Microbial Eukaryotes Research Articles

Interoperable vocabulary for marine microbial flow cytometry

The recent development of biological sensors has extended marine plankton studies from conducting laboratory bench work to in vivo and real-time observations. Flow cytometry (FCM) has shed new light on marine microorganisms since the 1980s through its single-cell approach and robust detection of the smallest cells. FCM records valuable optical properties of light scattering and fluorescence from cells passing in a single file in front of a narrow-collimated light source, recording tens of thousands of cells within a few minutes. Depending on the instrument settings, the sampling strategy, and the automation level, it resolves the spatial and temporal distribution of microbial marine prokaryotes and eukaryotes. Cells are usually classified and grouped on cytograms by experts and are still lacking standards, reducing data sharing capacities. Therefore, the need to make FCM data sets FAIR (Findability, Accessibility, Interoperability, and Reusability of digital assets) is becoming critical. In this paper, we present a consensus vocabulary for the 13 most common marine microbial groups observed with FCM using blue and red-light excitation. The authors designed a common layout on two-dimensional log-transformed cytograms reinforced by a decision tree that facilitates the characterization of groups. The proposed vocabulary aims at standardising data analysis and definitions, to promote harmonisation and comparison of data between users and instruments. This represents a much-needed step towards FAIRification of flow cytometric data collected in various marine environments.

Concepts towards Functional Eukaryotic Microbial Biogeography in the Ocean

High-throughput sequencing technologies have revolutionized microbial diversity studies, shedding light on the oceans’ plankton evolution, distribution, and biological activity. Whereas marine prokaryotes have been more extensively studied and specific methods developed, the research on microbial eukaryotes (protists) is falling behind, with major groups still largely unknown regarding their ecology and function. Because of numerous anthropogenic pressures, it is increasingly important to highlight the functional roles of protists in marine ecosystems. This review outlines the practices, challenges, and opportunities of high-throughput sequencing approaches (i.e., metabarcoding, metagenomics, and metatranscriptomics) to disentangle evolutionary, ecological, and functional aspects of protists in the ocean. These multidimensional approaches allow us to move from the classic picture of microbial biogeography towards functional microbial biogeography, explicitly highlighting the role of protists therein. We provide resources for functional classification and reflect on the current and future potential. We outline aspects of detecting and describing ecosystem changes at the species, population, and community levels, advancing methodological approaches for studying taxonomic diversity towards functional and evolutionary biodiversity concepts, seeking a more complete understanding and monitoring of ocean ecosystems.

Microbiome–Gut Dissociation in the Neonate: Autism-Related Developmental Brain Disease and the Origin of the Placebo Effect

While the importance of the intestinal microbiome has been realised for a number of years, the significance of the phrase microbiota–gut–brain axis is only just beginning to be fully appreciated. Our recent work has focused on the microbiome as if it were a single entity, modifying the expression of the genetic inheritance of the individual by the generation of interkingdom signalling molecules, semiochemicals, such as dopamine. In our view, the purpose of the microbiome is to convey information about the microbial environment of the mother so as to calibrate the immune system of the new-born, giving it the ability to distinguish harmful pathogens from the harmless antigens of pollen, for example, or to help distinguish self from non-self. In turn, this requires the partition of nutrition between the adult and its microbiome to ensure that both entities remain viable until the process of reproduction. Accordingly, the failure of a degraded microbiome to interact with the developing gut of the neonate leads to failure of this partition in the adult: to low faecal energy excretion, excessive fat storage, and concomitant problems with the immune system. Similarly, a weakened gut–brain axis distorts interoceptive input to the brain, increasing the risk of psychiatric diseases such as autism. These effects account for David Barker’s 1990 suggestion of “the fetal and infant origins of adult disease”, including schizophrenia, and David Strachan’s 1989 observation of childhood immune system diseases, such as hay fever and asthma. The industrialisation of modern life is increasing the intensity and scale of these physical and psychiatric diseases and it seems likely that subclinical heavy metal poisoning of the microbiome contributes to these problems. Finally, the recent observation of Harald Brüssow, that reported intestinal bacterial composition does not adequately reflect the patterns of disease, would be accounted for if microbial eukaryotes were the key determinant of microbiome effectiveness. In this view, the relative success of “probiotic” bacteria is due to their temporary immune system activation of the gut–brain axis, in turn suggesting a potential mechanism for the placebo effect.

Summer Dynamics of Microbial Diversity on a Mountain Glacier.

Glaciers are rapidly receding under climate change. A melting cryosphere will dramatically alter global sea levels, carbon cycling, and water resource availability. Glaciers host rich biotic communities that are dominated by microbial diversity, and this biodiversity can impact surface albedo, thereby driving a feedback loop between biodiversity and cryosphere melt. However, the microbial diversity of glacier ecosystems remains largely unknown outside of major ice sheets, particularly from a temporal perspective. Here, we characterized temporal dynamics of bacteria, eukaryotes, and algae on the Paradise Glacier, Mount Rainier, USA, over nine time points spanning the summer melt season. During our study, the glacier surface steadily darkened as seasonal snow melted and darkening agents accumulated until new snow fell in late September. From a community-wide perspective, the bacterial community remained generally constant while eukaryotes and algae exhibited temporal progression and community turnover. Patterns of individual taxonomic groups, however, were highly stochastic. We found little support for our a priori prediction that autotroph abundance would peak before heterotrophs. Notably, two different trends in snow algae emerged-an abundant early- and late-season operational taxonomic unit (OTU) with a different midsummer OTU that peaked in August. Overall, our results highlight the need for temporal sampling to clarify microbial diversity on glaciers and that caution should be exercised when interpreting results from single or few time points. IMPORTANCE Microbial diversity on mountain glaciers is an underexplored component of global biodiversity. Microbial presence and activity can also reduce the surface albedo or reflectiveness of glaciers, causing them to absorb more solar radiation and melt faster, which in turn drives more microbial activity. To date, most explorations of microbial diversity in the mountain cryosphere have only included single time points or focused on one microbial community (e.g., bacteria). Here, we performed temporal sampling over a summer melt season for the full microbial community, including bacteria, eukaryotes, and fungi, on the Paradise Glacier, Washington, USA. Over the summer, the bacterial community remained generally constant, whereas eukaryote and algal communities temporally changed through the melt season. Individual taxonomic groups, however, exhibited considerable stochasticity. Overall, our results highlight the need for temporal sampling on glaciers and that caution should be exercised when interpreting results from single or few time points.

Short-Term Evaluation of the Spatial Distribution of Trophic Groups of Amoebae in the Rhizosphere of Zea mays Inoculated with Rhizophagus intraradices.

Primary production in terrestrial ecosystems is sustained by plants, microbiota, and fungi, which are the major organic matter providers in the root zone, setting in motion the soil food webs. Predators like soil amoebae voraciously feed on bacteria, fungi, and microbial eukaryotes releasing the nutrients sequestered in their biomass. Early food web setting up is crucial for seedling nutrition and its further development after establishment. Mycorrhizal fungi are more than phosphorus providers, and we wonder what their role is in structuring the predators' trophic groups in the root zone. We evaluated the effect of Rhizophagus intraradices inoculated in Zea mays (mycorrhizosphere), on the structuration of amoebae trophic groups along vertical and horizontal (3, 6, and 9cm) soil distribution when compared to un-inoculated plants, after 20days in microcosms. Amoebae species richness was highest in non-mycorrhizal seedlings in the root zone at 6- to 9-cm depth, and 3cm away from plants. More bacterial species are needed when plants are devoid of mycorrhiza, and their influence is constrained 3cm away from roots. Higher diversity of trophic groups was recorded at mycorrhizal seedlings and at the compartment influenced by the mycelium at 6- to 9-cm depth. The highest bacterivorous diversity, higher number of rare species and protozoa-eating amoebae, and the absence of fungivorous group recorded at the mycorrhizosphere of Z. mays, indicate that the community was very different from the non-mycorrhizal plants. We conclude that the arbuscular mycorrhizal fungus exerts significant changes on the community of trophic groups of amoebae.

Contrasting sea ice conditions shape microbial food webs in Hudson Bay (Canadian Arctic)

The transition from ice-covered to open water is a recurring feature of the Arctic and sub-Arctic, but microbial diversity and cascading effects on the microbial food webs is poorly known. Here, we investigated microbial eukaryote, bacterial and archaeal communities in Hudson Bay (sub-Arctic, Canada) under sea-ice cover and open waters conditions. Co-occurrence networks revealed a <3 µm pico‒phytoplankton-based food web under the ice and a >3 µm nano‒microphytoplankton-based food web in the open waters. The ice-edge communities were characteristic of post-bloom conditions with high proportions of the picophytoplankton Micromonas and Bathycoccus. Nano‒ to micro‒phytoplankton and ice associated diatoms were detected throughout the water column, with the sympagic Melosira arctica exclusive to ice-covered central Hudson Bay and Thalassiosira in open northwestern Hudson Bay. Heterotrophic microbial eukaryotes and prokaryotes also differed by ice-state, suggesting a linkage between microbes at depth and surface phytoplankton bloom state. The findings suggest that a longer open water season may favor the establishment of a large phytoplankton-based food web at the subsurface chlorophyll maxima (SCM), increasing carbon export from pelagic diatoms to deeper waters and affect higher trophic levels in the deep Hudson Bay.

A cap 0-dependent mRNA capture method to analyze the yeast transcriptome.

Analysis of the protein coding transcriptome by the RNA sequencing requires either enrichment of the desired fraction of coding transcripts or depletion of the abundant non-coding fraction consisting mainly of rRNA. We propose an alternative mRNA enrichment strategy based on the RNA-binding properties of the human IFIT1, an antiviral protein recognizing cap 0 RNA. Here, we compare for Saccharomyces cerevisiae an IFIT1-based mRNA pull-down with yeast targeted rRNA depletion by the RiboMinus method. IFIT1-based RNA capture depletes rRNA more effectively, producing high quality RNA-seq data with an excellent coverage of the protein coding transcriptome, while depleting cap-less transcripts such as mitochondrial or some non-coding RNAs. We propose IFIT1 as a cost effective and versatile tool to prepare mRNA libraries for a variety of organisms with cap 0 mRNA ends, including diverse plants, fungi and eukaryotic microbes.

Potential Contribution of Coastal Upwelling to Carbon Sink through Interaction between Cyanobacteria and Microbial Eukaryotes

Upwelling, a common oceanographic event, can make great contributions, directly or indirectly, to deep ocean carbon sequestration. However, the extent of its contribution indirectly depends on the composition of microbial communities and the interactions between bacterioplankton and other microorganisms. This study provides insights into the influence of upwelling on bacterioplankton at the whole community level and predicts their potential functional profiles. The α diversity of the bacterial community exhibited no significant differences between the upwelling area and non-upwelling area, while the community composition varied clearly in different habitats. Proteobacteria, Cyanobacteria, Bacteroidota, Firmicutes, and Actinobacteria were the five dominant phyla in all of the habitats. The proportions of members of Firmicutes were increased whereas Cyanobacteria were reduced in upwelling water. However, the percentage of Cyanobacteria was enhanced in the upwelling deep water. Functional genes that are involved in signal transductions, which belong to environmental information processing, were more active in upwelling surface water than in the other habitats. Closer and more complex relationships between bacterioplankton and microbial eukaryotes were found in the upwelling area, which altered with the variation of the external environmental conditions. Cyanobacteria showed a positive correlation with microbial eukaryotes in upwelling deep water. Combined with the high proportions of Cyanobacteria in upwelling deep water, this might be strong evidence that Cyanobacteria contribute to a deep ocean carbon sink. Overall, our study reveals the impacts of upwelling on the bacterial community composition, metabolic functions, and microbial interactions, which are significant to further understanding the carbon sink effects of upwelling.

DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes.

DNA extraction and preservation bias is a recurring topic in DNA sequencing‐based microbial ecology. The different methodologies can lead to distinct outcomes, which has been demonstrated especially in studies investigating prokaryotic community composition. Eukaryotic microbes are ubiquitous, diverse, and increasingly a subject of investigation in addition to bacteria and archaea. However, little is known about how the choice of DNA preservation and extraction methodology impacts perceived eukaryotic community composition. In this study, we compared the effect of two DNA preservation methods and six DNA extraction methods on the community profiles of both eukaryotes and prokaryotes in phototrophic biofilms on seagrass (Zostera marina) leaves from the Baltic Sea. We found that, whereas both DNA preservation and extraction method caused significant bias in perceived community composition for both eukaryotes and prokaryotes, extraction bias was more pronounced for eukaryotes than for prokaryotes. In particular, soft‐bodied and hard‐shelled eukaryotes like nematodes and diatoms, respectively, were differentially abundant depending on the extraction method. We conclude that careful consideration of DNA preservation and extraction methodology is crucial to achieving representative community profiles of eukaryotes in marine biofilms and likely all other habitats containing diverse eukaryotic microbial communities.

Does filter pore size introduce bias in DNA sequence-based plankton community studies?

The cell size of microbial eukaryotic plankton normally ranges from 0.2 to 200 μm. During the past decade, high-throughput sequencing of DNA has been revolutionizing their study on an unprecedented scale. Nonetheless, it is currently unclear whether we can accurately, effectively, and quantitatively depict the microbial eukaryotic plankton community using size-fractionated filtration combined with environmental DNA (eDNA) molecular methods. Here we assessed the microbial eukaryotic plankton communities with two filtering strategies from two subtropical reservoirs, that is one-step filtration (0.2–200 μm) and size-fractionated filtration (0.2–3 and 3–200 μm). The difference of 18S rRNA gene copy abundance between the two filtering treatments was less than 50% of the 0.2–200 μm microbial eukaryotic community for 95% of the total samples. Although the microbial eukaryotic plankton communities within the 0.2–200 μm and the 0.2–3 and 3–200 μm size fractions had approximately identical 18S rRNA gene copies, there were significant differences in their community composition. Furthermore, our results demonstrate that the systemic bias introduced by size-fractionation filtration has more influence on unique OTUs than shared OTUs, and the significant differences in abundance between the two eukaryotic plankton communities largely occurred in low-abundance OTUs in specific seasons. This work provides new insights into the use of size-fractionation in molecular studies of microbial eukaryotes populating the plankton.

Using average nucleotide identity (ANI) to evaluate microsporidia species boundaries based on their genetic relatedness.

Microsporidia are obligatory intracellular parasites related to fungi and since their discovery their classification and origin has been controversial due to their unique morphology. Early taxonomic studies of microsporidia were based on ultrastructural spore features, characteristics of their life cycle and transmission modes. However, taxonomy and phylogeny based solely on these characteristics can be misleading. SSU rRNA is a traditional marker used in taxonomical classifications, but the power of SSU rRNA to resolve phylogenetic relationships between microsporidia is considered weak at the species level, as it may not show enough variation to distinguish closely related species. Overall genome relatedness indices (OGRI), such as average nucleotide identity (ANI), allows fast and easy-to-implement comparative measurements between genomes to assess species boundaries in prokaryotes, with a 95% cutoff value for grouping genomes of the same species. Due to the increasing availability of complete genomes, metrics of genome relatedness have been applied for eukaryotic microbes taxonomy such as microsporidia. However, the distribution of ANI values and cutoff values for species delimitation have not yet been fully tested in microsporidia. In this study we examined the distribution of ANI values for 65 publicly available microsporidian genomes and tested whether the 95% cutoff value is a good estimation for circumscribing species based on their genetic relatedness.

More than just hitchhikers: a survey of bacterial communities associated with diatoms originating from sea turtles.

Diatoms and bacteria are known for being the first colonizers of submerged surfaces including the skin of marine reptiles. Sea turtle carapace and skin harbor diverse prokaryotic and eukaryotic microbes, including several epizoic diatoms. However, the importance of diatom-bacteria associations is hardly investigated in biofilms associated with animal hosts. This study provides an inventory of diatoms, bacteria and diatom-associated bacteria originating from loggerhead sea turtles using both metabarcoding and culturing approaches. Amplicon sequencing of the carapace and skin samples chloroplast gene rbcL and 16S rRNA gene detected, in total, 634 diatom amplicon sequence variants (ASVs) and 3661 bacterial ASVs, indicating high diversity. Cultures of putative epizoic and non-epizoic diatoms contained 458 bacterial ASVs and their bacterial assemblages reflected those of their host. Diatom strains allowed for enrichment and isolation of bacterial families rarely observed on turtles, such as Marinobacteraceae, Alteromonadaceae and Alcanivoracaceae. When accounting for phylogenetic relationships between bacterial ASVs, we observed that related diatom genera might retain similar microbial taxa in culture, regardless of the turtle's skin or carapace source. These data provide deeper insights into the sea turtle-associated microbial communities, and reveal the potential of epizoic biofilms as a source of novel microbes and possibly important diatom-bacteria associations.

Interactions between bacteria and eukaryotic microorganisms and their response to soil properties and heavy metal exchangeability nearby a coal-fired power plant.

Persistent heavy metal (HM) contaminated soil provides special habitat for microorganisms, HM stress and complex abiotic factors bring great uncertainty for the development of bacteria and eukaryotic microbes. Despite numerous studies about HMs' effect on soil microorganisms, the key factors affecting microbial communities in severe HM contaminated soil and their interactions are still not definite. In this study, the effect of HM fractions and soil properties on the interaction between bacterial communities and eukaryotic microorganisms was studied by high-throughput Illumina sequencing and simplified continuous extraction of HM in severe HM contaminated soil. Based on amplification and sequencing of the 18S rRNA gene, this study revealed that protists and algae were the most predominant eukaryotic microorganisms, and the dominant phyla were SAR, Opisthokonta and Archaeplastida in HM seriously polluted soil. These results also showed that exchangeable As was negatively correlated with bacterial Shannon and Simpson indexes, while exchangeable Zn was positively correlated with Shannon and Simpson indexes of eukaryotic microbes. Moreover, the structural equation model illustrated that pH, moisture content, available potassium and phosphorus, and exchangeable Cd, As and Zn were the dominant factors shaping bacterial communities, while total organic carbon and exchangeable Zn made the predominant contributions to variations in eukaryotic microbes. In addition, eukaryotic microbes were intensely affected by the bacterial communities, with a standardized regression weight of 0.53, which exceeded the influence of other abiotic factors. It was suggested that community-level adaptions through cooperative interactions under serious HM stress in soil.

Genome-powered classification of microbial eukaryotes: focus on coral algal symbionts.

Modern microbial taxonomy generally relies on the use of single marker genes or sets of concatenated genes to generate a framework for the delineation and classification of organisms at different taxonomic levels. However, given that DNA is the 'blueprint of life', and hence the ultimate arbiter of taxonomy, classification systems should attempt to use as much of the blueprint as possible to capture a comprehensive phylogenetic signal. Recent analysis of whole-genome sequences from coral reef symbionts (dinoflagellates of the family Symbiodiniaceae) and other microalgal groups has uncovered extensive divergence not recognised by current algal taxonomic approaches. In the era of 'sequence everything', we argue that whole-genome data are pivotal to guide informed taxonomic inference, particularly for microbial eukaryotes.

Foraminifera as a model of the extensive variability in genome dynamics among eukaryotes.

Knowledge of eukaryotic life cycles and associated genome dynamics stems largely from research on animals, plants, and a small number of "model" (i.e., easily cultivable) lineages. This skewed sampling results in an underappreciation of the variability among the many microeukaryotic lineages, which represent the bulk of eukaryotic biodiversity. The range of complex nuclear transformations that exists within lineages of microbial eukaryotes challenges the textbook understanding of genome and nuclear cycles. Here, we look in-depth at Foraminifera, an ancient (∼600million-year-old) lineage widely studied as proxies in paleoceanography and environmental biomonitoring. We demonstrate that Foraminifera challenge the "rules" of life cycles developed largely from studies of plants and animals. To this end, we synthesize data on foraminiferal life cycles, focusing on extensive endoreplication within individuals (i.e., single cells), the unusual nuclear process called Zerfall, and the separation of germline and somatic function into distinct nuclei (i.e., heterokaryosis). These processes highlight complexities within lineages and expand our understanding of the dynamics of eukaryotic genomes.

Total RNA sequencing of Phlebotomus chinensis sandflies in China revealed viral, bacterial, and eukaryotic microbes potentially pathogenic to humans

ABSTRACT Phlebotomus chinensis sandfly is a neglected insect vector in China that is well-known for carrying Leishmania. Recent studies have expanded its pathogen repertoire with two novel arthropod-borne phleboviruses capable of infecting humans and animals. Despite these discoveries, our knowledge of the general pathogen diversity and overall microbiome composition of this vector species is still very limited. Here we carried out a meta-transcriptomics analysis that revealed the actively replicating/transcribing RNA viruses, DNA viruses, bacteria, and eukaryotic microbes, namely, the “total microbiome”, of several sandfly populations in China. Strikingly, “microbiome” made up 1.8% of total non-ribosomal RNA and comprised more than 87 species, among which 70 were novel, including divergent members of the genera Flavivirus and of the family Trypanosomatidae. Importantly, among these microbes we were able to reveal four distinguished types of human and/or mammalian pathogens, including two phleboviruses (hedi and wuxiang viruses), one novel Spotted fever group rickettsia, as well as a member of Leishmania donovani complex, among which hedi virus and Leishmania each had > 50% pool prevalence rate and relatively high abundance levels. Our study also showed the ubiquitous presence of an endosymbiont, namely Wolbachia, although no anti-viral or anti-pathogen effects were detected based on our data. In summary, our results uncovered the much un-explored diversity of microbes harboured by sandflies in China and demonstrated that high pathogen diversity and abundance are currently present in multiple populations, implying disease potential for exposed local human population or domestic animals.

Vegetation drives the response of the active fraction of the rhizosphere microbial communities to soil warming in Antarctic vascular plants.

In the Antarctic Peninsula, increases in mean annual temperature are associated with the coverage and population density of the two Antarctic vascular plant species-Deschampsia antarctica and Colobanthus quitensis-potentially modifying critical soil processes. In this study, we characterized the diversity and community composition of active microorganisms inhabiting the vascular plant rhizosphere in two sites with contrasting vegetation cover in King George Island, Western Antarctic Peninsula. We assessed the interplay between soil physicochemical properties and microbial diversity and composition, evaluating the effect of an in situ experimental warming on the microbial communities of the rhizosphere from D. antarctica and C. quitensis. Bacteria and Eukarya showed different responses to warming in both sites, and the effect was more noticeable in microbial eukaryotes from the low vegetation site. Furthermore, important changes were found in the relative abundance of Tepidisphaerales (Bacteria) and Ciliophora (Eukarya) between warming and control treatments. Our results showed that rhizosphere eukaryal communities are more sensitive to in situ warming than bacterial communities. Overall, our results indicate that vegetation drives the response of the active fraction of the microbial communities from the rhizosphere of Antarctic vascular plants to soil warming.

Genomic diversity and biosynthetic capabilities of sponge-associated chlamydiae

Sponge microbiomes contribute to host health, nutrition, and defense through the production of secondary metabolites. Chlamydiae, a phylum of obligate intracellular bacteria ranging from animal pathogens to endosymbionts of microbial eukaryotes, are frequently found associated with sponges. However, sponge-associated chlamydial diversity has not yet been investigated at the genomic level and host interactions thus far remain unexplored. Here, we sequenced the microbiomes of three sponge species and found high, though variable, Chlamydiae relative abundances of up to 18.7% of bacteria. Using genome-resolved metagenomics 18 high-quality sponge-associated chlamydial genomes were reconstructed, covering four chlamydial families. Among these, Candidatus Sororchlamydiaceae shares a common ancestor with Chlamydiaceae animal pathogens, suggesting long-term co-evolution with animals. Based on gene content, sponge-associated chlamydiae resemble members from the same family more than sponge-associated chlamydiae of other families, and have greater metabolic versatility than known chlamydial animal pathogens. Sponge-associated chlamydiae are also enriched in genes for degrading diverse compounds found in sponges. Unexpectedly, we identified widespread genetic potential for secondary metabolite biosynthesis across Chlamydiae, which may represent an unexplored source of novel natural products. This finding suggests that Chlamydiae members may partake in defensive symbioses and that secondary metabolites play a wider role in mediating intracellular interactions. Furthermore, sponge-associated chlamydiae relatives were found in other marine invertebrates, pointing towards wider impacts of the Chlamydiae phylum on marine ecosystems.

Assessment of biological community in riparian zone contaminated by PAHs: Linking source apportionment to biodiversity

Riparian zone, an important land-water interface, plays an essential role in maintaining the ecological health of rivers, whereas the effects of Polycyclic aromatic hydrocarbons (PAHs) on the health of biological communities in riparian groundwater remain undetermined. To understand the responses of multiple communities to environmental variables, the distribution and ecosystem risk of 16 PAHs have been investigated in the Beiluo River, China. The distribution of multiple communities in riparian groundwater was investigated by environmental DNA metabarcoding, including 16S rRNA, 18S rRNA, and COI gene sequencing for bacteria, microbial eukaryotes (including algae, fungi, and protozoa), and metazoan, respectively, followed by correlation analysis between multiple communities and PAH contamination levels. The concentration of PAHs in the Beiluo River ranged largely from 35.32 to 728.59 ng/L. Here, the Shannon's diversity index of bacteria (Firmicutes) decreased possibly due to the occurrence of Pyrene, which mainly derives from coal and biomass combustion. Furthermore, the reduced richness of fungi (Ascomycota, Basidiomycota) and algae (Chlorophyta, Chrysophyceae) can be attributed to the presence of medium molecular weight (MMW) PAHs (Pyrene, Benz(a)anthracene, Chrysene), and low molecular weight (LMW) PAHs (Naphthalene, Fluorene, Phenanthrene). The richness and Shannon's diversity index of metazoan (Arthropoda) were promoted owing to MMW PAHs (Chrysene, Fluoranthene) generated from coal and biomass combustion and traffic emission. The ecological risk of PAHs in the groundwater environment of the Beiluo River was characterized as low to medium, where LMW and MMW PAHs posed higher risk than the high molecular weight (HMW) compounds. Overall, this study provides insights into the structures of riparian multi-biological communities altered by PAHs.

FreshOmics: A manually curated and standardized -omics database for investigating freshwater microbiomes.

Freshwater is a critical resource for human survival but severely threatened by anthropogenic activities and climate change. These changes strongly impact the abundance and diversity of the microbial communities which are key players in the functioning of these aquatic ecosystems. Although widely documented since the emergence of high-throughput sequencing approaches, the information on these natural microbial communities is scattered among thousands of publications and it is therefore difficult to investigate the temporal dynamics and the spatial distribution of microbial taxa within or across ecosystems. To fill this gap and in the FAIR principles context we built a manually curated and standardized microbial freshwater -omics database (FreshOmics). Based on recognized ontologies (ENVO, MIMICS, GO, ISO), FreshOmics describes 29 different types of freshwater ecosystems and uses standardized attributes to depict biological samples, sequencing protocols and article attributes for more than 2487 geographical locations across 71 countries around the world. The database contains 24,808 sequence identifiers (i.e., Run_Id / Exp_ID, mainly from SRA/DDBJ SRA/ENA, GSA and MG-RAST repositories) covering all sequence-based -omics approaches used to investigate bacteria, archaea, microbial eukaryotes, and viruses. Therefore, FreshOmics allows accurate and comprehensive analyses of microbial communities to answer questions related to their roles in freshwater ecosystems functioning and resilience, especially through meta-analysis studies. This collection also highlights different sort of errors in published works (e.g., wrong coordinates, sample type, material, spelling).