Agriculture Reference
In-Depth Information
alter their morphology or physiology for dessication and starvation resistance (Lappin-Scott
and Costerton, 1990).
Despite mention of a role for ectomycorrhizae (and thus by extension basidiomycetes) in
soil aggregation in a relatively early assessment of the microbial ecology of soil aggregation
(Tisdall, 1994), such fungi were subsequently largely unexplored for their role in soil
aggregation until recently. A study by the senior author showed polysaccharide production as
the basis of the ability of a basidiomycete fungus to form soil aggregates, (Caesar-TonThat
and Cochran, 2000). In this study, pure cultures of the fungus and development of an assay
for formation of water stable aggregates allowed the authors through experimentally derived
data to contribute knowledge of the role of a basidiomycete to soil aggregation.
5.
M
ICROBIAL
D
IVERSITY IN
S
OIL
A
GGREGATES
Inventories of species within any given ecological niche, thereby establishing the
diversity index of that niche have been of enormous value in ecology. When this diversity is
inventoried with molecular based methods, clearly the most comprehensive means to
establish the magnitude of diversity, a picture emerges of a greater totality of species than any
other means. Such measurements of total diversity move beyond the purely descriptive when
they can be related to such questions as whether soil fertility or disease suppressiveness are
affected or enhanced by microbial diversity per se or whether management methods or
restoration efforts affect it and vice versa (Garbeva et al., 2006, Hartmann and Franco, 2006,
Hiddink et al., 2005). The culturability/activity thesis described previously, unchallenged
since its introduction, applies here. The ecological utility of assessing total bacterial diversity
in water stable microaggregates with molecular methods compared to culturing the most
abundant bacteria can be considered with an analogy drawn from this same authors work. The
total microbial diversity in microaggregates can be likened to the seed-bank in plant ecology,
which would represent “potential diversity”, whereas the culturable species represent the
plant community or “realized diversity” (Prosser et al., 2007). The uncultured species, as the
analogous dormant members of a seed-bank, likely represent the adaptability to
environmental change of either ecosystem rather than active members of the community.
Thus, while great stress is placed on the low proportion of microbial species in soil that are
typically culturable among the larger set of taxonomic units detected using molecular
methods, whether the larger set represents other than inactive species, i.e., “potential
diversity”, remains to be shown. It remains true that most significant functions in soil such as
nitrogen cycling, beneficial symbiotic associations between bacteria and plants, the
mineralization of plant nutrients and suppressiveness to plant diseases are attributable
(entirely or predominantly) to bacterial species that are culturable. In addition, a closer
examination of the gap between species culturable and those not yet cultured indicates that
the ability to culture representatives of the phylogenetic diversity in soil is better than the 1%
often quoted (Janssen, 2006).
Typically in molecular studies the specification of the most abundant members of any
measured community and their precise taxonomic identity have either not been directly
addressed or remain elusive. These issues impede the practical application of the results for
developing a fuller understanding of the microbial ecology and physiology of soil
