Chuck begin ecol strategy re-write  about 9 years ago

Commit id: d19f8490756abfc3730b7997e18704a2af9d9e4e

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\subsection{Ecological strategies of soil microorganisms participating in the  decomposition of organic matter}  We assessed the ecology of $^{13}$C-responsive OTUs by estimating each OTU's  \textit{rrn} gene copy number and the BD shift upon labeling. \textit{rrn} gene  copy number is positively correlated with growth rate and BD shift is  indicative of substrate specificity. 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.  $^{13}$C-cellulose responsive OTUs grow slower (Figure~XX), have greater  substrate specificity (Figure~XX), and are generally lower abundance than  $^{13}$C-xylose responsive OTUs (Figure~XX). There are only faint ecological  differences between $^{13}$C-cellulose responsive OTUs but the combination of  \textit{rrn} gene copy number, BD shift, abundance rank and relative abundance  change over time does appears to be consistent with phylum membership  (Figure~XX). $^{13}$C-xylose responsive OTU growth rate was negatively  correlated with the time at which the OTU was first found to incorporate  $^{13}$C into DNA (Figure~XX).   Ecological metrics suggest cellulose degraders are substrate specialists that  grow slow and are in low bulk abundance. Labile C responder ecology is more  varied perhaps because some $^{13}$C labeled microorganisms did not primarily  assimilate xylose but became labeled via predatory interactions 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 trophic interactions or functional groups tuned to different substrate  concentrations. Each temporally defined response group appeared to be  phylogenetically clustered suggesting a uniform ecological strategy, however  (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). Predatory interactions could impact soil  C storage and turnover. Our results suggest that are large group of soil  microorganisms may be predators that consume fast-growing opportunistic  spore-formers that are primary labile C utilizers.  % Fakesubsubsection:Ecological strategies of soil microorganisms  We quantified the \textit{rrn} gene copy number, relative abundance changes  with time in the bulk community and substrate specificity for the