Biology subjects

Anslan, S.

Publications and source records attributed to Anslan, S..

9 recordsLinked to original sources

bioRxiv2026

The hidden multiverse of ecological roles in Fungi

Ecological roles are treated as discrete, bounded units of biological organization, even as evidence shows that many taxa are versatile, performing more than one of them. Each record of versatility represents a boundary crossing, yet current categorical paradigms prevent this cumulative evidence from reshaping the roles themselves. We solve this by introducing the ecological multiverse, a self-correcting framework that turns boundary crossings into a network of role connectivity. Applied to Fungi, the multiverse recasts the major form of plant pathogenicity from an isolated disease role into a central hub linking much of fungal functional space, especially benign plant symbioses and decomposition. By exposing this topology, the multiverse transforms categorical views of ecological function into a dynamic map, revealing pathways of role change as organisms and knowledge evolve.

ecology↗

bioRxiv2026

Full-length COI barcodes improve eDNA metabarcoding data denoising relative to mini-barcodes

Animal COI (mitochondrial cytochrome oxidase I) metabarcoding of environmental DNA (eDNA) is increasingly used to assess biodiversity in complex substrates such as soil. However, due to read-length constraints of second-generation sequencing platforms, mini-barcodes have been used instead of the full barcode region. Long-read sequencing technologies now enable the recovery of full-length barcode sequences, and are more commonly applied for studying microbes, but their use for metabarcoding the full-length standard COI barcoding region in animals remains limited. In this study, we compared three COI amplicon sets - 313 bp, 660 bp, and 1,256 bp - amplified from soil eDNA samples and sequenced using Illumina and PacBio platforms to evaluate their overall concurrence, the effectiveness of identifying nuclear mitochondrial DNA segments (NUMTs) and chimeras, as well as their respective taxonomic resolution. The long-read datasets exhibited a higher identification rate of NUMTs and true chimeras, suggesting that longer sequences improve the detection of noise in COI metabarcoding data, thereby reducing the occurrence of spurious taxa. Taxonomy assignment confidence was similar between the 313 bp and 660 bp datasets, whereas extending the amplicon beyond the standard COI barcode region (1,256 bp) reduced confidence, likely because longer reads extend into regions poorly represented in barcode reference databases. Despite substantially lower sequencing depth in the 660 bp dataset, per-sample OTU richness did not differ significantly from that recovered with the Illumina 313 bp amplicon set. Similarly, the relationships between samples were strongly correlated across the detected OTU communities, indicating consistent ecological interpretations between short and long amplicons. We conclude that the standard [~]658 bp COI barcode is an optimal marker for soil animal metabarcoding from eDNA, balancing target recovery, artifact detection, taxonomic assignment and ecological interpretability. As COI eDNA metabarcoding becomes increasingly used in biodiversity assessment and is increasingly adopted in large-scale monitoring initiatives, this study provides methodological guidance for improving the robustness of soil animal community biomonitoring.

ecology↗

bioRxiv2026

Benchmarking full-length ITS metabarcoding across Illumina 2x500, PacBio, and Oxford Nanopore sequencing using mock and soil communities

Metabarcoding is a powerful tool for biodiversity comparisons, where standard-size DNA barcodes (>500 bases) offer better taxonomic resolution than shorter ones. Still, the choice of sequencing platforms and bioinformatics pipelines may strongly affect inferred diversity due to various technical biases. We assessed the relative performance of Illumina MiSeq i100 (2x500 paired-end), PacBio Revio and Oxford Nanopore MinION sequencing and bioinformatics pipelines, using full-length ITS amplicon sequencing datasets from a 103-species mock community and 45 composite soil samples. Despite numerous low-quality reads, PacBio yielded the lowest overall error rate and highest number of taxa. Illumina revealed the highest proportion of chimeric and index-switched reads, along with a strong bias towards shorter amplicons. MinION data analysed using PRONAME and Minovar - a bioinformatics pipeline presented here - had the largest proportion of low-quality data, and rare taxa were lost during data filtering and read polishing steps. Although Minovar enabled amplicon sequence variant (ASV) level precision for common taxa, we recommend clustering ASVs into OTUs. For PacBio, standard filtering approaches outperformed the ASV approach because they retained rare taxa. For Illumina, a stringent ASV approach or removal of rare OTUs would limit artefacts. Across all platforms, excess PCR cycles promoted chimeric and low-quality reads and lost quantitativity in biodiversity assessments. With moderate differences in effect sizes, all analytical approaches supported the conclusion that sampling design determines how we see soil biodiversity responses to land use. For biodiversity surveys based on the full-length ITS metabarcoding, we recommend using PacBio sequencing with standard, non-ASV pipelines.

bioinformatics↗

bioRxiv2024

Common to rare transfer learning (CORAL) enables inference and prediction for a quarter million rare Malagasy arthropods

Modern DNA-based biodiversity surveys result in massive-scale data, including up to millions of species - of which most are rare. Making the most of such data for inference and prediction requires modelling approaches that can relate species occurrences to environmental and spatial predictors, while incorporating information about their taxonomic or phylogenetic placement. Even if the scalability of joint species distribution models to large communities has greatly advanced, incorporating hundreds of thousands of species has not been feasible to date, leading to compromised analyses. Here we present a novel "common to rare transfer learning" approach (CORAL), based on borrowing information from the common species to enable statistically and computationally efficient modelling of both common and rare species. We illustrate that CORAL leads to much improved prediction and inference in the context of DNA metabarcoding data from Madagascar, comprising 255,188 arthropod species detected in 2874 samples.

ecology↗

bioRxiv2023

What mycologists should talk about when they are talking about the International Code of Nomenclature for algae, fungi, and plants

Fungal metabarcoding of substrates such as soil, wood, and water are uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside of the ambit of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings challenge the present stance of the mycological community - that "the code" works fine and that these complications will somehow sort themselves out given enough time and a following wind - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. However, the present authors fear that no waves of change will be lapping the shores of mycology for the foreseeable future, leaving the overwhelming majority of extant fungi without formal names and thus scientific and environmental agency. It is not clear to us who benefits from that, but neither fungi nor mycology are likely to be on the winning side.

scientific communication and education↗

bioRxiv2022

Towards understanding diversity, endemicity and global change vulnerability of soil fungi

Fungi play pivotal roles in ecosystem functioning, but little is known about their global patterns of diversity, endemicity, vulnerability to global change drivers and conservation priority areas. We applied the high-resolution PacBio sequencing technique to identify fungi based on a long DNA marker that revealed a high proportion of hitherto unknown fungal taxa. We used a Global Soil Mycobiome consortium dataset to test relative performance of various sequencing depth standardization methods (calculation of residuals, exclusion of singletons, traditional and SRS rarefaction, use of Shannon index of diversity) to find optimal protocols for statistical analyses. Altogether, we used six global surveys to infer these patterns for soil-inhabiting fungi and their functional groups. We found that residuals of log-transformed richness (including singletons) against log-transformed sequencing depth yields significantly better model estimates compared with most other standardization methods. With respect to global patterns, fungal functional groups differed in the patterns of diversity, endemicity and vulnerability to main global change predictors. Unlike -diversity, endemicity and global-change vulnerability of fungi and most functional groups were greatest in the tropics. Fungi are vulnerable mostly to drought, heat, and land cover change. Fungal conservation areas of highest priority include wetlands and moist tropical ecosystems.

ecology↗

bioRxiv2019

Microbiomes from feces vs. gut in aquatic vertebrates: distinct community compositions between substrates and preservation methods

Sample type and preservation methods are likely to influence microbiome analysis results. Relatively few studies have explored the differences between feces and gut as well as ethanol-stored and frozen samples. Here, we sampled the same individuals of three aquatic vertebrates from the Qinghai-Tibetan Plateau non-invasively for feces, and subsequently for hindgut through dissection. Our study species, two fishes (Gymnocypris cf. namensis and Triplophysa sp.) and one amphibian (tadpoles of Nanorana parkeri), were all collected at the same time and site. Gut and fecal samples were stored in ethanol, and additionally, part of the gut samples were frozen, but temporarily thawed during transport as it often happens under difficult field conditions. Our results showed that both substrate (gut content vs. feces) as well as preservation method can influence the analysis of intestinal microbiomes. Frozen gut samples strongly differed from ethanol-stored samples, and especially in Nanorana most frozen samples were dominated (in relative abundance) by a set of Proteobacteria OTUs that were completely absent from the ethanol-stored samples. This blooming of contaminant bacteria occurred after less than 12 h of thawing, thus caution should be taken when constancy of cold temperatures cannot be maintained in the field for sample preservation purposes. Among ethanol-stored samples, bacterial communities from feces differed from those recovered from guts, but in part recovered similar patterns, such as a higher bacterial richness in the more herbivorous Nanorana tadpoles. Although our results argue against combining gut and fecal samples in analyses of host-specific microbiome differences, they also confirm that non-invasive sampling of feces can provide useful information of gut microbiomes in aquatic vertebrates, which may be important especially when working with endangered species.

microbiology↗

bioRxiv2019

Comparative genomic analysis reveals a monophyletic cold adapted Arthrobacter cluster from polar and alpine regions

Decrease in the frequency of arginine and increase in lysine are the trends that have been identified in the genomes of cold adapted bacteria. However, some cold adapted taxa show only limited or no detectable changes in the frequencies of amino acid composition. Here, we examined Arthrobacter spp. genomes from a wide range of environments on whether the genomic adaptations can be conclusively identified across genomes of taxa from polar and alpine regions. Phylogenetic analysis with a concatenated alignment of 119 orthologous proteins revealed a monophyletic clustering of seven polar and alpine isolated strains. Significant changes in amino acid composition related to cold adaptation were exclusive to seven of the twenty-nine strains from polar and alpine regions. Analysis of significant indicator genes and cold shock genes also revealed that clear differences could only be detected in the same seven strains. These unique characteristics may result from a vast exchange of genome content at the node leading to the monophyletic cold adapted Arthrobacter cluster predicted by the birth-and-death model. We then experimentally validated that strains with significant changes in amino acid composition have a better capacity to grow at low temperature than the mesophilic strains.\n\nImportanceAcquisition of novel traits through horizontal gene transfer at the early divergence of the monophyletic cluster may accelerate their adaptation to low temperature. Our study reached a clear relationship between adaptation to cold and genomic features and would advanced in understanding the ambiguous results produced by the previous studies on genomic adaption to cold temperature.

microbiology↗

bioRxiv2019

Relative performance of Oxford Nanopore MinION vs. Pacific Biosciences Sequel third-generation sequencing platforms in identification of agricultural and forest pathogens

Culture-based molecular characterization methods have revolutionized detection of pathogens, yet these methods are either slow or imprecise. The second-generation sequencing tools have much improved precision and sensitivity of detection, but the analysis processes are costly and take several days. Of third-generation techniques, the portable Oxford Nanopore MinION device has received much attention because of its small size and possibility of rapid analysis at reasonable cost. Here, we compare the relative performance of two third-generation sequencing instruments, MinION and Pacific Biosciences Sequel in identification and diagnostics of pathogens from conifer needles and potato leaves and tubers. We demonstrate that Sequel is efficient in metabarcoding of complex samples, whereas MinION is not suited for this purpose due to the high error rate and multiple biases. However, we find that MinION can be utilized for rapid and accurate identification of dominant pathogenic organisms from plant tissues following both amplicon-based and metagenomics-based approaches. Using the PCR-free approach with shortened extraction and incubation times, we performed the entire MinION workflow from sample preparation through DNA extraction, sequencing, bioinformatics and interpretation in two and half hours. We advocate the use of MinION for rapid diagnostics of pathogens, but care needs to be taken to control or account for all potential technical biases.\n\nIMPORTANCEWe develop new and rapid protocols for MinION-based third-generation diagnostics of plant pathogens that greatly improves the speed and precision of diagnostics. Due to high error rate and technical biases in MinION, PacBio Sequel platform is more useful for amplicon-based metabarcoding from complex biological samples.

microbiology↗