Micah Dunthorn
YOU?
Author Swipe
View article: Long Term Copepod Culture Houses a Rich Microbial Eukaryotic Community Including New and Known Symbionts
Long Term Copepod Culture Houses a Rich Microbial Eukaryotic Community Including New and Known Symbionts Open
Copepods, dominant marine zooplankton, are hosts to microbial eukaryotic symbionts, but the copepod eukaryome remains largely unexplored. We used 18S rRNA gene primers with reduced metazoan amplification to identify microbial eukaryotes in…
View article: Towards a trait-based framework for protist ecology and evolution
Towards a trait-based framework for protist ecology and evolution Open
Protists comprise the vast majority of eukaryotic genetic and functional diversity. While they have traditionally been difficult to study due to their small size and varied phenotypes, environmental sequencing studies have revealed the stu…
View article: Diversity and assembly mechanisms of zooplankton communities in freshwater aquaculture ponds
Diversity and assembly mechanisms of zooplankton communities in freshwater aquaculture ponds Open
Ecological succession is vital for forecasting ecosystem responses to environmental changes and their future states. Zooplankton, a primary natural food source in aquaculture, plays a crucial role in maintaining ecosystem function. Thus, u…
View article: Comparing the precision of two digital PCR applications for copy number comparisons in protists
Comparing the precision of two digital PCR applications for copy number comparisons in protists Open
View article: Investigating the dynamics of the aquatic community in Oslofjord through time series analysis of <scp>eDNA</scp>
Investigating the dynamics of the aquatic community in Oslofjord through time series analysis of <span>eDNA</span> Open
Understanding the 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 an…
View article: Distinct ecological processes shape micro-eukaryotic generalists and specialists in a canal-disturbed wetland, Lake Weishan, China
Distinct ecological processes shape micro-eukaryotic generalists and specialists in a canal-disturbed wetland, Lake Weishan, China Open
Micro-eukaryotic communities are highly sensitive to environmental changes, and their structure offers crucial insights into the impact of human activities on aquatic habitats. Despite their significance, the assembly mechanisms of micro-e…
View article: O short-branch Microsporidia, where art thou? Identifying diversity hotspots for future sampling
O short-branch Microsporidia, where art thou? Identifying diversity hotspots for future sampling Open
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 characte…
View article: Harnessing eDNA metabarcoding to investigate fish community composition and its seasonal changes in the Oslo fjord
Harnessing eDNA metabarcoding to investigate fish community composition and its seasonal changes in the Oslo fjord Open
View article: O Short-branch Microsporidia, Where Art Thou? Identifying diversity hotspots for future sampling
O Short-branch Microsporidia, Where Art Thou? Identifying diversity hotspots for future sampling Open
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 characte…
View article: Using digital <scp>PCR</scp> to predict ciliate abundance from ribosomal <scp>RNA</scp> gene copy numbers
Using digital <span>PCR</span> to predict ciliate abundance from ribosomal <span>RNA</span> gene copy numbers Open
Ciliates play a key role in most ecosystems. Their abundance in natural samples is crucial for answering many ecological questions. Traditional methods of quantifying individual species, which rely on microscopy, are often labour‐intensive…
View article: Harnessing eDNA metabarcoding to investigate fish community composition and its seasonal changes in the Oslo fjord
Harnessing eDNA metabarcoding to investigate fish community composition and its seasonal changes in the Oslo fjord Open
In the face of global ecosystem changes driven by anthropogenic activities, effective biomonitoring strategies are crucial for mitigating impacts on vulnerable aquatic habitats. Time series analysis underscores a great significance in unde…
View article: Harnessing eDNA metabarcoding to investigate fish community composition and its seasonal changes in the Oslo fjord
Harnessing eDNA metabarcoding to investigate fish community composition and its seasonal changes in the Oslo fjord Open
In the face of global ecosystem changes driven by anthropogenic activities, effective biomonitoring strategies are crucial for mitigating impacts on vulnerable aquatic habitats. Time series analysis underscores a great significance in unde…
View article: Interpreting phylogenetic placements for taxonomic assignment of environmental <scp>DNA</scp>
Interpreting phylogenetic placements for taxonomic assignment of environmental <span>DNA</span> Open
Taxonomic assignment of operational taxonomic units (OTUs) is an important bioinformatics step in analyzing environmental sequencing data. Pairwise alignment and phylogenetic‐placement methods represent two alternative approaches to taxono…
View article: Cationic Solution and Solid‐State Emitters – Robust Imaging Agents for Cells, Bacteria, and Protists
Cationic Solution and Solid‐State Emitters – Robust Imaging Agents for Cells, Bacteria, and Protists Open
A library of eight different cationic emitters with emission properties in solution and in solid‐state (solution and solid‐state emitters – SSSE) is presented. These compounds, bearing either ammonium or pyridinium groups, have been invest…
View article: Comparing Microsporidia-targeting primers for environmental DNA sequencing
Comparing Microsporidia-targeting primers for environmental DNA sequencing Open
Metabarcoding is a powerful tool to detect classical, and well-known “long-branch” Microsporidia in environmental samples. Several primer pairs were developed to target these unique microbial parasites, the majority of which remain undetec…
View article: Comparison of phylogenetic placements to pairwise alignments for taxonomic assignment of ciliate OTUs
Comparison of phylogenetic placements to pairwise alignments for taxonomic assignment of ciliate OTUs Open
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 res…
View article: Report of the 2022 Protistology Nordics meeting
Report of the 2022 Protistology Nordics meeting Open
PROTISTOLOGY Nordics (PiN) met May 10–11, 2022, at the Natural History Museum of the University of Oslo, Norway. PiN was designed to promote scientists in Nordic countries who study genetics, cell biology, ecology, and evolution of protist…
View article: Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade
Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade Open
Phylogenetic placement refers to a family of tools and methods to analyze, visualize, and interpret the tsunami of metagenomic sequencing data generated by high-throughput sequencing. Compared to alternative (e. g., similarity-based) metho…
View article: Molecular insight reveals broad-scale spatial patterns in floodplain ciliate assemblages, whereas morphology reflects local environmental controls
Molecular insight reveals broad-scale spatial patterns in floodplain ciliate assemblages, whereas morphology reflects local environmental controls Open
One of the major goals in microbial ecology is to understand whether the empirical biogeographic patterns of macroorganisms also apply to microorganisms. Here, we used morphological data from live organisms, along with molecular data, to i…
View article: Metagenomic Analysis using Phylogenetic Placement -- A Review of the\n First Decade
Metagenomic Analysis using Phylogenetic Placement -- A Review of the\n First Decade Open
Phylogenetic placement refers to a family of tools and methods to analyze,\nvisualize, and interpret the tsunami of metagenomic sequencing data generated\nby high-throughput sequencing. Compared to alternative (e. g.,\nsimilarity-based) me…
View article: Future prospects for investigating ciliate biodiversity
Future prospects for investigating ciliate biodiversity Open
Ciliates have a long history of being central in evolutionary and ecological studies on eukaryotic microorganisms. Although thousands of species have been discovered, their total diversity still remains unknown. Here, we will discuss two u…
View article: Metabarcoding advances for ecology and biogeography of Neotropical protists: what do we know, where do we go?
Metabarcoding advances for ecology and biogeography of Neotropical protists: what do we know, where do we go? Open
The Neotropics is one of the most diverse regions of the globe in terms of plants and animal species. Regarding the microbial world, however, little is known about the diversity and biogeography patterns of microorganisms in the Neotropics…
View article: Above‐ and below‐ground biodiversity responses to the prolonged flood pulse in central‐western Amazonia, Brazil
Above‐ and below‐ground biodiversity responses to the prolonged flood pulse in central‐western Amazonia, Brazil Open
Amazonia encompasses extensive forests in areas that are periodically inundated by overflowing rivers. The inundation depth and duration vary according to the slope of the terrain and distance to major water bodies. This creates a flooding…
View article: Indigenous microbial communities in heavy oil show a threshold response to salinity
Indigenous microbial communities in heavy oil show a threshold response to salinity Open
Microbial degradation influences the quality of oil resources. The environmental factors that shape the composition of oil microbial communities are largely unknown because most samples from oil fields are impacted by anthropogenic oil pro…
View article: Report of the 2021 meeting of the International Society of Protistologists
Report of the 2021 meeting of the International Society of Protistologists Open
The International Society of Protistologists (ISOP) met online from 26 to 30 July, 2021. The Program and Abstract book for this is available here (File S1). An in-person international meeting was not possible due to the continued COVID-19 …
View article: Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data
Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data Open
Although ciliates are one of the most dominant microbial eukaryotic groups in many environments, there is a lack of updated global ciliate alignments and reference trees that can be used for phylogenetic placement methods to analyze enviro…
View article: Swarm v3: towards tera-scale amplicon clustering
Swarm v3: towards tera-scale amplicon clustering Open
Motivation Previously we presented swarm, an open-source amplicon clustering programme that produces fine-scale molecular operational taxonomic units (OTUs) that are free of arbitrary global clustering thresholds. Here, we present swarm v3…
View article: Phylogenetic relatedness drives protist assembly in marine and terrestrial environments
Phylogenetic relatedness drives protist assembly in marine and terrestrial environments Open
Aim Assembly of protist communities is known to be driven mainly by environmental filtering, but the imprint of phylogenetic relatedness is unknown. In this study, we aimed to test the degree to which co‐occurrences and co‐exclusions of pr…
View article: Above- and below-ground biodiversity responses to the prolonged flood pulse in central-western Amazonia, Brazil
Above- and below-ground biodiversity responses to the prolonged flood pulse in central-western Amazonia, Brazil Open
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 affec…
View article: Assessing Biotic and Abiotic Interactions of Microorganisms in Amazonia through Co-Occurrence Networks and DNA Metabarcoding
Assessing Biotic and Abiotic Interactions of Microorganisms in Amazonia through Co-Occurrence Networks and DNA Metabarcoding Open