Heterotrophic flagellates (HF) are known as most important grazers of bacteria in many aquatic ecosystem. HF cannot be treated as a black box since HF generally contain a diverse community of species ...significantly differing in their feeding behaviour and other ecological properties. Today it seems that the dominant taxonomic groups among heterotrophic nano- and microflagellate communities within different marine, brackish and limnetic pelagic communities (heterokont taxa, dinoflagellates, choanoflagellates, kathablepharids) and benthic communities (euglenids, bodonids, thaumatomonads, apusomonads, cercomonads) are relatively similar. HF among protista incertae sedis, often neglected in ecological studies, are abundant bacterivores in all investigated habitats. Recent studies of flagellate feeding processes indicated that there are significant species-specific differences and individual variability regarding the food uptake and food selection of bacterivorous flagellates: Variability of bacterivory is discussed regarding the prevailing feeding modes, the energy budgets, the considerable importance of slight deviations in the time budgets of feeding phases, the ingestion rates and the feeding microhabitat, respectively. The significant flexibility of the grazing impact of bacterivorous flagellate communities creates a complex top-down pressure on bacteria which should have lead to the evolution of efficient predator avoidance mechanisms in bacteria and should be at least partly responsible for the diversity of present bacteria.
Aquatic environments are heavily impacted by human activities including climate warming and the introduction of xenobiotics. Due to the application of silver nanoparticles as bactericidal agent the ...introduction of silver into the environment strongly has increased during the past years. Silver ions affect the primary metabolism of algae, in particular photosynthesis. Mixotrophic algae are an interesting test case as they do not exclusively rely on photosynthesis which may attenuate the harmful effect of silver. In order to study the effect of silver ions on mixotrophs, cultures of the chrysophyte Poterioochromonas malhamensis were treated in a replicate design in light and darkness with silver nitrate at a sub-lethal concentration. At five time points samples were taken for the identification and quantitation of proteins by mass spectrometry. In our analysis, relative quantitative protein mass spectrometry has shown to be a useful tool for functional analyses in conjunction with transcriptome reference sequences. A total of 3,952 proteins in 63 samples were identified and quantified, mapping to 4,829 transcripts of the sequenced and assembled transcriptome. Among them, 720 and 104 proteins performing various cellular functions were differentially expressed after eight days in light versus darkness and after three days of silver treatment, respectively. Specifically pathways of the energy and primary carbon metabolism were differentially affected by light and the utilization of expensive reactions hints to an energy surplus of P. malhamensis under light conditions. The excess energy is not invested in growth, but in the synthesis of storage metabolites. The effects of silver were less explicit, observable especially in the dark treatments where the light effect could not mask coinciding but weaker effects of silver. Photosynthesis, particularly the light harvesting complexes, and several sulphur containing enzymes were affected presumably due to a direct interference with the silver ions, mainly affecting energy supply.
Summary
We isolated 28 strains of ‘Spumella‐like’ flagellates from different freshwater and soil habitats in Austria, People's Republic of China, Nepal, New Zealand, Uganda, Kenya, Tanzania and ...Hawaii by use of a modified filtration–acclimatization method. ‘Spumella‐like’ flagellates were found in all of the samples and were often among the dominant bacterivorous flagellates in the respective environments. The small subunit ribosomal RNA (SSU rRNA) gene sequence of the isolates was determined and aligned with previously published sequences of members belonging to the Chrysophyceae sensu stricto. Phylogenetic analysis of the 28 new sequences confirmed their position within the Chrysophyceae sensu stricto and positioned them within different clades. Most of the sequences grouped within clade C and formed several subclusters separated from each other by green taxa including flagellates belonging to Ochromonas, Dinobryon, Poterioochromonas and others. All soil isolates clustered together (subcluster C1) with the soil strain Spumella elongata and the undescribed soil strain ‘Spumella danica’. Aquatic isolates were affiliated with at least two branches (C2 and C3). Sequence similarity to the closest related member of the Chrysophyceae ranged between 92% and 99.6%, sequence divergence among the ‘Spumella‐like’ flagellates was as high as 10%. We conclude that (i) the ‘Spumella‐like’ flagellates are a diverse group both in terms of sequence dissimilarity between isolates and in terms of the number of genotypes, (ii) Spumella and Ochromonas are polyphyletic, and (iii) based on the SSU rRNA gene no biogeographical restriction of certain branches could be observed even though different ecotypes may be represented by the same genotype.
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. The molecular responses of
significantly changed in the presence of predators with different trophic modes and combinations of species. In the single-species samples we observed significant differences related to the relative importance of grazing and exudation in the protist-bacteria interaction, i.e., to the presence of either the heterotrophic
or the mixotrophic
. When grazing dominates the interaction, as in the presence of
, genes acting in stress response are up-regulated. Further genes associated with transcription and translation are down-regulated indicating a reduced growth of
. In contrast, when the potential use of algal exudates dominates the interaction, genes affiliated with iron transport are up-regulated. Rapid phototrophic growth of chrysophytes, with a high demand on soluble iron, could thus lead to iron-limitation and cause changes in the iron metabolism of
. Additionally, we observe a benefit for
from a more diverse protistan community, which could be due to shifts in the relative importance of phototrophy in the mixotrophic chrysophytes when competing for food with other species. Our study highlights the importance of biotic interactions and the specificity of such interactions, in particular the differential effect of grazing and algal exudation in the interaction of bacteria with mixotrophic protists.
Chrysophytes are protist model species in ecology and ecophysiology and important grazers of bacteria-sized microorganisms and primary producers. However, they have not yet been investigated in ...detail at the molecular level, and no genomic and only little transcriptomic information is available. Chrysophytes exhibit different trophic modes: while phototrophic chrysophytes perform only photosynthesis, mixotrophs can gain carbon from bacterial food as well as from photosynthesis, and heterotrophs solely feed on bacteria-sized microorganisms. Recent phylogenies and megasystematics demonstrate an immense complexity of eukaryotic diversity with numerous transitions between phototrophic and heterotrophic organisms. The question we aim to answer is how the diverse nutritional strategies, accompanied or brought about by a reduction of the plasmid and size reduction in heterotrophic strains, affect physiology and molecular processes.
We sequenced the mRNA of 18 chrysophyte strains on the Illumina HiSeq platform and analysed the transcriptomes to determine relations between the trophic mode (mixotrophic vs. heterotrophic) and gene expression. We observed an enrichment of genes for photosynthesis, porphyrin and chlorophyll metabolism for phototrophic and mixotrophic strains that can perform photosynthesis. Genes involved in nutrient absorption, environmental information processing and various transporters (e.g., monosaccharide, peptide, lipid transporters) were present or highly expressed only in heterotrophic strains that have to sense, digest and absorb bacterial food. We furthermore present a transcriptome-based alignment-free phylogeny construction approach using transcripts assembled from short reads to determine the evolutionary relationships between the strains and the possible influence of nutritional strategies on the reconstructed phylogeny. We discuss the resulting phylogenies in comparison to those from established approaches based on ribosomal RNA and orthologous genes. Finally, we make functionally annotated reference transcriptomes of each strain available to the community, significantly enhancing publicly available data on Chrysophyceae.
Our study is the first comprehensive transcriptomic characterisation of a diverse set of Chrysophyceaen strains. In addition, we showcase the possibility of inferring phylogenies from assembled transcriptomes using an alignment-free approach. The raw and functionally annotated data we provide will prove beneficial for further examination of the diversity within this taxon. Our molecular characterisation of different trophic modes presents a first such example.
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. We verified altitudinal diversity gradients of freshwater protists with decreasing richness and diversity across altitudes similar to those observed for plants and animals. Alpine specialists and generalists could be identified differing significantly in richness and diversity, but hardly in occurrence and proportions of major taxonomic groups. High proportions of region‐specific alpine specialists indicate an increased occurrence of distinct lineages within each mountain range and thus, suggested either separated glacial refugia or post‐glacial diversification within mountain ranges. However, a few alpine specialists were shared between mountain ranges suggesting a post‐glacial recolonization from a common lowland pool. Our results identified generalists with wide distribution ranges and putatively wide tolerance ranges toward environmental conditions as main drivers of protist diversification (specification) in alpine lakes, while there was hardly any diversification in alpine specialists.
Deviations of high‐mountain protist communities from lowland communities are well known but the underlying diversification processes are hardly understood. Here, we studied protist communities in several European high‐mountain ranges and analyzed commonalities and deviations between these sites. We further analyzed patterns of diversification of specialized and generalistic taxa of mountain ranges, as well as of lowlands, and showed that particularly the high mountain specialist taxa have low‐diversification rates.
The loss of photosynthesis has occurred often in eukaryotic evolution, even more than its acquisition, which occurred at least nine times independently and which generated the evolution of the ...supergroups Archaeplastida, Rhizaria, Chromalveolata and Excavata. This secondary loss of autotrophic capability is essential to explain the evolution of eukaryotes and the high diversity of protists, which has been severely underestimated until recently. However, the ecological and evolutionary scenarios behind this evolutionary "step back" are still largely unknown.
Using a dynamic model of heterotrophic and mixotrophic flagellates and two types of prey, large bacteria and ultramicrobacteria, we examine the influence of DOC concentration, mixotroph's photosynthetic growth rate, and external limitations of photosynthesis on the coexistence of both types of flagellates. Our key premises are: large bacteria grow faster than small ones at high DOC concentrations, and vice versa; and heterotrophic flagellates are more efficient than the mixotrophs grazing small bacteria (both empirically supported). We show that differential efficiency in bacteria grazing, which strongly depends on cell size, is a key factor to explain the loss of photosynthesis in mixotrophs (which combine photosynthesis and bacterivory) leading to purely heterotrophic lineages. Further, we show in what conditions an heterotroph mutant can coexist, or even out-compete, its mixotrophic ancestor, suggesting that bacterivory and cell size reduction may have been major triggers for the diversification of eukaryotes.
Our results suggest that, provided the mixotroph's photosynthetic advantage is not too large, the (small) heterotroph will also dominate in nutrient-poor environments and will readily invade a community of mixotrophs and bacteria, due to its higher efficiency exploiting the ultramicrobacteria. As carbon-limited conditions were presumably widespread throughout Earth history, such a scenario may explain the numerous transitions from phototrophy to mixotrophy and further to heterotrophy within virtually all major algal lineages. We challenge prevailing concepts that affiliated the evolution of phagotrophy with eutrophic or strongly light-limited environments only.
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. Over 10 days, community Bray–Curtis dissimilarities between treated and control mesocosm decreased (0.57 ± 0.058 to 0.26 ± 0.046) based on ribosomal protein S3 gene clustering, finally converging to nearly identical communities. Similarly, strain‐resolved metagenomics revealed a high diversity of bacteria and viruses after the introduction of treated wastewater; these microbes also decreased over time resulting in the same strain clusters in control and treatment at the end of the experiment. Specifically, 39.2% of viral strains detected in all samples were present after the introduction of treated wastewater only. Although bacteria present at low abundance in the treated wastewater introduced additional antibiotic resistance genes, signals of naturally occurring ARG‐encoding organisms resembled the resistome at the endpoint. Our results suggest that the previously stressed freshwater stream and its microbial community are resilient to a substantial introduction of treated wastewater.
Wastewater represents a substantial portion of river microbiomes worldwide, yet its effect on stream microbiomes remains challenging to study. Here, we use a mesocosm setup combined with strain‐resolved metagenomics to unravel the impacts of treated wastewater on previously stressed stream water. The disturbance resulted in a significant shift of the microbiome, which did not persist over 10 days, suggesting that previously stressed stream microbiomes are resilient to the introduction of treated wastewater.
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. Since we were able to detect a set of nine meiosis-specific and 29 meiosis-related genes shared by the chrysophytes, we conclude that they are secretively sexual and therefore should be investigated further using genome sequencing to uncover any missed genes from the transcriptomes.
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