Ashley Campbell edited introduction.tex  over 9 years ago

Commit id: c9eb5dead3d90c8fd1e66af5a31fdc1e1f04ab1c

deletions | additions      

       

An estimated 80-90\% of 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 methods limitations. Soils are biologically, chemically, and physically complex 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{Sollins_Homann_Caldwell_1996}. Further, rates of metabolism are often measured without knowing the identity of the microbial species involved \cite{ndi_Pietramellara_Renella_2003} leaving the importance of specific community members towards maintaining ecosystem functions unknown \cite{Allison_2008,ndi_Pietramellara_Renella_2003,Schimel_2012}. Litter bag experiments have shown that the community composition of soils can have quantitative and qualitative impacts on the breakdown of plant materials \cite{Schimel_1995}. Reciprocal exchange of litter type and microbial inocula under controlled environmental conditions reveals that differences in community composition can account for 85\% of the variation in litter carbon mineralization \cite{Strickland_2009}. In addition, assembled communities of cellulose degraders reveal that the composition of the community has significant impacts on the rate of cellulose degradation \cite{Wohl_2004}.   Carbon 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 \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} \cite{Hu_1997,Rui_2009}  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. 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.