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Chuck updates
almost 9 years ago
Commit id: 16b84fee04e75a8f41e67951b2b53237797ac52b
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diff --git a/Abstract.tex b/Abstract.tex
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in~49 and~63 OTUs, respectively. In the $^{13}$C-xylose treatment the types of
microorganisms that incorporated $^{13}$C into DNA changed over time dominated
by \textit{Firmicutes} at day~1 followed by \textit{Bacteroidetes} at day~3 and
then
\textit{Actinbacteria} \textit{Actinobacteria} at day~7. These dynamics of $^{13}$C-labeling
suggests suggest labile C traveled through different trophic levels within the soil
bacterial community. The microorganisms that metabolized cellulose-C increased
in relative abundance over the course of the experiment with the highest number
of OTUs exhibiting evidence for $^{13}$C-assimilation after 14 to 30 days.
Microbes that metabolized cellulose C belonged to cosmopolitan soil lineages
that remain uncharacterized including \textit{Spartobacteria},
\textit{Chloroflexi} and \textit{Planctomycetes}. Using an approach that
diff --git a/Methods.tex b/Methods.tex
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\section{Methods}
%
All code to take raw SSU rRNA gene sequencing reads to final publication
figures and through all presented analyses is located at the following URL:\\
\url{https://github.com/chuckpr/CSIP_succession_data_analysis}.\\ DNA sequences
are deposited on MG-RAST (Accession XXXXXXX).
% Fakesubsubsection: Twelve soil cores
Twelve soil cores (5 cm diameter x 10 cm depth) were collected from six
sampling locations within an organically managed agricultural field in Penn
diff --git a/Results.tex b/Results.tex
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relative abundance in non-fractionated DNA, demonstrated signal consistent with
higher atom \% $^{13}$C in labeled DNA, and had lower estimated \textit{rrn}
copy number (Figure~\ref{fig:shift}). In the non-fractionated DNA, cellulose
responders had lower relative abundance
(7 (3.8 x
10$^{-4}$ 10$^{-3}$ (s.d.
2 1.2
x 10$^{-3}$)) than xylose responders
(2 (3.5 x 10$^{-3}$ (s.d.
4 5.2 x 10$^{-3}$))
(Figure~\ref{fig:xyl_count},
P-value $=$ 0.00028, P-value~$=$~1.12 x 10$^{-5}$, Wilcoxon Rank
Sum test). Six of the ten most common OTUs observed in the non-fractionated DNA
responded to xylose, and,
eight seven of the ten most abundant responders to xylose
or cellulose in the non-fractionated DNA were xylose
responders. responders although
``OTU.6'' annotated as \textit{Cellvibrio} a cellulose responder at day 14 was
the responder found at highest relative abundance (3.3 \% or SSU rRNA genes at
day~14).
% Fakesubsubsection:DNA buoyant density increases as the amount
DNA buoyant density (BD) increases in proportion to atom \% $^{13}$C.