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

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\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}).  \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. The remaining x\% At the end of the 30 day experiment 30\%  of the original  \textsuperscript{13}C from xylose remained insoil over the 30 days of  the experiment. soil.  The \textsuperscript{13}C from xylose has likely been stabilized by assimilation into microbial biomass and/or microbial conversion into other forms of organic matter, though it is possible that some \textsuperscript{13}C-xylose remains unavailable to microbes due to abiotic interactions in soil (cite ref that shows mineral or SOm stabilization of labile SOM - ask Thea for a good ref here)/. 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}. Day 3 presents a decrease in Firmicutes responders (from 12 OTUs to 1) and an increase in Bacteroidetes (from 4 to 8) from day 1, as well as, the onset of Verrucomicrobia reponders. With the exception of the single Firmicutes (Paenibacillaceae), responders on day 3 possess 3-6 rRNA operon copies, less than responders on day 1. A substantial amount (75\%) of xylose responders for day 7 had not previously been identified as responders at earlier time points which attests to the wider number of taxa able to use xylose. Each of the 10 Actinobacteria responders, the most dominant response group (50\%) at day 7, belonged to a different family making it the phylum with the most wide-spread use of xylose. However, it should be noted that they were confined within two Actinobacterial Orders; Frankiales and Micrococcales. A Paenibacillus (100\% identity) was the only OTU to be identified at every time point (up to day 30) as a xylose responder. This result suggests that large numbers of cells from OTUXXXX sporulated after \textsuperscript{13}C-labeling of their DNA and that these spores remained throughout the experiment. It was the the second most enriched xylose responder, log2fold change (l2fc) of 3.5, measured in the time series second only to a Gammaproteobacteria (Xanthomonadaceae; l2fc = 3.7).