Mapping sources,sinks, and connectivity using a simulation model of northern spotted owls

Source-sink dynamics are an emergent property of complex species–landscape interactions. A better understanding of how human activities affect source-sink dynamics has the potential to inform and improve the management of species of conservation concern. Here we use a study of the northern spotted owl (Strix occidentalis caurina) to introduce new methods for quantifying source-sink dynamics that simultaneously describe the population-wide consequences of changes to landscape connectivity. Our spotted owl model is mechanistic, spatially-explicit, individual-based, and incorporates competition with barred owls (Strix varia). Our observations of spotted owl source-sink dynamics could not have been inferred solely from habitat quality, and were sensitive to landscape connectivity and the spatial sampling schemes employed by the model. We conclude that a clear understanding of source-sink dynamics can best be obtained from sampling simultaneously at multiple spatial scales. Our methodology is general, can be readily adapted to other systems, and will work with population models ranging from simple and low-parameter to complex and data-intensive.     

Investigating the mechanisms for the opposing pH relationships of fungal and bacterial growth in soil

Soil pH is one of the most influential variables in soil, and is a powerful factor in influencing the size, activity and community structure of the soil microbial community. It was previously shown in a century old artificial pH gradient in an arable soil (pH 4.0-8.3) that bacterial growth is positively related to pH, while fungal growth increases with decreasing pH. In an attempt to elucidate some of the mechanisms for this, plant material that especially promotes fungal growth (straw) or bacterial growth (alfalfa) was added to soil samples of the pH gradient in 5-day laboratory incubation experiments. Also, bacterial growth was specifically inhibited by applying a selective bacterial growth inhibitor (bronopol) along the entire pH gradient to investigate if competitive interaction caused the shift in the decomposer community along the gradient. Straw benefited fungal growth relatively more than bacterial, and vice versa for alfalfa. The general pattern of a shift in fungal:bacterial growth with pH was, however, unaffected by substrate additions, indicating that lack of a suitable substrate was not the cause of the pH effect on the microbial community. In response to the bacterial growth inhibition by bronopol, there was stimulation of fungal growth up to pH 7, but not beyond, both for alfalfa and straw addition. However, the accumulation of ergosterol (an indicator of fungal biomass) during the incubation period after adding alfalfa increased at all pHs, indicating that fungal growth had been high at some time during the 5-day incubation following joint addition of alfalfa and bronopol. This was corroborated in a time-series experiment. In conclusion, the low fungal growth at high pH in an arable soil was caused to a large extent by bacterial competition, and not substrate limitation.     

Enhanced biological cycling of phosphorus increases its availability to crops in low-input sub-Saharan farming systems

Many soils in sub-Saharan Africa, which are farmed by smallholders, are P deficient and highly P fixing. Furthermore, P inputs supplied as farmyard manure (FYM) or inorganic P fertilizer are normally too small to replace P offtakes by crops. Consequently most soils are in a negative P balance, which is reflected in small, and often declining, crop yields. The obvious solution of simply applying adequate P is seldom an option due to shortages of manure, which is usually low in nutrients in any case, and the high cost of inorganic P fertilizer relative to the likely cash value of the harvest. Our aim was to see if we could devise practical methods to increase soil P availability in this situation and to investigate the mechanisms involved. Two approaches were adopted. Firstly, to attempt to saturate the P-fixing sites in the soils by applying a large annual application of P (75 kg P ha⁻¹), which should serve for several seasons. Secondly, to attempt to keep the fertilizer P in biological forms by supplying fertilizer P and cattle manure (FYM) in combination. Here, the aim was to promote the cycling of P through the soil microbial biomass and associated metabolite pools, with the expected result of decreasing P fixation and increased plant availability of this P. These treatments were investigated using two field sites on smallholder farms in Kenya: one, considered a ‘high P fixing’ soil at Malava (Kakamega District) and one considered a ‘low P fixing’ soil at Mau Summit (Nakuru District). The following treatments were applied in 1997 and 1998: nil; 75 kg P ha⁻¹ as super phosphate (P); 25 kg P ha⁻¹; FYM at 1.9 t ha⁻¹ dry matter; FYM+25 kg P ha⁻¹. All treatments also received 100 kg inorganic N ha⁻¹. Maize was the test crop. There was no significant correlation in either year at either site between soil P, measured as NaHCO₃-extractable P, resin P or NaOH-extractable P and maize yield. However, the different soil P fractions were closely correlated with each other. Yields at the high P rate (75 kg ha⁻¹y⁻¹) were often little better than the control. There was, however, a significant positive relationship (P<0.05) between soil microbial biomass P and crop yield, again at both sites and in both years. The treatment giving the best yield and the largest biomass P was always FYM+P. Our results indicate that the combined use of organic and inorganic fertilizers in these low input systems may promote increased biological cycling, enhanced availability and consequently improved plant uptake of soil and fertiliser P, to the advantage of the small scale farmer. The results also indicate that biomass P measurements may provide a better indicator of soil P availability in these soils than some more conventional chemical extractants. However, both findings require further evaluation.     

Extraction of soil nitrogen by chloroform fumigation – A new index for the evaluation of soil nitrogen supply

The N extracted after chloroform (CHCl₃) fumigation was determined as a possible index of soil N supply to plants. The relationships between extractable N following fumigation and reference indices such as total N, alkali-hydrolyzable N, N released by the Stanford short-term incubation method, and the N extracted by KCl and by CaCl₂, were measured in nine soils of differing soil N supply capacity. A highly significant correlation was achieved between the extractable N released by fumigation and the N released by the Stanford method, i.e. a short-term aerobic incubation (r = 0.87). Similarly, the correlation between extractable N by fumigation and the N uptake by ryegrass was highly statistically significant (r = 0.93). Using the N extracted following fumigation has the advantage that laboratory results are available in two days and are both reproducible and of high precision. Therefore, the N extracted following fumigation is a valid, timesaving and precise index of soil N supply capacity.     

European bat lyssaviruses: Distribution, prevalence and implications for conservation

Worldwide, there are more than 1100 species of the Order Chiroptera, 45 of which are present in Europe, and 16 in the UK. Bats are reservoirs of, or can be infected by, several viral diseases, including rabies virus strains (in the Lyssavirus genus). Within this genus are bat variants that have been recorded in Europe; European bat lyssavirus 1 (EBLV-1), European bat lyssavirus 2 (EBLV-2) and, four currently unclassified isolates. Since 1977, 783 cases of EBLVs (by isolation of viral RNA) have been recorded in Europe. EBLV-1 or EBLV-2 has been identified in 12 bat species, with over 95% of EBLV-1 infections identified in Eptesicus serotinus. EBLV-2 is associated with Myotis species (Myotis daubentonii and Myotis dasycneme). A programme of passive surveillance in the United Kingdom between 1987 and 2004 tested 4871 bats for lyssaviruses. Of these, four M. daubentonii (3.57% of submitted M. daubentonii) were positive for EBLV-2. Potential bias in the passive surveillance includes possible over-representation of synanthropic species and regional biases caused by varying bat submission numbers from different parts of the UK. In 2003, active surveillance in the UK began, and has detected an antibody prevalence level of 1-5% of EBLV-2 in M. daubentonii (n = 350), and one bat with antibodies to EBLV-1 in E. serotinus (n = 52). No cases of live lyssavirus infection or lyssavirus viral RNA have been detected through active surveillance. Further research and monitoring regarding prevalence, transmission, pathogenesis and immunity is required to ensure that integrated bat conservation continues throughout Europe, whilst enabling informed policy decision regarding both human and wildlife health issues.     

Effects of repeated use of an area of heather Calluna vulgaris (L.) hull moor at Kindrogan,Scotland, for teaching purposes

A triangular plot of heather moor at Kindrogan was used for teaching botanical analysis for eight years, using the same set of random coordinates to locate sample points. Because of the method of point location, there was a gradient of trampling pressure across the plot, and there were also parts of the plot that were never analysed. At the end of the eight-year period heather cover and mean height were found to have declined with increasing levels of trampling. Mean numbers of species/m² did not however decline, and were actually minimal on untrampled ground. With moderate levels of trampling, quadrats that had been analysed for eight years contained more heather litter than those that had not been analysed before. No decline in species frequencies was found in previously analysed quadrats. The value of the plot for teaching purposes does not seem to have declined, and may have actually increased over the period of use.     

Mineralization of native soil organic matter is not regulated by the size,activity or composition of the soil microbial biomass—a new perspective

Soil organic matter is extensively humified; some fractions existing for more than 1000 years. The soil microbial biomass is surrounded by about 50 times its mass of soil organic matter, but can only metabolize it very slowly. Paradoxically, even if more than 90% of the soil microbial biomass is killed, the mineralization of soil organic matter proceeds at the same rate as in an unperturbed soil. Here we show that soil organic matter mineralization is independent of microbial biomass size, community structure or specific activity. We suggest that the rate limiting step is governed by abiological processes (which we term the Regulatory Gate hypothesis), which convert non-bioavailable soil organic matter into bioavailable soil organic matter, and cannot be affected by the microbial population. This work challenges one of the long held theories in soil microbiology proposed by Winogradsky, of the existence of autochthonous and zymogenous microbial populations. This has significant implications for our understanding of carbon mineralization in soils and the role of soil micro-organisms in the global carbon cycle. Here we describe experiments designed to determine if the Regulatory Gate operates. We conclude that there is sufficient experimental evidence for it to be offered as a working hypothesis.     

Correction to: Individual based modelling of fish migration in a 2-D river system: model description and case study

Landscape Ecology - In the original publication of the article, the third author name has been misspelt. The correct name is given in this Correction. The original version of this article was revised.     

Exploring animal rabies endemicity to inform control programmes in Punjab,India

Previous studies estimate that one‐third of the annual global burden of rabies (~20,000 cases) occurs in India. Elimination of canine rabies is essential to reduce this burden. Surveillance of animal cases can assess both the risk to humans and the efficacy of control strategies. The objective of this study was to describe the spatial and temporal occurrence of reported confirmed cases of rabies in animals in Punjab, India, from 2004 to 2014. We analysed passive surveillance data on 556 samples submitted from 2004 to 2014 to GADVASU, Ludhiana, Punjab, India. Regression and time series analyses were conducted to understand seasonal and long‐term variation of cases and identify cross‐correlation of monthly cases between species. Spatio‐temporal analyses assessed spatial autocorrelation of date of reporting, mean geographic centres of disease occurrence and clustering of cases using Kulldorff's space‐time permutation statistic. The annual number of submissions and proportion of confirmed cases were consistent throughout 2004–2014. Most submissions (320; 57.6%) were confirmed rabies cases, including dogs (40.6%), buffalo (29.7%) and cattle (23.1%). Regression analysis of monthly cases in dogs showed seasonal variation with significant increases in cases in March and August. Monthly case numbers in buffalo decreased over time. Long‐term temporal trend was not detected in dog and cattle cases. Time‐series models identified significant cross‐correlation between dog and buffalo cases, suggesting that buffalo cases were spillover events from dogs. Significant spatio‐temporal variation or clusters of cases were not detected. These results indicate that rabies cases in animals—and therefore, the potential for exposure to humans—were temporally and spatially stable during 2004–2014 in Punjab, India. The endemic nature of rabies transmission in this region demands a coordinated, sustained control programme. This study provides baseline information for assessing the efficacy of rabies control measures and developing seasonally targeted dog vaccination and rabies awareness strategies.