20\%), \textit{Verrucomicrobia} (20\%), \textit{Chloroflexi} (13\%) and \textit{Cyanobacteria} (3\%). \textit{Proteobacteria}, \textit{Verrucomicrobia}, and \textit{Chloroflexi} had relatively high numbers of responders with heavy response across multiple time points (ref l2fc figure).