Freshwater protists: unveiling the unexplored in a large floodplain system

Interpreting phylogenetic placements for taxonomic assignment of environmental DNA

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 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 OTU placements within a subtaxon, and the branch distances between equally likely placement locations. We also inferred the evolutionary and ecological characteristics of the colpodean OTUs using their placements within subtaxa. This study demonstrates how to fully analyze the output of EPA-ng, by using GAPPA in conjunction with knowledge of the taxonomic diversity of the clade of interest.

Diversity of protist genera in periphyton of tufa-depositing karstic river

Purpose

In aquatic ecosystems, protists play a crucial role and cover numerous ecological functions. The karstic Krka River (Croatia) is a unique hotspot for high diversity of aquatic organisms, especially protists. The main objective of the present study was to obtain a detailed overview of the protist community structure in the periphyton of the Krka River and to determine the differences in protist diversity along the river.

Methods

Protist diversity was detected by amplicon sequencing of the hypervariable region V9 of the 18S rRNA gene, using the universal eukaryotic primer pair.

Results

The three main groups of protists were as follows: Ciliophora, Cercozoa, and Bacillariophyta. In terms of abundance of protist OTUs, the shade plot revealed an evident difference from the upstream to downstream river section, which increased between locations from Krka spring to Skradinski buk. Diversity was explored using measures of alpha and beta diversity. Alpha diversity showed an increasing trend in the downstream direction of the river. The location effect, or clustering/grouping of samples by location, was confirmed by the PERMANOVA permutation test of beta diversity.

Conclusion

The combination of alpha and beta diversity can help provide deeper insight into the study of diversity patterns, but also point out to decline in species diversity and allow for effective ways to protect aquatic karst habitats in future management.

Perkinsus marinus in bioreactor: growth and a cost-reduced growth medium

Perkinsus marinus (Perkinsea) is an osmotrophic facultative intracellular marine protozoan responsible for "Dermo" disease in the eastern oyster, Crassostrea virginica. In 1993 in vitro culture of P. marinus was developed in the absence of host cells. Compared to most intracellular protozoan parasites, the availability of P. marinus to grow in the absence of host cells has provided the basis to explore its use as a heterologous expression system. As the genetic toolbox is becoming available, there is also the need for larger-scale cultivation and lower-cost media formulations. Here, we took an industrial approach to scaled-up growth from a small culture flask to bioreactors, which required developing new cultivation parameters, including aeration, mixing, pH, temperature control, and media formulation. Our approach also enabled more real-time data collection on growth. The bioreactor cultivation method showed similar or accelerated growth rates of P. marinus compared to culture in T-flasks. Redox measurements indicated sufficient oxygen availability throughout the cultivation. Replacing fetal bovine serum with chicken serum showed no differences in the growth rate and a 60% reduction in the medium cost. This study opens the door to furthering P. marinus as a valid heterologous expression system by showing the ability to grow in bioreactors.

ONE-SENTENCE SUMMARY

Perkinsus marinus, a microbial parasite of oysters that could be useful for developing vaccines for humans, has been shown to grow well in laboratory equipment that can be expanded to commercial scale using a less expensive growth formula than usual laboratory practice.

metaPR2 : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists

In recent years, metabarcoding has become the method of choice for investigating the composition and assembly of microbial eukaryotic communities. The number of environmental data sets published has increased very rapidly. Although unprocessed sequence files are often publicly available, processed data, in particular clustered sequences, are rarely available in a usable format. Clustered sequences are reported as operational taxonomic units (OTUs) with different similarity levels or more recently as amplicon sequence variants (ASVs). This hampers comparative studies between different environments and data sets, for example examining the biogeographical patterns of specific groups/species, as well analysing the genetic microdiversity within these groups. Here, we present a newly-assembled database of processed 18S rRNA metabarcodes that are annotated with the PR² reference sequence database. This database, called metaPR² , contains 41 data sets corresponding to more than 4000 samples and 90,000 ASVs. The database, which is accessible through both a web-based interface (https://shiny.metapr2.org) and an R package, should prove very useful to all researchers working on protist diversity in a variety of systems.

Chromosome-level genome of Pedinomonas minor (Chlorophyta) unveils adaptations to abiotic stress in a rapidly fluctuating environment

The Pedinophyceae (Viridiplantae) comprise a class of small uniflagellate algae with a pivotal position in the phylogeny of the Chlorophyta as the sister group of the 'core chlorophytes'. We present a chromosome-level genome assembly of the freshwater type species of the class, Pedinomonas minor. We sequenced the genome using Pacbio, Illumina and Hi-C technologies, performed comparative analyses of genome and gene family evolution, and analyzed the transcriptome under various abiotic stresses. Although the genome is relatively small (55 Mb), it shares many traits with core chlorophytes including number of introns and protein-coding genes, messenger RNA (mRNA) lengths, and abundance of transposable elements. Pedinomonas minor is only bounded by the plasma membrane, thriving in temporary habitats that frequently dry out. Gene family innovations and expansions and transcriptomic responses to abiotic stresses have shed light on adaptations of P. minor to its fluctuating environment. Horizontal gene transfers from bacteria and fungi have possibly contributed to the evolution of some of these traits. We identified a putative endogenization site of a nucleocytoplasmic large DNA virus and hypothesized that endogenous viral elements donated foreign genes to the host genome, their spread enhanced by transposable elements, located at gene boundaries in several of the expanded gene families.