Toxic metals in Amazonian soil modify the bacterial community associated with Diplopoda. - Related Documents




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766201.0000Toxic metals in Amazonian soil modify the bacterial community associated with Diplopoda. Toxic metal pollution in the Amazon is a serious problem that reduces the quality of water, soil, air, and consequently alters communities of fauna, flora, and microbiota, harming human health and well-being. Our aim was to determine the impact of toxic metals on the structure of the bacterial community associated with Diplopoda in the Amazon rainforest. Animals were kept in microcosms contaminated with cadmium (50 mg.kg(-1)), mercury (35 mg.kg(-1)) and no toxic metal (control). The intestinal and molting chamber microbiota were accessed by culture-dependent and culture-independent methods (16S metabarcoding). The cultivated strains were identified, and their functional traits evaluated: secretion of enzymes, growth at different pH, resistance to metals and antibiotics, and ability to reduce toxic effects of metals on plants. Our research described Brachyurodesmus albus, a new species of Diplopoda. We obtained 177 isolates distributed in 35 genera and 61 species of bacteria (Pseudomonadota, Bacillota, Bacteroidota and Actinomycetota) associated with the gut and molting chamber of B. albus. Metabarcoding data provided a more robust access to the bacterial community, resulting in 24 phyla, 561 genera and 6792 ASVs. The presence of metal Cd and Hg alters the composition and abundance of bacteria associated with B. albus (PERMANOVA p < 0.05). The microhabitat (gut and molting chamber) harbours bacterial communities that differ in composition and abundance (PERMANOVA p < 0.05). The presence of Cd and Hg alters important metabolic pathways related to the prokaryotic defense system; antimicrobial resistance genes, endocytosis and secretion system, estimated by PICRUSt. Bacteria selected with high resistance to Cd and Hg buffer the toxic effect of metals on tomato seedlings. This work describes B. albus and concludes that its diverse bacterial microbiota is altered by soil contamination by toxic metals, as well as being an important repository for prospecting strains to be applied in bioremediation programs.202439419211
741610.9994Effect of copper and zinc as sulfate or nitrate salts on soil microbiome dynamics and bla(VIM)-positive Pseudomonas aeruginosa survival. The exposure of soil to metals and to antibiotic resistant bacteria may lead to the progressive deterioration of soil quality. The persistence of antibiotic resistant bacteria or antibiotic resistance genes in soil can be influenced by the microbial community or by soil amendments with metal salts. This work assessed the effect of soil amendment with copper and zinc, as sulfate or nitrate salts, on the fate of a carbapenem-resistant (bla(VIM)(+)) hospital effluent isolate of Pseudomonas aeruginosa (strain H1FC49) and on the variations of the microbial community composition. Microcosms with soil aged or not with copper and zinc salts (20 mM), and inoculated with P. aeruginosa H1FC49 were monitored at 0, 7, 14 and/or 30 days, for community composition (16S rRNA gene amplicon) and strain H1FC49 persistence. Data on culturable P. aeruginosa, quantitative PCR of the housekeeping gene ecf, and the presumably acquired genes bla(VIM)(+) and integrase (intI1), and community composition were interpreted based on descriptive statistics and multivariate analysis. P. aeruginosa and the presumably acquired genes, were quantifiable in soil for up to one month, in both metal-amended and non-amended soil. Metal amendments were associated with a significant decrease of bacterial community diversity and richness. The persistence of P. aeruginosa and acquired genes in soils, combined with the adverse effect of metals on the bacterial community, highlight the vulnerability of soil to both types of exogenous contamination.202133773246
771320.9994Metagenome analyses of corroded concrete wastewater pipe biofilms reveal a complex microbial system. BACKGROUND: Concrete corrosion of wastewater collection systems is a significant cause of deterioration and premature collapse. Failure to adequately address the deteriorating infrastructure networks threatens our environment, public health, and safety. Analysis of whole-metagenome pyrosequencing data and 16S rRNA gene clone libraries was used to determine microbial composition and functional genes associated with biomass harvested from crown (top) and invert (bottom) sections of a corroded wastewater pipe. RESULTS: Taxonomic and functional analysis demonstrated that approximately 90% of the total diversity was associated with the phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The top (TP) and bottom pipe (BP) communities were different in composition, with some of the differences attributed to the abundance of sulfide-oxidizing and sulfate-reducing bacteria. Additionally, human fecal bacteria were more abundant in the BP communities. Among the functional categories, proteins involved in sulfur and nitrogen metabolism showed the most significant differences between biofilms. There was also an enrichment of genes associated with heavy metal resistance, virulence (protein secretion systems) and stress response in the TP biofilm, while a higher number of genes related to motility and chemotaxis were identified in the BP biofilm. Both biofilms contain a high number of genes associated with resistance to antibiotics and toxic compounds subsystems. CONCLUSIONS: The function potential of wastewater biofilms was highly diverse with level of COG diversity similar to that described for soil. On the basis of the metagenomic data, some factors that may contribute to niche differentiation were pH, aerobic conditions and availability of substrate, such as nitrogen and sulfur. The results from this study will help us better understand the genetic network and functional capability of microbial members of wastewater concrete biofilms.201222727216
609130.9993Isolation of Heavy Metal-Tolerant and Anti-Phytopathogenic Plant Growth-Promoting Bacteria from Soils. In this study, multifunctional soil bacteria, which can promote plant development, resist heavy metals, exhibit anti-phytopathogenic action against plant diseaes, and produce extracellular enzymes, were isolated to improve the effectiveness of phytoremediation techniques. In order to isolate multifunctional soil bacteria, a variety of soil samples with diverse characteristics were used as sources for isolation. To look into the diversity and structural traits of the bacterial communities, we conducted amplicon sequencing of the 16S rRNA gene on five types of soils and predicted functional genes using Tax4Fun2. The isolated bacteria were evaluated for their multifunctional capabilities, including heavy metal tolerance, plant growth promotion, anti-phytopathogenic activity, and extracellular enzyme activity. The genes related to plant growth promotion and anti-phytopathogenic activity were most abundant in forest and paddy soils. Burkholderia sp. FZ3 and FZ5 demonstrated excellent heavy metal resistance (≤ 1 mM Cd and ≤ 10 mM Zn), Pantoea sp. FC24 exhibited the highest protease activity (24.90 μmol tyrosine·g-DCW(-1)·h(-1)), and Enterobacter sp. PC20 showed superior plant growth promotion, especially in siderophore production. The multifunctional bacteria isolated using traditional methods included three strains (FC24, FZ3, and FZ5) from the forest and one strain (PC20) from paddy field soil. These results indicate that, for the isolation of beneficial soil microorganisms, utilizing target gene information obtained from isolation sources and subsequently exploring target microorganisms is a valuable strategy.202439468992
795340.9993Rapid impact of phenanthrene and arsenic on bacterial community structure and activities in sand batches. The impact of both organic and inorganic pollution on the structure of soil microbial communities is poorly documented. A short-time batch experiment (6 days) was conducted to study the impact of both types of pollutants on the taxonomic, metabolic and functional diversity of soil bacteria. For this purpose sand spiked with phenanthrene (500 mg kg(-1) sand) or arsenic (arsenite 0.66 mM and arsenate 12.5 mM) was supplemented with artificial root exudates and was inoculated with bacteria originated from an aged PAH and heavy-metal-polluted soil. The bacterial community was characterised using bacterial strain isolation, TTGE fingerprinting and proteomics. Without pollutant, or with phenanthrene or arsenic, there were no significant differences in the abundance of bacteria and the communities were dominated by Pseudomonas and Paenibacillus genera. However, at the concentrations used, both phenanthrene or arsenic were toxic as shown by the decrease in mineralisation activities. Using community-level physiological profiles (Biolog Ecoplates™) or differential proteomics, we observed that the pollutants had an impact on the community physiology, in particular phenanthrene induced a general cellular stress response with changes in the central metabolism and membrane protein synthesis. Real-time PCR quantification of functional genes and transcripts revealed that arsenic induced the transcription of functional arsenic resistance and speciation genes (arsB, ACR3 and aioA), while no transcription of PAH-degradation genes (PAH-dioxygenase and catechol-dioxygenase) was detected with phenanthrene. Altogether, in our tested conditions, pollutants do not have a major effect on community abundance or taxonomic composition but rather have an impact on metabolic and functional bacterial properties.201424189653
771450.9993Functional traits and health implications of the global household drinking-water microbiome retrieved using an integrative genome-centric approach. The biological safety of drinking water plays a crucial role in public health protection. However, research on the drinking water microbiome remains in its infancy, especially little is known about the potentially pathogenic bacteria in and functional characteristics of the microbiome in household tap water that people are directly exposed to. In this study, we used a genomic-centric approach to construct a genetic catalogue of the drinking water microbiome by analysing 116 metagenomic datasets of household tap water worldwide, spanning nine countries/regions on five continents. We reconstructed 859 high-quality metagenome-assembled genomes (MAGs) spanning 27 bacterial and 2 archaeal phyla, and found that the core MAGs belonging to the phylum Proteobacteria encoded the highest metabolic functional diversity of the 33 key complete metabolic modules. In particular, we found that two core MAGs of Brevibacillus and Methylomona encoded genes for methane metabolism, which may support the growth of heterotrophic organisms observed in the oligotrophic ecosystem. Four MAGs of complete ammonia oxidation (comammox) Nitrospira were identified and functional metabolic analysis suggested these may enable mixotrophic growth and encode genes for reactive oxygen stress defence and arsenite reduction that could aid survival in the environment of oligotrophic drinking water systems. Four MAGs were annotated as potentially pathogenic bacteria (PPB) and thus represented a possible public health concern. They belonged to the genera Acinetobacter (n = 3) and Mycobacterium (n = 1), with a total relative abundance of 1.06 % in all samples. The genomes of PPB A. junii and A. ursingii were discovered to contain antibiotic resistance genes and mobile genetic elements that could contribute to antimicrobial dissemination in drinking water. Further network analysis suggested that symbiotic microbes which support the growth of pathogenic bacteria can be targets for future surveillance and removal.202438183799
735960.9993Shallow-Water Hydrothermal Vents as Natural Accelerators of Bacterial Antibiotic Resistance in Marine Coastal Areas. Environmental contamination by heavy metals (HMs) poses several indirect risks to human health, including the co-spreading of genetic traits conferring resistance to both HMs and antibiotics among micro-organisms. Microbial antibiotic resistance (AR) acquisition is enhanced at sites anthropogenically polluted by HMs, as well as in remote systems naturally enriched in HMs, such as hydrothermal vents in the deep sea. However, to date, the possible role of hydrothermal vents at shallower water depths as hot spots of microbial AR gain and spreading has not been tested, despite the higher potential risks associated with the closer vicinity of such ecosystems to coasts and human activities. In this work, we collected waters and sediments at the Panarea shallow-water hydrothermal vents, testing the presence of culturable marine bacteria and their sensitivity to antibiotics and HMs. All of the bacterial isolates showed resistance to at least one antibiotic and one HM and, most notably, 80% of them displayed multi-AR on average to 12 (min 8, max 15) different antibiotics, as well as multi-HM tolerance. We show that our isolates displayed high similarity (≥99%) to common marine bacteria, affiliating with Actinobacteria, Gammaproteobacteria, Alphaproteobacteria and Firmicutes, and all displayed wide growth ranges for temperature and salinity during in vitro physiological tests. Notably, the analysis of the genomes available in public databases for their closest relatives highlighted the lack of genes for AR, posing new questions on the origin of multi-AR acquisition in this peculiar HM-rich environment. Overall, our results point out that shallow-water hydrothermal vents may contribute to enhance AR acquisition and spreading among common marine bacteria in coastal areas, highlighting this as a focus for future research.202235208933
610270.9993Isolation of highly copper-resistant bacteria from deep-sea hydrothermal fields and description of a novel species Marinobacter metalliresistant sp. nov. INTRODUCTION: Hydrothermal vents, rich in heavy metals, provided a unique niche for heavy metal resistant microbes. However, knowledge about copper resistant microbes in deep sea hydrothermal vents is still limited. METHODS: The copper-resistant bacteria were isolated from deep-sea hydrothermal vent samples and conducted thorough physical, phylogenetic, and genomic analyses to elucidate their copper resistance capability and related genes. RESULTS: Twelve highly copper-resistant bacteria (up to 6-10 mM) were isolated from deep sea hydrothermal fields They were affiliated with the Pseudoalteromonas (4), Marinobacter (3), Halomonas (2), Psychrobacter (1), and Pseudomonas (1) genus in the α-Proteobacteria, and the Sphingomonas (1) genus in the β-Proteobacteria. The presence of copper in the medium obviously induced the amount of polysaccharides and proteins in the crude extracellular polymeric substances (EPS) produced by Halomonas sp. CuT 3-1, Pseudoalteromonas sp. CuT 4-3 and Marinobacter metalliresistant CuT 6, which could absorb 40 to 50 mg•g(-1) copper. We further described a novel species, Marinobacter metalliresistant sp. nov. CuT 6(T), which exhibited a higher copper resistance and encoded more heavy metal resistance-related genes than other Marinobacter species. DISCUSSION: It revealed that the copper resistance capability exhibited by these strains in hydrothermal fields is likely attributed to the production of exopolymeric substances, such as polysaccharides and proteins, as well as active transport or efflux mechanisms for heavy metals.202439234539
772480.9993Taxonomic and functional analyses reveal existence of virulence and antibiotic resistance genes in beach sand bacterial populations. Coastal sands are important natural recreational facilities that have become hotspots for tourism and economic development. However, these sands harbour diverse microbial assemblages that play a critical role in the balance between public health and ecology. In this study, targeted high-throughput sequencing analysis was used to identify sand-borne bacterial populations at four public beaches in Durban. The effect of heavy metal in shaping the distribution of bacterial metacommunities was determined using canonical correspondence analysis (CCA), while the functional gene profiles were predicted using PICRUSt2 analysis. Sequences matching those of the bacterial phylum Proteobacteria were the most abundant in all samples, followed by those of the phyla Firmicutes, Actinobacteria, Bacteroidetes, and Gemmatimonadetes. Genus-level taxonomic analysis showed the presence of 1163 bacterial genera in all samples combined. The distribution of bacterial communities was shaped by heavy metal concentrations, with the distribution of Flavobacteria, Bacteroidia, and Deltaproteobacteria influenced by Pb and Zn, while B and Cr influenced the distribution of Clostridia and Gammaproteobacteria, respectively. Identified antibiotic resistance genes included the peptidoglycan biosynthesis gene II, III, IV, and V, as well as the polymyxin resistance gene, while the virulence genes included the sitA, fimB, aerobactin synthase, and pilL gene. Our findings demonstrate that beach sand-borne bacteria are reservoirs of virulence and antibiotic resistance genes. Contamination of beach sands with heavy metals selects for both heavy metal resistance and antibiotic resistance in beach sand bacterial communities. Children and immunocompromised people engaging in recreational activities on beaches may be exposed to higher risk of infection.202133474608
610490.9993The Pseudomonas community in metal-contaminated sediments as revealed by quantitative PCR: a link with metal bioavailability. Pseudomonas bacteria are ubiquitous Gram-negative and aerobic microorganisms that are known to harbor metal resistance mechanisms such as efflux pumps and intracellular redox enzymes. Specific Pseudomonas bacteria have been quantified in some metal-contaminated environments, but the entire Pseudomonas population has been poorly investigated under these conditions, and the link with metal bioavailability was not previously examined. In the present study, quantitative PCR and cell cultivation were used to monitor and characterize the Pseudomonas population at 4 different sediment sites contaminated with various levels of metals. At the same time, total metals and metal bioavailability (as estimated using an HCl 1 m extraction) were measured. It was found that the total level of Pseudomonas, as determined by qPCR using two different genes (oprI and the 16S rRNA gene), was positively and significantly correlated with total and HCl-extractable Cu, Co, Ni, Pb and Zn, with high correlation coefficients (>0.8). Metal-contaminated sediments featured isolates of the Pseudomonas putida, Pseudomonas fluorescens, Pseudomonas lutea and Pseudomonas aeruginosa groups, with other bacterial genera such as Mycobacterium, Klebsiella and Methylobacterium. It is concluded that Pseudomonas bacteria do proliferate in metal-contaminated sediments, but are still part of a complex community.201425102022
7518100.9993Deciphering the toxic effects of metals in gold mining area: Microbial community tolerance mechanism and change of antibiotic resistance genes. Mine tailing dumps represent significant threats to ecological environments due to the presence of toxic substances. The present work investigated the relationship among microbial activity, the community, antibiotic resistance genes (ARGs) and trace metals in soil surrounding gold mine tailings. Using microbial metabolic activity and high-throughput sequencing analysis, we found the trace metals Cd and Hg could be main factors influencing the microbial community. According to bacterial co-occurrence pattern analysis, the effects of total cadmium and total mercury on bacterial diversity are potentially mediated by influencing bacteria community in the keystone module II. Additionally, most of metal-resistant bacteria belong to Actinobacteria and Proteobacteria, and the metal tolerance suggested to be linked with various functions including replication, recombination and repair, as well as inorganic ion transport and metabolism based on PICRUSt2 analysis. We also found that metals generated by mining activity may trigger the co-selection of antibiotic resistance in the phyla Actinobacteria and Proteobacteria due to co-resistance or cross resistance. Additionally, PLS-PM analysis revealed that metals could indirectly affect ARGs by influencing bacterial diversity in gold mining areas.202032678731
3711110.9993Characterization of aerobic polycyclic aromatic hydrocarbon-degrading bacteria from Bizerte lagoon sediments, Tunisia. AIMS: To characterize polycyclic aromatic hydrocarbon (PAH)-degrading bacteria from sediments of the Bizerte lagoon, and to determine their ability to resist other pollutants such as antibiotics and heavy metals. METHODS AND RESULTS: More than 100 strains were isolated for their ability to use fluoranthene as the sole carbon and energy source. Most of them showed antibiotic and heavy metal resistance; 20 representative strains were selected for further analysis. 16S rRNA coding sequences analysis showed that the majority of the selected bacteria (75%) were affiliated to the Gammaproteobacteria. The selected strains also utilized high molecular weight PAHs containing up to four benzene rings and showed different profiles of PAH substrate usage suggesting different PAH degradation pathways. These results are consistent with the fact that nah-like genes and idoA-like genes, involved in PAH degradation, were detected in 6 and 1 strains respectively. CONCLUSIONS: The Bizerte lagoon, polluted by many human activities, leads to the co-selection of strains able to cope with multiple contaminants. SIGNIFICANCE AND IMPACT OF THE STUDY: Polluted areas are often characterized by the concomitant presence of organic pollutants, heavy metals and antibiotics. This study is one of the first showing bacterial strains adapted to multiple contaminants, a promising potential for the development of bioremediation processes.200817973912
7516120.9993Functional gene array-based analysis of microbial communities in heavy metals-contaminated lake sediments. Lake DePue (IL, USA) has been contaminated for > 80 years by an adjacent Zn-smelting facility. Previous work indicated that sulfate reduction increased and biomass declined as pore-water metal concentrations increased, while 16S rRNA gene profiles remained relatively stable. To better understand this phenomenon, the sediment microbial community structure and functional potential were investigated using a functional gene microarray (GeoChip) targeting > 10,000 functional genes. Nonmetric multidimensional scaling and clustering analyses showed that the overall community structure was similar across all sites based on the relative abundance of all detected genes, but some individual gene categories did show differences. A subset of sulfate reduction genes (dsr) and the most relevant metal resistance genes were more abundant than other categories and were highly correlated with metal contamination. The most significant correlations were between pore-water metal concentrations and dsr, with Zn, Cd, and Mn as the most predictive for the presence of dsr. These results suggest that metal contamination influences sediment microbial community structure and function by increasing the abundance of relevant metal-resistant and sulfate-reducing populations. These populations therefore appear to contribute significantly to the resistance and stability of the microbial communities throughout the gradient of metal contamination in Lake DePue.201323710534
7403130.9993Effect of Enrofloxacin on the Microbiome, Metabolome, and Abundance of Antibiotic Resistance Genes in the Chicken Cecum. Enrofloxacin is an important antibiotic for the treatment of Salmonella infections in livestock and poultry. However, the effects of different concentrations of enrofloxacin on the bacterial and metabolite compositions of the chicken gut and changes in the abundance of resistance genes in cecum contents remain unclear. To investigate the effects of enrofloxacin on chickens, we orally administered different concentrations of enrofloxacin to 1-day-old chickens and performed 16S rRNA gene sequencing to assess changes in the gut microbiomes of chickens after treatment. The abundance of fluoroquinolone (FQ) resistance genes was measured using quantitative PCR. Metabolomics techniques were used to examine the cecal metabolite composition. We found that different concentrations of enrofloxacin had different effects on cecum microorganisms, with the greatest effect on cecum microbial diversity in the low-concentration enrofloxacin group at day 7. Enrofloxacin use reduced the abundance of beneficial bacteria such as Lactobacillaceae and Oscillospira. Furthermore, cecum microbial diversity was gradually restored as the chickens grew. In addition, enrofloxacin increased the abundance of resistance genes, and there were differences in the changes in abundance among different antibiotic resistance genes. Moreover, enrofloxacin significantly affected linoleic acid metabolism, amino acid metabolism, and signaling pathways. This study helps improve our understanding of how antibiotics affect host physiological activities and provides new insights into the rational use of drugs in poultry farming. The probiotics and metabolites that we identified could be used to modulate the negative effects of antibiotics on the host, which requires further study. IMPORTANCE In this study, we investigated changes in the cecum flora, metabolites, and abundances of fluoroquinolone antibiotic resistance genes in chickens following the use of different concentrations of enrofloxacin. These results were used to determine the effects of enrofloxacin on chick physiology and the important flora and metabolites that might contribute to these effects. In addition, these results could help in assessing the effect of enrofloxacin concentrations on host metabolism. Our findings could help guide the rational use of antibiotics and mitigate the negative effects of antibiotics on the host.202336840593
3155140.9993In silico mapping of microbial communities and stress responses in a porcine slaughterhouse and pork products through its production chain, and the efficacy of HLE disinfectant. The use of shotgun metagenomic sequencing to understand ecological-level spread of microbes and their genes has provided new insights for the prevention, surveillance and control of microbial contaminants in the slaughterhouse environment. Here, microbial samples were collected from products and surrounding areas though a porcine slaughter process; shotgun metagenomic DNA-sequencing of these samples revealed a high community diversity within the porcine slaughterhouse and pork products, in zones originating from animal arrival through to the sale zones. Bacteria were more prevalent in the first zones, such as arrival- and anesthesia-zones, and DNA viruses were prevalent in the scorching-and-whip zone, animal products and sale zone. Data revealed the dominance of Firmicutes and Proteobacteria phyla followed by Actinobacteria, with a clear shift in the relative abundance of lactic acid bacteria (mainly Lactobacillus sp.) from early slaughtering steps to Proteobacteria and then to viruses suggesting site-specific community compositions occur in the slaughterhouse. Porcine-type-C oncovirus was the main virus found in slaughterhouse, which causes malignant diseases in animals and humans. As such, to guarantee food safety in a slaughterhouse, a better decipher of ecology and adaptation strategies of microbes becomes crucial. Analysis of functional genes further revealed high abundance of diverse genes associated with stress, especially in early zones (animal and environmental surfaces of arrival zone with 57,710 and 40,806 genes, respectively); SOS responsive genes represented the most prevalent, possibly associated with genomic changes responsible of biofilm formation, stringent response, heat shock, antimicrobial production and antibiotic response. The presence of several antibiotic resistance genes suggests horizontal gene transfer, thus increasing the likelihood for resistance selection in human pathogens. These findings are of great concern, with the suggestion to focus control measures and establish good disinfection strategies to avoid gene spread and microbial contaminants (bacteria and viruses) from the animal surface into the food chain and environment, which was achieved by applying HLE disinfectant after washing with detergent.202032846568
7710150.9993Reduced Antibiotic Resistance in the Rhizosphere of Lupinus albus in Mercury-Contaminated Soil Mediated by the Addition of PGPB. The emergence of antibiotic resistance (AR) poses a threat to the "One Health" approach. Likewise, mercury (Hg) pollution is a serious environmental and public health problem. Its ability to biomagnify through trophic levels induces numerous pathologies in humans. As well, it is known that Hg-resistance genes and AR genes are co-selected. The use of plant-growth-promoting bacteria (PGPB) can improve plant adaptation, decontamination of toxic compounds and control of AR dispersal. The cenoantibiogram, a technique that allows estimating the minimum inhibitory concentration (MIC) of a microbial community, has been postulated as a tool to effectively evaluate the evolution of a soil. The present study uses the metagenomics of 16S rRNA gene amplicons to understand the distribution of the microbial soil community prior to bacterial inoculation, and the cenoantibiogram technique to evaluate the ability of four PGPB and their consortia to minimize antibiotic resistance in the rhizosphere of Lupinus albus var. Orden Dorado grown in Hg-contaminated soils. Results showed that the addition of A1 strain (Brevibacterium frigoritolerans) and its consortia with A2, B1 and B2 strains reduced the edaphic community´s MIC against cephalosporins, ertapenem and tigecycline. The metagenomic study revealed that the high MIC of non-inoculated soils could be explained by the bacteria which belong to the detected taxa,. showing a high prevalence of Proteobacteria, Cyanobacteria and Actinobacteria.202337372086
7419160.9993The bacterial microbiota in florfenicol contaminated soils: The antibiotic resistome and the nitrogen cycle. Soil antibiotic resistome and the nitrogen cycle are affected by florfenicol addition to manured soils but their interactions have not been fully described. In the present study, antibiotic resistance genes (ARGs) and nitrogen cycle genes possessed by soil bacteria were characterized using real-time fluorescence quantification PCR (qPCR) and metagenomic sequencing in a short-term (30 d) soil model experiment. Florfenicol significantly changed in the abundance of genes conferring resistance to aminoglycosides, β-lactams, tetracyclines and macrolides. And the abundance of Sphingomonadaceae, the protein metabolic and nitrogen metabolic functions, as well as NO reductase, nitrate reductase, nitrite reductase and N(2)O reductase can also be affected by florfenicol. In this way, ARG types of genes conferring resistance to aminoglycosides, β-lactamases, tetracyclines, colistin, fosfomycin, phenicols and trimethoprim were closely associated with multiple nitrogen cycle genes. Actinobacteria, Chlorobi, Firmicutes, Gemmatimonadetes, Nitrospirae, Proteobacteria and Verrucomicrobia played an important role in spreading of ARGs. Moreover, soil physicochemical properties were important factors affecting the distribution of soil flora. This study provides a theoretical basis for further exploration of the transmission regularity and interference mechanism of ARGs in soil bacteria responsible for nitrogen cycle.202032023788
8656170.9993Genome-centric metagenomics insights into functional divergence and horizontal gene transfer of denitrifying bacteria in anammox consortia. Denitrifying bacteria with high abundances in anammox communities play crucial roles in achieving stable anammox-based systems. Despite the relative constant composition of denitrifying bacteria, their functional diversity remains to be explored in anammox communities. Herein, a total of 77 high-quality metagenome-assembled genomes (MAGs) of denitrifying bacteria were recovered from the anammox community in a full-scale swine wastewater treatment plant. Among these microbes, a total of 26 MAGs were affiliated with the seven dominant denitrifying genera that have total abundances higher than 1%. A meta-analysis of these species suggested that external organics reduced the abundances of genus Ignavibacterium and species MAG.305 of UTPRO2 in anammox communities. Comparative genome analysis revealed functional divergence across different denitrifying bacteria, largely owing to their distinct capabilities for carbohydrate (including endogenous and exogenous) utilization and vitamin (e.g., pantothenate and thiamine) biosynthesis. Serval microbes in this system contained fewer genes encoding biotin, pantothenate and methionine biosynthesis compared with their related species from other habitats. In addition, the genes encoding energy production and conversion (73 genes) and inorganic ion transport (53 genes) putatively transferred from other species to denitrifying bacteria, while these denitrifying bacteria (especially genera UTPRO2 and SCN-69-89) likely donated the genes encoding nutrients (e.g., inorganic ion and amino acid) transporter (64 genes) for other members to utilize new metabolites. Collectively, these findings highlighted the functional divergence of these denitrifying bacteria and speculated that the genetic interactions within anammox communities through horizontal gene transfer may be one of the reasons for their functional divergence.202236116192
3689180.9993Virome-associated antibiotic-resistance genes in an experimental aquaculture facility. We report the comprehensive characterization of viral and microbial communities within an aquaculture wastewater sample, by a shotgun sequencing and 16S rRNA gene profiling metagenomic approach. Caudovirales had the largest representation within the sample, with over 50% of the total taxonomic abundance, whereas approximately 30% of the total open reading frames (ORFs) identified were from eukaryotic viruses (Mimiviridae and Phycodnaviridae). Antibiotic resistance genes (ARGs) within the virome accounted for 0.85% of the total viral ORFs and showed a similar distribution both in virome and in microbiome. Among the ARGs, those encoding proteins involved in the modulation of antibiotic efflux pumps were the most abundant. Interestingly, the taxonomy of the bacterial ORFs identified in the viral metagenome did not reflect the microbial taxonomy as deduced by 16S rRNA gene profiling and shotgun metagenomic analysis. A limited number of ARGs appeared to be mobilized from bacteria to phages or vice versa, together with other bacterial genes encoding products involved in general metabolic functions, even in the absence of any antibiotic treatment within the aquaculture plant. Thus, these results confirm the presence of a complex phage-bacterial network in the aquaculture environment.201626738553
7962190.9993Linking the Effect of Antibiotics on Partial-Nitritation Biofilters: Performance, Microbial Communities and Microbial Activities. The emergence and spread of antibiotics resistance in wastewater treatment systems have been pointed as a major environmental health problem. Nevertheless, research about adaptation and antibiotics resistance gain in wastewater treatment systems subjected to antibiotics has not been successfully developed considering bioreactor performance, microbial community dynamics and microbial activity dynamics at the same time. To observe this in autotrophic nitrogen removal systems, a partial-nitritation biofilter was subjected to a continuous loading of antibiotics mix of azithromycin, norfloxacin, trimethoprim, and sulfamethoxazole. The effect of the antibiotics mix over the performance, bacterial communities and bacterial activity in the system was evaluated. The addition of antibiotics caused a drop of ammonium oxidation efficiency (from 50 to 5%) and of biomass concentration in the bioreactor, which was coupled to the loss of ammonium oxidizing bacteria Nitrosomonas in the bacterial community from 40 to 3%. Biomass in the partial nitritation biofilter experienced a sharp decrease of about 80% due to antibiotics loading, but the biomass adapted and experienced a growth by stabilization under antibiotics feeding. During the experiment several bacterial genera appeared, such as Alcaligenes, Paracoccus, and Acidovorax, clearly dominating the bacterial community with >20% relative abundance. The system reached around 30% ammonium oxidation efficiency after adaptation to antibiotics, but no effluent nitrite was found, suggesting that dominant antibiotics-resistant phylotypes could be involved in nitrification-denitrification metabolisms. The activity of ammonium oxidation measured as amoA and hao gene expression dropped a 98.25% and 99.21%, respectively, comparing the system before and after the addition of antibiotics. On the other hand, denitrifying activity increased as observed by higher expression of nir and nos genes (83.14% and 252.54%, respectively). In addition, heterotrophic nitrification cyt c-551 was active only after the antibiotics addition. Resistance to the antibiotics was presumably given by ermF, carA and msrA for azithromycin, mutations of the gyrA and grlB for norfloxacin, and by sul123 genes for sulfamethoxazole. Joined physicochemical and microbiological characterization of the system were used to investigate the effect of the antibiotics over the bioprocess. Despite the antibiotics resistance, activity of Bacteria decreased while the activity of Archaea and Fungi increased.201829535704