Body-size shifts in aquatic and terrestrial urban communities.

Body size is intrinsically linked to metabolic rate and life-history traits, and is a crucial determinant of food webs and community dynamics1,2. The increased temperatures associated with the urban-heat-island effect result in increased metabolic costs and are expected to drive shifts to smaller body sizes 3 . Urban environments are, however, also characterized by substantial habitat fragmentation 4 , which favours mobile species. Here, using a replicated, spatially nested sampling design across ten animal taxonomic groups, we show that urban communities generally consist of smaller species. In addition, although we show urban warming for three habitat types and associated reduced community-weighted mean body sizes for four taxa, three taxa display a shift to larger species along the urbanization gradients. Our results show that the general trend towards smaller-sized species is overruled by filtering for larger species when there is positive covariation between size and dispersal, a process that can mitigate the low connectivity of ecological resources in urban settings 5 . We thus demonstrate that the urban-heat-island effect and urban habitat fragmentation are associated with contrasting community-level shifts in body size that critically depend on the association between body size and dispersal. Because body size determines the structure and dynamics of ecological networks 1 , such shifts may affect urban ecosystem function.

Back to the roots, desiccation and radiation resistances are ancestral characters in bdelloid rotifers.

BACKGROUND: Bdelloid rotifers are micro-invertebrates distributed worldwide, from temperate latitudes to the most extreme areas of the planet like Antarctica or the Atacama Desert. They have colonized any habitat where liquid water is temporarily available, including terrestrial environments such as soils, mosses, and lichens, tolerating desiccation and other types of stress such as high doses of ionizing radiation (IR). It was hypothesized that bdelloid desiccation and radiation resistance may be attributed to their potential ability to repair DNA double-strand breaks (DSBs). Here, these properties are investigated and compared among nine bdelloid species collected from both mild and harsh habitats, addressing the correlation between the ability of bdelloid rotifers to survive desiccation and their capacity to repair massive DNA breakage in a phylogenetically explicit context. Our research includes both specimens isolated from habitats that experience frequent desiccation (at least 1 time per generation), and individuals sampled from habitats that rarely or never experienced desiccation. RESULTS: Our analysis reveals that DNA repair prevails in somatic cells of both desiccation-tolerant and desiccation-sensitive bdelloid species after exposure to X-ray radiation. Species belonging to both categories are able to withstand high doses of ionizing radiation, up to 1000 Gy, without experiencing any negative effects on their survival. However, the fertility of two desiccation-sensitive species, Rotaria macrura and Rotaria rotatoria, was more severely impacted by low doses of radiation than that of desiccation-resistant species. Surprisingly, the radioresistance of desiccation-resistant species is not related to features of their original habitat. Indeed, bdelloids isolated from Atacama Desert or Antarctica were not characterized by a higher radioresistance than species found in more temperate environments. CONCLUSIONS: Tolerance to desiccation and radiation are supported as ancestral features of bdelloid rotifers, with a group of species of the genus Rotaria having lost this trait after colonizing permanent water habitats. Together, our results provide a comprehensive overview of the evolution of desiccation and radiation resistance among bdelloid rotifers.

Urbanization drives cross-taxon declines in abundance and diversity at multiple spatial scales.

The increasing urbanization process is hypothesized to drastically alter (semi-)natural environments with a concomitant major decline in species abundance and diversity. Yet, studies on this effect of urbanization, and the spatial scale at which it acts, are at present inconclusive due to the large heterogeneity in taxonomic groups and spatial scales at which this relationship has been investigated among studies. Comprehensive studies analysing this relationship across multiple animal groups and at multiple spatial scales are rare, hampering the assessment of how biodiversity generally responds to urbanization. We studied aquatic (cladocerans), limno-terrestrial (bdelloid rotifers) and terrestrial (butterflies, ground beetles, ground- and web spiders, macro-moths, orthopterans and snails) invertebrate groups using a hierarchical spatial design, wherein three local-scale (200 m × 200 m) urbanization levels were repeatedly sampled across three landscape-scale (3 km × 3 km) urbanization levels. We tested for local and landscape urbanization effects on abundance and species richness of each group, whereby total richness was partitioned into the average richness of local communities and the richness due to variation among local communities. Abundances of the terrestrial active dispersers declined in response to local urbanization, with reductions up to 85% for butterflies, while passive dispersers did not show any clear trend. Species richness also declined with increasing levels of urbanization, but responses were highly heterogeneous among the different groups with respect to the richness component and the spatial scale at which urbanization impacts richness. Depending on the group, species richness declined due to biotic homogenization and/or local species loss. This resulted in an overall decrease in total richness across groups in urban areas. These results provide strong support to the general negative impact of urbanization on abundance and species richness within habitat patches and highlight the importance of considering multiple spatial scales and taxa to assess the impacts of urbanization on biodiversity.

Finding the perfect pairs: A matchmaking of plant markers and primers for multi-marker eDNA metabarcoding.

As the scope of plant eDNA metabarcoding diversifies, so do the primers, markers and methods. A wealth of primers exists today, but their comparative evaluation is lacking behind. Similarly, multi-marker approaches are recommended but debates persist regarding barcode complementarity and optimal combinations. After a literature compilation of used primers, we compared in silico 102 primer pairs based on amplicon size, coverage and specificity, followed by an experimental evaluation of 15 primer pairs on a mock community sample covering 268 plant species and genera, and about 100 families. The analysis was done for the four most common plant metabarcoding markers, rbcL, trnL, ITS1 and ITS2 and their complementarity was assessed based on retrieved species. By focusing on existing primers, we identify common designs, promote alternatives and enhance prior-supported primers for immediate applications. The ITS2 was the best-performing marker for flowering vascular plants and was congruent to ITS1. However, the combined taxonomic breadth of ITS2 and rbcL surpassed any other combination, highlighting their high complementarity across Streptophyta. Overall, our study underscores the significance of comprehensive primer and barcode evaluations tailored to metabarcoding applications.

Weak effect of urbanization on bdelloid rotifers living in lichens.

Human activities have an overwhelming impact on the natural environment, leading to a deep biodiversity crisis whose effects range from genes to ecosystems. Here, we analysed the effect of such anthropogenic impacts on bdelloid rotifers (Rotifera Bdelloidea), for whom these effects are poorly understood. We targeted bdelloid rotifers living in lichen patches across urbanization gradients in Flanders and Brussels (Belgium). Urbanization was measured as the percentage of built-up area (BU) across different spatial scales, at circles from 50 to 3200 m of radius around the lichen. Urbanization effects on biodiversity were assessed on abundance, species richness and community-weighted mean body size of bdelloid rotifers, as well as on genetic diversity of a mitochondrial marker (cytochrome c oxidase subunit I) of one of the most common and widespread bdelloid species, Adineta vaga. Overall, no negative effect of urbanization was found at any diversity level and any spatial scale. Counterintuitively, the BU area quantified at the largest spatial scale had a positive effect on abundance. These results leave open the question of whether negative effects of urbanization are present for bdelloid rotifers, if they are mediated by other unexplored drivers, or if such effects are only visible at even larger spatial scales.

Minimal requirements for ISO15189 validation and accreditation of three next generation sequencing procedures for SARS-CoV-2 surveillance in clinical setting.

Rapid and recurrent breakthroughs of new SARS-CoV-2 strains (variants) have prompted public health authorities worldwide to set up surveillance networks to monitor the circulation of variants of concern. The use of next-generation sequencing technologies has raised the need for quality control assessment as required in clinical laboratories. The present study is the first to propose a validation guide for SARS-CoV-2 typing using three different NGS methods fulfilling ISO15189 standards. These include the assessment of the risk, specificity, accuracy, reproducibility, and repeatability of the methods. Among the three methods used, two are amplicon-based involving reverse transcription polymerase chain reaction (Artic v3 and Midnight v1) on Oxford Nanopore Technologies while the third one is amplicon-based using reverse complement polymerase chain reaction (Nimagen) on Illumina technology. We found that all methods met the quality requirement (e.g., 100% concordant typing results for accuracy, reproducibility, and repeatability) for SARS-CoV-2 typing in clinical setting. Additionally, the typing results emerging from each of the three sequencing methods were compared using three widely known nomenclatures (WHO, Pangolineage, and Nextclade). They were also compared regarding single nucleotide variations. The outcomes showed that Artic v3 and Nimagen should be privileged for outbreak investigation as they provide higher quality results for samples that do not meet inclusion criteria for analysis in a clinical setting. This study is a first step towards validation of laboratory developed NGS tests in the context of the new European regulation for medical devices and in vitro diagnostics.

A Revised Phylogeny of the Mentha spicata Clade Reveals Cryptic Species.

The genus Mentha is taxonomically and phylogenetically challenging due to complex genomes, polyploidization and an extensive historical nomenclature, potentially hiding cryptic taxa. A straightforward interpretation of phylogenetic relationships within the section Mentha is further hindered by dominant but outdated concepts on historically identified hybrid taxa. Mentha spicata is traditionally considered to be of hybrid origin, but the evidence for this is weak. Here, we aim to understand the phylogenetic relationships within the section Mentha using large sample sizes and to revisit the hybrid status and identity of M. spicata. We show that two of three traditional species in the subsection Spicatae are polyphyletic, as is the subsection as a whole, while the real number of cryptic species was underestimated. Compared to previous studies we present a fundamentally different phylogeny, with a basal split between M. spicata s.s. and M. longifolia s.s. Cluster analyses of morphological and genotypic data demonstrate that there is a dissociation between morphologically and genotypically defined groups of samples. We did not find any evidence that M. spicata is of hybrid origin, and we conclude its taxonomic status should be revised. The combination of genetic and phenotypic information is essential when evaluating hyperdiverse taxonomic groups.

Response to Signorovitch et al.

Signorovitch et al.[1] comment that an Oenothera-like meiosis [2] could produce a pattern similar to what we observed in our study of natural isolates of the bdelloid rotifer Adineta vaga, which we attributed to horizontal gene transfers (HGTs) [3]. Indeed, our HGT hypothesis appears at first sight difficult to conciliate with their observation of a congruent pattern of allele sharing at four large loci possibly located on different chromosomes [4]. However, one might imagine conditions under which massive horizontal gene transfer between bdelloid individuals could produce such a pattern, notably if the individuals involved had previously lost most of their heterozygosity because of their exposure to frequent desiccation (which produces DNA double-strand breaks [5]). In the published A. vaga genome the loss of heterozygosity due to large-scale gene conversion events or break-induced replication covers only about 10% of the genome [6], but this percentage may be much higher in environmental isolates that often experience dessication. Besides, if an Oenothera-like mode of meiosis occurs in bdelloids frequently enough to be detected in a single sampling of 29 individuals (as in [4]), one would expect males and meiosis to be observed at least occasionally, and instances of congruent allele sharing across loci should turn up frequently in genetic surveys. This was not the case in [3]: among the 82 A. vaga individuals sequenced for four nuclear markers, no trio of individuals presented congruent patterns of shared sequences at different loci. For these reasons, and in the absence of any direct evidence for an Oenothera-like meiosis in bdelloids, we still consider inter-bdelloid HGTs a more parsimonious explanation for our results.

Genetic Exchange among Bdelloid Rotifers Is More Likely Due to Horizontal Gene Transfer Than to Meiotic Sex.

Although strict asexuality is supposed to be an evolutionary dead end, morphological, cytogenetic, and genomic data suggest that bdelloid rotifers, a clade of microscopic animals, have persisted and diversified for more than 60 Myr in an ameiotic fashion. Moreover, the genome of bdelloids of the genus Adineta comprises 8%-10% of genes of putative non-metazoan origin, indicating that horizontal gene transfers are frequent within this group and suggesting that this mechanism may also promote genetic exchanges among bdelloids as well. To test this hypothesis, we used five independent sequence markers to study the genetic diversity of 576 Adineta vaga individuals from a park in Belgium. Haplowebs and GMYC analyses revealed the existence of six species among our sampled A. vaga individuals, with strong evidence of both intra- and interspecific recombination. Comparison of genomic regions of three allele-sharing individuals further revealed signatures of genetic exchanges scattered among regions evolving asexually. Our findings suggest that bdelloids evolve asexually but exchange DNA horizontally both within and between species.