Agriculture Reference
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between activity and cell size, cell size and culturability and activity and culturability. We
believe based on this reasoning that isolating the bacteria occurring at the highest population
levels in soil microaggregates is a necessary step to the elucidation of the key microbial
effectors of soil aggregation. While it cannot be precluded that less abundant members of
prokaryote communities associated with microaggregates might have some role in
aggregation, it would be reasonable to conclude that the most abundant prokaryotic species
found (by culturing) in microaggregates play the key roles in aggregation. Since the means
for aggregating soil are regarded as essentially through binding with extracellular
polysaccharides, one could conclude that the main players would tend to be culturable. And if
they are to exert a major effect on their soil environment, they would need to be among the
more numerous organisms in that environment.
While it has become almost axiomatic that the value of culture-based studies is highly
compromised (such as to be negligible, judging from passing references made to, and quite
unequivocally dismissive comments by the reviewers of a paper by the authors employing
culture-based methods) the value of such studies has been alluded to quite often (Ellis et al.,
2003; Janssen, 2006; Palleroni, 1997; Zinder and Salyers, 2001). This value deserves some
emphasis here. The need for culture-based methods has been acknowledged by advocates of
molecular methods for studying soil biology (Muyzer and Smalla, 1998), as providing
“phylogenetic frameworks of protein-encoding gene sequences as well as for the
classification and identification of closely related bacteria”. The culture of even highly
fastidious microbes is viewed as indispensable because pure cultures “allow a comprehensive
understanding of the physiology, cell-cell interactions and permit access to metabolic
pathways” of such microbes (Darby and Welburn, 2006). The latter authors further saw
isolation in culture as “a limiting factor in the study of these organisms…”, and the same
applies to soil aggregation by microbes. The overall issue of the burgeoning of molecular
methods in microbial ecology elicited this comment by others: “We need to guard against the
research becoming too technology driven” (O'Donnell et al., 2001). A consensus has since
developed that “new technologies will increasingly lead us down blind, non-generalist and
expensive alleyways if studies are not directed and driven by theory” (Prosser et al., 2007).
These workers further stressed the need to bridge the gap between descriptive studies of soil
microbial diversity and soil function and between disciplines for microbial ecology to
advance. It is also important to recall that knowledge of quorum sensing, discussed above,
was initially derived from and has progressed chiefly through studies using culturable
bacterial species, and perhaps this will be true of soil aggregation as well. Future studies
suggested in the present review such as the role of bacterial lectins, quorum sensing, and
biofilm networks or by others such as the need to determine which species are the most
effective stabilizers (aggregators) of soil (Tisdall, 1994), will all rely on the need to culture
the bacteria involved.
The isolation of the most abundant species of bacterial communities of microaggregates
is thus supported by the several points outlined above: the correlation of culturability with
activity, the need for culturable species to initiate ecological and physiological studies of the
bacterial role in soil aggregation. For example, individual isolates found to be occurring at the
highest dilution levels should be assessed for their ability to aggregate soil singly or in
combination.
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