Biology subjects

Łukasik, P.

Publications and source records attributed to Łukasik, P..

13 recordsLinked to original sources

bioRxiv2026

Selection for high metabolic rate reduces gut microbiota responsiveness to dietary restriction in bank voles

Host-microbiota interactions are crucial in adapting to environmental changes, such as fluctuating energy availability. Yet, the extent to which hosts and their microbiota exhibit coordinated plasticity in response to transient energy limitation remains unclear. Here, we examined the capacity for parallel reversible plasticity in hosts and gut microbiota to temporary dietary restriction in hosts with differing energy needs. We subjected bank voles (Clethrionomys glareolus) from a long-term artificial selection experiment for high aerobic metabolism (A-lines) and control lines (C-lines) to dietary restriction (food dilution with insoluble fiber) followed by a recovery period. We measured traits relevant for vole energy consumption and fecal microbiota composition at baseline, after dietary restriction, and after recovery. We hypothesized that A-line voles would experience more severe and prolonged physiological effects of dietary restriction than C-line voles, which might be counteracted by higher microbiota responsiveness. Dietary restriction caused a temporary increase in food consumption, decrease in body mass and resting metabolic rate, and significant shifts in gut microbiota composition, all of which returned to near baseline levels during the recovery period. These effects were largely similar for the selection lines, but contrary to our prediction, the effect of dietary restriction on bacterial diversity was stronger in C-lines. This suggests higher resistance of the A-line microbiota to dietary changes, perhaps resulting from increased host control over microbial communities due to the directional selection for high metabolic capacity. Overall, our findings highlight a substantial capacity for reversible plasticity in host physiology and gut microbiota in fluctuating environments.

evolutionary biology↗

bioRxiv2026

Insect COI barcoding data as an untapped resource for surveying Wolbachia symbioses

O_LIDNA barcoding of the mitochondrial cytochrome c oxidase I (COI) gene is widely used to characterise insect diversity and distributions; however, its potential to reveal information on species interactions, including host-symbiont associations, remains largely unexplored. Here, we assess whether COI amplicon data can be used to identify Wolbachia - one of the most widely distributed bacterial symbionts known to profoundly affect their hosts biology. C_LIO_LIWe demonstrate that several commonly used invertebrate COI primer sets perfectly match many reference Wolbachia genomes, leading to frequent co-amplification. C_LIO_LIBy screening 7,901 individual-insect COI amplicon libraries obtained with the popular BF3-BR2 primer set, we detected Wolbachia sequences in over 35% of samples, revealing that co-amplification is indeed widespread. After removing low-abundance reads, Wolbachia detection based on COI amplicons showed over 90% agreement with simultaneously generated 16S-V4 rRNA amplicon data from the same specimens. The degree of agreement, however, varied depending on the thresholds used, among datasets and insect clades. C_LIO_LIFurther, we show that Wolbachia abundance inferred from COI amplicons correlated with their abundance in metagenomic datasets for 152 specimens, supporting the quantitative relevance of the signal. C_LIO_LIFinally, we find that Wolbachia COI sequences provide greater phylogenetic resolution than 16S-V4 rRNA data (mean pairwise genetic distance of COI sequences - 9.6%, 16S-V4 rRNA - 2.8%), and the reconstructed Wolbachia COI-based genotype network largely agrees with genome-based phylogenies. C_LIO_LICollectively, our results demonstrate that off-target Wolbachia sequences recovered from standard insect COI barcoding data may reliably detect symbiont presence, provide phylogenetic insight, and guide sample selection for metagenomics. Given the rapid expansion of global insect barcoding initiatives, these findings highlight an opportunity for cost-effective monitoring of their most prevalent bacterial symbionts, offering new perspectives on how host-microbe interactions may shape insect communities. C_LI

ecology↗

bioRxiv2025

Contrasting genomic trajectories of Bartonellaceae symbionts of planthoppers

Symbioses with microorganisms have shaped the nutritional biology and evolution of many insects. For example, several ant clades have adapted to nutrient-poor diets through symbiosis with a specific clade of bacteria in the family Bartonellaceae (Hyphomicrobiales), notorious for also including virulent vertebrate pathogens. Here we show that Bartonellaceae phylogenetically placed within the clade that has only encompassed ant symbionts to date - Candidatus genus Tokpelaia - have established as symbionts in four different clades of planthoppers (Insecta: Hemiptera: Fulgoromorpha). Genome size and contents indicate different levels of integration of these strains into the planthopper host biology and their diverse roles. Symbionts infecting one of the clades have some of the largest genomes among Bartonellaceae, at ca. 2 Mb, two others are under 700 kb, and the fourth is reduced to barely 158 kb. The planthopper-associated Tokpelaia strains with larger genomes, similarly to ant symbionts, encode multiple amino acid and vitamin biosynthesis genes, complementing the degraded nutritional capabilities of their hosts ancient heritable endosymbionts. Strikingly, the smallest Tokpelaia genome lacks any genes linked to essential amino acid biosynthesis, in contrast to all other known insect-associated bacteria with genomes of comparable size. We identified a single vitamin biosynthesis gene and iron-sulfur cluster assembly genes as its only putative contributions to the host biology. Our results broaden the host spectrum of non-pathogenic Bartonellaceae, indicating that they have contributed to nutrition and symbiotic consortium function in diverse diet-restricted host clades. They also highlight an unexpectedly broad range of evolutionary outcomes for this important bacterial group. SignificanceMany insects rely on bacterial partners to overcome nutrient-poor diets, yet the diversity and evolutionary trajectories and outcomes for these associations remain unclear. Our discovery of Bartonellaceae bacteria in planthoppers improves the understanding of the host range of these broadly relevant bacteria best-known as vertebrate pathogens. The finding that these planthopper symbionts generally have the capacity to produce essential amino acids and vitamins relevant to hosts and likely form long-term symbiotic associations agree with the expectations for sap-sucking hemipteran symbionts. However, the breadth of sizes and functions of the newly assembled genomes substantially expand the known range of states for Bartonellaceae, and their evolutionary trajectories. In particular, the identification of a strain with an ultra-reduced genome of only 158kb with no amino acid biosynthetic functions contrasts with all other known insect-symbiotic bacteria with genomes in a similar size range. This study also indicates how symbionts may enable the degeneration, functional loss, and evolution of other bacteria residing in the same host.

ecology↗

bioRxiv2025

Dissecting multitrophic interactions: the relationships among Entomophthora, their dipteran hosts, and associated bacteria

Interactions with microorganisms from across a range of mutualism-to-pathogenicity spectrums shape the biology of insects at all levels - from individual traits to populations and communities. However, the understanding of pathogens attacking non-model insect species in natural ecosystems, or their interactions with other insect-associated microorganisms, is fragmentary. Here, we tested a conceptually novel approach - the simultaneous sequencing of insect, fungal, and bacterial marker gene amplicons - as a means of dissecting interactions among entomopathogenic fungi in the genus Entomophthora and their dipteran hosts in South Greenland. We aimed to describe the taxonomic diversity of Entomophthora-killed flies, their pathogens, and the bacterial diversity within a set of field-collected dead insects exhibiting signs of Entomophthora infection. Across nine collected dipteran species, we identified multiple Entomophthora genotypes, with strong but not perfect patterns of host-specificity across the five targeted marker regions. Additionally, we found consistent differences in bacterial community composition among fungus-killed fly species and sampling sites. Our results substantially expand the knowledge of Entomopthora diversity and host associations while providing the very first insights into associated bacteria and their potential roles. We also conclude that multi-target amplicon sequencing can be a powerful tool for addressing broad questions about biological interactions in diverse natural communities.

ecology↗

bioRxiv2024

High-throughput biodiversity surveying sheds new light on the brightest of insect taxa

Sampling of species-rich taxa followed by DNA metabarcoding is quickly becoming a popular high-throughput method for biodiversity inventories. Unfortunately, we know little about its accuracy and efficiency, as the results mostly pertain to poorly-known organism groups in underexplored environments or regions of the world. Here we ask what an extensive sampling effort based on Malaise trapping and metabarcoding can tell us about the lepidopteran fauna of Sweden - one of the best-understood insect taxa in one of the most-surveyed countries of the world. Specifically, we deployed 197 Malaise traps for a single year across Sweden in a systematic sampling design, then metabarcoded the resulting 4,749 bulk samples, and compared the results to existing data sources. We detected more than half (1,535) of the 2,990 lepidopteran species ever recorded as occurring in Sweden, and 323 species not reported during the sampling period by other data providers. Full-length barcoding of individual specimens confirmed three new species for the country and extensive range extensions for two species. It also corroborated eight genetically distinct COI variants that may represent new species to science, one of which has since been described. Most of the new records are for small and inconspicuous species and poorly surveyed regions, suggesting that they represent previously overlooked components of the fauna. Our findings, corroborated by independent metagenomic analyses, show that DNA metabarcoding can be a highly efficient and accurate method of biodiversity sampling, to the extent that it can generate significant new discoveries even for the most well-known of insect faunas.

zoology↗

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

Biotic and abiotic drivers of ecosystem functioning differ between a temperate and a tropical region

Any single ecosystem will provide many ecosystem functions. Whether these functions tend to increase in concert or trade off against each other is a question of much current interest. Equally topical are the drivers behind ecosystem function rates. Yet, we lack large-scale systematic studies that investigate how abiotic factors can directly or indirectly -- via effects on biodiversity -- drive ecosystem functioning. In this study, we assessed the impact of climate, landscape and biotic community on ecosystem functioning and multifunctioning in the temperate and tropical zone, and investigated potential trade-offs among ecosystem functions in both zones. To achieve this, we measured a diverse set of insect-related ecosystem functions -- including herbivory, seed dispersal, predation, decomposition and pollination -- at 50 sites across Madagascar and 171 sites across Sweden, and characterized the insect community at each site using Malaise traps. We used structural equations models to infer causality of the effects of climate, landscape, and biodiversity on ecosystem functioning. For the temperate zone, we found that abiotic factors were more important than biotic factors in driving ecosystem functioning, while in the tropical zone, effects of biotic drivers were most pronounced. In terms of trade-offs among functions, in the temperate zone, only seed dispersal and predation were positively correlated, while all other functions were uncorrelated. By contrast, in the tropical zone, most ecosystem functions increased in concert, highlighting that tropical ecosystems can simultaneously provide a diverse set of functions. These correlated functions in Madagascar could for the most part be explained by similar responses to local climate, landscape, and biota. Our study suggests that the functioning of temperate and tropical ecosystems differs fundamentally in patterns and drivers. Without a better understanding of these differences, it will be impossible to correctly predict shifts in ecosystem functioning in response to environmental disturbances. To identify global patterns and drivers of ecosystem functioning, we will next need replicate sampling across biomes - as here achieved for two regions, thus paving the road and setting the baseline expectations.

ecology↗

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↗

bioRxiv2023

No Transcriptional Compensation for Extreme Gene Dosage Imbalance in Fragmented Bacterial Endosymbionts of Cicadas

Bacteria that form long-term intracellular associations with host cells lose many genes, a process that often results in tiny, gene-dense, and stable genomes. Paradoxically, the same evolutionary processes that drive genome reduction and simplification may also sometimes cause genome expansion and complexification. A bacterial endosymbiont of cicadas, Hodgkinia cicadicola, exemplifies this paradox. In many cicada species, a single Hodgkinia lineage with a tiny, gene-dense genome has split into several interdependent cell and genome lineages. Each new Hodgkinia lineage encodes a unique subset of the ancestral unsplit genome in a complementary way, such that the collective gene contents of all lineages sum to the total found in the ancestral single genome. This splitting process creates genetically distinct Hodgkinia cells that must function together to carry out basic cellular processes, but also creates a gene dosage problem where some genes are encoded by only a small fraction of cells while others are much more abundant. Here, by sequencing DNA and RNA of Hodgkinia from different cicada species with different amounts of splitting - along with those of its structurally stable, unsplit partner endosymbiont Sulcia muelleri - we show that Hodgkinia does not transcriptionally compensate to rescue the wildly unbalanced gene and genome ratios that result from lineage splitting. We also find evidence that Hodgkinia has a reduced capacity for basic transcriptional control independent of the splitting process. Collectively, these findings reveal another layer of degeneration that further pushes the limits of canonical molecular and cell biology in Hodgkinia, and may in part explain its propensity to go extinct through symbiont replacement. SignificanceMany cicadas host two bacterial endosymbionts, Hodgkinia and Sulcia, which produce essential amino acids missing from the insects xylem sap diet. Following 100+ million years of strict host association, both bacteria have lost many genes and posses extremely tiny genomes. In some cicadas, Hodgkinia has split into multiple cell lineages, distributing its genes, with little respect to their function, among separate lineages present at (sometimes wildly) different abundances. We find no transcriptional response to this in Hodgkinia, resulting in similarly imbalanced mRNA abundances. We also find less control of transcription in Hodgkinia compared to Sulcia. Hodgkinias transcriptome embodies an extreme, even relative to other highly-reduced endosymbionts, and raises questions about how cell biology in multi-lineage Hodgkinia can function at all.

evolutionary biology↗

bioRxiv2021

In their sister's footsteps: Taxonomic divergence obscures substantial functional overlap among the metabolically diverse symbiotic gut communities of adult and larval turtle ants

Gut bacterial symbionts can support animal nutrition by facilitating digestion and providing valuable metabolites. While the composition of gut symbiont communities shifts with host development in holometabolous insects, changes in symbiotic roles between immature and adult stages are not well documented, especially in ants. Here, we explored the metabolic capabilities of microbiomes sampled from herbivorous turtle ant (Cephalotes sp.) larvae and adult workers through genomic and metagenomic screenings and targeted in vitro metabolic assays. We reveal that larval guts harbor bacterial symbionts from the Enterobacteriales, Lactobacillales and Rhizobiales orders, with impressive metabolic capabilities, including catabolism of plant and fungal recalcitrant fibers common in turtle ant diets, and energy-generating fermentation. Additionally, several members of the specialized turtle ant adult gut microbiome, sampled downstream of an anatomical barrier that dams large food particles, show a conserved potential to depolymerize many dietary fibers and other carbohydrates. Symbionts from both life stages have the genomic capacity to recycle nitrogen, synthesize amino acids and B-vitamins, and perform several key aspects of sulfur metabolism. We also document, for the first time in ants, an adult-associated Campylobacterales symbiont with an apparent capacity to anaerobically oxidize sulfide, reduce nitrate, and fix carbon dioxide. With help of their gut symbionts, including several bacteria likely acquired from the environment, turtle ant larvae appear as an important component of turtle ant colony digestion and nutrition. In addition, the conserved nature of the digestive, energy-generating, and nutritive capacities among adult-enriched symbionts suggests that nutritional ecology of turtle ant colonies has long been shaped by specialized, behaviorally-transferred gut bacteria with over 46 million years of residency.

evolutionary biology↗

bioRxiv2018

Changes in endosymbiont complexity drive host-level compensatory adaptations in cicadas

For insects that depend on one or more bacterial endosymbionts for survival, it is critical that these bacteria are faithfully transmitted between insect generations. Cicadas harbor two essential bacterial endosymbionts, Sulcia muelleri and Hodgkinia cicadicola. In some cicada species, Hodgkinia has fragmented into multiple distinct cellular and genomic lineages that can differ in abundance by more than two orders of magnitude. This complexity presents a potential problem for the host cicada, because low-abundance-but-essential Hodgkinia lineages risk being lost during the symbiont transmission bottleneck from mother to egg. Here we show that all cicada eggs seem to receive the full complement of Hodgkinia lineages, and that in cicadas with more complex Hodgkinia this outcome is achieved by increasing the number of Hodgkinia cells transmitted by up to six-fold. We further show that cicada species with varying Hodgkinia complexity do not visibly alter their transmission mechanism at the resolution of cell biological structures. Together these data suggest that a major cicada adaptation to changes in endosymbiont complexity is an increase in the number of Hodgkinia cells transmitted to each egg. We hypothesize that the requirement to increase the symbiont titer is one of the costs associated with Hodgkinia fragmentation.

evolutionary biology↗

bioRxiv2017

Idiosyncratic genome degradation in a bacterial endosymbiont of periodical cicadas

When a free-living bacterium transitions to a host-beneficial endosymbiotic lifestyle, it almost invariably loses a large fraction of its genome [1, 2]. The resulting small genomes often become unusually stable in size, structure, and coding capacity [3-5]. Candidatus Hodgkinia cicadicola (Hodgkinia), a bacterial endosymbiont of cicadas, sometimes exemplifies this genomic stability. The Hodgkinia genome has remained completely co-linear in some cicadas diverged by tens of millions of years [6, 7]. But in the long-lived periodical cicada Magicicada tredecim, the Hodgkinia genome has split into dozens of tiny, gene-sparse genomic circles that sometimes reside in distinct Hodgkinia cells [8]. Previous data suggested that other Magicicada species harbor similarly complex Hodgkinia populations, but the timing, number of origins, and outcomes of the splitting process were unknown. Here, by sequencing Hodgkinia metagenomes from the remaining six Magicicada species and two sister species, we show that all Magicicada species harbor Hodgkinia populations of at least twenty genomic circles each. We find little synteny among the 256 Hodgkinia circles analyzed except between the most closely related species. Individual gene phylogenies show that Hodgkinia first split in the common ancestor of Magicicada and its closest known relatives, but that most splitting has occurred within Magicicada and has given rise to highly variable Hodgkinia gene dosages between cicada species. These data show that Hodgkinia genome degradation has proceeded down different paths in different Magicicada species, and support a model of genomic degradation that is stochastic in outcome and likely nonadaptive for the host. These patterns mirror the genomic instability seen in some mitochondria.

evolutionary biology↗

bioRxiv2017

Dramatic differences in gut bacterial densities help to explain the relationship between diet and habitat in rainforest ants

Abundance is a key parameter in microbial ecology, and important to estimates of potential metabolite flux, impacts of dispersal, and sensitivity of samples to technical biases such as laboratory contamination. However, modern amplicon-based sequencing techniques by themselves typically provide no information about the absolute abundance of microbes. Here, we use fluorescence microscopy and quantitative PCR as independent estimates of microbial abundance to test the hypothesis that microbial symbionts have enabled ants to dominate tropical rainforest canopies by facilitating herbivorous diets, and compare these methods to microbial diversity profiles from 16S rRNA amplicon sequencing. Through a systematic survey of ants from a lowland tropical forest, we show that the density of gut microbiota varies across several orders of magnitude among ant lineages, with median individuals from many genera only marginally above detection limits. Supporting the hypothesis that microbial symbiosis is important to dominance in the canopy, we find that the abundance of gut bacteria is positively correlated with stable isotope proxies of herbivory among canopy-dwelling ants, but not among ground-dwelling ants. Notably, these broad findings are much more evident in the quantitative data than in the 16S rRNA sequencing data. Our results help to resolve a longstanding question in tropical rainforest ecology, and have broad implications for the interpretation of sequence-based surveys of microbial diversity.

ecology↗