Microbial regulation of natural antibiotic resistance: Understanding the protist-bacteria interactions for evolution of soil resistome

Characterization of the natural bacterial microbiota of pathogenic free-living amoebae (Acanthamoeba spp. and Naegleria fowleri) isolated from rivers and tap water in Guadeloupe

Free-living amoebae (FLA) are ubiquitous protists found in water, feeding mainly on bacteria. While most FLA are harmless, Acanthamoeba spp. and Naegleria fowleri can cause keratitis and/or meningitis. FLA can host amoeba-resistant bacteria (ARB), but their natural bacterial microbiota is largely unknown. This study aimed to identify the natural bacterial microbiota of Naegleria fowleri, Acanthamoeba castellanii, Acanthamoeba lenticulata, and Acanthamoeba sp. T17, isolated from untreated (rivers) and treated (tap) waters in Guadeloupe. The whole bacterial microbiota of the water source and the FLA grown with E. coli and under axenic culture conditions, during successive passages, were characterized using 16S rRNA gene metabarcoding. The culturable subset of ARB was identified by mass spectrometry (MALDI-TOF MS) followed by conventional 16S PCR, and bacterial antibiotic resistance was analyzed using the disk diffusion method. Transmission electron microscopy was used to locate ARB within the amoebae. The metabarcoding analyses identified Salmonella, Enterobacter and Klebsiella genera as the most abundant bacteria in untreated and treated waters. However, the most frequently detected amoeba-resistant bacteria (ARB) were from the Bosea, Escherichia-Shigella, Microbacterium, and Pseudomonas genera. Our findings revealed, for the first time, the natural occurrence of several bacteria within N. fowleri, including Pseudomonas spp. and Escherichia coli. Additionally, we detected Legionella in A. castellanii and Bordetella in A. lenticulata. The four pathogenic FLA showed both temporary and permanent associations with various bacterial genera, depending on the number of passages and culture conditions. Pseudomonas species isolated from distinct FLA exhibited resistance to different antibiotics. ARB were detected within the cytoplasm of trophozoites. The presence of pathogenic FLA and ARB in untreated and treated water in Guadeloupe's drinking systems pose health risks. Our results highlight the need for regular monitoring to ensure water safety and understanding amoebae-bacteria interactions for better management. The natural presence of ARB in pathogenic FLA also questions the host immune response during amoeba infection.

Unveiling the critical role of overlooked consumer protist-bacteria interactions in antibiotic resistance gene dissemination in urban sewage systems

Antibiotic resistance genes (ARGs) are emerging contaminants of significant concern due to their role in facilitating the spread of antibiotic resistance, especially high-risk ARGs, which are characterized by high human accessibility, gene mobility, pathogenicity, and clinical availability. Studies have shown that cross-domain interactions, such as those between consumer protists (consumers) and bacteria, can influence bacterial diversity, distribution, and function through top-down control. The consumers-bacteria interactions may also affect the occurrence and distribution of ARGs, yet this has been scarcely explored in field investigations. We conducted a city-scale investigation of ARGs, protists, and bacterial communities across each unit of the urban sewage system (USS), including 49 sewage pumping stations (SW), as well as influent (IF), activated sludge (AS), and effluent (EF) from seven wastewater treatment plants. Interestingly, consumers-bacteria interactions, as indicated by indices of bipartite relevance networks (i.e., connectedness and cohesion), increased from SW and IF to AS and EF. Structural equation modelling (SEM) revealed that consumers-bacteria interactions had a greater influence on the abundance of total ARGs and high-risk ARGs than seasonal or environmental factors. Notably, the total effects of consumers-bacteria interactions in SEM were significant (P < 0.05) and comparable in both IF and EF, even with the decrease in ARG abundance from IF to EF. This suggests a potential risk of ARG spread to the environment, facilitated by consumer protists in the EF. Additionally, the relevance network also demonstrated an increasing trend in the relationships between consumer protists and potential hosts of high-risk ARGs from raw sewage (SW and IF) to AS and EF. Overall, this study emphasizes the importance of integrating multitrophic microbial interactions to better understand and mitigate the dissemination of ARGs in sewage systems.

Acquired Bacterial Resistance to Antibiotics and Resistance Genes: From Past to Future

The discovery, commercialization, and regular administration of antimicrobial agents have revolutionized the therapeutic paradigm, making it possible to treat previously untreatable and fatal infections. However, the excessive use of antibiotics has led to develop resistance soon after their use in clinical practice, to the point of becoming a global emergency. The mechanisms of bacterial resistance to antibiotics are manifold, including mechanisms of destruction or inactivation, target site modification, or active efflux, and represent the main examples of evolutionary adaptation for the survival of bacterial species. The acquirement of new resistance mechanisms is a consequence of the great genetic plasticity of bacteria, which triggers specific responses that result in mutational adaptation, acquisition of genetic material, or alteration of gene expression, virtually producing resistance to all currently available antibiotics. Understanding resistance processes is critical to the development of new antimicrobial agents to counteract drug-resistant microorganisms. In this review, both the mechanisms of action of antibiotic resistance (AMR) and the antibiotic resistance genes (ARGs) mainly found in clinical and environmental bacteria will be reviewed. Furthermore, the evolutionary background of multidrug-resistant bacteria will be examined, and some promising elements to control or reduce the emergence and spread of AMR will be proposed.

Protozoa-enhanced conjugation frequency alters the dissemination of soil antibiotic resistance

Protozoa, as primary predators of soil bacteria, represent an overlooked natural driver in the dissemination of antibiotic resistance genes (ARGs). However, the effects of protozoan predation on ARGs dissemination at the community level, along with the underlying mechanisms, remain unclear. Here we used fluorescence-activated cell sorting, qPCR, combined with metagenomics and reverse transcription quantitative PCR, to unveil how protozoa (Colpoda steinii and Acanthamoeba castellanii) influence the plasmid-mediated transfer of ARGs to soil microbial communities. Protozoan predation reduced the absolute abundance of plasmids but promoted the expression of conjugation-associated genes, leading to a 5-fold and 4.5-fold increase in conjugation frequency in the presence of C. steinii and A. castellanii, respectively. Excessive oxidative stress, increased membrane permeability, and the provoked SOS response closely associated with the increased conjugative transfer. Protozoan predation also altered the plasmid host range and selected for specific transconjugant taxa along with ARGs and virulence factors carried by transconjugant communities. This study underscores the role of protozoa in the plasmid-mediated conjugative transfer of ARGs, providing new insights into microbial mechanisms that drive the dissemination of environmental antibiotic resistance.

Urbanization enhances consumer protist-driven ARGs dissemination in riverine ecosystems

Despite the emergence of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARBs), how biological inter-trophic interactions, modulated by watershed urbanization, shape the resistome remains unexplored. We collected water samples from the highly urbanized (western: 65 % built land, sewage-affected) and lesser-urbanized (northern: 25 % built land, drinking water source) downstream tributaries of the Jiulong River in southeast China over dry and wet seasons. We utilized metagenomic and amplicon (16S and 18S rDNA) sequencing to investigate the relationships among microeukaryotic algae, consumer protists, bacterial communities, and the resistome. Metagenomic results showed that ARG-MGE-carrying contigs (mobile ARGs), rather than ARG-carrying contigs (non-mobile ARGs), exhibited more pronounced discrepancies between tributaries. A higher total abundance of ARGs and a greater number of co-shared ARGs between pathogen and non-pathogen bacteria were observed in the more urbanized western tributary. Structural equation modeling revealed that consumer protist-bacteria and algae-bacteria cohesions predominantly influenced the resistome in the western and northern tributaries, respectively. Additionally, consumer protists had more significant associations (511 out of 634) with bacteria carrying mobile ARGs in western tributary, while algae had more significant associations (73 out of 105) in northern tributary. These results highlight the distinct inter-trophic driving factors of the resistome modulated by watershed urbanization.

Soil Amoebae Are Unexpected Hotspots of Environmental Antibiotics and Antibiotic Resistance Genes

Antibiotic resistance poses a significant threat to human health. While most studies focus on bacteria, interactions between antibiotics and other crucial microbial groups like protists remain uncertain. This study investigates how protists interact with antibiotics and examines how these interactions impact the fate of resistance genes. It reveals that amoebae exhibit high resistance to eight high-risk environmental antibiotics, accumulating significant quantities within their cells. Wild amoeboid strains from distant locations carry substantial antibiotic resistance genes (ARGs) and metal resistance genes (MRGs), with significant heterogeneity within a single species. Amoeboid symbionts and pathogens predominantly carry these genes. Paraburkholderia symbionts have reduced genomes and fewer resistance genes compared to free-living strains, while amoeba-endogenous Stenotrophomonas maltophilia does not exhibit a significantly reduced genome size. This suggests that the amoeboid hosts serve as a temporary medium facilitating its transmission. In summary, the study unveils that soil amoebae represent unexpected hotspots for antibiotics and resistance genes. Future research should assess the effects of antibiotics on often-overlooked protists and explore their role in spreading ARGs and MRGs in ecosystems. Incorporating protists into broader antibiotic resistance research is recommended, highlighting their significance within a One Health perspective.

Sources, interactions, influencing factors and ecological risks of microplastics and antibiotic resistance genes in soil: A review

Microplastics (MPs) and antibiotic resistance genes (ARGs) are gaining increasing attention as they pose a threat to the ecological environment and human health as emerging contaminants. MPs has been proved to be a hot spot in ARGs, and although it has been extensively studied in water environment, the results of bibliometrics statistical analysis in this paper showed that relevant studies in soil ecological environment are currently in the initial stage. In view of this, the paper provides a systematic review of the sources, interactions, influencing factors, and ecological risks associated with MPs and ARGs in soil environments. Additionally, the mechanism and influencing factors of plastisphere formation and resistance are elaborated in detail. The MPs properties, soil physicochemical properties, soil environmental factors and agricultural activities are the primarily factors affecting the interaction between MPs and ARGs in soil. Challenges and development directions of related research in the future are also prospected. It is hoped that the review could assist in a deeper comprehension and exploration of the interaction mechanism between MPs and ARGs in soil as well as the function of MPs in the transmission process of ARGs among diverse environmental media and organisms, and provide theory basis and reference for the MPs and ARGs pollution control and remediation in soil.

Combined use of digestate and inorganic fertilizer alleviates the burden of class 1 integrons in perennial ryegrass rhizosphere without compromising aerial biomass production

Antimicrobial resistance (AMR) is one of the main global health challenges. Anaerobic digestion (AD) can significantly reduce the burden of antibiotic resistance genes (ARGs) in animal manures. However, the reduction is often incomplete. The agronomic use of digestates requires assessments of their effects on soil ARGs. The objective of this study was to assess the effect of digestate on the abundance of ARGs and mobile genetic elements (MGEs) in the rhizosphere of ryegrass (Lolium perenne L.) and to determine whether half-dose replacement of digestate with urea (combined fertilizer) can be implemented as a safer approach while maintaining a similar biomass production. A greenhouse assay was conducted during 190 days under a completely randomized design with two experimental factors: fertilizer type (unfertilized control and fertilized treatments with equal N dose: digestate, urea and combined fertilizer) and sampling date (16 and 148 days after the last application). The results indicated that the digestate significantly increased the abundance of clinical class 1 integrons (intI1 gene) relative to the unfertilized control at both sampling dates (P < 0.05), while the combined fertilizer only increased them at the first sampling. Sixteen days after completing the fertilization scheme only the combined fertilizer and urea significantly increased the biomass production relative to the control (P < 0.05). Additionally, by the end of the assay, the combined fertilizer showed significantly lower levels of the macrolide-resistance gene ermB than digestate and a cumulative biomass similar to urea or digestate. Overall, the combined fertilizer can alleviate the burden of integrons and ermB while simultaneously improving biomass production.

Functional Genomics of a Collection of Gammaproteobacteria Isolated from Antarctica

Antarctica, one of the most extreme environments on Earth, hosts diverse microbial communities. These microbes have evolved and adapted to survive in these hostile conditions, but knowledge on the molecular mechanisms underlying this process remains limited. The Italian Collection of Antarctic Bacteria (Collezione Italiana Batteri Antartici (CIBAN)), managed by the University of Messina, represents a valuable repository of cold-adapted bacterial strains isolated from various Antarctic environments. In this study, we sequenced and analyzed the genomes of 58 marine Gammaproteobacteria strains from the CIBAN collection, which were isolated during Italian expeditions from 1990 to 2005. By employing genome-scale metrics, we taxonomically characterized these strains and assigned them to four distinct genera: Pseudomonas, Pseudoalteromonas, Shewanella, and Psychrobacter. Genome annotation revealed a previously untapped functional potential, including secondary metabolite biosynthetic gene clusters and antibiotic resistance genes. Phylogenomic analyses provided evolutionary insights, while assessment of cold-shock protein presence shed light on adaptation mechanisms. Our study emphasizes the significance of CIBAN as a resource for understanding Antarctic microbial life and its biotechnological potential. The genomic data unveil new horizons for insight into bacterial existence in Antarctica.

Interaction patterns and keystone taxa of bacterial and eukaryotic communities during sulfamethoxazole mineralization in lake sediment

Sulfamethoxazole (SMX) is a common antibiotic pollutant in aquatic environments, which is highly persistent under various conditions and significantly contributes to the spread of antibiotic resistance. Biodegradation is the major pathway to eliminate antibiotics in the natural environment. The roles of bacteria and eukaryotes in the biodegradation of antibiotics have received considerable attention; however, their successions and co-occurrence patterns during the biodegradation of antibiotics remain unexplored. In this study, 13C-labled SMX was amended to sediment samples from Zhushan Bay (ZS), West Shore (WS), and Gonghu Bay (GH) in Taihu Lake to explore the interplay of bacterial and eukaryotic communities during a 30-day incubation period. The cumulative SMX mineralization on day 30 ranged from 5.2 % to 19.3 %, which was the highest in WS and the lowest in GH. The bacterial community showed larger within-group interactions than between-group interactions, and the positive interactions decreased during incubation. However, the eukaryotic community displayed larger between-group interactions than within-group interactions, and the positive interactions increased during incubation. The proportion of negative interactions between bacteria and eukaryotes increased during incubation. Fifty genera (including 46 bacterial and 4 eukaryotic genera) were identified as the keystone taxa due to their dominance in the co-occurrence network and tolerance to SMX. The cumulative relative abundance of these keystone taxa significantly increased during incubation and was consistent with the SMX mineralization rate. These taxa closely cooperated and played vital roles in co-occurrence networks and microbial community interactions, signifying their crucial role in SMX mineralization. These findings broadened our understanding of the complex interactions of microorganisms under SMX exposure and their potential functions during SMX mineralization, providing valuable insights for in situ bioremediation.

Sustainable strategies: Nature-based solutions to tackle antibiotic resistance gene proliferation and improve agricultural productivity and soil quality

The issue of antibiotic resistance is now recognized by the World Health Organisation (WHO) as one of the major problems in human health. Although its effects are evident in the healthcare settings, the root cause should be traced back to the One Health link, extending from animals to the environment. In fact, the use of organic fertilizers in agroecosystems represents one, if not the primary, cause of the introduction of antibiotics and antibiotic-resistant bacteria into the soil. Since the concentrations of antibiotics introduced into the soil are residual, the agroecosystem has become a perfect environment for the selection and proliferation of antibiotic resistance genes (ARGs). The continuous influx of these emerging contaminants (i.e., antibiotics) into the agroecosystem results in the selection and accumulation of ARGs in soil bacteria, occasionally giving rise to multi-resistant bacteria. These bacteria may harbour ARGs related to various antibiotics on their plasmids. In this context, these bacteria can potentially enter the human sphere when individuals consume food from contaminated agroecosystems, leading to the acquisition of multi-resistant bacteria. Once introduced into the nosocomial environment, these bacteria pose a significant threat to human health. In this review, we analyse how the use of digestate as an organic fertilizer can mitigate the spread of ARGs in agroecosystems. Furthermore, we highlight how, according to European guidelines, digestate can be considered a Nature-Based Solution (NBS). This NBS not only has the ability to mitigate the spread of ARGs in agroecosystems but also offers the opportunity to further improve Microbial-Based Solutions (MBS), with the aim of enhancing soil quality and productivity.

Effect of composting and storage on the microbiome and resistome of cattle manure from a commercial dairy farm in Poland

Manure from food-producing animals, rich in antibiotic-resistant bacteria and antibiotic resistance genes (ARGs), poses significant environmental and healthcare risks. Despite global efforts, most manure is not adequately processed before use on fields, escalating the spread of antimicrobial resistance. This study examined how different cattle manure treatments, including composting and storage, affect its microbiome and resistome. The changes occurring in the microbiome and resistome of the treated manure samples were compared with those of raw samples by high-throughput qPCR for ARGs tracking and sequencing of the V3-V4 variable region of the 16S rRNA gene to indicate bacterial community composition. We identified 203 ARGs and mobile genetic elements (MGEs) in raw manure. Post-treatment reduced these to 76 in composted and 51 in stored samples. Notably, beta-lactam, cross-resistance to macrolides, lincosamides and streptogramin B (MLSB), and vancomycin resistance genes decreased, while genes linked to MGEs, integrons, and sulfonamide resistance increased after composting. Overall, total resistance gene abundance significantly dropped with both treatments. During composting, the relative abundance of genes was lower midway than at the end. Moreover, higher biodiversity was observed in samples after composting than storage. Our current research shows that both composting and storage effectively reduce ARGs in cattle manure. However, it is challenging to determine which method is superior, as different groups of resistance genes react differently to each treatment, even though a notable overall reduction in ARGs is observed.

Carbon starvation raises capacities in bacterial antibiotic resistance and viral auxiliary carbon metabolism in soils

Organic carbon availability in soil is crucial for shaping microbial communities, yet, uncertainties persist concerning microbial adaptations to carbon levels and the ensuing ecological and evolutionary consequences. We investigated organic carbon metabolism, antibiotic resistance, and virus-host interactions in soils subjected to 40 y of chemical and organic fertilization that led to contrasting carbon availability: carbon-poor and carbon-rich soils, respectively. Carbon-poor soils drove the enrichment of putative genes involved in organic matter decomposition and exhibited specialization in utilizing complex organic compounds, reflecting scramble competition. This specialization confers a competitive advantage of microbial communities in carbon-poor soils but reduces their buffering capacity in terms of organic carbon metabolisms, making them more vulnerable to environmental fluctuations. Additionally, in carbon-poor soils, viral auxiliary metabolic genes linked to organic carbon metabolism increased host competitiveness and environmental adaptability through a strategy akin to "piggyback the winner." Furthermore, putative antibiotic resistance genes, particularly in low-abundance drug categories, were enriched in carbon-poor soils as an evolutionary consequence of chemical warfare (i.e., interference competition). This raises concerns about the potential dissemination of antibiotic resistance from conventional agriculture that relies on chemical-only fertilization. Consequently, carbon starvation resulting from long-term chemical-only fertilization increases microbial adaptations to competition, underscoring the importance of implementing sustainable agricultural practices to mitigate the emergence and spread of antimicrobial resistance and to increase soil carbon storage.

Enterobacter cloacae from urinary tract infections: frequency, protein analysis, and antimicrobial resistance

The genus Enterobacter belongs to the ESKAPE group, which includes Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. This group is characterized by the development of resistance to various antibiotics. In recent years, Enterobacter cloacae (E. cloacae) has emerged as a clinically important pathogen responsible for a wide range of healthcare-associated illnesses. Identifying Enterobacter species can be challenging due to their similar phenotypic characteristics. The emergence of multidrug-resistant E. cloacae is also a significant problem in healthcare settings. Therefore, our study aimed to identify and differentiate E. cloacae using Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) as a fast and precise proteomic analytical technique. We also tested hospital-acquired E. cloacae isolates that produce Extended-spectrum beta-lactamases (ESBL) against commonly used antibiotics for treating urinary tract infections (UTIs). We used a total of 189 E. cloacae isolates from 2300 urine samples of patients with UTIs in our investigation. We employed culturing techniques, as well as the BD Phoenix™ automated identification system (Becton, Dickinson) and Analytical Profile Index (API) system for the biochemical identification of E. cloacae isolates. We used the MALDI Biotyper (MBT) device for peptide mass fingerprinting analysis of all isolates. We utilized the single peak intensities and Principal Component Analysis (PCA) created by MBT Compass software to discriminate and cluster the E. cloacae isolates. Additionally, we evaluated the sensitivity and resistance of ESBL-E. cloacae isolates using the Kirby Bauer method. Out of the 189 E. cloacae isolates, the BD Phoenix system correctly identified 180 (95.24%) isolates, while the API system correctly identified 165 (87.30%) isolates. However, the MBT accurately identified 185 (98.95%) isolates with a score of 2.00 or higher. PCA positively discriminated the identified E. cloacae isolates into one group, and prominent peaks were noticed between 4230 mass-to-charge ratio (m/z) and 8500 m/z. The ESBL-E. cloacae isolates exhibited a higher degree of resistance to ampicillin, amoxicillin-clavulanate, cephalothin, cefuroxime, and cefoxitin. Several isolates were susceptible to carbapenems (meropenem, imipenem, and ertapenem); however, potential future resistance against carbapenems should be taken into consideration. In conclusion, MALDI-TOF MS is a powerful and precise technology that can be routinely used to recognize and differentiate various pathogens in clinical samples. Additionally, the growing antimicrobial resistance of this bacterium may pose a significant risk to human health.

Different long-term fertilization regimes affect soil protists and their top-down control on bacterial and fungal communities in Mollisols

Soil protists represent a vastly diverse component of soil microbial communities and significantly contribute to biogeochemical cycling. However, how different fertilization regimes impact the protistan communities and their top-down control on bacteria and fungi remain largely unknown. Here, using high-throughput sequencing, we investigated the differences in protist communities and their relationships with bacterial and fungal communities in Mollisols of Northeast China that were subjected to chemical and organic fertilization over 30 years. The results showed that manure addition rather than chemical fertilization significantly increased protistan alpha diversity and changed protistan community structure. Manure amendments markedly increased the relative abundances of protistan consumers (such as Cercozoa) and reduced the proportion of phototrophic protists (such as Chlorophyta). Soil pH was the most influential factor driving microbial communities, and protists were less sensitive to environmental disturbances than bacteria and fungi. Protistan communities exhibited more stronger relationships with bacterial communities than fungal communities, and Chlorococcum was the most important contributor in regulation of microbial taxa and functional genes. Furthermore, manure addition slightly simplified the microbial network, and chemical plus manure fertilization improved network stability with the highest robustness. Manure addition specifically mitigated the negative interactions between protists and bacteria while reinforced the positive interactions between protists and fungi. This study advanced our knowledge about the roles of protistan groups in regulating microbial communities and ecosystem functions associated with chemical and organic fertilization.

Host genetic variation and specialized metabolites from wheat leaves enriches for phyllosphere Pseudomonas spp. with enriched antibiotic resistomes

Antibiotic resistance in plant-associated microbiomes poses significant risks for agricultural ecosystems and human health. Although accumulating evidence suggests a role for plant genotypes in shaping their microbiome, almost nothing is known about how the changes of plant genetic information affect the co-evolved plant microbiome carrying antibiotic resistance genes (ARGs). Here, we selected 16 wheat cultivars and experimentally explored the impact of host genetic variation on phyllosphere microbiome, ARGs, and metabolites. Our results demonstrated that host genetic variation significantly influenced the phyllosphere resistomes. Wheat genotypes exhibiting high phyllosphere ARGs were linked to elevated Pseudomonas populations, along with increased abundances of Pseudomonas aeruginosa biofilm formation genes. Further analysis of 350 Pseudomonas spp. genomes from diverse habitats at a global scale revealed that nearly all strains possess multiple ARGs, virulence factor genes (VFGs), and mobile genetic elements (MGEs) on their genomes, albeit with lower nucleotide diversity compared to other species. These findings suggested that the proliferation of Pseudomonas spp. in the phyllosphere significantly contributed to antibiotic resistance. We further observed direct links between the upregulated leaf metabolite DIMBOA-Glc, Pseudomonas spp., and enrichment of phyllosphere ARGs, which were corroborated by microcosm experiments demonstrating that DIMBOA-Glc significantly enhanced the relative abundance of Pseudomonas spp. Overall, alterations in leaf metabolites resulting from genetic variation throughout plant evolution may drive the development of highly specialized microbial communities capable of enriching phyllosphere ARGs. This study enhances our understanding of how plants actively shape microbial communities and clarifies the impact of host genetic variation on the plant resistomes.

Protist predation promotes antimicrobial resistance spread through antagonistic microbiome interactions

Antibiotic resistance has grown into a major public health threat. In this study, we reveal predation by protists as an overlooked driver of antibiotic resistance dissemination in the soil microbiome. While previous studies have primarily focused on the distribution of antibiotic resistance genes, our work sheds light on the pivotal role of soil protists in shaping antibiotic resistance dynamics. Using a combination of metagenomics and controlled experiments in this study, we demonstrate that protists cause an increase in antibiotic resistance. We mechanistically link this increase to a fostering of antimicrobial activity in the microbiome. Protist predation gives a competitive edge to bacteria capable of producing antagonistic secondary metabolites, which secondary metabolites promote in turn antibiotic-resistant bacteria. This study provides insights into the complex interplay between protists and soil microbiomes in regulating antibiotic resistance dynamics. This study highlights the importance of top-down control on the spread of antibiotic resistance and directly connects it to cross-kingdom interactions within the microbiome. Managing protist communities may become an important tool to control outbreaks of antibiotic resistance in the environment.

Protist predation selects for the soil resistome

A key aspect of "One Health" is to comprehend how antibiotic resistomes evolve naturally. In this issue, Nguyen and colleagues pioneered an in situ investigation on the impact of protist predations on the soil microbial community and its antibiotic resistance genes (ARGs). They found that bacterivorous protists consistently increased the abundance of ARGs, such as tetracycline resistant genes. Indeed, antibiotic production is a common strategy for bacteria to evade protist predation. The rise of ARGs can be explained by the balance between antibiotic producers and resisters shaped by predatory selection. This work suggests that ARG enrichment due to biotic interactions may be less worrisome than previously thought. Unless, these ARGs are carried by or disseminated among pathogens. Therefore, it is essential to monitor the occurrence, dissemination and pathogenic hosts of ARGs, enhancing our capacity to combat antibiotic resistance.

Urban greenspaces shape soil protist communities in a location-specific manner

The impacts of urbanization on aboveground biodiversity are well studied, and its impact on soil microorganisms are also receiving increased attention. However, the impact of urbanization on the soil protists are hardly investigated. Here, we studied how urbanization and distinct urban greenspaces affect protist communities. We used amplicon sequencing of the18 S rRNA gene of samples from five types of urban greenspaces (parks, greenbelts, industrial areas, residential areas and hospital lawns), neighboring natural forests and agricultural ecosystems in Ningbo, China. We found that urban greenspaces harbored higher protist α-diversity than forests, while protist β-diversity increased from agricultural systems to urban greenspaces to forests. Among the studied driving factors, soil bacterial α- and β-diversity best predicted phagotrophic protist α- and β-diversity in urban greenspaces, while differences in α- and β-diversity of phototrophic protists were best explained by soil carbon-to-nitrogen ratio and fungal β-diversity, respectively. Abiotic factors i.e., total phosphorus and carbon-to-nitrogen ratio, best predicted the α- and β-diversity of protist parasites in urban greenspaces, respectively. The results revealed that the composition and drivers of protist communities vary between functional groups and urban ecosystems. Overall, our findings contribute to a better understanding of drivers of soil protist communities and indicate that soil protist communities and associated soil functions could be managed in predictable ways in urban greenspaces.

Protists regulate microbially mediated organic carbon turnover in soil aggregates

Soil protists, the major predator of bacteria and fungi, shape the taxonomic and functional structure of soil microbiome via trophic regulation. However, how trophic interactions between protists and their prey influence microbially mediated soil organic carbon turnover remains largely unknown. Here, we investigated the protistan communities and microbial trophic interactions across different aggregates-size fractions in agricultural soil with long-term fertilization regimes. Our results showed that aggregate sizes significantly influenced the protistan community and microbial hierarchical interactions. Bacterivores were the predominant protistan functional group and were more abundant in macroaggregates and silt + clay than in microaggregates, while omnivores showed an opposite distribution pattern. Furthermore, partial least square path modeling revealed positive impacts of omnivores on the C-decomposition genes and soil organic matter (SOM) contents, while bacterivores displayed negative impacts. Microbial trophic interactions were intensive in macroaggregates and silt + clay but were restricted in microaggregates, as indicated by the intensity of protistan-bacterial associations and network complexity and connectivity. Cercozoan taxa were consistently identified as the keystone species in SOM degradation-related ecological clusters in macroaggregates and silt + clay, indicating the critical roles of protists in SOM degradation by regulating bacterial and fungal taxa. Chemical fertilization had a positive effect on soil C sequestration through suppressing SOM degradation-related ecological clusters in macroaggregate and silt + clay. Conversely, the associations between the trophic interactions and SOM contents were decoupled in microaggregates, suggesting limited microbial contributions to SOM turnovers. Our study demonstrates the importance of protists-driven trophic interactions on soil C cycling in agricultural ecosystems.

Antibacterial Activities of Ag/Cellulose Nanocomposites Derived from Marine Environment Algae against Bacterial Tooth Decay

Dental caries is an infectious oral disease caused by the presence of different bacteria in biofilms. Multidrug resistance (MDR) is a major challenge of dental caries treatment. Swabs were taken from 65 patients with dental caries in Makkah, Saudi Arabia. Swabs were cultivated on mitis salivarius agar and de Man, Rogosa, and Sharpe (MRS) agar. VITEK 2 was used for the identification of isolated bacteria. Antibiotic susceptibility testing of the isolated bacteria was performed using commercial antibiotic disks. Ulva lactuca was used as a reducing agent and cellulose source to create nanocellulose and Ag/cellulose nanocomposites. Fourier-transform infrared spectroscopy (FTIR), transmission electron microscopy (TEM), scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), and X-ray diffraction spectroscopy (XRD) were used to characterize nanocellulose and Ag/cellulose nanocomposites. The results showed that most bacterial isolates were Streptococcus spp., followed by Staphylococcus spp. on mitis salivarius media. Lactobacillus spp. and Corynebacterium group f-1 were the bacterial isolates on de Man, Rogosa, and Sharpe (MRS) media. The antibiotic susceptibility test revealed resistance rates of 77%, 93%, 0, 83%, 79%, and 79% against penicillin G, Augmentin, metronidazole, ampicillin, ciprofloxacin, and cotrimoxazole, respectively. Ag/cellulose nanocomposites and Ag/cellulose nanocomposites with fluoride were the most effective antibacterial agents. The aim of this work was to assess the antibacterial activity of Ag/cellulose nanocomposites with and without fluoride against bacteria isolated from the oral cavities of patients with dental caries. This study demonstrated that Ag/cellulose nanocomposites have antibacterial properties against multidrug-resistant bacteria that cause dental caries.

Protistan predation selects for antibiotic resistance in soil bacterial communities

Understanding how antibiotic resistance emerges and evolves in natural habitats is critical for predicting and mitigating antibiotic resistance in the context of global change. Bacteria have evolved antibiotic production as a strategy to fight competitors, predators and other stressors, but how predation pressure of their most important consumers (i.e., protists) affects soil antibiotic resistance genes (ARGs) profiles is still poorly understood. To address this gap, we investigated responses of soil resistome to varying levels of protistan predation by inoculating low, medium and high concentrations of indigenous soil protist suspensions in soil microcosms. We found that an increase in protistan predation pressure was strongly associated with higher abundance and diversity of soil ARGs. High protist concentrations significantly enhanced the abundances of ARGs encoding multidrug (oprJ and ttgB genes) and tetracycline (tetV) efflux pump by 608%, 724% and 3052%, respectively. Additionally, we observed an increase in the abundance of numerous bacterial genera under high protistan pressure. Our findings provide empirical evidence that protistan predation significantly promotes antibiotic resistance in soil bacterial communities and advances our understanding of the biological driving forces behind the evolution and development of environmental antibiotic resistance.

Nanoparticle therapy for antibiotic-resistant bacteria: current methods and prospects

Emerging diseases due to antibiotic-resistant bacteria cause severe health concerns while increasing their negative effects on human health. The overuse or misuse of antimicrobial agents has contributed to the evolution of bacterial resistance to current medications. Bacteria can develop resistance by altering drugs, changing their target sites, forming biofilms and spending more time in the intracellular environment. Due to this, efforts are being made to create novel, alternative nanoantibiotics as a promising strategy to treat bacteria that cause disease and have developed resistance to a variety of drugs. Utilizing their biocidal properties, nanoparticles can be directed for medication delivery to particular tissues and employed as antibacterial agents against a range of illnesses. Targeted medication delivery-related toxicity problems may be solved with the aid of nanoencapsulation technology. This review paper generally provides a conceptual foundation for understanding the complexity of the problem of the development of antibiotic-resistant bacteria, particularly for brand-new synthetic antibiotics. This information will allow researchers to explore the use of nanoparticles in the treatment of multidrug-resistant bacteria.

Bacterial microbiota management in free-living amoebae (Heterolobosea lineage) isolated from water: The impact of amoebae identity, grazing conditions, and passage number

Free-living amoebae (FLA) are ubiquitous protozoa mainly found in aquatic environments. They are well-known reservoirs and vectors for the transmission of amoeba-resistant bacteria (ARB), most of which are pathogenic to humans. Yet, the natural bacterial microbiota associated with FLA remains largely unknown. Herein, we characterized the natural bacterial microbiota of different FLA species isolated from recreational waters in Guadeloupe. Monoxenic cultures of Naegleria australiensis, Naegleria sp. WTP3, Paravahlkampfia ustiana and Vahlkampfia sp. AK-2007 (Heterolobosea lineage) were cultivated under different grazing conditions, during successive passages. The whole bacterial microbiota of the waters and the amoebal cysts was characterized using 16S rRNA gene metabarcoding. The culturable subset of ARB was analyzed by mass spectrometry (MALDI-TOF MS), conventional 16S PCR, and disk diffusion method (to assess bacterial antibiotic resistance). Transmission electron microscopy was used to locate the ARB inside the amoebae. According to alpha and beta-diversity analyses, FLA bacterial microbiota were significantly different from the ones of their habitat. While Vogesella and Aquabacterium genera were detected in water, the most common ARB belonged to Pseudomonas, Bosea, and Escherichia/Shigella genera. The different FLA species showed both temporary and permanent associations with differentially bacterial taxa, suggesting host specificity. These associations depend on the number of passages and grazing conditions. Additionally, Naegleria, Vahlkampfia and Paravahlkampfia cysts were shown to naturally harbor viable bacteria of the Acinetobacter, Escherichia, Enterobacter, Pseudomonas and Microbacterium genera, all being pathogenic to humans. To our knowledge, this is the first time Paravahlkampfia and Vahlkampfia have been demonstrated as hosts of pathogenic ARB in water. Globally, the persistence of these ARB inside resistant cysts represents a potential health risk. To ensure the continued safety of recreational waters, it is crucial to (i) regularly control both the amoebae and their ARB and (ii) improve knowledge on amoebae-bacteria interactions to establish better water management protocols.

Pristine and Sulfidized Zinc Oxide Nanoparticles Promote the Release and Decomposition of Organic Carbon in the Legume Rhizosphere

The effects and mechanisms of zinc oxide nanoparticles (ZnO NPs) and their aging products, sulfidized (s-) ZnO NPs, on the carbon cycling in the legume rhizosphere are still unclear. We observed that, after 30 days of cultivation, in the rhizosphere soil of Medicago truncatula, under ZnO NP and s-ZnO NP treatments, the dissolved organic carbon (DOC) concentrations were significantly increased by 1.8- to 2.4-fold compared to Zn²⁺ treatments, although the soil organic matter (SOM) contents did not change significantly. Compared to Zn²⁺ additions, the additions of NPs significantly induced the production of root metabolites such as carboxylic acids and amino acids and also stimulated the growth of microbes involved in the degradations of plant-derived and recalcitrant SOM, such as bacteria genera RB41 and Bryobacter, and fungi genus Conocybe. The bacterial co-occurrence networks indicated that microbes associated with SOM formation and decomposition were significantly increased under NP treatments. The adsorption of NPs by roots, the generation of root metabolites (e.g., carboxylic acid and amino acid), and enrichment of key taxa (e.g., RB41 and Gaiella) were the major mechanisms by which ZnO NPs and s-ZnO NPs drove DOC release and SOM decomposition in the rhizosphere. These results provide new perspectives on the effect of ZnO NPs on agroecosystem functions in soil-plant systems.

Hydraulic characteristics in channel confluence affect the nitrogen dynamics through altering interactions among multi-trophic microbiota

Identifying the distribution of multi-trophic microbiota under the complicated hydrodynamic characteristics of channel confluences and evaluating the microbial contributions to biogeochemical processes are vital for river regulation and ecological function protection. However, relevant studies mainly focus on bacterial community distribution in confluence, neglecting the essential role of multi-trophic microbiota in the aquatic ecosystems and biogeochemical processes. To address this knowledge gap, this study investigated the distribution of multi-trophic microbiota and the underlying assembly process under the hydraulic characteristics in the confluence and described the direct and indirect effects of multi-trophic microbiota on the nitrogen dynamics. Results revealed that, in a river confluence, eukaryotic communities were governed by deterministic processes (52.4%) and bacterial communities were determined by stochastic processes (74.3%). The response of higher trophic levels to environmental factors was intensively higher than that of lower trophic microbiota, resulting in higher trophic microbiota were significantly different between regions with varied environmental conditions (P < 0.05). Flow velocity was the driving force controlling the assembly and composition of multi-trophic microbiota and interactions among multi-trophic levels, and further made a significant difference to nitrogen dynamics. In regions with lower flow velocity, interactions among multi-trophic levels were more complex. There were intense nitrate and nitrite reduction and anammox reactions via direct impacts of protozoan and metazoan and the top-down control (protozoan and metazoan prey on heterotrophic bacteria) among multi-trophic microbiota. Results and findings reveal the ecological effect on river nitrogen removal in a river confluence under complex hydraulic conditions and provide useful information for river management.

Exposure to benzalkonium chloride disinfectants promotes antibiotic resistance in sewage sludge microbiomes

Disinfectants are routinely used in human environments to control and prevent the transmission of microbial disease, and this is particularly true during the current COVID-19 crisis. However, it remains unclear whether the increased disinfectant loadings to wastewater treatment plants facilitate the dissemination of antibiotic resistance genes (ARGs) in sewage sludge microbiomes. Here, we investigated the impacts of benzalkonium chlorides (BACs), widely used disinfectants, on ARGs profiles and microbial community structures in sewage sludge by using high-throughput quantitative PCR and Illumina sequencing. A total of 147 unique ARGs and 39 mobile genetic elements (MGEs) were detected in all sewage sludge samples. Our results show that exposure to BACs disinfectants at environmentally relevant concentrations significantly promotes both the diversity and absolute abundance of ARGs in sludge microbiomes, indicating the co-selection of ARGs by BACs disinfectants. The enrichment of ARGs abundance varied from 2.15-fold to 3.63-fold compared to controls. In addition, BACs exposure significantly alters bacterial and protistan communities, resulting in dysbiosis of the sludge microbiota. The Mantel test and Procrustes analysis confirm that bacterial communities are significantly correlated with ARGs profiles under BACs treatments. The structural equation model explains 83.8 % of the total ARGs variation and further illustrates that the absolute abundance of MGEs exerts greater impacts on the variation of absolute abundance of ARGs than microbial communities under BACs exposure, suggesting BACs may promote antibiotic resistance by enhancing the horizontal gene transfer of ARGs across sludge microbiomes. Collectively, our results provide new insights into the proliferation of antibiotic resistance through disinfectant usage during the pandemic and highlight the necessity to minimize the environmental release of disinfectants into the non-target environment for combating antibiotic resistance.

Trophic interrelationships of bacteria are important for shaping soil protist communities

Protists occupy multiple trophic positions in soil food webs and significantly contribute to organic matter decomposition and biogeochemical cycling. Protists can ingest bacteria and fungi as main food sources while being subjected to predation of invertebrates, but our understanding of how bottom-up and top-down regulations structure protists in natural soil habitats is limited. Here, we disentangle the effects of trophic regulations to the diversity and structure of soil protists in natural settings across northern and eastern Australia. Bacterial and invertebrate diversity were identified as important drivers of the diversity of functional groups of protists. Moreover, the compositions of protistan taxonomic and functional groups were better predicted by bacteria and fungi, than by soil invertebrates. There were strong trophic interconnections between protists and bacteria in multiple organismic network analysis. Altogether, the study provided new evidence that, bottom-up control of bacteria played an important role in shaping the soil protist community structure, which can be derived from feeding preferences of protists on microbial prey, and their intimate relationships in soil functioning or environmental adaptation. Our findings advance our knowledge about the impacts of different trophic groups on key soil organismic communities, with implications for ecosystem functions and services.

Antimicrobial resistomes in food chain microbiomes

The safety and integrity of the global food system is in a constant state of flux with persistent chemical and microbial risks. While chemical risks are being managed systematically, microbial risks pose extra challenges. Antimicrobial resistant microorganism and persistence of related antibiotic resistance genes (ARGs) in the food chain adds an extra dimension to the management of microbial risks. Because the food chain microbiome is a key interface in the global health system, these microbes can affect health in many ways. In this review, we systematically summarize the distribution of ARGs in foods, describe the potential transmission pathway and transfer mechanism of ARGs from farm to fork, and discuss potential food safety problems and challenges. Modulating antimicrobial resistomes in the food chain facilitates a sustainable global food production system.

Temporal dynamics of soil bacterial network regulate soil resistomes

Soil bacteria are diverse and form complicated ecological networks through various microbial interactions, which play important roles in soil multi-functionality. However, the seasonal effects on the bacterial network, especially the relationship between bacterial network topological features and soil resistomes remains underexplored, which impedes our ability to unveil the mechanisms of the temporal-dynamics of antibiotic resistance genes (ARGs). Here, a field investigation was conducted across four seasons at the watershed scale. We observed significant seasonal variation in bacterial networks, with lower complexity and stability in autumn, and a wider bacterial community niche in summer. Similar to bacterial communities, the co-occurrence networks among ARGs also shift with seasonal change, particularly with respect to the topological features of the node degree, which on average was higher in summer than in the other seasons. Furthermore, the nodes with higher betweenness, stress, degree, and closeness centrality in the bacterial network showed strong relationships with the 10 major classes of ARGs. These findings highlighted the changes in the topological properties of bacterial networks that could further alter antibiotic resistance in soil. Together, our results reveal the temporal dynamics of bacterial ecological networks at the watershed scale, and provide new insights into antibiotic resistance management under environmental changes.

Plant associated protists-Untapped promising candidates for agrifood tools

The importance of host-associated microorganisms and their biotic interactions for plant health and performance has been increasingly acknowledged. Protists, main predators and regulators of bacteria and fungi, are abundant and ubiquitous eukaryotes in terrestrial ecosystems. Protists are considered to benefit plant health and performance, but the community structure and functions of plant-associated protists remain surprisingly underexplored. Harnessing plant-associated protists and other microbes can potentially enhance plant health and productivity and sustain healthy food and agriculture systems. In this review, we summarize the knowledge of multifunctionality of protists and their interactions with other microbes in plant hosts, and propose a future framework to study plant-associated protists and utilize protists as agrifood tools for benefiting agricultural production.

Cyanobacterial blooms: A player in the freshwater environmental resistome with public health relevance?

Cyanobacterial harmful algal blooms (cyanoHABs) are an ecological concern because of large ecosystem-disrupting blooms and a global public health concern because of the cyanotoxins produced by certain bloom-forming species. Another threat to global public health is the dissemination of antibiotic resistance (AR) in freshwater environmental reservoirs from anthropogenic sources, such as wastewater discharge and urban and agricultural runoff. In this study, cyanobacteria are now hypothesized to play a role in the environmental resistome. A non-systematic literature review of studies using molecular techniques (such as PCR and metagenomic sequencing) was conducted to explore indirect and direct ways cyanobacteria might contribute to environmental AR. Results show cyanobacteria can host antibiotic resistance genes (ARGs) and might promote the spread of ARGs in bacteria due to the significant contribution of mobile genetic elements (MGEs) located in genera such as Microcystis. However, cyanobacteria may promote or inhibit the spread of ARGs in environmental freshwater bacteria due to other factors as well. The purpose of this review is to 1) consider the role of cyanobacteria as AR hosts, since cyanoHABs are historically considered to be a separate problem from AR, and 2) to identify the knowledge gap in understanding cyanobacteria as ARG reservoirs. Cyanobacterial blooms, as well as other biotic (e.g. interactions with protists or cyanophages) and abiotic factors, should be studied further using advanced methods such as shotgun metagenomic and long read sequencing to clarify the extent of their functional ARGs/MGEs and influences on environmental AR.

Bioaccumulation of antibiotics and resistance genes in lettuce following cattle manure and digestate fertilization and their effects on soil and phyllosphere microbial communities

The degradation and bioaccumulation of selected antibiotics such as the sulfonamide sulfamethoxazole (SMX) and the fluoroquinolones enrofloxacin (ENR) and ciprofloxacin (CIP) were investigated in soil microcosm experiments where Lactuca sativa was grown with manure or digestate (1%) and spiked with a mixture of the three antibiotics (7.5 mg/kg each). The soil, rhizosphere and leaf phyllosphere were sampled (at 0 and 46 days) from each microcosm to analyze the antibiotic concentrations, main resistance genes (sul1, sul2, qnrS, aac-(6')-Ib-crand qepA), the intI1and tnpA mobile genetic elements and the microbial community structure.Overall results showed that SMX and CIP decreased (70-85% and 55-79%, respectively), and ENR was quite persistent during the 46-day experiment. In plant presence, CIP and ENR were partially up-taken from soil to plant. In fact the bioaccumulation factors were > 1, with higher values in manure than digestate amended soils. The most abundant gene in soil was sul2 in digestate- and aac-(6')-Ib-cr in the manure-amended microcosms. In soil, neither sulfamethoxazole-resistance (sul1 and sul2), nor fluoroquinolone-resistance (aac-(6')-Ib-cr, qepA and qnrS) gene abundances were correlated with any antibiotic concentration. On the contrary, in lettuce leaves, the aac-(6')-Ib-cr gene was the most abundant, in accordance with the fluoroquinolone bioaccumulation. Finally, digestate stimulated a higher soil microbial biodiversity, introducing and promoting more bacterial genera associated with antibiotic degradation and involved in soil fertility and decreased fluoroquinolone bioaccumulation.

A review of some medicinal plants with the potential to defeat antimicrobial resistance: Cases of Benin, Togo, Ghana, Burkina Faso, and Cape Verde

Antimicrobial resistance (AMR) is a global public health problem. In the alternatives being explored for developing new antimicrobials, medicinal plants occupy an important place, particularly in Africa, where they are widely used. This review aims to analyze the potential of medicinal plants from Benin, Togo, Ghana, Burkina-Faso, and Cape Verde in the fight against AMR. A bibliographic search was conducted to explore scientific databases such as PubMed and Google Scholar. During this search, particular attention was given to epidemiological data related to AMR in these countries, medicinal plants traditionally used to treat microbial infections and medicinal plants that have been shown to be active on multidrug-resistant microbial strains. In total, 94 manuscripts were investigated. Epidemiological data showed that the problem of AMR is worsening in each target country. In addition, several medicinal plants have been demonstrated to be effective against microbial strains resistant to conventional antibiotics. A total of 532 medicinal plants were identified according to their ethnomedical uses for the treatment of microbial infections. Scientific evidence was collected on the antimicrobial potential of 91 plants. This study showed the potential of medicinal plants in the fight against AMR. Their documented traditional use, coupled with the evidence of efficacy provided, make them interesting sources for developing new antimicrobials.

Metagenomic characterization of bacterial community and antibiotic resistance genes found in the mass transit system in Seoul, South Korea

Mass transit systems, including subways and buses, are useful environments for studying the urban microbiome, as the vast majority of populations in urban areas use public transportation. Microbial communities in urban environments include both human- and environment-associated bacteria that play roles in health and pathogen transmission. In this study, we used shotgun metagenomic sequencing to profile microbial communities sampled from various surfaces found in subway stations and bus stops within the Seoul mass transit system. The metagenomic approach and network analysis were used to investigate broad-spectrum antibiotic resistance genes (ARGs) and their co-occurrence patterns. We uncovered 598 bacterial species in 76 samples collected from various surfaces within the Seoul mass transit system. All samples were dominated by the potential human pathogen Salmonella enterica (40 %) and the human skin bacterium Cutibacterium acnes (19 %). Significantly abundant biomarkers detected in subway station samples were associated with bacteria typically found in the human oral cavity and respiratory tract, whereas biomarkers detected in bus stop samples were associated with bacteria commonly found in soil, water, and plants. Temperature and location had significant effects on microbial community structure and diversity. In total, 41 unique ARG subtypes were identified, associated with single-drug or multidrug resistance to clinically important and extensively used antibiotics, including aminoglycosides, carbapenem, glycopeptide, and sulfonamides. We revealed that Seoul subway stations and bus stops possess unique microbiomes containing potential human pathogens and ARGs. These findings provide insights for refining location-specific responses to reduce exposure to potentially causative agents of infectious diseases, improving public health.

Microbial Multitrophic Communities Drive the Variation of Antibiotic Resistome in the Gut of Soil Woodlice (Crustacea: Isopoda)

Multitrophic communities inhabit in soil faunal gut, including bacteria, fungi, and protists, which have been considered a hidden reservoir for antibiotic resistance genes (ARGs). However, there is a dearth of research focusing on the relationships between ARGs and multitrophic communities in the gut of soil faunas. Here, we studied the contribution of multitrophic communities to variations of ARGs in the soil woodlouse gut. The results revealed diverse and abundant ARGs in the woodlouse gut. Network analysis further exhibited strong connections between key ecological module members and ARGs, suggesting that multitrophic communities in the keystone ecological cluster may play a pivotal role in the variation of ARGs in the woodlouse gut. Moreover, long-term application of sewage sludge significantly altered the woodlice gut resistome and interkingdom communities. The variation portioning analysis indicated that the fungal community has a greater contribution to variations of ARGs than bacterial and protistan communities in the woodlice gut after long-term application of sewage sludge. Together, our results showed that changes in gut microbiota associated with agricultural practices (e.g., sewage sludge application) can largely alter the gut interkingdom network in ecologically relevant soil animals, with implications for antibiotic resistance, which advances our understanding of the microecological drivers of ARGs in terrestrial ecosystem.

High Frequency of Antibiotic Resistance Genes (ARGs) in the Lerma River Basin, Mexico

The spread of beta-lactamase-producing bacteria is of great concern and the environment has been found to be a main source of contamination. Herein, it was proposed to determine the frequency of antimicrobial-resistant-Gram-negative bacteria throughout the Lerma River basin using phenotypic and molecular methods. Resistant bacteria were isolated with chromogenic media and antimicrobial susceptibility tests were used to characterize their resistance. ARGs for beta-lactams, aminoglycosides, and quinolones were detected by PCR. Species were identified by Sanger sequencing the 16S rRNA gene and the representative genomes of MDR strains were sequenced by NGS. A high variation in the number of isolates was observed in the 20 sampled sites, while observing a low diversity among the resistant bacteria. Of the 12 identified bacterial groups, C. freundii, E. coli, and S. marcescens were more predominant. A high frequency of resistance to beta-lactams, quinolones, and aminoglycosides was evidenced, where the bla_CTX,qnrB, qnrS y, and aac(6')lb-cr genes were the most prevalent. C. freundii showed the highest frequency of MDR strains. Whole genome sequencing revealed that S. marcescens and K. pneumoniae showed a high number of shared virulence and antimicrobial resistance genes, while E. coli showed the highest number of unique genes. The contamination of the Lerma River with MDR strains carrying various ARGs should raise awareness among environmental authorities to assess the risks and regulations regarding the optimal hygienic and sanitary conditions for this important river that supports economic activities in the different communities in Mexico.

Insights into the impact of manure on the environmental antibiotic residues and resistance pool

The intensive use of antibiotics in the veterinary sector, linked to the application of manure-derived amendments in agriculture, translates into increased environmental levels of chemical residues, AR bacteria (ARB) and antibiotic resistance genes (ARG). The aim of this review was to evaluate the current evidence regarding the impact of animal farming and manure application on the antibiotic resistance pool in the environment. Several studies reported correlations between the prevalence of clinically relevant ARB and the amount and classes of antibiotics used in animal farming (high resistance rates being reported for medically important antibiotics such as penicillins, tetracyclines, sulfonamides and fluoroquinolones). However, the results are difficult to compare, due to the diversity of the used antimicrobials quantification techniques and to the different amounts and types of antibiotics, exhibiting various degradation times, given in animal feed in different countries. The soils fertilized with manure-derived products harbor a higher and chronic abundance of ARB, multiple ARG and an enriched associated mobilome, which is also sometimes seen in the crops grown on the amended soils. Different manure processing techniques have various efficiencies in the removal of antibiotic residues, ARB and ARGs, but there is only a small amount of data from commercial farms. The efficiency of sludge anaerobic digestion appears to be dependent on the microbial communities composition, the ARB/ARG and operating temperature (mesophilic vs. thermophilic conditions). Composting seems to reduce or eliminate most of antibiotics residues, enteric bacteria, ARB and different representative ARG in manure more rapidly and effectively than lagoon storage. Our review highlights that despite the body of research accumulated in the last years, there are still important knowledge gaps regarding the contribution of manure to the AMR emergence, accumulation, spread and risk of human exposure in countries with high clinical resistance rates. Land microbiome before and after manure application, efficiency of different manure treatment techniques in decreasing the AMR levels in the natural environments and along the food chain must be investigated in depth, covering different geographical regions and countries and using harmonized methodologies. The support of stakeholders is required for the development of specific best practices for prudent – cautious use of antibiotics on farm animals. The use of human reserve antibiotics in veterinary medicine and of unprescribed animal antimicrobials should be stopped and the use of antibiotics on farms must be limited. This integrated approach is needed to determine the optimal conditions for the removal of antibiotic residues, ARB and ARG, to formulate specific recommendations for livestock manure treatment, storage and handling procedures and to translate them into practical on-farm management decisions, to ultimately prevent exposure of human population.

Nodules of wild legumes as unique natural hotspots of antibiotic resistance genes

Root nodules (RN) of legumes have distinct microenvironment from their symbiotic roots and surrounding soils. The rhizobia can withstand the host-produced phytoalexins and antimicrobial compounds. We thus hypothesize that the wild legume RN may develop unique natural resistome and be antibiotic resistance gene (ARG) hotspots. In this study, in comparison with rhizosphere soil (RS) and bulk soil (BS), we characterized the feature of antibiotic resistance in the RN of two wild legumes, Medicago polymorpha and Astragalus sinicus, by metagenomics. It was shown that the total relative abundance of ARGs followed the order of RN > RS > BS for both legumes. ARGs encoding antibiotic efflux pump predominated in all samples with increased proportion from BS to RN samples for both legumes. Totally 275 ARG subtypes were detected, and diversity of ARGs in RN was significantly lower than in BS samples for both legumes. 32 and 25 unique ARGs subtypes were detected in RN of both legumes. Bacterial community played a key role in shaping nodule-associated resistome because both ARG profiles and bacterial community differed greatly among BS, RS and RN. Rhizobia potentially hosted 10 and 15 ARGs subtypes for both legumes. The number and proportion of plasmid- and ARG-carrying contigs (ACCs) were higher in RN than in BS. Host tracking analysis of plasmid-ACCs suggests that proportion of rhizobial bacteria identified as their hosts decreased from BS to RN samples. No plasmid-ACCs with multiple ARGs were observed in BS samples, whereas they were detected in RN samples of both legumes. Our study showed that even wild legume nodules are unique natural ARG hotspots and enough attention should be paid to the dissemination risk of ARGs posed by globally produced legume crops.

Distinct aggregate stratification of antibiotic resistome in farmland soil with long-term manure application

Agricultural soils, which are closely linked to human health via food supply, have been recognized as an important reservoir for antibiotic resistance genes (ARGs). However, there is still a lack of knowledge regarding the role of soil aggregates in shaping ARG profile. In this study, we collected soils from long-term experimental farmland plots receiving inorganic and/or organic fertilizers and examined the patterns of antibiotic resistome distribution among differently sized soil aggregates using high-throughput quantitative polymerase chain reaction (HT-qPCR). Our results showed that the distribution of soil ARGs could be affected by manure application and aggregate size individually but not interactively. More diverse and abundant ARGs were found in the manured soils, compared to the non-manured soils. The aggregate size fraction of <53 μm exhibited the highest diversity and abundance of ARGs. Variation partitioning analysis revealed that soil traits, mobile genetic elements, and bacterial community collectively contributed to the variation of soil antibiotic resistance. The knowledge about aggregation stratification of soil ARGs obtained in this study is fundamental and essential to understanding the fate of soil ARGs at the microscale.

Investigation of dirigent like domains from bacterial genomes

BACKGROUND

DIRs are mysterious protein that have the ability to scavenge free radicals, which, are highly reactive with molecules in their vicinity. What is even more fascinating is that they carry out from these highly unstable species, a selective reaction (i.e., stereoenantioselective) from a well-defined substrate to give a very precise product. Unfortunately, to date, only three products have been demonstrated following studies on DIRs from the plant world, which until now was the kingdom where these proteins had been demonstrated. Within this kingdom, each DIR protein has its own type of substrate. The products identified to date, have on the other hand, a strong economic impact: in agriculture for example, the biosynthesis of (+)-gossypol could be highlighted (a repellent antifood produced by the cotton plant) by the DIRs of cotton. In forsythia plant species, it is the biosynthesis of (-)-pinoresinol, an intermediate leading to the synthesis of podophyllotoxine (a powerful anicancerous agent) which has been revealed. Recently, a clear path of study, potentially with strong impact, appeared by the hypothesis of the potential existence of protein DIR within the genomes of prokaryotes. The possibility of working with this type of organism is an undeniable advantage: since many sequenced genomes are available and the molecular tools are already developed. Even easier to implement and working on microbes, of less complex composition, offers many opportunities for laboratory studies. On the other hand, the diversity of their environment (e.g., soil, aquatic environments, extreme environmental conditions (pH, temperature, pressure) make them very diverse and varied subjects of study. Identifying new DIR proteins from bacteria means identifying new substrate or product molecules from these organisms. It is the promise of going further in understanding the mechanism of action of these proteins and this will most likely have a strong impact in the fields of agricultural, pharmaceutical and/or food chemistry.

RESULTS

Our goal is to obtain as much information as possible about these proteins to unlock the secrets of their exceptional functioning. Analyzes of structural and functional genomic data led to the identification of the Pfam PF03018 domain as characteristic of DIR proteins. This domain has been further identified in the sequence of bacterial proteins therefore named as DIR-like (DIRL). We have chosen a multidisciplinary bioinformatic approach centered on bacterial genome identification, gene expression and regulation signals, protein structures, and their molecular information content. The objective of this study was to perform a thorough bioinformatic analysis on these DIRLs to highlight any information leading to the selection of candidate bacteria for further cloning, purification, and characterization of bacterial DIRs.

CONCLUSIONS

From studies of DIRL genes identification, primary structures, predictions of their secondary and tertiary structures, prediction of DIRL signals sequences, analysis of their gene organization and potential regulation, a list of primary bacterial candidates is proposed.

Enhanced removal of antibiotics and antibiotic resistance genes in a soil microbial fuel cell via in situ remediation of agricultural soils with multiple antibiotics

Soil microbial fuel cells (MFCs) have been applied for the in situ remediation of soils polluted by single antibiotics. However, the investigation of only single antibiotic pollution has hindered MFC application in real-world soil remediation, where the effects of multiple antibiotics with similar chemical structures on the fate of antibiotics and their corresponding antibiotic resistance genes (ARGs) remain unknown. In this study, antibiotic removal rates, microbial community compositions, metabolite compositions, and ARG abundances were investigated in soil MFCs by adding two commonly used antibiotics (sulfadiazine, SDZ, and sulfamethoxazole, SMX), and comparing them with the addition of only a single antibiotic (SDZ). The antibiotic removal rate was higher in the soil MFC with addition of mixed antibiotics compared to the single antibiotic due to enhanced biodegradation efficiency in both the upper (57.24% of the initial antibiotic concentration) and lower layers (57.07% of the initial concentration) of the antibiotic-polluted soils. Bacterial community diversity in the mixed antibiotic conditions increased, and this likely resulted from the decreased toxicity of intermediates produced during antibiotic biodegradation. Moreover, the addition of mixed antibiotics led to lower risks of ARG release into soil environments, as reflected by higher abundances of host bacteria in the single antibiotic treatment. These results encourage the further development of soil MFC technology for in situ remediation of antibiotic-polluted soils.

Pedogenesis shapes predator-prey relationships within soil microbiomes

Pedogenesis determines soil physicochemical properties and many biodiversity facets, including belowground microbial bacteria and fungi. At the local scale, top-down predation by microbial protists regulates the soil microbiome, while the microbiome also affects protistan communities. However, it remains unknown how pedogenesis affects protistan communities and the potential protist-microbiome predator-prey relationships. With 435 soil samples representing different stages of pedogenesis ranging in soil age from centuries to millennia, we examined the influence of pedogenesis on the main protistan groups, and the interrelationships between protistan predators and microbial prey biomass. We revealed an enrichment in the diversity of total protists across pedogenesis and increasing richness of phototrophic protists in the medium compared with the early stages of pedogenesis. The richness of predatory protists accumulated throughout pedogenesis, which was more strongly determined by microbial biomass than environmental factors. Predator-prey associations were stronger in the young and the medium soils than in the older soils, likely because prey biomass accumulated in the latter and might be no longer limit predators. Together, our work provides evidence that pedogenesis shapes predatory protists differently than their prey, leading to shifts in predator-prey relationships. This knowledge is critical to better understand how soil food webs develop across soil development which might lead to changes in ecosystem functions.

Analysis of antibiotic resistance genes reveals their important roles in influencing the community structure of ocean microbiome

Antibiotic resistance gene (ARG) content is a well-established driver of microbial abundance and diversity in an environment. By reanalyzing 132 metagenomic datasets from the Tara Oceans project, we aim to unveil the associations between environmental factors, the ocean microbial community structure and ARG contents. We first investigated the structural patterns of microbial communities including both prokaryotes such as bacteria and eukaryotes such as protists. Additionally, several ARG-dominant horizontal gene transfer events between Protist and Prokaryote have been identified, indicating the potential roles of ARG in shaping the ocean microbial communities. For a deeper insight into the role of ARGs in ocean microbial communities on a global scale, we identified 1926 unique types of ARGs and discovered that the ARGs are more abundant and diverse in the mesopelagic zone than other water layers, potentially caused by limited resources. Finally, we found that ARG-enriched genera were often more abundant compared to their ARG-less neighbors in the same environment (e.g. coastal oceans). A deeper understanding of the ARG-microbiome relationships could help in the conservation of the oceanic ecosystem.

Climate warming increases the proportions of specific antibiotic resistance genes in natural soil ecosystems

Understanding the future distribution of antibiotic resistance in natural soil ecosystems is important to forecast their impacts on ecosystem and human health under projected climate change scenarios. Therefore, it is critical and timely to decipher the links between climate warming and antibiotic resistance, two of Earth's most imminent problems. Here, we explored the role of five-year simulated climate warming (+ 4 °C) on the diversity and proportions of soil antibiotic resistance genes (ARGs) across three seasons in both plantation and natural forest ecosystems. We found that the positive effects of warming on the number and proportions of ARGs were dependent on the sampling seasons (summer, autumn and winter), and seasonality was a key factor driving the patterns of ARG compositions in forest soils. Fifteen ARGs, conferring resistance to common antibiotics including aminoglycoside, beta-lactam, macrolide-lincosamide-streptogramin B, multidrug, sulfonamide, and tetracycline, were significantly enriched in the warming treatment. We showed that changes in soil properties and community compositions of bacteria, fungi and protists can explain the changes in soil ARGs under climate warming. Taken together, these findings advance our understanding of environmental ARGs under the context of future climate change and suggest that elevated temperature may promote the abundance of specific soil ARGs, with important implications for ecosystem and human health.

An Overview of Antibiotic Resistance and Abiotic Stresses Affecting Antimicrobial Resistance in Agricultural Soils

Excessive use of antibiotics in the healthcare sector and livestock farming has amplified antimicrobial resistance (AMR) as a major environmental threat in recent years. Abiotic stresses, including soil salinity and water pollutants, can affect AMR in soils, which in turn reduces the yield and quality of agricultural products. The objective of this study was to investigate the effects of antibiotic resistance and abiotic stresses on antimicrobial resistance in agricultural soils. A systematic review of the peer-reviewed published literature showed that soil contaminants derived from organic and chemical fertilizers, heavy metals, hydrocarbons, and untreated sewage sludge can significantly develop AMR through increasing the abundance of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) in agricultural soils. Among effective technologies developed to minimize AMR's negative effects, salinity and heat were found to be more influential in lowering ARGs and subsequently AMR. Several strategies to mitigate AMR in agricultural soils and future directions for research on AMR have been discussed, including integrated control of antibiotic usage and primary sources of ARGs. Knowledge of the factors affecting AMR has the potential to develop effective policies and technologies to minimize its adverse impacts.

Livestock manure spiked with the antibiotic tylosin significantly altered soil protist functional groups

With the increasing global antibiotic uses in livestock husbandry, animal manures upon land application pose potential threats to the environments and soil microbiome. Nevertheless, effects of manures and antibiotic-administered manures on soil protists, an integral component of soil food web and primary regulators of bacteria, remain unknown. Here, we assessed impacts of cattle and poultry manures with or without an antibiotic tylosin on soil protists and their functional groups in a 130-day microcosm incubation. Protists were highly responsive to manure application, with a significant decline in their alpha diversity in all manure treatments. There were also significant temporal changes in the alpha diversity and composition of soil protists and their functional groups. Poultry manures had stronger negative influences on the community structure of protists compared to cattle manures, and more pronounced effects on protists were observed in tylosin-spiked manure treatments. Furthermore, many consumer, phototrophic and parasitic taxa were highly susceptible to all manure treatments at Day 50 and 130. Altogether, our findings demonstrate negative effects of animal manures and tylosin on soil protists. This study suggests that the applications of livestock manures and antibiotics may subsequently alter ecological functions of protists and their interactions with other soil microorganisms in agricultural systems.

Antibiotics and antibiotic resistance genes in anaerobic digesters and predicted concentrations in agroecosystems

In recent decades, the innovative practice of management and valorization of agrozootechnical waste as energy through anaerobic digestion (AD) has been rapidly growing. However, whether applying digestate to soil as biofertilizer can be a source of antibiotics (ABs) and antibiotic resistance genes (ARGs) has not been fully investigated so far. In this work the ARGs responsible for sulfamethoxazole (SMX) resistance (sul1, sul2), ciprofloxacin (CIP) resistance (qnrS, qepA, aac-(6')-Ib-cr) and the mobile genetic element intl1, together with the concentrations of the antibiotics SMX and CIP, were measured in several anaerobic digesters located in Central Italy. Based on these results, the concentrations of antibiotics and ARGs which can potentially reach soil through amendment with digestate were also estimated. The highest CIP and SMX concentrations were found during winter and spring in anaerobic digesters. The highest ARG abundances were found for the aac-(6')-Ib-cr and sul2 genes. The overall results showed that application of digestate to soil does not exclude AB contamination and spread of ARGs in agroecosystems, especially in the case of ciprofloxacin, owing to its high intrinsic persistence.

Graphene-based ZnCr layered double hydroxide nanocomposites as bactericidal agents with high sonophotocatalytic performances for degradation of rifampicin

Herein, ZnCr layered double hydroxide (ZnCr LDH), and its nanocomposites with GO and rGO were synthesized using the co-precipitation method. The samples were characterized using XRD, FT-IR, SEM, TEM, BET, and XPS techniques. The sonophotocatalytic activity of the ZnCr LDH, ZnCr LDH/GO, and ZnCr LDH/rGO was investigated via the degradation of rifampicin (RIF) in the ultrasonic bath under visible light irradiation. The synergy index of more than 1 determined for ZnCr LDH/rGO indicated the positive interaction of sonocatalysis and photocatalysis resulted by hybridizing the LDH nanosheets with rGO. The maximum sonophotocatalytic degradation efficiency of 87.3% was achieved in the presence of ZnCr LDH/rGO nanocomposite with the concentration of 1.5 g L^-1 for degradation of RIF with an initial concentration of 15 mg L^-1 within 60 min sonication under visible light irradiation. The addition of different scavengers indicated that hydroxyl radicals, superoxide anion radicals, and the generated holes played a dominant role in the degradation of the pollutant molecules. A possible degradation mechanism was suggested based on the intermediates. The antibacterial tests confirmed the higher antibacterial activity of ZnCr LDH/GO compared with ZnCr LDH and ZnCr LDH/rGO against Gram-positive Staphylococcus aureus.

Legacy and Emerging Pollutants in an Urban River Stretch and Effects on the Bacterioplankton Community

River contamination is due to a chemical mixture of point and diffuse pollution, which can compromise water quality. Polycyclic Aromatic Hydrocarbons (PAHs) and emerging compounds such as pharmaceuticals and antibiotics are frequently found in rivers flowing through big cities. This work evaluated the presence of fifteen priority PAHs, eight pharmaceuticals including the antibiotics ciprofloxacin (CIP) and sulfamethoxazole (SMX), together with their main antibiotic resistant genes (ARGs) and the structure of the natural bacterioplankton community, in an urbanized stretch of the river Danube. SMX and diclofenac were the most abundant chemicals found (up to 20 ng/L). ARGs were also found to be detected as ubiquitous contaminants. A principal component analysis of the overall microbiological and chemical data revealed which contaminants were correlated with the presence of certain bacterial groups. The highest concentrations of naphthalene were associated with Deltaproteobacteria and intI1 gene. Overall, the most contaminated site was inside the city and located immediately downstream of a wastewater treatment plant. However, both the sampling points before the river reached the city and in its southern suburban area were still affected by emerging and legacy contamination. The diffuse presence of antibiotics and ARGs causes particular concern because the river water is used for drinking purposes.