this is for holding javascript data
Chuck changes to discussion
about 9 years ago
Commit id: c6e1d9851802db39f421155eeb5b7aceb5842772
deletions | additions
diff --git a/Discussion.tex b/Discussion.tex
index f0dd818..e0d445b 100644
--- a/Discussion.tex
+++ b/Discussion.tex
...
OTUs that responded beginning at day 3 had greater \textit{rrn} gene copy
number than OTUs that responded to $^{13}$C-xylose later
(Figure~\ref{fig:shift}, Figure~\ref{fig:copy}) suggesting fast-growing
microbes assimilated $^{13}$C from xylose before slow growers.
% Fakesubsubsection:NRI values have been used to assess
NRI values are useful metrics for assessing phylogenetic clustering
...
$^{13}$C-xylose responsive organisms were labeled as a result of primary xylose
assimilation (see below), and therefore it's not clear if $^{13}$C-xylose
responsive OTUs in this experiment constitute a single ecologically meaningful
group or multiple ecological groups.
TALK ABOUT PHLO COHERENT TEMPORAL
RESPONSE.
\subsection{Implications for soil C cycling models}
% Fakesubsubsection:Land management, climate, pollution and
...
decomposition but there is not working quantitative definition of what
constitutes ``narrow'' versus ``broad'' in the literature. HGT SENTENCE.
% Fakesubsubsection:For community composition to influence ecological processes
For community composition to influence ecological processes several criteria
must be satisfied CITE Schimel 2012: microorganisms must differ in functional
capacity, and biological reactions must influence C fate or be rate limiting.
We demonstrate that the microbes participating in cellulose decomposition are
largely different than those participating in xylose decomposition which
satisfies the first criterion above. The other criteria were not directly
tested in our study but we propose several mechanisms suggested by our results
wherein C dynamics and fate would be affected by community composition. Genomic
evidence shows cellulose degradation is likely a conserved trait CITE Allison.
To our knowledge this study is the first to evaluate the phylogenetic
conservation of cellulose degradation \textit{in situ} via DNA-SIP and our
results are remarkably consistent with genomic evidence. A decrease in active
cellulose degraders could decrease cellulose decomposition process rates as the
phylogenetic conservation of cellulose degradation likely means few soil
microorganisms can fill the cellulose degradation niche. If cellulose
decomposers are readily dispersed, however, dispersed microorganisms could fill
the cellulose degradation void renewing ecosystem function. For labile
C decomposition, if dispersal does not enable rapid recolonization CITE,
a decrease in fast growing spore former abundance could enable the labile
C degradation niche to be occupied by different labile C degraders. The primary
labile C degraders in this study were fast growers, and have a distinct
lifestyle (spore formation) which might indicate a distinct C use dynamics
and/or resource allocation signature. Both attributes are unlikely to be
mimicked by substitution with a different functional group and thus this
substitution might influence labile C dynamics and fate. Further, it is unclear
how labile C degrader substitution would affect biomass C turnover by predatory
bacteria that appeared to feed on fast growing, spore forming labile
C decomposers. Spore formation, however, might enable dispersal. The
consistency of labile C decomposition rates across soils is hypothesized to be
a manifestation of the wide ability to use labile materials across
microorganisms CITE. An alternative hypothesis is that labile C degraders are
easily dispersed. Other lineages implicated in rapid labile C turnover include
members of the \textit{Actinobacteria} CITE Placella and Many soil
\textit{Actinobacteria} form hyphae that facilitate dispersal CITE. The two
hypotheses are not mutually exclusive, however, but our results suggest that
environmental conditions unfavorable to fast-growing spore-formers and/or
quickly resusitated, hyphal \textit{Actinobacteria} CITE may impact labile
C dynamics and fate.
% Fakesubsubsection:It's not clear whether the observed activity
The activity succession from \textit{Firmicutes} to \textit{Bacteroidetes} and
finally \textit{Actinobacteria} in response to $^{13}$C-xylose addition is
...
interactions in soil C cycling are rarely considered (e.g.
\citep{Moore1988}).
% Fakesubsubsection:We propose two scenarios wherein C dynamics
We propose two scenarios wherein C dynamics and fate would be affected
by community composition in the context of our results. Genomic evidence shows
cellulose degradation is a phylogenetically conserved trait CITE Allison. This
study is the first to evaluate the phylogenetic conservation of soil cellulose
degradation \textit{in situ} via DNA-SIP and our results are consistent with
genomic evidence. Decreasing cellulose degraders would diminish cellulose
decomposition process rates. Few soil microorganisms can fill the
phylogenetically conserved cellulose degradation niche. Ecosystem function
could be renewed by dispersed cellulose decomposers, however. For labile
C decomposition, the absence fast growing spore formers would enable other
microbes to assimilate labile C when dispersal does not enable rapid
recolonization CITE. The primary labile C degraders in this study were fast
growers, and had a distinct lifestyle (spore formation) which might indicate
distinct C use dynamics and/or resource allocation. New labile C degraders may
metabolize and allocate labile C differently changing labile C dynamics and
fate. Further, labile C degrader substitution could affect biomass C turnover
by predatory bacteria that feed on fast growing, spore forming labile
C decomposers. On the other hand, spore formation enables dispersal CITE. One
proposed mechanism for similar labile C decomposition rates across soils that
vary in community composition is that labile materials can be used widely by
microorganisms CITE. An alternative hypothesis for consistent labile C process
rates across soils is that labile C degraders are easily dispersed. Notably,
other lineages implicated in rapid labile C turnover include members of the
\textit{Actinobacteria} CITE Placella and many soil \textit{Actinobacteria}
form hyphae that facilitate dispersal CITE. The two hypotheses are not mutually
exclusive, however, but our results suggest that environmental conditions
unfavorable to fast-growing spore-formers and/or quickly resuscitated, hyphal
\textit{Actinobacteria} CITE may impact labile C dynamics and fate.
% Fakesubsubsection:Intuitively C cycling trait diversity is inferred
Intuitively C cycling functional guild diversity is inferred from the
distribution of diagnostic genes CITE. For instance, the wide distribution of
the glycolysis operon is interpreted as evidence many soil microorganisms
participate in glucose turnover CITE. We suggest that \textit{in situ}
functional guild diversity can vary significantly from guild diversity assessed
by functionally screening isolates and/or genomes. Xylose use in soil, for
instance, may be less a function of catabolic pathway distribution among
genomes and more a function of microorganism lifestyle. Soil is characterized
by pulse delivery of nutrients that coincide with phenomena including seasonal
change, land management, and rainfall CITE. Therefore, rapid growth rates
and/or the rapid resuscitation upon wet up may control labile soil
C assimilation. Growth rate and dessication resistance are phylogenetically
conserved unlike labile C degradation so labile C assimilation may be
deceivingly conserved as well. DNA-SIP is useful for establishing \textit{in
situ} phylogenetic clustering and diversity of functional guilds because
DNA-SIP can incorporate life history strategies into trait functional guild
identification.
Paenibacillus Neufeld
Thompson "all bands enriched"
\subsection{Conclusion}
% Fakesubsubsection:Microorganisms sequester atmospheric C and respire
Microorganisms sequester atmospheric C and respire SOM influencing climate