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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 to
soil 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 number
was 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