Ecological adaptation of diverse honey bee (Apis mellifera) populations

Increasing temperature and time in glasshouses increases honey bee activity and affects internal brood conditions

Honey bees are globally important pollinators, key to many aspects of ecosystem function and agricultural production. However they are facing an increasing array of stress factors. These stressors include exposure to pathogens and pesticides, agricultural intensification, and changes in climate, and likely contribute to colony dysfunction and colony losses. Here we use temperature-controlled glasshouse experiments to investigate the impact of a field-realistic temperature-range on honey bee colonies, including temperatures based on projections for near-future local conditions. We show that increased temperatures have a significant impact on honey bee worker activity, with increased worker movement in and out of colonies, particularly over 30 °C. In addition, increased glasshouse temperatures led to significantly higher brood (egg, larval and pupal cells) humidity. Finally, temperature had a more severe impact at the later end of the experiment than at the start (on worker movement and brood conditions), suggesting that colonies under stress (either due to exposure to thermal stress or glasshouse confinement) have more difficulty in manging thermoregulation. These results indicate the potential impact of higher temperatures on the healthy functioning of these important pollinators.

Queen quality, performance, and winter survival of imported and domestic honey bee queen stocks

Canadian beekeepers have faced high colony mortality each winter over the last decade. Frequently citing "poor queen quality" as a top contributing factor to colony loss, Canadian beekeepers report needing to replace half their queens each year. Domestic queen production exists throughout Canada but is limited due to the short season and can be further limited when colony mortality is high. Consequently, Canadian beekeepers import over 260,000 queens annually, primarily from locations with warmer climates. In this study, newly mated imported queens from Hawaii (USA) and New Zealand were compared to domestic Canadian queens produced in British Columbia; these stocks were evaluated on their morphological and sperm storage characteristics. Stock quality was also evaluated in the field at two locations in Alberta, Canada over two production seasons. Our results show initial variation in queen morphology and fertility among imported and domestic queen stocks. Most striking, the New Zealand queens weighed 10-13% less than the Hawaii and British Columbia queens, respectively upon arrival. Colony performance over a two-year field study suggests: (1) brood pattern solidness has a positive nonlinear correlation with honey production regardless of queen stock and environment; (2) environment (i.e., apiary location) and queen stock variably predict colony health and productivity depending on year; specifically, apiary site appears to be a stronger predictor of colony health and productivity than queen stock in year one, but in year two, queen stock appears to be a stronger predictor than apiary site; (3) high clinical symptoms of chalkbrood may explain the prevalence of poor brood patterns in colonies headed by queens from New Zealand; (4) domestic queens are 25% more likely to survive winter in Alberta than imported queens. Therefore, it is important to consider possible mismatches in disease immunity and climate conditioning of imported queen stocks heading colonies in temperate regions that face drastically different seasonal climates and disease ecology dynamics.

Observation of Genetic Gain with Instrumental Insemination of Honeybee Queens

Controlling mating in the honeybee (Apis mellifera) is part of one of the greatest challenges for the beekeeping industry's genetic selection programs due to specific characteristics of their reproduction. Several techniques for supervising honeybee mating with relative effective control have been developed over the years to allow honeybee selection. As part of this project, we compared the genetic gains for several colony performance traits, obtained using the BLUP-animal method, according to the selection pressure applied in controlled reproduction (directed fertilization versus instrumental insemination). Our results show similar genetic gains for hygienic behavior and honey production between colonies whether queens were fertilized naturally or via instrumental insemination, as well as similar or lower genetic gains for colonies with queens inseminated for spring development. In addition, we noticed greater fragility in queens following insemination. These findings show that instrumental insemination is an effective tool for reproductive control in genetic selection and for estimating breeding values more precisely. However, this technique does not result in queens of superior genetic quality for commercial purposes.

Applications of Alginate-Based Nanomaterials in Enhancing the Therapeutic Effects of Bee Products

Since the ancient times, bee products (i.e., honey, propolis, pollen, bee venom, bee bread, and royal jelly) have been considered as natural remedies with therapeutic effects against a number of diseases. The therapeutic pleiotropy of bee products is due to their diverse composition and chemical properties, which is independent on the bee species. This has encouraged researchers to extensively study the therapeutic potentials of these products, especially honey. On the other hand, amid the unprecedented growth in nanotechnology research and applications, nanomaterials with various characteristics have been utilized to improve the therapeutic efficiency of these products. Towards keeping the bee products as natural and non-toxic therapeutics, the green synthesis of nanocarriers loaded with these products or their extracts has received a special attention. Alginate is a naturally produced biopolymer derived from brown algae, the desirable properties of which include biodegradability, biocompatibility, non-toxicity and non-immunogenicity. This review presents an overview of alginates, including their properties, nanoformulations, and pharmaceutical applications, placing a particular emphasis on their applications for the enhancement of the therapeutic effects of bee products. Despite the paucity of studies on fabrication of alginate-based nanomaterials loaded with bee products or their extracts, recent advances in the area of utilizing alginate-based nanomaterials and other types of materials to enhance the therapeutic potentials of bee products are summarized in this work. As the most widespread and well-studied bee products, honey and propolis have garnered a special interest; combining them with alginate-based nanomaterials has led to promising findings, especially for wound healing and skin tissue engineering. Furthermore, future directions are proposed and discussed to encourage researchers to develop alginate-based stingless bee product nanomedicines, and to help in selecting suitable methods for devising nanoformulations based on multi-criteria decision making models. Also, the commercialization prospects of nanocomposites based on alginates and bee products are discussed. In conclusion, preserving original characteristics of the bee products is a critical challenge in developing nano-carrier systems. Alginate-based nanomaterials are well suited for this task because they can be fabricated without the use of harsh conditions, such as shear force and freeze-drying, which are often used for other nano-carriers. Further, conjunction of alginates with natural polymers such as honey does not only combine the medicinal properties of alginates and honey, but it could also enhance the mechanical properties and cell adhesion capacity of alginates.

The Life Span and Levels of Oxidative Stress in Foragers Between Feral and Managed Honey Bee Colonies

Molecular damage caused by oxidative stress may lead to organismal aging and result in acute mortality to organisms. Thus, oxidative stress resistance and longevity are closely linked. Honey bees (Apis mellifera) are the most important managed pollinator in agriculture, but the long-term survival of honey bees is seriously threatened. Feral honey bee colonies can be used as natural resources to improve honey bee health. One question we ask here is whether feral honey bees are stress resistant or survive longer than managed bee populations. More work is needed to determine the impact of oxidative stress on honey bee health and survival. In this study, we used paired colony designs to compare the life span of worker bees (foragers) between feral and managed colonies and their levels of oxidative stress. Each pair of colonies shared similar foraging resources. The results indicated that foragers in feral colonies had longer survival times and life spans than those in managed colonies. The levels of oxidative stress from lipid damage content in feral colonies were higher than those in managed colonies, indicating that they used a tolerance mechanism rather than a repair mechanism to survive. Our study provides new insights into a colony difference in the physiology and oxidative stress resistance of feral honey bees compared with managed colony stocks.

Effects of Insecticides and Microbiological Contaminants on Apis mellifera Health

Over the past two decades, there has been an alarming decline in the number of honey bee colonies. This phenomenon is called Colony Collapse Disorder (CCD). Bee products play a significant role in human life and have a huge impact on agriculture, therefore bees are an economically important species. Honey has found its healing application in various sectors of human life, as well as other bee products such as royal jelly, propolis, and bee pollen. There are many putative factors of CCD, such as air pollution, GMO, viruses, or predators (such as wasps and hornets). It is, however, believed that pesticides and microorganisms play a huge role in the mass extinction of bee colonies. Insecticides are chemicals that are dangerous to both humans and the environment. They can cause enormous damage to bees' nervous system and permanently weaken their immune system, making them vulnerable to other factors. Some of the insecticides that negatively affect bees are, for example, neonicotinoids, coumaphos, and chlorpyrifos. Microorganisms can cause various diseases in bees, weakening the health of the colony and often resulting in its extinction. Infection with microorganisms may result in the need to dispose of the entire hive to prevent the spread of pathogens to other hives. Many aspects of the impact of pesticides and microorganisms on bees are still unclear. The need to deepen knowledge in this matter is crucial, bearing in mind how important these animals are for human life.

Mitochondrial DNA Suggests the Introduction of Honeybees of African Ancestry to East-Central Europe

Simple Summary

In Europe, a well-known threat to the conservation of honeybee diversity is the loss of genetic uniqueness of local populations due to beekeepers’ preference for a few genetic lineages. However, due to climate change and large-scale ongoing movement of breeding individuals, the expansion of bees of African origin could represent another threat. This issue has not yet been recognised in detail, although bees bearing African mitochondrial DNA occur in South-West and South Europe due to natural gene flow. Here, we determine the diversity of mitochondrial DNA in honey bees from East-Central Europe. We sequenced the COI-COII region in 427 bees sampled along two 900 km transects (17.5° N and 23° E). We found that 1.64% of bees (95% CI: 0.66–3.35%) had African mitochondrial DNA. It is unlikely that their presence in the area resulted from natural migration but instead human-driven introductions of hybrids of African ancestry. This expansion deserves more attention, as it may contribute to the dissemination of undesirable traits, parasites and diseases.

Abstract

In Europe, protecting the genetic diversity of Apis mellifera is usually perceived in the context of limiting the spread of the evolutionary C-lineage within the original range of the M-lineage. However, due to climate change and large-scale ongoing movement of breeding individuals, the expansion of bees from the African A-lineage could represent another threat. This issue has not yet been investigated in detail, although A-mitotypes occur in South-West and South Europe due to natural gene flow. Here, we determine the diversity of mtDNA in honey bees from East-Central Europe. We sequenced the COI-COII region in 427 bees sampled along two 900 km transects (17.5° N and 23° E). We found that 1.64% of bees (95% CI: 0.66–3.35 %) had A-mitotypes. It is unlikely that their presence in the area resulted from natural migration but instead human driven introductions of hybrids of African ancestry. This expansion deserves more attention, as it may contribute to the dissemination of undesirable traits, parasites and diseases.

The Importance of Time and Place: Nutrient Composition and Utilization of Seasonal Pollens by European Honey Bees (Apis mellifera L.)

Simple Summary

Honey bees rely on pollen and nectar to provide nutrients to support their yearly colony cycle. Specifics of the cycle differ among geographic regions as do the species of flowering plants and the nutrients they provide. We examined responses of honey bees from two different queen lines fed pollens from locations that differed in floral species composition and yearly colony cycles. We detected differences between the queen lines in the amount of pollen they consumed and the size of their hypopharyngeal glands (HPG). There were also seasonal differences between the nutrient composition of pollens. Spring pollens collected from colonies in both locations had higher amino and fatty acid concentrations than fall pollens. There also were seasonal differences in responses to the pollens consumed by bees from both queen lines. Bees consumed more spring than fall pollen, but digested less of it so that bees consumed more protein from fall pollens. Though protein consumption was higher with fall pollen, HPG were larger in spring bees.

Abstract

Honey bee colonies have a yearly cycle that is supported nutritionally by the seasonal progression of flowering plants. In the spring, colonies grow by rearing brood, but in the fall, brood rearing declines in preparation for overwintering. Depending on where colonies are located, the yearly cycle can differ especially in overwintering activities. In temperate climates of Europe and North America, colonies reduce or end brood rearing in the fall while in warmer climates bees can rear brood and forage throughout the year. To test the hypothesis that nutrients available in seasonal pollens and honey bee responses to them can differ we analyzed pollen in the spring and fall collected by colonies in environments where brood rearing either stops in the fall (Iowa) or continues through the winter (Arizona). We fed both types of pollen to worker offspring of queens that emerged and open mated in each type of environment. We measured physiological responses to test if they differed depending on the location and season when the pollen was collected and the queen line of the workers that consumed it. Specifically, we measured pollen and protein consumption, gene expression levels (hex 70, hex 110, and vg) and hypopharyngeal gland (HPG) development. We found differences in macronutrient content and amino and fatty acids between spring and fall pollens from the same location and differences in nutrient content between locations during the same season. We also detected queen type and seasonal effects in HPG size and differences in gene expression between bees consuming spring vs. fall pollen with larger HPG and higher gene expression levels in those consuming spring pollen. The effects might have emerged from the seasonal differences in nutritional content of the pollens and genetic factors associated with the queen lines we used.

Adaptations to thermal stress in social insects: recent advances and future directions

Thermal stress is a major driver of population declines and extinctions. Shifts in thermal regimes create new environmental conditions, leading to trait adaptation, population migration, and/or species extinction. Extensive research has examined thermal adaptations in terrestrial arthropods. However, little is known about social insects, despite their major role in ecosystems. It is only within the last few years that the adaptations of social insects to thermal stress have received attention. Herein, we discuss what is currently known about thermal tolerance and thermal adaptation in social insects - namely ants, termites, social bees, and social wasps. We describe the behavioural, morphological, physiological, and molecular adaptations that social insects have evolved to cope with thermal stress. We examine individual and collective responses to both temporary and persistent changes in thermal conditions and explore the extent to which individuals can exploit genetic variability to acclimatise. Finally, we consider the costs and benefits of sociality in the face of thermal stress, and we propose some future research directions that should advance our knowledge of individual and collective thermal adaptations in social insects.

Genetic Parameters of Honey Bee Colonies Traits in a Canadian Selection Program

Genetic selection has led to spectacular advances in animal production in many domestic species. However, it is still little applied to honey bees (Apis mellifera), whose complex genetic and reproductive characteristics are a challenge to model statistically. Advances in informatics now enable creation of a statistical model consistent with honey bee genetics, and, consequently, genetic selection for this species. The aim of this project was to determine the genetic parameters of several traits important for Canadian beekeepers with a view to establishing a breeding program in a northern context. Our results show that the five traits measured (Varroa destructor infestation, spring development, honey production, winter consumption, and hygienic behavior) are heritable. Thus, the rate of V. destructor infestation has a high heritability (h² = 0.44 ± 0.56), spring development and honey production have a medium heritability (respectively, h² = 0.30 ± 0.14 and h² = 0.20 ± 0.13), and winter consumption and hygienic behavior have a low heritability (respectively, h² = 0.11 ± 0.09 and h² = 0.18 ± 0.13). Furthermore, the genetic correlations between these traits are all positive or null, except between hygienic behavior and V. destructor infestation level. These genetic parameters will be instrumental to the development of a selection index that will be used to improve the capacity of honey bees to thrive in northern conditions.

Population genomics of honey bees reveals a selection signature indispensable for royal jelly production

In order to interpret the molecular mechanisms that modulating the organism variations and selection signatures to drive adaptive evolutionary changes are indispensable goals in the new evolutionary ecological genetics. Here, we identified the gene locus associated to royal jelly production through whole-genome sequencing of the DNA from eight populations of honeybees. The analysis of the samples was composed of 120 individuals and each pointed extremely opposite trait values for a given phenotype. We identified functional single nucleotide polymorphisms (SNPs) candidate that might be essential in regulating the phenotypic traits of honeybee populations. Moreover, selection signatures were investigated using pooling sequencing of eight distinct honeybee populations, and the results provided the evidence of signatures of recent selection among populations under different selection objectives. Furthermore, gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that selected genes were potentially involved in several biological processes and molecular functioning, which could directly or indirectly influence the production of royal jelly. Our findings can be used to understand the genomic signatures, as well as implicate a profound glance on genomic regions that control the production trait of royal jelly in honey bees.

The genomic basis of adaptation to high-altitude habitats in the eastern honey bee (Apis cerana)

The eastern honey bee (Apis cerana) is of central importance for agriculture in Asia. It has adapted to a wide variety of environmental conditions across its native range in southern and eastern Asia, which includes high-altitude regions. eastern honey bees inhabiting mountains differ morphologically from neighbouring lowland populations and may also exhibit differences in physiology and behaviour. We compared the genomes of 60 eastern honey bees collected from high and low altitudes in Yunnan and Gansu provinces, China, to infer their evolutionary history and to identify candidate genes that may underlie adaptation to high altitude. Using a combination of F_ST -based statistics, long-range haplotype tests and population branch statistics, we identified several regions of the genome that appear to have been under positive selection. These candidate regions were strongly enriched for coding sequences and had high haplotype homozygosity and increased divergence specifically in highland bee populations, suggesting they have been subjected to recent selection in high-altitude habitats. Candidate loci in these genomic regions included genes related to reproduction and feeding behaviour in honey bees. Functional investigation of these candidate loci is necessary to fully understand the mechanisms of adaptation to high-altitude habitats in the eastern honey bee.

Differences in protein expression among five species of stream stonefly (Plecoptera) along a latitudinal gradient in Japan

Proteome variation among natural populations along an environmental gradient may provide insights into how the biological functions of species are related to their local adaptation. We investigated protein expression in five stream stonefly species from four geographic regions along a latitudinal gradient in Japan with varying climatic conditions. The extracted proteins were separated by two-dimensional gel electrophoresis and identified by matrix-assisted laser desorption/ionization of time-of-flight (MALDI TOF/TOF), yielding 446 proteins. Low interspecies variation in the proteome profiles was observed among five species within geographical regions, presumably due to the co-occurring species sharing the environments. However, large spatial variations in protein expression were found among four geographic regions, suggesting strong regulation of protein expression in heterogeneous environments, where the spatial variations were positively correlated with water temperature. We identified 21 unique proteins expressed specifically in a geographical region and six common proteins expressed throughout all regions. In warmer regions, metabolic proteins were upregulated, whereas proteins related to cold stress, the photoperiod, and mating were downregulated. Oxygen-related and energy-production proteins were upregulated in colder regions with higher altitudes. Thus, our proteomic approach is useful for identifying and understanding important biological functions related to local adaptations by populations of stoneflies.

Peptide biomarkers used for the selective breeding of a complex polygenic trait in honey bees

We present a novel way to select for highly polygenic traits. For millennia, humans have used observable phenotypes to selectively breed stronger or more productive livestock and crops. Selection on genotype, using single-nucleotide polymorphisms (SNPs) and genome profiling, is also now applied broadly in livestock breeding programs; however, selection on protein/peptide or mRNA expression markers has not yet been proven useful. Here we demonstrate the utility of protein markers to select for disease-resistant hygienic behavior in the European honey bee (Apis mellifera L.). Robust, mechanistically-linked protein expression markers, by integrating cis- and trans- effects from many genomic loci, may overcome limitations of genomic markers to allow for selection. After three generations of selection, the resulting marker-selected stock outperformed an unselected benchmark stock in terms of hygienic behavior, and had improved survival when challenged with a bacterial disease or a parasitic mite, similar to bees selected using a phenotype-based assessment for this trait. This is the first demonstration of the efficacy of protein markers for industrial selective breeding in any agricultural species, plant or animal.

Pathogenic Acinetobacter species have a functional type I secretion system and contact-dependent inhibition systems

Pathogenic Acinetobacter species, including Acinetobacter baumannii and Acinetobacter nosocomialis, are opportunistic human pathogens of increasing relevance worldwide. Although their mechanisms of drug resistance are well studied, the virulence factors that govern Acinetobacter pathogenesis are incompletely characterized. Here we define the complete secretome of A. nosocomialis strain M2 in minimal medium and demonstrate that pathogenic Acinetobacter species produce both a functional type I secretion system (T1SS) and a contact-dependent inhibition (CDI) system. Using bioinformatics, quantitative proteomics, and mutational analyses, we show that Acinetobacter uses its T1SS for exporting two putative T1SS effectors, an Repeats-in-Toxin (RTX)-serralysin-like toxin, and the biofilm-associated protein (Bap). Moreover, we found that mutation of any component of the T1SS system abrogated type VI secretion activity under nutrient-limited conditions, indicating a previously unrecognized cross-talk between these two systems. We also demonstrate that the Acinetobacter T1SS is required for biofilm formation. Last, we show that both A. nosocomialis and A. baumannii produce functioning CDI systems that mediate growth inhibition of sister cells lacking the cognate immunity protein. The Acinetobacter CDI systems are widely distributed across pathogenic Acinetobacter species, with many A. baumannii isolates harboring two distinct CDI systems. Collectively, these data demonstrate the power of differential, quantitative proteomics approaches to study secreted proteins, define the role of previously uncharacterized protein export systems, and observe cross-talk between secretion systems in the pathobiology of medically relevant Acinetobacter species.

Whole-genome resequencing of honeybee drones to detect genomic selection in a population managed for royal jelly

Four main evolutionary lineages of A. mellifera have been described including eastern Europe (C) and western and northern Europe (M). Many apiculturists prefer bees from the C lineage due to their docility and high productivity. In France, the routine importation of bees from the C lineage has resulted in the widespread admixture of bees from the M lineage. The haplodiploid nature of the honeybee Apis mellifera, and its small genome size, permits affordable and extensive genomics studies. As a pilot study of a larger project to characterise French honeybee populations, we sequenced 60 drones sampled from two commercial populations managed for the production of honey and royal jelly. Results indicate a C lineage origin, whilst mitochondrial analysis suggests two drones originated from the O lineage. Analysis of heterozygous SNPs identified potential copy number variants near to genes encoding odorant binding proteins and several cytochrome P450 genes. Signatures of selection were detected using the hapFLK haplotype-based method, revealing several regions under putative selection for royal jelly production. The framework developed during this study will be applied to a broader sampling regime, allowing the genetic diversity of French honeybees to be characterised in detail.

Identification of Avian Corticosteroid-binding Globulin (SerpinA6) Reveals the Molecular Basis of Evolutionary Adaptations in SerpinA6 Structure and Function as a Steroid-binding Protein

Corticosteroid-binding globulin (CBG) was isolated from chicken serum and identified by mass spectrometry and genomic analysis. This revealed that the organization and synteny of avian and mammalian SerpinA6 genes are conserved. Recombinant zebra finch CBG steroid-binding properties reflect those of the natural protein in plasma and confirm its identity. Zebra finch and rat CBG crystal structures in complex with cortisol resemble each other, but their primary structures share only ∼40% identity, and their steroid-binding site topographies differ in several unexpected ways. Remarkably, a tryptophan that anchors ligands in mammalian CBG steroid-binding sites is replaced by an asparagine. Phylogenetic comparisons show that reptilian CBG orthologs share this unexpected property. Glycosylation of this asparagine in zebra finch CBG does not influence its steroid-binding affinity, but we present evidence that it may participate in protein folding and steroid-binding site formation. Substitutions of amino acids within zebra finch CBG that are conserved only in birds reveal how they contribute to their distinct steroid-binding properties, including their high (nanomolar) affinities for glucocorticoids, progesterone, and androgens. As in mammals, a protease secreted by Pseudomonas aeruginosa cleaves CBG in zebra finch plasma within its reactive center loop and disrupts steroid binding, suggesting an evolutionarily conserved property of CBGs. Measurements of CBG mRNA in zebra finch tissues indicate that liver is the main site of plasma CBG production, and anti-zebra finch CBG antibodies cross-react with CBGs in other birds, extending opportunities to study how CBG regulates the actions of glucocorticoids and sex steroids in these species.

Quantitative metabolome, proteome and transcriptome analysis of midgut and fat body tissues in the mountain pine beetle, Dendroctonus ponderosae Hopkins, and insights into pheromone biosynthesis

Bark beetles (Coleoptera: Scolytinae) are pests of many forests around the world. The mountain pine beetle (MPB), Dendroctonus ponderosae Hopkins, is a significant pest of western North American pine forests. The MPB is able to overcome the defences of pine trees through pheromone-assisted aggregation that results in a mass attack of host trees. These pheromones, both male and female produced, are believed to be biosynthesized in the midgut and/or fat bodies of these insects. We used metabolite analysis, quantitative proteomics (iTRAQ) and transcriptomics (RNA-seq) to identify proteins and transcripts differentially expressed between sexes and between tissues when treated with juvenile hormone III. Juvenile hormone III induced frontalin biosynthesis in males and trans-verbenol biosynthesis in females, as well as affected the expression of many proteins and transcripts in sex- and tissue-specific ways. Based on these analyses, we identified candidate genes involved in the biosynthesis of frontalin, exo-brevicomin, and trans-verbenol pheromones.

Phenotypic Variation in Fitness Traits of a Managed Solitary Bee, Osmia ribifloris (Hymenoptera: Megachilidae)

We investigated fitness in natural populations of a managed solitary bee Osmia ribifloris Cockerell (Hymenoptera: Megachilidae) from sites separated from 400 to 2,700 km. Parental wild bees originated in central Texas (TX), central-northern Utah (UT), and central California (CA). They were then intercrossed and raised inside a mesh enclosure in southern Mississippi (MS). Females from all possible mated pairs of O. ribifloris produced F1 broods with 30-40% female cocoons and outcrossed progeny were 30% heavier. Mitochondrial (COI) genomes of the four populations revealed three distinct clades, a TX-CA clade, a UT clade, and an MS clade, the latter (MS) representing captive progeny of CA and UT bees. Although classified as separate subspecies, TX and CA populations from 30° N to 38° N latitude shared 98% similarity in COI genomes and the greatest brood biomass per nest straw (600- to 700-mg brood). Thus, TX and CA bees show greater adaptation for southern U.S. sites. In contrast, UT-sourced bees were more distantly related to TX and CA bees and also produced ∼50% fewer brood. These results, taken together, confirm that adult O. ribifloris from all trap-nest sites are genetically compatible, but some phenotypic variation exists that could affect this species performance as a commercial blueberry pollinator. Males, their sperm, or perhaps a substance in their sperm helped stabilize our captive bee population by promoting legitimate nesting over nest usurpation. Otherwise, without insemination, 50% fewer females nested (they nested 14 d late) and 20% usurped nests, killing 33-67% of brood in affected nests.

Phosphoproteomic Analysis of Cell-Based Resistance to BRAF Inhibitor Therapy in Melanoma

The treatment of melanoma by targeted inhibition of the mutated kinase BRAF with small molecules only temporarily suppresses metastatic disease. In the face of chemical inhibition tumor plasticity, both innate and adaptive, promotes survival through the biochemical and genetic reconfiguration of cellular pathways that can engage proliferative and migratory systems. To investigate this process, high-resolution mass spectrometry was used to characterize the phosphoproteome of this transition in vitro. A simple and accurate, label-free quantitative method was used to localize and quantitate thousands of phosphorylation events. We also correlated changes in the phosphoproteome with the proteome to more accurately determine changes in the activity of regulatory kinases determined by kinase landscape profiling. The abundance of phosphopeptides with sites that function in cytoskeletal regulation, GTP/GDP exchange, protein kinase C, IGF signaling, and melanosome maturation were highly divergent after transition to a drug resistant phenotype.

A search for protein biomarkers links olfactory signal transduction to social immunity

Background

The Western honey bee (Apis mellifera L.) is a critical component of human agriculture through its pollination activities. For years, beekeepers have controlled deadly pathogens such as Paenibacillus larvae, Nosema spp. and Varroa destructor with antibiotics and pesticides but widespread chemical resistance is appearing and most beekeepers would prefer to eliminate or reduce the use of in-hive chemicals. While such treatments are likely to still be needed, an alternate management strategy is to identify and select bees with heritable traits that allow them to resist mites and diseases. Breeding such bees is difficult as the tests involved to identify disease-resistance are complicated, time-consuming, expensive and can misidentify desirable genotypes. Additionally, we do not yet fully understand the mechanisms behind social immunity. Here we have set out to discover the molecular mechanism behind hygienic behavior (HB), a trait known to confer disease resistance in bees.

Results

After confirming that HB could be selectively bred for, we correlated measurements of this behavior with protein expression over a period of three years, at two geographically distinct sites, using several hundred bee colonies. By correlating the expression patterns of individual proteins with HB scores, we identified seven putative biomarkers of HB that survived stringent control for multiple hypothesis testing. Intriguingly, these proteins were all involved in semiochemical sensing (odorant binding proteins), nerve signal transmission or signal decay, indicative of the series of events required to respond to an olfactory signal from dead or diseased larvae. We then used recombinant versions of two odorant-binding proteins to identify the classes of ligands that these proteins might be helping bees detect.

Conclusions

Our data suggest that neurosensory detection of odors emitted by dead or diseased larvae is the likely mechanism behind a complex and important social immunity behavior that allows bees to co-exist with pathogens.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-014-1193-6) contains supplementary material, which is available to authorized users.

Honey bees avoid nectar colonized by three bacterial species, but not by a yeast species, isolated from the bee gut

The gut microflora of the honey bee, Apis mellifera, is receiving increasing attention as a potential determinant of the bees' health and their efficacy as pollinators. Studies have focused primarily on the microbial taxa that appear numerically dominant in the bee gut, with the assumption that the dominant status suggests their potential importance to the bees' health. However, numerically minor taxa might also influence the bees' efficacy as pollinators, particularly if they are not only present in the gut, but also capable of growing in floral nectar and altering its chemical properties. Nonetheless, it is not well understood whether honey bees have any feeding preference for or against nectar colonized by specific microbial species. To test whether bees exhibit a preference, we conducted a series of field experiments at an apiary using synthetic nectar inoculated with specific species of bacteria or yeast that had been isolated from the bee gut, but are considered minor components of the gut microflora. These species had also been found in floral nectar. Our results indicated that honey bees avoided nectar colonized by the bacteria Asaia astilbes, Erwinia tasmaniensis, and Lactobacillus kunkeei, whereas the yeast Metschnikowia reukaufii did not affect the feeding preference of the insects. Our results also indicated that avoidance of bacteria-colonized nectar was caused not by the presence of the bacteria per se, but by the chemical changes to nectar made by the bacteria. These findings suggest that gut microbes may not only affect the bees' health as symbionts, but that some of the microbes may possibly affect the efficacy of A. mellifera as pollinators by altering nectar chemistry and influencing their foraging behavior.

Proteomic properties reveal phyloecological clusters of Archaea

In this study, we propose a novel way to describe the variety of environmental adaptations of Archaea. We have clustered 57 Archaea by using a non-redundant set of proteomic features, and verified that the clusters correspond to environmental adaptations to the archaeal habitats. The first cluster consists dominantly of hyperthermophiles and hyperthermoacidophilic aerobes. The second cluster joins together halophilic and extremely halophilic Archaea, while the third cluster contains mesophilic (mostly methanogenic) Archaea together with thermoacidophiles. The non-redundant subset of proteomic features was found to consist of five features: the ratio of charged residues to uncharged, average protein size, normalized frequency of beta-sheet, normalized frequency of extended structure and number of hydrogen bond donors. We propose this clustering to be termed phyloecological clustering. This approach could give additional insights into relationships among archaeal species that may be hidden by sole phylogenetic analysis.

Proteomic evidence of a paedomorphic evolutionary process within a marine snail species: a strategy for adapting to extreme ecological conditions?

The exposed and sheltered ecotypes of the marine snail Littorina saxatilis from European rocky shores are considered a key model system to study adaptation and ecological speciation. Previous studies showed that two ecotypes (RB and SU) of this species in NW Spain have adapted differently to different shore levels and microhabitats. In order to understand how this divergent adaptive process has been accomplished, we followed a quantitative proteomic approach to investigate the proteome variation in a number of different biological factors, that is, ecotype, ontogeny and their interactions. This approach allowed testing the hypothesis that one of the ecotypes has evolved by paedomorphosis, and also whether or not the molecular mechanisms related to ecotype differentiation are set up in early developmental stages. Additionally, the identification of some candidate proteins using mass spectrometry provides some functional insights into these evolutionary processes. Results from this study provided evidence of higher ontogenetic differentiation at proteome level in the RB (metamorphic) than in SU (paedomorphic) ecotype that point to the possibility of juvenile stage retention in this latter ecotype. The level of protein expression (proteome) differences between ecotypes maintained nearly constant from late embryonic stages to adulthood, although some proteins involved in these changes considerably differed in embryonic compared to other ontogenetic stages. Paedomorphosis may be the evolutionary response of the SU ecotype of solving the trade-off during sexually immaturity that is caused by the evolution of small size arising from adaptation to the wave-exposed habitat. Some potential candidate genes of adaptation related to energetic metabolism have been identified, providing a promising baseline for future functional analyses.

Correlation of proteome-wide changes with social immunity behaviors provides insight into resistance to the parasitic mite, Varroa destructor, in the honey bee (Apis mellifera)

BACKGROUND

Disease is a major factor driving the evolution of many organisms. In honey bees, selection for social behavioral responses is the primary adaptive process facilitating disease resistance. One such process, hygienic behavior, enables bees to resist multiple diseases, including the damaging parasitic mite Varroa destructor. The genetic elements and biochemical factors that drive the expression of these adaptations are currently unknown. Proteomics provides a tool to identify proteins that control behavioral processes, and these proteins can be used as biomarkers to aid identification of disease tolerant colonies.

RESULTS

We sampled a large cohort of commercial queen lineages, recording overall mite infestation, hygiene, and the specific hygienic response to V. destructor. We performed proteome-wide correlation analyses in larval integument and adult antennae, identifying several proteins highly predictive of behavior and reduced hive infestation. In the larva, response to wounding was identified as a key adaptive process leading to reduced infestation, and chitin biosynthesis and immune responses appear to represent important disease resistant adaptations. The speed of hygienic behavior may be underpinned by changes in the antenna proteome, and chemosensory and neurological processes could also provide specificity for detection of V. destructor in antennae.

CONCLUSIONS

Our results provide, for the first time, some insight into how complex behavioural adaptations manifest in the proteome of honey bees. The most important biochemical correlations provide clues as to the underlying molecular mechanisms of social and innate immunity of honey bees. Such changes are indicative of potential divergence in processes controlling the hive-worker maturation.

Proteomics in evolutionary ecology: linking the genotype with the phenotype

The study of the proteome (proteomics), which includes the dynamics of protein expression, regulation, interactions and its function, has played a less prominent role in evolutionary and ecological investigations in comparison with the study of the genome and transcriptome. There are, however, a number of arguments suggesting that this situation should change. First, the proteome is closer to the phenotype than the genome or the transcriptome, and as such may be more directly responsive to natural selection, and thus closely linked to adaptation. Second, there is evidence of a low correlation between protein and transcript expression levels across genes in many different organisms. Finally, there have been some recent important technological improvements in proteomics methods that make them feasible, practical and useful to address a wide range of evolutionary questions even in nonmodel organisms. The different proteomic methods, their limitations and problems when interpreting empirical data are described and discussed. In addition, the proteomic literature pertaining to evolutionary ecology is reviewed with examples, and potential applications of proteomics in a variety of evolutionary contexts are outlined. New proteomic research trends such as the study of posttranslational modifications and protein-protein interactions, as well as the combined use of the different -omics approaches, are discussed in relation to the development of a more functional and integrated perspective, needed for achieving a more comprehensive knowledge of evolutionary change.

A honey bee (Apis mellifera L.) PeptideAtlas crossing castes and tissues

BACKGROUND

Honey bees are a mainstay of agriculture, contributing billions of dollars through their pollination activities. Bees have been a model system for sociality and group behavior for decades but only recently have molecular techniques been brought to study this fascinating and valuable organism. With the release of the first draft of its genome in 2006, proteomics of bees became feasible and over the past five years we have amassed in excess of 5E+6 MS/MS spectra. The lack of a consolidated platform to organize this massive resource hampers our ability, and that of others, to mine the information to its maximum potential.

RESULTS

Here we introduce the Honey Bee PeptideAtlas, a web-based resource for visualizing mass spectrometry data across experiments, providing protein descriptions and Gene Ontology annotations where possible. We anticipate that this will be helpful in planning proteomics experiments, especially in the selection of transitions for selected reaction monitoring. Through a proteogenomics effort, we have used MS/MS data to anchor the annotation of previously undescribed genes and to re-annotate previous gene models in order to improve the current genome annotation.

CONCLUSIONS

The Honey Bee PeptideAtlas will contribute to the efficiency of bee proteomics and accelerate our understanding of this species. This publicly accessible and interactive database is an important framework for the current and future analysis of mass spectrometry data.