Diverse Eukaryotes Research Articles

Merging and concatenation of sequencing reads: a bioinformatics workflow for the comprehensive profiling of microbiome from amplicon data.

A comprehensive profiling of microbial diversity is essential to understand the ecosystem functions. Universal primer sets such as the 515Y/926R could amplify a part of 16S and 18S rRNA and infer the diversity of prokaryotes and eukaryotes. However, the analyses of mixed sequencing data pose a bioinformatics challenge; the 16S and 18S rRNA sequences need to be separated first and analysed individually/independently due to variations in the amplicon length. This study describes an alternative strategy, a merging and concatenation workflow, to analyse the mixed amplicon data without separating the 16S and 18S rRNA sequences. The workflow was tested with 24 mock community (MC) samples, and the analyses resolved the composition of prokaryotes and eukaryotes adequately. In addition, there was a strong correlation (cor=0.950; P-value=4.754e-10) between the observed and expected abundances in the MC samples, which suggests that the computational approach could infer the microbial proportions accurately. Further, 18 samples collected from the Sundarbans mangrove region were analysed as a case study. The analyses identified Proteobacteria, Bacteroidota, Actinobacteriota, Cyanobacteria, and Crenarchaeota as dominant bacterial phyla and eukaryotic divisions such as Metazoa, Gyrista, Cryptophyta, Chlorophyta, and Dinoflagellata were found to be dominant in the samples. Thus, the results support the applicability of the method in environmental microbiome research. The merging and concatenation workflow presented here requires considerably less computational resources and uses widely/commonly used bioinformatics packages, saving researchers analyses time (for equivalent sample numbers, compared to the conventional approach) required to infer the diversity of major microbial domains from mixed amplicon data at comparable accuracy.

High amino acid osmotrophic incorporation by marine eukaryotic phytoplankton revealed by click chemistry.

The osmotrophic uptake of dissolved organic compounds in the ocean is considered to be dominated by heterotrophic prokaryotes, whereas the role of planktonic eukaryotes is still unclear. We explored the capacity of natural eukaryotic plankton communities to incorporate the synthetic amino acid L-homopropargylglycine (HPG, analogue of methionine) using biorthogonal noncanonical amino acid tagging (BONCAT), and we compared it with prokaryotic HPG use throughout a 9-day survey in the NW Mediterranean. BONCAT allows to fluorescently identify translationally active cells, but it has never been applied to natural eukaryotic communities. We found a large diversity of photosynthetic and heterotrophic eukaryotes incorporating HPG into proteins, with dinoflagellates and diatoms showing the highest percentages of BONCAT-labelled cells (49 ± 25% and 52 ± 15%, respectively). Among them, pennate diatoms exhibited higher HPG incorporation in the afternoon than in the morning, whereas small (≤5μm) photosynthetic eukaryotes and heterotrophic nanoeukaryotes showed the opposite pattern. Centric diatoms (e.g. Chaetoceros, Thalassiosira, and Lauderia spp.) dominated the eukaryotic HPG incorporation due to their high abundances and large sizes, accounting for up to 86% of the eukaryotic BONCAT signal and strongly correlating with bulk 3H-leucine uptake rates. When including prokaryotes, eukaryotes were estimated to account for 19-31% of the bulk BONCAT signal. Our results evidence a large complexity in the osmotrophic uptake of HPG, which varies over time within and across eukaryotic groups and highlights the potential of BONCAT to quantify osmotrophy and protein synthesis in complex eukaryotic communities.

Phylogenomic analysis expands the known repertoire of single-stranded DNA viruses in benthic zones of the South Indian Ocean.

Single-stranded (ss) DNA viruses are ubiquitous and constitute some of the most diverse entities on Earth. Most studies have focused on ssDNA viruses from terrestrial environments resulting in a significant deficit in benthic ecosystems including aphotic zones of the South Indian Ocean (SIO). Here, we assess the diversity and phylogeny of ssDNA in deep waters of the SIO using a combination of established viral taxonomy tools and a Hidden Markov Model based approach. Replication initiator protein-associated (Rep) phylogenetic reconstruction and sequence similarity networks were used to show that the SIO hosts divergent and as yet unknown circular Rep-encoding ssDNA viruses. Several sequences appear to represent entirely novel families, expanding the repertoire of known ssDNA viruses. Results suggest that a small proportion of these viruses may be circular genetic elements, which may strongly influence the diversity of both eukaryotes and prokaryotes in the SIO. Taken together, our data show that the SIO harbours a diverse assortment of previously unknown ssDNA viruses. Due to their potential to infect a variety of hosts, these viruses may be crucial for marine nutrient recycling through their influence of the biological carbon pump.

Chlamydiae as symbionts of photosynthetic dinoflagellates.

Chlamydiae are ubiquitous intracellular bacteria and infect a wide diversity of eukaryotes, including mammals. However, chlamydiae have never been reported to infect photosynthetic organisms. Here, we describe a novel chlamydial genus and species, Candidatus Algichlamydia australiensis, capable of infecting the photosynthetic dinoflagellate Cladocopium sp. (originally isolated from a scleractinian coral). Algichlamydia australiensis was confirmed to be intracellular by fluorescence in situ hybridization and confocal laser scanning microscopy and temporally stable at the population level by monitoring its relative abundance across four weeks of host growth. Using a combination of short- and long-read sequencing, we recovered a high-quality (completeness 91.73% and contamination 0.27%) metagenome-assembled genome of A. australiensis. Phylogenetic analyses show that this chlamydial taxon represents a new genus and species within the Simkaniaceae family. Algichlamydia australiensis possesses all the hallmark genes for chlamydiae-host interactions, including a complete type III secretion system. In addition, a type IV secretion system is encoded on a plasmid and has previously been observed for only three other chlamydial species. Twenty orthologous groups of genes are unique to A. australiensis, one of which is structurally similar to a protein known from Cyanobacteria and Archaeplastida involved in thylakoid biogenesis and maintenance, hinting at potential chlamydiae interactions with the chloroplasts of Cladocopium cells. Our study shows that chlamydiae infect dinoflagellate symbionts of cnidarians, the first photosynthetic organism reported to harbor chlamydiae, thereby expanding the breadth of chlamydial hosts and providing a new contribution to the discussion around the role of chlamydiae in the establishment of the primary plastid.

Eukaryotic diversity patterns in the Red Sea: from the surface to the deep

Understanding how biological communities are assembled is central to many ecological studies. The semi-confined nature of the Red Sea, with limited exchange of waters with other seas and strong environmental gradients, is an ideal ecosystem to investigate assembly processes of biological communities. Sampling through the water column (surface, deep chlorophyll maximum (DCM), oxygen minimum zone (OMZ), and bottom) along the latitudinal axis of the Red Sea was undertaken during cruises in 2015/2016. The composition and assembly of eukaryotic communities were assessed using high-throughput sequencing of the 18S rRNA gene. Distinct differences were noted in the composition of the eukaryotic community across the different depth layers. Dinophyceae were more prevalent in the euphotic zone (surface = 35.3%; DCM = 18.1%), while Syndiniales had the highest relative abundances in the OMZ (45.9%) and the bottom waters (52.6%). We showed that the assembly of eukaryotic communities through the water column was primarily determined by deterministic processes, especially variable selection due to different environmental conditions. The exception was between the OMZ and the bottom, where deterministic and stochastic processes were balanced with homogeneous selection and homogenizing dispersal dominating, indicating similar environmental conditions and high levels of dispersal between the layers. Across the latitudinal gradient, environmental variable selection was predominant in the euphotic zone, most likely driven by the strong environmental gradients present in the Red Sea. In the aphotic zones, homogenizing dispersal was more prevalent, especially in the OMZ. Our study highlights the contrasting assembly mechanisms governing the distribution of eukaryotic planktonic communities through the water column.

Constraining the oxygen requirements for modern microbial eukaryote diversity.

Eukaryotes originated prior to the establishment of modern marine oxygen (O2) levels. According to the body fossil and lipid biomarker records, modern (crown) microbial eukaryote lineages began diversifying in the ocean no later than ~800 Ma. While it has long been predicted that increasing atmospheric O2 levels facilitated the early diversification of microbial eukaryotes, the O2 levels needed to permit this diversification remain unconstrained. Using time-resolved geochemical parameter and gene sequence information from a model marine oxygen minimum zone spanning a range of dissolved O2 levels and redox states, we show that microbial eukaryote taxonomic richness and phylogenetic diversity remain the same until O2 declines to around 2 to 3% of present atmospheric levels, below which these diversity metrics become significantly reduced. Our observations suggest that increasing O2 would have only directly promoted early crown-eukaryote diversity if atmospheric O2 was below 2 to 3% of modern levels when crown-eukaryotes originated and then later met or surpassed this range as crown-eukaryotes diversified. If atmospheric O2 was already consistently at or above 2 to 3% of modern levels by the time that crown-eukaryotes originated, then the subsequent diversification of modern microbial eukaryotes was not directly driven by atmospheric oxygenation.

Eukaryotic plankton species diversity and community structure in the Xiao Jiang River (the primary tributary of Upper Yangtze River), Yunnan.

The Xiao Jiang River, as a crucial element of ecological restoration in the upper reaches of the Yangtze River, plays an indispensable role in agricultural water utilization and water ecology within its watersheds. The water quality status of the Xiao Jiang River not only impacts local water-ecological equilibrium and economic benefits but also holds paramount importance for sustaining ecosystem health in the Yangtze River basin. Plankton surveys and environmental physicochemical detection were conducted in the major channel region of the Xiao Jiang River in dry and wet periods in 2022 to better understand the diversity of eukaryotic plankton and its community structure characteristics. Environmental DNA is an emerging method that combines traditional ecology with second-generation sequencing technology. It can detect species from a single sample that are difficult to find by traditional microscopy, making the results of plankton diversity studies more comprehensive. For the first time, environmental DNA was used to investigate eukaryotic plankton in the Xiao Jiang River . The results showed that a total of 881 species of plankton from 592 genera in 17 phyla were observed. During the dry period, 480 species belonging to 384 genera within17 phyla were detected, while, during the wet period, a total of 805 species belonging to 463 genera within 17 phyla were recorded. The phylum Ciliophora dominated the zooplankton, while the phylum Chlorophyta and Bacillariophyta dominated the phytoplankton. The presence of these dominant species indicate that the water quality conditions in the study area are oligotrophic and mesotrophic. Principal coordinate analysis and difference test showed that the number of plankton ASVs, abundance, species richness, dominating species, and diversity indices differed between the dry and wet periods. Spearman correlation analysis and redundancy analysis (RDA) of relative abundance data with environmental physicochemical factors revealed that water temperature (WT), dissolved oxygen (DO), potential of hydrogenacidity (pH), ammonia nitrogen (NH3-N), total nitrogen (TN), electrical conductivity (EC) and the determination of redox potential (ORP) were the main environmental physicochemical factors impacting the plankton community structure. The results of this study can serve as a provide data reference at the plankton level for water pollution management in the Xiao Jiang River, and they are extremely important for river ecological restoration and biodiversity recovery in the Yangtze River basin.

Microbial eukaryote community succession over hundreds of years in Chinese lakes

Microbial eukaryotes play critical roles in maintaining the health and stability of lake ecosystems. Consequently, investigating the spatial and temporal evolution of microbial eukaryotic community structures and associated environmental drivers can inform water ecology studies and water environmental protection efforts. In this study, sediment core samples were collected from Lakes Chaohu, Erhai, Lugu and Fuxian in China to reconstruct lake microbial eukaryotic community succession using sediment DNA profiling methods. Mantel tests were used to identify the key factors influencing community succession and explore the mechanisms underlying ecological network changes. Statistical analyses revealed that community structures and diversity in Lakes Chaohu and Erhai shifted in the 2000s and 1980s, respectively, while the communities of Lakes Fuxian and Lugu did not exhibit significant changes during the study period, which may be due to the oligotrophic state of these two lakes. Ciliophora and Chlorophyta were the primary eukaryotic microbial taxa in the four lakes during the study period, with overall relative abundances of 27.2 % and 22.3 %, respectively. The diversities of microbial eukaryotic communities in the lakes were significantly correlated with nutrient enrichment and meteorological factors. Lastly, the ecological niche gap of microbial eukaryotes gradually overlapped after community shifts in Lake Chaohu, while biased interactions strengthened. Overall, this study reveals the impacts of long-term human activities and climate change on lake ecosystems from multiple perspectives of microbial eukaryotic community structure, diversity and ecological network, these findings will contribute to integrate microbial indicators in freshwater environmental monitoring in the future.

Biodiversity and core microbiota of key-stone ecological clusters regulate compost maturity during cow-dung-driven composting

The primary objectives of this study were to explore the community-level succession of bacteria, fungi, and protists during cow-dung-driven composting and to elucidate the contribution of the biodiversity and core microbiota of key-stone microbial clusters on compost maturity. Herein, we used high-throughput sequencing, polytrophic ecological networks, and statistical models to visualize our hypothesis. The results showed significant differences in the richness, phylogenetic diversity, and community composition of bacteria, fungi, and eukaryotes at different composting stages. The ASV191 (Sphingobacterium), ASV2243 (Galibacter), ASV206 (Galibacter), and ASV62 (Firmicutes) were the core microbiota of key-stone bacterial clusters relating to compost maturity; And the ASV356 (Chytridiomycota), ASV470 (Basidiomycota), and ASV299 (Ciliophora) were the core microbiota of key-stone eukaryotic clusters relating to compost maturity based on the data of this study. Compared with the fungal taxa, the biodiversity and core microbiota of key-stone bacterial and eukaryotic clusters contributed more to compost maturity and could largely predict the change in the compost maturity. Structural equation modeling revealed that the biodiversity of total microbial communities and the biodiversity and core microbiota of the key-stone microbial clusters in the compost directly and indirectly regulated compost maturity by influencing nutrient availability (e.g., NH4+-N and NO3−-N), hemicellulose, humic acid content, and fulvic acid content, respectively. These results contribute to our understanding of the biodiversity and core microbiota of key-stone microbial clusters in compost to improve the performance and efficiency of cow-dung-driven composting.

Soil organic carbon loss decreases biodiversity but stimulates multitrophic interactions that promote belowground metabolism.

Soil organic carbon (SOC) plays an essential role in mediating community structure and metabolic activities of belowground biota. Unraveling the evolution of belowground communities and their feedback mechanisms on SOC dynamics helps embed the ecology of soil microbiome into carbon cycling, which serves to improve biodiversity conservation and carbon management strategy under global change. Here, croplands with a SOC gradient were used to understand how belowground metabolisms and SOC decomposition were linked to the diversity, composition, and co-occurrence networks of belowground communities encompassing archaea, bacteria, fungi, protists, and invertebrates. As SOC decreased, the diversity of prokaryotes and eukaryotes also decreased, but their network complexity showed contrasting patterns: prokaryotes increased due to intensified niche overlap, while that of eukaryotes decreased possibly because of greater dispersal limitation owing to the breakdown of macroaggregates. Despite the decrease in biodiversity and SOC stocks, the belowground metabolic capacity was enhanced as indicated by increased enzyme activity and decreased enzymatic stoichiometric imbalance. This could, in turn, expedite carbon loss through respiration, particularly in the slow-cycling pool. The enhanced belowground metabolic capacity was dominantly driven by greater multitrophic network complexity and particularly negative (competitive and predator-prey) associations, which fostered the stability of the belowground metacommunity. Interestingly, soil abiotic conditions including pH, aeration, and nutrient stocks, exhibited a less significant role. Overall, this study reveals a greater need for soil C resources across multitrophic levels to maintain metabolic functionality as declining SOC results in biodiversity loss. Our researchers highlight the importance of integrating belowground biological processes into models of SOC turnover, to improve agroecosystem functioning and carbon management in face of intensifying anthropogenic land-use and climate change.

Lakes-scale pattern of eukaryotic phytoplankton diversity and assembly process shaped by electrical conductivity in central Qinghai-Tibet Plateau.

Phytoplankton are the main primary producers in aquatic ecosystems and play an important role in food web and geochemical cycles. Its diversity, community structure, and assembly process are influenced by several factors. Alpine lake ecosystems are relatively weak and extremely sensitive to global climate change. However, the impact of climate change on phytoplankton in Qinghai-Tibet Plateau lakes and their responses are still unclear. In this study, we analyzed the diversity, environmental drivers, and assembly process of phytoplankton community in the central QTP lakes. The phytoplankton of these lakes can be primarily distinguished into freshwater and brackish types, with significant differences in species diversity and community dissimilarity. Both shared nearly same key environmental factors that significantly affecting phytoplankton such as EC, and brackish lakes were also positively correlative with TN. Stochastic process was predominant in phytoplankton assembly. Additionally, freshwater and brackish lakes were dominated by dispersal limitation and heterogeneous selection respectively. Alpine lakes had significant EC thresholds, and their diversity and assembly processes changed significantly around the thresholds. The present findings have important implications for understanding and predicting the response of lake phytoplankton communities to climate change and for making decisions to protect the ecological resources of alpine lakes.

Life through an Ediacaran glaciation: Shale- and diamictite-hosted organic-walled microfossil assemblages from the late Neoproterozoic of the Tanafjorden area, northern Norway

New organic-walled microfossil (OWM) assemblages are reported from upper Neoproterozoic glacial and interglacial siliciclastic deposits in Finnmark, northern Norway. A nearly continuous sedimentary succession of the Vestertana Group contains two glaciogenic units, the Smalfjorden and Mortensnes formations, interpreted as end-Cryogenian Marinoan and Ediacaran glaciations, respectively. We investigated the OWM record in the Nyborg, Mortensnes, and Stáhpogieddi formations to assess the impact of a glacial interval on the diversity of microscopic eukaryotes. A modified acid-extraction technique was applied to recover OWM from the diamictite matrix. The upper Nyborg Formation contains morphologically complex Doushantuo-Pertatataka acritarchs (DPA), restricting the age of the Nyborg Formation to early-mid Ediacaran. DPA occur below the dolostones that record a negative carbon isotope excursion correlated with the Shuram anomaly and below a glacial diamictite. A decline in species richness and compositional change is observed in the Mortensnes glacial assemblage. DPA are replaced by bacterial filaments and cell aggregates. The overlying Indreelva Member, Stáhpogieddi Formation contains Ediacara-type biota and palaeopascichnids, but only a depauperate OWM assemblage of leiosphaerids and flask-shaped microfossils characteristic of the late Ediacaran.The succession of assemblages in the Vestertana Group demonstrates a turnover from large eukaryotic OWM to a microbial community in the glacial interval, to a low diversity post-glacial assemblage during the rise of macroscopic life. We compared the Vestertana record to global DPA occurrences. Although one DPA assemblage zone postdates the Shuram excursion, no DPA occur above Ediacaran glacial diamictites in successions where those deposits are present. Considering this, and the community changes in the Vestertana succession, we suggest that DPA were affected by the onset of an Ediacaran glaciation. Lastly, we combined the biostratigraphic markers in the Vestertana Group to constrain the age of the Mortensnes diamictite.

Effect of dietary phytase on water and fecal prokaryotic and eukaryotic microbiomes in a hybrid tilapia (Oreochromis aureus x O. niloticus) mixotrophic biofloc production system

In this study we evaluated feed and temporal effects on prokaryotic (16S) and eukaryotic (18S) microbiome dynamics in an outdoor mixotrophic biofloc system used to grow hybrid tilapia (Oreochromis aureus x O. niloticus) to market size. The dicalcium phosphate -free practical feed treated with 6-phytase (3000 FTU/kg; P-Free+Phytase) and positive (Control) and negative (P-Free) control practical feeds used were formulated to contain 27.7% digestible protein and 4% lipid. Sex reversed, all-male hybrid tilapia (28.9 g/fish) were stocked (29 fish/m3) in 9 outdoor rectangular tanks (16.6 m3) and grown for 154 days. The Control feed was fed to all fish during the 14-day acclimation period after which each test feed was fed to fish in three tanks/feed. Biofloc water and fecal samples were collected from all tanks at time 0 (T0, study day 15) and T7, T70, and T140; prokaryotic and eukaryotic abundance and diversity were assessed using high-throughput amplicon sequencing of the 16S and 18S rRNA genes, respectively. Fecal 16S microbiome in all treatments was dominated by Fusobacteria (namely Cetobacterium) with minority representation by Proteobacteria, Firmicutes, Bacteroidetes, and Planctomycetes. Opisthokonts (namely Capsaspora) were the dominant eukaryote detected overall in all fecal samples. Fecal 16S and 18S relative abundances varied significantly with time. Relative abundance of fecal 16S differed significantly between Control and P-Free+Phytase feed treatments only at T140 (harvest). Fecal 18S relative abundance differences among feed treatments were detected only at T0 and T7 and only at the supergroup taxonomic level. Prokaryotic communities in biofloc water among feed treatments and across times were highly diverse and dominated by Proteobacteria, Bacteroidetes, Fusobacteria, Chloroflexi, Planctomycetes, and Actinobacteria. High relative abundances of Capsaspora across time characterized eukaryotic communities. Relative abundances of 16S and 18S taxa in water varied significantly over time. Control and P-Free feed 16S relative abundances in water differed significantly at T0 and T7. Time was the factor that explained most of the variation observed for 16S and 18S beta diversity. Overall, results of the present experiment suggest minimal influence of phytase-treated or dicalcium phosphate-free feeds on hybrid tilapia 16S and 18S water and fecal microbiomes throughout the experiment, particularly because the base feed formulation was the same for all treatments. During this experiment and at harvest tilapia in all treatments appeared healthy and robust, and no known pathogenic bacteria or eukaryotes were detected in any sample, suggesting the observed microbiomes may represent system-specific “healthy” core microbiomes.

SpliceWiz: interactive analysis and visualization of alternative splicing in R.

Alternative splicing (AS) is a crucial mechanism for regulating gene expression and isoform diversity in eukaryotes. However, the analysis and visualization of AS events from RNA sequencing data remains challenging. Most tools require a certain level of computer literacy and the available means of visualizing AS events, such as coverage and sashimi plots, have limitations and can be misleading. To address these issues, we present SpliceWiz, an R package with an interactive Shiny interface that allows easy and efficient AS analysis and visualization at scale. A novel normalization algorithm is implemented to aggregate splicing levels within sample groups, thereby allowing group differences in splicing levels to be accurately visualized. The tool also offers downstream gene ontology enrichment analysis, highlighting ASEs belonging to functional pathways of interest. SpliceWiz is optimized for speed and efficiency and introduces a new file format for coverage data storage that is more efficient than BigWig. Alignment files are processed orders of magnitude faster than other R-based AS analysis tools and on par with command-line tools. Overall, SpliceWiz streamlines AS analysis, enabling reliable identification of functionally relevant AS events for further characterization. SpliceWiz is a Bioconductor package and is also available on GitHub (https://github.com/alexchwong/SpliceWiz).

Openly available illustrations as tools to describe eukaryotic microbial diversity.

Microbial life maintains nearly all the support systems that keep the Earth habitable, yet the diversity of this vast microbial world is greatly understudied, misrepresented, and misunderstood. Even what we do know is difficult to communicate broadly because an intuitive grasp of what these tiny organisms are like is abstract, and we lack tools that would help to describe them. In this Essay, we present a series of openly available technical diagrams that illustrate the diverse range of complex body plans of microbial eukaryotes (or "protists"), as well as an illustrated tree to show the vast diversity they encompass and how they are related to the more familiar macroscopic animals, fungi, and plants. These sorts of tools are desperately needed for teaching and communication about the microbial world, which is a pressingly important problem where much improvement is needed.

Effects of tidal cycles on the variability of microbial communities in a semiclosed bay

Shallow sediment-water plays an important role in transforming organic matter in estuaries. As a shallow bay often flanks a large estuary, the estuarine water enters the shallow bay during flood tides and exits during ebb tides. The inundation between flood and ebb tides in the shallow bay serves as an incubation of the bay water and sediment. However, little is known about the effects of tidal cycles on microbial diversity and biogeochemical processes. In Tangjiawan Bay, which is a small bay located on the west side of the Pearl River estuary, we examined changes in microbial diversity and environmental factors by collecting surface water samples between floods and ebbs. Using high-throughput sequencing targeting 16S and 18S rRNA genes, the results indicated that between floods and ebbs, the community composition of bacteria and eukaryotes differed significantly, the alpha diversity of bacteria and eukaryotes differed significantly, with floods harboring higher diversity. The analysis of RDA suggested that salinity and TOC were important in explaining community variation in both bacteria and eukaryotes. Moreover, the co-occurrence networks between bacteria and eukaryotes showed higher negative relationships in ebbs (83.87%) than in floods (64.29%), suggesting increased interactions between bacteria and eukaryotes during ebbs as the water was incubated in the bay. These findings demonstrated the dynamics of biogeochemical processes of nutrients and plankton communities in the shallow bay and tidal cycles are a dominant driving force in regulating variability in phytoplankton and bacterial community and the sediment-water interface exchange. The results indicate that we should not overlook at the importance of shallow water column fringing the shore lines.

Investigating non-fungal eukaryotic diversity in snow in the Antarctic Peninsula region using DNA metabarcoding.

Snow is a unique microhabitat, despite being a harsh environment, multiple life forms have adapted to survive in it. While algae, bacteria and fungi are dominant microorganisms in Antarctic snow, little is known about other organisms that may be present in this habitat. We used metabarcoding to investigate DNA sequence diversity of non-fungal eukaryotes present in snow obtained from six different sites across the Maritime Antarctica. A total of 20 taxa were assigned to obtained sequences, representing five Kingdoms (Chromista, Protozoa, Viridiplantae and Metazoa) and four phyla (Ciliophora, Cercozoa, Chlorophyta and Cnidaria). The highest diversity indices were detected in Trinity Peninsula followed by Robert Island, Arctowski Peninsula, Deception Island, King George Island and Snow Island. The most abundant assignments were to Trebouxiophyceae, followed by Chlamydomonas nivalis and Chlamidomonadales. No taxa were detected at all sites. Three potentially new records for Antarctica were detected: two Ciliophora (Aspidisca magna and Stokesia sp.) and the green algae Trebouxia potteri. Our data suggested that similarities found between the sites may be more related with snow physicochemical properties rather than geographic proximity or latitude. This study provides new insights into the diversity and distribution of eukaryotic organisms in Antarctic snow.

Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton.

Single-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers' efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.

Balanced biogeographic and local environmental effects determine the patterns of microbial diversity in biocrusts at multi-scales.

Biodiversity maintenance and its underlying mechanisms are central issues of ecology. However, predicting the composition turnovers of microbial communities at multiple spatial scales remains greatly challenging because they are obscured by the inconsistent impacts of climatic and local edaphic conditions on the assembly process. Based on the Illumina MeSeq 16S/18S rRNA sequencing technology, we investigated soil bacterial and eukaryotic communities in biocrusts with different successional levels at a subcontinental scale of Northern China. Results showed that irrespective of spatial scale, bacterial α diversity increased but eukaryotic diversity decreased with the primary succession, whereas both β diversities decreased at the subcontinental scale compared with smaller scales, indicating that the biogeographic pattern of soil microorganisms was balanced by successional convergence and distance decay effect. We found that the convergence of bacterial and eukaryotic communities was attributed to the turnovers of generalist and specialist species, respectively. In this process, edaphic and climatic factors showed unique roles in the changes of diversity at local/subcontinental scales. Moreover, the taxonomic diversity tended to be more susceptible to climatic and edaphic conditions, while biotic factors (photosynthesis and pigments) were more important to phylogenetic diversity. Taken together, our study provided comprehensive insights into understanding the pattern of microbial diversity at multiple spatial scales of drylands.

Functional diversity of microbial eukaryotes in a meromictic lake: Coupling between metatranscriptomic and a trait-based approach.

The advent of high-throughput sequencing has led to the discovery of a considerable diversity of microbial eukaryotes in aquatic ecosystems, nevertheless, their function and contribution to the trophic food web functioning remain poorly characterized especially in freshwater ecosystems. Based on metabarcoding data obtained from a meromictic lake ecosystem (Pavin, France), we performed a morpho-physio-phenological traits-based approach to infer functional groups of microbial eukaryotes. Metatranscriptomic data were also analysed to assess the metabolic potential of these groups across the diel cycle, size fraction, sampling depth, and periods. Our analysis highlights a huge microbial eukaryotic diversity in the monimolimnion characterized by numerous saprotrophs expressing transcripts related to sulfur and nitrate metabolism as well as dissolved and particulate organic matter degradation. We also describe strong seasonal variations of microbial eukaryotes in the mixolimnion, especially for parasites and mixoplankton. It appears that the water mixing (occurring during spring and autumn) which benefits photosynthetic host communities also promotes parasitic fungi dissemination and over-expression of genes involved in the zoospore phototaxis and stage transition in the parasitic cycle. Mixoplanktonic haptophytes over-expressing photosynthesis-, endocytosis- and phagosome-linked genes under nutrient limitation also suggest that phagotrophy may provide them an advantage over non-phagotrophic phytoplankton.