Insights from single-strain and mixed culture experiments on the effects of heatwaves on freshwater flagellates.

The increasing frequency and intensity of heatwaves driven by climate change significantly impact microbial communities in freshwater habitats, particularly eukaryotic microorganisms. Heterotrophic nanoflagellates are important bacterivorous grazers and play a crucial role in aquatic food webs, influencing the morphological and taxonomic structure of bacterial communities. This study investigates the responses of three flagellate taxa to heatwave conditions through single-strain and mixed culture experiments, highlighting the impact of both biotic and abiotic factors on functional redundancy between morphologically similar protist species under thermal stress.

Microbial, holobiont, and Tree of Life eDNA/eRNA for enhanced ecological assessment.

Microbial environmental DNA and RNA (collectively 'eNA') originate from a diverse and abundant array of microbes present in environmental samples. These eNA signals, largely representing whole organisms, serve as a powerful complement to signals derived from fragments or remnants of larger organisms. Integrating microbial data into the toolbox of ecosystem assessments and biotic indices therefore has the potential to transform how we use eNA data to understand biodiversity dynamics and ecosystem functions, and to inform the next generation of environmental monitoring.

Exploring the efficacy of metabarcoding and non-target screening for detecting treated wastewater.

Wastewater treatment processes can eliminate many pollutants, yet remainder pollutants contain organic compounds and microorganisms released into ecosystems. These remainder pollutants have the potential to adversely impact downstream ecosystem processes, but their presence is currently not being monitored. This study was set out with the aim of investigating the effectiveness and sensitivity of non-target screening of chemical compounds, 18S V9 rRNA gene, and full-length 16S rRNA gene metabarcoding techniques for detecting treated wastewater in receiving waters.

Temporal disturbance of a model stream ecosystem by high microbial diversity from treated wastewater.

Microbial communities in freshwater streams play an essential role in ecosystem functioning via biogeochemical cycling. Yet, the impacts of treated wastewater influx into stream ecosystems on microbial strain diversity remain mostly unexplored. Here, we coupled full-length 16S ribosomal RNA gene Nanopore sequencing and strain-resolved metagenomics to investigate the impact of treated wastewater on a mesocosm system (AquaFlow) run with restored river water.

The Asymmetric Response Concept explains ecological consequences of multiple stressor exposure and release.

Our capacity to predict trajectories of ecosystem degradation and recovery is limited, especially when impairments are caused by multiple stressors. Recovery may be fast or slow and either complete or partial, sometimes result in novel ecosystem states or even fail completely. Here, we introduce the Asymmetric Response Concept (ARC) that provides a basis for exploring and predicting the pace and magnitude of ecological responses to, and release from, multiple stressors.

Microbial community shifts induced by plastic and zinc as substitutes of tire abrasion.

Aquatic environments serve as a sink for anthropogenic discharges. A significant part of the discharge is tire wear, which is increasingly being released into the environment, causing environmental disasters due to their longevity and the large number of pollutants they contain. Main components of tires are plastic and zinc, which therefore can be used as substitutes for tire abrasion to study the effect on microbial life.

Paramecium epigenetics in development and proliferation.

The term epigenetics is used for any layer of genetic information aside from the DNA base-sequence information. Mammalian epigenetic research increased our understanding of chromatin dynamics in terms of cytosine methylation and histone modification during differentiation, aging, and disease. Instead, ciliate epigenetics focused more on small RNA-mediated effects.

The relationship between land cover and microbial community composition in European lakes.

Microbes are essential for element cycling and ecosystem functioning. However, many questions central to understanding the role of microbes in ecology are still open. Here, we analyze the relationship between lake microbiomes and the lakes' land cover.

Patterns of protist distribution and diversification in alpine lakes across Europe.

Biogeography in Europe is known to be crucially influenced by the large mountain ranges serving as biogeographical islands for cold-adapted taxa and geographical barriers for warm-adapted taxa. While biogeographical patterns are well-known for plants and animals in Europe, we here investigated diversity and distribution patterns of protist freshwater communities on a European scale (256 lakes) in the light of the well-studied post-glacial distribution patterns of macroorganisms. Thus, our study compared 43 alpine protist communities of lakes located in the Alps, Carpathians, Pyrenees, and the Sierra Nevada with that of surrounding lowland lakes.

A multi-omics study on quantifying antimicrobial resistance in European freshwater lakes.

The surveillance of wastewater for the Covid-19 virus during this unprecedented pandemic and mapped to the distribution and magnitude of the infected in the population near real-time exemplifies the importance of tracking rapidly changing trends of pathogens or public health problems at a large scale. The rising trends of antimicrobial resistance (AMR) with multidrug-resistant pathogens from the environmental water have similarly gained much attention in recent years. Wastewater-based epidemiology from water samples has shown that a wide range of AMR-related genes is frequently detected.

Nutrient-driven genome evolution revealed by comparative genomics of chrysomonad flagellates.

Phototrophic eukaryotes have evolved mainly by the primary or secondary uptake of photosynthetic organisms. A return to heterotrophy occurred multiple times in various protistan groups such as Chrysophyceae, despite the expected advantage of autotrophy. It is assumed that the evolutionary shift to mixotrophy and further to heterotrophy is triggered by a differential importance of nutrient and carbon limitation.

Quantification of the covariation of lake microbiomes and environmental variables using a machine learning-based framework.

It is known that microorganisms are essential for the functioning of ecosystems, but the extent to which microorganisms respond to different environmental variables in their natural habitats is not clear. In the current study, we present a methodological framework to quantify the covariation of the microbial community of a habitat and environmental variables of this habitat. It is built on theoretical considerations of systems ecology, makes use of state-of-the-art machine learning techniques and can be used to identify bioindicators.

Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring.

Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have been recognized for their importance in environmental processes. Recently, the use of molecular methods has revealed unexpected diversity within known functional groups and novel metabolic pathways that are particularly important in energy and nutrient cycling.

Protistan and fungal diversity in soils and freshwater lakes are substantially different.

Freshwater and soil habitats hold rich microbial communities. Here we address commonalities and differences between both habitat types. While freshwater and soil habitats differ considerably in habitat characteristics organismic exchange may be high and microbial communities may even be inoculated by organisms from the respective other habitat.

Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads.

Background: Sequencing of marker genes amplified from environmental samples, known as amplicon sequencing, allows us to resolve some of the hidden diversity and elucidate evolutionary relationships and ecological processes among complex microbial communities. The analysis of large numbers of samples at high sequencing depths generated by high throughput sequencing technologies requires efficient, flexible, and reproducible bioinformatics pipelines. Only a few existing workflows can be run in a user-friendly, scalable, and reproducible manner on different computing devices using an efficient workflow management system.

Centers of endemism of freshwater protists deviate from pattern of taxon richness on a continental scale.

Here, we analyzed patterns of taxon richness and endemism of freshwater protists in Europe. Even though the significance of physicochemical parameters but also of geographic constraints for protist distribution is documented, it remains unclear where regional areas of high protist diversity are located and whether areas of high taxon richness harbor a high proportion of endemics. Further, patterns may be universal for protists or deviate between taxonomic groups.

Factors shaping community patterns of protists and bacteria on a European scale.

Factors shaping community patterns of microorganisms are controversially discussed. Physical and chemical factors certainly limit the survival of individual taxa and maintenance of diversity. In recent years, a contribution of geographic distance and dispersal barriers to distribution patterns of protists and bacteria has been demonstrated.

Ecological Differentiation in Two Major Freshwater Bacterial Taxa Along Environmental Gradients.

(, ) and (, ) are abundant freshwater bacteria comprising large genetic and taxonomic diversities, with species adapted to physico-chemically distinct types of freshwater systems. The relative importance of environmental drivers, i.e.

Intraspecific Variation in Protists: Clues for Microevolution from Poteriospumella lacustris (Chrysophyceae).

Species delimitation in protists is still a challenge, attributable to the fact that protists are small, difficult to observe and many taxa are poor in morphological characters, whereas most current phylogenetic approaches only use few marker genes to measure genetic diversity. To address this problem, we assess genome-level divergence and microevolution in strains of the protist Poteriospumella lacustris, one of the first free-living, nonmodel organisms to study genome-wide intraspecific variation. Poteriospumella lacustris is a freshwater protist belonging to the Chrysophyceae with an assumed worldwide distribution.

Interaction-Specific Changes in the Transcriptome of Caused by Varying Protistan Communities.

We studied the impact of protist grazing and exudation on the growth and transcriptomic response of the prokaryotic prey species . Different single- and multi-species communities of chrysophytes were used to determine a species-specific response to the predators and the effect of chrysophyte diversity. We sequenced the mRNA of in communities with three single chrysophyte species ( and ) and all combinations.

Putatively asexual chrysophytes have meiotic genes: evidence from transcriptomic data.

Chrysophytes are a large group of heterotrophic, phototrophic, or even mixotrophic protists that are abundant in aquatic as well as terrestrial environments. Although much is known about chrysophyte biology and ecology, it is unknown if they are sexual or not. Here we use available transcriptomes of 18 isolates of 15 putatively asexual species to inventory the presence of genes used in meiosis.

SEDE-GPS: socio-economic data enrichment based on GPS information.

Background: Microbes are essentail components of all ecosystems because they drive many biochemical processes and act as primary producers. In freshwater ecosystems, the biodiversity in and the composition of microbial communities can be used as indicators for environmental quality. Recently, some environmental features have been identified that influence microbial ecosystems.

Silver stress differentially affects growth of phototrophic and heterotrophic chrysomonad flagellate populations.

Silver ions are among the predominant anthropogenic introduced pollutants in aquatic systems. As silver has effects on species at all trophic levels the community composition in aquatic habitats can be changed as a result of silver stress. The response of planktonic protists to environmental stressors is particularly important as they act both as producers and consumers in complex planktonic communities.