Biology subjects

Prus-Frankowska, M.

Publications and source records attributed to Prus-Frankowska, M..

7 recordsLinked to original sources

bioRxiv2024

Cold and lonely: low-abundance microbiota and no core microbiome across a broad geographic sampling of a mosquito species in Greenland

Microbial symbionts are key players in insect ecology and evolution, but microbiota vary widely across and within host species. The microbiota of insect clades such as high-latitude mosquitoes remain understudied, despite their abundance and potential economic and medical relevance. Here, we resolve temporal and spatial variation in the abundance and diversity of bacteria and fungi associated with Ochlerotatus mosquitoes in Greenland. To this aim, we apply a comprehensive workflow combining the simultaneous characterization of host, bacterial, and fungal marker regions, contamination filtering, as well as bacterial quantification and joint species distribution modelling. We find that 573 mosquitoes collected in five regions of Greenland between 2009 and 2024 represented two species (O. nigripes and O. impiger). Their microbial communities were low-abundance, highly diverse, and dominated by environmentally versatile taxa, showing high individual-to-individual-rather than spatio-temporal variation, although taxa such as Pseudomonas and Serratia exhibited sex-specific associations. DNA from local vertebrates and potential vertebrate pathogens (e.g., Bartonella) was detected, likely reflecting blood meals. These findings suggest that Greenland Ochlerotatus mosquitoes do not rely on core microbiota, but engage in flexible associations with diverse, low-abundance microbial communities. They also point to mosquitoes as likely vectors of bacterial and fungal pathogens in the Arctic.

ecology↗

bioRxiv2024

What lurks beneath the humped back? - The patterns of bacterial abundance, diversity and distribution across communities of a dipteran family

Symbiotic microorganisms can profoundly impact insects, their life history traits, population dynamics, and evolutionary trajectories. However, microbiota remain poorly understood in natural insect communities, especially in dark taxa - i.e., hyperdiverse, yet understudied clades. Here, we implemented a novel multi-target amplicon sequencing approach to study microbiota in complex, species-rich communities. It combines four methodological innovations: (1) To establish a host taxonomic framework, we sequenced amplicons of the host marker gene (COI) and reconstructed barcodes alongside microbiota characterisation. (2) To assess microbiota abundance, we incorporated spike-in-based quantification. (3) To improve the phylogenetic resolution for the dominant endosymbiont, Wolbachia, we analysed bycatch data from the COI amplicon sequencing. (4) To investigate the primary drivers of host-microbe associations in massive multi-dimensional datasets, we performed HMSC modelling. Applying this approach to 1,842 wild-caught scuttle flies (Diptera: Phoridae) from northern Sweden, we organised them into 480 genotypes and 186 species and gained unprecedented insights into their microbiota. We found orders-of-magnitude differences in bacterial abundance and massive within-population variation in microbiota composition. Patterns and drivers differed among microbial functional categories: the distribution and abundance of facultative endosymbionts (Wolbachia, Rickettsia, Spiroplasma) were shaped by host species, genotype and sex. In contrast, many other bacterial taxa were broadly distributed across species and sites. This study highlights facultative endosymbionts as key players in insect microbiota and reveals striking variations in distributional patterns of microbial clades. It also demonstrates the power of integrative sequencing approaches in uncovering the ecological complexity and significance of symbiotic microorganisms in multi-species natural communities.

ecology↗

bioRxiv2024

A new tool in a toolbox: Addressing challenges in high-throughput microbiota surveys across diverse wild insects

With their significant effects on the biology of higher organisms, host-associated microbiota has attracted the research communitys attention. The rapid progress in sequencing techniques has greatly facilitated microbial community characterization. However, the most popular surveying technique, marker gene amplicon sequencing, has multiple caveats that are not often addressed satisfactorily, including the uncertainty about the identity of the surveyed wild-caught specimens, variable and sometimes very low abundance of microbes in some samples, or reagent- and cross-contamination. As a result, researchers often obtain incomplete, biased, and sometimes totally incorrect microbial community profiles. Here, we present a versatile, cost-effective, and high-throughput quantitative multi-target amplicon sequencing workflow for the characterization of host-associated microbial communities, combining laboratory and bioinformatic steps and addressing most of the known methodological issues. Optimized for the study of the microbiota of wild insects, it can be easily adapted for other sample types. Outputs include contamination-controlled data on the absolute abundance and identity of microbes present in insect samples, both at genotype- and OTU-level, as well as host barcodes alongside information on parasite infections. Using 1384 samples from Zackenberg Valley, NE Greenland, we demonstrate the potential of the workflow to study insect and symbiont diversity patterns across a large portion of a diverse natural community.

ecology↗

bioRxiv2024

Phylogenomics resolves the relationship and the evolutionary history of planthoppers (Insecta: Hemiptera: Fulgoromorpha)

Planthoppers (Hemiptera: Fulgoromorpha) are a species-rich and globally distributed insect clade with high economic, ecological, and evolutionary importance. However, the relationships among planthopper lineages and families remain unclear. Previous efforts based on inconsistent morphological traits, a few genes, or limited sampling often resulted in conflicting tree topologies. Here, we used genome-level data to assemble 1164 nuclear single-copy genes and 13 mitochondrial protein-coding genes for 149 planthopper species representing 19 out of 21 extant families. Additional markers were added from published mitogenomes, expanding our sampling to 285 species. These markers were used for Maximum Likelihood-based tree inference and dating analyses. The newly inferred phylogenies validated well-accepted relationships and recovered novel placements. Taxonomic conclusions include the establishment of a new family Borysthenidae stat. rev. within Delphacoidea and a new superfamily Meenoploidea superfam. nov. including redefined Kinnaridae stat. rev. and Meenoplidae stat. rev., the confirmation of the monophyletic family Achilixiidae outside the Achilidae-Derbidae clade, and the transfer of tribes Lyncidini and Amyclini to Dictyopharidae and the genus Madagascaritia to Fulgoridae. The time analyses based on 57 nuclear markers and 30 fossils dated the origin of crown Fulgoromorpha back to Guadalupian, Permian ([~]263 Ma), close to the maximum constraint at 267.3 Ma, while applying an older root constraint resulted in an origin in Mississippian, Carboniferous ([~]332 Ma). While future sampling of unstudied fauna in unexplored regions or habitats may change the topology, the current phylogenomic analysis will serve as a solid foundation for research into planthopper ecology, evolution, and significance.

evolutionary biology↗

bioRxiv2024

Limited variation in microbial communities across populations of Macrosteles leafhoppers (Hemiptera: Cicadellidae)

Microbial symbionts play important roles in insect biology, but their diversity, distribution, and dynamics over time across host populations are poorly understood. We surveyed the spatio-temporal distribution of bacterial symbionts in the broadly distributed and economically significant leafhopper genus Macrosteles, with emphasis on Macrosteles laevis, using host and symbiont marker gene amplicon sequencing. The cytochrome oxidase I (COI) gene data revealed no strong genetic differentiation across M. laevis populations, significant levels of heteroplasmy, and multiple cases of parasitoid infections. 16S rRNA data confirmed the universal presence of the ancient nutritional endosymbionts Sulcia and Nasuia and a high prevalence of Arsenophonus. Interestingly, in contrast to most previously surveyed species, in M. laevis we found only occasional cases of infection with facultative endosymbionts and other bacteria. There was no significant variation in symbiont prevalence across populations, or among sampling years for the same population. Facultative endosymbionts including Rickettsia, Wolbachia, Cardinium, and Lariskella, were more common in other Macrosteles species. Combined, our data demonstrate that not all species show clear spatial and temporal variation in genetic structure and microbial prevalence. However, simultaneous characterization of host and symbiont marker gene amplicons in large insect collections can help understand the dynamics of host-microbe interactions.

evolutionary biology↗

bioRxiv2024

Pinpointing the microbiota of tardigrades: what is really there?

Microbiota have been proposed as an important aspect of tardigrade biology, but little is known about their diversity and distribution. Here, we attempted to characterize the microbiota of 44 cultured species of tardigrades using 16S rRNA amplicon sequencing, using different specimen pooling strategies, various DNA extraction kits, and multiple types of controls. We also estimated the number of microbes in samples using synthetic DNA spike-ins. Additionally, we reanalyzed data from previous studies. Our results suggest that the microbial community profiles of cultured tardigrades are dominated by bacterial OTUs and genotypes originating from food, medium, or laboratory reagents. We found microbial strains consistently enriched in certain tardigrades (relative to the culture media and controls), which indicates likely symbiotic associations, but the reads representing putative true tardigrade-associated microbes rarely exceeded 20% of the datasets. Some of the identified tardigrade-associated microbes matched symbionts identified by other studies. However, we also identified serious contamination issues with previous studies of tardigrade microbiome, making some of their conclusions questionable. We conclude that tardigrades are not universally dependent on specialized microbes and highlight the necessary safeguards in future studies of the microbiota of microscopic organisms.

microbiology↗

bioRxiv2022

Genome comparison reveals inversions and alternative evolutionary history of nutritional endosymbionts in planthoppers (Hemiptera: Fulgoromorpha)

The evolutionary success of sap-feeding hemipteran insects in the suborder Auchenorrhyncha was enabled by nutritional contributions from their heritable endosymbiotic bacteria. However, the symbiont diversity, functions, and evolutionary origins in this large insect group have not been broadly characterized using genomic tools. In particular, the origins and relationships among ancient betaproteobacterial symbionts Vidania (in Fulgoromorpha) and Nasuia/Zinderia (in Cicadomorpha) are uncertain. Here, we characterized the genomes of Vidania and Sulcia from three Pyrops planthoppers (family Fulgoridae) to understand their metabolic functions and evolutionary histories. Like in previously characterized planthoppers, these symbionts share nutritional responsibilities, with Vidania providing seven out of ten essential amino acids. Sulcia lineages across the Auchenorrhyncha have a highly conserved genome but with multiple independent rearrangements occurring in an early ancestor of Cicadomorpha or Fulgoromorpha and in a few succeeding lineages. Genomic synteny was also observed within each of the betaproteobacterial symbiont genera Nasuia, Zinderia, and Vidania, but not across them, which challenges the expectation of a shared ancestry for these symbionts. The further comparison of other biological traits strongly suggests an independent origin of Vidania early in the planthopper evolution and possibly of Nasuia and Zinderia in their respective host lineages. Originality-Significance StatementWe sequenced and characterized the genomes of two ancient nutritional symbionts, Sulcia and Vidania, in three species from the genus Pyrops in the species- and symbiont-rich but understudied insect clade, Fulgoromorpha (planthoppers). We describe--for the first time--several independent genome rearrangements in Sulcia, which is often cited as a premier example of extreme genome stability spanning hundreds of millions of years. We also show a global lack of synteny across the genomes of the Auchenorrhynchan betaproteobacterial symbionts (Vidania, Nasuia, and Zinderia). This result is unexpected given previous hypotheses of a common origin for these symbionts >250 million years ago alongside Sulcia. Taken together, we suggest an independent origin of Vidania and possibly of Nasuia and Zinderia symbiont lineages as well. This hypothesis further links the potential acquisition of novel nutritional endosymbiont lineages with the emergence of auchenorrhyncham superfamilies.

genomics↗