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\subsection{Phylogeneitic affiliation of $^{13}$C-cellulose and $^{13}$C-xylose -responsive microorganisms}
% Fakesubsubsection:\textit{Verrucomicrobia} are ubiquitous in soil
\textit{Verrucomicrobia} are
ubiquitous in cosmopolitan soil
worldwide
\citep{Bergmann_2011}. \textit{Verrucomicrobia} microbes \citep{Bergmann_2011}
and can comprise up to 23\%
of 16S rRNA gene sequences in high-throughput DNA sequencing surveys of
SSU rRNA genes in soil \citep{Bergmann_2011} and represent as high as
9.8\% of soil 16S rRNA \citep{Buckley_2001}. Many \textit{Verrucomicrobia}
cultivars have been established were first isolated in the last decade \cite{Wertz_2011} but
only one of the 15 most abundant verrucomicrobial phylotypes in a global
soil sample collection shared greater than 93\% sequence identity with an
cultured isolate \citep{Bergmann_2011}. Genomic analyses and physiological
profiling of \textit{Verrucomicrobia} isolates revealed
\texit{Verrucomicrobia}
are capable of methanotrophy and
diazotrophy \citep{Wertz_2011}
within \textit{Verrucomicrobia} (CITE and
reviewed by
\citet{Wertz_2011}). \citet{Wertz_2011}. \textit{Verrucomicrobia} cultivars
degrade cellulose in culture and
select \textit{Verrucomicrobia} genomes possess
the genes necessary to degrade cellulose \citep{Otsuka_2012, Wertz_2011}.
Although, we have learned many functional roles of
\textit{Verrucomicrobia} in the environment, the The function and or global
significance of soil \textit{Verrucomicrobia} in global C-cycling is
unknown. unknown, however. For example, only one of the putative verrucomicrobial cellulose
degraders identified in this experiment is closely related to a named
cultivar (OTU.XX, Table~\ref{tab:cell}) and only XX\% of all
verrucomicrobial OTUs found in this study share at least 97\% sequence
...
distributed soil samples \citep{Bergmann_2011}. \textit{Verrucomicrobia}
lineages particularly \textit{Spartobacteria}, given their ubiquity and
abundance in soil as well as their demonstrated incorporation of $^{13}$C from
$^{13}$C-cellulose, may be
decomposing contributos to cellulose
in soil worldwide. decomposition on a
global scale.
% Fakesubsubsection:Soil \textit{Chloroflexi} have been found to assimilate
Soil \textit{Chloroflexi} have been found to assimilate cellulose before in
DNA-SIP studies with $^{13}$C-cellulose \citep{Schellenberger_2010}. Previously
identified \textit{Chloroflexi} $^{13}$C-cellulose-responders were
similarly
underrepresented in culture collections
as the \citep{Schellenberger_2010}.
The \textit{Chloroflexi} identified
as cellulose degraders in this study
\citep{Schellenberger_2010}. are also only distantly related to
isolates (TABLE XX).
Chloroflexi are among the six most abundant soil phyla commonly recovered from
soil microbial diversity surveys CITE. Chloroflexi are typically not as as
abundant as \textit{Verrucomicrobia}, XX, and XX but have similar abundance as
...
the SSU rRNA gene sequences from this study share at most XX\% sequence
identity with the type strain for the \textit{Herpetosiphon} genus (\textit{H.
geysericola} CHECK SPELLING). \textit{H. geysericola} is a predatory bacterium
shown to prey upon XX in culture. In our
study study, "Herpetosiphon"
$^{13}$C-cellulose responders did not show a delayed response to
$^{13}$C-cellulose as compared to other responders but nonetheless could have
become labeled by feeding on primary $^{13}$C-cellulose degraders. The prey
specificity of predatory bacteria is not well established especially \textit{in
situ}. $^{13}$C-labeling
by as would be positively correlated with prey
specificity. If the predator specifically preyed upon one population then it
could take on the same labeling \% as that population. Preying on multiple
types would produce a mixed and potentially diluted labeling signature if some
of the prey populations were
unlabeled. not isotopically labeled.
% Fakesubsubsection:\textit{Acidobacteria} did not incorporate $^{13}$C
We also observed $^{13}$C-incorporation from cellulose from \textit{Proteobacteria}, \textit{Planctomycetes} and \textit{Bacteroidetes}.
...
earliest assimilated C will be converted into biomass. Leftover labile C and
new biomass C is assimilated by slower growing \textit{Actinobacteria},
\textit{Proteobacteria} and \textit{Bacteroidetes} types that are tuned to
lower C substrate concentrations,
are predatory bacteria (e.g.
\textit{Agromyces}) \textit{Agromyces}),
and/or
are specialized for consuming viral lysate. Polymeric C is likely
assimilated by fungal cellulose degraders before bacterial degraders but the
differences in fungal and bacterial soil C assimilation are outside the scope
of this study. Polymeric C enters the bacterial community after several weeks.
Canonical cellulose degrading bacteria such as \textit{Cellvibrio} are major
cellulose degraders but uncharacterized lineages in the \textit{Chloroflexi}
and \textit{Verrucomicrobia}, specifically the
\textit{Spartobacteria} \textit{Spartobacteria}, are
significant contributors to
soil cellulose decomposition. C originally from
polymeric substrates may also enter the bacterial community via predatory
actions of lineages that specifically prey upon cellulose degraders that are
perhaps members of the \textit{Herpetosiphon} genus although it is not known at
this time the
scale, relative contibution, if
it exists, any, of
the this predatory action. The assimilation of
C from polymeric substrates precipitates a smaller trophic cascade because
polymeric C degraders exhibit lower growth efficiency than their labile C
degrading
counterparts. counterparts and thus less assimilated C is converted into biomass that
can move higher tropic levels.
\subsection{DNA-SIP methods considerations}
% Fakesubsubsection:We found that control gradients yield amplifiable
We found that control gradients yield amplifiable DNA well into the heavy
