Ashley Campbell edited introduction.tex  about 10 years ago

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There are 2,300 Pg of carbon (C) stored in soils worldwide, excluding plant biomass, which accounts for \sim 80\% 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). Current climate change models concur on atmospheric and ocean C predictions but not terrestrial (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 & Badalucco 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}. 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 (Allison & Martiny 2008, \cite{ndi_Pietramellara_Renella_2003}.   Degradative succession refers to the temporal changes in species or functional guilds that occurs during the sequential degradation of constituents of a nutrient resource (Townsend et al 2003). The decomposition of a nutrient source is hypothesized to promote succession of active community members as compounds are sequentially degraded (Biddanda & Pomeroy 1988). A classic example of plant litter degradative succession is characterized by a series of stages in which sugar fungi dominate in stage one, followed by cellulolytic fungi in stage two, and lignin degrading fungi in the final stage (Gessner et al 2010). This demonstrates not only the succession of detritivores but also the sequential degradation of litter constituents starting with consumption of the most labile C sources followed by degradation of more complex and polymeric C sources. These single substrate 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 on and subsequent polymeric C degradation. We propose this temporal cascade from labile C degraders preceeding the polymeric C degraders occurs in natural microbial communities, called herein microbial community succession.  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 (O’Donnell et al 2001). Stable-isotope probing (SIP) provides a unique opportunity to link microbial identity to activity (\cite{Chen_Murrell_2010}). SIP has been utilized to expanded our knowledge of a myriad of important biogeochemical processes (Chen & Murrell 2011), 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 (Lueders et al 2004b, Chauhan et al 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.  Degradative succession refers to the temporal changes in species or functional guilds that occurs during the sequential degradation of constituents of a nutrient resource (Townsend et al 2003). The decomposition of a nutrient source is hypothesized to promote succession of active community members as compounds are sequentially degraded (Biddanda & Pomeroy 1988). A classic example of plant litter degradative succession is characterized by a series of stages in which sugar fungi dominate in stage one, followed by cellulolytic fungi in stage two, and lignin degrading fungi in the final stage (Gessner et al 2010). This demonstrates not only the succession of detritivores but also the sequential degradation of litter constituents starting with consumption of the most labile C sources followed by degradation of more complex and polymeric C sources. These single substrate 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 on and subsequent polymeric C degradation. We propose this temporal cascade from labile C degraders preceeding the polymeric C degraders occurs in natural microbial communities, called herein microbial community succession.  The aim of this study is to track the path of C added to soil as a complex C mixture to provide insight into these dynamic systems. A previous study has shown that 13C labeled plant residues enable tracking of C through microbial pathways (Evershed et al 2006). Utilizing this technique with single 13C labeled substrates added as a complex C mixture will allow us to test how different C containing components cascade through discrete taxa within the soil microbial community. Powerful techniques such as nucleic acid stable isotope probing (SIP) coupled with 454 pyrosequencing can then be used to parse out and identify these 13C labeled portions of the microbial community to reveal the community members that are responsible for the transformation of the labeled C. Coupling complex C additions additions to microcosm incubations with nucleic acid stable isotope probing (SIP) provides a means of looking into microbial community functions while minimizing other factors affecting the fate of C. This allows us to sift out the specific organisms or functional guilds that are responsible for the cycling of that specific C substrate.