Impact of management practices on soil microflora : implications for subsequent effects on plants and insects

Abstract

The perceived benefits of food grown under organic (low-input) management practices include lower levels of potentially harmful pesticides and an increased awareness of environmental protection. It is also believed that such crops are inherently more tolerant to biotic stresses, although there is little evidence to support this. The aims of this thesis are to investigate differential effects of conventional and organic management practices on soil microbial community structure and consequences for plant growth using Arabidopsis thaliana, as the model plant species. Soil used in the study was from ‘Palace Leas hay plots long term field trial’ where Plot 2 is fertilised using farmyard manure (FYM) and Plot 13 is fertilised using inorganic fertilisers. Changes in community structure of the two different fertiliser amendments were measured over time using T-RFLP. The laboratory addition of inorganic fertiliser had a significant effect on the bacterial community (p=0.047); however, neither initial field treatment nor time had any effect (p=0.263, p=0.842, respectively). The fungal community showed no significant effect from field treatment, laboratory amendment or time (p=0.342, p=0.131, p=0.219). A. thaliana plants grown in conventionally fertilised soil (Plot 13) grew slower and were smaller than those grown in FYM amended soil (Plot 2). After 28 days, rosette area was 552.1cm2 and 418.4cm2 for plants grown with FYM and mineral amendment, respectively (p=0.01). Dry weights of the rosette were 92.6mg and 72.8mg for FYM and conventionally grown plants respectively (p=0.044). Levels of boron (org=0.73ppm, conv=0.31ppm at 30 days), calcium (org=177.7ppm, conv=124.9ppm, at 30 days), potassium (org=331.0ppm, conv=161.5ppm at 30 days) and magnesium (org=29.5ppm, conv=18.3ppm at 30 days) were all significantly higher in FYM grown plants. The ratios of K:Ca and K:Mg in plants grown on FYM amended soil were higher than for those grown on mineral fertiliser amended soil, indicating that the latter plants were under increased stress. Analysis of the leaf proteome demonstrated that nitrilase 1, 14-3-3 like protein GF14, Heat Shock Cognate 70kDa Protein 1, and glutathione-S-transferases PM24 and ERD13 were up-regulated in conventionally grown plants, whilst lipoxygenase and Annexin D6 were downregulated. Again, this indicates that A.thaliana is under increased stress when grown in conventionally treated soil. Glucosinolates and volatiles, produced as part of the plant’s inducible defence system, were investigated by HPLC/MS. There were both qualitative and quantitative differences in glucosinolate profiles. Plants grown on FYM amended soils had higher levels of the alkyl glucoside gluconaprin, whilst those on the conventionally treated soil contained glucoraphanin and glucoerucin. Subsequent aphid infestation resulted in a small (7% and 8% for conventionally and FYM grown plants, respectively) increase in the indole glucosides. Those grown on the conventionally amended soil produced 26 different volatile chemicals compared to 18 from the FYM amended soil (Plot 2); average levels of volatiles released where higher from the former than the latter. The results indicate that there was little effect of amendment practice on direct defence mechanisms in A. thaliana, although indirect defence was altered by amendment practice. The interactions between fertiliser amendment, soil microbial community, and plant and aphid herbivores were investigated using Structural Equation Modelling. The only significant relationship was a positive correlation between organic FYM amendment and rate of plant growth (p=0.004), indicating that the use of FYM as an additional amendment increased plant growth. The effect of the rate of plant growth on the rate of aphid reproduction was almost significant and negative (p=0.067), indicating that the rate of plant growth negatively impacted the rate of aphid reproduction.