Activated sludge (AS), a common biological secondary treatment process in wastewater treatment plants (WWTPs), is known to remove a large spectrum of microorganisms. Yet little is known about its ...effect on the entire viral community. After compiling 3 Tbp of next-generation sequencing (NGS) metagenomic/viromic datasets consisted of 119 sub-datasets of influent, effluent, and AS samples from 27 WWTPs, viral removal efficacy is evaluated through data mining. The normalized abundance of viruses suggests effluents exhibit the highest viral prevalence (3.21 ± 3.26%, n = 13) followed by the AS (0.48 ± 0.25%, n = 57) and influents (0.23 ± 0.17%, n = 17). In contrast, plasmids, representing genetic element of bacteria, show higher average prevalence (0.73 ± 0.82%, n = 17) in influents than those of the AS (0.63 ± 0.26%, n = 57) and effluents (0.35 ± 0.42%, n = 13). Furthermore, the abundance-occupancy analysis identifies 142 core phage viruses and 17 non-phages core viruses, including several pathogenic viruses in the AS virome. The persistent occurrence of pathogenic viruses, coupled with non-favorable virus removal by the AS treatment, reveals the hidden virus threats in biologically treated domestic wastewater. The mechanisms for why viruses persist and the possibility that WWTPs are potential hotspots for viral survival deserve attention.
•WWTP effluents exhibit higher viral prevalence than influents and activated sludge.•Influents, activated sludge and effluents show distinct viral communities.•The persistent viruses reveal virus threats in biologically treated wastewater.
Metagenomic strategy serves as the foundation for the ecological exploration of novel bioresources (e.g., industrial enzymes and bioactive molecules) and biohazards (e.g., pathogens and antibiotic ...resistance genes) in natural and engineered microbial systems across multiple disciplines. Recent advancements in sequencing technology have fostered rapid development in the field of microbiome research where an increasing number of studies have applied both illumina short reads (SRs) and nanopore long reads (LRs) sequencing in their metagenomic workflow. However, given the high complexity of an environmental microbiome data set and the bioinformatic challenges caused by the unique features of these sequencing technologies, integrating SRs and LRs is not as straightforward as one might assume. The fast renewal of existing tools and growing diversity of new algorithms make access to this field even more difficult. Therefore, here we systematically summarized the complete workflow from DNA extraction to data processing strategies for applying illumina and nanopore‐integrated metagenomics in the investigation in environmental microbiomes. Overall, this review aims to provide a timely knowledge framework for researchers that are interested in or are struggling with the SRs and LRs integration in their metagenomic analysis. The discussions presented will facilitate improved ecological understanding of community functionalities and assembly of natural, engineered, and human microbiomes, benefiting researchers from multiple disciplines.
Strategies and tools in illumina and nanopore‐integrated metagenomic analysis of microbiome data.
Highlights
A timely knowledge framework to integrate nanopore long reads and illumina short reads is provided.
Workflow of common strategies for illumina and nanopore integration is illustrated in Figure 1.
Algorithm basis and application properties of tools are summarized in Table 3.
Nanomaterials have been widely used in many fields, especially in biomedical and stem cell therapy. However, the potential risks associated with nanomaterials applications are also gradually ...increasing. Therefore, effective and robust toxicology models are critical to evaluate the developmental toxicity of nanomaterials. The development of stem cell research provides a new idea of developmental toxicology. Recently, many researchers actively investigated the effects of nanomaterials with different sizes and surface modifications on various stem cells (such as embryonic stem cells (ESCs), adult stem cells, etc.) to study the toxic effects and toxic mechanisms. In this review, we summarized the effects of nanomaterials on the proliferation and differentiation of ESCs, mesenchymal stem cells and neural stem cells. Moreover, we discussed the advantages of stem cells in nanotoxicology compared with other cell lines. Finally, combined with the latest research methods and new molecular mechanisms, we analyzed the application of stem cells in nanotoxicology.
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•The application of stem cells in the analysis of toxic effects and mechanism of nanoparticles were summarized.•Organoids and omics technology has expanded the application of stem cells in nanotoxicology.•The application prospect of stem cells in nanotoxicology was identified.•Stem cells are more effectively than other cell lines in studying developmental toxic effects of nanoparticles.
•Typhoon increased microplastics abundance in water, while converse for sediment.•Typhoon had promptly uniformed plastisphere community of sediment.•Typhoon caused the steep increases abundance of ...nitrogen fixer of plastisphere.
The increasing microplastic pollution together with the plastisphere-associated ecological threats in coastal areas have aroused global concern. Tropical cyclones have been increased in both frequency and intensity under global warming, causing intense impact on the microplastics distribution and the structure of coastal ecosystems. However, until most currently, the extent to which typhoon impacts the microplastics and plastisphere community remains poorly known. This study analyzed the effects of Typhoon Wipha (Code: 1907) on microplastics abundance and composition in surface water and sediment crossed coastal areas of Shenzhen. Here we found a significant typhoon-induced increase in microplastics abundance in surface water, whereas an opposite trend was observed in sediment. Despite the evident transportation of microplastics from sediment to surface water by agitation, a possible microplastics influx was introduced by typhoon as evidenced by the large attribution of unknown force in source tracking analysis. Furthermore, typhoon had adeptly uniformed the plastisphere community in the sediment along the 190 km costal line overnight. A significant increase of nitrogen fixer, Bradyrhizobiaceae, was observed ubiquitously after typhoon, which might alter the nitrogen cycling and increase eutrophic condition of the coastal ecological system. Together, this study expanded the knowledge about the impact of typhoon-induced influx of the microplastics on coastal biogeochemical cycling. Moreover, the microplastics and the plastisphere compositional pattern revealed here will underpin future studies on adsorption behavior, interfacial processes and ecotoxicity of the coastal microplastic pollution.
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•This study firstly explored the biogeography of anammox consortia at micron-scale.•Individual taxa in anammox consortia distributed heterogeneously at micron-scale.•There was no significant ...symbiosis between anammox bacteria and heterotrophs.•Conserved co-associations of anammox bacteria were restricted to brocadia species.•Quorum sensing potentially held on the conserved cooperation among brocadia species.
Micron-scale resolution can help to reliably identify true taxon-taxon interactions in complex microbial communities. Despite widespread recognition of the critical role of metabolic interactions in anaerobic ammonium oxidation (anammox) system performance, no studies have examined microbial interactions at the micron-scale in anammox consortia. To fill this gap, we extensively sampled (totally 242 samples) the consortia of a lab-scale anammox reactor at different length scales, including bulk-scale (∼cm), macro-scale (300–500 µm) and micron-scale (70–100 µm). We firstly observed evident micron-scale heterogeneity in anammox consortia, with the relative abundance of anammox bacteria fluctuated greatly across individual clusters (2.0%–79.3%), indicating that the biotic interactions play a significant role in the assembly of anammox communities under well-controlled and well-mixed condition. Importantly, by mapping the spatial associations in anammox consortia at micron-scale, we demonstrated that the conserved co-associations for anammox bacteria were restricted to three different Brocadia species over time, and their co-associations with heterotrophs were random, implying that there was no statistically significant symbiotic interaction between anammox bacteria and other heterotrophic populations. Further metagenomic binning revealed that the quorum sensing with secondary messenger c-di-GMP potentially holding on the conservative metabolic cooperation among Brocadia species. These results shed new light on the social behavior of the anammox community. Overall, delineating of biological structures at micron-scale opens a new way of monitoring the microbial spatial structure and interactions, paving the way for improved community engineering of biotreatment systems.
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Rare species are vital members of a microbial community, but retrieving their genomes is difficult because of their low abundance. The ReadUntil (RU) approach allows nanopore devices to sequence ...specific DNA molecules selectively in real time, which provides an opportunity for enriching rare species. Despite the robustness of enriching rare species by reducing the sequencing depth of known host sequences, such as the human genome, there is still a gap in RU-based enriching of rare species in environmental samples whose community composition is unclear, and many rare species have poor or incomplete reference genomes in public databases. Therefore, here we present metaRUpore to overcome this challenge. When we applied metaRUpore to a thermophilic anaerobic digester (TAD) community and human gut microbial community, it reduced coverage of the high-abundance populations and modestly increased (∼2×) the genome coverage of the rare taxa, facilitating successful recovery of near-finished metagenome-assembled genomes (nf-MAGs) of rare species. The simplicity and robustness of the approach make it accessible for laboratories with moderate computational resources, and hold the potential to become the standard practice in future metagenomic sequencing of complicated microbiomes.
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•Hospital air-conditioners can form resistome and accumulate pathogens.•The Outpatient hall can distribute ARGs to other departments.•Evidence-based network strategy proves that ...plasmid-mediated ARG transfer can occur frequently.
As a symbol of the defense mechanisms that bacteria have evolved over time, the genes that make bacteria resist antibiotics are overwhelmingly present in the environment. Currently, bacterial antibiotic resistance genes (ARGs) in the air are a serious concern. Previous studies have identified bacterial communities and summarized putative routes of transmissions for some dominant hospital-associated pathogens from hospital indoor samples. However, little is known about the possible indoor air ARG transportation. In this study, we mainly surveyed air-conditioner air dust samples under different airflow conditions and analyzed these samples using a metagenomic-based method. The results show air dust samples exhibited a complex resistome, and the average concentration is 0.00042 copies/16S rRNA gene, which is comparable to some other environments. The hospital air-conditioners can form resistome over time and accumulate pathogens. In addition, our results indicate that the Outpatient hall is one of the main ARG transmission sources, which can distribute ARGs to other departments (explains >80% resistome). We believe that the management should focus on ARG carrier genera such as Staphylococcus, Micrococcus, Streptococcus, and Enterococcus in this hospital and our novel evidence-based network strategy proves that plasmid-mediated ARG transfer can occur frequently. Overall, these results provide insights into the characteristics of air dust resistome and possible route for how ARGs are spread in air.
The microbiological ecology of a low-nutrient shallow aquifer with high arsenic content in the Yinchuan Plain was investigated in this study. Amplicon sequencing data from five samples (depths: ...1.5 m, 3.5 m, 11.2 m, 19.3 m, and 25.5 m) revealed diverse and adaptable microbial community. Among the microbial community, Comamonas was the most prominent, accounting for 10.52 % of the total. This genus displayed high growth rates, with a maximum growth rate of 12.06 d−1 and a corresponding doubling time of 1.38 days, as determined through an analysis of codon usage bias. Functional annotation of Metagenome-Assembled Genomes (MAGs) for samples at 1.5 m and 11.2 m depths revealed Comamonas' metabolic versatility, including various carbon pathways, assimilative sulfate reduction (ASR), and dissimilatory reduction to ammonium (DNRA). The TPM (Transcripts Per Kilobase of exon model per Million mapped reads) of MAGs at 11.2 m sample was 15.7 and 12.3. The presence of arsenic resistance genes in Comamonas aligns with sediment arsenic levels (65.8 mg/kg for 1.5 m depth, 32.8 mg/kg for 11.2 m depth). This study highlights the role of Comamonas as a ‘generalist’ bacteria in challenging oligotrophic sediments, emphasizing the significance of such organisms in community stability and ecological functions.
Low-biomass limits the microbial activity and biogeochemical study in oligotrophic environments, which is the typical condition for underground aquatic ecosystems. Facilitated by growth rate estimation, our research focuses on active functional microorganisms and their biogeochemical metabolic in oligotrophic aquifer sediments, revealing their impact on the environment and response to arsenic threats. Findings illuminate the metabolic advantage of a ‘generalist life-style’ in carbon-scarce environments and contribute to a broader understanding of bacterial ecosystems and environmental impacts in oligotrophic aquifer sediments worldwide.
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•Comamonas was the most abundant and active genus.•Comamonas demonstrates versatile metabolic capabilities.•Metabolic “generalists” are important in oligotrophic aquifers.
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•Human relevant doses of AgNPs slightly affected human ectoderm differentiation.•AgNPs disrupted human embryonic stem cell-based specification of cranial placode.•AgNP effects on ...cranial placode may be mediated by the FGF signaling pathway.
Silver nanoparticles (AgNPs) are compounds used in numerous consumer products because of their desirable optical, conductive and antibacterial properties. However, several in vivo and in vitro studies have raised concerns about their potential developmental toxicity. Here, we employed a human embryonic stem cell model to evaluate the potential ectodermal toxicity of AgNPs, at human relevant concentrations. Among the four major ectodermal lineages tested, only cranial placode specification was significantly affected by AgNPs and AgNO3, morphology-wise and in the expression of specific markers, such as SIX3 and PAX6. Mechanistically, we found that the effects of AgNPs on the cranial placode differentiation were probably due to Ag ion leakage and mediated by the FGF signaling. Thus, AgNPs may have the ability to alter the early stages of embryonic development.
Filter mating experiment is widely used to study the conjugation behavior of plasmids and associated antibiotic resistance in environmental settings, however, the influence and biases brought by ...sample storage conditions (temperature and duration) were not yet systematically elaborated. This study systematically investigated the influence of standard storage conditions (4 °C, −20 °C, −80 °C) on plasmid conjugation behavior in influent (Inf) and activated sludge (AS) samples from sewage treatment plants (STP). The findings revealed a significant reduction in conjugation efficiency under all the tested storage conditions except for 1-week storage at 4 °C. Notably, storing at −80 °C maintained conjugation activities in activated sludge more effectively compared to −20 °C. However, the preservation performance was less effective for influent samples, which consist mainly of anaerobe-dominant communities. Systematic loss of IncH-type plasmids was observed in influent samples stored at 4 °C and −20 °C. Correspondingly, the plasmid-carrying resistome genotypes detected in the influent samples showed a clear downward trend with the increase in storage duration when stored at 4 °C and −20 °C. A relatively uniform composition in terms of incompatibility type and resistome profile was observed across activated sludge samples, regardless of the varied storage conditions. This study highlights the critical impact of storage conditions on plasmid conjugation behavior and resistome composition, offering valuable insights for optimal sample handling in resistome research.
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•Except 1-week storage at 4 °C, conjugation efficiency reduced in all samples.•Influent samples show a decline in IncH-type plasmids under 4 °C and −20 °C storage.•Beta-Lactam and multidrug-resistant genes sharply decrease when stored at −20 °C.•Antibiotic resistance gene subtypes tend to stabilize when stored at −80 °C.
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