Plant biodiversity assessment through soil eDNA reflects temporal and local diversity

1. Several studies have shown the potential of eDNA-based proxies for plant identification, but little is known about their spatial and temporal resolution. This limits its use for plant biodiversity assessments and monitoring of vegetation responses to environmental changes. Here we calibrate the temporal and spatial plant signals detected with soil eDNA surveys by comparing with a standard visual above-ground vegetation survey. 2. Our approach compares vegetation in an old-growth boreal forest in southern Norway, surveyed in 100 permanent 1-m2 plots seven times over a 30-year period, with a single soil eDNA metabarcoding-based survey from soil samples collected at the same 100 plots in the year of the last vegetation survey. 3. On average, 60% and 10% of the vascular plants and bryophytes recorded across all vegetation surveys were detected by soil eDNA. Taxa detected by soil eDNA were more representative for the local taxa pool than for the specific plot, and corresponded to those surveyed over the 30-year period although most closely matched the current taxa composition. Soil eDNA detected abundant taxa better than rare ones although both rare taxa and taxa unrecorded by the visual survey were detected. 4. Our study highlights the potential of soil eDNA assessments for monitoring of vegetation responses over broad spatial and temporal scales. The method's ability to detect abundant taxa makes it suitable for assessment of vegetation composition in a specific area and for broad-scale plant diversity assessments

The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

Behavioural and social immunity in a eusocial insect, the bumblebee Bombus terrestris

Die Abwehrmechanismen der Hummeln gegen Parasiten sind gut untersucht, vor allem ihr Immunsystem. Allerdings ist wenig über ihre verhaltensbezogene Immunität bekannt. Einer der häufigsten und spezifischen Hummelsparasiten ist Crithidia bombi, ein Trypanosomatide, welcher den Hummeldarm infiziert. C. bombi reduziert die Fitness der Hummelkolonien. Seine Transmission wird durch die gemeinsame Nutzung vorhandener Blüten durch mehrere Hummeln begünstigt. Daher habe ich das Futtersuchverhalten der Hummeln von C. bombi-belasteten und -unbelasteten künstlichen Blüten erforscht. Hummeln zeigen die Fähigkeit, kontaminierte Blüten zu erkennen und zu vermeiden. Diese Leistung wird verstärkt, wenn die Blüten anstatt mit C. bombi mit einem allgemeinen Erreger (Escherichia coli) kontaminiert waren. Diese Leistung wurde zudem im Laufe der Zeit verstärkt, welches auf einen Lernprozess der Hummeln schließen lässt. Dieses Lernen scheint durch den Einsatz sozialer Signale vermittelt zu werden. Bienen können Duftmarken auf Blüten, zurückgelassen von Artgenossen, und visuelle Hinweise (Anwesenheit von Artgenossen auf Blüten) wahrnehmen, die sie bei der Nahrungssuche an Blüten unterstützen. In diesem Fall werden die Duftmarken der Artgenossen nicht von den Sammlerinnen verwendet. Sie verlassen sich auf den Geruch, der durch die Interaktion von C. bombi Zellen mit dem Blütennektar zustande kommt. Dennoch wirken die visuellen Hinweisen als stimulierende Verstärkung für naive Sammlerinnen, wodurch der Lernprozess auf Kolonie-Ebene erklärt werden könnte. Zudem verglich ich auch zwei molekulare Methoden, um C. bombi Infektionsraten in Hummeln zu messen. Beide Methoden sind zuverlässig und erlauben eine schnelle und effiziente Abschätzung von C. bombi Infektionsraten in Hummeln.The defence mechanisms of bumblebees against parasites has been well studied, mainly their immune system. However, little is known about their behavioural immunity. One of the most common and specific parasites of bumblebees is Crithidia bombi, a trypanosome infecting bumblebee guts. C. bombi reduces the fitness of bumblebee colonies and is transmitted through the shared use of flowers. Therefore, I investigated the foraging behaviour of bees facing contaminated and uncontaminated flowers. Bumblebees showed the ability to recognise and avoid contaminated flowers. They perform better when the flowers are contaminated by C. bombi rather than contaminated by a common pathogen (Escherichia coli). They also perform better over time, showing a learning process. This learning appears to be mediated through the use of social cues. Bees can use scent-marks deposited on flowers by conspecifics and visual cues (presence of conspecifics on flowers) to help them foraging on flowers. In this case, the scent-marks are not used by foraging bees; they rely on the odour produced by the interaction of C. bombi cells with the flower nectar. Nevertheless, the visual cues act as a local/stimulus enhancement for naïve foraging bees, which can explain the learning process at a colony level. I also compared two molecular methods to measure C. bombi infection rates in bumblebees. Both methods are reliable and allow a rapid and efficient assessment of C. bombi infection rates in bees.von Bertrand Joseph Jean-Baptiste Fouk

Data for: The presence of a larval honey bee parasite, Ascosphaera apis, on flowers reduces pollinator visitation to several plant species

Observations of pollinator visits between Ascosphaera apis spores-sprayed (CH) and water-sprayed (WA) flowers. Visits are categorized as Apporaches (VWL), Landings (V) and Feedings (F)

Recognition and Avoidance of Contaminated Flowers by Foraging Bumblebees (Bombus terrestris)

Bumblebee colonies are founded by a single-mated queen. Due to this life history trait, bumblebees are more susceptible to parasites and diseases than polyandrous and/or polygynous social insects. A greater resistance towards parasites is shown when the genetic variability within a colony is increased. The parasite resistance may be divided into different levels regarding the step of the parasite infection (e.g. parasite uptake, parasite intake, parasite's establishment in the nest, parasite transmission).We investigate the prophylactic behaviour of bumblebees. Bumblebees were observed during their foraging flights on two artificial flowers; one of these was contaminated by Crithidia bombi, a naturally occurring gut parasite of bumblebees (in a control experiment the non-specific pathogen Escherichia coli was used). For C. bombi, bumblebees were preferentially observed feeding on the non-contaminated flower. Whereas for E. coli, the number of visits between flowers was the same, bumblebees spent more time feeding on the non-contaminated flower.These results demonstrate the ability of bumblebees to recognise the contamination of food sources. In addition, bumblebees have a stronger preference for the non-contaminated flower when C. bombi is present in the other flower than with E. coli which might be explained as an adaptive behaviour of bumblebees towards this specific gut parasite. It seems that the more specific the parasite is, the more it reduces the reward of the flower

DNA Transposons Favor De Novo Transcript Emergence Through Enrichment of Transcription Factor Binding Motifs

The files containing processed data is available in the Zenodo archive https://doi.org/10.5281/zenodo.8403184, and is referred in the main text as "Supplemental Deposit". Supplemental figures, information, analyses and models are found in the Supplementary Information (SI). All programs are stored on GitHub (https://github.com/MarieLebh). The position frequency matices (PFM) of the studied motifs can be downloaded from https://jaspar2020.genereg.net/collection/POLII/ (Pol II database for core motifs) and https://jaspar2022.genereg.net/downloads/ (tFBS motifs, download the insect core non redundant database).International audienceAbstract: De novo genes emerge from noncoding regions of genomes via succession of mutations. Among others, such mutations activate transcription and create a new open reading frame (ORF). Although the mechanisms underlying ORF emergence are well documented, relatively little is known about the mechanisms enabling new transcription events. Yet, in many species a continuum between absent and very prominent transcription has been reported for essentially all regions of the genome. In this study, we searched for de novo transcripts by using newly assembled genomes and transcriptomes of seven inbred lines of Drosophila melanogaster, originating from six European and one African population. This setup allowed us to detect sample specific de novo transcripts, and compare them to their homologous nontranscribed regions in other samples, as well as genic and intergenic control sequences. We studied the association with transposable elements (TEs) and the enrichment of transcription factor motifs upstream of de novo emerged transcripts and compared them with regulatory elements. We found that de novo transcripts overlap with TEs more often than expected by chance. The emergence of new transcripts correlates with regions of high guanine-cytosine content and TE expression. Moreover, upstream regions of de novo transcripts are highly enriched with regulatory motifs. Such motifs are more enriched in new transcripts overlapping with TEs, particularly DNA TEs, and are more conserved upstream de novo transcripts than upstream their ‘nontranscribed homologs’. Overall, our study demonstrates that TE insertion is important for transcript emergence, partly by introducing new regulatory motifs from DNA TE families.Graphical Abstract: https://academic.oup.com/view-large/figure/476385418/evae134_ga.jpgSignificance: In the present study, we used inbred lines of Drosophila melanogaster to detect earlier stages of de novo emerged transcripts in samples. We determined and studied the impact of transposable elements (TEs) and TFBS motifs on the emergence of de novo transcripts. We show that the insertion of DNA transposons plays a role in de novo transcripts emergence. We demonstrate enrichment of transcription factor binding motif (motifs whose identity to a reference motif is low) upstream de novo transcripts compared to regions upstream annotated genes and control non transcribed intergenic sequences.This enrichment is even more frequent upstream de novo transcripts overlapping with DNA TEs. Our findings help elucidate main molecular drivers of transcription gain, namely insertions of DNA TEs and enrichment in transcription factor motifs with lower similarity to the reference