Freshwater Environments Research Articles

Occurrence, Transport, and Risk Assessment of Brominated Flame Retardants in Northern Wetland Multimedia

Current studies have paid extensive attention to the occurrence of brominated flame retardants (BFRs) in aquatic environments; however, there is a lack of exploration of BFRs in ice media in freshwater environments, and there are fewer studies on the distribution patterns and ecological risks of BFRs in different media. In order to fill this gap in the current research status, this study conducted four seasonal samplings in the Songhua River wetland in Northeast China. The distribution and risk of 14 polybrominated diphenyl ethers (PBDEs) and 22 new brominated flame retardants (NBFRs) in water, ice, sediment, and soil were analyzed using liquid–liquid extraction sample pretreatment and gas chromatography–mass spectrometry instrumentation. A total of 18, 5, 8, 19, and 18 BFRs were detected in non-ice-covered water, ice-covered water, ice, sediment, and soil, respectively. NBFRs dominated contaminant concentrations in each medium. Significant correlations were found between BFRs in ice and subglacial water, suggesting that the sources of BFRs in these two media are similar and there is an exchange between them. The ice enrichment factor (IEF) revealed the water–ice distribution mechanism of BFRs, indicating that wetland ice acts as a temporary sink for 2-(Allyloxy)-1,3,5-tribromobenzene (ATE), 1,2-Dibromo-4-(1,2-dibromoethyl)cyclohexane (α-TBECH), 1,2,5,6-Tetrabromocyclooctane (TBCO), and 2-Bromoallyl 2,4,6-tribromophenyl ether (BATE). In order to achieve dynamic equilibrium, the exchange profile of BFRs between water and sediment requires the release of BFRs into water. The risk quotient (RQ) indicated that TBCO in water and ice poses a moderate risk to aquatic organisms, and its potential impact on wetland ecology cannot be ignored.

Deciphering the carbon and nitrogen cycling in selected tropical coastal fish: revelations from stable isotope fluctuations and feeding patterns.

This study investigated the availability, abundance, and seasonal variations of fish in Msimbazi, Kizinga, and Mbezi Rivers, Tanzania. Nine species, Schilbe mystus, Megalops cyprinoides, Terapon jarbua, Liza sp., Tilapia sp., Gerres filamentosus,Lutjanus fulvus, Clarias gariepinus, and Periophthalmus argentilineatus, were identified, with varying abundance across rivers and seasons. Fluctuations of mean %TOC and %TN in fish tissues were observed across seasons, with mean %TOC values varying from 30.4 ± 0.5% (during the dry season) to 35.1 ± 2.1% (during the wet season) and average %TN ranging from 9.3 ± 0.1% (in the dry season) to 10.7 ± 1.3% (in the wet season). Stable isotope ratios (δ13C, δ15N) also exhibited seasonal variations, with δ13C values ranging from - 21.3 ± 0.6‰ to - 16.0 ± 0.1‰ (dry season) and - 21.3 ± 1.1‰ to - 13.7 ± 0.1‰ (wet season), and δ15N values ranging from 9.3 ± 0.0‰ to 15.9 ± 2.7‰ (dry season) and 10.0 ± 0.1‰ to 17.9 ± 0.6‰ (wet season). These variations suggest diverse feeding habits and potential movement patterns between freshwater and marine environments. This study emphasizes the significance of factoring in seasonal fluctuations and dietary origins when investigating the ecology of fish inhabiting coastal rivers. Future research should focus on the impact of environmental factors (temperature, pH, dissolved oxygen) and human activities (land-use changes, pollution) on these ecosystems, with long-term monitoring programs being crucial for the sustainable management of these vital resources.

Fluvial flooding and plastic pollution - The delivery of potential human pathogenic bacteria into agricultural fields.

The frequency of plastic debris entering agricultural land is likely going to increase due to increased discharge into surface waters and more frequent flood events. Microbial biofilm on the surfaces of plastic pollution (known as the 'plastisphere') in freshwater environments often includes human pathogenic bacteria capable of causing disease. Pathogens have been detected on the surface of plastics in freshwater environments, but it is yet to be determined whether plastic debris can also transport pathogens into agricultural fields during flooding. Therefore, this study quantified the presence of viable pathogenic bacteria on the surface of plastic pollution at five agricultural fields along two rivers. All visible plastic debris, including sewage-associated plastic waste, were collected along a perpendicular 100m transect from the riparian zone into each field. All plastic pieces were screened for five target bacteria (Escherichia coli, intestinal enterococci, Salmonella spp., Campylobacter spp., and Klebsiella spp.) using selective media, and positively identified colonies subsequently tested for antimicrobial resistance. In all five fields, there were higher volumes of plastic in the areas closer to the river, with 75%±24% of plastic collected within 30m from the riverbank. Overall, 49% of all plastic collected in agricultural fields was colonised by phenotypically positive colonies for at least one or more target bacteria, with resistance to commonly prescribed antibiotics detected among several of these target bacteria. Therefore, the transport of contaminated plastic debris from fluvial floodwater into agricultural fields could pose an as yet unquantified risk of introducing potentially harmful bacteria into agricultural systems and the ultimately into the food chain.

Microplastic ingestion by an aquatic ciliate: Functional response, modulation, and reduced population growth.

Microplastic particles are ubiquitous in aquatic environments and are considered a major threat to the large range of heterotrophic organisms that involuntarily consume them. However, there is current uncertainty around the mechanisms underpinning microplastic uptake by aquatic consumers and the consequences for both the fate of the microplastics and the growth potential of consumer populations. We performed a feeding experiment, exposing a model freshwater ciliate, Tetrahymena pyriformis, to six different microplastic concentrations and measured microplastic uptake and population growth over the course of several generations. Microplastic uptake increased in a saturating fashion with concentration, consistent with a Type II functional response, with a maximum feeding rate of 22 microplastic particles individual-1h-1. Interestingly, microplastic uptake decreased through time and we observed that, after egestion, microplastic particles aggregated, rendering them too large for re-consumption. We built and tested a simulation model which matched rates of microplastic uptake when incorporating functional response parameters and assuming 50% immobilisation of microplastics after egestion. Nevertheless, ciliate population growth was compromised by the presence of microplastics, decreasing by 43% over the full microplastic concentration range. Taken together, our results demonstrate the potential for aquatic ciliates to play an important role in the uptake, transfer, and modification of microplastics in freshwater environments with associated negative impacts on population fitness.

Effects of low-salt stress on biological characteristics and transcriptomic profiles of Vibrio parahaemolyticus.

Studies have proved that halophilic Vibrio parahaemolyticus is widely detected in freshwater environments (salinity <0.5%). However, the growth and colonization of V. parahaemolyticus in low-salt environments remain unclear. This study was envisaged to assess the effects of low-salt stress on the growth, motility and biofilm formation of V. parahaemolyticus and the transcriptomic changes that the bacterium responds to such stress. The results indicated that low salt concentrations supported the growth (allowing growth to proceed, though at a lower speed) of V. parahaemolyticus, prolonged the lag time (LT), and decreased the maximum specific growth rate (μmax) of V. parahaemolyticus. Additionally, this low salinity inhibited its motility and enhanced its biofilm formation capacity. Notably, the growth of V. parahaemolyticus on both freshwater and marine-cultured Litopenaeus vannamei exhibited a similar trend, suggesting that V. parahaemolyticus might have adapted to thrive in freshwater food. Furthermore, the reasons for the support of V. parahaemolyticus growth in 0.25% NaCl was analyzed by transcriptome sequencing (RNA-seq). RNA-seq revealed that V. parahaemolyticus can improve resistance to adverse environments by reducing energy consumption and enhancing oxidative stress resistance to adapt to a low-salt environment. This study revealed that the freshwater environment supported the growth of V. parahaemolyticus and its influence on the growth of V. parahaemolyticus, providing valuable theoretical support for risk assessment.

The Atlantic salmon gill transcriptional response to natural infection with HPR0-ISAV (Isavirus salaris) in three Norwegian smolt farms.

Infectious Salmon Anaemia virus (ISAV) is an orthomyxovirus that causes large economic losses in Atlantic salmon (Salmo salar L.) aquaculture. All virulent ISAV variants originally emerged from a non-virulent subtype, ISAV-HPR0. Transient ISAV-HPR0 infections are common in both freshwater and marine environments. ISAV-HPR0 infects juveniles, marine salmon at on-growing sites, and broodstock salmon. The shift in virulence from ISAV-HPR0 to the virulent HPRΔ is suggested to be a stochastic event that depends on the virus's replication frequency. Therefore, reducing the capacity to maintain ISAV-HPR0 infection within individual farms may limit the risk of emerging pathogenic ISAV variants and ISA disease. The absence of infection-related clinical signs and the lack of experimental models limit our understanding of ISAV-HPR0-host interactions. We characterise the host transcriptional response to natural ISAV-HPR0 infection, using Atlantic salmon gill tissues collected on three Norwegian smolt farms. The comparison of all infected (qPCR-positive) and non-infected (qPCR-negative) individuals revealed a classic antiviral response in the gills of ISAV-HPR0 infected fish in a site-independent transcriptomic analysis. Complementary analyses showed that the response to infection varied considerably between sites. Site-specific differences could be associated with a range of factors that are challenging to control in field studies, such as fish size, the stage of infection, and the presence of additional microorganisms. Our findings enhance our understanding of how Atlantic salmon respond to ISAV-HPR0 infection, pinpointing common HPR0-induced antiviral response genes. Future studies should investigate whether these candidate genes limit virus replication in the gill for risk of novel transitions to virulence.

Distribution of early-branching Cyanobacteriia and the potential habitats that gave rise to the earliest oxygenic phototrophs.

The evolution of oxygenic photosynthesis in the Cyanobacteria was one of the most transformative events in Earth history, eventually leading to the oxygenation of Earth's atmosphere. However, it is difficult to understand how the earliest Cyanobacteria functioned or evolved on early Earth in part because we do not understand their ecology, including the environments in which they lived. Here, we use a cutting-edge bioinformatics tool to survey nearly 500,000 metagenomes for relatives of the taxa that likely bookended the evolution of oxygenic photosynthesis to identify the modern environments in which these organisms live. Ancestral state reconstruction suggests that the common ancestors of these organisms lived in terrestrial (soil and/or freshwater) environments. This restricted distribution may have increased the lag between the evolution of oxygenic photosynthesis and the oxygenation of Earth's atmosphere.IMPORTANCECyanobacteria generate oxygen as part of their metabolism and are responsible for the rise of oxygen in Earth's atmosphere over two billion years ago. However, we do not know how long this process may have taken. To help constrain how long this process would have taken, it is necessary to understand where the earliest Cyanobacteria may have lived. Here, we use a cutting-edge bioinformatics tool called branch water to examine the environments where modern Cyanobacteria and their relatives live to constrain those inhabited by the earliest Cyanobacteria. We find that these species likely lived in non-marine environments. This indicates that the rise of oxygen may have taken longer than previously believed.

Morphological and molecular phylogeny of Clinostomum sp. (Digenea: Clinostomidae) metacercariae, using DNA barcode from a South American freshwater fish.

Here, we present a comprehensive morphological and molecular phylogenetic analysis of Clinostomum sp. (Digenea: Clinostomidae) metacercariae parasitizing two freshwater fish species from Southeast Brazil: Serrasalmus spilopleura (piranha) and Callichthys callichthys (tambuatá). The morphological examination revealed distinct characteristics of metacercariae in each host. Using the cytochrome c oxidase I (COI) gene barcode region, we obtained DNA sequences that allowed for accurate phylogenetic placement. Phylogenetic analyses revealed that Clinostomum sp. HM41 (metacercariae), isolated from S. spilopleura, exhibited 86% similarity to Ithyoclinostomum yamagutii, while Clinostomum sp. HM125 (metacercariae), from C. callichthys, showed 98.7% similarity to Clinostomum sp. Cr_Ha1. The phylogenetic trees constructed through Bayesian Inference and Maximum Likelihood methods indicated high biodiversity within the Clinostomum genus and strong support for distinct lineages. These findings enhance our understanding of the diversity and ecological distribution of Clinostomum species in South American freshwater environments.

Chromosome-Level Genome Assembly and Comparative Genomic Analysis of Planiliza haematocheilus: Insights into Environmental Adaptation and Hypoxia Tolerance Mechanisms.

Planiliza haematocheilus, a teleostan species noted for its ecological adaptability and economic significance, thrives in both freshwater and marine environments. This study presents a novel chromosome-level genome assembly through Hi-C, PacBio CCS, and Illumina sequencing methods. The assembled genome has a final size of 651.58Mb, with 24 chromosomes anchoring 91.94% of contigs. Contig N50 and scaffold N50 are respectively measured at 25.52Mb and 28.59Mb. Of the 22,476 protein-coding genes identified in the genome, 21,834 have functional annotations. BUSCO (Benchmarking Universal Single-Copy Orthologs) genome and gene annotation assessments yielded scores of 96% and 96.6%, respectively. The genome of P. haematocheilus revealed 228 expanded and 1433 contracted gene families. Comparative genomic analyses highlight adaptations and hypoxia tolerance, linked to protein synthesis, immune response, and metabolic regulation. The high-quality genome assembly supports advanced studies on gene expression patterns under different environmental stressors, contributing to genetic enhancement efforts for this economically important aquaculture species.

Seasonal Dynamics of Phytoplankton Diversity in Ranchi Lake: Indicators of Water Quality and Ecosystem Health

A British soldier named Colonel Onsely created Ranchi lake, which the locals call Bada Talab, as a freshwater environment. Evaluating phytoplankton diversity and its connection to water quality is the goal. The evaluation of phytoplankton which are mostly found in water bodies is the focus of this research. The majority of the phytoplanktonic species found in Bada Talab belong to the Chlorophyceae, Bascilariophyceae and Cyanophyceae groups and this assessment carried out at regular intervals. Thus it can be concluded that April 2023- June 2023 is the ideal time period for Cyanophyceae members to grow followed by January2023- March 2023 for Chlorophyceae and January 2023-March 2023 for Bascilariophyceae. The most common species which are trustworthy markers of pollution and water quality were Microcystis, Spirogyra, Nostoc, Oscilatoria, Scendesmus, Pinnularia and Volvox. Certain genera such as Microcystis and Spirogyra are dominant and serve as indicators of pollution.

Combined application of metagenomics and FEAST to trace sources of microbial eukaryotic contamination in the Pasig-Marikina-San Juan (PAMARISAN) river system in Metro Manila, Philippines.

Microbial eukaryotes are vital to global microbial diversity, but there is limited information about their composition and sources in contaminated surface waters. This study examined the pathogens and potential sources of microbial eukaryotic communities in polluted sink environments using the 18S rDNA amplicon sequencing combined with the fast expectation-maximization for microbial source tracking (FEAST) program. Six sampling sites were selected along the Pasig-Marikina-San Juan (PAMARISAN) River System, representing different locations within the waterway and classified as sinks (n = 12), whereas animal fecal samples collected from various farms were classified as sources (n = 29). Taxonomic composition revealed Stramenopila, Alveolata, Rhizaria (SAR), Archaeplastida, and Excavata in the rivers, accounting for 85.1%, 13.2%, and 0.36% mean abundance of microbial sink communities, respectively. Clinically relevant human pathogens were also observed in sink environments. The correlation test demonstrated that dissolved oxygen, total suspended solids, pH, temperature, fecal coliform count, and phosphates were important environmental factors driving community variations. Moreover, FEAST results indicated that sewage (19.6%) was the primary source of microbial eukaryotes, followed by duck (0.644%) and cow (0.566%) feces. Spatio-seasonal variations showed higher contributions at downstream stations and during the wet season, highlighting the role of rainfall in enhancing microbial dispersal. Results from community-based microbial source tracking can be used to explore factors shaping microbial eukaryotes in freshwater environments, assess potential pathogen-related hazards, and inform river conservation and management strategies. Furthermore, this also serves as preliminary data for microbial eukaryotic source tracking in the Philippines, laying groundwork for future research.

Phylogeny of the planthopper genus Megamelus (Hemiptera, Delphacidae), with the description of two new species from South America.

Megamelus is a genus of Delphacidae widely distributed and mostly associated with plants in freshwater environments. Despite various taxonomic revisions and thorough research, the delimitation of the genus, its diversity, and its evolutionary history need to be further explored. Moreover, features originally considered distinctive of the genus exhibit variation and should be reassessed. Here, the genus Megamelus in South America was examined, describing two new species, Megamelusdelticus Remes Lenicov & Mariani, sp. nov. and Megamelusserpentinus Mariani & Remes Lenicov, sp. nov., and providing information on their host plants and geographical distribution. The distribution and host range knowledge of Megamelusiphigeniae and Megamelustimehri are also expanded, the male brachypter of M.timehri described for the first time, and a key to distinguish the species, based on male and female genitalia and their external morphology, is provided. Moreover, the first phylogenetic analysis of the genus is presented, based on the mitochondrial COI gene to clarify the interspecific relationships among its members. Our combined findings support the monophyly of the genus and refine diagnostic features, including the importance of the pygofer's lobed appearance. This comprehensive revision highlights the need for further multidisciplinary approaches to fully understand the evolutionary history of Megamelus and its interactions with host plants and environments.

A metagenomic perspective on the microbial prokaryotic genome census.

Following 30 years of sequencing, we assessed the phylogenetic diversity (PD) of >1.5 million microbial genomes in public databases, including metagenome-assembled genomes (MAGs) of uncultivated microbes. As compared to the vast diversity uncovered by metagenomic sequences, cultivated taxa account for a modest portion of the overall diversity, 9.73% in bacteria and 6.55% in archaea, while MAGs contribute 48.54% and 57.05%, respectively. Therefore, a substantial fraction of bacterial (41.73%) and archaeal PD (36.39%) still lacks any genomic representation. This unrepresented diversity manifests primarily at lower taxonomic ranks, exemplified by 134,966 species identified in 18,087 metagenomic samples. Our study exposes diversity hotspots in freshwater, marine subsurface, sediment, soil, and other environments, whereas human samples yielded minimal novelty within the context of existing datasets. These results offer a roadmap for future genome recovery efforts, delineating uncaptured taxa in underexplored environments and underscoring the necessity for renewed isolation and sequencing.

Progress in the Study of Toxic Effects of Microplastics on Organisms in Freshwater Environments and Human Health

Progress in the Study of Toxic Effects of Microplastics on Organisms in Freshwater Environments and Human Health

Exploring Diversity within Chytridiales and Rhizophydiales (Chytridiomycota) in Korea

Chytridiomycota is the most species-rich phylum of basal lineage fungi with a worldwide distribution. Its species constitute essential components of freshwater ecosystems. However, the diversity of this group in Korea remains understudied. A survey of Chytridiales and Rhizophydiales fungi was conducted in soil and freshwater environments in Korea, and seven strains were isolated. Based on morphological and molecular data, a previously unidentified, novel Rhizophydium species was discovered, designated Rhizophydium multiplex sp. nov. In addition, Chytriomyces hyalinus and Globomyces pollinis-pini were isolated for the first time in Korea. Detailed descriptions and illustrations of the three species are provided. This study highlights the potential diversity of chytrid fungi in Korea.

Paraplaconeis dorofeyukae sp. nov. (Cymbellales, Bacillariophyceae)—a new species from Mongolia, described based on molecular and morphological investigations

An unknown species of the diatom genus Paraplaconeis was discovered during a field study of freshwater environments in Central Mongolia. In the course of further study, two monoclonal strains were acquired for the unknown species. The strains were utilized for molecular-genetic analysis on SSU rRNA and rbcL genes. As a result of the molecular investigation and careful morphological examination of valve structure with light and scanning electron microscopy, we propose the description of a new species—Paraplaconeis dorofeyukae sp. nov.—in this article. The new species is morphologically compared to similar taxa from the Paraplaconeis placentula group. Paraplaconeis dorofeyukae sp. nov. can be distinguished from related species by a combination of valve dimensions, morphology of apices and central area, and external valve ultrastructure.

Seasonal and Spatial Variation in the Diet of Gambusia holbrooki in Different Water Bodies of Karaburun Peninsula (Western Türkiye)

The Eastern mosquitofish Gambusia holbrooki Girard, 1859, has been widely introduced into tropical and temperate countries as a biological agent to control mosquitos, which are associated with diseases such as malaria and yellow fever. However, the species exhibits invasive characteristics by competing with native species for food and habitat use. This study investigates the feeding ecology of G. holbrooki populations from three distinct freshwater environments (Lake Iris, Eğlenhoca Reservoir, and Parlak Reservoir) on the Karaburun Peninsula (North-Western Türkiye), a region outside its native range. The primary aim was to evaluate seasonal and spatial variations in the diet of the species. A total of 871 specimens were analysed: 247 from Iris Lake, 318 from Parlak Reservoir, and 306 from Eğlenhoca Reservoir. Low percentages of empty stomachs (≤20%) across all populations indicate high feeding intensity. The results reveal that G. holbrooki exhibits a generalist feeding strategy, consuming a wide range of food items such as insects, zooplankton, and plant material across all the investigated environments. The relative importance of food groups (determined by the Importance Index, MI%) varied seasonally but not spatially. In all three populations, the most important food source in the spring was dipterans, followed by plants in the summer and fall, and cladocerans in the winter. Plants accounted for the largest percentage of the diet in every population (MI% &gt;65%). These findings suggest that G. holbrooki adapts its diet to seasonal food availability.

MICROPLASTICS IN A LOTIC FRESHWATER ENVIRONMENT: TYPOLOGY AND PROFILE OF OCCURRENCE ALONG JOUMINE STREAM, AFFLUENT OF THE ICHKEUL WETLAND (NORTHERN TUNISIA)

The intensifying plastic production and poor management of its waste have led to a tremendous rise in the dumping into aquatic ecosystems, thus resulting in harmful effects on living organisms as well as biodiversity loss and wetland threat. The study aims to assess the availability of microplastics in a freshwater environment (the Joumine stream, Northern Tunisia) by determining their abundance, shape, type, color, and size in both water and sediment. Thirty samples were collected from five sites and analyzed for MPs using stereomicroscopy and FTIR spectroscopy. The average value of microplastics was found to be 8.87±3.94/L (in water) and 18.2±8.27/50g dry weight (in sediment). The most dominant form in all samples was fibers, while the color category varied according to the two considered matrices and sites. Microplastic particles in the samples ranged from 0.24 to 1.45 mm in length. Polypropylene and polyethylene were the identified types of polymers. Overall, the level of microplastic pollution along the Joumine stream was found to be relatively average compared to the global pollution level. It underlined the fact that MPs are widespread even in freshwater environments and provides a baseline for future surveys and management sustainable decisions.

Freshwater life-cycle timing of Pacific salmon and steelhead (Oncorhynchus spp.) in Canada

Information on species’ phenology and distribution is essential for assessing and mitigating exposure to pressures that vary over space and time, such as development projects or climate changes. Pacific salmon (Oncorhynchus spp.) have complex life cycles that span freshwater and marine environments and unfold over several years and many thousands of kilometers. Currently, there is no central repository of life-cycle timing for salmon and steelhead populations throughout their Canadian range, hindering conservation and recovery efforts. To fill this gap, we have compiled timing data for fry migration from incubation to rearing grounds, juvenile migration from rearing grounds to the ocean, adult entry into rivers, and spawning for salmon and steelhead from British Columbia and the Yukon, Canada. For each species, we analysed the compiled data using linear models to describe patterns in population-specific timing across latitude, distance from the ocean, river gradient, and life-history types. Although we found significant data gaps in remote regions, our compiled dataset represents the best-available information on life-history timing that can inform environmental planning and salmon conservation actions

Microplastics as Emerging Contaminants: Challenges in Inland Aquatic Food Web

Microplastic (MP) pollution in inland water bodies, such as rivers, lakes, and reservoirs, is a growing environmental concern, yet research on its ecological impacts in freshwater ecosystems remains limited compared to marine environments. Microplastics, defined as particles smaller than 5 mm, have been detected in freshwater systems globally, and their presence is widespread across diverse aquatic habitats. This review examines the sources, distribution, persistence, and ecological consequences of microplastics in freshwater ecosystems, emphasizing their bioaccumulation in organisms from plankton to fish, and the potential risks to human health through microplastic-contaminated fish consumption. Ingestion of microplastics by aquatic organisms can cause physical harm, such as entanglement, and chemical toxicity, including oxidative stress and the accumulation of harmful substances. The trophic transfer of microplastics through the food web raises concerns about higher-level organisms, including humans. Despite these risks, significant knowledge gaps exist regarding the long-term effects of microplastics on freshwater ecosystems. The review calls for improved monitoring, mitigation strategies, and regulatory frameworks to address this issue. Further research is needed to understand the full extent of microplastic pollution in freshwater environments and its impacts on both biodiversity and human health.