Protist Diversity Research Articles

DNA Barcoding Using 18S rRNA Gene Fragments for Identification of Tick-Borne Protists in Ticks in the Republic of Korea

The objective of this study was to evaluate the diversity and prevalence of tick-borne protists in the Republic of Korea via DNA barcoding using 18S rRNA gene fragments and PCR. Between 2021 and 2022, questing ticks were collected using the flagging method, with a total of 13,375 ticks collected and pooled into 1003 samples. Of these, 50 tick pools were selected for DNA barcoding targeting the V4 and V9 regions of 18S rRNA using the MiSeq platform. A taxonomic analysis of the amplicon sequence variants identified three genera of protozoa, namely Hepatozoon canis, Theileria luwenshuni, and Gregarine sp. However, the number and abundance of protists detected were different depending on the primer sets, and T. gondii was not identified in DNA barcoding. Furthermore, conventional PCR confirmed the presence of H. canis, Toxoplasma gondii, T. luwenshuni, and Theileria sp. in the collected ticks. This study identified H. canis and T. gondii in Ixodes nipponensis for the first time. It demonstrated that the results of DNA barcoding using 18S rRNA gene fragments can vary depending on the primer sets and further optimization is required for library construction to identify tick-borne protists in ticks. Despite these limitations, the findings highlight the potential of DNA barcoding using 18S rRNA gene fragments for screening the diversity of tick-borne protists in ticks.

The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations

Marine microbial eukaryotes (protists) perform essential metabolic functions in oceanic ecosystems. The diversity of protist functions remains poorly understood as few species have been isolated in laboratory settings. Metatranscriptomes provide an invaluable tool for exploring protist diversity and genetic capacities within their natural habitats. Here, we introduce the North Pacific Eukaryotic Gene Catalog, a compilation of metatranscriptome data derived from a total of 261 metatranscriptomes: 169 metatranscriptomes were derived from samples collected on three meridional surface transects along 158°W, each spanning ~20 degrees of latitude from the North Pacific Subtropical Gyre (NPSG) to the North Pacific Transition Zone (NPTZ); 92 metatranscriptomes were derived from two diel-resolved field studies, one in the NPSG at 157°W, 23°N, one in the NPTZ at 158°W, 41°N. The metatranscriptome sequences were de novo assembled into 175 assemblies and pooled into five datasets each containing between 22 M and 49 M contigs clustered at 99% protein identity. Assemblies were annotated by taxonomy and function, and enumerated by short read alignment. All data are available in the Zenodo repository, with underlying code available on github.

National-scale distribution of protists associated with sorghum leaves and roots.

Protists, as integral constituents of the plant microbiome, are posited to confer substantial benefits to plant health and performance. Despite their significance, protists have received considerably less attention compared to other constituents of the plant microbiome, such as bacteria and fungi. To investigate the diversity and community structure of protists in sorghum leaves and roots, we employed amplicon sequencing of the eukaryotic 18S rRNA gene in 563 leaf and root samples collected from 57 locations across China. We found significant differences in the diversity and community structure of protists in sorghum leaves and roots. The leaf was taxonomically dominated by Evosea, Cercozoa and Ciliophora, while the root was dominated by Endomyxa, Cercozoa and Oomycota. The functional taxa of protists exhibited notable differences between leaves and roots, with the former being predominantly occupied by consumers and the latter by parasites. The community composition of protists in the leaf was predominantly influenced by mean annual precipitation, whereas soil pH played a more significant role in the root. The present study identified the most abundant and distributed protists in sorghum leaves and roots and elucidated the underlying factors that govern their community structure. The present study offers a novel perspective on the factors that shape plant-associated protist communities and their potential roles in enhancing the functionality of plant ecosystems.

Exploring the impact of urban pollution on ciliate diversity along the Sapucaí River (Minas Gerais, Brazil) via DNA metabarcoding.

Protists are diverse single-celled eukaryotes found in various habitats. They exhibit a wide range of forms and functions, representing a significant portion of the eukaryotic tree of life, which also includes animals, plants, and fungi. Due to their high sensitivity to environmental changes, these organisms are widely used as biological indicators of organic pollution. We investigated the molecular diversity of ciliate protists at seven strategic points along the Sapucaí River (Itajubá, Minas Gerais State, Brazil), to assess the impact of urban pollution on the richness, abundance, and diversity indexes of these communities. For each sampling point, values of physicochemical parameters were also recorded. DNA sequences were obtained by high-throughput sequencing (HTS) and analyzed using the V4 18S-rRNA molecular marker, employing the DNA metabarcoding method. We recorded 125 ciliate taxonomic units (OTUs), with nearly 80% corresponding to the classes Spirotrichea, Oligohymenophorea, and Litostomatea. At the genus level, 54 OTUs (43.2%) were identified, spanning 28 genera. The composition of ciliates varied significantly along the river's course, from upstream to downstream of Itajubá city. Samples collected from the urban area displayed the lowest richness and diversity, corroborating the influence of the pollution gradient on these communities. The physicochemical parameters showed little variation among the samples and were not linked to the observed changes in ciliate communities, revealing that these organisms are strongly affected by environmental changes and respond more sensitively to these disturbances than physicochemical parameters, emphasizing their potential as bioindicators.

The eukaryome of modern microbialites reveals distinct colonization across aquatic ecosystems

Protists are less studied for their role and diversity in ecosystems. Notably, protists have played and still play an important role in microbialites. Microbialites, or lithified microbial mats, represent the oldest evidence of fossil biofilms (~3.5 Gyr). Modern microbialites may offer a unique proxy to study the potential role of protists within a geological context. We examined protist diversity in freshwater (Kelly and Pavilion Lake in British Columbia, Canada) and marine (Highborne Cay, Bahamas) to hypersaline (Shark Bay, Australia) microbialites to decipher their geomicrobiological role. The freshwater microbialite communities were clearly distinct from their marine and hypersaline counterparts. Chlorophytes had higher numerical abundance in freshwater microbialites; whereas pennate diatoms dominated numerically in marine microbialites. Despite the differences, protists across ecosystems may have adopted similar roles and functions. We suggest a consistent biogeochemical role of protists across microbialites globally; but that salinity may shape protist composition and evolution in these ecosystems.

Structural variability of protist assemblages in surface sediments across Italian Mediterranean marine subregions

Marine sediments host heterogeneous protist communities consisting of both living benthic microorganisms and planktonic resting stages. Despite their key functions in marine ecosystem processes and biogeochemical cycles, their structure and dynamics are largely unknown. In the present study, with a spatially intensive sampling design we investigated benthic protist diversity and function of surface sediment samples from three subregions of the Mediterranean Sea, through an environmental DNA metabarcoding approach targeting the 18S V4 region of rRNA gene. Protists were characterized at the taxonomic level and trophic function, both in terms of alpha diversity and community composition, testing for potential differences among marine subregions and bathymetric groups. Overall, Alveolata and Stramenopiles were the two divisions that dominated the communities. These dominant groups exhibited significant differences among the three Mediterranean subregions in the alpha diversity estimates based on the detected ASVs, for all computed indices (ASV richness, Shannon and Simpson indices). Protist communities were also found to be significantly different in terms of composition at the order rank in the three subregions p-value < 0.01). These differences were mainly driven by Anoecales, Peridiniales, Borokales, Paraliales and Gonyaulacales, which together contributed almost 80% of the average dissimilarity. Anoecales was the dominant order in the Ionian – Central Mediterranean and Adriatic Sea, but with considerably different relative abundances (52% and 36%, respectively), while Borokales was the dominant order in the Western Mediterranean Sea (33%). Similarly, significant differences among the three marine subregions were also highlighted when protist assemblages were examined in terms of trophic function, both in terms of alpha diversity (calculated on the ASVs for each trophic group) and community composition p-value < 0.01. In particular, the Adriatic Sea stood out for having the highest relative abundance of autotrophic/mixotrophic components in the surface sediments analyzed. Conversely, no significant differences in protist assemblages were found among depth groups. This study provided new insights into the taxonomic and trophic composition of benthic protist communities found in Mediterranean surface sediments, revealing geographical differences among regional seas. The results were discussed in relation to the Mediterranean environmental features that could generate the differences among benthic protist communities.

Flourishing in Darkness: Protist Communities of Water Sites in Shulgan-Tash Cave (Southern Urals, Russia)

Karst caves, formed by the erosion of soluble carbonate rocks, provide unique ecosystems characterized by stable temperatures and high humidity. These conditions support diverse microbial communities, including wall microbial fouling, aquatic biofilms, and planktonic communities. This study discloses the taxonomic diversity of protists in aquatic biotopes of Shulgan-Tash Cave, a culturally significant site and popular tourist destination, by 18S rRNA gene metabarcoding. Our findings reveal the rich protist communities in the cave’s aquatic biotopes, with the highest diversity observed in Blue Lake at the cave entrance. In contrast, Distant Lake in the depth of the cave was inhabited by specific communities of plankton, mats, and pool fingers, which exhibited lower richness and evenness, and were adapted to extreme conditions (cold, darkness, and limited nutrients). High-rank taxa including Opisthokonta, Stramenopiles, and Rhizaria dominated all biotopes, aligning with observations from other subterranean environments. Specific communities of biotopes inside the cave featured distinct dominant taxa: amoeboid stramenopile (Synchromophyceae) and flagellates (Choanoflagellatea and Sandona) in mats; flagellates (Choanoflagellatea, Bicoecaceae, Ancyromonadida) and amoeboid protists (Filasterea) in pool fingers; flagellates (Ochromonadales, Glissomonadida, Synchromophyceae), fungi-like protists (Peronosporomycetes), and fungi (Ustilaginomycotina) in plankton. The specificity of the communities was supported by LEfSe analysis, which revealed enriched or differentially abundant protist taxa in each type of biotope. The predominance of Choanoflagellatea in the communities of cave mats and pool fingers, as well as the predominance of Synchromophyceae in the cave mats, appears to be a unique feature of Shulgan-Tash Cave. The cold-tolerant yeast Malassezia recorded in other caves was present in both plankton and biofilm communities, suggesting its resilience to low temperatures. However, no potentially harmful fungi were detected, positioning this research as a baseline for future monitoring. Our results emphasize the need for ongoing surveillance and conservation efforts to protect the fragile ecosystems of Shulgan-Tash Cave from human-induced disturbances and microbial invasions.

Urbanization reduces the stability of soil microbial community by reshaping the diversity and network complexity

Rapid urbanization considerably alters soil environment, biodiversity, and stability of terrestrial ecosystems. Soil microbial community, a key component of global biodiversity, plays a pivotal role in ecosystem stability and is highly vulnerable to urbanization. However, effects of urbanization on the diversity, stability, and network structure of soil microbial community remain poorly understood. Herein, we investigated the diversity and stability of soil microbial communities, including bacteria, fungi, and protists, across three regions with different levels of urbanization—urban, suburb, and ecoregion—using high-throughput sequencing techniques. Our results revealed that urbanization led to a notable decrease in the alpha diversity of soil microbial community, causing a significant reduction in soil stability, as assessed by the average variation degree (AVD). The loss of stability was linked to the diminished alpha diversity of the soil fungal and protistan communities, along with weakened interactions among bacteria, fungi, and protists. Notably, the majority of keystone species identified through network analysis were classified as bacteria (Proteobacteria) and displayed a strong positive correlation with the environmental factors influencing AVD. This highlights that the variability of bacteria and the immutability of fungi and protists are important to sustain soil microbial stability. Furthermore, structural equation models indicated that protistan diversity primarily drove soil microbial stability across all regions studied. In the suburban and ecoregion areas, soil microbial stability was directly influenced by the soil properties, bacterial diversity, and keystone species, as well as indirectly affected by heavy metals. These results underscore how urbanization can reduce the stability of soil microbial community via declined diversity and network complexity, whereas the establishment of ecoregions maybe contribute to preserve the diversity and stability of soil microbial community.

Microbial assemblages and associated biogeochemical processes in Lake Bonney, a permanently ice-covered lake in the McMurdo Dry Valleys, Antarctica

BackgroundLake Bonney, which is divided into a west lobe (WLB) and an east lobe (ELB), is a perennially ice-covered lake located in the McMurdo Dry Valleys of Antarctica. Despite previous reports on the microbial community dynamics of ice-covered lakes in this region, there is a paucity of information on the relationship between microbial genomic diversity and associated nutrient cycling. Here, we applied gene- and genome-centric approaches to investigate the microbial ecology and reconstruct microbial metabolic potential along the depth gradient in Lake Bonney.ResultsLake Bonney is strongly chemically stratified with three distinct redox zones, yielding different microbial niches. Our genome enabled approach revealed that in the sunlit and relatively freshwater epilimnion, oxygenic photosynthetic production by the cyanobacterium Pseudanabaena and a diversity of protists and microalgae may provide new organic carbon to the environment. CO-oxidizing bacteria, such as Acidimicrobiales, Nanopelagicales, and Burkholderiaceae were also prominent in the epilimnion and their ability to oxidize carbon monoxide to carbon dioxide may serve as a supplementary energy conservation strategy. In the more saline metalimnion of ELB, an accumulation of inorganic nitrogen and phosphorus supports photosynthesis despite relatively low light levels. Conversely, in WLB the release of organic rich subglacial discharge from Taylor Glacier into WLB would be implicated in the possible high abundance of heterotrophs supported by increased potential for glycolysis, beta-oxidation, and glycoside hydrolase and may contribute to the growth of iron reducers in the dark and extremely saline hypolimnion of WLB. The suboxic and subzero temperature zones beneath the metalimnia in both lobes supported microorganisms capable of utilizing reduced nitrogens and sulfurs as electron donors. Heterotrophs, including nitrate reducing sulfur oxidizing bacteria, such as Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), and denitrifying bacteria, such as Gracilimonas (MAG7), Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), dominated the hypolimnion of WLB, whereas the environmental harshness of the hypolimnion of ELB was supported by the relatively low in metabolic potential, as well as the abundance of halophile Halomonas and endospore-forming Virgibacillus.ConclusionsThe vertical distribution of microbially driven C, N and S cycling genes/pathways in Lake Bonney reveals the importance of geochemical gradients to microbial diversity and biogeochemical cycles with the vertical water column.

Age-Dependent Changes in Protist and Fungal Microbiota in a Peruvian Cattle Genetic Nucleus.

In this research, the connection between age and microbial diversity in cattle was explored, revealing significant changes in both protist diversity and fungal microbiota composition with age. Using fecal samples from 21 Simmental cattle, microbial communities were analyzed through 18S rRNA gene sequencing. Results indicated significant differences in alpha protist diversity among the three age groups, while fungal composition varied notably with age and was linked to hematological parameters. Despite the stability of fungal alpha diversity, compositional changes suggest the gut as a stable niche for microbial colonization influenced by diet, clinical parameters, and microbial interactions. All cattle were maintained on a consistent diet, tailored to meet the specific nutritional needs of each age group. These findings emphasize the importance of understanding age-related microbial dynamics to enhance livestock management and animal health, contributing to broader ecological and biomedical research. This study was limited by the lack of comprehensive metabolic analyses correlating microbiota changes with specific age-related variations, indicating a need for further research in this area.

Life cycle strategies in free-living unicellular eukaryotes: Diversity, evolution, and current molecular tools to unravel the private life of microorganisms.

An astonishing range of morphologies and life strategies has arisen across the vast diversity of protists, allowing them to thrive in most environments. In model protists, like Tetrahymena, Dictyostelium, or Trypanosoma, life cycles involving multiple life stages with different morphologies have been well characterized. In contrast, knowledge of the life cycles of free-living protists, which primarily consist of uncultivated environmental lineages, remains largely fragmentary. Various life stages and lineage-specific cellular innovations have been observed in the field for uncultivated protists, but such innovations generally lack functional characterization and have unknown physiological and ecological roles. In the actual state of knowledge, evidence of sexual processes is confirmed for 20% of free-living protist lineages. Nevertheless, at the onset of eukaryotic diversification, common molecular trends emerged to promote genetic recombination, establishing sex as an inherent feature of protists. Here, we review protist life cycles from the viewpoint of life cycle transitions and genetics across major eukaryotic lineages. We focus on the scarcely observed sexual cycle of free-living protists, summarizing evidence for its existence and describing key genes governing its progression, as well as, current methods for studying the genetics of sexual cycles in both cultivable and uncultivated protist groups.

Earthworms alleviate microplastics stress on soil microbial and protist communities

Microplastic (MP) pollution can exert significant pressure on soil ecosystems, however, the interactive effects of MPs on soil bacterial, fungal and protist communities remains poorly understood. Soil macrofauna, such as earthworms, can be directly affected by MPs, potentially leading to a range of feedbacks on the soil microbial community. To address this, we conducted a microcosm experiment to examine the effects of conventional (i.e., polyethylene, polystyrene) and biodegradable MPs (i.e. PBAT, polylactic acid) on the structure of the soil bacterial, fungal, and protist communities in the presence or absence of earthworms. We found that MP contamination negatively affected the diversity and composition of soil microbial and protist communities, with smaller-sized conventional MPs having the most pronounced effects. For example, compared with the unamended control, small-sized polyethylene MPs both significantly reduced the Shannon diversity of soil bacteria, fungi, and protist by 4.3 %, 37.0 %, and 9.1 %, respectively. Biodegradable MPs increased negative correlations among bacteria, fungi, and protists. However, earthworms mitigated these effects, enhancing the diversity and altering the composition of these communities. They also increased the niche width and stability of the soil microbial food web network. Our study indicated that earthworms help attenuate the response of soil microorganisms to MPs stress by influencing the diversity and composition of soil microorganisms and soil physicochemical properties and underscores the importance of considering macrofauna in MPs research.

The polinton-like supergroup of viruses: evolution, molecular biology, and taxonomy.

SUMMARYPolintons are 15-20 kb-long self-synthesizing transposons that are widespread in eukaryotic, and in particular protist, genomes. Apart from a transposase and a protein-primed DNA polymerase, polintons encode homologs of major and minor jelly-roll capsid proteins, DNA-packaging ATPases, and proteases involved in capsid maturation of diverse eukaryotic viruses of kingdom Bamfordvirae. Given the conservation of these structural and morphogenetic proteins among polintons, these elements are predicted to alternate between transposon and viral lifestyles and, although virions have thus far not been detected, are classified as viruses (class Polintoviricetes) in the phylum Preplasmiviricota. Related to polintoviricetes are vertebrate adenovirids; unclassified polinton-like viruses (PLVs) identified in various environments or integrated into diverse protist genomes; virophages (Maveriviricetes), which are part of tripartite hyperparasitic systems including protist hosts and giant viruses; and capsid-less derivatives, such as cytoplasmic linear DNA plasmids of fungi and transpovirons. Phylogenomic analysis indicates that the polinton-like supergroup of viruses bridges bacterial tectivirids (preplasmiviricot class Tectiliviricetes) to the phylum Nucleocytoviricota that includes large and giant eukaryotic DNA viruses. Comparative structural analysis of proteins encoded by polinton-like viruses led to the discovery of previously undetected functional domains, such as terminal proteins and distinct proteases implicated in DNA polymerase processing, and clarified the evolutionary relationships within Polintoviricetes. Here, we leverage these insights into the evolution of the polinton-like supergroup to develop an amended megataxonomy that groups Polintoviricetes, PLVs (new class 'Aquintoviricetes'), and virophages (renamed class 'Virophaviricetes') together with Adenoviridae (new class 'Pharingeaviricetes') in a preplasmiviricot subphylum 'Polisuviricotina' sister to a subphylum including Tectiliviricetes ('Prepoliviricotina').

Jeremy David Pickett-Heaps. 5 June 1940—11 April 2021

Jeremy Pickett-Heaps was a biologist whose acute observational powers were fed by a deep fascination for how cells work; he had an affinity for the myriad diversity of algae and other protists in general, and for what they could teach us about all cells. An early adopter of the electron microscope, he made fundamental discoveries in plant cell division and green algal phylogeny that developed into studies on cell division in general: first with the highly ordered diatoms and other protists, and later with animal cells. In the latter part of his career, Jeremy mastered time-lapse microcinematography to document the dynamic lives of cells and, through the resultant movies and his enthusiastic teaching, introduced many to the wonders of microscopic life.

Trophic strategies of picoeukaryotic phytoplankton vary over time and with depth in the North Pacific Subtropical Gyre.

In oligotrophic oceans, the smallest eukaryotic phytoplankton are both significant primary producers and predators of abundant bacteria such as Prochlorococcus. However, the drivers and consequences of community dynamics among these diverse protists are not well understood. Here, we investigated how trophic strategies along the autotrophy-mixotrophy spectrum vary in importance over time and across depths at Station ALOHA in the North Pacific Subtropical Gyre. We combined picoeukaryote community composition from a 28-month time-series with traits of diverse phytoplankton isolates from the same location, to examine trophic strategies across 13 operational taxonomic units and 8 taxonomic classes. We found that autotrophs and slower-grazing mixotrophs tended to prevail deeper in the photic zone, while the most voracious mixotrophs were relatively abundant near the surface. Within the mixed layer, there was greater phagotrophy when conditions were most stratified and when Chl a concentrations were lowest, although the greatest temporal variation in trophic strategy occurred at intermediate depths (45-100 m). Dynamics at this site are consistent with previously described spatial patterns of trophic strategies. The success of relatively phagotrophic phytoplankton at shallower depths in the most stratified waters suggests that phagotrophy is a competitive strategy for acquiring nutrients when energy from light is plentiful.

Colonization ability and uniformity of resources and environmental factors determine biological homogenization of soil protists in human land-use systems.

Humans have substantially transformed the global land surface, resulting in the decline in variation in biotic communities across scales, a phenomenon known as "biological homogenization." However, different biota are affected by biological homogenization to varying degrees, but this variation and the underlying mechanisms remain little studied, particularly in soil systems. To address this topic, we used metabarcoding to investigate the biogeography of soil protists and their prey/hosts (prokaryotes, fungi, and meso- and macrofauna) in three human land-use ecosystem types (farmlands, residential areas, and parks) and natural forest ecosystems across subtropical and temperate regions in China. Our results showed that the degree of community homogenization largely differed between taxa and functional groups of soil protists, and was strongly and positively linked to their colonization ability of human land-use systems. Removal analysis showed that the introduction of widespread, generalist taxa (OTUs, operational taxonomic units) rather than the loss of narrow-ranged, specialist OTUs was the major cause of biological homogenization. This increase in generalist OTUs seemingly alleviated the negative impact of land use on specialist taxa, but carried the risk of losing functional diversity. Finally, homogenization of prey/host biota and environmental conditions were also important drivers of biological homogenization in human land-use systems, with their importance being more pronounced in phagotrophic than parasitic and phototrophic protists. Overall, our study showed that the variation in biological homogenization strongly depends on the colonization ability of taxa in human land-use systems, but is also affected by the homogenization of resources and environmental conditions. Importantly, biological homogenization is not the major cause of the decline in the diversity of soil protists, and conservation and study efforts should target at taxa highly sensitive to local extinction, such as parasites.

Measurements of soil protist richness and community composition are influenced by primer pair, annealing temperature, and bioinformatics choices.

Protists are a diverse and understudied group of microbial eukaryotic organisms especially in terrestrial environments. Advances in molecular methods are increasing our understanding of the distribution and functions of these creatures; however, there is a vast array of choices researchers make including barcoding genes, primer pairs, PCR settings, and bioinformatic options that can impact the outcome of protist community surveys. Here, we tested four commonly used primer pairs targeting the V4 and V9 regions of the 18S rRNA gene using different PCR annealing temperatures and processed the sequences with different bioinformatic parameters in 10 diverse soils to evaluate how primer pair, amplification parameters, and bioinformatic choices influence the composition and richness of protist and non-protist taxa using Illumina sequencing. Our results showed that annealing temperature influenced sequencing depth and protist taxon richness for most primer pairs, and that merging forward and reverse sequencing reads for the V4 primer pairs dramatically reduced the number of sequences and taxon richness of protists. The data sets of primers that targeted the same 18S rRNA gene region (e.g., V4 or V9) had similar protist community compositions; however, data sets from primers targeting the V4 18S rRNA gene region detected a greater number of protist taxa compared to those prepared with primers targeting the V9 18S rRNA region. There was limited overlap of protist taxa between data sets targeting the two different gene regions (80/549 taxa). Together, we show that laboratory and bioinformatic choices can substantially affect the results and conclusions about protist diversity and community composition using metabarcoding.IMPORTANCEEcosystem functioning is driven by the activity and interactions of the microbial community, in both aquatic and terrestrial environments. Protists are a group of highly diverse, mostly unicellular microbes whose identity and roles in terrestrial ecosystem ecology have been largely ignored until recently. This study highlights the importance of choices researchers make, such as primer pair, on the results and conclusions about protist diversity and community composition in soils. In order to better understand the roles protist taxa play in terrestrial ecosystems, biases in methodological and analytical choices should be understood and acknowledged.

Bacteria, Fungi, and Protists Exhibit Distinct Responses to Managed Vegetation Restoration in the Karst Region.

Bacteria, fungi, and protists occupy a pivotal position in maintaining soil ecology. Despite limited knowledge on their responses to managed vegetation restoration strategies in karst regions, we aimed to study the essential microbial communities involved in the process of vegetation restoration. We compared microbial characteristics in four land use types: planted forests (PF), forage grass (FG), a mixture of plantation forest and forage grass (FF), and cropland (CR) as a reference. Our findings revealed that the richness of bacteria and protists was higher in FF compared to PF, while fungal richness was lower in both PF and FF than in CR. Additionally, the bacterial Shannon index in FF was higher than that in CR and PF, while the fungal and protist Shannon indices were similar across all four land use types. Significant differences were observed in the compositions of bacterial, fungal, and protist communities between FF and the other three land use types, whereas bacterial, fungal, and protist communities were relatively similar in PF and FG. In FF, the relative abundance of bacterial taxa Acidobacteria, Firmicutes, and Gemmatimonadetes was significantly higher than in PF and CR. Fungal communities were dominated by Ascomycota and Basidiomycota, with the relative abundance of Ascomycota significantly higher in FF compared to other land use types. Regarding protistan taxa, the relative abundance of Chlorophyta was higher in FF compared to CR, PF, and FG, while the relative abundance of Apicomplexa was higher in CR compared to FF. Importantly, ammonium nitrogen, total phosphorus, and microbial biomass nitrogen were identified as key soil properties predicting changes in the diversity of bacteria, fungi, and protists. Our results suggest that the microbial community under FF exhibits greater sensitivity to vegetation restoration compared to PF and FG. This sensitivity may stem from differences in soil properties, the formation of biological crusts and root systems, and management activities, resulting in variations in bacterial, fungal, and protist diversity and taxa in PF. As a result, employing a combination restoration strategy involving plantation forest and forage grass proves to be an effective approach to enhance the microbial community and thereby improve ecosystem functionality in ecologically fragile areas.

Exploring the landscape of symbiotic diversity and distribution in unicellular ciliated protists

BackgroundThe eukaryotic-bacterial symbiotic system plays an important role in various physiological, developmental, and evolutionary processes. However, our current understanding is largely limited to multicellular eukaryotes without adequate consideration of diverse unicellular protists, including ciliates.ResultsTo investigate the bacterial profiles associated with unicellular organisms, we collected 246 ciliate samples spanning the entire Ciliophora phylum and conducted single-cell based metagenome sequencing. This effort has yielded the most extensive collection of bacteria linked to unicellular protists to date. From this dataset, we identified 883 bacterial species capable of cohabiting with ciliates, unveiling the genomes of 116 novel bacterial cohabitants along with 7 novel archaeal cohabitants. Highlighting the intimate relationship between ciliates and their cohabitants, our study unveiled that over 90% of ciliates coexist with bacteria, with individual hosts fostering symbiotic relationships with multiple bacteria concurrently, resulting in the observation of seven distinct symbiotic patterns among bacteria. Our exploration of symbiotic mechanisms revealed the impact of host digestion on the intracellular diversity of cohabitants. Additionally, we identified the presence of eukaryotic-like proteins in bacteria as a potential contributing factor to their resistance against host digestion, thereby expanding their potential host range.ConclusionsAs the first large-scale analysis of prokaryotic associations with ciliate protists, this study provides a valuable resource for future research on eukaryotic-bacterial symbioses.89id7Mc_Y_Zgt6kKNc3JJ4Video

Diversity and composition of gut protist in young rural Zimbabwean children

Diversity and composition of gut protist in young rural Zimbabwean children