Gary D. Bending

Phyllosphere microbiology with special reference to diversity and plant genotype

The phyllosphere represents the habitat provided by the aboveground parts of plants, and on a global scale supports a large and complex microbial community. Microbial interactions in the phyllosphere can affect the fitness of plants in natural communities, the productivity of agricultural crops, and the safety of horticultural produce for human consumption. The structure of phyllosphere communities reflects immigration, survival and growth of microbial colonists, which is influenced by numerous environmental factors in addition to leaf physico‐chemical properties. The recent use of culture‐independent techniques has demonstrated considerable previously unrecognized diversity in phyllosphere bacterial communities. Furthermore, there is significant recent evidence that plant genotype can play a major role in determining the structure of phyllosphere microbial communities. The main aims of this review are: (i) to discuss the diversity of phyllosphere microbial populations; (ii) to consider the processes by which microbes colonize the phyllosphere; (iii) to address the leaf characteristics and environmental factors that determine the survival and growth of colonists; (iv) to discuss microbial adaptations that allow establishment in the phyllosphere habitat and (v) to evaluate evidence for plant genotypic control of phyllosphere communities. Finally, we suggest approaches and priority areas for future research on phyllosphere microbiology.

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.

Microbial degradation of isoproturon and related phenylurea herbicides in and below agricultural fields

Abstract The phenylurea herbicides are an important group of pesticides used extensively for pre- or post-emergence weed control in cotton, fruit and cereal crops worldwide. The detection of phenylurea herbicides and their metabolites in surface and ground waters has raised the awareness of the important role played by agricultural soils in determining water quality. The degradation of phenylurea herbicides following application to agricultural fields is predominantly microbial. However, evidence suggests a slow degradation of the phenyl ring, and substantial spatial heterogeneity in the distribution of active degradative populations, which is a key factor determining patterns of leaching losses from agricultural fields. This review summarises current knowledge on the microbial metabolism of isoproturon and related phenylurea herbicides in and below agricultural soils. It addresses topics such as microbial degradation of phenylurea herbicides in soil and subsurface environments, characteristics of known phenylurea-degrading soil micro-organisms, and similarities between metabolic pathways for different phenylurea herbicides. Finally, recent studies in which molecular and microbiological techniques have been used to provide insight into the in situ microbial metabolism of isoproturon within an agricultural field will be discussed.

Spatial variability in the degradation rate of isoproturon in soil.

Thirty samples of soil were taken at 50-m intersections on a grid pattern over an area of 250 x 200 m within a single field with nominally uniform soil characteristics. Incubations of isoproturon (3-(4-isopropylphenyl)-1,1-dimethylurea) under standard conditions (15 degrees C; -33 kPa soil water potential) indicated considerable variation in degradation rate of the herbicide, with the time to 50% loss (DT50) varying from 6.5 to 30 days. The kinetics of degradation also varied between the sub-samples of soil. In many of them, there was an exponential decline in isoproturon residues; in others, exponential loss was followed by more rapid rates of decline; in a few soil samples, rapid rates of loss began shortly after the start of the incubations. In more detailed studies with soils from a smaller number of sub-sites (20), measurements were again made of isoproturon degradation rate, and the soils were analysed for organic matter content, pH, and nutrient status (N, P, K). Measurements were also made of isoproturon adsorption by the soils and of soil microbial biomass. Patterns of microbial metabolism were assessed using 95 substrates in Biolog GN plates. Soils showing rapid biodegradation were generally of higher pH and contained more available potassium than those showing slower degradation rates. They also had a larger microbial biomass and greater microbial metabolic diversity as determined by substrate utilisation on Biolog GN plates. The implications of the results for the efficacy and environmental behaviour of isoproturon are discussed.

Development of novel assays for lignin degradation: comparative analysis of bacterial and fungal lignin degraders

Two spectrophotometric assays have been developed to monitor breakdown of the lignin component of plant lignocellulose: a continuous fluorescent assay involving fluorescently modified lignin, and a UV-vis assay involving chemically nitrated lignin. These assays have been used to analyse lignin degradation activity in bacterial and fungal lignin degraders, and to identify additional soil bacteria that show activity for lignin degradation. Two soil bacteria known to act as aromatic degraders, Pseudomonas putida and Rhodococcus sp. RHA1, consistently showed activity in these assays, and these strains were shown in a small scale experiment to breakdown lignocellulose, producing a number of monocyclic phenolic products. Using milled wood lignin prepared from wheat straw, pine, and miscanthus, some bacterial lignin degraders were found to show specificity for lignin type. These assays could be used to identify novel lignin degraders for breakdown of plant lignocellulose.

Meeting the demand for crop production : the challenge of yield decline in crops grown in short rotations

There is a trend world‐wide to grow crops in short rotation or in monoculture, particularly in conventional agriculture. This practice is becoming more prevalent due to a range of factors including economic market trends, technological advances, government incentives, and retailer and consumer demands. Land‐use intensity will have to increase further in future in order to meet the demands of growing crops for both bioenergy and food production, and long rotations may not be considered viable or practical. However, evidence indicates that crops grown in short rotations or monoculture often suffer from yield decline compared to those grown in longer rotations or for the first time. Numerous factors have been hypothesised as contributing to yield decline, including biotic factors such as plant pathogens, deleterious rhizosphere microorganisms, mycorrhizas acting as pathogens, and allelopathy or autotoxicity of the crop, as well as abiotic factors such as land management practices and nutrient availability. In many cases, soil microorganisms have been implicated either directly or indirectly in yield decline. Although individual factors may be responsible for yield decline in some cases, it is more likely that combinations of factors interact to cause the problem. However, evidence confirming the precise role of these various factors is often lacking in field studies due to the complex nature of cropping systems and the numerous interactions that take place within them. Despite long‐term knowledge of the yield‐decline phenomenon, there are few tools to counteract it apart from reverting to longer crop rotations or break crops. Alternative cropping and management practices such as double‐cropping or inter‐cropping, tillage and organic amendments may prove valuable for combating some of the negative effects seen when crops are grown in short rotation. Plant breeding continues to be important, although this does require a specific breeding target to be identified. This review identifies gaps in our understanding of yield decline, particularly with respect to the complex interactions occurring between the different components of agro‐ecosystems, which may well influence food security in the 21st Century.

In-Field Spatial Variability in the Degradation of the Phenyl-Urea Herbicide Isoproturon Is the Result of Interactions between Degradative Sphingomonas spp. and Soil pH

ABSTRACT Substantial spatial variability in the degradation rate of the phenyl-urea herbicide isoproturon (IPU) [3-(4-isopropylphenyl)-1,1-dimethylurea] has been shown to occur within agricultural fields, with implications for the longevity of the compound in the soil, and its movement to ground- and surface water. The microbial mechanisms underlying such spatial variability in degradation rate were investigated at Deep Slade field in Warwickshire, United Kingdom. Most-probable-number analysis showed that rapid degradation of IPU was associated with proliferation of IPU-degrading organisms. Slow degradation of IPU was linked to either a delay in the proliferation of IPU-degrading organisms or apparent cometabolic degradation. Using enrichment techniques, an IPU-degrading bacterial culture (designated strain F35) was isolated from fast-degrading soil, and partial 16S rRNA sequencing placed it within the Sphingomonas group. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified bacterial community 16S rRNA revealed two bands that increased in intensity in soil during growth-linked metabolism of IPU, and sequencing of the excised bands showed high sequence homology to the Sphingomonas group. However, while F35 was not closely related to either DGGE band, one of the DGGE bands showed 100% partial 16S rRNA sequence homology to an IPU-degrading Sphingomonas sp. (strain SRS2) isolated from Deep Slade field in an earlier study. Experiments with strains SRS2 and F35 in soil and liquid culture showed that the isolates had a narrow pH optimum (7 to 7.5) for metabolism of IPU. The pH requirements of IPU-degrading strains of Sphingomonas spp. could largely account for the spatial variation of IPU degradation rates across the field.

Changes in microbial community metabolism and labile organic matter fractions as early indicators of the impact of management on soil biological quality

Abstract Changes to the metabolic profiles of soil microbial communities could have potential for use as early indicators of the impact of management or other perturbations on soil functioning and soil quality. We compared the relative susceptibility to management of microbial community metabolism with a number of soil organic matter (OM) and microbial parameters currently used as indicators of changes in soil biological quality. Following long-term cereal cropping, plots were subjected to a 16-month treatment period consisting of either a mixed cropping sequence of vetch, spring barley and clover or a continuous grass-clover ley which was periodically mown and mulched. The treatments had no effect on soil biomass N or respiration of microbial populations inoculated into Biolog Gram negative (GN) plates. After 16 months there were no management-induced changes to total OM, light-fraction OM C and N, labile organic N or water-soluble carbohydrates. However, patterns of substrate utilization by the soil microbial population following inoculation into Biolog GN plates were found to be highly sensitive to management practice. In the mixed cropping sequence, substrate utilization changed markedly following plough-in of the vetch crop, with a smaller change occurring after harvesting of the barley. In the ley treatment, substrate utilization was not affected until the onset of mowing, when the pattern changed to become similar to that in the mixed cropping sequence. Metabolic diversity of the Biolog-culturable microbial population was increased by the ley treatment, but was not affected by the cropping sequence. We conclude that patterns of microbial substrate utilization and metabolic diversity are more sensitive to the effects of management than are OM and biomass pools, and therefore have value as early indicators of the impacts of management on soil biological properties, and hence soil quality.

Inhibition of soil nitrifying bacteria communities and their activities by glucosinolate hydrolysis products

During microbial degradation of crucifer tissues in soil, a range of low molecular weight volatile S-containing compounds is produced. While a number of these compounds are known to have potent nitrification inhibiting properties, the eAects of isothiocyanates (ITCs), which are derived from glucosinolates, are not known. We investigated the eAects of glucosinolate hydrolysis products on communities and activities of nitrifying bacteria in bioassays using contrasting sandy- and clay-loam soils. In both soils, ITCs reduced populations of NH4 -oxidizing bacteria and inhibited their growth. ITCs had no apparent inhibitory eAect on populations of NO2 -oxidizing bacteria in sandy-loam, but did reduce growth of these bacteria in clay-loam. Individual application of an aliphatic and an aromatic ITC inhibited nitrification of applied NH4 in the two soils, with the eAect being longer lived in sandy-loam relative to clay-loam. After 42 days, mineralization of N in sandy-loam amended with 2phenethyl-ITC was greater than in unamended soil, suggesting that this compound had a general fumigant eAect on the soil microbiota. ITCs were more eAective inhibitors of nitrification than intact glucosinolates or nitriles. Phenyl-ITC was found to be the most toxic of the ITCs tested, but generally there were no diAerences between the nitrifying inhibitory properties of aliphatic and aromatic ITCs. The capacity of 2-propenyl-ITC to inhibit nitrification was shown to be less than that of dimethyldisulphide. However, when concentrations of 2-propenyl-ITC and dimethyl-sulphide, which had no eAect on nitrification when applied to soil individually, were mixed, nitrification was strongly inhibited. No such synergistic interaction was found for either of these compounds with dimethyl-disulphide. The significance of these findings is discussed. 7 2000 Elsevier Science Ltd. All rights reserved.

The role of local environment and geographical distance in determining community composition of arbuscular mycorrhizal fungi at the landscape scale

Arbuscular fungi have a major role in directing the functioning of terrestrial ecosystems yet little is known about their biogeographical distribution. The Baas-Becking hypothesis (‘everything is everywhere, but, the environment selects’) was tested by investigating the distribution of arbuscular mycorrhizal fungi (AMF) at the landscape scale and the influence of environmental factors and geographical distance in determining community composition. AMF communities in Trifolium repens and Lolium perenne roots were assessed in 40 geographically dispersed sites in Ireland representing different land uses and soil types. Field sampling and laboratory bioassays were used, with AMF communities characterised using 18S rRNA terminal-restriction fragment length polymorphism. Landscape-scale distribution of AMF was driven by the local environment. AMF community composition was influenced by abiotic variables (pH, rainfall and soil type), but not land use or geographical distance. Trifolium repens and L. perenne supported contrasting communities of AMF, and the communities colonising each plant species were consistent across pasture habitats and over distance. Furthermore, L. perenne AMF communities grouped by soil type within pasture habitats. This is the largest and most comprehensive study that has investigated the landscape-scale distribution of AMF. Our findings support the Baas-Becking hypothesis at the landscape scale and demonstrate the strong influence the local environment has on determining AMF community composition.