Cadmium-induced developmental alteration and upregulation of serine-type endopeptidase transcripts in wild freshwater populations of Chironomus plumosus

The trophic interaction of freshwater chironomids using DNA metabarcoding and stable isotope analysis in stream ecosystem

Identifying the food sources of aquatic insects is crucial for understanding their ecological roles and ecosystem dynamics. However, obtaining direct information on food sources in freshwater ecosystems can be challenging. This study employed DNA metabarcoding and stable isotope analysis to identify the primary food sources of chironomids, the first dominant group of aquatic insects, and to monitor their response to water temperature changes. We conducted field sampling surveys to identify the most dominant taxonomy and analyze the gut contents of chironomids in the urban stream of Yeosu City Center, South Korea. DNA metabarcoding analysis of chironomid gut contents revealed that algae were the dominant food source, with a high relative abundance of diatoms (Bacillariophyta) and green algae (Chlorophyta). Stable isotope analysis of chironomid tissues and their habitat environment supported these findings, indicating that particulate organic matter and algae were the primary dietary components. We found that seasonal changes influenced chironomid community composition and food source preferences. The genus Cricotopus (Orthocladiinae) was dominant in cooler water temperatures, while Chironomus (Chironominae) became dominant as water temperatures increased. DNA metabarcoding analysis revealed that Cricotopus consumed a wider variety of algae, including diatoms and green algae, while Chironomus primarily consumed diatoms. This study highlights the importance of DNA metabarcoding and stable isotope analysis as effective tools to assess food source diversity and trophic levels in aquatic insects and their associated environmental conditions. The findings provide new insights into the trophic relationships within freshwater ecosystems and the potential impacts of environmental changes on aquatic insect communities.

Identifying potential trace metal contamination impacts of a coal ash landfill on the largest Chesapeake Bay tributary (Chester, VA, USA)

Coal fly ash is a highly heterogeneous waste product that becomes concentrated with metals after combustion that have been shown to act as neurotoxins and/or carcinogens in both wildlife and humans. As such, increased understanding of the presence, concentrations, and potential ecosystem impacts is needed. The Chesterfield power station contains more than 15 million tons of ash and is located adjacent to the James River, which serves as a tributary to the Chesapeake Bay. Our study investigated (1) the presence and concentrations of aluminum (Al), aresnic (As), cadmium (Cd), chromium (Cr), copper (Cu), iron (Fe), magnesium (Mg), manganese (Mn), lead (Pb), selenium (Se), and zinc (Zn) in surface water, deep water, and sediment samples obtained from the surrounding area and (2) the presence of various teleost species, using environmental DNA (eDNA) sampling. Universal cokriging was used to estimate the spatial variability of metals in sediments and the extent of pollution interpreted using enrichment factors (EF). Little contamination was observed in water samples compared to sediment samples. Elevated concentrations of Al, As, Cd, Cr, Fe, Pb, and Zn were observed in areas immediately adjacent to the coal ash landfills. Arsenic, Cd, and Pb showed increased EF in sites adjacent to the landfills, suggesting that the contamination observed is due to anthropogenic factors. Environmental DNA analyses revealed the presence of 22 teleost species, several of which have been identified as threatened, endangered, diadromous, and/or consumed by anglers who use the James River. Collectively, our results provide novel insight regarding the impacts of coal ash on an important Chesapeake Bay watershed and guidance for future risk assessment.

The Divergent Responses of Salinity Generalists to Hyposaline Stress Provide Insights Into the Colonisation of Freshwaters by Diatoms

Environmental transitions, such as the salinity divide separating marine and fresh waters, shape biodiversity over both shallow and deep timescales, opening up new niches and creating opportunities for accelerated speciation and adaptive radiation. Understanding the genetics of environmental adaptation is central to understanding how organisms colonise and subsequently diversify in new habitats. We used time-resolved transcriptomics to contrast the hyposalinity stress responses of two diatoms. Skeletonema marinoi has deep marine ancestry but has recently invaded brackish waters. Cyclotella cryptica has deep freshwater ancestry and can withstand a much broader salinity range. Skeletonema marinoi is less adept at mitigating even mild salinity stress compared to Cyclotella cryptica, which has distinct mechanisms for rapid mitigation of hyposaline stress and long-term growth in low salinity. We show that the cellular mechanisms underlying low salinity tolerance, which has allowed diversification across freshwater habitats worldwide, includes elements that are both conserved and variable across the diatom lineage. The balance between ancestral and lineage-specific environmental responses in phytoplankton have shaped marine-freshwater transitions on evolutionary timescales and, on contemporary timescales, will affect which lineages survive and adapt to changing ocean conditions.

Genome-wide identification of crustacyanin and function analysis of one isoform high-expression in carapace from Neocaridina denticulata sinensis

Lipocalin proteins transport hydrophobic molecules, including apolipoprotein D, retinol-binding protein, and crustacyanin (CRCN). CRCN can combine with astaxanthin to cause a bathochromic shift in the emission spectrum of astaxanthin from red to blue. Therefore, CRCN influences the colors and patterns of crustaceans, which are important for various biological functions such as camouflage, reproduction, and communication. For aquatic organisms, body color is economically important and can be indicative of habitat water quality. In this study, thirteen CRCN genes (NdCRCNs) were first discovered in Neocaridina denticulata sinensis, contradicting prior findings of a few isoform genes in a species. The expression pattern of NdCRCNs in tissues showed that the expression of one CRCN isoform gene, named NdCRCN-30, was the highest in the carapace. In situ hybridization (ISH) analysis revealed that NdCRCN-30 was predominantly distributed in the outer epidermis of shrimp. Interference of NdCRCN-30 could cause a change in the color of the carapace. RNA-seq was performed after knockdown with the NdCRCN-30, and differential gene enrichment analysis revealed that this gene is primarily associated with antioxidant function, pigmentation, and molting. Overall, our results will provide new insights into the biological function of the CRCN and genetic breeding for changing body color in economic crustaceans.

Molecular level toxicity effects of As(V) on Folsomia candida: Integrated transcriptomics and metabolomics analyses

Arsenic (As) is a widespread metalloid with well-known toxicity. To date, numerous studies have focused on individual level toxicity (e.g., growth and reproduction) of As to typical invertebrate springtails in soils, however, the molecular level toxicity and mechanism was poorly understood. Here, an integrated transcriptomics and metabolomics approach was used to reveal responses of Folsomia candida exposed to As(V) of 10 and 60 mg kg-1 at which the individual level endpoints were influenced. Transcriptomics identified 5349 and 4020 differentially expressed genes (DEGs) in low and high concentration groups, respectively, and the most DEGs were down-regulated. Enrichment analysis showed that low and high concentrations of As(V) significantly inhibited chromatin/chromosome-related biological processes (chromatin/chromosome organization, nucleosome assembly and organization, etc.) in springtails. At high concentration treatment, structural constituent of cuticle, chitin metabolic process and peptidase activity (serine-type peptidase activity, endopeptidase activity, etc.) were inhibited or disturbed. Moreover, the apoptosis pathway was significantly induced. Metabolomics analysis identified 271 differential changed metabolites (DCMs) in springtails exposed to high concentration of As. Steroid hormone biosynthesis was the most significantly affected pathway. Several DCMs that related to chitin metabolism could further support above transcriptomic results. These findings further extended the knowledge of As toxic mechanisms to soil fauna and offer important information for the environmental risk assessment.

Growth retardation and suppression of ubiquitin-dependent catabolic processes in the brackish water clam Corbicula japonica in response to salinity changes and bioaccumulation of toxic heavy metals

The brackish water clam (Corbicula japonica) is constantly exposed to stressful salinity gradients and high levels of heavy metals in the freshwater-saltwater interface of estuary environments, which are introduced from upstream regions and land. To identify the key molecular pathways involved in the response to salinity changes and heavy metal bioaccumulation, we obtained the transcriptomes of C. japonica inhabiting different salinities and heavy metal distributions in Gwangyang Bay (Korea) using RNA sequencing. Among a total of 404,486 assembled unigenes, 5534 differentially expressed genes were identified in C. japonica inhabiting different conditions, 1549 of which were significantly upregulated and 1355 were significantly downregulated. Correlation analyses revealed distinct gene expression patterns between the low and high conditions of salinity and heavy metal bioaccumulation. Functional annotation revealed significant downregulation of genes involved in "ubiquitin-dependent protein catabolic process," "tricarboxylic acid cycle," and "intracellular protein transport" in C. japonica from the high condition compared to the low condition. Transcription and translation pathways were significantly enriched in the high condition. Additionally, upon comparison of the low and high conditions by qRT-PCR and proteasome enzyme activity analyses, our findings demonstrated that environmental stress could suppress the ubiquitin-proteasome complex (UPC). Additionally, transcriptomic changes under high salinity stress conditions may be related to an increase in cellular protection by defense enzymes, which leads to more energy being required and a disruption of energy homeostasis. Ultimately, this could cause growth retardation in the clam C. japonica. In summary, this study provides the first evidence of UPC suppression induced by a combination of high salinity and heavy metal bioaccumulation stress in C. japonica, which could compromise the survival and growth of estuarine bivalves.

RNA sequencing analysis revealed differentially expressed genes and their functional annotation in porcine longissimus dorsi muscle affected by dietary lysine restriction

The objective of this study was to investigate the effects of dietary lysine restriction on the global gene expression profile of skeletal muscle in growing pigs. Twelve crossbred (Yorkshire × Landrace) barrows (initial BW 22.6 ± 2.04 kg) were randomly assigned to two dietary treatments (LDD: a lysine-deficient diet; LAD: a lysine-adequate diet) according to a completely randomized experiment design (n = 6). After feeding for 8 weeks, skeletal muscle was sampled from the longissimus dorsi of individual pigs. The muscle total RNA was isolated and cDNA libraries were prepared for RNA sequencing (RNA-Seq) analysis. The RNA-Seq data obtained was then analyzed using the CLC Genomics Workbench to identify differentially expressed genes (DEGs). A total of 80 genes (padj ≤ 0.05) were differentially expressed in the longissimus dorsi muscle of the pigs fed LDD vs. LAD, of which 46 genes were downregulated and 34 genes were upregulated. Gene Ontology (GO) analysis of the DEGs (padj ≤ 0.05) for functional annotation identified those GO terms that are mostly associated with the molecular functions of structural molecules and metabolic enzymes (e.g., oxidoreductase and endopeptidase), biological process of acute-phase response, and amino acid metabolism including synthesis and degradation in the extracellular matrix region. Collectively, the results of this study have provided some novel insight regarding the molecular mechanisms of muscle growth that are associated with dietary lysine supply.

Surveillance spilled Chironomidae (Diptera) larvae from drinking water treatment plants in South Korea using morphogenetic species analysis and eDNA metabarcoding

Chironomid larvae (Diptera: Chironomidae) are tremendous indicator species that can tolerate a broad range of environmental conditions, from polluted to unimpaired water ecosystems. These species are ubiquitously observed in all bioregions and can even be found in drinking water treatment plants (DWTPs). Detection of chironomid larvae in DWTPs is a critical issue because their presence may be indicative of the water quality in the supply of tap water for human consumption. Therefore, the aim of the present study was to identify the chironomid communities that reflect the water quality of DWTPs and develop a biomonitoring tool to detect biological contamination of the chironomids in DWTPs. To do so, we investigated the identity and distribution of chironomid larvae in seven DWTP areas using morphological identification, DNA barcoding, and sediment environmental DNA (eDNA) analysis. A total of 7924 chironomid individuals encompassing three subfamilies and 25 species of 19 genera were identified in 33 sites within the DWTPs. The Gongchon and Bupyeong DWTPs were dominated by Chironomus spp. larvae, which were correlated with low levels of dissolved oxygen in the water. In the Samgye DWTP and Hwajeong DWTP, Chironomus spp. were almost absent, and instead, Tanytarsus spp. were abundant. Additionally, the Gangjeong DWTP was dominated by a Microtendipes sp., and two species of Orthocladiinae (a Parametriocnemus sp. and a Paratrichocladius sp.) were found only in the Jeju DWTP. We also identified the eight most abundant Chironomidae larvae found in the DWTPs. Furthermore, eDNA metabarcoding of DWTP sediment indicated the presence of different eukaryotic fauna and confirmed the presence of chironomids in DWTPs. These data provide useful morphological and genetic information regarding chironomid larvae that can be used for the water quality biomonitoring of DWTPs to support the supply of clean drinking water.

Evaluation of Cd2+ stress on Synechocystis sp. PCC6803 based on single-cell elemental accumulation and algal toxicological response

With the development of single cell analysis techniques, the concept of precision toxicology has been proposed in recent years. Due to the heterogeneity of cells, we need to perform toxicological assessments on individual cells. Microalgae, one kind of important primary producers, play as a major pathway by which heavy metals enter the food chain and thus accumulate/transfer to higher trophic levels. Herein, the biosorption of Cd (Ex-Cd) and bioaccumulation of Cd (In-Cd) for Synechocystis sp. PCC 6803 were investigated by online 3D droplet microfluidic device combined with inductively coupled plasma mass spectrometry detection. Meanwhile, the algal toxicological responses of the algae cell to Cd²⁺ exposure under different concentration (50, 100, and 150 μg L ^- 1) and time (15 min, 24, 48 and 96 h) were studied. Combining single-cell analysis with toxicological indicators, the toxicity mechanism of Cd²⁺to algal was discussed. The single cell analysis results revealed heterogeneity in cellular uptake of Cd²⁺. The proportion of Cd-containing cells and Cd content in single algal cells all reached the maximum at 24 h. The uptake of Cd²⁺ occurred within 15 min under all tested exposure concentrations and a large part of Cd²⁺ were adsorbed on the algal cells surface. The Pearson correlation analysis showed that cell density, chlorophyll a and carotenoids were significantly negatively correlated with Cd accumulation, whereas ROS level and SOD activity were significantly positively correlated with Cd accumulation. It suggested that Cd²⁺accumulated intracellular would show toxic effects on the algal cells and oxidative stress is the main mechanism of Cd toxicity to algal cells. This work promotes our understanding of the toxicological responses of microalgae under Cd stress at single cells level.

Analysis of Differential Gene Expression of the Aquatic Insect Protohermes costalis (Walker) (Megaloptera: Corydalidae) in Response to Cadmium Exposure

Heavy metal pollution in freshwater ecosystems is a serious threat to aquatic organisms. Species of Megaloptera are important predators of aquatic invertebrates and have been widely used as bioindicators in assessing the quality of freshwater ecosystems. In this study, we determined the differential gene expression profile of Protohermes costalis (Walker) (Megaloptera: Corydalidae) in response to cadmium (Cd) exposure by using transcriptome analysis. A total of 60,627 unigenes were obtained in the transcriptomes of 150 mg/liter (PL), 1,000 mg/liter (PH) CdCl2 treatment, and the no Cd control (PC). Differential expression gene (DEG) analysis by pairwise comparison identified 2,794 DEGs after filtering the noninsect genes and repetitive counts. 606 DEGs were shared in comparisons of PL versus PC and PH versus PC, with 165 DEGs consistently up-regulated and 441 down-regulated by both PL and PH. Six heat shock proteins (HSPs) in the HSP70 family were identified in P. costalis and PcosHSP68 was up-regulated by both PL and PH. Real-time quantitative polymerase chain reaction (RT-qPCR) confirmed that the expression levels of PcosHSP68 in PL and PH were higher than that of PC by 31 and 197%, respectively. These results showed that exposure to Cd altered the gene expression profiles of P. costalis and the transcriptome data presented in this study provide insight into future studying on molecular mechanisms of Cd toxicity to these insects.

Toxicity evaluation of pyraclostrobin exposure in farmland soils and co-exposure with nZnO to Eisenia fetida

Although the toxicity of pyraclostrobin (PYRA) to earthworms in artificial soil is well known, the toxicity of PYRA in farmland soils is yet to be explored in detail. Additionally, with more zinc oxide nanoparticles (nZnO) entering the soil environment, the risk of PYRA co-exposure with nZnO is increasing alarmingly. However, toxicity caused by this co-exposure of PYRA and nZnO is still unknown. Therefore, we assessed the biomarkers responses to reveal the toxicity of PYRA (0.1, 1, 2.5 mg/kg) on earthworms in farmland soils (black soil, fluvo-aquic soil, and red clay) and evaluated the biomarkers responses of Eisenia fetida exposed to PYRA (0.5 mg/kg)/PYRA+nZnO (10 mg/kg). Moreover, transcriptomic analysis was performed on E. fetida exposed to PYRA/PYRA+nZnO for 28 days to reveal the mechanism of genotoxicity. The Integrated Biomarker Responses (IBR) showed PYRA induced more severe oxidative stress and damage to E. fetida in farmland soils than that in artificial soil. The oxidative stress and damage induced by PYRA+nZnO were greater than that induced by PYRA. Transcriptomic analysis showed that PYRA and PYRA+nZnO significantly altered gene expression of both biological processes and molecular functions. These results provided toxicological data for PYRA exposure in three typical farmland soils and co-exposure with nZnO.

Transcriptome profiling reveals sex-specific gene expressions in pupal and adult stages of the mosquito Culex pipiens

Understanding the development process of male and female mosquitoes provides important basic information for sterile insect release programmes and is important for improving other vector control strategies. However, little is known about the molecular mechanisms that distinguish male from female-specific developmental processes in this species. We used IlluminaRNA-seq to identify sex-specific genes during pupal and adult stages. One hundred and forty-seven genes were expressed only in pupal males, 56 genes were expressed in adult males and another 82 genes were commonly expressed in both male samples. In addition, 26 genes were expressed only in the pupal females, 163 genes were found in the adult females and only one gene was expressed in both female samples. A further quantitative real-time PCR validation of selected genes from the RNA sequencing (RNA-seq) analysis confirmed upregulation of those genes in a sex-specific manner, including: fibrinogen and fibronectin, a zinc finger protein, phospholipase A(2) and a serine protein for female pupae; venom allergen 3, a perlecan, testis-specific serine/threonine-protein kinase 1, testis-specific serine/threonine-protein kinase 6 and cytochrome c-2 for male pupae; a salivary protein, D7 protein precursor, trypsin 7 precursor, D7 protein and nanos for female adults; and tetraspanin F139, cytosol aminopeptidase, testis-specific serine/threonine-protein kinase 1, a testis-specific serine/threonine-protein kinase 6 and a C-type lectin for male adults. These findings provide insight into the development and physiology of Culex mosquitoes, which will help in the development of more effective control methods for these disease vectors.

Study on molecular level toxicity of Sb(V) to soil springtails: using a combination of transcriptomics and metabolomics

To date, numerous studies have focused on the toxicity of antimony (Sb) to soil-dwelling organisms at the individual level. However, little is known about Sb-caused molecular level toxicity. Here, an integrated transcriptomics and metabolomics approach was used to better reveal toxicity of Sb(V) to springtails Folsomia candida considering environmentally relevant speciation of Sb. No significant effects of Sb(V) on survival, reproduction and growth of springtails were observed using the ISO standard test. Transcriptomics analysis identified 1015 and 3367 differentially expressed genes (DEGs) after 2 and 7 d of exposure, indicating an increasing transcriptomal changes with time. Significantly enriched top GO (Gene Ontology) terms (chitin metabolic process, chitin binding and extracellular region) were shared between the two time exposure groups. However, no enriched KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway was shared, with fatty acid metabolism and apoptosis-fly being the most significant pathway, respectively. Metabolomics analysis identified 155 differential changed metabolites (DCMs) in springtails after 7 d of exposure. Antifolate resistance was the most significantly enriched pathway, in which dihydrofolic acid was up-regulated and three purine nucleotides (adenosine 5'-monophosphate, inosine 5'-monophosphate, guanosine 5'-monophosphate) were down-regulated. This indicated obvious repression of DNA replication, which was also observed by transcriptomics. Additionally, metabolites level related to chitin, oxidative stress, and protein metabolism significantly changed, and these metabolites could also support and confirm main transcriptomic results. Thus, the combination of multiomics facilitated better understanding of the molecular level of toxicity of Sb(V) in Collembola.

Multi-Level Gene Expression in Response to Environmental Stress in Aquatic Invertebrate Chironomids: Potential Applications in Water Quality Monitoring

In freshwater ecosystems, aquatic invertebrates are influenced continuously by both physical stress and xenobiotics. Chironomids (Diptera; Chironomidae), or non-biting midges, are the most diverse and abundant invertebrates in freshwater habitats. They are a fundamental link in food chains of aquatic ecosystems. Chironomid larvae tolerate stress factors in their environments via various physiological processes. At the molecular level, environmental pollutants induce multi-level gene responses in Chironomus that regulate cellular protection through the activation of defense processes. This paper reviews literature on the transcriptional responses of biomarker genes to environmental stress in chironomids at the molecular level, in studies conducted from 1991 to 2020 (120 selected literatures of 374 results with the keywords "Chironomus and gene expression" by PubMed search tool). According to these studies, transcriptional responses in chironomids vary depending on the type of stress factor and defensive responses associated with antioxidant activity, the endocrine system, detoxification, homeostasis and stress response, energy metabolism, ribosomal machinery, apoptosis, DNA repair, and epigenetics. These data could provide a comprehensive overview of how Chironomus species respond to pollutants in aquatic environments. Furthermore, the transcriptomic data could facilitate the development of genetic tools for water quality and environmental monitoring based on resident chironomid species.