chuckpr removed degradative succession hypothesis material  over 8 years ago

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the development and refinement of global C models  \citep{Bradford2008,Neff_2001,McGuire2010,Wieder2013}.  % Fakesubsubsection: The degradative succession hypothesis  The degradative succession hypothesis is a simple framework that explains  the impact of microbial ecophysiology on the decomposition of plant biomass.  Most plant C is comprised of cellulose (30-50\%) followed by hemicellulose  (20-40\%), and lignin (15-25\%) \citep{Lynd2002}. Hemicellulose, being the most  soluble, degrades in the early stages of decomposition. Xylans are often an  abundant component of hemicellulose, and xylose is often the most abundant  sugar in hemicellulose, comprising as much as 60-90\% of xylan in some plants  (e.g switchgrass \citep{Bunnell2013}). The degradative succession hypothesis  posits that fast growing organisms proliferate in response to the labile  fraction of plant biomass such as sugars \citep{Garrett1963,Bremer1994}  followed by slow growing organisms that target structural C such as cellulose  \citep{Garrett1963}. Evidence to support the degradative succession hypothesis  comes from observing soil respiration dynamics and characterizing  microorganisms cultured at different stages of decomposition. Microorganisms  that consume labile C in the form of sugars proliferate during the initial  stages of decomposition \citep{Garrett1951,Alexander1964}, and metabolize as  much as 75\% of sugar C during the first 5 days \citep{Engelking2007}. In  contrast, cellulose decomposition proceeds more slowly with rates increasing  for approximately 15~days while degradation continues for 30-90~days  \citep{Hu1997,Engelking2007}. This hypothesis is generally consistent with the  common categorization of soil microorganisms as either fast growing copiotrophs  or slow growing oligotrophs \citep{Fierer2007}. The degree to which the  degradative succession hypothesis presents an accurate model of litter  decomposition has been questioned  \citep{AnneliseHKjoller2002,Frankland_1998,Osono_2005} and it's clear that we  need new approaches to dissect microbial contributions to C transformations in  soils.  % Fakesubsubsection:Though microorganisms mediate  Though microorganisms mediate 80-90\% of the soil C-cycle  \citep{ColemanCrossley_1996,Nannipieri_2003}, and microbial community 

microbial communities (based on surveys of the SSU rRNA genes in soil)  \citep{Janssen2006,Buckley2002}.   % Fakesubsubsection: Functional niche characterization  In addition to understanding the C-cycling roles of specific microbial taxa in  soil, characterizing the functional niches soil microorganisms is necessary to  predict whether and how biogeochemical processes vary with microbial community  composition. Functional niches are defined by soil microbiologists and have  been successfully incorporated into biogeochemical process models (E.g.  \citep{wieder_2014a,Kaiser2014a}). In some C models ecological strategies such  as growth rate and substrate specificity are parameters for functional niche  behavior \citep{Kaiser2014a}. The phylogenetic breadth of a functionally  defined group is often inferred from the distribution of diagnostic genes  across genomes \citep{Berlemont2013} or from the physiology of isolates  cultured on laboratory media \citep{Martiny2013}. For instance, the wide  distribution of the glycolysis operon in microbial genomes is interpreted as  evidence that many soil microorganisms participate in glucose turnover  \citep{McGuire2010}. However, the functional niche may depend less on the  distribution of diagnostic genes across genomes and more on life history traits  that allow organisms to compete for a given substrate as it occurs in the soil.  For instance, fast growth and rapid resuscitation allow microorganisms to  compete for labile C which may often be transient in soil. Hence, life history  traits may constrain the diversity of microbes that metabolize a given C source  in the soil under a given set of conditions. Therefore, it is important to  contrast characterizations of microbial traits from genomic and/or culture  based studies with observations of active microorganisms in microcosms and  under \textit{in situ} conditions to fully understand the breadth of   functional niches in soil.  % Fakesubsubsection:Nucleic acid SIP  Nucleic acid stable-isotope probing (SIP) links genetic identity and activity  without the need diagnostic genetic markers or cultivation and has expanded our 

environmentally realistic experimental conditions. It is also possible to  sequence rRNA genes from numerous density gradient fractions across multiple  samples thereby increasing the resolution of a typical nucleic acid SIP  experiment \citep{Verastegui_2014}. With this improved resolution the activity  of more soil microorganisms can be assessed. Further, since microbial  activities can be more comprehensively assessed, we can begin to determine the  ecological properties of functional groups defined by a specific activity in a  DNA-SIP experiment.  We have employed such a high resolution DNA stable isotope probing approach to explore the assimilation of both xylose and cellulose into bacterial DNA in an agricultural soil. % Fakesubsubsection: We add a complex amendment  We added to soil a complex amendment representative of organic