Transport of antibiotic resistance genes in the landfill plume: Experiment and numerical modeling

Antibiotic resistance genes (ARGs) in the landfill site would potentially seep into groundwater by leachate infiltration, which poses great threat of ARGs dissemination through groundwater flow. However, the transport characteristics of ARGs in the landfill plume are still unclear, impeding the risk management and remediation of landfill sites. This study carried out a series of column experiments to investigate the transport of various ARGs in the landfill plume and its influencing factors. Besides, a numerical model was also developed to simulate the transport of ARGs in the porous media, which could determine the attachment and decay rates of ARGs in various scenarios. Experimental results showed that high contents of organic matter and corresponding antibiotics in the landfill plume promoted the transport of antibiotic-resistant bacteria (ARB) and reduced the decay rates of intracellular ARGs (iARGs) in the porous media. Inorganic ions such as Cl- and SO42- inhibited the mobility of ARB, while they had little influence on iARGs decay. Extracellular ARGs (eARGs) in plasmids exhibited higher decay rate in pore water, leading to shorter transport distance in porous media. In the landfill plume, sul1 had higher mobility than aadA and ermB, which was tightly correlated with its lower decay rate in groundwater and the smaller bacterial host. The decrease of particle size greatly inhibited the transport of ARGs in porous media due to the attachment of ARB on sand surface, while the attached ARGs would easily detach from sand surface during background water flushing. This study could guide the accurate risk assessment of ARGs in the landfill plume as well as the optimization of management strategy for landfill site.

A roadmap to understanding and anticipating microbial gene transfer in soil communities

SUMMARYEngineered microbes are being programmed using synthetic DNA for applications in soil to overcome global challenges related to climate change, energy, food security, and pollution. However, we cannot yet predict gene transfer processes in soil to assess the frequency of unintentional transfer of engineered DNA to environmental microbes when applying synthetic biology technologies at scale. This challenge exists because of the complex and heterogeneous characteristics of soils, which contribute to the fitness and transport of cells and the exchange of genetic material within communities. Here, we describe knowledge gaps about gene transfer across soil microbiomes. We propose strategies to improve our understanding of gene transfer across soil communities, highlight the need to benchmark the performance of biocontainment measures in situ, and discuss responsibly engaging community stakeholders. We highlight opportunities to address knowledge gaps, such as creating a set of soil standards for studying gene transfer across diverse soil types and measuring gene transfer host range across microbiomes using emerging technologies. By comparing gene transfer rates, host range, and persistence of engineered microbes across different soils, we posit that community-scale, environment-specific models can be built that anticipate biotechnology risks. Such studies will enable the design of safer biotechnologies that allow us to realize the benefits of synthetic biology and mitigate risks associated with the release of such technologies.

A qPCR assay for the detection of Phytophthora abietivora, an emerging pathogen on fir species cultivated as Christmas trees

Emerging species of the Phytophthora genus are among the most important threats to global plant biodiversity, horticulture and trade. For instance, Phytophthora root rot (PRR) of Christmas trees, mainly Fraser (Abies fraseri) and balsam (Abies balsamea) firs, is responsible for an average of 10% of the observed diseased trees in plantations. Diagnosing PRR involves isolation followed by morphological and molecular identification of the causal agents. However, these methods are rarely adapted to larger scale monitoring such as in situ detection. For these applications, molecular detection of environmental DNA (eDNA) provides the fast and high-throughput results needed. Phytophthora abietivora was associated with PRR in firs (Abies spp.) cultivated as Christmas trees in the province of Québec (Canada). This study focused on developing a sensitive and specific qPCR assay targeting P. abietivora and validating its efficiency on DNA extracted from soil and roots. A set of primers and probe was designed for this assay, and parameters such as the limit of detection (LOD95%) and limit of quantification (LOQ) were measured. The assay was tested on DNA obtained from healthy-looking and PRR symptomatic Fraser and balsam firs. The assay was shown to be semi-specific because it cross-reacted with P. europaea and three other phylogenetically close species, but deemed specific in the context of PRR of firs. The LOD95% was estimated at 10 copies per reaction (Cq of 35.7) and the LOQ to 33 P. abietivora oospores per gram of soil. Out of 488 DNA samples from soil, 68 were positive for P. abietivora from which 42 (61.7%) were from PRR symptomatic trees. Only a slight overlap (3 out of 7 samples) was observed with previously obtained baiting results. This assay will be useful for rapid diagnostics of P. abietivora infected trees and as a prospecting tool to better characterize the natural distribution and dissemination of the disease.

Could the inhibition of systemic NLRP3 inflammasome mediate central redox effects of yerba mate? An in silico and pre-clinical translational approach

ETHNOPHARMACOLOGICAL RELEVANCE

Empirically, Ilex paraguariensis A. St. Hil, or yerba-mate, has been used by natives of South America as a stimulant. Nowadays, this plant has gained popularity due to its neuroprotective effects. However, there are few studies on the biochemical-molecular mechanisms of action involved in its effect.

AIM OF THE STUDY

Chemically characterize an aqueous extract of yerba mate (YME) and evaluate if it could suppress the aberrant inflammatory response related to neurodegeneration.

MATERIALS AND METHODS

Macrophages and microglia cells were exposed to lipopolysaccharide (LPS; 100 ng/mL) plus nigericin (100 μM) or quinolinic acid (QA; 5 mM). Cellular viability, oxidative, and inflammatory markers were evaluated. Chemical matrix (HPLC - DAD), antioxidant activity, safety profile in vitro and in vivo, and an in silico docking of main targets were also assessed.

RESULTS

Pre-treatment with YME (15 μg/mL) prevented impairments in redox metabolism and inflammatory markers in BV-2 cells. In macrophages, YME showed similar results to MCC950, an inflammasome inhibitor. YME presented 282.88 mg EAG/g total phenolic content and a redox capacity of 32.94 ± 1.30 μg/mL (IC50), and its major compounds were chlorogenic acid > rutin > ferulic acid > catechin > sinapic acid. Chlorogenic acid and rutin presented a high affinity to the MCC950 region. Additionally, YME did not cause genotoxicity and was safe in vivo.

CONCLUSION

YME has significantly affected macrophages and microglia by regulating the NLRP3 inflammatory pathway.

Hand-to-surface bacterial transfer and healthcare-associated infections prevention: a pilot study on skin microbiome in a molecular biology laboratory

Background

Healthcare-associated infections (HAIs) are a major global public health problem, contributing significantly to patient morbidity and mortality. This study analyses differences in type and amounts of bacteria transferred from volunteers' dominant palm to two healthcare-relevant surfaces (glass and laminate table), both before and after hand washing with water and antibacterial soap. The aim was to understand hand-to-surface microbial contamination and support the development of HAI prevention strategies.

Methods

Microbial DNA was extracted and sequenced to identify bacteria species. Taxonomic and statistical analyses were performed to evaluate bacterial diversity and abundance across the experimental groups.

Results

The results confirmed greater bacteria abundance and species richness on palm compared to surfaces, with a significant reduction after hand washing, especially on glass. Taxa analysis highlighted the increased persistence of Gram-negative HAIs-related bacteria on laminate surface, while Gram-positive opportunistic bacteria were more abundant on palms and glass surface. Beta diversity confirmed significant differences in microbial composition between the groups, highlighting the importance of bacteria-surface characteristics in designing preventive measures.

Conclusion

Despite some limitations, our study emphasizes the importance of microbiological surveillance for all opportunistic bacteria with pathogenic potential. These findings can contribute to more effective guidelines for surface disinfection and hand washing, key elements in preventing HAIs.

Controllable Supply-Demand Effect during Superior Fe Single-Atom Catalyst Synthesis for Targeted Guanine Oxidation of Antibiotic Resistance Genes

Nonradical Fenton-like catalysis offers an opportunity to degrade extracellular antibiotic resistance genes (eARGs). However, high-loading single-atom catalysts (SACs) with controllable configurations are urgently required to selectively generate high-yield nonradicals. Herein, we constructed high-loading Fe SACs (5.4-34.2 wt %) with uniform Fe-N4 sites via an optimized coordination balance of supermolecular assembly for peroxymonosulfate activation. The selectivity of singlet oxygen (1O2) generation and its contribution to eARGs degradation were both >98%. This targeting strategy of oxidizing guanines with low ionization potentials by 1O2 allowed 7 log eARGs degradation within 10 min and eliminated their transformation within 2 min, outperforming most reported advanced oxidation processes. Relevant interactions between 1O2 and guanines were revealed at a single-molecule resolution. The high-loading Fe SACs exhibited excellent universality and stability for different eARGs and water matrices. These findings provide a promising route for constructing high-loading SACs for efficient and selective Fenton-like water treatment.

Detection of Live Shiga Toxin-Producing Escherichia coli with Long-Read Sequencing

A requirement of any foodborne pathogen testing method is that it only detects live bacteria. Ethidium monoazide (EMA) and propidium monoazide (PMA) are dyes that penetrate the membranes of dead cells and form cross-linkages in the DNA, which prevents its amplification in PCR. This study investigated whether treatment with EMA or PMA would inhibit the sequencing of DNA from dead Escherichia coli. Range finding experiments with qPCR were conducted to determine the optimal concentrations of EMA and PMA needed to inhibit the amplification of DNA from dead cells while not influencing live cells. An EMA concentration that differentiated between live and dead cells could not be established. However, a PMA concentration of 25 µM effectively prevented qPCR amplification of DNA from dead E. coli while not impacting the amplification of live E. coli DNA. Sequencing experiments were conducted with PMA-treated live, untreated live, PMA-treated dead, and untreated dead E. coli. There were no significant differences in the detection of virulence genes of interest between the PMA-treated live, untreated live, and untreated dead E. coli. However, no DNA sequencing data were obtained from the PMA-treated dead E. coli. These results suggest that PMA could be incorporated into sample preparation methods prior to sequencing to selectively detect live cells of foodborne pathogens.

Relic DNA obscures bacterial diversity and interactions in ballast tank sediment

The dark and anoxic environment of ballast tank sediment (BTS) harbors substantial amounts of relic DNA, yet its impact on microbial diversity estimates in BTS management remains poorly understood. This study employed propidium monoazide (PMA) treatment to eliminate relic DNA and used 16S amplicon high-throughput sequencing to characterize both total and viable bacteria. Our findings revealed that relic DNA is abundant in BTS. When removed, it led to variable reductions in species richness, which fluctuated from a 3.15% increase to a 37.52% decrease. Additionally, 6.27%-15.79% of OTUs were absent in the PMA-treated samples. These findings indicate that relic DNA has diverse effects on microbial diversity estimates. Moreover, relic DNA removal altered the relative abundances of a wide range of taxa, thereby facilitating the detection of rare taxa. Furthermore, the absence of relic DNA resulted in an overestimation of co-occurrence network size, complexity, and competitiveness, which could lead to misinterpretations of community assembly processes. In conclusion, our findings indicate that relic DNA obscures microbial diversity estimates and risk assessments in BTS, highlighting the critical need for monitoring viable bacteria in ballast sediment management.

Propidium Monoazide is Unreliable for Quantitative Live-Dead Molecular Assays

Propidium monoazide (PMA) is a dye that distinguishes between live and dead cells in molecular assays like the Polymerase Chain Reaction (PCR). It works by cross-linking to the DNA of cells that have compromised membranes or extracellular DNA upon photoactivation, making the DNA inaccessible for amplification. Currently, PMA is used to detect viable pathogens and alleviate systemic bias in the microbiome analysis of samples using 16S rRNA gene sequencing. In these applications, treated samples consist of different amounts of dead bacteria and a range of bacterial strains, variables that can affect the performance of PMA and lead to inconsistent findings across various research studies. To evaluate the effectiveness of PMA, we used a sensitive qPCR assay and post-treatment sample concentration to determine PMA cross-linkage and activity accurately under varying sample conditions. We report that PMA is unreliable for viability assays when the concentration and composition of the bacterial mixtures are unknown. PMA is suitable only for qualitatively assessing viability in samples containing a known number of dead microbes or extracellular DNA.

Influence of Environmental Conditions on the Escape Rates of Biocontained Genetically Engineered Microbes

The development of genetically engineered microbes (GEMs) has resulted in an urgent need to control their persistence in the environment. The use of biocontainment such as kill switches is a critical approach to prevent the unintended proliferation of GEMs; however, the effectiveness of kill switches─reported as escape rates, i.e., the ratio of the number of viable microbes when the kill switch is triggered relative to the number when it is not triggered─is typically assessed under laboratory conditions that do not resemble environmental conditions under which biocontainment must perform. In this study, we discovered that the escape rate of an Escherichia coli GEM biocontained with a CRISPR-based kill switch triggered by anhydrotetracycline (aTc) increased by 3-4 orders of magnitude when deployed in natural surface waters as compared to rich laboratory media. We identified that environmental conditions (e.g., pH, nutrient levels) may contribute to elevated escape rates in multiple ways, including by altering the chemical speciation of the kill switch trigger to reduce its uptake and providing limited nutrients required for the kill switch to function. Our study demonstrated that conditions in the intended environment must be considered in order to design effective GEM biocontainment strategies.

Environmental RNA metabarcoding for ballast water microbial diversity: Minimizing false positives

While maritime transport boosts global trade by shipping bulk goods, it raises concerns about the spread of harmful bacteria via ballast water. Moreover, the dark and cold environments of ballast tanks often harbor extracellular DNA from dead organisms, leading to false positives in traditional environmental DNA (eDNA) metabarcoding analyses. Here, we alternatively employed environmental RNA (eRNA) metabarcoding to assess its potential for reducing false positive in ballast water monitoring. We collected eDNA and eRNA in parallel from ballast water before and after disinfection in three vessels. High-throughput sequencing of the 16S rRNA V4-V5 regions and cDNA counterparts was conducted to compare bacterial community composition. Our findings showed that over 80 % of the top 150 abundant amplicon sequence variants (ASVs) were detected by both eRNA and eDNA metabarcoding. Samples sequenced separately using DNA and RNA consistently clustered together, indicating similar community recovery efficacy. However, 42 % of ASVs were detected exclusively in DNA, resulting in significantly higher bacterial diversity compared to RNA, which suggests false positives in the DNA method. In treated samples with higher dead cell counts, the RNA method showed significantly lower bacterial diversity, indicating its effectiveness in detecting live bacteria. In summary, eRNA metabarcoding offers comparable recovery efficiency while maintaining a lower false-positive rate than eDNA metabarcoding.

Increasing phosphorus ratios between overlying and surface water inhibits intracellular antibiotic resistance gene transformation in a large shallow lake

The rising prevalence of antibiotic resistance genes (ARGs) in the surface waters of lakes poses a significant threat to human health. The overlying water in these lakes serves as a critical hotspot for the accumulation of ARGs in surface water. However, the mobility of extracellular (adsorbed ARGs (a-eARGs) and free ARGs (f-eARGs)), and intracellular ARGs (i-ARGs) from overlying water to surface water remains unknown. This study examined the mobility of ARGs between water layers, as well as the underlying mechanisms involved. Significant variations in ARG abundance were observed between overlying and surface water according to PCoA analysis (p < 0.05), with significant reductions in i-ARGs (p < 0.05) in surface water and no significant difference in a-eARGs and f-eARGs. Aminoglycoside and tetracycline i-ARGs had the highest and lowest mobility from overlying water to surface water, respectively. Additionally, the transformation of i-ARGs from overlying water to surface water was significantly correlated with total phosphorus ratio. According to the direct analysis of partial least squares-path modeling, the key drivers of a- and f-eARGs movement from overlying water to surface water were free-living and particle-attached bacteria, respectively, whereas heavy metals gradually became the driving force for i-ARGs by regulating mobile genetic elements. This study illustrated the transmission mechanisms of ARGs from overlying water to surface water in lakes, which will be useful for ARG treatment strategies, especially in eutrophic water.

Monitoring the Persistence of Pseudomonas sivasensis Strain CF10PS3 in Cereal Fields

The persistence and efficacy of biocontrol agents in agricultural fields are crucial for sustainable crop production. In this study, we investigated the persistence of the introduced bacterial strain Pseudomonas sivasensis CF10PS3 in the wheat phyllosphere using a novel qPCR probe protocol. The CF10PS3 strain, known for its in vitro biocontrol properties against wheat pathogens, was applied through foliar spray, and its persistence was monitored over 7 weeks. Our qPCR assays, designed to specifically detect CF10PS3, distinguished it from naturally occurring P. sivasensis strains, providing precise insights into its dynamics in the field. The experimental results indicated that CF10PS3 was already present on the wheat leaves before its application, suggesting its natural adaptation to the foliar environment. Following initial application, a significant increase in CF10PS3 was observed, though subsequent environmental factors such as rain and wind might have caused notable fluctuations in its population. Despite these variations, the introduced strain showed considerable persistence, with population levels significantly higher than those in untreated plots by the end of the study period. This research underscores the importance of understanding bacteria dynamics in the field, highlighting the influence of environmental conditions on their efficacy. The use of specific qPCR probes proved effective in monitoring introduced strains, offering valuable insights for optimizing biocontrol agent application strategies. Our findings contribute to the development of robust biocontrol methods, promoting sustainable agricultural practices and enhancing crop protection.

Characterization of a widespread sugar phosphate-processing bacterial microcompartment

Many prokaryotes form Bacterial Microcompartments (BMCs) that encapsulate segments of specialized metabolic pathways to enhance catalysis. The various functions of metabolosomes, catabolic BMCs, are dictated by the signature enzyme that processes initial substrates of the confined pathway. The components and native functions of several metabolosomes have been experimentally characterized; however one of the most prevalent across all bacteria has yet to be studied. Sugar Phosphate Utilizing (SPU) BMC loci encode enzymes predicted to be involved in sugar phosphate metabolism. The SPU genetic loci are found in organisms occupying habitats ranging from soils to hot springs, highlighting the ubiquity of the SPU BMC. We bioinformatically characterized seven SPU subtypes, all which contain an enzyme unique to SPU BMCs, a deoxyribose 5-phosphate aldolase (DERA). Here, we define the fundamental characteristics of SPU BMCs and have expressed, purified, and characterized a set of SPU core enzymes. These include a protein-protein complex formed between a SPU BMC DERA and a predicted ribose 5-phosphate isomerase. Further, we show that the SPU BMC DERA is catalytically active and propose that it acts as the universal signature enzyme for the SPU BMC, with implications for fundamental understanding and biotechnological applications of SPU BMCs.

Fate of intracellular and extracellular antibiotic resistance genes in sewage sludge by full-scale anaerobic digestion

Storage tank (ST) is a promising strategy for solid-liquid separation following anaerobic digestion (AD). However, little is known regarding the effects of ST on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and microbial communities. Therefore, this study first investigated eight typical ARGs (sul1, sul2, tetW, tetA, tetO, tetX, ermF, and ermB) and three MGEs (int1, int2, and tnpA) during full-scale AD of sludge and the liquid and biosolids phases of ST. Following that, intracellular ARGs (iARGs), extracellular polymeric substances (EPS)-associated ARGs, and cell-free ARGs removal were quantified in AD process, which is largely unknown for full-scale AD of sludge. The qPCR results showed that both AD and ST significantly removed ARGs, with ST biosolids showing the highest removal efficiency for the total measured relative (82.27 ± 2.09 %) and absolute (92.38 ± 0.89 %) abundance of ARGs compared to the raw sludge. Proteobacteria, Bacteroidota, Firmicutes and Campilobacterota were the main potential ARGs hosts in the sludge. Moreover, the results of different ARGs fractions showed that the total relative and absolute abundance of iARGs decreased by 90.12 ± 0.83 % and 79.89 ± 1.41 %, respectively, following AD. The same trend was observed for the abundance of EPS-associated ARGs, while those of cell-free ARGs increased after AD. These results underscore the risk of extracellular ARGs and provided new insights on extracellular ARGs dissemination evaluation.

Illumina Sequencing in Conjunction with Propidium Monoazide to Identify Live Bacteria After Antiseptic Treatment in a Complex Oral Biofilm: A Study Using an Ex Vivo Supragingival Biofilm Model

Background/Objectives: The evaluation of the efficacy of antibacterial treatments in complex oral ecosystems is limited by the inability to differentiate live from dead bacteria using omic techniques. The objective of this study was therefore to assess the ability of the combination of the 16S rRNA Illumina sequencing methodology and the action of propidium monoazide (PMA) to study viable bacterial profiles in oral biofilms after exposure to an antiseptic compound. Methods: Cariogenic supragingival biofilms were developed in an ex vivo model for 96 h, using saliva from healthy volunteers. The biofilms were treated with 0.12% chlorhexidine (CHX) combined with 0.05% cetylpyridinium chloride (CPC), for 60 s, using phosphate buffered saline as a control. After exposure, each biofilm was treated or not with PMA to then extract the bacterial DNA, quantify it by Qubit, quantify the bacterial population using qPCR, and perform the metataxonomic study of the samples using Illumina 16S rRNA sequencing. Results: A significantly lower DNA concentration in the PMA-treated biofilms (p < 0.05 compared with those not exposed to PMA) was observed. The viable bacterial count obtained by qPCR differed significantly from the total bacterial count in the biofilm samples exposed to the antiseptic (p < 0.05). The viable microbiome differed significantly from the total bacterial profile of the samples treated with CHX/CPC after exposure to PMA (p < 0.05 at the α- and β-diversity levels). Conclusions: The combination of Illumina 16S rRNA sequencing and PMA helps solve the inability to evaluate the efficacy of antibacterial treatments in the bacterial profile of complex ecosystems such as oral biofilms.

Effect of environmental DNA sampling resolution in detecting nearshore fish biodiversity compared to capture surveys

Sampling and sequencing marine environmental DNA (eDNA) provides a tool that can increase our ability to monitor biodiversity, but movement and mixing of eDNA after release from organisms before collection could affect our inference of species distributions. To assess how conditions at differing spatial scales influence the inferred species richness and compositional turnover, we conducted a paired eDNA metabarcoding and capture (beach seining) survey of fishes on the coast of British Columbia. We found more taxa were typically detected using eDNA compared to beach seining. eDNA identified more taxa with alternative habitat preferences, and this richness difference was greater in areas of high seawater movement, suggesting eDNA has a larger spatial grain influenced by water motion. By contrast, we found that eDNA consistently missed low biomass species present in seining surveys. Spatial turnover of communities surveyed using beach seining differed from that of the eDNA and was better explained by factors that vary at small (10-1000s meters) spatial scales. Specifically, vegetation cover and shoreline exposure explained most species turnover from seining, while eDNA turnover was not explained by those factors and showed a distance decay pattern (a change from 10% to 25% similarity from 2 km to 10 km of distance), suggesting unmeasured environmental variation at larger scales drives its turnover. Our findings indicate that the eDNA sample grain is larger than that of capture surveys. Whereas seining can detect differences in fish distributions at scales of 10s-100s of meters, eDNA can best summarize fish biodiversity at larger scales possibly more relevant to regional biodiversity assessments.

Quantitative assessment of reef foraminifera community from metabarcoding data

Describing living community compositions is essential to monitor ecosystems in a rapidly changing world, but it is challenging to produce fast and accurate depiction of ecosystems due to methodological limitations. Morphological methods provide absolute abundances with limited throughput, whereas metabarcoding provides relative abundances of genes that may not correctly represent living communities from environmental DNA assessed with morphological methods. However, it has the potential to deliver fast descriptions of living communities provided that it is interpreted with validated species-specific calibrations and reference databases. Here, we developed a quantitative approach to retrieve from metabarcoding data the assemblages of living large benthic foraminifera (LBF), photosymbiotic calcifying protists, from Indonesian coral reefs that are under increasing anthropogenic pressure. To depict the diversity, we calculated taxon-specific correction factors to reduce biological biases by comparing surface area, biovolume and calcite volume, and the number of mitochondrial gene copies in seven common LBF species. To validate the approach, we compared calibrated datasets of morphological communities from mock samples with bulk reef sediment; both sample types were metabarcoded. The calibration of the data significantly improved the estimations of genus relative abundance, with a difference of ±5% on average, allowing for comparison of past morphological datasets with future molecular ones. Our results also highlight the application of our quantitative approach to support reef monitoring operations by capturing fine-scale processes, such as seasonal and pollution-driven dynamics, that require high-throughput sampling treatment.

Assessing eDNA capture method from aquatic environment to optimise recovery of human mt-eDNA

Previous studies have shown that environmental DNA (eDNA) from human sources can be recovered from natural bodies of water, and the generation of DNA profiles from such environmental samples may assist in forensic investigations. However, fundamental knowledge gaps exist around the factors influencing the probability of detecting human eDNA and the design of optimal sampling protocols. One of these is understanding the particle sizes eDNA signals are most strongly associated with and the most appropriate filter size needed for efficiently capturing eDNA particles. This study assessed the amount of mitochondrial eDNA associated with different particle sizes from human blood and skin cells recovered from freshwater samples. Samples (300 mL) were taken from experimental 10 L tanks of freshwater spiked with 50 µL of human blood or skin cells deposited by vigorously rubbing hands together for two minutes in freshwater. Subsamples were collected by passing 250 mL of experimental water sample through six different filter pore sizes (from 0.1 to 8 µm). This process was repeated at four time intervals after spiking over 72 hours to assess if the particle size of the amount of eDNA recovered changes as the eDNA degrades. Using a human-specific quantitative polymerase chain reaction (qPCR) assay targeting the HV1 mitochondrial gene region, the total amount of mitochondrial eDNA associated with different particle size fractions was determined. In the case of human blood, at 0 h, the 0.45 µm filter pore size captured the greatest amount of mitochondrial eDNA, capturing 42 % of the eDNA detected. The pattern then changed after 48 h, with the 5 µm filter pore size capturing the greatest amount of eDNA (67 %), and 81 % of eDNA at 72 h. Notably, a ten-fold dilution proved to be a valuable strategy for enhancing eDNA recovery from the 8 µm filter at all time points, primarily due to the PCR inhibition observed in hemoglobin. For human skin cells, the greatest amounts of eDNA were recovered from the 8 µm filter pore size and were consistent through time (capturing 37 %, 56 %, and 88 % of eDNA at 0 hours, 48 hours, and 72 hours respectively). There is a clear variation in the amount of eDNA recovered between different cell types, and in some forensic scenarios, there is likely to be a mix of cell types present. These results suggest it would be best to use a 5 µm filter pore size to capture human blood and an 8 µm filter pore size to capture human skin cells to maximize DNA recovery from freshwater samples. Depending on the cell type contributing to the eDNA, a combination of different filter pore sizes may be employed to optimize the recovery of human DNA from water samples. This study provides the groundwork for optimizing a strategy for the efficient recovery of human eDNA from aquatic environments, paving the way for its broader application in forensic and environmental sciences.

Seasonal dynamics of free-living (FL) and particle-attached (PA) bacterial communities in a plateau reservoir

In terms of lifestyle, bacterioplankton can be classified as free-living (FL) and particle-attached (PA) forms, and both play essential roles in biogeochemical cycling in aquatic ecosystems. Structure, distribution, and community assembly of FL and PA bacteria in plateau riverine waterbodies are largely unknown. Therefore, we explored the seasonal dynamics of FLand PA bacterial communities in the Wujiangdu reservoir, Yungui Plateau using 16S rRNA gene high-throughput sequencing. Results revealed there was a significant environmental heterogeneity in Wujiangdu reservoir seasonally. The dominant phylum was Actinomycetota for FL and Pseudomonadota for PA bacteria. Species richness and diversity was higher in autumn and winter compared to spring and summer. In general, PA diversity was greater than FL, but with some temporal variations. Species turnover was the major contributor to β-diversity of both FL and PA lifestyles, and significant differences were noticed between FL and PA bacterial community composition. Distinct co-occurrence network patterns implied that more connections exist between FL bacteria, while more complex PA networks were in parallel to their greater diversity and stronger interactions in biofilms on particles. Dispersal limitation was the major driving force for both FL and PA bacterial community assembly. Deterministic processes were of relatively low importance, with homogeneous selection for FL and heterogeneous selection for PA bacteria. Temperature was the most important environmental driver of seasonal bacterial dynamics, followed by nitrate for FL and Secchi depth for PA bacteria. This study allows for a better understanding of the temporal variability of different bacteria lifestyles in reservoirs in the vulnerable and rapidly changing plateau environment, facilitating further microbial research related to global warming and eutrophication.

Enhanced sensitivity of extracellular antibiotic resistance genes (ARGs) to environmental concentrations of antibiotic

As emerging contaminants, antibiotics are frequently present in various environments, particularly rivers, albeit often at sublethal concentrations (ng/L∼μg/L). Assessing the risk associated with these low levels, which are far below the lethal threshold for most organisms, remains challenging. In this study, using microcosms containing planktonic bacteria and biofilm, we examined how antibiotic resistance genes (ARGs) in different physical states, including intracellular ARGs (iARGs) and extracellular ARGs (eARGs) responded to these low-level antibiotics. Our findings reveal a positive correlation between sub-lethal antibiotic exposure (ranging from 0.1 to 10 μg/L) and increased prevalence (measured as ARG copies/16s rDNA) of both iARGs and eARGs in planktonic bacteria. Notably, eARGs demonstrated greater sensitivity to antibiotic exposure compared to iARGs, with a lower threshold (0.1 μg/L for eARGs versus 1 μg/L for iARGs) for abundance increase. Moreover, ARGs in biofilms demonstrates higher sensitivity to antibiotic exposure compared to planktonic bacteria. To elucidate the underlying mechanisms, we established an integrated population dynamics-pharmacokinetics-pharmacodynamics (PD-PP) model. This model indicates that the enhanced sensitivity of eARGs is primarily driven by an increased potential for plasmid release from cells under low antibiotic concentrations. Furthermore, the accumulation of antibiotic in biofilms induces a greater sensitivity of ARG compared to the planktonic bacteria. This study provides a fresh perspective on the development of antibiotic resistance and offers an innovative approach for assessing the risk of sublethal antibiotic in the environment.

Effects of eutrophication on the horizontal transfer of antibiotic resistance genes in microalgal-bacterial symbiotic systems

Overloading of nutrients such as nitrogen causes eutrophication of freshwater bodies. The spread of antibiotic resistance genes (ARGs) poses a threat to ecosystems. However, studies on the enrichment and spread of ARGs from increased nitrogen loading in algal-bacterial symbiotic systems are limited. In this study, the transfer of extracellular kanamycin resistance (KR) genes from large (RP4) small (pEASY-T1) plasmids into the intracellular and extracellular DNA (iDNA, eDNA) of the inter-algal environment of Chlorella pyrenoidosa was investigated, along with the community structure of free-living (FL) and particle-attached (PA) bacteria under different nitrogen source concentrations (0-2.5 g/L KNO3). The results showed that KR gene abundance in the eDNA adsorbed on solid particles (D-eDNA) increased initially and then decreased with increasing nitrogen concentration, while the opposite was true for the rest of the free eDNA (E-eDNA). Medium nitrogen concentrations promoted the transfer of extracellular KR genes into the iDNA attached to algal microorganisms (A-iDNA), eDNA attached to algae (B-eDNA), and the iDNA of free microorganisms (C-iDNA); high nitrogen contributed to the transfer of KR genes into C-iDNA. The highest percentage of KR genes was found in B-eDNA with RP4 plasmid treatment (66.2%) and in C-iDNA with pEASY-T1 plasmid treatment (86.88%). In addition, dissolved oxygen (DO) significantly affected the bacterial PA and FL community compositions. Nephelometric turbidity units (NTU) reflected the abundance of ARGs in algae. Proteobacteria, Cyanobacteria, Bacteroidota, and Actinobacteriota were the main potential hosts of ARGs. These findings provide new insights into the distribution and dispersal of ARGs in the phytoplankton inter-algal environment.

Utilization of qPCR to Determine Duration and Environmental Drivers Contributing to the Persistence of Human DNA in Soil

Little is known about the underlying mechanisms that contribute to the persistence and degradation of DNA within soil. The goals of this study are to determine the duration of mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) persistence in soils enriched by surface-level human decomposition and to better understand the contribution of environmental factors. The surface-level decomposition of three human cadavers was documented over 11 weeks. Based on quantitative PCR results, we found nuDNA to persist in soils six weeks post-placement, while mtDNA was recoverable for the entire 11-week decomposition period. Principle components analyses and Spearman's rank correlations revealed that (1) time, (2) total body score, and (3) weekly average air temperature were significantly correlated with concentrations of nuDNA and mtDNA in soil, suggesting these factors play a role in the degradation of DNA in soils.

A neoteric antibacterial ceria-silver nanozyme for abiotic surfaces

Community-associated and hospital-acquired infections caused by bacteria continue to yield major global challenges to human health. Bacterial contamination on abiotic surfaces is largely spread via high-touch surfaces and contemporary standard disinfection practices show limited efficacy, resulting in unsatisfactory therapeutic outcomes. New strategies that offer non-specific and broad protection are urgently needed. Herein, we report our novel ceria-silver nanozyme engineered at a molar ratio of 5:1 and with a higher trivalent (Ce3+) surface fraction. Our results reveal potent levels of surface catalytic activity on both wet and dry surfaces, with rapid, and complete eradication of Pseudomonas aeruginosa, Staphylococcus aureus, and methicillin resistant S. aureus, in both planktonic and biofilm form. Preferential electrostatic adherence of anionic bacteria to the cationic nanozyme surface leads to a catastrophic loss in both aerobic and anaerobic respiration, DNA damage, osmodysregulation, and finally, programmed bacterial lysis. Our data reveal several unique mechanistic avenues of synergistic ceria-Ag efficacy. Ag potentially increases the presence of Ce3+ sites at the ceria-Ag interface, thereby facilitating the formation of harmful H2O2, followed by likely permeation across the cell wall. Further, a weakened Ag-induced Ce-O bond may drive electron transfer from the Ec band to O2, thereby further facilitating the selective reduction of O2 toward H2O2 formation. Ag destabilizes the surface adsorption of molecular H2O2, potentially leading to higher concentrations of free H2O2 adjacent to bacteria. To this end, our results show that H2O2 and/or NO/NO2-/NO3- are the key liberators of antibacterial activity, with a limited immediate role being offered by nanozyme-induced ROS including O2•- and OH•, and likely other light-activated radicals. A mini-pilot proof-of-concept study performed in a pediatric dental clinic setting confirms residual, and continual nanozyme antibacterial efficacy over a 28-day period. These findings open a new approach to alleviate infections caused by bacteria for use on high-touch hard surfaces.

Plasmid size determines adsorption to clay and breakthrough in a saturated sand column

Horizontal gene transfer (HGT) is a major factor in the spread of antibiotic resistant genes (ARG). Transformation, one mode of HGT, involves the acquisition and expression of extracellular DNA (eDNA). eDNA in soils is degraded rapidly by extracellular nucleases. However, if bound to a clay particle, eDNA can persist for long periods of time without losing its transformation ability. To better understand the mechanism of eDNA persistence in soil, this experiment assessed the effects of 1) clay mineralogy, 2) mixed salt solution, 3) plasmid size on DNA adsorption to clay and 4) breakthrough behavior of three differently sized plasmids in an environmentally relevant solution. Batch test methods were used to determine adsorption trends of three differently sized DNA plasmids, pUC19, pBR322, and pTYB21, to several pure clay minerals, goethite (α-FeOOH), illite, and kaolinite, and one environmental soil sample. Results show not all sorbents have equal adsorption capacity based on surface area with adsorption capacities decreasing from goethite > illite = kaolinite > bulk soil, and low ionic strength solutions will likely not significantly alter sorption trends. Additionally, plasmid DNA size (i.e., length) was shown to be a significant predictor of adsorption efficiency and that size affects DNA breakthrough, with breakthroughs occurring later with larger plasmids. Given that DNA persistence is linked to its adsorption to soil constituents and breakthrough, eDNA size is likely an important contributor to the spread of ARG within natural microbial communities.

eDNA Adsorption onto Microplastics: Impacts of Water Chemistry and Polymer Physiochemical Properties

Adsorption of biomacromolecules onto polymer surfaces, including microplastics (MPs), occurs in multiple environmental compartments, forming an ecocorona. Environmental DNA (eDNA), genetic material shed from organisms, can adsorb onto MPs which can potentially either (1) promote long-range transport of antibiotic resistant genes or (2) serve to gain insights into the transport pathways and origins of MPs by analyzing DNA sequences on MPs. However, little is known about the capacity of MPs to adsorb eDNA or the factors that influence sorption, such as polymer and water chemistries. Here we investigated the adsorption of extracellular linear DNA onto a variety of model MP fragments composed of three of the most environmentally prevalent polymers (polyethylene, polyethylene terephthalate, and polystyrene) in their pristine and photochemically weathered states. Batch adsorption experiments in a variety of water chemistries were complemented with nonlinear modeling to quantify the rate and extent of eDNA sorption. Ionic strength was shown to strongly impact DNA adsorption by reducing or inhibiting electrostatic repulsion. Polyethylene terephthalate exhibited the highest adsorption capacity when normalizing for MP specific surface area, likely due to the presence of ester groups. Kinetics experiments showed fast adsorption (majority adsorbed under 30 min) before eventually reaching equilibrium after 1-2 h. Overall, we demonstrated that DNA quickly binds to MPs, with pseudo-first- and -second-order models describing adsorption kinetics and the Freundlich model describing adsorption isotherms most accurately. These insights into DNA sorption onto MPs show that there is potential for MPs to act as vectors for genetic material of interest, especially considering that particle-bound DNA typically persists longer in the environment than dissolved DNA.

Invasibility of a North American soil ecosystem to amphibian-killing fungal pathogens

North American salamanders are threatened by intercontinental spread of chytridiomycosis, a deadly disease caused by the fungal pathogen Batrachochytrium salamandrivorans (Bsal). To predict potential dispersal of Bsal spores to salamander habitats, we evaluated the capacity of soil microbial communities to resist invasion. We determined the degree of habitat invasibility using soils from five locations throughout the Great Smoky Mountains National Park, a region with a high abundance of susceptible hosts. Our experimental design consisted of replicate soil microcosms exposed to different propagule pressures of the non-native pathogen, Bsal, and an introduced but endemic pathogen, B. dendrobatidis (Bd). To compare growth and competitive interactions, we used quantitative PCR, live/dead cell viability assays, and full-length 16S rRNA sequencing. We found that soil microcosms with intact bacterial communities inhibited both Bsal and Bd growth, but inhibitory capacity diminished with increased propagule pressure. Bsal showed greater persistence than Bd. Linear discriminant analysis (LDA) identified the family Burkolderiaceae as increasing in relative abundance with the decline of both pathogens. Although our findings provide evidence of environmental filtering in soils, such barriers weakened in response to pathogen type and propagule pressure, showing that habitats vary their invasibility based on properties of their local microbial communities.

Negative plant-soil feedback in Arabidopsis thaliana: Disentangling the effects of soil chemistry, microbiome, and extracellular self-DNA

Nutrient deficiency, natural enemies and litter autotoxicity have been proposed as possible mechanisms to explain species-specific negative plant-soil feedback (PSF). Another potential contributor to negative PSF is the plant released extracellular self-DNA during litter decay. In this study, we sought to comprehensively investigate these hypotheses by using Arabidopsis thaliana (L.) Heynh as a model plant in a feedback experiment. The experiment comprised a conditioning phase and a response phase in which the conditioned soils underwent four treatments: (i) addition of activated carbon, (ii) washing with tap water, (iii) sterilization by autoclaving, and (iv) control without any treatment. We evaluated soil chemical properties, microbiota by shotgun sequencing and the amount of A. thaliana extracellular DNA in the differently treated soils. Our results showed that washing and sterilization treatments mitigated the negative PSF effect. While shifts in soil chemical properties were not pronounced, significant changes in soil microbiota were observed, especially after sterilization. Notably, plant biomass was inversely associated with the content of plant self-DNA in the soil. Our results suggest that the negative PSF observed in the conditioned soil was associated to increased amounts of soilborne pathogens and plant self-DNA. However, fungal pathogens were not limited to negative conditions, butalso found in soils enhancing A.thaliana growth. In-depth multivariate analysis highlights that the hypothesis of negative PSF driven solely by pathogens lacks consistency. Instead, we propose a multifactorial explanation for the negative PSF buildup, in which the accumulation of self-DNA weakens the plant's root system, making it more susceptible to pathogens.

Larger particle size distribution of environmental RNA compared to environmental DNA: a case study targeting the mitochondrial cytochrome b gene in zebrafish (Danio rerio) using experimental aquariums

Environmental RNA (eRNA) analysis is conventionally expected to infer physiological information about organisms within their ecosystems, whereas environmental DNA (eDNA) analysis only infers their presence and abundance. Despite the promise of eRNA application, basic research on eRNA characteristics and dynamics is limited. The present study conducted aquarium experiments using zebrafish (Danio rerio) to estimate the particle size distribution (PSD) of eRNA in order to better understand the persistence state of eRNA particles. Rearing water samples were sequentially filtered using different pore-size filters, and the resulting size-fractioned mitochondrial cytochrome b (CytB) eDNA and eRNA data were modeled with the Weibull complementary cumulative distribution function (CCDF) to estimate the parameters characterizing the PSDs. It was revealed that the scale parameter (α) was significantly higher (i.e., the mean particle size was larger) for eRNA than eDNA, while the shape parameter (β) was not significantly different between them. This result supports the hypothesis that most eRNA particles are likely in a protected, intra-cellular state, which mitigates eRNA degradation in water. Moreover, these findings also imply the heterogeneous dispersion of eRNA relative to eDNA and suggest an efficient method of eRNA collection using a larger pore-size filter. Further studies on the characteristics and dynamics of eRNA particles should be pursued in the future.

Employing a triple metabarcoding approach to differentiate active, dormant and dead microeukaryotes in sediments

Microbial communities are commonly characterised through the metabarcoding of environmental DNA. This DNA originates from both viable (including dormant and active) and dead organisms, leading to recent efforts to distinguish between these states. In this study, we further these approaches by distinguishing not only between viable and dead cells but also between dormant and actively growing cells. This is achieved by sequencing both rRNA and rDNA, in conjunction with propidium monoazide cross-linked rDNA, to partition the active, dormant and relic fractions in environmental samples. We apply this method to characterise the diversity and assemblage structure of these fractions of microeukaryotes in intertidal sediments during a wet-dry-rewet incubation cycle. Our findings indicate that a significant proportion of microeukaryotic phylotypes detected in the total rDNA pools originate from dormant and relic microeukaryotes in the sediments, both in terms of richness (dormant, 13 ± 2%; relic, 47 ± 5%) and read abundance (dormant, 20 ± 7%; relic, 14 ± 5%). The richness and sequence proportion of dormant microeukaryotes notably increase during the transition from wet to dry conditions. Statistical analyses suggest that the dynamics of diversity and assemblage structure across different activity fractions are influenced by various environmental drivers. Our strategy offers a versatile approach that can be adapted to characterise other microbes in a wide range of environments.

Active soil microbial composition and proliferation are directly affected by the presence of biocides from building materials

Combinations of biocides are commonly added to building materials to prevent microbial growth and thereby cause degradation of the façades. These biocides reach the environment by leaching from façades posing an environmental risk. Although ecotoxicity to the aquatic habitat is well established, there is hardly any data on the ecotoxicological effects of biocides on the soil habitat. This study aimed to characterize the effect of the biocides terbutryn, isoproturon, octhilinone, and combinations thereof on the total and metabolically active soil microbial community composition and functions. Total soil microbial community was retrieved directly from the nucleic acid extracts, while the DNA of the active soil microbial community was separated after bromodeoxyuridine labeling. Bacterial 16S rRNA gene and fungal internal transcribed spacer region gene-based amplicon sequencing was carried out for both active and total, while gene copy numbers were quantified only for the total soil microbial community. Additionally, soil respiration and physico-chemical parameters were analyzed to investigate overall soil microbial activity. The bacterial and fungal gene copy numbers were significantly affected by single biocides and combined biocide soil treatment but not soil respiration and physico-chemical parameters. While the total soil microbiome experienced only minor effects from single and combined biocide treatment, the active soil microbiome was significantly impacted in its diversity, richness, composition, and functional patterns. The active bacterial richness was more sensitive than fungal richness. However, the adverse effects of the biocide combination treatments on soil bacterial richness were highly dependent on the identities of the biocide combination. Our results demonstrate that the presence of biocides frequently used in building materials affects the active soil microbiome. Thereby, the approach described herein can be used as an ecotoxicological measure for the effect on complex soil environments in future studies.

Biochar induces different responses of intracellular and extracellular antibiotic resistance genes and suppresses horizontal transfer during lincomycin fermentation dregs composting

This study aims to indicate the influence of biochar on extracellular and intracellular ARGs (e/iARGs) variation and proliferation during lincomycin fermentation dregs (LFDs) compost. Biochar addition made iARGs keep reducing but eARGs increase to the maximum at the middle thermophilic phase and reduce at the end of the compost. Compared to control 3.15-log and 5.42-log reduction of iARGs and eARGs were observed, respectively. Biochar addition, bacterial community, and MGEs were the major contributors to iARGs and eARGs removal, with the contribution percentages of 38.4%, 31.0%, 23.7%, and 27.2%, 29.1%, and 34.9%, respectively. Moreover, biochar significantly inhibited eARGs transformation and RP4 plasmid conjugative transfer among E. coli DH5α and Pseudomonas aeruginosa HLS-6. The underlying mechanism involved in broken cell membranes of bacteria, and altered expression of oxidative stress genes and save our souls (SOS) response-related genes. The results indicated that biochar addition in composting could limit the dissemination of ARGs.

DNA and RNA Stability of Marine Microalgae in Cold-Stored Sediments and Its Implications in Metabarcoding Analyses

The ever-increasing applications of metabarcoding analyses for environmental samples demand a well-designed assessment of the stability of DNA and RNA contained in cells that are deposited or buried in marine sediments. We thus conducted a qPCR quantification of the DNA and RNA in the vegetative cells of three microalgae entrapped in facsimile marine sediments and found that >90% of DNA and up to 99% of RNA for all microalgal species were degraded within 60 days at 4 °C. A further examination of the potential interference of the relic DNA of the vegetative cells with resting cyst detection in sediments was performed via a metabarcoding analysis in artificial marine sediments spiked with the vegetative cells of two Kareniaceae dinoflagellates and the resting cysts of another three dinoflagellates. The results demonstrated a dramatic decrease in the relative abundances of the two Kareniaceae dinoflagellates in 120 days, while those of the three resting cysts increased dramatically. Together, our results suggest that a positive detection of microalgae via metabarcoding analysis in DNA or RNA extracted from marine sediments strongly indicates the presence of intact or viable cysts or spores due to the rapid decay of relic DNA/RNA. This study provides a solid basis for the data interpretation of metabarcoding surveys, particularly in resting cyst detection.

Changes in the behavior of Staphylococcus aureus strains in the presence of oxacillin under the effect of gamma radiation

Staphylococcus aureus (S. aureus) as a major pathogen is implicated in a wide range of foodborne and hospital-acquired infections, its methicillin resistant variants contribute to the spread of β-lactam antibiotic resistance. It is essentially important to destroy these pathogens, their resistance genes and the antibiotics in wastewaters. For this purpose reactions of reactive radicals (advanced oxidation processes), first of all hydroxyl radicals (•OH), are suggested. Here the radiolysis of water supplied these radicals. In the experiments B.01755 oxacillin sensitive and B.02174 resistant S. aureus strains were used to study their behaviorr in suspensions under the effect of irradiation in presence and absence of oxacillin. Oxacillin inactivation depended on concentration of the antibiotic used (0.042 and 1 g dm-3), higher concentration required a higher dose. When 106-109 CFU cm-3 S. aureus suspensions were irradiated with γ-radiation the bacteria were inactivated at low absorbed doses: 4 orders of magnitude decrease ocurred in the number of culturable cells at ∼0.6 kGy dose. Both cell membrane and DNA suffered considerable damages during irradiation. Due to the membrane damage the cells could not be stained, and the DNA content of cells in several days period was released into the solution. In DNA damage the oxacillin resistance mecA gene was also modified, it did not multiply in PCR test. These findings are important from the point of view of applying irradiation technology to stop the spread of antibiotic resistance.

Engineering E. coli strains using antibiotic-resistance-gene-free plasmids

We created a generalizable pipeline for antibiotic-resistance-gene-free plasmid (ARGFP)-based cloning using a dual auxotrophic- and essential-gene-based selection strategy. We use auxotrophic selection to construct plasmids in engineered E. coli DH10B cloning strains and both auxotrophic- and essential-gene-based selection to (1) select for recombinant strains and (2) maintain a plasmid in E. coli Nissle 1917, a common chassis for engineered probiotic applications, and E. coli MG1655, the laboratory "wild-type" E. coli strain. We show that our approach has comparable efficiency to that of antibiotic-resistance-gene-based cloning. We also show that the double-knockout Nissle and MG1655 strains are simple to transform with plasmids of interest. Notably, we show that the engineered Nissle strains are amenable to long-term plasmid maintenance in repeated culturing as well as in the mouse gut, demonstrating the potential for broad applications while minimizing the risk of antibiotic resistance spread via horizontal gene transfer.

Microbial communities of a variety of 75 homemade fermented vegetables

Fermentation is an ancient practice of food preservation. Fermented vegetables are popular in Eastern European and Asian countries. They have received a growing interest in Western countries, where they are mainly manufactured at domestic and artisanal scales and poorly characterized. Our aim was to investigate the microbial communities and the safety of French homemade fermented vegetables, in the frame of a citizen science project. Fermented vegetables and the data associated with their manufacture were collected from citizens and characterized for pH, NaCl concentration, and microbiology by culturomics and 16S DNA metabarcoding analysis. Lactic acid bacteria (LAB) and yeast isolates were identified by 16S rRNA gene sequencing and D1/D2 domains of the large subunit of the rRNA gene, respectively. The 75 collected samples contained 23 types of vegetables, mainly cabbage, followed by carrots and beets, and many mixtures of vegetables. They were 2 weeks to 4 years old, and their median pH was 3.56, except for two samples with a pH over 4.5. LAB represented the dominant viable bacteria. LAB concentrations ranged from non-detectable values to 8.7 log colony-forming units (CFU)/g and only depended on the age of the samples, with the highest most frequently observed in the youngest samples (<100 days). The 93 LAB isolates identified belonged to 23 species, the two mains being Lactiplantibacillus pentosus/plantarum and Levilactobacillus brevis. The other microbial groups enumerated (total aerobic bacteria, halotolerant bacteria, Gram-negative bacteria, and acetic acid bacteria) generally showed lower concentrations compared to LAB concentrations. No pathogenic bacteria were detected. Viable yeasts were observed in nearly half the samples, at concentrations reaching up to 8.0 log CFU/g. The 33 yeast clones identified belonged to 16 species. Bacterial metabarcoding showed two main orders, namely, Lactobacillales (i.e., LAB, 79% of abundance, 177 of the 398 total ASVs) and Enterobacterales (19% of abundance, 191 ASVs). Fifteen LAB genera were identified, with Lactiplantibacillus and Levilactobacillus as the most abundant, with 41 and 12% of total reads, respectively. Enterobacterales members were mainly represented by Enterobacteriaceae and Yersiniaceae. This study is the first wide description of the microbiota of a large variety of homemade fermented vegetables and documents their safety.

Exploring the impact of oral bacteria remnants on stem cells from the Apical papilla: mineralization potential and inflammatory response

Introduction

Bacterial persistence is considered one of the main causal factors for regenerative endodontic treatment (RET) failure in immature permanent teeth. This interference is claimed to be caused by the interaction of bacteria that reside in the root canal with the stem cells that are one of the essentials for RET. The aim of the study was to investigate whether prolonged exposure of stem cells from the apical papilla (SCAP) to bacterial remnants of Fusobacterium nucleatum, Actinomyces gerensceriae, Slackia exigua, Enterococcus faecalis, Peptostreptococcaceae yurii, commonly found in infected traumatized root canals, and the probiotic bacteria Lactobacillus gasseri and Limosilactobacillus reuteri, can alter SCAP's inflammatory response and mineralization potential.

Methods

To assess the effect of bacterial remnants on SCAP, we used UV-C-inactivated bacteria (as cell wall-associated virulence factors) and bacterial DNA. Histochemical staining using Osteoimage Mineralization Assay and Alizarin Red analysis was performed to study SCAP mineralization, while inflammatory and osteo/odontogenic-related responses of SCAPs were assessed with Multiplex ELISA.

Results

We showed that mineralization promotion was greater with UV C-inactivated bacteria compared to bacterial DNA. Immunofluorescence analysis detected that the early mineralization marker alkaline phosphatase (ALP) was increased by the level of E. coli lipopolysaccharide (LPS) positive control in the case of UV-C-inactivated bacteria; meanwhile, DNA treatment decreased the level of ALP compared to the positive control. SCAP's secretome assessed with Multiplex ELISA showed the upregulation of pro-inflammatory factors IL-6, IL-8, GM-CSF, IL-1b, neurotrophic factor BDNF, and angiogenic factor VEGF, induced by UV-C-killed bacteria.

Discussion

The results suggest that long term stimulation (for 21 days) of SCAP with UV-C-inactivated bacteria stimulate their mineralization and inflammatory response, while DNA influence has no such effect, which opens up new ideas about the nature of RET failure.

Application of environmental DNA metabarcoding and quantitative PCR to detect blooming jellyfish in a temperate bay of northern China

Frequently occurring jellyfish blooms have severe impacts on the socioeconomics of coastal areas, which stress the importance of early detection and assessments of blooming jellyfish taxa. Environmental DNA (eDNA) techniques (quantitative PCR and eDNA metabarcoding) have the advantage of high sensitivity and are an emerging powerful tool for investigations of target species. However, a comprehensive analysis of the biodiversity and biomass of jellyfish taxa in the target area by combining the two eDNA techniques is still lacking. Here, we developed eDNA metabarcoding and quantitative PCR for the detection and assessment of jellyfish taxa in the temperate Yantai Sishili Bay (YSB) and estimated the spatial distribution of Aurelia coerulea. Species-specific quantitative PCR assays targeting the mitochondrial cytochrome c oxidase subunit I gene of A. coerulea were developed. Additionally, eDNA metabarcoding based on the mitochondrial 16S rDNA sequences identified six jellyfish species in YSB. Moreover, our results indicate that A. coerulea aggregations were more likely to occur in the inner part of the bay than in the outer part, and they gathered in the bottom layer of seawater rather than in the surface layer. Our results demonstrate the potential of two eDNA techniques in jellyfish biomass investigation and jellyfish taxa detection. These eDNA techniques may contribute to the discovery of jellyfish aggregation so as to achieve early warning of large-scale jellyfish blooms in coastal areas.

Binding of Dissolved Organic Matter to RNA and Protection from Nuclease-Mediated Degradation

The persistence of RNA in environmental systems is an important parameter for emerging applications, including ecological surveys, wastewater-based epidemiology, and RNA interference biopesticides. RNA persistence is controlled by its rate of biodegradation, particularly by extracellular enzymes, although the specific factors determining this rate have not been characterized. Due to prior work suggesting that nucleic acids-specifically DNA-interact with dissolved organic matter (DOM), we hypothesized that DOM may bind RNA and impede its biodegradation in natural systems. We first adapted a technique previously used to assess RNA-protein binding to differentiate RNA that is bound at all sites by DOM from RNA that is unbound or partially bound by DOM. Results from this technique suggested that humic acids bound RNA more extensively than fulvic acids. At concentrations of 8-10 mgC/L, humic acids were also found to be more effective than fulvic acids at suppressing enzymatic degradation of RNA. In surface water and soil extract containing DOM, RNA degradation was suppressed by 39-46% relative to pH-adjusted controls. Due to the ability of DOM to both bind and suppress the enzymatic degradation of RNA, RNA biodegradation may be slowed in environmental systems with high DOM concentrations, which may increase its persistence.

Microplastic biofilm: An important microniche that may accelerate the spread of antibiotic resistance genes via natural transformation

Microplastic (MP) biofilms provide a specific microniche for microbial life and are a potential hotspot for the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Nevertheless, the acquisition of ARGs in MP biofilms via natural transformation mediated by extracellular DNA (eDNA) has been rarely explored. This study demonstrated that MP biofilms promoted the natural transformation of extracellular ARGs at the single-cell and multi-species levels, compared to natural substrate (NS) biofilms and bacterioplankton. The transformation frequency on MP biofilms was up to 1000-fold compare to that on NS. The small MPs and aged MPs enhanced the ARG transformation frequencies up to 77.16-fold and 32.05-fold, respectively, compared with the large MPs and pristine MPs. The transformation frequencies on MP biofilms were significantly positively correlated with the bacterial density and extracellular polymeric substance (EPS) content (P < 0.05). Furthermore, MPs significantly increased the expression of the biofilm formation related genes (motA and pgaA) and DNA uptake related genes (pilX and comA) compared to NS and bacterioplankton. The more transformants colonized on MPs contributed to the enhanced transformation frequencies at the community-wide level. Overall, eDNA-mediated transformation in MP biofilms may be an important path of ARG spread, which was promoted by heterogeneous biofilm.

A glimpse of the paleome in endolithic microbial communities

BACKGROUND

The terrestrial subsurface is home to a significant proportion of the Earth's microbial biomass. Our understanding about terrestrial subsurface microbiomes is almost exclusively derived from groundwater and porous sediments mainly by using 16S rRNA gene surveys. To obtain more insights about biomass of consolidated rocks and the metabolic status of endolithic microbiomes, we investigated interbedded limestone and mudstone from the vadose zone, fractured aquifers, and deep aquitards.

RESULTS

By adapting methods from microbial archaeology and paleogenomics, we could recover sufficient DNA for downstream metagenomic analysis from seven rock specimens independent of porosity, lithology, and depth. Based on the extracted DNA, we estimated between 2.81 and 4.25 × 105 cells × g-1 rock. Analyzing DNA damage patterns revealed paleome signatures (genetic records of past microbial communities) for three rock specimens, all obtained from the vadose zone. DNA obtained from deep aquitards isolated from surface input was not affected by DNA decay indicating that water saturation and not flow is controlling subsurface microbial survival. Decoding the taxonomy and functional potential of paleome communities revealed increased abundances for sequences affiliated with chemolithoautotrophs and taxa such as Cand. Rokubacteria. We also found a broader metabolic potential in terms of aromatic hydrocarbon breakdown, suggesting a preferred utilization of sedimentary organic matter in the past.

CONCLUSIONS

Our study suggests that limestones function as archives for genetic records of past microbial communities including those sensitive to environmental stress at modern times, due to their specific conditions facilitating long-term DNA preservation. Video Abstract.

Quantification of nitrogen cycle functional genes from viable archaea and bacteria in paddy soil

AIMS

One of the main challenges of culture-independent soil microbiology is distinguishing the microbial community's viable fraction from dead matter. Propidium monoazide (PMA) binds the DNA of dead cells, preventing its amplification. This dye could represent a robust means to overcome the drawbacks of other selective methods, such as ribonucleic acid-based analyses.

METHODS AND RESULTS

We quantified functional genes from viable archaea and bacteria in soil by combining the use of PMA and quantitative polymerase chain reaction. Four N-cycle-related functional genes (bacterial and archaeal ammonia monooxygenase, nitrate reductase, and nitrite reductase) were successfully quantified from the living fraction of bacteria and archaea of a paddy soil. The protocol was also tested with pure bacterial cultures and soils with different physical and chemical properties.

CONCLUSIONS

The experiment results revealed a contrasting impact of mineral and organic fertilizers on the abundance of microbial genes related to the N-cycle in paddy soil.

Technological variations, microbial diversity and quality characteristics of maize ogi used for akpan production in Benin

Fermented maize starch, called ogi in Benin, is used for preparing akpan, a traditional yoghurt-like food that contributes to the food and nutrition security of its consumers. Current ogi processing technologies used by two socio-cultural groups of Benin, namely the Fon and the Goun, and aspects of the quality of the fermented starches were studied to assess the current state-of-the-art, explore changes in key product characteristics over time and identify priorities for follow-up research to increase product quality and shelf life. A survey on processing technologies was conducted in five municipalities in south Benin and samples of maize starch were collected, which were analysed after the fermentation required to obtain ogi. Four processing technologies were identified, two from the Goun (G1, G2) and two from the Fon (F1, F2). The main difference between the four processing technologies was the steeping procedure used for the maize grains. The pH of the ogi samples ranged between 3.1 and 4.2, with the highest values for G1 samples, which also contained relatively higher concentrations of sucrose (0.05-0.3 g/L) than F1 samples (0.02-0.08 g/L), and lower citrate and lactate concentrations (0.2-0.3 and 5.6-16.9 g/L, respectively) than F2 samples (0.4-0.5 and 14-27.7 g/L, respectively). Fon samples collected in Abomey were particularly rich in volatile organic compounds and free essential amino acids. Members of the genera Lactobacillus (8.6-69.3%), Limosilactobacillus (5.4-79.1%), Streptococcus (0.6-59.3%) and Weissella (2.6-51.2%) dominated the bacterial microbiota of ogi with a significant abundance of Lactobacillus spp. in Goun samples. Sordariomycetes (10.6-81.9%) and Saccharomycetes (6.2-81.4%) dominated the fungal microbiota. The yeast community of ogi samples mainly consisted of the genera Diutina, Pichia, Kluyveromyces, Lachancea and unclassified members of the Dipodascaceae family. Hierarchical clustering of metabolic data showed similarities between samples from different technologies at a default threshold of 0.05. No obvious trend in the composition of the samples' microbial communities reflected the clusters observed for the metabolic characteristics. The results indicate that beyond the general impact of the use of Fon or Goun technologies on fermented maize starch, the individual contribution of processing practices warrants study, under controlled conditions, to determine the drivers of difference or similarity between maize ogi samples to further contribute to improving product quality and shelf life.

Earthworms restructure the distribution of extracellular antibiotics resistance genes of sludge by modifying the structure of extracellular polymeric substances during vermicomposting

The role of earthworms in reducing the antibiotic resistance genes (ARGs) in sludge vermicompost remains unclear. The structure of extracellular polymeric substance (EPS) of sludge may be associated with the horizontal gene transfer behavior of ARGs in the vermicomposting of sludge. Therefore, this study aimed to investigate the effects of earthworms on the structural characteristics of EPS associated with the fate of ARGs in EPS during the vermicomposting of sludge. The results showed vermicomposting could diminish the abundance of ARGs and mobile genetic elements (MGEs) in the EPS of sludge by 47.93 % and 7.75 %, compared to the control, respectively. Relative to the control, vermicomposting also led to the reduction of MGEs abundances in the soluble EPS of 40.04 %, lightly bound EPS of 43.53 %, and tightly bound EPS of 70.49 %, respectively. The total abundances of certain ARGs dramatically diminished 95.37 % in tightly bound EPS of sludge during vermicomposting. In vermicomposting, the main influencing factor of ARGs distribution was the proteins in LB-EPS, accounting for 48.5 % of the variation. This study suggests that the earthworms lower the total abundances of ARGs by regulating the microbial community and modifying the microbial metabolic pathways associated with ARGs and MGEs in the EPS of sludge.

RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities

BACKGROUND

Characterization of microbial activity is essential to the understanding of the basic biology of microbial communities, as the function of a microbiome is defined by its biochemically active ("viable") community members. Current sequence-based technologies can rarely differentiate microbial activity, due to their inability to distinguish live and dead sourced DNA. As a result, our understanding of microbial community structures and the potential mechanisms of transmission between humans and our surrounding environments remains incomplete. As a potential solution, 16S rRNA transcript-based amplicon sequencing (16S-RNA-seq) has been proposed as a reliable methodology to characterize the active components of a microbiome, but its efficacy has not been evaluated systematically. Here, we present our work to benchmark RNA-based amplicon sequencing for activity assessment in synthetic and environmentally sourced microbial communities.

RESULTS

In synthetic mixtures of living and heat-killed Escherichia coli and Streptococcus sanguinis, 16S-RNA-seq successfully reconstructed the active compositions of the communities. However, in the realistic environmental samples, no significant compositional differences were observed in RNA ("actively transcribed - active") vs. DNA ("whole" communities) spiked with E. coli controls, suggesting that this methodology is not appropriate for activity assessment in complex communities. The results were slightly different when validated in environmental samples of similar origins (i.e., from Boston subway systems), where samples were differentiated both by environment type as well as by library type, though compositional dissimilarities between DNA and RNA samples remained low (Bray-Curtis distance median: 0.34-0.49). To improve the interpretation of 16S-RNA-seq results, we compared our results with previous studies and found that 16S-RNA-seq suggests taxon-wise viability trends (i.e., specific taxa are universally more or less likely to be viable compared to others) in samples of similar origins.

CONCLUSIONS

This study provides a comprehensive evaluation of 16S-RNA-seq for viability assessment in synthetic and complex microbial communities. The results found that while 16S-RNA-seq was able to semi-quantify microbial viability in relatively simple communities, it only suggests a taxon-dependent "relative" viability in realistic communities.  Video Abstract.

RNA outperforms DNA-based metabarcoding in assessing the diversity and response of microeukaryotes to environmental variables in the Arctic Ocean

The Arctic Ocean (AO) has a harsh environment characterized by low temperatures, extensive ice coverage, and periodic freezing and melting of sea ice, which has provided diverse habitats for microorganisms. Prior studies primarily focused on microeukaryote communities in the upper water or sea ice based on environmental DNA, leaving the composition of active microeukaryotes in the diverse AO environments largely unknown. This study provided a vertical assessment of microeukaryote communities in the AO from snow and ice to sea water at a depth of 1670 m using high-throughput sequencing of co-extracted DNA and RNA. RNA extracts depicted microeukaryote community structure and intergroup correlations more accurately and responded more sensitively to environmental conditions than those derived from DNA. Using RNA:DNA ratios as a proxy for relative activity of major taxonomic groups, the metabolic activities of major microeukaryote groups were determined along depth. Analysis of co-occurrence networks showed that parasitism between Syndiniales and dinoflagellates/ciliates in the deep ocean may be significant. This study increased our knowledge of the diversity of active microeukaryote communities and highlighted the importance of using RNA-based sequencing over DNA-based sequencing to examine the relationship between microeukaryote assemblages and the responses of microeukaryotes to environmental variables in the AO.

Photocatalysis enhanced constructed wetlands effectively remove antibiotic resistance genes from domestic wastewater

Antibiotic resistance genes (ARGs) is a new class of environmental pollutants that endanger both humans and the environment. So far, removing ARGs economically and efficiently has remained a challenge. In this study, combining photocatalytic technology with constructed wetlands (CWs) were used to remove ARGs, which can remove both intracellular and extracellular ARGs and reduce the risk of resistance gene spread. This study includes three devices: a series photocatalytic treatment-constructed wetland (S-PT-CW), a built photocatalytic treatment into a constructed wetland (B-PT-CW), and a single constructed wetland (S-CW). Results demonstrated that photocatalysis and CWs together increased the efficiency of removing ARGs, particularly intracellular ARGs (iARGs). The log values of iARGs removal ranged from 1.27 to 1.72, while the log values of eARGs removal were only 0.23-0.65. The iARG removal effectiveness was ranked as B-PT-CW > S-PT-CW > S-CW, and the removal effectiveness for extracellular ARGs (eARGs) was ranked as S-PT-CW > B-PT-CW > S-CW. Further investigation into the removal mechanisms of S-PT-CW and B-PT-CW revealed that CWs represented primary pathways for iARG removal, whereas photocatalysis was the primary pathways for eARG removal. The addition of nano-TiO₂ altered the diversity and structure of the microorganisms in CWs, leading to an increase in the abundance of nitrogen and phosphorus removal microorganisms. The main potential hosts for target ARGs (sul1, sul2 and tetQ), were the genera Vibrio, Gluconobacter, Streptococcus, Fusobacterium, and Halomonas; the removal of these potential hosts from wastewater may result from their decreased abundance.

Environmental concentrations of surfactants as a trigger for climax of horizonal gene transfer of antibiotic resistance

Ubiquitous antibiotic resistance genes (ARGs) is a significant global human health concern. Surfactants have been extensively used worldwide, and the consumption of surfactants containing hygiene, cleaning agents and disinfectants was multiplied during COVID-19 pandemic, which have caused significantly increased pollution of surfactants in aquatic environment. Whether such ever-increasing surfactant concentration boost dissemination risk of ARGs still remains unknown. Here the effects of three typical surfactants such as sodium dodecyl sulfate, cetyltrimethylammonium bromide and benzalkonium chloride on the transformation of pUC19 plasmid (2686 bp)-borne ARGs to recipient bacteria E. coli DH5ɑ were investigated. It was found that these surfactants at environmental concentrations facilitated horizonal gene transfer (HGT) via transformation. The transformation triggering concentrations for the three surfactants were 0.25-0.34 mg/L with a maximum increased transformation frequency of 13.51-22.93-fold. The mechanisms involved in activated HGT of ARGs via transformation triggered by surfactants could be mainly attributed to the increased production of reactive oxygen species, which further enhanced cell membrane permeability. These findings provide new sights for understanding of ARG propagation and also imply that the drastic rise of surfactant concentration in aquatic environment may significantly increase the dissemination risk of antibiotic resistance.

Utilizing the state of environmental DNA (eDNA) to incorporate time-scale information into eDNA analysis

Environmental DNA (eDNA) analysis allows cost-effective and non-destructive biomonitoring with a high detection sensitivity in terrestrial and aquatic environments. However, the eDNA results can sometimes include false-positive inferences of target organisms owing to the detection of aged eDNA that has long since been released from the individual and is more likely to be detected at a site further away from its source. In order to address the issue, this manuscript focuses on the state of eDNA, proposing new methodologies to estimate the age of eDNA: (1) DNA damage rate, (2) eDNA particle size distribution, and (3) viable cell-derived eDNA. In addition, the manuscript also focuses on the shorter persistence of environmental RNA (eRNA) compared with eDNA, highlighting the application of eRNA and environmental nucleic acid ratio for assessing the age of the genetic materials in water. Although substantial further research is essential to support the feasibility of these methodologies, incorporating time-scale information into eDNA analysis would update current eDNA analysis, improve the accuracy and reliability of eDNA-based monitoring, and further refine eDNA analysis as a useful monitoring tool in ecology, fisheries and various environmental sciences.

Differential dose-response patterns of intracellular and extracellular antibiotic resistance genes under sub-lethal antibiotic exposure

Although antibiotics are one of the most significant factors contributing to the propagation of antibiotic resistance genes (ARGs), studies on the dose-response relationship at sub-lethal concentrations of antibiotics remain scarce, despite their importance for assessing the risks of antibiotics in the environment. In this study, we constructed a series of microcosms to investigate the propagation of intracellular (iARGs) and extracellular (eARGs) ARGs in both water and biofilms when exposed to antibiotics at various concentrations (1-100 μg/L) and frequencies. Results showed that eARGs were more abundant than iARGs in water, while iARGs were the dominant ARGs form in biofilms. eARGs showed differentiated dose-response relationships from iARGs. The abundance of iARGs increased with the concentration of antibiotics as enhanced selective pressure overcame the metabolic burden of antibiotic-resistant bacteria carrying ARGs. However, the abundance of eARGs decreased with increasing antibiotic concentrations because less ARGs were secreted from bacterial hosts at higher concentrations (100 μg/L). Furthermore, combined exposure to two antibiotics (tetracycline & imipenem) showed a synergistic effect on the propagation of iARGs, but an antagonistic effect on the propagation of eARGs compared to exposure to a single antibiotic. When exposed to antibiotic at a fixed total dose, one-time dosing (1 time/10 d) favored the propagation of iARGs, while fractional dosing (5 times /10 d) favored the propagation of eARGs. This study sheds light on the propagation of antibiotic resistance in the environment and can help in assessing the risks associated with the use of antibiotics.