deletions | additions
diff --git a/Discussion.tex b/Discussion.tex
index fa5ce2f..356af41 100644
--- a/Discussion.tex
+++ b/Discussion.tex
...
important pure cultures from soil included nine genera \textit{Agrobacterium},
\textit{Alcaligenes}, \textit{Arthrobacter}, \textit{Bacillus},
\textit{Flavobacterium}, \textit{Micromonospora}, \textit{Nocardia},
\textit{Pseudomonas}, and \textit{Streptomyces}
(CITE Anderson, (\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
104 114 OTUs in an agricultural soil that can
incorporate C from xylose
or and/or cellulose into biomass. 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
show used DNA-SIP to assay substrate specificity and
temporal dynamics of
C-cycling. 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 soil follows the following path
(Figure~XX): (Figure~\ref{fig:foodweb}): Labile C such as xylose is assimilated by
fast-growing opportunistic \textit{Firmicutes} spore formers. The remaining
labile C and new biomass C is assimilated in succession by slower growing
\textit{Bacteroidetes}, \textit{Actinobacteria} and \textit{Proteobacteria}
phylotypes that are either tuned to lower C substrate concentrations, are
predatory bacteria (e.g. \textit{Agromyces}), and/or are specialized for
consuming viral lysate. Polymeric C enters the bacterial community after
several weeks. Canonical cellulose degrading bacteria such as
\textit{Cellvibrio} are major cellulose degraders but uncharacterized lineages
in the \textit{Chloroflexi}, \textit{Planctomycetes} and
\textit{Verrucomicrobia}, specifically the \textit{Spartobacteria}, are
...
% Fakesubsubsection:We assessed
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
CITE \citep{11125085} and BD shift is indicative of substrate
specificity CITE. 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. Ecological metrics show
$^{13}$C-cellulose responsive OTUs grow slower
(Figure~XX), (Figure~\ref{fig:copy}),
have greater substrate specificity
(Figure~XX), (Figure~\ref{fig:shift}), and are
generally lower abundance than $^{13}$C-xylose responsive OTUs
(Figure~XX). (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~XX). (Figure~RADVIZ). $^{13}$C-xylose responsive
OTU \textit{rrn} gene copy number was negatively correlated with the time at
which the OTU was first found to incorporate $^{13}$C into DNA
(Figure~XX) (Figure~\ref{fig:copy}) suggesting that fast-growing microbes assimilated
$^{13}$C from xylose before slower growing types.
% Fakesubsubsection:Ecological metrics suggest
Ecological metrics suggest cellulose degraders are substrate specialists that
