Microbial Abundance and Distribution in Soil

Unfortunately for the soil ecologist, the distribution and abundance of microorganisms is so patchy that it is very difficult to make an accurate determination of their mean abundances without dealing with a very high variance about that mean, when viewed on a macro scale. Part of this variation is due to the close "tracking" of organic matter "patches" by the microbes. There are aggregations of microbes around roots (the often-cited "rhizosphere") (Lynch, 1990), around fecal pellets and other patches of organic matter (Foster, 1994), and in pore necks (Fig. 3.3) (Foster and Dormaar, 1991). In addition, microorganisms concentrate in the mucus secretions that line the burrows of earthworms (the "drilosphere," as defined by Bouché [1975] and reviewed by Lee [1985]). The phenomenon of "patches" is discussed more in Chapter 6.

A large proportion of soil ecology studies has focused on processes occurring in the O and upper A horizons because so much of the short-term dynamics occurs there. With tools of microbial community analysis, Fierer et al. (2003) used phospholipid fatty acid (PLFA) analysis to examine the vertical distribution of specific microbial groups and their diversity in two soil profiles down to a depth of 2 m. The number of individual PLFAs decreased by about one-third from the soil surface down to 2 m. Changes in certain ratios of fatty acid precursors and ratios of total saturated to total monounsaturated fatty acids increased with soil depth, indicating that microbes in the lower horizons were more carbon limited at greater depths. Interestingly, approximately 35% of the total amount of microbial biomass was found in soil below a depth of 25 centimeters (cm). Gram-positive bacteria and actinomycetes tended to increase in proportional abundance with depth, whereas Gramnegative bacteria, fungi, and protozoa were highest at the soil surface.

Soil is an impressively heterogeneous matrix of minerals and organic matter. Ways in which this heterogeneity in organic matter and texture can influence microbial populations have been widely studied for more than a century. A number of studies using transmission electron microscopy (TEM) and scanning electron microscopy (SEM) have revealed the intimate associations of bacteria and fungi with soil aggregates (Figs. 3.4 and 3.5) (V. V. S. R. Gupta, personal communication).

With the development of more sophisticated imaging tools and statistical analyses of data, there have been several studies of microbial spatial patterns at the field or plot scale. Unfortunately, these studies have not spanned the range of spatial variability, which may exist at levels well below the millimeter scale (Nunan et al., 2002). Taking a large vol-

FIGURE 3.3. (a) An amoeba probing a soil microaggregate containing cell wall remnants (CWR) and a microcolony of bacteria (B); P, pseudopodium; R, root; S, soil minerals; bar, 1 Mm (from Foster and Dormaar, 1991). (b) An amoeba with an elongated pseudopodium reaching into a soil pore. The amoeba contains intact ingested bacteria in its food vacuoles (from Foster and Dormaar, 1991). (c) An amoeba with partly digested bacteria in food vacuoles; note bacterium enclosed by a pseudopodium (P) (from Foster and Dormaar, 1991). (d) A pseudopodium associated with a Gram-positive microorganism (from Foster and Dormaar, 1991).

FIGURE 3.3. (a) An amoeba probing a soil microaggregate containing cell wall remnants (CWR) and a microcolony of bacteria (B); P, pseudopodium; R, root; S, soil minerals; bar, 1 Mm (from Foster and Dormaar, 1991). (b) An amoeba with an elongated pseudopodium reaching into a soil pore. The amoeba contains intact ingested bacteria in its food vacuoles (from Foster and Dormaar, 1991). (c) An amoeba with partly digested bacteria in food vacuoles; note bacterium enclosed by a pseudopodium (P) (from Foster and Dormaar, 1991). (d) A pseudopodium associated with a Gram-positive microorganism (from Foster and Dormaar, 1991).

FIGURE 3.4. Scanning electron microscopy (SEM) picture of a macroaggregate (250- to 500-|im diameter) with particulate organic matter and hyphae (V. V. S. R. Gupta, with permission).
FIGURE 3.5. Amoebae feeding on fungi (V. V. S. R. Gupta, with permission).

ume of soil, both topsoil and subsoil (3 x 3 x 0.9m) from an arable field, Nunan et al. (2002) prepared subsampled cores and biological thin sections in which the in situ distribution of bacteria could be quantified. They acquired spatially referenced RGB digital images using epifluo-rescence microscopy at 630x magnification. Average bacterial numbers per thin section were calculated using nine replicate images captured from each thin section (Fig. 3.6). Analysis of spatial dependence or continuity of soil bacterial density was performed using geostatistical tools at three scales: (1) centimeter to meter, (2) millimeter to centimeter, and (3) micrometer to millimeter scale, using appropriate semivariogram formulas (for more information on use of semivariograms, see Robertson and Gross [1994]). Spatial structure was found only at the micrometer

FIGURE 3.6. Spatial distribution of sampling points in topsoil (a). Solid circles form systematic random lattice and open circles form a biased random cluster. An undisturbed core (b) was sampled at each point and a thin section (c) cut from the horizontal plane. Nine spatially referenced images, in which bacteria were mapped, were acquired from each thin section. Average bacterial density per thin section was calculated and the values used to study large-scale variability. Bacterial maps were divided into 100 quadrats and bacterial density in each quadrat calculated. There were 900 quadrats per thin section and these bacterial density values were used to study microscale spatial variability (from Nunan et al., 2002).

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