Defense systems of soil microorganisms in response to compound contamination by arsenic and polycyclic aromatic hydrocarbons.

Arsenic and PAHs impose environmental stress on soil microorganisms, yet their compound effects remain poorly understood. While soil microorganisms possess the ability to metabolize As and PAHs, the mechanisms of microbial response are not fully elucidated. In our study, we established two simulated soil systems using soil collected from Xixi Wetland Park grassland, Hangzhou, China. The As-600 Group was contaminated with 600 mg/kg sodium arsenite, while the As-600-PAHs-30 Group received both 600 mg/kg sodium arsenite and 30 mg/kg PAHs (phenanthrene:fluoranthene:benzo[a]pyrene = 1:1:1). These systems were operated continuously for 270 days, and microbial responses were assessed using high-throughput sequencing and metagenomic analysis. Our findings revealed that compound contamination significantly promoted the abundance of microbial defense-related genes, with general defense genes increasing by 11.07 % ~ 74.23 % and specific defense genes increasing by 44.13 % ~ 55.74 %. The dominate species Rhodococcus adopts these general and specific defense mechanisms to resist compound pollution stress and gain ecological niche advantages, making it a candidate strain for soil remediation. Our study contributes to the assessment of ecological damage caused by As and PAHs from a microbial perspective and provides valuable insights for soil remediation.

The microbial community structure and nitrogen cycle of high-altitude pristine saline lakes on the Qinghai-Tibetan plateau.

The nitrogen (N) cycle is the foundation of the biogeochemistry on Earth and plays a crucial role in global climate stability. It is one of the most important nutrient cycles in high-altitude lakes. The biogeochemistry of nitrogen is almost entirely dependent on redox reactions mediated by microorganisms. However, the nitrogen cycling of microbial communities in the high-altitude saline lakes of the Qinghai-Tibet Plateau (QTP), the world's "third pole" has not been investigated extensively. In this study, we used a metagenomic approach to investigate the microbial communities in four high-altitude pristine saline lakes in the Altun mountain on the QTP. We observed that Proteobacteria, Bacteroidota, and Actinobacteriota were dominant in these lakes. We reconstructed 1,593 bacterial MAGs and 8 archaeal MAGs, 1,060 of which were found to contain nitrogen cycle related genes. Our analysis revealed that nitrite reduction, nitrogen fixation, and assimilatory nitrate reduction processes might be active in the lakes. Denitrification might be a major mechanism driving the potential nitrogen loss, while nitrification might be inactive. A wide variety of microorganisms in the lake, dominated by Proteobacteria, participate together in the nitrogen cycle. The prevalence of the dominant taxon Yoonia in these lakes may be attributed to its well-established nitrogen functions and the coupled proton dynamics. This study is the first to systematically investigate the structure and nitrogen function of the microbial community in the high-altitude pristine saline lakes in the Altun mountain on the QTP. As such, it contributes to a better comprehension of biogeochemistry of high-altitude saline lakes.

Methane-dependent denitrification by Methylomirabilis: an indirect nitrous oxide sink?

Methane-dependent complete denitrification primarily involves nitrate reduction to nitrite by ANME-2d archaea and nitrite reduction to dinitrogen by Methylomirabilis bacteria. 'Candidatus Methylomirabilis sinica' integrates the divisional labor. Physiological traits of this bacterium potentially enable the simultaneous reduction of N2O and CH4 emissions. This forum article explores these traits and possible microbial mechanisms for co-reduction, providing guidance for greenhouse gas management strategies.

Impact of arsenic and PAHs compound contamination on microorganisms in coking sites: From a community to individual perspective.

Arsenic (As) and polycyclic aromatic hydrocarbons (PAHs) are highly toxic, carcinogenic and teratogenic, and are commonly found in soils of industrial sites such as coking plants. They exert environmental stresses on soil microorganisms, but their compounding effects have not been systematically studied. Exploring the effects of compound contamination on microbial communities, species and genes is important for revealing the ecological damage caused by compound contamination and offering scientific insights into soil remediation strategies. In this study, we selected soil samples from 0 to 100 cm depth of a coking site with As, PAHs and compound contamination. We investigated the compound effects of As and PAHs on microbial communities by combining high-throughput sequencing, metagenomic sequencing and genome assembly. Compared with single contamination, compound contamination reduced the microbial community diversity by 10.68%-12.07% and reduced the community richness by 8.39%-18.61%. The compound contamination decreased 32.41%-46.02% of microbial PAHs metabolic gene abundance, 11.36%-19.25% of cell membrane transport gene abundance and 12.62%-57.77% of cell motility gene abundance. Xanthobacteraceae, the biomarker for compound contaminated soils, harbors arsenic reduction genes and PAHs degradation pathways of naphthalene, benzo [a]pyrene, fluorene, anthracene, and phenanthrene. Its broad metabolic capabilities, encompassing sulfur metabolism and quorum sensing, facilitate the acquisition of energy and nutrients, thereby conferring ecological niche advantages in compound contaminated environments. This study underscores the significant impacts of As and PAHs on the composition and function of microbial communities, thereby enriching our understanding of their combined effects and providing insights for the remediation of compound contaminated sites.

Fluoranthene slow down sulfamethazine migration in soil via π-π interaction to increase the abundance of antibiotic resistance genes.

Sulfonamide antibiotics and polycyclic aromatic hydrocarbons (PAHs) often coexist in soil, leading to compound pollution through various pathways. This study focuses on sulfamethazine (SMZ) and PAHs (fluoranthene) as the subject for compound pollution research. Using a soil-groundwater simulation system, we investigated the migration characteristics of SMZ under coexistence with fluoranthene (Fla) and observed variations in the abundance of antibiotic resistance genes (ARGs). Through molecular docking simulations and isothermal adsorption experiments, we discovered that Fla bound with SMZ via π-π interactions, resulting in a 20.9% increase in the SMZ soil-water partition coefficient. Under compound conditions, the concentration of SMZ in surface soil could reach 1.4 times that of SMZ added alone, with an 13.4% extension in SMZ half-life. The deceleration of SMZ's vertical migration rate placed additional stress on surface soil microbiota, leading to a proliferation of ARGs by 66.3%-125.8%. Moreover, under compound pollution, certain potential hosts like Comamonadaceae and Gemmatimonas exhibited a significant positive correlation with resistance genes such as sul 1 and sul 2. These findings shed light on the impact of PAHs on sulfonamide antibiotic migration and the abundance of ARGs. They also provide theoretical insights for the development of technologies aimed at mitigating compound pollution in soil.

Prediction of developmental toxic effects of fine particulate matter (PM2.5) water-soluble components via machine learning through observation of PM2.5 from diverse urban areas.

The global health implications of fine particulate matter (PM2.5) underscore the imperative need for research into its toxicity and chemical composition. In this study, zebrafish embryos exposed to the water-soluble components of PM2.5 from two cities (Harbin and Hangzhou) with differences in air quality, underwent microscopic examination to identify primary target organs. The Harbin PM2.5 induced dose-dependent organ malformation in zebrafish, indicating a higher level of toxicity than that of the Hangzhou sample. Harbin PM2.5 led to severe deformities such as pericardial edema and a high mortality rate, while the Hangzhou sample exhibited hepatotoxicity, causing delayed yolk sac absorption. The experimental determination of PM2.5 constituents was followed by the application of four algorithms for predictive toxicological assessment. The random forest algorithm correctly predicted each of the effect classes and showed the best performance, suggesting that zebrafish malformation rates were strongly correlated with water-soluble components of PM2.5. Feature selection identified the water-soluble ions F- and Cl- and metallic elements Al, K, Mn, and Be as potential key components affecting zebrafish development. This study provides new insights into the developmental toxicity of PM2.5 and offers a new approach for predicting and exploring the health effects of PM2.5.

Dynamic migration and risk of cephalosporin antibiotic resistance genes: Move from pharmaceutical plants through wastewater treatment plants to coastal tidal flats sediments.

The migration and dissemination of antibiotics and their corresponding antibiotic resistance genes (ARGs) from pharmaceutical plants through wastewater treatment to the environment introduce exogenous ARGs, increasing the risk of antibiotic resistance. Cephalosporin antibiotics (Ceps) are among the most widely used antibiotics with the largest market scale today, and the issue of resistance is becoming increasingly severe. In this study, a cephalosporin pharmaceutical plant was selected and metagenomic analysis was employed to investigate the dissemination patterns of cephalosporin antibiotics (Ceps) and their ARGs (CepARGs) from the pharmaceutical plant through the wastewater treatment plant to tidal flats sediments. The findings revealed a significant reduction in the total concentration of Ceps by 90.32 % from the pharmaceutical plant's Pioneer Bio Reactor (PBR) to the effluent of the wastewater treatment plant, and a notable surge of 172.13 % in the relative abundance of CepARGs. It was observed that CepARGs originating from the PBR could migrate along the dissemination chain, contributing to 60 % of the CepARGs composition in tidal flats sediments. Microorganisms play a crucial role in the migration of CepARGs, with efflux-mediated CepARGs, as an intrinsic resistance mechanism, exhibiting a higher prospensity for migration due to their presence in multiple hosts. While Class I risk CepARGs are present at the pharmaceutical and wastewater plant stages, Class I ina-CepARGs are completely removed during wastewater treatment and do not migrate to the environment. This study reveals the dynamic migration characteristics and potential risk changes regarding Ceps and CepARGs in real dissemination chains, providing new theoretical evidence for the mitigation, control, and risk prevention of CepARGs.

Fungi play a crucial role in sustaining microbial networks and accelerating organic matter mineralization and humification during thermophilic phase of composting.

Fungi play an important role in the mineralization and humification of refractory organic matter such as lignocellulose during composting. However, limited research on the ecological role of fungi in composting system hindered the development of efficient microbial agents. In this study, six groups of lab-scale composting experiments were conducted to reveal the role of fungal community in composting ecosystems by comparing them with bacterial community. The findings showed that the thermophilic phase was crucial for organic matter degradation and humic acid formation. The Richness index of the fungal community peaked at 1165 during this phase. PCoA analysis revealed a robust thermal stability in the fungal community. Despite temperature fluctuations, the community structure, predominantly governed by Pichia and Candida, remained largely unaltered. The stability of fungal community and the complexity of ecological networks were 1.26 times and 5.15 times higher than those observed in bacterial community, respectively. Fungi-bacteria interdomain interaction markedly enhanced network complexity, contributing to maintain microbial ecological functions. The core fungal species belonging to the family Saccharomycetaceae drove interdomain interaction during thermophilic phase. This study demonstrated the key role of fungi in the composting system, which would provide theoretical guidance for the development of high efficiency composting agents to strengthen the mineralization and humification of organic matter.

Aptamer-free upconversion nanoparticle/silk biosensor system for low-cost and highly sensitive detection of antibiotic residues.

The detection of antibiotics is crucial for safeguarding the environment, ensuring food safety, and promoting human health. However, developing a rapid, convenient, low-cost, and sensitive method for antibiotic detection presents significant challenges. Herein, an aptamer-free biosensor was successfully constructed using upconversion nanoparticles (UCNPs) coated with silk fibroin (SF), based on Förster resonance energy transfer (FRET) and the charge-transfer effect, for detecting roxithromycin (RXM). A synergistic FRET efficiency was achieved by utilizing alizarin red and RXM complexes as energy acceptors, with UCNP as the energy donor, and immobilizing an ultrathin SF protein corona within 10 nm. The biosensor detects RXM in deionized water with high sensitivity primarily through monolayer adsorption, with a detection range of 1.0 nM-141.6 nM and a detection limit as low as 0.68 nM. The performance of this biosensor was compared with the ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS) method for detecting antibiotics in river water separately and a strong correlation between the two methods was observed. The biosensor exhibited long-term stability in aqueous solutions (up to 60 d) with no attenuation of fluorescence intensity. Furthermore, the biosensor's applicability extended to the highly sensitive detection of other antibiotics, such as azithromycin. This study introduces a low-cost, eco-friendly, and highly sensitive method for antibiotic detection, with broad potential for future applications in environmental, healthcare, and food-related fields.

Mobile genetic elements mediate the cross-media transmission of antibiotic resistance genes from pig farms and their risks.

Manure composting in traditional small-scale pig farms leads to the migration and diffusion of antibiotics and antibiotics resistance genes (ARGs) along the chain of transmission to the surrounding environment, increasing the risk of environmental resistance. Understanding the transmission patterns, driving factors, and health risks of ARGs on small-scale pig farms is important for effective control of ARGs transmission. This study was conducted on a small pig farm and its surrounding environment. The cross-media transmission of ARGs and their risks in the farming habitat were investigated using Metagenomic annotation and qPCR quantitative detection. The results indicate that ARGs in farms spread with manure pile-soil-channel sediment-mudflat sediment. Pig farm manure contributed 22.49 % of the mudflat sediment ARGs. Mobile genetic elements mediate the spread of ARGs across different media. Among them, tnpA and IS26 have the highest degree. Transmission of high-risk ARGs sul1 and tetM resulted in a 50 % and 116 % increase in host risk for sediment, respectively. This study provides a basis for farm manure management and control of the ARGs spread.

Low-intensity alternating ventilation achieves effective humification during food waste composting by enhancing the intensity of microbial interaction and carbon metabolism.

Vertical static composting is an efficient and convenient technology for the treatment of food waste. Exploring the impact of oxygen concentration levels on microbial community structure and functional stability is crucial for optimizing ventilation technology. This study set three experimental groups with varying ventilation intensities based on self-made alternating ventilation composting reactor (AL2: 0.2 L kg-1 DM·min-1; AL4: 0.4 L kg-1 DM·min-1; AL6: 0.6 L kg-1 DM·min-1) to explore the optimal alternating ventilation rate. The results showed that the cumulative ammonia emission of AL2 group reduced by 25.13% and 12.59% compared to the AL4 and AL6 groups. The humification degree of the product was 1.18 times and 1.25 times higher than the other two groups. AL2 increased the relative abundance of the core species Saccharomonospora, thereby strengthening microbial interaction. Low-intensity alternating ventilation increased the carbon metabolism levels, especially aerobic_chemoheterotrophy, carbohydrate and lipid metabolism. However, it simultaneously reduced nitrogen metabolism. Structural equation model analysis demonstrated that alternating low-intensity ventilation effectively regulated both microbial diversity (0.81, p < 0.001) and metabolism (0.81, p < 0.001) by shaping the composting environment. This study optimized the intensity of alternating ventilation and revealed the regulatory mechanism of community structure and metabolism. This study provides guidance for achieving efficient and low-consumption composting.

Field-based investigation reveals selective enrichment of companion microbes in vegetables leading to specific accumulation of antibiotic resistance genes.

Vegetables capture antibiotic resistance genes (ARGs) from the soil and then pass them on to consumers through the delivery chain and food chain, and are therefore the key node that may increase the risk of human exposure to ARGs. This study investigates the patterns and driving forces behind the transmission of ARGs from soil to vegetables by the commonly planted cash crops in the coastal region of southern China, i.e. broccoli, pumpkin, and broad bean, to investigate. The study used metagenomic data to reveal the microbial and ARGs profiles of various vegetables and the soil they are grown. The results indicate significant differences in the accumulation of ARGs among different vegetables harvested in the same area at the same time frame, and the ARGs accumulation ability of the three vegetables was in the order of broccoli, broad bean, and pumpkin. In addition, broccoli collected the highest number of ARGs in types (n = 14), while pumpkin (n = 13) does not obtain trimethoprim resistance genes and broad beans (n = 10) do not obtain chloramphenicol, fosmidomycin, quinolone, rifamycin, or trimethoprim resistance genes. Host tracking analysis shows a strong positive correlation (|rho| > 0.8, p < 0.05) between enriched ARGs and plant companion microbes. Enrichment analysis of metabolic pathways of companion microbes shows that vegetables exhibit a discernible enrichment of companion microbes, with significant differences among vegetables. This phenomenon is primarily due to the screening of carbohydrate metabolism capabilities among companion microbes and leads varied patterns of ARGs that spread from the soil to vegetables. This offers a novel insight into the intervention of foodborne transmission of ARGs.

Unveiling the unique role of iron in the metabolism of methanogens: A review.

Methanogens are the main participants in the carbon cycle, catalyzing five methanogenic pathways. Methanogens utilize different iron-containing functional enzymes in different methanogenic processes. Iron is a vital element in methanogens, which can serve as a carrier or reactant in electron transfer. Therefore, iron plays an important role in the growth and metabolism of methanogens. In this paper, we cast light on the types and functions of iron-containing functional enzymes involved in different methanogenic pathways, and the roles iron play in energy/substance metabolism of methanogenesis. Furthermore, this review provides certain guiding significance for lowering CH4 emissions, boosting the carbon sink capacity of ecosystems and promoting green and low-carbon development in the future.

Methane-dependent complete denitrification by a single Methylomirabilis bacterium.

Methane-dependent nitrate and nitrite removal in anoxic environments is thought to rely on syntrophy between ANME-2d archaea and bacteria in the genus 'Candidatus Methylomirabilis'. Here we enriched and purified a single Methylomirabilis from paddy soil fed with nitrate and methane, which is capable of coupling methane oxidation to nitrate reduction via nitrite to dinitrogen independently. Isotope labelling showed that this bacterium we name 'Ca. Methylomirabilis sinica' stoichiometrically performed methane-dependent complete nitrate reduction to dinitrogen gas. Multi-omics analyses collectively demonstrated that 'M. sinica' actively expressed a well-established pathway for this process, especially including nitrate reductase Nap. Furthermore, 'M. sinica' exhibited a higher nitrate affinity than most denitrifiers, implying its competitive fitness under oligotrophic nitrogen-limited conditions. Our findings revise the paradigm of methane-dependent denitrification performed by two organisms, and the widespread presence of 'M. sinica' in public databases suggests that the coupling of methane oxidation and complete denitrification in single cells substantially contributes to global methane and nitrogen budgets.

Alternating ventilation accelerates the mineralization and humification of food waste by optimizing the temperature-oxygen-moisture distribution in the static composting reactor.

Traditional unidirectional ventilation often leads to the loss of heat and moisture during composting, disrupting the favorable microenvironment required for aerobic microbes. This study developed a pulse alternating ventilation composting reactor and investigated the effects of alternating ventilation on composting efficiency compared with upward ventilation and downward ventilation. The results demonstrated that alternating ventilation stabilized the moisture content at approximately 60 % while reducing the temperature and oxygen concentration range within the reactor. Moreover, it extended the duration of high-temperature (>50 °C) by 31 % and 75 % compared to other two groups. It improved the microbial cooperation intensity and stimulated the core microbe (Tepidimicrobium). Seed germination index (GI) of the compost was improved (GI = 91.27 %), and the humic acid content was 1.23 times and 1.37 times higher than other two groups. These results showed that alternating ventilation can be used for efficient resource disposal of food waste.

D-Ring Modifications of Tetracyclines Determine Their Ability to Induce Resistance Genes in the Environment.

The widespread utilization of tetracyclines (TCs) in agriculture and medicine has led to the borderless spread of tetracycline resistance in humans, animals, and the environment, posing huge risks to both the ecosystem and human society. Changes in the functional group modifications resulted in a higher bacteriostatic efficacy of the new generation of TCs, but their effect on the emergence and evolution of antibiotic resistance genes (ARGs) is not yet known. To this end, four TCs from three generations were chosen to compare their structural effects on influencing the evolution of ARGs in soil microbial communities. The findings revealed that low-generation TCs, such as tetracycline and oxytetracycline, exhibited a greater propensity to stimulate the production and proliferation of ARGs than did high-generation tigecycline. Molecular docking analysis demonstrated that modifications of the D-ring functional group determined the binding capacity of TCs to the substrate-binding pocket of transcriptional regulators and efflux pumps mainly involved in drug resistance. This can be further evidenced by reverse transcription-quantitative polymerase chain reaction quantification and intracellular antibiotic accumulation assessment. This study sheds light on the mechanism of the structural effect of antibiotic-induced ARG production from the perspective of compound-protein binding, therefore providing theoretical support for controlling the dissemination of antibiotic resistance.

Inter-bacterial mutualism promoted by public goods in a system characterized by deterministic temperature variation.

Mutualism is commonly observed in nature but not often reported for bacterial communities. Although abiotic stress is thought to promote microbial mutualism, there is a paucity of research in this area. Here, we monitor microbial communities in a quasi-natural composting system, where temperature variation (20 °C-70 °C) is the main abiotic stress. Genomic analyses and culturing experiments provide evidence that temperature selects for slow-growing and stress-tolerant strains (i.e., Thermobifida fusca and Saccharomonospora viridis), and mutualistic interactions emerge between them and the remaining strains through the sharing of cobalamin. Comparison of 3000 bacterial pairings reveals that mutualism is common (~39.1%) and competition is rare (~13.9%) in pairs involving T. fusca and S. viridis. Overall, our work provides insights into how high temperature can favour mutualism and reduce competition at both the community and species levels.

Vertical migration and dissipation of oxytetracycline induces the recoverable shift in microbial community and antibiotic resistance.

Antibiotic resistance gene (ARG) spread in anthropogenic polluted soils is believed to be accelerated by the incidental inputs of antibiotics via fertilizing and irrigation, and endangering food and human health. However, due to the complex nature of substrates and uncertain microbial responses, the primary drivers of ARG dissemination remain unclear. To address this concern, the effects of antibiotic inputs on soil microbes and antibiotic resistance under simulated natural conditions was investigated in this study. Specifically, four flow-through reactors with gravity flow were established, and the oxytetracycline (OTC) a typical antibiotic in agricultural soils was studied at environmental concentrations (i.e. 0.1, 1 and 10 mg/kg) for 31 days. The vertical distribution and dissipation of OTC were profiled by measuring the residuals in layers over time. Correspondingly, the effects of antibiotic exposure on microbial communities and ARG abundances were studied. The results showed that the average exposure intensity of OTC in different soil layers ranged in 0.03-6.45 mg/kg, and resulted in different dissipation kinetics. In addition, top layer was found to be the main site of OTC reduction, where OTC dissipated at magnitude of 74.0-96.6 %, depending on the initial OTC concentration. OTC migration and dissipation resulted in the shift of community composition to the extent of 0.25-0.33 in terms of Bray-Curtis distance, which partially recovered over time. And the achievement of alternative community compositions was supposed to be largely affected by the microbial interaction. Along with the community changes, a short-term accumulation of resistance genes was detected, while the relative abundance of indicator ARGs, i.e. tetG and mexB, rising up to 10-fold higher than the initial, although eventually decayed. Collective findings of this study indicated that antibiotics at environmental concentrations might trigger extra microbial interactions and thereby reducing the demand for ARGs accumulation. It provided valuable understandings in the risk of antibiotic spillage, especially for the incident exposure at the environmentally relevant concentrations.

Ecological distribution of anaerobic granular sludge towards efficient anaerobic reactor.

Anaerobic reactors often underperform compared to expectations. To identify the key factors, an ecological anaerobic reactor (EAR) with vertical partitions was developed and compared to a physical anaerobic reactor (PAR) as the control. It was observed that EAR achieved a much higher organic loading rate (OLR) compared to PAR (>100 vs 45 kg/m3·d). The different vertical distribution characteristics of anaerobic granular sludge could be ascribed to two vertical distribution patterns dominated in EAR and PAR, i.e., ecological and physical distributions. It was revealed that ecological distribution was formed by the habitat selection, resulting in promoted substrate availability and higher OLR. While physical distribution was mainly affected by hydraulic selection via granule settleability, causing declined substrate availability and lower OLR. Consequently, the promoted ecological distribution and weakened hydraulic selection in EAR contributed to its good performance. Overall, these findings could offer novel concepts for the development of reactors towards high performance.

Directed regulation of anammox communities based on exogenous siderophores for highly efficient nitrogen removal.

It is expected that the quicker domestication of anaerobic ammonia oxidation (anammox) communities and the enhancement of their nitrogen transformation capability can be achieved through targeted regulation of anammox communities. Iron cast a vital role in the growth and metabolism of anammox bacteria. Specific siderophores offer promising prospects for the targeted regulation of anammox communities by facilitating the efficient utilization of iron. Two siderophores-enterobactin and putrebactin-exclusively for Ca. Brocadia and Ca. Kuenenia were developed to specifically regulate anammox communities towards different directions, respectively. Anammox communities in the reactors evoluted targetedly towards Ca. Brocadia-dominated communities and Ca. Kuenenia-dominated communities, respectively, leading to a maximum increase in community nitrogen removal capacity by 84.64±0.55% and 210.26±0.57%, respectively, under different nitrogen concentrations. It was indicated that siderophores could regulate anammox communities by redistributing iron resources in a targeted manner based on the analyses of transcriptome and proteome. This study provides novel insights into the rational selection and utilization of exogenous siderophores as an effective implement to manipulate anammox communities and create communities with high nitrogen removal ability fleetly.