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\subsection{Soil microcosm microbial community changes with time}
% Fakesubsubsection:Changes in the soil microcosm microbial community structure
Bulk soil DNA sequencing revealed changes in the soil microcosm microbial community structure and membership
correlated was significantly
correlated with incubation time (Figure~\ref{fig:bulk_ord}B, p-value 0.23,
R$^{2}$ 0.63, Adonis test \citet{Anderson2001a}).
The identity of the Substituting $^{13}$C-labeled
substrate added to substrates in the
microcosms amendments did not significantly correlate with
the overall soil microcosm
community structure and membership (p-value 0.35). Additionally,
microcosm bulk sample
beta diversity was significantly less than gradient fraction beta diversity
(p-value 0.003, \citet{Anderson2006}). Twenty-nine OTUs significantly changed
in relative abundance with time ("BH" adjusted p-value $<$ 0.10,
\citet{YBenjamini1995})
(Figure~\ref{fig:time}). \citet{YBenjamini1995}). OTUs that significantly increased in relative
abundance with time included OTUs in the \textit{Verrucomicrobia},
\textit{Proteobacteria}, \textit{Planctomycetes}, \textit{Cyanobacteria},
\textit{Chloroflexi} and \textit{Acidobacteria}. OTUs that significantly
decreased in relative abundance with time included OTUs in the
\textit{Proteobacteria}, \textit{Firmicutes}, \textit{Bacteroidetes} and
\textit{Actinobacteria}
(Figure~\ref{fig:time}). (Figure~XX). \textit{Proteobacteria} was the only
phylum that had OTUs
which increased that significantly
increased and OTUs that
decreased significantly
decreased in abundance with time. If sequences were grouped by taxonomic
annotations at the class level, only four classes significantly changed in
abundance, \textit{Bacilli} (decreased), \textit{Flavobacteria} (decreased),
\textit{Gammaproteobacteria} (decreased) and \textit{Herpetosiphonales}
(increased)
(Figure~\ref{fig:time_class}). (Figure~XX). Of the 29 OTUs that changed significantly in relative
abundance with time, 14 are labeled substrate responders
(Figure~\ref{fig:time}). (Figure~XX).
\subsection{OTUs that assimilated $^{13}$C from xylose}
% Fakesubsubsection:Isotope incorporation by an OTU is revealed by
...
$^{13}$C-cellulose responders is in the \textit{Streptomyces}, a genus known to
possess cellulose degraders, while the other two share high sequence identity
to cultured isolates \textit{Allokutzneriz albata} \citep{Labeda_2008,
Tomita_1993} and \textit{Lentzea waywayandensis}
\citep{LABEDA_1989,Labeda_2001}; \citep{LABEDA_1989,
Labeda_2001}; neither isolate decomposes cellulose in culture. Nine
\textit{Planctomycetes} OTUs responded to $^{13}$C-cellulose but none are within
described genera (closest cultured isolate match 91\% sequence identity,
Table~\ref{tab:cell}) (Figure~\ref{fig:trees}). Interestingly, one