Jacqueline M. Potts

A Rapid Microtiter Plate Method To Measure Carbon Dioxide Evolved from Carbon Substrate Amendments so as To Determine the Physiological Profiles of Soil Microbial Communities by Using Whole Soil

ABSTRACT Sole-carbon-source tests (Biolog), designed to identify bacteria, have become very popular for metabolically fingerprinting soil microbial communities, despite disadvantages associated with the use of carbon source profiles that primarily select for fast-growing bacteria. In this paper we describe the use of an alternative method that combines the advantages of the Biolog community-level physiological profile (CLPP) method, in which microtiter-based detection plates are used, with the ability to measure carbon dioxide evolution from whole soil. This method facilitates measurement over short periods of time (4 to 6 h) and does not require the extraction and culturing of organisms. Deep-well microtiter plates are used as test wells into which soil is placed. The apparatus to fill the deep-well plates and interface it with a second removable detection plate is described. Two detection systems, a simple colorimetric reaction in absorbent alkali and scintillation counting with radioactive carbon sources, are described. The methods were compared to the Biolog-CLPP system by using soils under different vegetation types and soil treated with wastewater sludge. We aimed to test the hypothesis that using whole soil would have specific advantages over using extracts in that more immediate responses to substrates could be obtained that would reflect activity rather than growth. The whole-soil method was more rapid and gave earlier detection of C source use. Also, the metabolic fingerprints obtained could discriminate between sludge treatments.

Spatial and temporal ecology of Scots pine ectomycorrhizas

Spatial analysis was used to explore the distribution of individual species in an ectomycorrhizal (ECM) fungal community to address: whether mycorrhizas of individual ECM fungal species were patchily distributed, and at what scale; and what the causes of this patchiness might be. Ectomycorrhizas were extracted from spatially explicit samples of the surface organic horizons of a pine plantation. The number of mycorrhizas of each ECM fungal species was recorded using morphotyping combined with internal transcribed spacer (ITS) sequencing. Semivariograms, kriging and cluster analyses were used to determine both the extent and scale of spatial autocorrelation in species abundances, potential interactions between species, and change over time. The mycorrhizas of some, but not all, ECM fungal species were patchily distributed and the size of patches differed between species. The relative abundance of individual ECM fungal species and the position of patches of ectomycorrhizas changed between years. Spatial and temporal analysis revealed a dynamic ECM fungal community with many interspecific interactions taking place, despite the homogeneity of the host community. The spatial pattern of mycorrhizas was influenced by the underlying distribution of fine roots, but local root density was in turn influenced by the presence of specific fungal species.

Changes in fungal community composition in response to vegetational succession during the natural regeneration of cutover peatlands

Despite the importance of peatlands as a major store of sequestered carbon and the role of fungi in releasing sequestered C, we know little about the community structure of fungi in peatlands. We investigated these across a gradient of naturally regenerating peatland vegetation using denaturing gradient gel electrophoresis (DGGE) and clone libraries of fragments of the fungal rRNA internal transcribed spacer (ITS) region. Significant changes in the fungal community structure of peat samples at different stages of regeneration were observed, which relate to the composition of the vegetation recolonizing these sites. Cloning and sequence analysis also demonstrated a potential shift in the relative abundance of the main fungal phyla. Some of the clones identified to genus level were highly related to fungi known to play a role in the degradation of plant litter or wood in similar ecosystems and/or form mycorrhizal associations. In addition, several fungal isolates highly related to peat clones were obtained, and their enzymic capacity to degrade structural plant tissues was assessed. Together, these results suggest that the fungal community composition of peat may be an important indicator of the status of regeneration and potential carbon sequestration of cutover peatlands.

Estimating the spatial scales of regionalized variables by nested sampling, hierarchical analysis of variance and residual maximum likelihood

The variogram is essential for local estimation and mapping of any variable by kriging. The variogram itself must usually be estimated from sample data. The sampling density is a compromise between precision and cost, but it must be sufficiently dense to encompass the principal spatial sources of variance. A nested, multi-stage, sampling with separating distances increasing in geometric progression from stage to stage will do that. The data may then be analyzed by a hierarchical analysis of variance to estimate the components of variance for every stage, and hence lag. By accumulating the components starting from the shortest lag one obtains a rough variogram for modest effort. For balanced designs the analysis of variance is optimal; for unbalanced ones, however, these estimators are not necessarily the best, and the analysis by residual maximum likelihood (reml) will usually be preferable. The paper summarizes the underlying theory and illustrates its application with data from three surveys, one in which the design had four stages and was balanced and two implemented with unbalanced designs to economize when there were more stages. A Fortran program is available for the analysis of variance, and code for the reml analysis is listed in the paper.

Long-term trends in hydro-climatology of a major Scottish mountain river.

The River Dee, in North East Scotland, is a mountainous river strongly influenced by patterns of snow accumulation and melt from the Cairngorm Mountains. Analysis of this rivers flow record from 1929-2004, the longest in Scotland, supports anecdotal evidence that river extreme flows are increasing. There was no detectable change in the overall annual flow patterns. However, an analysis of seasonal data suggested a shift towards increased flows in spring (March-May) and decreased flows in summer (June-August) over the 75 years of the record. Flows in spring exceeded 29 m(3) s(-1) for 50% of the time over the earliest part of the record (1930 to 1954), whereas in the last 25 years of the record (1979 to 2004) 50% of the flows exceeded 35 m(3) s(-1). Precipitation is increasing in the spring and decreasing in July and August. If these trends continue they have important implications for water management in the Dee, with a potential increase in flood risk in spring and the increased possibility of drought in summer. Combined with this increase in flows the river appears to be more responsive to precipitation events in the catchment. In large heterogeneous catchments with a marginal alpine/high latitude climate it is difficult to assess the amount of precipitation falling as snow and its relative accumulation and ablation dynamics on daily to seasonal time scales. Changes in the temporal pattern of coherence between flow and precipitation are thought to be linked to changing snow patterns in the upland part of the catchment. A decreased amount of precipitation occurring as snow has led to higher coherence. We also show that in responsive systems it is important to record river flows at an hourly rather than daily time step in order to characterise peak flow events.

Microbial pollution of water by livestock: approaches to risk assessment and mitigation.

In this study, we investigate the extent to which the incidence of Escherichia coli O157:H7 can be predicted in human faeces, from human intake and infection via water contaminated by livestock and carrying this zoonotic pathogen in North-East (NE) and South-West (SW) regions of Scotland. In SW Scotland, there is a risk of coastal recreational waters failing EU standards for faecal indicator organisms, and this is assumed to be the main potential waterborne route of infection. In NE Scotland, the main waterborne route is assumed to be the many private drinking water supplies; these are mainly derived from shallow groundwater and surveys show that there is potential for significant levels of microbial contamination from livestock. The risk to human health from these sources has been assessed using a combination of process models, epidemiological risk-assessment methods and survey data. A key assumption in the calculations is the amount of mixing of pathogenic and non-pathogenic E. coli between animal faecal sources and contaminated water intake by humans. Using the probability distributions of the E. coli O157 content of individual faecal pat material (which would imply no mixing between source and human intake), based on three recent surveys of animal faeces in Scotland, led to predicted annual risks of infection slightly higher than observed human infection incidence. Using the geometric mean to represent partial mixing (which theoretically may over- or underestimate incidence with a concave dose-response curve) gave infection rates similar to those observed for two of the three faecal surveys. Using the arithmetic mean led to over-prediction of risk. This is to be expected if the true dose-response curve is (such as the Beta-Poisson curve used here) concave. Other factors that may lead to over-prediction of incidence are discussed, including under-reporting, loss of infectivity as a result of environmental exposure, immunity and the appropriateness of the Beta-Poisson curve. It is concluded that better epidemiological data for calibration of the dose-response curve, better knowledge of the degree of mixing and understanding of immunity are key requirements for progress in process model-based predictions of infection rate. The paper also explores the potential of improved farm and catchment scale management to deliver cost-effective mitigation of pollution of bathing and drinking water by livestock zoonoses.

Evaluating the use of in - situ turbidity measurements to quantify fluvial sediment and phosphorus concentrations and fluxes in agricultural streams

Accurate quantification of suspended sediments (SS) and particulate phosphorus (PP) concentrations and loads is complex due to episodic delivery associated with storms and management activities often missed by infrequent sampling. Surrogate measurements such as turbidity can improve understanding of pollutant behaviour, providing calibrations can be made cost-effectively and with quantified uncertainties. Here, we compared fortnightly and storm intensive water quality sampling with semi-continuous turbidity monitoring calibrated against spot samples as three potential methods for determining SS and PP concentrations and loads in an agricultural catchment over two-years. In the second year of sampling we evaluated the transferability of turbidity calibration relationships to an adjacent catchment with similar soils and land cover. When data from nine storm events were pooled, both SS and PP concentrations (all in log space) were better related to turbidity than they were to discharge. Developing separate calibration relationship for the rising and falling limbs of the hydrograph provided further improvement. However, the ability to transfer calibrations between adjacent catchments was not evident as the relationships of both SS and PP with turbidity differed both in gradient and intercept on the rising limb of the hydrograph between the two catchments. We conclude that the reduced uncertainty in load estimation derived from the use of turbidity as a proxy for specific water quality parameters in long-term regulatory monitoring programmes, must be considered alongside the increased capital and maintenance costs of turbidity equipment, potentially noisy turbidity data and the need for site-specific prolonged storm calibration periods.

Developing monitoring protocols for cost-effective surveillance of lichens

The criteria set out by the International Union for Conservation of Nature to identify threatened species requires information on population trends which, for priority lichen species within Scotland, is lacking. Collecting such data is problematic as there is a lack of empirical information on the performance of different sampling designs and survey methodologies. Using Pseudocyphellaria norvegica as an example species, we tested differences in the efficiency of 3 transect patterns and a 20 minute search for surveying 100×100 m cells of potentially suitable habitat. The methods were not intended to census the total population of the cells but, rather, to provide a standardized, repeatable estimate of the population density to allow detection of trends through time. We also tested the repeatability of the methods between surveyors. The results provided no evidence to suggest that controlled survey methodologies using fixed transect patterns were any better in terms of consistency between surveyors or numbers of occupied trees found than 20 minute searches of the areas within each 100×100 m cell deemed suitable for the target species by an experienced surveyor. Given that following the fixed transect patterns took approximately twice as long as a 20 minute search, the search method would clearly be more cost-effective when there are large numbers of cells to survey. For all survey methods variability between surveyors was high, meaning that it would be extremely difficult to detect temporal changes in populations, and hence identify population trends. We also examined the extent to which recording presence/absence at the 1 ha scale might improve consistency between surveyors and found that it reduced, but did not eliminate, the surveyor variability. Recording only presence/absence would allow greater numbers of cells to be surveyed using the same level of resources, but would reduce the amount of information available per cell for use in analysis of population trends. We conclude that controlling inter-surveyor variability while collecting adequate data for population trend analysis is a major issue when planning and implementing any large-scale survey of lichen species.

Recent trends in water quality in an agricultural catchment in Eastern Scotland: elucidating the roles of hydrology and land use.

Across the EU, programmes of measures have been introduced as part of river basin management planning as a means of tackling problems of diffuse pollution from agriculture. Evidence is required to demonstrate the effectiveness of these measures and with this overarching objective, monitoring of an agricultural catchment in Eastern Scotland was initiated in 2007. As a precursor to evaluating the effect of new management measures it is essential to understand how other factors, including hydrology and land use changes, could have influenced water quality. This study undertook an analysis of the trends in concentrations and loads of nitrate, soluble reactive phosphorus (SRP), suspended solids (SS) and turbidity measured at six points in the catchment over a six year period. The results identified both differing trends between determinands and differing trends occurring over varying spatial scales. The only direct relationships between land use and water quality that could be identified based on annual data was a positive link between arable cropping and nitrate concentrations. At the sub-catchment scale some temporal changes in land use and management explained short-term trends in nitrate but not in SRP. Lags in the system were identified due to soil adsorption, in-stream/loch processing and groundwater transport making the identification of cause and effect problematic. The results have implications for the demonstration of effectiveness of measures over the shorter term and the timescales of recovery from diffuse pollution. Longer term monitoring at small scales will be important in this regard.

Decline in atmospheric sulphur deposition and changes in climate are the major drivers of long-term change in grassland plant communities in Scotland

The predicted long lag time between a decrease in atmospheric deposition and a measured response in vegetation has generally excluded the investigation of vegetation recovery from the impacts of atmospheric deposition. However, policy-makers require such evidence to assess whether policy decisions to reduce emissions will have a positive impact on habitats. Here we have shown that 40 years after the peak of SOx emissions, decreases in SOx are related to significant changes in species richness and cover in Scottish Calcareous, Mestrophic, Nardus and Wet grasslands. Using a survey of vegetation plots across Scotland, first carried out between 1958 and 1987 and resurveyed between 2012 and 2014, we test whether temporal changes in species richness and cover of bryophytes, Cyperaceae, forbs, Poaceae, and Juncaceae can be explained by changes in sulphur and nitrogen deposition, climate and/or grazing intensity, and whether these patterns differ between six grassland habitats: Acid, Calcareous, Lolium, Nardus, Mesotrophic and Wet grasslands. The results indicate that Calcareous, Mesotrophic, Nardus and Wet grasslands in Scotland are starting to recover from the UK peak of SOx deposition in the 1970s. A decline in the cover of grasses, an increase in cover of bryophytes and forbs and the development of a more diverse sward (a reversal of the impacts of increased SOx) was related to decreased SOx deposition. However there was no evidence of a recovery from SOx deposition in the Acid or Lolium grasslands. Despite a decline in NOx deposition between the two surveys we found no evidence of a reversal of the impacts of increased N deposition. The climate also changed significantly between the two surveys, becoming warmer and wetter. This change in climate was related to significant changes in both the cover and species richness of bryophytes, Cyperaceae, forbs, Poaceae and Juncaceae but the changes differed between habitats.