Long-term effectiveness of sowing high and low diversity seed mixtures to enhance plant community development on ex-arable fields

Questions: How is succession on ex-arable land affected by sowing high and low diversity mixtures of grassland species as compared to natural succession? How long do effects persist? Location: Experimental plots installed in the Czech Republic, The Netherlands, Spain, Sweden and the United Kingdom. Methods: The experiment was established on ex-arable land, with five blocks, each containing three 10 m x 10 m experiment tal plots: natural colonization, a low- (four species) and high-diversity (15 species) seed mixture. Species composition and biomass was followed for eight years. Results: The sown plants considerably affected the whole successional pathway and the effects persisted during the whole eight year period. Whilst the proportion of sown species (characterized by their cover) increased during the study period, the number of sown species started to decrease from the third season onwards. Sowing caused suppression of natural colonizing species, and the sown plots had more biomass. These effects were on average larger in the high diversity mixtures. However, the low diversity replicate sown with the mixture that produced the largest biomass or largest suppression of natural colonizers fell within the range recorded at the five replicates of the high diversity plots. The natural colonization plots usually had the highest total species richness and lowest productivity at the end of the observation period. Conclusions: The effect of sowing demonstrated dispersal limitation as a factor controlling the rate of early secondary succession. Diversity was important primarily for its 'insurance effect': the high diversity mixtures were always able to compensate for the failure of some species.

Dietary iron depletion at weaning imprints low microbiome diversity and this is not recovered with oral nano Fe(III)

Alterations in the gut microbiota have been recently linked to oral iron. We conducted two feeding studies including an initial diet-induced iron-depletion period followed by supplementation with nanoparticulate tartrate-modified ferrihydrite (Nano Fe(III): considered bioavailable to host but not bacteria) or soluble ferrous sulfate (FeSO4: considered bioavailable to both host and bacteria). We applied denaturing gradient gel electrophoresis and fluorescence in situ hybridization for study-1 and 454-pyrosequencing of fecal 16S rRNA in study-2. In study-1, the within-community microbial diversity increased with FeSO4 (P = 0.0009) but not with Nano Fe(III) supplementation. This was confirmed in study-2, where we also showed that iron depletion at weaning imprinted significantly lower within- and between-community microbial diversity compared to mice weaned onto the iron-sufficient reference diet (P < 0.0001). Subsequent supplementation with FeSO4 partially restored the within-community diversity (P = 0.006 in relation to the continuously iron-depleted group) but not the between-community diversity, whereas Nano Fe(III) had no effect. We conclude that (1) dietary iron depletion at weaning imprints low diversity in the microbiota that is not, subsequently, easily recovered; (2) in the absence of gastrointestinal disease iron supplementation does not negatively impact the microbiota; and (3) Nano Fe(III) is less available to the gut microbiota.

Management of plant communities on set-aside land and its effects on earthworm communities

Plant communities of set-aside agricultural land in a European project were managed in order to enhance plant succession towards weed-resistant, mid-successional grassland. Here, we ask if the management of a plant community affects the earthworm community. Field experiments were established in four countries, the Netherlands, Sweden, the UK, and the Czech Republic. High (15 plant species) and low diversity (four plant species) seed mixtures were sown as management practice, with natural colonization as control treatment in a randomized block design. The response of the earthworrns to the management was studied after three summers since establishment of the sites. Samples were also taken from plots with continued agricultural practices included in the experimental design and from a site with a late successional plant community representing the target plant community. The numbers and biomass of individuals were higher in the set-aside plots than in the agricultural treatment in two countries out of four. The numbers of individuals at one site (The Netherlands) was higher in the naturally colonized plots than in the sowing treatments, otherwise there were no differences between the treatments. Species diversity was lower in the agricultural plots in one country. The species composition had changed from the initial community of the agricultural field, but was still different from a late successional target community. The worm biomass was positively related to legume biomass in Sweden and to grass biomass in the UK. (C) 2005 Elsevier SAS. All rights reserved.

The impact of genome defense on mobile elements in Microbotryum

Repeat induced point mutation (RIP), a mechanism causing hypermutation of repetitive DNA sequences in fungi, has been described as a ‘genome defense’ which functions to inactivate mobile elements and inhibit their deleterious effects on genome stability. Here we address the interactions between RIP and transposable elements in the Microbotryum violaceum species complex. Ten strains of M. violaceum, most of which belong to different species of the fungus, were all found to contain intragenomic populations of copia-like retrotransposons. Intragenomic DNA sequence variation among the copia-like elements was analyzed for evidence of RIP. Among species with RIP, there was no significant correlation between the frequency of RIP-induced mutations and inferred transposition rate based on diversity. Two strains of M. violaceum, from two different plant species but belonging to the same fungal lineage, contained copia-like elements with very low diversity, as would result from a high transposition rate, and these were also unique in showing no evidence of the hypermutation patterns indicative of the RIP genome defense. In this species, evidence of RIP was also absent from a Class II helitron-like transposable element. However, unexpectedly the absolute repetitive element load was lower than in other strains.

A global quantitative synthesis of local and landscape effects on wild bee pollinators in agroecosystems

Bees provide essential pollination services that are potentially affected both by local farm management and the surrounding landscape. To better understand these different factors, we modelled the relative effects of landscape composition (nesting and floral resources within foraging distances), landscape configuration (patch shape, interpatch connectivity and habitat aggregation) and farm management (organic vs. conventional and local-scale field diversity), and their interactions, on wild bee abundance and richness for 39 crop systems globally. Bee abundance and richness were higher in diversified and organic fields and in landscapes comprising more high-quality habitats; bee richness on conventional fields with low diversity benefited most from high-quality surrounding land cover. Landscape configuration effects were weak. Bee responses varied slightly by biome. Our synthesis reveals that pollinator persistence will depend on both the maintenance of high-quality habitats around farms and on local management practices that may offset impacts of intensive monoculture agriculture.

Low genetic diversity in a marine nature reserve: re-evaluating diversity criteria in reserve design

Little consideration has been given to the genetic composition of populations associated with marine reserves, as reserve designation is generally to protect specific species, communities or habitats. Nevertheless, it is important to conserve genetic diversity since it provides the raw material for the maintenance of species diversity over longer, evolutionary time-scales and may also confer the basis for adaptation to environmental change. Many current marine reserves are small in size and isolated to some degree (e.g. sea loughs and offshore islands). While such features enable easier management, they may have important implications for the genetic structure of protected populations, the ability of populations to recover from local catastrophes and the potential for marine reserves to act as sources of propagules for surrounding areas. Here, we present a case study demonstrating genetic differentiation, isolation, inbreeding and reduced genetic diversity in populations of the dogwhelk Nucella lapillus in Lough Hyne Marine Nature Reserve (an isolated sea lough in southern Ireland), compared with populations on the local adjacent open coast and populations in England, Wales and France. Our study demonstrates that this sea lough is isolated from open coast populations, and highlights that there may be long-term genetic consequences of selecting reserves on the basis of isolation and ease of protection.

Reliability comparison of transmit/receive diversity and error control coding in low-power medium access control protocols

Low-power medium access control (MAC) protocols used for communication of energy constraint wireless embedded devices do not cope well with situations where transmission channels are highly erroneous. Existing MAC protocols discard corrupted messages which lead to costly retransmissions. To improve transmission performance, it is possible to include an error correction scheme and transmit/receive diversity. It is possible to add redundant information to transmitted packets in order to recover data from corrupted packets. It is also possible to make use of transmit/receive diversity via multiple antennas to improve error resiliency of transmissions. Both schemes may be used in conjunction to further improve the performance. In this study, the authors show how an error correction scheme and transmit/receive diversity can be integrated in low-power MAC protocols. Furthermore, the authors investigate the achievable performance gains of both methods. This is important as both methods have associated costs (processing requirements; additional antennas and power) and for a given communication situation it must be decided which methods should be employed. The authors’ results show that, in many practical situations, error control coding outperforms transmission diversity; however, if very high reliability is required, it is useful to employ both schemes together.

Improving transmission reliability of low-power medium access control protocols using average diversity combining

Embedded computer systems equipped with wireless communication transceivers are nowadays used in a vast number of application scenarios. Energy consumption is important in many of these scenarios, as systems are battery operated and long maintenance-free operation is required. To achieve this goal, embedded systems employ low-power communication transceivers and protocols. However, currently used protocols cannot operate efficiently when communication channels are highly erroneous. In this study, we show how average diversity combining (ADC) can be used in state-of-the-art low-power communication protocols. This novel approach improves transmission reliability and in consequence energy consumption and transmission latency in the presence of erroneous channels. Using a testbed, we show that highly erroneous channels are indeed a common occurrence in situations, where low-power systems are used and we demonstrate that ADC improves low-power communication dramatically.

High prevalence of undernutrition and low dietary diversity in institutionalised elderly living in Sri Lanka

This research received no specific grant from any funding agency in the public, commercial and not-for-profit sectors. The authors wish to thank the participants, administrators and caregivers of the homes for elders for their enthusiastic cooperation and also the Nutrition Research Team of the Department of Applied Nutrition, Wayamba University of Sri Lanka, for their valuable assistance during the course of the study. The authors also wish to thank Mr. S. Rahanan for coordination and the assistance given in data collection especially in Tamil speaking participants. K.M.R designed and managed the study, interpreted the data and drafted the manuscript. M.P.P.M contributed to the data collection, data analysis and coordination of the study. M.W, K.G.J and J.A.L assisted in data interpretation and critical revision of the manuscript. The authors declare that there is no conflict of interest of any kind involved in this study or this publication. Ethical clearance for this study was obtained from the Ethical Review Committee of the Sri Lanka Medical Association (ERC/13-037).

Intersections of Jane Jacobs’ conditions for diversity and low-carbon urban systems: a look at four global cities

Countless cities are rapidly developing across the globe, pressing the need for clear urban planning and design recommendations geared towards sustainability. This article examines the intersections of Jane Jacobs’ four conditions for diversity with low-carbon and low-energy use urban systems in four cities around the world: Lyon (France), Chicago (United-States), Kolkata (India), and Singapore (Singapore). After reviewing Jacobs’ four conditions for diversity, we introduce the four cities and describe their historical development context. We then present a framework to study the cities along three dimensions: population and density, infrastructure development/use, and climate and landscape. These cities differ in many respects and their analysis is instructive for many other cities around the globe. Jacobs’ conditions are present in all of them, manifested in different ways and to varying degrees. Overall we find that the adoption of Jacobs' conditions seems to align well with concepts of low-carbon urban systems, with their focus on walkability, transit-oriented design, and more efficient land use (i.e., smaller unit sizes). Transportation sector emissions seems to demonstrate a stronger influence from the presence of Jacobs' conditions, while the link was less pronounced in the building sector. Kolkata, a low-income, developing world city, seems to possess many of Jacobs' conditions, while exhibiting low per capita emissions - maintaining both of these during its economic expansion will take careful consideration. Greenhouse gas mitigation, however, is inherently an in situ problem and the first task must therefore be to gain local knowledge of an area before developing strategies to lower its carbon footprint.

Response of plant-pollinator communities to fire: changes in diversity, abundance and floral reward structure

Globally, plant-pollinator communities are subject to a diverse array of perturbations and in many temperate and semi-arid systems fire is a dominant structuring force. We present a novel and highly integrated approach, which quantifies, in parallel, the response to fire of pollinator communities, floral communities and floral reward structure. Mt Carmel, Israel is a recognised bee-flower biodiversity hotspot, and using a chronosequence of habitats with differing post-fire ages, we follow the changes in plant-pollinator community organisation from immediately following a burn until full regeneration of vegetation. Initially, fire has a catastrophic effect on these communities, however, recovery is rapid with a peak in diversity of both flowers and bees in the first 2 years post-fire, followed by a steady decline over the next 50 years. The regeneration of floral communities is closely matched by that of their principal pollinators. At the community level we quantify, per unit area of habitat, key parameters of nectar and pollen forage known to be of importance in structuring pollinator communities. Nectar Volume, nectar water content, nectar concentration and the diversity of nectar foraging niches are all greatest immediately following fire with a steady decrease as regeneration proceeds. Temporal changes in energy availability for nectar, pollen, total energy (nectar + pollen) and relative importance of pollen to nectar energy show a similar general decline with site age, however, the pattern is less clear owing to the highly patchy distribution of floral resources. Changes in floral reward structure reflect the general shift from annuals (generally low-reward open access flowers) to perennials (mostly high-reward and restricted access flowers) as post-fire regeneration ensues. The impact of fire on floral communities and their associated rewards have clear implications for pollinator community structure and we discuss this and the role of other disturbance factors on these systems.

Measuring bee diversity in different European habitats and biogeographical regions

Bee pollinators are currently recorded with many different sampling methods. However, the relative performances of these methods have not been systematically evaluated and compared. In response to the strong need to record ongoing shifts in pollinator diversity and abundance, global and regional pollinator initiatives must adopt standardized sampling protocols when developing large-scale and long-term monitoring schemes. We systematically evaluated the performance of six sampling methods (observation plots, pan traps, standardized and variable transect walks, trap nests with reed internodes or paper tubes) that are commonly used across a wide range of geographical regions in Europe and in two habitat types (agricultural and seminatural). We focused on bees since they represent the most important pollinator group worldwide. Several characteristics of the methods were considered in order to evaluate their performance in assessing bee diversity: sample coverage, observed species richness, species richness estimators, collector biases (identified by subunit-based rarefaction curves), species composition of the samples, and the indication of overall bee species richness (estimated from combined total samples). The most efficient method in all geographical regions, in both the agricultural and seminatural habitats, was the pan trap method. It had the highest sample coverage, collected the highest number of species, showed negligible collector bias, detected similar species as the transect methods, and was the best indicator of overall bee species richness. The transect methods were also relatively efficient, but they had a significant collector bias. The observation plots showed poor performance. As trap nests are restricted to cavity-nesting bee species, they had a naturally low sample coverage. However, both trap nest types detected additional species that were not recorded by any of the other methods. For large-scale and long-term monitoring schemes with surveyors with different experience levels, we recommend pan traps as the most efficient, unbiased, and cost-effective method for sampling bee diversity. Trap nests with reed internodes could be used as a complementary sampling method to maximize the numbers of collected species. Transect walks are the principal method for detailed studies focusing on plant-pollinator associations. Moreover, they can be used in monitoring schemes after training the surveyors to standardize their collection skills.

Inbreeding depression and founder diversity among captive and free-living populations of the endangered pink pigeon Columba mayeri

The endemic pink pigeon has recovered from less than 20 birds in the mid-1970s to 355 free-living individuals in 2003. A major concern for the species' recovery has been the potential genetic problem of inbreeding. Captive pink pigeons bred for reintroduction were managed to maximise founder representation and minimise inbreeding. In this paper, we quantify the effect of inbreeding on survival and reproductive parameters in captive and wild populations and quantify DNA sequence variation in the mitochondrial d-loop region for pink pigeon founders. Inbreeding affected egg fertility, squab, juvenile and adult survival, but effects were strongest in highly inbred birds (F≥0.25). Inbreeding depression was more apparent in free-living birds where even moderate levels of inbreeding affected survival, although highly inbred birds were equally compromised in both captive and wild populations. Mitochondrial DNA haplotypic diversity in pink pigeon founders is low, suggesting that background inbreeding is contributing to low fertility and depressed productivity in this species, as well as comparable survival of some groups of non-inbred and nominally inbred birds. Management of wild populations has boosted population growth and may be required long-term to offset the negative effects of inbreeding depression and enhance the species' survival.

Genetic structure and systematic relationships within the Ophrys fuciflora aggregate (Orchidaceae: Orchidinae): high diversity in Kent and a wind-induced discontinuity bisecting the Adriatic

A recent phylogenetic study based on multiple datasets is used as the framework for a more detailed examination of one of the ten molecularly circumscribed groups identified, the Ophrys fuciflora aggregate. The group is highly morphologically variable, prone to phenotypic convergence, shows low levels of sequence divergence and contains an unusually large proportion of threatened taxa, including the rarest Ophrys species in the UK. The aims of this study were to (a) circumscribe minimum resolvable genetically distinct entities within the O. fuciflora aggregate, and (b) assess the likelihood of gene flow between genetically and geographically distinct entities at the species and population levels. Fifty-five accessions sampled in Europe and Asia Minor from the O. fuciflora aggregate were studied using the AFLP genetic fingerprinting technique to evaluate levels of infraspecific and interspecific genetic variation and to assess genetic relationships between UK populations of O. fuciflora s.s. in Kent and in their continental European and Mediterranean counterparts. The two genetically and geographically distinct groups recovered, one located in England and central Europe and one in south-eastern Europe, are incongruent with current species delimitation within the aggregate as a whole and also within O. fuciflora s.s. Genetic diversity is higher in Kent than in the rest of western and central Europe. Gene flow is more likely to occur between populations in closer geographical proximity than those that are morphologically more similar. Little if any gene flow occurs between populations located in the south-eastern Mediterranean and those dispersed throughout the remainder of the distribution, revealing a genetic discontinuity that runs north-south through the Adriatic. This discontinuity is also evident in other clades of Ophrys and is tentatively attributed to the long-term influence of prevailing winds on the long-distance distribution of pollinia and especially seeds. A cline of gene flow connects populations from Kent and central and southern Europe; these individuals should therefore be considered part of an extensive meta-population. Gene flow is also evident among populations from Kent, which appear to constitute a single metapopulation. They show some evidence of hybridization, and possibly also introgression, with O. apifera.

Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens

Background: Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species. Results: Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome. Conclusions: P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.