Ashley Campbell edited Results_and_Discussion.tex  over 9 years ago

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\textbf{Patterns of carbon use vary dramatically within phylum.} Dynamic patterns of \textsuperscript{13}C-assimilation from xylose and cellulose occur at discrete, fine-scale taxonomic units (\href{https://authorea.com/users/3537/articles/3612/master/file/figures/bacteria_tree/bacteria_tree.png}{Fig. 4}). Responders for xylose and cellulose are widespread across 6 and 7 phyla, respectively (\href{https://authorea.com/users/3537/articles/3612/master/file/figures/bacteria_tree/bacteria_tree.png}{Fig. 4}). There are 5 phyla containing responders for both treatments; of all the responder OTUS detected within those phyla for either xylose or cellulose, there are only six OTUs that respond to both xylose and cellulose (discussed previously). This result suggests that phyla do not represent coherent ecological units with respect to the soil C-cycle, that is, taxa within phyla exhibit differences in substrate use, level of substrate specialization, and dynamics of incorporation.   In this study, we have identified Actinobacteria responders for both substrateswith a peak shift of ~0.036 g mL\textsuperscript{-1} for cellulose and ~x g mL\textsuperscript{-1} for xylose, suggesting a strong substrate specificity  (\href{https://authorea.com/users/3537/articles/8459/master/file/figures/xylose_resp_profiles/xylose_resp_profiles.png}{Figs. S5} \href{https://authorea.com/users/3537/articles/8459/master/file/figures/cellulose_resp_profiles/cellulose_resp_profiles.png}{, S6}). Although there were no shared Actinobacteria OTUs that responded to both xylose (Microbacteriaceae, Micrococcaceae, Cellulomonadaceae, Nakamurellaceae, Promicromonosporaceae, and Geodermatophilaceae) and cellulose (Streptomycetaceae and Pseudonocardiaceae). This information may suggest that while Actinobacteria exhibit an ability to utilize an array of carbon substrates, substrate use may be more clade specific and not widespread throughout the phylum (\href{https://authorea.com/users/3537/articles/3612/master/file/figures/bacteria_tree/bacteria_tree.png}{Fig. 4}). Similarly, Bacteroidetes responders were identified for both substrates, yet, at a finer taxonomic resolution there is a clear differential response for xylose (Flavobacteriaceae and Chitinophagaceae) and cellulose (Cytophagaceae). Whole phylum responses were not detected for xylose or cellulose yet utilization of these substrates spanned many phylogenetically diverse groups. Within each phylum we observed substrate utilization at the clade or single taxa level with each exhibiting a unique pattern of \textsuperscript{13}C-assimilation over time (\href{https://authorea.com/users/3537/articles/3612/master/file/figures/bacteria_tree/bacteria_tree.png}{Fig. 4, heatmap}). It has previously been suggested that all taxa within a phylum are unlikely to share ecological characteristics \cite{Fierer_2007}, and furthermore, within a species population \cite{Choudoir_2012,Preheim_2011,Hunt_2008}. Habitat traits of coastal Vibrio isolates were mapped onto microbial phylogeny revealing discrete ecological populations based on seasonal occurrence and particulate size fractionation \cite{Preheim_2011,Hunt_2008}. Yet, it has been proposed that the microbial community functionality responsible for soil C cycling appear at the level of phlya rather than species/genera \cite{Schimel_2012}. The traditional phylum level assignment conventions could in part be due to limitations in finer scale taxonomic identifications or methodological limitations (ie sequencing depth), but our data in concert with others \cite{Goldfarb_2011,Fierer_2007,Choudoir_2012,Preheim_2011,Hunt_2008} would suggest that portraying the response of a few OTUs or clades as a phylum level response would be overreaching and serves as a strong argument towards moving away from assigning substrate utilization to phylum level responses.