Differential Responses of Bird Species to Habitat Condition in a Coastal Kenyan Forest Reserve: Implications for Conservation

The management of assemblages of species across many taxa is a common concern in conservation. Consequently, the use of one or a few surrogate or indicator species to represent an entire assemblage has become an increasingly important tool in conservation science. However, conservation schemes based on the needs of one or two focal species often fail to account for individualistic responses of larger assemblages of species. Data from bird point counts along with vegetation characteristics from a coastal tropical dry forest in Kenya that is subject to elephant disturbance were used to explore the differential responses of bird species to environmental conditions in a forest reserve where wildlife management includes both endangered birds and mammals. Results revealed that even birds with similar foraging habits had idiosyncratic responses to both environmental traits and elephant disturbance. While overall species responded to important characteristics such as percent canopy cover and leaf litter depth, individualistic responses of different species trait diversity defied easy characterization of optimal forest management schemes. Taken together, our analyses highlight the difficulty in basing the development of management plans for entire assemblages of species on the response of a single or a few species. Implications for wildlife conservation in Arabuko-Sokoke Forest and similar forest reserves are discussed, emphasizing the need for a better understanding of individual species’ responses to forest conditions

The use of natural products in the leather industry: Depilation without damage

Content: Sheepskin, a by-product of the meat industry, is then often processed to leather, primarily for the clothing industry. Where the tanneries are distant from the abattoirs and freezing works, the raw skins have to be transported long distances to be processed. In warm weather, there is the potential for putrefaction of the skins which then have to be disposed of at a cost. Depilation, the first step of leather processing, is designed to remove the wool from the skin without damaging it. Conventional depilation involves the use of strong alkali and sulfides, that are harmful to both the environment and the personnel carrying out the process due to the potential production of hydrogen sulfide, a toxic, flammable gas. To solve this problem, scientists have been looking to depilate skins using enzymes as these are environmentally friendly. Various enzymes, such as collagenase, keratinase, protease and lipase have been shown to be able to remove hair from skin, but unfortunately usually damage it. Furthermore, at present, they are not cost effective at an industrial level. We have found a simple solution, a derivative of a dairy by-product, that prevents putrefaction, preserving the skin for days at room temperature. In addition, it allows easy removal of the wool from the skin. Scanning electron microscopy showed there was no obvious damage to the surface of the depilated skin and that the wool is cleanly removed from the hair follicle. To assess any less visible damage that may have occurred as a result of soaking the skin, biochemical analyses were carried out to measure the changes to the amino acid composition, collagen crosslinks and proteoglycan concentrations of the depilated skins. Sheepskin depilated with this method was processed to leather and its physical properties such as tear, and tensile strength analysed. Culture dependent methods were used to isolate the microorganisms present in the solution after depilation, showed that only four main species were consistently found in the depilation fluid and on the skins. Metagenomic analysis, confirmed these findings and was used to follow the changes in the microbiome during the course of depilation. This presentation will describe the progress that has been made to understand the science behind these observations and compare the properties of skins depilated using this method with those depilated using the traditional beamhouse process. Take-Away: We are using a natural product to depilate sheepskin. The sheepskin is also preserved while depilation. Microscopy, chemical analyses, physical tests, and metagenomics analysis were done to understand the process

Global expansion of Vibrio parahaemolyticus threatens the seafood industry: Perspective on controlling its biofilm formation

As global warming increases the geographical range and frequency of Vibrio parahaemolyticus infections, its formation of biofilms providing bacteria greater resistance to stress and contributing to the persistence of pathogens, is threatening the seafood industry. V. parahaemolyticus has a number of advantages leading to biofilm formation. This study reviews recent advances in understanding V. parahaemolyticus biofilm formation on biotic and abiotic surfaces, discusses research gaps in the mechanism of biofilm formation and examines promising biofilm control strategies to overcome current limitations of chemical disinfectant. This information will deepen our understanding of V. parahaemolyticus biofilm formation, as well as help design and optimize V. parahaemolyticus biofilm control strategies for the seafood industry

Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community

BACKGROUND: In silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical, considering that the metasecretome open reading frames (ORFs) comprise only 10% to 30% of total metagenome, and are poorly represented in the dataset due to overall low coverage of metagenomic gene pool, even in large-scale projects. RESULTS: By combining secretome-selective phage display and next-generation sequencing, we focused the sequence analysis of complex rumen microbial community on the metasecretome component of the metagenome. This approach achieved high enrichment (29 fold) of secreted fibrolytic enzymes from the plant-adherent microbial community of the bovine rumen. In particular, we identified hundreds of heretofore rare modules belonging to cellulosomes, cell-surface complexes specialised for recognition and degradation of the plant fibre. CONCLUSIONS: As a method, metasecretome phage display combined with next-generation sequencing has a power to sample the diversity of low-abundance surface and secreted proteins that would otherwise require exceptionally large metagenomic sequencing projects. As a resource, metasecretome display library backed by the dataset obtained by next-generation sequencing is ready for i) affinity selection by standard phage display methodology and ii) easy purification of displayed proteins as part of the virion for individual functional analysis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-356) contains supplementary material, which is available to authorized users

Exploring rumen microbe-derived fibre-degrading activities for improving feed digestibility

Ruminal fibre degradation is mediated by a complex community of rumen microbes, and its efficiency is crucial for optimal dairy productivity. Enzymes produced by rumen microbes are primarily responsible for degrading the complex structural polysaccharides that comprise fibre in the plant cell walls of feed materials. Because rumen microbes have evolved with their ruminant hosts over millions of years to perform this task, their enzymes are hypothesised to be optimally suited for activity at the temperature, pH range, and anaerobic environment of the rumen. However, fibre-rich diets are not fully digested, which represents a loss in potential animal productivity. Thus, there is opportunity to improve fibre utilisation through treating feeds with rumen microbe-derived fibrolytic enzymes and associated activities that enhance fibre degradation. This research aims to gain a better understanding of the key rumen microbes involved in fibre degradation and the mechanisms they employ to degrade fibre, by applying cultivation-based and culture-independent genomics approaches to rumen microbial communities of New Zealand dairy cattle. Using this knowledge, we aim to identify new opportunities for improving fibre degradation to enhance dairy productivity. Rumen content samples were taken over the course of a year from a Waikato dairy production herd. Over 1,000 rumen bacterial cultures were obtained from the plant-adherent fraction of the rumen contents. Among these cultures, two, 59 and 103 potentially new families, genera and species of rumen bacteria were identified, respectively. Many of the novel strains are being genome sequenced within the Hungate 1000 rumen microbial reference genome programme, which is providing deeper insights into the range of mechanisms used by the individual strains for fibre degradation. This information has been used to guide the selection of rumen bacterial strains with considerable potential as fibrolytic enzyme producers in vitro, with the intent of developing the strains so that their enzymes may be used as feed pre-treatments for use on farm. Culture-independent metagenomic approaches were also used to explore the activities involved in fibre degradation from the rumen microbial communities. Functional screening has revealed a range of novel enzymes and a novel fibre disrupting activity. Enrichment for the cell-secreted proteins from the community revealed evidence of a diverse range of cellulosomes, which are cell-surface associated multi-enzyme complexes that efficiently degrade plant cell wall polysaccharides. Biochemical and structural characterisation of these proteins has been conducted. In conclusion, cultivation and culture-independent genomic approaches have been applied to New Zealand bovine rumen microbial communities, and have provided considerable new insights into ruminal fibre degradation processes. Novel activities and bacterial species that display desirable activities on fibrous substrates in vitro are now being explored for their potential to improve ruminal fibre degradation, to allow the development of new technologies that will enhance dairy productivity

The effect of protective covers on pollinator health and pollination service delivery

Protective covers (i.e., glasshouses, netting enclosures, and polytunnels) are increasingly used in crop production to enhance crop quality, yield, and production efficiency. However, many protected crops require insect pollinators to achieve optimal pollination and there is no consensus about how best to manage pollinators and crop pollination in these environments. We conducted a systematic literature review to synthesise knowledge about the effect of protective covers on pollinator health and pollination services and identified 290 relevant studies. Bees were the dominant taxon used in protected systems (90%), represented by eusocial bees (e.g., bumble bees (Bombus spp.), honey bees (Apis spp.), stingless bees (Apidae: Meliponini)) and solitary bees (e.g., Amegilla spp., Megachile spp., and Osmia spp.). Flies represented 9% of taxa and included Calliphoridae, Muscidae, and Syrphidae. The remaining 1% of taxa was represented by Lepidoptera and Coleoptera. Of the studies that assessed pollination services, 96% indicate that pollinators were active on the crop and/or their visits resulted in improved fruit production compared with flowers not visited by insects (i.e., insect visits prevented, or flowers were self- or mechanically pollinated). Only 20% of studies evaluated pollinator health. Some taxa, such as mason or leafcutter bees, and bumble bees can function well in covered environments, but the effect of covers on pollinator health was negative in over 50% of the studies in which health was assessed. Negative effects included decreased reproduction, adult mortality, reduced forager activity, and increased disease prevalence. These effects may have occurred as a result of changes in temperature/humidity, light quality/quantity, pesticide exposure, and/or reduced access to food resources. Strategies reported to successfully enhance pollinator health and efficiency in covered systems include: careful selection of bee hive location to reduce heat stress and improve dispersal through the crop; increased floral diversity; deploying appropriate numbers of pollinators; and manipulation of flower physiology to increase attractiveness to pollinating insects. To improve and safeguard crop yields in pollinator dependent protected cropping systems, practitioners need to ensure that delivery of crop pollination services is compatible with suitable conditions for pollinator health

Seed Transmission of Epichloë Endophytes in Lolium perenne Is Heavily Influenced by Host Genetics

Vertical transmission of symbiotic Epichloë endophytes from host grasses into progeny seed is the primary mechanism by which the next generation of plants is colonized. This process is often imperfect, resulting in endophyte-free seedlings which may have poor ecological fitness if the endophyte confers protective benefits to its host. In this study, we investigated the influence of host genetics and environment on the vertical transmission of Epichloë festucae var. lolii strain AR37 in the temperate forage grass Lolium perenne. The efficiency of AR37 transmission into the seed of over 500 plant genotypes from five genetically diverse breeding populations was determined. In Populations I–III, which had undergone previous selection for high seed infection by AR37, mean transmission was 88, 93, and 92%, respectively. However, in Populations IV and V, which had not undergone previous selection, mean transmission was 69 and 70%, respectively. The transmission values, together with single-nucleotide polymorphism data obtained using genotyping-by-sequencing for each host, was used to develop a genomic prediction model for AR37 seed transmission. The predictive ability of the model was estimated at r = 0.54. While host genotype contributed greatly to differences in AR37 seed transmission, undefined environmental variables also contributed significantly to seed transmission across different years and geographic locations. There was evidence for a small host genotype-by-environment effect; however this was less pronounced than genotype or environment alone. Analysis of endophyte infection levels in parent plants within Populations I and IV revealed a loss of endophyte infection over time in Population IV only. This population also had lower average tiller infection frequencies than Population I, suggesting that AR37 failed to colonize all the daughter tillers and therefore seeds. However, we also observed that infection of seed by AR37 may fail during or after initiation of floral development from plants where all tillers remained endophyte-infected over time. While the effects of environment and host genotype on fungal endophyte transmission have been evaluated previously, this is the first study that quantifies the relative impacts of host genetics and environment on endophyte vertical transmission

Meta-analysis reveals that pollinator functional diversity and abundance enhance crop pollination and yield

How insects promote crop pollination remains poorly understood in terms of the contribution of functional trait differences between species. We used meta-analyses to test for correlations between community abundance, species richness and functional trait metrics with oilseed rape yield, a globally important crop. While overall abundance is consistently important in predicting yield, functional divergence between species traits also showed a positive correlation. This result supports the complementarity hypothesis that pollination function is maintained by non-overlapping trait distributions. In artificially constructed communities (mesocosms), species richness is positively correlated with yield, although this effect is not seen under field conditions. As traits of the dominant species do not predict yield above that attributed to the effect of abundance alone, we find no evidence in support of the mass ratio hypothesis. Management practices increasing not just pollinator abundance, but also functional divergence, could benefit oilseed rape agriculture

A global synthesis reveals biodiversity-mediated benefits for crop production

Human land use threatens global biodiversity and compromises multiple ecosystem functions critical to food production. Whether crop yield-related ecosystem services can be maintained by a few dominant species or rely on high richness remains unclear. Using a global database from 89 studies (with 1475 locations), we partition the relative importance of species richness, abundance, and dominance for pollination; biological pest control; and final yields in the context of ongoing land-use change. Pollinator and enemy richness directly supported ecosystem services in addition to and independent of abundance and dominance. Up to 50% of the negative effects of landscape simplification on ecosystem services was due to richness losses of service-providing organisms, with negative consequences for crop yields. Maintaining the biodiversity of ecosystem service providers is therefore vital to sustain the flow of key agroecosystem benefits to society

The interplay of landscape composition and configuration: new pathways to manage functional biodiversity and agroecosystem services across Europe

Managing agricultural landscapes to support biodiversity and ecosystem services is a key aim of a sustainable agriculture. However, how the spatial arrangement of crop fields and other habitats in landscapes impacts arthropods and their functions is poorly known. Synthesising data from 49 studies (1515 landscapes) across Europe, we examined effects of landscape composition (% habitats) and configuration (edge density) on arthropods in fields and their margins, pest control, pollination and yields. Configuration effects interacted with the proportions of crop and non‐crop habitats, and species’ dietary, dispersal and overwintering traits led to contrasting responses to landscape variables. Overall, however, in landscapes with high edge density, 70% of pollinator and 44% of natural enemy species reached highest abundances and pollination and pest control improved 1.7‐ and 1.4‐fold respectively. Arable‐dominated landscapes with high edge densities achieved high yields. This suggests that enhancing edge density in European agroecosystems can promote functional biodiversity and yield‐enhancing ecosystem services