Chuck updates  almost 9 years ago

Commit id: 16b84fee04e75a8f41e67951b2b53237797ac52b

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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         

\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         

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.