Automated pre-processing strategies for species occurrence data used in biodiversity modelling

To construct Biodiversity richness maps from Environmental Niche Models (ENMs) of thousands of species is time consuming. A separate species occurrence data pre-processing phase enables the experimenter to control test AUC score variance due to species dataset size. Besides, removing duplicate occurrences and points with missing environmental data, we discuss the need for coordinate precision, wide dispersion, temporal and synonymity filters. After species data filtering, the final task of a pre-processing phase should be the automatic generation of species occurrence datasets which can then be directly ’plugged-in’ to the ENM. A software application capable of carrying out all these tasks will be a valuable time-saver particularly for large scale biodiversity studies.

Iron Uptake and Homeostasis in Microorganisms

Preface. Iron is considered to be a minor element employed, in a variety of forms, by nearly all living organisms. In some cases, it is utilised in large quantities, for instance for the formation of magnetosomes within magnetotactic bacteria or during use of iron as a respiratory donor or acceptor by iron oxidising or reducing bacteria. However, in most cases the role of iron is restricted to its use as a cofactor or prosthetic group assisting the biological activity of many different types of protein. The key metabolic processes that are dependent on iron as a cofactor are numerous; they include respiration, light harvesting, nitrogen fixation, the Krebs cycle, redox stress resistance, amino acid synthesis and oxygen transport. Indeed, it is clear that Life in its current form would be impossible in the absence of iron. One of the main reasons for the reliance of Life upon this metal is the ability of iron to exist in multiple redox states, in particular the relatively stable ferrous (Fe2+) and ferric (Fe3+) forms. The availability of these stable oxidation states allows iron to engage in redox reactions over a wide range of midpoint potentials, depending on the coordination environment, making it an extremely adaptable mediator of electron exchange processes. Iron is also one of the most common elements within the Earth’s crust (5% abundance) and thus is considered to have been readily available when Life evolved on our early, anaerobic planet. However, as oxygen accumulated (the ‘Great oxidation event’) within the atmosphere some 2.4 billion years ago, and as the oceans became less acidic, the iron within primordial oceans was converted from its soluble reduced form to its weakly-soluble oxidised ferric form, which precipitated (~1.8 billion years ago) to form the ‘banded iron formations’ (BIFs) observed today in Precambrian sedimentary rocks around the world. These BIFs provide a geological record marking a transition point away from the ancient anaerobic world towards modern aerobic Earth. They also indicate a period over which the bio-availability of iron shifted from abundance to limitation, a condition that extends to the modern day. Thus, it is considered likely that the vast majority of extant organisms face the common problem of securing sufficient iron from their environment – a problem that Life on Earth has had to cope with for some 2 billion years. This struggle for iron is exemplified by the competition for this metal amongst co-habiting microorganisms who resort to stealing (pirating) each others iron supplies! The reliance of micro-organisms upon iron can be disadvantageous to them, and to our innate immune system it represents a chink in the microbial armour, offering an opportunity that can be exploited to ward off pathogenic invaders. In order to infect body tissues and cause disease, pathogens must secure all their iron from the host. To fight such infections, the host specifically withdraws available iron through the action of various iron depleting processes (e.g. the release of lactoferrin and lipocalin-2) – this represents an important strategy in our defence against disease. However, pathogens are frequently able to deploy iron acquisition systems that target host iron sources such as transferrin, lactoferrin and hemoproteins, and thus counteract the iron-withdrawal approaches of the host. Inactivation of such host-targeting iron-uptake systems often attenuates the pathogenicity of the invading microbe, illustrating the importance of ‘the battle for iron’ in the infection process. The role of iron sequestration systems in facilitating microbial infections has been a major driving force in research aimed at unravelling the complexities of microbial iron transport processes. But also, the intricacy of such systems offers a challenge that stimulates the curiosity. One such challenge is to understand how balanced levels of free iron within the cytosol are achieved in a way that avoids toxicity whilst providing sufficient levels for metabolic purposes – this is a requirement that all organisms have to meet. Although the systems involved in achieving this balance can be highly variable amongst different microorganisms, the overall strategy is common. On a coarse level, the homeostatic control of cellular iron is maintained through strict control of the uptake, storage and utilisation of available iron, and is co-ordinated by integrated iron-regulatory networks. However, much yet remains to be discovered concerning the fine details of these different iron regulatory processes. As already indicated, perhaps the most difficult task in maintaining iron homeostasis is simply the procurement of sufficient iron from external sources. The importance of this problem is demonstrated by the plethora of distinct iron transporters often found within a single bacterium, each targeting different forms (complex or redox state) of iron or a different environmental condition. Thus, microbes devote considerable cellular resource to securing iron from their surroundings, reflecting how successful acquisition of iron can be crucial in the competition for survival. The aim of this book is provide the reader with an overview of iron transport processes within a range of microorganisms and to provide an indication of how microbial iron levels are controlled. This aim is promoted through the inclusion of expert reviews on several well studied examples that illustrate the current state of play concerning our comprehension of how iron is translocated into the bacterial (or fungal) cell and how iron homeostasis is controlled within microbes. The first two chapters (1-2) consider the general properties of microbial iron-chelating compounds (known as ‘siderophores’), and the mechanisms used by bacteria to acquire haem and utilise it as an iron source. The following twelve chapters (3-14) focus on specific types of microorganism that are of key interest, covering both an array of pathogens for humans, animals and plants (e.g. species of Bordetella, Shigella, , Erwinia, Vibrio, Aeromonas, Francisella, Campylobacter and Staphylococci, and EHEC) as well as a number of prominent non-pathogens (e.g. the rhizobia, E. coli K-12, Bacteroides spp., cyanobacteria, Bacillus spp. and yeasts). The chapters relay the common themes in microbial iron uptake approaches (e.g. the use of siderophores, TonB-dependent transporters, and ABC transport systems), but also highlight many distinctions (such as use of different types iron regulator and the impact of the presence/absence of a cell wall) in the strategies employed. We hope that those both within and outside the field will find this book useful, stimulating and interesting. We intend that it will provide a source for reference that will assist relevant researchers and provide an entry point for those initiating their studies within this subject. Finally, it is important that we acknowledge and thank wholeheartedly the many contributors who have provided the 14 excellent chapters from which this book is composed. Without their considerable efforts, this book, and the understanding that it relays, would not have been possible. Simon C Andrews and Pierre Cornelis

Water reuse for irrigated agriculture in Jordan: challenges of soil sustainability and the role of management strategies

Reclaimed water provides an important contribution to the water balance in water-scarce Jordan, but the quality of this water presents both benefits and challenges. Careful management of reclaimed water is required to maximize the nutrient benefits while minimizing the salinity risks. This work uses a multi-disciplinary research approach to show that soil response to irrigation with reclaimed water is a function of the management strategies adopted on the farm by the water user. The adoption of management methods to maintain soil productivity can be seen to be a result of farmers’ awareness to potentially plant-toxic ions in the irrigation water (70% of Jordan Valley farmers identified salinization as a hazard from irrigation with reclaimed water). However, the work also suggests that farmers’ management capacity is affected by the institutional management of water. About a third (35%) of farmers in the Jordan Valley claimed that their ability to manage salinization was limited by water shortages. Organizational interviews revealed that institutional awareness of soil management challenges was quite high (34% of interviewees described salinization as a risk from water reuse), but strategies to address this challenge at the institutional level require greater development.

An economic decision support tool for simulating paratuberculosis control strategies in a UK suckler beef herd

A dynamic, deterministic, economic simulation model was developed to estimate the costs and benefits of controlling Mycobacterium avium subsp. paratuberculosis (Johne's disease) in a suckler beef herd. The model is intended as a demonstration tool for veterinarians to use with farmers. The model design process involved user consultation and participation and the model is freely accessible on a dedicated website. The 'user-friendly' model interface allows the input of key assumptions and farm specific parameters enabling model simulations to be tailored to individual farm circumstances. The model simulates the effect of Johne's disease and various measures for its control in terms of herd prevalence and the shedding states of animals within the herd, the financial costs of the disease and of any control measures and the likely benefits of control of Johne's disease for the beef suckler herd over a 10-year period. The model thus helps to make more transparent the 'hidden costs' of Johne's in a herd and the likely benefits to be gained from controlling the disease. The control strategies considered within the model are 'no control', 'testing and culling of diagnosed animals', 'improving management measures' or a dual strategy of 'testing and culling in association with improving management measures'. An example 'run' of the model shows that the strategy 'improving management measures', which reduces infection routes during the early stages, results in a marked fall in herd prevalence and total costs. Testing and culling does little to reduce prevalence and does not reduce total costs over the 10-year period.

Public values for badgers, bovine TB reduction and management strategies

This paper applies an attribute-based stated choice experiment approach to estimate the value that society places on changes to the size of the badger population in England and Wales. The study was undertaken in the context of a rising incidence of bovine tuberculosis (bTB) in cattle and the government's review of current bTB control policy. This review includes consideration of culling badgers to reduce bTB in cattle, since badgers are thought to be an important wildlife reservoir for the disease. The design of the CE involved four attributes (size of badger population, cattle slaughtered due to bTB, badger management strategy and household tax) at four levels with eight choice sets of two alternatives presented to respondents. Telephone interviews were undertaken with over 400 respondents, which elicited their attitudes and preferences concerning badgers, bTB in cattle and badger management strategies. The study estimated a willingness to pay of 0.10 pound per household per year per 100,000 badgers and 1.52 pound per household per year per 10,000 cattle slaughtered due to bTB which aggregated to 22 per badger and 3298 pound per bTB slaughtered animal for all households in England and Wales. Management strategy toward badgers had a very high valuation, highlighting the emotive issue of badger culling for respondents and the importance of government policy towards badgers.

Exploring options for managing strategies for pea-barley intercropping using a modeling approach

A modeling Study was carried out into pea-barley intercropping in northern Europe. The two objectives were (a) to compare pea-barley intercropping to sole cropping in terms of grain and nitrogen yield amounts and stability, and (b) to explore options for managing pea-barley intercropping systems in order to maximize the biomass produced and the grain and nitrogen yields according to the available resources, such as light, water and nitrogen. The study consisted of simulations taking into account soil and weather variability among three sites located in northern European Countries (Denmark, United Kingdom and France), and using 10 years of weather records. A preliminary stage evaluated the STICS intercrop model's ability to predict grain and nitrogen yields of the two species, using a 2-year dataset from trials conducted at the three sites. The work was carried out in two phases, (a) the model was run to investigate the potentialities of intercrops as compared to sole crops, and (b) the model was run to explore options for managing pea-barley intercropping, asking the following three questions: (i) in order to increase light capture, Would it be worth delaying the sowing dates of one species? (ii) How to manage sowing density and seed proportion of each species in the intercrop to improve total grain yield and N use efficiency? (iii) How to optimize the use of nitrogen resources by choosing the most suitable preceding crop and/or the most appropriate soil? It was found that (1) intercropping made better use of environmental resources as regards yield amount and stability than sole cropping, with a noticeable site effect, (2) pea growth in intercrops was strongly linked to soil moisture, and barley yield was determined by nitrogen uptake and light interception due to its height relative to pea, (3) sowing barley before pea led to a relative grain yield reduction averaged over all three sites, but sowing strategy must be adapted to the location, being dependent on temperature and thus latitude, (4) density and species proportions had a small effect on total grain yield, underlining the interspecific offset in the use of environmental growth resources which led to similar total grain yields whatever the pea-barley design, and (5) long-term strategies including mineralization management through organic residue supply and rotation management were very valuable, always favoring intercrop total grain yield and N accumulation. (C) 2009 Elsevier B.V. All rights reserved.

Strategies, effectiveness and rationale of vector-borne disease control in the pastoralist system of south-western Uganda

In Uganda, control of vector-borne diseases is mainly in form of vector control, and chemotherapy. There have been reports that acaricides are being misused in the pastoralist systems in Uganda. This is because of the belief by scientists that intensive application of acaricide is uneconomical and unsustainable particularly in the indigenous cattle. The objective of this study was to investigate the strategies, rationale and effectiveness of vector-borne disease control by pastoralists. To systematically carry out these investigations, a combination of qualitative and quantitative research methods was used, in both the collection and the analysis of data. Cattle keepers were found to control tick-borne diseases (TBDs) mainly through spraying, in contrast with the control of trypanosomosis for which the main method of control was by chemotherapy. The majority of herders applied acaricides weekly and used an acaricide of lower strength than recommended by the manufacturers. They used very little acaricide wash, and spraying was preferred to dipping. Furthermore, pastoralists either treated sick animals themselves or did nothing at all, rather than using veterinary personnel. Oxytetracycline (OTC) was the drug commonly used in the treatment of TBDs. Nevertheless, although pastoralists may not have been following recommended practices in their control of ticks and tick-borne diseases, they were neither wasteful nor uneconomical and their methods appeared to be effective. Trypanosomosis was not a problem either in Sembabule or Mbarara district. Those who used trypanocides were found to use more drugs than were necessary.