Ashley Campbell edited Results.tex  about 9 years ago

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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 thatdecreased  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