Towards a strategy for the conservation of the freshwater pearl mussel Margaritifera margaritifera in County Donegal, Ireland

This study attempts to identify the habitat requirements of the pearl mussel Margaritifea margaritifera in County Donegal, in north west Ireland, an area with little urban, industrial or intensive agricultural development. No mussels occur in rivers where calcium and conductivity levels are high or where the substratum is predominantly bedrock or fine sediment but it was not possible to distinguish clearly between mussel and non-mussel sites on the basis of ordination analysis. However, rivers which still support mussels and rivers with historical records of mussels are loosely grouped. Rivers which formerly supported mussels but lack living M. margaritifera appear to have suitable habitat for mussels; pearl fishing is the most likely reason for the extinction of these mussel populations. Where population densities are high, for example in locations on the rivers Eske, Clady and Owenea, conservation may necessitate the establishment of reserves. The prospect for the successful reintroduction of mussels into former mussel rivers such as the Finn and Eany Water, where suitable habitat exists and water quality is high, is very good.

Consistent patterns and the idiosyncratic effects of biodiversity in marine ecosystems

Revealing the consequences of species extinctions for ecosystem function has been a chief research goal(1-7) and has been accompanied by enthusiastic debate(8-11). Studies carried out predominantly in terrestrial grassland and soil ecosystems have demonstrated that as the number of species in assembled communities increases, so too do certain ecosystem processes, such as productivity, whereas others such as decomposition can remain unaffected(12). Diversity can influence aspects of ecosystem function, but questions remain as to how generic the patterns observed are, and whether they are the product of diversity, as such, or of the functional roles and traits that characterize species in ecological systems. Here we demonstrate variable diversity effects for species representative of marine coastal systems at both global and regional scales. We provide evidence for an increase in complementary resource use as diversity increases and show strong evidence for diversity effects in naturally assembled com-munities at a regional scale. The variability among individual species responses is consistent with a positive but idiosyncratic pattern of ecosystem function with increased diversity.

How many dimensions of biodiversity do we need?

Biodiversity is not a commodity, nor a service (ecosystem or otherwise), it is a scientific measure of the complexity of a biological system. Rather than directly valuing biodiversity, economists have tended to value its services, more often the services of 'key' species. This is understandable given the confusion of definitions and measures of biodiversity, but weakly justified if biodiversity is not substitutable. We provide a quantitative and comprehensive definition of biodiversity and propose a framework for examining its substitutability as the first step towards valuation. We define biodiversity as a measure of semiotic information. It is equated with biocomplexity and measured by Algorithmic Information Content (AIC). We argue that the potentially valuable component of this is functional information content (FIC) which determines biological fitness and supports ecosystem services. Inspired by recent extensions to the Noah's Ark problem, we show how FIC/AIC can be calculated to measure the degree of substitutability within an ecological community. From this, we derive a way to rank whole communities by Indirect Use Value, through quantifying the relation between system complexity and production rate of ecosystem services. Understanding biodiversity as information evidently serves as a practical interface between economics and ecological science.

A quorum-quenching approach to investigate the conservation of quorum-sensing-regulated functions within the Burkholderia cepacia complex

Taxonomic studies of the past few years have shown that the Burkholderia cepacia complex, a heterogeneous group of B. cepacia-like organisms, consists of at least nine species. B. cepacia complex strains are ubiquitously distributed in nature and have been used for biocontrol, bioremediation, and plant growth promotion purposes. At the same time, B. cepacia complex strains have emerged as important opportunistic pathogens of humans, particularly those with cystic fibrosis. All B. cepacia complex species investigated thus far use quorum-sensing (QS) systems that rely on N-acylhomoserine lactone (AHL) signal molecules to express certain functions, including the production of extracellular proteases, swarming motility, biofilm formation, and pathogenicity, in a population-density-dependent manner. In this study we constructed a broad-host-range plasmid that allowed the heterologous expression of the Bacillus sp. strain 240B1 AiiA lactonase, which hydrolyzes the lactone ring of various AHL signal molecules, in all described B. cepacia complex species. We show that expression of AiiA abolished or greatly reduced the accumulation of AHL molecules in the culture supernatants of all tested B. cepacia complex strains. Phenotypic characterization of wild-type and transgenic strains revealed that protease production, swarming motility, biofilm formation, and Caenorhabditis elegans killing efficiency was regulated by AHL in the large majority of strains investigated.

Identification of 100 fundamental ecological questions

Fundamental ecological research is both intrinsically interesting and provides the basic knowledge required to answer applied questions of importance to the management of the natural world. The 100th anniversary of the British Ecological Society in 2013 is an opportune moment to reflect on the current status of ecology as a science and look forward to high-light priorities for future work. To do this, we identified 100 important questions of fundamental importance in pure ecology. We elicited questions from ecologists working across a wide range of systems and disciplines. The 754 questions submitted (listed in the online appendix) from 388 participants were narrowed down to the final 100 through a process of discussion, rewording and repeated rounds of voting. This was done during a two-day workshop and thereafter. The questions reflect many of the important current conceptual and technical pre-occupations of ecology. For example, many questions concerned the dynamics of environmental change and complex ecosystem interactions, as well as the interaction between ecology and evolution. The questions reveal a dynamic science with novel subfields emerging. For example, a group of questions was dedicated to disease and micro-organisms and another on human impacts and global change reflecting the emergence of new subdisciplines that would not have been foreseen a few decades ago. The list also contained a number of questions that have perplexed ecologists for decades and are still seen as crucial to answer, such as the link between population dynamics and life-history evolution. Synthesis. These 100 questions identified reflect the state of ecology today. Using them as an agenda for further research would lead to a substantial enhancement in understanding of the discipline, with practical relevance for the conservation of biodiversity and ecosystem function. © 2013 The Authors. Journal of Ecology © 2013 British Ecological Society.

An Integrated Toolkit for the Conservation of Stone-Built Heritage

Rapid in situ diagnosis of damage is a key issue in the preservation of stone-built cultural heritage. This is evident in the increasing number of congresses, workshops and publications dealing with this issue. With this increased activity has come, however, the realisation that for many culturally significant artefacts it is not possible either to remove samples for analysis or to affix surface markers for measurement. It is for this reason that there has been a growth of interest in non-destructive and minimally invasive techniques for characterising internal and external stone condition. With this interest has come the realisation that no single technique can adequately encompass the wide variety of parameters to be assessed or provide the range of information required to identify appropriate conservation. In this paper we describe a strategy to address these problems through the development of an integrated `tool kit' of measurement and analytical techniques aimed specifically at linking object-specific research to appropriate intervention. The strategy is based initially upon the acquisition of accurate three-dimensional models of stone-built heritage at different scales using a combination of millimetre accurate LiDAR and sub-millimetre accurate Object Scanning that can be exported into a GIS or directly into CAD. These are currently used to overlay information on stone characteristics obtained through a combination of Ground Penetrating Radar, Surface Permeametry, Colorimetry and X-ray Fluorescence, but the possibility exists for adding to this array of techniques as appropriate. In addition to the integrated three-dimensional data array provided by superimposition upon Digital Terrain Models, there is the capability of accurate re-measurement to show patterns of surface loss and changes in material condition over time. Thus it is possible to both record and base-line condition and to identify areas that require either preventive maintenance or more significant pre-emptive intervention. In pursuit of these goals the authors are developing, through a UK Government supported collaboration between University Researchers and Conservation Architects, commercially viable protocols for damage diagnosis, condition monitoring and eventually mechanisms for prioritizing repairs to stone-built heritage. The understanding is, however, that such strategies are not age-constrained and can ultimately be applied to structures of any age.

Application of low temperature plasmas for restoration/conservation of archaeological objects

The low-temperature low-pressure hydrogen based plasmas were used to study the influence of processes and discharge conditions on corrosion removal. The capacitive coupled RF discharge in the continuous or pulsed regime was used at operating pressure of 100-200 Pa. Plasma treatment was monitored by optical emission spectroscopy. To be able to study influence of various process parameters, the model corroded samples with and without sandy incrustation were prepared. The SEM-EDX analyzes were carried out to verify corrosion removal efficiency. Experimental conditions were optimized for the selected most frequent materials of original metallic archaeological objects (iron, bronze, copper, and brass). Chlorides removal is based on hydrogen ion reactions while oxides are removed mainly by neutral species interactions. A special focus was kept for the samples temperature because it was necessary to avoid any metallographic changes in the material structure. The application of higher power pulsed regime with low duty cycle seems be the best treatment regime. The low pressure hydrogen plasma is not applicable for objects with a very broken structure or for nonmetallic objects due to the non-uniform heat stress. Due to this fact, the new developed plasmas generated in liquids were applied on selected original archaeological glass materials.

Granular gland transcriptomes in stimulated amphibian skin secretions.

Amphibian defensive skin secretions are complex, species-specific cocktails of biologically active molecules, including many uncharacterized peptides. The study of such secretions for novel peptide discovery is time-limited, as amphibians are in rapid global decline. While secretion proteome analysis is non-lethal, transcriptome analysis has until now required killing of specimens prior to skin dissection for cDNA library construction. Here we present the discovery that polyadenylated mRNAs encoding dermal granular gland peptides are present in defensive skin secretions, stabilized by endogenous nucleic acid-binding amphipathic peptides. Thus parallel secretory proteome and transcriptome analyses can be performed without killing the specimen in this model amphibian system--a finding that has important implications in conservation of biodiversity within this threatened vertebrate taxon and whose mechanistics may have broader implications in biomolecular science.

Population enumeration and assessing conservation status in a widespread amphibian: A case study of Rana temporaria in Ireland

Global amphibian declines are a major element of the current biodiversity crisis. Monitoring changes in the distribution and abundance of target species is a basic component in conservation decision making and requires robust and repeatable sampling. For EU member states, surveillance of designated species, including the common frog Rana temporaria, is a formal requirement of the 'EC Habitats & Species Directive'. We deployed established methods for estimating frog population density at local water bodies and extrapolated these to the national and ecoregion scale. Spawn occurred at 49.4% of water bodies and 70.1% of independent 500-m survey squares. Using spawn mat area, we estimated the number of adult breeding females and subsequently the total population assuming a sex ratio of 1:1. A negative binomial model suggested that mean frog density was 23.5 frogsha [95% confidence interval (CI) 14.9-44.0] equating to 196M frogs (95%CI 124M-367M) throughout Ireland. A total of 86% of frogs bred in drainage ditches, which were a notably common feature of the landscape. The recorded distribution of the species did not change significantly between the last Article 17 reporting period (1993-2006) and the current period (2007-2011) throughout the Republic of Ireland. Recording effort was markedly lower in Northern Ireland, which led to an apparent decline in the recorded distribution. We highlight the need to coordinate biological surveys between adjacent political jurisdictions that share a common ecoregion to avoid apparent disparities in the quality of distributional information. Power analysis suggested that a reduced sample of 40-50 survey squares is sufficient to detect a 30% decline (consistent with the International Union for Conservation of Nature Category of 'Vulnerable') at 80% power providing guidance for minimizing future survey effort. Our results provin assessments for R. temporaria and other clump-spawning amphibians. 2013 The Zoological Society of London.

Building on IUCN regional red lists to produce lists of species of conservation priority: a model with Irish bees

A World Conservation Union (IUCN) regional red list is an objective assessment of regional extinction risk and is not the same as a list of conservation priority species. Recent research reveals the widespread, but incorrect, assumption that IUCN Red List categories represent a hierarchical list of priorities for conservation action. We developed a simple eight-step priority-setting process and applied it to the conservation of bees in Ireland. Our model is based on the national red list but also considers the global significance of the national population; the conservation status at global, continental, and regional levels; key biological, economic, and societal factors; and is compatible with existing conservation agreements and legislation. Throughout Ireland, almost one-third of the bee fauna is threatened (30 of 100 species), but our methodology resulted in a reduced list of only 17 priority species. We did not use the priority species list to broadly categorize species to the conservation action required; instead, we indicated the individual action required for all threatened, near-threatened, and data-deficient species on the national red list based on the IUCN's conservation-actions template file. Priority species lists will strongly influence prioritization of conservation actions at national levels, but action should not be exclusive to listed species. In addition, all species on this list will not necessarily require immediate action. Our method is transparent, reproducible, and readily applicable to other taxa and regions.