Open-set deep learning-enabled single-cell Raman spectroscopy for rapid identification of airborne pathogens in real-world environments.

Pathogenic bioaerosols are critical for outbreaks of airborne disease; however, rapidly and accurately identifying pathogens directly from complex air environments remains highly challenging. We present an advanced method that combines open-set deep learning (OSDL) with single-cell Raman spectroscopy to identify pathogens in real-world air containing diverse unknown indigenous bacteria that cannot be fully included in training sets. To test and further enhance identification, we constructed the Raman datasets of aerosolized bacteria.

Single-cell Raman and functional gene analyses reveal microbial P solubilization in agriculture waste-modified soils.

Application of agricultural waste such as rapeseed meal (RM) is regarded as a sustainable way to improve soil phosphorus (P) availability by direct nutrient supply and stimulation of native phosphate-solubilizing microorganisms (PSMs) in soils. However, exploration of the in situ microbial P solubilizing function in soils remains a challenge. Here, by applying both phenotype-based single-cell Raman with DO labeling (Raman-DO) and genotype-based high-throughput chips targeting carbon, nitrogen and P (CNP) functional genes, the effect of RM application on microbial P solubilization in three typical farmland soils was investigated.

Mapping the profiles and underlying driving mechanisms of the antibiotic resistome and microbiome within a subtropical complex river watershed.

Antibiotic resistance is an escalating global concern, leading to millions of annual deaths worldwide. Human activities can impact antibiotic resistance gene (ARG) prevalence in aquatic ecosystems, but the intricate interplay between anthropogenic disturbances and river system resilience, and their respective contributions to the dynamics of different river segments, remains poorly understood. In this study, we investigate the antibiotic resistome and microbiome in water and sediment samples from two distinct sub-watersheds within a specific watershed.

Impact of Airborne Pathogen-Derived Extracellular Vesicles on Macrophages Revealed by Raman Spectroscopy and Multiomics.

Long-term exposure to the indoor environment may pose threats to human health due to the presence of pathogenic bacteria and their byproducts. Nanoscale extracellular vesicles (EVs) extensively secreted from pathogenic bacteria can traverse biological barriers and affect physio-pathological processes. However, the potential health impact of EVs from indoor dust and the underlying mechanisms remain largely unexplored.

Quantifying health risks of plastisphere antibiotic resistome and deciphering driving mechanisms in an urbanizing watershed.

Microplastics (MPs) ubiquitous in environments promote the dissemination of antibiotic resistance genes (ARGs), threatening ecosystem safety and human health. However, quantitative assessments of the health risks of ARGs (HRA) in plastisphere and an in-depth exploration of their driving mechanisms are still lacking. Here, the microbiomes, ARGs, and community assembly processes of five types of MPs in an urbanizing watershed were systematically investigated.

An Isotope-Labeled Single-Cell Raman Spectroscopy Approach for Tracking the Physiological Evolution Trajectory of Bacteria toward Antibiotic Resistance.

Understanding evolution of antibiotic resistance is vital for containing its global spread. Yet our ability to in situ track highly heterogeneous and dynamic evolution is very limited. Here, we present a new single-cell approach integrating D O-labeled Raman spectroscopy, advanced multivariate analysis, and genotypic profiling to in situ track physiological evolution trajectory toward resistance.

Seasonal hydrological dynamics govern lifestyle preference of aquatic antibiotic resistome.

Antibiotic resistance genes (ARGs) are a well-known environmental concern. Yet, limited knowledge exists on the fate and transport of ARGs in deep freshwater reservoirs experiencing seasonal hydrological changes, especially in the context of particle-attached (PA) and free-living (FL) lifestyles. Here, the ARG profiles were examined using high-throughput quantitative PCR in PA and FL lifestyles during four seasons representing two hydrological phenomena (vertical mixing and thermal stratification) in the Shuikou Reservoir (SR), Southern China.

Metagenomic insights into environmental risk of field microplastics in an urban river.

Microplastics (MPs) are emerging as anthropogenic vectors for the colonization and transportation of microbial communities in aquatic ecosystems. However, the composition of the microbiome and its environmental risk on field MPs at watershed scale has rarely been explored. Here, geographical distributions of microbiome, antibiotic resistance genes (ARGs) and virulence factors (VFs) on field MPs at watershed scale were characterized and their potential environmental risks were evaluated based on the data from metagenomic analyzes.

Urbanization drives the succession of antibiotic resistome and microbiome in a river watershed.

Urbanization is a process of ecosystem evolution mediated by human activities. One of the main consequences is the alteration of antibiotic resistome and microbiome in aquatic environment, which may transfer from water to sediments and exert a long-term health concern to aquatic animals and even humans. However, the role of urbanization in shaping resistome and microbiome in water and sediments is largely unknown.

Viral diversity and potential environmental risk in microplastic at watershed scale: Evidence from metagenomic analysis of plastisphere.

Microplastics (MPs) have been considered as a new vector for the long-distance transport of pathogens in aquatic ecosystems. However, the composition of viral communities attached on MPs and their environmental risk are largely unknown. Here, we profiled the viral diversity and potential risk in five different MPs collected from the Beilun River based on metagenomic analysis.

Impact of Urbanization on Antibiotic Resistome in Different Microplastics: Evidence from a Large-Scale Whole River Analysis.

Microplastics (MPs) are becoming ubiquitous in environments and viewed as carriers of antibiotic resistance genes (ARGs). Rivers connecting differently urbanized areas contribute a significant input of MPs and ARGs to the environment. However, a systematic study assessing the role of urbanization in shaping antibiotic resistome and mobilome in riverine MPs is lacking.

Background noise analysis and improvement for the water vapor and oxygen transmission rate test of free-standing films.

The background noise (BGN) of test equipment affects the lower detection limit of the measurement range, and achieving an ultralow BGN is identified as a formidable challenge for highly accurate testing of a free-standing film. In this paper, a new gas transmission rate test apparatus is designed by detecting the electrical resistance increase with calcium corrosion. Thanks to the new design strategy, the only permeable place of this apparatus is the clamping and holding site.

Selective pressures of heavy metals on microbial community determine microbial functional roles during composting: Sensitive, resistant and actor.

Heavy metals (HM) pollution exerts an effect on microbial community composition and structure during composting, the way how microbial community responses to HM pressure is remain poorly understood though. The aim of this study was to explore functional roles of microorganisms based on selective pressures of HM (Cu, Zn and Cd). The results of microbial resistance showed that the toxicity of metals to microorganisms were Cu > Zn > Cd during composting.

Effect of Fenton pretreatment combined with bacteria inoculation on humic substances formation during lignocellulosic biomass composting derived from rice straw.

The goal of this work was to explore the effect of Fenton pretreatment combined with bacteria inoculation on the formation of humic substances (HS) during rice straw composting. In this study, the compound bacterial agents were inoculated after Fenton pretreatment during rice straw composting. The results suggested that the coupling effects of Fenton pretreatment and bacteria inoculation promoted the humification process, which might be the reason of organic fractions degradation and transformation.

Elucidating the negative effect of denitrification on aromatic humic substance formation during sludge aerobic fermentation.

Humic substance (HS), as an aromatic compound, is the core product of aerobic fermentation. Denitrification-dependent degradation of aromatic compounds have been repeatedly observed in environment. However, few studies have elucidated the relationship between denitrification and aromatic HS during sludge aerobic fermentation.

Core microorganisms promote the transformation of DOM fractions with different molecular weights to improve the stability during composting.

Transformation of DOM fractions with different molecular weights during composting of chicken manure (CM), garden waste (GW) and municipal solid waste (MSW) was evaluated in this study. The results revealed that DOM concentrations decreased by 49.8%, 53.

Biochar combined with montmorillonite amendments increase bioavailable organic nitrogen and reduce nitrogen loss during composting.

This study aimed to compare the effects of biochar, montmorillonite and their mixture on nitrogen availability and nitrogen loss during chicken manure composting. Four lab-scale composting experiments, the control (CK), 5% biochar addition (BC), 5% montmorillonite addition (M) and 2.5% biochar + 2.

Roles of adding biochar and montmorillonite alone on reducing the bioavailability of heavy metals during chicken manure composting.

The aim of this study was to explore the effects of adding biochar and montmorillonite alone on the correlations between bacteria and bioavailability of heavy metals (HM) during chicken manure composting. Three composting experiments were conducted, containing the without ameliorant, 10% biochar and 10% montmorillonite. The results showed that biochar and montmorillonite ameliorants significantly reduced the bioavailability of Cu by 90.

Role of NH recycling on nitrogen fractions during sludge composting.

The aim of this study is to reduce nitrogen (N) loss and investigate the role of ammonia (NH) recycling on N fractions, environmental factors and bacterial communities. In this study, collected NH from composting and recycled in it. The results showed that NH recycling affected N-cycling processes such as nitrification.

A novel method for removing heavy metals from composting system: The combination of functional bacteria and adsorbent materials.

The aim of this study was to remove heavy metals from composting system using a novel method combined functional bacteria with adsorbent materials. Four types of adsorbent materials were selected in this study. Results showed that Cr had significant removal efficiency, especially in sponge treatment (19.