Agriculture Reference
In-Depth Information
aggregation. For example, clarification is needed when the term “abundance” is used when
describing the occurrence of microbial taxa in studies of diversity and community
composition within microaggregates and soils in general. Also, the term “dominance” has
been applied based on the frequency with which sequences of particular taxa are encountered
from cloning procedures or sequencing of bands from denaturing or temperature gradient gel
electrophoresis. Dominance and abundance applied this way may not be readily analogous to
their relative abundance as cells or as a proportion of active cells in soil. This is because of
the pitfalls affecting molecular-based, culture-independent methods, particularly when DNA
is isolated from whole soils. These include differential lysis efficiencies of cells, the
harshness of DNA extraction methods such as bead beating, purification steps leading to loss
of DNA, differential target amplification, and intraspecies variation in rDNA repeated
sequences (Witzengerode et al., 1997, Kirk et al., 2004, Green and Martin, 2006).
6.
T
ECHNIQUES FOR
A
SSESSING
M
ICROBIAL
A
GGREGATIVE
F
UNCTION
I
N
S
OIL
A
GGREGATES AND
B
IOFILMS
Various physical measurement techniques including resistance to pressure of artificial
soil aggregates (Caesar-TonThat et al. 2007) or biofilms (Chen et al. 1998, Kreth et al. 2004;
Xavier et al. 2005; Ahimou et al., 2007) amended with individual bacterial species have been
used to pattern the degree of adhesiveness of the binding agents produced by microorganisms.
Our research group has extended this work, using reflectance to measure the ability of
individual species to sediment soil particles.
Electromagnetic spectrum is used for the measurement of spectral response of
biomaterials (Alupoaei et al. 2004; Bohren and Huffman, 1983) and configured into three
reactions: reflectance, absorptance, and transmittance. When the biomaterials receive
incoming irradiation, a portion of the light is absorbed. When the incoming photons impinge
on an object at a certain angle, a portion of the photons is reflected. Light neither absorbed
nor reflected is transmitted. The portions of three spectral reactions vary in the
electromagnetic wavelength of the illumination source and the physical properties of the
target object. The measurement of the transmittance has been widely used to estimate the
density of aggregate solutions (Ramos and McBride, 1996; Dontsova and Norton, 2002;
Joyce and Smith, 2003; Kim et al., 2004), but requires special and expensive equipment
combined with a time-consuming dilution procedure performed on one sample at a time and
is often limited by a short measurement range (Gributs and Burns, 2004). Image-based
reflectance measurement offers an advantage of quick and cost-effective measurement of the
solution density by using a spectral camera capturing an image of the reflected light for
multiple samples at a time. The captured image is calibrated by referencing white (255 in
gray-scale value) and black (0 in gray-scale value) image spots as 100% and 0% reflectance,
respectively, then the reflectance of each target solution image is converted to a gray-scale
value that directly correlates to relative differences of the solution density.
We utilized the image-based reflectance method described above to measure the
aggregative function of predominant culturable bacterial species isolated from
microaggregates collected from a field study with different irrigation and tillage treatments
(details of the field study are described in Sainju et al. (in press)). Bacteria from soils cropped
