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.

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.

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.

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.

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.

The dynamics and transmission of antibiotic resistance associated with plant microbiomes

Antibiotic resistance genes (ARGs) have been widely found and studied in soil and water environments. However, the propagation of ARGs in plant microbiomes has attracted insufficient attention. Plant microbiomes, especially the rhizosphere microorganisms, are closely connected with water, soil, and air, which allows ARGs to spread widely in ecosystems and pose a threat to human health after entering the human body with bacteria. Therefore, it is necessary to deeply understand and explore the dynamics and the transmission of ARGs in rhizosphere microorganisms and endophytes of plants. In this review, the transmission and influencing factors of ARGs in the microorganisms associated with plants, especially the influence of root exudates on plant microbiomes, are analyzed. Notably, the role of intrinsic genes of plants in determining root exudates and their potential effects on ARGs are proposed and analyzed. The important role of phyllosphere microorganisms and endophytes in the transmission of ARGs and co-resistance of antibiotics and other substances are also emphasized. The proliferation and transmission of ARGs associated with plant microbiomes addressed in this review is conducive to revealing the fate of ARGs in plant microorganisms and alleviating ARG pollution.

Using cyanobacteria and other phytoplankton to assess trophic conditions: A qPCR-based, multi-year study in twelve large rivers across the United States

Phytoplankton is the essential primary producer in fresh surface water ecosystems. However, excessive phytoplankton growth due to eutrophication significantly threatens ecologic, economic, and public health. Therefore, phytoplankton identification and quantification are essential to understanding the productivity and health of freshwater ecosystems as well as the impacts of phytoplankton overgrowth (such as Cyanobacterial blooms) on public health. Microscopy is the gold standard for phytoplankton assessment but is time-consuming, has low throughput, and requires rich experience in phytoplankton morphology. Quantitative polymerase chain reaction (qPCR) is accurate and straightforward with high throughput. In addition, qPCR does not require expertise in phytoplankton morphology. Therefore, qPCR can be a useful alternative for molecular identification and enumeration of phytoplankton. Nonetheless, a comprehensive study is missing which evaluates and compares the feasibility of using qPCR and microscopy to assess phytoplankton in fresh water. This study 1) compared the performance of qPCR and microscopy in identifying and quantifying phytoplankton and 2) evaluated qPCR as a molecular tool to assess phytoplankton and indicate eutrophication. We assessed phytoplankton using both qPCR and microscopy in twelve large freshwater rivers across the United States from early summer to late fall in 2017, 2018, and 2019. qPCR- and microscope-based phytoplankton abundance had a significant positive linear correlation (adjusted R2 = 0.836, p-value < 0.001). Phytoplankton abundance had limited temporal variation within each sampling season and over the three years studied. The sampling sites in the midcontinent rivers had higher phytoplankton abundance than those in the eastern and western rivers. For instance, the concentration (geometric mean) of Bacillariophyta, Cyanobacteria, Chlorophyta, and Dinoflagellates at the sampling sites in the midcontinent rivers was approximately three times that at the sampling sites in the western rivers and approximately 18 times that at the sampling sites in the eastern rivers. Welch's analysis of variance indicates that phytoplankton abundance at the sampling sites in the midcontinent rivers was significantly higher than that at the sampling sites in the eastern rivers (p-value = 0.013) but was comparable to that at the sampling sites in the western rivers (p-value = 0.095). The higher phytoplankton abundance at the sampling sites in the midcontinent rivers was presumably because these rivers were more eutrophic. Indeed, low phytoplankton abundance occurred in oligotrophic or low trophic sites, whereas eutrophic sites had greater phytoplankton abundance. This study demonstrates that qPCR-based phytoplankton abundance can be a useful numerical indicator of the trophic conditions and water quality in freshwater rivers.

Reductions in abundances of intracellular and extracellular antibiotic resistance genes by SiO2 nanoparticles during composting driven by mobile genetic elements

Applying exogenous additives during the aerobic composting of livestock manure is effective for slowing down the spread of antibiotic resistance genes (ARGs) in the environment. Nanomaterials have received much attention because only low amounts need to be added and they have a high capacity for adsorbing pollutants. Intracellular ARGs (i-ARGs) and extracellular ARGs (e-ARGs) comprise the resistome in livestock manure but the effects of nanomaterials on the fates of these different fractions during composting are still unclear. Thus, we investigated the effects of adding SiO₂ nanoparticles (SiO₂NPs) at four levels (0 (CK), 0.5 (L), 1 (M), and 2 g/kg (H)) on i-ARGs, e-ARGs, and the bacterial community during composting. The results showed that i-ARGs represented the main fraction of ARGs during aerobic composting of swine manure, and their abundance was lowest under M. Compared with CK, M increased the removal rates of i-ARGs and e-ARGs by 17.9% and 100%, respectively. SiO₂NPs enhanced the competition between ARGs hosts and non-hosts. M optimized the bacterial community by reducing the abundances of co-hosts (Clostridium_sensu_stricto_1, Terrisporobacter, and Turicibacter) of i-ARGs and e-ARGs (by 96.0% and 99.3%, respectively) and killing 49.9% of antibiotic-resistant bacteria. Horizontal gene transfer dominated by mobile genetic elements (MGEs) played a key role in the changes in the abundances of ARGs. i-intI1 and e-Tn916/1545 were key MGEs related closely to ARGs, and the maximum decreases of 52.8% and 100%, respectively, occurred under M, which mainly explained the decreased abundances of i-ARGs and e-ARGs. Our findings provide new insights into the distribution and main drivers of i-ARGs and e-ARGs, as well as demonstrating the possibility of adding 1 g/kg SiO₂NPs to reduce the propagation of ARGs.

The hidden diversity of microbes in ballast water and sediments revealed by metagenomic sequencing

With the rapid globalization of trade, the worldwide spread of pathogens through ballast water is becoming a major concern. Although the international maritime organization (IMO) convention has been adopted to prevent the spread of harmful pathogens, the limited species resolution of the current microbe-monitoring methods challenged the ballast water and sediments management (BWSM). In this study, we explored metagenomic sequencing to investigate the species composition of microbial communities in four international vessels for BWSM. Our results showed the largest species diversity (14,403) in ballast water and sediments, including bacteria (11,710), eukaryotes (1007), archaea (829), and viruses (790). A total of 129 phyla were detected, among which the Proteobacteria, followed by Bacteroidetes, and Actinobacteria were the most abundant. Notably, 422 pathogens that are potentially harmful to marine environments and aquaculture were identified. The co-occurrence network analysis showed that most of these pathogens were positively correlated with the commonly used indicator bacteria Vibrio cholerae, Escherichia coli, and intestinal Enterococci species, validating the D-2 standard in BWSM. The functional profile showed prominent pathways of methane and sulfur metabolism, indicating that the microbial community in the severe tank environment still utilizes the energy to sustain such a high level of microbe diversity. In conclusion, metagenomic sequencing provides novel information for BWSM.

Extracellular DNA includes an important fraction of high-risk antibiotic resistance genes in treated wastewaters

Wastewater treatment plants are among the main hotspots for the release of antibiotic resistance genes (ARGs) into the environment. ARGs in treated wastewater can be found in the intracellular DNA (iDNA) and in the extracellular DNA (eDNA). In this study, we investigated the fate and the distribution (either in eDNA or in iDNA) of ARGs in the treated wastewaters pre and post-disinfection by shotgun metagenomics. The richness of the intracellular resistome was found to be higher than the extracellular one. However, the latter included different high risk ARGs. About 11% of the recovered metagenome assembled genomes (MAGs) from the extracted DNA was positive for at least one ARG and, among them, several were positive for more ARGs. The high-risk ARG bacA was the most frequently detected gene among the MAGs. The disinfection demonstrated to be an important driver of the composition of the antibiotic resistomes. Our results demonstrated that eDNA represents an important fraction of the overall ARGs, including a number of high-risk ARGs, which reach the environment with treated wastewater effluents. The studied disinfections only marginally affect the whole antibiotic resistome but cause important shifts from intracellular to extracellular DNA, potentially threating human health.

Cell-to-cell non-conjugative plasmid transfer between Bacillus subtilis and lactic acid bacteria

Bacillus subtilis is a soil-dwelling bacterium that can interact with a plethora of other microorganisms in its natural habitat. Due to the versatile interactions and its ability to form nanotubes, i.e., recently described membrane structures that trade cytoplasmic content between neighbouring cells, we investigated the potential of HGT from B. subtilis to industrially-relevant members of lactic acid bacteria (LAB). To explore the interspecies HGT events, we developed a co-culturing protocol and provided proof of transfer of a small high copy non-conjugative plasmid from B. subtilis to LABs. Interestingly, the plasmid transfer did not involve conjugation nor activation of the competent state by B. subtilis. Moreover, our study shows for the first time non-conjugative cell-to-cell intraspecies plasmid transfer for non-competent Lactococcus lactis sp. cremoris strains. Our study indicates that cell-to-cell transformation is a ubiquitous form of HGT and can be potentially utilized as an alternative tool for natural (non-GMO) strain improvement.

Biocontainment Techniques and Applications for Yeast Biotechnology

Biocontainment techniques for genetically modified yeasts (GMYs) are pivotal due to the importance of these organisms for biotechnological processes and also due to the design of new yeast strains by using synthetic biology tools and technologies. Due to the large genetic modifications that many yeast strains display, it is highly desirable to avoid the leakage of GMY cells into natural environments and, consequently, the spread of synthetic genes and circuits by horizontal or vertical gene transfer mechanisms within the microorganisms. Moreover, it is also desirable to avoid patented yeast gene technologies spreading outside the production facility. In this review, the different biocontainment technologies currently available for GMYs were evaluated. Interestingly, uniplex-type biocontainment approaches (UTBAs), which rely on nutrient auxotrophies induced by gene mutation or deletion or the expression of the simple kill switches apparatus, are still the major biocontainment approaches in use with GMY. While bacteria such as Escherichia coli account for advanced biocontainment technologies based on synthetic biology and multiplex-type biocontainment approaches (MTBAs), GMYs are distant from this scenario due to many reasons. Thus, a comparison of different UTBAs and MTBAs applied for GMY and genetically engineered microorganisms (GEMs) was made, indicating the major advances of biocontainment techniques for GMYs.

Profiling of intracellular and extracellular antibiotic resistance genes in municipal wastewater treatment plant and their effluent-receiving river

The presence of antibiotic resistance genes (ARGs) and heavy metal resistance genes (MRGs) in extracellular and intracellular DNA (eDNA and iDNA) has received considerable attention in recent years owing to the potential threat to human health and the ecosystem. As a result, we investigated six ARGs, three MRGs, and two mobile genetic elements (MGEs) in the municipal wastewater treatment plant (MWWTP) and its adjacent environments. Results revealed that the absolute abundances of eARGs and eMRGs were lower than iARGs and iMRGs in MWWTP. By contrast, eARGs and eMRGs were higher in river sediments. Among ARGs, aminoglycoside resistance genes (aadA) was the most abundant gene (3.13 × 10² to 2.31 × 10⁶ copies/mL in iDNA; 1.27 × 10³ to 7.23 × 10⁵ copies/mL in eDNA) in MWWTP, while zntA gene (9.4 × 10² to 3.97 × 10⁶ copies/mL in iDNA; 3.2 × 10³ to 6 × 10⁵ copies/mL in eDNA) was amongst the MRGs. Notably, intI1 was enriched and positively correlated with iDNA (tetA, sul1, blaCTX-M, ermB, and merA) and eDNA (blaCTX-M, ermB, and merA), demonstrating its function in the proliferation of resistance genes. This widespread distribution of ARGs, MRGs, and MGEs in MWWTP and its adjacent river sediments will help clarify the transmission routes within these environments and provide a theoretical basis for better monitoring and mitigation of such dissemination.

New and traditional methods for antibiotic resistance genes removal: Constructed wetland technology and photocatalysis technology

Antibiotic resistance genes (ARGs) are a new environmental contaminant that poses a major hazard to humans and the environment. This research discusses the methods and drawbacks of two ARG removal approaches, constructed wetlands (CWs) and photocatalysis. CWs primarily rely on the synergistic effects of substrate adsorption, plant uptake, and microbial processes to remove ARGs. The removal of ARGs can be influenced by wetland plants, substrate type, wetland type, and hydraulic conditions. The absolute abundance of ARGs in effluent decreased, but their relative abundance increased. Photocatalysis deactivates ARGs predominantly through reactive oxygen species, with removal effectiveness determined by catalyst type, radiation type, and radiation intensity. The drawback is that it exposes intracellular resistance genes, perhaps increasing the risk of ARG spread. To address the current shortcomings, this paper proposes the feasibility of combining a constructed wetland with photocatalysis technology, which provides a novel strategy for ARG removal.

Solid-liquid interface adsorption of antibiotic resistance plasmids induced by nanoplastics aggravates gene pollution in aquatic ecosystems

Antibiotic resistance genes (ARGs) and nanoplastics (NPs) have been identified as emerging pollutants in water environment; the interactions between antibiotic resistance plasmids (ARPs) and NPs will influence ARG transport in sediments. Herein, the adsorption experiments of a typical ARP onto polystyrene nanoplastics (PS-NPs) in river and lake sediments were conducted to elucidate the adsorption mechanisms and the effects of environmental factors. Results indicated that the adsorption amounts of PS-NPs increased with the dosages while decreased with the particle size of sediments. Multi-layer adsorption of PS-NPs was found to exist mainly in sand and silt sediments, whereas the filling adsorption dominated in the clay. Moreover, the adsorbed PS-NPs enhanced the physisorption of ARPs in sediments through stimulating the intraparticle diffusion of ARPs induced by electrostatic force. Besides, the adsorption amounts of ARPs onto the PS-NPs decreased with the increasing pH and dissolve organic matter due to the enhanced electrostatic repulsion and competitive adsorption. The ion strength played catalytic roles by increasing the electrostatic attraction and adsorption sites of ARPs on PS-NPs. The adsorbed ARPs in sediments were closely related with the ARGs in extra/intracellular DNA of biofilms, influencing the distribution and proliferation of ARGs largely. The findings indicate that ARG-associated pollution might be enhanced by the solid-liquid interface adsorption induced by NPs, which was controlled by pH, ion strength and dissolve organic matter. This study provides supplementary insights into the roles of NPs as carriers of ARP in sediments, and advances our understanding on the risks of NP-ARG co-occurring contamination in aquatic ecosystems.

Parallel engineering of environmental bacteria and performance over years under jungle-simulated conditions

Engineered bacteria could perform many functions in the environment, for example, to remediate pollutants, deliver nutrients to crops or act as in-field biosensors. Model organisms can be unreliable in the field, but selecting an isolate from the thousands that naturally live there and genetically manipulating them to carry the desired function is a slow and uninformed process. Here, we demonstrate the parallel engineering of isolates from environmental samples by using the broad-host-range XPORT conjugation system (Bacillus subtilis mini-ICEBs1) to transfer a genetic payload to many isolates in parallel. Bacillus and Lysinibacillus species were obtained from seven soil and water samples from different locations in Israel. XPORT successfully transferred a genetic function (reporter expression) into 25 of these isolates. They were then screened to identify the best-performing chassis based on the expression level, doubling time, functional stability in soil, and environmentally-relevant traits of its closest annotated reference species, such as the ability to sporulate and temperature tolerance. From this library, we selected Bacillus frigoritolerans A3E1, re-introduced it to soil, and measured function and genetic stability in a contained environment that replicates jungle conditions. After 21 months of storage, the engineered bacteria were viable, could perform their function, and did not accumulate disruptive mutations.

Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects

Global food production, food supply chains and food security are increasingly stressed by human population growth and loss of arable land, becoming more vulnerable to anthropogenic and environmental perturbations. Numerous mutualistic and antagonistic species are interconnected with the cultivation of crops and livestock and these can be challenging to identify on the large scales of food production systems. Accurate identifications to capture this diversity and rapid scalable monitoring are necessary to identify emerging threats (i.e. pests and pathogens), inform on ecosystem health (i.e. soil and pollinator diversity), and provide evidence for new management practices (i.e. fertiliser and pesticide applications). Increasingly, environmental DNA (eDNA) is providing rapid and accurate classifications for specific organisms and entire species assemblages in substrates ranging from soil to air. Here, we aim to discuss how eDNA is being used for monitoring of agricultural ecosystems, what current limitations exist, and how these could be managed to expand applications into the future. In a systematic review we identify that eDNA-based monitoring in food production systems accounts for only 4 % of all eDNA studies. We found that the majority of these eDNA studies target soil and plant substrates (60 %), predominantly to identify microbes and insects (60 %) and are biased towards Europe (42 %). While eDNA-based monitoring studies are uncommon in many of the world's food production systems, the trend is most pronounced in emerging economies often where food security is most at risk. We suggest that the biggest limitations to eDNA for agriculture are false negatives resulting from DNA degradation and assay biases, as well as incomplete databases and the interpretation of abundance data. These require in silico, in vitro, and in vivo approaches to carefully design, test and apply eDNA monitoring for reliable and accurate taxonomic identifications. We explore future opportunities for eDNA research which could further develop this useful tool for food production system monitoring in both emerging and developed economies, hopefully improving monitoring, and ultimately food security.

The Origin, Function, Distribution, Quantification, and Research Advances of Extracellular DNA

In nature, DNA is ubiquitous, existing not only inside but also outside of the cells of organisms. Intracellular DNA (iDNA) plays an essential role in different stages of biological growth, and it is defined as the carrier of genetic information. In addition, extracellular DNA (eDNA) is not enclosed in living cells, accounting for a large proportion of total DNA in the environment. Both the lysis-dependent and lysis-independent pathways are involved in eDNA release, and the released DNA has diverse environmental functions. This review provides an insight into the origin as well as the multiple ecological functions of eDNA. Furthermore, the main research advancements of eDNA in the various ecological environments and the various model microorganisms are summarized. Furthermore, the major methods for eDNA extraction and quantification are evaluated.

A Carotenoid- and Nuclease-Producing Bacterium Can Mitigate Enterococcus faecalis Transformation by Antibiotic Resistance Genes

Dissemination of antibiotic resistance genes (ARGs) through natural transformation is facilitated by factors that stabilize extracellular DNA (eDNA) and that induce reactive oxygen species (ROS) that permeabilize receptor cells and upregulate transformation competence genes. In this study, we demonstrate that Deinococcus radiodurans can mitigate this ARG dissemination pathway by removing both eDNA and ROS that make recipient cells more vulnerable to transformation. We used plasmid RP4 as source of extracellular ARGs (tetA, aphA, and blaTEM-2) and the opportunistic pathogen Enterococcus faecalis as receptor. The presence of D. radiodurans significantly reduced the transformation frequency from 2.5 ± 0.7 × 10^-6 to 7.4 ± 1.4 × 10^-7 (p < 0.05). Based on quantification of intracellular ROS accumulation and superoxide dismutase (SOD) activity, and quantitative polymerase chain reaction (qPCR) and transcriptomic analyses, we propose two mechanisms by which D. radiodurans mitigates E. faecalis transformation by ARGs: (a) residual antibiotics induce D. radiodurans to synthesize liposoluble carotenoids that scavenge ROS and thus mitigate the susceptibility of E. faecalis for eDNA uptake, and (b) eDNA induces D. radiodurans to synthesize extracellular nucleases that degrade eARGs. This mechanistic insight informs biological strategies (including bioaugmentation) to curtail the spread of ARGs through transformation.

Why eDNA fractions need consideration in biomonitoring

The analysis of environmental DNA (eDNA) is revolutionizing the monitoring of biodiversity as it allows to assess organismic diversity at large scale and unprecedented taxonomic detail. However, eDNA consists of an extracellular and intracellular fraction, each characterized by particular properties that determine the retrievable information on when and where organisms live or have been living. Here, we review the fractions of eDNA, describe how to obtain them from environmental samples and present a four-scenario concept that aims at enhancing spatial and temporal resolution of eDNA-based monitoring. Importantly, we highlight how the appropriate choice of eDNA fractions precludes misinterpretation of eDNA-based biodiversity data. Finally, future avenues of research towards eDNA fraction-specific analyses are outlined to unravel the full potential of eDNA-based studies targeting micro- and macro-organisms.

Intra-/extra-cellular antibiotic resistance responses to sewage sludge composting and salinization of long-term compost applied soils

Municipal sewage sludge, a reservoir of antibiotic resistance genes (ARGs), is usually composted as fertilizer for agricultural application especially in arid and semi-arid areas. The evolution patterns of intracellular ARGs (iARGs) and extracellular ARGs (eARGs) during composting and their responses to soil salinization after long-term compost application kept unclear previously, which were systematically studied in the current study. The variation and dissemination risk of eARGs and iARGs with the salinization of farmland soils was also evaluated. Extra/intra-cellular ARGs relative abundance varied drastically through composting process. Generally, the relative abundance of the cell-free eARGs (f-eARGs) and the cell-adsorbed eARGs (a-eARGs) were 4.62 and 3.54 folds (median) higher than that of iARGs, respectively, during the entire composting process, which held true even before the sludge composting (false discovery rate, FDR p < 0.05). There was no significant difference in relative abundance between f-eARGs and a-eARGs. The relative abundance of eARGs gradually decreased with composting time but was relatively higher than iARGs. It was worth noting that iARGs rebounded in the maturation phase. However, an over ten-year application of the eARG-rich compost led to much more severe contamination of iARGs than eARGs in soil. Soil salinization caused remarkable rise of eARGs by 943.34-fold (FDR p < 0.05). The variation of ARGs during composting and soil salinization was closely related to the change of microbial community structure. In compost, the bacterial communities mainly interacting with ARGs were the Firmicutes (54 unique and 35 shared core genera); and the bacterial communities playing major roles in ARGs during soil salinization were Proteobacteria (116 unique and 53 shared core genera) and Actinobacteria (52 unique and 27 shared core genera). These findings are important for assessing the transmission risk of ARGs in compost application to farmland in arid and semi-arid areas.

Effect of Calcium Ion Supplementation on Oral Microbial Composition and Biofilm Formation In Vitro

The oral cavity contains a variety of ecological niches with very different environmental conditions that shape biofilm structure and composition. The space between the periodontal tissue and the tooth surface supports a unique anaerobic microenvironment that is bathed in the nutrient-rich gingival crevicular fluid (GCF). During the development of periodontitis, this environment changes and clinical findings reported a sustained level of calcium ion concentration in the GCF collected from the periodontal pockets of periodontitis patients. Here, we report the effect of calcium ion supplementation on human oral microbial biofilm formation and community composition employing an established SHI medium-based in vitro model system. Saliva-derived human microbial biofilms cultured in calcium-supplemented SHI medium (SHICa) exhibited a significant dose-dependent increase in biomass and metabolic activity. The effect of SHICa medium on the microbial community composition was evaluated by 16S rRNA gene sequencing using saliva-derived microbial biofilms from healthy donors and periodontitis subjects. In this study, intracellular microbial genomic DNA (iDNA) and extracellular DNA (eDNA) were analyzed separately at the genus level. Calcium supplementation of SHI medium had a differential impact on iDNA and eDNA in the biofilms derived from healthy individuals compared to those from periodontitis subjects. In particular, the genus-level composition of the eDNA portion was distinct between the different biofilms. This study demonstrated the effect of calcium in a unique microenvironment on oral microbial complex supporting the dynamic transformation and biofilm formation.

Lack of robust evidence for a Wolbachia infection in Anopheles gambiae from Burkina Faso

The endosymbiont Wolbachia can have major effects on the reproductive fitness, and vectorial capacity of host insects and may provide new avenues to control mosquito-borne pathogens. Anopheles gambiae s.l is the major vector of malaria in Africa but the use of Wolbachia in this species has been limited by challenges in establishing stable transinfected lines and uncertainty around native infections. High frequencies of infection of Wolbachia have been previously reported in An. gambiae collected from the Valle du Kou region of Burkina Faso in 2011 and 2014. Here, we re-evaluated the occurrence of Wolbachia in natural samples, collected from Valle du Kou over a 12-year time span, and in addition, expanded sampling to other sites in Burkina Faso. Our results showed that, in contrast to earlier reports, Wolbachia is present at an extremely low prevalence in natural population of An. gambiae. From 5341 samples analysed, only 29 were positive for Wolbachia by nested PCR representing 0.54% of prevalence. No positive samples were found with regular PCR. Phylogenetic analysis of 16S rRNA gene amplicons clustered across supergroup B, with some having similarity to sequences previously found in Anopheles from Burkina Faso. However, we cannot discount the possibility that the amplicon positive samples we detected were due to environmental contamination or were false positives. Regardless, the lack of a prominent native infection in An. gambiae s.l. is encouraging for applications utilizing Wolbachia transinfected mosquitoes for malaria control.

d. Maas P, Heederik D, Mevius D, Sørensen SJ, Schmitt H. Horizontal Gene Transfer of an IncP1 Plasmid to Soil Bacterial Community Introduced by Escherichia coli through Manure Amendment in Soil Microcosms

The quantification and identification of new plasmid-acquiring bacteria in representative mating conditions is critical to characterize the risk of horizontal gene transfer in the environment. This study aimed to quantify conjugation events resulting from manure application to soils and identify the transconjugants resulting from these events. Conjugation was quantified at multiple time points by plating and flow cytometry, and the transconjugants were recovered by fluorescence-activated cell sorting and identified by 16S rRNA sequencing. Overall, transconjugants were only observed within the first 4 days after manure application and at values close to the detection limits of this experimental system (1.00-2.49 log CFU/g of manured soil, ranging between 10^-5 and 10^-4 transconjugants-to-donor ratios). In the pool of recovered transconjugants, we found amplicon sequence variants (ASVs) of genera whose origin was traced to soils (Bacillus and Nocardioides) and manure (Comamonas and Rahnella). This work showed that gene transfer from fecal to soil bacteria occurred despite the less-than-optimal conditions faced by manure bacteria when transferred to soils, but these events were rare, mainly happened shortly after manure application, and the plasmid did not colonize the soil community. This study provides important information to determine the risks of AMR spread via manure application.