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Microbial Ecology Jun 2024Plastic pollution poses a worldwide environmental challenge, affecting wildlife and human health. Assessing the biodegradation capabilities of natural microbiomes in...
Plastic pollution poses a worldwide environmental challenge, affecting wildlife and human health. Assessing the biodegradation capabilities of natural microbiomes in environments contaminated with microplastics is crucial for mitigating the effects of plastic pollution. In this work, we evaluated the potential of landfill leachate (LL) and estuarine sediments (ES) to biodegrade polyethylene (PE), polyethylene terephthalate (PET), and polycaprolactone (PCL), under aerobic, anaerobic, thermophilic, and mesophilic conditions. PCL underwent extensive aerobic biodegradation with LL (99 ± 7%) and ES (78 ± 3%) within 50-60 days. Under anaerobic conditions, LL degraded 87 ± 19% of PCL in 60 days, whereas ES showed minimal biodegradation (3 ± 0.3%). PE and PET showed no notable degradation. Metataxonomics results (16S rRNA sequencing) revealed the presence of highly abundant thermophilic microorganisms assigned to Coprothermobacter sp. (6.8% and 28% relative abundance in anaerobic and aerobic incubations, respectively). Coprothermobacter spp. contain genes encoding two enzymes, an esterase and a thermostable monoacylglycerol lipase, that can potentially catalyze PCL hydrolysis. These results suggest that Coprothermobacter sp. may be pivotal in landfill leachate microbiomes for thermophilic PCL biodegradation across varying conditions. The anaerobic microbial community was dominated by hydrogenotrophic methanogens assigned to Methanothermobacter sp. (21%), pointing at possible syntrophic interactions with Coprothermobacter sp. (a H-producer) during PCL biodegradation. In the aerobic experiments, fungi dominated the eukaryotic microbial community (e.g., Exophiala (41%), Penicillium (17%), and Mucor (18%)), suggesting that aerobic PCL biodegradation by LL involves collaboration between fungi and bacteria. Our findings bring insights on the microbial communities and microbial interactions mediating plastic biodegradation, offering valuable perspectives for plastic pollution mitigation.
Topics: Biodegradation, Environmental; Microbiota; Microplastics; Waste Disposal Facilities; Bacteria; Water Pollutants, Chemical; Polyesters; Geologic Sediments; RNA, Ribosomal, 16S; Estuaries; Polyethylene; Polyethylene Terephthalates
PubMed: 38943017
DOI: 10.1007/s00248-024-02399-8 -
International Journal of Antimicrobial... Jun 2024Bacteroides fragilis is the most frequent cause of anaerobic bacteraemia. Although recent data suggest a rise in antimicrobial resistance (AMR) of this and other...
BACKGROUND
Bacteroides fragilis is the most frequent cause of anaerobic bacteraemia. Although recent data suggest a rise in antimicrobial resistance (AMR) of this and other anaerobic bacteria, surveillance remains limited due to a lack of both data availability and comparability. However, a newly introduced standardised method for antimicrobial susceptibility testing (AST) of anaerobic bacteria has made larger scale surveillance possible for the first time.
AIM
To investigate phenotypic AMR of Bacteroides fragilis isolates from bacteraemia across Europe in 2022.
METHODS
In a multicentre approach, clinical microbiology laboratories in Europe were invited to contribute results of AST for Bacteroides fragilis blood culture isolates (including only the first isolate per patient and year). AST of a selection of four antibiotics was performed locally by participating laboratories in a prospective or retrospective manner, using the new EUCAST disc diffusion method on fastidious anaerobe agar (FAA-HB).
RESULTS
A total of 16 European countries reported antimicrobial susceptibilities in 449 unique isolates of Bacteroides fragilis from blood cultures in 2022. Clindamycin demonstrated the highest resistance rates (20.9%, range 0 - 63.6%), followed by piperacillin-tazobactam (11.1%, 0 - 54.5%), meropenem (13.4%, 0 - 45.5%), and metronidazole (1.8%, 0 - 20.0%), all with wide variation between countries.
CONCLUSION
Considering that the mean resistance rates across Europe were higher than expected for three of the four anti-anaerobic antibiotics under surveillance, both local AST of clinically relevant isolates of Bacteroides fragilis and continued surveillance on an international level is warranted.
PubMed: 38942247
DOI: 10.1016/j.ijantimicag.2024.107241 -
Acta Microbiologica Et Immunologica... Jun 2024The aim of this prospective pilot study was to compare culture and microbiome results of the removed tonsils of patients with assumed distant focal disease (11 patients)...
The aim of this prospective pilot study was to compare culture and microbiome results of the removed tonsils of patients with assumed distant focal disease (11 patients) and those who underwent a tonsillectomy, due to other reasons, such as recurrent tonsillitis, tonsil stones or snoring (nine patients). Aerobic culture was carried out for samples taken from the surface of the tonsils by swabs before tonsillectomy for all 20 patients. The squeezed detritus and the tissue samples of removed tonsils, taken separately for the right and left tonsils, were incubated aerobically and anaerobically. The microbiome composition of tissue samples of removed tonsils was also evaluated. Based on the culture results of the deep samples Staphylococcus aureus was the dominating pathogen, besides a great variety of anaerobic and facultative anaerobic bacteria present in the oral microbiota in those patients who underwent tonsillectomy due to distant focal diseases. Microbiome study of the core tissue samples showed a great diversity on genus and species level among patients of the two groups however, S. aureus and Prevotella nigrescens were present in higher proportion in those, whose tonsils were removed due to distant focal diseases. Our results may support previous findings about the possible triggering role of S. aureus and P. nigrescens leading to distant focal diseases. Samples taken by squeezing the tonsils could give more information about the possible pathogenic/triggering bacteria than the surface samples cultured only aerobically.
PubMed: 38941152
DOI: 10.1556/030.2024.02279 -
MSystems Jun 2024We use metagenome-assembled genomes (MAGs) to understand single-carbon (C1) compound-cycling-particularly methane-cycling-microorganisms in montane riparian floodplain...
Diverse and unconventional methanogens, methanotrophs, and methylotrophs in metagenome-assembled genomes from subsurface sediments of the Slate River floodplain, Crested Butte, CO, USA.
We use metagenome-assembled genomes (MAGs) to understand single-carbon (C1) compound-cycling-particularly methane-cycling-microorganisms in montane riparian floodplain sediments. We generated 1,233 MAGs (>50% completeness and <10% contamination) from 50- to 150-cm depth below the sediment surface capturing the transition between oxic, unsaturated sediments and anoxic, saturated sediments in the Slate River (SR) floodplain (Crested Butte, CO, USA). We recovered genomes of putative methanogens, methanotrophs, and methylotrophs ( = 57). Methanogens, found only in deep, anoxic depths at SR, originate from three different clades (, , and ), each with a different methanogenesis pathway; putative methanotrophic MAGs originate from within the Archaea ( Methanoperedens) in anoxic depths and uncultured bacteria (. Binatia) in oxic depths. Genomes for canonical aerobic methanotrophs were not recovered. Methanoperedens were exceptionally abundant (~1,400× coverage, >50% abundance in the MAG library) in one sample that also contained aceticlastic methanogens, indicating a potential C1/methane-cycling hotspot. . Methylomirabilis MAGs from SR encode pathways for methylotrophy but do not harbor methane monooxygenase or nitrogen reduction genes. Comparative genomic analysis supports that one clade within the . Methylomirabilis genus is not methanotrophic. The genetic potential for methylotrophy was widespread, with over 10% and 19% of SR MAGs encoding a methanol dehydrogenase or substrate-specific methyltransferase, respectively. MAGs from uncultured archaea in the . Gimiplasmatales (UBA10834) contain pathways that may allow for anaerobic methylotrophic acetogenesis. Overall, MAGs from SR floodplain sediments reveal a potential for methane production and consumption in the system and a robust potential for methylotrophy.IMPORTANCEThe cycling of carbon by microorganisms in subsurface environments is of particular relevance in the face of global climate change. Riparian floodplain sediments contain high organic carbon that can be degraded into C1 compounds such as methane, methanol, and methylamines, the fate of which depends on the microbial metabolisms present as well as the hydrological conditions and availability of oxygen. In the present study, we generated over 1,000 MAGs from subsurface sediments from a montane river floodplain and recovered genomes for microorganisms that are capable of producing and consuming methane and other C1 compounds, highlighting a robust potential for C1 cycling in subsurface sediments both with and without oxygen. Archaea from the . Methanoperedens genus were exceptionally abundant in one sample, indicating a potential C1/methane-cycling hotspot in the Slate River floodplain system.
PubMed: 38940520
DOI: 10.1128/msystems.00314-24 -
Case Reports in Pediatrics 2024In infants and children, bacterial meningitis caused by anaerobic bacteria is rare. However, a serious infection with the anaerobe can occur in previously healthy...
In infants and children, bacterial meningitis caused by anaerobic bacteria is rare. However, a serious infection with the anaerobe can occur in previously healthy children with a peak incidence in preschool children and in adolescents. As the clinical presentation can be very similar to meningitis caused by aerobic bacteria, one should consider as the causative agent when preceded by or associated with otitis media with purulent otorrhea or mastoiditis, in combination with minimal or no improvement on empiric antibiotic treatment. As this pathogen can be difficult to culture, anaerobic cultures should be obtained. Prompt treatment with a third-generation cephalosporin and metronidazole should be initiated once suspected or confirmed. Surgical source control is often necessary, but even with adequate and prompt treatment, the morbidity and mortality in children with a meningitis remains high. In this report, we describe a case of meningitis in a previously healthy child and review the available literature.
PubMed: 38939326
DOI: 10.1155/2024/6365796 -
Cureus May 2024is a new genus of anaerobic bacteria discovered in the year 2000. It is one of the most common bacteria present in the host microbial flora of dental plaque. The levels...
Comparative Evaluation of Mogibacterium timidum in the Subgingival Plaque of Periodontally Healthy and Chronic Periodontitis Patients: A Real-Time Polymerase Chain Reaction (PCR) Study.
BACKGROUND
is a new genus of anaerobic bacteria discovered in the year 2000. It is one of the most common bacteria present in the host microbial flora of dental plaque. The levels of are supposedly higher in inflammatory conditions.
AIMS AND OBJECTIVES
This study aimed to quantify the levels of species in the subgingival plaque samples of healthy patients and patients with chronic periodontitis.
MATERIALS AND METHODS
A total of 24 samples of the subgingival plaque, 12 healthy samples and 12 samples of chronic periodontitis patients, were collected in a buffer solution using a sterile Gracey curette. These samples were then sent to a laboratory for real-time polymerase chain reaction (PCR) testing.
RESULTS
was found in higher quantities in plaque samples taken from chronic periodontitis patients when compared to healthy patients.
CONCLUSION
can be said to be associated with chronic periodontitis condition. Further studies are required to know the exact nature of the pathogen.
PubMed: 38939247
DOI: 10.7759/cureus.61211 -
Plant Disease Jun 2024Blackleg and soft rot diseases represent a major threat to the health of potato () and other vegetable, ornamental and fruit crops worldwide; their main causal agents...
Blackleg and soft rot diseases represent a major threat to the health of potato () and other vegetable, ornamental and fruit crops worldwide; their main causal agents are species of and . In May 2022, 60% of potato plants (cv. Spunta) in a production field in Córdoba, Argentina (31°32'36''S 64°09'46''W) showed soft rot, blackleg and wilt. To isolate the causal agent, decayed plant tissues were disinfected in 2% NaClO, macerated in sterile water and streaked on crystal violet pectate (CVP) medium. Plates were incubated at 28°C for 48 h. Colonies that produced a pit on CVP medium were purified on nutrient agar. Two of the isolates, called 1Aia and 1B, were characterized by tests commonly employed for the identification of pectinolytic bacteria (Schaad et al. 2001). Both produced Gram-negative rods that were facultatively anaerobic, oxidase negative, nonfluorescent on King´s B, resistant to erythromycin and caused soft rot of potato slices. In addition, these isolates did not produce the blue pigment indigoidine and grew on nutrient glucose agar containing 5% NaCl. Phenotypic characteristics of the isolates 1Aia and 1B were compatible with spp. Genomic DNA was extracted using the commercially available Wizard® Genomic DNA Purification Kit (Promega) according to the manufacturer's instructions for the purification of DNA from Gram-negative bacteria. The isolates were positive in a PCR assay for (Duarte et al. 2004). The purified DNA of isolate 1Aia was used to construct a pooled Illumina library, which was sequenced at the Genomics Unit from the National Institute of Agricultural Technology (INTA, Argentina), by using high-throughput Illumina sequencing technology. Average nucleotide identity (ANI) calculation performed by FastANI v0.1.3 (Jain et al. 2018) showed 96.11% identity between the genome of the type strain LMG 21371 of (Acc. no. JQOE00000000) and our strain 1Aia (Acc. no. JAYGXQ000000000). For pathogenicity test, 3-weeks-old potato plants (cv. Spunta) planted in pots were infiltrated with 10 µl of a bacterial suspension (1x107 CFU/ml) 5 cm above the base of the stem using a sterile syringe. Negative controls were infiltrated with sterile water. Plants were kept under greenhouse conditions and regularly watered. The experiment was performed twice with six plants per treatment. Two days after inoculation, plants treated with strain 1Aia or 1B showed necrotic lesions on the stems and tubers soft rot symptoms while control plants remained asymptomatic. To fulfill Koch´s postulates, bacteria were re-isolated from symptomatic plants. Re-isolated bacteria, called 1Aia d and 1B d, were confirmed as according to biochemical and PCR results, as outlined above. Also, the % ANI value between isolates 1Aia and 1Aia d was 99.99% (Acc. no. JAYGXR000000000). To our knowledge, this is the first report of the occurrence of in Argentina. This pathogen has been observed causing blackleg and tuber soft rot on potato in Brazil (Duarte et al. 2004), Netherlands (Nunes Leite et al. 2014), Switzerland (de Werra et al. 2015), Russia (Voronina et al. 2019), Serbia (Loc et al. 2022) and USA (Zhang et al. 2023), among other countries worldwide. Due to the important economic and nutritional value of the crop, the distribution of needs to be investigated and monitored in order to develop effective control strategies.
PubMed: 38937930
DOI: 10.1094/PDIS-03-24-0558-PDN -
The Science of the Total Environment Jun 2024Schwertmannite (Sch) is found in environments abundant in iron and sulfate. Microorganisms that utilize iron or sulfate can induce the phase transition of...
Schwertmannite (Sch) is found in environments abundant in iron and sulfate. Microorganisms that utilize iron or sulfate can induce the phase transition of Schwertmannite, consequently leading to the redistribution of coexisting pollutants. However, the impact of the molar ratio of sulfate to iron (S/Fe) on the microbial-mediated transformation of Schwertmannite and its implications for the fate of cadmium (Cd) have not been elucidated. In this study, we examined how S/Fe influenced mineral transformation and the fate of Cd during microbial reduction of Cd-loaded Schwertmannite by Desulfovibrio vulgaris. Our findings revealed that an increase in the S/Fe ratio facilitated sulfate-reducing bacteria (SRB) in mitigating the toxicity of Cd, thereby expediting the generation of sulfide (S(-II)) and subsequently triggering mineral phase transformation. As the S/Fe ratio increased, the predominant minerals in the system transitioned from prismatic-cluster vivianite to rose-shaped mackinawite. The Cd phase and distribution underwent corresponding alterations. Cd primarily existed in its oxidizable state, with its distribution being directly linked not only to FeS content but also showing a robust correlation with phosphorus. The coexistence of vivianite and FeS minerals proved to be more favorable for Cd immobilization. These findings have significant implications for understanding the biogeochemistry of iron (oxyhydr)oxides and Cd fate in anaerobic environments.
PubMed: 38936727
DOI: 10.1016/j.scitotenv.2024.174275 -
Environmental Pollution (Barking, Essex... Jun 2024The environmental transmission of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) exerted devastating threats to global public health, and their...
The environmental transmission of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) exerted devastating threats to global public health, and their interactions with other emerging contaminants (ECs) have raised increasing concern. This study investigated that the abundances of ARGs and MRGs with the predominant type of efflux pump were simultaneously increased (8.4-59.1%) by disinfectant polyhexamethylene guanidine (PHMG) during waste activated sludge (WAS) anaerobic digestion. The aggregation of the same microorganisms (i.e., Hymenobacter and Comamonas) and different host bacteria (i.e., Azoarcus and Thauera) were occurred upon exposure to PHMG, thereby increasing the co-selection and propagation of MRGs and ARGs by vertical gene transfer. Moreover, PHMG enhanced the process of horizontal gene transfer (HGT), facilitating their co-transmission by the same mobile genetic elements (20.2-223.7%). Additionally, PHMG up-regulated the expression of critical genes (i.e., glnB, trpG and gspM) associated with the HGT of ARGs and MRGs (i.e., two-component regulatory system and quorum sensing) and exocytosis system (i.e., bacterial secretion system). Structural equation model analysis further verified that the key driver for the simultaneous enrichment of ARGs and MRGs under PHMG stress was microbial community structure. The study gives new insights into the aggravated environmental risks and mechanisms of ECs in sludge digestion system, providing guidance for subsequent regulation and control of ECs.
PubMed: 38936038
DOI: 10.1016/j.envpol.2024.124453 -
Frontiers in Microbiology 2024Microbial inhibition by high ammonia concentrations is a recurring problem that significantly restricts methane formation from intermediate acids, i.e., propionate and...
Microbial inhibition by high ammonia concentrations is a recurring problem that significantly restricts methane formation from intermediate acids, i.e., propionate and acetate, during anaerobic digestion of protein-rich waste material. Studying the syntrophic communities that perform acid conversion is challenging, due to their relatively low abundance within the microbial communities typically found in biogas processes and disruption of their cooperative behavior in pure cultures. To overcome these limitations, this study examined growth parameters and microbial community dynamics of highly enriched mesophilic and ammonia-tolerant syntrophic propionate and acetate-oxidizing communities and analyzed their metabolic activity and cooperative behavior using metagenomic and metatranscriptomic approaches. Cultivation in batch set-up demonstrated biphasic utilization of propionate, wherein acetate accumulated and underwent oxidation before complete degradation of propionate. Three key species for syntrophic acid degradation were inferred from genomic sequence information and gene expression: a syntrophic propionate-oxidizing bacterium (SPOB) " Syntrophopropionicum ammoniitolerans", a syntrophic acetate-oxidizing bacterium (SAOB) and a novel hydrogenotrophic methanogen, for which we propose the provisional name " Methanoculleus ammoniitolerans". The results revealed consistent transcriptional profiles of the SAOB and the methanogen both during propionate and acetate oxidation, regardless of the presence of an active propionate oxidizer. Gene expression indicated versatile capabilities of the two syntrophic bacteria, utilizing both molecular hydrogen and formate as an outlet for reducing equivalents formed during acid oxidation, while conserving energy through build-up of sodium/proton motive force. The methanogen used hydrogen and formate as electron sources. Furthermore, results of the present study provided a framework for future research into ammonia tolerance, mobility, aggregate formation and interspecies cooperation.
PubMed: 38933034
DOI: 10.3389/fmicb.2024.1389257