Eukaryotic molecular diversity at different steps of the wastewater treatment plant process reveals more phylogenetic novel lineages

Quantification of the dark fungal taxon Cryptomycota using qPCR

Fungi are present in a wide variety of natural environments, and in the last years, various studies have shown that they are quite abundant in aquatic ecosystems. In addition, a whole new highly diverse phylum, the Cryptomycota, was discovered. Nevertheless, research on aquatic fungi and a detailed evaluation of their functions and distribution are still sparse. One of the main reasons is a limitation in reliable identification and quantification methods. To bridge part of the research gap, this study aims to implement a quantitative PCR method to detect and quantify the newly discovered phylum. We developed and validated a Cryptomycota-specific qPCR primer pair targeting the 5.8S region that detects the majority of Cryptomycota, but Microsporidia. The resulting amplicon is 102 bp long. We used different environmental samples to evaluate the primer pair, various fungal sequences as negative control and positive control sequences. Obtained amplicons were sequenced using Illumina, and the obtained ASVs were all classified as Cryptomycota. The qPCR method works reliably and specifically for the quantification of Cryptomycota in environmental samples.

Metabarcoding and Metabolomics Reveal the Effect of the Invasive Alien Tree Miconia calvescens DC. on Soil Diversity on the Tropical Island of Mo'orea (French Polynesia)

Miconia calvescens is a dominant invasive alien tree species that threatens several endemic plants in French Polynesia (South Pacific). While most analyses have been performed at the scale of plant communities, the effects on the rhizosphere have not been described so far. However, this compartment can be involved in plant fitness through inhibitory activities, nutritive exchanges, and communication with other organisms. In particular, it was not known whether M. calvescens forms specific associations with soil organisms or has a specific chemical composition of secondary metabolites. To tackle these issues, the rhizosphere of six plant species was sampled on the tropical island of Mo'orea in French Polynesia at both the seedling and tree stages. The diversity of soil organisms (bacteria, microeukaryotes, and metazoa) and of secondary metabolites was studied using high-throughput technologies (metabarcoding and metabolomics, respectively). We found that trees had higher effects on soil diversity than seedlings. Moreover, M. calvescens showed a specific association with microeukaryotes of the Cryptomycota family at the tree stage. This family was positively correlated with the terpenoids found in the soil. Many terpenoids were also found within the roots of M. calvescens, suggesting that these molecules were probably produced by the plant and favored the presence of Cryptomycota. Both terpenoids and Cryptomycota were thus specific chemicals and biomarkers of M. calvescens. Additional studies must be performed in the future to better understand if they contribute to the success of this invasive tree.

Fate of Functional Bacterial and Eukaryotic Community Regulated by Earthworms during Vermicomposting of Dewatered Sludge, Studies Based on the 16S rDNA and 18S rDNA Sequencing of Active Cells

DNA sequencing of active cells involved in vermicomposting can clarify the roles of earthworms in regulating functional microorganisms. This study aimed to investigate the effect of earthworms on functional microbial communities in sludge by comparing biodegradation treatments with and without earthworms. PCR and high throughput sequencing based on pretreatment of propidium monoazide (PMA) were used to detect the changes in active bacterial 16S rDNA and eukaryotic 18S rDNA during vermicomposting. The results showed that the nitrate in sludge vermicomposting and control were significantly different from day 10, with a more stable product at day 30 of vermicomposting. Compared with the control, the Shannon indexes of active bacteria and eukaryotes decreased by 1.9% and 31.1%, respectively, in sludge vermicompost. Moreover, Proteobacteria (36.2%), Actinobacteria (25.6%), and eukaryotic Cryptomycota (80.3%) were activated in the sludge vermicompost. In contrast, the control had Proteobacteria (44.8%), Bacteroidetes (14.2%), Cryptomycota (50.00%), and Arthropoda (36.59%). Network analysis showed that environmental factors had different correlations between active bacterial and eukaryotic community structures. This study suggests that earthworms can decrease the diversity of bacterial and eukaryotic communities, forming a specific-functional microbial community and thus accelerating organic matter decomposition during vermicomposting of dewatered sludge.

The wastewater protist Rhogostoma minus (Thecofilosea, Rhizaria) is abundant, widespread, and hosts Legionellales

Wastewater is treated by concerted actions of the microbial communities within bioreactors. Although protists (unicellular eukaryotes) are good bioindicators and important players influencing denitrification, nitrification, and flocculation, they are the least known organisms in WWTPs. The few recent environmental surveys of the protistan diversity in WWTPs show that the most abundant protistan sequences in WWTPs belong to Thecofilosea (Rhizaria). We re-investigated previously published environmental sequencing data and gathered strains from seven WWTPs to determine which species dominate WWTPs worldwide. We found that all highly abundant thecofilosean sequences represent a single species - Rhogostoma minus. Considering that Thecofilosea are frequent hosts for Legionellales, i.e. bacteria linked to waterborne diseases, we confirm that Rhogostoma minus functions as a host for Legionellales in WWTPs. Whether the highly abundant Rhogostoma minus also serves as a host for known human pathogenic Legionellales requires further attention.

Salinity is the major driver of the global eukaryotic community structure in fish-canning wastewater treatment plants

Fish-canning wastewater is characterized frequently by a high content of salt (NaCl), making its treatment particularly difficult; however, the knowledge of the effect of NaCl on eukaryotic communities is very limited. In the present study, the global diversity of eukaryotes in activated sludges (AS) from 4 different wastewater treatment plants (WWTPs) treating fish-canning effluents varying in salinity (0.47, 1.36, 1.72 and 12.76 g NaCl/L) was determined by sequencing partial 18S rRNA genes using Illumina MiSeq. A greater diversity than previously reported was observed in the AS community, which comprised 37 and 330 phylum-like and genera-like groups, respectively. In this sense, the more abundant genus-like groups (average relative abundance (RA) > 5%) were Adineta (6.80%), Lecane (16.80%), Dictyostelium (7.36%), Unclassified_Fungi7 (6.94%), Procryptobia (5.13) and Oocystis (5.07%). The eukaryotic communities shared a common core of 25 phylum-like clades (95% of total sequences); therefore, a narrow selection of the eukaryotic populations was found, despite the differences in the abiotic characteristics of fish-canning effluents and reactor operational conditions inflicted. The differences in NaCl concentration were the main factor that influenced the structure of the eukaryotic community, modulating the RAs of the different phylum-like clades of the common core. Higher levels of salt increased the RAs of Ascomycota, Chlorophyta, Choanoflagellata, Cryptophyta, Mollusca, Nematoda, Other Protists and Unclassified Fungi. Among the different eukaryotic genera here found, the RA of Oocystis (Chlorophyta) was intimately correlated to increasing NaCl concentrations and it is proposed as a bioindicator of the global eukaryotic community of fish-canning WWTPs.

Specificity of RNA Folding and Its Association with Evolutionarily Adaptive mRNA Secondary Structures

The secondary structure is a fundamental feature of both noncoding and messenger RNAs. However, our understanding of the secondary structure of mRNA, especially that of the coding regions, remains elusive, likely due to translation and the lack of RNA-binding proteins that sustain the consensus structure, such as those that bind to noncoding RNA. Indeed, mRNA has recently been found to adopt diverse alternative structures, the overall functional significance of which remains untested. We hereby approached this problem by estimating the folding specificity, i.e., the probability that a fragment of RNA folds back to the same partner once refolded. We showed that the folding specificity of mRNA is lower than that of noncoding RNA and exhibits moderate evolutionary conservation. Notably, we found that specific rather than alternative folding is likely evolutionarily adaptive since specific folding is frequently associated with functionally important genes or sites within a gene. Additional analysis in combination with ribosome density suggests the ability to modulate ribosome movement as one potential functional advantage provided by specific folding. Our findings revealed a novel facet of the RNA structurome with important functional and evolutionary implications and indicated a potential method for distinguishing the mRNA secondary structures maintained by natural selection from molecular noise.

Clarifying prokaryotic and eukaryotic biofilm microbiomes in anaerobic membrane bioreactor by non-destructive microscopy and high-throughput sequencing

Anaerobic membrane bioreactor (AnMBR) is used for the treatment of organic solid waste. Clogging of filtration membrane pores, called membrane fouling, is one of the most serious issues for the sustainable operation of AnMBR. Although the physical and chemical mechanisms of the membrane fouling have been widely studied, the biological mechanisms are still unclear. The biofilm formation and development on the membrane might cause the membrane fouling. In this study, the prokaryotic and eukaryotic microbiomes of the membrane-attached biofilms in an AnMBR treating a model slurry of organic solid waste were investigated by non-destructive microscopy and high-throughput sequencing of 16S and 18S rRNA genes. The non-destructive visualization indicated that the biofilm was layered with different structures. The lowermost residual fouling layer was mesh-like and composed of filamentous microorganisms, while the upper cake layer was mainly the non-dense and non-cell region. The principal coordinate and phylogenetic analyses of the sequence data showed that the biofilm microbiomes were different from the sludge. The lowermost layer consisted of operational taxonomic units that were related to Leptolinea tardivitalis and Methanosaeta concilii (9.53-10.07% and 1.14-1.64% of the total prokaryotes, respectively) and Geotrichum candidum (30.22-82.31% of the total eukaryotes), all of which exhibited the filamentous morphology. Moreover, the upper layer was inhabited by the presumably cake-degrading bacteria and predatory eukaryotes. The biofilm microbiome features were consistent with the microscope-visualized structure. These results demonstrated that the biofilm structure and microbiome were the layer specific, which provides better understanding of biological mechanisms of membrane fouling in the AnMBR.

Colonization kinetics and implantation follow-up of the sewage microbiome in an urban wastewater treatment plant

The Seine-Morée wastewater treatment plant (SM_WWTP), with a capacity of 100,000 population-equivalents, was fed with raw domestic wastewater during all of its start-up phase. Its microbiome resulted from the spontaneous evolution of wastewater-borne microorganisms. This rare opportunity allowed us to analyze the sequential microbiota colonization and implantation follow up during the start-up phase of this WWTP by means of regular sampling carried out over 8 months until the establishment of a stable and functional ecosystem. During the study, biological nitrification–denitrification and dephosphatation occurred 68 days after the start-up of the WWTP, followed by flocs decantation 91 days later. High throughput sequencing of 18S and 16S rRNA genes was performed using Illumina's MiSeq and PGM Ion Torrent platforms respectively, generating 584,647 16S and 521,031 18S high-quality sequence rDNA reads. Analyses of 16S and 18S rDNA datasets show three colonization phases occurring concomitantly with nitrification, dephosphatation and floc development processes. Thus, we could define three microbiota profiles that sequentially colonized the SM_WWTP: the early colonizers, the late colonizers and the continuous spectrum population. Shannon and inverse Simpson diversity indices indicate that the highest microbiota diversity was reached at days 133 and 82 for prokaryotes and eukaryotes respectively; after that, the structure and complexity of the wastewater microbiome reached its functional stability. This study demonstrates that physicochemical parameters and microbial metabolic interactions are the main forces shaping microbial community structure, gradually building up and maintaining a functionally stable microbial ecosystem.

Fungi in aquatic ecosystems

Fungi are phylogenetically and functionally diverse ubiquitous components of almost all ecosystems on Earth, including aquatic environments stretching from high montane lakes down to the deep ocean. Aquatic ecosystems, however, remain frequently overlooked as fungal habitats, although fungi potentially hold important roles for organic matter cycling and food web dynamics. Recent methodological improvements have facilitated a greater appreciation of the importance of fungi in many aquatic systems, yet a conceptual framework is still missing. In this Review, we conceptualize the spatiotemporal dimensions, diversity, functions and organismic interactions of fungi in structuring aquatic food webs. We focus on currently unexplored fungal diversity, highlighting poorly understood ecosystems, including emerging artificial aquatic habitats.

Performance and microbial community structure of an aerobic granular sludge system at different phenolic acid concentrations

The present work aims to use aerobic granular sludge technology for the treatment of wastewater containing high organic matter loads and a mixture of phenolic compounds normally present in olive washing water. The physicochemical performance of five bioreactors treating different concentrations of mixture of phenolic acid was monitored to observe the response of the systems. The bioreactors that operated at 50, 100 and 300 mg L^-1 did not show relevant changes in terms of performance and granules properties, showing high ratio of phenolic compound removal ratio. However, the bioreactors operated with high phenolic compound concentrations showed low rates of organic matter, nitrogen and phenolic acid removal. In the same way, high concentrations of phenolic compounds determined the disintegration of the granular biomass. Next-generation sequencing studies showed a stable community structure in the bioreactors operating with 50, 100 and 300 mg L^-1 of phenolic acids, with the genera Lampropedia and Arenimonas, family Xanthobacteraceae and Fungi Pezizomycotina as the dominant phylotypes. Conversely, the reactors operated at 500 and 600 mg L^-1 of phenolic substances promoted the proliferation of Oligohymenophorea ciliates. Thus, this study suggests that aerobic granular sludge technology could be useful for the treatment of wastewaters such as olive washing water.

Acetate promotes microbial reductive debromination of tetrabromobisphenol A during the startup phase of anaerobic wastewater sludge bioreactors

The detection of increasing concentrations of tetrabromobisphenol A (TBBPA) in wastewater treatment plants is raising concerns as TBBPA has been identified as a potentially toxic flame retardant. The objectives of this study were to evaluate the effect of acetate biostimulation on TBBPA microbial reductive debromination, and the response of anaerobic sludge associated microbial communities repeatedly exposed to TBBPA. Results indicate that the bulk of the microbial community did not experience significant shifts as a result of TBBPA exposure, and that only a small fraction of the community responded to the presence of TBBPA. Taxa most likely responsible for TBBPA transformation affiliated to Clostridiales and the wastewater sludge group Blvii28. The biostimulating effect of acetate was only observed during reactor startup, when acetogenesis was likely not yet occurring. However, when acetate likely started to be microbially generated in the reactor, acetate addition resulted in a slight but significant inhibiting effect on TBBPA transformation. A significant increase of hydrogenotrophic methanogens in the TBBPA-spiked reactor overtime implies that TBBPA degraders were not in direct competition with methanogens for H₂. These results strongly suggest that TBBPA degrading taxa might have been primarily using acetate as an electron donor for the reductive debromination of TBBPA.

Pinning down the role of common luminal intestinal parasitic protists in human health and disease - status and challenges

While some single-celled intestinal parasites are direct causes of diarrhoea and other types of intestinal pathology, the impact of other gut micro-eukaryotes on human health remains elusive. The fact that some common luminal intestinal parasitic protists (CLIPPs) have lately been found more often in healthy than in diseased individuals has fuelled the hypothesis that some parasites might in fact be protective against disease. To this end, the use of new DNA technologies has helped us investigate trans-kingdom relationships in the gut. However, research into these relationships is currently hampered by the limited data available on the genetic diversity within the CLIPPs genera, which results in limited efficacy of publicly available DNA sequence databases for taxonomic annotation of sequences belonging to the eukaryotic component of the gut microbiota. In this paper, I give a brief overview of the status on CLIPPs in human health and disease and challenges related to the mapping of intestinal eukaryotic diversity of the human gut.