Synthetic microbial communities: Novel strategies to enhance the quality of traditional fermented foods.

Consumers are attracted to traditional fermented foods due to their unique flavor and nutritional value. However, the traditional fermentation technique can no longer accommodate the requirements of the food industry. Traditional fermented foods produce hazardous compounds, off-odor, and anti-nutritional factors, reducing product stability. The microbial system complexity of traditional fermented foods resulting from the open fermentation process has made it challenging to regulate these problems by modifying microbial behaviors. Synthetic microbial communities (SynComs) have been shown to simplify complex microbial communities and allow for the targeted design of microbial communities, which has been applied in processing traditional fermented foods. Herein, we describe the theoretical information of SynComs, particularly microbial physiological processes and their interactions. This paper discusses current approaches to creating SynComs, including designing, building, testing, and learning, with typical applications and fundamental techniques. Based on various traditional fermented food innovation demands, the potential and application of SynComs in enhancing the quality of traditional fermented foods are highlighted. SynComs showed superior performance in regulating the quality of traditional fermented foods using the interaction of core microorganisms to reduce the hazardous compounds of traditional fermented foods and improve flavor. Additionally, we presented the current status and future perspectives of SynComs for improving the quality of traditional fermented foods.

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. Here, Raman spectroscopy combined with multiomics (genomics and proteomics) was used to address these issues. Genomic analysis revealed that Pseudomonas was an efficient producer of EVs that harbored 68 types of virulence factor-encoding genes. Upon exposing macrophages to environmentally relevant doses of Pseudomonas aeruginosa PAO1-derived EVs, macrophage internalization was observed, and release of inflammatory factors was determined by RT-PCR. Subsequent Raman spectroscopy and unsupervised surprisal analysis of EV-affected macrophages distinguished metabolic alterations, particularly in proteins and lipids. Proteomic analysis further revealed differential expression of proteins in inflammatory and metabolism-related pathways, indicating that EV exposure induced macrophage metabolic reprogramming and inflammation. Collectively, our findings revealed that pathogen-derived EVs in the indoor environments can act as a new mediator for pathogens to exert adverse health effects. Our method of Raman integrated with multiomics offers a complementary approach for rapid and in-depth understanding of EVs' impact.

Unraveling the Role of Microalgae in Mitigating Antibiotics and Antibiotic Resistance Genes in Photogranules Treating Antibiotic Wastewater.

Harnessing the potential of specific antibiotic-degrading microalgal strains to optimize microalgal-bacterial granular sludge (MBGS) technology for sustainable antibiotic wastewater treatment and antibiotic resistance genes (ARGs) mitigation is currently limited. This article examined the performance of bacterial granular sludge (BGS) and MBGS (of Haematococcus pluvialis, an antibiotic-degrading microalga) systems in terms of stability, nutrient and antibiotic removal, and fate of ARGs and mobile genetic elements (MGEs) under multiclass antibiotic loads. The systems exhibited excellent performance under none and 50 µg/L mixed antibiotics and a decrease in performance at a higher concentration. The MBGS showed superior potential, higher nutrient removal, 53.9 mg/L/day higher chemical oxygen demand (COD) removal, and 5.2-8.2% improved antibiotic removal, notably for refractory antibiotics, and the system removal capacity was predicted. Metagenomic analysis revealed lower levels of ARGs and MGEs in effluent and biomass of MBGS compared to the BGS bioreactor. Particle association niche and projection pursuit regression models indicated that microalgae in MBGS may limit gene transfers among biomass and effluent, impeding ARG dissemination. Moreover, a discrepancy was found in the bacterial antibiotic-degrading biomarkers of BGS and MBGS systems due to the microalgal effect on the microcommunity. Altogether, these findings deepened our understanding of the microalgae's value in the MBGS system for antibiotic remediation and ARG propagation control.

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 D2 O-labeled Raman spectroscopy, advanced multivariate analysis, and genotypic profiling to in situ track physiological evolution trajectory toward resistance. Physiological diversification of individual cells from isogenic population with cyclic ampicillin treatment is captured. Advanced multivariate analysis of spectral changes classifies all individual cells into four subsets of sensitive, intrinsic tolerant, evolved tolerant and resistant. Remarkably, their dynamic shifts with evolution are depicted and spectral markers of each state are identified. Genotypic analysis validates the phenotypic shift and provides insights into the underlying genetic basis. The new platform advances rapid phenotyping resistance evolution and guides evolution control.

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. Here, we conducted a large-scale study by placing five types of MPs (polyethylene, polypropylene, polystyrene, polyethylene-fiber, and polyethylene-fiber-polyethylene) into Beilun River with an urbanization gradient. A total of 314 ARGs and 57 mobile genetic elements (MGEs) were detected in MPs by high-throughput quantitative polymerase chain reaction (PCR). The ARGs in MPs showed a clear spatial distribution with the abundance increased by 2 orders of magnitude from rural to urban regions. A holistic analysis of 13 socioeconomic and environmental factors identified that urbanization predominantly contributed to both the abundance and potential MGE-mediated dissemination of ARGs in riverine MPs. Notably, MPs types were found to significantly affect the resistome and dissemination risk of ARGs, with polypropylene being the preferred substrates to acquire and spread ARGs. This work highlights the necessity of controlling MPs and ARGs pollution in urban areas and provides an important guide for the future usage and disposal of plastics.

Assessing the environmental impact of phenanthrene in different types of land use based on the binding characteristics with dissolved organic matter.

The binding characteristics of phenanthrene with dissolved organic matter (DOM) were studied by the excitation emission matrix fluorescence spectroscopy with parallel factor analysis in four types of land use which derived from forest (F), meadow (M), cropland (C), and greenhouse (G). The results showed that the humification degree and binding characteristics of phenanthrene with DOM were distinct differences in the four soils. The binding capacities of humic-like components with phenanthrene were stronger than those of protein-like components. The log K derived from the Stern-Volmer equation significantly correlated with the humification degree of DOM (p < 0.05) in different types of land use. Besides, correlation analysis demonstrated that the potential binding index (Fk) obtained from the modified Stern-Volmer model was a more accurate parameter to describe the combination degree of DOM with phenanthrene than log K, which presented a decrease order of C > F > M > G. Therefore, the environmental impact of phenanthrene in different types of land use could be assessed deeply based on the Fk and DOM concentration.

Characterization of atrazine binding to dissolved organic matter of soil under different types of land use.

Atrazine is widely used in agriculture. In this study, dissolved organic matter (DOM) from soils under four types of land use (forest (F), meadow (M), cropland (C) and wetland (W)) was used to investigate the binding characteristics of atrazine. Fluorescence excitation-emission matrix-parallel factor (EEM-PARAFAC) analysis, two-dimensional correlation spectroscopy (2D-COS) and Stern-Volmer model were combined to explore the complexation between DOM and atrazine. The EEM-PARAFAC indicated that DOM from different sources had different structures, and humic-like components had more obvious quenching effects than protein-like components. The Stern-Volmer model combined with correlation analysis showed that log K values of PARAFAC components had a significant correlation with the humification of DOM, especially for C3 component, and they were all in the same order as follows: meadow soil (5.68)>wetland soil (5.44)>cropland soil (5.35)>forest soil (5.04). The 2D-COS further confirmed that humic-like components firstly combined with atrazine followed by protein-like components. These findings suggest that DOM components can significantly influence the bioavailability, mobility and migration of atrazine in different land uses.

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. Results show a decrease in the number of core ARGs downstream in water, while sediments near densely populated areas exhibit an increase. PCoA ordination reveals clear geographic clustering of resistome and microbiome among samples from strong anthropogenic disturbed areas, reservoir areas, and estuary area. Co-occurrence networks highlight a higher connectivity of mobile genetic elements (MGEs) in disturbed areas compared to reservoir areas, presenting a threat to densely populated areas. Water quality parameters and antibiotics concentration were the key factors shaping the ARG profiles in sediment samples from urban regions. Overall, our study reveals distinct patterns of ARGs in sediment and water samples, emphasizing the importance of considering both anthropogenic and natural factors in comprehending and managing ARG distribution in river systems.

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 D2O labeling (Raman-D2O) 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. The abundances of PSMs increased in two alkaline soils after RM application identified by single-cell Raman D2O. RM application reduced the diversity of bacterial communities and increased the abundance of a few bacteria with reported P solubilization function. Genotypic analysis indicated that RM addition generally increased the relative abundance of CNP functional genes. A correlation analysis of the abundance of active PSMs with the abundance of soil microbes or functional genes was carried out to decipher the linkage between the phenotype and genotype of PSMs. Myxococcota and C degradation genes were found to potentially contribute to the enhanced microbial P release following RM application. This work provides important new insights into the in situ function of soil PSMs. It will lead to better harnessing of agricultural waste to mobilize soil legacy P and mitigate the P crisis.

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. By fully considering the abundance, clinical availability, human pathogenicity, human accessibility, and mobility of 660 ARGs in plastisphere, the HRA on MPs were quantified and compared. Polyethylene had the highest HRA among the five MP types, and urbanization further increased its risk index. In addition to abiotic factors, more complex biotic factors have been shown to drive HRA in plastisphere. Specifically, dispersal limitation accounted for the increasing diversity and interaction of bacteria that determined HRA in plastisphere. Further analysis of metabolic functions indicated that a higher HRA was accompanied by decreased normal metabolic functions of plastisphere microbiota due to the higher fitness costs of ARGs. This study advances the quantitative surveillance of HRA in plastisphere and understanding of its driving mechanisms. This will be helpful for the management of both MPs and ARGs treatments for human health.

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. The results indicated that seasonal hydrological dynamics were critical for influencing the ARGs in PA and FL and the transition of ARGs between the two lifestyles. ARG profiles both in PA and FL were likely to be shaped by horizontal gene transfer. However, they exhibited distinct responses to the physicochemical (e.g., nutrients and dissolved oxygen) changes under seasonal hydrological dynamics. The particle-association niche (PAN) index revealed 94 non-conservative ARGs (i.e., no preferences for PA and FL) and 23 and 16 conservative ARGs preferring PA and FL lifestyles, respectively. A sharp decline in conservative ARGs under stratified hydrologic suggested seasonal influence on the ARGs transition between PA and FL lifestyles. Remarkably, the conservative ARGs (in PA or FL lifestyle) were more closely related to bacterial OTUs in their preferred lifestyle than their counterparts, indicating lifestyle-dependent ARG enrichment. Altogether, these findings enhanced our understanding of the ARG lifestyles and the role of seasonal hydrological changes in governing the ARG transition between the lifestyles in a typical deep freshwater ecosystem.

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. Here, a typical watershed with a significant gradient of urbanization was selected, and the resistome and microbiome in both water and sediments were profiled. In water, the relative abundance of ARGs and bacterial diversity increased gradually along the urbanization, but were relatively stable in sediments. The abundance of potential multidrug-resistant bacteria in peri-urban and urban water were significantly higher than rural water, while in sediments, unique potential multidrug-resistant bacteria were detected at different urbanization levels. Population size was identified as the key factor shaping the ARGs profiles. Finally, environmental risk assessment based on the projection pursuit regression model suggested that the water in urban region had higher potential environmental risk of antibiotic resistance, in contrary to the sediments in rural and peri-urban regions. Our findings revealed distinct responses of water and sediment to urbanization in terms of antibiotic resistome and microbiome. This work provides important guide for hierarchically controlling ARGs dissemination in watershed.

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. Nearly 2863 million raw reads were produced and assembled, and annotation resulted in the identification of 1719 different species of viruses in MPs. Viruses in polypropylene (PP) displayed the highest diversity, with about 250 specific viruses detected. Source tracking of viruses in MPs by the fast expectation-maximization microbial source tracking method (FEAST) demonstrated that viruses in upstream and downstream MPs are two major sources of viruses in estuary. Furthermore, the MP-type-dependent potential environmental risk of viruses was significant based on both antibiotic resistance genes (ARGs) and virulence factors (VFs) detected in viral metagenomes, and PP was confirmed with the highest potential environmental risk. This study reveals the high diversity and potential environmental risk of viruses in different MPs, and provides an important guidance for future environmental monitoring and understanding the potential risks associated with both viral transmission and MPs pollution.

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. The succession of microbial communities on MPs was observed along the watershed, and some ARGs and VFs were significantly enriched on MPs in urban region in comparison with rural region. Potential environmental risk of MPs conducted by Projection Pursuit Regression model in midstream (peri-urban region) and downstream (urban region) were significantly higher than that in upstream (rural region), and exhibit close relationships with MPs concentration and water velocity. Furthermore, our source tracking results demonstrated that the microbiome, ARGs and VFs in urban region MPs were largely derived from rural region MPs. Our results caution us that special attention should be paid to the risks posed by MPs in urban water bodies, and highlight the threat of MPs from rural upstream areas.

Temporal variation of antibiotic resistome and pathogens in food waste during short-term storage.

The massive food wastes pose a growing health concern for spreading of antibiotic resistance and pathogens due to food spoilage. However, little is known about these microbial hazards during collection, classification, and transportation before eventual treatment. Here, we profiled the temporal variations of antibiotic resistance genes (ARGs), pathogens, bacterial and fungal communities across four typical food wastes (vegetable, fish, meat, and rice) during storage at room temperature in summer (maximum 28-29 °C) of typical southeast city in China. A total of 171 ARGs and 32 mobile genetic elements were detected, and the absolute abundance of ARGs significantly increased by up to 126-fold with the storage time. Additionally, five bacterial pathogens containing virulence factor genes were detected, and Klebsiella pneumoniae was persistently detected throughout the storage time in all food types except rice. Moreover, fungal pathogens (e.g., Aspergillus, Penicillium, and Fusarium) were also frequently detected. Notably, animal food wastes were demonstrated to harbor higher abundance of ARGs and more types of pathogens, indicating a higher level of hazard. Mobile genetic elements and food types were demonstrated to mainly impact ARG profiles and pathogens, respectively. This work provides a comprehensive understanding of the microbial hazards associated with food waste recycling, and will contribute to optimize the food waste management to ensure biosecurity and benefit human health.

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. Mathematical methods for calculating the molecular permeation behaviors and magnitude of BGN are devised. The results show that the properties and structures of the materials significantly affect the BGN value. By using a sealant with low permeability (2.25 × 10-15 g cm cm-2 s-1 Pa-1) and a clamping ring with small width (2.5 mm) and testing an ultrahigh barrier (WVTR: 10-6 g m-2 day-1), the BGN could reach a level of 10-11 g m-2 day-1. With theoretical guidance, after optimization, one sealing structure obtained an ultralow BGN value (∼10-6 g m-2 day-1) in the actual test. The electrical resistance test has many advantages over existing methods. Additionally, the computational method devised in this study to examine the effects of materials provides a useful tool to achieve high-accuracy testing.

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%, 53.9% and 86.4% during CM, GW and MSW composting, respectively. Meanwhile, low molecular weight (<650 Da) DOM was visibly transformed into high molecular weight (>10 kDa) DOM for enhancing their stability during composting. Core microorganisms promoting DOM stabilization were identified by network analysis, such as Prosthecobacter, Paenalcaligenes and Solibacillus. In addition, DOM composition was also related to the relative abundance of microbial metabolic function, such as chemoheterotrophy and aerobic chemoheterotrophy. Moreover, temperature, moisture and pH were identified as the key physicochemical factors affecting the DOM stabilization mediated by core microorganisms during composting. These above findings are helpful to regulate the DOM stabilization during composting and improve the quality of final composts.

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. This study was conducted to investigate the effect of enhanced denitrification on aromatic HS formation. On the 24th day of sludge aerobic fermentation, five tests (CK, Run1, Run2, Run3 and Run4) were executed, and nitrate concentrations were adjusted to 480 ± 20, 500 ± 20, 1000 ± 20, 1500 ± 20 and 2000 ± 20 mg/kg with potassium nitrate, respectively. Analytical results demonstrated that nitrate addition increased denitrifying genes abundance and enhanced denitrification, which further reduced aromatic HS formation (p < 0.05). Especially in Run3, the concentrations of HS and humic acid on the 52nd day dramatically decreased by 12.9 % and 34.2 % in comparison with those on the 31st day. High-throughput sequencing revealed that enhanced denitrification effectively stimulated the metabolism of denitrifying microorganisms with aromatic-degrading capability. Co-occurring network analysis indicated that some keystone taxa of denitrification aromatic-degrading microorganisms involved in the conversion of nitrate to nitrite were the most crucial for enhancing denitrification and reducing aromatic HS formation.

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. In addition, the bacterial communities structure and diversity were changed by Fenton pretreatment and inoculation. Key microbial genera linking to the transformation of organic fractions were determined by network analysis. Redundancy analysis and structural equation model analysis indicated that Fenton pretreatment, inoculation, amino acid, soluble sugar and beta-diversity as the key factors affecting organic fractions transformation during composting. Therefore, the combined application Fenton pretreatment with bacteria inoculation provided a new method to promote the HS amount.

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. Cu and Zn were more toxic for microorganisms during composting when compared with Cd. However, microorganisms had a longer lag period to grow under Zn stress through microbial tolerance determination. In addition, the microbial catalase activity generally decreased and protease activity generally increased, thus microorganisms became more adaptable to HM stress during composting. The experimental results confirmed the existence of sensitive, resistant and actor microorganisms during beef cattle and chicken manures composting. Ultimately, the resistant, sensitive and actor microorganisms at genus level were distinguished under HM pressure based on the network analysis and structural equation models, including 85 resistant microorganisms, 5 sensitive microorganisms and 6 actor microorganisms. This would be helpful to understand the microbial succession process under HM stress and identify functional strains of HM remediation.