Soil ecology and agroecosystem studies - Microbial Ecology in Sustainable Agroecosystems - page 8

nitrogen than they require for growth (i.e., invertebrates are net mineralizers of nitrogen),
enhanced microbial growth through grazing leads to increased nitrogen availability for
plants. When this process plays itself out within the rooting zone of plants, a positive
feedback can occur—plants and the soil food web feed off one another's excess and waste.
Under this scenario, plants exude excess photosynthate in the form of labile carbon sub-
strates from their roots, which in turn are utilized by microbes and subsequently as food
for microbivorous invertebrates, which release nitrogenous waste that is utilized by plants
(Gupta et al., 1999; Ingham et al., 1985).
Many invertebrates feed directly on plant materials and organic substrates. The
fragmentation or comminution of these materials enhances their decomposition. For
plant structural materials, comminution increases the surface areas of the materials and
exposes cytoplasm, thereby enabling greater access by microbes. Decomposition is fur-
ther accelerated as the feeding activity often results in the translocation of nitrogen from
the soil to the substrate in the form of fecal material and through fungal hyphae. Grazing
by invertebrates disseminates microbes from one organic source to another as many
microbes adhere to invertebrate exoskeletons and cuticles and survive passage through
their digestive tracts.
The diversity of archaea and bacteria is as yet little known, but with the use of new
massive parallel sequencing devices (Roche 454 and other pyrosequencing techniques;
Buée et al., 2009), we are beginning to approach an understanding of the very large bio-
diversity of these organisms. Metagenomics encompasses the full array of microorgan-
isms present in ecosystems at any point in time (Handelsman, 2004; Van Elsas et al.,
2008). Metatranscriptomics refers to the number of microbes in a given community or
ecosystem that are active, namely, respiring or synthesizing at a given time. Stable isotope
probing (SIP) platforms provide additional avenues to track a specific element (C or nutri-
ents) through microbial and faunal communities, facilitating the linkage of diversity to
function. “At any moment, an estimated 10 30 bacterial and archaeal genes are mediating
essential ecological processes throughout the world” (Moran, 2009). In a number of marine
microbial ecological studies, diurnal patterns have been measured. Thus, bacterioplank-
ton communities in oligotrophic waters of the North Pacific Ocean showed greater invest-
ments in energy acquisition and metabolism (photosynthesis, oxidative phosphorylation,
and C1 compound metabolism) during the day and in biosynthesis (of membranes, amino
acids, and vitamins) at night, according to an analysis of RNA transcripts from these peri-
ods (Poretsky et al., 2009).
1.3 An integrative framework
A framework as described that links soil microbes and invertebrates directly to pedogenic
processes is beginning to emerge. Soil food webs and the differences in microbial and
invertebrate life-forms within them offer a starting point for connecting the components
of the detrital food web to soil pedogenesis and SOM dynamics (Coleman et al., 1983, 2004).
Coleman et al. (1983) identified a bacterial-based fast cycle and fungal-based slow cycle
within soils. Subsequent studies revealed that these fast cycles and slow cycles were borne
from the trophic interactions of detritus to bacteria and their consumers and from detritus
to fungi and their consumers ( Figure 1.2 ; Hunt et al., 1987; Moore et al., 1988; de Ruiter et
al., 1996). These dominant trophic pathways, or “energy channels,” are ubiquitous across
ecosystem types and grounded in the basic architecture of soil food webs and their struc-
tural stability (Moore and Hunt, 1988).