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\section{Discussion}
% Fakesubsubsection: We
demonstrate that establish ecological
We establish ecological characteristics of microorganisms participating in soil
C cycling using a nucleic acid SIP approach. We distributed SSU rRNA genes from
our experimental soil into 5,940 OTUs and observed assimilation of $^{13}$C
from either $^{13}$C-xylose or $^{13}$C-cellulose into DNA by 104 OTUs.
$^{13}$C label
was observed appeared to move into and then out of groups of related OTUs
over time. By coupling nucleic acid SIP to high throughput sequencing we
we
able to observe diagnosed OTU activity
across a wide range of natural abundances; For
instance,we observed $^{13}$C-incorporation into DNA for OTUs present at even low relative abundance
(as low as XX\%) in non-fractionated DNA
from the
experimental soil. (as
low as XX\%). Our results support the degradative succession hypothesis,
elucidate ecophysiological properties of soil microorganisms, reveal activity
of widespread uncultured soil bacteria, and
demonstrate a begin to piece together the
microbial food web in soils.
% Fakesubsubsection: The degradative succession hypothesis
The degradative succession hypothesis predicts an ecological transition in
activity from microbes that decompose labile plant biomass C to those that
decompose structural more recalcitrant C.
We observed rapid consumption of
$^{13}$C-xylose and soil microorganisms Microorganisms quickly assimilated
$^{13}$C-label $^{13}$C from
$^{13}$C-xylose xylose into DNA
during days~1, 3, and 7. relative to cellulose. Xylose is the major
monomer of xylan and xylan itself is a major constituent of hemicellulose.
Thus, xylose represents an abundant sugar present in
the early phases of fresh plant
biomass
degradation. litter. The
phylogenetic composition of
$^{13}$C labeled $^{13}$C-labeled OTUS in response to the
$^{13}$C-xylose amendment changed over time and the
total number of
$^{13}$C-labeled OTUs in response to $^{13}$C xylose
addition diminished responders almost entirely
diminished by the end of the incubation. In
contrast,
degradation of cellulose
decomposition proceeded slower.
Assimilation of $^{13}$C-label into DNA from
$^{13}$C-cellulose sharply increased from day~7 to day~14 and was maintained
through day~30. Finally,
the vast majority of xylose or cellulose responders
had unique activity for either cellulose or xylose as only 8 of 104 OTUs
were observed to metabolize both xylose and
cellulose. cellulose demonstrating
a succession in activity from xylose responders to cellulose responders. Our
results agree with the degradative succession hypothesis and highlight
additional ecological phenomena potentially associated with plant biomass
decomposition including several waves of activity in response to labile
C inputs.
% Fakesubsubsection: Correlations between community composition
Correlations between community composition and environmental characteristics
often reveal the ecology of microorganisms \citep{Fierer2007}. In this
experiment, we similarly define microbial ecology albeit through SIP as opposed
to spatio-temporal
variation. variation in the context of environmental gradients. We
further characterized microbial ecological strategies by inferring \textit{rrn}
gene copy number. High \textit{rrn} copy number may allow microorganisms to
rapidly respond to nutrients influx \citep{Klappenbach_2000}. Several lines of
evidence suggest that the xylose responders
are were able to grow rapidly and
assimilate C from multiple sources. The xylose responders
were characterized by rapid
assimilation of quickly (within 24
hours) assimilated xylose-C into
DNA but they DNA. Xylose responders also had relatively low
$\Delta\hat{BD}$ potentially indicating
that xylose was not the sole C source
used for growth. Xylose represented only 20\% of the nutrient and resource
microcosm amendment and~3.5\% of total soil C. Xylose responders
were also highly often included
the most abundant
OTUs within the non-fractionated DNA and had relatively high
estimated \textit{rrn} copy number. However, to some degree, high \textit{rrn}
gene copy number may inflate observed xylose responder relative abundance.
It is also notable that Notably, the majority of xylose
responders responder SSU rRNA genes (86\%)
are well represented among matched
cultured
isolates. isolates' at high sequence identity ($>$ 97\%).
% Fakesubsubsection: In contrast, the results
In contrast, cellulose Cellulose responders appeared to
be specialize in using cellulose as
a C
specialists. source. Cellulose responders grew relatively slowly over a span of weeks
and had relatively high $\Delta\hat{BD}$ indicating
that, although multiple sources of
C were present, cellulose remained the
dominant C source for cellulose
responders. They responders even though multiple sources of
C were present. Cellulose responders were also
present at generally lower
in relative
abundance within the non-fractionated DNA and had lower estimated \textit{rrn}
copy number than xylose responders.
While The majority of cellulose responders were
not close relatives of cultured isolates although a number of cellulose
responders shared high SSU rRNA gene sequence identity
to cultured
isolates in the
\textit{Proteobacteria} (e.g. \textit{Cellvibrio}),
the majority of cellulose
responders were not close relatives of cultured isolates. . We identified
cellulose responders among phyla such as \textit{Verrucomicrobia},
\textit{Chloroflexi}, and \textit{Planctomycetes} whose functions within soil
communities remain poorly characterized.
