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

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\textit{Cellulose}. In contrast with xylose responders, there were only three \textsuperscript{13}C-cellulose responders detected within the first 7 days of incubation and 46 for days 14 and 30. An average of 16\% of the \textsuperscript{13}C-cellulose added was respired within the first 7 days, 38\% by day 14, and 60\% by day 30. The earliest responders detected for \textsuperscript{13}C-cellulose assimilation were a canonical cellulose degrader, Cellvibrio, in Proteobacteria and a novel clade in Chloroflexi (\href{https://www.authorea.com/users/3537/articles/3612/master/file/figures/l2fc_fig1/l2fc_fig.pdf}{Fig. 2}, \href{https://authorea.com/users/3537/articles/8459/master/file/figures/l2fc_fig_pVal/l2fc_fig_pVal.png}{Fig. S4}). At day 14, 54\% of the responders belong to Proteobacteria (65\% Alpha-, 23\% Gamma-, and 12\% Beta-), 13\% Chloroflexi, 13\% Planctomycetes, 10\% Verrucomicrobia, and 6\% Actinobacteria.  All cellulose responders for day 30 (n = 15) had been identified as responders at earlier time points in this study except two; a Deltaproteobacteria (Sandaracinaceae family) and a Bacteroidetes (Cytophagaceae family). While there are known cellulose degraders in the Bacteroidetes Cytophagaceae family, there are currently no known cellulose degraders in the Sandaracinaceae family although it's sister family Polyangiaceae has known cellulose degraders (\cite{Reichenbach_2006}, Bergey's ISBN:978-0-387-24145-6). Throughout the time series, responders with the greatest enrichment were Verrucomicrobia (Verrucomicrobiaceae), Chloroflexi, Cyanobacteria, Proteobacteria (Cellvibrio, Brevundimonas, Stenotrophomonas, Devosia), and Planctomycetes (Planctomycetaceae). (Planctomycetaceae) (\href{https://authorea.com/users/3537/articles/3612/master/file/figures/bacteria_tree/bacteria_tree.png}{Fig. 4}).  Verrucomicrobia, a phylum found to be ubiquitous and in high abundance in soil \cite{Zhang_2008, Bergmann_2011, Fierer_2013}, \cite{Fierer_2013},  have been noted for degradation of polysaccharides in soil, aquatic, and anoxic rice patty soils \cite{Fierer_2013,Herlemann_2013,10543821}. In this study, Verrucomicrobia comprise ~11\% of the total cellulose responder OTUs detected, detected (\href{https://www.authorea.com/users/3537/articles/3612/master/file/figures/l2fc_fig1/l2fc_fig.pdf}{Fig. 2}, \href{https://authorea.com/users/3537/articles/8459/master/file/figures/l2fc_fig_pVal/l2fc_fig_pVal.png}{Fig. S4}, \href{https://authorea.com/users/3537/articles/8459/master/file/figures/cellulose_resp_profiles/cellulose_resp_profiles.png}{Fig. S6})  most of which belong to the uncultured FukuN18 clade originally identified in freshwater lakes \cite{14602613, Glockner_2000, Parveen_2013}. Yet the largest enrichment measured (l2fc = 3.7) during the whole time series for \textsuperscript{13}C-cellulose assimilation was by an uncultured Verrucomicrobia in the Verrucomicrobiaceae family on day 14. 14 (\href{https://authorea.com/users/3537/articles/3612/master/file/figures/bacteria_tree/bacteria_tree.png}{Fig. 4}).  Chloroflexi, ubitiquous across many diverse environments, are traditionally known for their metabolically dynamic lifestyles ranging from anoxygenic phototropy to organohalide respiration \cite{Yamada_2009,14527284,Hug_2013,Seshadri_2005,Tang_2011,dworkin2006the}. Yet, only recently have we shifter focus towards the metabolic functions of Chloroflexi in C cycling \cite{Hug_2013,Goldfarb_2011,Cole_2013}. In this study, we identified a previously undescribed clade within the Chloroflexi class (closest relative at a 96\% identity being Herpetosiphon) that exhibited a high substrate specificity based on a density shift peak between 0.03-0.04 gmL\textsuperscript{-1}. gmL\textsuperscript{-1} (\href{https://authorea.com/users/3537/articles/8459/master/file/figures/cellulose_resp_profiles/cellulose_resp_profiles.png}{Fig. S6}).  We observed no other cellulose utilization in Chloroflexi outside of this clade although many members of this phylum have previously been demonstrated or implicated in cellulose utilization \cite{Goldfarb_2011,Cole_2013,Hug_2013}. One of the most interesting findings is a single Cyanobacterial responder OTU, which exhibit the third greatest enrichment measured (l2fc = 3.35). This OTU falls into the recently described candidate phylum Melainabacteria \cite{Di_Rienzi_2013}, although its phylogenetic position is debated \cite{Soo_2014}. More importantly, the catalog of metabolic capabilities associated with Cyanobacteria are quickly expanding \cite{Di_Rienzi_2013, Soo_2014}. Our findings provide evidence of cellulose degradation for Melainabacteria, supporting hypothesized polysaccharide degradation suggested by genomic analysis \cite{Di_Rienzi_2013}.