Chuck discussion edits  about 9 years ago

Commit id: f419f564f37237fb7879b7abe4ad74028403f9c1

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\section{Discussion}  % Fakesubsubsection:Early soil microbial ecology was informed Fakesubsubsection:Pure culture based studies drove early  Pure culture based studies drove early soil microbial ecology. Historically  important ecology research.  Important  pure cultures from soil historically  included nine genera \textit{Agrobacterium}, \textit{Alcaligenes}, \textit{Arthrobacter}, \textit{Bacillus}, \textit{Flavobacterium}, \textit{Micromonospora}, \textit{Nocardia}, \textit{Pseudomonas}, and \textit{Streptomyces} (\citep{Alexander1977} and reviewed by \citet{Janssen2006}) but culture-independent surveys of soil microbial diversity revealed soil can harbor 5,000 OTUs per half gram \citep{Schloss2006}. We recovered almost 6,000 OTUs in this study. Although culturing techniques can produce isolates from diverse soil lineages \citep{Janssen2002}, numerically dominant soil microorganisms are still uncultured and we know little of their ecophysiology \citep{Janssen2006}. In contrast DNA-SIP can characterize functional roles for thousands of phylotypes in a single experiment. We found 114 OTUs in an agricultural soil that can incorporate C from xylose and/or cellulose into biomass. We also used DNA-SIP to assay substrate specificity  and temporal dynamics of C-cycling or soluble and polymeric C degraders.  Included in the $^{13}$C-xylose and $^{13}$C-cellulose responsive OTUs were members of numerically dominant yet functionally uncharacterized soil phylogenetic groups such as \textit{Verrucomicrobia}, \textit{Planctomycetes} and \textit{Chloroflexi}.We also used DNA-SIP to assay substrate specificity and  temporal dynamics of C-cycling or soluble and polymeric C degraders.  \subsection{Microbial response to isotopic labels}  % Fakesubsubsection: We propose that microbial decomposition  We propose that organic matter in C added to  soil follows microcosms in this experiment followed  the following path through the microbial food web  (Figure~\ref{fig:foodweb}): Labile First, labile  C such as xylose is was  assimilated by fast-growing opportunistic \textit{Firmicutes} spore formers. The remaining labile C and new biomass C is was  assimilated in succession by slower growing \textit{Bacteroidetes}, \textit{Actinobacteria} and \textit{Proteobacteria} phylotypes that are were  either tuned to lower C substrate concentrations, are were  predatory bacteria (e.g. \textit{Agromyces}), and/or are were  specialized for consuming viral lysate.Polymeric  C enters from polymeric substrates entered  the bacterial community after several weeks. 14 days.  Canonical cellulose degrading bacteria such as \textit{Cellvibrio} are major degraded  cellulose degraders but uncharacterized lineages in the \textit{Chloroflexi}, \textit{Planctomycetes} and \textit{Verrucomicrobia}, specifically the \textit{Spartobacteria}, are were also  significant contributors tosoil  cellulose decomposition as well. decomposition.  \subsection{Ecological strategies of soil microorganisms participating in the  decomposition of organic matter} 

We assessed the ecology of $^{13}$C-responsive OTUs by estimating the  \textit{rrn} gene copy number and the BD shift upon labeling for each OTU.  \textit{rrn} gene copy number correlates positively with growth rate  \citep{11125085} and BD shift is indicative of substrate specificity. specificity (see  results).  We also observed how $^{13}$C-substrate responsive OTUs changed in relative abundance with time in the microcosms and the abundance rank of $^{13}$C-substrate responsive OTUs in the bulk DNA. Ecological metrics show  $^{13}$C-cellulose responsive OTUs grow slower (Figure~\ref{fig:copy}), have greater substrate specificity (Figure~\ref{fig:shift}), and are generally lower abundance than $^{13}$C-xylose responsive OTUs (Figure~\ref{fig:shift}). There are only faint ecological differences within the $^{13}$C-cellulose responsive OTUs but the combination of \textit{rrn} gene copy number, BD shift, abundance rank and relative abundance change over time is consistent with phylum membership (Figure~RADVIZ). $^{13}$C-xylose responsive OTU \textit{rrn} gene copy numberwas negatively  correlated inversely  with the time at which the OTU was first found to incorporate $^{13}$C into DNA (Figure~\ref{fig:copy}) suggesting that fast-growing microbes assimilated $^{13}$C from xylose before slower growing types. slow growers.  % Fakesubsubsection:Ecological metrics suggest  Ecological metrics suggest cellulose degraders are substrate specialists that  grow slow and are in low bulk abundance. Labile C responder ecology is ecological  strategies were  more varied perhaps because some $^{13}$C labeled microorganisms did not primarily assimilate xylose but became labeled via predatory interactions and/or are saprophytes. $^{13}$C-xylose responsive OTUs are generalists, grow faster and are more abundant when compared to $^{13}$C-cellulose responders. $^{13}$C-xylose responders vary in growth rate and while generally lower abundance than $^{13}$C-cellulose responders can also be low abundance microorganisms. It's not clear whether the observed activity succession from \textit{Firmicutes} to \textit{Bacteroidetes} and finally \textit{Actinobacteria} in response to $^{13}$C-xylose addition marks a trophic  cascade or functional groups tuned to different resource concentrations or  both. Notably, each temporally defined response group clustered  phylogenetically suggesting a uniform ecological strategy (Figure~XX). It's also clear that some of the non-\textit{Firmicutes} $^{13}$C-xylose responders are closely related to known predators (\textit{Agromyces}) and many marine predatory bacteria are members of the \textit{Bacteroidetes} (CITE). If the temporal dynamics of $^{13}$C-xylose incorporation are due to trophic interactions, our results suggest that there many predatory soil bacteria that consume fast-growing, opportunistic, primary labile C assimilating, gram-positive spore-formers. Hence, trophic interactions among soil bacteria may be of importance in soil C turnover models. % Fakesubsubsection:C substrate specificity  ARE OUR RESULTS CONSISTENT WITH SUBSTRATE SPECIFICITY STUDIES? C substrate