Ashley Campbell edited introduction.tex  over 10 years ago

Commit id: e2f38ed89abd9b08fd6176d7871d981272cf7177

deletions | additions      

       

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. 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).   \indent \setlength\parindent  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 constrained resolution of identification by fingerprinting and cloning techniques and to our knowledge are usually conducted as single substrate experimental designs with few exceptions (refs). SIP studies use single substrate additions to minimize signal dilution, however, it detracts from how microbes may experience that substrate in nature, likely in a complex C mixture, making it challenging to estimate it's biological relevance in the environment. Plant residues represent the largest proportion of C entering soil systems and are composed primarily of cellulose making it the most abundant biopolymer globally (Paul & Clark 1989, Berg & Laskowski 2005, Klemm et al 2005, Coleman & Crossley 1996, Nannipieri & Badalucco 2003). Much work has been done to study cellulose degradation by microorganisms (Beguin & Aubert 1994, Lynd et al 2002, Haicher et al 2007, Eichorst & Kuske 2012). With the advent of culture independent techniques, we have discovered that there are far more cellulose degraders than our limited culture collection represents. Some studies have used labeled leaf litter to identify soil decomposers, however, this makes it difficult to differentiate which organisms are responsible for the actual degradation of the cellulose (Evershed et al 2006). Other cellulose degradation studies add cellulose as a single substrate addition to a cultured cellulose degrader or to soil (Haichar et al 2007, Li et al 2009, Eichorst & Kuske 2012). This method may present false positives, as an organism that might not normally consume a given C substrate may opportunistically do so under the circumstances that it is the only C source available. Additionally, organisms may behave quite differently when given a large dose of a nutrient source versus a complex C mixture which they may actually encounter in nature.