deletions | additions
diff --git a/Results.tex b/Results.tex
index 0484323..f295b3a 100644
--- a/Results.tex
+++ b/Results.tex
...
1929 who named it for its cellulose degrading abilities
\citep{boone2001bergeys}. All $^{13}$C-cellulose responding
\textit{Proteobacteria} share high sequence identity with 16S rRNA genes from
sequenced cultured isolatets
(Table XX) (Table~\ref{tab:cell}) except for OTU.442 (best cultured
isolate match 92\% sequence identity in the \textit{Chrondomyces} genus) and
OTU.663 (best cultured isolate match outside \textit{Proteobacteria} entirely,
\textit{Clostridium} genus, 89\% sequence identity). Some
...
identity (97\%) with an isolate from Norway tundra soil \citep{Jiang_2011}
although growth on cellulose was not assessed for this isolate. Only one other
$^{13}$C-cellulose responding verrucomicrobium shared high DNA sequence
identity with a sequenced type strain, ``OTU.638''
(Table XX) (Table~\ref{tab:cell}) with
\textit{Roseimicrobium gellanilyticum} (100\% sequence identity).
\textit{Roseimicrobium gellanilyticum} grows on soluble celluose
\citep{Otsuka_2012}. The remaining $^{13}$C-cellulose \textit{Verrucomicrobia}
...
\citep{Di_Rienzi_2013}. Although we highlight $^{13}$C-cellulose responders
that share high sequence identity with described genera, most
$^{13}$C-cellulose responders uncovered in this experiment are not closely
related to cultured isolates
(Table~XX). (Table~\ref{tab:cell}).
\subsection{Putative spore-formers in the Firmicutes assimilate $^{13}$C from
xylose within first day after soil amendment followed by Bacteroidetes and then
...
All of the $^{13}$-xylose responders in the \textit{Firmicutes} phylum are
closely related (at least 99\% sequence idetity) to cultured isolates from
genera that are known to form endospores
(Table XX). (Table~\ref{tab:xyl}). Each responder is closely
related to strains annotated as members of \textit{Bacillus},
\textit{Paenibacillus} or \textit{Lysinibacillus}. \textit{Bacteroidetes}
$^{13}$C-xylose responders are predominantly closely related to
...
\textit{Actinobacteria} $^{13}$C-xylose responders are in the
\textit{Micrococcales} order. One $^{13}$C-xylose responding
\textit{Actinobacteria} OTU shares 100\% seqeunce identity with
\textit{Agromyces ramosus}
(Table~XX). (Table~\ref{tab:xyl}). \textit{Agromyces ramosus} is a known
predatotry bacterium but is not dependent on a host for growth in culture
\citep{16346402}. It is not possible to determine the specific origin of assimilated
$^{13}$C in a DNA-SIP experiment. The isotopically labeled C can be passed down
...
$^{13}$C-xylose responders are generally more abundant members based on relative abundance in bulk DNA SSU rRNA gene content than $^{13}$C-cellulose responders (Figure~XX, p-value).
However, both $^{13}$C-xylose and $^{13}$C-cellulose responders were found in abundant and
rare OTUs (Figure~XX). For instance, a \textit{Delftia} $^{13}$C-cellulose responder is fairly
abundant in the bulk samples ("OTU.5",
Table~XX) Table~\ref{tab:cell}) with a mean bulk rank of 13 (\textit{i.e.}
on average the 13th most abundant OTU) and a $^{13}$C-xylose responder ("OTU.1040,
Table~XX) Table~\ref{tab:xyl}) has
a mean abundance in bulk relative abundance in samples of 2.85e$^{-05}$. Only one substrate
responder ($^{13}$C-cellulose) was not found in any bulk samples ("OTU.862",
Table~XX). Table~\ref{tab:cell}). Of the top 10 responders sorted by descending mean rank (essentially the 10 most abundandant responders
in the bulk samples), 8 are $^{13}$C-xylose responders and 5 of these 8 have mean ranks less than
10 in bulk samples.