Ashley Campbell edited introduction.tex  almost 10 years ago

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\section{Introduction}    There are 2,300 Pg of carbon (C) stored in soils worldwide, excluding plant biomass, which accounts for \texttt{\char`\~}80\% \texttt{~}80\%  of the global terrestrial C pool \cite{Amundson_2001,Mendelsohn_2001,IPCC2007Synth,elsen_Ayres_Wall_Bardgett_2011,Lal_2008,BATJES_1996,Lal_2008}. Current climate change models concur on atmospheric and ocean C predictions but not terrestrial \cite{Friedlingstein_2006}. The disagreeable predictive power between models for terrestrial ecosystems reflects how little we know about belowground C cycling dynamics. It is estimated that 80-90\% of the 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 our limitations in methodologies. Soils consist of an overwhelming biological, chemical, and physical complexity which affects microbial community composition, diversity, and structure (refs). 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{Schlesinger_1977,dgett_Wall_Hattenschwiler_2010,Sollins_Homann_Caldwell_1996,Torn_Vitousek_Trumbore_2005,TRUMBORE_2006,Schimel_2012}. Furthermore, rates of metabolism are often measured without knowing the identity of the microbial species specifically involved \cite{ndi_Pietramellara_Renella_2003} resulting in uncertainty in importance of community diversity in maintaining ecosystem functioning \cite{Allison_2008,ndi_Pietramellara_Renella_2003,Schimel_2012}. The first step in teasing out belowground C cycling dynamics is to identify microbial groups responsible for the measured process and understand the relationship between genetic diversity, community structure, and function \cite{O_Donnell_2002}. Stable-isotope probing (SIP) provides a unique opportunity to link microbial identity to activity \cite{Chen_Murrell_2010}. SIP has been utilized to expand our knowledge of a myriad of important biogeochemical processes \cite{Chen_Murrell_2010}, yet, there remain limitations. Frequently utilized SIP-coupled molecular applications such as TRFLP, DGGE, and cloning provide insufficient resolution of taxon identity and depth of coverage and, to our knowledge, are usually conducted under the narrow scope of single substrate additions with few exceptions \cite{Lueders_2003,Chauhan_2009}. SIP studies use single substrate experimental designs to minimize isotope signal dilution, however, it detracts from how microbes may experience that substrate naturally, calling into question its environmental and biological relevance.