New reference genomes of honey bee-associated bacteria Paenibacillus melissococcoides, Paenibacillus dendritiformis, and Paenibacillus thiaminolyticus.

We sequenced the genomes of recently discovered Paenibacillus melissococcoides (CCOS 2000) and of the type strains of closely related P. thiaminolyticus (DSM 7262) and P. dendritiformis (LMG 21716). The three genomes set the basis to unambiguous diagnostic of these honey bee associated Paenibacillus bacteria.

Prospects, challenges and perspectives in harnessing natural selection to solve the 'varroa problem' of honey bees.

Honey bees, Apis mellifera, of European origin are major pollinators of crops and wild flora. Their endemic and exported populations are threatened by a variety of abiotic and biotic factors. Among the latter, the ectoparasitic mite Varroa destructor is the most important single cause behind colony mortality. The selection of mite resistance in honey bee populations has been deemed a more sustainable solution to its control than varroacidal treatments. Because natural selection has led to the survival of some European and African honey bee populations to V. destructor infestations, harnessing its principles has recently been highlighted as a more efficient way to provide honey bee lineages that survive infestations when compared with conventional selection on resistance traits against the parasite. However, the challenges and drawbacks of harnessing natural selection to solve the varroa problem have only been minimally addressed. We argue that failing to consider these issues could lead to counterproductive results, such as increased mite virulence, loss of genetic diversity reducing host resilience, population collapses or poor acceptance by beekeepers. Therefore, it appears timely to evaluate the prospects for the success of such programmes and the qualities of the populations obtained. After reviewing the approaches proposed in the literature and their outcomes, we consider their advantages and drawbacks and propose perspectives to overcome their limitations. In these considerations, we not only reflect on the theoretical aspects of host-parasite relationships but also on the currently largely neglected practical constraints, that is, the requirements for productive beekeeping, conservation or rewilding objectives. To optimize natural selection-based programmes towards these objectives, we suggest designs based on a combination of nature-driven phenotypic differentiation and human-directed selection of traits. Such a dual strategy aims at allowing field-realistic evolutionary approaches towards the survival of V. destructor infestations and the improvement of honey bee health.

Identification of runs of homozygosity in Western honey bees (Apis mellifera) using whole-genome sequencing data.

Runs of homozygosity (ROH) are continuous homozygous segments that arise through the transmission of haplotypes that are identical by descent. The length and distribution of ROH segments provide insights into the genetic diversity of populations and can be associated with selection signatures. Here, we analyzed reconstructed whole-genome queen genotypes, from a pool-seq data experiment including 265 Western honeybee colonies from Apis mellifera mellifera and Apis mellifera carnica. Integrating individual ROH patterns and admixture levels in a dynamic population network visualization allowed us to ascertain major differences between the two subspecies. Within A. m. mellifera, we identified well-defined substructures according to the genetic origin of the queens. Despite the current applied conservation efforts, we pinpointed 79 admixed queens. Genomic inbreeding (F ROH) strongly varied within and between the identified subpopulations. Conserved A. m. mellifera from Switzerland had the highest mean F ROH (3.39%), while queens originating from a conservation area in France, which were also highly admixed, showed significantly lower F ROH (0.45%). The majority of A. m. carnica queens were also highly admixed, except 12 purebred queens with a mean F ROH of 2.33%. Within the breed-specific ROH islands, we identified 14 coding genes for A. m. mellifera and five for A. m. carnica, respectively. Local adaption of A. m. mellifera could be suggested by the identification of genes involved in the response to ultraviolet light (Crh-BP, Uvop) and body size (Hex70a, Hex70b), while the A. m. carnica specific genes Cpr3 and Cpr4 are most likely associated with the lighter striping pattern, a morphological phenotype expected in this subspecies. We demonstrated that queen genotypes derived from pooled workers are useful tool to unravel the population dynamics in A. mellifera and provide fundamental information to conserve native honey bees.

Evaluating the Potential of Brood Recapping to Select Varroa destructor (Acari: Varroidae) Resistant Honey Bees (Hymenoptera: Apidae).

Several resistance traits have been proposed to select honey bees (Apis mellifera L.) that can survive in the presence of parasitic mite Varroa destructor (Anderson and Trueman) and enable a more sustainable apiculture. The interest for uncapping-recapping has recently increased following its identification in several naturally surviving honey bee populations, yet the utility of this trait for human-mediated selection is poorly known. Here, we evaluated the repeatability of recapping and its correlations with mite infestation levels, and assessed the expression of the trait in the often neglected drone brood. We also calculated correlations between recapping, mite infertility, and mite fecundity, expressed either at the level of individual brood cells or of the whole colony. Recapping measured in worker brood showed moderate repeatability (ranging between 0.30 and 0.46). Depending on sample, recapping slightly correlated negatively with colony infestation values. Recapping was also measured in drone brood, with values often comparable to recapping in worker brood, but no significant correlations were obtained between castes. At cell level, recapped cells in drone brood (but not in workers) were significantly less infested than nonrecapped cells, whereas in workers (but not in drones), recapped cells hosted mites with significantly lower fecundity. At colony level, with a few exceptions, recapping did not significantly correlate with mite infertility and fecundity, caste, sample, or number of infested cells considered. These results indicate limited possibilities of impeding mite reproduction and possibly mite infestation of honey bee colonies by recapping, which would need to be confirmed on larger, different populations.

Influence of Honey bee Nutritive Jelly Type and Dilution on its Bactericidal Effect on Melissococcus plutonius, the Etiological Agent of European Foulbrood.

To defend themselves against pathogenic microorganisms, honey bees resort to social immunity mechanisms, such as the secretion of antibiotic compounds in the jelly they feed to their larvae. Whereas the bactericidal activity of jelly fed to queen larvae is well studied, little is known about the bioactivity of compositionally different jelly fed to worker larvae. However, the numerous worker larvae are likely to drive the spread of the microorganism and influence its virulence and pathogenesis. Diluted jelly or extracts are mostly used for jelly bioactivity tests, which may bias the evaluation of the pathogen's resistance and virulence. Here, we compared the bactericidal effect of pure and diluted jellies destined for queen and worker larvae on Melissococcus plutonius, the etiological agent of the European foulbrood (EFB) disease of honey bees, and on a secondary invader bacteria, Enterococcus faecalis. We tested three strains of M. plutonius with varying virulence to investigate the association between resistance to antibacterial compounds and virulence. The resistance of the bacteria varied but was not strictly correlated with their virulence and was lower in pure than in diluted jelly. Resistance differed according to whether the jelly was destined for queen or worker larvae, with some strains being more resistant to queen jelly and others to worker jelly. Our results provide a biologically realistic assessment of host defenses via nutritive jelly and contribute to a better understanding of the ecology of M. plutonius and of secondary invaders bacteria in the honey bee colony environment, thus shedding light on the selective forces affecting their virulence and on their role in EFB pathogenesis.

Lack of evidence for trans-generational immune priming against the honey bee pathogen Melissococcus plutonius.

Trans-generational immune priming involves the transfer of immunological experience, acquired by the parents after exposure to pathogens, to protect their progeny against infections by these pathogens. Such natural mechanisms could be exploited to prevent disease expression in economically important insects, such as the honey bee. This mechanism occurs when honey bee queens are exposed to the pathogenic bacterium Paenibacillus larvae. Here, we tested whether natural or experimental exposure to Melissococcus plutonius-another bacterium triggering a disease in honey bee larvae-reduced the susceptibility of the queen's progeny to infection by this pathogen. Because the immunological response upon pathogen exposure can lead to fitness costs, we also determined whether experimental exposure of the queens affected them or their colony negatively. Neither natural nor experimental exposure induced protection in the honey bee larvae against the deleterious effects of M. plutonius. Our results provided no evidence for the occurrence of trans-generational immune priming upon exposure of the queen to M. plutonius. Whether this lack was due to confounding genetic resistance, to unsuitable exposure procedure or to the absence of trans-generational immune priming against this pathogen in honey bees remains to be determined.

Decreased Mite Reproduction to Select Varroa destructor (Acari: Varroidae) Resistant Honey Bees (Hymenoptera: Apidae): Limitations and Potential Methodological Improvements.

The invasive parasitic mite, Varroa destructor (Anderson and Trueman), is the major biotic threat to the survival of European honey bees, Apis mellifera L. To improve colony survival against V. destructor, the selection of resistant lineages against this parasite is considered a sustainable solution. Among selected traits, mite fertility and fecundity, often referred to as suppressed mite reproduction are increasingly used in breeding programmes. However, the current literature leaves some gaps in the assessment of the effectiveness of selecting these traits toward achieving resistance. In the population studied here, we show a low repeatability and reproducibility of mite fertility and fecundity phenotypes, as well as a low correlation of these traits with infestation rates of colonies. Phenotyping reliability could neither be improved by increasing the number of worker brood cells screened, nor by screening drone brood, which is highly attractive for the parasite and available early in the season, theoretically allowing a reduction of generation time and thus an acceleration of genetic progress in selected lineages. Our results provide an evaluation of the potential and limitations of selecting on decreased mite reproduction traits to obtain V. destructor-resistant honeybee colonies. To allow for a more precise implementation of such selection and output reporting, we propose a refined nomenclature by introducing the terms of decreased mite reproduction and reduced mite reproduction, depending on the extent of mite reproduction targeted. We also highlight the importance of ensuring accurate phenotyping ahead of initiating long-lasting selection programmes.

Exploring Two Honey Bee Traits for Improving Resistance Against Varroa destructor: Development and Genetic Evaluation.

For the development of novel selection traits in honey bees, applicability under field conditions is crucial. We thus evaluated two novel traits intended to provide resistance against the ectoparasitic mite Varroa destructor and to allow for their straightforward implementation in honey bee selection. These traits are new field estimates of already-described colony traits: brood recapping rate ('Recapping') and solidness ('Solidness'). 'Recapping' refers to a specific worker characteristic wherein they reseal a capped and partly opened cell containing a pupa, whilst 'Solidness' assesses the percentage of capped brood in a predefined area. According to the literature and beekeepers' experiences, a higher recapping rate and higher solidness could be related to resistance to V. destructor. During a four-year field trial in Switzerland, the two resistance traits were assessed in a total of 121 colonies of Apis mellifera mellifera. We estimated the repeatability and the heritability of the two traits and determined their phenotypic correlations with commonly applied selection traits, including other putative resistance traits. Both traits showed low repeatability between different measurements within each year. 'Recapping' had a low heritability (h2 = 0.04 to 0.05, depending on the selected model) and a negative phenotypic correlation to non-removal of pin-killed brood (r = -0.23). The heritability of 'Solidness' was moderate (h2 = 0.24 to 0.25) and did not significantly correlate with resistance traits. The two traits did not show an association with V. destructor infestation levels. Further research is needed to confirm the results, as only a small number of colonies was evaluated.

Advances and perspectives in selecting resistance traits against the parasitic mite Varroa destructor in honey bees.

BACKGROUND: In spite of the implementation of control strategies in honey bee (Apis mellifera) keeping, the invasive parasitic mite Varroa destructor remains one of the main causes of colony losses in numerous countries. Therefore, this parasite represents a serious threat to beekeeping and agro-ecosystems that benefit from the pollination services provided by honey bees. To maintain their stocks, beekeepers have to treat their colonies with acaricides every year. Selecting lineages that are resistant to infestations is deemed to be a more sustainable approach. REVIEW: Over the last three decades, numerous selection programs have been initiated to improve the host-parasite relationship and to support honey bee survival in the presence of the parasite without the need for acaricide treatments. Although resistance traits have been included in the selection strategy of honey bees, it has not been possible to globally solve the V. destructor problem. In this study, we review the literature on the reasons that have potentially limited the success of such selection programs. We compile the available information to assess the relevance of selected traits and the potential environmental effects that distort trait expression and colony survival. Limitations to the implementation of these traits in the field are also discussed. CONCLUSIONS: Improving our knowledge of the mechanisms underlying resistance to V. destructor to increase trait relevance, optimizing selection programs to reduce environmental effects, and communicating selection outcomes are all crucial to efforts aiming at establishing a balanced relationship between the invasive parasite and its new host.

Genome of the small hive beetle (Aethina tumida, Coleoptera: Nitidulidae), a worldwide parasite of social bee colonies, provides insights into detoxification and herbivory.

Background: The small hive beetle (Aethina tumida; ATUMI) is an invasive parasite of bee colonies. ATUMI feeds on both fruits and bee nest products, facilitating its spread and increasing its impact on honey bees and other pollinators. We have sequenced and annotated the ATUMI genome, providing the first genomic resources for this species and for the Nitidulidae, a beetle family that is closely related to the extraordinarily species-rich clade of beetles known as the Phytophaga. ATUMI thus provides a contrasting view as a neighbor for one of the most successful known animal groups. Results: We present a robust genome assembly and a gene set possessing 97.5% of the core proteins known from the holometabolous insects. The ATUMI genome encodes fewer enzymes for plant digestion than the genomes of wood-feeding beetles but nonetheless shows signs of broad metabolic plasticity. Gustatory receptors are few in number compared to other beetles, especially receptors with known sensitivity (in other beetles) to bitter substances. In contrast, several gene families implicated in detoxification of insecticides and adaptation to diverse dietary resources show increased copy numbers. The presence and diversity of homologs involved in detoxification differ substantially from the bee hosts of ATUMI. Conclusions: Our results provide new insights into the genomic basis for local adaption and invasiveness in ATUMI and a blueprint for control strategies that target this pest without harming their honey bee hosts. A minimal set of gustatory receptors is consistent with the observation that, once a host colony is invaded, food resources are predictable. Unique detoxification pathways and pathway members can help identify which treatments might control this species even in the presence of honey bees, which are notoriously sensitive to pesticides.

Characterisation of the British honey bee metagenome.

The European honey bee (Apis mellifera) plays a major role in pollination and food production. Honey bee health is a complex product of the environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of these factors will help manage modern challenges to bee health. Here we used DNA sequencing to characterise the genomes and metagenomes of 19 honey bee colonies from across Britain. Low heterozygosity was observed in many Scottish colonies which had high similarity to the native dark bee. Colonies exhibited high diversity in composition and relative abundance of individual microbiome taxa. Most non-bee sequences were derived from known honey bee commensal bacteria or pathogens. However, DNA was also detected from additional fungal, protozoan and metazoan species. To classify cobionts lacking genomic information, we developed a novel network analysis approach for clustering orphan DNA contigs. Our analyses shed light on microbial communities associated with honey bees and demonstrate the power of high-throughput, directed metagenomics for identifying novel biological threats in agroecosystems.

Publisher Correction: Social context influences the expression of DNA methyltransferase genes in the honeybee.

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An improved DNA method to unambiguously detect small hive beetle Aethina tumida, an invasive pest of honeybee colonies.

The scavenger and invasive species Aethina tumida threatening the honey bee has been recently introduced in Europe. We present a new, reliable and rapid multiplex real-time PCR for efficient diagnostics enabling surveillance programs. © 2018 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Social context influences the expression of DNA methyltransferase genes in the honeybee.

DNA methylation is a reversible epigenetic modification that alters gene expression without altering the nucleotide sequence. Epigenetic modifications have been suggested as crucial mediators between social interactions and gene expression in mammals. However, little is known about the role of DNA methylation in the life cycle of social invertebrates. Recently, honeybees have become an attractive model to study epigenetic processes in social contexts. Although DNA methyltransferase (DNMT) enzymes responsible for DNA methylation are known in this model system, the influence of social stimuli on this process remains largely unexplored. By quantifying the expression of DNMT genes (dnmt1a, dnmt2 and dnmt3) under different demographical conditions characterized by the absence or presence of immatures and young adults, we tested whether the social context affected the expression of DNMT genes. The three DNMT genes had their expression altered, indicating that distinct molecular processes were affected by social interactions. These results open avenues for future investigations into regulatory epigenetic mechanisms underlying complex traits in social invertebrates.

Triplex real-time PCR method for the qualitative detection of European and American foulbrood in honeybee.

The bacteria Melissococcus plutonius and Paenibacillus larvae, causative agents of respectively European and American foulbrood, damage honeybee health worldwide. Here, we present a specific and sensitive qualitative triplex real-time PCR method to detect simultaneously those microbial agents and a honeybee gene, validated through a study involving 7 laboratories through Europe.

Social regulation of ageing by young workers in the honey bee, Apis mellifera.

Organisms' lifespans are modulated by both genetic and environmental factors. The lifespan of eusocial insects is determined by features of the division of labor, which itself is influenced by social regulatory mechanisms. In the honey bee, Apis mellifera, the presence of brood and of old workers carrying out foraging tasks are important social drivers of ageing, but the influence of young adult workers is unknown, as it has not been experimentally teased apart from that of brood. In this study, we test the role of young workers in the ageing of their nestmates. We measured the impact of different social contexts characterized by the absence of brood and/or young adults on the lifespan of worker nestmates in field colonies. To acquire insight into the physiological processes occurring under these contexts, we analyzed the expression of genes known to affect honey bee ageing. The data showed that young workers significantly reduced the lifespan of nestmate workers, similar to the effect of brood on its own. Differential expression of vitellogenin, major royal jelly protein-1, and methylase transferase, but not methyl farneosate epoxidase genes suggests that young workers and brood influence ageing of adult nestmate workers via different physiological pathways. We identify young workers as an essential part of the social regulation of ageing in honey bee colonies.

The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions.

As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the microbiome. The bee microbiome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee microbiome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health.

Overwintering Is Associated with Reduced Expression of Immune Genes and Higher Susceptibility to Virus Infection in Honey Bees.

The eusocial honey bee, Apis mellifera, has evolved remarkable abilities to survive extreme seasonal differences in temperature and availability of resources by dividing the worker caste into two groups that differ in physiology and lifespan: summer and winter bees. Most of the recent major losses of managed honey bee colonies occur during the winter, suggesting that winter bees may have compromised immune function and higher susceptibility to diseases. We tested this hypothesis by comparing the expression of eight immune genes and naturally occurring infection levels of deformed wing virus (DWV), one of the most widespread viruses in A. mellifera populations, between summer and winter bees. Possible interactions between immune response and physiological activity were tested by measuring the expression of vitellogenin and methyl farnesoate epoxidase, a gene coding for the last enzyme involved in juvenile hormone biosynthesis. Our data show that high DWV loads in winter bees correlate with reduced expression of genes involved in the cellular immune response and physiological activity and high expression of humoral immune genes involved in antibacterial defense compared with summer bees. This expression pattern could reflect evolutionary adaptations to resist bacterial pathogens and economize energy during the winter under a pathogen landscape with reduced risk of pathogenic viral infections. The outbreak of Varroa destructor infestation could have overcome these adaptations by promoting the transmission of viruses. Our results suggest that reduced cellular immune function during the winter may have increased honey bee's susceptibility to DWV. These results contribute to our understanding of honey bee colony losses in temperate regions.

Population-genomic variation within RNA viruses of the Western honey bee, Apis mellifera, inferred from deep sequencing.

BACKGROUND: Deep sequencing of viruses isolated from infected hosts is an efficient way to measure population-genetic variation and can reveal patterns of dispersal and natural selection. In this study, we mined existing Illumina sequence reads to investigate single-nucleotide polymorphisms (SNPs) within two RNA viruses of the Western honey bee (Apis mellifera), deformed wing virus (DWV) and Israel acute paralysis virus (IAPV). All viral RNA was extracted from North American samples of honey bees or, in one case, the ectoparasitic mite Varroa destructor. RESULTS: Coverage depth was generally lower for IAPV than DWV, and marked gaps in coverage occurred in several narrow regions (< 50 bp) of IAPV. These coverage gaps occurred across sequencing runs and were virtually unchanged when reads were re-mapped with greater permissiveness (up to 8% divergence), suggesting a recurrent sequencing artifact rather than strain divergence. Consensus sequences of DWV for each sample showed little phylogenetic divergence, low nucleotide diversity, and strongly negative values of Fu and Li's D statistic, suggesting a recent population bottleneck and/or purifying selection. The Kakugo strain of DWV fell outside of all other DWV sequences at 100% bootstrap support. IAPV consensus sequences supported the existence of multiple clades as had been previously reported, and Fu and Li's D was closer to neutral expectation overall, although a sliding-window analysis identified a significantly positive D within the protease region, suggesting selection maintains diversity in that region. Within-sample mean diversity was comparable between the two viruses on average, although for both viruses there was substantial variation among samples in mean diversity at third codon positions and in the number of high-diversity sites. FST values were bimodal for DWV, likely reflecting neutral divergence in two low-diversity populations, whereas IAPV had several sites that were strong outliers with very low FST. CONCLUSIONS: This initial survey of genetic variation within honey bee RNA viruses suggests future directions for studies examining the underlying causes of population-genetic structure in these economically important pathogens.