Biology subjects

Macher, J.-N.

Publications and source records attributed to Macher, J.-N..

10 recordsLinked to original sources

bioRxiv2025

Urbanisation drives non-linear, guild-specific restructuring of fungal communities in coastal dune habitats

Coastal dunes form dynamic ecosystems where fungal communities play critical roles in nutrient cycling and plant establishment. Urban expansion increasingly fragments these habitats through trampling, beach grooming, and nutrient inputs, yet the effects of urbanization on below{square}ground fungal diversity remain poorly understood. We used eDNA metabarcoding on 294 soil cores from 49 transects spanning 35 km of the Dutch coast to test how urban proximity influences total fungal diversity and composition in different functional guilds (litter saprotrophs, plant pathogens, mycorrhizal fungi) across incipient (early-successional) and established dunes. Urban effects were habitat-specific and generally strongest in incipient dunes. In incipient dunes, total alpha diversity showed a U-shaped relationship with city distance, with minima at intermediate distances, whereas established dunes showed weak responses. Fungal guilds diverged in their responses as predicted: litter saprotroph diversity increased with distance from cities in both habitats (consistent with greater organic inputs by vegetation), plant pathogens showed U-shaped diversity in incipient dunes, suggesting distinct urban-associated and native-associated assemblages, and mycorrhizal diversity increased with distance in both habitats, consistent with limited suitable hosts and higher disturbance near cities. Partitioning of beta diversity revealed that turnover, rather than nestedness, accounted for almost all variation in community composition, indicating taxon replacement rather than directional loss. Community uniqueness was higher near cities, particularly in incipient dunes and for most guilds, implying that urban environments foster compositionally atypical assemblages relative to the regional pool. Overall, urbanization acts as a trait-based environmental filter, restructuring fungal communities without necessarily reducing fungal diversity. Stronger responses in early-successional dunes highlight their vulnerability to combined natural and urban stressors and the need to prioritize protection of incipient coastal habitats under intensifying urban pressure.

ecology↗

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↗

bioRxiv2023

Comparative mitogenomics of native European and alien Ponto-Caspian amphipods

European inland surface waters harbor an extensive diversity of native amphipod crustaceans with many species facing threats from invasive counterparts of Ponto-Caspian origin. Herein, we examine mitochondrial genomes to infer phylogenetic relationships and compare gene order and nucleotide composition between representative native European and invasive Ponto-Caspian taxa belonging to five families, ten genera, and 20 species (13 newly sequenced herein). We observe diverse gene rearrangement patterns in the phylogenetically disparate native species pool. Pallaseopsis quadrispinosa and Synurella ambulans show significant departures from the typical organization, with extensive translocations of tRNAs and the nad1 gene, as well as a tRNA-F polarity switch in the latter. The monophyletic alien Ponto-Caspian gammarids display a conserved gene order, mainly differing from the native species by a tRNA-E and tRNA-R translocation, which strengthens previous findings. However, extensive rearrangement is observed in Chaetogammarus warpachowskyi with translocations of six tRNAs. The alien corophiid, Chelicorophium curvispinum, displays a very conserved gene order despite its distant phylogenetic position. We also find that native species have a significantly higher GC and lower AT content than invasive ones. The observed mitogenomic differences between native and invasive amphipods need further investigation and could shed light on the mechanisms underlying invasion success.

molecular biology↗

bioRxiv2023

Single-cell genomics reveals the divergent mitochondrial genomes of Retaria (Foraminifera and Radiolaria)

Mitochondria originated from an ancient bacterial endosymbiont that underwent reductive evolution by gene loss and endosymbiont gene transfer to the nuclear genome. The diversity of mitochondrial genomes published to date has revealed that gene loss and transfer processes are ongoing in many lineages. Most well-studied eukaryotic lineages are represented in mitochondrial genome databases, except for the superphylum Retaria--the lineage comprising Foraminifera and Radiolaria. Using single-cell approaches, we present two complete mitochondrial genomes of Foraminifera and two near-complete mitochondrial genomes of radiolarians. We report the complete coding content of an additional 14 foram species. We show that foraminiferan and radiolarian mitochondrial genomes encode a nearly fully overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. In contrast to animals and fungi, many protists encode a diverse set of proteins on their mitochondrial genomes, including several ribosomal genes; however, some aerobic eukaryotic lineages (euglenids, myzozoans, and chlamydomonas-like algae) have reduced mitochondrial gene content and lack all ribosomal genes. Similar to these reduced outliers, we show that retarian mitochondrial genomes lack ribosomal protein and tRNA genes, contain truncated and divergent small and large rRNA genes, and encode only 14-15 protein-coding genes, including nad1, 3, 4, 4L, 5, 7, cob, cox1, 2, 3, atp1, 6, and 9, with forams and radiolarians additionally encoding nad2 and nad6, respectively. In radiolarian mitogenomes, a non-canonical genetic code was identified in which all three stop codons encode amino acids. Collectively, these results add to our understanding of mitochondrial genome evolution and fill in one of the last major gaps in mitochondrial sequence databases.

genomics↗

bioRxiv2023

Comparative phylogeography of Ponto-Caspian amphipods throughout the invaded Baltic and native NW Black Sea donor ranges. Can introduction mode affect genetic diversity?

The Baltic countries harbor a diverse assemblage of alien amphipods of Ponto-Caspian origin. The composition of this fauna was shaped by three invasion waves: 1) pre-20th century dispersals via watershed-connecting canals, 2) deliberate introductions in the 1960s, and 3) new dispersals during the last decade via shipping and pre-existing canals. Given this rich invasion history, we test whether genetic diversity (mitochondrial and nuclear) differs between the native and invaded ranges and between the deliberately introduced species and the ones that dispersed on their own. Our results show a significant decrease in mitochondrial but not nuclear genetic diversity in the invaded Baltic range. We also find that in the invaded range the introduced species exhibit a higher mitochondrial and nuclear genetic diversity than the species that dispersed on their own, while in the native range only the nuclear diversity is higher in introduced species. Mitochondrial diversity was more structured geographically in the native range and the dominant invasive haplotypes were detected in the native populations of all but one species, further highlighting the utility of this marker in tracing invasion sources. Our comparative approach provides important insight into the inter-range genetic diversity of Ponto-Caspian invaders, highlighting the role of introduction mode.

evolutionary biology↗

bioRxiv2020

Metabarcoding reveals different zooplankton communities in northern and southern areas of the North Sea

Zooplankton are key players in marine ecosystems, linking primary production to higher trophic levels. The high abundance and high taxonomic diversity renders zooplankton ideal for biodiversity monitoring. However, taxonomic identification of the zooplankton assemblage is challenging due to its high diversity, subtle morphological differences and the presence of many meroplanktonic species, especially in coastal seas. Molecular techniques such as metabarcoding can help with rapid processing and identification of taxa in complex samples, and are therefore promising tools for identifying zooplankton communities. In this study, we applied metabarcoding of the mitochondrial cytochrome c oxidase I gene to zooplankton samples collected along a latitudinal transect in the North Sea, a shelf sea of the Atlantic Ocean. Northern regions of the North Sea are influenced by inflow of oceanic Atlantic waters, whereas the southern parts are characterised by more coastal waters. Our metabarcoding results indicated strong differences in zooplankton community composition between northern and southern areas of the North Sea, particularly in the classes Copepoda, Actinopterygii (ray-finned fishes) and Polychaeta. We compared these results to the known distributions of species reported in previous studies, and by comparing the abundance of copepods to data obtained from the Continuous Plankton Recorder (CPR). We found that our metabarcoding results are mostly congruent with the reported distribution and abundance patterns of zooplankton species in the North Sea. Our results highlight the power of metabarcoding to rapidly assess complex zooplankton samples, and we suggest that the technique could be used in future monitoring campaigns and biodiversity assessments. HighlightsO_LIZooplankton communities are different in northern and southern areas of the North Sea C_LIO_LIMetabarcoding results are consistent with known species distributions and abundance C_LIO_LIMetabarcoding allows for fast identification of meroplanktonic species C_LI

molecular biology↗

bioRxiv2020

The mitochondrial genomes of 11 aquatic macroinvertebrate species from Cyprus

Aquatic macroinvertebrates are often identified based on morphology, but molecular approaches like DNA barcoding, metabarcoding and metagenomics are increasingly used for species identification. These approaches require the availability of DNA references deposited in public databases. Here we report the mitochondrial genomes of 11 aquatic macroinvertebrates species from Cyprus, a European Union island country in the Mediterranean. Only three of the molecularly identified species could be assigned to a species name, highlighting the need for taxonomic work that leads to the formal description and naming of species, and the need for further genetic work to fill the current gaps in reference databases containing aquatic macroinvertebrates.Competing Interest StatementThe authors have declared no competing interest.View Full Text

molecular biology↗

bioRxiv2017

Environmental DNA metabarcoding of rivers: Not all eDNA is everywhere, and not all the time

Environmental DNA metabarcoding has become a popular tool for the assessment of freshwater biodiversity, but it is largely unclear how sampling time and location influence the assessment of communities. Abiotic factors in rivers can change on small spatial and temporal scale and might greatly influence eDNA metabarcoding results. In this study, we sampled three German rivers at four locations per sampling site: 1. Left river side, surface water 2. Right river side, surface water, 3. Left side, close to the riverbed, 4. Right side, close to the riverbed. For the rivers Ruhr and Mohne, sampling was conducted three times in spring, each sampling one week apart. The Ruhr was again sampled in autumn and the Gillbach was sampled in winter. Sequencing on an Illumina MiSeq with COI primers Bf2/BR2 revealed diverse communities (6493 Operational taxonomic units, OTUs), which largely differed between rivers. Communities changed significantly over time in the Ruhr, but not in the Mohne. Sampling location influenced recovered communities in the Mohne and in the Ruhr in autumn. Our results have important implications for future eDNA studies, which should take into account that not all eDNA in rivers is everywhere and not at all times.

molecular biology↗