Transcriptional profiling of antioxidant defense system and heat shock protein (Hsp) families in the cadmium- and copper-exposed marine ciliate Euplotes crassu

Multiple biological responses and transcriptome plasticity of the model unicellular eukaryote paramecium for cadmium toxicity aggravated by freshwater acidification

Cadmium (Cd) pollution is a widespread threat to aquatic life, and ongoing freshwater acidification (FA) can be expected to interact with Cd compounds to disrupt freshwater ecosystems. However, the effects of FA on Cd biotoxicity remain unclear. Herein, the model ciliate Paramecium tetraurelia, a model unicellular eukaryotic organism, was used to explore the response to environmental relevant concentrations of Cd under acidification conditions. We show for the first time that exposure to acidified freshwater accelerated Cd bioaccumulation and enhanced Cd bioavailability in P. tetraurelia, suggesting the synergistic interaction of Cd and FA. The co-exposure greatly reduced the abundance and carbon biomass, altered lysosomal membrane stability, induced oxidative stress, and consumed more ATP in exposed ciliates. Transcriptome plasticity enabled P. tetraurelia to develop a Cd stress-adaptive transcriptional profile (upregulation of transport and detoxification and downregulation of energy metabolism) under acidification. With a concomitant inhibition in energy production, the exposed ciliates might have diverted the energy from growth and cell replication to compensate for the energetic cost from stress response and detoxification. Collectively, acidified freshwater could aggravate Cd toxicity, which, in turn, arouses the response strategy of ciliates to cope with stress, providing a mechanistic understanding of the interaction between freshwater acidification and Cd pollution in the basic trophic level ciliated protozoa in freshwater ecosystems.

Comparative Transcriptome Analysis of the Hepatopancreas from Macrobrachium rosenbergii Exposed to the Heavy Metal Copper

The contamination of aquatic ecosystems by the heavy metal copper (Cu) is an important environmental issue and poses significant risks to the physiological functions of aquatic organisms. Macrobrachium rosenbergii is one of the most important freshwater-cultured prawns in the world. The hepatopancreas of crustaceans is a key organ for immune defense, heavy metal accumulation, and detoxification, playing a pivotal role in toxicological research. However, research on the molecular response of the hepatopancreas in M. rosenbergii to Cu exposure is still lacking. In this study, the transcriptomic response in the hepatopancreas of M. rosenbergii was studied after Cu exposure for 3 and 48 h. Compared with the control group, 11,164 (7288 up-regulated and 3876 down-regulated genes) and 10,937 (6630 up-regulated and 4307 down-regulated genes) differentially expressed genes (DEGs) were identified after 3 and 48 h exposure, respectively. Most of these DEGs were up-regulated, implying that gene expressions were largely induced by Cu. Functional enrichment analysis of these DEGs revealed that immunity, copper homeostasis, detoxification, DNA damage repair, and apoptosis were differentially regulated by Cu. Seven genes involved in immunity, detoxification, and metabolism were selected for validation by qRT-PCR, and the results confirmed the reliability of RNA-Seq. All these findings suggest that M. rosenbergii attempts to resist the toxicity of Cu by up-regulating the expression of genes related to immunity, metabolism, and detoxification. However, with the excessive accumulation of reactive oxygen species (ROS), the antioxidant enzyme system was destroyed. As a result, DNA damage repair and the cellular stress response were inhibited, thereby exacerbating cell damage. In order to maintain the normal function of the hepatopancreas, M. rosenbergii removes damaged cells by activating the apoptosis mechanism. Our study not only facilitates an understanding of the molecular response mechanisms of M. rosenbergii underlying Cu toxicity effects but also helps us to identify potential biomarkers associated with the stress response in other crustaceans.

Phytodegradation of neonicotinoids in Cyperus papyrus from enzymatic and transcriptomic perspectives

Neonicotinoids are widely used but environmentally hazardous insecticides. Constructed wetlands offer potential for neonicotinoid removal, but the corresponding metabolic pathways and mechanisms in wetland plants are incompletely understood. This study investigated the fate of six neonicotinoids and their metabolites in Cyperus papyrus, a common wetland plant, and the underlying metabolic mechanisms through enzymatic and transcriptomic analyses. Neonicotinoids were absorbed by roots and translocated upward, causing high levels in shoots. Concentrations of neonicotinoids and their metabolites declined to their minimum at day 28 of exposure. Nitro reduction, hydroxylation, and demethylation were the major metabolic reactions with which C. papyrus responded to neonicotinoids. These reactions may be mediated by cytochrome P450 enzyme, aldehyde oxidase, glutathione-disulfide reductase, and glucuronate reductase. The toxicity of neonicotinoids in C. papyrus was evaluated according to the peroxidase and catalase enzymatic activities. Transcriptomic analysis revealed that differentially expressed genes (DEGs) mainly encoded proteins related to immune processes and cell growth regulation. Co-expression correlation analysis of DEGs revealed that the genes encoding P450s, peroxidase and glutathione S-transferase were the key functional genes. This study elucidates the stress response and degradation mechanism of neonicotinoids in wetland plants, providing new insights into the phytoremediation of organic contaminants in constructed wetlands.

Cadmium exposure-triggered growth retardation in Hyphantria cunea larvae involves disturbances in food utilization and energy metabolism

Serious environmental pollution in the ecosystem makes phytophagous insects face a great risk of exposure to pollutants, especially heavy metals. This study aims to understand the effects of Cd exposure on the growth and development of Hyphantria cunea and to elucidate the mechanism of growth toxicity induced by Cd from the perspective of food utilization and energy metabolism. Our results showed that the larval basal growth data, growth index, fitness index, and standard growth index were significantly decreased after feeding on Cd-containing artificial diets. The Cd-treated larvae had significantly higher digestibility than the untreated larvae. However, the food consumption, efficiency of conversion of digested food, and efficiency of conversion of ingested food were significantly lower than those of untreated larvae. Eight key metabolites in the glycolysis pathway and six key metabolites in the tricarboxylic acid cycle pathway were significantly reduced in Cd-treated larvae. The mRNA expression levels of two regulatory genes (6-phosphofructokinase 1 and hexokinase-1) belonging to two key enzymes in the glycolysis pathway and four regulatory genes (isocitrate dehydrogenase-1, isocitrate dehydrogenase-3, citrate synthase, and oxoglutarate dehydrogenase) belonging to three key enzymes in the tricarboxylic acid cycle pathway were significantly lower in the Cd-treated group than in the control group. Furthermore, most fitness-related traits were significantly and positively correlated with food utilization (except approximate digestibility) or energy metabolism parameters. Taken together, Cd exposure-triggered growth retardation of H. cunea larvae is a consequence of disturbances in food utilization and energy metabolism, thereby emphasizing the toxicity of heavy metals.

Legacy Metal Contaminants and Excess Nutrients in Low Flow Estuarine Embayments Alter Composition and Function of Benthic Bacterial Communities

Coastal systems such as estuaries are threatened by multiple anthropogenic stressors worldwide. However, how these stressors and estuarine hydrology shape benthic bacterial communities and their functions remains poorly known. Here, we surveyed sediment bacterial communities in poorly flushed embayments and well flushed channels in Sydney Harbour, Australia, using 16S rRNA gene sequencing. Sediment samples were collected monthly during the Austral summer-autumn 2014 at increasing distance from a large storm drain in each channel and embayment. Bacterial communities differed significantly between sites that varied in proximity to storm drains, with a gradient of change apparent for sites within embayments. We explored this pattern for embayment sites with analysis of RNA-Seq gene expression patterns and found higher expression of multiple genes involved in bacterial stress response far from storm drains, suggesting that bacterial communities close to storm drains may be more tolerant of localised anthropogenic stressors. Several bacterial groups also differed close to and far from storm drains, suggesting their potential utility as bioindicators to monitor contaminants in estuarine sediments. Overall, our study provides useful insights into changes in the composition and functioning of benthic bacterial communities as a result of multiple anthropogenic stressors in differing hydrological conditions.

Morpholino-Mediated Knockdown of Ciliary Genes in Euplotes vannus, a Novel Marine Ciliated Model Organism

Cilia are highly conserved organelles present in almost all types of eukaryotic cells, and defects in cilia structure and/or function are related to many human genetic disorders. Single-celled ciliated protists, which possess diverse types of cilia, are remarkable model organisms for studying cilia structures and functions. Euplotes vannus is a representative ciliate with many intriguing features; for example, it possesses extensively fragmented somatic genomes and a high frequency of + 1 programmed ribosomal frameshifting. However, the molecular mechanisms underlying these remarkable traits remain largely unknown, mainly due to the lack of efficient genetic manipulation tools. Here, we describe the first application of a morpholino-based strategy to knockdown gene expression in E. vannus. Through interfering with the function of two ciliary genes, ZMYND10 and C21ORF59, we showed that these two genes are essential for the ciliary motility and proliferation of E. vannus cells. Strikingly, both ZMYND10- and C21ORF59-knockdown cells developed shorter cilia in the ventral cirri, a special type of ciliary tuft, suggesting a novel role for these genes in the regulation of cilia length. Our data provide a new method to explore gene function in E. vannus, which may help us to understand the functions of evolutionarily conserved cilia-related genes as well as other biological processes in this intriguing model.

TiO2 nanoparticles and multi-walled carbon nanotubes monitoring and bioremediation potential using ciliates Pseudocohnilembus persalinus

In recent years, the release of nanomaterials pollutants to water bodies, to a great extent, attributed to anthropogenic activities. Their impacts on aquatic organisms as well as nanomaterial monitoring and bioremediation using organism have drawn much attentions. However, studies on relationship of nano-contaminants and aquatic organisms are very scarce. Our results showed that titanium dioxide nanoparticles (TiO₂-NPs) and Multi-walled carbon nanotubes (MWCNTs) caused an obvious cell decreases on the whole, but a significant increase at 48 h TiO₂-NPs exposure, indicating a resistant mechanism in ciliates for nano-toxic. Besides, MWCNTs was more toxic to Pseudocohnilembus persalinus than that of TiO₂-NPs in terms of EC₅₀ value. It is firstly found that P. persalinus ingested and released TiO₂-NPs through cytostome and cytoproct, which might be the reason that TiO₂-NPs less toxic than MWCNTs. The significantly increased superoxide dismutase (SOD) and glutathione S-transferase (GST) enzyme activities and expression levels were evaluated by reactive oxygen species ROS generation, which demonstrated that P. persalinus antioxidant defense enzyme played roles on nano-toxic resistant in ciliates. Moreover, the integrated biomarker response (IBR) was also determined, which demonstrated that MWCNTs had comparatively higher values than those of TiO₂-NPs after higher concentration exposure to ciliates. In addition, it was confirmed by the present work that sod, gst and cat played different roles on immunity, and the sensitivity of cat gene expression to these two nanomaterials exposure was dissimilar. Damages of shrunk as well as losses of cilia on the cell surface caused by TiO₂-NPs and MWCNTs exposure in P. persalinus using SEM revealed possible physical hazards of aggregated nanomaterials. Our findings will be helpful to understand the effect mechanisms of NPs on ciliates, and also demonstrated the possibility of P. persalinus as bio-indicator of nanomaterials in aquatic and potentials on bioremediation.

Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors

As a model organism for studies of cell and environmental biology, the free-living and cosmopolitan ciliate Euplotes vannus shows intriguing features like dual genome architecture (i.e., separate germline and somatic nuclei in each cell/organism), "gene-sized" chromosomes, stop codon reassignment, programmed ribosomal frameshifting (PRF) and strong resistance to environmental stressors. However, the molecular mechanisms that account for these remarkable traits remain largely unknown. Here we report a combined analysis of de novo assembled high-quality macronuclear (MAC; i.e., somatic) and partial micronuclear (MIC; i.e., germline) genome sequences for E. vannus, and transcriptome profiling data under varying conditions. The results demonstrate that: (a) the MAC genome contains more than 25,000 complete "gene-sized" nanochromosomes (~85 Mb haploid genome size) with the N50 ~2.7 kb; (b) although there is a high frequency of frameshifting at stop codons UAA and UAG, we did not observe impaired transcript abundance as a result of PRF in this species as has been reported for other euplotids; (c) the sequence motif 5'-TA-3' is conserved at nearly all internally-eliminated sequence (IES) boundaries in the MIC genome, and chromosome breakage sites (CBSs) are duplicated and retained in the MAC genome; (d) by profiling the weighted correlation network of genes in the MAC under different environmental stressors, including nutrient scarcity, extreme temperature, salinity and the presence of ammonia, we identified gene clusters that respond to these external physical or chemical stimulations, and (e) we observed a dramatic increase in HSP70 gene transcription under salinity and chemical stresses but surprisingly, not under temperature changes; we link this temperature-resistance to the evolved loss of temperature stress-sensitive elements in regulatory regions. Together with the genome resources generated in this study, which are available online at Euplotes vannus Genome Database (http://evan.ciliate.org), these data provide molecular evidence for understanding the unique biology of highly adaptable microorganisms.

Techniques and tools for species identification in ciliates: a review

Ciliates are highly divergent unicellular eukaryotic organisms with nuclear dualism and a highly specialized ciliary pattern. They inhabit all biotopes and play crucial roles in regulating microbial food webs as they prey on bacteria, protists and even on microscopic animals. Nevertheless, subtle morphological differences and tiny sizes hinder proper species identification for many ciliates. In the present review, an attempt has been made to elaborate the various approaches used by modern day ciliate taxonomists for species identification. The different approaches involved in taxonomic characterization of ciliates such as classical (using live-cell observations, staining techniques, etc.), molecular (involving various marker genes) and statistical (delimitation of cryptic species) methods have been reviewed. Ecological and behavioural aspects in species identification have also been discussed. In present-day taxonomy, it is important to use a ‘total evidence’ approach in identifying ciliates, relying on both classical and molecular information whenever possible. This integrative approach will help in the mergence of classical methods with modern-day tools for comprehensive species description in future.

Identification and molecular characterization of two Cu/Zn-SODs and Mn-SOD in the marine ciliate Euplotes crassus: Modulation of enzyme activity and transcripts in response to copper and cadmium

The superoxide dismutase (SOD) family is a first line antioxidant enzyme group involved in transformation of the superoxide anion (O₂^-) into hydrogen peroxide (H₂O₂) and O₂. SOD gene expression patterns and enzyme activities therefore have a role as molecular biomarkers in evaluating the oxidative stress status of aquatic organisms. However, antioxidant enzyme systems are yet to be fully explored in the marine ciliates. In this study, we identified and characterized two types of Cu/Zn SODs (Ec-Cu/ZnSOD1 and Ec-Cu/ZnSOD2) and Ec-Mn SOD in the marine ciliate Euplotes crassus. Subsequently, SOD activity and transcriptional modulation of the relevant genes were investigated after the exposure to Cd and Cu for 8 h. All Ec-SODs showed conserved domains and metal binding sites on their active sites. Total SOD activity was induced at 1 h after exposure to Cd (125 and 1000 μg/L), and showed a marginal increase at 1-h exposure to Cu (10 and 100 μg/L). However, SOD activity was maintained at a steady level under Cd and decreased under Cu exposure conditions at 3 h and 8 h. mRNA expression of both the Ec-Cu/Zn-SODs and Mn-SOD were remarkably elevated after the exposure to Cd (250-1000 μg/L, maximum 4-fold, p < 0.05) and, in particular, Cu (25-100 μg/L, maximum > 20-fold, p < 0.05), in a concentration - dependent manner. These findings suggest that Ec-SODs may be actively involved in cellular protection against metal - mediated oxidative stress. This study is therefore helpful in understanding the molecular responses for metal toxicity in the ciliates.