Chapter 2: LITERATURE REVIEW
2.3 FACTORS AFFECTING SOIL MICROBIAL DIVERSITY
2.3.1 The rhizosphere
The application of information theory to diversity measurement suggests that heterogeneity (or a combination of richness and equitability) can be equated with the amount of uncertainty regarding the species of an individual selected at random from a population. The more species there are and the more even their distribution, the greater the diversity (Peet, 1974; Pielou, 1977).
An alternative approach to conventional statistical methods for environmental studies is the use of artificial neural networks (ANNs) (Dollhopf et al., 2001; Kim et al., 2008). Two different ANN algorithms which are useful in ecological informatics are self-organizing maps (SOMs) and multilayer perceptrons (MLPs). These were used successfully to model convective flows and the associated oxygen transport in a wetland pond. These models were able to ‘learn’ the mechanism of convective transport, resulting in an ability to forecast oxygen saturation near the bottom of the wetland bed (Schramm et al., 2003). In a different study, SOMs and MLPs were efficient at revealing community associations and environmental effects in an inter- taxa study of microbes and benthic macroinvertebrates subjected to different pollution levels in a stream (Kim et al., 2008).
of the plant community critically determine the structural and functional diversity and biomass of the microbial species, as most soil microorganisms depend on autotrophic organisms, including bacteria and plants, for a carbon supply (Johnson et al., 2003a).
Plants in turn are dependent on the soil microbial community. This relationship is often highly specific and is mediated by chemical communication such as that in legume/rhizobial symbioses (Broeckling et al., 2008).
2.3.1.1 Rhizosphere communities
As land use and management are known to affect the rhizosphere, Smalla et al. (2001) determined how dependent the rhizosphere effect was on plants and whether this effect increased by growing the same crop over two consecutive years. They found plant-dependent shifts in the abundance of bacterial rhizosphere communities that were more apparent in the second year, and seasonal shifts in the abundance and structure of these communities in both years. In bulk soils, Bacillus megaterium and Arthrobacter sp. predominated, whereas in the rhizosphere, the proportion of gram- positive bacteria increased. Evenness in the rhizosphere was reduced compared to the bulk soil.
Conflicting reports regarding the relative importance of the effects of soil type or plant species in determining rhizosphere bacterial community composition, have prompted several studies. Marschner et al. (2001) analysed soil- and plant-specific effects on the abundance and diversity of bacterial communities in the rhizospheres of chickpea (Cicer arietinum), rape (Brassica napus) and Sudan grass (Sorghum bicolor). Both soil type and nitrogen fertilization affected plant growth but nitrogen had no significant effect on the bacterial population. It was concluded that complex interactions of soil type, plant species and root zone location influenced rhizosphere bacterial population structure.
In contrast, Miethling et al. (2000) considered that crop species was the main determinant of microbial population characteristics with soil having only a minor effect. This conclusion was based on the comparison of the effects of alfalfa (Medicago sativa) and rye (Secale cereale), soil origin and inoculation with
Sinorhizobium meliloti strain L33, on the establishment of rhizobial communities. In a subsequent study, however, Miethling et al. (2003) found that both soil type and plant species affected structural diversity in the rhizosphere communities of three legumes, namely; alfalfa (M. sativa); common bean (Phaseolus vulgaris) and clover (Trifolium pratense). In the same soil, significant differences were found in the composition of leguminous rhizosphere communities and plant-specific organisms. Dominant alfalfa rhizosphere populations differed in two soils with distinct agricultural histories, and the three leguminous rhizosphere populations could be differentiated.
Anthropogenic disturbance has drastically altered the composition and productivity of plant communities in the arid land ecosystem of the Colorado (USA) plateau grasslands. Kuske et al. (2002) made comparisons at different depths of rhizosphere bacterial communities of the native bunchgrasses Stipa hymenoides and Hilaria jamesii, the invading annual grass Bromus tectorum and of interspaces colonised by cyanobacterial soil crusts. A significant difference was found in the total bacterial population structure and in the Acidobacterium division between the soil crust interspaces and the plant rhizospheres, with large differences also seen among the three rhizospheres, particularly in the Acidobacterium analysis. It was shown that soil depth in plant rhizospheres as well as in the interspaces affected both the total bacterial community and bacteria from the Acidobacterium division, with different members of this division occupying specific niches in the grassland soil.
The effects of genetically engineered (GE) crops on agricultural practice, human health and the environment were studied by Schmalenberger and Tebbe (2003).
Bacterial community diversity in the rhizosphere of a transgenic, herbicide (glufosinate)-resistant sugar beet (Beta vulgaris) was compared with that of its non- engineered counterpart. Differences in community composition due to field and annual variability were evident but there was no detectable effect of transgenic herbicide resistance on the microbial community. In a similar study, Heuer et al.
(2002) investigated the possibility that GE plants could change rhizosphere bacterial consortia through transgenic T4 lysozyme release or by a change in root exudate composition, and thereby change agroecosystems. Bacterial populations from transgenic potato rhizospheres were compared with those of wild-type plants and non- lysozyme producing transgenic controls. The authors found environmental factors
such as season, year and field site influenced the rhizosphere populations but T4 lysozyme expression by GE plants did not.
As little is known of the role of fungi in the rhizosphere, Gomes et al. (2003) investigated fungal communities in bulk and maize rhizosphere soil of two maize cultivars, differing in N utilization. A rhizosphere effect for fungal communities at all stages of plant development was observed, with marked changes in fungal population composition during plant growth. In young maize plant rhizospheres, ascomycetes of the order Pleosporales were selected for, whereas in senescent maize rhizospheres, different members of ascomycetes and basidiomycetic yeasts were found.
At the community level, fungal community response to plants is less well documented than that of bacteria. To clarify the role of plants and root exudates in the structuring of soil fungal communities, Broeckling et al. (2008) investigated the effect of a novel plant species on an existing soil fungal community and also the relative importance of root exudates in structuring this community. Their results showed that the two study plant species (Arabidopsis thaliana and Medicago truncata) could maintain resident soil fungal populations but not non-resident populations and that this was mediated largely through root exudates. They concluded that root exudates were a mechanism by which plants regulate soil fungal community composition.
The indigenous arbuscular mycorrhizal (AM) community in the rhizosphere of maize (Zea mays) genotypes with contrasting phosphorus uptake efficiency was investigated by Oliveira et al. (2009). They showed that the maize genotypes had a greater influence on the rhizosphere mycorrhizal community than soil P levels. Some mycorrhizal groups were found only in the rhizospheres of P-efficient maize genotypes cultivated in low P soils and more mycorrhizal OTUs were present in no- till (NT) maize than in maize under conventional tillage (CT).