Genomic signatures of strain selection and enhancement in Bacillus atrophaeus var. globigii, a historical biowarfare simulant

Superior hydrogen production during sodium borohydride methanolysis using monodisperse copper nanoparticles grafted on the peptidoglycan layer of Bacillus atrophaeus bacteria

Recently, "Bacillus atrophaeus", which has a cell wall structure consisting of peptidoglycan layers, has attracted the attention of researchers due to its different usage areas. In particular, research focuses on the technology of obtaining bio‑hydrogen with various techniques. This research involves, for the first time, the use of the Bacillus atrophaeus bacteria as a bio-supporting material for monodisperse copper nanoparticles (CuNPs@Bacillus atrophaeus) and the manufacture of hydrogen through catalytic NaBH4-methanolysis (SB-methanolysis) in the presence of the resulting nanoparticles. Here, detailed kinetic studies were carried out during the SB-methanolysis by taking CuNPs and bacteria in varying amounts and at varying temperatures, and the activation energy and lifetime of monodisperse CuNPs@Bacillus atrophaeus was found to be 31.76 kJ mol-1 and 30,903 mol H2 (mol Cu)-1, respectively. The chemical and physical structure of the CuNPs@Bacillus atrophaeus was observed during the SB-methanolysis, so only detailed characterization of bacteria and monodisperse CuNPs@Bacillus atrophaeus was performed, and the particle size of the catalyst was calculated as 3.29 nm. The results showed that the monodisperse CuNPs@Bacillus atrophaeus, which has superior features and high catalytic activity, is a "clean", very well methanol-soluble, and quite surprising catalyst in terms of hydrogen production.

Phosphorelay changes and plasticity underlie the life history evolution of Bacillus subtilis sporulation and germination in serial batch culture

Bacterial endospores facilitate survival in extreme and unpredictably fluctuating environments. However, under abundant nutrient conditions, the production of endospores is quickly reduced or lost. We hypothesized that endospore-forming bacteria exposed to frequent cycling of nutrient availability would evolve reduced sporulation efficiency. We employed replicated batch culture for 11 transfers to test the effects of rapid nutrient cycles on the evolution of the life history traits of sporulation, germination and growth in Bacillus subtilis. We periodically measured total cell and endospore densities during the period between transfers. Replicates evolved in parallel behaviourally and genetically. By the fourth transfer, we saw a reduction in endospore production, which continued to decline throughout the experiment. Our results support a decreased likelihood of sporulation being driven by frequent nutrient renewal. The proportion of endospores germinating after transfer increased significantly by the end of the experiment through the effects of plasticity alone. Every evolved replicate culture displayed colony dimorphism: the dominant morphology being translucent with reduced sporulation ability and the rarer being opaque with accelerated sporulation and highly efficient germination. Colony dimorphism was reflected in the genomes, with all isolates with reduced sporulation having mutations in elements of the sporulation phosphorelay, particularly kinA. Some opaque colonies had no mutations, indicating that those adaptive changes occurred through plasticity. These results suggest that our selection conditions of nutrient cycling resulted in the parallel evolution of communities of ecologically diverse strains, where most reduced sporulation while a smaller proportion accelerated it.

Decontamination of Soil Contaminated at the Surface with Bacillus anthracis (Anthrax) Surrogate Spores Using Steam Vapor

In the event of a wide-area release of Bacillus anthracis spores, soils and other outdoor materials will likely become contaminated with the biological agent. Soils may also become contaminated with B. anthracis when livestock or wildlife succumb to anthrax disease. This study was conducted to assess the in situ remediation of soil using steam vapor to inactivate a B. anthracis spore surrogate (Bacillus atrophaeus) inoculated into soil samples. Tests were conducted using small columns (~0.04 m3 of soil) filled with either loam, clay, or a sandy soil. Following steam treatment, the B. atrophaeus spores were recovered from the test and positive control soil samples via liquid extraction and this liquid was subsequently dilution plated to quantify viable spores in terms of colony-forming units. Decontamination efficacy was assessed as a function of soil type, soil depth, soil moisture, soil temperature, and steam exposure time. Results showed that spore inactivation improved with increasing steam exposure time and diminished with depth. The clay soil generally exhibited the highest soil temperatures and correspondingly showed the highest inactivation of spores. Adding moisture to the soil prior to the steam treatment increased heat transfer within the soil column, and sealing the columns to mitigate steam leakage increased spore inactivation. The results showed that a steam mass of 40-50 kg applied per square meter of soil surface was sufficient to inactivate bacterial spores to depths between 7 and 10 cm. With bacterial spores on the soil column surface, a contact time of 15 min with the steam vapor at 99°C was sufficient for complete inactivation. These findings provide a foundation for estimating costs and time requirements for applying steam to the soil surface, and further confirmatory testing at field-scale is suggested.

Comparison of liquid and filter sampling techniques for recovery of Bacillus spores and Escherichia coli from environmental water

Historically, detecting water contamination has involved collecting and directly analyzing liquid samples, but recent advances in filter sampling methods offer numerous potential advantages. Emerging technologies, including environmental DNA (eDNA) samplers, could be used for remote microbial contamination sampling, but work is needed to determine if target microorganisms can be recovered from filters at comparable levels to traditional sampling methods. In this study, Escherichia coli and a surrogate for Bacillus anthracis spores were sampled from synthetic stormwater and quantified using both direct liquid and filter methods, and dwell time tests compared microorganism persistence in water and on filters. At nearly all tested timepoints, the recoveries of spores from membrane filters were within 0.5 log10 colony forming units per sample (CFU/sample) compared to the liquid-only samples, suggesting that the use of filter sampling is a feasible alternative to liquid-based sampling, and samples were held for up to 4 weeks without significant sample degradation. Recoveries for E. coli remained relatively consistent for ∼3 days in phosphate buffered saline (PBS), in synthetic stormwater, and on membrane filters, but decreases in recoveries were observed for samples held for >3 days. These results indicate that emerging water sampling technologies, which reduce logistical burdens and offer potential cost savings, can be leveraged to characterize biological contamination in water matrices with multiple types of microbiological agents.

Fomite disinfection using spray systems: A computational multi-physics framework

Disinfecting inanimate objects or materials carrying infectious agents, i.e., fomites, using spray systems reduces healthcare-associated infections in medical settings and community-acquired infections in non-medical environments. However, an accurate prediction of such systems is challenging as these systems embrace multi-physics phenomena depending on several parameters. Therefore, this paper presents a computational modeling-based multi-physics framework to evaluate the performance and effectiveness of spray systems employed in disinfecting fomites with non-porous hydrophilic surfaces. The framework includes four key phases: (i) atomizing the liquid disinfectant jet into the disinfectant droplets; (ii) interactions between disinfectant droplets and the surrounding air; (iii) impingements created by the disinfectant droplets on the fomite surface; (iv) interactions between the disinfectant depositions and pathogens causing fomite disinfection. The accuracy of the framework is evaluated using two sets of experimental data on the reduction of viable Bacillus atrophaeus spores over an 1800-second period. The results show that the framework can predict fomite disinfection via spray systems, with the deviations from the measured data being 2.73% and 2.38%. By presenting a detailed perception of the dynamics involved in fomite disinfection, this framework has the potential to improve public health practices and lead to the development of more effective and targeted disinfection strategies in diverse settings.

Fate and transport of viable Bacillus anthracis simulant spores in ambient air during a large outdoor decontamination field exercise

The Wide Area Demonstration (WAD) was a field exercise conducted under the U.S. EPA's Analysis of Coastal Operational Resiliency program, in conjunction with the U.S. Department of Homeland Security and the U.S. Coast Guard. The purpose of the WAD was to operationalize at field scale aspects of remediation activities that would occur following an outdoor release of Bacillus anthracis spores, including sampling and analysis, decontamination, data management, and waste management. The WAD was conducted in May 2022 at Fort Walker (formerly known as Fort A.P. Hill) and utilized Bacillus atrophaeus as a benign simulant for B. anthracis. B. atrophaeus spores were inoculated onto the study area at the beginning of the study, and air samples were collected daily during each of the different phases of the WAD using Dry Filter Units (DFUs). Ten DFU air samplers were placed at the perimeter of the study area to collect bioaerosols onto two parallel 47-mm diameter polyester felt filters, which were then subsequently analyzed in a microbiological laboratory for the quantification of B. atrophaeus. The study demonstrated the use of DFUs as a rugged and robust bioaerosol collection device. The results indicated that the highest B. atrophaeus spore air concentrations (up to ~ 5 colony forming units/m3) occurred at the beginning of the demonstration (e.g. during inoculation and characterization sampling phases) and generally downwind from the test site, suggesting transport of the spores was occurring from the study area. Very few B. atrophaeus spores were detected in the air after several weeks and following decontamination of exterior surfaces, thus providing an indication of the site decontamination procedures' effectiveness. No B. atrophaeus spores were detected in any of the blank or background samples.Implications: Following an incident involving a release of Bacillus anthracis spores or other biological threat agent into the outdoor environment, understanding the factors that may affect the bioagent's fate and transport can help predict viable contaminant spread via the ambient air. This paper provides scientific data for the first time on ambient air concentrations of bacterial spores over time and location during different phases of a field test in which Bacillus atrophaeus (surrogate for B. anthracis) spores were released outdoors as part of a full-scale study on sampling and decontamination in an urban environment. This study advances the knowledge related to the fate and transport of bacterial spores (such as those causing anthrax disease) as an aerosol in the outdoor environment over the course of three weeks in a mock urban environment and has exposure and health risk implications. The highest spore air concentrations occurred at the beginning of the study (e.g. during inoculation of surfaces and characterization sampling), and in the downwind direction, but diminished over time; few B. atrophaeus spores were detected in the air after several weeks and following decontamination. Therefore, in an actual incident, potential reaerosolization of the microorganism and subsequent transport in the air during surface sampling and remediation efforts should be considered for determining exclusion zone locations and estimating potential risk to neighboring communities. The data also provide evidence suggesting that the large-scale decontamination of outdoor surfaces may reduce air concentrations of the bioagent, which is important since exposure of B. anthracis via inhalation is a primary concern.

Use of semi-permeable bag materials to facilitate on-site treatment of biological agent-contaminated waste

Clean up following the wide-area release of a persistent biological agent has the potential to generate significant waste. Waste containing residual levels of biological contaminants may require off-site shipment under the U.S. Department of Transportation's (US DOT) solid waste regulations for Category A infectious agents, which has packaging and size limitations that do not accommodate large quantities. Treating the waste on-site to inactivate the bio-contaminants could alleviate the need for Category A shipping and open the possibility for categorizing the waste as conventional solid waste with similar shipping requirements as municipal garbage. To collect and package waste for on-site treatment, a semi-permeable nonwoven-based fabric was developed. The fabric was designed to contain residual bio-contaminants while providing sufficient permeability for penetration by a gaseous decontamination agent. The nonwoven fabric was tested in two bench-scale experiments. First, decontamination efficacy and gas permeability were evaluated by placing test coupons inoculated with spores of a Bacillus anthracis surrogate inside the nonwoven material. After chlorine dioxide fumigation, the coupons were analyzed for spore viability and results showed a ≥6 Log reduction on all test materials except glass. Second, filters cut from the nonwoven material were tested in parallel with commercially available cellulose acetate filters having a known pore size (0.45 μm) and results demonstrate that the two materials have similar permeability characteristics. Overall, results suggest that the nonwoven material could be used to package waste at the point of generation and then moved to a nearby staging area where it could be fumigated to inactivate bio-contaminants.

Impact of filter material and holding time on spore sampling efficiency in water

Bacillus anthracis and other environmentally persistent pathogens pose a significant threat to human and environmental health. If contamination is spread over a wide area (e.g. resulting from a bioterrorism or biowarfare incident), readily deployable and scalable sample collection methods will be necessary for rapidly developing and implementing effective remediation strategies. A recent surge in environmental (eDNA) sampling technologies could prove useful for quantifying the extent and levels of contamination from biological agents in environmental and drinking water. In this study, three commonly used membrane filtration materials (cellulose acetate, cellulose nitrate, and nylon) were evaluated for spore filtration efficiency, yielding recoveries from 17%-68% to 25%-117% for high and low titer samples, respectively, where cellulose nitrate filters generated the highest recoveries. A holding time test revealed no statistically significant differences between spore recoveries when analyzed at the specified timepoints, suggesting that eDNA filter sampling techniques can yield and maintain a relatively high recovery of spores for an extended period of time between filtration and analysis without a detrimental impact on spore recoveries. The results shown here indicate that emerging eDNA technologies could be leveraged for sampling following a wide-area contamination incident and for other microbiological water sampling applications.

Effective inactivation of Bacillus atrophaeus spores and Escherichia coli on disposable face masks using ultraviolet laser irradiation

Due to the widespread emergence of COVID-19, face masks have become a common tool for reducing transmission risk between people, increasing the need for sterilization methods against mask-contaminated microorganisms. In this study, we measured the efficacy of ultraviolet (UV) laser irradiation (266 nm) as a sterilization technique against Bacillus atrophaeus spores and Escherichia coli on three different types of face mask. The UV laser source demonstrated high penetration of inner mask layers, inactivating microorganisms in a short time while maintaining the particle filtration efficiency of the masks. This study demonstrates that UV laser irradiation is an efficient sterilization method for removing pathogens from face masks.

Sterilization effects of UV laser irradiation on Bacillus atrophaeus spore viability, structure, and proteins

Bacillus spores are highly resistant to toxic chemicals and extreme environments. Because some Bacillus species threaten public health, spore inactivation techniques have been intensively investigated. We exposed Bacillus atrophaeus spores to a 266 nm Nd:YVO₄ laser at a laser power of 1 W and various numbers of scans. As a result, the UV laser reduced the viability of Bacillus atrophaeus spores. Although the outer coat of spores remained intact after UV laser irradiation of 720 scans, damage inside the spores was observed. Spore proteins were identified by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry during the course of UV laser irradiation. Photochemical and photothermal processes are believed to be involved in the UV laser sterilization of Bacillus spores. Our findings suggest that a UV laser is capable of sterilizing Bacillus atrophaeus spores.

Comparative genomic analysis of azasugar biosynthesis

Azasugars are monosaccharide analogs in which the ring oxygen is replaced with a nitrogen atom. These well-known glycosidase inhibitors are of interest as therapeutics, yet several aspects of azasugars remain unknown including their distribution, structural diversity, and chemical ecology. The hallmark signature of bacterial azasugar biosynthesis is a three gene cluster (3GC) coding for aminotransferase, phosphatase, and dehydrogenase enzymes. Using the bioinformatics platform Enzyme Similarity Tool (EST), we identified hundreds of putative three gene clusters coding for azasugar production in microbial species. In the course of this work, we also report a consensus sequence for the aminotransferase involved in azasugar biosynthesis as being: SGNXFRXXXFPNXXXXXXXLXVPXPYCXRC. Most clusters are found in Bacillus and Streptomyces species which typically inhabit soil and the rhizosphere, but some clusters are found with diverse species representation such as Photorhabdus and Xenorhabdus which are symbiotic with entomopathogenic nematodes; the human skin commensal Cutibacterium acnes, and the marine Bacillus rugosus SPB7, a symbiont to the sea sponge Spongia officinalis. This pan-taxonomic survey of the azasugar 3GC signature may lead to the identification of new azasugar producers, facilitate studies of their natural functions, and lead to new potential therapeutics.

Decontamination of soil contaminated at the surface with Bacillus anthracis spores using dry thermal treatment

In the event of a large, aerosol release of Bacillus anthracis spores in a major metropolitan area, soils and other outdoor materials may become contaminated with the biological agent. A study was conducted to assess the in-situ remediation of soil using a dry thermal treatment approach to inactivate a B. anthracis spore surrogate inoculated into soil samples. The study was conducted in two phases, using loam, clay and sand-based soils, as well as biological indicators and spore-inoculated stainless-steel coupons. Initial experiments were performed in an environmental test chamber with temperatures controlled between 80 and 110 °C, with and without added humidity, and with contact times ranging from 4 h to 7 weeks. Tests were then scaled up to assess the thermal inactivation of spores in small soil columns, in which a heating plate set to 141 °C was applied to the soil surface. These column tests were conducted to assess time requirements to inactivate spores as a function of soil depth and soil type. Results from the initial phase of testing showed that increasing the temperature and relative humidity reduced the time requirements to achieve samples in which no surrogate spores were detected. For the test at 80 °C with no added humidity, 49 days were required to achieve soil samples with no spores detected in clay and loam. At 110 °C, 24 h were required to achieve samples in which no spores were detected. In the column tests, no spores were detected at the 2.5 cm depth at four days and at the 5.1 cm depth at 21 days, for two of the three soils. The experiments described in the study demonstrate the feasibility of using dry thermal techniques to decontaminate soils that have been surficially contaminated with B. anthracis spores.

A spore quality-quantity tradeoff favors diverse sporulation strategies in Bacillus subtilis

Quality–quantity tradeoffs govern the production of propagules across taxa and can explain variability in life-history traits in higher organisms. A quality–quantity tradeoff was recently discovered in spore forming bacteria, but whether it impacts fitness is unclear. Here we show both theoretically and experimentally that the nutrient supply during spore revival determines the fitness advantage associated with different sporulation behaviors in Bacillus subtilis. By tuning sporulation rates we generate spore-yield and spore-quality strategists that compete with each other in a microscopic life-cycle assay. The quality (yield) strategist is favored when spore revival is triggered by poor (rich) nutrients. We also show that natural isolates from the gut and soil employ different life-cycle strategies that result from genomic variations in the number of rap-phr signaling systems. Taken together, our results suggest that a spore quality–quantity tradeoff contributes to the evolutionary adaptation of sporulating bacteria.

Iturinic Lipopeptide Diversity in the Bacillus subtilis Species Group - Important Antifungals for Plant Disease Biocontrol Applications

Iturins and closely related lipopeptides constitute a family of antifungal compounds known as iturinic lipopeptides that are produced by species in the Bacillus subtilis group. The compounds that comprise the family are: iturin, bacillomycin D, bacillomycin F, bacillomycin L, mycosubtilin, and mojavensin. These lipopeptides are prominent in many Bacillus strains that have been commercialized as biological control agents against fungal plant pathogens and as plant growth promoters. The compounds are cyclic heptapeptides with a variable length alkyl sidechain, which confers surface activity properties resulting in an affinity for fungal membranes. Above a certain concentration, enough molecules enter the fungal cell membrane to create a pore in the cell wall, which leads to loss of cell contents and cell death. This study identified 330 iturinic lipopeptide clusters in publicly available genomes from the B. subtilis species group. The clusters were subsequently assigned into distinguishable types on the basis of their unique amino acid sequences and then verified by HPLC MS/MS analysis. The results show some lipopeptides are only produced by one species, whereas certain others can produce up to three. In addition, four species previously not known to produce iturinic lipopeptides were identified. The distribution of these compounds among the B. subtilis group species suggests that they play an important role in their speciation and evolution.

Review of Decontamination Techniques for the Inactivation of Bacillus anthracis and Other Spore-Forming Bacteria Associated with Building or Outdoor Materials

Since the intentional release of Bacillus anthracis spores through the U.S. Postal Service in the fall of 2001, research and development related to decontamination for this biological agent have increased substantially. This review synthesizes the advances made relative to B. anthracis spore decontamination science and technology since approximately 2002, referencing the open scientific literature and publicly available, well-documented scientific reports. In the process of conducting this review, scientific knowledge gaps have also been identified. This review focuses primarily on techniques that are commercially available and that could potentially be used in the large-scale decontamination of buildings and other structures, as well as outdoor environments. Since 2002, the body of scientific data related to decontamination and microbial sterilization has grown substantially, especially in terms of quantifying decontamination efficacy as a function of several factors. Specifically, progress has been made in understanding how decontaminant chemistry, the materials the microorganisms are associated with, environmental factors, and microbiological methods quantitatively impact spore inactivation. While advancement has been made in the past 15 years to further the state of the science in the inactivation of bacterial spores in a decontamination scenario, further research is warranted to close the scientific gaps that remain.

Surrogate strains of human pathogens for field release

Surrogate microorganisms, in short surrogates, are an essential part of pathogen research. Compared to surrogates used in controlled laboratory environments, surrogates for field release are restricted by concerns about human and environmental safety. For field research of food-borne pathogens, strains of an attenuated pathogen or strains of genetically close non-pathogenic species have been used as surrogates. Genetic modification is usually performed to attenuate virulence, through for examples deletion of genes of virulence and transcriptional regulators and removal of virulence plasmids, and to facilitate detection and monitoring through observing antibiotic resistance, fluorescence, and bioluminescence. For field research of a biological warfare agent Bacillus anthracis, strains of genetically close non-pathogenic species or strains of genetically distant non-pathogenic species have been used, mostly without any genetic modification. Recently, we constructed strains of Bacillus thuringiensis as surrogates for B. anthracis, demonstrating that strain engineering could significantly enhance the utility of surrogates, and that the application of a simple genetic circuit could significantly impact surrogate safety. Thus far, enormous potential of biotechnology has not been exploited enough due to safety concerns regarding the field release of genetically engineered microorganisms. However, synthetic biology is rapidly developing, providing new concepts for biocontainment as well as ingenious genetic circuits and devices, which should be applied in future research of field-use surrogates.

Aerobiological Stabilities of Different Species of Gram-Negative Bacteria, Including Well-Known Biothreat Simulants, in Single-Cell Particles and Cell Clusters of Different Compositions

The ability to perform controlled experiments with bioaerosols is a fundamental enabler of many bioaerosol research disciplines. A practical alternative to using hazardous biothreat agents, e.g., for detection equipment development and testing, involves using appropriate model organisms (simulants). Several species of Gram-negative bacteria have been used or proposed as biothreat simulants. However, the appropriateness of different bacterial genera, species, and strains as simulants is still debated. Here, we report aerobiological stability characteristics of four species of Gram-negative bacteria (Pantoea agglomerans, Serratia marcescens, Escherichia coli, and Xanthomonas arboricola) in single-cell particles and cell clusters produced using four spray liquids (H₂O, phosphate-buffered saline[PBS], spent culture medium[SCM], and a SCM-PBS mixture). E. coli showed higher stability in cell clusters from all spray liquids than the other species, but it showed similar or lower stability in single-cell particles. The overall stability was higher in cell clusters than in single-cell particles. The highest overall stability was observed for bioaerosols produced using SCM-containing spray liquids. A key finding was the observation that stability differences caused by particle size or compositional changes frequently followed species-specific patterns. The results highlight how even moderate changes to one experimental parameter, e.g., bacterial species, spray liquid, or particle size, can strongly affect the aerobiological stability of Gram-negative bacteria. Taken together, the results highlight the importance of careful and informed selection of Gram-negative bacterial biothreat simulants and also the accompanying particle size and composition. The outcome of this work contributes to improved selection of simulants, spray liquids, and particle size for use in bioaerosol research.IMPORTANCE The outcome of this work contributes to improved selection of simulants, spray liquids, and particle size for use in bioaerosol research. Taken together, the results highlight the importance of careful and informed selection of Gram-negative bacterial biothreat simulants and also the accompanying particle size and composition. The results highlight how even moderate changes to one experimental parameter, e.g., bacterial species, spray liquid, or particle size, can strongly affect the aerobiological stability of Gram-negative bacteria. A key finding was the observation that stability differences caused by particle size or compositional changes frequently followed species-specific patterns.

Holographic deep learning for rapid optical screening of anthrax spores

Establishing early warning systems for anthrax attacks is crucial in biodefense. Despite numerous studies for decades, the limited sensitivity of conventional biochemical methods essentially requires preprocessing steps and thus has limitations to be used in realistic settings of biological warfare. We present an optical method for rapid and label-free screening of Bacillus anthracis spores through the synergistic application of holographic microscopy and deep learning. A deep convolutional neural network is designed to classify holographic images of unlabeled living cells. After training, the network outperforms previous techniques in all accuracy measures, achieving single-spore sensitivity and subgenus specificity. The unique "representation learning" capability of deep learning enables direct training from raw images instead of manually extracted features. The method automatically recognizes key biological traits encoded in the images and exploits them as fingerprints. This remarkable learning ability makes the proposed method readily applicable to classifying various single cells in addition to B. anthracis, as demonstrated for the diagnosis of Listeria monocytogenes, without any modification. We believe that our strategy will make holographic microscopy more accessible to medical doctors and biomedical scientists for easy, rapid, and accurate point-of-care diagnosis of pathogens.

Holographic deep learning for rapid optical screening of anthrax spores

Establishing early warning systems for anthrax attacks is crucial in biodefense. Despite numerous studies for decades, the limited sensitivity of conventional biochemical methods essentially requires preprocessing steps and thus has limitations to be used in realistic settings of biological warfare. We present an optical method for rapid and label-free screening of Bacillus anthracis spores through the synergistic application of holographic microscopy and deep learning. A deep convolutional neural network is designed to classify holographic images of unlabeled living cells. After training, the network outperforms previous techniques in all accuracy measures, achieving single-spore sensitivity and subgenus specificity. The unique "representation learning" capability of deep learning enables direct training from raw images instead of manually extracted features. The method automatically recognizes key biological traits encoded in the images and exploits them as fingerprints. This remarkable learning ability makes the proposed method readily applicable to classifying various single cells in addition to B. anthracis, as demonstrated for the diagnosis of Listeria monocytogenes, without any modification. We believe that our strategy will make holographic microscopy more accessible to medical doctors and biomedical scientists for easy, rapid, and accurate point-of-care diagnosis of pathogens.

Comparative analysis of the sensitivity of metagenomic sequencing and PCR to detect a biowarfare simulant (Bacillus atrophaeus) in soil samples

To evaluate the sensitivity of high-throughput DNA sequencing for monitoring biowarfare agents in the environment, we analysed soil samples inoculated with different amounts of Bacillus atrophaeus, a surrogate organism for Bacillus anthracis. The soil samples considered were a poorly carbonated soil of the silty sand class, and a highly carbonated soil of the silt class. Control soil samples and soil samples inoculated with 10, 10³, or 10⁵ cfu were processed for DNA extraction. About 1% of the DNA extracts was analysed through the sequencing of more than 10⁸ reads. Similar amounts of extracts were also studied for Bacillus atrophaeus DNA content by real-time PCR. We demonstrate that, for both soils, high-throughput sequencing is at least equally sensitive than real-time PCR to detect Bacillus atrophaeus DNA. We conclude that metagenomics allows the detection of less than 10 ppm of DNA from a biowarfare simulant in complex environmental samples.

Aerosol and Surface Deposition Characteristics of Two Surrogates for Bacillus anthracis Spores

Spores of an acrystalliferous derivative of Bacillus thuringiensis subsp. kurstaki, termed Btcry-, are morphologically, aerodynamically, and structurally indistinguishable from Bacillus anthracis spores. Btcry- spores were dispersed in a large, open-ended barn together with spores of Bacillus atrophaeus subsp. globigii, a historically used surrogate for Bacillus anthracis Spore suspensions (2 × 10¹² CFU each of B. atrophaeus subsp. globigii and Btcry-) were aerosolized in each of five spray events using a backpack misting device incorporating an air blower; a wind of 4.9 to 7.6 m s^-1 was also flowing through the barn in the same direction. Filter air samplers were situated throughout the barn to assess the aerosol density of the spores during each release. Trays filled with a surfactant in aqueous buffer were placed on the floor near the filter samplers to assess spore deposition. Spores were also recovered from arrays of solid surfaces (concrete, aluminum, and plywood) that had been laid on the floor and set up as a wall at the end of the barn. B. atrophaeus subsp. globigii spores were found to remain airborne for significantly longer periods, and to be deposited on horizontal surfaces at lower densities, than Btcry- spores, particularly near the spray source. There was a 6-fold-higher deposition of Btcry- spores than of B. atrophaeus subsp. globigii spores on vertical surfaces relative to the surrounding airborne density. This work is relevant for selecting the best B. anthracis surrogate for the prediction of human exposure, hazard assessment, and hazard management following a malicious release of B. anthracis IMPORTANCE: There is concern that pathogenic bacteria could be maliciously disseminated in the air to cause human infection and disruption of normal life. The threat from spore-forming organisms, such as the causative agent of anthrax, is particularly serious. In order to assess the extent of this risk, it is important to have a surrogate organism that can be used to replicate the dispersal characteristics of the threat agent accurately. This work compares the aerosol dispersal and deposition behaviors of the surrogates Btcry- and B. atrophaeus subsp. globigii Btcry- spores remained in the air for a shorter time, and were markedly more likely to adhere to vertical surfaces, than B. atrophaeus subsp. globigii spores.

Longitudinal Metagenomic Analysis of Hospital Air Identifies Clinically Relevant Microbes

We describe the sampling of sixty-three uncultured hospital air samples collected over a six-month period and analysis using shotgun metagenomic sequencing. Our primary goals were to determine the longitudinal metagenomic variability of this environment, identify and characterize genomes of potential pathogens and determine whether they are atypical to the hospital airborne metagenome. Air samples were collected from eight locations which included patient wards, the main lobby and outside. The resulting DNA libraries produced 972 million sequences representing 51 gigabases. Hierarchical clustering of samples by the most abundant 50 microbial orders generated three major nodes which primarily clustered by type of location. Because the indoor locations were longitudinally consistent, episodic relative increases in microbial genomic signatures related to the opportunistic pathogens Aspergillus, Penicillium and Stenotrophomonas were identified as outliers at specific locations. Further analysis of microbial reads specific for Stenotrophomonas maltophilia indicated homology to a sequenced multi-drug resistant clinical strain and we observed broad sequence coverage of resistance genes. We demonstrate that a shotgun metagenomic sequencing approach can be used to characterize the resistance determinants of pathogen genomes that are uncharacteristic for an otherwise consistent hospital air microbial metagenomic profile.

Surfactin variants mediate species-specific biofilm formation and root colonization in Bacillus

Cyclic lipopeptides (cLP) and especially surfactins produced by Bacillus spp. trigger biofilm formation and root colonization and are crucial for biocontrol activity and systemic resistance in plants. Bacillus atrophaeus 176s isolated from the moss Tortella tortuosa produces the cLP fengycins, iturins and surfactins, possesses antifungal activities and can protect tomato, lettuce and sugar beet against Rhizoctonia solani infection. In B. atrophaeus we identified for the first time the variant surfactin C, which differs from surfactin A produced by B. subtilis and B. amyloliquefaciens by an isoleucine instead of a leucine at position 7 of the lipopeptide backbone. The analysis of the complete surfactin gene clusters revealed that the dissimilarity is encoded in the adenylation domain of srfC and show that surfactin variations are distributed in a species-specific manner in bacilli. We demonstrate that the surfactin A and C with subtle structural differences have varying signal strengths on biofilm formation and root colonization and act specifically on the respective producing strain. This became evident as biofilm formation and root colonization but not swarming motility in surfactin biosynthesis mutants was restored differentially in the presence of exogenously supplemented cognate and non-cognate surfactin variants.

Whole-Genome Sequencing in Microbial Forensic Analysis of Gamma-Irradiated Microbial Materials

Effective microbial forensic analysis of materials used in a potential biological attack requires robust methods of morphological and genetic characterization of the attack materials in order to enable the attribution of the materials to potential sources and to exclude other potential sources. The genetic homogeneity and potential intersample variability of many of the category A to C bioterrorism agents offer a particular challenge to the generation of attributive signatures, potentially requiring whole-genome or proteomic approaches to be utilized. Currently, irradiation of mail is standard practice at several government facilities judged to be at particularly high risk. Thus, initial forensic signatures would need to be recovered from inactivated (nonviable) material. In the study described in this report, we determined the effects of high-dose gamma irradiation on forensic markers of bacterial biothreat agent surrogate organisms with a particular emphasis on the suitability of genomic DNA (gDNA) recovered from such sources as a template for whole-genome analysis. While irradiation of spores and vegetative cells affected the retention of Gram and spore stains and sheared gDNA into small fragments, we found that irradiated material could be utilized to generate accurate whole-genome sequence data on the Illumina and Roche 454 sequencing platforms.

Integrative and Conjugative Elements (ICEs): What They Do and How They Work

Horizontal gene transfer plays a major role in microbial evolution, allowing microbes to acquire new genes and phenotypes. Integrative and conjugative elements (ICEs, a.k.a. conjugative transposons) are modular mobile genetic elements integrated into a host genome and are passively propagated during chromosomal replication and cell division. Induction of ICE gene expression leads to excision, production of the conserved conjugation machinery (a type IV secretion system), and the potential to transfer DNA to appropriate recipients. ICEs typically contain cargo genes that are not usually related to the ICE life cycle and that confer phenotypes to host cells. We summarize the life cycle and discovery of ICEs, some of the regulatory mechanisms, and how the types of cargo have influenced our view of ICEs. We discuss how ICEs can acquire new cargo genes and describe challenges to the field and various perspectives on ICE biology.

Draft Genome Sequence of the Biowarfare Simulant Bacillus atrophaeus Strain 930029

We report here the draft genome sequence of Bacillus atrophaeus strain 930029. Strain 930029 shows evidence of drift, based on a comparison to the corresponding source strain publicly available today.

Differential proteomics analysis of Bacillus amyloliquefaciens and its genome-shuffled mutant for improving surfactin production

Genome shuffling technology was used as a novel whole-genome engineering approach to rapidly improve the antimicrobial lipopeptide yield of Bacillus amyloliquefaciens. Comparative proteomic analysis of the parental ES-2-4 and genome-shuffled FMB38 strains was conducted to examine the differentially expressed proteins. The proteome was separated by 2-DE (two dimensional electrophoresis) and analyzed by MS (mass spectrum). In the shuffled strain FMB38, 51 differentially expressed protein spots with higher than two-fold spot density were detected by gel image comparison. Forty-six protein spots were detectable by silver staining and further MS analysis. The results demonstrated that among the 46 protein spots expressed particularly induced in the genome-shuffled mutant, 15 were related to metabolism, five to DNA replication, recombination and repair, six to translation and post-translational modifications, one to cell secretion and signal transduction mechanisms, three to surfactin synthesis, two to energy production and conversion, and 14 to others. All these indicated that the metabolic capability of the mutant was improved by the genome shuffling. The study will enable future detailed investigation of gene expression and function linked with surfactin synthesis. The results of proteome analysis may provide information for metabolic engineering of Bacillus amyloliquefaciens for overproduction of surfactin.

Bacillus thuringiensis HD-1 Cry- : development of a safe, non-insecticidal simulant for Bacillus anthracis

AIMS

A representative simulant for spores of Bacillus anthracis is needed for field testing. Bacillus thuringiensis is gaining recognition as a suitable organism. A strain that does not form the insecticidal, parasporal crystals that are characteristic of this species is a more accurate physical representative of B. anthracis spores. We developed noninsecticidal derivatives of two isolates of B. thuringiensis HD-1.

METHODS AND RESULTS

Two plasmid-cured derivatives of B. thuringiensis HD-1, unable to make crystal toxins ('Cry(-) '), were isolated. These isolates and the existing Cry(-) strain, B. thuringiensis Al Hakam, were probed with PCR assays against the known insecticidal genes cry, vip and cyt. Their genomic DNA was sequenced to demonstrate a lack of insecticidal genes. This was confirmed by bioassays against a number of invertebrate species. Real-time PCR assays were developed to identify the B. thuringiensis HD-1 Cry(-) derivatives and an effective differential and selective medium was assessed.

CONCLUSIONS

All three Cry(-) isolates are devoid of known insecticidal determinants. The B. thuringiensis HD-1 Cry(-) derivatives can easily be recovered from soil and identified by PCR with some selectivity.

SIGNIFICANCE AND IMPACT OF THE STUDY

The B. thuringiensis HD-1 Cry(-) derivatives represent accurate, nongenetically manipulated simulants for B. anthracis with excellent human and environmental safety records.

Life cycle and spore resistance of spore-forming Bacillus atrophaeus

Bacillus endospores have a wide variety of important medical and industrial applications. This is an overview of the fundamental aspects of the life cycle, spore structure and factors that influence the spore resistance of spore-forming Bacillus. Bacillus atrophaeus was used as reference microorganism for this review because their spores are widely used to study spore resistance and morphology. Understanding the mechanisms involved in the cell cycle and spore survival is important for developing strategies for spore killing; producing highly resistant spores for biodefense, food and pharmaceutical applications; and developing new bioactive molecules and methods for spore surface display.

Molecular signatures for Bacillus species: demarcation of the Bacillus subtilis and Bacillus cereus clades in molecular terms and proposal to limit the placement of new species into the genus Bacillus

The genus Bacillus is a phylogenetically incoherent taxon with members of the group lacking a common evolutionary history. Comprising aerobic and anaerobic spore-forming bacteria, no characteristics are known that can distinguish species of this genus from other similar endospore-forming genera. With the availability of complete genomic data from over 30 different species from this group, we have constructed detailed phylogenetic trees to determine the relationships among Bacillus and other closely related taxa. Additionally, we have performed comparative genomic analysis for the determination of molecular markers, in the form of conserved signature indels (CSIs), to assist in the understanding of relationships among species of the genus Bacillus in molecular terms. Based on the analysis, we report here the identification of 11 and 6 CSIs that clearly differentiate a ‘ Bacillus subtilis clade’ and a ‘ Bacillus cereus clade’, respectively, from all other species of the genus Bacillus . No molecular markers were identified that supported a larger clade within this genus. The subtilis and the cereus clades were also the largest observed monophyletic groupings among species from the genus Bacillus in the phylogenetic trees based on 16S rRNA gene sequences and those based upon concatenated sequences for 20 conserved proteins. Thus, the relationships observed among these groups of species through CSIs are independently well supported by phylogenetic analysis. The molecular markers identified in this study provide a reliable means for the reorganization of the currently polyphyletic genus Bacillus into a more evolutionarily consistent set of groups. It is recommended that the genus Bacillus sensu stricto should comprise only the monophyletic subtilis clade that is demarcated by the identified CSIs, with B. subtilis as its type species. Members of the adjoining cereus clade (referred to as the Cereus clade of bacilli), although they are distinct from the subtilis clade, will also retain the Bacillus genus name as they contain several clinically important species, and their transfer into a new genus could have serious consequences. However, all other species that are currently part of the genus Bacillus and not part of these two clades should be eventually transferred to other genera. We also propose that all novel species of the genus Bacillus must meet minimal requirements, foremost among which is that the branching of the prospective species with the Bacillus sensu stricto clade or the Cereus clade of bacilli should be strongly supported by 16S rRNA gene sequence trees or trees based upon concatenated protein sequences. Additionally, the presence of one or more of the CSIs that are specific for these clades may be used to confirm molecularly the placement of the species into these clades. The identified CSIs, in addition to their usefulness for taxonomic and diagnostic purposes, also provide novel probes for genetic and biochemical studies of these bacteria.

Genetic barcodes for improved environmental tracking of an anthrax simulant

The development of realistic risk models that predict the dissemination, dispersion and persistence of potential biothreat agents have utilized nonpathogenic surrogate organisms such as Bacillus atrophaeus subsp. globigii or commercial products such as Bacillus thuringiensis subsp. kurstaki. Comparison of results from outdoor tests under different conditions requires the use of genetically identical strains; however, the requirement for isogenic strains limits the ability to compare other desirable properties, such as the behavior in the environment of the same strain prepared using different methods. Finally, current methods do not allow long-term studies of persistence or reaerosolization in test sites where simulants are heavily used or in areas where B. thuringiensis subsp. kurstaki is applied as a biopesticide. To create a set of genetically heterogeneous yet phenotypically indistinguishable strains so that variables intrinsic to simulations (e.g., sample preparation) can be varied and the strains can be tested under otherwise identical conditions, we have developed a strategy of introducing small genetic signatures ("barcodes") into neutral regions of the genome. The barcodes are stable over 300 generations and do not impact in vitro growth or sporulation. Each barcode contains common and specific tags that allow differentiation of marked strains from wild-type strains and from each other. Each tag is paired with specific real-time PCR assays that facilitate discrimination of barcoded strains from wild-type strains and from each other. These uniquely barcoded strains will be valuable tools for research into the environmental fate of released organisms by providing specific artificial detection signatures.

Effect of the Bacillus atrophaeus subsp. globigii Spo0F H101R mutation on strain fitness

Sporulation is a critical developmental process in Bacillus spp. that, once initiated, removes the possibility of further growth until germination. Therefore, the threshold conditions triggering sporulation are likely to be subject to evolutionary constraint. Our previous studies revealed two spontaneous hypersporulating mutants of Bacillus atrophaeus subsp. globigii, both containing point mutations in the spo0F gene. One of these strains (Detrick-2; contains the spo0F101 allele with a C:T [His101Arg] substitution) had been deliberately selected in the early 1940s as an anthrax surrogate. To determine whether the experimental conditions used during the selection of the "military" strains could have supported the emergence of hypersporulating variants, the relative fitness of strain Detrick-2 was measured in several experimental settings modeled on experimental conditions employed during its development in the 1940s as a simulant. The congenic strain Detrick-1 contained a wild-type spo0F gene and sporulated like the wild-type strain. The relative fitness of Detrick-1 and Detrick-2 was evaluated in competition experiments using quantitative single nucleotide polymorphism (SNP)-specific real-time PCR assays directed at the C:T substitution. The ancestral strain Detrick-1 had a fitness advantage under all conditions tested except when competing cultures were subjected to frequent heat shocks. The hypersporulating strain gained the maximum fitness advantage when cultures were grown at low oxygen tension and when heat shock was applied soon after the formation of the first heat-resistant spores. This is interpreted as gain of fitness by the hypersporulating strain in fast-changing fluctuating environments as a result of the increased rate of switching to the sporulating phenotype.

Detection and tracking of a novel genetically tagged biological simulant in the environment

A variant of Bacillus thuringiensis subsp. kurstaki containing a single, stable copy of a uniquely amplifiable DNA oligomer integrated into the genome for tracking the fate of biological agents in the environment was developed. The use of genetically tagged spores overcomes the ambiguity of discerning the test material from pre-existing environmental microflora or from previously released background material. In this study, we demonstrate the utility of the genetically "barcoded" simulant in a controlled indoor setting and in an outdoor release. In an ambient breeze tunnel test, spores deposited on tiles were reaerosolized and detected by real-time PCR at distances of 30 m from the point of deposition. Real-time PCR signals were inversely correlated with distance from the seeded tiles. An outdoor release of powdered spore simulant at Aberdeen Proving Ground, Edgewood, MD, was monitored from a distance by a light detection and ranging (LIDAR) laser. Over a 2-week period, an array of air sampling units collected samples were analyzed for the presence of viable spores and using barcode-specific real-time PCR assays. Barcoded B. thuringiensis subsp. kurstaki spores were unambiguously identified on the day of the release, and viable material was recovered in a pattern consistent with the cloud track predicted by prevailing winds and by data tracks provided by the LIDAR system. Finally, the real-time PCR assays successfully differentiated barcoded B. thuringiensis subsp. kurstaki spores from wild-type spores under field conditions.

Complete genome sequence of Paenibacillus mucilaginosus 3016, a bacterium functional as microbial fertilizer

Paenibacillus mucilaginosus is a ubiquitous functional bacterium in microbial fertilizer. Here we report the complete sequence of P. mucilaginosus 3016. Multiple sets of functional genes have been found in the genome. To the best of our knowledge, this is the first announcement about the complete genome sequence of a P. mucilaginosus strain.