Bacterivory by heterotrophic flagellates: community structure and feeding strategies

Checklist of colourless euglenoids of the Czech Republic, with several taxonomic additions

This study presents the results of a complex survey of freshwater heterotrophic euglenoids in the Czech Republic, including both literature data and own field surveys of 469 sites visited in the course of three years. The checklist includes 189 taxa in 28 genera: Anisonema (10), Astasia (26), Atraktomonas (1), Calycimonas (2), Chasmostoma (1), Dinematomonas (3), Distigma (8), Dylakosoma (1), Entosiphon (4), Euglena (1), Gyropaigne (1), Heteronema (19), Jenningsia (11), Khawkinea (1), Lepocinclis (1), Menoidium (7), Neometanema (3), Notosolenus (18), Petalomonas (40), Phacus (1), Ploeotia (2), Pseudoperanema (7), Rhabdomonas (5), Scytomonas (1), Sphenomonas (5), Teloprocta (1) Tropidocyphus (1), Urceolus (4), and 4 species of uncertain identity. In addition, a general description of habitat types in which the taxa were found and a review of the current taxonomy and nomenclature of included taxa are provided. Several taxonomic and nomenclatural novelties are proposed, based on the review of morphological features, mostly applying to the genera Notosolenus and Jenningsia.

The effect of external flow on 3D orientation of a microscopic sessile suspension feeder, Vorticella convallaria

Vorticella convallaria are microscopic sessile suspension feeders that live attached to substrates in aquatic environments. They feed using a self-generated current and help maintain the health of aquatic ecosystems and wastewater treatment facilities by consuming bacteria and detritus. Their environmental impact is mediated by their feeding rate. In ambient flow, feeding rates are highly dependent on an individual's orientation relative to the substrate and the flow. Here, we investigate how this orientation is impacted by flow speed. Furthermore, we examined whether individuals actively avoid orientations unfavorable for feeding. We exposed individuals to unidirectional laminar flow at shear rates of 0, 0.5, 1.0, and 1.5 s-1, and recorded their 3D orientation using a custom biplanar microscope. We determined that V. convallaria orientation became progressively tilted downstream as the shear rate increased, but individuals were still able to actively reorient. Additionally, at higher shear rates, individuals spent a larger fraction of their time in orientations with reduced feeding rates. Our shear rates correspond to freestream flows on the scale of mm s-1 to cm s-1 in natural environments.

Size dependent uptake and trophic transfer of polystyrene microplastics in unicellular freshwater eukaryotes

Microplastics (MP) have become a well-known and widely investigated environmental pollutant. Despite the huge amount of new studies investigating the potential threat posed by MP, the possible uptake and trophic transfer in lower trophic levels of freshwater ecosystems remains understudied. This study aims to investigate the internalization and potential trophic transfer of fluorescent polystyrene (PS) beads (0.5 μm, 3.6 × 108 particles/mL; 6 μm, 2.1 × 105 particles/mL) and fragments (<30 μm, 5 × 103 particles/mL) in three unicellular eukaryotes. This study focuses on the size-dependent uptake of MP by two freshwater Ciliophora, Tetrahymena pyriformis, Paramecium caudatum and one Amoebozoa, Amoeba proteus, serving also as predator for experiments on potential trophic transfer. Size-dependent uptake of MP in all three unicellular eukaryotes was shown. P. caudatum is able to take up MP fragments up to 27.7 μm, while T. pyriformis ingests particles up to 10 μm. In A. proteus, small MP (PS0.5μm and PS6μm) were taken up via pinocytosis and were detected in the cytoplasm for up to 14 days after exposure. Large PS-MP (PS<30μm) were detected in A. proteus only after predation on MP-fed Ciliophora. These results indicate that A. proteus ingests larger MP via predation on Ciliophora (PS<30μm), which would not be taken up otherwise. This study shows trophic transfer of MP at the base of the aquatic food web and serves as basis to study the impact of MP in freshwater ecosystems.

Integrating depth-dependent protist dynamics and microbial interactions in spring succession of a freshwater reservoir

BACKGROUND

Protists are essential contributors to eukaryotic diversity and exert profound influence on carbon fluxes and energy transfer in freshwaters. Despite their significance, there is a notable gap in research on protistan dynamics, particularly in the deeper strata of temperate lakes. This study aimed to address this gap by integrating protists into the well-described spring dynamics of Římov reservoir, Czech Republic. Over a 2-month period covering transition from mixing to established stratification, we collected water samples from three reservoir depths (0.5, 10 and 30 m) with a frequency of up to three times per week. Microbial eukaryotic and prokaryotic communities were analysed using SSU rRNA gene amplicon sequencing and dominant protistan groups were enumerated by Catalysed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). Additionally, we collected samples for water chemistry, phyto- and zooplankton composition analyses.

RESULTS

Following the rapid changes in environmental and biotic parameters during spring, protistan and bacterial communities displayed swift transitions from a homogeneous community to distinct strata-specific communities. A prevalence of auto- and mixotrophic protists dominated by cryptophytes was associated with spring algal bloom-specialized bacteria in the epilimnion. In contrast, the meta- and hypolimnion showcased a development of a protist community dominated by putative parasitic Perkinsozoa, detritus or particle-associated ciliates, cercozoans, telonemids and excavate protists (Kinetoplastida), co-occurring with bacteria associated with lake snow.

CONCLUSIONS

Our high-resolution sampling matching the typical doubling time of microbes along with the combined microscopic and molecular approach and inclusion of all main components of the microbial food web allowed us to unveil depth-specific populations' successions and interactions in a deep lentic ecosystem.

Enhanced transport of bacteria along root systems by protists can impact plant health

Soil protists have been shown to contribute to the structure and function of the rhizosphere in a variety of ways. Protists are key contributors to nutrient cycling through the microbial loop, where biomass is digested by protists and otherwise stored nutrients are returned to the environment. Protists have also been shown to feed on plant pathogenic bacteria and alter root microbiomes in ways that may benefit plants. Recently, a mechanism involving bacterial transport, facilitated by protists, has been hypothesized to contribute to the spatial distribution of bacteria in the rhizosphere. Here, we observe the differential abilities of three soil protists: a ciliate (Colpoda sp.), a flagellate (Cercomonas sp.), and a naked amoeba (Acanthamoeba castellanii) to transport nitrogen-fixing Sinorhizobium meliloti to infectible root tips. Co-inoculation of protists plus S. meliloti resulted in the movement of bacteria, as measured by the presence of nitrogen-fixing nodules, up to 15 cm farther down the root systems when compared to plants inoculated with S. meliloti alone. Co-inoculation of the ciliate, Colpoda sp., with S. meliloti, resulted in shoot weights that were similar to plants that grew in nitrogen-replete potting mix. Colpoda sp.-feeding style and motility likely contributed to their success at transporting bacteria through the rhizosphere. We observed that the addition of protists alone without the co-inoculum of S. meliloti resulted in plants with larger shoot weights than control plants. Follow-up experiments showed that protists plus their associated microbiomes were aiding in plant health, likely through means of nutrient cycling.IMPORTANCEProtists represent a significant portion of the rhizosphere microbiome and have been shown to contribute to plant health, yet they are understudied compared to their bacterial and fungal counterparts. This study elucidates their role in the rhizosphere community and suggests a mechanism by which protists can be used to move bacteria along plant roots. We found that the co-inoculation of protists with nitrogen-fixing beneficial bacteria, Sinorhizobium meliloti, resulted in nodules farther down the roots when compared to plants inoculated with S. meliloti alone, and shoot weights similar to plants that received nitrogen fertilizer. These data illustrate the ability of protists to transport viable bacteria to uninhabited regions of the root system.

Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton

Single-cell transcriptomics has the potential to provide novel insights into poorly studied microbial eukaryotes. Although several such technologies are available and benchmarked on mammalian cells, few have been tested on protists. Here, we applied a microarray single-cell sequencing (MASC-seq) technology, that generates microscope images of cells in parallel with capturing their transcriptomes, on three species representing important plankton groups with different cell structures; the ciliate Tetrahymena thermophila, the diatom Phaeodactylum tricornutum, and the dinoflagellate Heterocapsa sp. Both the cell fixation and permeabilization steps were adjusted. For the ciliate and dinoflagellate, the number of transcripts of microarray spots with single cells were significantly higher than for background spots, and the overall expression patterns were correlated with that of bulk RNA, while for the much smaller diatom cells, it was not possible to separate single-cell transcripts from background. The MASC-seq method holds promise for investigating "microbial dark matter", although further optimizations are necessary to increase the signal-to-noise ratio.

Predation in a Microbial World: Mechanisms and Trade-Offs of Flagellate Foraging

Heterotrophic nanoflagellates are the main consumers of bacteria and picophytoplankton in the ocean and thus play a key role in ocean biogeochemistry. They are found in all major branches of the eukaryotic tree of life but are united by all being equipped with one or a few flagella that they use to generate a feeding current. These microbial predators are faced with the challenges that viscosity at this small scale impedes predator-prey contact and that their foraging activity disturbs the ambient water and thus attracts their own flow-sensing predators. Here, I describe some of the diverse adaptations of the flagellum to produce sufficient force to overcome viscosity and of the flagellar arrangement to minimize fluid disturbances, and thus of the various solutions to optimize the foraging-predation risk trade-off. I demonstrate how insights into this trade-off can be used to develop robust trait-based models of microbial food webs.

Kaonashia insperata gen. et sp. nov., a eukaryotrophic flagellate, represents a novel major lineage of heterotrophic stramenopiles

Eukaryotrophic protists are ecologically significant and possess characteristics key to understanding the evolution of eukaryotes; however, they remain poorly studied, due partly to the complexities of maintaining predator-prey cultures. Kaonashia insperata, gen. nov., et sp. nov., is a free-swimming biflagellated eukaryotroph with a conspicuous ventral groove, a trait observed in distantly related lineages across eukaryote diversity. Di-eukaryotic (predator-prey) cultures of K. insperata with three marine algae (Isochrysis galbana, Guillardia theta, and Phaeodactylum tricornutum) were established by single-cell isolation. Growth trials showed that the studied K. insperata clone grew particularly well on G. theta, reaching a peak abundance of 1.0 × 105  ± 4.0 × 104 cells ml-1 . Small-subunit ribosomal DNA phylogenies infer that K. insperata is a stramenopile with moderate support; however, it does not fall within any well-defined phylogenetic group, including environmental sequence clades (e.g. MASTs), and its specific placement remains unresolved. Electron microscopy shows traits consistent with stramenopile affinity, including mastigonemes on the anterior flagellum and tubular mitochondrial cristae. Kaonashia insperata may represent a novel major lineage within stramenopiles, and be important for understanding the evolutionary history of the group. While heterotrophic stramenopile flagellates are considered to be predominantly bacterivorous, eukaryotrophy may be relatively widespread amongst this assemblage.

Molecular phylogenetics of sessile Dolium sedentarium, a petalomonad euglenid

The euglenids are a species-rich group of flagellates with varying modes of nutrition that can be found in diverse habitats. Phagotrophic members of this group gave rise to phototrophs and hold the key to understanding the evolution of euglenids as a whole, including the evolution of complex morphological characters like the euglenid pellicle. Yet to understand the evolution of these characters, a comprehensive sampling of molecular data is needed to correlate morphological and molecular data, and to estimate a basic phylogenetic backbone of the group. While the availability of SSU rDNA and, more recently, multigene data from phagotrophic euglenids has improved, several "orphan" taxa remain without any molecular data whatsoever. Dolium sedentarium is one such taxon: It is a rarely-observed phagotrophic euglenid that inhabits tropical benthic environments and is one of few known sessile euglenids. Based on morphological characters, it has been thought of as part of the earliest branch of euglenids, the Petalomonadida. We report the first molecular sequencing data for Dolium using single-cell transcriptomics, adding another small piece in the puzzle of euglenid evolution. Both SSU rDNA and multigene phylogenies confirm it as a solitary branch within Petalomonadida.

Climate Change Causes Salinity To Become Determinant in Shaping the Microeukaryotic Spatial Distribution among the Lakes of the Inner Mongolia-Xinjiang Plateau

Climate change greatly affects lake microorganisms in arid and semiarid zones, which alters ecosystem functions and the ecological security of lakes. However, the responses of lake microorganisms, especially microeukaryotes, to climate change are poorly understood. Here, using 18S ribosomal RNA (rRNA) high-throughput sequencing, we investigated the distribution patterns of microeukaryotic communities and whether and how climate change directly or indirectly affected the microeukaryotic communities on the Inner Mongolia-Xinjiang Plateau. Our results showed that climate change, as the main driving force of lake change, drives salinity to become a determinant of the microeukaryotic community among the lakes of the Inner Mongolia-Xinjiang Plateau. Salinity shapes the diversity and trophic level of the microeukaryotic community and further affects lake carbon cycling. Co-occurrence network analysis further revealed that increasing salinity reduced the complexity but improved the stability of microeukaryotic communities and changed ecological relationships. Meanwhile, increasing salinity enhanced the importance of deterministic processes in microeukaryotic community assembly, and the dominance of stochastic processes in freshwater lakes transformed into deterministic processes in salt lakes. Furthermore, we established lake biomonitoring and climate sentinel models by integrating microeukaryotic information, which would provide substantial improvements to our predictive ability of lake responses to climate change. IMPORTANCE Our findings have important implications for understanding the distribution patterns and the driving mechanisms of microeukaryotic communities among the lakes of the Inner Mongolia-Xinjiang Plateau and whether and how climate change directly or indirectly affects microeukaryotic communities. Our study also establishes the groundwork to use the lake microbiome for the assessment of aquatic ecological health and climate change, which is critical for ecosystem management and for projecting the ecological consequences of future climate warming.

Identification of the heterotrophic nanoflagellate Bilabrum latius in the southern Adriatic (Mediterranean Sea)

Heterotrophic flagellates (HF) represent an important protist group in marine ecosystem functioning. Characterised by high taxonomic diversity, identification and classification of HF is often difficult using classical methods of light microscopy (LM). Complementing LM with molecular methods, such as barcoding, enables reliable taxonomic identification of even small size nanoflagellates that share similar or unnoticeable morphological features. The order Bicosoecida is a group of heterotrophic nanoflagellates that are important part of protist plankton and benthic communities of the world oceans. Recently, on the basis of high-resolution light microscopy and barcoding, a new bicosoecid genus, Bilabrum, was described with B. latius sp. as a type species. Our study reports on identification of B. latius from co-culture with the diatom species Chaetoceros affinis isolated from fresh plankton samples collected in the southern Adriatic. This detection of the Adriatic B.latius represents first record of this species outside itś up to now known and described habitat (deep-sea sediment of the South - East Atlantic Ocean) and in diatom co-culture.

Grazing on Marine Viruses and Its Biogeochemical Implications

Viruses are the most abundant biological entities in the ocean and show great diversity in terms of size, host specificity, and infection cycle. Lytic viruses induce host cell lysis to release their progeny and thereby redirect nutrients from higher to lower trophic levels. Studies continue to show that marine viruses can be ingested by nonhost organisms. However, not much is known about the role of viral particles as a nutrient source and whether they possess a nutritional value to the grazing organisms. This review seeks to assess the elemental composition and biogeochemical relevance of marine viruses, including roseophages, which are a highly abundant group of bacteriophages in the marine environment. We place a particular emphasis on the phylum Nucleocytoviricota (NCV) (formerly known as nucleocytoplasmic large DNA viruses [NCLDVs]), which comprises some of the largest viral particles in the marine plankton that are well in the size range of prey for marine grazers. Many NCVs contain lipid membranes in their capsid that are rich carbon and energy sources, which further increases their nutritional value. Marine viruses may thus be an important nutritional component of the marine plankton, which can be reintegrated into the classical food web by nonhost organism grazing, a process that we coin the "viral sweep." Possibilities for future research to resolve this process are highlighted and discussed in light of current technological advancements.

The Effect of Protozoa Indigenous to Lakewater and Wastewater on Decay of Fecal Indicator Bacteria and Coliphage

Fecal indicator bacteria (FIB: Escherichia coli and enterococci) are used to assess recreational water quality. Viral indicators (i.e., somatic and F+ coliphage), could improve the prediction of viral pathogens in recreational waters, however, the impact of environmental factors, including the effect of predatory protozoa source, on their survival in water is poorly understood. We investigated the effect of lakewater or wastewater protozoa, on the decay (decreasing concentrations over time) of culturable FIB and coliphages under sunlight and shaded conditions. FIB decay was generally greater than the coliphages and was more rapid when indicators were exposed to lake vs. wastewater protozoa. F+ coliphage decay was the least affected by experimental variables. Somatic coliphage decayed fastest in the presence of wastewater protozoa and sunlight, though their decay under shaded conditions was-10-fold less than F+ after 14 days. The protozoa source consistently contributed significantly to the decay of FIB, and somatic, though not the F+ coliphage. Sunlight generally accelerated decay, and shade reduced somatic coliphage decay to the lowest level among all the indicators. Differential responses of FIB, somatic, and F+ coliphages to environmental factors support the need for studies that address the relationship between the decay of coliphages and viral pathogens under environmentally relevant conditions.

Planktonic prey size selection reveals an emergent keystone predator effect and niche partitioning

Marine herbivorous protists are often the dominant grazers of primary production. We developed a size-based model with flexible size-based grazing to encapsulate taxonomic and behavioral diversity. We examined individual and combined grazing impacts by three consumer sizes that span the size range of protistan grazers- 5, 50, and 200 μm-on a size-structured phytoplankton community. Prey size choice and dietary niche width varied with consumer size and with co-existence of other consumers. When all consumer sizes were present, distinct dietary niches emerged, with a range of consumer-prey size ratios spanning from 25:1 to 0.4:1, encompassing the canonical 10:1 often assumed. Grazing on all phytoplankton size classes maximized the phytoplankton size diversity through the keystone predator effect, resulting in a phytoplankton spectral slope of approximately -4, agreeing with field data. This mechanistic model suggests the observed size structure of phytoplankton communities is at least in part the result of selective consumer feeding.

Protists' microbiome: A fine-scale, snap-shot field study on the ciliate Euplotes

Host-microbiome relationships play a fundamental role in the evolution and ecology of any living being. As unicellular organisms, protists represent a unique eukaryotic model to investigate selection mechanisms of the prokaryotic microbiome at the cellular level. Field investigations are central to disentangle relative importance of selective drivers in nature. Here we performed an analysis on data from a snap-shot field study reported previously on bacterial microbiomes associated to natural populations of protist ciliates of the genus Euplotes to detect at a fine scale any influence of habitat and/or host identity in microbiome selection. Comparative analyses revealed environment at a relatively large scale (sampling area) as the main driving factor in shaping prokaryotic communities' structures. No evidence of habitat as key-factor emerged when a smaller spatial scale was considered (pond/channel or site). When only microbiomes of ciliates from the same site were compared, a clear assessment on the influence of host identity at the species level was not achieved, probably due to the small and unbalanced number of individuals for the two considered host species. Starting from this point, wider sampling campaigns will contribute in the future to depict a general view of the drivers influencing the prokaryotic microbiomes of natural protist populations.

First putative occurrence in the fossil record of choanoflagellates, the sister group of Metazoa

Choanoflagellates are microeukaryotes that inhabit freshwater and marine environments and have long been regarded as the closest living relatives of Metazoa. Knowledge on the evolution of choanoflagellates is key for the understanding of the ancestry of animals, and although molecular clock evidence suggests the appearance of choanoflagellates by late Neoproterozoic, no specimens of choanoflagellates are known to occur in the fossil record. Here the first putative occurrence of choanoflagellates in sediments from the Cretaceous (Cenomanian-Turonian) is described by means of several cutting-edge petrographic techniques, and a discussion of its paleoenvironmental significance is performed. Furthermore, their placement in the organic matter classification systems is argued, with a placement in the Zoomorph Subgroup (Palynomorph Group) of the dispersed organic matter classification system being proposed. Regarding the ICCP System 1994, incorporation of choanoflagellates is, at a first glance, straightforward within the liptinite group, but the definition of a new maceral may be necessary to accommodate the genetic origin of these organisms. While modern choanoflagellates may bring light to the cellular foundations of animal origins, this discovery may provide an older term of comparison to their extant specimens and provide guidelines for possible identification of these organic components in other locations and ages throughout the geological record.

Cryptic and ubiquitous aplastidic cryptophytes are key freshwater flagellated bacterivores

Morphology-based microscopic approaches are insufficient for a taxonomic classification of bacterivorous heterotrophic nanoflagellates (HNF) in aquatic environments since their cells do not display reliably distinguishable morphological features. This leads to a considerable lack of ecological insights into this large and taxonomically diverse functional guild. Here, we present a combination of fluorescence in situ hybridization followed by catalyzed reporter deposition (CARD-FISH) and environmental sequence analyses which revealed that morphologically indistinguishable, so far largely cryptic and uncultured aplastidic cryptophytes are ubiquitous and prominent protistan bacterivores in diverse freshwater ecosystems. Using a general probe for Cryptophyceae and its heterotrophic CRY1 lineage, we analyzed different water layers in 24 freshwater lakes spanning a broad range of trophic states, sizes and geographical locations. We show that bacterivorous aplastidic cryptophytes and the CRY1 lineage accounted for ca. 2/3 and ¼ of total HNF, respectively, in both epilimnetic and hypolimnetic samples. These heterotrophic cryptophytes were generally smaller and more abundant than their chloroplast-bearing counterparts. They had high uptake rates of bacteria, hinting at their important roles in channeling carbon flow from prokaryotes to higher trophic levels. The worldwide ubiquity of Cryptophyceae and its CRY1 lineage was supported by 18S rRNA gene sequence analyses across a diverse set of 297 freshwater metagenomes. While cryptophytes have been considered to be mainly plastidic "algae", we show that it is the aplastidic counterparts that contribute considerably to bacterial mortality rates. Additionally, our results suggest an undiscovered diversity hidden amongst these abundant and morphologically diverse aplastidic cryptophytes.

Formation of multicellular colonies by choanoflagellates increases susceptibility to capture by amoeboid predators

Many heterotrophic microbial eukaryotes are size-selective feeders. Some microorganisms increase their size by forming multicellular colonies. We used choanoflagellates, Salpingoeca helianthica, which can be unicellular or form multicellular colonies, to study the effects of multicellularity on vulnerability to predation by the raptorial protozoan predator, Amoeba proteus, which captures prey with pseudopodia. Videomicrography used to measure the behavior of interacting S. helianthica and A. proteus revealed that large choanoflagellate colonies were more susceptible to capture than were small colonies or single cells. Swimming colonies produced larger flow fields than did swimming unicellular choanoflagellates, and the distance of S. helianthica from A. proteus when pseudopod formation started was greater for colonies than for single cells. Prey size did not affect the number of pseudopodia formed and the time between their formation, pulsatile kinematics and speed of extension by pseudopodia, or percent of prey lost by the predator. S. helianthica did not change swimming speed or execute escape maneuvers in response to being pursued by pseudopodia, so size-selective feeding by A. proteus was due to predator behavior rather than prey escape. Our results do not support the theory that the selective advantage of becoming multicellular by choanoflagellate-like ancestors of animals was reduced susceptibility to protozoan predation.

Differing Escape Responses of the Marine Bacterium Marinobacter adhaerens in the Presence of Planktonic vs. Surface-Associated Protist Grazers

Protist grazing pressure plays a major role in controlling aquatic bacterial populations, affecting energy flow through the microbial loop and biogeochemical cycles. Predator-escape mechanisms might play a crucial role in energy flow through the microbial loop, but are yet understudied. For example, some bacteria can use planktonic as well as surface-associated habitats, providing a potential escape mechanism to habitat-specific grazers. We investigated the escape response of the marine bacterium Marinobacter adhaerens in the presence of either planktonic (nanoflagellate: Cafeteria roenbergensis) or surface-associated (amoeba: Vannella anglica) protist predators, following population dynamics over time. In the presence of V. anglica, M. adhaerens cell density increased in the water, but decreased on solid surfaces, indicating an escape response towards the planktonic habitat. In contrast, the planktonic predator C. roenbergensis induced bacterial escape to the surface habitat. While C. roenbergensis cell numbers dropped substantially after a sharp initial increase, V. anglica exhibited a slow, but constant growth throughout the entire experiment. In the presence of C. roenbergensis, M. adhaerens rapidly formed cell clumps in the water habitat, which likely prevented consumption of the planktonic M. adhaerens by the flagellate, resulting in a strong decline in the predator population. Our results indicate an active escape of M. adhaerens via phenotypic plasticity (i.e., behavioral and morphological changes) against predator ingestion. This study highlights the potentially important role of behavioral escape mechanisms for community composition and energy flow in pelagic environments, especially with globally rising particle loads in aquatic systems through human activities and extreme weather events.

Plankton food webs in the oligotrophic Gulf of Mexico spawning grounds of Atlantic bluefin tuna

We used linear inverse ecosystem modeling techniques to assimilate data from extensive Lagrangian field experiments into a mass-balance constrained food web for the Gulf of Mexico open-ocean ecosystem. This region is highly oligotrophic, yet Atlantic bluefin tuna (ABT) travel long distances from feeding grounds in the North Atlantic to spawn there. Our results show extensive nutrient regeneration fueling primary productivity (mostly by cyanobacteria and other picophytoplankton) in the upper euphotic zone. The food web is dominated by the microbial loop (>70% of net primary productivity is respired by heterotrophic bacteria and protists that feed on them). By contrast, herbivorous food web pathways from phytoplankton to metazoan zooplankton process <10% of the net primary production in the mixed layer. Nevertheless, ABT larvae feed preferentially on podonid cladocerans and other suspension-feeding zooplankton, which in turn derive much of their nutrition from nano- and micro-phytoplankton (mixotrophic flagellates, and to a lesser extent, diatoms). This allows ABT larvae to maintain a comparatively low trophic level (~4.2 for preflexion and postflexion larvae), which increases trophic transfer from phytoplankton to larval fish.

CARD-FISH and prey tracer techniques reveal the role of overlooked flagellate groups as major bacterivores in freshwater hypertrophic shallow lakes

Heterotrophic nanoflagellates (HNF) and ciliates are major protistan planktonic bacterivores. The term HNF, however, describes a functional guild only and, in contrast to the morphologically distinguishable ciliates, does not reflect the phylogenetic diversity of flagellates in aquatic ecosystems. Associating a function with taxonomic affiliation of key flagellate taxa is currently a major task in microbial ecology. We investigated seasonal changes in the HNF and ciliate community composition as well as taxa-specific bacterivory in four hypertrophic freshwater lakes. Taxa-specific catalyzed reporter deposition-fluorescence in situ hybridization probes assigned taxonomic affiliations to 51%-96% (average ±SD, 75 ± 14%) of total HNF. Ingestion rates of fluorescently labelled bacteria unveiled that HNF contributed to total protist-induced bacterial mortality rates more (56%) than ciliates (44%). Surprisingly, major HNF bacterivores were aplastidic cryptophytes and their Cry1 lineage, comprising on average 53% and 24% of total HNF abundance and 67% and 21% of total HNF bacterivory respectively. Kinetoplastea were important consumers of bacteria during summer phytoplankton blooms, reaching 38% of total HNF. Katablepharidacea (7.5% of total HNF) comprised mainly omnivores, with changing contributions of bacterivorous and algivorous phylotypes. Our results show that aplastidic cryptophytes, accompanied by small omnivorous ciliate genera Halteria/Pelagohalteria, are the major protistan bacterivores in hypertrophic freshwaters.

Seasonal Succession and Coherence Among Bacteria and Microeukaryotes in Lake Baikal

Microorganisms exhibit seasonal succession governed by physicochemical factors and interspecies interactions, yet drivers of this process in different environments remain to be determined. We used high-throughput sequencing of 16S rRNA and 18S rRNA genes to study seasonal dynamics of bacterial and microeukaryotic communities at pelagic site of Lake Baikal from spring (under-ice, mixing) to autumn (direct stratification). The microbial community was subdivided into distinctive coherent clusters of operational taxonomic units (OTUs). Individual OTUs were consistently replaced during different seasonal events. The coherent clusters change their contribution to the microbial community depending on season. Changes of temperature, concentrations of silicon, and nitrates are the key factors affected the structure of microbial communities. Functional prediction revealed that some bacterial or eukaryotic taxa that switched with seasons had similar functional properties, which demonstrate their functional redundancy. We have also detected specific functional properties in different coherent clusters of bacteria or microeukaryotes, which can indicate their ability to adapt to seasonal changes of environment. Our results revealed a relationship between seasonal succession, coherency, and functional features of freshwater bacteria and microeukaryotes.

Identification and feeding characteristics of the mixotrophic flagellate Poterioochromonas malhamensis, a microalgal predator isolated from planting water of Pontederia cordata

The microorganisms and allelochemicals in Pontederia cordata planting water may have a synergistic inhibitory effect on algae. To study this synergy, an algae-inhibiting organism was isolated and identified, and its growth and feeding characteristics were studied. The organism was identified as Poterioochromonas malhamensis yzs924 based on both its morphology and molecular barcoding employing 18S rDNA gene sequences.The growth and feeding of P. malhamensis were affected by environmental factors and the state of its prey. (1) P. malhamensis is a mixotrophic flagellate. Its heterotrophic growth was the fastest in a wheat grain medium, and its growth rate in this study reached 2.5 day^-1. (2) Within a short period of time (2 days), P. malhamensis growth was slower under continuous dark conditions than under alternating light and dark conditions, but it fed on Microcystis aeruginosa more rapidly under dark conditions. (3) High pH was disadvantageous to the growth and grazing of P. malhamensis. When the pH was kept stable at 9, P. malhamensis could not grow continuously. (4) When the initial density of M. aeruginosa was 5 × 10⁷ cells/mL or is in a period of decline, P. malhamensis could not remove all M. aeruginosa. The combined use of P. malhamensis and allelochemicals may represent a method of M. aeruginosa control, but this approach requires further research.

Salinity Is a Key Determinant for the Microeukaryotic Community in Lake Ecosystems of the Inner Mongolia Plateau, China

The arid and semiarid areas experienced remarkable lake shrinkage during recent decades due to intensive human activities and climate change, which would result in unprecedented changes of microeukaryotic communities. However, little is known about how climate change affects the structure and ecological mechanisms of microeukaryotic communities in this area. Here, we used an 18S rRNA gene-based high-throughput sequencing approach to explore the structure, interspecies interaction, and assembly processes of the microeukaryotic community in lake ecosystems of the Inner Mongolia Plateau. As a direct result of climate change, salinity has become the key determinant of the lacustrine microeukaryotic community in this region. The microeukaryotic community in this ecosystem can be divided into three groups: salt (Lake Daihai), brackish (Lake Dalinuoer) and freshwater lakes. Co-occurrence network analysis revealed that salinity shapes the interspecies interactions of the microeukaryotic community. This causes interspecies interactions to change from antagonistic to cooperative with an increase in salinity. Phylogenetic-based β-nearest taxon distance analyses revealed that stochastic processes mainly dominated the microeukaryotic community assembly in lake ecosystems of the Inner Mongolia Plateau, and salinity stress drove the assembly processes of the microeukaryotic community from stochastic to deterministic. Overall, these findings expand the current understanding of interspecies interactions and assembly processes of microeukaryotic communities during climate change in lake ecosystems of the Inner Mongolia Plateau.

Microeukaryotic Community Shifting Along a Lentic-Lotic Continuum

As an important regulator of ecosystem functions in river systems, microeukaryotes play an important role in energy and material conversion, yet little is known about the shift along a lentic-lotic continuum. In this study, the 18S rRNA genes sequencing was used to identify the microeukaryotic communities at 82 sites along a lentic-lotic continuum with the aim of understanding the impact of upstream inlet river on microeukaryotic communities in Baiyang Lake (BYD) and its downstream. Our results showed that the upstream inlet river affected the diversity and community composition of microeukaryotes in BYD and downstream rivers, and environmental variables greatly affected the composition of microeukaryotic community. The community composition in BYD had lower variabilities. Co-occurrence network analysis revealed that the network was non-random and clearly parsed into three modules, and different modules were relatively more abundant to a particular area. As keystone taxa, some nodes of the upstream microeukaryotic network played an important role in structuring network and maintaining the stability of the ecosystem. In BYD and downstream, the microeukaryotic network was highly fragmented, and the loss of keystone taxa would have an adverse impact on the integrity and function of the microeukaryotic community. Microeukaryotes had strong tendencies to co-occur, which may contribute to the stability and resilience of microeukaryotic communities. Overall, these findings extend the current understanding of the diversity and community composition of microeukaryotic along a lentic-lotic continuum.

Revision of the phylogeny of Placididea (Stramenopiles): Molecular and morphological diversity of novel placidid protists from extreme aquatic environments

Recent studies suggested that the diversity of microbial eukaryotes in hypersaline environments is widely underestimated. Placidids are a group of heterotrophic stramenopile flagellates that are frequently found in these environments, but up to now only very few species were isolated and fully described, mostly from marine or brackish water sites. In this study, we extend the known diversity of Placididea by three new genera (Allegra, Haloplacidia, and Placilonga) compromising nine new species, isolated from athalassic, mostly hypersaline environments (Allegra dunaii, Allegra atacamiensis, Allegra hypersalina, Haloplacidia cosmopolita, Suigetsumonas keniensis) and marine waters (Placilonga atlantica, Placidia azorensis, Placidia abyssalis, Wobblia pacifica) including a description of their morphology and molecular phylogeny. In total, 36 strains were comparatively analysed. Studies from athalassic waters revealed an especially high number of different genotypes. A multigene analysis based on a ten genes dataset revealed a clear separation into marine, athalassic and brackish water clades. Several representatives were found to cope with hypersaline conditions from 20 to 250 PSU, even up to 284 PSU, suggesting that they may form a halotolerant group.

Microbial eukaryotes assemblages and potential novel diversity in four tropical East-African Great Lakes

East-African Great Lakes are old and unique natural resources heavily utilized by their bordering countries. In those lakes, ecosystem functioning is dominated by pelagic processes, where microorganisms are key components, however protistan diversity is barely known. We investigated the community composition of small eukaryotes (< 10 µm) in surface waters of four African Lakes (Kivu, Edward, Albert and Victoria) by sequencing the 18S rRNA gene. Moreover, in the meromictic Lake Kivu, two stations were vertically studied. We found high protistan diversity distributed in 779 operational taxonomic units (OTUs), spanning in eleven high-rank lineages, being Alveolata (31%), Opisthokonta (20%) and Stramenopiles (17%) the most represented supergroups. Surface protistan assemblage were associated to conductivity and productivity gradients; whereas depth, had a strong effect on protistan community in Kivu, with higher contribution of heterotrophic organisms. Approximately 40% of OTUs had low similarity (< 90%) with reported sequences in public databases, these were mostly coming from deep anoxic waters of Kivu, suggesting a high extent of novel diversity. We also detected several taxa so far considered exclusive of marine ecosystems. Our results unveiled a complex and largely undescribed protistan community, in which several lineages have adapted to different niches after crossing the salinity boundary.

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. 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.

Experimental identification and in silico prediction of bacterivory in green algae

While algal phago-mixotrophs play a major role in aquatic microbial food webs, their diversity remains poorly understood. Recent studies have indicated several species of prasinophytes, early diverging green algae, to be able to consume bacteria for nutrition. To further explore the occurrence of phago-mixotrophy in green algae, we conducted feeding experiments with live fluorescently labeled bacteria stained with CellTracker Green CMFDA, heat-killed bacteria stained with 5-(4,6-dichlorotriazin-2-yl) aminofluorescein (DTAF), and magnetic beads. Feeding was detected via microscopy and/or flow cytometry in five strains of prasinophytes when provided with live bacteria: Pterosperma cristatum NIES626, Pyramimonas parkeae CCMP726, Pyramimonas parkeae NIES254, Nephroselmis pyriformis RCC618, and Dolichomastix tenuilepis CCMP3274. No feeding was detected when heat-killed bacteria or magnetic beads were provided, suggesting a strong preference for live prey in the strains tested. In parallel to experimental assays, green algal bacterivory was investigated using a gene-based prediction model. The predictions agreed with the experimental results and suggested bacterivory potential in additional green algae. Our observations underline the likelihood of widespread occurrence of phago-mixotrophy among green algae, while additionally highlighting potential biases introduced when using prey proxy to evaluate bacterial ingestion by algal cells.

High and specific diversity of protists in the deep-sea basins dominated by diplonemids, kinetoplastids, ciliates and foraminiferans

Heterotrophic protists (unicellular eukaryotes) form a major link from bacteria and algae to higher trophic levels in the sunlit ocean. Their role on the deep seafloor, however, is only fragmentarily understood, despite their potential key function for global carbon cycling. Using the approach of combined DNA metabarcoding and cultivation-based surveys of 11 deep-sea regions, we show that protist communities, mostly overlooked in current deep-sea foodweb models, are highly specific, locally diverse and have little overlap to pelagic communities. Besides traditionally considered foraminiferans, tiny protists including diplonemids, kinetoplastids and ciliates were genetically highly diverse considerably exceeding the diversity of metazoans. Deep-sea protists, including many parasitic species, represent thus one of the most diverse biodiversity compartments of the Earth system, forming an essential link to metazoans.

Small freshwater ecosystems with dissimilar microbial communities exhibit similar temporal patterns

Despite small freshwater ecosystems being biodiversity reservoirs and contributing significantly to greenhouse fluxes, their microbial communities remain largely understudied. Yet, microorganisms intervene in biogeochemical cycling and impact water quality. Because of their small size, these ecosystems are in principle more sensitive to disturbances, seasonal variation and pluri-annual climate change. However, how microbial community composition varies over space and time, and whether archaeal, bacterial and microbial eukaryote communities behave similarly remain unanswered. Here, we aim to unravel the composition and intra/interannual temporal dynamic patterns for archaea, bacteria and microbial eukaryotes in a set of small freshwater ecosystems. We monitored archaeal and bacterial community composition during 24 consecutive months in four ponds and one brook from northwestern France by 16S rRNA gene amplicon sequencing (microbial eukaryotes were previously investigated for the same systems). Unexpectedly for oxic environments, bacterial Candidate Phyla Radiation (CPR) were highly diverse and locally abundant. Our results suggest that microbial community structure is mainly driven by environmental conditions acting over space (ecosystems) and time (seasons). A low proportion of operational taxonomic units (OTUs) (<1%) was shared by the five ecosystems despite their geographical proximity (2-9 km away), making microbial communities almost unique in each ecosystem and highlighting the strong selective influence of local environmental conditions. Marked and similar seasonality patterns were observed for archaea, bacteria and microbial eukaryotes in all ecosystems despite strong turnovers of rare OTUs. Over the 2-year survey, microbial community composition varied despite relatively stable environmental parameters. This suggests that biotic associations play an important role in interannual community assembly.

Euglenozoa: taxonomy, diversity and ecology, symbioses and viruses

Euglenozoa is a species-rich group of protists, which have extremely diverse lifestyles and a range of features that distinguish them from other eukaryotes. They are composed of free-living and parasitic kinetoplastids, mostly free-living diplonemids, heterotrophic and photosynthetic euglenids, as well as deep-sea symbiontids. Although they form a well-supported monophyletic group, these morphologically rather distinct groups are almost never treated together in a comparative manner, as attempted here. We present an updated taxonomy, complemented by photos of representative species, with notes on diversity, distribution and biology of euglenozoans. For kinetoplastids, we propose a significantly modified taxonomy that reflects the latest findings. Finally, we summarize what is known about viruses infecting euglenozoans, as well as their relationships with ecto- and endosymbiotic bacteria.

Novel Endosymbionts in Rhizarian Amoebae Imply Universal Infection of Unrelated Free-Living Amoebae by Legionellales

Legionellales-infected water is a frequent cause of local outbreaks of Legionnaires’ disease and Pontiac fever. Decontaminations are difficult because Legionellales reproduce in eukaryotic microorganisms (protists). Most often, Legionellales have been isolated from amoebae; however, the culture-based sampling methods are taxonomically biased. Sequencing studies show that amoebae in the cercozoan class Thecofilosea are dominant in soils and wastewater treatment plants, prompting us to screen their capability to serve as potential hosts of endosymbiotic bacteria. Environmental isolates of Thecofilosea contained a surprising richness of endosymbiotic Legionellales, including Legionella. Considering the widespread dispersal of Legionellales in apparently unrelated amoeboid protist taxa, it appears that the morphotype and not the evolutionary origin of amoebae determines their suitability as hosts for Legionellales. We further provide a protocol for gnotobiotic cultivation of Legionellales and their respective hosts, facilitating future genomic and transcriptomic research of host–symbiont relationships.

Cascading effects in freshwater microbial food webs by predatory Cercozoa, Katablepharidacea and ciliates feeding on aplastidic bacterivorous cryptophytes

Heterotrophic nanoflagellates (HNF) are considered as major planktonic bacterivores, however, larger HNF taxa can also be important predators of eukaryotes. To examine this trophic cascading, natural protistan communities from a freshwater reservoir were released from grazing pressure by zooplankton via filtration through 10- and 5-µm filters, yielding microbial food webs of different complexity. Protistan growth was stimulated by amendments of five Limnohabitans strains, thus yielding five prey-specific treatments distinctly modulating protistan communities in 10- versus 5-µm fractions. HNF dynamics was tracked by applying five eukaryotic fluorescence in situ hybridization probes covering 55-90% of total flagellates. During the first experimental part, mainly small bacterivorous Cryptophyceae prevailed, with significantly higher abundances in 5-µm treatments. Larger predatory flagellates affiliating with Katablepharidacea and one Cercozoan lineage (increasing to up to 28% of total HNF) proliferated towards the experimental endpoint, having obviously small phagocytized HNF in their food vacuoles. These predatory flagellates reached higher abundances in 10-µm treatments, where small ciliate predators and flagellate hunters also (Urotricha spp., Balanion planctonicum) dominated the ciliate assemblage. Overall, our study reports pronounced cascading effects from bacteria to bacterivorous HNF, predatory HNF and ciliates in highly treatment-specific fashions, defined by both prey-food characteristics and feeding modes of predominating protists.

CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology

Phagotrophic protists are key players in aquatic food webs. Although sequencing-based studies have revealed their enormous diversity, ecological information on in situ abundance, feeding modes, grazing preferences, and growth rates of specific lineages can be reliably obtained only using microscopy-based molecular methods, such as Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). CARD-FISH is commonly applied to study prokaryotes, but less so to microbial eukaryotes. Application of this technique revealed that Paraphysomonas or Spumella-like chrysophytes, considered to be among the most prominent members of protistan communities in pelagic environments, are omnipresent but actually less abundant than expected, in contrast to little known groups such as heterotrophic cryptophyte lineages (e.g., CRY1), cercozoans, katablepharids, or the MAST lineages. Combination of CARD-FISH with tracer techniques and application of double CARD-FISH allow visualization of food vacuole contents of specific flagellate groups, thus considerably challenging our current, simplistic view that they are predominantly bacterivores. Experimental manipulations with natural communities revealed that larger flagellates are actually omnivores ingesting both prokaryotes and other protists. These new findings justify our proposition of an updated model of microbial food webs in pelagic environments, reflecting more authentically the complex trophic interactions and specific roles of flagellated protists, with inclusion of at least two additional trophic levels in the nanoplankton size fraction. Moreover, we provide a detailed CARD-FISH protocol for protists, exemplified on mixo- and heterotrophic nanoplanktonic flagellates, together with tips on probe design, a troubleshooting guide addressing most frequent obstacles, and an exhaustive list of published probes targeting protists.

Shift and Metabolic Potentials of Microbial Eukaryotic Communities Across the Full Depths of the Mariana Trench

Microbial eukaryotes are widespread and play important roles in marine ecosystems. However, their ecological characteristics in the deep sea (>1,000 m), especially hadal trenches, were largely unknown. Here, we investigated the diversity and metabolic potentials of microbial eukaryotes along the whole water column of the Mariana Trench by metagenomics. Our results showed clear depth-related distribution of microbial eukaryotic community and associated metabolic potentials. Surface seawater was dominated by phototrophic/mixotrophic groups (e.g., Dinoflagellata) and genes involved in biosynthesis (photosynthesis and fatty acid biosynthesis), while deep (bathypelagic and/or hadal) seawaters were enriched with heterotrophic groups (e.g., Bicoecea) and genes related to digestion (lysosomal enzymes and V-type ATPase) and carbohydrate metabolism. Co-occurrence analysis revealed high intra-domain connectivity, indicating that microbial eukaryotic composition was more influenced by microbial eukaryotes themselves than bacteria. Increased abundance of genes associated with unsaturated fatty acid biosynthesis likely plays a role in resisting high hydrostatic pressure. Top1 and hupB genes, responsible for the formation and stabilization of DNA structure, were unique and abundant in the hadal zone and thus may be helpful to stabilize DNA structure in the deep sea. Overall, our results provide insights into the distribution and potential adaptability of microbial eukaryotes in the hadal zone.

The microbiome of a polluted urban lake harbors pathogens with diverse antimicrobial resistance and virulence genes

Bacterial resistance to antibiotics is one of the greatest threats to the modern human population. Paradoxically, urban settlements are often culpable in generating such resistance by influencing the adaptation of bacterial communities via pollution of natural ecosystems. Urban lakes are well-known examples of this problem, as they often receive discharges of both domestic and industrial wastewater. In this study, we used shotgun metagenome sequencing to examine the microbial diversity of water and sediment samples of Lake Alalay, a polluted urban lake near Cochabamba, Bolivia. We found that Proteobacteria dominated the relative abundance of both water and sediment samples at levels over 25% and that a significant proportion of the microbial diversity could not be classified (about 9% in water and 22% in sediment). Further metagenomic investigation of antimicrobial resistance (AR) genes identified 277 and 150 AR genes in water and sediment samples, respectively. These included genes with functional annotations for resistance to fluoroquinolones, tetracyclines, phenicols, macrolides, beta-lactams, and rifamycin. A high number of genes involved in bacterial virulence also occurred in both water and sediment samples (169 and 283, respectively), where the virulence gene pscP normally found in the Pseudomonas aeruginosa type III secretion system had the highest relative abundance. Isolated and identified bacteria from water samples also revealed the presence of pathogenic bacteria among the microbiota of Lake Alalay. Seeing as most AR and virulence genes detected in this study are commonly described in nosocomial infections, we provide evidence suggesting that the microbial ecosystem of Lake Alalay presents a severe health risk to the surrounding population.

Molecular Phylogeny and Taxonomy of the Genus Spumella (Chrysophyceae) Based on Morphological and Molecular Evidence

The genus Spumella, established by Cienkowsky in 1870, is characterized by omnivory, two (rarely three) flagella, a short stick-like structure beneath the flagella, a threadlike stalk, cell division via constriction and cyst formation. Since the first phylogenetic study of Spumella-like flagellates, their paraphyly has consistently been shown, with separation into several genera. More recently, Spumella was carefully investigated using molecular and morphological data to propose seven new species. Classification of this genus and knowledge of its species diversity remain limited because Spumella-like flagellates are extremely difficult to identify based on limited morphological characters. To understand the phylogeny and taxonomy of Spumella, we analyzed molecular and morphological data from 47 strains, including 18 strains isolated from Korean ponds or swamps. Nuclear SSU, ITS and LSU rDNA data were used for maximum likelihood and Bayesian analyses. The molecular data divided the strains into 15 clades, including seven new lineages, each with unique molecular signatures for nuclear SSU rRNA from the E23-2 to E23-5 domains, the spacer between the E23-8 and E23-9 domains of the V4 region and domain 29 of the V5 region. Our results revealed increased species diversity in Spumella. In contrast to the molecular phylogeny results, the taxa showed very similar cell morphologies, suggesting morphological convergence into simple nanoflagellates to enable heterotrophy. Three new species produced stomatocysts in culture. Aspects of stomatocyst morphology, including collar structure, surface ornamentation, and cyst shape, were very useful in differentiating the three species. The general ultrastructure of Spumella bureschii strain Baekdongje012018B8 and S. benthica strain Hwarim032418A5 showed the typical chrysophyte form for the leucoplast, a vestigial chloroplast surrounded by four envelope membranes, supporting the hypothesis that Spumella evolved from a phototroph to a heterotroph via the loss of its photosynthetic ability. Seven new species are proposed: S. benthica, S. communis, S. longicolla, S. oblata, S. rotundata, S. similis, and S. sinechrysos.

Weekly variations of viruses and heterotrophic nanoflagellates and their potential impact on bacterioplankton in shallow waters of the central Red Sea

Bacterioplankton play a pivotal role in marine ecosystems. However, their temporal dynamics and underlying control mechanisms are poorly understood in tropical regions such as the Red Sea. Here, we assessed the impact of bottom-up (resource availability) and top-down (viruses and heterotrophic nanoflagellates) controls on bacterioplankton abundances by weekly sampling a coastal central Red Sea site in 2017. We monitored microbial abundances by flow cytometry together with a set of environmental variables including temperature, salinity, dissolved organic and inorganic nutrients and chlorophyll a. We distinguished five groups of heterotrophic bacteria depending on their physiological properties relative nucleic acid content, membrane integrity and cell-specific respiratory activity, two groups of Synechococcus cyanobacteria and three groups of viruses. Viruses controlled heterotrophic bacteria for most of the year, as supported by a negative correlation between their respective abundances and a positive one between bacterial mortality rates and mean viral abundances. On the contrary, heterotrophic nanoflagellates abundance covaried with that of heterotrophic bacteria. Heterotrophic nanoflagellates showed preference for larger bacteria from both the high and low nucleic acid content groups. Our results demonstrate that top-down control is fundamental in keeping heterotrophic bacterioplankton abundances low (< 5 × 10 ⁵ cells mL⁻¹) in Red Sea coastal waters.

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. We analyze diversity pattern and the overlap of taxa of eukaryotic microbial communities in freshwater and soil based on Illumina HiSeq high-throughput sequencing of the amplicon V9 diversity. We analyzed corresponding freshwater and soil samples from 30 locations, i.e. samples from different lakes across Germany and soil samples from the respective catchment areas. Aside from principle differences in the community composition of soils and freshwater, in particular with respect to the relative contribution of fungi and algae, soil habitats have a higher richness. Nevertheless, community similarity between different soil sites is considerably lower as compared to the similarity between different freshwater sites. We show that the overlap of organisms co-occurring in freshwater and soil habitats is surprisingly low. Even though closely related taxa occur in both habitats distinct OTUs were mostly habitat–specific and most OTUs occur exclusively in either soil or freshwater. The distribution pattern of the few co-occurring lineages indicates that even most of these are presumably rather habitat-specific. Their presence in both habitat types seems to be based on a stochastic drift of particularly abundant but habitat-specific taxa rather than on established populations in both types of habitats.

A freshwater radiation of diplonemids

Diplonemids are considered marine protists and have been reported among the most abundant and diverse eukaryotes in the world oceans. Recently we detected the presence of freshwater diplonemids in Japanese deep freshwater lakes. However, their distribution and abundances in freshwater ecosystems remain unknown. We assessed abundance and diversity of diplonemids from several geographically distant deep freshwater lakes of the world by amplicon-sequencing, shotgun metagenomics and catalysed reporter deposition-fluorescent in situ hybridization (CARD-FISH). We found diplonemids in all the studied lakes, albeit with low abundances and diversity. We assembled long 18S rRNA sequences from freshwater diplonemids and showed that they form a new lineage distinct from the diverse marine clades. Freshwater diplonemids are a sister-group to a marine clade, which are mainly isolates from coastal and bay areas, suggesting a recent habitat transition from marine to freshwater habitats. Images of CARD-FISH targeted freshwater diplonemids suggest they feed on bacteria. Our analyses of 18S rRNA sequences retrieved from single-cell genomes of marine diplonemids show they encode multiple rRNA copies that may be very divergent from each other, suggesting that marine diplonemid abundance and diversity both have been overestimated. These results have wider implications on assessing eukaryotic abundances in natural habitats by using amplicon-sequencing alone.

Single Cell Genomics Reveals Viruses Consumed by Marine Protists

The predominant model of the role of viruses in the marine trophic web is that of the “viral shunt,” where viral infection funnels a substantial fraction of the microbial primary and secondary production back to the pool of dissolved organic matter. Here, we analyzed the composition of non-eukaryotic DNA associated with individual cells of small, planktonic protists in the Gulf of Maine (GoM) and the Mediterranean Sea. We found viral DNA associated with a substantial fraction cells from the GoM (51%) and the Mediterranean Sea (35%). While Mediterranean SAGs contained a larger proportion of cells containing bacterial sequences (49%), a smaller fraction of cells contained bacterial sequences in the GoM (19%). In GoM cells, nearly identical bacteriophage and ssDNA virus sequences where found across diverse lineages of protists, suggesting many of these viruses are non-infective. The fraction of cells containing viral DNA varied among protistan lineages and reached 100% in Picozoa and Choanozoa. These two groups also contained significantly higher numbers of viral sequences than other identified taxa. We consider mechanisms that may explain the presence of viral DNA in protistan cells and conclude that protistan predation on free viral particles contributed to the observed patterns. These findings confirm prior experiments with protistan isolates and indicate that the viral shunt is complemented by a viral link in the marine microbial food web. This link may constitute a sink of viral particles in the ocean and has implications for the flow of carbon through the microbial food web.

Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate

Phagocytosis is a fundamental process in marine ecosystems by which prey organisms are consumed and their biomass incorporated in food webs or remineralized. However, studies searching for the genes underlying this key ecological process in free-living phagocytizing protists are still scarce, in part due to the lack of appropriate ecological models. Our reanalysis of recent molecular datasets revealed that the cultured heterotrophic flagellate Cafeteria burkhardae is widespread in the global oceans, which prompted us to design a transcriptomics study with this species, grown with the cultured flavobacterium Dokdonia sp. We compared the gene expression between exponential and stationary phases, which were complemented with three starvation by dilution phases that appeared as intermediate states. We found distinct expression profiles in each condition and identified 2056 differentially expressed genes between exponential and stationary samples. Upregulated genes at the exponential phase were related to DNA duplication, transcription and translational machinery, protein remodeling, respiration and phagocytosis, whereas upregulated genes in the stationary phase were involved in signal transduction, cell adhesion, and lipid metabolism. We identified a few highly expressed phagocytosis genes, like peptidases and proton pumps, which could be used to target this ecologically relevant process in marine ecosystems.

Tannins from senescent Rhizophora mangle mangrove leaves have a distinctive effect on prokaryotic and eukaryotic communities in a Distichlis spicata salt marsh soil

Due to climate warming, tannin-rich Rhizophora mangle migrates into tannin-poor salt marshes, where the tannins interfere with the biogeochemistry in the soil. Changes in biogeochemistry are likely associated with changes in microbial communities. This was studied in microcosms filled with salt marsh soil and amended with leaf powder, crude condensed tannins, purified condensed tannins (PCT), all from senescent R. mangle leaves, or with tannic acid. Size and composition of the microbial communities were determined by denaturing gradient gel electrophoresis, high-throughput sequencing and real-time PCR based on the 16S and 18S rRNA genes. Compared with the control, the 16S rRNA gene abundance was lowered by PCT, while the 18S rRNA gene abundance was enhanced by all treatments. The treatments also affected the composition of the 16S rRNA and 18S rRNA gene assemblies, but the effects on the 18S rRNA gene were greater. The composition of the 18S rRNA gene, but not of the 16S rRNA gene, was significantly correlated with the mineralization of carbon, nitrogen and phosphorus. Distinctive microbial groups emerged during the different treatments. This study revealed that migration of mangroves may affect both the prokaryotic and the eukaryotic communities in salt marsh soils, but that the effects on the eukaryotes will likely be greater.

The Molecular Diversity of Phagotrophic Euglenids Examined Using Single-cell Methods

Euglenids are a diverse group of euglenozoan flagellates that includes phototrophs, osmotrophs, and phagotrophs. Despite making up most of the phylogenetic diversity of euglenids, phagotrophs remain understudied, and recent work has focused on 'deep-branching' groups. Spirocuta is the large clade encompassing all flexible euglenids including the phototroph and primary osmotroph clades, plus various phagotrophs. Understanding the phylogenetic diversity of phagotrophic spirocutes is crucial for tracing euglenid evolution, including how phototrophs arose. We used single-cell approaches to greatly increase sampling of SSU rDNA for phagotrophic euglenids, particularly spirocutes, including the first sequences from Urceolus, Jenningsia, Chasmostoma, and Sphenomonas, and expanded coverage for Dinema and Heteronema sensu lato, amongst others. Urceolus monophyly is unconfirmed. Organisms referred to Jenningsia form two distinct clades. Heteronema vittatum and similar cells branch separately from Heteronema (c.f.) globuliferum and Teloprocta/Heteronema scaphurum, while Dinema appears as 2-3 clades. Sphenomonas is monophyletic and the deepest branch within Petalomonadida. The census of genera markedly underestimates the phylogenetic diversity of phagotrophs, but taxonomic restraint is necessary when sequences are not available from type species or reasonable surrogates. SSU rDNA phylogenies do not resolve most deep relationships within Spirocuta, but identify units of diversity to sample in future multigene analyses.