Effects of different assembly strategies on gene annotation in activated sludge.

Activated sludge comprises diverse bacteria, fungi, and other microorganisms, featuring a rich repertoire of genes involved in antibiotic resistance, pollutant degradation, and elemental cycling. In this regard, hybrid assembly technology can revolutionize metagenomics by detecting greater gene diversity in environmental samples. Nonetheless, the optimal utilization and comparability of genomic information between hybrid assembly and short- or long-read technology remain unclear. To address this gap, we compared the performance of the hybrid assembly, short- and long-read technologies, abundance and diversity of annotated genes, and taxonomic diversity by analysing 46, 161, and 45 activated sludge metagenomic datasets, respectively. The results revealed that hybrid assembly technology exhibited the best performance, generating the most contiguous and longest contigs but with a lower proportion of high-quality metagenome-assembled genomes than short-read technology. Compared with short- or long-read technologies, hybrid assembly technology can detect a greater diversity of microbiota and antibiotic resistance genes, as well as a wider range of potential hosts. However, this approach may yield lower gene abundance and pathogen detection. Our study revealed the specific advantages and disadvantages of hybrid assembly and short- and long-read applications in wastewater treatment plants, and our approach could serve as a blueprint to be extended to terrestrial environments.

Global biogeography of microbes driving ocean ecological status under climate change.

Microbial communities play a crucial role in ocean ecology and global biogeochemical processes. However, understanding the intricate interactions among diversity, taxonomical composition, functional traits, and how these factors respond to climate change remains a significant challenge. Here, we propose seven distinct ecological statuses by systematically considering the diversity, structure, and biogeochemical potential of the ocean microbiome to delineate their biogeography. Anthropogenic climate change is expected to alter the ecological status of the surface ocean by influencing environmental conditions, particularly nutrient and oxygen contents. Our predictive model, which utilizes machine learning, indicates that the ecological status of approximately 32.44% of the surface ocean may undergo changes from the present to the end of this century, assuming no policy interventions. These changes mainly include poleward shifts in the main taxa, increases in photosynthetic carbon fixation and decreases in nutrient metabolism. However, this proportion can decrease significantly with effective control of greenhouse gas emissions. Our study underscores the urgent necessity for implementing policies to mitigate climate change, particularly from an ecological perspective.

Deciphering Microbial Community and Nitrogen Fixation in the Legume Rhizosphere.

Nitrogen is the most limiting factor in crop production. Legumes establish a symbiotic relationship with rhizobia and enhance nitrogen fixation. We analyzed 1,624 rhizosphere 16S rRNA gene samples and 113 rhizosphere metagenomic samples from three typical legumes and three non-legumes. The rhizosphere microbial community of the legumes had low diversity and was enriched with nitrogen-cycling bacteria (Sphingomonadaceae, Xanthobacteraceae, Rhizobiaceae, and Bacillaceae). Furthermore, the rhizosphere microbiota of legumes exhibited a high abundance of nitrogen-fixing genes, reflecting a stronger nitrogen-fixing potential, and Streptomycetaceae and Nocardioidaceae were the predominant nitrogen-fixing bacteria. We also identified helper bacteria and confirmed through metadata analysis and a pot experiment that the synthesis of riboflavin by helper bacteria is the key factor in promoting nitrogen fixation. Our study emphasizes that the construction of synthetic communities of nitrogen-fixing bacteria and helper bacteria is crucial for the development of efficient nitrogen-fixing microbial fertilizers.

Neonicotinoid insecticides and metabolites levels in neonatal first urine from southern China: Exploring links to preterm birth.

Neonicotinoids (NEOs) have indeed become the most widely used insecticides worldwide. Concerns have been raised about their potential impact on newborns due to maternal exposure and their unique neurotoxic mode of action. However, it is still poorly understood whether in utero exposure of pregnant women to environmental NEOs and their metabolites can cause carryover effects on vulnerable newborns and subsequent health consequences. In this study, we determined the concentrations of 13 NEOs and their metabolites in the first urine collected from 92 newborns, both preterm and full-term, in southern China during 2020 and 2021. NEOs and their metabolites were identified in 91 urine samples, with over 93% of samples containing a cocktail of these compounds, confirming their maternal-fetal transfer. N-desmethyl-acetamiprid, imidaclothiz, clothianidin and flonicamid were the most commonly detected analytes, with detection frequencies of 59-87% and medians of 0.024-0.291 ng/mL in the urine. The relative abundance of imidaclothiz was significantly higher in preterm newborns, those with head circumferences below 33 cm, birth lengths less than 47 cm, and weights below 2500 g (p < 0.05). When comparing newborns in the 2nd quartile of imidaclothiz concentrations with those in the 1st quartile, we observed a significant increase in the odds of preterm outcomes in the unadjusted model (odds ratio = 3.24, 95% confidence interval = 1.02-10.3). These results suggest that exposure to elevated concentrations of imidaclothiz may be associated with preterm birth.

Phages in different habitats and their ability to carry antibiotic resistance genes.

As the most abundant organisms on Earth, phages play a key role in the evolution of bacterial antibiotic resistance. Although previous studies have demonstrated the molecular mechanisms of horizontal gene transfer mediated by mobile genetic elements, our understanding of the intertwined relationships between antibiotic resistance genes (ARGs) and phages is limited. In this study, we analysed 2781 metagenomic samples to reveal the composition and species interactions of phage communities in different habitats as well as their capacity to carry ARGs with health risks. The composition of phage communities varies in different habitats and mainly depends on environmental conditions. Terrestrial habitats display more complex and robust interactions between phages than aquatic and human-associated habitats, resulting in the highest biodiversity of phages. Several types of phages in certain taxa (4.95-7.67%, mainly belonging to Caudoviricetes) have the capacity to carry specific ARGs and display a high potential risk to human health, especially in human-associated habitats. Overall, our results provide insights into the assembly mechanisms of phage communities and their effects on the dissemination of antibiotic resistance.

Lipid Metabolites as Potential Regulators of the Antibiotic Resistome in Tetramorium caespitum.

Antibiotic resistance genes (ARGs) are ancient but have become a modern critical threat to health. Gut microbiota, a dynamic reservoir for ARGs, transfer resistance between individuals. Surveillance of the antibiotic resistome in the gut during different host growth phases is critical to understanding the dynamics of the resistome in this ecosystem. Herein, we disentangled the ARG profiles and the dynamic mechanism of ARGs in the egg and adult phases of Tetramorium caespitum. Experimental results showed a remarkable difference in both gut microbiota and gut resistome with the development of T. caespitum. Meta-based metagenomic results of gut microbiota indicated the generalizability of gut antibiotic resistome dynamics during host development. By using Raman spectroscopy and metabolomics, the metabolic phenotype and metabolites indicated that the biotic phase significantly changed lipid metabolism as T. caespitum aged. Lipid metabolites were demonstrated as the main factor driving the enrichment of ARGs in T. caespitum. Cuminaldehyde, the antibacterial lipid metabolite that displayed a remarkable increase in the adult phase, was demonstrated to strongly induce ARG abundance. Our findings show that the gut resistome is host developmental stage-dependent and likely modulated by metabolites, offering novel insights into possible steps to reduce ARG dissemination in the soil food chain.

Glyphosate Disorders Soil Enchytraeid Gut Microbiota and Increases Its Antibiotic Resistance Risk.

Pesticides promote the stable development of intensive global agriculture. Nevertheless, their residues in the soil can cause ecological and human health risks. Glyphosate is a popular herbicide and is generally thought to be ecologically safe and nontoxic, but this conclusion has been questioned. Herein, we investigated the interaction among soil fauna (Enchytraeus crypticus) exposed to glyphosate and found that glyphosate induced oxidative stress and detoxification responses in E. crypticus and disturbed their lipid metabolism and digestive systems. We further demonstrated that glyphosate disordered the gut microbiota of E. crypticus and increased the abundance of resistance determinants with significant human health risks. Empirical tests and structural equation models were then used to confirm that glyphosate could cause E. crypticus to generate reactive oxygen species, indirectly interfering with their gut microbiota. Our study provides important implications for deciphering the mechanisms of the ecotoxicity of pesticides under the challenge of worldwide pesticide contamination.

Effects of organic fertilizers on plant growth and the rhizosphere microbiome.

Application of organic fertilizers is an important strategy for sustainable agriculture. The biological source of organic fertilizers determines their specific functional characteristics, but few studies have systematically examined these functions or assessed their health risk to soil ecology. To fill this gap, we analyzed 16S rRNA gene amplicon sequencing data from 637 soil samples amended with plant- and animal-derived organic fertilizers (hereafter plant fertilizers and animal fertilizers). Results showed that animal fertilizers increased the diversity of soil microbiome, while plant fertilizers maintained the stability of soil microbial community. Microcosm experiments verified that plant fertilizers were beneficial to plant root development and increased carbon cycle pathways, while animal fertilizers enriched nitrogen cycle pathways. Compared with animal fertilizers, plant fertilizers harbored a lower abundance of risk factors such as antibiotic resistance genes and viruses. Consequently, plant fertilizers might be more suitable for long-term application in agriculture. This work provides a guide for organic fertilizer selection from the perspective of soil microecology and promotes sustainable development of organic agriculture.IMPORTANCEThis study provides valuable guidance for use of organic fertilizers in agricultural production from the perspective of the microbiome and ecological risk.

Structural Element of Vitamin U-Mimicking Antibacterial Polypeptide with Ultrahigh Selectivity for Effectively Treating MRSA Infections.

Antimicrobial peptides (AMPs) exhibit mighty antibacterial properties without inducing drug resistance. Achieving much higher selectivity of AMPs towards bacteria and normal cells has always been a continuous goal to be pursued. Herein, a series of sulfonium-based polypeptides with different degrees of branching and polymerization were synthesized by mimicking the structure of vitamin U. The polypeptide, G2 -PM-1H+ , shows both potent antibacterial activity and the highest selectivity index of 16000 among the reported AMPs or peptoids (e.g., the known index of 9600 for recorded peptoid in "Angew. Chem. Int. Ed., 2020, 59, 6412."), which can be attributed to the high positive charge density of sulfonium and the regulation of hydrophobic chains in the structure. The antibacterial mechanisms of G2 -PM-1H+ are primarily ascribed to the interaction with the membrane, production of reactive oxygen species (ROS), and disfunction of ribosomes. Meanwhile, altering the degree of alkylation leads to selective antibacteria against either gram-positive or gram-negative bacteria in a mixed-bacteria model. Additionally, both in vitro and in vivo experiments demonstrated that G2 -PM-1H+ exhibited superior efficacy against methicillin-resistant Staphylococcus aureus (MRSA) compared to vancomycin. Together, these results show that G2 -PM-1H+ possesses high biocompatibility and is a potential pharmaceutical candidate in combating bacteria significantly threatening human health.

Reverse transcription recombinase-aided amplification assay combined with a lateral flow dipstick for detection of duck Tembusu virus.

Duck Tembusu virus disease, caused by duck Tembusu virus (DTMUV), brings great harm to duck industry. Early diagnosis is of great significance for the prevention and control of this disease. In order to develop a specific and sensitive method for rapid diagnosis of DTMUV, reverse-transcriptase recombinase aided amplification combined with lateral flow dipstick (RT-RAA-LFD) method for detection of DTMUV was established. Firstly, downstream primer was labeled with biotin and probe was labeled with FAM, and primer concentration, reaction time, and reaction temperature were optimized. Then, the specificity and sensitivity of this method was investigated. The results of specificity test showed that it had no cross reaction with other common pathogens such as low pathogenic avian influenza virus (AIV), Newcastle disease virus (NDV), duck hepatitis A virus (DHV), and duck Reovirus. The results of sensitivity test showed that the minimum detection limit of this method was 10 copies/µL, which was 1000 times than conventional RT-PCR (104 copies/µL), and equivalent to that of fluorescent quantitative PCR. Furthermore, this RT-RAA-LFD method demonstrated excellent intragroup and intergroup consistency. Finally, the RT-RAA-LFD assay and real-time PCR were both utilized to examine 58 clinical samples concurrently. The results showed that the RT-RAA-LFD method (5/58) was more sensitive than the fluorescence quantitative PCR method (4/58). In summary, RT-RAA-LFD method established in this study had a strong specificity and high sensitivity, which provided technical support for clinical detection of DTMUV.

A global atlas of marine antibiotic resistance genes and their expression.

Oceans serve as global reservoirs of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). However, little is known about the traits and expression of ARGs in response to environmental factors. We analyzed 347 metagenomes and 182 metatranscriptomes to determine the distribution, hosts, and expression of ARGs in oceans. Our study found that the diversity and abundance of ARGs varied with latitude and depth. The core marine resistome mainly conferred glycopeptide and multidrug resistance. The hosts of this resistome were mainly limited to the core marine microbiome, with phylogenetic barriers to the horizontal transfer of ARGs, transfers being more frequent within species than between species. Sixty-five percent of the marine ARGs identified were expressed. More than 90% of high-risk ARGs were more likely to be expressed. Anthropogenic activity might affect the expression of ARGs by altering nitrate and phosphate concentrations and ocean temperature. Machine-learning models predict >97% of marine ARGs will change expression by 2100. High-risk ARGs will shift to low latitudes and regions with high anthropogenic activity, such as the Pacific and Atlantic Oceans. Certain ARGs serve a dual role in antibiotic resistance and potentially participate in element cycling, along with other unknown functions. Determining whether changes in ARG expression are beneficial to ecosystems and human health is challenging without comprehensive understanding of their functions. Our study identified a core resistome in the oceans and quantified the expression of ARGs for the development of future control strategies under global change.

Microrod crystals formed via Rhein-mediated mineralization.

Herein, a Rhein-mineralized microrod crystal (H-RMM) with an ultra-high drug loading capacity was reported for anti-inflammation. Due to a dense crystal structure, the H-RMM achieved improved biocompatibility and sustained controlled release of Rhein. Also, the Rhein nanofibers released from H-RMM were favorable to be internalized by cells, leading to enhanced anti-inflammation effects.

Effect of chlorpyrifos on freshwater microbial community and metabolic capacity of zebrafish.

Chlorpyrifos is a widely used organophosphorus insecticide because of its high efficiency and overall effectiveness, and it is commonly detected in aquatic ecosystems. However, at present, the impact of chlorpyrifos on the aquatic micro-ecological environment is still poorly understood. Here, we established aquatic microcosm systems treated with 0.2 and 2.0 µg/L chlorpyrifos, and employed omics biotechnology, including metagenomics and 16S rRNA gene sequencing, to investigate the effect of chlorpyrifos on the composition and functional potential of the aquatic and zebrafish intestinal microbiomes after 7 d and 14 d chlorpyrifos treatment. After 14 d chlorpyrifos treatment, the aquatic microbial community was adversely affected in terms of its composition, structure, and stability, while its diversity showed only a slight impact. Most functions, especially capacities for environmental information processing and metabolism, were destroyed by chlorpyrifos treatment for 14 d. We observed that chlorpyrifos increased the number of risky antibiotic resistance genes and aggravated the growth of human pathogens. Although no clear effects on the structure of the zebrafish intestinal microbial community were observed, chlorpyrifos treatment did alter the metabolic capacity of the zebrafish. Our study highlights the ecological risk of chlorpyrifos to the aquatic environment and provides a theoretical basis for the rational use of pesticides in agricultural production.

Water-Triggered Segment Orientation of Long-Lasting Anti-Biofouling Polyurethane Coatings on Biomedical Catheters via Solvent Exchange Strategy.

The formation of biofilm and thrombus on medical catheters poses a significant life-threatening concern. Hydrophilic anti-biofouling coatings upon catheter surfaces with complex shapes and narrow lumens are demonstrated to have the potential in reducing complications. However, their effectiveness is constrained by poor mechanical stability and weak substrate adhesion. Herein, a novel zwitterionic polyurethane (SUPU) with strong mechanical stability and long-term anti-biofouling is developed by controlling the ratio of sulfobetaine-diol and ureido-pyrimidinone. Once immersed in water, as-synthesized zwitterionic coating (SUPU3 SE) would undergo a water-driven segment reorientation to obtain much higher durability than its direct drying one, even under various extreme treatments, including acidic solution, abrasion, ultrasonication, flushing, and shearing, in PBS at 37 °C for 14 days. Moreover, SUPU3 SE coating could achieve a 97.1% of exceptional reducing protein fouling, complete prevention of cell adhesion, and long-lasting anti-biofilm performance even after 30 days. Finally, the good anti-thrombogenic formations of SUPU3 SE coating with bacterial treatment are validated in blood circulation through an ex vivo rabbit arteriovenous shunt model. This work provides a facile approach to fabricating stable hydrophilic coating through a simple solvent exchange to reduce thrombosis and infection of biomedical catheters.

Antimicrobial Peptides in the Global Microbiome: Biosynthetic Genes and Resistance Determinants.

Antimicrobial peptides are a promising new class of antimicrobials that could address the antibiotic resistance crisis, which poses a major threat to human health. These peptides are present in all kingdoms of life, but especially in microorganisms, having multiple origins in diverse taxa. To date, there has been no global study on the diversity of antimicrobial peptides, the hosts in which these occur, and the potential for resistance to these agents. Here, we investigated the diversity and number of antimicrobial peptides in four main habitats (aquatic, terrestrial, human, and engineered) by analyzing 52,515 metagenome-assembled genomes. The number of antimicrobial peptides was higher in the human gut microbiome than in other habitats, and most hosts of antimicrobial peptides were habitat-specific. The relative abundance of genes that confer resistance to antimicrobial peptides varied between habitats and was generally low, except for the built environment and on human skin. The horizontal transfer of potential resistance genes among these habitats was probably constrained by ecological barriers. We systematically quantified the risk of each resistance determinant to human health and found that nearly half of them pose a threat, especially those that confer resistance to multiple AMPs and polymyxin B. Our results help identify the biosynthetic potential of antimicrobial peptides in the global microbiome, further identifying peptides with a low risk of developing resistance.

Metatranscriptome deciphers the effects of non-antibiotic antimicrobial agents on antibiotic resistance and virulence factors in freshwater microcosms.

The emergence and transmission of antibiotic resistance genes (ARGs) and virulence factors (VFs) pose health risks to the ecosystem and humans. Understanding how non-antibiotic antimicrobial agents drive the expression of ARGs and VFs in freshwater ecosystems, however, remains large challenges. Here, we employed freshwater microcosms and performed metatranscriptomic analysis to investigate the expression profiles of ARGs and VFs in response to pollutants of non-antibiotic antimicrobial agents, including silver nanoparticles (AgNPs) and azoxystrobin. Results showed that AgNPs significantly inhibited the total expression of ARGs and VFs and decreased the number of pathogenic microorganisms expressing these genes. Azoxystrobin increased the total expression of ARGs and VFs, as well as the number of pathogens expressing VFs, but concomitantly reduced the number of pathogens expressing ARGs. Two tested pollutants dramatically changed the expression profiles of ARGs and VFs, with distinct patterns: AgNPs displayed a negative effect, while azoxystrobin showed a positive effect on their expression profiles. Our findings provided a systematical insight to demonstrate that non-antibiotic antimicrobial agents with different mechanisms of action showed various effects on ARGs and VFs, and therefore represented different ecological risks.

Global distribution of marine microplastics and potential for biodegradation.

Microplastics are a growing marine environmental concern globally due to their high abundance and persistent degradation. We created a global map for predicting marine microplastic pollution using a machine-learning model based on 9445 samples and found that microplastics converged in zones of accumulation in subtropical gyres and near polar seas. The predicted global potential for the biodegradation of microplastics in 1112 metagenome-assembled genomes from 485 marine metagenomes indicated high potential in areas of high microplastic pollution, such as the northern Atlantic Ocean and the Mediterranean Sea. However, the limited number of samples hindered our prediction, a priority issue that needs to be addressed in the future. We further identified hosts with microplastic degradation genes (MDGs) and found that Proteobacteria accounted for a high proportion of MDG hosts, mainly Alphaproteobacteria and Gammaproteobacteria, with host-specific patterns. Our study is essential for raising awareness, identifying areas with microplastic pollution, providing a prediction method of machine learning to prioritize surveillance, and identifying the global potential of marine microbiomes to degrade microplastics, providing a reference for selecting bacteria that have the potential to degrade microplastics for further applied research.

A campaign of mass drug administration with artemisinin-piperaquine to antimalaria in Trobriand Islands.

We conducted a study on the Trobriand Islands of Papua New Guinea (PNG) in 2018 to verify the safety and efficacy of the artemisinin-piperaquine (AP) mass drug administration (MDA) campaign in regions with moderate to high mixed malaria transmission. Based on the natural topography of the Trobriand Islands, 44,855 residents from 92 villages on the islands were enrolled and divided into the main and outer islands. Three rounds of MDA were conducted using grid-based management. The primary endpoint was the coverage rate. Adverse reactions, parasitemia, and malaria morbidity were the secondary endpoints. There were 36,716 people living in 75 villages on the main island, and the MDA coverage rate was 92.58-95.68%. Furthermore, 8,139 people living in 17 villages on the outer islands had a coverage rate of 94.93-96.11%. The adverse reactions were mild in both groups, and parasitemia decreased by 87.2% after one year of surveillance. The average annual malaria morbidity has decreased by 89.3% after the program for four years. High compliance and mild adverse reactions indicated that the MDA campaign with AP was safe. The short-term effect is relatively ideal, but the evidence for long-term effect evaluation is insufficient.

Geographic patterns of microbial traits of river basins in China.

River microbiotas contribute to critical geochemical processes and ecological functions of rivers but are sensitive to variations of environmental drivers. Understanding the geographic pattern of river microbial traits in biogeochemical processes can provide important insights into river health. Many studies have characterized river microbial traits in specific situations, but the geographic patterns of these traits and environmental drivers at a large scale are unknown. We reanalyzed 4505 raw 16S rRNA sequences samples for microbiota from river basins in China. The results indicated differences in the diversity, composition, and structure of microbiotas across diverse river basins. Microbial diversity and functional potential in the river basins decreased over time in northern China and increased in southern China due to niche differentiation, e.g., the Yangtze River basin was the healthiest ecosystem. River microbiotas were mainly involved in the cycling of carbon and nitrogen in the river ecosystems and participated in potential organic metabolic functions. Anthropogenic pollutants discharge was the most critical environmental driver for the microbial traits, e.g., antibiotic discharge, followed by climate change. The prediction by machine-learning models indicated that the continuous discharge of antibiotics and climate change led to high ecological risks for the rivers. Our study provides guidelines for improving the health of river ecosystems and for the formulation of strategies to restore the rivers.

Shaping effects of rice, wheat, maize, and soybean seedlings on their rhizosphere microbial community.

The rhizosphere microbiome plays critical roles in plant growth and is an important interface for resource exchange between plants and the soil environment. Crops at various growing stages, especially the seedling stage, have strong shaping effects on the rhizosphere microbial community, and such community reconstruction will positively feed back to the plant growth. In the present study, we analyzed the variations of bacterial and fungal communities in the rhizosphere of four crop species: rice, soybean, maize, and wheat during successive cultivations (three repeats for the seedling stages) using 16S rRNA gene and internal transcribed spacer (ITS) high-throughput sequencing. We found that the relative abundances of specific microorganisms decreased after different cultivation times, e.g., Sphingomonas, Pseudomonas, Rhodanobacter, and Caulobacter, which have been reported as plant-growth beneficial bacteria. The relative abundances of potential plant pathogenic fungi Myrothecium and Ascochyta increased with the successive cultivation times. The co-occurrence network analysis showed that the bacterial and fungal communities under maize were much more stable than those under rice, soybean, and wheat. The present study explored the characteristics of bacteria and fungi in crop seedling rhizosphere and indicated that the characteristics of indigenous soil flora might determine the plant growth status. Further study will focus on the use of the critical microorganisms to control the growth and yield of specific crops.