Identification of plastic-associated species in the Mediterranean Sea using DNA metabarcoding with Nanopore MinION

Metagenomic analysis of soil from landfill site reveals a diverse microbial community involved in plastic degradation

In this study, we have investigated microbial communities structure and function using high throughput amplicon sequencing and whole metagenomic sequencing of DNA extracted from different depths of a plastic-laden landfill site. With diverse taxonomic groups inhabiting the plastic-rich soil, our study demonstrates the remarkable adaptability of microbes to use this new substrate as a carbon source. FTIR spectroscopic analysis of soil indicated degradation of plastic as perceived from the carbonyl index of 0.16, 0.72, and 0.44 at 0.6, 0.9 and 1.2 m depth, respectively. Similarly, water contact angles of 108.7 degree, 99.7 degree, 62.7 degree, and 77.8 degree of plastic pieces collected at 0.3, 0.6, 0.9, and 1.2 m depths respectively showed increased wettability and hydrophilicity of the plastic. Amplicon analysis of 16S and 18 S rRNA revealed a high abundance of several plastic-degrading bacterial groups, including Pseudomonas, Rhizobiales, Micrococcaceae, Chaetomium, Methylocaldum, Micromonosporaceae, Rhodothermaceae and fungi, including Trichoderma, Aspergillus, Candida at 0.9 m. The co-existence of specific microbial groups at different depths of landfill site indicates importance of bacterial and fungal interactions for plastic. Whole metagenome analysis of soil sample at 0.9 m depth revealed a high abundance of genes encoding enzymes that participate in the biodegradation of PVC, polyethylene, PET, and polyurethane. Curation of the pathways related to the degradation of these materials provided a blueprint for plastic biodegradation in this ecosystem. Altogether, our study has highlighted the importance of microbial cooperation for the biodegradation of pollutants. Our metagenome-based investigation supports the current perception that consortia of fungi-bacteria are preferable to axenic cultures for effective bioremediation of the environment.

Zooming in the plastisphere: the ecological interface for phytoplankton-plastic interactions in aquatic ecosystems

Phytoplankton is an essential resource in aquatic ecosystems, situated at the base of aquatic food webs. Plastic pollution can impact these organisms, potentially affecting the functioning of aquatic ecosystems. The interaction between plastics and phytoplankton is multifaceted: while microplastics can exert toxic effects on phytoplankton, plastics can also act as a substrate for colonisation. By reviewing the existing literature, this study aims to address pivotal questions concerning the intricate interplay among plastics and phytoplankton/phytobenthos and analyse impacts on fundamental ecosystem processes (e.g. primary production, nutrient cycling). This investigation spans both marine and freshwater ecosystems, examining diverse organisational levels from subcellular processes to entire ecosystems. The diverse chemical composition of plastics, along with their variable properties and role in forming the "plastisphere", underscores the complexity of their influences on aquatic environments. Morphological changes, alterations in metabolic processes, defence and stress responses, including homoaggregation and extracellular polysaccharide biosynthesis, represent adaptive strategies employed by phytoplankton to cope with plastic-induced stress. Plastics also serve as potential habitats for harmful algae and invasive species, thereby influencing biodiversity and environmental conditions. Processes affected by phytoplankton-plastic interaction can have cascading effects throughout the aquatic food web via altered bottom-up and top-down processes. This review emphasises that our understanding of how these multiple interactions compare in impact on natural processes is far from complete, and uncertainty persists regarding whether they drive significant alterations in ecological variables. A lack of comprehensive investigation poses a risk of overlooking fundamental aspects in addressing the environmental challenges associated with widespread plastic pollution.

Identification of phytoplankton isolates from the eastern Canadian waters using long-read sequencing

As important primary producers and key components of biogeochemical processes, phytoplankton communities are highly diverse and continually adapt to changes in the environment, impacting the entire marine ecosystem. Consequently, it remains important to isolate, culture and properly describe new phytoplankton strains to provide relevant model organisms for laboratory research and accurate reference sequences for identification. Here, 73 phytoplankton strains from the eastern Canadian waters were isolated and genetically characterized using a long rRNA fragment (~4000 bp) covering the 18S, ITS and 28S rRNA regions generated with long-read sequencing technology. While most strains (66%) were accurately identified using the partial 18S rRNA gene (~1200 bp-V4-V9), this study broadens the current 28S rRNA reference database by incorporating 41 distinct strains including 30 unique species. In addition, previously unpublished long-read reference sequences were generated for a few genera, including Picochlorum and Droopiella. Species that were previously poorly described in the eastern Canadian waters were also genetically characterized, including a Chaetoceros similis strain. Overall, this work expands the total number of long-read references, an essential resource for accurate identification of phytoplankton and environmental sequences, thereby advancing the taxonomic resolution that could lead to a better understanding of environmental microbial diversity.

Community composition and seasonal dynamics of microplastic biota in the Eastern Mediterranean Sea

Marine plastic pollution poses a growing environmental threat, with microplastics accumulating in the global oceans. This study profiles the seasonal dynamics and taxonomic composition of the plastisphere, the microplastic ecosystem, in the Eastern Mediterranean Sea. Using long-read 16 S and 18 S metabarcoding, we analyzed offshore microplastic and whole seawater samples across each season over a two-year period. The analysis revealed a higher richness of prokaryotic communities on microplastics compared to seawater, which was predominantly composed of Proteobacteria and Bacteroidota and exhibited notable seasonal variability. Benthic eukaryotes were enriched on microplastics compared to the surrounding seawater. Diatoms (Bacillariophyceae), in particular, showed significant enrichment within the microplastic eukaryotic community with primarily pennate diatoms of Amphora, Navicula, and Nitzschia genera, whereas the seawater included mostly centric diatoms. Seasonal fluctuations were less pronounced in the microplastic communities than in seawater, highlighting the relative stability of this new human-made ecosystem. These findings underscore the unique ecological niche of microplastic-associated communities in marine environments.

What Quality Suffices for Nanopore Metabarcoding? Reconsidering Methodology and Ectomycorrhizae in Decaying Fagus sylvatica Bark as Case Study

Nanopore raw read accuracy has improved to over 99%, making it a potential tool for metabarcoding. For broad adoption, guidelines on quality filtering are needed to ensure reliable taxonomic unit recovery. This study aims to provide those guidelines for a fungal metabarcoding context and to apply them to a case study of ectomycorrhizae in the decaying bark of Fagus sylvatica. We introduce the eNano pipeline to test two standard metabarcoding approaches: (1) Reference-based mapping leveraging UNITE's species hypothesis system (SH approach); (2) Constructing 98% OTUs (OTU approach). Our results demonstrate that both approaches are effective with Nanopore data. When using a reference database, we recommend strict mapping criteria rather than Phred-based filtering. Leveraging the SH-system further enhances reproducibility and facilitates cross-study communication. For the 98% OTUs, filtering reads at ≥Q25 is recommended. Our case study reveals that the decay gradient is a primary determinant of community composition and that specific mycorrhizal fungi colonize decaying bark. Complementing our metabarcoding results with root tip morphotypification, we identify Laccaria amethystina and Tomentella sublilacina as key ectomycorrhizae of saplings on decaying logs. These findings demonstrate that Nanopore sequencing can provide valuable ecological insights and support its broader use in fungal metabarcoding as read quality continues to improve.

Primed and ready: nanopore metabarcoding can now recover highly accurate consensus barcodes that are generally indel-free

BACKGROUND

DNA metabarcoding applies high-throughput sequencing approaches to generate numerous DNA barcodes from mixed sample pools for mass species identification and community characterisation. To date, however, most metabarcoding studies employ second-generation sequencing platforms like Illumina, which are limited by short read lengths and longer turnaround times. While third-generation platforms such as the MinION (Oxford Nanopore Technologies) can sequence longer reads and even in real-time, application of these platforms for metabarcoding has remained limited possibly due to the relatively high read error rates as well as the paucity of specialised software for processing such reads.

RESULTS

We show that this is no longer the case by performing nanopore-based, cytochrome c oxidase subunit I (COI) metabarcoding on 34 zooplankton bulk samples, and benchmarking the results against conventional Illumina MiSeq sequencing. Nanopore R10.3 sequencing chemistry and super accurate (SUP) basecalling model reduced raw read error rates to ~ 4%, and consensus calling with amplicon_sorter (without further error correction) generated metabarcodes that were ≤ 1% erroneous. Although Illumina recovered a higher number of molecular operational taxonomic units (MOTUs) than nanopore sequencing (589 vs. 471), we found no significant differences in the zooplankton communities inferred between the sequencing platforms. Importantly, 406 of 444 (91.4%) shared MOTUs between Illumina and nanopore were also found to be free of indel errors, and 85% of the zooplankton richness could be recovered after just 12-15 h of sequencing.

CONCLUSION

Our results demonstrate that nanopore sequencing can generate metabarcodes with Illumina-like accuracy, and we are the first study to show that nanopore metabarcodes are almost always indel-free. We also show that nanopore metabarcoding is viable for characterising species-rich communities rapidly, and that the same ecological conclusions can be obtained regardless of the sequencing platform used. Collectively, our study inspires confidence in nanopore sequencing and paves the way for greater utilisation of nanopore technology in various metabarcoding applications.

Phototrophs as the central components of the plastisphere microbiome in coastal environments

Upon entering the marine environment, plastics are colonized by a plethora of microorganisms to form a plastisphere, influencing the fate and transport of the plastic debris and the health of marine ecosystems. The assembly of marine plastisphere is generally believed to be dominated by stochastic processes. However, it remains elusive whether microbial interaction in the assembly of plastisphere microbial communities is conserved or not. We analyzed the plastisphere microbiomes of 137 plastic debris samples from intertidal zones at different geographical locations and habitats (seagrass, coral, mangrove, beach, and open ocean) and compared them with the surrounding sediment and seawater microbiomes. Microbial community structures of the plastisphere from different locations were more similar to each other but differed substantially from the surrounding sediment and water microbiomes, implying a common mechanism of plastisphere assembly. We used different machine learning algorithms (Multinomial Logistic Regression, Support Vector Machine, Decision Trees, Random Forest, and Artificial Neural Networks) to classify plastic debris samples with high sensitivity based on the microbiome composition. Eukaryotic and prokaryotic phototrophic organisms such as green algae, diatoms, and cyanobacteria, were found to be enriched on the plastic surfaces. Network analysis revealed the central role of the phototrophic organisms in the formation and sustenance of the plastispheres. We found that phototrophs served as core members interacting strongly with heterotrophic organisms in marine plastisphere, irrespective of the sampling location, habitats, and polymer types. This would explain the stochastic assembly of the plastisphere along with conserved properties driven by the phototrophs in the surrounding environment. Our results highlight the importance of phototrophic organisms in shaping the marine plastisphere microbial communities.

Biodegradation of polyethylene by the marine fungus Parengyodontium album

Plastic pollution in the marine realm is a severe environmental problem. Nevertheless, plastic may also serve as a potential carbon and energy source for microbes, yet the contribution of marine microbes, especially marine fungi to plastic degradation is not well constrained. We isolated the fungus Parengyodontium album from floating plastic debris in the North Pacific Subtropical Gyre and measured fungal-mediated mineralization rates (conversion to CO2) of polyethylene (PE) by applying stable isotope probing assays with 13C-PE over 9 days of incubation. When the PE was pretreated with UV light, the biodegradation rate of the initially added PE was 0.044 %/day. Furthermore, we traced the incorporation of PE-derived 13C carbon into P. album biomass using nanoSIMS and fatty acid analysis. Despite the high mineralization rate of the UV-treated 13C-PE, incorporation of PE-derived 13C into fungal cells was minor, and 13C incorporation was not detectable for the non-treated PE. Together, our results reveal the potential of P. album to degrade PE in the marine environment and to mineralize it to CO2. However, the initial photodegradation of PE is crucial for P. album to metabolize the PE-derived carbon.

Plastisphere-hosted viruses: A review of interactions, behavior, and effects

Microbial communities, including bacteria, diatoms, and fungi, colonize plastic surfaces, forming biofilms known as the "plastisphere." Recent research has revealed that plastispheres also host a wide range of viruses, sparking interest in microbial ecology and virology. This shared habitat allows viruses to replicate, interact, infect, and spread, potentially impacting the environment and human health. Consequently, viruses attached to microplastics are now recognized to have broad effects on cellular and immune responses. However, the ecology and implications of viruses hosted in plastisphere habitats remain poorly understood, highlighting their fundamental importance as a subject of study. This review explores various pathways for virus attachment to plastispheres, factors influencing these interactions, their impacts within plastisphere and host-associated environments, and associated issues. It also summarizes current research and identifies knowledge gaps. We anticipate that this paper will help improve our predictive understanding of plastisphere viruses in natural settings and emphasizes the need for more research in real-world environments to advance the field.

Wuchereria bancrofti Lymphatic Filariasis, Barrancabermeja, Colombia, 2023

We describe a recent case of lymphatic filariasis in Colombia caused by Wuchereria bancrofti nematodes. Our study combines clinical-epidemiologic findings with phylogenetic data. Resurgence of lymphatic filariasis may be linked to increasing urbanization trends and migration from previously endemic regions. Fieldwork can be a beneficial tool for screening and containing transmission.

Comparative analysis of bottom trawl and nanopore sequencing in fish biodiversity assessment: The sylt outer reef example

The assessment of fish diversity is crucial for effective conservation and management strategies, especially in ecologically sensitive regions such as marine protected areas. This study contrasts the effectiveness of environmental DNA (eDNA) metabarcoding analysis employing Nanopore technology with compare beam trawl surveys at the Sylt Outer Reef, a Natura 2000 site in the North Sea, Germany. Out of the 17 fish species caught in a bottom trawl (using a 3m beam trawl), 14 were also identified through eDNA extracted from water samples. The three species not detected in the eDNA results were absent because they lacked representation in public DNA databases. The eDNA method detected twice as many fish species as the beam trawl, totalling 36 species, of which 14 were also detected by the trawl. Additionally, the selection of primers (Mifish) facilitated the identification of one marine mammal species, the harbour porpoise. In conclusion, the findings underscore the potential of eDNA coupled with MinION sequencing (Long read technology) as a robust tool for biodiversity assessment, surpassing traditional methods in detecting species richness.

Microbial hitchhikers on microplastics: The exchange of aquatic microbes across distinct aquatic habitats

Microplastics (MPs) have the potential to modify aquatic microbial communities and distribute microorganisms, including pathogens. This poses a potential risk to aquatic life and human health. Despite this, the fate of 'hitchhiking' microbes on MPs that traverse different aquatic habitats remains largely unknown. To address this, we conducted a 50-day microcosm experiment, manipulating estuarine conditions to study the exchange of bacteria and microeukaryotes between river, sea and plastisphere using a long-read metabarcoding approach. Our findings revealed a significant increase in bacteria on the plastisphere, including Pseudomonas, Sphingomonas, Hyphomonas, Brevundimonas, Aquabacterium and Thalassolituus, all of which are known for their pollutant degradation capabilities, specifically polycyclic aromatic hydrocarbons. We also observed a strong association of plastic-degrading fungi (i.e., Cladosporium and Plectosphaerella) and early-diverging fungi (Cryptomycota, also known as Rozellomycota) with the plastisphere. Sea MPs were primarily colonised by fungi (70%), with a small proportion of river-transported microbes (1%-4%). The mere presence of MPs in seawater increased the relative abundance of planktonic fungi from 2% to 25%, suggesting significant exchanges between planktonic and plastisphere communities. Using microbial source tracking, we discovered that MPs only dispersed 3.5% and 5.5% of river bacterial and microeukaryotic communities into the sea, respectively. Hence, although MPs select and facilitate the dispersal of ecologically significant microorganisms, drastic compositional changes across distinct aquatic habitats are unlikely.

Exploitation of environmental DNA (eDNA) for ecotoxicological research: A critical review on eDNA metabarcoding in assessing marine pollution

The rise in worldwide population has led to a noticeable spike in the production, consumption, and transportation of energy and food, contributing to elevated environmental pollution. Marine pollution is a significant global environmental issue with ongoing challenges, including plastic waste, oil spills, chemical pollutants, and nutrient runoff, threatening marine ecosystems, biodiversity, and human health. Pollution detection and assessment are crucial to understanding the state of marine ecosystems. Conventional approaches to pollution evaluation usually represent laborious and prolonged physical and chemical assessments, constraining their efficacy and expansion. The latest advances in environmental DNA (eDNA) are valuable methods for the detection and surveillance of pollution in the environment, offering enhanced sensibility, efficacy, and involvement. Molecular approaches allow genetic information extraction from natural resources like water, soil, or air. The application of eDNA enables an expanded evaluation of the environmental condition by detecting both identified and unidentified organisms and contaminants. eDNA methods are valuable for assessing community compositions, providing indirect insights into the intensity and quality of marine pollution through their effects on ecological communities. While eDNA itself is not direct evidence of pollution, its analysis offers a sensitive tool for monitoring changes in biodiversity, serving as an indicator of environmental health and allowing for the indirect estimation of the impact and extent of marine pollution on ecosystems. This review explores the potential of eDNA metabarcoding techniques for detecting and identifying marine pollutants. This review also provides evidence for the efficacy of eDNA assessment in identifying a diverse array of marine pollution caused by oil spills, harmful algal blooms, heavy metals, ballast water, and microplastics. In this report, scientists can expand their knowledge and incorporate eDNA methodologies into ecotoxicological research.

Tar patties are hotspots of hydrocarbon turnover and nitrogen fixation during a nearshore pollution event in the oligotrophic southeastern Mediterranean Sea

Weathered oil, that is, tar, forms hotspots of hydrocarbon degradation by complex biota in marine environment. Here, we used marker gene sequencing and metagenomics to characterize the communities of bacteria, archaea and eukaryotes that colonized tar patties and control samples (wood, plastic), collected in the littoral following an offshore spill in the warm, oligotrophic southeastern Mediterranean Sea (SEMS). We show potential aerobic and anaerobic hydrocarbon catabolism niches on tar interior and exterior, linking carbon, sulfur and nitrogen cycles. Alongside aromatics and larger alkanes, short-chain alkanes appear to fuel dominant populations, both the aerobic clade UBA5335 (Macondimonas), anaerobic Syntropharchaeales, and facultative Mycobacteriales. Most key organisms, including the hydrocarbon degraders and cyanobacteria, have the potential to fix dinitrogen, potentially alleviating the nitrogen limitation of hydrocarbon degradation in the SEMS. We highlight the complexity of these tar-associated communities, where bacteria, archaea and eukaryotes co-exist, likely exchanging metabolites and competing for resources and space.

Nanopore sequencing of full rRNA operon improves resolution in mycobiome analysis and reveals high diversity in both human gut and environments

High-throughput sequencing has substantially improved our understanding of fungal diversity. However, the short read (<500 bp) length of current second-generation sequencing approaches provides limited taxonomic and phylogenetic resolution for species discrimination. Longer sequences containing more information are highly desired to provide greater taxonomic resolution. Here, we amplified full-length rRNA operons (~5.5 kb) and established a corresponding fungal rRNA operon database for ONT sequences (FRODO), which contains ONT sequences representing eight phyla, 41 classes, 109 orders, 256 families, 524 genera and 1116 species. We also benchmarked the optimal method for sequence classification and determined that the RDP classifier based on our FRODO database was capable of improving the classification of ONT reads, with an average of 98%-99% reads correctly classified at the genus or species level. We investigated the applicability of our approach in three representative mycobiomes, namely, the soil, marine and human gut mycobiomes, and found that the gut contains the largest number of unknown species (over 90%), followed by the marine (42%) and soil (33.8%) mycobiomes. We also observed a distinct difference in the composition of the marine and soil mycobiomes, with the highest richness and diversity detected in soils. Overall, our study provides a systematic approach for mycobiome studies and revealed that the previous methods might have underestimated the diversity of mycobiome species. Future application of this method will lead to a better understanding of the taxonomic and functional diversity of fungi in environmental and health-related mycobiomes.

DNA metabarcoding reveals the dietary profiles of a benthic marine crustacean, Nephrops norvegicus

Norwegian lobster, Nephrops norvegicus, are a generalist scavenger and predator capable of short foraging excursions but can also suspension feed. Existing knowledge about their diet relies on a combination of methods including morphology-based stomach content analysis and stable isotopes, which often lack the resolution to distinguish prey items to species level particularly in species that thoroughly masticate their prey. DNA metabarcoding overcomes many of the challenges associated with traditional methods and it is an attractive approach to study the dietary profiles of animals. Here, we present the diet of the commercially valuable Nephrops norvegicus using DNA metabarcoding of gut contents. Despite difficulties associated with host amplification, our cytochrome oxidase I (COI) molecular assay successfully achieves higher resolution information than traditional approaches. We detected taxa that were likely consumed during different feeding strategies. Dinoflagellata, Chlorophyta and Bacillariophyta accounted for almost 50% of the prey items consumed, and are associated with suspension feeding, while fish with high fisheries discard rates were detected which are linked to active foraging. In addition, we were able to characterise biodiversity patterns by considering Nephrops as natural samplers, as well as detecting parasitic dinoflagellates (e.g., Hematodinium sp.), which are known to influence burrow related behaviour in infected individuals in over 50% of the samples. The metabarcoding data presented here greatly enhances a better understanding of a species' ecological role and could be applied as a routine procedure in future studies for proper consideration in the management and decision-making of fisheries.

The first report of Dirofilaria repens infection in dogs from Colombia

Dirofilariasis is a mosquito-borne disease caused by Dirofilaria parasites, affecting both wild and domestic animals, including humans considered as accidental hosts. Dirofilaria repens is the principal causative agent of dirofilariasis in the Old World, with increasing reports of the parasite in countries where it has not been previously identified, due to several factors such as the expansion of mosquito vectors' geographical distribution. By utilizing newly designed primers for molecular detection and confirming through next-generation sequencing, here, we report the first plausible cases of D. repens in dogs from Colombia. Our results support the classification of this species as an emergent pathogen in the Americas. Finally, we encourage an increase in diagnostic and surveillance efforts to prevent and control the current and future dirofilariasis cases in this region.

Inter-comparison of marine microbiome sampling protocols

Research on marine microbial communities is growing, but studies are hard to compare because of variation in seawater sampling protocols. To help researchers in the inter-comparison of studies that use different seawater sampling methodologies, as well as to help them design future sampling campaigns, we developed the EuroMarine Open Science Exploration initiative (EMOSE). Within the EMOSE framework, we sampled thousands of liters of seawater from a single station in the NW Mediterranean Sea (Service d'Observation du Laboratoire Arago [SOLA], Banyuls-sur-Mer), during one single day. The resulting dataset includes multiple seawater processing approaches, encompassing different material-type kinds of filters (cartridge membrane and flat membrane), three different size fractionations (>0.22 µm, 0.22-3 µm, 3-20 µm and >20 µm), and a number of different seawater volumes ranging from 1 L up to 1000 L. We show that the volume of seawater that is filtered does not have a significant effect on prokaryotic and protist diversity, independently of the sequencing strategy. However, there was a clear difference in alpha and beta diversity between size fractions and between these and "whole water" (with no pre-fractionation). Overall, we recommend care when merging data from datasets that use filters of different pore size, but we consider that the type of filter and volume should not act as confounding variables for the tested sequencing strategies. To the best of our knowledge, this is the first time a publicly available dataset effectively allows for the clarification of the impact of marine microbiome methodological options across a wide range of protocols, including large-scale variations in sampled volume.

Plastisphere composition in a subtropical estuary: Influence of season, incubation time and polymer type on plastic biofouling

Plastics are abundant artificial substrates in aquatic systems that host a wide variety of organisms (the plastisphere), including potential pathogens and invasive species. Plastisphere communities have many complex, but not well-understood ecological interactions. It is pivotal to investigate how these communities are influenced by the natural fluctuations in aquatic ecosystems, especially in transitional environments such as estuaries. Further study is needed in sub-tropical regions in the Southern Hemisphere, where plastic pollution is ever increasing. Here we applied DNA-metabarcoding (16S, 18S and ITS-2) as well Scanning Electron Microscopy (SEM) to assess the diversity of the plastisphere in the Patos Lagoon estuary (PLE), South Brazil. Through a one-year in situ colonization experiment, polyethylene (PE) and polypropylene (PP) plates were placed in shallow waters, and sampled after 30 and 90 days within each season. Over 50 taxa including bacteria, fungi and other eukaryotes were found through DNA analysis. Overall, the polymer type did not influence the plastisphere community composition. However, seasonality significantly affected community composition for bacteria, fungi and general eukaryotes. Among the microbiota, we found Acinetobacter sp., Bacillus sp., and Wallemia mellicola that are putative pathogens of aquatic organisms, such as algae, shrimp and fish, including commercial species. In addition, we identified organisms within genera that can potentially degrade hydrocarbons (e.g. Pseudomonas and Cladosporium spp). This study is the first to assess the full diversity and variation of the plastisphere on different polymers within a sub-tropical southern hemisphere estuary, significantly expanding knowledge on plastic pollution and the plastisphere in estuarine regions.

Plastisphere microbiome: Methodology, diversity, and functionality

Broad topics of the plastisphere in various environments are reviewed, including its methodologies, diversity, functionality, and outlook.

Biological effects on the migration and transformation of microplastics in the marine environment

Microplastics(MPs) are ubiquitous, difficult to degrade, and potentially threatening to organisms in marine environment, so it is important to clarify the factors that affect their biogeochemical processes. The impact of biological activities on the MPs in marine environment is ubiquitous and complex, and there is currently a lack of systematic summaries. This paper reviews the effects of biological actions on the migration, distribution and degradation of MPs in marine environment from four aspects: biological ingestion and digestion, biological movement, biological colonization and biological adhesion. MPs in seawater and sediments can be closely combined with organisms through three pathways: biological ingestion, biofilm formation or adhesion to organisms, and are passed between species at different trophic levels through the food chain. The generation and degradation of faecal pellets and biofilms can alter the density of "environmental MPs", thereby affecting their vertical migration and deposition in water bodies. The movement of swimming organisms and the disturbance by benthic organisms can promote the migration of MPs in water and vertical migration and resuspension in sediments, thereby changing the distribution of MPs in local sea areas. The grinding effect of the digestive tract and the secretion of chemicals from the biofilm (such as enzymes and acids) can reduce the particle size and increase surface roughness of MPs, or even degrade them completely. Besides, biological adhesion may be an important mechanism affecting the distribution, migration and preservation of MPs. There may be complex interactions and linkages among marine dynamical processes, photochemical degradation and biological processes that collectively affect the biogeochemical processes of MPs, but their relative contributions remain to be more studied.

Ecological insights into the resilience of marine plastisphere throughout a storm disturbance

Among numerous research about marine plastisphere, the community living on the surface of plastic debris, little attention was given to the ecological mechanisms governing prokaryotes compared to eukaryotes, and even less focused on their resilience in a changing climate with more storm prevalence. Our current research recruited an integrated approach involving community succession across temporal dimension, ecological mechanisms that govern the assembly, and resilience to environmental perturbations to highlight the ecology of different kingdoms in the plastisphere. Towards this goal, we examined the succession of the prokaryotic and eukaryotic communities on artificial plastic nets in a sidestream of seawater from the Gulf of Aqaba over 35 days. A robust local storm enabled investigation of the alterations before, during, and after this disturbance, aiming at the community's potential to recover. Data from 16S and 18S rRNA sequencing and microscopic analyses decrypted the plastisphere diversity, community assembly, and stochasticity, followed by further analyses of functional and co-occurrence networks for the prokaryotic group. Prokaryotic and eukaryotic communities underwent exact opposite ecological mechanisms. While determinism driven by a robust environmental selection dictated the prokaryotic community assembly, stochasticity prevailed when this condition was relaxed. Interestingly, resilience against disturbance was observed in prokaryotes but not in eukaryotes. The decrease in compositional, functional diversity and network complexity in the prokaryotic community was reversed, presumably due to the niche specification process and high dispersal. Niche specification following perturbation was evident in some bacteria by selected functions associated with plastic degradation, stress response, and antibiotic resistance. On the contrary, eukaryotes decreased in diversity and were dominated by the commonly found Chlorophyta towards the later successional period. Novel findings on the ecology of marine plastisphere during perturbation encourage the integration of this aspect into prediction research.

Epiplastic microhabitats for epibenthic organisms: a new inland water frontier for diatoms

Plastic pollution is widespread in each type of ecosystems. However, the colonization events of microorganisms on plastics seem to be neglected in inland waters. Therefore, in this study we analyze the possible colonization on the surface (hereafter epiplastic microhabitats) of two typology of plastic supports by diatom community. Specifically, we located 20 supports in expanded polystyrene and 20 in polyethylene terephthalate both floating and dipped (~ 1 m) in a central Italian shallow water pond, in order to evaluate the diachronic colonization of diatoms from November 2019 to August 2020. Our result showed the tendency in colonizing both epiplastic microhabitats without significant differences in number of species; additionally, depth does not appear to affect the number of species. As regard the temporal colonization, the number of species tends to increase over time from autumn-winter to spring-summer in both types of epiplastic microhabitats and depth. Instead, increase in dominance of some species over time has been demonstrated: only a few species keep a high number of individuals compared to the others; therefore, the number of individuals within the species is not uniformly distributed. These results suggest the tendency of diatom community to colonize plastic supports in lentic waters, and this evidence can be very important because artificial supports can increase the surface available for the settlement of the algae community with an increase of productivity and the colonization of new communities of different taxa. Further studies are mandatory to investigate the possible effects on the epiplastic community and the ecological implications in freshwater environments.

Isolation and characterization of crude-oil-dependent bacteria from the coast of Ghana using oxford nanopore sequencing

The utilization and improper use of crude oil can have irreparable damage on the environment and human populations. This study sought to isolate hydrocarbon utilizing bacteria from 1% v/v pristine seawater and 1% v/v crude oil using enrichment culture techniques. Whole genome sequencing of DNA using the Oxford Nanopore sequencing technique with Fastq WIMP as the workflow at 3% abundance was undertaken. The results showed that the most abundant isolates identified using this technique at specific sampling sites were, Acinetobacter junii (51.9%), Alcanivarax pacificus (15.8%), Acinetobacter haemolyticus (21.6%), Pseudomonas aeruginosa (23.4%), Alcanivorax xenomutans (24.7%), Alcanivorax xenomutans (23.0%) Acinetobacter baumannii (40.0%) and Acinetobacter junii (14.2%). Cumulatively, the most abundant isolates in the 8 sampling sites were Acinetobacter junii (17.91%), Alcanivorax xenomutans (11.68%), Pseudomonas aeruginosa (7.68%), Escherichia coli (7.67%), Acinetobacter haemolyticus (3.40%), and Alkanivorax pacificus (3.10%). Spearman's rank correlation analysis to examine the strength of relationship between the physicochemical parameters and type of bacteria isolated, revealed that salinity (0.8046) and pH (0.7252) were the highest. Isolated bacteria from pristine seawater, especially Escherichia coli have shown their capacity for bioremediating oil spill pollution in oceanic environments in Ghana.

Designing Knowledge-Based Bioremediation Strategies Using Metagenomics

Functional capacities for bioremediation are governed by metabolic mechanisms of inhabiting microbial communities at polluted niches. Process fluctuations lead to stress scenarios where microbes evolve continuously to adapt to sustain the harsh conditions. The biological wastewater treatment (WWT) process harbors the potential of these catabolic microbes for the degradation of organic molecules. In a typical biological WWT or soil bioremediation process, several microbial species coexist which code for enzymes that degrade complex compounds.High throughput DNA sequencing techniques for microbiome analysis in bioremediation processes have led to a powerful paradigm revealing the significance of metabolic functions and microbial diversity. The present chapter describes techniques in taxonomy and functional gene analysis for understanding bioremediation potential and novel strategies built on in silico analysis for the improvisation of existing aerobic wastewater treatment methods. Methods explaining comparative metagenomics by Metagenome Analysis server (MG-RAST) are described with successful case studies by focusing on industrial wastewaters and soil bioremediation studies.

Plastic-microbe interaction in the marine environment: Research methods and opportunities

Approximately 9 million metric tons of plastics enters the ocean annually, and once in the marine environment, plastic surfaces can be quickly colonised by marine microorganisms, forming a biofilm. Studies on plastic debris-biofilm associations, known as plastisphere, have increased exponentially within the last few years. In this review, we first briefly summarise methods and techniques used in exploring plastic-microbe interactions. Then we highlight research gaps and provide future research opportunities for marine plastisphere studies, especially, on plastic characterisation and standardised biodegradation tests, the fate of "environmentally friendly" plastics, and plastisphere of coastal habitats. Located in the tropics, Southeast Asian (SEA) countries are significant contributors to marine plastic debris. However, plastisphere studies in this region are lacking and therefore, we discuss how the unique environmental conditions in the SEA seas may affect plastic-microbe interaction and why there is an imperative need to conduct plastisphere studies in SEA marine environments. Finally, we also highlight the lack of understanding of the pathogenicity and ecotoxicological effects of plastisphere on marine ecosystems.

The geographical and seasonal effects on the composition of marine microplastic and its microbial communities: The case study of Israel and Portugal

Introduction

Floating microplastic debris are found in most marine environments around the world. Due to their low density and high durability, plastic polymers such as polyethylene, polypropylene, and polystyrene serve as stable floating substrates for the colonization of diverse communities of marine organisms. Despite the high abundance of microplastic debris in the oceans, it is not clear how the geographical location and season affect the composition of marine microplastic and its bacterial microbiome in the natural environment.

Methods

To address this question, microplastic debris were collected from the sea surface near estuaries in the Mediterranean Sea (Israel) and in the Atlantic Ocean (Portugal) during summer and winter of 2021. The microplastic physical characteristics, including shape, color, and polymer composition, were analyzed and the taxonomic structure of the microplastic bacterial microbiome was characterized using a high-resolution metabarcoding pipeline.

Results

Our results, supported by previously published data, suggest that the plastisphere is a highly diverse ecosystem which is strongly shaped by spatial and temporal environmental factors. The geographical location had the highest impact on the plastisphere physical characteristics and its microbiome composition, followed by the season. Our metabarcoding analysis showed great variability between the different marine environments with a very limited microbiome "core."

Discussion

This notion further emphasizes the importance of plastisphere studies in different geographical locations and/or seasons for the characterization of the plastisphere and the identification of plastic-associated species.

Five Previously Unrecorded Fungal Species Isolated from Marine Plastic Wastes in South Korea

Plastic wastes have a negative impact on marine environments; however, they can be used as carbon sources and habitats by certain microbes. Microbes in the marine plastisphere can migrate worldwide through the ocean and cause serious environmental problems when they encounter suitable environments. Therefore, efforts to investigate the microbes inhabiting the marine plastisphere are increasing. In the present study, fungal strains were isolated from plastic wastes buried in Korean sea sands and mudflats and identified using molecular and morphological analyses. Five species were identified that were previously unrecorded from South Korea: Cladosporium funiculosum, Neosetophoma poaceicola, Neosetophoma rosigena, Parasarocladium gamsii, and Trichoderma fomiticola. Their molecular phylogenies and morphological characteristics are described in this study.

UV stabilizers can foster early development of biofilms on freshwater microplastics

Interactions between microbes and microplastics are important as of emerging plastic loads in the global environment. Although diverse plastic additives are used in large amounts, there are very few studies on a quantitative comparison of plastisphere on plastics with different plastic additives. We studied the effects of two widely used UV stabilizers (benzotriazole-type UV-327 and benzophenone-type UV-531 were selected based on their persistence and toxicity) in low-density polyethylene (LDPE) on freshwater microbes. This is the first study on the sole effects of UV stabilizers used as plastic additives on freshwater in situ plastisphere biofilm development. Confocal laser scanning microscopy, assisted with proper differentiating fluorochromes and threshold-based 3D segmentation of data, was used to visualize and quantify biofilm. On the first week of biofilm growth, there was very little biovolume and a negligible amount of phototrophs on pristine LDPE contrasting other substrates. Biovolumes were significantly higher on LDPE with UV stabilizers (up to 159% higher than pristine LDPE), although the biomass was mostly dead due to toxicity (>100% higher dead biovolume than live biovolume in LDPE with UV stabilizers). After the fourth week, marginally higher biovolumes along with a revival of the biomass on LDPE with UV stabilizers were observed. The ability to induce microorganismic intracellular reactive oxygen species by UV stabilizers was detected, which may stimulate biofilm growth during the primary phase of biofilm development. Atomic force microscopy analysis denoted that LDPE with UV stabilizers exhibit considerably stronger adhesion force than pristine LDPE. These observations suggest that UV stabilizers can foster the early attachment of microbes to microplastics while killing the surface contacting layer. An alive upper layer of microbes can get developed on the dead biofilm without much disruption due to the toxicity of UV stabilizers. This occurrence can eventually boost the early development of biofilms on plastics.

Co-occurrences enhance our understanding of aquatic fungal metacommunity assembly and reveal potential host-parasite interactions

Our knowledge of aquatic fungal communities, their assembly, distributions and ecological roles in marine ecosystems is scarce. Hence, we aimed to investigate fungal metacommunities of coastal habitats in a subarctic zone (northern Baltic Sea, Sweden). Using a novel joint species distribution model and network approach, we quantified the importance of biotic associations contributing to the assembly of mycoplankton, further, detected potential biotic interactions between fungi-algae pairs, respectively. Our long-read metabarcoding approach identified 493 fungal taxa, of which a dominant fraction (44.4%) was assigned as early-diverging fungi (i.e. Cryptomycota and Chytridiomycota). Alpha diversity of mycoplankton declined and community compositions changed along inlet-bay-offshore transects. The distributions of most fungi were rather influenced by environmental factors than by spatial drivers, and the influence of biotic associations was pronounced when environmental filtering was weak. We found great number of co-occurrences (120) among the dominant fungal groups, and the 25 associations between fungal and algal OTUs suggested potential host-parasite and/or saprotroph links, supporting a Cryptomycota-based mycoloop pathway. We emphasize that the contribution of biotic associations to mycoplankton assembly are important to consider in future studies as it helps to improve predictions of species distributions in aquatic ecosystems.

Microbial communities on plastic particles in surface waters differ from subsurface waters of the North Pacific Subtropical Gyre

The long-term fate of plastics in the ocean and their interactions with marine microorganisms remain poorly understood. In particular, the role of sinking plastic particles as a transport vector for surface microbes towards the deep sea has not been investigated. Here, we present the first data on the composition of microbial communities on floating and suspended plastic particles recovered from the surface to the bathypelagic water column (0-2000 m water depth) of the North Pacific Subtropical Gyre. Microbial community composition of suspended plastic particles differed from that of plastic particles afloat at the sea surface. However, in both compartments, a diversity of hydrocarbon-degrading bacteria was identified. These findings indicate that microbial community members initially present on floating plastics are quickly replaced by microorganisms acquired from deeper water layers, thus suggesting a limited efficiency of sinking plastic particles to vertically transport microorganisms in the North Pacific Subtropical Gyre.

Plastisphere community assemblage of aquatic environment: plastic-microbe interaction, role in degradation and characterization technologies

It is undeniable that plastics are ubiquitous and a threat to global ecosystems. Plastic waste is transformed into microplastics (MPs) through physical and chemical disruption processes within the aquatic environment. MPs are detected in almost every environment due to their worldwide transportability through ocean currents or wind, which allows them to reach even the most remote regions of our planet. MPs colonized by biofilm-forming microbial communities are known as the ''plastisphere". The revelation that this unique substrate can aid microbial dispersal has piqued interest in the ground of microbial ecology. MPs have synergetic effects on the development, transportation, persistence, and ecology of microorganisms. This review summarizes the studies of plastisphere in recent years and the microbial community assemblage (viz. autotrophs, heterotrophs, predators, and pathogens). We also discussed plastic-microbe interactions and the potential sources of plastic degrading microorganisms. Finally, it also focuses on current technologies used to characterize those microbial inhabitants and recommendations for further research.

Seedborne Cercospora beticola Can Initiate Cercospora Leaf Spot from Sugar Beet (Beta vulgaris) Fruit Tissue

Cercospora leaf spot (CLS) is a globally important disease of sugar beet (Beta vulgaris) caused by the fungus Cercospora beticola. Long-distance movement of C. beticola has been indirectly evidenced in recent population genetic studies, suggesting potential dispersal via seed. Commercial sugar beet "seed" consists of the reproductive fruit (true seed surrounded by maternal pericarp tissue) coated in artificial pellet material. In this study, we confirmed the presence of viable C. beticola in sugar beet fruit for 10 of 37 tested seed lots. All isolates harbored the G143A mutation associated with quinone outside inhibitor resistance, and 32 of 38 isolates had reduced demethylation inhibitor sensitivity (EC₅₀ > 1 µg/ml). Planting of commercial sugar beet seed demonstrated the ability of seedborne inoculum to initiate CLS in sugar beet. C. beticola DNA was detected in DNA isolated from xylem sap, suggesting the vascular system is used to systemically colonize the host. We established nuclear ribosomal internal transcribed spacer region amplicon sequencing using the MinION platform to detect fungi in sugar beet fruit. Fungal sequences from 19 different genera were identified from 11 different sugar beet seed lots, but Fusarium, Alternaria, and Cercospora were consistently the three most dominant taxa, comprising an average of 93% relative read abundance over 11 seed lots. We also present evidence that C. beticola resides in the pericarp of sugar beet fruit rather than the true seed. The presence of seedborne inoculum should be considered when implementing integrated disease management strategies for CLS of sugar beet in the future.

High-Resolution Screening for Marine Prokaryotes and Eukaryotes With Selective Preference for Polyethylene and Polyethylene Terephthalate Surfaces

Marine plastic debris serve as substrates for the colonization of a variety of prokaryote and eukaryote organisms. Of particular interest are the microorganisms that have adapted to thrive on plastic as they may contain genes, enzymes or pathways involved in the adhesion or metabolism of plastics. We implemented DNA metabarcoding with nanopore MinION sequencing to compare the 1-month-old biomes of hydrolyzable (polyethylene terephthalate) and non-hydrolyzable (polyethylene) plastics surfaces vs. those of glass and the surrounding water in a Mediterranean Sea marina. We sequenced longer 16S rRNA, 18S rRNA, and ITS barcode loci for a more comprehensive taxonomic profiling of the bacterial, protist, and fungal communities, respectively. Long read sequencing enabled high-resolution mapping to genera and species. Using previously established methods we performed differential abundance screening and identified 30 bacteria and five eukaryotic species, that were differentially abundant on plastic compared to glass. This approach will allow future studies to characterize the plastisphere communities and to screen for microorganisms with a plastic-metabolism potential.

Insights into microbial diversity on plastisphere by multi-omics

Plastic pollution is a major concern in marine environment as it takes many years to degrade and is one of the greatest threats to marine life. Plastic surface, referred to as plastisphere, provides habitat for growth and proliferation of various microorganisms. The discovery of these microbes is necessary to identify significant genes, enzymes and bioactive compounds that could help in bioremediation and other commercial applications. Conventional culture techniques have been successful in identifying few microbes from these habitats, leaving majority of them yet to be explored. As such, to recognize the vivid genetic diversity of microbes residing in plastisphere, their structure and corresponding ecological roles within the ecosystem, an emerging technique, called metagenomics has been explored. The technique is expected to provide hitherto unknown information on microbes from the plastisphere. Metagenomics along with next generation sequencing provides comprehensive knowledge on microbes residing in plastisphere that identifies novel microbes for plastic bioremediation, bioactive compounds and other potential benefits. The following review summarizes the efficiency of metagenomics and next generation sequencing technology over conventionally used methods for culturing microbes. It attempts to illustrate the workflow mechanism of metagenomics to elucidate diverse microbial profiles. Further, importance of integrated multi-omics techniques has been highlighted in discovering microbial ecology residing on plastisphere for wider applications.

Amplicon_sorter: A tool for reference‐free amplicon sorting based on sequence similarity and for building consensus sequences

Oxford Nanopore Technologies (ONT) is a third‐generation sequencing technology that is gaining popularity in ecological research for its portable and low‐cost sequencing possibilities. Although the technology excels at long‐read sequencing, it can also be applied to sequence amplicons. The downside of ONT is the low quality of the raw reads. Hence, generating a high‐quality consensus sequence is still a challenge. We present Amplicon_sorter, a tool for reference‐free sorting of ONT sequenced amplicons based on their similarity in sequence and length and for building solid consensus sequences.

Floating plastics and their associated biota in the Western South Atlantic

The lack of information about plastic pollution in many marine regions hinders firm actions to manage human activities and mitigate their impacts. This study conducted for the first time a quali-quantitative evaluation of floating plastics and their associated biota from coastal and oceanic waters in South Brazil. Plastics were collected using a manta net, and were categorized according to their shape, size, malleability and polymer composition. Multi-marker DNA metabarcoding (16S, and 18S V4 and V9 rRNA regions) was performed to identify prokaryotes and eukaryotes associated to plastics. We found 371 likely plastic particles of several sizes, shapes and polymers, and the average concentration of plastics at the region was 4461 items.km^-2 (SD ± 3914). Microplastics (0.5 - 5 mm) were dominant in most sampling stations, with fragments and lines representing the most common shapes. Diverse groups of prokaryotes (20 bacteria phyla) and eukaryotes (41 groups) were associated with plastics. Both the community composition and richness of epiplastic organisms were highly variable between individual plastics but, in general, were not influenced by plastic categories. Organisms with potential pathogenicity (e.g. Vibrio species. and Alexandrium tamarense), as well as potential plastic degraders (e.g. Ralstonia, Pseudomonas, and Alcanivorax species), were found. The information generated here is pivotal to support strategies to prevent the input and mitigate the impacts of plastics and their associated organisms on marine environments.

A review on marine plastisphere: biodiversity, formation, and role in degradation

The pollution of plastic waste has become an increasingly serious environmental crisis. Recently, plastic has been detected in various kinds of environments, even in human tissues, which is an increasing threat to the ecosystems and humans. In the ocean, the plastic waste is eventually fragmentized into microplastics (MPs) under the disruption of physical and chemical processes. MPs are colonized by microbial communities such as fungi, diatoms, and bacteria, which form biofilms on the surface of the plastic called “plastisphere”. In this review, we summarize the studies related to microorganisms in the plastisphere in recent years and describe the microbial species in the plastisphere, mainly including bacteria, fungi, and autotrophs. Secondly, we explore the interactions between MPs and the plastisphere. The depth of MPs in the ocean and the nutrients in the surrounding seawater can have a great impact on the community structure of microorganisms in the plastisphere. Finally, we discuss the types of MP-degrading bacteria in the ocean, and use the “seed bank” theory to speculate on the potential sources of MP-degrading microorganisms. Challenges and future research prospects are also discussed.

Diversity and predicted inter- and intra-domain interactions in the Mediterranean Plastisphere

This study investigated the biogeography, the presence and diversity of potentially harmful taxa harbored, and potential interactions between and within bacterial and eukaryotic domains of life on plastic debris in the Mediterranean. Using a combination of high-throughput DNA sequencing (HTS), Causal Network Analysis, and Scanning Electron Microscopy (SEM), we show regional differences and gradients in the Mediterranean microbial communities associated with marine litter, positive causal effects between microbes including between and within domains of life, and how these might impact the marine ecosystems surrounding them. Adjacent seas within the Mediterranean region showed a gradient in the microbial communities on plastic with non-overlapping endpoints (Adriatic and Ligurian Seas). The largest predicted inter-domain effects included positive effects of a novel red-algal Plastisphere member on its potential microbiome community. Freshwater and marine samples housed a diversity of fungi including some related to disease-causing microbes. Algal species related to those responsible for Harmful Blooms (HABs) were also observed on plastic pieces including members of genera not previously reported on Plastic Marine Debris (PMD).

Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic Rodents

The effective control of rodent populations on farms is crucial for food safety, as rodents are reservoirs and vectors for several zoonotic pathogens. Clear links have been identified between rodents and farm-level outbreaks of pathogens throughout Europe and Asia; however, comparatively little research has been devoted to studying the rodent–agricultural interface in the USA. Here, we address this knowledge gap by metabarcoding bacterial communities of rodent pests collected from Minnesota and Wisconsin food animal farms. We leveraged the Oxford Nanopore MinION sequencer to provide a rapid real-time survey of putative zoonotic foodborne pathogens, among others. Rodents were live trapped (n = 90) from three dairy and mixed animal farms. DNA extraction was performed on 63 rodent colons along with 2 shrew colons included as outgroups in the study. Full-length 16S amplicon sequencing was performed. Our farm-level rodent-metabarcoding data indicate the presence of multiple foodborne pathogens, including Salmonella spp., Campylobacter spp., Staphylococcus aureus, and Clostridium spp., along with many mastitis pathogens circulating within five rodent species (Microtus pennsylvanicus, Mus musculus, Peromyscus leucopus, Peromyscus maniculatus, and Rattus norvegicus) and a shrew (Blarina brevicauda). Interestingly, we observed a higher abundance of enteric pathogens (e.g., Salmonella) in shrew feces compared to the rodents analyzed in our study. Knowledge gained from our research efforts will directly inform and improve farm-level biosecurity efforts and public health interventions to reduce future outbreaks of foodborne and zoonotic disease.

CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology

Phagotrophic protists are key players in aquatic food webs. Although sequencing-based studies have revealed their enormous diversity, ecological information on in situ abundance, feeding modes, grazing preferences, and growth rates of specific lineages can be reliably obtained only using microscopy-based molecular methods, such as Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). CARD-FISH is commonly applied to study prokaryotes, but less so to microbial eukaryotes. Application of this technique revealed that Paraphysomonas or Spumella-like chrysophytes, considered to be among the most prominent members of protistan communities in pelagic environments, are omnipresent but actually less abundant than expected, in contrast to little known groups such as heterotrophic cryptophyte lineages (e.g., CRY1), cercozoans, katablepharids, or the MAST lineages. Combination of CARD-FISH with tracer techniques and application of double CARD-FISH allow visualization of food vacuole contents of specific flagellate groups, thus considerably challenging our current, simplistic view that they are predominantly bacterivores. Experimental manipulations with natural communities revealed that larger flagellates are actually omnivores ingesting both prokaryotes and other protists. These new findings justify our proposition of an updated model of microbial food webs in pelagic environments, reflecting more authentically the complex trophic interactions and specific roles of flagellated protists, with inclusion of at least two additional trophic levels in the nanoplankton size fraction. Moreover, we provide a detailed CARD-FISH protocol for protists, exemplified on mixo- and heterotrophic nanoplanktonic flagellates, together with tips on probe design, a troubleshooting guide addressing most frequent obstacles, and an exhaustive list of published probes targeting protists.