Mangrove sediments are environmental hotspots for pathogenic protists

Mangrove sediments are unique ecosystems providing habitats for diverse organisms, especially microbial communities. However, little is known about the diversity and environmental risk of a critical group of microorganisms, the protists. To address this gap, we employed metagenome sequencing technologies to provide the first comprehensive view of the protistan community in the mangrove sediment. Our results surprisingly showed that parasitic protists dominated the protistan community in mangrove sediments, with an average abundance of 59.67%, one of the highest in all ecosystems on Earth. We also found that the relative abundance of protists decreased significantly (R = -0.21, p = 0.045) with latitude but increased with depths (R = 0.7099, p < 0.001). The parasitic communities were positively influenced by microbial (bacteria, fungi, and archaea) communities, including horizontal-scale and vertical-scale. In addition, sulfate and salinity had the most significant influence on the protistan community. Our findings provide new insights into our understanding of protistan variation in mangrove sediments, including abundance, composition, and possible functions, and indicate that mangrove sediments are hotspots for environmental pathogens, posing a potential risk to human health.

Long-term conservation tillage enhances microbial carbon use efficiency by altering multitrophic interactions in soil

Microbial carbon (C) use efficiency (CUE) plays a key role in soil C storage. The predation of protists on bacteria and fungi has potential impacts on the global C cycle. However, under conservation tillage conditions, the effects of multitrophic interactions on soil microbial CUE are still unclear. Here, we investigate the multitrophic network (especially the keystone ecological cluster) and its regulation of soil microbial CUE and soil organic C (SOC) under different long-term (15-year) tillage practices. We found that conservation tillage (CT) significantly enhanced microbial CUE, turnover, and SOC (P < 0.05) compared to traditional tillage (control, CK). At the same time, tillage practice and soil depth had significant effects on the structure of fungal and protistan communities. Furthermore, the soil biodiversity of the keystone cluster was positively correlated with the microbial physiological traits (CUE, microbial growth rate (MGR), microbial respiration rate (Rs), microbial turnover) and SOC (P < 0.05). Protistan richness played the strongest role in directly shaping the keystone cluster. Compared with CK, CT generally enhanced the correlation between microbial communities and microbial physiological characteristics and SOC. Overall, our results illustrate that the top-down control (the organisms at higher trophic levels affect the organisms at lower trophic levels) of protists in the soil micro-food web plays an important role in improving microbial CUE under conservation tillage. Our findings provide a theoretical basis for promoting the application of protists in targeted microbial engineering and contribute to the promotion of conservation agriculture and the improvement of soil C sequestration potential.

The coupling effects of carbon fractions, bacteria, and protists on carbon emissions among various ditch levels in the Lower Yellow River

Inland waters are receiving increasing attention due to their importance in the global carbon cycle. However, the dynamics of CO2 emissions and the related mechanisms from ditches remain unclear. In this study, field sampling and an incubation experiment were conducted to explore the effects and mechanisms, especially the coupling effects between carbon fractions, bacteria, and protists on carbon dynamics of different ditch levels (sublateral ditch, farm ditch, and lateral ditch) and sediment depths (0-20cm, 20-40cm) in the Lower Yellow River. Results indicated that sublateral ditches nearest to farmland had the highest accumulative carbon mineralization (0-20 cm 1.38 g C kg-1; 20-40 cm 0.89 g C kg-1), equivalent to that of farmland, followed by the lateral ditch (0-20 cm 0.84 g C kg-1; 20-40 cm 0.50 g C kg-1) and the farm ditch (0-20 cm 0.67 g C kg-1; 20-40 cm 0.26 g C kg-1). Carbon emissions from ditches are mainly regulated by SOC (36.97 %), bacteria (29.2 %), and protists (18.95 %). Specifically, the mineralization of flooded lateral ditches is attributed to protist diversity. SOC, bacterial and protistan diversity in the farm ditch significantly impacted carbon emissions, with SOC as the dominant factor, while the bacterial composition and SOC contributed more to CO2 emissions in the sublateral ditch. Our results highlight the importance of carbon emissions from ditches, especially those closest to farmland. This study provides new insights into the construction and management of farmland irrigation and drainage in the aspects of carbon sequestration.

Viral Chemotaxis of Paramecium Bursaria Altered by Algal Endosymbionts

Chemotaxis is widespread across many taxa and often aids resource acquisition or predator avoidance. Species interactions can modify the degree of movement facilitated by chemotaxis. In this study, we investigated the influence of symbionts on Paramecium bursaria's chemotactic behavior toward chloroviruses. To achieve this, we performed choice experiments using chlorovirus and control candidate attractors (virus stabilization buffer and pond water). We quantified the movement of Paramecia grown with or without algal and viral symbionts toward each attractor. All Paramecia showed some chemotaxis toward viruses, but cells without algae and viruses showed the most movement toward viruses. Thus, the endosymbiotic algae (zoochlorellae) appeared to alter the movement of Paramecia toward chloroviruses, but it was not clear that ectosymbiotic viruses (chlorovirus) also had this effect. The change in behavior was consistent with a change in swimming speed, but a change in attraction remains possible. The potential costs and benefits of chemotactic movement toward chloroviruses for either the Paramecia hosts or its symbionts remain unclear.

Molecular characterization of Blastocystis and Entamoeba of muskoxen and sheep in Greenland

Molecular characterisation of endobionts that are shared among human and non-human hosts can help shed light on the epidemiology and inform studies that aim to unravel the role of these organisms in health and disease. Two of the most common of shared endobionts include the single-celled intestinal protists Blastocystis and Entamoeba. Here, we present the first known data on genetic diversity and host specificity of these two genera in Greenland. Faecal DNA samples from 243 muskoxen and 44 sheep were submitted to metabarcoding of nuclear small subunit ribosomal DNA. Entamoeba- and Blastocystis-specific sequences were clustered, and consensus sequences were subjected to taxonomic query. Using MinION-based sequencing, near-complete nuclear small subunit ribosomal DNA sequences were obtained from four faecal samples. Of the 243 muskox samples, 180 (74%) and 19 (8%) were positive for Blastocystis and Entamoeba, respectively. Forty (91%) and six (14%) of the 44 sheep samples were positive for Blastocystis and Entamoeba, respectively. Blastocystis subtypes (ST) 10, 14, 21, 24-26, and a novel subtype (ST40) were identified. Colonisation by more than one subtype was common. ST40 was common in muskoxen but limited to Northeast Greenland. Entamoeba bovis and the E. bovis-associated ribosomal lineages (RL) 1 and 8 were found, and three conditional lineages (CL) 3, 4, and 10 were confirmed; CL10 was promoted to RL12. Several novel lineages were identified, all of which were linked to the E. bovis complex. In conclusion, Blastocystis was far more common than Entamoeba and found in approximately three of every four animals; both can be considered common colonisers of large herbivorous mammals in Greenland. Multiple subtypes/lineages of both genera were commonly observed, some of which were novel, but most of which are seen in many other parts of the world.

Shining the spotlight on the neglected: new high-quality genome assemblies as a gateway to understanding the evolution of Trypanosomatidae

BACKGROUND

Protists of the family Trypanosomatidae (phylum Euglenozoa) have gained notoriety as parasites affecting humans, domestic animals, and agricultural plants. However, the true extent of the group's diversity spreads far beyond the medically and veterinary relevant species. We address several knowledge gaps in trypanosomatid research by undertaking sequencing, assembly, and analysis of genomes from previously overlooked representatives of this protistan group.

RESULTS

We assembled genomes for twenty-one trypanosomatid species, with a primary focus on insect parasites and Trypanosoma spp. parasitizing non-human hosts. The assemblies exhibit sizes consistent with previously sequenced trypanosomatid genomes, ranging from approximately 18 Mb for Obscuromonas modryi to 35 Mb for Crithidia brevicula and Zelonia costaricensis. Despite being the smallest, the genome of O. modryi has the highest content of repetitive elements, contributing nearly half of its total size. Conversely, the highest proportion of unique DNA is found in the genomes of Wallacemonas spp., with repeats accounting for less than 8% of the assembly length. The majority of examined species exhibit varying degrees of aneuploidy, with trisomy being the most frequently observed condition after disomy.

CONCLUSIONS

The genome of Obscuromonas modryi represents a very unusual, if not unique, example of evolution driven by two antidromous forces: i) increasing dependence on the host leading to genomic shrinkage and ii) expansion of repeats causing genome enlargement. The observed variation in somy within and between trypanosomatid genera suggests that these flagellates are largely predisposed to aneuploidy and, apparently, exploit it to gain a fitness advantage. High heterogeneity in the genome size, repeat content, and variation in chromosome copy numbers in the newly-sequenced species highlight the remarkable genome plasticity exhibited by trypanosomatid flagellates. These new genome assemblies are a robust foundation for future research on the genetic basis of life cycle changes and adaptation to different hosts in the family Trypanosomatidae.

Three new species of Gromia (Protista, Rhizaria) identified from the Romanian Black Sea shelf

The protist genus Gromia was first described in 1835 by Dujardin and while gromiids are prominent in the marine environment, Gromia oviformis was, for a long time, the only valid species regularly recorded. To date, 16 species that are morphologically and/or genetically distinct have been described. While recent studies are documenting their diversity and their ecological importance, G. oviformis has been the sole gromiid species identified in the Black Sea, although unnamed Gromia species have also been recorded. We collected sediment samples from the Romanian continental shelf at varying depths (48 - 58 m) to study the morphological and genetic diversity of gromiids in this part of the Black Sea. Three new species, Gromia bugnae sp. nov., Gromia dianae sp. nov. and Gromia fabi sp. nov., were identified based on an integrative taxonomic approach, thus bringing the total described gromiid species to 19. Analysis of partial SSU rRNA gene sequences confirms that these are distinct species. Additionally, an undescribed species is represented by a sequence from the northern part of the Black Sea (Sevastopol, Kazachya Bay). The study provides further evidence of the diversity of gromiids in the Black Sea and underlines the importance of this little-known group in marginal seas.

Subunit composition of mitochondrial dehydrogenase complexes in diplonemid flagellates

In eukaryotes, pyruvate, a key metabolite produced by glycolysis, is converted by a tripartite mitochondrial pyruvate dehydrogenase (PDH) complex to acetyl-coenzyme A, which is fed into the tricarboxylic acid cycle. Two additional enzyme complexes with analogous composition catalyze similar oxidative decarboxylation reactions albeit using different substrates, the branched-chain ketoacid dehydrogenase (BCKDH) complex and the 2-oxoglutarate dehydrogenase (OGDH) complex. Comparative transcriptome analyses of diplonemids, one of the most abundant and diverse groups of oceanic protists, indicate that the conventional E1, E2, and E3 subunits of the PDH complex are lacking. E1 was apparently replaced in the euglenozoan ancestor of diplonemids by an AceE protein of archaeal type, a substitution that we also document in dinoflagellates. Here we demonstrate that the mitochondrion of the model diplonemid Paradiplonema papillatum displays pyruvate and 2-oxoglutarate dehydrogenase activities. Protein mass spectrometry of mitochondria reveal that the AceE protein is as abundant as the E1 subunit of BCKDH. This corroborates the view that the AceE subunit is a functional component of the PDH complex. We hypothesize that by acquiring AceE, the diplonemid ancestor not only lost the eukaryotic-type E1, but also the E2 and E3 subunits of the PDH complex, which are present in other euglenozoans. We posit that the PDH activity in diplonemids seems to be carried out by a complex, in which the AceE protein partners with the E2 and E3 subunits from BCKDH and/or OGDH.

RNA outperforms DNA-based metabarcoding in assessing the diversity and response of microeukaryotes to environmental variables in the Arctic Ocean

The Arctic Ocean (AO) has a harsh environment characterized by low temperatures, extensive ice coverage, and periodic freezing and melting of sea ice, which has provided diverse habitats for microorganisms. Prior studies primarily focused on microeukaryote communities in the upper water or sea ice based on environmental DNA, leaving the composition of active microeukaryotes in the diverse AO environments largely unknown. This study provided a vertical assessment of microeukaryote communities in the AO from snow and ice to sea water at a depth of 1670 m using high-throughput sequencing of co-extracted DNA and RNA. RNA extracts depicted microeukaryote community structure and intergroup correlations more accurately and responded more sensitively to environmental conditions than those derived from DNA. Using RNA:DNA ratios as a proxy for relative activity of major taxonomic groups, the metabolic activities of major microeukaryote groups were determined along depth. Analysis of co-occurrence networks showed that parasitism between Syndiniales and dinoflagellates/ciliates in the deep ocean may be significant. This study increased our knowledge of the diversity of active microeukaryote communities and highlighted the importance of using RNA-based sequencing over DNA-based sequencing to examine the relationship between microeukaryote assemblages and the responses of microeukaryotes to environmental variables in the AO.

Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly

BACKGROUND

Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses. Increasingly, these communities are being understood through the lens of omics tools, which enable high-throughput processing of diverse communities. Metatranscriptomics offers an understanding of near real-time gene expression in microbial eukaryotic communities, providing a window into community metabolic activity.

RESULTS

Here we present a workflow for eukaryotic metatranscriptome assembly, and validate the ability of the pipeline to recapitulate real and manufactured eukaryotic community-level expression data. We also include an open-source tool for simulating environmental metatranscriptomes for testing and validation purposes. We reanalyze previously published metatranscriptomic datasets using our metatranscriptome analysis approach.

CONCLUSION

We determined that a multi-assembler approach improves eukaryotic metatranscriptome assembly based on recapitulated taxonomic and functional annotations from an in-silico mock community. The systematic validation of metatranscriptome assembly and annotation methods provided here is a necessary step to assess the fidelity of our community composition measurements and functional content assignments from eukaryotic metatranscriptomes.

The Mixoplankton Database - diversity of photo-phago-trophic plankton in form, function and distribution across the global ocean

Protist plankton are major members of open-water marine food webs. Traditionally divided between phototrophic phytoplankton and phagotrophic zooplankton, recent research shows many actually combine phototrophy and phagotrophy in the one cell; these protists are the 'mixoplankton'. Under the mixoplankton paradigm, 'phytoplankton' are incapable of phagotrophy (diatoms being exemplars), while 'zooplankton' are incapable of phototrophy. This revision restructures marine food webs, from regional to global levels. Here we present the first comprehensive database of marine mixoplankton, bringing together extant knowledge of the identity, allometry, physiology and trophic interactivity of these organisms. This Mixoplankton Database (MDB) will aid researchers that confront difficulties in characterizing life traits of protist plankton, and it will benefit modellers needing to better appreciate ecology of these organisms with their complex functional and allometric predator-prey interactions. The MDB also identifies knowledge gaps, including the need to better understand, for different mixoplankton functional types, sources of nutrition (use of nitrate, prey types and nutritional states), and to obtain vital rates (e.g., growth, photosynthesis, ingestion, factors affecting photo' versus phago' -trophy). It is now possible to revisit and re-classify protistan 'phytoplankton' and 'zooplankton' in extant databases of plankton life forms so as to clarify their roles in marine ecosystems.

Characterizing potential pathogens from intracellular bacterial community of protists in wastewater treatment plants

Protists are a trophically diverse and biogeochemically significant component of water environments and are widely reported as hosts of bacteria. However, the potential role of protists in wastewater treatment plants (WWTPs) as reservoirs for human pathogens does not appear to have received adequate attention. Here, a combination of fluorescence-activated cell sorting and Illumina sequencing was applied to characterize the dynamics of the internalized bacterial community of the enriched protists from the influents and effluents of five WWTPs. The results showed that Proteobacteria (mainly Betaproteobacteria) dominate the intracellular bacterial communities of protists in both influents and effluents of WWTPs, accounting for 72.6% of the total intracellular bacterial communities. The most frequently detected genus was Sulfuricurvum in the influent samples, Chryseobacterium and Pseudomonas were most prevalent in the effluent samples. Compared with the influents, a more diverse and abundant intracellular bacterial community was observed in the effluents. Moreover, the potential intracellular bacterial pathogens were 26 times higher in effluents than in influents, with Pseudomonas fluorescens and Pseudomonas putida significantly enriched in effluents. This work provides insights into the dynamics of bacterial communities and potential pathogens harbored by protists in the influents and effluents from WWTPs, contributing to the improved evaluation of biosafety in WWTPs.

Response of soil protists to antimony and arsenic contamination

Microorganisms can mediate antimony (Sb) and arsenic (As) transformation and thus change their mobility and toxicity. Having similar geochemical behavior, Sb and As are generally considered to exert similar environmental pressure on microbiome. However, it needs further validation, especially for protists. In this study, the responses of protistan communities to Sb and As were investigated by collecting soils from Xikuangshan Sb mine and Shimen As mine in China. Antimony and As contamination taxonomically and functionally (consumer and phototroph) changed the alpha and beta diversities of protistan communities, but exerted different impacts on the parasitic community. Based on multiple statistical tools, As contamination had a greater impact on protistan communities than Sb. The ecological networks of highly contaminated sites were less complex but highly positively connected compared to less contaminated sites. High As contamination raised the ratio of consumers and decreased the ratio of phototrophs in ecological networks, while the opposite tendency was observed in Sb contaminated soils. High Sb and As contamination enriched different keystone taxa resistant to Sb and As. These results demonstrate that protistan community respond differently to Sb and As.

Experimental evidence for enzymatic cell wall dissolution in a microbial protoplast feeder (Orciraptor agilis, Viridiraptoridae)

BACKGROUND

Several protists have evolved the ability to perforate the cell walls of algae and fungi to specifically feed on their cell contents. These phagotrophic "protoplast feeders" represent an interesting mechanistic intermediate between predators and parasites and pose a number of cell biological questions. Although their fascinating feeding behaviour has been observed for the last 150 years, it is still unknown how protoplast feeders produce the well-defined and species-specific perforations in biochemically diverse cell walls. Differential expression analyses of the algivorous flagellate Orciraptor agilis (Viridiraptoridae, Cercozoa, Rhizaria) suggested the involvement of a highly expressed putative glycoside hydrolase of family GH5_5. To assess the importance of this carbohydrate-active enzyme in the feeding act of Orciraptor, we recombinantly produced its catalytic domain and studied the enzymatic activity, cellular localisation and function.

RESULTS

The GH5_5 catalytic domain from Orciraptor showed pronounced activity on soluble cellulose derivatives and mixed-linkage glucans, with reaction optima comparable to known GH5_5 representatives. Crystalline cellulose was not digested by the enzyme, which suggests a typical endocellulase activity. Immunocytochemistry with a polyclonal antibody raised against the GH5_5 domain revealed that the native endocellulase localises to the contact zone of Orciraptor and the algal cell wall (= perforation zone) and to intracellular granules, which were enriched during attack. Furthermore, the anti-GH5_5 antibody applied to live cells significantly reduced the feeding success of Orciraptor. The cells attacked the algae, which, however, resulted in numerous incomplete perforations.

CONCLUSIONS

Our experimental data from enzymatic assays, immunocytochemistry and inhibition experiments strongly suggest a key role of the GH5_5 endocellulase in cell wall dissolution by Orciraptor agilis. With that, we provide evidence that the well-defined perforations produced by protoplast feeders are caused by extracellular carbohydrate-active enzymes and made a first step towards establishing the molecular basis of a fascinating, yet poorly understood microbial feeding strategy.

Fertilization drives distinct biotic and abiotic factors in regulating functional groups of protists in a 5-year fertilization system

Introduction

Protists play an important role in nutrient cycling, microbiome stability and soil fertility maintenance. However, the driving force of protistan functional groups remains poorly understood in agricultural ecosystems.

Methods

We investigated the impacts of fertilization regimes on the diversity, composition and functional groups of protists and further disentangled the effects of multiple factors shaping the community composition of functional groups in a 5-year fertilization regime (CK, no fertilization; M, organic fertilization; MNPK, combined inorganic and organic fertilization; NPK, inorganic fertilization).

Results

Fertilization significantly changed the community composition of protists rather than diversity. The MNPK treatment significantly increased the relative abundance of phototrophs and decreased that of the parasites and consumers. Partial least squares path modeling indicated that fertilization indirectly regulated protistan consumers via changes in the P content, which affected the composition of consumers mainly by regulating fungal community composition. Soil moisture (SM) and available phosphorus (AP) were identified as the top predictors for the composition of parasites, and the composition of phototrophs was mainly affected by SM, indicating that parasites and phototrophs were more sensitive to abiotic factors in the fertilization system.

Discussion

Taken together, our findings highlight that fertilization significantly affects the composition of functional groups of protists and their biotic or abiotic regulatory processes, which have implications for the potential changes in their ecosystem functions for soil management systems.

A metabolic, phylogenomic and environmental atlas of diatom plastid transporters from the model species Phaeodactylum

Diatoms are an important group of algae, contributing nearly 40% of total marine photosynthetic activity. However, the specific molecular agents and transporters underpinning the metabolic efficiency of the diatom plastid remain to be revealed. We performed in silico analyses of 70 predicted plastid transporters identified by genome-wide searches of Phaeodactylum tricornutum. We considered similarity with Arabidopsis thaliana plastid transporters, transcriptional co-regulation with genes encoding core plastid metabolic pathways and with genes encoded in the mitochondrial genomes, inferred evolutionary histories using single-gene phylogeny, and environmental expression trends using Tara Oceans meta-transcriptomics and meta-genomes data. Our data reveal diatoms conserve some of the ion, nucleotide and sugar plastid transporters associated with plants, such as non-specific triose phosphate transporters implicated in the transport of phosphorylated sugars, NTP/NDP and cation exchange transporters. However, our data also highlight the presence of diatom-specific transporter functions, such as carbon and amino acid transporters implicated in intricate plastid-mitochondria crosstalk events. These confirm previous observations that substrate non-specific triose phosphate transporters (TPT) may exist as principal transporters of phosphorylated sugars into and out of the diatom plastid, alongside suggesting probable agents of NTP exchange. Carbon and amino acid transport may be related to intricate metabolic plastid-mitochondria crosstalk. We additionally provide evidence from environmental meta-transcriptomic/meta- genomic data that plastid transporters may underpin diatom sensitivity to ocean warming, and identify a diatom plastid transporter (J43171) whose expression may be positively correlated with temperature.

Spatial dynamics of active microeukaryotes along a latitudinal gradient: Diversity, assembly process, and co-occurrence relationships

Recent global warming is profoundly and increasingly influencing the Arctic ecosystem. Understanding how microeukaryote communities respond to changes in the Arctic Ocean is crucial for understanding their roles in the biogeochemical cycles of nutrients and elements. Between July 22 and August 19, 2016, during cruise ARA07, seawater samples were collected along a latitudinal transect extending from the East Sea of Korea to the central Arctic Ocean. Environmental RNA was extracted and the V4 hypervariable regions of the reverse transcribed SSU rRNA were amplified. The sequences generated by high throughput sequencing were clustered into zero-radius OTUs (ZOTUs), and the taxonomic identities of each ZOTU were assigned using SINTAX against the PR2 database. Thus, the diversity, community composition, and co-occurrence networks of size fractionated microeukaryotes were revealed. The present study found: 1) the alpha diversity of pico- and nano-sized microeukaryotes showed a latitudinal diversity gradient; 2) three distinct communities were identified, i.e., the Leg-A, Leg-B surface, and Leg-B subsurface chlorophyll a maximum (SCM) groups; 3) distinct network structure and composition were found in the three groups; and 4) water temperature was identified as the primary factor driving both the alpha and beta diversities of microeukaryotes. This study conducted a comprehensive and systematic survey of active microeukaryotes along a latitudinal gradient, elucidated the diversity, community composition, co-occurrence relationships, and community assembly processes among major microeukaryote assemblages, and will help shed more light on our understanding of the responses of microeukaryote communities to the changing Arctic Ocean.

The effect of short-term temperature exposure on vital physiological processes of mixoplankton and protozooplankton

Sudden environmental changes like marine heatwaves will become more intense and frequent in the future. Understanding the physiological responses of mixoplankton and protozooplankton, key members of marine food webs, to temperature is crucial. Here, we studied two dinoflagellates (one protozoo- and one mixoplanktonic), two ciliates (one protozoo- and one mixoplanktonic), and two cryptophytes. We report the acute (24 h) responses on growth and grazing to a range of temperatures (5-34 °C). We also determined respiration and photosynthetic rates for the four grazers within 6 °C of warming. The thermal performance curves showed that, in general, ciliates have higher optimal temperatures than dinoflagellates and that protozooplankton is better adapted to warming than mixoplankton. Our results confirmed that warmer temperatures decrease the cellular volumes of all species. Q₁₀ coefficients suggest that grazing is the rate that increases the most in response to temperature in protozooplankton. Yet, in mixoplankton, grazing decreased in warmer temperatures, whereas photosynthesis increased. Therefore, we suggest that the Metabolic Theory of Ecology should reassess mixoplankton's position for the correct parameterisation of future climate change models. Future studies should also address the multigenerational response to temperature changes, to confirm whether mixoplankton become more phototrophic than phagotrophic in a warming scenario after adaptation.

Water masses and their associated temperature and cross-domain biotic factors co-shape upwelling microbial communities

Disentangling the drivers and mechanisms that shape microbial communities in a river-influenced coastal upwelling system requires considering a hydrologic dimension that can drive both deterministic and stochastic community assembly by generating hydrological heterogeneity and dispersal events. Additionally, ubiquitous and complex microbial interactions can play a significant role in community structuring. However, how the hydrology, biotic, and abiotic factors collectively shape microbial distribution in the hydrologically complicated river plume-upwelling coupling system remains unknown. Through underway sampling and daily observations, we employed 16S and 18S ribosomal RNA sequencing to disentangle drivers and mechanisms shaping the protist-bacteria microbiota in a river-influenced coastal upwelling system. Our findings indicate that the composition of microbial communities was water mass specific. Collectively, water mass, local water chemistry (mostly temperature) and biotic interaction (mostly cross-domain biotic interaction) shaped the protistan-bacterial communities. In comparison to protists, bacteria were more influenced by abiotic factors such as temperature than by cross-domain biotic factors, implying a stronger coupling of geochemical cycles. Both deterministic and stochastic processes had an effect on the distribution of microbial communities, but deterministic processes were more important for bacteria and were especially pronounced for upwelling communities. The co-occurrence network revealed strong associations between the protistan assemblages Orchrophyta and Ciliophora and the bacterial assemblages Alphaproteobacteria, Deltaproteobacteria, and Bacteroidetes, which may reflect predation and mutualism interactions. Overall, this study emphasizes the importance of taking water masses, temperature and domains of life into account when seeking to understand the drivers and assemblies of protist-bacteria microbiome dynamics in coastal upwelling systems, which is especially true given the complex and dynamic nature of the coastal ecosystem.

The composition, biotic network, and assembly of plastisphere protistan taxonomic and functional communities in plastic-mulching croplands

The increasing use of plastic film mulching has caused the accumulation of plastic film residue in soil. To date, most researches on the plastisphere have focused on bacterial and fungal communities, with few on protistan community, especially in terrestrial ecosystems. To understand plastisphere protistan communities, we collected plastic film residues from plastic-mulching croplands. The plastisphere significantly altered the alpha-diversity, structure, and composition of taxonomic and functional (consumers, phototrophs, and parasites) communities. In both the plastisphere and surrounding soil, although some consumers dominated the protistan community network, while their performance was weakened by mulch application. The ecological networks of the plastisphere community presented higher modularity, less complexity, and a lower proportion of positive connections than the networks of surrounding soil. In addition, the enriched plant pathogens (e.g., Spongospora) and keystone taxa classified as plant pathogens (e.g., Pythium) in the plastisphere imply that plastic film residues may pose a risk to soil health and plant performance. Neutral-based processes dominated the assembly of the plastisphere protistan communities, whereas niche-based processes governed the protistan community assembly of surrounding soil. This study reveals that plastic film residues generate a unique niche for protistan colonization, which disturbs protistan communities and threatens agricultural ecosystem health and function.

Impacts of inorganic nutrients on the physiology of a mixoplanktonic ciliate and its cryptophyte prey

Many marine planktonic ciliates retain functional chloroplasts from their photosynthetic prey and use them to incorporate inorganic carbon via photosynthesis. While this strategy provides the ciliates with carbon, little is known about their ability to incorporate major dissolved inorganic nutrients, such as nitrogen and phosphorus. Here, we studied how ciliates respond to different concentrations of dissolved inorganic nitrogen and phosphorus. Specifically, we tested the direct and indirect effects of nutrient availability on the ciliate Strombidium cf. basimorphum fed the cryptophyte prey Teleaulax amphioxeia. We assessed responses in the rates of growth, ingestion, photosynthesis, inorganic nutrient uptake, and excretion. Our results show that the prey changed its carbon content depending on the nutrient concentrations. Low inorganic nutrient concentrations increased S. cf. basimorphum growth and prey ingestion. The higher carbon content of the prey under these low nutrient conditions likely supported the growth of the ciliate, while the higher carbon:nutrient stoichiometry of the prey led to the higher ingestion rates. The low carbon content of the prey at high nutrient concentrations resulted in reduced growth of S. cf. basimorphum, which indicates that carbon acquired via photosynthesis in the ciliate cannot compensate for the ingestion of prey with low carbon content. In conclusion, our findings show S. cf. basimorphum is not able to utilize dissolved inorganic nitrogen and phosphorus for growth, and this species seems to be well adapted to exploit its prey when grown at low nutrient conditions.

The strengths and weaknesses of Live Fluorescently Labelled Algae (LFLA) to estimate herbivory in protozooplankton and mixoplankton

The Live Fluorescently Labelled Algae (LFLA) technique has been used numerous times to estimate microzooplankton herbivory. Yet, it is unknown how mixoplankton (i.e., single-cell organisms that can combine phototrophy and phagotrophy) affect the outcome of this technique. Hence, we conducted a broad-spectrum assessment of the strengths and weaknesses of the LFLA technique, using several mixoplanktonic and protozooplanktonic grazers. Species from different taxonomic groups and different feeding mechanisms were tested in short-term experiments (ca. 5 h) in the laboratory, at different prey concentrations and during light and dark periods of the day. Overall, our findings suggest that the LFLA technique, due to its short-term nature, is an effective tracker of diel ingestion and digestion rates, and can detect new mixoplanktonic predators. We recommend that, irrespective of the prey concentration, incubations to measure grazing rates with this technique should generally be concluded within 1 h (adaptable to the environmental temperature). Nevertheless, our results also call for caution whenever using LFLA in the field: feeding mechanisms other than direct engulfment (like peduncle feeding) may provide severely biased ingestion rates. Furthermore, size and species selectivity are very hard to circumvent. To reduce the effects of selectivity, we propose the combined use of two distinctly coloured fluorochromes (i.e., distinct emission spectra). With this modification, one could either label different size ranges of prey or account for species-specific interactions in the food web.

House fly larval grazing alters dairy cattle manure microbial communities

Background

House fly larvae (Musca domestica L.) require a live microbial community to successfully develop. Cattle manure is rich in organic matter and microorganisms, comprising a suitable substrate for larvae who feed on both the decomposing manure and the prokaryotic and eukaryotic microbes therein. Microbial communities change as manure ages, and when fly larvae are present changes attributable to larval grazing also occur. Here, we used high throughput sequencing of 16S and 18S rRNA genes to characterize microbial communities in dairy cattle manure and evaluated the changes in those communities over time by comparing the communities in fresh manure to aged manure with or without house fly larvae.

Results

Bacteria, archaea and protist community compositions significantly differed across manure types (e.g. fresh, aged, larval-grazed). Irrespective of manure type, microbial communities were dominated by the following phyla: Euryarchaeota (Archaea); Proteobacteria, Firmicutes and Bacteroidetes (Bacteria); Ciliophora, Metamonanda, Ochrophyta, Apicomplexa, Discoba, Lobosa and Cercozoa (Protists). Larval grazing significantly reduced the abundances of Bacteroidetes, Ciliophora, Cercozoa and increased the abundances of Apicomplexa and Discoba. Manure aging alone significantly altered the abundance bacteria (Acinetobacter, Clostridium, Petrimonas, Succinovibro), protists (Buxtonella, Enteromonas) and archaea (Methanosphaera and Methanomassiliicoccus). Larval grazing also altered the abundance of several bacterial genera (Pseudomonas, Bacteroides, Flavobacterium, Taibaiella, Sphingopyxis, Sphingobacterium), protists (Oxytricha, Cercomonas, Colpodella, Parabodo) and archaea (Methanobrevibacter and Methanocorpusculum). Overall, larval grazing significantly reduced bacterial and archaeal diversities but increased protist diversity. Moreover, total carbon (TC) and nitrogen (TN) decreased in larval grazed manure, and both TC and TN were highly correlated with several of bacterial, archaeal and protist communities.

Conclusions

House fly larval grazing altered the abundance and diversity of bacterial, archaeal and protist communities differently than manure aging alone. Fly larvae likely alter community composition by directly feeding on and eliminating microbes and by competing with predatory microbes for available nutrients and microbial prey. Our results lend insight into the role house fly larvae play in shaping manure microbial communities and help identify microbes that house fly larvae utilize as food sources in manure. Information extrapolated from this study can be used to develop manure management strategies to interfere with house fly development and reduce house fly populations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02418-5.

Remote regulation of type 2 immunity by intestinal parasites

The intestinal tract is the target organ of most parasitic infections, including those by helminths and protozoa. These parasites elicit prototypical type 2 immune activation in the host's immune system with striking impact on the local tissue microenvironment. Despite local containment of these parasites within the intestinal tract, parasitic infections also mediate immune adaptation in peripheral organs. In this review, we summarize the current knowledge on how such gut-tissue axes influence important immune-mediated resistance and disease tolerance in the context of coinfections, and elaborate on the implications of parasite-regulated gut-lung and gut-brain axes on the development and severity of airway inflammation and central nervous system diseases.

Composition change and decreased diversity of microbial eukaryotes in the coastal upwelling waters of South China Sea

Upwelling plays an important role in marine ecosystems and potentially reshapes microbial communities by enhanced dispersal and distinct environmental drivers. Relative to that of bacterioplankton, however, the response of eukaryotic microbes to upwelling is largely unknown. Here, we investigated the influence of coastal upwelling in South China Sea on the microbial eukaryotic communities. Unlike several folds of increase in the cell abundance of bacterioplankton in upwelling than non-upwelling stations at corresponding water layers, no significant difference was detected for the total microbial eukaryotic 18S rRNA gene abundance. Moreover, the microbial eukaryotes in the upwelling stations exhibited increasing 18S rRNA gene abundance from the surface to the deep, contrasting the vertical cell abundance pattern of the bacterioplankton; but their vertical abundance patterns were similar in non-upwelling stations. Importantly, the coastal upwelling significantly reduced the community evenness of the microbial eukaryotes and slightly reduced their Shannon diversity. Their community composition also varied obviously especially between the surface waters of upwelling and non-upwelling stations. Among the dominant supergroups, Alveolata was found to be less abundant while Stramenopiles, particularly thraustochytrids and diatoms, to be more abundant in the surface water of upwelling than non-upwelling stations. Temperature was identified as the most important factor of the microbial eukaryotic community composition, suggesting potential effects of the cold upwelling water masses on specific taxa. Overall, our results reveal significant and distinct impacts of coastal upwelling on the abundance, diversity, and community structure of microbial eukaryotes, filling the knowledge gap about the microbial responses to this important marine phenomenon.

Insights into the roles of fungi and protist in the giant panda gut microbiome and antibiotic resistome

The mammal gut is a rich reservoir of antibiotic resistance genes (ARGs), and the relationship between bacterial communities and ARGs has been widely studied. Despite ecological significance of microeukaryotes (fungi and protists), our understanding of their roles in the mammal gut microbiome and antibiotic resistome is still limited. Here, we used amplicon sequencing, metagenomic sequencing and high-throughput quantitative PCR to examine microbiomes and antibiotic resistomes of 41 giant panda fecal samples from individuals with different genders, ages, sampling sites and diet. Our results show that diverse protists inhabit in the giant panda gut ecosystem, dominated by consumers. Higher abundance of protistan consumers was detected in the elder compared to sub-adult and adult giant pandas. Diet is the main driving factor of variation in ARGs in the giant panda gut microbiome. Weighted correlation network analysis identified two key microbial modules from multitrophic communities, which all contributed to the variation in ARGs in the giant panda gut. Protists occupied an important position in the two modules which were dominated by fungal taxa. Deterministic processes made a more important contribution to microbial community assembly of the two modules than to bacterial, fungal and protistan communities. This study sheds new light on how key microbial modules contribute to the variation in ARGs, which is crucial in understanding dynamics of antibiotic resistome in the mammal gut, particularly endangered species.

Inheritance of the reduced mitochondria of Giardia intestinalis is coupled to the flagellar maturation cycle

Background

The presence of mitochondria is a distinguishing feature between prokaryotic and eukaryotic cells. It is currently accepted that the evolutionary origin of mitochondria coincided with the formation of eukaryotes and from that point control of mitochondrial inheritance was required. Yet, the way the mitochondrial presence has been maintained throughout the eukaryotic cell cycle remains a matter of study. Eukaryotes control mitochondrial inheritance mainly due to the presence of the genetic component; still only little is known about the segregation of mitochondria to daughter cells during cell division. Additionally, anaerobic eukaryotic microbes evolved a variety of genomeless mitochondria-related organelles (MROs), which could be theoretically assembled de novo, providing a distinct mechanistic basis for maintenance of stable mitochondrial numbers. Here, we approach this problem by studying the structure and inheritance of the protist Giardia intestinalis MROs known as mitosomes.

Results

We combined 2D stimulated emission depletion (STED) microscopy and focused ion beam scanning electron microscopy (FIB/SEM) to show that mitosomes exhibit internal segmentation and conserved asymmetric structure. From a total of about forty mitosomes, a small, privileged population is harnessed to the flagellar apparatus, and their life cycle is coordinated with the maturation cycle of G. intestinalis flagella. The orchestration of mitosomal inheritance with the flagellar maturation cycle is mediated by a microtubular connecting fiber, which physically links the privileged mitosomes to both axonemes of the oldest flagella pair and guarantees faithful segregation of the mitosomes into the daughter cells.

Conclusion

Inheritance of privileged Giardia mitosomes is coupled to the flagellar maturation cycle. We propose that the flagellar system controls segregation of mitochondrial organelles also in other members of this supergroup (Metamonada) of eukaryotes and perhaps reflects the original strategy of early eukaryotic cells to maintain this key organelle before mitochondrial fusion-fission dynamics cycle as observed in Metazoa was established.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-021-01129-7.

Both viable and inactivated amoeba spores protect their intracellular bacteria from drinking water disinfection

In drinking water systems, waterborne pathogens constitute a significant threat. While most studies focus on a single infectious agent, such as bacteria, fungi, viruses, and protists, the effect of interactions among these infectious agents on disinfection treatment has largely been ignored. In this study, we find that dormant amoeba spores, a frequently found protist in drinking water systems, can protect their intracellular bacteria from drinking water disinfection. Bacteria-containing amoeba spores were constructed and treated with various disinfection techniques (Cl₂, ClO_2, and UV₂₅₄). The three disinfection methods could kill the bacteria alone efficiently (6-log inactivation). However, the inactivation efficiency of bacteria that hid within amoeba spore was significantly inhibited (2-3-log inactivation). We also found that inactivated amoeba spores can still protect their intracellular bacteria. This study provides direct evidence that viable and inactivated amoeba spores can protect their hitchhiking bacteria from disinfection treatment, which is crucial for future decision-making about the dosage for sufficient bacterial disinfection in drinking water systems.

An Illumina MiSeq-Based Amplicon Sequencing Method for the Detection of Mixed Parasite Infections Using the Blastocystis SSU rRNA Gene as an Example

Parasite mixed infections remain a relatively unexplored field in part due to the difficulties of unraveling complex mixtures of parasite DNA using classical methods of sequencing. Next-generation amplicon sequencing (NGS) is a powerful tool for exploring mixed infections of multiple genetic variants of the same parasite in clinical, environmental (water or soil), or food samples. Here, we provide a method for NGS-based detection of mixed parasite infections which uses the Blastocystis SSU rRNA gene as an example and includes steps for parasite concentration, DNA extraction, sequencing library preparation, and bioinformatic analysis.

Short term response of plankton community to nutrient enrichment in central eastern Arabian Sea: Elucidation through mesocosm experiments

Oligotrophic waters (OW), generally favour longer food chain facilitated by the microbial loop. In such ecosystems, physical mixing (e.g. upwelling, and winter convection) inject nutrients and propagules from subsurface to the photic zone. Such events are expected to alter the food chain through shifts in the plankton community. Mesocosm experiments were carried out to evaluate the influence of nutrient enrichment from the deep (100-150 m) on the surface plankton community for the first time in the Arabian Sea, through custom-designed enclosures in OW of the central-eastern Arabian Sea (CEAS). Surface water was characterized by low nutrients and phytoplankton biomass (chlorophyll-a of <0.2 μg m^-3) and upon nutrient enrichment yielded differing response. Higher abundance of picophytoplankton, bacteria and protists was noticed at a depth of ~100 m than at surface. The inoculation of such a population to the surface, resulted in a significant enhancement of autotrophic (picophytoplankton) and heterotrophic (bacteria and protists) populations. However, significant changes in the abundance of larger plankton was not evident till three days of incubation. Even though autotrophic picophytoplankton responded positively, a distinct increase in chlorophyll-a was not evident. This study points out that the lack of sufficient viable microphytoplankton propagules, neither at the surface nor at the depth (inoculum) are the possible reasons for the lack of their distinct positive response. These experiments suggest the dominance of microbial community response to physical mixing in the OW regions of the Arabian Sea and the importance of propagule diversity. The insights from this experiment will serve as a precursor for appropriate modifications in ocean modelling and forecasting studies and help in building global environmental management tools.

Cloning and characterization of glycogen branching and debranching enzymes from the parasitic protist Trichomonas vaginalis

The protist Trichomonas vaginalis is an obligate parasite of humans and the causative agent of trichomoniasis, a common sexually transmitted infection. The organism has long been known to accumulate glycogen, a branched polymer of glucose, and to mobilize this reserve in response to carbohydrate limitation. However, the enzymes required for the synthesis and degradation of glycogen by T. vaginalis have been little studied. Previously, we characterized T. vaginalis glycogen synthase and glycogen phosphorylase, the key enzymes of glycogen synthesis and degradation, respectively. We determined that their regulatory properties differed from those of well-characterized animal and fungal enzymes. Here, we turn our attention to how glycogen attains its branched structure. We first determined that the glycogen from T. vaginalis resembled that from a related organism, T. gallinae. To determine how the branched structure of T. vaginalis glycogen arose, we identified open reading frames encoding putative T. vaginalis branching and debranching enzymes. When the open reading frames TVAG_276310 and TVAG_330630 were expressed recombinantly in bacteria, the resulting proteins exhibited branching and debranching activity, respectively. Specifically, recombinant TVAG_276310 had affinity for polysaccharides with long outer branches and could add branches to both amylose and amylopectin. TVAG_330630 displayed both 4-α-glucanotransferase and α1,6-glucosidase activity and could efficiently debranch phosphorylase limit dextrin. Furthermore, expression of TVAG_276310 and TVAG_330630 in yeast cells lacking endogenous glycogen branching or debranching enzyme activity, restored normal glycogen accumulation and branched structure. We now have access to the suite of enzymes required for glycogen synthesis and degradation in T. vaginalis.

Sediment resuspension drives protist metacommunity structure and assembly in grass carp (Ctenopharyngodonidella) aquaculture ponds

Protists in aquaculture ponds are key components associated with primary productivity, nutrient cycling, and fish healthy. However, the protist metacommunity diversity, as well as the ecological and environmental factors that structure protist metacommunity in aquaculture ponds remain poorly understood. This study examined protist metacommunities in water and sediment of larval, small juvenile and large juvenile grass carp ponds. The results indicated sediment resuspension became stronger with the increased fish size, which led to high levels of total suspended solids and nitrogen but low levels of phosphate, chlorophyll a and transparency in water. Moreover, sediment resuspension subsequently increased the alpha diversity indexes (i.e., OTU number, Shannon index and Simpson index) of protist communities in water and sediment. Meanwhile, sediment resuspension increased the relative abundance of heterotrophic Ciliophora and Cercozoa, but decreased the relative abundance of autotrophic Chlorophyta, Stramenopiles X, and Ochrophyta. Besides, some mixotrophic and heterotrophic protists showed competitive advantages in the turbidity water, which led to the increase of negative interactions in the protist co-occurrence networks. Based on the null model, sediment resuspension strengthened homogeneous selection (deterministic process) and weakened dispersal limitation (stochastic process) processes of protist community assembly. Indeed, protist community dissimilarity within each local community and each habitat (water or sediment) both decreased while the community dissimilarity between habitats increased with the increase of fish size. Therefore, sediment resuspension did not enhance the dispersal path between water and sediment, but decreased the dispersal limitation within sediment and water coupled with the strengthening of environmental selection. These results indicated that grass carp could restructure the protist metacommunity in aquaculture ponds through bottom up way of sediment resuspension. This study advances our understanding of the relationship between fish and protist metacommunity assembly in aquaculture systems.

Patterns and drivers of microeukaryotic distribution along the North Equatorial Current from the Central Pacific Ocean to the South China Sea

Microeukaryotes have been recognized as highly abundant and diverse both in form and function, however, data on their diversity and distribution along marine currents remain scarce. Herein, the distribution of microeukaryotes in surface seawaters was analyzed along a 9000 km stretch of the North Equatorial Current (NEC) and its bifurcation using high throughput DNA sequencing. Significant distance-decay patterns were detected, and the microeukaryote communities were further divided into Central Pacific Ocean (CPO), Western Pacific Ocean (WPO), and South China Sea (SCS) groups. Statistical analyses suggested that the microeukaryotic assembly in the WPO is maintained by the CPO community transported via the NEC. Environmental selection contributed more to community variations than spatial processes did. Temperature and salinity were the two most important environmental factors to shape the examined communities. Altogether, characterizing the microeukaryotic diversity and distribution along the NEC provided an insight into the drivers of their distribution in open oceans.

Seasonal plankton succession is in accordance with phycotoxin occurrence in Disko Bay, West Greenland

Harmful algal blooms (HABs) are occurring more frequently in the world's oceans, probably as a consequence of climate change. HABs have not been considered a serious concern in the Arctic, even though the Arctic warms faster than any other region. While phycotoxins and toxin-producing phytoplankton have been found in Arctic waters on several occasions, there is a lack of information on seasonal succession of species and whether the occurrence of harmful species correlates with the presence of their respective phycotoxins. Hence, there is no baseline to assess future changes of HABs in this area. Here, we investigated two periods, from winter to spring and from the spring bloom until summer, in Disko Bay, West Greenland and followed the succession of toxins and their producers using metabarcoding, as well as analyses of particulate and dissolved toxins. We observed a typical seasonal succession with a spring bloom dominated by diatoms, followed by dinoflagellates in summer, with the two most important potentially toxic taxa found being Pseudo-nitzschia spp. and Alexandrium ostenfeldii. The Pseudo-nitzschia spp. peak correlated with a clear increase in particulate domoic acid, reaching 0.05 pg/L. Presence of Alexandrium ostenfeldii could be linked to an increase in spirolides, up to 56.4 pg/L in the particulate phase. Generally, the majority of detected dissolved toxins followed the succession pattern of the particulate toxins with a delay in time. Our results further show that Arctic waters are a suitable habitat for various toxin producers and that the strong seasonality of this environment is reflected by changing abundances of different toxins that pose a potential threat to the ecosystem and its beneficiaries.

A gene co-association network regulating gut microbial communities in a Duroc pig population

BACKGROUND

Analyses of gut microbiome composition in livestock species have shown its potential to contribute to the regulation of complex phenotypes. However, little is known about the host genetic control over the gut microbial communities. In pigs, previous studies are based on classical "single-gene-single-trait" approaches and have evaluated the role of host genome controlling gut prokaryote and eukaryote communities separately.

RESULTS

In order to determine the ability of the host genome to control the diversity and composition of microbial communities in healthy pigs, we undertook genome-wide association studies (GWAS) for 39 microbial phenotypes that included 2 diversity indexes, and the relative abundance of 31 bacterial and six commensal protist genera in 390 pigs genotyped for 70 K SNPs. The GWAS results were processed through a 3-step analytical pipeline comprised of (1) association weight matrix; (2) regulatory impact factor; and (3) partial correlation and information theory. The inferred gene regulatory network comprised 3561 genes (within a 5 kb distance from a relevant SNP-P < 0.05) and 738,913 connections (SNP-to-SNP co-associations). Our findings highlight the complexity and polygenic nature of the pig gut microbial ecosystem. Prominent within the network were 5 regulators, PRDM15, STAT1, ssc-mir-371, SOX9 and RUNX2 which gathered 942, 607, 588, 284 and 273 connections, respectively. PRDM15 modulates the transcription of upstream regulators of WNT and MAPK-ERK signaling to safeguard naive pluripotency and regulates the production of Th1- and Th2-type immune response. The signal transducer STAT1 has long been associated with immune processes and was recently identified as a potential regulator of vaccine response to porcine reproductive and respiratory syndrome. The list of regulators was enriched for immune-related pathways, and the list of predicted targets includes candidate genes previously reported as associated with microbiota profile in pigs, mice and human, such as SLIT3, SLC39A8, NOS1, IL1R2, DAB1, TOX3, SPP1, THSD7B, ELF2, PIANP, A2ML1, and IFNAR1. Moreover, we show the existence of host-genetic variants jointly associated with the relative abundance of butyrate producer bacteria and host performance.

CONCLUSIONS

Taken together, our results identified regulators, candidate genes, and mechanisms linked with microbiome modulation by the host. They further highlight the value of the proposed analytical pipeline to exploit pleiotropy and the crosstalk between bacteria and protists as significant contributors to host-microbiome interactions and identify genetic markers and candidate genes that can be incorporated in breeding program to improve host-performance and microbial traits. Video Abstract.

Bathymetric gradient shapes the community composition rather than the species richness of deep-sea benthic ciliates

The bathymetric gradient is one of the most important factors that regulate the distribution of life. However, community variations of benthic ciliates along bathymetric gradients in the deep sea remain rather unexplored. In this study, we hypothesize that in the deep sea, the bathymetric gradient shapes the benthic ciliate community composition rather than the species richness. Here, we evaluated the distribution patterns and drivers of benthic ciliate communities of an abyssal plain, a seamount, and a trench with water depths ranging from 800 m down to 6600 m by high throughput eDNA sequencing and statistical analyses. We observed no significant correlation between ciliate operated taxonomic unit (OTU) richness and water depth. A meta-analysis, which combined our previously published data from the neritic habitats, supports the notion that water depth exceeding 800 m has little effect on the richness of benthic ciliate species. In contrast, the composition of deep-sea ciliate communities was significantly distinct in different habitats along the bathymetric gradients. A SourceTracker analysis revealed extremely low connectivity among ciliate communities along the bathymetric gradients. More than 95% of the community dissimilarity in the deep-sea floor was attributed to species replacement, which might be caused by environmental sorting or historical constraints. Furthermore, the observed community variations could be ascribed more to water depth than to geographic distance. The findings imply that the strong force of environmental sorting along the bathymetric gradients and the low connectivity among the ciliate communities might lead to an isolated evolution. This could shape the community composition rather than the species richness, which is mainly determined by the limited nutrient availability and the extreme environmental conditions in the deep sea.

Autolysis of Chlorella variabilis in Starving Paramecium bursaria Help the Host Cell Survive Against Starvation Stress

The endosymbiosis between Paramecium bursaria and Chlorella spp. is mutualistic. Symbiotic algae localize beneath the host Paramecium cell cortex compete for their attachment sites with preexisting organelle trichocysts. To examine the relationship between P. bursaria trichocysts and their symbiotic algae, algae-bearing or alga-free P. bursaria were starved for several days and the changes in the number of Chlorella sp. and presence or absence of trichocysts were evaluated. We conducted an indirect immunofluorescence microscopy with an anti-trichocyst monoclonal antibody against P. bursaria cells. Indirect immunofluorescence microscopy demonstrated that under starvation and darkness conditions, the immunofluorescence of trichocysts in alga-free P. bursaria decreased much faster than that in the normal algae-bearing P. bursaria. In the latter case, our observations proposed the possibility that the nutrition obtained from symbiotic algal digestion may promote trichocysts synthesis. This algal digestion mechanism may permit host P. bursaria cells to survive for a longer time under starvation condition. To the best of our knowledge, this may be a new benefit that host P. bursaria gain from harboring symbiotic algae.

Disseminated protozoal infection in a wild feathertail glider (Acrobates pygmaeus) in Australia

This is the first report of a disseminated protozoal infection in a wild feathertail glider (Acrobates pygmaeus) from south-eastern Australia. The glider was found dead in poor body condition. Histologically, large numbers of zoites were seen predominantly in macrophages in the liver, spleen and lung, with protozoal cysts present in the liver. Molecular and phylogenetic analyses inferred that the protozoan parasite belongs to the family Sarcocystidae and is closely related to previously identified apicomplexans found in yellow-bellied gliders (Petaurus australis) in Australia and southern mouse opossums (Thylamys elegans) in Chile.

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A novel apicomplexan parasite caused a disseminated fatal disease in a wild feathertail glider.

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The apicomplexan parasite is a member of the family Sarcocystidae.

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It is most closely related to parasites previously identified in yellow-bellied gliders in Australia and southern mouseopossums in Chile.

Molecular investigation of Phryganella acropodia Hertwig et Lesser, 1874 (Arcellinida, Amoebozoa)

Phryganella acropodia Hertwig and Lesser, 1874, is one of the most common and abundant testate amoeba species. It represents the type species of the genus Phryganella Penard, 1902, which in turn is the type genus for the suborder Phryganellina (Arcellinida) Bovee, 1985, but despite its taxonomic importance it was not yet analyzed with molecular methods. We established two cultures of putative Phryganella acropodia, designed Phryganellina-specific primers, amplified SSU rDNA data and subjected these sequences to phylogenetic analyses. Morphological and genetic differences were found between both strains. With SSU rDNA phylogenetic analyses we confirm that Phryganella acropodia branches with Phryganella paradoxa Penard, 1902 and Cryptodifflugia Penard, 1890 in the Phryganellina. We thus give further evidence that pseudopodia morphology in the Arcellinida is a character of high taxonomic value, as suggested by Bovee and Jung when erecting the suborder Phryganellina. Moreover, we provide evidence for cryptic diversity and for the first time confirm the existence of a naked life stage in Arcellinida by molecular means.

Identification and evolutionary analysis of the nucleolar proteome of Giardia lamblia

Background

The nucleoli, including their proteomes, of higher eukaryotes have been extensively studied, while few studies about the nucleoli of the lower eukaryotes – protists were reported. Giardia lamblia, a protist with the controversy of whether it is an extreme primitive eukaryote or just a highly evolved parasite, might be an interesting object for carrying out the nucleolar proteome study of protists and for further examining the controversy.

Results

Using bioinformatics methods, we reconstructed G. lamblia nucleolar proteome (GiNuP) and the common nucleolar proteome of the three representative higher eukaryotes (human, Arabidopsis, yeast) (HEBNuP). Comparisons of the two proteomes revealed that: 1) GiNuP is much smaller than HEBNuP, but 78.4% of its proteins have orthologs in the latter; 2) More than 68% of the GiNuP proteins are involved in the “Ribosome related” function, and the others participate in the other functions, and these two groups of proteins are much larger and much smaller than those in HEBNuP, respectively; 3) Both GiNuP and HEBNuP have their own specific proteins, but HEBNuP has a much higher proportion of such proteins to participate in more categories of nucleolar functions.

Conclusion

For the first time the nucleolar proteome of a protist - Giardia was reconstructed. The results of comparison of it with the common proteome of three representative higher eukaryotes -- HEBNuP indicated that the simplicity of GiNuP is most probably a reflection of primitiveness but not just parasitic reduction of Giardia, and simultaneously revealed some interesting evolutionary phenomena about the nucleolus and even the eukaryotic cell, compositionally and functionally.

The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome

Background

Comparative analyses have indicated that the mitochondrion of the last eukaryotic common ancestor likely possessed all the key core structures and functions that are widely conserved throughout the domain Eucarya. To date, such studies have largely focused on animals, fungi, and land plants (primarily multicellular eukaryotes); relatively few mitochondrial proteomes from protists (primarily unicellular eukaryotic microbes) have been examined. To gauge the full extent of mitochondrial structural and functional complexity and to identify potential evolutionary trends in mitochondrial proteomes, more comprehensive explorations of phylogenetically diverse mitochondrial proteomes are required. In this regard, a key group is the jakobids, a clade of protists belonging to the eukaryotic supergroup Discoba, distinguished by having the most gene-rich and most bacteria-like mitochondrial genomes discovered to date.

Results

In this study, we assembled the draft nuclear genome sequence for the jakobid Andalucia godoyi and used a comprehensive in silico approach to infer the nucleus-encoded portion of the mitochondrial proteome of this protist, identifying 864 candidate mitochondrial proteins. The A. godoyi mitochondrial proteome has a complexity that parallels that of other eukaryotes, while exhibiting an unusually large number of ancestral features that have been lost particularly in opisthokont (animal and fungal) mitochondria. Notably, we find no evidence that the A. godoyi nuclear genome has or had a gene encoding a single-subunit, T3/T7 bacteriophage-like RNA polymerase, which functions as the mitochondrial transcriptase in all eukaryotes except the jakobids.

Conclusions

As genome and mitochondrial proteome data have become more widely available, a strikingly punctuate phylogenetic distribution of different mitochondrial components has been revealed, emphasizing that the pathways of mitochondrial proteome evolution are likely complex and lineage-specific. Unraveling this complexity will require comprehensive comparative analyses of mitochondrial proteomes from a phylogenetically broad range of eukaryotes, especially protists. The systematic in silico approach described here offers a valuable adjunct to direct proteomic analysis (e.g., via mass spectrometry), particularly in cases where the latter approach is constrained by sample limitation or other practical considerations.

Transformation of the Model Microalga Chlamydomonas reinhardtii Without Cell-Wall Removal

The green alga Chlamydomonas reinhardtii has been widely used to study many biological processes, including photosynthesis, flagellar motility, sexual reproduction, metabolism, and genetics. Here, we describe a step-by-step protocol of rapid and efficient transformation method for wild type cell-walled Chlamydomonas strains without cell-wall removal using a square electric pulses-generating electroporator. This method could be applied to the transformation of other industrially useful algae including diatom by optimizing the electric conditions.

Organic amendment strengthens interkingdom associations in the soil and rhizosphere of barley (Hordeum vulgare)

Anthropogenic modification of soil systems has diverse impacts on food web interactions and ecosystem functioning. To understand the positive, neutral or adverse effects of agricultural practices on the associations of community members of soil microbes and microfaunal biomes, we characterized the effects of different fertilization types (organic, inorganic and a combination of organic and inorganic) on the food web active communities in the bulk soil and rhizosphere compartments in field conditions. We examined the influence of fertilization on (i) individual groups (bacteria, protozoa and fungi as microbe representatives and metazoans as microfauna representatives) and (ii) inter-kingdom interactions (focusing on the interactions between bacteria and eukaryotic groups) both neglecting and considering environmental factors in our analysis in combination with the microbial compositional data. Our results revealed different patterns of biota communities under organic versus inorganic fertilization, which shaped food web associations in both the bulk and rhizosphere compartments. Overall, organic fertilization increased the complexity of microbial-microfaunal ecological associations with inter- and intra- connections among categories of primary decomposers (bacteria and fungi) and predators (protozoa and microfauna) and differences in potential function in the soil food web in both the bulk and rhizosphere compartments. Furthermore, the inter-connections between primary decomposers and predators in bulk soil were more pronounced when environmental factors were considered. We suggest that organic fertilization selects bacterial orders with different potential ecological functions and interactions as survival, predation and cooperation due to more complex environment than those of inorganic or combined fertilization. Our findings support the importance of a comprehensive understanding of trophic food web patterns for soil management systems.

Contrasted Micro-Eukaryotic Diversity Associated with Sphagnum Mosses in Tropical, Subtropical and Temperate Climatic Zones

Sphagnum-dominated ecosystem plays major roles as carbon sinks at the global level. Associated microbial communities, in particular, eukaryotes, play significant roles in nutrient fixation and turnover. In order to understand better the ecological processes driven by these organisms, the first step is to characterise these associated organisms. We characterised the taxonomic diversity, and from this, inferred the functional diversity of microeukaryotes in Sphagnum mosses in tropical, subtropical and temperate climatic zones through an environmental DNA diversity metabarcoding survey of the V9 region of the gene coding for the RNA of the small subunit of the ribosomes (SSU rRNA). As microbial processes are strongly driven by temperatures, we hypothesised that saprotrophy would be highest in warm regions, whereas mixotrophy, an optimal strategy in oligotrophic environments, would peak under colder climates. Phylotype richness was higher in tropical and subtropical climatic zones than in the temperate region, mostly due to a higher diversity of animal parasites (i.e. Apicomplexa). Decomposers, and especially opportunistic yeasts and moulds, were more abundant under warmer climates, while mixotrophic organisms were more abundant under temperate climates. The dominance of decomposers, suggesting a higher heterotrophic activity under warmer climates, is coherent with the generally observed faster nutrient cycling at lower latitudes; this phenomenon is likely enhanced by higher inputs of nutrients most probably brought in the system by Metazoa, such as arthropods.

Transcriptomic response in symptomless roots of clubroot infected kohlrabi (Brassica oleracea var. gongylodes) mirrors resistant plants

BACKGROUND

Clubroot disease caused by Plasmodiophora brassicae (Phytomyxea, Rhizaria) is one of the economically most important diseases of Brassica crops. The formation of hypertrophied roots accompanied by altered metabolism and hormone homeostasis is typical for infected plants. Not all roots of infected plants show the same phenotypic changes. While some roots remain uninfected, others develop galls of diverse size. The aim of this study was to analyse and compare the intra-plant heterogeneity of P. brassicae root galls and symptomless roots of the same host plants (Brassica oleracea var. gongylodes) collected from a commercial field in Austria using transcriptome analyses.

RESULTS

Transcriptomes were markedly different between symptomless roots and gall tissue. Symptomless roots showed transcriptomic traits previously described for resistant plants. Genes involved in host cell wall synthesis and reinforcement were up-regulated in symptomless roots indicating elevated tolerance against P. brassicae. By contrast, genes involved in cell wall degradation and modification processes like expansion were up-regulated in root galls. Hormone metabolism differed between symptomless roots and galls. Brassinosteroid-synthesis was down-regulated in root galls, whereas jasmonic acid synthesis was down-regulated in symptomless roots. Cytokinin metabolism and signalling were up-regulated in symptomless roots with the exception of one CKX6 homolog, which was strongly down-regulated. Salicylic acid (SA) mediated defence response was up-regulated in symptomless roots, compared with root gall tissue. This is probably caused by a secreted benzoic acid/salicylic acid methyl transferase from the pathogen (PbBSMT), which was one of the highest expressed pathogen genes in gall tissue. The PbBSMT derived Methyl-SA potentially leads to increased pathogen tolerance in uninfected roots.

CONCLUSIONS

Infected and uninfected roots of clubroot infected plants showed transcriptomic differences similar to those previously described between clubroot resistant and susceptible hosts. The here described intra-plant heterogeneity suggests, that for a better understanding of clubroot disease targeted, spatial analyses of clubroot infected plants will be vital in understanding this economically important disease.

Phylogeny of the ciliate family Psilotrichidae (Protista, Ciliophora), a curious and poorly-known taxon, with notes on two algae-bearing psilotrichids from Guam, USA

Background

The classification of the family Psilotrichidae, a curious group of ciliated protists with unique morphological and ontogenetic features, is ambiguous and poorly understood particularly due to the lack of molecular data. Hence, the systematic relationship between this group and other taxa in the subclass Hypotrichia remains unresolved. In this paper the morphology and phylogenetics of species from two genera of Psilotrichida are studied to shed new light on the phylogeny and species diversity of this group of ciliates.

Results

The 18S rRNA gene sequences of species from two psilotrichid genera were obtained. In the phylogenetic trees, the available psilotrichid sequences are placed in a highly supported clade, justifying the establishment of the family Psilotrichidae. The morphology of two little-known species, packed with green algae, including a new species, Hemiholosticha kahli nov. spec., and Psilotrichides hawaiiensis Heber et al., 2018, is studied based on live observation, protargol impregnation, and scanning electron microscopy. Both species are easily recognized by their green coloration due to the intracellular algae, and a comprehensive discussion as to the possible roles of the intracellular algae is provided.

Conclusions

The 18S rRNA gene phylogeny supports the morphological argument that Hemiholosticha, Psilotrichides and Urospinula belong to the same family, Psilotrichidae. However, the single-gene analysis, not surprisingly, does not resolve the deeper relationships of Psilotrichidae within the subclass Hypotrichia. Two little-known psilotrichid genera with green algae were collected from the same puddle on the island of Guam, indicating a high species diversity and broader geographic distribution of this group of ciliates than previously supposed. Phylogenetic inferences from transcriptomic and/or genomic data will likely be necessary to better define the systematic position and evolution of the family Psilotrichidae. Further studies are also needed to clarify the role of the intracellular eyespot-bearing algae in these ciliates.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1450-z) contains supplementary material, which is available to authorized users.

The Hidden World of Rickettsiales Symbionts: "Candidatus Spectririckettsia obscura," a Novel Bacterium Found in Brazilian and Indian Paramecium caudatum

Symbioses between bacteria and eukaryotes are widespread and may have significant impact on the evolutionary history of symbiotic partners. The order Rickettsiales is a lineage of intracellular Alphaproteobacteria characterized by an obligate association with a wide range of eukaryotic hosts, including several unicellular organisms, such as ciliates and amoebas. In this work, we characterized the Rickettsiales symbionts associated with two different genotypes of the freshwater ciliate Paramecium caudatum originated from freshwater environments in distant geographical areas. Phylogenetic analyses based on 16S rRNA gene showed that the two symbionts are closely related to each other (99.4% identity), belong to the family Rickettsiaceae, but are far-related with respect to previously characterized Rickettsiales. Consequently, they were assigned to a new species of a novel genus, namely "Candidatus Spectririckettsia obscura." Screening on a database of short reads from 16S rRNA gene amplicon-based profiling studies confirmed that bacterial sequences related to the new symbiont are preferentially retrieved from freshwater environments, apparently with extremely scarce occurrence (< 0.1% positive samples). The present work provides new information on the still under-explored biodiversity of Rickettsiales, in particular those associated to ciliate host cells.

Oxygen induces the expression of invasion and stress response genes in the anaerobic salmon parasite Spironucleus salmonicida

Background

Spironucleus salmonicida is an anaerobic parasite that can cause systemic infections in Atlantic salmon. Unlike other diplomonad parasites, such as the human pathogen Giardia intestinalis, Spironucleus species can infiltrate the blood stream of their hosts eventually colonizing organs, skin and gills. How this presumed anaerobe can persist and invade oxygenated tissues, despite having a strictly anaerobic metabolism, remains elusive.

Results

To investigate how S. salmonicida response to oxygen stress, we performed RNAseq transcriptomic analyses of cells grown in the presence of oxygen or antioxidant-free medium. We found that over 20% of the transcriptome is differentially regulated in oxygen (1705 genes) and antioxidant-depleted (2280 genes) conditions. These differentially regulated transcripts encode proteins related to anaerobic metabolism, cysteine and Fe-S cluster biosynthesis, as well as a large number of proteins of unknown function. S. salmonicida does not encode genes involved in the classical elements of oxygen metabolism (e.g., catalases, superoxide dismutase, glutathione biosynthesis, oxidative phosphorylation). Instead, we found that genes encoding bacterial-like oxidoreductases were upregulated in response to oxygen stress. Phylogenetic analysis revealed some of these oxygen-responsive genes (e.g., nadh oxidase, rubrerythrin, superoxide reductase) are rare in eukaryotes and likely derived from lateral gene transfer (LGT) events into diplomonads from prokaryotes. Unexpectedly, we observed that many host evasion- and invasion-related genes were also upregulated under oxidative stress suggesting that oxygen might be an important signal for pathogenesis.

Conclusion

While oxygen is toxic for related organisms, such as G. intestinalis, we find that oxygen is likely a gene induction signal for host invasion- and evasion-related pathways in S. salmonicida. These data provide the first molecular evidence for how S. salmonicida could tolerate oxic host environments and demonstrate how LGT can have a profound impact on the biology of anaerobic parasites.

Electronic supplementary material

The online version of this article (10.1186/s12915-019-0634-8) contains supplementary material, which is available to authorized users.

Identification of the evolutionarily conserved nuclear envelope proteins Lem2 and MicLem2 in Tetrahymena thermophila

Lem2 family proteins, i.e. the LAP2-Emerin-MAN1 (LEM) domain-containing nuclear envelope proteins, are well-conserved from yeasts to humans, both of which belong to the Opisthokonta supergroup. However, whether their homologs are present in other eukaryotic phylogenies remains unclear. In this study, we identified two Lem2 homolog proteins, which we named as Lem2 and MicLem2, in a ciliate Tetrahymena thermophila belonging to the SAR supergroup. Lem2 was localized to the nuclear envelope of the macronucleus (MAC) and micronucleus (MIC), while MicLem2 was exclusively localized to the nuclear envelope of the MIC. Immunoelectron microscopy revealed that Lem2 in T. thermophila was localized to both the inner and outer nuclear envelopes of the MAC and MIC, while MicLem2 was mostly localized to the nuclear pores of the MIC. Molecular domain analysis using GFP-fused protein showed that the N-terminal and luminal domains, including the transmembrane segments, are responsible for nuclear envelope localization. During sexual reproduction, enrichment of Lem2 occurred in the nuclear envelopes of the MAC and MIC to be degraded, while MicLem2 was enriched in the nuclear envelope of the MIC that escaped degradation. These findings suggest the unique characteristics of Tetrahymena Lem2 proteins. Our findings provide insight into the evolutionary divergence of nuclear envelope proteins.

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Conserved nuclear envelope proteins Lem2 and MicLem2 are identified in Tetrahymena.

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Lem2 is localized to the nuclear envelope of the macronucleus and the micronucleus.

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MicLem2 is localized to the nuclear pore complex of the micronucleus.

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In sexual reproduction, Lem2 is enriched to the nuclei assigned to degradation.

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MicLem2 is enriched to the micronuclei that are escaped from degradation.

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. Chrysomonad flagellates are of major interest, since this group includes heterotrophic, mixotrophic and phototrophic taxa, and therefore allows analysis of silver stress in organisms with contrasting nutritional strategies independent of a potential taxonomic bias. In a series of lab experiments, we compared the response of different trophic chrysophyte strains to low (5 μg L^-1), medium (10 μg L^-1) and high (20 μg L^-1) nominal Ag concentrations in combination with changes in temperature and light intensity (phototrophs), temperature and food concentration (heterotrophs), or a combination of the above settings (mixotrophs). All tested strains were negatively affected by silver in their growth rates. The phototrophic strains reacted strongly to silver stress, whereas light intensity and temperature had only minor effects on growth rates. For heterotrophic strains, high food concentration toned down the effect of silver, whereas temperatures outside the growth optimum had a combined stress effect. The mixotrophic strains reacted differently depending on whether their nutritional mode was dominated by heterotrophy or by phototrophy. The precise response pattern across all variables was uniquely different for every single species we tested. The present work contributes to a deeper understanding of the effects of environmental stressors on complex planktonic communities. It indicates that silver will negatively impact planktonic communities and may create shifts in their composition and functioning.