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\section{Discussion}
% Fakesubsubsection:
We highlight to key results
We highlight two key results with implications for understanding structure-function
relationships in soils, and for applying DNA-SIP in future studies of the soil-C
cycle. First, cellulose responders were members of physiologically undescribed
...
comprehensively describe which microorganisms consume $^{13}$C-labeled
substrates in nucleic acid SIP incubations.
% Fakesubsubsection:
Microorganisms that consumed
Microorganisms that consumed $^{13}$C-cellulose were not closely related to any
physiologically characterized cultured isolates but were members of
cosmopolitan phylogenetic groups in soil including \textit{Spartobacteria},
...
plant biomass cellulose. These structural differences might select for different
decomposers and caution should be taken when extrapolating our results.
% Fakesubsubsection:
In addition to taxonomic identity, we quantified
In addition to taxonomic identity, we quantified several ecological
properties of microorganisms that were actively engaged in labile and
structural C decomposition in an agricultural soil over time. Labile C was consumed
...
to changes in community composition CITE (see SI note 2 for further discussion
with respect to soil-C modelling).
% Fakesubsubsection:
We propose that the temporal fluctuations
We propose that the temporal fluctuations in $^{13}$C-labeling in the
$^{13}$C-xylose treatment are due to trophic exchange of $^{13}$C.
Alternatively, the temporal dynamics could be caused by microorganisms tuned to
different substrate concentrations and/or cross-feeding. Only trophic exchange,
however, can account for the precipitous drop in abundance of
\textit{Paenibacillus} with subsequent $^{13}$C-labeling of
\textit{Bacteroidetes} at day 3 followed by Micrococcales at day 7.
Furthermore, \textit{Bacteroidetes} types have been shown to become $^{13}$C
labeled after the addition of live $^{13}$C-labeled \textit{Escherichia coli}
to soil CITE and a member of the \textit{Micrococcales}, \textit{Agromyces
ramosus} (with which one of the $^{13}$C-xylose responders shared 100\% SSU
rRNA gene sequence identity), is a known predator that preys on many
microorganisms including yeast and \textit{Micrococcus luteus} CITE.
\textit{Agromyces} are abundant microorganisms in many soils and the most
abundant xylose responder in our experiment -- the fourth most abundant OTU in
our pooled dataset -- shares 100\% SSU rRNA gene sequence identity to
\textit{Agromyces
ramosus}. ramosus} (see SI note 3 for further discussion of trophic C
exchange). Climate change is expected to enhance the availability of labile C
in soil and soil predators may mitigate the response of microorganisms to
increased labile C CITE though the extent of bacterial predatory activity in
soil is unknown. Elucidating the identities of bacterial predator in soil will
assist in assessing the implications of climate change on global soil-C
storage.
\subsection{Implications for soil C cycling models}
% Fakesubsubsection: Models of soil
Functional niche characterization for soil microorganisms is necessary to
predict whether and how biogeochemical processes vary with microbial community
composition. Functional niches are defined by soil microbiologists and have
been successfully incorporated into biogeochemical process models (E.g.
\citep{wieder_2014a,Kaiser2014a}). In some C models ecological strategies such
as growth rate and substrate specificity are parameters for functional niche
behavior \citep{Kaiser2014a}. The phylogenetic breadth of a functionally
defined group is often inferred from the distribution of diagnostic genes
across genomes \citep{Berlemont2013} or from the physiology of isolates
cultured on laboratory media \citep{Martiny2013}. For instance, the wide
distribution of the glycolysis operon in microbial genomes is interpreted
as evidence that many soil microorganisms participate in glucose turnover
\citep{McGuire2010}. However, the functional niche may depend less on the
distribution of diagnostic genes across genomes and more on life history
traits that allow organisms to compete for a given substrate as it occurs
in the soil. For instance, fast growth and rapid resuscitation allow
microorganisms to compete for labile C which may often be transient in
soil. Hence, life history traits may constrain the diversity of microorganisms
that metabolize a given C source in the soil under a given set of
conditions.
% Fakesubsubsection: Biogeochemical processes
Biogeochemical processes mediated by a broad array of taxa are assumed
insensitive to community change relative to
processes mediated by a narrow suite of microorganisms
\citep{Schimel_1995,McGuire2010}. In addition, the diversity of
a functionally defined group engaged in a specific C transformation is
expected to correlate positively with C lability \citep{McGuire2010}.
However, the diversity of labile C and structural C decomposers in soil
has not been quantified directly. We found comparable numbers of OTUs
responded to $^{13}$C-cellulose and $^{13}$C-xylose (63 and~49,
respectively). Cellulose responders were phylogenetically clustered
suggesting that the ability to degrade cellulose is phylogenetically
conserved. The clade depth of cellulose responders, 0.028 SSU rRNA gene
sequence dissimilarity, is on the same order as that observed for
glycoside hydrolases which are diagnostic enzymes for cellulose
degradation \citep{Berlemont2013}. Xylose responders clustered in terminal
branches indicating groups of closely related taxa metabolized xylose but
xylose responders also clustered phylogenetically with respect to time of
response (Figure~\ref{fig:tiledtree}, Figure~\ref{fig:xyl_count}).
For example, xylose responders on day~1 are dominated by members of
\textit{Paenibacillus}. Thus, microorganisms that degraded labile C and
structural C were both limited in diversity. Although the genes for xylose
metabolism are likely widespread in the soil community, it's possible only
a limited diversity of organisms had the ecological characteristics
required to degrade xylose under experimental conditions. Therefore it's
possible that only a limited number of taxa actually participate in the
metabolism of labile C-sources under a given set of conditions, and hence
changes in community composition may alter the dynamics of structural
\textit{and} labile C-transformations in soil.
% Fakesubsubsection: Broadly, we observed
Broadly, we observed labile C use by fast growing generalists and structural
C use by slow growing specialists. These results agree with the MIMICS model
which simulates leaf litter decomposition by modeling microbial decomposers
as two functionally defined groups, copiotrophs or oligotrophs
\citep{wieder_2014a}. Including these functional types improved predictions
of C storage in response to environmental change. We identified
microbial lineages engaged in labile and structural C decomposition that
can be defined as copiotrophs or oligotrophs, respectively. We highlight two
additional considerations for soil-C process models based on our results.
First, soil-C may travel through multiple trophic levels within the bacterial
community where each C transfer represents an opportunity for C stabilization
in association with soil minerals or C loss by respiration. And second,
although labile C consumption is generally considered to be a broad process in
terms of microbial participants, we observed that only a small number of
related OTUs conclusively consumed xylose-C (see SI for additional discussion) and
that fast growth, as opposed the ability to use xylose, may constrain the diversity
of microorganisms that process labile-C \textit{in situ} which may often be
pulse delivered and transient. The diversity of microbial participants in a
biogeochemical process is thought to determine how robust process rates are to
changes in community composition. Our understanding of soil C dynamics will
likely improve as we develop a more granular understanding of the ecological
diversity of microorganisms that mediate C transformations in soil.
\subsection{Conclusion}
% Fakesubsubsection: Microorganisms sequester atmospheric C