Julie Jones

Interactions between crop residue and soil organic matter quality and the functional diversity of soil microbial communities

Abstract The effect of crop residue and soil organic matter (SOM) quality on the functional characteristics of soil microbial communities was investigated. Five shoot and root materials with contrasting biochemical qualities were incorporated into soil taken from a cultivated field (FC) and a field edge (FE). These soils had contrasting native SOM qualities, with organic C contents of 0.9 and 2.5%, respectively. The amended soils were incubated under controlled environment conditions before the metabolic characteristics of the soil microbial community were determined by analysis of the activities of 19 hydrolytic enzymes, by substrate utilization within Biolog GN microplates, and C and N mineralization dynamics. For enzyme and Biolog data, metabolic diversity and community level physiological profiles (CLPP) were determined by calculating Shannons diversity index and performing canonical variate analysis, respectively. Soil type significantly affected mineralization of N from the residues, although the size and direction of the effect varied according to the crop residue material added. Both enzyme and Biolog metabolic diversity were affected by the type of crop residue incorporated. Enzyme diversity was higher in FE relative to FC soil, but soil type had no effect on metabolic diversity recorded in Biolog microplates. There were significant interactions between soil type and crop residue material for respiration, N mineralization and enzyme diversity. During the early stages of decomposition, there were similarities in the response of enzyme and Biolog CLPP to crop residue quality and soil type. In the high OM soil, there was evidence for convergence of CLPP in treatments receiving low and high quality crop residue types. However, in the low SOM soil, CLPP of low and high quality crop residue treatments were clearly different. The length of time required for the CLPP of residue amended soil to converge with that of unamended control soil depended on both residue and soil type. We conclude that both crop residue and SOM quality can affect the functional diversity of the soil microbial community, and that enzyme and Biolog analyses reflect complementary, but not inter-changeable, analyses.

Distribution and diversity of Paraglomus spp. in tilled agricultural soils

Understanding of the ecology of arbuscular mycorrhizal fungi comes primarily from the order Glomerales, and relatively little is known of the ecology of other orders including the Paraglomerales. We investigated the distribution of the Paraglomerales across the English agricultural landscape under different management systems. Soils were collected from 11 tilled agricultural sites. Presence of Paraglomerales was assessed using PCR amplification of 18S/ITS region ribosomal DNA isolated from trap plants, terminal restriction fragment length polymorphism and cloning. Paraglomus spp. were detected in all samples from one location and sporadically in six more, but not at the other locations. Distribution was not related to soil physiochemical characteristics, but the Paraglomaceae were significantly more common in soils under organic management. Cloning of samples from three sites produced sequences closely related to Paraglomus laccatum but only distantly related to Paraglomus brasilianum and Paraglomus occultum. Individual sites had between 10 and 27 separate terminal restriction fragments (T-RFs). The large number of T-RFs reflected a significant sequence diversity in the ITS region. Paraglomerales were, therefore, widely distributed across the agricultural landscape, though with patchy distribution and low diversity. More intensive agricultural management appeared to impact negatively on Paraglomus spp.

Evidence for functional redundancy in arbuscular mycorrhizal fungi and implications for agroecosystem management

Arbuscular mycorrhizal (AM) fungi provide benefits to host plants and show functional diversity, with evidence of functional trait conservation at the family level. Diverse communities of AM fungi ought therefore to provide increased benefits to the host, with implications for the management of sustainable agroecosystems. However, this is often not evident in the literature, with diversity saturation at low species number. Growth and nutrient uptake were measured in onions in the glasshouse on AM-free phosphorus (P)-poor soil, inoculated with between one and seven species of AM fungi in all possible combinations. Inoculation with AM fungi increased shoot dry weight as well as P and copper concentrations in shoots but reduced the concentration of potassium and sulphur. There was little evidence of increased benefit from high AM fungal diversity, and increasing diversity beyond three species did not result in significantly higher shoot weight or P or Cu concentrations. Species of Glomeraceae had the greatest impact on growth and nutrient uptake, while species of Acaulospora and Racocetra did not have a significant impact. Failure to show a benefit from high AM fungal diversity in this and other studies may be the result of experimental conditions, with the benefits of AM fungal diversity only becoming apparent when the host plant is faced with multiple stress factors. Replicating the complex interactions between AM fungi, the host plant and their environment in the laboratory in order to fully understand these interactions is a major challenge to AM research.

Study of the spatial variation of the biodegradation rate of the herbicide bentazone with soil depth using contrasting incubation methods

Vertical and horizontal spatial variability in the biodegradation of the herbicide bentazone was compared in sandy-loam soil from an agricultural field using sieved soil and intact soil cores. An initial experiment compared degradation at five depths between 0 and 80 cm using sieved soil. Degradation was shown to follow the first-order kinetics, and time to 50% degradation (DT(50)), declined progressively with soil depth from 56 d at 0-10 cm to 520 d at 70-80 cm. DT(50) was significantly correlated with organic matter, pH and dehydrogenase activity. In a subsequent experiment, degradation rate was compared after 127 d in sieved soil and intact cores from 0 to 10 and 50 to 60 cm depth from 10 locations across a 160x90 m portion of the field. Method of incubation significantly affected mean dissipation rate, although there were relatively small differences in the amount of pesticide remaining in intact cores and sieved soil, accounting for between 4.6% and 10.6% of that added. Spatial variability in degradation rate was higher in soil from 0 to 10 cm depth relative to that from 50 and 60 cm depth in both sieved soil and intact core assessments. Patterns of spatial variability measured using cores and sieved soil were similar at 50-60 cm, but not at 0-10 cm depth. This could reflect loss of environmental context following processing of sieved soil. In particular, moisture content, which was controlled in sieved soil, was found to be variable in cores, and was significantly correlated with degradation rate in intact topsoil cores from 0 to 10 cm depth.

Growth and nutritional responses to arbuscular mycorrhizal fungi are dependent on onion genotype and fungal species

Plant roots associate with diverse communities of arbuscular mycorrhizal fungi (AMF), providing the plant with mineral nutrients in exchange for carbohydrates. We investigated how onion genotype and fungal species interact to determine the benefit of the symbiosis to the plant and the potential benefit of a mixed AMF community. Ten onion genotypes were inoculated with five different AMF species, or a mixture of all five, then plant growth/nutrient uptake was compared to non-inoculated controls. 18S ribosomal RNA (rRNA) terminal restriction fragment length polymorphism was used to compare the abundance of each AMF species between genotypes. Growth and nutrient uptake were significantly different between genotypes and AMF species, but no genotype × AMF interaction was observed, indicating a general response to AMF. Potentially useful pre-breeding material was identified for use in low-input systems. Inoculation of plants with AMF led to significant increases in the concentrations of N, P and Cu, whereas significant decreases in Ca, K, Na, Fe, Mn and Zn were observed. There were significant differences between AMF species in their effect on plant nutrition. Inoculation with Acaulospora spinosa led to a significant increase in shoot S concentration which may have implications for plant defence and pungency. No additive effect of a mixed community was observed. Contrasting genotypes showed subtly different preferences for associating with AMF from a mixed community, suggesting a selection process controlled by the plant and/or the fungi. The implications of this work for the development of sustainable, low-input systems are discussed.

Towards new sources of resistance to the currant-lettuce aphid (Nasonovia ribisnigri)

Domesticated lettuce varieties encompass much morphological variation across a range of crop type groups, with large collections of cultivars and landrace accessions maintained in genebanks. Additional variation not captured during domestication, present in ancestral wild relatives, represents a potentially rich source of alleles that can deliver to sustainable crop production. However, these large collections are difficult and costly to screen for many agronomically important traits. In this paper, we describe the generation of a diversity collection of 96 lettuce and wild species accessions that are amenable to routine phenotypic analysis and their genotypic characterization with a panel of 682 newly developed expressed sequence tag (EST)-linked KASP™ single nucleotide polymorphism (SNP) markers that are anchored to the draft Lactuca sativa genome assembly. To exemplify the utility of these resources, we screened the collection for putative sources of resistance to currant-lettuce aphid (Nasonovia ribisnigri) and carried out association analyses to look for potential SNPs linked to resistance.