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\section{Introduction}
We have only a rudimentary understanding of how carbon flows through soil microbial communities. This deficiency is driven by the staggering complexity of soil microbial food webs and the opacity of these biological systems to current methods for describing microbial metabolism in the environment. Relating community composition to overall soil processes, such as nitrification and denitrification, which are mediated by defined functional groups has been a useful approach. However, carbon-cycling processes have proven more recalcitrant to study due to the wide range of organisms participating in these reactions and our inability to discern discrete functional
genes for these processes. genes.
Excluding plant biomass, there are 2,300 Pg of carbon (C) stored in soils worldwide which accounts for $\sim$80\% of the global terrestrial C pool \cite{Amundson_2001,BATJES_1996}. When organic C from plants reaches soil it is degraded by fungi, archaea, and bacteria. This C is rapidly returned to the atmosphere as CO\textsubscript{2} or remains in the soil as humic substances that can persist up to 2000 years \cite{yanagita1990natural}. The majority of plant biomass C is respired and, on an annual basis, soil respiration produces 10 times more CO\textsubscript{2} than anthropogenic emissions \cite{chapin2002principles}. Global changes in atmospheric CO\textsubscript{2}, temperature, and ecosystem nitrogen inputs, are expected to impact primary production and C inputs to soils \cite{Groenigen_2006} but it remains difficult to predict the response of soil processes to anthropogenic change \cite{DAVIDSON_2006}. Current climate change models concur on atmospheric and ocean C predictions but not terrestrial
\cite{Friedlingstein_2006} reflecting \cite{Friedlingstein_2006}. Contrasting terrestrial ecosystem model predictions reflect how little is known about soil C cycling
dynamics. It dynamics and it has been suggested that incosistencies in terrestial modeling could be improved by elucidating the relationship between dissolved organic carbon and microbial communities in soils \cite{Neff_2001}.
An estimated 80-90\% of C cycling in soil is mediated by microorganisms \cite{ColemanCrossley_1996,Nannipieri_2003}. Understanding microbial processing of nutrients in soils presents a special challenge due to the hetergeneous nature of soil ecosystems and methods limitations. Soils are biologically, chemically, and physically complex which affects microbial community composition, diversity, and structure
(refs). \cite{Nannipieri_2003}. Confounding factors such as physical protection/aggregation, moisture content, pH, temperature, frequency and type of land disturbance, soil history, mineralogy, N quality and availability, and litter quality have all been shown to affect the ability of the soil microbial community to access and metabolize C substrates \cite{Sollins_Homann_Caldwell_1996}. Further, rates of metabolism are often measured without knowing the identity of the microbial species involved \cite{ndi_Pietramellara_Renella_2003} leaving the importance of specific community members towards maintaining ecosystem functions unknown \cite{Allison_2008,ndi_Pietramellara_Renella_2003,Schimel_2012}. Litter bag experiments have shown that the community composition of soils can have quantitative and qualitative impacts on the breakdown of plant materials \cite{Schimel_1995}. Reciprocal exchange of litter type and microbial inocula under controlled environmental conditions reveals that differences in community composition can account for 85\% of the variation in litter carbon mineralization \cite{Strickland_2009}. In addition, assembled communities of cellulose degraders reveal that the composition of the community has significant impacts on the rate of cellulose degradation \cite{Wohl_2004}.
Carbon An important step in
plant biomass is found primarily in cellulose (30-50\%), hemicellulose (20-40\%), and lignin (15-25\%) \cite{Lynd_2002}. Hemicellulose understanding soil C cycling dynamics is
composed mostly to identify individual contributions of
xylose with varying lesser amounts of arabinose, galactose, glucose, mannose, discrete microorganisms and
rhamnose. In plant biomass decomposition, hemicellulose and simple sugars are decomposed first while polymeric C degradation lags. As such, to investigate the
deposition relationship between genetic diversity, community structure, and function \cite{O_Donnell_2002}. The vast majority of
plant litter is hypothesized microorganisms continue to
induce ecological succession within resist cultivation in the
soil community as different plant compounds are degraded sequentially laboratory, and even when cultivation is achieved, the traits expressed by
organisms a microorganism in
differenct ecological niches \cite{Hu_1997,Rui_2009}. The degree culture may not be representative of those expressed when in its natural habitat. Stable-isotope probing (SIP) provides a unique opportunity to link microbial identity to
activity and has been utilized to expand our knowledge of a myriad of important biogeochemical processes \cite{Chen_Murrell_2010}. The most successful applications of this technique have identified organisms which
the succession hypothesis presents an accurate model mediate processes performed by a narrow set of
litter decomposition functional guilds such as methanogens \cite{Lu_2005}. The technique has been
questioned \cite{Kj_ller_1982,Frankland_1998,Osono_2005} and new approaches are needed less applicable to
reveal the study of soil C cycling
processes and because of limitations in resolving power as a result of simultaneous labeling of many different organisms in the
manner community. Additionally, molecular applications such as TRFLP, DGGE, and cloning that are frequently used in
conjunction with SIP provide insufficient resolution of taxon identity and depth of coverage. We have developed an approach that employs a complex mixture of substrates, added at low concentration relative to soil organic matter pools, along with massively parallel DNA sequencing, which
C is transformed by greatly expands the
soil food web. ability of nucleic acid SIP to explore complex patterns of C-cycling in microbial communities.
An important step A temporal cascade occurs in
understanding soil natural microbial communities during the plant biomass degradation in which labile C
cycling dynamics degradation preceeds polymeric C \cite{Hu_1997,Rui_2009}. The aim of this study is to
identify individual contributions track the temporal dynamics of
C assimilation through discrete
microorganisms and to investigate individuals of the
relationship between genetic diversity, soil microbial community
structure, and function \cite{O_Donnell_2002}. The vast majority of microorganisms continue to
resist cultivation in the laboratory, and even when cultivation is achieved, provide greater insight into soil C-cycling. Our experimental approach employs the
traits expressed by a microorganism in culture may not be representative addition of
those expressed when in its natural habitat. Stable-isotope probing (SIP) provides a
unique opportunity to link microbial identity to activity soil organic matter simulant (a complex mixture of model carbon sources and
has been utilized inorganic nutrients common to
expand our knowledge of plant biomass), where a
myriad of important biogeochemical processes \cite{Chen_Murrell_2010}. The most successful applications single C constituent is substituted for its \textsuperscript{13}C-labeled equivalent, to soil. Parallel incubations of
soils amended with this
technique have identified organisms which mediate processes performed by a narrow set of functional guilds such as methanogens\cite{Lu_2005}. The technique has been less applicable complex C mixture allows us to
test how different C substrates cascade through discrete taxa within the
study of soil
C cycling because of limitations in resolving power microbial community. In this study we use \textsuperscript{13}C-xylose and \textsuperscript{13}C-cellulose as a
result proxy for labile and polymeric C, respectively. A previous study has shown that \textsuperscript{13}C labeled plant residues enable tracking of
simultaneous labeling C through microbial pathways \cite{Evershed_2006}. Using a novel approach we couple nucleic acid stable isotope probing coupled with next generation sequencing (SIP-NGS) to elucidating soil microbial community members responsible for specific C transformations. Amplicon sequencing of
16S rRNA gene fragments from many
gradient fractions and multiple gradients make it possible to track carbon assimilation by hundreds of different
taxa. Ultimately we identify specific organisms
in or functional guilds responsible for the
community. Additionally, molecular applications such cycling of specific C substrates. Illuminating these microbial contributions associated with decomposition in soil are important because as
TRFLP, DGGE, and cloning that environments change, there are
frequently used in conjunction with SIP provide insufficient resolution of taxon identity measurable and
depth of coverage. We have developed an approach that employs a complex mixture of substrates, added at low concentration relative to functional changes in soil
organic matter pools, along with massively parallel DNA sequencing, C \cite{Grandy_2008} which
greatly expands the ability of nucleic acid SIP to explore complex patterns of C-cycling in microbial communities. could cumulatively have large impacts at a global scale.
The aim of this study is to track To minimize isotope signal dilution, SIP studies use single substrate experimental designs with few exceptions \cite{Lueders_2003,Chauhan_2009}. This differs from how microbes experience the
temporal dynamics of substrate naturally undermining its environmental and biological relevance. C
assimilation through discrete individuals in plant biomass is found primarily in cellulose (30-50\%), hemicellulose (20-40\%), and lignin (15-25\%) \cite{Lynd_2002}. Hemicellulose is composed mostly of
the soil microbial community to provide greater insight into soil C-cycling xylose with varying lesser amounts of arabinose, galactose, glucose, mannose, and
the transformation rhamnose. The deposition of
plant litter is hypothesized to induce ecological succession within the
microbial soil community
during plant biomass degradation. To test this, we use \textsuperscript{13}C-xylose and \textsuperscript{13}C-cellulose as
a proxy for labile different plant compounds are degraded sequentially by organisms in differenct ecological niches. Hemicellulose and
simple sugars are decomposed first while polymeric
C, respectively, C degradation lags. There is a great deal of evidence in
an experimental approach that employs the addition support of
this \cite{GARRETT_1951, Alexander_1964, Engelking_2007, Hu_1997, Anderson_1973, Stotzky_1961, Alden_2001, Furukawa_1996, Fontaine_2003, Blagodatskaya_2007, Jenkins_2010, Rui_2009, Fierer_2010, Gessner_2010} and these studies suggest that if a
soil organic matter simulant (a complex mixture of
model carbon sources labile and
inorganic nutrients common to plant biomass) polymeric C were added to
soil. Parallel incubations soil two waves of
soils amended with this complex degradation could be observed; labile C
mixture, where a single degradation early followed by polymeric C
constituent is substituted for its \textsuperscript{13}C-labeled equivalent, allows us degradation. The degree to
test how different C substrates cascade through discrete taxa within which the
soil microbial community. A previous study has shown that \textsuperscript{13}C labeled plant residues enable tracking succession hypothesis presents an accurate model of
C through microbial pathways \cite{Evershed_2006}. Using a novel approach we couple nucleic acid stable isotope probing with next generation sequencing (SIP-NGS) litter decomposition has been questioned \cite{Kj_ller_1982,Frankland_1998,Osono_2005}. New approaches are needed to
elucidate reveal soil
microbial community members responsible for specific C
transformations. Amplicon sequencing of 16S rRNA gene fragments from many gradient fractions cycling processes and
multiple gradients make it possible to track carbon assimilation the manner in which C is transformed by
hundreds of different taxa. This approach allows us to identify specific microbial taxa that assimilate different forms of soil C, and to evaluate the
assimilation dynamics of these substrates into DNA. soil food web.