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Model suicide vector for containment of genetically engineered microorganisms.

A model suicide vector (pBAP19h), designed for the potential containment of genetically engineered microorganisms, was made by constructing a plasmid with the hok gene, which codes for a lethal polypeptide, under the control of the lac promoter. The vector plasmid also codes for carbenicillin resistance. In the absence of carbenicillin, induction of the hok gene in vitro caused elimination of all detectable cells containing the suicide vector; pBAP19h-free cells of the culture survived and grew exponentially. In the presence of carbenicillin, however, the number of cells containing pBAP19h initially declined after induction of hok but then multiplied exponentially. The surviving cells still had a fully functional hok gene and had apparently developed resistance to the action of the Hok polypeptide. Thus, high selective pressure against the loss of the suicide vector led to a failure of the system. Soil microcosm experiments confirmed the ability of a suicide vector to restrict the growth of a genetically engineered microorganism in the absence of selective pressure against the loss of the plasmid, with 90 to 99% elimination of hok-bearing cells within 24 h of hok induction. However, some pBAP19h-bearing cells survived in the soil microcosms after hok induction. The surviving cells contained an active hok gene but were not capable of normal growth even after elimination of the hok gene; it appears that a mutation that made them Hok resistant also reduced their capacity for membrane functions needed for energy generation and exponential cell growth. Thus, the model suicide vector was shown to be functional in soil as well as in vitro.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacterial Proteins

A day in the life of an inpatient: an experiential game to promote empathy for individuals in a psychiatric hospital.

The attitudes of hospital staff toward individuals with mental illness have been investigated, described in the literature, and discussed at national conferences. It has been suggested that attitudes are the precursors or determinants of behavior. Although the precise effect of staff attitude on patients is unclear, attitudes of the staff do appear to be related to their behavior and to have an impact on patients and their subsequent recovery. There are few precise answers on how to promote positive attitudes. While hospital policies and procedures can prescribe behaviors of staff, attitude cannot be dictated. Some studies have evaluated the effect of training and participation in milieu programs on the attitude of psychiatric staff. Simulation games recently have been explored as a possible way to influence the attitude of staff toward those with mental illness. This article describes an attempt at one state psychiatric hospital to influence in a positive way the attitude of the staff by using a simulation game called, A Day in the Life of an Inpatient. Adapted from Into Aging by Hoffman and Reif (1978), the game used by the authors provides a microcosmic experience for staff of a hospitalized patient's ward experience.

Empathy

Long-term PFOA and cadmium Co-contamination alters soil carbon, nitrogen, and phosphorus cycling: Insights from metagenomics and metabolomics.

The co-existence of perfluorooctanoic acid (PFOA) and cadmium (Cd) in soil poses a combined threat to microbial communities. However, the ecological effects and underlying mechanisms of their long-term combined exposure remain poorly understood. This study conducted a 90-day soil microcosm experiment to systematically investigate the effects of individual and combined effects of PFOA and Cd on microbial communities. Our results demonstrated that combined pollution of PFOA and Cd significantly affected four soil enzyme activities associated with carbon, nitrogen, and phosphorus cycling. It also influenced microbial thermal activity with an IC50 of PFOA at 0.94 mg/kg. The toxic interaction between PFOA and Cd varied with both toxicity indicators and exposure time. At the community level, PFOA and Cd synergistically reduced bacterial diversity and richness, while exerting more complex interactive effects on fungal communities. Metagenomic analysis revealed that PFOA and Cd significantly affected carbon, nitrogen, and phosphorus cycling by inhibiting inorganic phosphorus solubilization genes (gcd, pqqC) and altering key genes in carbon fixation and nitrogen transformation. Metabolomic profiling further demonstrated that PFOA disrupted membrane lipid homeostasis and amino acid metabolism. Meanwhile, the co-existence of Cd exacerbated disturbances in sugar and carbon metabolism. Our findings provide genetic-level insights into microbial responses to long-term PFOA and Cd co-contamination. These results are essential for risk assessment at such co-contamination sites.

Cadmium

Novel bacterial hosts and mobile genetic structure of tet(X) variants in tetracycline-contaminated aquatic environment uncovered by culture and long-read metagenomics.

Clinically important tigecycline (3rd-generation tetracycline) resistance tet(X) variants were inferred to have evolutionarily originated from environmental bacteria, and have been recognized among environment, human and animals. However, genetic basis for environmental proliferation and dissemination of tet(X) variants remains ambiguous. This study profiled tet(X) variants at gene, contig, isolate, and community levels in environmental community subjected to long-term stepwise increasing oxytetracycline (1st-generation tetracycline) or tigecycline pressure using long-term microcosm experiments, quantitative PCR, bacterial isolation, whole-genome sequencing, and Nanopore-based long-read metagenomics. We confirmed that both oxytetracycline and tigecycline enriched the abundance of tetracycline resistance genes especially oxytetracycline-enriched tet(X3). Unexpectedly diverse bacterial hosts and genetic structure of tet(X)-positive mobile elements in the environment microbiome were identified using bacterial isolation and long-read Nanopore metagenomics. Pseudomonas defluvii was first reported to carry tet(X3) in the chromosome, forming IS26-tet(X3)-res-ISCR2 circular intermediate to transfer between different DNA molecules. Database mining revealed similar mobile segments have prevailed among animal-derived Acinetobacter species. Unlike the widely reported ISCR2-mediated transfer of tet(X6), we identified a novel mobile multidrug transposon TnAs3 where tet(X6) and class 1 integron co-transferred as its passenger region. Mobile tet(X2)-ere(D)-aadS-erm(F)-blaOXA-347 segment was annotated in Runella, and co-occurrences of tet(X2) and ere(D), aadS, blaOXA-347 were also found in Flavobacterium, Arsenicibacter, Chryseobacterium and Pedobacter. Overall, tetracycline-contaminated aquatic microbiome harboured diverse mobile tet(X)-positive segments which have not yet been acquired by clinical pathogens, and thus served as the genetic pool of tet(X) variants together with indigenous bacterial hosts, especially the newly reported Pseudomonas defluvii. Reducing pollution of older-generation tetracyclines would be a proactive way to mitigate environmental evolution and possible clinical effects of tet(X) variants.

Metagenomics

Plasmid transfer between strains of Pseudomonas aeruginosa on membrane filters attached to river stones.

A naturally occurring mercury-resistance, conjugative plasmid, designated pQM1, was isolated from a bacterial population on the surface of stones from a river using Pseudomonas aeruginosa as a recipient. This was a narrow-host-range plasmid [IncP-13; 165 MDa; Tra+, Hgr, fluorescein mercuric acetater, merbrominr, Phi(E79), UVr] confined to some Pseudomonas spp. It was used to demonstrate transfer between bacteria on stones in laboratory microcosm experiments and in situ. Transfer occurred (3.3 X 10(-1) to 6.8 X 10(-9) per recipient) at all the temperatures used (6-20 degrees C), although frequencies were lower in the cold. Nutrient status also affected transfer frequency, rich conditions promoting transfer. The presence of competing bacteria in the natural epilithon lowered transfer frequencies, but when unscrubbed stones were heat treated, transfer was enhanced, perhaps because of nutrient release from the heated epilithon.

Fresh Water

Maintenance of plasmids pBR322 and pUC8 in nonculturable Escherichia coli in the marine environment.

Maintenance of plasmids pBR322 and pUC8 in Escherichia coli that was nonculturable after exposure to seawater was studied. E. coli JM83 and JM101, which contained plasmids pBR322 and pUC8, respectively, were placed in sterile artificial seawater for 21 days. Culturability was determined by plating on both nonselective and selective agar, and plasmid maintenance was monitored by direct isolation of plasmid nucleic acid from bacteria collected on Sterivex filters. E. coli JM83 became nonculturable after incubation for 6 days in seawater yet maintained plasmid pBR322 for the entire period of the study, i.e., 21 days. E. coli JM101 was nonculturable after incubation in seawater for 21 days and also maintained plasmid pUC8 throughout the duration of the microcosm experiment. Direct counts of bacterial cells did not change significantly during exposure to seawater, even though plate counts yielded no viable (i.e., platable) cells. We concluded that E. coli cells are capable of maintaining high-copy-number plasmids, even when no longer culturable, after exposure to the estuarine or marine environment.

DNA, Bacterial

Microbial decomposer diversity and metabolic function during the decomposition of brine shrimp carcasses in a saline lake.

BACKGROUND: Decomposition of brine shrimp carcasses has a crucial role in carbon cycling of saline lakes, yet the microbial dynamics remain poorly understood. RESULTS: Here we integrated metagenomics, metatranscriptomics, culturomics, metabolomics, and microcosm experiments to investigate microbial community succession and function during brine shrimp (Artemia sp.) carcass decomposition in Barkol Lake, a hypersaline lake in China. A total of 149 metagenome-assembled genomes (MAGs) and 77 pure culture genomes were recovered across 33 phyla, with 72.12% genomes representing species-level novel lineages. Our results reveal diverse bacterial and archaeal taxa, including novel lineages from CG03, T1Sed10-126 and rare archaeal taxa (Asgardarchaeota, Thermoplasmatota, Nanoarchaeota, and Halobacteriota), involved in degradation of biomacromolecules-proteins, carbohydrates, lipids, and nucleic acids-via extracellular hydrolysis, nutrient transport, and intracellular catabolism. These taxa exhibit substrate preferences, rapidly responding to the breakdown of polysaccharides and proteins, followed by lipids and nucleic acids. Hydrolyzed oligomers are further oxidized by various microbes through fermentation, sulfate reduction, and methanogenesis via metabolic handoffs. Additionally, viral auxiliary metabolic genes (AMGs) further enhance microbial host functions, contributing to key ecological processes such as carbon cycling and stress response. A temporally structured microbial decomposer network (MDN) was observed, driving mineralization cascades from fermentation to sulfate reduction and methanogenesis. CONCLUSIONS: This study reveals microbial metabolic handoffs and virus-mediated modulation as critical mechanisms for organic matter turnover, expanding the known diversity and function of decomposers in saline ecosystems. Our findings offer new insights into biogeochemical processes in saline lakes and highlight a synergistic microbial decomposer network involving bacteria, archaea, and viruses that collectively drive nutrient cycling during brine shrimp carcass decomposition. Video Abstract.

Animals

Eco-evolutionary dynamics sustain a potent yet rare antibiotic gene cluster in Streptomyces.

Microbial secondary metabolites have been recognized and utilized for nearly a century. Nevertheless, the eco-evolutionary mechanisms governing their distribution among microorganisms remain largely unresolved. In this study, we examined intraspecific interactions within Streptomyces albidoflavus and identified a strain exhibiting potent antagonistic activity against conspecifics. This "killer" phenotype was attributed to the production of kosinostatin, a hybrid aromatic polyketide antibiotic. Evolutionary genomic analyses provided strong evidence that the kosinostatin biosynthetic gene cluster was horizontally acquired in S. albidoflavus over a relatively short evolutionary timescale, a finding consistent with its sparse distribution within this species, across the genus Streptomyces, and even throughout the phylum Actinomycetota. Using microcosm assays, we demonstrated that the kosinostatin producer outcompeted sensitive conspecifics in liquid culture but not in soil, indicating that environmental context plays a key role in altering the fitness benefits of this cluster. Moreover, the competitive advantage was observed only in the presence of sensitive strains, revealing a trade-off between fitness benefits and metabolic costs. These results highlight the role of context-dependent selection in shaping the evolutionary persistence of the kosinostatin cluster. The current distribution pattern of this cluster in S. albidoflavus likely results from a dynamic interplay of intraspecific horizontal gene transfer, vertical inheritance, and recurrent gene loss. Overall, our findings establish an eco-evolutionary framework that explains the rarity of a potent antibiotic gene cluster in Streptomyces, illustrating how environmental constraints, fitness trade-offs, and gene flux collectively orchestrate the biosynthetic architecture of Streptomyces species.

Streptomyces

Kinetics of chromium transformations in the environment.

Kinetics of chromium transformations under typical environmental conditions were systematically investigated using batch, microcosm and column experiments. Oxidation and reduction rates were evaluated in single phase water systems and in two phase water-solid systems. Natural and reference waters, sediments and soils representing a broad range of characteristics were used. Some of the investigated reactions, such as the reduction of Cr(VI) by S2- or Fe2+ ions under anaerobic conditions, were instantaneous and the experimental results exactly followed the stoichiometric and equilibrium calculations. Other reactions, such as the reduction of Cr(VI) by organics in sediments and soils, or the oxidation of Cr(III) by MnO2, were much slower and clearly exhibited kinetic controls. Reduction of Cr(VI) by organics was dependent on both the type and amount of organic material. Dissolved oxygen by itself did not induce measurable oxidation of Cr(III), spiked to the experimental waters, after 128 days. Slow Cr(III) oxidation to Cr(VI) was only noted in one of the natural waters and sediments with half-lives ranging from 2 to 9 years. In all cases the extent of Cr(III) oxidation did not exceed 15% of the initial Cr(III) present. The overall results indicate that the transport and transformation of chromium can be predicted using kinetics data derived from a simplified laboratory experiment, the Eh-pH data and the aquatic system characteristics. Results of the microcosm and laboratory experiments were in good agreement with the predicted concentrations.

Chemical Phenomena

[Systemic thrombolysis using streptokinase. Experiences at the Civic Hospital of Lugano in the framework of the ISIS-2 study].

With a small group of Swiss hospitals we had an opportunity of participating in ISIS-2, the major study on thrombolysis in acute myocardial infarction. Experience with our microcosm (Ospedale Civico Lugano) was compared with the macrocosm of the results of ISIS-2 in 17,187 randomized patients (in brackets). Mortality was 5.1% (7.8%) in our streptokinase group and 15.8% (12.8%) in our placebo group. In the ISIS-2 study the combination of thrombolytic therapy with streptokinase, and of antiplatelet therapy with aspirin, showed a reduction of approximately one third in acute mortality of myocardial infarction, stroke and reinfarction. Our experience confirms the reduced incidence of allergic side effects (3.5%), major bleeding (0.3%) and minor bleeding (2.9%) during or after thrombolytic therapy.

Administration, Oral

Bacterial conjugation between Escherichia coli and Pseudomonas spp. donor and recipient cells in soil.

Experiments conducted in microcosms containing loam soil samples inoculated with either E. coli or Pseudomonas spp. donor and recipient cells showed that bacterial cells survived and conjugated over a 24-h incubation period. E. coli transconjugants were detected 6 h after donor and recipient strains were introduced into sterile soil samples. In non-sterile soil samples, transconjugants were detected between 8 and 24 h incubation. Pseudomonas transconjugants were recovered from sterile soil samples between 6 and 12 h after their introduction and as early as 2 h in non-sterile soil. The results show that genetic interactions occur in non-sterile soil in relatively short periods of time at relatively high transfer frequencies (10(-3) to 10(-4]. Studies on genetic interactions in soil are becoming necessary in risk assessment/environmental impact studies prior to the release of genetically engineered or modified organisms into uncontained environments.

Conjugation, Genetic

Evolve III: a discrete events model of an evolutionary ecosystem.

Evolve III is a discrete events model of an evolutionary ecosystem. The model includes three levels of organization: population, organism and genetic structure. Each of these components was modeled independently, so that selective replacement of subsystems can be used to create families of models capable of testing alternative hypotheses about the real system. To demonstrate the use of the model we describe an experiment on the relationship between adaptability of populations and the variability of the environment. Populations cultured in a constant environment usually dominated those cultured in a variable environment when both were placed in a variable environment at an early stage of development, whereas the opposite is the case at later stages of development. This agrees with experiments on laboratory microcosms and lends credence to the potential predictive value of the model.

Biological Evolution

Twenty-five years of residents: what and where are they now.

To evaluate the effectiveness of our program in meeting the subsequent career needs of our graduates and to describe their professional experiences as a microcosm of pediatrics, a survey was completed of the 419 pediatricians who had completed the Harriet Lane Residency Program at The Johns Hopkins Hospital between 1960 and 1984. Overall, the 326 respondents found the program to have been effective in the areas they deemed appropriate to be taught in residency years. In decreasing order, the chief resident, fellow house officers, and full-time faculty were rated to have had the greatest teaching effectiveness. The women respondents were less likely to be married (76% vs 89%), had fewer children on average (1.2 vs 2.31), missed more work, and were more likely to enter postresidency training (89% vs 78%) than the men. Of all respondents, 73% reported being certain of their career goals during residency and 77% of those reported a reasonable similarity with current positions. More than 93% reported being satisfied with their current careers, and 87% would still choose pediatrics. They are generally well reimbursed financially, with academician salaries matching those of private practitioners 10 years after completing residency and surpassing them, slightly, thereafter. This information provides much food for thought in preparing tomorrow's pediatricians.

Attitude of Health Personnel

Sampling culturable heterotrophs from microcosms: a statistical analysis.

The contributions of different sources of error in sampling mixed and unmixed bacterial microcosms were evaluated by using analysis of variance. Culturable heterotrophic bacteria from a turbid freshwater impoundment were sampled from 9-liter tanks that were unagitated or mixed with magnetic stirrers or pumps and from dilution bottles that were unagitated or agitated with a mechanical shaker. Axenic cultures of Enterobacter aerogenes were also sampled from manually shaken test tubes. In both agitated and unagitated tanks and in unagitated dilution bottles, dilutions made from the same sampling pipette were significantly different, showing a clumping of bacteria on the scale of millimeters. Also, microcosms within a single experiment differed from one another by a large margin. Dilution mean squares and tank or bottle mean squares were homogeneous for all types of tanks and unagitated bottles, indicating that the gentle mixing provided by pumps and stir bars did not reduce either millimeter scale or intermicrocosm variability over what prevailed in unagitated microcosms. By contrast, the vigorously shaken bottles and test tubes showed no millimeter scale variability. Intermicrocosm variability was undetectable in test tubes and two orders of magnitude less in shaken bottles than in unshaken bottles. When these facts are coupled with the inherent statistical advantage of replicating large rather than small experimental units, it is concluded that sampling error in the enumeration of aquatic bacteria in microcosms will be reduced by using numerous, small, violently agitated microcosms with a minimum of subsampling per microcosm.

Analysis of Variance

The changing face of cardiac transplantation: the Washington University Program, 1985-1987.

Since January, 1985, 59 patients have undergone 62 heart transplantations at Washington University School of Medicine. The experience in this program serves as a useful microcosm of the field of cardiac transplantation as a whole to demonstrate certain trends that are becoming evident. Of the patients, 47% had coronary artery disease compared with 40% with cardiomyopathy. Fourteen patients (24%) were 55 years old or older at the time of transplantation. Sixteen patients (27%) required mechanical support of respiration or circulation or both prior to transplantation. Six patients were maintained with a left ventricular or biventricular assist device, and all survived; 1 patient received extracorporeal membrane oxygenation and lived; 7 patients were maintained with an intraaortic balloon pump, 6 of whom survived; and 2 were maintained with a mechanical ventilator and survived. The preoperative waiting period averaged 51 days for the group as a whole. Status-3 patients experienced an average 81-day waiting period, and those in blood group O waited 155 days. In contrast, critically ill patients (status 0) underwent transplantation within an average of 9 days. Actuarial survival at 12 months for all patients, operative survivors, patients age 55 years old or more, and patients bridged to transplantation was 87%, 92%, 84%, and 87%, respectively. Utilizing the combination therapy of cyclosporine, azathioprine, and prednisone introduced by one of us in 1983 and administered to all patients in this series, 50% of patients were rejection free and 56% were infection free at 12 months.(ABSTRACT TRUNCATED AT 250 WORDS)

Academic Medical Centers

Survival and function of a genetically engineered Pseudomonad in aquatic sediment microcosms.

Pseudomonas sp. strain B13 FR1(pFRC20P) is a genetically engineered microorganism (GEM) which is able to degrade chloro- and methylaromatics through a constructed ortho cleavage pathway. The fate of the GEM and its ability to degrade substituted aromatic compounds in two different aquatic sediments was investigated by using a microcosm system which consisted of intact layered sediment cores with an overlying water column. The GEM survived in Lake Plussee and in Rhine river sediments at densities of approximately 10(5) bacteria per g (dry weight) (1 to 5% of the total CFU) throughout a 4-week period of investigation. According to several criteria, the microcosm system was stable and healthy throughout the experiment and the addition of the GEM did not affect the total number of extractable CFU (I. Wagner-Döbler, R. Pipke, K. N. Timmis, and D. F. Dwyer, Appl. Environ. Microbiol. 58:1249-1258, 1992). When compared with uninoculated controls, the presence of the GEM enhanced the rate of degradation of a mixture of 3-chlorobenzoate and 4-methylbenzoate (25 microns each) which had been added to the water column of the sediment cores.

Biodegradation, Environmental

The effects of atrazine on microcosms developed from four natural plankton communities.

Comparisons were made among Leffler microcosms developed from four different natural communities and exposed to 0, 20, 100, 200, 500, 1,000, and 5,000 micrograms/L atrazine, a commonly used herbicide. Atrazine reduced net primary productivity, pH, and net productivity/respiration ratios in all four microcosm communities. In three of the four communities, the lowest observed (P less than 0.05) effect concentration (LOEL) was 100 micrograms/L. In the fourth community the LOEL was 200 micrograms/L atrazine. The sensitivity and accuracy of bioassays with four different microcosm communities were evaluated by comparing results with values reported for acute and chronic single species bioassays, other types of microcosms, and experimental ponds exposed to similar concentrations of atrazine. The ranges of sensitivity noted in these experiments were less than the range reported for single species bioassays using common test organisms and similar to those reported for other microcosms. The similarity between Leffler microcosm results and the responses reported for the experimental ponds suggests that the Leffler microcosms accurately reflected concentrations causing ecosystem level changes in the experimental ponds.

Animals