Microbial community adaptation to quaternary ammonium biocides as revealed by metagenomics

Effects of different quaternary ammonium compounds on intracellular and extracellular resistance genes in nitrification systems under the pre-contamination of benzalkyl dimethylammonium compounds

As the harm of benzalkyl dimethylammonium compounds (BACs) on human health and environment was discovered, alkyltrimethyl ammonium compound (ATMAC) and dialkyldimethyl ammonium compound (DADMAC), which belong to quaternary ammonium compounds (QACs), were likely to replace BACs as the main disinfectants. This study simulated the iterative use of QACs to explore their impact on resistance genes (RGs) in nitrification systems pre-contaminated by BACs. ATMAC could initiate and maintain partial nitrification. DADMAC generated higher levels of reactive oxygen species and lactate dehydrogenase, leading to increased biological toxicity in bacteria. The abundance of intracellular RGs of sludge was higher with the stress of QACs. DADMAC also induced higher extracellular polymeric substance secretion. Moreover, it facilitated the transfer of RGs from sludge to water, with ATMAC disseminating RGs through si-tnpA-04 and DADMAC through si-intI1. Sediminibacterium might be potential hosts for RGs. This study offered insights into disinfectant usage in the post-COVID-19 era.

Challenges of quaternary ammonium antimicrobial agents: Mechanisms, resistance, persistence and impacts on the microecology

Quaternary ammonium compounds (QACs) served as broad spectrum antimicrobial agents are widely applied for surface disinfection, skin and mucous disinfection, and mouthwash. The daily applications of QACs have significantly increased, especially during the COVID-19 pandemic. However, the environmental residues of QACs have demonstrated harmful impacts on the environment, leading to an increase in environmental contamination, resistant microbes and disruption of microecology. The actions of QACs were related to their cationic character, which can impact the negatively charged cell membranes, but the details are still unclear. Moreover, bacteria with lower sensitivity and resistant pathogens have been detected in clinics and environments, while QACs were also reported to induce the formation of bacterial persisters. Even worse, the resistant bacteria even showed co-resistance and cross-resistance with traditional antibiotics, decreasing therapeutic effectiveness, and disrupting the microecology homeostasis. Unfortunately, the resistance and persistence mechanisms of QACs and the effects of QACs on microecology are still not clear, which even neglected during their daily usages. Therefore, we summarized and discussed current understandings on the antimicrobial actions, resistance, persistence and impacts on the microecology to highlight the challenges in the QACs applications and discuss the possible strategies for overcoming their drawbacks.

Bushy-Tailed QACs: The Development of Multicationic Quaternary Ammonium Compounds with a High Degree of Alkyl Chain Substitution

Quaternary ammonium compounds have served as a first line of protection for human health as surface disinfectants and sanitizers for nearly a century. However, increasing levels of bacterial resistance have spurred the development of novel QAC architectures. In light of the observed reduction in eukaryotic cell toxicity when the alkyl chains on QACs are shorter in nature (≤10 C), we prepared 47 QAC architectures that bear multiple short alkyl chains appended to up to three cationic groups, thus rendering them "bushy-tailed" multiQACs. Antibacterial activity was strong (often ~1-4 μM) in a varied set of bushy-tailed architectures, though observed therapeutic indices were not significantly improved over QAC structures bearing fewer and longer alkyl chains.

Multi-species biofilms of environmental microbiota isolated from fruit packing facilities promoted tolerance of Listeria monocytogenes to benzalkonium chloride

Listeria monocytogenes may survive and persist in food processing environments due to formation of complex multi-species biofilms of environmental microbiota that co-exists in these environments. This study aimed to determine the effect of selected environmental microbiota on biofilm formation and tolerance of L. monocytogenes to benzalkonium chloride in formed biofilms. The studied microbiota included bacterial families previously shown to co-occur with L. monocytogenes in tree fruit packing facilities, including Pseudomonadaceae, Xanthomonadaceae, Microbacteriaceae, and Flavobacteriaceae. Biofilm formation ability and the effect of formed biofilms on the tolerance of L. monocytogenes to benzalkonium chloride was measured in single- and multi-family assemblages. Biofilms were grown statically on polystyrene pegs submerged in a R2A broth. Biofilm formation was quantified using a crystal violet assay, spread-plating, confocal laser scanning microscopy, and its composition was assessed using amplicon sequencing. The concentration of L. monocytogenes in biofilms was determined using the most probable number method. Biofilms were exposed to the sanitizer benzalkonium chloride, and the death kinetics of L. monocytogenes were quantified using a most probable number method. A total of 8, 8, 6, and 3 strains of Pseudomonadaceae, Xanthomonadaceae, Microbacteriaceae, and Flavobacteriaceae, respectively, were isolated from the environmental microbiota of tree fruit packing facilities and were used in this study. Biofilms formed by Pseudomonadaceae, Xanthomonadaceae, and all multi-family assemblages had significantly higher concentration of bacteria, as well as L. monocytogenes, compared to biofilms formed by L. monocytogenes alone. Furthermore, multi-family assemblage biofilms increased the tolerance of L. monocytogenes to benzalkonium chloride compared to L. monocytogenes mono-species biofilms and planktonic multi-family assemblages. These findings suggest that L. monocytogenes control strategies should focus not only on assessing the efficacy of sanitizers against L. monocytogenes, but also against biofilm-forming microorganisms that reside in the food processing built environment, such as Pseudomonadaceae or Xanthomonadaceae.

Transcriptomic signature of bacteria exposed to benzalkonium chloride

The COVID-19 pandemic has highlighted our reliance on biocides, the increasing prevalence of resistance to biocides is a risk to public health. Bacterial exposure to the biocide, benzalkonium chloride (BAC), resulted in a unique transcriptomic profile, characterised by both a short and long-term response. Differential gene expression was observed in four main areas: motility, membrane composition, proteostasis, and the stress response. A metabolism shift to protect the proteome and the stress response were prioritised suggesting these are main resistance mechanisms. Whereas "well-established" mechanisms, such as biofilm formation, were not found to be differentially expressed after exposure to BAC.

Microbial response and recovery strategy of the anammox process under ciprofloxacin stress from pure strain and consortia perspectives

Ciprofloxacin (CIP) poses a high risk of resistance development in water environments. Therefore, comprehensive effects and recovery strategies of CIP in anaerobic ammonia oxidation (anammox) process were systematically elucidated from consortia and pure strains perspectives. The anammox consortia was not significantly affected by the stress of 10 mg L-1 CIP, while the higher concentration (20 mg L-1) of CIP caused a dramatic reduction in the nitrogen removal performance of anammox system. Simultaneously, the abundances of dominant functional bacteria and corresponding genes also significantly decreased. Such inhibition could not be mitigated by the recovery strategy of adding hydrazine and hydroxylamine. Reducing nitrogen load rate from 5.1 to 1.4 kg N m-3 d-1 promoted the restoration of three reactors. In addition, the robustness and recovery of anammox systems was evaluated using starvation and shock strategies. Simultaneously, antibiotic resistance genes and key metabolic pathways of anammox consortia were upregulated, such as carbohydrate and energy metabolisms. In addition, 11 pure stains were isolated from the anammox system and identified through phylogenetic analysis, 40 % of which showed multidrug resistance, especially Pseudomonas. These findings provide deep insights into the responding mechanism of anammox consortia to CIP stress and promote the application of anammox process for treating wastewater containing antibiotics.

Does Environmental Exposure to Pharmaceutical and Personal Care Product Residues Result in the Selection of Antimicrobial-Resistant Microorganisms, and is this Important in Terms of Human Health Outcomes?

The environment plays a critical role in the development, dissemination, and transmission of antimicrobial resistance (AMR). Pharmaceuticals and personal care products (PPCPs) enter the environment through direct application to the environment and through anthropogenic pollution. Although there is a growing body of evidence defining minimal selective concentrations (MSCs) of antibiotics and the role antibiotics play in horizontal gene transfer (HGT), there is limited evidence on the role of non-antibiotic PPCPs. Existing data show associations with the development of resistance or effects on bacterial growth rather than calculating selective endpoints. Research has focused on laboratory-based systems rather than in situ experiments, although PPCP concentrations found throughout wastewater, natural water, and soil environments are often within the range of laboratory-derived MSCs and at concentrations shown to promote HGT. Increased selection and HGT of AMR by PPCPs will result in an increase in total AMR abundance in the environment, increasing the risk of exposure and potential transmission of environmental AMR to humans. There is some evidence to suggest that humans can acquire resistance from environmental settings, with water environments being the most frequently studied. However, because this is currently limited, we recommend that more evidence be gathered to understand the risk the environment plays in regard to human health. In addition, we recommend that future research efforts focus on MSC-based experiments for non-antibiotic PPCPS, particularly in situ, and investigate the effect of PPCP mixtures on AMR. Environ Toxicol Chem 2024;43:623-636. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

A laboratory ice machine as a cold oligotrophic artificial microbial niche for biodiscovery

Microorganisms are ubiquitously distributed in nature and usually appear as biofilms attached to a variety of surfaces. Here, we report the development of a thick biofilm in the drain pipe of several standard laboratory ice machines, and we describe and characterise, through culture-dependent and -independent techniques, the composition of this oligotrophic microbial community. By using culturomics, 25 different microbial strains were isolated and taxonomically identified. The 16S rRNA high-throughput sequencing analysis revealed that Bacteroidota and Proteobacteria were the most abundant bacterial phyla in the sample, followed by Acidobacteriota and Planctomycetota, while ITS high-throughput sequencing uncovered the fungal community was clearly dominated by the presence of a yet-unidentified genus from the Didymellaceae family. Alpha and beta diversity comparisons of the ice machine microbial community against that of other similar cold oligotrophic and/or artificial environments revealed a low similarity between samples, highlighting the ice machine could be considered a cold and oligotrophic niche with a unique selective pressure for colonisation of particular microorganisms. The recovery and analysis of high-quality metagenome-assembled genomes (MAGs) yielded a strikingly high rate of new species. The functional profiling of the metagenome sequences uncovered the presence of proteins involved in extracellular polymeric substance (EPS) and fimbriae biosynthesis and also allowed us to detect the key proteins involved in the cold adaptation mechanisms and oligotrophic metabolic pathways. The metabolic functions in the recovered MAGs confirmed that all MAGs have the genes involved in psychrophilic protein biosynthesis. In addition, the highest number of genes for EPS biosynthesis was presented in MAGs associated with the genus Sphingomonas, which was also recovered by culture-based method. Further, the MAGs with the highest potential gene number for oligotrophic protein production were closely affiliated with the genera Chryseoglobus and Mycobacterium. Our results reveal the surprising potential of a cold oligotrophic microecosystem within a machine as a source of new microbial taxa and provide the scientific community with clues about which microorganisms are able to colonise this ecological niche and what physiological mechanisms they develop. These results pave the way to understand how and why certain microorganisms can colonise similar anthropogenic environments.

Risks of benzalkonium chlorides as emerging contaminants in the environment and possible control strategies from the perspective of ecopharmacovigilance

An unprecedented increase in the use of disinfection products triggered by the coronavirus disease 2019 (COVID-19) pandemic is resulting in aggravating environmental loads of disinfectants as emerging contaminants, which has been considered a cause for worldwide secondary disasters. This review analyzed the literature published in the last decade about occurrence, bioaccumulation, and possible environmental risks of benzalkonium chlorides (BKCs) as emerging contaminants. Results indicated that BKCs globally occurred in municipal wastewater, surface water, groundwater, reclaimed water, sludge, sediment, soil, roof runoff, and residential dust samples across 13 countries. The maximum residual levels of 30 mg/L and 421 μg/g were reported in water and solid environmental samples, respectively. Emerging evidences suggested possible bioaccumulation of BKCs in plants, even perhaps humans. Environmentally relevant concentrations of BKCs exert potential adverse impacts on aquatic and terrestrial species, including genotoxicity, respiratory toxicity, behavioural effects and neurotoxicity, endocrine disruption and reproductive impairment, phytotoxicity, etc. Given the intrinsic biocidal and preservative properties of disinfectants, the inductive effects of residual BKCs in environment in terms of resistance and imbalance of microorganisms have been paid special attention. Considering the similarities of disinfectants to pharmaceuticals, from the perspective of ecopharmacovigilance (EPV), a well-established strategy for pharmaceutical emerging contaminants, we use the control of BKC pollution as a case, and provide some recommendations for employing the EPV measures to manage environmental risks posed by disinfectant emerging contaminants.

Sustained Ability of a Natural Microbial Community to Remove Nitrate from Groundwater

Microbial-mediated nitrate removal from groundwater is widely recognized as the predominant mechanism for nitrate attenuation in contaminated aquifers and is largely dependent on the presence of a carbon-bearing electron donor. The repeated exposure of a natural microbial community to an electron donor can result in the sustained ability of the community to remove nitrate; this phenomenon has been clearly demonstrated at the laboratory scale. However, in situ demonstrations of this ability are lacking. For this study, ethanol (electron donor) was repeatedly injected into a groundwater well (treatment) for six consecutive weeks to establish the sustained ability of a microbial community to remove nitrate. A second well (control) located upgradient was not injected with ethanol during this time. The treatment well demonstrated strong evidence of sustained ability as evident by ethanol, nitrate, and subsequent sulfate removal up to 21, 64, and 68%, respectively, as compared to the conservative tracer (bromide) upon consecutive exposures. Both wells were then monitored for six additional weeks under natural (no injection) conditions. During the final week, ethanol was injected into both treatment and control wells. The treatment well demonstrated sustained ability as evident by ethanol and nitrate removal up to 20 and 21%, respectively, as compared to bromide, whereas the control did not show strong evidence of nitrate removal (5% removal). Surprisingly, the treatment well did not indicate a sustained and selective enrichment of a microbial community. These results suggested that the predominant mechanism(s) of sustained ability likely exist at the enzymatic- and/or genetic-levels. The results of this study demonstrated the in situ ability of a microbial community to remove nitrate can be sustained in the prolonged absence of an electron donor.

Whole genome strategies and bioremediation insight into dehalogenase-producing bacteria

An integral approach to decoding both culturable and uncultured microorganisms' metabolic activity involves the whole genome sequencing (WGS) of individual/complex microbial communities. WGS of culturable microbes, amplicon sequencing, metagenomics, and single-cell genome analysis are selective techniques integrating genetic information and biochemical mechanisms. These approaches transform microbial biotechnology into a quick and high-throughput culture-independent evaluation and exploit pollutant-degrading microbes. They are windows into enzyme regulatory bioremediation pathways (i.e., dehalogenase) and the complete bioremediation process of organohalide pollutants. While the genome sequencing technique is gaining the scientific community's interest, it is still in its infancy in the field of pollutant bioremediation. The techniques are becoming increasingly helpful in unraveling and predicting the enzyme structure and explore metabolic and biodegradation capabilities.

Increased Use of Quaternary Ammonium Compounds during the SARS-CoV-2 Pandemic and Beyond: Consideration of Environmental Implications

Quaternary ammonium compounds (QACs) are active ingredients in over 200 disinfectants currently recommended by the U.S. EPA for use to inactivate the SARS-CoV-2 (COVID-19) virus. The amounts of these compounds used in household, workplace, and industry settings has very likely increased, and usage will continue to be elevated given the scope of the pandemic. QACs have been previously detected in wastewater, surface waters, and sediments, and effects on antibiotic resistance have been explored. Thus, it is important to assess potential environmental and engineering impacts of elevated QAC usage, which may include disruption of wastewater treatment unit operations, proliferation of antibiotic resistance, formation of nitrosamine disinfection byproducts, and impacts on biota in surface waters. The threat caused by COVID-19 is clear, and a reasonable response is elevated use of QACs to mitigate spread of infection. Exploration of potential effects, environmental fate, and technologies to minimize environmental releases of QACs, however, is warranted.

Long-term exposure of activated sludge in chemostats leads to changes in microbial communities composition and enhanced biodegradation of 4-chloroaniline and N-methylpiperazine

Exposure history and adaptation of the inoculum to chemicals have been shown to influence the outcome of ready biodegradability tests. However, there is a lack of information about the mechanisms involved in microbial adaptation and the implication thereof for the tests. In the present study, we investigated the impact of a long-term exposure to N-methylpiperazine (NMP) and 4-chloroaniline (4CA) of an activated sludge microbial community using chemostat systems. The objective was to characterize the influence of adaptation to the chemicals on an enhanced biodegradation testing, following the OECD 310 guideline. Cultures were used to inoculate the enhanced biodegradability tests, in batch, before and after exposure to each chemical independently in chemostat culture. Composition and diversity of the microbial communities were characterised by 16s rRNA gene amplicon sequencing. Using freshly sampled activated sludge, NMP was not degraded within the 28 d frame of the test while 4CA was completely eliminated. However, after one month of exposure, the community exposed to NMP was adapted and could completely degrade it. This result was in complete contrast with that from the culture exposed for 3 months to 4CA. Long term incubation in the chemostat system led to a progressive loss of the initial biodegradation capacity of the community, as a consequence of the loss of key degrading microorganisms. This study highlights the potential of chemostat systems to induce adaptation to a specific chemical, ultimately resulting in its biodegradation. At the same time, one should be critical of these observations as the dynamics of a microbial community are difficult to maintain in chemostat, as the loss of 4CA biodegradation capacity demonstrates.

Biodegradability of Dental Care Antimicrobial Agents Chlorhexidine and Octenidine by Ligninolytic Fungi

Chlorhexidine (CHX) and octenidine (OCT), antimicrobial compounds used in oral care products (toothpastes and mouthwashes), were recently revealed to interfere with human sex hormone receptor pathways. Experiments employing model organisms—white-rot fungi Irpex lacteus and Pleurotus ostreatus—were carried out in order to investigate the biodegradability of these endocrine-disrupting compounds and the capability of the fungi and their extracellular enzyme apparatuses to biodegrade CHX and OCT. Up to 70% ± 6% of CHX was eliminated in comparison with a heat-killed control after 21 days of in vivo incubation. An additional in vitro experiment confirmed manganese-dependent peroxidase and laccase are partially responsible for the removal of CHX. Up to 48% ± 7% of OCT was removed in the same in vivo experiment, but the strong sorption of OCT on fungal biomass prevented a clear evaluation of the involvement of the fungi or extracellular enzymes. On the other hand, metabolites indicating the enzymatic transformation of both CHX and OCT were detected and their chemical structures were proposed by means of liquid chromatography–mass spectrometry. Complete biodegradation by the ligninolytic fungi was not achieved for any of the studied analytes, which emphasizes their recalcitrant character with low possibility to be removed from the environment.

Microbial Community Enhances Biodegradation of Bisphenol A Through Selection of Sphingomonadaceae

Bisphenol A (BPA) is a common ingredient in plastic wares and epoxy resins that are essential for our daily life. Despite the obvious benefits, BPA may act as an environmental endocrine disruptor, causing metabolic, reproductive, and/or developmental consequences and diseases in humans and other organisms. Although previous studies have yielded progress toward the microbial breakdown of BPA, the work has primarily been focused on pure cultures rather than complex microbial communities. In this study, we examined microbial communities in bioreactors that control the fate of BPA at various levels (up to 5000 μg L^-1). Microbial communities rapidly increased removal rates of 500-5000 μg L^-1 BPA from 23-29 to 89-99% during the first 2 weeks of the acclimation period, after which > 90% stable removal rates were maintained over 3 months. Biochemical assays demonstrated that BPA was removed by biodegradation, rather than other abiotic removal routes (e.g., adsorption and volatilization). The 16S rRNA gene-based community analysis revealed that 50-5000 μg L^-1 of BPA exposure systematically selected for three Sphingomonadaceae species (Sphingobium, Novosphingobium, and Sphingopyxis). The Sphingomonadaceae-enriched communities acclimated to BPA showed a 7.0-L gVSS^-1 day^-1 BPA degradation rate constant, which is comparable to that (4.1-6.3) of Sphingomonadaceae isolates and is higher than other potential BPA degraders. Taken together, our results advanced the understanding of how microbial communities acclimate to environmentally relevant levels of BPA, gradually enhancing BPA degradation via selective enrichment of a few Sphingomonadaceae populations with higher BPA metabolic activity.

Comparing the selective and co-selective effects of different antimicrobials in bacterial communities

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Selective and co-selective effects of antimicrobials were compared for the first time.

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Ciprofloxacin and trimethoprim were more co-selective than selective.

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Benzalkonium chloride (BAC) did not select for antibiotic/metal/qac resistance genes.

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Metagenomics could identify highly co-selective compounds for further study.

Bacterial communities are exposed to a cocktail of antimicrobial agents, including antibiotics, heavy metals and biocidal antimicrobials such as quaternary ammonium compounds (QACs). The extent to which these compounds may select or co-select for antimicrobial resistance (AMR) is not fully understood. In this study, human-associated, wastewater-derived bacterial communities were exposed to either benzalkonium chloride (BAC), ciprofloxacin or trimethoprim at sub-point-of-use concentrations for one week to determine selective and co-selective potential. Metagenome analyses were performed to determine effects on bacterial community structure and prevalence of antibiotic resistance genes (ARGs) and metal or biocide resistance genes (MBRGS). Ciprofloxacin had the greatest co-selective potential, significantly enriching for resistance mechanisms to multiple antibiotic classes. Conversely, BAC exposure significantly reduced relative abundance of ARGs and MBRGS, including the well characterised qac efflux genes. However, BAC exposure significantly impacted bacterial community structure. Therefore BAC, and potentially other QACs, did not play as significant a role in co-selection for AMR as antibiotics such as ciprofloxacin at sub-point-of-use concentrations in this study. This approach can be used to identify priority compounds for further study, to better understand evolution of AMR in bacterial communities exposed to sub-point-of-use concentrations of antimicrobials.

Ecological processes underpinning microbial community structure during exposure to subinhibitory level of triclosan

Ecological processes shaping the structure and diversity of microbial communities are of practical importance for managing the function and resilience of engineered biological ecosystems such as activated sludge processes. This study systematically evaluated the ecological processes acting during continuous exposure to a subinhibitory level of antimicrobial triclosan (TCS) as an environmental stressor. 16S rRNA gene-based community profiling revealed significant perturbations on the community structure and dramatic reduction (by 20-30%) in species diversity/richness compared to those under the control conditions. In addition, community profiling determined the prevalence of the deterministic processes overwhelming the ecological stochasticity. Analysis of both community composition and phenotypes in the TCS-exposed communities suggested the detailed deterministic mechanism: selection of TCS degrading (Sphingopyxis) and resistant (Pseudoxanthomonas) bacterial populations. The analysis also revealed a significant reduction of core activated sludge members, Chitinophagaceae (e.g., Ferruginibacter) and Comamonadaceae (e.g., Acidovorax), potentially affecting ecosystem functions (e.g., floc formation and nutrient removal) directly associated with system performance (i.e., wastewater treatment efficiency and effluent quality). Overall, our study provides new findings that inform the mechanisms underlying the community structure and diversity of activated sludge, which not only advances the current understanding of microbial ecology in activated sludge, but also has practical implications for the design and operation of environmental bioprocesses for treatment of antimicrobial-bearing waste streams.

Widely Used Benzalkonium Chloride Disinfectants Can Promote Antibiotic Resistance

While the misuse of antibiotics has clearly contributed to the emergence and proliferation of resistant bacterial pathogens, with major health consequences, it remains less clear if the widespread use of disinfectants, such as benzalkonium chlorides (BAC), a different class of biocides than antibiotics, has contributed to this problem. Here, we provide evidence that exposure to BAC coselects for antibiotic-resistant bacteria and describe the underlying genetic mechanisms. After inoculation with river sediment, BAC-fed bioreactors selected for several bacterial taxa, including the opportunistic pathogen Pseudomonas aeruginosa, that were more resistant to several antibiotics than their counterparts in a control (no BAC) bioreactor. A metagenomic analysis of the bioreactor microbial communities, confirmed by gene cloning experiments with the derived isolates, suggested that integrative and conjugative elements encoding a BAC efflux pump together with antibiotic resistance genes were responsible for these results. Furthermore, the exposure of the P. aeruginosa isolates to increasing concentrations of BAC selected for mutations in pmrB (polymyxin resistance) and physiological adaptations that contributed to a higher tolerance to polymyxin B and other antibiotics. The physiological adaptations included the overexpression of mexCD-oprJ multidrug efflux pump genes when BAC was added in the growth medium at subinhibitory concentrations. Collectively, our results demonstrated that disinfectants promote antibiotic resistance via several mechanisms and highlight the need to remediate (degrade) disinfectants in nontarget environments to further restrain the spread of antibiotic-resistant bacteria.IMPORTANCE Benzalkonium chlorides (BAC) are biocides broadly used in disinfectant solutions. Disinfectants are widely used in food processing lines, domestic households, and pharmaceutical products and are typically designed to have a different mode of action than antibiotics to avoid interfering with the use of the latter. Whether exposure to BAC makes bacteria more resistant to antibiotics remains an unresolved issue of obvious practical consequences for public health. Using an integrated approach that combines metagenomics of natural microbial communities with gene cloning experiments with isolates and experimental evolution assays, we show that the widely used benzalkonium chloride disinfectants promote clinically relevant antibiotic resistance. Therefore, more attention should be given to the usage of these disinfectants, and their fate in nontarget environments should be monitored more tightly.

Impacts of Glutaraldehyde on Microbial Community Structure and Degradation Potential in Streams Impacted by Hydraulic Fracturing

The environmental impacts of hydraulic fracturing, particularly those of surface spills in aquatic ecosystems, are not fully understood. The goals of this study were to (1) understand the effect of previous exposure to hydraulic fracturing fluids on aquatic microbial community structure and (2) examine the impacts exposure has on biodegradation potential of the biocide glutaraldehyde. Microcosms were constructed from hydraulic fracturing-impacted and nonhydraulic fracturing-impacted streamwater within the Marcellus shale region in Pennsylvania. Microcosms were amended with glutaraldehyde and incubated aerobically for 56 days. Microbial community adaptation to glutaraldehyde was monitored using 16S rRNA gene amplicon sequencing and quantification by qPCR. Abiotic and biotic glutaraldehyde degradation was measured using ultra-performance liquid chromatography--high resolution mass spectrometry and total organic carbon. It was found that nonhydraulic fracturing-impacted microcosms biodegraded glutaraldehyde faster than the hydraulic fracturing-impacted microcosms, showing a decrease in degradation potential after exposure to hydraulic fracturing activity. Hydraulic fracturing-impacted microcosms showed higher richness after glutaraldehyde exposure compared to unimpacted streams, indicating an increased tolerance to glutaraldehyde in hydraulic fracturing impacted streams. Beta diversity and differential abundance analysis of sequence count data showed different bacterial enrichment for hydraulic fracturing-impacted and nonhydraulic fracturing-impacted microcosms after glutaraldehyde addition. These findings demonstrated a lasting effect on microbial community structure and glutaraldehyde degradation potential in streams impacted by hydraulic fracturing operations.

A Rieske-Type Oxygenase of Pseudomonas sp. BIOMIG1 Converts Benzalkonium Chlorides to Benzyldimethyl Amine

Recently, an array of eight genes involved in the biotransformation of benzalkonium chlorides (BACs)-an active ingredient of many disinfectants-to benzyldimethyl amine (BDMA) was identified in the genome of Pseudomonas sp. BIOMIG1, which is a bacterium present in various environments and mineralizes BACs. In this study, we showed that heterologous expression of an oxygenase gene (oxyBAC) present in this gene array in E. coli resulted in formation of BDMA from BACs at a rate of 14 μM h^-1. oxyBAC is phylogenetically classified as a Rieske-type oxygenase (RO) and belongs to a group which catalyzes the cleavage of C-N⁺ bond between either methyl or alkyl ester and a quaternary nitrogen (N) of natural quaternary ammonium compounds such as stachydrine, carnitine, and trimethylglycine. Insertion of two glycines into the Rieske domain and substitution of tyrosine with leucine in the mononuclear iron center differentiate oxyBAC from other ROs that cleave C-N⁺, and presumably facilitate the cleavage of saturated alkyl chain from quaternary N via N-dealkylation reaction. In addition, unlike other ROs, oxyBAC did not require a specific reductase to function. Our results demonstrate that oxyBAC represents a new member of RO associated with BAC degradation, and have applications for controlling the fate of BACs in the environment.

Metagenomics Reveals a Novel Virophage Population in a Tibetan Mountain Lake

Virophages are parasites of giant viruses that infect eukaryotic organisms and may affect the ecology of inland water ecosystems. Despite the potential ecological impact, limited information is available on the distribution, diversity, and hosts of virophages in ecosystems. Metagenomics revealed that virophages were widely distributed in inland waters with various environmental characteristics including salinity and nutrient availability. A novel virophage population was overrepresented in a planktonic microbial community of the Tibetan mountain lake, Lake Qinghai. Our study identified coccolithophores and coccolithovirus-like phycodnaviruses in the same community, which may serve as eukaryotic and viral hosts of the virophage population, respectively.

Spills of Hydraulic Fracturing Chemicals on Agricultural Topsoil: Biodegradation, Sorption, and Co-contaminant Interactions

Hydraulic fracturing frequently occurs on agricultural land. Yet the extent of sorption, transformation, and interactions among the numerous organic frac fluid and oil and gas wastewater constituents upon environmental release is hardly known. Thus, this study aims to advance our current understanding of processes that control the environmental fate and toxicity of commonly used hydraulic fracturing chemicals. Poly(ethylene glycol) surfactants were completely biodegraded in agricultural topsoil within 42-71 days, but their transformation was impeded in the presence of the biocide glutaraldehyde and was completely inhibited by salt at concentrations typical for oil and gas wastewater. At the same time, aqueous glutaraldehyde concentrations decreased due to sorption to soil and were completely biodegraded within 33-57 days. While no aqueous removal of polyacrylamide friction reducer was observed over a period of 6 months, it cross-linked with glutaraldehyde, further lowering the biocide's aqueous concentration. These findings highlight the necessity to consider co-contaminant effects when we evaluate the risk of frac fluid additives and oil and gas wastewater constituents in agricultural soils in order to fully understand their human health impacts, likelihood for crop uptake, and potential for groundwater contamination.

Similar Microbial Consortia and Genes Are Involved in the Biodegradation of Benzalkonium Chlorides in Different Environments

Benzalkonium chlorides (BACs) are emerging pollutants. Identification of microorganisms and the genes involved in the biodegradation of BACs is crucial for better understanding the fate of BACs in the environment and developing treatment strategies. Four microbial communities degrading BACs were developed from sewage (SEW), activated sludge (AS), soil (SOIL) and sea sediment (SEA) samples. According to 16S rRNA pyrosequencing and shotgun metagenome sequencing analyses, the most abundant species represented uncharacterized members of the Pseudomonas and Achromobacter genera. BAC biotransformation rates of the enriched microbial communities were 2.8, 3.2, 17.8, and 24.3 μM hr(-1) for SEA, AS, SOIL, and SEW, respectively, and were positively correlated with the relative abundance of a particular Pseudomonas sp. strain, BIOMIG1. The strain BIOMIG1 mineralizes BACs at a rate up to 2.40 μmol hr(-1) 10(-11) cells. Genomes of four BAC degrading and nondegrading BIOMIG1 phenotypes were sequenced and differentially compared with each other. As a result, a gene cluster encoding for transporters, an integrase and a dioxygenase were involved in BAC biotransformation. Our results suggest that BIOMIG1 plays a key role on the fate of BACs in the environment and genes, other than those reported to date, are involved in BAC biotransformation in various habitats.

Widespread Microbial Adaptation to l-Glutamate-N,N-diacetate (L-GLDA) Following Its Market Introduction in a Consumer Cleaning Product

l-Glutamate-N,N-diacetate (L-GLDA) was recently introduced in the United States (U.S.) market as a phosphate replacement in automatic dishwashing detergents (ADW). Prior to introduction, L-GLDA exhibited poor biodegradation in OECD 301B Ready Biodegradation Tests inoculated with sludge from U.S. wastewater treatment plants (WWTPs). However, OECD 303A Activated Sludge WWTP Simulation studies showed that with a lag period to allow for growth (40-50 days) and a solids retention time (SRT) that allows establishment of L-GLDA degraders (>15 days), significant biodegradation (>80% dissolved organic carbon removal) would occur. Corresponding to the ADW market launch, a study was undertaken to monitor changes in the ready biodegradability of L-GLDA using activated sludge samples from various U.S. WWTPs. Initially all sludge inocula showed limited biodegradation ability, but as market introduction progressed, both the rate and extent of degradation increased significantly. Within 22 months, L-GLDA was ready biodegradable using inocula from 12 WWTPs. In an OECD 303A study repeated 18 months post launch, significant and sustained carbon removal (>94%) was observed after a 29-day acclimation period. This study systematically documented field adaptation of a new consumer product chemical across a large geographic region and confirmed the ability of laboratory simulation studies to predict field adaptation.

Development of a New Monomer for the Synthesis of Intrinsic Antimicrobial Polymers with Enhanced Material Properties

The use of biocidal compounds in polymers is steadily increasing because it is one solution to the need for safety and hygiene. It is possible to incorporate an antimicrobial moiety to a polymer. These polymers are referred to as intrinsic antimicrobial. The biocidal action results from contact of the polymer to the microorganisms, with no release of active molecules. This is particularly important in critical fields like food technology, medicine and ventilation technology, where migration or leaching is crucial and undesirable. The isomers N-(1,1-dimethylethyl)-4-ethenyl-benzenamine and N-(1,1-dimethyl-ethyl)-3-ethenyl-benzenamine (TBAMS) are novel (Co-)Monomers for intrinsic anti-microbial polymers. The secondary amines were prepared and polymerized to the corresponding water insoluble polymer. The antimicrobial activity was analyzed by the test method JIS Z 2801:2000. Investigations revealed a high antimicrobial activity against Staphylococcus aureus and Escherichia coli with a reduction level of >4.5 log10 units. Furthermore, scanning electron microscopy (SEM) of E. coli. in contact with the polymer indicates a bactericidal action which is caused by disruption of the bacteria cell membranes, leading to lysis of the cells.

Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data

Background

Antimicrobial resistance remains a growing and significant concern in human and veterinary medicine. Current laboratory methods for the detection and surveillance of antimicrobial resistant bacteria are limited in their effectiveness and scope. With the rapidly developing field of whole genome sequencing beginning to be utilised in clinical practice, the ability to interrogate sequencing data quickly and easily for the presence of antimicrobial resistance genes will become increasingly important and useful for informing clinical decisions. Additionally, use of such tools will provide insight into the dynamics of antimicrobial resistance genes in metagenomic samples such as those used in environmental monitoring.

Results

Here we present the Search Engine for Antimicrobial Resistance (SEAR), a pipeline and web interface for detection of horizontally acquired antimicrobial resistance genes in raw sequencing data. The pipeline provides gene information, abundance estimation and the reconstructed sequence of antimicrobial resistance genes; it also provides web links to additional information on each gene. The pipeline utilises clustering and read mapping to annotate full-length genes relative to a user-defined database. It also uses local alignment of annotated genes to a range of online databases to provide additional information. We demonstrate SEAR’s application in the detection and abundance estimation of antimicrobial resistance genes in two novel environmental metagenomes, 32 human faecal microbiome datasets and 126 clinical isolates of Shigella sonnei.

Conclusions

We have developed a pipeline that contributes to the improved capacity for antimicrobial resistance detection afforded by next generation sequencing technologies, allowing for rapid detection of antimicrobial resistance genes directly from sequencing data. SEAR uses raw sequencing data via an intuitive interface so can be run rapidly without requiring advanced bioinformatic skills or resources. Finally, we show that SEAR is effective in detecting antimicrobial resistance genes in metagenomic and isolate sequencing data from both environmental metagenomes and sequencing data from clinical isolates.

Biocides in hydraulic fracturing fluids: a critical review of their usage, mobility, degradation, and toxicity

Biocides are critical components of hydraulic fracturing ("fracking") fluids used for unconventional shale gas development. Bacteria may cause bioclogging and inhibit gas extraction, produce toxic hydrogen sulfide, and induce corrosion leading to downhole equipment failure. The use of biocides such as glutaraldehyde and quaternary ammonium compounds has spurred a public concern and debate among regulators regarding the impact of inadvertent releases into the environment on ecosystem and human health. This work provides a critical review of the potential fate and toxicity of biocides used in hydraulic fracturing operations. We identified the following physicochemical and toxicological aspects as well as knowledge gaps that should be considered when selecting biocides: (1) uncharged species will dominate in the aqueous phase and be subject to degradation and transport whereas charged species will sorb to soils and be less bioavailable; (2) many biocides are short-lived or degradable through abiotic and biotic processes, but some may transform into more toxic or persistent compounds; (3) understanding of biocides' fate under downhole conditions (high pressure, temperature, and salt and organic matter concentrations) is limited; (4) several biocidal alternatives exist, but high cost, high energy demands, and/or formation of disinfection byproducts limits their use. This review may serve as a guide for environmental risk assessment and identification of microbial control strategies to help develop a sustainable path for managing hydraulic fracturing fluids.

Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities

BACKGROUND

Environmental shotgun sequencing (metagenomics) provides a new way to study communities in microbial ecology. We here use sequence data from the Global Ocean Sampling (GOS) expedition to investigate toxicant selection pressures revealed by the presence of detoxification genes in marine bacteria. To capture a broad range of potential toxicants we selected detoxification protein families representing systems protecting microorganisms from a variety of stressors, such as metals, organic compounds, antibiotics and oxygen radicals.

RESULTS

Using a bioinformatics procedure based on comparative analysis to finished bacterial genomes we found that the amount of detoxification genes present in marine microorganisms seems surprisingly small. The underrepresentation is particularly evident for toxicant transporters and proteins involved in detoxifying metals. Exceptions are enzymes involved in oxidative stress defense where peroxidase enzymes are more abundant in marine bacteria compared to bacteria in general. In contrast, catalases are almost completely absent from the open ocean environment, suggesting that peroxidases and peroxiredoxins constitute a core line of defense against reactive oxygen species (ROS) in the marine milieu.

CONCLUSIONS

We found no indication that detoxification systems would be generally more abundant close to the coast compared to the open ocean. On the contrary, for several of the protein families that displayed a significant geographical distribution, like peroxidase, penicillin binding transpeptidase and divalent ion transport protein, the open ocean samples showed the highest abundance. Along the same lines, the abundance of most detoxification proteins did not increase with estimated pollution. The low level of detoxification systems in marine bacteria indicate that the majority of marine bacteria have a low capacity to adapt to increased pollution. Our study exemplifies the use of metagenomics data in ecotoxicology, and in particular how anthropogenic consequences on life in the sea can be examined.

Microbial community degradation of widely used quaternary ammonium disinfectants

Benzalkonium chlorides (BACs) are disinfectants widely used in a variety of clinical and environmental settings to prevent microbial infections, and they are frequently detected in nontarget environments, such as aquatic and engineered biological systems, even at toxic levels. Therefore, microbial degradation of BACs has important ramifications for alleviating disinfectant toxicity in nontarget environments as well as compromising disinfectant efficacy in target environments. However, how natural microbial communities respond to BAC exposure and what genes underlie BAC biodegradation remain elusive. Our previous metagenomic analysis of a river sediment microbial community revealed that BAC exposure selected for a low-diversity community, dominated by several members of the Pseudomonas genus that quickly degraded BACs. To elucidate the genetic determinants of BAC degradation, we conducted time-series metatranscriptomic analysis of this microbial community during a complete feeding cycle with BACs as the sole carbon and energy source under aerobic conditions. Metatranscriptomic profiles revealed a candidate gene for BAC dealkylation, the first step in BAC biodegradation that results in a product 500 times less toxic. Subsequent biochemical assays and isolate characterization verified that the putative amine oxidase gene product was functionally capable of initiating BAC degradation. Our analysis also revealed cooperative interactions among community members to alleviate BAC toxicity, such as the further degradation of BAC dealkylation by-products by organisms not encoding amine oxidase. Collectively, our results advance the understanding of BAC aerobic biodegradation and provide genetic biomarkers to assess the critical first step of this process in nontarget environments.

Soil microbial community responses to a decade of warming as revealed by comparative metagenomics

Soil microbial communities are extremely complex, being composed of thousands of low-abundance species (<0.1% of total). How such complex communities respond to natural or human-induced fluctuations, including major perturbations such as global climate change, remains poorly understood, severely limiting our predictive ability for soil ecosystem functioning and resilience. In this study, we compared 12 whole-community shotgun metagenomic data sets from a grassland soil in the Midwestern United States, half representing soil that had undergone infrared warming by 2°C for 10 years, which simulated the effects of climate change, and the other half representing the adjacent soil that received no warming and thus, served as controls. Our analyses revealed that the heated communities showed significant shifts in composition and predicted metabolism, and these shifts were community wide as opposed to being attributable to a few taxa. Key metabolic pathways related to carbon turnover, such as cellulose degradation (∼13%) and CO2 production (∼10%), and to nitrogen cycling, including denitrification (∼12%), were enriched under warming, which was consistent with independent physicochemical measurements. These community shifts were interlinked, in part, with higher primary productivity of the aboveground plant communities stimulated by warming, revealing that most of the additional, plant-derived soil carbon was likely respired by microbial activity. Warming also enriched for a higher abundance of sporulation genes and genomes with higher G+C content. Collectively, our results indicate that microbial communities of temperate grassland soils play important roles in mediating feedback responses to climate change and advance the understanding of the molecular mechanisms of community adaptation to environmental perturbations.

Long-term exposure to benzalkonium chloride disinfectants results in change of microbial community structure and increased antimicrobial resistance

The effect of benzalkonium chlorides (BACs), a widely used class of quaternary ammonium disinfectants, on microbial community structure and antimicrobial resistance was investigated using three aerobic microbial communities: BACs-unexposed (DP, fed a mixture of dextrin/peptone), BACs-exposed (DPB, fed a mixture of dextrin/peptone and BACs), and BACs-enriched (B, fed only BACs). Long-term exposure to BACs reduced community diversity and resulted in the enrichment of BAC-resistant species, predominantly Pseudomonas species. Exposure of the two microbial communities to BACs significantly decreased their susceptibility to BACs as well as three clinically relevant antibiotics (penicillin G, tetracycline, ciprofloxacin). Increased resistance to BACs and penicillin G of the two BACs-exposed communities is predominantly attributed to degradation or transformation of these compounds, whereas resistance to tetracycline and ciprofloxacin is largely due to the activity of efflux pumps. Quantification of several key multidrug resistance genes showed a much higher number of copies of these genes in the DPB and B microbial communities compared to the DP community. Collectively, our findings indicate that exposure of a microbial community to BACs results in increased antibiotic resistance, which has important implications for both human and environmental health.