Agriculture Reference
In-Depth Information
such conditions would limit populations of anaerobes. However, in the limited number of
recent studies, a range of aerotolerant anaerobes have been isolated and identified from
diverse habitats (Kato et al., 2004; Matthies et al., 2004; Gossner et al., 2006; Kusel et al.,
2006) and there is a documented ability of aerobic and anaerobic bacteria to stably coexist
with aerobes in artificial communities and plant rhizospheres (Kato et al., 2005; Nikolausz, et
al., 2006). This would perhaps indicate that less stringent and accessible conditions would be
feasible for working with such anaerobes than the conditions prescribed for their study
(Kaspar and Tiedje, 1994). Thus, studies of the role of anaerobes in soil aggregation need not
be restricted to specialists.
3.
T
HE
N
EED FOR
C
ULTURE
-B
ASED
M
ETHODS
Cause-and-effect investigation of the role of specific bacteria in the important issue of
soil aggregation is highly constrained without cultural methods. Even a sophisticated study
like that of Vaisenen et al. (2005) lacked direct evidence and identification of prominent or
predominant players in the process of aggregation. Determination of key bacterial species in
soil aggregation was to our knowledge last called for in a major work more than a decade
previous (Tisdall, 1994) to the writing of the present paper. This need remained unmet to our
knowledge until we initiated work to address it in a recent study (Caesar-TonThat et al.,
2007). Progress in this area need not await the development of methods that overcome the
admitted flaws of culture- (or molecularly-) based methods. We feel the most useful
information currently would be to know what culturable organisms are predominant within
soil aggregates and their likelihood to cause aggregation. This avenue has not been pursued to
date. We are interested in culturable aggregators because it affords the ability to amend the
soil with them in further work, and to develop means of assaying for their ability to form
water-stable so aggregates. Much molecular method-based work in soil aggregation, while
contributing in essential ways to the field, is not cause-and-effect in nature. Several practical
handicaps of molecular methods presently preclude other than descriptive or correlative
studies: the lack of a sufficient blast database of taxa with which to compare sequences for
reliable identification, the up-front time and expense of methods such as real-time PCR (for
which accurate primers must be developed and this would rely on identified, cultured
organisms from which DNA would be extracted) that might allow quantification and the
overall lack of any background on which to base studies that would compare those that could
be identified using molecular methods with known aggregating bacteria. As described above,
there is a documented relationship between rhizosphere-driven stimulation of bacterial
populations, production of extracellular polysaccharides by such bacteria (and root mucigels,
possibly partly in response to rhizosphere bacterial activity (Barber and Lynch, 1977) and
resulting soil aggregation. We interpret this to be a relationship between an enrichment in the
rhizosphere of larger populations of bacteria, the rhizosphere effect, (Katznelson 1965), the
production of extracellular polysaccharides by fast-growing species such as
Pseudomonas
and
Serratia
spp. (Marilley and Aragno, 1999; Berg et al., 2005) and aggregation of soil. Thus, it
is reasonable to hypothesize that population levels of bacteria that tend to be culturable would
be determinative in soil aggregation. This is essentially an extension of the reasoning set forth
by Ellis et al. (2003): that previous studies have shown that there are positive correlations
