Stephen Rushton

Visualization, modelling and prediction in soil microbiology

The introduction of new approaches for characterizing microbial communities and imaging soil environments has benefited soil microbiology by providing new ways of detecting and locating microorganisms. Consequently, soil microbiology is poised to progress from simply cataloguing microbial complexity to becoming a systems science. A systems approach will enable the structures of microbial communities to be characterized and will inform how microbial communities affect soil function. Systems approaches require accurate analyses of the spatio–temporal properties of the different microenvironments present in soil. In this Review we advocate the need for the convergence of the experimental and theoretical approaches that are used to characterize and model the development of microbial communities in soils.

Classification and ordination of habitats of ground beetles (Coleoptera, Carabidae) in north-east England

Species lists of Carabidae from 248 localities in north-east England were classified by Two-Way Indicator Species Analysis (TWINSPAN) and ordinated by Detrended Correspondence Analysis (DECORANA). 2. The classification lead to the recognition of ten ecologically meaningful habitat groups: coastal (1), upland (2), woodland (1), grassland (2), riverside (3) and marsh (1). 3. Ordination showed that all these groups were distinct, and suggested that moisture, substrate porosity and altitude may be the main factors determining the carabid communities.

Soil, vegetation and space: an analysis of their effects on the invertebrate communities of a moorland in north-east England

1. The role of spatial factors in determining the structure and function of plant and invertebrate communities on a 117 ha upland moor in north-east England was investigated using ordination and Mantel tests. 2. The vegetation species composition was spatially autocorrelated and associated with the soil conditions. The species composition of Auchenorrhyncha (Hemiptera) communities appeared to be determined by both the soil conditions and vegetation species composition, whereas Heteroptera (Hemiptera) were associated primarily with the vegetation. Araneae were not found to be directly related with either the soil conditions or vegetation, but were linked to the spatial location of the sample. Carabidae (Coleoptera) were associated with variation in soil conditions, but not directly to spatial location or vegetation. 3. The implications of these results for the management of vegetation in upland landscapes are discussed.

Disease threats posed by alien species: the role of a poxvirus in the decline of the native red squirrel in Britain

Red squirrels are declining in the United Kingdom. Competition from, and squirrel poxvirus (SQPV) disease carried by, grey squirrels are assumed to be determining the decline. We analyse the incidence of disease and changes in distribution of the two species in Cumbria, from 1993 to 2003 and compare these to the predictions of an individual-based (IB) spatially explicit disease model simulating the dynamics of both squirrel species and SQPV in the landscape. Grey squirrels increased whilst red squirrels declined over 10 years. The incidence of disease in red squirrels was related to the time since grey squirrels arrived in the landscape. Analysis of rates of decline in red squirrel populations in other areas showed that declines are 17-25 times higher in regions where SQPV is present in grey squirrel populations than in those where it is not. The IB model predicted spatial overlap of 3-4 years between the species that was also observed in the field. The model predictions matched the observed data best when contact rates and rates of infection between the two species were low. The model predicted that a grey squirrel population control of >60% effective kill was needed to stop the decline in red squirrel populations in Cumbria.

Classification and prediction of grassland habitats using ground beetles (Coleoptera, Carabidae)

Ground beetle species assemblages were sampled by pitfall trapping from 69 grassland sites in north-east England. A TWINSPAN classification, based on the percentage occurrence of each species in the total catch from each site, identified 10 habitat groups within grasslands. DECORANA ordination was used to examine the relationships between sites. Positions of sites along the first two axes of the ordination were most clearly related to soil characteristics. The third axis was associated with intensity of management. Data from replicated sites fitted well into the same habitat groups. Discriminant analysis showed that habitat groups could be separated on the basis of site management, soil water, soil bulk density and altitude. 62% of sites were assigned to the correct habitat group on a basis of these environmental factors. Seven of 10 new sites were classified into identical habitat groups by a method based on ordination analysis using their ground beetle fauna and by discriminant functions derived from analysis of environmental factors. These results should enable the ground beetle fauna of further sites to be assessed and used quantitatively as indicators of environmental quality and change.

Effects of pasture improvement and management on the ground beetle and spider communities of upland grasslands

(1) The effects of pasture improvement procedures and subsequent pesticide use on the ground beetle and spider faunas of semi-natural upland grasslands in Northumberland in 1985-87 were analysed using pitfall trapping and multivariate techniques. (2) The sites were classified and ordinated on the basis of their species lists of spiders and ground beetles. Stepwise linear discriminant analyses were used to identify the major environmental features influencing the distribution of species across sites. (3) The effects of pasture improvement were dramatic: species composition of improved sites was poor and similar to that on intensively managed pastures at lower altitudes. (4) The frequency of use of the organo-phosphorus pesticide chlorpyrifos appeared to be an important factor influencing the species composition of improved sites for both the ground beetle and spider communities.

Bacillus Calmette-Guérin vaccination reduces the severity and progression of tuberculosis in badgers

Control of bovine tuberculosis (TB) in cattle has proven particularly challenging where reservoirs of infection exist in wildlife populations. In Britain and Ireland, control is hampered by a reservoir of infection in Eurasian badgers (Meles meles). Badger culling has positive and negative effects on bovine TB in cattle and is difficult, costly and controversial. Here we show that Bacillus Calmette-Guérin (BCG) vaccination of captive badgers reduced the progression, severity and excretion of Mycobacterium bovis infection after experimental challenge. In a clinical field study, BCG vaccination of free-living badgers reduced the incidence of positive serological test results by 73.8 per cent. In common with other species, BCG did not appear to prevent infection of badgers subjected to experimental challenge, but did significantly reduce the overall disease burden. BCG vaccination of badgers could comprise an important component of a comprehensive programme of measures to control bovine TB in cattle.

Modelling the distribution of the red and grey squirrel at the landscape scale : a combined GIS and population dynamics approach

An integrated Geographical Information System (GIS)-Spatially Explicit Population Dynamics Model (SEPM) for investigating the dynamics of red squirrel Sciurus vulgaris and grey squirrel S. carolinensis populations in different landscapes is described. Using the model, we simulated processes of reproduction, mortality and dispersal in individual populations of squirrels in habitat blocks identified within a GIS. We modelled dispersal as a process whereby individual animals moved between blocks of habitat separated by areas of unsuitable habitat. An interference model simulating the effects of competition between the grey and red squirrels was incorporated where both species occupied the same habitat blocks. The model was used to investigate the spread of grey squirrels and its impact on the distribution of red squirrels in Norfolk, UK, where historical information on the decline in the red squirrel and the expansion of the grey squirrel were available. We examined the effect of a range of life history scenarios differing in terms of adult mortality, juvenile mortality, fecundity, habitat carrying capacity and maximum dispersal distances. Model predictions were closest to the observed expansion of the grey squirrel and decline in the red squirrel when mortality was lower and fecundity higher than the averages recorded for the grey squirrel in the United Kingdom.

Poxviral disease in red squirrels Sciurus vulgaris in the UK: spatial and temporal trends of an emerging threat.

The squirrel poxvirus (SQPV) is the probable mediator of apparent competition between the introduced invading gray squirrel (Sciurus carolinensis) and the red squirrel (Sciurus vulgaris) in the UK, and modeling studies have shown that this viral disease has had a significant impact on the decline of the red squirrel in the UK. However, given our limited understanding of the epidemiology of the disease, and more generally the effects of invasive species on parasite ecology, there is a need to investigate the transmission dynamics and the relative pathogenicity of the virus between species. We aimed to increase our knowledge of these processes through an empirical study in which we: (i) used pathological signs and transmission electron microscopy (TEM) to diagnose SQPV disease in red squirrels found dead during scanning surveillance between 1993 and 2005; (ii) detected antibody to SQPV using an enzyme-linked immunosorbent assay (ELISA) in the same animals; and (iii) mapped cases of the disease, and the gray squirrel distribution, using a geographical information system. We analyzed the distribution of cases of SQPV disease according to woodland type, a measure of squirrel density. SQPV disease occurred only in areas of England also inhabited by seropositive gray squirrels, and as the geographical range of gray squirrels expanded, SQPV disease occurred in these new gray squirrel habitats, supporting a role for the gray squirrel as a reservoir host of the virus. There was a delay between the establishment of invading gray squirrels and cases of the disease in red squirrels which implies gray squirrels must reach a threshold number or density before the virus is transmitted to red squirrels. The spatial and temporal trend in SQPV disease outbreaks suggested that SQPV disease will have a significant effect on Scottish populations of red squirrels within 25 years. The even spread of cases of disease across months suggested a direct rather than vector-borne transmission route is more likely. Eight juvenile and sub-adult free-living red squirrels apparently survived exposure to SQPV by mounting an immune response, the first evidence of immunity to SQPV in free-living red squirrels, which possibly suggests a changing host-parasite relationship and that the use of a vaccine may be an effective management tool to protect remnant red squirrel populations.

Ambient air pollution and congenital heart disease: a register-based study.

Maternal exposure to ambient air pollution has increasingly been linked to adverse pregnancy outcomes. The evidence linking this exposure to congenital anomalies is still limited and controversial. This case-control study investigated the association between maternal exposure to ambient particulate matter with aerodynamic diameter less than 10 μm (PM(10)), sulfur dioxide (SO(2)), nitrogen dioxide, nitric oxide (NO), ozone (O(3)), and carbon monoxide (CO) and the occurrence of congenital heart disease in the population of Northeast England (1993-2003). Each case and control was assigned weekly average (weeks 3-8 of pregnancy) of pollutant levels measured by the closest monitor to the mothers residential postcode. Using exposure as both continuous and categorical variables, logistic regression models were constructed to quantify the adjusted odds ratios of exposure to air pollutants and the occurrence of each outcome group. We found exposure to CO and NO to be associated with ventricular septal defect and cardiac septa malformations. CO was also associated with congenital pulmonary valve stenosis and NO with pooled cases of congenital heart disease and tetralogy of Fallot. Findings for SO(2), O(3) and PM(10) were less consistent.