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\subsection{Putative spore-formers in the Firmicutes assimilate $^{13}$C from
xylose within first day after soil amendment followed by Bacteroidetes and then
Actinobacteria OTUs}
Within the first 7 days of incubation
an average 63\%
on average of $^{13}$C-xylose was
respired and only an additional 6\% more was respired
between days from day 7
and to 30. At
the end of the 30 day
experiment incubation 30\% of the
original $^{13}$C from
added xylose
remained in the soils. The $^{13}$C remaining in the soil from $^{13}$C-xylose
addition
has was likely
been stabilized by assimilation into microbial biomass
and/or microbial conversion into other forms of organic
matter, though it matter. It is
also
possible that some $^{13}$C-xylose remains unavailable to microbes due to
abiotic interactions in soil \citep{Kalbitz_2000}.
At day 1, 84\% of
xylose $^{13}$C-xylose responsive OTUs belong to
Firmicutes, \textit{Firmicutes}, 11\% to \textit{Proteobacteria} and 5\% to
\textit{Bacteroidetes}. At day 3,
Firmicutes \textit{Firmicutes} responders decreased to
5\% (from 16 OTUs to 1) while \textit{Bacteroidetes} increased to 63\% (from 1
to 12 OTUs) of day 3 responders. The remaining day 3 responders are members of
the \textit{Proteobacteria} (26\%) and the \textit{Verrucomicrobia} (5\%). Day
7 responders were 53\%
Actinobacteria, \textit{Actinobacteria}, 40\%
Proteobacteria, \textit{Proteobacteria},
and 7\%
Firmicutes. A
substantial amount (XX\%) of xylose responders for day 7 had not previously
been identified as responders at earlier time points. \textit{Firmicutes}. The identities of $^{13}$C-xylose responders
change with
time at the phylum level. time. The numerically dominant
xylose $^{13}$C-xylose responder phylum
shifts from \textit{Firmicutes} to \textit{Bacteroidetes} and then to
\textit{Actinobacteria} across days 1, 3 and 7 (Figure~\ref{fig:l2fc},
Figure~\ref{fig:xyl_count}).
All of the $^{13}$C-xylose responders in the \textit{Firmicutes} phylum are
closely related (at least 99\% sequence
idetity) identity) to cultured isolates from
genera that are known to form endospores (Table~\ref{tab:xyl}). Each
$^{13}$C-xylose responder is closely related to
strains isolates annotated as members
of \textit{Bacillus}, \textit{Paenibacillus} or \textit{Lysinibacillus}.
\textit{Bacteroidetes} $^{13}$C-xylose responders are predominantly closely
related to \textit{Flavobacterium} species (5 of 8 total
responders). responders)
(Table~\ref{tab:xyl}. Only one \textit{Bacteroidetes}
$^{13}$C-xylose
responder is not closely related to a cultured isolate, ``OTU.183'' (closest
LTP BLAST hit, \textit{Chitinophaca sp.}, 89.5\% sequence
identity). identity,
Table~\ref{tab:xyl}). OTU.183 shares high sequence identity with environmental
clones derived from rhizosphere samples (accession AM158371, unpublished) and
the skin microbiome (accession JF219881, \citet{Kong_2012}). Other
\textit{Bacteroidetes} responders share high sequence identities with canonical
soil genera including \textit{Dyadobacer}, \textit{Solibius} and
\textit{Terrimonas}. Six of the 8 \textit{Actinobacteria} $^{13}$C-xylose
responders are in the \textit{Micrococcales} order. One $^{13}$C-xylose
responding \textit{Actinobacteria} OTU shares 100\%
seqeunce sequence identity with
\textit{Agromyces ramosus} (Table~\ref{tab:xyl}).
\textit{Agromyces \textit{A. ramosus} is a
known
predatotry predatory 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 $^{13}$C can be passed down
through trophic levels although heavy isotope representation in C pools
targeted by cross-feeders and predators would
decrease be diluted with depth into the
trohpic trophic cascade. It's possible, however, that the $^{13}$C labeled
\textit{Agromyces} OTU
is was assimilating $^{13}$C primarily by
predatation predation if
the
\textit{Agromyces}
is OTU was selective enough with respect to its prey
such that it
primarily attacked $^{13}$C-xylose assimilating
organisms. organisms and that those
$^{13}$C-xylose assimilating organisms utilized $^{13}$C-xylose as a sole
carbon source.
\subsection{Cellulose degrader DNA exhibits greater bouyant density shifts upon
$^{13}$C incorporation than xylose degrader DNA}
