Ashley Campbell edited introduction.tex  over 9 years ago

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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  communitystructure, 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  ofthose 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  thestudy 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  communityduring 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  asoil 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  soilmicrobial 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  byhundreds 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.