-
Microbiome May 2024Antibiotics and microplastics are two major aquatic pollutants that have been associated to antibiotic resistance selection in the environment and are considered a risk...
BACKGROUND
Antibiotics and microplastics are two major aquatic pollutants that have been associated to antibiotic resistance selection in the environment and are considered a risk to human health. However, little is known about the interaction of these pollutants at environmental concentrations and the response of the microbial communities in the plastisphere to sub-lethal antibiotic pollution. Here, we describe the bacterial dynamics underlying this response in surface water bacteria at the community, resistome and mobilome level using a combination of methods (next-generation sequencing and qPCR), sequencing targets (16S rRNA gene, pre-clinical and clinical class 1 integron cassettes and metagenomes), technologies (short and long read sequencing), and assembly approaches (non-assembled reads, genome assembly, bacteriophage and plasmid assembly).
RESULTS
Our results show a shift in the microbial community response to antibiotics in the plastisphere microbiome compared to surface water communities and describe the bacterial subpopulations that respond differently to antibiotic and microplastic pollution. The plastisphere showed an increased tolerance to antibiotics and selected different antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs). Several metagenome assembled genomes (MAGs) derived from the antibiotic-exposed plastisphere contained ARGs, virulence factors, and genes involved in plasmid conjugation. These include Comamonas, Chryseobacterium, the opportunistic pathogen Stenotrophomonas maltophilia, and other MAGs belonging to genera that have been associated to human infections, such as Achromobacter. The abundance of the integron-associated ciprofloxacin resistance gene aac(6')-Ib-cr increased under ciprofloxacin exposure in both freshwater microbial communities and in the plastisphere. Regarding the antibiotic mobilome, although no significant changes in ARG load in class 1 integrons and plasmids were observed in polluted samples, we identified three ARG-containing viral contigs that were integrated into MAGs as prophages.
CONCLUSIONS
This study illustrates how the selective nature of the plastisphere influences bacterial response to antibiotics at sub-lethal selective pressure. The microbial changes identified here help define the selective role of the plastisphere and its impact on the maintenance of environmental antibiotic resistance in combination with other anthropogenic pollutants. This research highlights the need to evaluate the impact of aquatic pollutants in environmental microbial communities using complex scenarios with combined stresses. Video Abstract.
Topics: Anti-Bacterial Agents; Bacteria; Microbiota; RNA, Ribosomal, 16S; Integrons; Drug Resistance, Bacterial; Water Pollutants, Chemical; Microplastics; High-Throughput Nucleotide Sequencing; Metagenome; Plasmids; Water Microbiology; Drug Resistance, Microbial
PubMed: 38790062
DOI: 10.1186/s40168-024-01803-2 -
Computational and Structural... Dec 2024Antlers are hallmark organ of deer, exhibiting a relatively high growth rate among mammals, and requiring large amounts of nutrients to meet its development. The rumen...
Antlers are hallmark organ of deer, exhibiting a relatively high growth rate among mammals, and requiring large amounts of nutrients to meet its development. The rumen microbiota plays key roles in nutrient metabolism. However, changes in the microbiota and metabolome in the rumen during antler growth are largely unknown. We investigated rumen microbiota (liquid, solid, ventral epithelium, and dorsal epithelium) and metabolic profiles of sika deer at the early (EG), metaphase (MG) and fast growth (FG) stages. Our data showed greater concentrations of acetate and propionate in the rumens of sika deer from the MG and FG groups than in those of the EG group. However, microbial diversity decreased during antler growth, and was negatively correlated with short-chain fatty acid (SCFA) levels. , , and were the dominant bacteria in the liquid, solid, ventral epithelium, and dorsal epithelium fractions. The proportions of , , and increased significantly in the liquid or dorsal epithelium fractions. Untargeted metabolomics analysis revealed that the metabolites also changed significantly, revealing 237 significantly different metabolites, among which the concentrations of γ-aminobutyrate and creatine increased during antler growth. Arginine and proline metabolism and alanine, aspartate and glutamate metabolism were enhanced. The co-occurrence network results showed that the associations between the rumen microbiota and metabolites different among the three groups. Our results revealed that the different rumen ecological niches were characterized by distinct microbiota compositions, and the production of SCFAs and the metabolism of specific amino acids were significantly changed during antler growth.
PubMed: 38680874
DOI: 10.1016/j.csbj.2024.04.018 -
Metabolites Apr 2024Heavy metal pollution poses significant environmental challenges, and understanding how plants and endophytic bacteria interact to mitigate these challenges is of utmost...
Heavy metal pollution poses significant environmental challenges, and understanding how plants and endophytic bacteria interact to mitigate these challenges is of utmost importance. In this study, we investigated the roles of endophytic bacteria, particularly and , in Swartz () in response to chromium and nickel co-pollution. Our results demonstrated the remarkable tolerance of and to heavy metals, and their potential to become dominant species in the presence of co-pollution. We observed a close relationship between these endophytic bacteria and the significant differences in metabolites, particularly carbohydrates, flavonoids, and amino acids in . These findings shed light on the potential of endophytic bacteria to promote the production of aspartic acid and other metabolites in plants as a response to abiotic stressors. Furthermore, our study presents a new direction for plant and bioremediation strategies in heavy metal pollution and enhances our understanding of 's mechanisms for heavy metal tolerance.
PubMed: 38668359
DOI: 10.3390/metabo14040231 -
Bioresources and Bioprocessing Dec 2023The escalating crisis of polyethylene terephthalate (PET) microplastic contamination in biological wastewater treatment systems is a pressing environmental concern....
The escalating crisis of polyethylene terephthalate (PET) microplastic contamination in biological wastewater treatment systems is a pressing environmental concern. These microplastics inevitably accumulate in sewage sludge due to the absence of effective removal technologies. Addressing this urgent issue, this study introduces a novel approach using DuraPETase, a potent enzyme with enhanced PET hydrolytic activity at ambient temperatures. Remarkably, this enzyme was successfully secreted from Comamonas testosteroni CNB-1, a dominant species in the active sludge. The secreted DuraPETase showed significant hydrolytic activity toward p-NPB and PET nanoplastics. Furthermore, the CNB-1 derived whole-cell biocatalyst was able to depolymerize PET microplastics under ambient temperature, achieving a degradation efficiency of 9% within 7 days. The CNB-1-based whole biocatalysts were also capable of utilizing PET degradation intermediates, such as terephthalic acid (TPA) and ethylene glycol (EG), and bis(2-hydroxyethyl)-TPA (BHET), for growth. This indicates that it can completely mineralize PET, as opposed to merely breaking it down into smaller molecules. This research highlights the potential of activated sludge as a potent source for insitu microplastic removal.
PubMed: 38647778
DOI: 10.1186/s40643-023-00715-7 -
IScience May 2024The advancement of regenerative life support systems (RLSS) is crucial to allow long-distance space travel. Within the Micro-Ecological Life Support System Alternative...
The advancement of regenerative life support systems (RLSS) is crucial to allow long-distance space travel. Within the Micro-Ecological Life Support System Alternative (MELiSSA), efficient nitrogen recovery from urine and other waste streams is vital to produce liquid fertilizer to feed food and oxygen production in subsequent photoautotrophic processes. This study explores the effects of ionizing radiation on nitrogen cycle bacteria that transform urea to nitrate. In particular, we assess the radiotolerance of , , and after exposure to acute γ-irradiation. Moreover, a comprehensive whole transcriptome analysis elucidates the effects of spaceflight-analogue low-dose ionizing radiation on the individual axenic strains and on their synthetic community o. This research sheds light on how the spaceflight environment could affect ureolysis and nitrification processes from a transcriptomic perspective.
PubMed: 38638570
DOI: 10.1016/j.isci.2024.109596 -
Frontiers in Microbiology 2024This study aimed to investigate the impact of temperature and the presence of other microorganisms on the susceptibility of STEC to biocides. Mature biofilms were formed...
This study aimed to investigate the impact of temperature and the presence of other microorganisms on the susceptibility of STEC to biocides. Mature biofilms were formed at both 10°C and 25°C. An inoculum of planktonic bacteria comprising 10 CFU/mL of spoilage bacteria and 10 CFU/mL of a single strain (O157, O111, O103, and O12) was used to form mixed biofilms. The following bacterial combinations were tested: T1: + + STEC, T2: + + STEC, and T3: + + STEC. Tested biocides included quaternary ammonium compounds (Quats), sodium hypochlorite (Shypo), sodium hydroxide (SHyd), hydrogen peroxide (HyP), and BioDestroy®-organic peroxyacetic acid (PAA). Biocides were applied to 6-day-old biofilms. Minimum Bactericidal Concentrations (MBC) and Biofilm Eradication Concentrations (BEC) were determined. Planktonic cells and single-species biofilms exhibited greater susceptibility to sanitizers ( < 0.0001). and were more susceptible than the rest of the tested bacteria (p < 0.0001). Single species biofilms formed by O111, O121, O157, and O45 showed resistance (100%) to Shypo sanitizer (200 ppm) at 25°C. From the most effective to the least effective, sanitizer performance on single-species biofilms was PAA > Quats > HyP > SHyd > Shypo. In multi-species biofilms, spoilage bacteria within T1, T2, and T3 biofilms showed elevated resistance to SHyd (30%), followed by quats (23.25%), HyP (15.41%), SHypo (9.70%), and BioDestroy® (3.42%; < 0.0001). Within T1, T2, and T3, the combined STEC strains exhibited superior survival to Quats (23.91%), followed by HyP (19.57%), SHypo (18.12%), SHyd (16.67%), and BioDestroy® (4.35%; < 0.0001). O157:H7-R508 strains were less tolerant to Quats and Shypo when combined with T2 and T3 ( < 0.0001). O157:H7 and O103:H2 strains in mixed biofilms T1, T2, and T3 exhibited higher biocide resistance than the weak biofilm former, O145:H2 ( < 0.0001). The study shows that STEC within multi-species biofilms' are more tolerant to disinfectants.
PubMed: 38633705
DOI: 10.3389/fmicb.2024.1360645 -
MicroPublication Biology 2024animals with a compromised pharynx accumulate bacteria in their intestinal lumen and activate a transcriptional response that includes anti-bacterial response genes....
animals with a compromised pharynx accumulate bacteria in their intestinal lumen and activate a transcriptional response that includes anti-bacterial response genes. In this study, we demonstrate that animals with defective pharynxes are resistant to Orsay virus (OrV) infection. This resistance is observed for animals grown on OP50 and on BIGb0172, a bacterium naturally associated with . The viral resistance observed in defective-pharynx mutants does not seem to result from constitutive transcriptional immune responses against viruses. OrV resistance is also observed in mutants with defective defecation, which share with the pharynx-defective perturbations in the regulation of their intestinal contents and altered lipid metabolism. The underlying mechanisms of viral resistance in pharynx- and defecation-defective mutants remain elusive.
PubMed: 38590801
DOI: 10.17912/micropub.biology.001166 -
Nanowarriors from Mentha: Unleashing Nature's Antimicrobial Arsenal with Cerium Oxide Nanoparticles.ACS Omega Apr 2024Medicinal plant-based cerium oxide nanoparticles (CeONPs) possessed excellent antimicrobial properties against multiple strains of Gram-positive and Gram-negative...
Medicinal plant-based cerium oxide nanoparticles (CeONPs) possessed excellent antimicrobial properties against multiple strains of Gram-positive and Gram-negative bacteria. The CeONPs are popular because their electropositive charged surface causes oxidation of plasma membrane and facilitates the penetration of CeONPs inside the pathogen body. In the present research work, CeONPs stabilized with Mentha leaf extract; as a result, nanoparticles surface-bonded with various functional groups of phytochemicals which enhanced the therapeutic potential of CeONPs. The inhibition percentage of CeONPs was evaluated against eight pathogenic Gram-positive bacteria and Gram-negative bacteria , , sp., sp., and and plant bacteria sp. The antifungal properties of CeONPs were evaluated against three pathogenic fungal species , , and via the streak plate method. The antimicrobial inhibitory activity of CeONPs was good to excellent. The current research work clearly shows that three different medicinal plants , , and based CeONPs, variation in nanoparticle sizes, and surface-to-volume ratio of green CeONPs are three factors responsible to generate and provoke antimicrobial activities of CeONPs against human pathogenic bacteria and plant infecting fungi. The results show that CeONPs possessed good antimicrobial properties and are effective to use for pharmaceutical applications and as a food preservative because of low toxicity, organic coating, and acceptable antimicrobial properties. This study showed a rapid and well-organized method to prepare stable phytochemical-coated CeONPs with three different plants , , and with remarkable antibacterial and antifungal characteristics.
PubMed: 38585053
DOI: 10.1021/acsomega.4c00236 -
Frontiers in Cellular and Infection... 2024This study aimed to investigate the composition of ocular surface microbiota in patients with obesity.
PURPOSE
This study aimed to investigate the composition of ocular surface microbiota in patients with obesity.
METHODS
This case-control study, spanning from November 2020 to March 2021 at Henan Provincial People's Hospital, involved 35 patients with obesity and an equivalent number of age and gender-matched healthy controls. By employing 16S rRNA sequencing, this study analyzed the differences in ocular surface microbiota between the two groups. The functional prediction analysis of the ocular surface microbiota was conducted using PICRUSt2.
RESULTS
The alpha diversity showed no notable differences in the richness or evenness of the ocular surface microbiota when comparing patients with obesity to healthy controls (Shannon index, =0.1003). However, beta diversity highlighted significant variances in the microbiota composition of these two groups (ANOSIM, =0.005). LEfSe analysis revealed that the relative abundances of , , , , , and in patients with obesity were significantly increased (<0.05). Predictive analysis using PICRUSt2 highlighted a significant enhancement in certain metabolic pathways in patients with obesity, notably xenobiotics metabolism via cytochrome P450 (CYP450), lipid metabolism, and the oligomerization domain (NOD)-like receptor signaling pathway (<0.05).
CONCLUSIONS
Patients with obesity exhibit a distinct ocular surface core microbiome. The observed variations in this microbiome may correlate with increased activity in CYP450, changes in lipid metabolism, and alterations in NOD-like receptor signaling pathways.
Topics: Humans; Case-Control Studies; RNA, Ribosomal, 16S; Eye; Obesity; Microbiota
PubMed: 38533385
DOI: 10.3389/fcimb.2024.1356197 -
Scientific Reports Mar 2024In the Anthropocene, plastic pollution has become a new environmental biotope, the so-called plastisphere. In the oceans, nano- and micro-sized plastics are omnipresent...
In the Anthropocene, plastic pollution has become a new environmental biotope, the so-called plastisphere. In the oceans, nano- and micro-sized plastics are omnipresent and found in huge quantities throughout the water column and sediment, and their large surface area-to-volume ratio offers an excellent surface to which hydrophobic chemical pollutants (e.g. petrochemicals and POPs) can readily sorb to. Our understanding of the microbial communities that breakdown plastic-sorbed chemical pollutants, however, remains poor. Here, we investigated the formation of 500 nm and 1000 nm polystyrene (PS) agglomerations in natural seawater from a coastal environment, and we applied DNA-based stable isotope probing (DNA-SIP) with the 500 nm PS sorbed with isotopically-labelled phenanthrene to identify the bacterial members in the seawater community capable of degrading the hydrocarbon. Whilst we observed no significant impact of nanoplastic size on the microbial communities associated with agglomerates that formed in these experiments, these communities were, however, significantly different to those in the surrounding seawater. By DNA-SIP, we identified Arcobacteraceae, Brevundimonas, Comamonas, uncultured Comamonadaceae, Delftia, Sphingomonas and Staphylococcus, as well as the first member of the genera Acidiphilum and Pelomonas to degrade phenanthrene, and of the genera Aquabacterium, Paracoccus and Polymorphobacter to degrade a hydrocarbon. This work provides new information that feeds into our growing understanding on the fate of co-pollutants associated with nano- and microplastics in the ocean.
Topics: Microplastics; Plastics; Polystyrenes; Comamonadaceae; DNA Probes; Environmental Pollutants; Isotopes; Microbiota; Phenanthrenes; DNA
PubMed: 38433255
DOI: 10.1038/s41598-024-55825-9