Biology subjects

Hagenbeek, A.

Publications and source records attributed to Hagenbeek, A..

6 recordsLinked to original sources

bioRxiv2025

Genomic diversity and functional potential of facultative bacterial symbionts across scale insects

Microbial symbionts play pivotal roles in the physiology, ecology, and evolution of insects. While obligate symbionts have been extensively characterized in insects feeding on nutritionally poor diets, the diversity and functional roles of facultative bacterial symbionts remain largely unexplored in many insect lineages, including scale insects (Hemiptera: Coccomorpha). Here, we present a genome-resolved metagenomic and comparative genomic analysis of facultative bacterial symbionts across 120 scale insect metagenomes from 20 different families. Our analyses reveal rich and taxonomically diverse facultative symbiont communities, dominated by the Pseudomonadota, such as Wolbachia, Rickettsia, Arsenophonus, and Sodalis. Genomic features reveal substantial variation in genome sizes, coding densities, metabolic potentials, and hostinteraction genes among symbiont clades, indicating lineage-specific lifestyles and host interactions. Interestingly, alphaproteobacterial and gammaproteobacterial symbionts mostly co-occur within their respective hosts. Gammaproteobacterial symbionts exhibit broader metabolic repertoires and potential defense capabilities via the APSE phage toxin cassettes, while alphaproteobacterial symbionts retain reduced metabolic capabilities, Type IV secretion systems, and reproductive manipulation genes (cifAB and wmk). We propose how the symbiont genes related to nutritional provisioning, defensive symbiosis, and reproductive manipulation may influence the biology and evolution of scale insects. Our results provide the first comprehensive genomic overview of facultative bacterial symbionts in scale insects, revealing their evolutionary dynamics and putative functions.

genomics↗

bioRxiv2025

Non-photosynthetic Plastid Replacement by a Primary Plastid in the Making

The integration of a cyanobacterium into a heterotrophic eukaryote gave rise to the primary plastid [~]1.5 Gya. This rare cyanobacterium-to-plastid transition has only been reported once more in Paulinella chromatophora [~]100 Mya. Unfortunately, the order and relative importance of organellogenesis events have been blurred by time in primary plastids and obscured by P. chromatophora becoming phototrophic. Here, we characterize the tripartite symbiosis in a benthic dinoflagellate (Sinophysis sp.) using diverse single-cell methods. Sinophysis houses a photosynthetic cyanobacterium closely interacting with an alphaproteobacterial endosymbiont. The cyanobacterium is in the intermediate stage of symbiont-to-organelle transition, with the host likely supporting it with metabolites and proteins, and controlling its cell division. Surprisingly, it seems to have replaced the hosts remnant non-photosynthetic plastid. Our results support mixotrophy, horizontal gene transfer, co-symbioses, and cell division control as early drivers of primary plastid origin and highlight the importance of protists for deciphering organellogenesis events.

evolutionary biology↗

bioRxiv2025

A Midichloriaceae endosymbiont of terrestrial arthropods found as an endosymbiont in a marine nematode

The obligate endosymbiont Candidatus Lariskella (Alphaproteobacteria, Candidatus Midichloriaceae) has been found across a wide diversity of terrestrial arthropods, including ticks, true bugs, beetles, fleas, wasps and moths. However, to date, Ca. Lariskella had never been detected in nematodes or marine animals. Here we report the first known occurrence of Ca. Lariskella infecting a population of marine nematodes (Enoplida, Thoracostomopsideae). This nematode-infecting Ca. Lariskella is closely related to insect-infecting Ca. Lariskella, despite the drastic shift in both host phylum and habitat. TEM and FISH microscopy showed Ca. Lariskella is localized within both somatic cells and developing oocytes, strongly suggesting that Ca. Lariskella is a vertically transmitted endosymbiont within the nematode population. We found that Ca. Lariskella was present within approximately 20% of the nematode population, but notably failed to detect any Ca. Lariskella within adult males, potentially hinting at reproductive manipulation. Overall, our findings show that Ca. Lariskella is not limited to arthropods or terrestrial hosts, indicating a larger host range than previously described. Its presence within marine nematodes demonstrates the ability of Ca. Lariskella to infect nematode hosts, as well as hosts from marine environments, suggesting terrestrial nematodes, marine arthropods, and perhaps even other marine invertebrates could be potential hosts of Ca. Lariskella.

microbiology↗

bioRxiv2025

Adaptive pangenomic remodeling in the Azolla cyanobiont amid a transient microbiome

Plants fix nitrogen in concert with diverse microbial symbionts, often recruiting them from the surrounding environment each generation. Vertical transmission of a microbial symbiont from parent to offspring can produce extreme evolutionary consequences, including metabolic codependence, genome reduction, and synchronized life cycles. One of the few examples of vertical transmission of N-fixing symbionts occurs in Azolla ferns, which maintain an obligate mutualism with the cyanobacterium Trichormus azollae--but the genomic consequences of this interaction, and whether the symbiosis involves other vertically transmitted microbial partners, are currently unknown. We generated high-coverage metagenomes across the genus Azolla and reconstructed metagenome assembled genomes to investigate whether a core microbiome exists within Azolla leaf cavities, and how the genomes of T. azollae diverged from their free-living relatives. Our results suggest that T. azollae is the only consistent symbiont across all Azolla accessions, and that other bacterial groups are transient or facultative associates. Pangenomic analyses of T. azollae indicate extreme pseudogenization and gene loss compared to free-living relatives--especially in defensive, stress-tolerance, and secondary metabolite pathways--yet the key functions of nitrogen fixation and photosynthesis remain intact. Additionally, differential codon bias and intensified (rather than relaxed) selection on photosynthesis, intracellular transport, and carbohydrate metabolism genes suggest ongoing evolution in response to the unique conditions within Azolla leaf cavities. These findings highlight how genome erosion and shifting selection pressures jointly drive the evolution of this unique mutualism, while broadening the taxonomic scope of genomic studies on vertically transmitted symbioses.

microbiology↗

bioRxiv2021

Antibiotic breakdown by susceptible bacteria enhances the establishment of β-lactam resistant mutants

For a better understanding of the evolution of antibiotic resistance, it is imperative to study the factors that determine the initial establishment of mutant resistance alleles. In addition to the antibiotic concentration, the establishment of resistance alleles may be affected by interactions with the surrounding susceptible cells from which they derive, for instance via the release of nutrients or removal of the antibiotic. Here, we investigate the effects of social interactions with surrounding susceptible cells on the establishment of Escherichia coli mutants with increasing {beta}-lactamase activity (i.e. the capacity to hydrolyze {beta}-lactam antibiotics) from single cells under the exposure of the antibiotic cefotaxime on agar plates. We find that mutant establishment probability is increased in the presence of susceptible cells due to the active breakdown of the antibiotic, but the rate of breakdown by the susceptible strain is much higher than expected based on its low enzymatic activity. A detailed theoretical model suggests that this observation can be explained by cell filamentation causing delayed lysis. While susceptible cells may hamper the spread of higher-resistant {beta}-lactamase mutants at relatively high frequencies, our findings show that they could promote establishment during their emergence.

evolutionary biology↗

bioRxiv2021

Stochastic effects on the establishment of mutants resistant to β-lactam antibiotics

For antibiotic resistance to arise, new resistant mutants must establish in a bacterial population before they can spread via natural selection. Comprehending the stochastic factors that influence mutant establishment is crucial for a quantitative understanding of antibiotic resistance emergence. Here, we quantify the single-cell establishment probability of four Escherichia coli strains expressing {beta}-lactamase alleles with different activity against the antibiotic cefotaxime, as a function of antibiotic concentration in both unstructured (liquid) and structured (agar) environments. We show that concentrations well below the minimum inhibitory concentration (MIC) can substantially hamper establishment, particularly for highly resistant mutants. While the pattern of establishment suppression is comparable in both tested environments, we find greater variability in establishment probability on agar. Using a simple branching model, we investigate possible sources of this stochasticity, including environment-dependent lineage variability. Lastly, we use the single-cell establishment probability to predict each strains MIC in the absence of social interactions. We observe substantially higher measured than predicted MIC values, particularly for highly resistant strains, which indicates cooperative effects among resistant cells at large cell numbers, such as in standard MIC assays.

evolutionary biology↗