Holistic screening of collapsing honey bee colonies in Spain: a case study

Promastigote EPS secretion and haptomonad biofilm formation as evolutionary adaptations of trypanosomatid parasites for colonizing honeybee hosts

Bees are major pollinators involved in the maintenance of all terrestrial ecosystems. Biotic and abiotic factors placing these insects at risk is a research priority for ecological and agricultural sustainability. Parasites are one of the key players of this global decline and the study of their mechanisms of action is essential to control honeybee colony losses. Trypanosomatid parasites and particularly the Lotmaria passim are widely spread in honeybees, however their lifestyle is poorly understood. In this work, we show how these parasites are able to differentiate into a new parasitic lifestyle: the trypanosomatid biofilms. Using different microscopic techniques, we demonstrated that the secretion of Extracellular Polymeric Substances by free-swimming unicellular promastigote forms is a prerequisite for the generation and adherence of multicellular biofilms to solid surfaces in vitro and in vivo. Moreover, compared to human-infective trypanosomatid parasites our study shows how trypanosomatid parasites of honeybees increases their resistance and thus resilience to drastic changes in environmental conditions such as ultralow temperatures and hypoosmotic shock, which would explain their success thriving within or outside their hosts. These results set up the basis for the understanding of the success of this group of parasites in nature and to unveil the impact of such pathogens in honeybees, a keystones species in most terrestrial ecosystems.

Prevalence and genome features of lake sinai virus isolated from Apis mellifera in the Republic of Korea

Lake Sinai Virus (LSV) is an emerging pathogen known to affect the honeybee (Apis mellifera). However, its prevalence and genomic characteristics in the Republic of Korea (ROK) remain unexplored. This study aimed to assess the prevalence of and analyze the LSVs by examining 266 honeybee samples from the ROK. Our findings revealed that LSV exhibited the highest infection rate among the pathogens observed in Korean apiaries, particularly during the reported period of severe winter loss (SWL) in A. mellifera apiaries in 2022. Three LSV genotypes- 2, 3, and 4 -were identified using RNA-dependent RNA polymerase gene analysis. Importantly, the infection rates of LSV2 (65.2%) and LSV3 (73.3%) were significantly higher in colonies experiencing SWL than in those experiencing normal winter loss (NWL) (p < 0.03). Furthermore, this study provides the first near-complete genome sequences of the Korean LSV2, LSV3, and LSV4 strains, comprising 5,759, 6,040, and 5,985 nt, respectively. Phylogenetic analysis based on these near-complete genome sequences demonstrated a close relationship between LSVs in the ROK and China. The high LSV infection rate in colonies experiencing a heightened mortality rate during winter suggests that this pathogen might contribute to SWL in ROK. Moreover, the genomic characteristic information on LSVs in this study holds immense potential for epidemiological information and the selection of specific genes suitable for preventing and treating LSV, including the promising utilization of RNA interference medicine in the future.

Frequent Parasitism of Apis mellifera by Trypanosomatids in Geographically Isolated Areas with Restricted Beekeeping Movements

Trypanosomatids form a group of high prevalence protozoa that parasitise honey bees, with Lotmaria passim as the predominant species worldwide. However, the knowledge about the ecology of trypanosomatids in isolated areas is limited. The Portuguese archipelagos of Madeira and Azores provide an interesting setting to investigate these parasites because of their geographic isolation, and because they harbour honey bee populations devoid of two major enemies: Varroa destructor and Nosema ceranae. Hence, a total of 661 honey bee colonies from Madeira and the Azores were analysed using different molecular techniques, through which we found a high prevalence of trypanosomatids despite the isolation of these islands. L. passim was the predominant species and, in most colonies, was the only one found, even on islands free of V. destructor and/or N. ceranae with severe restrictions on colony movements to prevent the spread of them. However, islands with V. destructor had a significantly higher prevalence of L. passim and, conversely, islands with N. ceranae did not shown any significant correlation with the trypanosomatid. Crithidia bombi was detected in Madeira and on three islands of the Azores, almost always coincident with L. passim. By contrast, Crithidia mellificae was not detected in any sample. A high-throughput sequencing analysis distinguished two main haplotypes of L. passim, which accounted for 98% of the total sequence reads. This work suggests that L. passim and C. bombi are parasites that have been associated with honey bees predating the spread of V. destructor and N. ceranae.

Trypanosomatids in honey bee colonies in Spain: A new specific qPCR method for specific quantification of Lotmaria passim, Crithidia mellificae and Crithidia bombi

Bee trypanosomatids have not been widely studied due to the original belief that these organisms were not pathogenic to honey bees. However, trypanosomatids have been linked to increased winter mortality in honey bee colonies in recent years and it has been shown that these pathogens can shorten a honey bee worker's lifespan in laboratory conditions. These studies found that this mortality corresponded to dose-dependent infection. Although Lotmaria passim is the most prevalent species worldwide, the natural load in colonies remains poorly investigated. Here we describe a new highly specific and sensitive qPCR method that allows the differentiation and quantification of the parasitic load of each of the three most common trypanosomatid species described to date in honey bee colonies: L. passim, Crithidia mellificae, and Crithidia bombi. We have used this new method to analyze honey bee colonies in central Spain and confirm that L. passim is the most common species and the one with higher parasitic loads in the colonies, which increased over the years, being higher in spring than in autumn. Crithidia mellificae was present along the study, with the highest prevalence in autumn 2019 and lately it was only found in non-quantifiable loads. Crithidia bombi was not detected in any of the colonies analyzed.

Significant, but not biologically relevant: Nosema ceranae infections and winter losses of honey bee colonies

The Western honey bee Apis mellifera, which provides about 90% of commercial pollination, is under threat from diverse abiotic and biotic factors. The ectoparasitic mite Varroa destructor vectoring deformed wing virus (DWV) has been identified as the main biotic contributor to honey bee colony losses worldwide, while the role of the microsporidium Nosema ceranae is still controversially discussed. In an attempt to solve this controversy, we statistically analyzed a unique data set on honey bee colony health collected from a cohort of honey bee colonies over 15 years and comprising more than 3000 data sets on mite infestation levels, Nosema spp. infections, and winter losses. Multivariate statistical analysis confirms that V. destructor is the major cause of colony winter losses. Although N. ceranae infections are also statistically significantly correlated with colony losses, determination of the effect size reveals that N. ceranae infections are of no or low biological relevance.

Development of a TaqMan qPCR assay for trypanosomatid multi-species detection and quantification in insects

BACKGROUND

Trypanosomatid parasites are widely distributed in nature and can have a monoxenous or dixenous life-cycle. These parasites thrive in a wide number of insect orders, some of which have an important economic and environmental value, such as bees. The objective of this study was to develop a robust and sensitive real-time quantitative PCR (qPCR) assay for detecting trypanosomatid parasites in any type of parasitized insect sample.

METHODS

A TaqMan qPCR assay based on a trypanosomatid-conserved region of the α-tubulin gene was standardized and evaluated. The limits of detection, sensitivity and versatility of the α-tubulin TaqMan assay were tested and validated using field samples of honeybee workers, wild bees, bumblebees and grasshoppers, as well as in the human infective trypanosomatid Leishmania major.

RESULTS

The assay showed a detection limit of 1 parasite equivalent/µl and successfully detected trypanosomatids in 10 different hosts belonging to the insect orders Hymenoptera and Orthoptera. The methodology was also tested using honeybee samples from four apiaries (n = 224 worker honeybees) located in the Alpujarra region (Granada, Spain). Trypanosomatids were detected in 2.7% of the honeybees, with an intra-colony prevalence of 0% to 13%. Parasite loads in the four different classes of insects ranged from 40.6 up to 1.1 × 10⁸ cell equivalents per host.

CONCLUSIONS

These results show that the α-tubulin TaqMan qPCR assay described here is a versatile diagnostic tool for the accurate detection and quantification of trypanosomatids in a wide range of environmental settings.

Bee Trypanosomatids: First Steps in the Analysis of the Genetic Variation and Population Structure of Lotmaria passim, Crithidia bombi and Crithidia mellificae

Trypanosomatids are among the most prevalent parasites in bees but, despite the fact that their impact on the colonies can be quite important and that their infectivity may potentially depend on their genotypes, little is known about the population diversity of these pathogens. Here we cloned and sequenced three non-repetitive single copy loci (DNA topoisomerase II, glyceraldehyde-3-phosphate dehydrogenase and RNA polymerase II large subunit, RPB1) to produce new genetic data from Crithidia bombi, C. mellificae and Lotmaria passim isolated from honeybees and bumblebees. These were analysed by applying population genetic tools in order to quantify and compare their variability within and between species, and to obtain information on their demography and population structure. The general pattern for the three species was that (1) they were subject to the action of purifying selection on nonsynonymous variants, (2) the levels of within species diversity were similar irrespective of the host, (3) there was evidence of recombination among haplotypes and (4) they showed no haplotype structuring according to the host. C. bombi exhibited the lowest levels of synonymous variation (π_S= 0.06 ± 0.04 %) - and a mutation frequency distribution compatible with a population expansion after a bottleneck - that contrasted with the extensive polymorphism displayed by C. mellificae (π_S= 2.24 ± 1.00 %), which likely has a more ancient origin. L. passim showed intermediate values (π_S= 0.40 ± 0.28 %) and an excess of variants a low frequencies probably linked to the spread of this species to new geographical areas.

Detection of Lotmaria passim and Crithidia mellificae in Selected Bumblebee Species

Bumblebees (Bombus spp.) are an essential element of the ecosystem and the global economy. They are valued pollinators in many countries around the word. Unfortunately, there has been a decline in the bumblebee population, which is attributed to, among others, pathogens and reduced access to food due to the loss of natural nesting sites. Lotmaria passim and Crithidia mellificae, protozoan pathogens of the family Trypanosomatidae, commonly infect bumblebees, including in Poland. In this study, a Polish population of bumblebees was screened for L. passim and C. mellificae. The experiment was performed on 13 adult bumblebees belonging to 4 species: B. lapidarius, B. lucorum, B. pascuorum, and B. terrestris. Protozoa of the family Trypanosomatidae were identified by PCR. Only L. passim was identified in one B. pascuorum individual. Further research is needed to confirm the effect of concurrent pathogens on the decline of bumblebee populations.

First detection of Lake Sinai virus in the Czech Republic: a potential member of a new species

Lake Sinai virus (LSV) is one of over 20 honey bee viruses. Variants of LSV have been classified as members of two officially recognised species, Lake Sinai virus 1 and Lake Sinai virus 2. However, there are currently a limited number of whole-genome sequences, and the genetic variability of the virus indicates that additional species may need to be established. Extracted nucleic acid of 209 honey bee samples was screened by PCR for 11 honey bee viruses. LSV was the third most abundant virus (36.9% of positive samples), after Apis mellifera filamentous virus (72.2%) and deformed wing virus (52.5%). LSV-positive samples were analyzed further by PCR with primers targeting the region encoding the viral RNA-dependent RNA polymerase. Subsequently, the PCR products were sequenced, and the resulting sequences were used for a first round of phylogenetic analysis. Based on those results, several isolates were selected for whole-genome sequencing, and the complete genome sequences were used for additional phylogenetic analysis. The results indicated the presence of at least three genetically distinct groups of LSV in the Czech Republic, the most prevalent one being related to LSV 2 but too dissimilar to be considered a member of the same species. Two sequences of a major LSV strain cluster native to the Czech Republic were determined, representing the first Czech LSV strains published to date.

Glucosinolates as Markers of the Origin and Harvesting Period for Discrimination of Bee Pollen by UPLC-MS/MS

Bee pollen is currently one of the most commonly consumed food supplements, as it is considered to be a good source of bioactive substances and energy. It contains various health-promoting compounds, such as proteins, amino acids, lipids, as well as glucosinolates. In the present study, the glucosinolate content was determined, by means of ultra-performance liquid chromatography coupled to a quadrupole time-of-flight mass detector, in 72 bee pollen samples from four different apiaries in Guadalajara (Spain), harvested in three different periods. In addition, 11 commercial multifloral samples from different Spanish regions were also analyzed. The aim was to verify the suitability of these compounds as biomarkers of their geographical origin, and to test their potential for distinguishing the harvesting period. By means of a canonical discriminant analysis, it was possible to differentiate the apiary of origin of most of the samples, and these could also be clearly differentiated from the commercial ones, simply as a result of the glucosinolate content. In addition, it was also demonstrated for the first time that bee pollen samples were capable of being differentiated according to the time of harvesting and their glucosinolate content.

Effects of Thiamethoxam-Dressed Oilseed Rape Seeds and Nosema ceranae on Colonies of Apis mellifera iberiensis, L. under Field Conditions of Central Spain. Is Hormesis Playing a Role?

Simple Summary

The collapse of the honey bee colonies is a complex phenomenon in which different factors may participate in an interrelated manner (e.g., pathogen interactions, exposure to chemicals, beekeeping practices, climatology, etc.). In light of the current debate regarding the interpretation of field and monitoring studies in prospective risk assessments, here we studied how exposure to thiamethoxam affects honey bee colonies in Central Spain when applied as a seed treatment to winter oilseed rape, according to the good agricultural practice in place prior to the EU restrictions. Under the experimental conditions, exposure to thiamethoxam, alone or in combination with other stressors, did not generate and maintain sufficient chronic stress as to provoke honey bee colony collapse. The stress derived from exposure to thiamethoxam and honey bee pathogens was compensated by adjustments in the colony’s dynamics, and by an increase in the worker bee population, a behavior known as hormesis. An analysis of the factors underlying this phenomenon should be incorporated into the prospective risk assessment of plant protection products in order to improve the future interpretation of field studies and management practices.

Abstract

To study the influence of thiamethoxam exposure on colony strength and pathogen prevalence, an apiary (5 colonies) was placed in front of a plot sown with winter oilseed rape (wOSR), just before the flowering phase. Before sowing, the seeds were treated with an equivalent application of 18 g thiamethoxam/ha. For comparison, a second apiary (5 colonies) was located in front of a separate 750 m plot sown with untreated wOSR. Dead foragers at the entrance of hives were assessed every 2–3 days throughout the exposure period, while the colony strength (number of combs covered with adult honey bees and brood) and pathogens were monitored each month until the following spring. Foraging on the wOSR crop was confirmed by melissopalynology determination of the corbicular pollen collected periodically, while the chemical analysis showed that exposure to thiamethoxam was mainly through nectar. There was an increase in the accumulation of dead bees in the apiary exposed to thiamethoxam relating with the control, which was coped with an increment of bee brood surface and adult bee population. However, we did not find statistically significant differences between apiaries (α = 0.05) in terms of the evolution of pathogens. We discuss these results under hormesis perspective.

Nosemosis Prevention and Control

Nosemosis is a serious microsporidian disease of adult European honey bees caused by the spore-forming unicellular fungi Nosema apis and Nosema ceranae. In this paper we describe the currently known techniques for nosemosis prevention and control including Good Beekeeping Practices (GBPs) and biosecurity measures (BMBs). Topics such as queen renewal, nosema-resistant bees and hygienic and control methods are described. Strong efforts are currently provided to find more a sustainable solution than the use of antibiotics. So far, it seems that the best way to approach nosemosis is given by an “integrated pest management strategy”, which foresees the contemporary application of different, specific GBPs and BMBs.

Screening of Honey Bee Pathogens in the Czech Republic and Their Prevalence in Various Habitats

Western honey bee (Apis mellifera) is one of the most important pollinators in the world. Thus, a recent honey bee health decline and frequent honey bee mass losses have drawn attention and concern. Honey bee fitness is primarily reduced by pathogens, parasites, and viral load, exposure to pesticides and their residues, and inadequate nutrition from both the quality and amount of food resources. This study evaluated the prevalence of the most common honey bee pathogens and viruses in different habitats across the Czech Republic. The agroecosystems, urban ecosystems, and national park were chosen for sampling from 250 colonies in 50 apiaries. Surprisingly, the most prevalent honey bee pathogens belong to the family Trypanosomatidae including Lotmaria passim and Crithidia mellificae. As expected, the most prevalent viruses were DWV, followed by ABPV. Additionally, the occurrence of DWV-B and DWV-C were correlated with honey bee colony mortality. From the habitat point of view, most pathogens occurred in the town habitat, less in the agroecosystem and least in the national park. The opposite trend was observed in the occurrence of viruses. However, the prevalence of viruses was not affected by habitat.

First description of Lotmaria passim and Crithidia mellificae haptomonad stages in the honeybee hindgut

The remodelling of flagella into attachment structures is a common and important event in the trypanosomatid life cycle. Lotmaria passim and Crithidia mellificae can parasitize Apis mellifera, and as a result they might have a significant impact on honeybee health. However, there are details of their life cycle and the mechanisms underlying their pathogenicity in this host that remain unclear. Here we show that both L. passim promastigotes and C. mellificae choanomastigotes differentiate into haptomonad stages covering the ileum and rectum of honeybees. These haptomonad cells remain attached to the host surface via zonular hemidesmosome-like structures, as revealed by transmission electron microscopy. This work describes for the first known time the haptomonad morphotype of these species and their hemidesmosome-like attachments in A. mellifera, a key trait used by other trypanosomatid species to proliferate in the insect host hindgut.

A Case Report of Chronic Stress in Honey Bee Colonies Induced by Pathogens and Acaricide Residues

In this case report, we analyze the possible causes of the poor health status of a professional Apis mellifera iberiensis apiary located in Gajanejos (Guadalajara, Spain). Several factors that potentially favor colony collapse were identified, including Nosema ceranae infection, alone or in combination with other factors (e.g., BQCV and DWV infection), and the accumulation of acaricides commonly used to control Varroa destructor in the beebread (coumaphos and tau-fluvalinate). Based on the levels of residues, the average toxic unit estimated for the apiary suggests a possible increase in vulnerability to infection by N. ceranae due to the presence of high levels of acaricides and the unusual climatic conditions of the year of the collapse event. These data highlight the importance of evaluating these factors in future monitoring programs, as well as the need to adopt adequate preventive measures as part of national and international welfare programs aimed at guaranteeing the health and fitness of bees.

Analysis of honey environmental DNA indicates that the honey bee (Apis mellifera L.) trypanosome parasite Lotmaria passim is widespread in the apiaries of the North of Italy

Lotmaria passim is a trypanosomatid that infects honey bees. In this study, we established an axenic culture of L. passim from Italian isolates and then used its DNA as a control in subsequent analyses that investigated environmental DNA (eDNA) to detect this trypasonosomatid. The source of eDNA was honey, which has been already demonstrated to be useful to detect honey bee parasites. DNA from a total of 164 honey samples collected in the North of Italy was amplified with three L. passim specific PCR primers and 78% of the analysed samples gave positive results. These results indicated a high prevalence rate of this trypanosomatid in the North of Italy, where it might be considered another threat to honey bee health.

Amplicon Sequencing of Variable 16S rRNA from Bacteria and ITS2 Regions from Fungi and Plants, Reveals Honeybee Susceptibility to Diseases Results from Their Forage Availability under Anthropogenic Landscapes

European Apis mellifera and Asian Apis cerana honeybees are essential crop pollinators. Microbiome studies can provide complex information on health and fitness of these insects in relation to environmental changes, and plant availability. Amplicon sequencing of variable regions of the 16S rRNA from bacteria and the internally transcribed spacer (ITS) regions from fungi and plants allow identification of the metabiome. These methods provide a tool for monitoring otherwise uncultured microbes isolated from the gut of the honeybees. They also help monitor the composition of the gut fungi and, intriguingly, pollen collected by the insect. Here, we present data from amplicon sequencing of the 16S rRNA from bacteria and ITS2 regions from fungi and plants derived from honeybees collected at various time points from anthropogenic landscapes such as urban areas in Poland, UK, Spain, Greece, and Thailand. We have analysed microbial content of honeybee intestine as well as fungi and pollens. Furthermore, isolated DNA was used as the template for screening pathogens: Nosema apis, N. ceranae, N. bombi, tracheal mite (Acarapis woodi), any organism in the parasitic order Trypanosomatida, including Crithidia spp. (i.e., Crithidia mellificae), neogregarines including Mattesia and Apicystis spp. (i.e., Apicistis bombi). We conclude that differences between samples were mainly influenced by the bacteria, plant pollen and fungi, respectively. Moreover, honeybees feeding on a sugar based diet were more prone to fungal pathogens (Nosema ceranae) and neogregarines. In most samples Nosema sp. and neogregarines parasitized the host bee at the same time. A higher load of fungi, and bacteria groups such as Firmicutes (Lactobacillus); γ-proteobacteria, Neisseriaceae, and other unidentified bacteria was observed for Nosema ceranae and neogregarine infected honeybees. Healthy honeybees had a higher load of plant pollen, and bacteria groups such as: Orbales, Gilliamella, Snodgrassella, and Enterobacteriaceae. Finally, the period when honeybees switch to the winter generation (longer-lived forager honeybees) is the most sensitive to diet perturbations, and hence pathogen attack, for the whole beekeeping season. It is possible that evolutionary adaptation of bees fails to benefit them in the modern anthropomorphised environment.

Workflow of Lotmaria passim isolation: Experimental infection with a low-passage strain causes higher honeybee mortality rates than the PRA-403 reference strain

The impact of trypanosomatid parasites on honeybee health may represent a major threat to bee colonies worldwide. However, few axenic isolates have been generated to date and with no details on cell culture passages, a parameter that could influence parasite virulence. To address this question, a trypanosomatid isolation protocol was developed and a new strain was obtained, named L. passim C1. Using experimental infection of worker honeybees, we compared the virulence and mortality rates of the ATCC PRA-403 reference strain and C1 strain, the latter showing higher virulence from 10 days post-infection onward. This study highlights the impact of cell culture passages on the pathogenicity of L. passim in honeybees, providing new evidence of its negative effects on honeybee health.

Experimental evidence of harmful effects of Crithidia mellificae and Lotmaria passim on honey bees

The trypanosomatids Crithidia mellificae and Lotmaria passim are very prevalent in honey bee colonies and potentially contribute to colony losses that currently represent a serious threat to honey bees. However, potential pathogenicity of these trypanosomatids remains unclear and since studies of infection are scarce, there is little information about the virulence of their different morphotypes. Hence, we first cultured C. mellificae and L. passim (ATCC reference strains) in six different culture media to analyse their growth rates and to obtain potentially infective morphotypes. Both C. mellificae and L. passim grew in five of the media tested, with the exception of M199. These trypanosomatids multiplied fastest in BHI medium, in which they reached a stationary phase after around 96 h of growth. Honey bees inoculated with either Crithidia or Lotmaria died faster than control bees and their mortality was highest when they were inoculated with 96 h cultured L. passim. Histological and Electron Microscopy analyses revealed flagellated morphotypes of Crithidia and Lotmaria in the lumen of the ileum, and adherent non-flagellated L. passim morphotypes covering the epithelium, although no lesions were evident. These data indicate that parasitic forms of these trypanosomatids obtained from the early stationary growth phase infect honey bees. Therefore, efficient infection can be achieved to study their intra-host development and to assess the potential pathogenicity of these trypanosomatids.

Prevalence of the Microsporidian Nosema spp. in Honey Bee Populations (Apis mellifera) in Some Ecological Regions of North Asia

Two species of microsporidia, Nosema apis and Nosema ceranae, are obligate intracellular parasites that are widespread in the world and cause the infectious disease (Nosemosis) of the Western honey bee Apis mellifera. Information on the prevalence and distribution of Nosema species in North Asia conditions is scarce. The main aim of the present study is to determine the prevalence of Nosema spp. (Nosemosis) in honey bees inhabiting some inland regions of North Asia (Western and Eastern Siberia, Altai Territory, Russia, and northeastern part of Kazakhstan). The objective of the paper is also to assess the influence of climatic factors on the spread of N. ceranae. Eighty apiaries in four ecological regions of North Asia (southern taiga, sub-taiga zone, forest steppe, and mountain taiga forests) were investigated with regard to distribution, prevalence, and diversity of Nosema infection in honey bees using duplex-PCR. Nosema infected bees were found in 65% apiaries of ecoregions studied, and coinfection was predominant (36.3% of Nosema-positive apiaries). Both N. apis and N. ceranae occur across subarctic and warm summer continental climates, but while N. apis predominates in the former, N. ceranae is more predominant in the latter. No statistically significant differences in Nosema distribution were identified in various climatic zones. In the sub-taiga zone (subarctic climate), low presence of colonies with pure N. ceranae and a significantly higher proportion of coinfection apiaries were revealed. Long-term epidemiological study of Nosema spp. prevalence in the sub-taiga zone showed a surprising percentage increase of Nosema-positive apiaries from 46.2% to 74.1% during 2012–2017. From 2012 to 2015, N. apis became a predominant species, but in 2016–2017, the coinfection was mainly detected. In conclusion, the results of this investigation showed that N. ceranae is widespread in all study ecoregions of North Asia where it exists in combination with the N. apis, but there is no replacement of N. apis by N. ceranae in the studied bee populations.

Longitudinal analysis on parasite diversity in honeybee colonies: new taxa, high frequency of mixed infections and seasonal patterns of variation

To evaluate the influence that parasites have on the losses of Apis mellifera it is essential to monitor their presence in the colonies over time. Here we analysed the occurrence of nosematids, trypanosomatids and neogregarines in five homogeneous colonies for up to 21 months until they collapsed. The study, which combined the use of several molecular markers with the application of a massive parallel sequencing technology, provided valuable insights into the epidemiology of these parasites: (I) it enabled the detection of parasite species rarely reported in honeybees (Nosema thomsoni, Crithidia bombi, Crithidia acanthocephali) and the identification of two novel taxa; (II) it revealed the existence of a high rate of co-infections (80% of the samples harboured more than one parasite species); (III) it uncovered an identical pattern of seasonal variation for nosematids and trypanosomatids, that was different from that of neogregarines; (IV) it showed that there were no significant differences in the fraction of positive samples, nor in the levels of species diversity, between interior and exterior bees; and (V) it unveiled that the variation in the number of parasite species was not directly linked with the failure of the colonies.

Analysing ambiguities in trypanosomatids taxonomy by barcoding

BACKGROUND

Biodiversity screens and phylogenetic studies are dependent on reliable DNA sequences in public databases. Biological collections possess vouchered specimens with a traceable history. Therefore, DNA sequencing of samples available at institutional collections can greatly contribute to taxonomy, and studies on evolution and biodiversity.

METHODS

We sequenced part of the glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH) and the SSU rRNA (V7/V8) genes from 102 trypanosomatid cultures, which are available on request at www.colprot.fiocruz.br.

OBJECTIVE

The main objective of this work was to use phylogenetic inferences, using the obtained DNA sequences and those from representatives of all Trypanosomatidae genera, to generate phylogenetic trees that can simplify new isolates screenings.

FINDINGS

A DNA sequence is provided for the first time for several isolates, the phylogenetic analysis allowed the classification or reclassification of several specimens, identification of candidates for new genera and species, as well as the taxonomic validation of several deposits.

MAIN CONCLUSIONS

This survey aimed at presenting a list of validated species and their associated DNA sequences combined with a short historical overview of each isolate, which can support taxonomic and biodiversity research and promote culture collections.

Trypanosomatid parasite dynamically changes the transcriptome during infection and modifies honey bee physiology

It is still not understood how honey bee parasite changes the gene expression to adapt to the host environment and how the host simultaneously responds to the parasite infection by modifying its own gene expression. To address this question, we studied a trypanosomatid, Lotmaria passim, which can be cultured in medium and inhabit the honey bee hindgut. We found that L. passim decreases mRNAs associated with protein translation, glycolysis, detoxification of radical oxygen species, and kinetoplast respiratory chain to adapt to the anaerobic and nutritionally poor honey bee hindgut during the infection. After the long term infection, the host appears to be in poor nutritional status, indicated by the increase and decrease of take-out and vitellogenin mRNAs, respectively. Simultaneous gene expression profiling of L. passim and honey bee during infection by dual RNA-seq provided insight into how both parasite and host modify their gene expressions.

The toxic unit approach as a risk indicator in honey bees surveillance programmes: A case of study in Apis mellifera iberiensis

The influence of genetic diversity and exposure to xenobiotics on the prevalence of pathogens was studied within the context of a voluntary epidemiological study in Spanish apiaries of Apis mellifera iberiensis, carried out during the spring season of years 2014 and 2015. As such, the evolutionary lineages of the honey bee colonies were identified, a multiresidue analysis of xenobiotics was carried out in beebread and worker bee samples, and the Toxic Unit (TUm) was estimated for each sampled apiary. The relationship between lineages and the most prevalent pathogens (Nosema ceranae, Varroa destructor, trypanosomatids, Black Queen Cell Virus; and Deformed Wing Virus) was analysed with contingency tables, and the possible relationships between TUm and the prevalence of these pathogens were studied by using a factor analysis. The statistical analysis supported the associations between V. destructor and Deformed Wing Virus (DWV), and between N. ceranae and Black Queen Cell Virus (BQCV), but the association between these pathogens and trypanosomatids was not observed. TUm values varied between 5.5 × 10^-6 and 3.65 × 10^-1. When TUm < 3.35 × 10^-4, it was mainly determined by coumaphos, tau-fluvalinate and/or chlorfenvinphos. At higher values, other insecticides also contributed to TUm, although a clear predominance was not seen up to TUm ≥ 1.83 × 10^-2, when it was mainly defined by acrinathrin, spinosad and/or imidacloprid. The possible cumulative effect from the joint action of xenobiotics was >10% in the 63% of the cases. The prevalence of pathogens did not appear to be influenced by the distribution of evolutionary lineages and, while the prevalence of V. destructor was not found to be determined by TUm, there was a trend towards an increasing prevalence of N. ceranae when TUm ≥ 23 10^-4. This study is an example of using TUm approach beyond the field of the ecotoxicology.

Nosema apis and Nosema ceranae Tissue Tropism in Worker Honey Bees (Apis mellifera)

The microsporidia Nosema apis and Nosema ceranae are major honey bee pathogens that possess different characteristics in terms of the signs they produce, as well as disease development and transmission. Although the ventricular epithelium is generally considered the target tissue, indirect observations led to speculation that N. ceranae may also target other structures, possibly explaining at least some of the differences between these 2 species. To investigate the tropism of Nosema for honey bee tissues, we performed controlled laboratory infections by orally administering doses of 50 000 or 100 000 fresh mature spores of either species. The fat body was isolated from the infected bees, as well as organs from the digestive (esophagus, ventriculus, ileum, rectum), excretory (Malpighian tubules), circulatory (aorta, heart), respiratory (thoracic tracheas), exocrine (hypopharyngeal, mandibular and labial, cephalic, thoracic salivary glands), and sensory/nervous (brain, eyes and associated nerve structures, thoracic nerve ganglia) systems. Tissues were examined by light and electron microscopy at 7, 10, and 15 days postinfection. Both Nosema species were found to infect epithelial cells and clusters of regenerative cells in the ventriculus, and while the ileum and rectum contained spores of the microsporidia in the lumen, these structures did not show overt lesions. No stages of the parasites or cellular lesions were detected in the other organs tested, confirming the high tropism of both species for the ventricular epithelium cells. Thus, these direct histopathological observations indicate that neither of these 2 Nosema species exhibit tropism for honey bee organs other than the ventriculus.

High Load of Deformed Wing Virus and Varroa destructor Infestation Are Related to Weakness of Honey Bee Colonies in Southern Spain

Many factors, including pathogens, contribute to the continuing losses of colonies of the honey bee Apis mellifera, which has led to steady population decline. In particular, colony losses have been linked to deformed wing virus (DWV) and the Varroa destructor mite. To clarify the potential role of these two pathogens in honey bee colony weakening and loss, we sampled colonies in southern Spain during a 21-month period and analyzed the samples for loads of four viruses and varroa. Loads of DWV and black queen cell virus as well as varroa infestation negatively correlated with colony vigor as measured using the subjective colony strength method. Logistic regression identified varroa and DWV as the main factors involved in colony weakening. Our results confirm that varroa and DWV play a key role in triggering colony weakening in southern Spain and provide evidence that experienced beekeepers’ and technicians’ assessments of colony vigor can accurately estimate colony strength.

Deformed Wing Virus in Honeybees and Other Insects

Deformed wing virus (DWV) has become the most well-known, widespread, and intensively studied insect pathogen in the world. Although DWV was previously present in honeybee populations, the arrival and global spread of a new vector, the ectoparasitic mite Varroa destructor, has dramatically altered DWV epidemiology. DWV is now the most prevalent virus in honeybees, with a minimum average of 55% of colonies/apiaries infected across 32 countries. Additionally, DWV has been detected in 65 arthropod species spanning eight insect orders and three orders of Arachnida. Here, we describe the significant progress that has been made in elucidating the capsid structure of the virus, understanding its ever-expanding host range, and tracking the constantly evolving DWV genome and formation of recombinants. The construction of molecular clones, working with DWV in cell lines, and the development of immunohistochemistry methods will all help the community to move forward. Identifying the tissues in which DWV variants are replicating and understanding the impact of DWV in non-honeybee hosts are major new goals.

The levels of natural Nosema spp. infection in Apis mellifera iberiensis brood stages

Nosema ceranae is the most prevalent endoparasite of Apis mellifera iberiensis and it is a major health problem for bees worldwide. The infective capacity of N. ceranae has been demonstrated experimentally in honey bee brood, however no data are available about its prevalence in brood under natural conditions. Thus, brood combs from 10 different hives were analyzed over two consecutive years, taking samples before and after winter. A total of 1433 larvae/pupae were analyzed individually and N. ceranae (3.53%) was the microsporidian most frequently detected, as opposed to Nosema apis (0.42%) which was more frequently detected in conjunction with N. ceranae (0.71%). The active multiplication of both microsporidians was confirmed by the expression (real-time-PCR) of the N. ceranae polar tube protein 3 gene and/or the N. apis RNA polymerase II gene in 24% of the brood samples positive for Nosema spp. Both genes are related to microsporidian multiplication. As such, N. ceranae multiplication was confirmed in 1.06% of the samples, while N. apis multiplication was only observed in co-infections with N. ceranae (0.07%). Brood cells were analyzed for the presence of Nosema spp., as those are the immediate environment where the brood stages develop. The brood samples infected by Nosema spp. were in brood cells in which that microsporidians were not detected, while brood cells positive for N. ceranae hosted brood stages that were not apparently infected, indicating that this is unlikely to be the main pathway of infection. Finally, the colonies with brood infected by N. ceranae showed higher levels (numbers) of infected adult bees, although the differences were not significant before (P = 0.260), during (P = 0.055) or after (P = 0.056) brood sampling. These results show that N. ceranae is a bee parasite ubiquitous to all members of the colony, irrespective of the age of the bee. It is also of veterinary interest and should be considered when studying the epidemiology of the disease.

Gene Disruption of Honey Bee Trypanosomatid Parasite, Lotmaria passim, by CRISPR/Cas9 System

Two trypanosomatid species, Lotmaria passim and Crithidia mellificae, have been shown to parasitize honey bees to date. L. passim appears to be more prevalent than C. mellificae and specifically infects the honey bee hindgut. Although the genomic DNA has been sequenced, the effects of infection on honey bee health and colony are poorly understood. To identify the genes that are important for infecting honey bees and to understand their functions, we applied the CRISPR/Cas9 system to establish a method to manipulate L. passim genes. By electroporation of plasmid DNA and subsequent selection by drug, we first established an L. passim clone expressing tdTomato or Cas9. We also successfully disrupted the endogenous miltefosine transporter and tyrosine aminotransferase genes by replacement with drug (hygromycin) resistant gene using the CRISPR/Cas9-induced homology-directed repair pathway. The L. passim clone expressing fluorescent marker, as well as the simple method for editing specific genes, could become useful approaches to understand the underlying mechanisms of honey bee-trypanosomatid parasite interactions.

Detection of two Microsporidia pathogens of the European honey bee Apis Mellifera (Insecta: Apidae) in Western Siberia

Two species of microsporidia, Nosema apis and Nosema ceranae, occur regularly and cause significant losses in apiculture throughout the world. N. ceranae is thought to be an emerging pathogen of the European honey bee which is replacing N. apis. Microscopic analysis of honey bees collected in Tyumen region, South-Western Siberia, suggested presence of two microsporidial pathogens slightly differing in spore size and shape. PCR detection using species-specific primer sets 312APIS and 218MITOC followed by PCR product sequencing confirmed the diagnosis of N. apis and N. ceranae, respectively. Microsporidia were present in private apiaries through 2008-2010, and among 21 colonies from 7 localities, two colonies were infected with both pathogens, while infections with N. apis only were detected in 8, and with N. ceranae only in 13 colonies. These data suggest that N. ceranae is widely spread in South-Western Siberia alongside with N. apis and is able to persist in the regions with average January temperatures below -18°C.

Detection of Lotmaria passim in Africanized and European honey bees from Uruguay, Argentina and Chile

Trypanosomatids affecting honey bees, Crithidia mellificae and Lotmaria passim, have been poorly studied in South America. We therefore analyzed their presence in Africanized and European honeybees from Uruguay, Argentina and Chile collected between 1990 and 2011 and assessed their association with other bee parasites and pathogens. Crithidia mellificae was not detected while L. passim was wide-spread. This report shows that L. passim has been present in this region at least since 2007 and it infects both Africanized and European honey bees. L. passim infected colonies showed high V. destructor parasitization levels, suggesting an association between them.

Recently identified bee viruses and their impact on bee pollinators

Bees are agriculturally and ecologically important plant pollinators. Recent high annual losses of honey bee colonies, and reduced populations of native and wild bees in some geographic locations, may impact the availability of affordable food crops and the diversity and abundance of native and wild plant species. Multiple factors including viral infections affect pollinator health. The majority of well-characterized bee viruses are picorna-like RNA viruses, which may be maintained as covert infections or cause symptomatic infections or death. Next generation sequencing technologies have been utilized to identify additional bee-infecting viruses including the Lake Sinai viruses and Rhabdoviruses. In addition, sequence data is instrumental for defining specific viral strains and characterizing associated pathogenicity, such as the recent characterization of Deformed wing virus master variants (DWV-A, DWV-B, and DWV-C) and their impact on bee health.

Honey bee (Apis mellifera) colony health and pathogen composition in migratory beekeeping operations involved in California almond pollination

Honey bees are important pollinators of agricultural crops. Pathogens and other factors have been implicated in high annual losses of honey bee colonies in North America and some European countries. To further investigate the relationship between multiple factors, including pathogen prevalence and abundance and colony health, we monitored commercially managed migratory honey bee colonies involved in California almond pollination in 2014. At each sampling event, honey bee colony health was assessed, using colony population size as a proxy for health, and the prevalence and abundance of seven honey bee pathogens was evaluated using PCR and quantitative PCR, respectively. In this sample cohort, pathogen prevalence and abundance did not correlate with colony health, but did correlate with the date of sampling. In general, pathogen prevalence (i.e., the number of specific pathogens harbored within a colony) was lower early in the year (January-March) and was greater in the summer, with peak prevalence occurring in June. Pathogen abundance in individual honey bee colonies varied throughout the year and was strongly associated with the sampling date, and was influenced by beekeeping operation, colony health, and mite infestation level. Together, data from this and other observational cohort studies that monitor individual honey bee colonies and precisely account for sampling date (i.e., day of year) will lead to a better understanding of the influence of pathogens on colony mortality and the effects of other factors on these associations.

Long-Term Temporal Trends of Nosema spp. Infection Prevalence in Northeast Germany: Continuous Spread of Nosema ceranae, an Emerging Pathogen of Honey Bees (Apis mellifera), but No General Replacement of Nosema apis

The Western honey bee (Apis mellifera) is widely used as commercial pollinator in worldwide agriculture and, therefore, plays an important role in global food security. Among the parasites and pathogens threatening health and survival of honey bees are two species of microsporidia, Nosema apis and Nosema ceranae. Nosema ceranae is considered an emerging pathogen of the Western honey bee. Reports on the spread of N. ceranae suggested that this presumably highly virulent species is replacing its more benign congener N. apis in the global A. mellifera population. We here present a 12 year longitudinal cohort study on the prevalence of N. apis and N. ceranae in Northeast Germany. Between 2005 and 2016, a cohort of about 230 honey bee colonies originating from 23 apiaries was sampled twice a year (spring and autumn) resulting in a total of 5,600 bee samples which were subjected to microscopic and molecular analysis for determining the presence of infections with N. apis or/and N. ceranae. Throughout the entire study period, both N. apis- and N. ceranae-infections could be diagnosed within the cohort. Logistic regression analysis of the prevalence data demonstrated a significant increase of N. ceranae-infections over the last 12 years, both in autumn (reflecting the development during the summer) and in spring (reflecting the development over winter) samples. Cell culture experiments confirmed that N. ceranae has a higher proliferative potential than N. apis at 27° and 33°C potentially explaining the increase in N. ceranae prevalence during summer. In autumn, characterized by generally low infection prevalence, this increase was accompanied by a significant decrease in N. apis-infection prevalence. In contrast, in spring, the season with a higher prevalence of infection, no significant decrease of N. apis infections despite a significant increase in N. ceranae infections could be observed. Therefore, our data do not support a general advantage of N. ceranae over N. apis and an overall replacement of N. apis by N. ceranae in the studied honey bee population.

Approaches and Challenges to Managing Nosema (Microspora: Nosematidae) Parasites in Honey Bee (Hymenoptera: Apidae) Colonies

The microsporidia Nosema apis (Zander) and Nosema ceranae (Fries) are common intestinal parasites in honey bee (Apis mellifera L.) colonies. Though globally prevalent, there are mixed reports of Nosema infection costs, with some regions reporting high parasite virulence and colony losses, while others

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high Nosema prevalence but few costs. Basic and applied studies are urgently needed to help beekeepers effectively manage Nosema spp., ideally through an integrated pest management approach that allows beekeepers to deploy multiple strategies to control Nosema when Nosema is likely to cause damage to the colonies, rather than using prophylactic treatments. Beekeepers need practical and affordable technologies that facilitate disease diagnosis and science-backed guidelines that recommend when, if at all, to treat infections. In addition, new treatment methods are needed, as there are several problems associated with the chemical use of fumagillin (the only currently extensively studied, but not globally available treatment) to control Nosema parasites. Though selective breeding of Nosema-resistant or tolerant bees may offer a long-term, sustainable solution to Nosema management, other treatments are needed in the interim. Furthermore, the validation of alternative treatment efficacy in field settings is needed along with toxicology assays to ensure that treatments do not have unintended, adverse effects on honey bees or humans. Finally, given variation in Nosema virulence, development of regional management guidelines, rather than universal guidelines, may provide optimal and cost-effective Nosema management, though more research is needed before regional plans can be developed.

Differential diagnosis of the honey bee trypanosomatids Crithidia mellificae and Lotmaria passim

Trypanosomatids infecting honey bees have been poorly studied with molecular methods until recently. After the description of Crithidia mellificae (Langridge and McGhee, 1967) it took about forty years until molecular data for honey bee trypanosomatids became available and were used to identify and describe a new trypanosomatid species from honey bees, Lotmaria passim (Evans and Schwarz, 2014). However, an easy method to distinguish them without sequencing is not yet available. Research on the related bumble bee parasites Crithidia bombi and Crithidia expoeki revealed a fragment length polymorphism in the internal transcribed spacer 1 (ITS1), which enabled species discrimination. In search of fragment length polymorphisms for differential diagnostics in honey bee trypanosomatids, we studied honey bee trypanosomatid cell cultures of C. mellificae and L. passim. This research resulted in the identification of fragment length polymorphisms in ITS1 and ITS1-2 markers, which enabled us to develop a diagnostic method to differentiate both honey bee trypanosomatid species without the need for sequencing. However, the amplification success of the ITS1 marker depends probably on the trypanosomatid infection level. Further investigation confirmed that L. passim is the dominant species in Belgium, Japan and Switzerland. We found C. mellificae only rarely in Belgian honey bee samples, but not in honey bee samples from other countries. C. mellificae was also detected in mason bees (Osmia bicornis and Osmia cornuta) besides in honey bees. Further, the characterization and comparison of additional markers from L. passim strain SF (published as C. mellificae strain SF) and a Belgian honey bee sample revealed very low divergence in the 18S rRNA, ITS1-2, 28S rRNA and cytochrome b sequences. Nevertheless, a variable stretch was observed in the gp63 virulence factor.

Genome analyses suggest the presence of polyploidy and recent human-driven expansions in eight global populations of the honeybee pathogen Nosema ceranae

Nosema ceranae is a microsporidian pathogen whose infections have been associated with recent global declines in the populations of western honeybees (Apis mellifera). Despite the outstanding economic and ecological threat that N. ceranae may represent for honeybees worldwide, many aspects of its biology, including its mode of reproduction, propagation and ploidy, are either very unclear or unknown. In the present study, we set to gain knowledge in these biological aspects by re-sequencing the genome of eight isolates (i.e. a population of spores isolated from one single beehive) of this species harvested from eight geographically distant beehives, and by investigating their level of polymorphism. Consistent with previous analyses performed using single gene sequences, our analyses uncovered the presence of very high genetic diversity within each isolate, but also very little hive-specific polymorphism. Surprisingly, the nature, location and distribution of this genetic variation suggest that beehives around the globe are infected by a population of N. ceranae cells that may be polyploid (4n or more), and possibly clonal. Lastly, phylogenetic analyses based on genome-wide single-nucleotide polymorphism data extracted from these parasites and mitochondrial sequences from their hosts all failed to support the current geographical structure of our isolates.

Microsporidia-host interactions

Microsporidia comprise one of the largest groups of obligate intracellular pathogens and can infect virtually all animals, but host response to these fungal-related microbes has been poorly understood. Several new studies of the host transcriptional response to microsporidia infection have found infection-induced regulation of genes involved in innate immunity, ubiquitylation, metabolism, and hormonal signaling. In addition, microsporidia have recently been shown to exploit host recycling endocytosis for exit from intestinal cells, and to interact with host degradation pathways. Microsporidia infection has also been shown to profoundly affect behavior in insect hosts. Altogether, these and other recent findings are providing much-needed insight into the underlying mechanisms of microsporidia interaction with host animals.

Recent worldwide expansion of Nosema ceranae (Microsporidia) in Apis mellifera populations inferred from multilocus patterns of genetic variation

Nosema ceranae has been found infecting Apismellifera colonies with increasing frequency and it now represents a major threat to the health and long-term survival of these honeybees worldwide. However, so far little is known about the population genetics of this parasite. Here, we describe the patterns of genetic variation at three genomic loci in a collection of isolates from all over the world. Our main findings are: (i) the levels of genetic polymorphism (πS≈1%) do not vary significantly across its distribution range, (ii) there is substantial evidence for recombination among haplotypes, (iii) the best part of the observed genetic variance corresponds to differences within bee colonies (up to 88% of the total variance), (iv) parasites collected from Asian honeybees (Apis cerana and Apis florea) display significant differentiation from those obtained from Apismellifera (8-16% of the total variance, p<0.01) and (v) there is a significant excess of low frequency variants over neutral expectations among samples obtained from A. mellifera, but not from Asian honeybees. Overall these results are consistent with a recent colonization and rapid expansion of N. ceranae throughout A. mellifera colonies.