Fungi are well associated with the degradation of hydrocarbons by the production of different enzymes, among which catalases (CBH), laccases (LCC) and peroxidases (LiP and MnP) are of immense importance. In this study, crude oil tolerance and enzyme secretions were demonstrated by rhizospheric fungal strains. Four most abundant strains were isolated from the rhizosphere of grasses growing in aged oil spill sites and identified through morphological characterization and molecular PCR-amplification of 5.8–28S ribosomal rRNA using ITS1 and ITS4 primers. These strains were subjected to crude oil tolerance test at 0–20% concentrations. Presence and transcriptase responses of putative genes lig (1–6), mnp, cbh (1.1, 1.1 and 11), and lcc encoding lignin peroxidase, manganese peroxidase, catalase, and laccase enzymes respectively were also studied in these strains using RT-PCR. In addition, activities of secreted enzymes by each strain were studied in aliquots. The strains were identified as Aspergillus niger asemoA (KY473958), Talaromyces purpurogenus asemoF (KY488463), Trichoderma harzianum asemoJ (KY488466), and Aspergillus flavus asemoM (KY488467) through sequencing and comparing the sequences’ data at NCBI BLAST search software. All the isolated strains showed tolerance to crude oil at 20% concentration, but the growth rate reduced with increasing in oil concentrations. All the isolated strains possess the tested genes and lig 1–6 gene was overexpressed in A. niger and T. harzianum while lcc and mnp genes were moderately expressed in all the four strains. Almost 145 U.mL⁻¹ of lignin and manganese peroxidase, 87 U.mL⁻¹ of catalase, and 180 U.mL⁻¹ of laccase enzymes were produced by these strains and it was also observed that these strain mostly produced studied enzymes in response to increasing crude oil concentrations. Considering the robust nature and diverse production of these catalytic enzymes by these strains, they can be exploited for various bioremediation technologies as well as other biotechnological applications.

Heavy metal tolerance of microorganisms is the basis of heavy metal removal by growing cells. In this study, a cross-protection effect generated by salt stress significantly enhanced the cadmium tolerance of multi-stress-tolerant Pichia kudriavzevii. Comparative transcriptome analysis using RNA-Seq linked with physiological and biochemical observation was used to elucidate the underlying mechanisms of the improved cadmium tolerance. The expression of cadmium transport related genes (GSTY2, GLR1, GLO2, YCF1 and YOR1), GSH content and GST activity were elevated by salt stress, suggesting enhanced cadmium conjugation and detoxification in yeast cells. The inhibited cadmium uptake by ZRT1 and enhanced cadmium efflux by YOR1 contributed to the decrease in the intracellular cadmium concentration. The improved expression of antioxidant enzyme genes (SOD1, SOD2, SOD6, CAT1 and PRXIID), along with the enhanced activities of antioxidant enzymes (SOD, CAT and POD) resulted in a decrease in cadmium-induced ROS production, protein carbonylation, lipid peroxidation and cell death. The abundant expression of heat shock protein genes (HSP12, HSP10 and SSC1) and genes related to trehalose synthesis (TPS1 and TSL1) induced by salt stress protected yeast cells against complex stress conditions, contributing to the improved cadmium tolerance. These findings will be useful to develop cadmium-tolerant yeasts for cadmium removal by growing cells.

The contribution of diesel exhaust to atmospheric pollution is a major concern for public health, especially in terms of occurrence of lung cancers. The present study aimed at addressing the toxic effects of a repeated exposure to these emissions in an animal study performed under strictly controlled conditions. Rats were repeatedly exposed to the exhaust of diesel engine. Parameters such as the presence of a particle filter or the use of gasoil containing rapeseed methyl ester were investigated. Various biological parameters were monitored in the lungs to assess the toxic and genotoxic effects of the exposure. First, a transcriptomic analysis showed that some pathways related to DNA repair and cell cycle were affected to a limited extent by diesel but even less by biodiesel. In agreement with occurrence of a limited genotoxic stress in the lungs of diesel-exposed animals, small induction of γ-H2AX and acrolein adducts was observed but not of bulky adducts and 8-oxodGuo. Unexpected results were obtained in the study of the effect of the particle filter. Indeed, exhausts collected downstream of the particle filter led to a slightly higher induction of a series of genes than those collected upstream. This result was in agreement with the formation of acrolein adducts and γH2AX. On the contrary, induction of oxidative stress remained very limited since only SOD was found to be induced and only when rats were exposed to biodiesel exhaust collected upstream of the particle filter. Parameters related to telomeres were identical in all groups. In summary, our results point to a limited accumulation of damage in lungs following repeated exposure to diesel exhausts when modern engines and relevant fuels are used. Yet, a few significant effects are still observed, mostly after the particle filter, suggesting a remaining toxicity associated with the gaseous or nano-particular phases.

Microplastics are widespread emerging contaminants that have been found globally in the marine and freshwater ecosystem, but there is limited knowledge regarding its impact on coral reef ecosystem and underpinning mechanism. In the present study, using Pocillopora damicornis as a model, we investigated cytological, physiological, and molecular responses of a scleractinian coral to acute microplastic exposure. No significant changes were observed in the density of symbiotic zooxanthellae during the entire period of microplastic exposure, while its chlorophyll content increased significantly at 12 h of microplastic exposure. We observed significant increases in the activities of antioxidant enzymes such as superoxide dismutase and catalase, significant decrease in the detoxifying enzyme glutathione S-transferase and the immune enzyme alkaline phosphatase, but no change in the other immune enzyme phenoloxidase during the whole experiment period. Transcriptomic analysis revealed 134 significantly up-regulated coral genes at 12 h after the exposure, enriched in 11 GO terms mostly related to stress response, zymogen granule, and JNK signal pathway. Meanwhile, 215 coral genes were significantly down-regulated at 12 h after exposure, enriched in 25 GO terms involved in sterol transport and EGF-ERK1/2 signal pathway. In contrast, only 12 zooxanthella genes exhibited significant up-regulation and 95 genes down-regulation at 12 h after the microplastic exposure; genes regulating synthesis and export of glucose and amino acids were not impacted. These results suggest that acute exposure of microplastics can activate the stress response of the scleractinian coral P. damicornis, and repress its detoxification and immune system through the JNK and ERK signal pathways. These demonstrate that microplastic exposure can compromise the anti-stress capacity and immune system of the scleractinian coral P. damicornis, despite the minimal impact on the abundance and major photosynthate translocation transporters of the symbiont in the short term.

Glyphosate has been the most widely used herbicide worldwide over the last three decades, raising increasing concerns for its potential impacts on environmental and human health. Recent studies revealed that glyphosate occurs in soil, surface water, and groundwater, and residues are found at all levels of the food chain, such as drinking water, plants, animals, and even in humans. While research has demonstrated that glyphosate can induce a broad range of biological effects in exposed organisms, the global molecular mechanisms of action still need to be elucidated, in particular for marine species. In this study, we characterized for the first time the molecular mechanisms of action of glyphosate in a marine bivalve species after exposure to environmentally realistic concentrations. To reach such a goal, Mediterranean mussels Mytilus galloprovincialis, an ecologically and economically relevant species, were exposed for 21 days to 10, 100, and 1000 μg/L and digestive gland transcriptional profiles were investigated through RNA-seq. Differential expression analysis identified a total of 111, 124, and 211 differentially regulated transcripts at glyphosate concentrations of 10, 100, and 1000 μg/L, respectively. Five genes were found consistently differentially expressed at all investigated concentrations, including SERP2, which plays a role in the protection of unfolded target proteins against degradation, the antiapoptotic protein GIMAP5, and MTMR14, which is involved in macroautophagy. Functional analysis of differentially expressed genes reveals the disruption of several key biological processes, such as energy metabolism and Ca2+ homeostasis, cell signalling, and endoplasmic reticulum stress response. Together, the results obtained suggest that the presence of glyphosate in the marine ecosystem should raise particular concern because of its significant effects even at the lowest concentration.

Assessing the toxicity posed by mixtures of unknown chemicals to aquatic organisms is challenging. In this study, water samples from six cross-sections along the Xitiaoxi River Basin (XRB) were monthly or bimonthly collected in 2014. The year-period physiochemical parameters as well as one-month-water sample based acute biotoxicity tests showed that the river water quality of the year was generally in a good status. High performance liquid chromatography (HPLC) screening based on one-month-water samples suggested that the organic pollutants might be non-to-moderately-polar chemicals in very low concentrations. One-month-water sample based RNA-seq was performed to measure the mRNA differential expression profile of zebrafish larvae to furtherly explore the potential bioeffect and the spatial water quality change of the river. Result indicated that the number of deferentially expressed genes (DEGs) tended to increase along the downstream direction of the river. Gene ontology (GO) enrichment analysis implied that the key pollutants might mainly be the function disruptors of biological processes. Principle components analysis (PCA) combining with transcripts and one-month-water sample based physiochemical parameters indicated that the pollution might be similar at TP, DP and CTB sites while pollution homology existed on some extent between YBQ and JW sites. Although the water quality of the river had a complex time-space alternation during the year, and the one-month-data based RNA-seq could not reflex the whole year-water quality of a watershed, the gene expression profile via RNA-seq provided an alternative way for assessing integrated biotoxicity of surface water, and it was relatively fit for early-warning of water quality of a watershed with unobservable acute toxicity. However, the identification of detail toxicants and the links between DEGs and pollution level as well as physiological-biochemical toxicity needed further investigation.

Diesel vehicle emissions are the major source of genotoxic compounds in ambient air from urban areas. These pollutants are linked to risks of cardiovascular diseases, lung cancer, respiratory infections and adverse neurological effects. Biological events associated with exposure to some air pollutants are widely unknown but applying omics techniques may help to identify the molecular processes that link exposure to disease risk. Most data on health risks are related to long-term exposure, so the aim of this study is to investigate the impact of short-term exposure (two hours) to air pollutants on the blood transcriptome and microRNA expression levels.We analyzed transcriptomics and microRNA expression using microarray technology on blood samples from volunteers participating in studies in London, the Oxford Street cohort, and, in Barcelona, the TAPAS cohort. Personal exposure levels measurements of particulate matter (PM₁₀, PM₂.₅), ultrafine particles (UFPC), nitrogen oxides (NO₂, NO and NOx), black carbon (BC) and carbon oxides (CO and CO₂) were registered for each volunteer. Associations between air pollutant levels and gene/microRNA expression were evaluated using multivariate normal models (MVN).MVN-models identified compound-specific expression of blood cell genes and microRNAs associated with air pollution despite the low exposure levels, the short exposure periods and the relatively small-sized cohorts. Hsa-miR-197-3p, hsa-miR-29a-3p, hsa-miR-15a-5p, hsa-miR-16-5p and hsa-miR-92a-3p are found significantly expressed in association with exposures. These microRNAs target also relevant transcripts, indicating their potential relevance in the research of omics-biomarkers responding to air pollution. Furthermore, these microRNAs are also known to be associated with diseases previously linked to air pollution exposure including several cancers such lung cancer and Alzheimer's disease. In conclusion, we identified in this study promising compound-specific mRNA and microRNA biomarkers after two hours of exposure to low levels of air pollutants during two hours that suggest increased cancer risks.

Hypoxia is as an endocrine disruptor, and, in crustaceans, the energy metabolic consequences of hypoxia in the brain tissue are still poorly understood. We combined gas chromatography-mass spectrometry (GC-MS)-based metabolomic analysis and high-throughput RNA sequencing to evaluate the metabolic effects and subjacent regulatory pathways in the brain tissue of the male Oriental river prawn (Macrobrachium nipponense) in response to hypoxia and reoxygenation. We recorded LC₅₀ and heartbeats per minute of male M. nipponense juveniles. Hypoxia resulted in the generation of reactive oxygen species in the brain cells and alterations in gene expression and metabolite concentrations in the prawn brain tissue in a time-dependent manner. The transcriptomic analyses revealed specific changes in the expression of genes associated with metabolism pathways, which was consistent with the changes in energy metabolism indicated by the GC-MS metabolomic analysis. Quantitative real-time polymerase chain reaction and western blot confirmed the transcriptional induction of these genes because of hypoxia. The lactate levels increased significantly during hypoxia and decreased to normal after reoxygenation; this is consistent with a shift towards anaerobic metabolism, which may cause metabolic abnormalities in the brain tissue of M. nipponense. Overall, these results are consistent with metabolic disruption in the brain of M. nipponense exposed to hypoxia and will help in understanding how crustacean brain tissue adapts and responds to hypoxia and reoxygenation.

Due to some similarity of innate immunity between insects and mammals, the study of the molecular mechanism of innate immunity in insects has become a focus of research. However, the exact molecular and cellular basis of immune system in insect remains poorly understood. Characterization of the transcriptomic response to Cd of spider is an effective approach to understanding the innate immunity mechanisms. In this study, we carried out transcriptome sequencing and gene expression analyses to develop molecular resources for Pardosa pseudoannulata venom glands with and without Cd treatments. A total of 92,778 assembled unigenes and 237 Cd stress-associated differentially expressed genes between the Cd-treated and control groups were obtained. Expression profile analysis demonstrated that immunity-related genes involved in bacterial invasion of epithelial cells, leukocyte transendothelial migration, platelet activation, apoptosis, phagosome, and Rap1 signaling pathway were upregulated by Cd exposure, except the genes involved in PPAR signaling pathway were downregulated. Our results provide the first comprehensive transcriptome dataset of venom glands in P. pseudoannulata response to Cd, which is valuable for throws light on the immunotoxicity mechanism of Cd, and the innate immunity complexity.