DNA base modifications in honey bee and fruit fly genomes suggest an active demethylation machinery with species- and tissue-specific turnover rates

Well-known epigenetic DNA modifications in mammals include the addition of a methyl group and a hydroxyl group to cytosine, resulting in 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) respectively. In contrast, the abundance and the functional implications of these modifications in invertebrate model organisms such as the honey bee (Apis mellifera) and the fruit fly (Drosophila melanogaster) are not well understood. Here we show that both adult honey bees and fruit flies contain 5mC and also 5hmC. Using a highly sensitive liquid chromatography/tandem mass spectrometry (LC/MS/MS) technique, we quantified 5mC and 5hmC in different tissues of adult honey bee worker castes and in adult fruit flies. A comparison of our data with reports from human and mouse shed light on notable differences in 5mC and 5hmC levels between tissues and species.     

Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifera

Background

Long non-coding RNAs (lncRNAs) are a class of RNAs that do not encode proteins. Recently, lncRNAs have gained special attention for their roles in various biological process and diseases.

Results

In an attempt to identify long intergenic non-coding RNAs (lincRNAs) and their possible involvement in honey bee development and diseases, we analyzed RNA-seq datasets generated from Asian honey bee (Apis cerana) and western honey bee (Apis mellifera). We identified 2470 lincRNAs with an average length of 1011 bp from A. cerana and 1514 lincRNAs with an average length of 790 bp in A. mellifera. Comparative analysis revealed that 5 % of the total lincRNAs derived from both species are unique in each species. Our comparative digital gene expression analysis revealed a high degree of tissue-specific expression among the seven major tissues of honey bee, different from mRNA expression patterns. A total of 863 (57 %) and 464 (18 %) lincRNAs showed tissue-dependent expression in A. mellifera and A. cerana, respectively, most preferentially in ovary and fat body tissues. Importantly, we identified 11 lincRNAs that are specifically regulated upon viral infection in honey bees, and 10 of them appear to play roles during infection with various viruses.

Conclusions

This study provides the first comprehensive set of lincRNAs for honey bees and opens the door to discover lincRNAs associated with biological and hormone signaling pathways as well as various diseases of honey bee.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1868-7) contains supplementary material, which is available to authorized users.     

Microbes from apiarian sources: Bacillus spp. in frass of the greater wax moth

Frass from the greater wax moth, Galleria mellonella, obtained from feral colonies of honey bees, Apis mellifera; from managed honey bee colonies; and from a laboratory culture of the wax moth was sampled for aerobic Gram-positive spore-forming rods. One hundred eighty-five strains belonging to the genus Bacillus were isolated, and most were identified. One hundred and three of the isolates were from frass from the wax moth culture, 61 were from frass from managed honey bee colonies, and 21 were from frass from feral honey bee colonies. The species most frequently isolated varied with the source. Fifty-eight isolates from frass from managed honey bee colonies were B. cereus which was isolated from this source only, but B. sphaericus was the most frequent isolate from frass from the wax moth culture. Bacillus megaterium and organisms belonging to the B. alvei-B. thiaminolyticus spectrum were the most frequent isolates from frass from feral honey bee colonies. Most strains isolated produced caprylate esterase-lipase, leucine aminopeptidase, and phosphoamidase. The numbers of isolates, the species, and the enzymatic activity of the strains varied with the source of the frass. In fact, the complete microbial complement varied with the source. These results are discussed in relation to possible roles of Bacillus spp. in the nutrition of the wax moth as well as the microbial ecology of the honey bee colony.     

Genetic diversity and phylogenetic relationship among the western and the Asian honey bees based on two mitochondrial gene segments (COI and ND5)

The Asian honey bee species i.e., Apis cerana (the eastern honey bee), A. dorsata (the giant honey bee), and the western or European honey bee (A. mellifera) collected from Pakistan were studied using partial sequences from two mitochondrial genes (i) the Cytochrome c oxidase I (COI) and (ii) the mitochondrially encoded NADH dehydrogenase 5 (ND5) and then compared with other honey bees sequences (already submitted from different countries around the globe) obtained after the national center for biotechnology information (NCBI). DNA sequences were analyzed employing molecular evolutionary genetics analysis and Kimura 2-parameter model, neighbor-joining method was applied to investigate phylogenetic relationships, and DNA sequence polymorphism was applied to measure the genetic diversity within the genus Apis. The phylogenetic analyses yielded consistent results. Based on COI gene fragment in two Asian and European honey bee species from Pakistan and from other countries showed considerable genetic diversity levels and deviation among the species. While in contrast the phylogenetic analyses based on ND5 gene fragment in Asian and European honey bee species from Pakistan and other countries showed comparatively higher genetic diversity indices and variations than the COI gene. So, in the genus Apis, the mitochondrial ND5 region has shown the possibility to answer the interactions among species. A further detailed work (by linking the analysis of other genomic and mitochondrial genes) is required for good quality solution to establish the concise genetic diversity and interaction among the Apis species. The objective of this study was to explore the extent of genetic differences and phylogenetic links among the three kinds of honey bee species from Pakistan and comparing them with other bee species around the globe.     

Isolation of the cytoplasmic form of malate dehydrogenase from honey bee (Apis mellifera) larvae.

A simplified system for the preparation of cytoplasmic MDH from honey bee larvae is presented. The study shows the enzyme to be a dimer with a subunit molecular weight of 34,000. The enzyme was found to have a lower specific activity than that found in Drosophila melanogaster.     

A new gene, SRP16, differentially expressed in the spermathecae of honeybee queens (Apis mellifera) related with reproduction status

Honey bee queens have the ability to store sperm in spermathecae for fertilizing eggs throughout their life. To investigate mechanisms for sperm storage in Apis mellifera, we employed suppression subtractive hybridization (SSH) to find differentially expressed fragments in spermathecae between virgin queens and newly mated queens. A new gene, named SRP16, was obtained by joining the SSH products with 5′-RACE and 3′-RACE. SRP16 is predicted to encode a 41?kDa protein with 363 amino acid residues. Its expression was found in the spermathecae dominantly in honey bee queens but not in honey bee workers, with the highest expression found in spermathecae of virgin and newly mated queens. SRP16 expression was weak in other tissues of queens other than in the spermathecae and showed no obvious change with reproductive status of queens. The results suggest that SRP16 may play important roles in sperm storage and honey bee reproduction.     

Imidacloprid Alters Foraging and Decreases Bee Avoidance of Predators

Concern is growing over the effects of neonicotinoid pesticides, which can impair honey bee cognition. We provide the first demonstration that sublethal concentrations of imidacloprid can harm honey bee decision-making about danger by significantly increasing the probability of a bee visiting a dangerous food source. Apis cerana is a native bee that is an important pollinator of agricultural crops and native plants in Asia. When foraging on nectar containing 40 µg/L (34 ppb) imidacloprid, honey bees (Apis cerana) showed no aversion to a feeder with a hornet predator, and 1.8 fold more bees chose the dangerous feeder as compared to control bees. Control bees exhibited significant predator avoidance. We also give the first evidence that foraging by A. cerana workers can be inhibited by sublethal concentrations of the pesticide, imidacloprid, which is widely used in Asia. Compared to bees collecting uncontaminated nectar, 23% fewer foragers returned to collect the nectar with 40 µg/L imidacloprid. Bees that did return respectively collected 46% and 63% less nectar containing 20 µg/L and 40 µg/L imidacloprid. These results suggest that the effects of neonicotinoids on honey bee decision-making and other advanced cognitive functions should be explored. Moreover, research should extend beyond the classic model, the European honey bee (A. mellifera), to other important bee species.     

Pollen diets and niche overlap of honey bees and native bees in protected areas

The decline of both managed and wild bee populations has been extensively reported for over a decade now, with growing concerns amongst the scientific community. Also, evidence is growing that both managed and feral honey bees may exacerbate threats to wild bees. In Australia, there are over 1600 native bee species and introduced European honey bees (Apis mellifera) have established throughout most landscapes. There is a major gap in knowledge of the interactions between honey bees and native bees in Australian landscapes, especially floral resource use.Here we report on the pollen diets of wild bees in protected areas of coastal heathland, an ecosystem characterised by mass flowering in late winter and spring. We sampled bees within three sites and DNA metabarcoding was used to compare the pollen diets of honey bees and native bees. We recorded 2, 772 bees in total, with 13 genera and 18 described species identified. Apis mellifera was the most common species across all locations, accounting for 42% of all bees collected. Native bee genera included eusocial Tetragonula (stingless bees) (37%), and semi-social Exoneura and Braunsapis (19.8% combined). Metabarcoding data revealed both Tetragonula and honey bees have wide foraging patterns, and the bipartite network overall was highly generalised (H₂’ = 0.24). Individual honey bees carried pollen of 7–29 plant species, and significantly more species than all other bees. We found niche overlap in the diets of honey bees and native bees generally (0.42), and strongest overlap with stingless bees (0.70) and species of Braunsapis (0.62). A surprising finding was that many species carried pollen from Restionaceae and Cyperaceae, families generally considered to be predominantly wind-pollinated in Australia. Our study showed introduced honey bee use of resources overlaps with that of native bees in protected heathlands, but there are clear differences in their diet preferences.     

Population structure of honey bees in the Carpathian Basin (Hungary) confirms introgression from surrounding subspecies

Carniolan honey bees (Apis mellifera carnica) are considered as an indigenous subspecies in Hungary adapted to most of the ecological and climatic conditions in this area. However, during the last decades Hungarian beekeepers have recognized morphological signs of the Italian honey bee (Apis mellifera ligustica). As the natural distribution of the honey bee subspecies can be affected by the importation of honey bee queens or by natural gene flow, we aimed at determining the genetic structure and characteristics of the local honey bee population using molecular markers. All together, 48 Hungarian and 84 foreign (Italian, Polish, Spanish, Liberian) pupae and/or workers were used for mitochondrial DNA analysis. Additionally, 53 sequences corresponding to 10 subspecies and the Buckfast hybrid were downloaded from GenBank. For the nuclear analysis, 236 Hungarian and 106 foreign honey bees were genotyped using nine microsatellites. Heterozygosity values, population‐specific alleles, FST values, principal coordinate analysis, assignment tests, structure analysis, and dendrograms were calculated. Haplotype and nucleotide diversity values showed moderate values. We found that one haplotype (H9) was dominant in Hungary. The presence of the black honey bee (Apis mellifera mellifera) was negligible, but a few individuals resembling other subspecies were identified. We proved that the Hungarian honey bee population is nearly homogeneous but also demonstrated introgression from the foreign subspecies. Both mitochondrial DNA and microsatellite analyses corroborated the observations of the beekeepers. Molecular analyses suggested that Carniolan honey bee in Hungary is slightly affected by Italian and black honey bee introgression. Genetic differences were detected between Polish and Hungarian Carniolan honey bee populations, suggesting the existence of at least two different gene pools within A. m. carnica.     

Laboratory Assay of Brood Care for Quantitative Analyses of Individual Differences in Honey Bee (Apis mellifera) Affiliative Behavior

Care of offspring is a form of affiliative behavior that is fundamental to studies of animal social behavior. Insects do not figure prominently in this topic because Drosophila melanogaster and other traditional models show little if any paternal or maternal care. However, the eusocial honey bee exhibits cooperative brood care with larvae receiving intense and continuous care from their adult sisters, but this behavior has not been well studied because a robust quantitative assay does not exist. We present a new laboratory assay that enables quantification of group or individual honey bee brood “nursing behavior” toward a queen larva. In addition to validating the assay, we used it to examine the influence of the age of the larva and the genetic background of the adult bees on nursing performance. This new assay also can be used in the future for mechanistic analyses of eusociality and comparative analyses of affilative behavior with other animals.     

A Cell Line Resource Derived from Honey Bee (Apis mellifera) Embryonic Tissues

A major hindrance to the study of honey bee pathogens or the effects of pesticides and nutritional deficiencies is the lack of controlled in vitro culture systems comprised of honey bee cells. Such systems are important to determine the impact of these stress factors on the developmental and cell biology of honey bees. We have developed a method incorporating established insect cell culture techniques that supports sustained growth of honey bee cells in vitro. We used honey bee eggs mid to late in their embryogenesis to establish primary cultures, as these eggs contain cells that are progressively dividing. Primary cultures were initiated in modified Leibovitz’s L15 medium and incubated at 32^°C. Serial transfer of material from several primary cultures was maintained and has led to the isolation of young cell lines. A cell line (AmE-711) has been established that is composed mainly of fibroblast-type cells that form an adherent monolayer. Most cells in the line are diploid (2n = 32) and have the Apis mellifera karyotype as revealed by Giemsa stain. The partial sequence for the mitochondrial-encoded cytochrome c oxidase subunit I (Cox 1) gene in the cell line is identical to those from honey bee tissues and a consensus sequence for A. mellifera. The population doubling time is approximately 4 days. Importantly, the cell line is continuously subcultured every 10–14 days when split at a 1:3 ratio and is cryopreserved in liquid nitrogen. The cell culture system we have developed has potential application for studies aimed at honey bee development, genetics, pathogenesis, transgenesis, and toxicology.     

Interactions between Cooccurring Lactic Acid Bacteria in Honey Bee Hives

In contrast to the honey bee gut, which is colonized by a few characteristic bacterial clades, the hive of the honey bee is home to a diverse array of microbes, including many lactic acid bacteria (LAB). In this study, we used culture, combined with sequencing, to sample the LAB communities found across hive environments. Specifically, we sought to use network analysis to identify microbial hubs sharing nearly identical operational taxonomic units, evidence which may indicate cooccurrence of bacteria between environments. In the process, we identified interactions between noncore bacterial members (Fructobacillus and Lactobacillaceae) and honey bee-specific “core” members. Both Fructobacillus and Lactobacillaceae colonize brood cells, bee bread, and nectar and may serve the role of pioneering species, establishing an environment conducive to the inoculation by honey bee core bacteria. Coculture assays showed that these noncore bacterial members promote the growth of honey bee-specific bacterial species. Specifically, Fructobacillus by-products in spent medium supported the growth of the Firm-5 honey bee-specific clade in vitro. Metabolic characterization of Fructobacillus using carbohydrate utilization assays revealed that this strain is capable of utilizing the simple sugars fructose and glucose, as well as the complex plant carbohydrate lignin. We tested Fructobacillus for antibiotic sensitivity and found that this bacterium, which may be important for establishment of the microbiome, is sensitive to the commonly used antibiotic tetracycline. Our results point to the possible significance of “noncore” and environmental microbial community members in the modulation of honey bee microbiome dynamics and suggest that tetracycline use by beekeepers should be limited.     

Longevity and aging in insects: Is reproduction costly; cheap; beneficial or irrelevant? A critical evaluation of the "trade-off" concept

The most prevalent hypothesis concerning the relationship between reproduction and longevity predicts that reproduction is costly, particularly in females. Specifically, egg production and sexual harassment of females by males reduce female longevity. This may apply to some short-lived species such as Drosophila, but not to some long-lived species such as the queens of ants and bees. Bee queens lay up to 2000 eggs a day for several years, but they nevertheless live at least 20 times longer than their sisters, the sterile workers. This discrepancy necessitates a critical reevaluation of the validity of both the trade-off concept as such, and of the current theories of aging. The widely accepted oxidative stress theory of aging with its links to metabolism and the insulin/IGF-I system has been disproven in Caenorhabditis elegans and mice, but not in Drosophila, necessitating other approaches. The recent spermidine/mitophagy theory is gaining momentum. Two major mechanisms may have been largely overlooked, namely epigenetic control of longevity by imprinting through DNA methylation as suggested by recent data in the honey bee, and especially, a mechanism of which the principles are outlined here, the progressive weakening of the “electrical dimension” of cells up to the point of total collapse, namely death.     

Lotmaria passim (Kinetoplastea: Trypanosomatidae) in honey bees from Argentina

Lotmaria passim (Kinetoplastea) is considered the most prevalent as well as the most virulent trypanosomatid associated to the European honey bee Apis mellifera. We used qPCR to screen for the presence of this parasite in 57 samples from ten Argentinian provinces, and were able to detect its presence throughout most of the country with 41% of the samples testing positive. In a retrospective analysis, we detected L. passim in 73% of honey bee samples from 2006 showing that this flagellate has been widely present in Argentina for at least ~15 years. Additionally, three primer sets for L. passim detection were compared, with the pair that produced smallest PCR product having the best detection capability. Finally, we also found L. passim DNA in 100% (n = 6) of samples of the mite Varroa destructor. The role of this ectoparasite in the lifecycle of Lotmaria, if any, remains unrevealed.     

Viral Infection Affects Sucrose Responsiveness and Homing Ability of Forager Honey Bees,Apis mellifera L.

Honey bee health is mainly affected by Varroa destructor, viruses, Nosema spp., pesticide residues and poor nutrition. Interactions between these proposed factors may be responsible for the colony losses reported worldwide in recent years. In the present study, the effects of a honey bee virus, Israeli acute paralysis virus (IAPV), on the foraging behaviors and homing ability of European honey bees (Apis mellifera L.) were investigated based on proboscis extension response (PER) assays and radio frequency identification (RFID) systems. The pollen forager honey bees originated from colonies that had no detectable level of honey bee viruses and were manually inoculated with IAPV to induce the viral infection. The results showed that IAPV-inoculated honey bees were more responsive to low sucrose solutions compared to that of non-infected foragers. After two days of infection, around 10⁷ copies of IAPV were detected in the heads of these honey bees. The homing ability of IAPV-infected foragers was depressed significantly in comparison to the homing ability of uninfected foragers. The data provided evidence that IAPV infection in the heads may enable the virus to disorder foraging roles of honey bees and to interfere with brain functions that are responsible for learning, navigation, and orientation in the honey bees, thus, making honey bees have a lower response threshold to sucrose and lose their way back to the hive.     

Stingless bee honey (Tetragonula laeviceps): Chemical composition and their potential roles as an immunomodulator in malnourished rats

Honey is rich in bioactive compounds, phenolic acids, and flavonoids and is an antioxidant and an immunomodulator. The objectives of this study were to determine the honey chemical composition of Indonesian stingless bees and their potential roles as an immunomodulator in the malnourished rats. Tetragonula laeviceps honey was used to analyses of chemical composition was obtained from three different geographical origins were Depok Sleman, Bayan Lombok, and Nglipar Gunungkidul. Thirty-two rats were divided into four groups of 8 rats and placed in individual cages. The experimental designed was as follows: T1 = normal rats + without honey (0–7 weeks), T2 = normal rats + with honey of 1.8 g/kg BW/day (0–7 weeks), T3 = malnourished honey of 1.8 g/kg BW/day started from 2 weeks after the malnourished condition (2–7 weeks). The results showed that the chemical composition of Tetragonula laeviceps honey from three different geographical origins were vitamin C content (6.49–13.58 mg/100 g), total phenolic content (0.65–2.30% GAE/100 g), total flavonoid content (0.28–1.00 mg QE/g), and antioxidant activity DPPH (61.43–90.28%). The application of fresh honey from stingless bee that was offered to either normal or malnourished rats were increased lymphocytes proliferation and decreased the production of both proinflammatory markers, interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) from tissue culture supernatant of lymphocytes (p < 0.01). Data from this study clearly indicates the potential role of honey from stingless bee as an immunomodulator in malnourished rats.     

Structure–Function Analysis of the DNA Translocating Portal of the Bacteriophage T4 Packaging Machine

Tailed bacteriophages and herpesviruses consist of a structurally well conserved dodecameric portal at a special 5-fold vertex of the capsid. The portal plays critical roles in head assembly, genome packaging, neck/tail attachment, and genome ejection. Although the structures of portals from phages φ29, SPP1, and P22 have been determined, their mechanistic roles have not been well understood. Structural analysis of phage T4 portal (gp20) has been hampered because of its unusual interaction with the Escherichia coli inner membrane. Here, we predict atomic models for the T4 portal monomer and dodecamer, and we fit the dodecamer into the cryo-electron microscopy density of the phage portal vertex. The core structure, like that from other phages, is cone shaped with the wider end containing the “wing” and “crown” domains inside the phage head. A long “stem” encloses a central channel, and a narrow “stalk” protrudes outside the capsid. A biochemical approach was developed to analyze portal function by incorporating plasmid-expressed portal protein into phage heads and determining the effect of mutations on head assembly, DNA translocation, and virion production. We found that the protruding loops of the stalk domain are involved in assembling the DNA packaging motor. A loop that connects the stalk to the channel might be required for communication between the motor and the portal. The “tunnel” loops that project into the channel are essential for sealing the packaged head. These studies established that the portal is required throughout the DNA packaging process, with different domains participating at different stages of genome packaging.     

The microRNA ame-miR-279a regulates sucrose responsiveness of forager honey bees (Apis mellifera)

Increasing evidence demonstrates that microRNAs (miRNA) play an important role in the regulation of animal behaviours. Honey bees (Apis mellifera) are eusocial insects, with honey bee workers displaying age-dependent behavioural maturation. Many different miRNAs have been implicated in the change of behaviours in honey bees and ame-miR-279a was previously shown to be more highly expressed in nurse bee heads than in those of foragers. However, it was not clear whether this difference in expression was associated with age or task performance. Here we show that ame-miR-279a shows significantly higher expression in the brains of nurse bees relative to forager bees regardless of their ages, and that ame-miR-279a is primarily localized in the Kenyon cells of the mushroom body in both foragers and nurses. Overexpression of ame-miR-279a attenuates the sucrose responsiveness of foragers, while its absence enhances their sucrose responsiveness. Lastly, we determined that ame-miR-279a directly target the mRNA of Mblk-1. These findings suggest that ame-miR-279a plays important roles in regulating honey bee division of labour.     

Replicative DWV type A in Bombus terrestris in Pantelleria island (Sicily,Italy)

The deformed wing virus (DWV) is one of the most common bee pathogens, deemed responsible for both honey bee colony losses and general pollinator decline. That virus may infect both managed and wild bumblebees. In this study, the DWV infection was investigated in 52 free-flying Bombus terrestris (L., 1758) individuals from Pantelleria. This is a volcanic island in the Sicilian Channel. Of the collected individuals, 59.62% scored positive for DWV, with a mean abundance of 2.97 × 10⁵ ± 1.46 × 10⁶ copies per bee. Active replication of the virus could be demonstrated in all positive samples. All the sequences belonged to DWV type A. However both phylogenetic and pairwise distance analysis indicated a low similarity to Italian and Tunisian strains. Further studies are needed to elucidate the epidemiology of DWV in B. terrestris and the drivers of possible genetic modifications of the virus on Pantelleria island.     

Expression and characterization of the chitinases from Serratia marcescens GEI strain for the control of Varroa destructor, a honey bee parasite

Serratia marcescens GEI strain was isolated from the gut of the workers of Chinese honey bee Apis cerana and evaluated in the laboratory for the control of Varroa destructor, a parasite of western honey bee A. mellifera. The supernatant and the collected proteins by ammonium sulfate from the bacterial cultures showed a strong miticidal effect on the female mites, with 100% mite mortality in 5 days. Heat (100 °C for 10 min) and proteinase K treatment of the collected proteins destroyed the miticidal activity. The improved miticial activity of this bacterial strain on chitin medium indicated the involvement of chitinases. The expressed chitinases ChiA, ChiB and ChiC1 from S. marcescens GEI by recombinant Escherichia coli showed pathogenicity against the mites in the laboratory. These chitinases were active in a broad pH range (5-9) and the optimum temperatures were between 60 and 75 °C. Synergistic effects of ChiA and ChiB on the miticidal activity against V. destructor were observed. The workers of both honey bee species were not sensitive to the spraying and feeding chitinases. These results provided alternative control strategies for Varroa mites, by formulating chitinase agents and by constructing transgenetic honey bees.