Biology subjects

Fontaneto, D.

Publications and source records attributed to Fontaneto, D..

16 recordsLinked to original sources

bioRxiv2026

Meiofaunal communities flourish in Antarctic marine sediments despite the harsh environmental conditions

While Antarctic terrestrial ecosystems support low metazoan diversity, the surrounding marine macrobenthos is rich. However, marine meiofauna remains historically neglected, leaving its diversity patterns unclear. In this study, we used 18S rRNA gene metabarcoding alongside an enhanced taxonomic annotation pipeline to characterize marine meiofauna diversity in the Ross Sea, comparing it to global datasets. We evaluated how depth, habitat type, and mesh size influence community structures to test if habitat heterogeneity drives diversity despite the harsh Southern Ocean conditions. Our results revealed exceptionally high diversity, with metazoans richness comparable to or higher than temperate regions. Although environmental variables had limited effects on taxonomic richness, they significantly shaped community composition, with habitat type explaining the highest proportion of variance. Interestingly, we detected several ASVs 100% identical to North Sea and North Atlantic sequences, likely reflecting the limited taxonomic resolution of the 18S marker rather than global dispersal (the "meiofaunal paradox"). Overall, these findings demonstrate that Antarctic marine sediments host rich meiofaunal communities where ecological processes operate similarly to other global regions, contrasting sharply with depauperate continental Antarctic ecosystems.

ecology↗

bioRxiv2025

Multilayered human activities shape the microbial communities of groundwater-dependent ecosystems in an arid oceanic island

Island coastal aquifers, though physically small compared to continental groundwater systems, are of huge ecological and societal importance, sustaining functions that connect to locally crucial provision, maintenance and culture ecosystem services. Those functions are largely dependent on the presence of highly adapted biological communities, for which, their microbial communities remain understudied. Our goal is to describe the bacterial communities across the groundwater-dependent ecosystems on Lanzarote, spanning a gradient of anthropogenic pollution using 16SrRNA amplicon sequencing. We sampled coastal caves and pools, wells and water galleries, springs, saltworks and marine bays affected by submarine groundwater discharge. Ecological analyses highlight that richness and composition of bacterial communities strongly depend on the type of habitats. Pathogens and human-derived species were ubiquitous in our samples, but, strikingly, caves and wells were strongly enriched with them compared to other habitats. We propose that our results highlight the susceptibility of groundwater environments to pollution and indicate that aquifers act as reservoirs of biological contamination in addition to natural diversity--regardless of their salinity. Since this enrichment might compromise some of the functions and services that groundwater-dependent ecosystems provide in oceanic islands, we call for integrative conservation strategies that include hydrological and biological perspectives into the decision making.

microbiology↗

bioRxiv2025

Urbanisation reshapes community assembly differently across coastal beach and dune habitats

Urbanisation can reduce biodiversity through environmental filtering, but its effects may differ among neighbouring habitats within ecotones. Beach-dune systems provide a useful test because strong environmental gradients occur over short distances and overlap with gradients in human pressure. We collected 660 sediment samples from 55 transects along the Dutch North Sea coast, covering established dunes, incipient dunes, the upper intertidal zone, and the lower intertidal zone. Using environmental DNA metabarcoding and habitat-specific joint species distribution models, we tested how distance-to-city was associated with community composition, operational taxonomic unit (OTU) richness, and OTU-level occurrence. We found compositional differentiation along the urban-proximity gradient in both dune habitats, particularly in incipient dunes, but not in the intertidal habitats. Across all habitats, communities far from cities were more similar to one another than communities near cities, indicating greater among-site compositional variation near urban areas. OTU richness and mean OTU occurrence probabilities increased with distance-to-city in the lower intertidal, upper intertidal, and established dunes. Incipient dunes showed no clear richness gradient or directional OTU-level response despite the strong compositional turnover, suggesting that the main response was community replacement rather than loss of OTUs. Overall, habitat position within the beach-dune ecotone influenced whether biodiversity responses to urban proximity led to directional filtering, compositional turnover, or increased community heterogeneity. Our findings show that biodiversity and impact assessments based on a single habitat may miss important ecological change in coastal habitats.

ecology↗

bioRxiv2024

Metacommunity theory and metabarcoding reveal the environmental, spatial, and biotic drivers of meiofaunal communities in sandy beaches

Sandy beaches are important ecosystems providing coastal protection and recreation, but they face significant threats from human activities and sea level rise. They are inhabited by meiofauna, small benthic invertebrates that are highly abundant and diverse, but are commonly understudied biotic components of beach ecosystems. Here, we investigate the factors shaping meiofaunal metacommunities by employing Generalised Dissimilarity Modelling (GDM) and Joint Species Distribution Modelling (JSDM) to study community turnover and assembly processes. We analysed over 550 meiofauna samples from a >650 km stretch of the southern North Sea coastline using a metabarcoding approach. Our findings reveal that environmental factors, especially Distance from Low Tide and Sediment Grain Size, are important drivers of meiofauna community turnover. This highlights the influence of the gradient from marine to terrestrial habitats and sediment conditions. Spatial factors, which indicate dispersal limitations, also significantly impact community composition, challenging the view that marine meiofauna have broad geographic distributions. The JSDM results show that species sorting by environmental conditions is the dominant process in community assembly with increasing environmental differences between sampling sites, but that biotic associations, or similar environmental preferences, are a major driver of community assembly at sites with similar environmental conditions. Further, we find that spatial factors also significantly influence community assembly across the study region. By facilitating the inference of ecological niches for a high number of meiofaunal taxa, JSDM provides a powerful framework for understanding the ecology of these animals. Our results highlight the importance of considering environmental gradients and dispersal limitations in meiofauna and beach ecosystem research, and future research should aim at adding information on functional traits and biotic interactions under varying environmental conditions to understand meiofauna community dynamics and resilience.

ecology↗

bioRxiv2024

Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: a case study on beach meiofauna

Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack of reference DNA sequences available for taxonomic annotation. Our study explores the benefits of combining targeted DNA barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches are globally important ecosystems and are inhabited by meiofauna, microscopic animals living in the interstitial space between the sand grains, which play a key role in coastal biodiversity and ecosystem dynamics. However, research on meiofauna faces challenges due to limited taxonomic expertise and sparse sampling. We generated 775 new cytochrome c oxidase I DNA barcodes from meiofauna specimens collected along the Netherlands west coast and combined them with the NCBI GenBank database. We analysed alpha and beta diversity in 561 metabarcoding samples from 24 North Sea beaches, a region extensively studied for meiofauna, using both the enriched reference database and the NCBI database without the additional reference barcodes. Our results show a 2.5-fold increase in sequence annotation and a doubling of species-level Operational Taxonomic Units (OTUs) identification when annotating the metabarcoding data with the enhanced database. Additionally, our analyses revealed a bell-shaped curve of OTU richness across the intertidal zone, aligning more closely with morphological analysis patterns, and more defined community dissimilarity patterns between supralittoral and intertidal sites. Our research highlights the importance of expanding molecular reference databases and combining morphological taxonomy with molecular techniques for biodiversity assessments, ultimately improving our understanding of coastal ecosystems.

molecular biology↗

bioRxiv2024

Zooplankton impacts on the persistence of the anthropogenic pollution marker intI1 in lake water

Wastewater treatment plants (WWTP) effluents can release microbiological pollutants, including the intI1 gene (integrases of class 1 integrons), which has been proposed as a target for monitoring anthropogenic pollution in surface waters. This gene has also a strong correlation with antibiotic resistance, making of it an important proxy to evaluate the level of genetic contamination in aquatic environments. he ecological factors that influence the abundance and dynamics of intI1 within natural water bodies are largely unknown. To better understand the fate of class 1 integrons in aquatic systems, we resorted to classical limnological monitoring of intI1 over multiple years. We also conducted experiments to elucidate the impact of Daphnia grazing on its abundance. The monitoring of different size fractions of the Lake Maggiore microbial community has shown a particle-bound life-style for intI1-harbouring bacteria. Most of the bacteria hosting intI1, originating from both a wastewater effluent that discharges intro Lake Maggiore and lake water itself, grow on particulate substrates in open waters, making them particularly vulnerable to grazing by large filter feeders such as Daphnia. Daphnia grazing is independent from the origin (lake water or wastewater) of the bacterial genera; it selectively removes bacteria that are present in aggregates or even filamentous forms from both origins. To understand if intI1 is related to viable bacteria or just DNA residues, it is important to study the persistence of class 1 integrons with their gene cassettes, which often contain antibiotic resistance genes in freshwater ecosystems. Significance StatementWhile faecal pollution of freshwaters is commonly monitored, genetic pollution through wastewater treatment plant outflows, such as antibiotic resistance genes, is difficult to monitor due to the diverse nature of genes present. The intI1 gene is proposed as a proxy for anthropogenic pollution; however, there is a major lack of understanding regarding the persistence of this gene in freshwaters. In this study, we demonstrate that intI1 in freshwaters is associated with both the natural microbial community and allochthonous microbes arriving from wastewater. Furthermore, we show that intI1 harbouring bacteria preferentially reside in the aggregated microbial fraction and are easily removed by zooplankton grazing. This study is the first limnological investigation of this gene and highlights a significant gap in our knowledge regarding the ecology of class 1 integrons. Genetic pollution of surface waters is however a global problem and of very broad interest on the one hand, on the other hand, the question of the establishment of an allochthonous gene into a natural microbial community is also an interesting fundamental question in ecology, thus this study has both more applied and more fundamental aspects. Therefore, we consider it perfect for the readership of L&O.

ecology↗

bioRxiv2023

Drivers of species knowledge across the Tree of Life

Knowledge of biodiversity is unevenly distributed across the Tree of Life. In the long run, such disparity in awareness unbalances our understanding of life on Earth, influencing policy decisions and the allocation of research and conservation funding. We investigated how humans accumulate knowledge of biodiversity by searching for consistent relationships between scientific (number of publications) and societal (number of views in Wikipedia) interest, and species-level morphological, ecological and socio-cultural factors. Across a random selection of 3,019 species spanning 29 Phyla/Divisions, we show that socio-cultural factors are the most important correlates of scientific and societal interest in biodiversity, including the fact that a species is useful or harmful to humans, has a common name and is listed in the IUCN Red List. Furthermore, large-bodied, broadly distributed and taxonomically unique species receive more scientific and societal attention, whereas colorfulness and phylogenetic proximity to humans correlates exclusively with societal attention. These results highlight a favoritism towards limited branches of the Tree of Life, and that scientific and societal priorities in biodiversity research broadly align. This suggests that we may be missing out on key species in our research and conservation agenda simply because they are not on our cultural radar.

ecology↗

bioRxiv2022

Climate change will redefine taxonomic, functional, and phylogenetic diversity patterns of Odonata in space and time

Climate change is rearranging the mosaic of biodiversity on our planet. These broad-scale species re-distributions will affect the structure of communities across multiple biodiversity facets (taxonomic, phylogenetic, and functional diversity). The current challenges to understand such effects involve focusing on organisms other than vertebrates and considering the signature of species redistribution on phylogenetic and functional diversity in addition to species composition. Using European dragonflies and damselflies (Odonata), we asked: i) how climate change will redefine taxonomic, phylogenetic, and functional diversity at continental scales; ii) which traits will mediate species response to global change; and iii) whether this response will be conserved across the phylogeny. First, we constructed stacked species distribution models for 107 species of Odonata under current and future climate conditions. Then, we quantified the temporal variation of taxonomic, functional and phylogenetic components, forecasting alpha and beta diversity changes through our geographical grid. Lastly, we used phylogenetic comparative models to test the influence of phylogeny and traits on range shifts. We observed broad latitudinal and altitudinal rearrangements in community composition driven by climate change. Given the high dispersal ability of Odonata, changes are predicted to be rapid, especially in areas experiencing faster climate change rates. According to our predictions, changes in species composition cascade to affect functional and phylogenetic diversity, determining broad turnovers in traits and evolutionary lineages. There was no clear phylogenetic signal in the range-shift response of European Odonata to climate change. According to our phylogenetic regression models, only body size and flight period can be partly correlated with observed range shifts. By considering all three primary facets of biodiversity, our results support the design of inclusive management and conservation strategies, accounting not only for the diversity of species, but also the services they provide and the phylogenetic heritage they carry in a targeted ecosystem.

ecology↗

bioRxiv2022

Taxonomic practice, creativity, and fashion: What's in a spider name?

Theres a secret pleasure in naming new species. Besides traditional etymologies recalling the sampling locality, habitat, or morphology of the species, etymologies may be tributes to some meaningful person (for example, the species collector, the authors husband or wife, or a celebrity), pop culture references, and even exercises of enigmatography. The possibility of choosing witty or even playful names for new species departs from the otherwise impersonal and old-fashioned writing style thats common in taxonomic papers; but, how has the descriptors choice for specific etymologies changed over the 300+ years since the introduction of the Linnaean binomial system of nomenclature? Using an unprecedented dataset of 48,464 etymologies (all valid species and subspecies of spiders described between 1757 and May 2020), we tested the hypothesis that species names given by taxonomists are deeply influenced by their cultural background. In particular, we asked whether naming practices change through space (continent in which the species was found) or have changed through time (year of description). We observed spatial and temporal differences in the way taxonomists name new species. In absolute terms, etymologies referring to morphology were the most frequently used. In relative terms, however, references to morphology peaked in 1850-1900 and then began to decline, with a parallel increase in etymologies dedicated to people and geography. Currently, these are the most widely used, with [~]38% of all etymologies of spider species described in the last ten years referring to geography, [~]25% to people, and [~]25% to morphology. Interestingly, there has been a dramatic increase in etymologies referring to pop culture and other cultural aspects in the last two decades, especially in Europe and the Americas. While such fashionable names often carry little or no biological information regarding the species itself, they help give visibility to the science of taxonomy, a discipline currently facing a profound crisis within academia. Taxonomy is among the most unchanged disciplines across the last centuries in terms of background, tools, rules, and writing style; but our analysis suggests that taxonomists remain deeply influenced by their living time and space.

scientific communication and education↗

bioRxiv2021

Zooplankton as a transitional host for Escherichia coli in freshwater

This study shows that Escherichia coli can be temporarily enriched in zooplankton in natural conditions and that these bacteria can belong to different phylogroups and sequence types including environmental as well as clinical and animal isolates. We isolated 10 E. coli strains and sequenced the genomes of two of them. Phylogenetically the two isolates were closer to strains isolated from poultry meat than with freshwater E. coli, albeit their genomes were smaller than those from poultry. After isolation and fluorescent protein tagging of strains ED1 and ED157 we show that Daphnia sp. can take up these strains and release them alive again, thus forming a temporary host for E. coli. In a chemostat experiment we show that the association does not prolong the bacterial long-term survival, but that at low abundances it does also not significantly reduce the bacterial numbers. We demonstrate that E. coli does not belong to the core microbiota of Daphnia, suffers from competition by the natural microbiota of Daphnia, but can profit from its carapax to survive in water. All in all, this study suggests that the association of E. coli to Daphnia is only temporary but that the cells are viable therein and this might allow encounters with other bacteria for genetic exchange and potential genomic adaptations to the freshwater environment. ImportanceThe contamination of freshwaters with faecal derived bacteria is of major concern regarding drinking water acquisition and recreational activities. Ecological interactions promoting their persistence are still very scarcely studied. This study, which analyses the survival of E. coli in the presence of zooplankton, is thus of ecological as well as water safety relevance.

ecology↗

bioRxiv2021

Meiofauna is an important, yet neglected, component of biodiversity of Posidonia oceanica

Posidonia oceanica meadows are biodiversity reservoirs and provide many ecosystem services in coastal Mediterranean regions. Marine meiofauna, on the other hand, not only represents a major component of regional marine biodiversity, but also a useful tool to address both theoretical and applied questions in ecology, evolution, and conservation. We review the meiofaunal diversity in the P. oceanica ecosystem combining a literature review and a case study. First, we gathered records of 664 species from 69 published studies as well as unpublished sources, including few species exclusive from this ecosystem. Eighteen of those studies quantified the spatial and temporal changes of species composition, highlighting habitat-specific assemblages that fluctuate following the annual changes experienced by P. oceanica. Hydrodynamics, habitat complexity, and food availability, all three inherently linked to the seagrass phenology, are recognised as the main factors at shaping the complex distribution patterns of meiofauna in the meadows. These drivers have been identified mainly from Copepoda and Nematoda, and depend ultimately on species-specific preferences. Second, we tested the generality of these observations using marine mites as a model group, showing that the same processes might be in place also for other less abundant meiofaunal groups. Overall, our study highlights an outstanding diversity of meiofauna in P. oceanica and shows its potential for future research, not only focused on exploring and describing new species of neglected meiofaunal organisms, but also providing a more complete understanding on the functioning of the iconic Mediterranean ecosystem created by P. oceanica.

ecology↗

bioRxiv2021

Climate-induced forest dieback drives compositional change in insect communities that is concentrated amongst rare species

Marked decline in insect species richness, abundance and biomass have recently been quantified in Europe. We metabarcoded 224 Malaise-trap samples to investigate whether drought-induced forest dieback and subsequent salvage logging have an impact on flying insects (ca. 3000 insect species) in silver fir Pyrenean forests. We found no evidence that climate-induced forest dieback impacted species richness of flying insects but revealed compositional turnover patterns consistent with those seen during natural forest succession, given that the key covariates explaining compositional variation were canopy openness versus microhabitat diversity and deadwood amount at local and landscape scales, respectively. Importantly, most change was driven by rare species. In contrast, observed levels of salvage logging did not explain change in species richness or composition. Hence, although forest dieback appears to cause changes in species assemblages mimicking natural forest succession, it also increases the risk of catastrophic loss of rare species through homogenization of environmental conditions.

ecology↗

bioRxiv2020

Habitat differences filter functional diversity of low dispersive microscopic animals

O_LIWhereas the study of patterns of distribution of microscopic animals has long been dominated by the ubiquity paradigm, we are starting to appreciate that microscopic animals are not as widespread as previously thought and that habitat preferences may have a strong role in structuring their patterns of occurrence. However, we still ignore to what extent and through which mechanisms the environment selects for specific communities or traits in microscopic animals. This gap is partly due to the lack of data on the relevant traits of many species, and partly because measuring environmental variables at an appropriate resolution may be problematic. C_LIO_LIWe here overcome both issues by analysing the functional space of marine mite communities living in a sea-grass (Posidonia oceanica) meadow across two habitats: the leaves and the matte. The strictly benthic lifestyle and the conserved morphology of mites allow for unambiguous characterization of their functional traits, while the discrete nature of the two habitats alleviates the uncertainty in their ecological characterization. C_LIO_LIOur results show that habitat filters the distribution of certain traits favouring a higher diversity, dispersion, and evenness of functional traits in the matte than in the leaves. We further observed temporal variations in the functional diversity of communities, potentially following the seasonal renovation and decay of seagrass leaves. However, in spite of the stark ecological differences between the two habitats and across seasons, the filtering effect is partial and affects mostly relative species abundances. C_LIO_LIWe conclude that in other microscopic organisms, habitat filtering might appear even more subtle especially if they are capable of long distance dispersal or occur in ecological systems where environmental variables vary continuously or fluctuate through time. Our study therefore emphasises the need of moving from a merely taxonomical toward a functional view of ecological studies of microscopic organisms if we want to achieve a mechanistic understanding of their habitat and distribution patterns. C_LI Data availability statementRaw data and R script to generate the analyses will be deposited in a public repository upon acceptance.

ecology↗

bioRxiv2020

Evolutionary dynamics of transposable elements in bdelloid rotifers

Transposable elements (TEs) are selfish genomic parasites whose ability to spread autonomously is facilitated by sexual reproduction in their hosts. If hosts become obligately asexual, TE frequencies and dynamics are predicted to change dramatically, but the long-term outcome is unclear. Here, we test current theory using whole-genome sequence data from eight species of bdelloid rotifers, a class of invertebrates where males are thus far unknown. Contrary to expectations, we find a diverse range of active TEs in bdelloid genomes, at an overall frequency within the range seen in sexual species. We find no evidence that TEs are spread by cryptic recombination or restrained by unusual DNA repair mechanisms, but we report that bdelloids share a large and unusual expansion of genes involved in RNAi-mediated TE suppression. This suggests that enhanced cellular defence mechanisms might mitigate the deleterious effects of active TEs and compensate for the consequences of long-term asexuality.

evolutionary biology↗

bioRxiv2020

Scientometric correlates of high-quality reference lists in ecological papers

It is said that the quality of a scientific publication is as good as the science it cites, but the properties of high-quality reference lists have never been numerically quantified. We examined seven numerical characteristics of reference lists of 50,878 primary research articles published in 17 ecological journals between 1997 and 2017. Over this 20-years period, there have been significant changes in reference lists’ properties. On average, more recent ecological papers have longer reference lists, cite more high Impact Factor papers, and fewer non-journal publications. Furthermore, we show that highly cited papers across the ecology literature have longer reference lists, cite more recent and impactful papers, and account for more self-citations. Conversely, the proportion of ‘classic’ papers and non-journal publications cited, as well as the temporal range of the reference list, have no significant influence on articles’ citations. From this analysis, we distill a recipe for crafting impactful reference lists.View Full Text

scientific communication and education↗

bioRxiv2017

Comparative genomics of bdelloid rotifers: evaluating the effects of asexuality and desiccation tolerance on genome evolution

Bdelloid rotifers are microscopic invertebrates that have existed for millions of years apparently without sex or meiosis. They inhabit a variety of temporary and permanent freshwater habitats globally, and many species are remarkably tolerant of desiccation. Bdelloids offer an opportunity to better understand the evolution of sex and recombination, but previous work has emphasized desiccation as the cause of several unusual genomic features in this group. Here, we evaluate the relative effects of asexuality and desiccation tolerance on genome evolution by comparing whole genome sequences for three bdelloid species: Adineta ricciae (desiccation tolerant), Rotaria macrura and Rotaria magnacalcarata (both desiccation intolerant) to the only published bdelloid genome to date, that of Adineta vaga (also desiccation tolerant). We find that tetraploidy is conserved among all four bdelloid species, but homologous divergence in obligately aquatic Rotaria genomes is low, well within the range observed between alleles in obligately sexual, diploid animals. In addition, we find that homologous regions in A. ricciae are largely collinear and do not form palindromic repeats as observed in the published A. vaga assembly. These findings are contrary to current understanding of the role of desiccation in shaping the bdelloid genome, and indicate that various features interpreted as genomic evidence for long-term ameiotic evolution are not general to all bdelloid species, even within the same genus. Finally, we substantiate previous findings of high levels of horizontally transferred non-metazoan genes encoded in both desiccating and non-desiccating bdelloid species, and show that this is a unique feature of bdelloids among related animal phyla. Comparisons within bdelloids and to other desiccation-tolerant animals, however, again call into question the purported role of desiccation in horizontal transfer.

evolutionary biology↗