Biology subjects

Dunthorn, M.

Publications and source records attributed to Dunthorn, M..

8 recordsLinked to original sources

bioRxiv2025

Investigating the dynamics of the aquatic community in Oslofjord through time series analysis of eDNA

Understanding temporal dynamics of marine communities is critical for assessing ecosystem health and guiding conservation efforts. Here, we conducted a survey using environmental DNA (eDNA) metabarcoding with two primer sets, MiFish and Elas02, to investigate seasonal and interannual changes in the fish community of Oslofjord (Norway) over two consecutive years. Using the MitoFish reference database through the GBIF querying tool, we identified 61 fish species and found significant changes in the dominant taxa between seasons and years. Clupea harengus (Atlantic herring) consistently peaked in early spring, while Scomber scombrus (Atlantic mackerel) dominated winter months in the second year. The MiFish primer set showed increased species richness in the second year, whereas the Elas02 primer set showed stable richness despite compositional turnover. Non-metric multidimensional scaling (NMDS) revealed distinct community separation between years in presence/absence data, driven by species turnover rather than abundance read changes. Our findings support the use of eDNA metabarcoding to capture fine-scale temporal dynamics and emphasise the importance of multi-year datasets for distinguishing ecological trends from stochastic changes. This strategy improves monitoring practices for marine ecosystems under anthropogenic stressors.

ecology↗

bioRxiv2020

The windblown: possible explanations for dinophyte DNA in forest soils

Dinophytes are widely distributed in marine- and fresh-waters, but have yet to be conclusively documented in terrestrial environments. Here we evaluated the presence of these protists from an environmental DNA metabarcoding dataset of Neotropical rainforest soils. Using a phylogenetic placement approach with a reference alignment and tree, we showed that the numerous sequencing reads that were assigned to the dinophytes did not associate with taxonomy, environmental preference, nutritional mode, or dormancy. All the dinophytes in the soils are most likely windblown dispersal units of aquatic species, and are not biologically active residents of terrestrial environments.

microbiology↗

bioRxiv2020

Evaluating geographic variation within molecular operational taxonomic units (OTUs) using network analyses in Scandinavian lakes

Operational taxonomic units (OTUs) are usually treated as if they are internally uniform in environmental metabarcoding studies of microbial and macrobial eukaryotes, even when the OTUs are being used to infer biogeographic patterns. The OTUs constructed by the program Swarm have underlying network topologies in which nodes represent amplicons and edges represent 1 nucleotide differences between nodes. Such networks can be exploited to search for biogeographic patterns within each OTU. To do this, here we used an available protistan metabarcoding dataset consisting of the hypervariable V4 region of the 18S rRNA locus amplified from 77 lakes collected across Norway and Sweden. The 82 most abundant and wide-spread OTUs constructed by Swarm were evaluated using shortest path, assortativity, and geographical analyses. We found that while pairs of amplicons from the same lake were usually connected directly to each other within the OTUs, these pairs of amplicons from the same lake did not form assortative clusters within the OTUs, and amplicons were not more connected with other amplicons occurring in neighboring lakes than expected by chance. This new approach to looking at within-OTU is applicable to other metabarcoding datasets and we provide code to perform these analyses.

microbiology↗

bioRxiv2020

Relating network analyses to phylogenetic relatedness to infer protistan co-occurrences and co-exclusions in marine and terrestrial environments

We used two large-scale metabarcoding datasets to evaluate phylogenetic signals at global marine and regional terrestrial scales using co-occurrence and co-exclusion networks. Phylogenetic relatedness was estimated using either global pairwise sequence distance or phylogenetic distance and the significance of observed patterns relating networks and phylogenies were evaluated against two null models. In all datasets, we found that phylogenetically close OTUs significantly co-occurred more often, and OTUs with intermediate phylogenetic relatedness co-occurred less often, than expected by chance. Phylogenetically close OTUs co-excluded less often than expected by chance in the marine datasets only. Simultaneous excess of co-occurrences and co-exclusions were observed in the inversion zone between close and intermediate phylogenetic distance classes in marine surface. Similar patterns were observed by using either pairwise sequence or phylogenetic distances, and by using both null models. These results suggest that environmental filtering and dispersal limitation are the preponderant forces driving co-occurrence of protists in both environments, while signal of competitive exclusion was only detected in the marine surface environment. The discrepancy in the co-exclusion pattern is potentially linked to the individual environments: water bodies are more homogeneous while tropical forest soils contain a myriad of nutrient rich micro-environment reducing the strength of mutual exclusion.

ecology↗

bioRxiv2018

Planktonic Protist Biodiversity and Biogeography in Lakes From Four Brazilian River-Floodplain Systems

While the biodiversity and biogeography of protists inhabiting many ecosystems have been intensely studied using different sequencing approaches, tropical ecosystems are relatively under-studied. Here we sampled planktonic waters from 32 lakes associated with four different river-floodplains systems in Brazil, and sequenced the DNA using a metabarcoding approach with general eukaryotic primers. The lakes were dominated by the largely free-living Discoba (mostly the Euglenida) and Ciliophora unlike previously sampled Neotropical environments, bu the community similarities between samples were likewise low. These protists inhabiting these floodplains potentially form part of the large diversity of unknown diversity in the tropics.

microbiology↗

bioRxiv2017

Persistent patterns of high alpha and low beta diversity in tropical parasitic and free-living protists

Animal and plant communities in tropical rainforests are known to have high alpha diversity within forests, but low beta diversity between forests. By contrast, it is unknown if the microbial protists inhabiting the same ecosystems exhibit similar biogeographic patterns. To evaluate the biogeographies of soil protists in three lowland Neotropical rainforests using metabarcoding data, we estimated taxa-area and distance-decay relationships for three large protist taxa and their subtaxa, at both the OTU and phylogenetic levels, with presence-absence and abundance based measures, and compared the estimates to null models. High local alpha and low regional beta diversity patterns were persistently found for both the parasitic Apicomplexa and the free-living Cercozoa and Ciliophora, even though they have different ecological functions and different dispersal modes. In comparison to the null models, both OTU and phylogenetic diversities showed spatial structures between forests, but only phylogenetic diversity showed spatial patterns within forests. These results suggest that the biogeographies of macro-and micro-organismal eukaryotes in lowland Neotropical rainforests are partially structured by the same general processes. As with arthropods, the protists high alpha diversity within forests presents problems for estimating their local diversity, and shows that regional diversity cannot be easily estimated because of low turnover between forests.

ecology↗

bioRxiv2017

Yeasts Dominate Soil Fungal Communities In Three Lowland Neotropical Rainforests

Forest soils typically harbour a vast diversity of fungi, but are usually dominated by filamentous (hyphae-forming) taxa. Compared to temperate and boreal forests, though, we have limited knowledge about the fungal diversity in tropical rainforest soils. Here we show, by environmental metabarcoding of soil samples collected in three Neotropical rainforests, that Yeasts dominate the fungal communities in terms of the number of sequencing reads and OTUs. These unicellular forms are commonly found in aquatic environments, and their hyperdiversity may be the result of frequent inundation combined with numerous aquatic microenvironments in these rainforests. Other fungi that are frequent in aquatic environments, such as the abundant Chytridiomycotina, were also detected. While there was low similarity in OTU composition within and between the three rainforests, the fungal communities in Central America were more similar to each other than the communities in South America, reflecting a general biogeographic pattern also seen in animals, plants, and protists.\n\nContactdunthorn@rhrk.uni-kl.de

microbiology↗

bioRxiv2017

Meiotic Genes In Colpodean Ciliates Support Secretive Sexuality

Colpodean ciliates potentially pose a problem to macro-organismic theories of evolution: they are putatively asexual and extremely ancient, and yet there is one apparently derived sexual species. If macro-organismic theories of evolution also broadly apply to microbial eukaryotes, though, then most or all of the colpodean ciliates should merely be secretively sexual. Here we show using de novo genome sequencing, that colpodean ciliates have the meiotic genes required for sex and these genes are under functional constraint. Along with these genomic data, we argue that these ciliates are sexual given the cytological observations of both micronuclei and macronuclei within their cells, and the behavioral observations of brief fusions as if the cells were mating. The challenge that colpodean ciliates pose is therefore not to evolutionary theory, but to our ability to induce microbial eukaryotic sex in the laboratory.\n\nContact: dunthorn@rhrk.uni-kl.de

evolutionary biology↗