Biology subjects

Rixen, C.

Publications and source records attributed to Rixen, C..

5 recordsLinked to original sources

bioRxiv2026

Exploring nematode diversity in soils: comparison of extraction methods and sequencing protocols

Soil nematodes play key roles in regulating organic matter decomposition, nutrient cycling and trophic interactions in the soil ecosystem, and are very useful bioindicators of soil condition and soil health. But to characterise them, we need reliable measurements of nematode biodiversity in soils. DNA-based techniques such as metabarcoding have recently explored their biodiversity, with successful results. However, there are many methodological steps that can modify the outcome considerably and require informed decisions. In this study, we tested the effect on nematode alpha and beta diversity metrics of three methodological steps, namely i) type of extraction of genetic material from the matrix, either from soil directly with different starting amount of material or extracting nematodes first via the Baermann or Oostenbrink methods, ii) the choice of taxonomically-relevant DNA segment for amplification, with a nematode specific primer (NemF/18Sr2b) and a universal eukaryotic primer (3NDf/1132rmod), both within 18S rDNA, and iii) the selection of appropriate reference library for taxonomic assignment (comparing three nematode specialised databases and three broad taxonomic databases). Observed differences in alpha diversity were more pronounced when comparing the nematode extraction vs soil extractions. In particular, direct soil extractions co-extracted many non-nematode taxa, especially if amplified with a universal primer, which can significantly reduce the number of nematode reads obtained and therefore the accuracy of nematode community indexes and other nematode-based metrics. The choice of the reference database strongly affected the taxonomic identification, which calls for extreme caution when making this selection. Notably, specialised databases tended to over assign reads to nematodes that were detected as non-nematodes by broad taxonomic databases. However, beta diversity metrics were consistent across methods, highlighting these metrics as robust against methodological choices. Our study clearly demonstrates that the choices of methods for nematode biodiversity studies using molecular tools can have a big impact on the results, and decisions should be made consciously and carefully.

ecology↗

bioRxiv2024

Variable responses of alpine-plant communities to warming and loss of dominant species

Responses of ecological communities to perturbations are inherently variable because responses of their constituent populations also vary. Species within a single community may show combinations of no response, positive responses, and negative responses to any given perturbation often canceling each other out resulting in small or no signal that the community level. Here we explore the impacts of warming and loss of the dominant species on alpine ecosystems in a global study. We investigate warming and species-loss treatments on population- and community-level dynamics across alpine-plant communities at two elevations in five globally-distributed mountain locations. Communities showed varied responses to treatments; no community showed strong responses to a single treatment. Rather, most sites were influenced by both perturbations. Populations within these communities responded idiosyncratically, suggesting that constituent species are not all equally robust to perturbations even when community-level effects appear weak. Our results highlight the challenge of making general predictions about population- and community-level responses of alpine ecosystems in the face of present and future perturbations.

ecology↗

bioRxiv2023

Female-biased population sex ratios caused by genetic rather than ecological mechanisms

1. Biased sex ratios among reproductive individuals are common in plants, but the underlying mechanisms, as well as the evolutionary consequences, are not well understood. The classical theory of Dusing and Fisher predicts an equal primary sex ratio at seed production, based on the selective advantage of the rare sex. Biased sex ratios among reproductive plants can arise from sexual dimorphism in survival and flowering. Sex ratio biases can also be present from seed; in these cases, assumptions of Dusings and Fishers theory, for example, random mating or demographic equilibrium, were not met. 2. We investigated mechanisms leading to female-biased sex ratios in the arctic-alpine dwarf willow Salix herbacea L. We studied sex ratios in three natural populations over three years as well as in 29 crosses (full-sib families) under controlled conditions over four growth periods. We tested whether sex ratio was associated with germination, survival or flowering, and whether females and males differed in habitat, size or flowering. 3. We detected a strong and consistent female bias, both in natural populations (sex ratio [proportion of females]: 0.71-0.82) and in our controlled experiment (overall sex ratio: 0.70-0-72). Our data did not support habitat segregation of the sexes or sexual dimorphism in size or flowering. Family sex ratios varied largely (from 0.25 to 1), including many female-biased families, but also unbiased families and two male-biased families. Families with lower germination, seedling establishment, survival or flowering did not have stronger female bias, indicating that intrinsically higher survival or flowering in females does not explain overall female bias. 4. Synthesis. Our results suggest that sex ratio bias in S. herbacea is already present in seeds and does not arise through intrinsic differences between sexes. Candidate mechanisms that can lead to both overall female bias and variation in sex ratio among families are meiotic drive or cyto-nuclear interactions. The pioneer habit of Salix may lead to non-equilibrium population dynamics that allow for the long-term persistence of variable genetic sex ratio distortion systems that arise from genetic conflict.

evolutionary biology↗

bioRxiv2023

Biotic interactions explain seasonal dynamics of the alpine soil microbiome

BackgroundThe soil alpine microbiome is dependent on season and elevation, yet there is limited understanding of how complex communities are differentially shaped by abiotic and biotic factors. Here we investigated the spring-to-summer dynamics of soil microbiomes in alpine grasslands, focussing on soil food web interactions. To this end, we conducted a survey along altitudinal transects in three mountains in the Alps, in spring at snowmelt and in the following summer, recorded vegetation and topographic, climatic and edaphic parameters for 158 soil samples. By using metatranscriptomics, we simultaneously assessed prokaryotic and eukaryotic communities, further classified by nutrition guilds. ResultsOur results show: (i) that biotic interactions could explain more variation of the microbial communities than topographic and edaphic variables, more for consumers than for preys, and this effect was stronger in summer than in spring; (ii) a seasonal dynamic in biotic interactions: the consumers pressure on preys increases from spring to summer, resulting in a higher diversity and evenness of preys. ConclusionIn alpine grasslands, consumers effectively contribute to maintain the diverse soil bacterial and fungal community essential for ecosystem functioning.

ecology↗

bioRxiv2017

New barcoded primers for efficient retrieval of cercozoan sequences in high-throughput environmental diversity surveys, with emphasis on worldwide biological soil crusts

We describe the performance of a new metabarcoding approach to investigate the environmental diversity of a prominent group of widespread unicellular organisms, the Cercozoa. Cercozoa is an immensely large group of protists and although it may dominate in soil and aquatic ecosystems, its environmental diversity remains undersampled. We designed PCR primers targeting the hyper-variable region V4 of the small subunit ribosomal RNA (SSU or 18S) gene, which is the recommended barcode marker for Cercozoa. The length of the amplified fragment (ca. 350 bp) is suitable for Illumina MiSeq, the most cost-effective platform for molecular environmental surveys. We provide barcoded primers, an economical alternative to multiple libraries for multiplex sequencing of over a hundred samples. In silico, our primers matched 68% of the cercozoan sequences of the reference database and performed better than previously proposed new generation sequencing primers. In mountain grasslands soils and in biological soil crusts from a variety of climatic regions, we were able to detect cercozoan sequences encompassing nearly the whole range of the phylum. We obtained 901 OTUs at 97% similarity threshold from 26 samples, with ca. 50,000 sequences per site, and only 8% of non-cercozoan sequences. We could contribute to a further increase of the diversity of Cercozoa, since only 43% of the OTUs were 97-100% similar to any known sequence. Our study thus provides an advanced tool for cercozoan metabarcoding and to investigate their diversity and distribution in the environment.

bioinformatics↗