Biology subjects

Dunthorn, M. E.

Publications and source records attributed to Dunthorn, M. E..

5 recordsLinked to original sources

bioRxiv2026

The Leray-XT COI primer pair is not suitable for observing ciliates and radiolarians

The Leray-XT primer pair has been widely used to amplify the mitochondrial cytochrome c oxidase subunit I (COI) gene from animals. In some marine metabarcoding studies, protists have also been amplified and sequenced using these primers. Here, we ask if the Leray-XT COI primer pair is suitable for observing ciliates and radiolarians, which are numerically and ecologically important components of marine protistan communities. We show that while there are sufficient COI reference sequences for ciliates in NCBI for taxonomic assignments, there are currently only two COI reference sequences for radiolarians. Using in-silico analyses, we additionally show that while the reverse primer Leray-XT primer can bind and potentially amplify both ciliates and radiolarians, the forward primer cannot bind to either taxon. These results show that the Leray-XT primer pair is not suitable for observing ciliates and radiolarians, although it may be useful for observing other marine protistan taxa.

microbiology↗

bioRxiv2024

O Short-branch Microsporidia, Where Art Thou? Identifying diversity hotspots for future sampling

Short-branch Microsporidia were previously shown to form a basal grade within the expanded Microsporidia clade and to branch near the classical, long-branch Microsporidia. Although they share simpler versions of some morphological characteristics, they do not show accelerated evolutionary rates, making them ideal candidates to study the evolutionary trajectories that has led to long-branch microsporidians unique characteristics. However, most sequences assigned to the short-branch Microsporidia are undescribed, novel environmental lineages for which the identification requires knowledge of where they can be found. To direct future isolation, we used the EukBank database of the global UniEuk initiative that contains the majority of the publicly available environmental V4 SSU-rRNA gene sequences of protists. The curated OTU table and corresponding metadata were used to evaluate the occurrence of short-branch Microsporidia across freshwater, hypersaline, marine benthic, marine pelagic, and terrestrial environments. Presence-absence analyses infer that short-branch Microsporidia are most abundant in freshwater and terrestrial environments, and alpha- and beta-diversity measures indicate that focusing our sampling effort on these two environments would cover a large part of their overall diversity. These results can be used to coordinate future isolation and sampling campaigns to better understand the mysterious evolution of microsporidians unique characteristics.

microbiology↗

bioRxiv2022

Comparison of phylogenetic placements to pairwise alignments for taxonomic assignment of ciliate OTUs

Taxonomic assignment of OTUs is an important bioinformatics step in analyzing environmental sequencing data. Pairwise-alignment and phylogenetic-placement methods represent two alternative approaches to taxonomic assignments, but their results can differ. Here we used available colpodean ciliate OTUs from forest soils to compare the taxonomic assignments of VSEARCH (which performs pairwise alignments) and EPA-ng (which performs phylogenetic placements). We showed that when there are differences in taxonomic assignments between pairwise alignments and phylogenetic placements at the subtaxon level, there is a low pairwise similarity of the OTUs to the reference database. We then showcase how the output of EPA-ng can be further evaluated using GAPPA to assess the taxonomic assignments when there exist multiple equally likely placements of an OTU, by taking into account the sum over the likelihood weights of the OUT placements within a subtaxon, and the branch distances between equally likely placement locations. We also inferred evolutionary and ecological characteristics of the colpodean OTUs using their placements within subtaxa. This study demonstrates how to fully analyse the output of EPA-ng, by using GAPPA in conjunction with knowledge of the taxonomic diversity of the clade of interest.

evolutionary biology↗

bioRxiv2021

Above- and below-ground biodiversity responses to the prolonged flood pulse in central-western Amazonia, Brazil.

Amazonia encompasses forests that grow in areas that are periodically inundated by overflowing rivers. The inundation depth and duration vary according to the slope of the terrain, creating a flooding gradient. This gradient directly affects the biota, but the effect on soil organisms remains elusive. Here, we use DNA metabarcoding to estimate prokaryote and eukaryote diversity from soil and litter samples in a seasonally flooded forest and its adjacent unflooded forest in central-western Amazonia using 16S and 18S gene sequences, respectively. We characterize the below-ground diversity and community composition based on Amplicon Sequence Variants (ASVs) along the flooding gradient. We test for the relationship of soil biota with the flooding gradient, soil properties and above-ground woody plant diversity. The flooding gradient did not explain below-ground biodiversity. Nor was the below-ground diversity explained by the above-ground woody plant diversity. However, we found taxonomic groups not previously reported in Amazonian seasonally flooded forests. Also, the flooding gradient and woody plant diversity did, in part, explain the community composition of soil bacteria. Although the effects of the flooding gradient, soil properties and above-ground woody plant diversity is hard to quantify, our results thus indicate that flood stress could influence below-ground bacterial community composition.

ecology↗

bioRxiv2020

Identifying potential hosts of short-branch Microsporidia

Microsporidia are obligate parasites that are closely related to Fungi. While the widely-known "long-branch" Microsporidia infect mostly animals, the hosts of "short-branch" Microsporidia are only partially characterized or not known at all. Here, we used network analyses from Neotropical rainforest soil metabarcoding data, to infer co-occurrences between environmental lineages of short-branch microsporidians and their potential hosts. We found significant co-occurrences with several taxa, especially with Apicomplexa, Cercozoa, Fungi, as well as some Metazoa. Our results are the first step to identify potential hosts of the environmental lineages of short-branch microsporidians, which can be targeted in future molecular and microscopic studies.

microbiology↗