Ashley Campbell edited introduction.tex  over 9 years ago

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An important step in understanding soil C cycling dynamics is to identify individual contributions of discrete microorganisms and to investigate the relationship between genetic diversity, 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, the traits expressed by a microorganism in 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 mediate processes performed by a narrow set of functional guilds such as methanogens\cite{Lu_2005}. The technique has been less applicable to the study of soil C cycling because of limitations in resolving power as a result of simultaneous labeling of many different organisms in the 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 greatly expands the ability of nucleic acid SIP to explore complex patterns of C-cycling in microbial communities.   A temporal cascade occurs in natural microbial communities during the plant biomass degradation in which labile C degradation preceeds polymeric C. C \cite{Hu_1997,Rui_2009}.  The aim of this study is to track the temporal dynamics of C assimilation in through discrete individuals of  the soil microbial community to provide greater insight into soil C-cycling. Our experimental approach employs the addition of a soil organic matter simulant (a complex mixture of model carbon sources and inorganic nutrients common to plant biomass), where a single C constituent is substituted for its \textsuperscript{13}C-labeled equivalent, to soil. Parallel incubations of soils amended with this complex C mixture allows us to test how different C substrates cascade through discrete taxa within the soil microbial community. In this study we use \textsuperscript{13}C-xylose and \textsuperscript{13}C-cellulose as a proxy for labile and polymeric C, respectively.  A previous study has shown that \textsuperscript{13}C labeled plant residues enable tracking of 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 or functional guilds responsible for the cycling of specific C substrates. Illuminating these microbial contributions associated with decomposition in soil are important because as environments change, there are measurable and functional changes in soil C \cite{Grandy_2008} which could cumulatively have large impacts at a global scale. 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 substrate naturally undermining its environmental and biological relevance. C 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 xylose with varying lesser amounts of arabinose, galactose, glucose, mannose, and rhamnose. The deposition of plant litter is hypothesized to induce ecological succession within the soil community as different plant compounds are degraded sequentially by organisms in differenct ecological niches. Hemicellulose and simple sugars are decomposed first while polymeric C degradation lags. There is a great deal of evidence in 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 complex mixture of labile and polymeric C were added to soil two waves of degradation could be observed; labile C degradation early followed by polymeric C degradation. The degree to which the succession hypothesis presents an accurate model of litter decomposition has been questioned \cite{Kj_ller_1982,Frankland_1998,Osono_2005}. New approaches are needed to reveal soil C cycling processes and the manner in which C is transformed by the soil food web.