For thousands of years, humans have domesticated animals and cultivated crops by managing reproduction and selecting for desirable traits. In contrast, microbial domestication has often occurred unintentionally, and the variation of life cycle as well as its impact on genome evolution remain poorly understood. Here, we systematically examined life cycle variation across a diverse panel of 771 diploid Saccharomyces cerevisiae isolates from both wild and domesticated lineages. We identified widespread alterations in sexual reproduction, including impairments of sporulation, spore viability, and mating-type switching. These changes led to the emergence of two distinct life cycle strategies, favoring either asexual or sexual reproduction, which were notably enriched in domesticated clades. Haplotype analyses of the HO mating-type switching gene revealed multiple, independent loss-of-function mutations, indicating convergent evolution of heterothallism. While a preference for sexual life cycle often correlated with increased genomic heterozygosity in domesticated and human-associated clades, this relationship was not uniform across all lineages. We propose that the co-occurrence of altered sexual and asexual cycle preferences results in a trade-off that balances outcrossing and the subsequent maintenance of heterozygosity in domesticated populations. Finally, we provide a CRISPR-based molecular toolbox and a stable haploid strain collection spanning global genetic diversity, enabling further genetic research and industrial applications.

This study explores the dynamic coupling between microplastics (MPs) accumulation and sulfate reduction within landfill systems, providing new insights into modern sulfur biogeochemical processes under human-influenced conditions. Simulated landfill experiments showed that redox perturbations, triggered by the addition of electron donors and acceptors, significantly enhanced both sulfate reduction and MP release. Final concentrations of volatile sulfur compounds (VSCs) were 6.24–10.53 times higher in high-plastic groups than in the no-plastic controls. Regression and modeling analyses identified dimethyl sulfide (DMS) as a key intermediate linking sulfur cycling with MP release, while sulfide and chemical oxygen demand acted as major controlling factors. Notably, redox reactivation induced a delayed yet amplified priming effect, with MP concentrations reaching 9.09–18.51 times those of the initial stage. These findings suggest that landfill systems, often considered controlled contaminant sinks, may act as active zones of plastic–microbial sulfur interactions influenced by plastic-derived inputs. These interactions may contribute to anthropogenic impacts on landfill biogeochemical processes and pose long-term risks to surrounding environments.

Natural genetic variation shapes how microbial populations adapt to environmental and chemical challenges, but scalable approaches to map genotype-phenotype relationships across diverse genetic backgrounds remain limited. Here, we developed a systematically barcoded collection of 520 Saccharomyces cerevisiae natural isolates that captures the ecological, geographical and genetic diversity of the species. Using pooled barcode sequencing, we profiled fitness responses to over 600 bioactive and natural compounds, revealing broader and more polarized bioactivity than the standard yeast gene-deletion collection. Fitness-based clustering defined six major compound groups with reproducible, population-structured sensitivity patterns. Genome-wide association analysis identified significant genetic variants across 107 compounds, linking natural polymorphisms to chemical responses and involving genes in genome maintenance, ribosome biogenesis, vesicular trafficking and stress tolerance. Together, our barcoded natural population provides a scalable framework for chemical-genetic screening, enabling systematic dissection of how genetic diversity shapes microbial fitness and adaptation.

Climate change has increased the frequency and intensity of extreme weather events, including hurricanes, floods, droughts, hot snaps, cold snaps, and storms. Such disturbances often trigger abrupt ecological changes, particularly habitat loss and degradation, thereby generating opportunities for invasive species. Subsequent biological invasions destabilize ecosystems, accelerate biodiversity loss, and compromise ecosystem services. Ecosystem conservation is facing unprecedented challenges in the context of biological invasions. However, the mechanisms through which extreme weather events promote invasions remain poorly understood, especially with respect to the physiological and ecological processes that underpin invasive success. Existing studies provide limited explanations of how invasive species so rapidly colonize ecological niches and displace native species following disturbance. This review summarizes current evidence linking extreme weather events to invasion dynamics, emphasizing the functional traits that enable invaders to thrive under stressful conditions. Key factors include broad environmental tolerance, adaptive responses to abiotic stresses, competitive superiority over native species, and highly efficient resource utilization. Our fundings highlight how these traits allow invasive species to resist disturbance, exploit newly available resources, and quickly adjust to altered environments, thereby intensifying threats to native biota and ecosystem resilience. We further discuss how trait-based perspectives can enhance predictive capacity for invasion trajectories under climate change and inform conservation planning. Understanding these processes is essential for developing proactive, ecologically grounded conservation strategies that mitigate biodiversity loss, safeguard ecosystem integrity, and support long-term resilience of socio-ecological systems in a rapidly changing world.

Perfluorooctanoic acid (PFOA) and microplastics are widespread aquatic pollutants, yet their combined toxicological effects remain unclear. This study investigates how polystyrene (PS) microplastics influence the toxicity of PFOA in zebrafish, focusing on transcriptomic, toxicological, and molecular dynamics insights. Zebrafish were exposed to PFOA alone or with PS of varying sizes (0.2, 2, and 20 μm). PFOA disrupted neurotransmitter release pathways, while PS modulated toxicity in a size-dependent manner. Specifically, 0.2 PS enhanced PFOA-induced inhibition of neurotransmission via activation of G protein-gated potassium channels and inhibition of calcium channels. 2 PS exacerbated disruptions in amino acid metabolism, including histidine, glycine, and arginine pathways. Survival rates decreased with increasing PFOA, and PS-particularly 2 PS and 20 PS-further reduced survival and increased PFOA accumulation. Histopathology revealed significant gut and muscle damage under high PFOA exposure, worsened by PS. Molecular simulations showed that PS increased binding energies and altered protein flexibility, weakening ligand-receptor interactions critical to metabolism and detoxification. Moreover, 20 PS amplified PFOA-induced inhibition of phase II conjugation pathways. Overall, PS significantly alters PFOA bioaccumulation and toxicity, underscoring the environmental risks associated with the co-occurrence of microplastics and persistent organic pollutants in aquatic ecosystems.

The leachate pressure-bearing zone in landfill sites is an important source and sink of microplastics (MPs), yet the formation processes and mechanisms under these conditions remain unclear. This study investigated MPs dynamics from plastic waste under simulated landfill conditions, revealing critical differences between plastic types. Polyethylene (PE) showed minimal fragmentation, while poly(butylene adipate-co-terephthalate)/polylactic acid (PBAT/PLA) generated substantial MPs (up to 1.39 × 106 items/L) under atmospheric pressure, with particles below 100 μm progressively dominating the size distribution. Temperature emerged as the primary driver of MP formation, accelerating PBAT/PLA depolymerization and leading to surface formation of carbonyl, hydroxyl, and ether groups. Conversely, pressure indirectly suppressed MP release by inhibiting microbial activity. Leachate parameters (DOC/COD) effectively predicted MP dynamics, providing practical monitoring indicators. These results elucidated the mechanisms of MP generation in landfill pressure environments, offering valuable insights for MP pollution control and waste management strategies.

Unravelling the genetic basis of the remarkable phenotypic diversity observed in natural populations remains a central challenge in biology1-4. Despite major advances5-19, no species has yet been characterized with a truly comprehensive atlas of genetic variation. Here we present an extensive genomic and phenotypic resource for the yeast Saccharomyces cerevisiae based on near telomere-to-telomere assemblies of 1,086 natural isolates. Leveraging these high-contiguity assemblies, we generated a highly complete species-wide structural variant atlas, gene-based pangenome and graph pangenome. By incorporating the full spectrum of genetic variation captured across the species, we conducted genome-wide association studies across 8,391 molecular and organismal traits19-22. The inclusion of structural variants and small insertion-deletion mutations improved heritability estimates by an average of 14.3% compared with analyses based only on single-nucleotide polymorphisms. Structural variants were more frequently associated with traits and exhibited greater pleiotropy than other variant types. Notably, the genetic architecture of molecular and organismal traits differed markedly. Together, this work provides a unique dataset that illuminates how diverse forms of genetic variation shape phenotypic diversity and lays the groundwork for integrative, genome-scale studies in other eukaryotic systems.

Co-exposure to low-density polyethylene microplastics (LDPE-MPs) and plastic additives like bisphenol A (BPA) and bisphenol AF (BPAF) poses a growing concern in aquatic environments, yet the role of LDPE-MPs in modulating their toxicity remains debated. This study integrates transcriptome sequencing, adsorption/desorption kinetics, and computational toxicology to assess how LDPE-MPs influence BPA- and BPAF-induced toxicity in zebrafish. We found that BPAF is more toxic than BPA, with 96 h lethal concentration 50 % (LC50) values of 1.659 mg/L for BPAF and 6.219 mg/L for BPA. LDPE-MPs act as dual modulators, alleviating or exacerbating toxicity in a chemical- and pathway-dependent manner. For BPA, LDPE-MPs mitigate its impact on phototransduction by adsorbing BPA, reducing its bioavailability, and preserving light signal conversion. In contrast, LDPE-MPs exacerbate BPA-induced nucleotide metabolism disruptions by enhancing inosine-5'-monophosphate dehydrogenase (IMPDH) activity, leading to increased gene transcription and accumulation of metabolic intermediates. For BPAF, LDPE-MPs alleviate glucose metabolism disruptions by enhancing ligand-receptor interactions, restoring glucose homeostasis. However, LDPE-MPs have little effect on BPAF-induced upregulation of steroid biosynthesis genes. These findings highlight the integration of multi-omics approaches (transcriptome sequencing, adsorption/desorption kinetics, and computational toxicology) to reveal the dual mechanisms of LDPE-MPs, addressing the knowledge gap in understanding pathway-specific toxicity mechanisms in existing studies. The results emphasize the necessity of prioritizing regulatory control of BPAF and integrating BPA/BPAF-MPs interactions into future pathway-based environmental risk assessment frameworks.

Microplastics (MPs) and per/polyfluoroalkyl substances (PFASs), as emerging pollutants widely present in aquatic environments, pose a significant threat to human health through the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Molecular dynamics simulations and machine learning can accurately capture the complex interactions between molecules. This study utilized them to identify the HGT risk between bacteria under MPs and PFASs stress. This study found that MPs and PFASs significantly increase the HGT risk between bacteria, up to 1.57 and 1.59 times, respectively. Notably, long-chain PFASs and perfluoroalkyl carboxylic acids increased the HGT risk by 1.38 and 1.40 times, respectively. Additionally, MPs primarily increase the HGT risk by enhancing hydrogen bonding interaction between key proteins in the HGT pathway and "active codons". The electronegativity and polarizability of PFASs critically influence the HGT risk, acting inversely and directly proportional, respectively. The HGT risk between bacteria under the combined stress from PP-MPs and PFASs exhibits a significant synergistic effect (synergistic effect value of 27.6), which markedly increases the HGT risk. Further analysis revealed that a smaller minimum distance and sharper RDF curve peaks between key proteins and "active codons" indicate higher HGT risk. This indicates that stronger interactions lead to higher HGT risk. This study identifies the characteristics of HGT risks between bacteria in aquatic environments under the individual and combined stresses from MPs and PFASs at the molecular level. It provides a theoretical basis for mitigating ARG transfer and comprehensively assessing the health risks posed by these emerging pollutants.

Phthalate acid esters (PAEs), widely used as plasticizers, are frequently detected in the environments and are known to exert toxic effects on aquatic organisms. However, whether these effects are recoverable after exposure-and the mechanisms underlying any recovery-remains poorly understood, limiting accurate risk assessment for these toxicants. In this study, zebrafish were exposed to three representative PAEs-dimethyl phthalate (DMP), dibutyl phthalate (DBP), and di-n-octyl phthalate (DNOP)-for 4 days, followed by a 7-day recovery in PAEs-free water. By combining accumulation assessment, survival analysis, and transcriptomic sequencing, we investigated the molecular mechanisms underlying these toxic effects and recovery. All three PAEs were detected in zebrafish during exposure and recovery periods. While no changes were observed in survival, transcriptomic sequencing revealed distinct molecular patterns: DMP interfered with PPAR signaling and tryptophan metabolism, leading to lipid dysregulation, neurotransmitter imbalance, and oxidative stress. DBP influenced glutathione metabolism, reducing antioxidant and detoxification capacity. DNOP suppressed the expressions of genes related to cell cycle and DNA replication, inhibiting cell proliferation and tissue repair. After 7-day recovery, PAE residues were still at high levels, and molecular alterations were aggravated: tryptophan metabolism was further inhibited in the DMP exposure, glutathione pathway remained downregulated under DBP, and DNOP-induced cell cycle arrest became more severe. Our results suggest that PAE exposures can induce persistent and compound-specific transcriptomic toxicity in zebrafish, even after toxicant removal. These findings highlight the importance of including post-exposure periods in future toxicological studies and provide molecular insights for improving environmental risk assessments for PAEs.

Sediments provide habitat and food for benthos, and phthalates (PAEs) have been detected in numerous river and marine sediments as a widely used plastic additive. PAEs in sediments is not only toxic to benthos, but also poses a threat to pelagic fish and human health through the food chain, so it is essential to comprehensively assess the contamination of sediments with PAEs. This paper presents a critical evaluation of PAEs in sediments, which is embodied in the analysis of the sources of PAEs in sediments from multiple perspectives. Biological production is indispensable, while artificial synthesis is the most dominant, thus the focus was on analyzing the industrial and commercial sources of synthetic PAEs. In addition, since the content of PAEs in sediments varies, some factors affecting the content of PAEs in sediments are summarized, such as the properties of PAEs, the properties of plastics, and environmental factors (sediments properties and hydrodynamic conditions). As endocrine disruptors, PAEs can produce toxicity to its direct contacts. Therefore, the effects of PAEs on benthos immunity, endocrinology, reproduction, development, and metabolism were comprehensively analyzed. In addition, we found that reciprocal inhibition and activation of the systems lead to genotoxicity and apoptosis. Finally, the paper discusses the feasible measures to control PAEs in wastewater and leachate from the perspective of source control, and summarizes the in-situ treatment measures for PAEs contamination in sediments. This paper provides a comprehensive review of PAEs contamination in sediments, toxic effects and removal strategies, and provides an important reference for reducing the contamination and toxicity of PAEs to benthos.

Summary Gene expression is an essential step in the translation of genotypes into phenotypes. However, little is known about the transcriptome architecture and the underlying genetic effects at a species-level. Here, we generated and analyzed the pan-transcriptome of ∼1,000 yeast natural isolates across 4,977 core and 1,468 accessory genes. We found that the accessory genome is an underappreciated driver of the transcriptome divergence. Global gene expression patterns combined with population structure show that the heritable expression variation mainly lies within subpopulation-specific signatures, for which the accessory genes are overrepresented. Genome-wide association analyses consistently highlight that the accessory genes are associated with proportionally more variants with larger effect sizes, illustrating the critical role of the accessory genome on the transcriptional landscape within and between populations.

Assessing the complexity and expressivity of traits at the species level is an essential first step to better dissect the genotype-phenotype relationship. As trait complexity behaves dynamically, the classic dichotomy between monogenic and complex traits is too simplistic. However, no systematic assessment of this complexity spectrum has been carried out on a population scale to date. In this context, we generated a large diallel hybrid panel composed of 190 unique hybrids coming from 20 natural isolates representative of the S. cerevisiae genetic diversity. For each of these hybrids, a large progeny of 160 individuals was obtained, leading to a total of 30,400 offspring individuals. Their mitotic growth was evaluated on 38 conditions inducing various cellular stresses. We developed a classification algorithm to analyze the phenotypic distributions of offspring and assess the trait complexity. We clearly found that traits are mainly complex at the population level. On average, we found that 91.2% of cross/trait combinations exhibit high complexity, while monogenic and oligogenic cases accounted for only 4.1% and 4.7%, respectively. However, the complexity spectrum is very dynamic, trait specific and tightly related to genetic backgrounds. Overall, our study provided greater insight into trait complexity as well as the underlying genetic basis of its spectrum in a natural population.

The toxicological impacts of different types of perfluorinated compounds on various life processes of marine bivalves will be summarized and interpreted in this chapter. The occurrence status of some perfluorinated compounds in marine environment and the corresponding environmental risks are explained and put forward. Growth and immune response are the main aspects of the life process of marine bivalves exposed to perfluorinated compounds. Moreover, the influence of perfluorinated compounds on bivalve nervous system and cell morphology is also discussed. Finally, considering the unique physical and chemical properties of perfluorinated compounds, the accumulation mode of perfluorinated compounds in organisms, and its potential toxicity mechanism are also discussed.

As a widely used brominated flame retardant, the widespread presence of decabromodiphenyl ether (BDE-209) in the natural environment and the toxicity risks it poses are well established, but the recoverability of BDE-209-induced individual injuries remains unknown. Therefore, a 7-day depuration experiment following a 4-day exposure of zebrafish to BDE-209 was conducted to confirm the recoverability and its mode of action. Oxidative stress after depuration was significantly reduced compared with BDE-209 exposure as indicated by the decreased expression level of oxidative stress-related genes and the reduced MDA, Gpx, and GST in zebrafish, indicating a gradual recovery of antioxidant activity. However, BDE-209 inhibition of extracellular matrix (ECM) proteins worsened after depuration. Mechanistically, BDE-209 mediated ECM production and secretion by down-regulating integrin expression. Furthermore, BDE-209 inhibition of collagen synthesis worsened after depuration. Biochemical assays and histopathological observations revealed a same result in zebrafish. Mechanistically, lysine hydroxylation is inhibited thereby affecting collagen synthesis. Interestingly, zebrafish showed arrhythmia after depuration compared to BDE-209 exposure, and abnormal changes in ATPase levels indicated that disturbances in Ca2+ homeostasis contributed to arrhythmia. Collectively, BDE-209-induced interference with ECM production and collagen synthesis persisted after depuration, which will provide new insights for understanding the recovery patterns of individuals under BDE-209 stress.

To investigate the underlying resistance mechanisms of Saccharomyces cerevisiae against Ag-NPs with different particle sizes and coatings, transcriptome sequencing (RNA-seq) technology was used to characterize the transcriptomes from S. cerevisiae exposed to 20-PVP-Ag, 100-PVP-Ag, 20-CIT-Ag and 100-CIT-Ag, respectively. The steroid biosynthesis was found as a general pathway for Ag-NPs stress responding, in which ERG6 and ERG3 were inhibited and ERG11, ERG25 and ERG5 were significantly up-regulated to resist the stress by supporting the later mutation and resistance and modulate drug efflux indirectly. The resistance mechanism of S. cerevisiae to 20-PVP-Ag seems different from that of 100-PVP-Ag, 20-CIT-Ag and 100-CIT-Ag. Under the 20-PVP-Ag, transmembrane transporter activity, transition metal ion homeostasis and oxidative phosphorylation pathway were main resistance pathways to enhance cell transport processes. While 100-PVP-Ag, 20-CIT-Ag and 100-CIT-Ag mainly impacted RNA binding, structural constituent of ribosome and ribosome pathway which can provide more energy to maintain the number and function of protein in cells. This study reveals the differences in resistance mechanisms of S. cerevisiae to Ag-NPs with different particle sizes and coatings, and explains several main regulatory mechanisms used to respond to silver stress. It will provide theoretical basis for the study of chemical risk assessment.

Gene expression variation, an essential step between genotype and phenotype, is collectively controlled by local (cis) and distant (trans) regulatory changes. Nevertheless, how these regulatory elements differentially influence gene expression variation remains unclear. Here, we bridge this gap by analyzing the transcriptomes of a large diallel panel consisting of 323 unique hybrids originating from genetically divergent Saccharomyces cerevisiae isolates. Our analysis across 5,087 transcript abundance traits showed that non-additive components account for 36% of the gene expression variance on average. By comparing allele-specific read counts in parent-hybrid trios, we found that trans-regulatory changes underlie the majority of gene expression variation in the population. Remarkably, most cis-regulatory variations are also exaggerated or attenuated by additional trans effects. Overall, we showed that the transcriptome is globally buffered at the genetic level mainly due to trans-regulatory variation in the population.

AgNPs are widely used for their excellent antimicrobial properties, whereas the cytotoxicity they possess makes them an unignorable environmental problem. Considering the impact of particle size and surface coating on the antibacterial properties, four types of AgNPs are selected: citrate-coated 20 nm (C20), polyvinylpyrrolidone-coated 20 nm (P20), citrate-coated 100 nm (C100), and polyvinylpyrrolidone-coated 100 nm (P100) AgNPs. All four AgNPs significantly affect the ribosome pathway, with stronger binding of large and small subunits. 20 nm and 100 nm AgNPs both affected the biosynthesis and metabolism of several amino acids (including arginine, glycine, serine, threonine, glyoxylic acid, and dicarboxylic acid). P20 and C100 exposure affected bacterial chemotaxis and flagellar motility. This study preliminarily explained the response mechanism of E. coli to AgNPs with different properties, which provided a theoretical basis for predicting the response mechanism of E. coli to metal nanoparticles with similar properties. Toxic effects of four different types of AgNPs on Escherichia coli. image

Unraveling the genetic sources of gene expression variation is essential to better understand the origins of phenotypic diversity in natural populations. Genome-wide association studies identified thousands of variants involved in gene expression variation, however, variants detected only explain part of the heritability. In fact, variants such as low-frequency and structural variants (SVs) are poorly captured in association studies. To assess the impact of these variants on gene expression variation, we explored a half-diallel panel composed of 323 hybrids originated from pairwise crosses of 26 natural Saccharomyces cerevisiae isolates. Using short- and long-read sequencing strategies, we established an exhaustive catalog of single nucleotide polymorphisms (SNPs) and SVs for this panel. Combining this dataset with the transcriptomes of all hybrids, we comprehensively mapped SNPs and SVs associated with gene expression variation. While SVs impact gene expression variation, SNPs exhibit a higher effect size with an overrepresentation of low-frequency variants compared to common ones. These results reinforce the importance of dissecting the heritability of complex traits with a comprehensive catalog of genetic variants at the population level.