Search

The radioactive nuclide 225Ac is one of the few promising candidates for cancer treatment by targeted-α\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym}\usepackage{amsfonts}\usepackage{amssymb}\usepackage{amsbsy}\usepackage{mathrsfs}\usepackage{upgreek}\setlength{\oddsidemargin}{-69pt}\begin{document}$$\alpha$$\end{document}-therapy, but worldwide production of 225Ac faces significant limitations. In this work, the Isotope Separation On-Line method was used to produce actinium by irradiating targets made of uranium carbide and thorium carbide with 1.4-GeV protons. Actinium fluoride molecules were formed, ionized through electron impact, then extracted and mass-separated as a beam of molecular ions. The composition of the mass-selected ion beam was verified using time-of-flight mass spectrometry, α\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym}\usepackage{amsfonts}\usepackage{amssymb}\usepackage{amsbsy}\usepackage{mathrsfs}\usepackage{upgreek}\setlength{\oddsidemargin}{-69pt}\begin{document}$$\alpha$$\end{document}- and γ\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym}\usepackage{amsfonts}\usepackage{amssymb}\usepackage{amsbsy}\usepackage{mathrsfs}\usepackage{upgreek}\setlength{\oddsidemargin}{-69pt}\begin{document}$$\gamma$$\end{document}-ray decay spectrometry. Extracted quantities of 225Ac19F2+\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym}\usepackage{amsfonts}\usepackage{amssymb}\usepackage{amsbsy}\usepackage{mathrsfs}\usepackage{upgreek}\setlength{\oddsidemargin}{-69pt}\begin{document}$$^{225}\textrm{Ac}^{19}\textrm{F}_2^{+}$$\end{document} particles per μ\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym}\usepackage{amsfonts}\usepackage{amssymb}\usepackage{amsbsy}\usepackage{mathrsfs}\usepackage{upgreek}\setlength{\oddsidemargin}{-69pt}\begin{document}$$\upmu$$\end{document}C of incident protons were 3.9(3)×107\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym}\usepackage{amsfonts}\usepackage{amssymb}\usepackage{amsbsy}\usepackage{mathrsfs}\usepackage{upgreek}\setlength{\oddsidemargin}{-69pt}\begin{document}$$3.9(3)\times 10^7$$\end{document} from a uranium carbide target and 4.3(4)×107\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym}\usepackage{amsfonts}\usepackage{amssymb}\usepackage{amsbsy}\usepackage{mathrsfs}\usepackage{upgreek}\setlength{\oddsidemargin}{-69pt}\begin{document}$$4.3(4)\times 10^7$$\end{document} for a thorium carbide target. Using a magnetic mass separator, the long-lived contamination 227 Ac is suppressed to <5.47×10-7\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym}\usepackage{amsfonts}\usepackage{amssymb}\usepackage{amsbsy}\usepackage{mathrsfs}\usepackage{upgreek}\setlength{\oddsidemargin}{-69pt}\begin{document}$$<5.47\times 10^{-7}$$\end{document} (95% confidence interval) with respect to 225Ac by activity. Measured rates scale to collections of 108 kBqμ\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym}\usepackage{amsfonts}\usepackage{amssymb}\usepackage{amsbsy}\usepackage{mathrsfs}\usepackage{upgreek}\setlength{\oddsidemargin}{-69pt}\begin{document}$$\upmu$$\end{document}A-1\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym}\usepackage{amsfonts}\usepackage{amssymb}\usepackage{amsbsy}\usepackage{mathrsfs}\usepackage{upgreek}\setlength{\oddsidemargin}{-69pt}\begin{document}$$^{-1}$$\end{document}h-1\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym}\usepackage{amsfonts}\usepackage{amssymb}\usepackage{amsbsy}\usepackage{mathrsfs}\usepackage{upgreek}\setlength{\oddsidemargin}{-69pt}\begin{document}$$^{-1}$$\end{document} of directly produced 225Ac19F2+\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym}\usepackage{amsfonts}\usepackage{amssymb}\usepackage{amsbsy}\usepackage{mathrsfs}\usepackage{upgreek}\setlength{\oddsidemargin}{-69pt}\begin{document}$$^{225}\textrm{Ac}^{19}\textrm{F}_2^{+}$$\end{document}. [ABSTRACT FROM AUTHOR]

Background and Objective: Peanut allergy (PA) is an IgE-mediated food allergy with variable clinical outcomes. Mild-to-severe symptoms affect various organs and, often, the gastrointestinal tract. The role of intestine-derived IgE antibodies in astrointestinal PA symptoms is poorly understood. This study aimed to examine fecal IgE responses in PA as a novel approach to patient endotyping., Methods: Feces and serum samples were collected from peanut-allergic and healthy children (n=26) to identify IgE and cytokines using multiplex assays. Shotgun metagenomics DNA sequencing and allergen database comparisons made it possible to identify microbial peptides with homology to known allergens., Results: Compared to controls, fecal IgE signatures showed broad diversity and increased levels for 13 allergens, including food, venom, contact, and respiratory allergens (P<.01-.0001). Overall, fecal IgE patterns were negatively correlated compared to sera IgE patterns in PA patients, with the greatest differences recorded for peanut allergens (P<.0001). For 83% of the allergens recognized by fecal IgE, we found bacterial homologs from PA patients' gut microbiome (eg, thaumatin-like protein Acinetobacter baumannii vs Act d 2, 109/124 aa identical). Compared to controls, PA patients had higher levels of fecal IgA, IL-22, and auto-IgE binding to their own fecal proteins (P<.001). Finally, levels of fecal IgE correlated with abdominal pain scores (P<.0001), suggesting a link between local IgE production and clinical outcomes., Conclusion: Fecal IgE release from the intestinal mucosa could be an underlying mechanism of severe abdominal pain through the association between leaky gut epithelia and anticommensal TH2 responses in PA.

Antibiotics have transformed medicine, saving millions of lives since they were first used to treat a bacterial infection. However, antibiotics administered to target a specific pathogen can also cause collateral damage to the patient's resident microbial population. These drugs can suppress the growth of commensal species which provide protection against colonization by foreign pathogens, leading to an increased risk of subsequent infection. At the same time, a patient's microbiota can harbour potential pathogens and, hence, be a source of infection. Antibiotic-induced selection pressure can cause overgrowth of resistant pathogens pre-existing in the patient's microbiota, leading to hard-to-treat superinfections. In this Review, we explore our current understanding of how antibiotic therapy can facilitate subsequent infections due to both loss of colonization resistance and overgrowth of resistant microorganisms, and how these processes are often interlinked. We discuss both well-known and currently overlooked examples of antibiotic-associated infections at various body sites from various pathogens. Finally, we describe ongoing and new strategies to overcome the collateral damage caused by antibiotics and to limit the risk of antibiotic-associated infections., (© 2023. Springer Nature Limited.)

The emergence and spread of antimicrobial resistance (AMR) and resistant bacteria, are a global public health challenge. Through horizontal gene transfer, potential pathogens can acquire antimicrobial resistance genes (ARGs) that can subsequently be spread between human, animal, and environmental reservoirs. To understand the dissemination of ARGs and linked microbial taxa, it is necessary to map the resistome within different microbial reservoirs. By integrating knowledge on ARGs in the different reservoirs, the One Health approach is crucial to our understanding of the complex mechanisms and epidemiology of AMR. Here, we highlight the latest insights into the emergence and spread of AMR from the One Health perspective, providing a baseline of understanding for future scientific investigations into this constantly growing global health threat., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Background: Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group., Results: We found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19-positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19-positive individuals compared to healthy controls., Conclusions: Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. Video Abstract., (© 2023. The Author(s).)

Antimicrobial resistance (AMR) is a universal phenomenon the origins of which lay in natural ecological interactions such as competition within niches, within and between micro- to higher-order organisms. To study these phenomena, it is crucial to examine the origins of AMR in pristine environments, i.e., limited anthropogenic influences. In this context, epilithic biofilms residing in glacier-fed streams (GFSs) are an excellent model system to study diverse, intra- and inter-domain, ecological crosstalk. We assessed the resistomes of epilithic biofilms from GFSs across the Southern Alps (New Zealand) and the Caucasus (Russia) and observed that both bacteria and eukaryotes encoded twenty-nine distinct AMR categories. Of these, beta-lactam, aminoglycoside, and multidrug resistance were both abundant and taxonomically distributed in most of the bacterial and eukaryotic phyla. AMR-encoding phyla included Bacteroidota and Proteobacteria among the bacteria, alongside Ochrophyta (algae) among the eukaryotes. Additionally, biosynthetic gene clusters (BGCs) involved in the production of antibacterial compounds were identified across all phyla in the epilithic biofilms. Furthermore, we found that several bacterial genera ( Flavobacterium , Polaromonas, Superphylum Patescibacteria) encode both atimicrobial resistance genes (ARGs) and BGCs within close proximity of each other, demonstrating their capacity to simultaneously influence and compete within the microbial community. Our findings help unravel how naturally occurring BGCs and AMR contribute to the epilithic biofilms mode of life in GFSs. Additionally, we report that eukaryotes may serve as AMR reservoirs owing to their potential for encoding ARGs. Importantly, these observations may be generalizable and potentially extended to other environments that may be more or less impacted by human activity. IMPORTANCE Antimicrobial resistance is an omnipresent phenomenon in the anthropogenically influenced ecosystems. However, its role in shaping microbial community dynamics in pristine environments is relatively unknown. Using metagenomics, we report the presence of antimicrobial resistance genes and their associated pathways in epilithic biofilms within glacier-fed streams. Importantly, we observe biosynthetic gene clusters associated with antimicrobial resistance in both pro- and eukaryotes in these biofilms. Understanding the role of resistance in the context of this pristine environment and complex biodiversity may shed light on previously uncharacterized mechanisms of cross-domain interactions.

Biological wastewater treatment plants (BWWTP) are considered to be hotspots for the evolution and subsequent spread of antimicrobial resistance (AMR). Mobile genetic elements (MGEs) promote the mobilization and dissemination of antimicrobial resistance genes (ARGs) and are thereby critical mediators of AMR within the BWWTP microbial community. At present, it is unclear whether specific AMR categories are differentially disseminated via bacteriophages (phages) or plasmids. To understand the segregation of AMR in relation to MGEs, we analyzed meta-omic (metagenomic, metatranscriptomic and metaproteomic) data systematically collected over 1.5 years from a BWWTP. Our results showed a core group of 15 AMR categories which were found across all timepoints. Some of these AMR categories were disseminated exclusively (bacitracin) or primarily (aminoglycoside, MLS and sulfonamide) via plasmids or phages (fosfomycin and peptide), whereas others were disseminated equally by both. Combined and timepoint-specific analyses of gene, transcript and protein abundances further demonstrated that aminoglycoside, bacitracin and sulfonamide resistance genes were expressed more by plasmids, in contrast to fosfomycin and peptide AMR expression by phages, thereby validating our genomic findings. In the analyzed communities, the dominant taxon Candidatus Microthrix parvicella was a major contributor to several AMR categories whereby its plasmids primarily mediated aminoglycoside resistance. Importantly, we also found AMR associated with ESKAPEE pathogens within the BWWTP, and here MGEs also contributed differentially to the dissemination of the corresponding ARGs. Collectively our findings pave the way toward understanding the segmentation of AMR within MGEs, thereby shedding new light on resistome populations and their mediators, essential elements that are of immediate relevance to human health., Competing Interests: Ld, SB, BK, PM, PW No competing interests declared, (© 2022, de Nies et al.)

The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and timescales shaping this resistome remain elusive. Using an antibiotic cocktail administered to a murine model along with a longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire antimicrobial resistance genes (ARGs) after a single antibiotic course. While most of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Enterobacteriaceae, Enterococcaceae, and Lactobacillaceae families acquire resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotics in the corresponding metagenome-assembled genomes (MAGs) and trace their origins within each genome. Here we show that, while mobile genetic elements (MGEs), including bacteriophages and plasmids, contribute to the spread of ARGs, integrons represent key factors mediating AMR in the antibiotic-treated mice. Our findings suggest that a single course of antibiotics alone may act as the selective sweep driving ARG acquisition and incidence in gut commensals over a single mammalian lifespan., (© 2022. The Author(s).)

In glacier-fed streams, ecological windows of opportunity allow complex microbial biofilms to develop and transiently form the basis of the food web, thereby controlling key ecosystem processes. Using metagenome-assembled genomes, we unravel strategies that allow biofilms to seize this opportunity in an ecosystem otherwise characterized by harsh environmental conditions. We observe a diverse microbiome spanning the entire tree of life including a rich virome. Various co-existing energy acquisition pathways point to diverse niches and the exploitation of available resources, likely fostering the establishment of complex biofilms during windows of opportunity. The wide occurrence of rhodopsins, besides chlorophyll, highlights the role of solar energy capture in these biofilms while internal carbon and nutrient cycling between photoautotrophs and heterotrophs may help overcome constraints imposed by oligotrophy in these habitats. Mechanisms potentially protecting bacteria against low temperatures and high UV-radiation are also revealed and the selective pressure of this environment is further highlighted by a phylogenomic analysis differentiating important components of the glacier-fed stream microbiome from other ecosystems. Our findings reveal key genomic underpinnings of adaptive traits contributing to the success of complex biofilms to exploit environmental opportunities in glacier-fed streams, which are now rapidly changing owing to global warming., (© 2022. The Author(s).)

Real-world evaluations of metagenomic reconstructions are challenged by distinguishing reconstruction artifacts from genes and proteins present in situ. Here, we evaluate short-read-only, long-read-only and hybrid assembly approaches on four different metagenomic samples of varying complexity. We demonstrate how different assembly approaches affect gene and protein inference, which is particularly relevant for downstream functional analyses. For a human gut microbiome sample, we use complementary metatranscriptomic and metaproteomic data to assess the metagenomic data-based protein predictions. Our findings pave the way for critical assessments of metagenomic reconstructions. We propose a reference-independent solution, which exploits the synergistic effects of multi-omic data integration for the in situ study of microbiomes using long-read sequencing data., (© The Author(s) 2021. Published by Oxford University Press.)

Background: Retinol binding protein 1 (Rbp1) acts as an intracellular regulator of vitamin A metabolism and retinoid transport. In mice, Rbp1 deficiency decreases the capacity of hepatic stellate cells to take up all-trans retinol and sustain retinyl ester stores. Furthermore, Rbp1 is crucial for visual capacity. Although the function of Rbp1 has been studied in the mature eye, its role during early anterior neural development has not yet been investigated in detail., Results: We showed that rbp1 is expressed in the eye, anterior neural crest cells (NCCs) and prosencephalon of the South African clawed frog Xenopus laevis. Rbp1 knockdown led to defects in eye formation, including microphthalmia and disorganized retinal lamination, and to disturbed induction and differentiation of the eye field, as shown by decreased rax and pax6 expression. Furthermore, it resulted in reduced rax expression in the prosencephalon and affected cranial cartilage. Rbp1 inhibition also interfered with neural crest induction and migration, as shown by twist and slug. Moreover, it led to a significant reduction of the all-trans retinoic acid target gene pitx2 in NCC-derived periocular mesenchyme. The Rbp1 knockdown phenotypes were rescued by pitx2 RNA co-injection., Conclusion: Rbp1 is crucial for the development of the anterior neural tissue., (© 2021 The Authors. Developmental Dynamics published by Wiley Periodicals LLC on behalf of American Association of Anatomists.)

In recent years, multi-omic studies have enabled resolving community structure and interrogating community function of microbial communities. Simultaneous generation of metagenomic, metatranscriptomic, metaproteomic, and (meta) metabolomic data is more feasible than ever before, thus enabling in-depth assessment of community structure, function, and phenotype, thus resulting in a multitude of multi-omic microbiome datasets and the development of innovative methods to integrate and interrogate those multi-omic datasets. Specifically, the application of reference-independent approaches provides opportunities in identifying novel organisms and functions. At present, most of these large-scale multi-omic datasets stem from spatial sampling (e.g., water/soil microbiomes at several depths, microbiomes in/on different parts of the human anatomy) or case-control studies (e.g., cohorts of human microbiomes). We believe that longitudinal multi-omic microbiome datasets are the logical next step in microbiome studies due to their characteristic advantages in providing a better understanding of community dynamics, including: observation of trends, inference of causality, and ultimately, prediction of community behavior. Furthermore, the acquisition of complementary host-derived omics, environmental measurements, and suitable metadata will further enhance the aforementioned advantages of longitudinal data, which will serve as the basis to resolve drivers of community structure and function to understand the biotic and abiotic factors governing communities and specific populations. Carefully setup future experiments hold great potential to further unveil ecological mechanisms to evolution, microbe-microbe interactions, or microbe-host interactions. In this article, we discuss the challenges, emerging strategies, and best-practices applicable to longitudinal microbiome studies ranging from sampling, biomolecular extraction, systematic multi-omic measurements, reference-independent data integration, modeling, and validation., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Martínez Arbas, Busi, Queirós, de Nies, Herold, May, Wilmes, Muller and Narayanasamy.)

Caesarean section delivery (CSD) disrupts mother-to-neonate transmission of specific microbial strains and functional repertoires as well as linked immune system priming. Here we investigate whether differences in microbiome composition and impacts on host physiology persist at 1 year of age. We perform high-resolution, quantitative metagenomic analyses of the gut microbiomes of infants born by vaginal delivery (VD) or by CSD, from immediately after birth through to 1 year of life. Several microbial populations show distinct enrichments in CSD-born infants at 1 year of age including strains of Bacteroides caccae, Bifidobacterium bifidum and Ruminococcus gnavus, whereas others are present at higher levels in the VD group including Faecalibacterium prausnitizii, Bifidobacterium breve and Bifidobacterium kashiwanohense. The stimulation of healthy donor-derived primary human immune cells with LPS isolated from neonatal stool samples results in higher levels of tumour necrosis factor alpha (TNF-α) in the case of CSD extracts over time, compared to extracts from VD infants for which no such changes were observed during the first year of life. Functional analyses of the VD metagenomes at 1 year of age demonstrate a significant increase in the biosynthesis of the natural antibiotics, carbapenem and phenazine. Concurrently, we find antimicrobial resistance (AMR) genes against several classes of antibiotics in both VD and CSD. The abundance of AMR genes against synthetic (including semi-synthetic) agents such as phenicol, pleuromutilin and diaminopyrimidine are increased in CSD children at day 5 after birth. In addition, we find that mobile genetic elements, including phages, encode AMR genes such as glycopeptide, diaminopyrimidine and multidrug resistance genes. Our results demonstrate persistent effects at 1 year of life resulting from birth mode-dependent differences in earliest gut microbiome colonisation., (© 2021. The Author(s).)

Background: Pathogenic microorganisms cause disease by invading, colonizing, and damaging their host. Virulence factors including bacterial toxins contribute to pathogenicity. Additionally, antimicrobial resistance genes allow pathogens to evade otherwise curative treatments. To understand causal relationships between microbiome compositions, functioning, and disease, it is essential to identify virulence factors and antimicrobial resistance genes in situ. At present, there is a clear lack of computational approaches to simultaneously identify these factors in metagenomic datasets., Results: Here, we present PathoFact, a tool for the contextualized prediction of virulence factors, bacterial toxins, and antimicrobial resistance genes with high accuracy (0.921, 0.832 and 0.979, respectively) and specificity (0.957, 0.989 and 0.994). We evaluate the performance of PathoFact on simulated metagenomic datasets and perform a comparison to two other general workflows for the analysis of metagenomic data. PathoFact outperforms all existing workflows in predicting virulence factors and toxin genes. It performs comparably to one pipeline regarding the prediction of antimicrobial resistance while outperforming the others. We further demonstrate the performance of PathoFact on three publicly available case-control metagenomic datasets representing an actual infection as well as chronic diseases in which either pathogenic potential or bacterial toxins are hypothesized to play a role. In each case, we identify virulence factors and AMR genes which differentiated between the case and control groups, thereby revealing novel gene associations with the studied diseases., Conclusion: PathoFact is an easy-to-use, modular, and reproducible pipeline for the identification of virulence factors, bacterial toxins, and antimicrobial resistance genes in metagenomic data. Additionally, our tool combines the prediction of these pathogenicity factors with the identification of mobile genetic elements. This provides further depth to the analysis by considering the genomic context of the pertinent genes. Furthermore, PathoFact's modules for virulence factors, toxins, and antimicrobial resistance genes can be applied independently, thereby making it a flexible and versatile tool. PathoFact, its models, and databases are freely available at https://pathofact.lcsb.uni.lu . Video abstract.

Reliable recognition of pain is difficult in ferrets as many currently available parameters are non-specific, inconsistent and/or impractical. Grimace scales have successfully been applied to assess pain in different animal species and might also be applicable to ferrets. To compose a Ferret Grimace Scale (FGS), we studied the facial musculature of ferrets and compared lateral photographs of 19 ferret faces at six time points before and after intraperitoneal telemetry probe implantation. We identified the Action Units (AUs) orbital tightening, nose bulging, cheek bulging, ear changes and whisker retraction as potential indicators of pain in ferrets. To evaluate whether these AUs could reliably be used to identify photographs taken before and after surgery, the photographs were scored 0, 1 or 2 (not, moderately or obviously present) by 11 observers that were blinded to the treatment and timing of the photographs. All AU-scores assigned to the photographs taken five hours after surgery were significantly higher compared to their time-matched baseline scores. Further analysis using the weights that were obtained using a Linear Discriminant Analysis revealed that scoring orbital tightening alone was sufficient to make this distinction with high sensitivity, specificity and accuracy. Including weighted scores for nose bulging, cheek bulging and ear change did not change this. As these AUs had more missing values than orbital tightening, their descriptions should be re-evaluated. Including whisker retraction, which had a negative weight, resulted in lower accuracy and should therefore in its current form be left out of the FGS. Overall, the results of this study suggest that the FGS and the AU orbital tightening in particular could be useful in a multifactorial pain assessment protocol for ferrets. However, before applying the FGS in practice, it should be further validated by incorporating more time points before and after applying (different) painful stimuli, and different levels of analgesia.

The performance and microbial community characteristics of a laboratory scale anaerobic baffled reactor (ABR) with four compartments (C1-C4) treating sugar refinery wastewater were investigated. The COD removal was 94.8 % with a CH4 yield of 0.21 L g(-1) CODremoved at total organic loading rate (OLR) of 5.33 kg COD/m(-3) day(-1). Fermentative bacteria were dominant in C1 and C2, while syntrophic acetogens and methanogens were dominant in C3 and C4. Some acid-tolerant methanogens were enriched in acidogenic phase. The present of the acid-tolerant methanogens could improve the efficiency and stability of the ABR as the most of the methanogens are vulnerable to low pH. In addition, high functional redundancy of the fermentative bacteria implicated that the microbial communities in acidogenic phase were stable functionally and allowed the ABR to balance perturbation. It was also found that syntrophic acetogenesis might be a weakness in the ABR as syntrophic acetogens were poor as compared with fermentative bacteria and methanogens.

Multi-phase extraction (MPE) is commonly used at petroleum-contaminated sites to volatilize and recover hydrocarbons from the vadose and saturated zones in contaminant source areas. Although primarily a physical treatment technology, the induced subsurface air flow can potentially increase oxygen supply and promote aerobic biodegradation of benzene, toluene, ethylbenzene, and xylenes (BTEX), the contaminants of concern at gasoline-contaminated sites. In this study, real-time PCR enumeration of aromatic oxygenase genes and PCR-DGGE profiles were used to elucidate the impact of MPE operation on the aquifer microbial community structure and function at a gasoline-contaminated site. Prior to system activation, ring-hydroxylating toluene monooxygenase (RMO) and naphthalene dioxygenase (NAH) gene copies were on the order of 10(6) to 10(10)copies L(-1) in groundwater samples obtained from BTEX-impacted wells. Aromatic oxygenase genes were not detected in groundwater samples obtained during continuous MPE indicating decreased populations of BTEX-utilizing bacteria. During periods of pulsed MPE, total aromatic oxygenase gene copies were not significantly different than prior to system activation, however, shifts in aromatic catabolic genotypes were noted. The consistent detection of RMO, NAH, and phenol hydroxylase (PHE), which catabolizes further oxidation of hydroxylated BTEX metabolites indicated the potential for aerobic biodegradation of dissolved BTEX during pulsed MPE.

Subsurface injection of oxygen-releasing materials (ORMs) is frequently performed at petroleum-contaminated sites to stimulate aerobic bioremediation of benzene, toluene, ethylbenzene, and xylenes (BTEX). In this study, qPCR enumeration of aromatic oxygenase genes and PCR-DGGE profiles of bacterial 16S rRNA genes were combined with groundwater monitoring to determine the impact of ORM injection on BTEX bioremediation at a gasoline-contaminated site. Prior to injection, BTEX concentrations were greater than 3 mg/L and DO levels were typically lessthan 2 mg/L, butphenol hydroxylase (PHE) and ring-hydroxylating toluene monooxygenase (RMO) genes were detected in impacted wells indicating the potential for aerobic BTEX biodegradation. Following injection, DO increased, BTEX concentrations decreased substantially, and PHE and RMO genes copies increased by 1-3 orders of magnitude. In addition, naphthalene dioxygenase (NAH) and xylene monooxygenase (TOL) genes were intermittently detected during periods of increased DO. Following depletion of the ORM, DO decreased, BTEX concentrations rebounded, and oxygenase genes were no longer detected. Temporal changes in PCR-DGGE microbial community profiles reflected the dynamic changes in subsurface conditions. Overall, the combination of chemical and geochemical analyses with quantification of aromatic oxygenase genes demonstrated that injection stimulated BTEX biodegradation until the ORM was depleted.

As the technological benefits of nanotechnology begin to rapidly move from laboratory to large-scale industrial application, release of nanomaterials to the environment is inevitable. Little is known about the fate and effects of nanomaterials in nature. Major environmental receptors of nanomaterials will be soil, sediment, and biosolids from wastewater treatment. Analysis of anaerobic microbial activity and communities provides needed information about the effects of nanoparticles in certain environments. In this study, biosolids from anaerobic wastewater treatment sludge were exposed to fullerene (C60) in order to model an environmentally relevant discharge scenario. Activity was assessed by monitoring production of CO2 and CH4. Changes in community structure were monitored by denaturing gradient gel electrophoresis (DGGE), using primer sets targeting the small subunit rRNA genes of Bacteria, Archaea, and Eukarya. Findings suggest that C60 fullerenes have no significant effect on the anaerobic community over an exposure period of a few months. This conclusion is based on the absence of toxicity indicated by no change in methanogenesis relative to untreated reference samples. DGGE results show no evidence of substantial community shifts due to treatment with C60, in any subset of the microbial community.

Because of the bioaccumulation of penta- and tetrapolybrominated diphenyl ether (PBDE) flame retardants in biota,the environmental biotransformation of decabromodiphenyl ether (BDE-209) is of interest. BDE-209 accounts for more than 80% by mass of PBDE production and is the dominant PBDE in sediments. Most sediments are anaerobic and reports of microbial reductive dehalogenation of hydrophobic persistent organohalogen pollutants are numerous. Reductive debromination of BDE-209 in the environment could provide a significant source of lesser-brominated PBDEs to biota. Moreover, a recent study showed that BDE-209 debrominates in sewage sludge, and another demonstrated that some halorespiring bacteria will debrominate BDE-209. To determine whether reductive debromination of BDE-209 occurs in sediments, parallel experiments were conducted using anaerobic sediment microcosms and a cosolvent-enhanced biomimetic system. In the biomimetic system, reductive debromination occurred at rates corresponding to bromine substitution levels with a BDE-209 half-life of only 18 s compared with a halflife of almost 60 days for 2,2',4,4'-tetrabromodiphenyl ether. In sediment, the measured debromination half-life of BDE-209 was well over a decade and was in good agreement with the predicted value obtained from the biomimetic experiment. Product congeners were predominantly double para-substituted. BDE-209 debrominated in sediment with a corresponding increase in nona-, octa-, hepta-, and hexa-PBDEs. Nine new PBDE congeners appeared in sediment from reductive debromination. Given the very large BDE-209 burden already in sediments globally, it is important to determine whether this transformation is a significant source of lesser-brominated PBDEs to the environment.

Monitoring groundwater benzene, toluene, ethylbenzene, and xylene (BTEX) concentrations is the typical method to assess monitored natural attenuation (MNA) and bioremediation as corrective actions at gasoline-contaminated sites. Conclusive demonstration of bioremediation, however, relies on converging lines of chemical and biological evidence to support a decision. In this study, real-time PCR quantification of aromatic oxygenase genes was used to evaluate the feasibility of MNA at two gasoline-impacted sites. Phenol hydroxylase (PHE), ring-hydroxylating toluene monooxygenase (RMO), naphthalene dioxygenase (NAH), toluene monooxygenase (TOL), toluene dioxygenase (TOD), and biphenyl dioxygenase (BPH4) genes were routinely detected in BTEX-impacted wells. Aromatic oxygenase genes were not detected in sentinel wells outside the plume indicating that elevated levels of oxygenase genes corresponded to petroleum hydrocarbon contamination. Total aromatic oxygenase gene copy numbers detected in impacted wells were on the order of 10(6)-10(9)copies L(-1). PHE, RMO, NAH, TOD, and BPH4 gene copies positively correlated to total BTEX concentration. Mann-Kendall analysis of benzene concentrations was used to evaluate the status of the dissolved BTEX plume. The combination of trend analysis of contaminant concentrations with quantification of aromatic oxygenase genes was used to assess the feasibility of MNA as corrective measures at both sites.

The nascent state of the nanoproduct industry calls for important early assessment of environmental impacts before significant releases have occurred. Clearly, the impact of manufactured nanomaterials on key soil processes must be addressed so that an unbiased discussion concerning the environmental consequences of nanotechnology can take place. In this study, soils were treated with either 1 microg C60 g(-1) soil in aqueous suspension (nC60) or 1000 microg C60 g(-1) soil in granularform, a control containing equivalent tetrahydrofuran residues as generated during nC60 formation process or water and incubated for up to 180 days. Treatment effects on soil respiration, both basal and glucose-induced, were evaluated. The effects on the soil microbial community size was evaluated using total phospholipid derived phosphate. The impact on community structure was evaluated using both fatty acid profiles and following extraction of total genomic DNA, by DGGE after PCR amplification of total genomic DNA using bacterial variable V3 region targeted primers. In addition, treatment affects on soil enzymatic activities for beta-glucosidase, acid-phosphatase, dehydrogenase, and urease were followed. Our observations show that the introduction of fullerene, as either C60 or nC60, has little impact on the structure and function of the soil microbial community and microbial processes.

Decabromodiphenyl ether (BDE-209) is a major component of a commercial flame retardant formulation; however, there is limited information on the fate of BDE-209 in the environment, including metal oxide mediated degradation. Laboratory experiments were conducted to investigate the birnessite (delta-MnO(2))-promoted debromination of BDE-209 in tetrahydrofuran (THF)-water systems as well as catechol solutions. Up to 100% (0.1044 micromol initial charge) of BDE-209 disappeared upon reaction with birnessite in THF/H(2)O (4:6-9:1). The formation of aqueous Br(-) from BDE-209 reduction was determined and up to 16 mole% of initial bromine was released over the course of the reaction indicating approximately 1.7 Br-C bonds were reduced per BDE-209 molecule. The distribution of debrominated congeners, however, indicated a much greater extent of debromination for some products than what was inferred from an average bromine mass balance. The produced congeners varied from tetra- to nona-bromodiphenyl ether, including BDE-47 and -99, during the 24 h reaction. Experiments with deuterated water indicated that water was not the major hydrogen donor in the reduction but rather THF provided the reducing power. This conclusion was supported by the presence of succinic acid, which was produced from oxidation of THF. The reactions with aqueous catechol, rather than THF-water mixtures, were performed to assess the possible role that compounds found in natural environments, such a tannin-like phenols, might have on the chemistry. These experiments indicated that birnessite mediated debromination of BDE-209 might occur in natural settings.