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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