Ashley Campbell edited introduction.tex  over 10 years ago

Commit id: d6295f4eddc7464eeaf917cfbf37478ed4314a2d

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Importance of Carbon   There are 2,300 Pg of carbon (C) stored in soils worldwide, excluding plant biomass, which accounts for \sim80\% of the global terrestrial C pool \cite{Amundson_2001,IPCC 2000,IPCC 2007,elsen_Ayres_Wall_Bardgett_2011,Lal_2008,BATJES_1996}, http://rstb.royalsocietypublishing.org/content/363/1492/815.full). It is estimated that 80-90\% of the C cycling in soil is mediated by microorganisms (\cite{ColemanCrossley_1996}, Nannipieri & Badalucco 2003). However, 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} which ultimately dictates the fate of C. \cite{Schlesinger_1977,dgett_Wall_Hattenschwiler_2010,Sollins_Homann_Caldwell_1996,Torn_Vitousek_Trumbore_2005,TRUMBORE_2006}.  Furthermore, rates of metabolism are often measured without knowing the identity of the microbial species specifically involved in the cycling of the measured process \cite{ndi_Pietramellara_Renella_2003}. The importance of community diversity in maintaining ecosystem functioning remains uncertain (Allison & Martiny 2008, \cite{ndi_Pietramellara_Renella_2003}. Therefore, the first step in teasing out this central problem is to identify microbial groups responsible for the measured process and understand the relations between genetic diversity, community structure, and function (O’Donnell et al 2001). Stable-isotope probing (SIP) provides a unique opportunity to link microbial identity to activity (\cite{Chen_Murrell_2010}). Since its development, the technique has been utilized for identifying key microorganisms and functional genes in a myriad of important biogeochemical processes including methane, cellulose, acetate (Chen & Murrell 2011). However, only two studies have employed SIP to better understand microbial food webs (Lueders et al 2004b, Chauhan et al 2009). SIP studies have expanded our knowledge of important biogeochemical processes, yet, there remain limitations including insufficient resolution of identification by fingerprinting and cloning techniques and, to our knowledge are, usually conducted under the narrow scope of single substrate additions with few exceptions (refs). 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.