Association of zoonotic protozoan parasites with microplastics in seawater and implications for human and wildlife health

Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing

The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA's versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions.

Microplastic contamination of intertidal sediment and cockles (Cerastoderma edule)

Microplastic pollution represents a new threat to both marine environments and the species that reside within them. This study examined the temporal concentrations of microplastics found in the commercially and ecologically important bivalve, Cerasastoderma edule and the presence of microplastics in intertidal sediment from the Special Area of Conservation (SAC) and Special Protected Area (SPA) of Dundalk Bay, Ireland. A microplastic range of 1.55 ± 1.38 to 1.92 ± 1.00 g-1 and 3.43 ± 2.47 to 6.90 ± 3.68 ind-1 was reported between seasons. Microfibres dominated the shape of microplastics present in both sediment and cockles. While a wider range of polymers were identified in cockles than in sediment, microplastic concentrations recovered from both intertidal sites studied were approximately double the estimated safe loading levels for this pollutant. The potential of cockles to perform as shallow environment biomonitors of microplastic pollution was identified as they presented buoyant microplastics that were not identified in sediment samples.

First description of Rhodococcus equi infection in common bottlenose dolphin (Tursiops truncatus)

Rhodococcus equi is a terrestrial bacterium and a common pathogen in foals (Equus caballus), in which causes pneumonia. This report describes for the first time the infection caused by R. equi in a common bottlenose dolphin (Tursiops truncatus) stranded in the Calabrian coast, Italy. The post mortem examination of the animal revealed lesions in lung and colon. The animal was also positive to dolphin morbillivirus. The histological study showed lesions attributable to R. equi infection, such as pyogranulomatous bacterial pneumonia and chronic granulomatous colitis. Whole genome sequencing of the isolated strain confirmed its identification as R. equi.

Like noodles in a soup: Anthropogenic microfibers are being ingested by juvenile fish in nursery grounds of the Southwestern Atlantic Ocean

The balance between marine health and ecosystem sustainability confronts a pressing threat from anthropogenic pollution. Estuaries are particularly susceptible to contamination, notably by anthropogenic microfibers originated from daily human activities in land and in fishing practices. This study examines the impact of anthropogenic microfibers on the whitemouth croaker in an estuarine environment of the Southwestern Atlantic Ocean during cold and warm seasons. The presence of anthropogenic microfibers was revealed in 64 % of juvenile gastrointestinal tracts, and 94 % of water samples, and concentrations were influenced by factors such as temperature, bay zone, and fish body length. Blue and black anthropogenic microfibers, with a rather new physical aspect, were dominant. This study highlights the impact of microfibers in a heavily anthropized body of water, subject to federal and local regulations due to the presence of commercially significant fish species inhabiting this area.

Unveiling the Microbial Realm with VEBA 2.0: A modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic, and viral multi-omics from either short- or long-read sequencing

The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA's versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible platform that bridges the gap between genomics and biotechnological solutions.

The role of species ecology in predicting Toxoplasma gondii prevalence in wild and domesticated mammals globally

Macroecological approaches can provide valuable insight into the epidemiology of globally distributed, multi-host pathogens. Toxoplasma gondii is a protozoan that infects any warm-blooded animal, including humans, in almost every habitat worldwide. Toxoplasma gondii infects its hosts through oocysts in the environment, carnivory of tissue cysts within intermediate host prey and vertical transmission. These routes of infection enable specific predictions regarding the ecological and life history traits that should predispose specific taxa to higher exposure and, thus infection rates of T. gondii. Using T. gondii prevalence data compiled from 485 studies representing 533 free-ranging wild mammalian species, we examined how ecological (habitat type, trophic level) and life history (longevity, vagility, gestation duration and torpor) traits influence T. gondii infection globally. We also compared T. gondii prevalence between wild and domesticated species from the same taxonomic families using data compiled from 540 studies of domestic cattle, sheep, and pigs. Across free-ranging wildlife, we found the average T. gondii prevalence was 22%, which is comparable to the global human estimate. Among ecological guilds, terrestrial species had lower T. gondii prevalence than aquatic species, with freshwater aquatic taxa having an increased prevalence compared to marine aquatic species. Dietary niches were also influential, with carnivores having an increased risk compared to other trophic feeding groups that have reduced tissue cyst exposure in their diet. With respect to influential life history traits, we found that more vagile wildlife species had higher T. gondii infection rates, perhaps because of the higher cumulative risk of infection during movement through areas with varying T. gondii environmental loads. Domestic farmed species had a higher T. gondii prevalence compared to free-ranging confamilial wildlife species. Through a macroecological approach, we determined the relative significance of transmission routes of a generalist pathogen, demonstrating an increased infection risk for aquatic and carnivorous species and highlighting the importance of preventing pathogen pollution into aquatic environments. Toxoplasma gondii is increasingly understood to be primarily an anthropogenically-associated pathogen whose dissemination is enhanced by ecosystem degradation and human subsidisation of free-roaming domestic cats. Adopting an ecosystem restoration approach to reduce one of the world's most common parasites would synergistically contribute to other initiatives in conservation, feline and wildlife welfare, climate change, food security and public health.

Using eRNA/eDNA metabarcoding to detect community-level impacts of nanoplastic exposure to benthic estuarine ecosystems

Plastic particles are ubiquitous in marine systems and fragment into smaller pieces, such as nanoplastics (NPs). The effects of NPs on marine organisms are of growing concern but are not well understood. Marine sediments act as a sink for many contaminants, like microplastics, and are rich habitats for benthic micro- and meiofauna which are ecologically-important components of marine food webs; however, little is known about the sensitivities of specific organisms to NPs or the effects on community diversity and composition. Utilizing molecular methods, such as metabarcoding of environmental DNA/RNA, allows for the rapid and comprehensive detection of microscopic organisms via high-throughput sequencing to assess adverse effects at the community level. The objective of this study was to use a metabarcoding approach to investigate the effects of NPs on benthic micro- and meiofaunal community diversity. Mesocosms were created with sediment cores collected from the Narrow River estuary (Rhode Island, USA) and exposed to 900 nm diameter weathered polystyrene beads at concentrations of 0.1, 1, 10, or 100 mg/kg dry weight in sediment for two weeks. Following exposure, RNA and DNA were co-extracted from the sediment, RNA was reverse-transcribed, 18S and COI markers were PCR-amplified, and amplicons were sequenced on an Illumina MiSeq. Using the 18S marker and eRNA template, increases to α-diversity and significant differences to β-diversity were observed in the highest NP exposures relative to the control. Observed differences in community composition were driven by the differential abundance of several types of protists and arthropods. Significant dose-dependent shifts in composition were observed in β-diversity Jaccard and Unweighted-Unifrac metrics with the 18S marker using the RNA template. To our knowledge, this is the first demonstration of a dose-response relationship for NPs at a community level, and it highlights the value of using community-level endpoints to assess environmental impacts of nanoparticles.

Plastics in an endemic fish species (Alburnus sellal) and its parasite (Ligula intestinalis) in the Upper Tigris River, Türkiye

Occurrence of micro-, meso- and macroplastics in Alburnus sellal and its parasite Ligula intestinalis is reported for the first time in the Tigris River, one of the two large rivers that defines Mesopotamia. Plastic occurrence was assessed from museum fish materials collected in the upper Tigris River between 2007 and 2021. Plastics were found in 57 % of A. sellal specimens (536 individuals) and in 74 % of L. intestinalis specimens (57 individuals). Mean plastic ingestion was 1.27 ± 1.30 items. fish-1 and 1.77 ± 1.79 items. parasite-1 considering all the fish and parasites analysed. Fibres were the most common types of plastics, comprising 96.2 % and 81 % of plastics in A. sellal and L. intestinalis, respectively. Black was the most common colour of plastics found in both fish (37 %) and parasite specimens (58 %). Microplastics comprised 95.5 % and 100 % of plastics found in A. sellal and L. intestinalis, respectively. In both specimens acrylic (PAN) was the most common polymer as confirmed by FTIR spectroscopy. Differences in plastic ingestion were not significantly over time and among regions. No significant correlation was found between plastics ingestion by fish and by parasites. The present assessment shows that native fish species of the Tigris River have been contaminated by plastics by more than a decade. Our results contribute to a better understanding of the status of plastic pollution in fish and parasites, provide plastic pollution baseline data for the Tigris River and highlight the urgent need to elucidate on the distribution and fate of plastics in freshwater environments and their effects on the ecosystem and humans.

Plastic leachate exposure drives antibiotic resistance and virulence in marine bacterial communities

Plastic pollution is a serious global problem, with more than 12 million tonnes of plastic waste entering the oceans every year. Plastic debris can have considerable impacts on microbial community structure and functions in marine environments, and has been associated with an enrichment in pathogenic bacteria and antimicrobial resistance (AMR) genes. However, our understanding of these impacts is largely restricted to microbial assemblages on plastic surfaces. It is therefore unclear whether these effects are driven by the surface properties of plastics, providing an additional niche for certain microbes residing in biofilms, and/or chemicals leached from plastics, the effects of which could extend to surrounding planktonic bacteria. Here, we examine the effects of polyvinyl chloride (PVC) plastic leachate exposure on the relative abundance of genes associated with bacterial pathogenicity and AMR within a seawater microcosm community. We show that PVC leachate, in the absence of plastic surfaces, drives an enrichment in AMR and virulence genes. In particular, leachate exposure significantly enriches AMR genes that confer multidrug, aminoglycoside and peptide antibiotic resistance. Additionally, enrichment of genes involved in the extracellular secretion of virulence proteins was observed among pathogens of marine organisms. This study provides the first evidence that chemicals leached from plastic particles alone can enrich genes related to microbial pathogenesis within a bacterial community, expanding our knowledge of the environmental impacts of plastic pollution with potential consequences for human and ecosystem health.

Foodborne protozoan parasites in fresh mussels and oysters purchased at retail in Canada

Studies worldwide have reported the presence of protozoan parasites in a variety of commercial bivalve shellfish. The uptake of these parasites by shellfish occurs during filter feeding in faecally-contaminated waters. The objective of the present study was to determine the prevalence of Giardia, Cryptosporidium and Toxoplasma in fresh, live shellfish purchased in three Canadian provinces as part of the retail surveillance activities led by FoodNet Canada (Public Health Agency of Canada). Packages containing mussels (n = 253) or oysters (n = 130) were purchased at grocery stores in FoodNet Canada sentinel sites on a biweekly basis throughout 2018 and 2019, and shipped in coolers to Health Canada for testing. A small number of packages were not tested due to insufficient quantity or poor quality. Following DNA extraction from homogenized, pooled tissues, nested PCR and DNA sequencing were used to detect parasite-specific sequences. Epifluorescence microscopy was used to confirm the presence of intact cysts and oocysts in sequence-confirmed PCR-positive samples. Giardia duodenalis DNA was present in 2.4 % of 247 packages of mussels and 4.0 % of 125 packages of oysters, while Cryptosporidium parvum DNA was present in 5.3 % of 247 packages of mussels and 7.2 % of 125 packages of oysters. Toxoplasma gondii DNA was only found in mussels in 2018 (1.6 % of 249 packages). Parasite DNA was detected in shellfish purchased in all three Canadian provinces sampled, and there was no apparent seasonal variation in prevalence. While the present study did not test for viability, parasites are known to survive for long periods in the marine environment, and these findings suggest that there is a risk of infection, especially when shellfish are consumed raw.

Tsunami-Driven Spread of Toxoplasma gondii and Other Microbial Pathogens: Implications for Cetacean Health and Conservation

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Microplastic Pollution: Chemical Characterization and Impact on Wildlife

Microplastics are small pieces of plastic that are less than 5 mm in size and can be found in most environments, including the oceans, rivers, and air. These small plastic particles can have negative impacts on wildlife and the environment. In this review of the literature, we analyze the presence of microplastics in various species of wildlife, including fish, birds, and mammals. We describe a variety of analytical techniques, such as microscopy and spectrometry, which identify and quantify the microplastics in the samples. In addition, techniques of sample preparation are discussed. Summary results show that microplastics are present in all the wildlife species studied, with the highest concentrations often found in fish and birds. The literature suggests that microplastics are widely distributed in the environment and have the potential to affect a wide range of species. Further research is required to fully understand the impacts of microplastics on wildlife and the environment.

Review of research on migration, distribution, biological effects, and analytical methods of microfibers in the environment

Microplastics have been proven to be one of the critical environmental pollution issues. Moreover, microfibers, the most prominent form of microplastics in the environment, have likewise attracted the attention of various countries. With the increase in global population and industrialization, the production and use of fibers continue to increase yearly. As a result, a large number of microfibers are formed. If fiber products are not used or handled correctly, it will cause direct/indirect severe microfiber environmental pollution. Microfibers will be further broken into smaller fiber fragments when they enter the natural environment. Presently, researchers have conducted extensive research in the identification of microfibers, laying the foundation for further resourcefulness research. This work used bibliometric analysis to review the microfiber contamination researches systematically. First, the primary sources of microfibers and the influencing factors are analyzed. We aim to summarize the influence of the clothing fiber preparation and care processes on microfiber formation. Then, this work elaborated on the migration in/between water, atmosphere, and terrestrial environments. We also discussed the effects of microfiber on ecosystems. Finally, microfibers' current and foreseeable effective treatment, disposal, and resource utilization methods were explained. This paper will provide a structured reference for future microfiber research.

Microplastic transfer from the American horseshoe crab to shorebirds through consumption of horseshoe crab eggs in Jamaica Bay, NY

Microplastic transfer between horseshoe crabs (Limulus polyphemus) and migratory shorebirds through consumption of crab eggs was examined in Jamaica Bay, New York. Fertilized and unfertilized crab eggs, shorebird fecal pellets, beach sand, and bay water were processed with a hydrogen peroxide solution to remove organic material, then stained with a Nile Red to identify microplastics using fluorescence microscopy. Microplastics were present in all samples and ranged from approximately26-1300 μm. Unfertilized and fertilized eggs contained significantly higher numbers of microplastic particles per gram than shorebird fecal pellets, beach sand, and bay water. The presence of microplastics in unfertilized egg samples indicates that microplastics undergo maternal transfer during oogenesis. We estimated that 1 g of horseshoe crab eggs could contain approximately 426 to 840 microplastic particles, suggesting that shorebirds feeding on this resource could be ingesting a substantial burden of microplastics during their migratory stopover, much of which appears to be retained by shorebirds, rather than being eliminated in their fecal pellets.

Food and human safety: the impact of microplastics

Plastic waste pollution is one of the biggest problems in the world today. The amount of plastic in the environment continues to increase, and human exposure to microplastic (MP) has become a reality. This subject has attracted the attention of the whole world. The MP problem has also been noticed by the scientific community. The term microplastic is mostly used to define synthetic material with a high polymer content that can have a size range from 0.1 to 5000 µm. This paper aims to characterize the routes of exposure to MP, define its pollution sources, and identify food types contaminated with plastics. This review addresses the current state of knowledge on this type of particles, with particular emphasis on their influence on human health. Adverse effects of MP depend on routes and sources of exposure. The most common route of exposure is believed to be the gastrointestinal tract. Sources of MP include fish, shellfish, water as well as tea, beer, wine, energy drinks, soft drinks, milk, salt, sugar, honey, poultry meat, fruits, and vegetables. Studies have shown that particles of PET, PE, PP, PS, PVC, PA, and PC are the most frequently found in food.

VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

BACKGROUND

With the advent of metagenomics, the importance of microorganisms and how their interactions are relevant to ecosystem resilience, sustainability, and human health has become evident. Cataloging and preserving biodiversity is paramount not only for the Earth's natural systems but also for discovering solutions to challenges that we face as a growing civilization. Metagenomics pertains to the in silico study of all microorganisms within an ecological community in situ, however, many software suites recover only prokaryotes and have limited to no support for viruses and eukaryotes.

RESULTS

In this study, we introduce the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite developed to recover genomes from all domains. To our knowledge, VEBA is the first end-to-end metagenomics suite that can directly recover, quality assess, and classify prokaryotic, eukaryotic, and viral genomes from metagenomes. VEBA implements a novel iterative binning procedure and hybrid sample-specific/multi-sample framework that yields more genomes than any existing methodology alone. VEBA includes a consensus microeukaryotic database containing proteins from existing databases to optimize microeukaryotic gene modeling and taxonomic classification. VEBA also provides a unique clustering-based dereplication strategy allowing for sample-specific genomes and genes to be directly compared across non-overlapping biological samples. Finally, VEBA is the only pipeline that automates the detection of candidate phyla radiation bacteria and implements the appropriate genome quality assessments. VEBA's capabilities are demonstrated by reanalyzing 3 existing public datasets which recovered a total of 948 MAGs (458 prokaryotic, 8 eukaryotic, and 482 viral) including several uncharacterized organisms and organisms with no public genome representatives.

CONCLUSIONS

The VEBA software suite allows for the in silico recovery of microorganisms from all domains of life by integrating cutting edge algorithms in novel ways. VEBA fully integrates both end-to-end and task-specific metagenomic analysis in a modular architecture that minimizes dependencies and maximizes productivity. The contributions of VEBA to the metagenomics community includes seamless end-to-end metagenomics analysis but also provides users with the flexibility to perform specific analytical tasks. VEBA allows for the automation of several metagenomics steps and shows that new information can be recovered from existing datasets.

Potential SARS-CoV-2 Susceptibility of Cetaceans Stranded along the Italian Coastline

Due to marine mammals' demonstrated susceptibility to SARS-CoV-2, based upon the homology level of their angiotensin-converting enzyme 2 (ACE2) viral receptor with the human one, alongside the global SARS-CoV-2 occurrence and fecal contamination of the river and marine ecosystems, SARS-CoV-2 infection may be plausibly expected to occur also in cetaceans, with special emphasis on inshore species like bottlenose dolphins (Tursiops truncatus). Moreover, based on immune and inflammatory responses to SARS-CoV-2 infection in humans, macrophages could also play an important role in antiviral defense mechanisms. In order to provide a more in-depth insight into SARS-CoV-2 susceptibility in marine mammals, we evaluated the presence of SARS-CoV-2 and the expression of ACE2 and the pan-macrophage marker CD68. Aliquots of tissue samples, belonging to cetaceans stranded along the Italian coastline during 2020-2021, were collected for SARS-CoV-2 analysis by real-time PCR (RT-PCRT) (N = 43) and Immunohistochemistry (IHC) (N = 59); thirty-two aliquots of pulmonary tissue sample (N = 17 Tursiops truncatus, N = 15 Stenella coeruleoalba) available at the Mediterranean Marine Mammal Tissue Bank (MMMTB) of the University of Padua (Legnaro, Padua, Italy) were analyzed to investigate ACE2 expression by IHC. In addition, ACE2 and CD68 were also investigated by Double-Labeling Immunofluorescence (IF) Confocal Laser Microscopy. No SARS-CoV-2 positivity was found in samples analyzed for the survey while ACE2 protein was detected in the lower respiratory tract albeit heterogeneously for age, gender/sex, and species, suggesting that ACE2 expression can vary between different lung regions and among individuals. Finally, double IF analysis showed elevated colocalization of ACE2 and CD68 in macrophages only when an evident inflammatory reaction was present, such as in human SARS-CoV-2 infection.