Characterization of bacterial diversity in contaminated groundwater using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Bactericidal effectors of the Stenotrophomonas maltophilia type IV secretion system: functional definition of the nuclease TfdA and structural determination of TfcB

Stenotrophomonas maltophilia expresses a type IV protein secretion system (T4SS) that promotes contact-dependent killing of other bacteria and does so partly by secreting the effector TfcB. Here, we report the structure of TfcB, comprising an N-terminal domain similar to the catalytic domain of glycosyl hydrolase (GH-19) chitinases and a C-terminal domain for recognition and translocation by the T4SS. Utilizing a two-hybrid assay to measure effector interactions with the T4SS coupling protein VirD4, we documented the existence of five more T4SS substrates. One of these was protein 20845, an annotated nuclease. A S. maltophilia mutant lacking the gene for 20845 was impaired for killing Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Moreover, the cloned 20845 gene conferred robust toxicity, with the recombinant E. coli being rescued when 20845 was co-expressed with its cognate immunity protein. The 20845 effector was an 899 amino-acid protein, comprised of a GHH-nuclease domain in its N-terminus, a large central region of indeterminant function, and a C-terminus for secretion. Engineered variants of the 20845 gene that had mutations in the predicted catalytic site did not impede E. coli, indicating that the antibacterial effect of 20845 involves its nuclease activity. Using flow cytometry with DNA staining, we determined that 20845, but not its mutant variants, confers a loss in DNA content of target bacteria. Database searches revealed that uncharacterized homologs of 20845 occur within a range of bacteria. These data indicate that the S. maltophilia T4SS promotes interbacterial competition through the action of multiple toxic effectors, including a potent, novel DNase.IMPORTANCEStenotrophomonas maltophilia is a multi-drug-resistant, Gram-negative bacterium that is an emerging pathogen of humans. Patients with cystic fibrosis are particularly susceptible to S. maltophilia infection. In hospital water systems and various types of infections, S. maltophilia co-exists with other bacteria, including other pathogens such as Pseudomonas aeruginosa. We previously demonstrated that S. maltophilia has a functional VirB/D4 type VI protein secretion system (T4SS) that promotes contact-dependent killing of other bacteria. Since most work on antibacterial systems involves the type VI secretion system, this observation remains noteworthy. Moreover, S. maltophilia currently stands alone as a model for a human pathogen expressing an antibacterial T4SS. Using biochemical, genetic, and cell biological approaches, we now report both the discovery of a novel antibacterial nuclease (TfdA) and the first structural determination of a bactericidal T4SS effector (TfcB).

The escalating threat of human-associated infectious bacteria in surface aquatic resources: Insights into prevalence, antibiotic resistance, survival mechanisms, detection, and prevention strategies

Anthropogenic activities and climate change profoundly impact water quality, leading to a concerning increase in the prevalence and abundance of bacterial pathogens across diverse aquatic environments. This rise has resulted in a growing challenge concerning the safety of water sources, particularly surface waters and marine environments. This comprehensive review delves into the multifaceted challenges presented by bacterial pathogens, emphasizing threads to human health within ground and surface waters, including marine ecosystems. The exploration encompasses the intricate survival mechanisms employed by bacterial pathogens and the proliferation of antimicrobial resistance, largely driven by human-generated antibiotic contamination in aquatic systems. The review further addresses prevalent pathogenic bacteria, elucidating associated risk factors, exploring their eco-physiology, and discussing the production of potent toxins. The spectrum of detection techniques, ranging from conventional to cutting-edge molecular approaches, is thoroughly examined to underscore their significance in identifying and understanding waterborne bacterial pathogens. A critical aspect highlighted in this review is the imperative for real-time monitoring of biomarkers associated with waterborne bacterial pathogens. This monitoring serves as an early warning system, facilitating the swift implementation of action plans to preserve and protect global water resources. In conclusion, this comprehensive review provides fresh insights and perspectives, emphasizing the paramount importance of preserving the quality of aquatic resources to safeguard human health on a global scale.

Delivering on sustainable development goals in wastewater reuse for agriculture: Initial prioritization of emerging pollutants in the Tula Valley, Mexico

Wastewater reuse for agricultural irrigation is a widespread beneficial practice, in line with the sustainable development goals. However, contaminants of emerging concern (CECs) present in wastewater, such as pharmaceuticals, pose an environmental risk. The Tula Valley in Mexico is one of the world's largest agricultural areas reusing wastewater for agriculture. However, no untargeted CEC monitoring has been undertaken there, limiting the information available to prioritise local environmental risk assessment. Furthermore, CEC environmental presence in the Global South remains understudied, compared to the Global North. There is a risk that current research efforts focus on CECs predominantly found in the Global North, leading to strategies that may not be appropriate for the Global South where the pollution profile may be different. To address these knowledge gaps, a sampling campaign at five key sites in the Tula Valley was undertaken and samples analysed using multi-residue targeted and untargeted liquid chromatography mass spectrometry methods. Using the targeted data, ten CECs were found to be of environmental risk for at least one sampling site: 4‑tert-octylphenol, acetaminophen, bezafibrate, diclofenac, erythromycin, levonorgestrel, simvastatin, sulfamethoxazole, trimethoprim and tramadol as well as total estrogenicity (combination of three steroid hormones). Six of these have not been previously quantified in the Tula Valley. Over one hundred pollutants never previously measured in the area were identified through untargeted analysis supported by library spectrum match. Examples include diclofenac and carbamazepine metabolites and area-specific pollutants such as the herbicide fomesafen. This research contributes to characterising the presence of CECs in the Global South, as well as providing site-specific data for the Tula Valley.

Versatility of Stenotrophomonas maltophilia: Ecological roles of RND efflux pumps

S. maltophilia is a widely distributed bacterium found in natural, anthropized and clinical environments. The genome of this opportunistic pathogen of environmental origin includes a large number of genes encoding RND efflux pumps independently of the clinical or environmental origin of the strains. These pumps have been historically associated with the uptake of antibiotics and clinically relevant molecules because they confer resistance to many antibiotics. However, considering the environmental origin of S. maltophilia, the ecological role of these pumps needs to be clarified. RND efflux systems are highly conserved within bacteria and encountered both in pathogenic and non-pathogenic species. Moreover, their evolutionary origin, conservation and multiple copies in bacterial genomes suggest a primordial role in cellular functions and environmental adaptation. This review is aimed at elucidating the ecological role of S. maltophilia RND efflux pumps in the environmental context and providing an exhaustive description of the environmental niches of S. maltophilia. By looking at the substrates and functions of the pumps, we propose different involvements and roles according to the adaptation of the bacterium to various niches. We highlight that i°) regulatory mechanisms and inducer molecules help to understand the conditions leading to their expression, and ii°) association and functional redundancy of RND pumps and other efflux systems demonstrate their complex role within S. maltophilia cells. These observations emphasize that RND efflux pumps play a role in the versatility of S. maltophilia.

Whole-Genome Sequencing of Alcaligenes faecalis HZ01, with Potential to Inhibit Nontuberculous Mycobacterial Growth

Alcaligenes faecalis is a Gram-negative rod that is ubiquitous in the environment and is an opportunistic human pathogen. Here, we report the whole-genome sequencing analysis of A. faecalis HZ01, which presents mycobacterial growth inhibitory activity and was isolated from a contaminated culture of Mycobacterium chubuense ATCC 27278.

Exploiting targeted and untargeted approaches for the analysis of bacterial metabolites under altered growth conditions

In the host, pathogenic microorganisms have developed stress responses to cope with constantly changing environments. Stress responses are directly related to changes in several metabolomic pathways, which could hamper microorganisms' unequivocal identification. We evaluated the effect of various in vitro stress conditions (acidic, basic, oxidative, ethanolic, and saline conditions) on the metabolism of Staphylococcus aureus, Bacillus cereus, and Pseudomonas aeruginosa, which are common lung pathogens. The metabolite profiles of the bacteria were analyzed using liquid chromatography coupled to triple quadrupole and quadrupole time-of-flight mass spectrometry. The advantages of targeted and untargeted analysis combined with univariate and multivariate statistical analysis (principal component analysis, hierarchical cluster analysis, partial least square discriminant analysis, random forest) were combined to unequivocally identify bacterial species. In normal in vitro conditions, the targeted methodology, based on the analysis of primary metabolites, enabled the rapid and efficient discrimination of the three bacteria. In changing in vitro conditions and specifically in presence of the various stressors, the untargeted methodology proved to be more valuable for the global and accurate differentiation of the three bacteria, also considering the type of stress environment within each species. In addition, species-specific metabolites (i.e., fatty acids, polysaccharides, peptides, and nucleotide bases derivatives) were putatively identified. Good intra-day repeatability and inter-day repeatability (< 10% RSD and < 15% RSD, respectively) were obtained for the targeted and the untargeted methods. This untargeted approach highlights its importance in unusual (and less known) bacterial growth environments, being a powerful tool for infectious disease diagnosis, where the accurate classification of microorganisms is sought.

Inactivation of waterborne fungal spores by 1-bromo-3-chloro-5,5-dimethylhydantoin: Kinetics, influencing factors and mechanisms

Fungal contamination in drinking water source has become a problem worth studying, as waterborne fungi may cause deterioration of water quality and outbreak of diseases. Various disinfection methods have been explored to control fungal spores in drinking water, such as chlor(am)ination, ozonation, chlorine dioxide treatment, but these methods are not appropriate for remote areas, owing to the difficulties in preparation, carriage and storage. In this study, a powdery disinfectant of 1-bromo-3-chloro-5,5-dimethylhydantoin (BCDMH), which facilitated transportation and preservation, was firstly chosen to inactivate opportunistic pathogens of Aspergillus niger (A. niger) and Penicillium polonicum (P. polonicum). The results revealed that the inactivation kinetics of fungal spores by BCDMH fitted to Chick-Watson model well, with the inactivation rate constant of 0.011 and 0.034 L mg^-1 min^-1 for A. niger and P. polonicum, respectively. Acidic condition and high temperature promoted the inactivation by BCDMH. Compared with chlorine, BCDMH showed relative weaker ability on inactivation of fungal spores. However, it was demonstrated that the inactivation efficiency of BCDMH was obviously enhanced by adding halide ions, with 11 or 36 folds for A. niger and 4 or 15 folds for P. polonicum by adding 40 μM Br^- or I^-. The inactivation mechanisms were detected by flow cytometry and scanning electron microscope. Fungal spores lost their culturability firstly, then membrane integrity was damaged. Meanwhile, the esterase activity and intracellular reactive oxygen species level changed, and finally intracellular adenosine triphosphate released.

Effectors of the Stenotrophomonas maltophilia Type IV Secretion System Mediate Killing of Clinical Isolates of Pseudomonas aeruginosa

Previously, we documented that Stenotrophomonas maltophilia encodes a type IV secretion system (T4SS) that allows the organism to kill, in contact-dependent fashion, heterologous bacteria, including wild-type Pseudomonas aeruginosa. Bioinformatic screens based largely on the presence of both a C-terminal consensus sequence and an adjacent gene encoding a cognate immunity protein identified 13 potential antibacterial effectors, most of which were highly conserved among sequenced strains of S. maltophilia. The immunity proteins of two of these proved especially capable of protecting P. aeruginosa and Escherichia coli against attack from the Stenotrophomonas T4SS. In turn, S. maltophilia mutants lacking the putative effectors RS14245 and RS14255 were impaired for killing not only laboratory E. coli but clinical isolates of P. aeruginosa, including ones isolated from the lungs of cystic fibrosis patients. That complemented mutants behaved as wild type did confirmed that RS14245 and RS14255 are required for the bactericidal activity of the S. maltophilia T4SS. Moreover, a mutant lacking both of these proteins was as impaired as a mutant lacking the T4SS apparatus, indicating that RS14245 and RS14255 account for (nearly) all of the bactericidal effects seen. Utilizing an interbacterial protein translocation assay, we determined that RS14245 and RS14255 are bona fide substrates of the T4SS, a result confirmed by examination of mutants lacking both the T4SS and the individual effectors. Delivery of the cloned 14245 protein (alone) into the periplasm resulted in the killing of target bacteria, indicating that this effector, a putative lipase, is both necessary and sufficient for bactericidal activity.

Advances in the Microbiology of Stenotrophomonas maltophilia

Stenotrophomonas maltophilia is an opportunistic pathogen of significant concern to susceptible patient populations. This pathogen can cause nosocomial and community-acquired respiratory and bloodstream infections and various other infections in humans. Sources include water, plant rhizospheres, animals, and foods. Studies of the genetic heterogeneity of S. maltophilia strains have identified several new genogroups and suggested adaptation of this pathogen to its habitats. The mechanisms used by S. maltophilia during pathogenesis continue to be uncovered and explored. S. maltophilia virulence factors include use of motility, biofilm formation, iron acquisition mechanisms, outer membrane components, protein secretion systems, extracellular enzymes, and antimicrobial resistance mechanisms. S. maltophilia is intrinsically drug resistant to an array of different antibiotics and uses a broad arsenal to protect itself against antimicrobials. Surveillance studies have recorded increases in drug resistance for S. maltophilia, prompting new strategies to be developed against this opportunist. The interactions of this environmental bacterium with other microorganisms are being elucidated. S. maltophilia and its products have applications in biotechnology, including agriculture, biocontrol, and bioremediation.

Characterizing anecdotal claims of groundwater contamination in shale energy basins

The increased societal monitoring of unconventional oil and gas development (UD) has brought forth tremendous scrutiny over the environmental stewardship and subsequent public health impacts of surface and sub-surface activities. Concerns over groundwater quality in shale energy basins have prompted concerned citizens into monitoring UD activities for a series of qualitative parameters, and even coordinating sampling efforts for chemical analysis. Here we present a list of analytical parameters, hierarchically structured to guide concerned citizens through an efficient and cost-effective monitoring program. Utilizing this multi-step testing regime, we assessed groundwater quality from 36 private water wells involved in 19 anecdotal claims of alleged UD-related contamination across the Barnett, Eagle Ford, Haynesville, and Marcellus Shale formations in the United States. Our analytical findings aligned with the landowners' accounts of their situation in only 5 of the 36 collected samples, with several cases revealing environmental abnormalities that were unbeknownst to the landowners but likely unrelated to UD activities. These data are some of the first to assess the relationship between landowner perception and analytical determination in a cohort of highly variable anecdotal cases of alleged groundwater contamination, revealing a notable disconnect that is likely attributable to a myriad of societal and environmental factors. The analytical modalities presented here also serve as a step-wise method in a weight of evidence approach to assess the presence or absence of anthropogenic contamination under the most variable hydrogeological conditions.

A review of the analytical methods used for beer ingredient and finished product analysis and quality control

Beer is an incredibly complex beverage containing more than 3000 different compounds, including carbohydrates, proteins, ions, microbes, organic acids, and polyphenols, among others. Beer becomes even more complex during storage, for over time it may undergo chemical changes that negatively affect the flavor, aroma, and appearance. Thus, it can be expected that maintaining the quality of beer throughout its lifetime is a difficult task. Since it is such a popular drink throughout the world, being familiar with proper analytical techniques for beer evaluation is useful for researchers and brewers. These techniques include, but are not limited to, gas chromatography, liquid chromatography, matrix assisted laser desorption/ionization, capillary electrophoresis, mass spectrometry, ultraviolet-visible spectroscopy, and flame ionization detection. This review aims to summarize the various ingredients and components of beer, discuss how they affect the finished product, and present some of the analytical methods used for quality control and understanding the formation of chemicals in beer during the brewing process.

Analysis of bacteria stress responses to contaminants derived from shale energy extraction

In order to survive environmental changes, bacteria have stress responses, which protect them from adverse and variable conditions. Contamination can be a source of stress and bacterial responses can serve as an indicator of environmental abnormality. In this work, the biochemical effects of toxic compounds that stem from hydraulic fracturing were measured on the whole cell-derived fatty acid and protein compositions of Escherichia coli, Klebsiella oxytoca, Pseudomonas aeruginosa, Pseudomonas putida, Pseudomonas stutzeri, Aeromonas hydrophila, Bacillus cereus, and Bacillus subtilis. These microorganisms were exposed to elevated levels of benzene, ethanol, propanol, toluene, and salt. These were chosen to represent significant subsurface contamination or a surface spill. The fatty acid and protein profiles for the bacteria were analyzed using gas chromatography - vacuum ultraviolet spectroscopy and matrix-assisted laser desorption ionization time-of-flight mass spectrometry, respectively. Overall, different fatty acid and protein profiles were observed when the microorganisms were grown in the presence of the toxic compounds. The cells exhibited an increase in the saturated/unsaturated ratio and displayed the presence of branched and cyclopropane fatty acids when in the presence of common fracture fluid constituents to decrease membrane permeability which was confirmed by the analysis of produced water. This approach provides a potentially useful tool for environmental diagnosis, since proteins and fatty acids can act as a harbinger of ecological health.

Antimicrobial-Resistant Escherichia coli from Environmental Waters in Northern Colorado

Waterborne Escherichia coli are a major reservoir of antimicrobial resistance (AMR), including but not limited to extended-spectrum beta-lactamase (ESBL) and Klebsiella pneumoniae carbapenemase (KPC) mechanisms. This study quantified and described ESBL- and KPC-producing E. coli in Northern Colorado from sewer water, surface water, and influent and effluent wastewater treatment sources. Total detected bacteria and E. coli abundances, and the percentages that contain ESBL and/or KPC, were compared between water sources. Seventy E. coli isolates from the various waters had drug resistance validated with a panel of 17 antibiotics using a broth microdilution assay. The diverse drug resistance observed across E. coli isolates was further documented by polymerase chain reaction of common ESBL genes and functional relatedness by PhenePlate assay-generated dendrograms (n=70). The total E. coli abundance decreased through the water treatment process as expected, yet the percentages of E. coli harboring ESBL resistance were increased (1.70%) in surface water. Whole-genome sequencing analysis was completed for 185 AMR genes in wastewater E. coli isolates and confirmed the presence of diverse AMR gene classes (e.g., beta-lactams and efflux pumps) in isolate genomes. This study completed surveillance of AMR patterns in E. coli that reside in environmental water systems and suggests a role for integrating both phenotypic and genotypic profiling beyond ESBL and KPC mechanisms. AMR screening via multiple approaches may assist in the prevention of drug-resistant E. coli spread from waters to animals and humans.

Characterizing variable biogeochemical changes during the treatment of produced oilfield waste

At the forefront of the discussions about climate change and energy independence has been the process of hydraulic fracturing, which utilizes large amounts of water, proppants, and chemical additives to stimulate sequestered hydrocarbons from impermeable subsurface strata. This process also produces large amounts of heterogeneous flowback and formation waters, the subsurface disposal of which has most recently been linked to the induction of anthropogenic earthquakes. As such, the management of these waste streams has provided a newfound impetus to explore recycling alternatives to reduce the reliance on subsurface disposal and fresh water resources. However, the biogeochemical characteristics of produced oilfield waste render its recycling and reutilization for production well stimulation a substantial challenge. Here we present a comprehensive analysis of produced waste from the Eagle Ford shale region before, during, and after treatment through adjustable separation, flocculation, and disinfection technologies. The collection of bulk measurements revealed significant reductions in suspended and dissolved constituents that could otherwise preclude untreated produced water from being utilized for production well stimulation. Additionally, a significant step-wise reduction in pertinent scaling and well-fouling elements was observed, in conjunction with notable fluctuations in the microbiomes of highly variable produced waters. Collectively, these data provide insight into the efficacies of available water treatment modalities within the shale energy sector, which is currently challenged with improving the environmental stewardship of produced water management.