Pseudomonas turukhanskensis sp. nov., isolated from oil-contaminated soils.

A bacterial strain named IB1.1T was isolated in a screening of hydrocarbon-degrading bacteria from oil-contaminated soils on the territory of the Turukhansk District of Krasnoyarsk Krai, East Siberia, Russia. The 16S rRNA gene sequence had 98.7 % identity with respect to the closest phylogenetic relative, Pseudomonas granadensis F-278,770T, and the next most closely related species with 98.6 % similarity was Pseudomonaspunonensis, suggesting that IB1.1T should be classified within the genus Pseudomonas. The analysis of housekeeping genes rpoB, rpoD and gyrB showed similarities lower than 90 % in all cases with respect to the closest relatives, confirming its phylogenetic affiliation. The strain showed a polar flagellum. The respiratory quinone was Q9. The major fatty acids were 16 : 1ω7c/16 : 1ω6c (summed feature 3), 18 : 1ω7c and 16 : 0. The strain was oxidase- and catalase-positive, but the arginine dihydrolase system was not present. Nitrate reduction, urease and ß-galactosidase production, and aesculin hydrolysis were negative. The temperature range for growth was 4-34 °C, and the strain could grow at pH 11. The DNA G+C content was 58.5 mol%. DNA-DNA hybridization results showed values of less than 30 % relatedness with respect to the type strains of the eight most closely related species. Therefore, the dataset of genotypic, phenotypic and chemotaxonomic data support the classification of strain IB1.1T into a novel species of the genus Pseudomonas, for which the name Pseudomonasturukhanskensis sp. nov. is proposed. The type strain is IB1.1T (=VKM B-2935T=CECT 9091T).

Effect of Plant Growth-Promoting Bacteria on Antioxidant Status, Acetolactate Synthase Activity, and Growth of Common Wheat and Canola Exposed to Metsulfuron-Methyl.

Metsulfuron-methyl, a widely used herbicide, could cause damage to the sensitive plants in crop-rotation systems at extremely low levels in the soil. The potential of plant growth-promoting bacteria (PGPB) for enhancing the resistance of plants against herbicide stress has been discovered recently. Therefore, it is poorly understood how physiological processes occur in plants, while PGPB reduce the phytotoxicity of herbicides for agricultural crops. In greenhouse studies, the effect of strains Pseudomonas protegens DA1.2 and Pseudomonas chlororaphis 4CH on oxidative damage, acetolactate synthase (ALS), enzymatic and non-enzymatic antioxidants in canola (Brassica napus L.), and wheat (Triticum aestivum L.) were investigated under two levels (0.05 and 0.25 mg∙kg-1) of metsulfuron-methyl using spectrophotometric assays. The inoculation of herbicide-exposed wheat with bacteria significantly increased the shoots fresh weight (24-28%), amount of glutathione GSH (60-73%), and flavonoids (5-14%), as well as activity of ascorbate peroxidase (129-140%), superoxide dismutase SOD (35-49%), and ALS (50-57%). Bacterial treatment stimulated the activity of SOD (37-94%), ALS (65-73%), glutathione reductase (19-20%), and the accumulation of GSH (61-261%), flavonoids (17-22%), and shoots weight (27-33%) in herbicide-exposed canola. Simultaneous inoculation prevented lipid peroxidation induced by metsulfuron-methyl in sensitive plants. Based on the findings, it is possible that the protective role of bacterial strains against metsulfuron-metil is linked to antioxidant system activation.

Improving Tree Seedling Quality Using Humates Combined with Bacteria to Address Decarbonization Challenges through Forest Restoration.

Improving the quality of tree planting material for carbon sequestration through reforestation can help solve environmental problems, including the need to reduce the concentration of carbon dioxide in the atmosphere. The purpose of this study was to investigate the possibility of using humic substances in combination with rhizosphere microorganisms Pseudomonas protegens DA1.2 and Pseudomonas sp. 4CH as a means to stimulate the growth of seedlings of pine, poplar, large-leaved linden, red oak, horse chestnut, and rowan. Humic substances stimulated the growth of shoots and roots of pine, large-leaved linden, and horse chestnut seedlings. The effects of bacteria depended on both plant and bacteria species: Pseudomonas protegens DA1.2 showed a higher stimulatory effect than Pseudomonas sp. 4CH on pine and linden, and Pseudomonas sp. 4CH was more effective in the case of chestnut. An additive effect of humates and Pseudomonas protegens DA1.2 on the growth rate of pine and linden saplings was discovered. Poplar, red oak, and rowan seedlings were unresponsive to the treatments. The growth-stimulating effects of the treatments are discussed in connection with the changes in carbon, chlorophyll, and nitrogen contents in plants. The results show the need for further research in bacterial species capable of stimulating the growth of plant species that were unresponsive in the present experiments.

Mitigation of the Negative Effect of Drought and Herbicide Treatment on Growth, Yield, and Stress Markers in Bread Wheat as a Result of the Use of the Plant Growth Regulator Azolen®.

Most chemical pesticides, in addition to their main functions (protection against diseases, weeds, and pests), also have a noticeable inhibitory effect on target crops. In a laboratory experiment and two-year field experiments (Russia, Trans-Urals), a study was made of the effect of the biopreparation Azolen® (Azotobacter vinelandii IB-4) on plants of the Ekada 113 wheat variety under conditions of drought and stress caused by the exposure to the herbicide Chistalan (2.4-D and dicamba). The biopreparation and the herbicide were used separately and together on wheat during the tillering phase. Treatment with the biological preparation under stressful conditions had a significant effect on the hormonal balance of plants (a decrease in the amount of abscisic acid and a normalization of the balance of indolyl-3-acetic acid and cytokinins in shoots and roots of plants was noted), while the osmoprotective, antioxidant, and photosynthetic systems of plants were activated. In drought conditions, the treatment of plants with biological preparation prevented the inhibition of root growth caused by the use of the herbicide. This, in turn, improved the absorption of water by plants and ensured an increase in wheat yield (1.6 times). The results obtained give reason to believe that microbiological preparations can be used as antidotes that weaken the phytotoxic effect of herbicidal treatments, including in drought conditions.

Independent evaluation of the accuracy of 5 artificial intelligence software for detecting lung nodules on chest X-rays.

Background: The integration of artificial intelligence (AI) into medicine is growing, with some experts predicting its standalone use soon. However, skepticism remains due to limited positive outcomes from independent validations. This research evaluates AI software's effectiveness in analyzing chest X-rays (CXR) to identify lung nodules, a possible lung cancer indicator. Methods: This retrospective study analyzed 7,670,212 record pairs from radiological exams conducted between 2020 and 2022 during the Moscow Computer Vision Experiment, focusing on CXR and computed tomography (CT) scans. All images were acquired during clinical routine. The final dataset comprised 100 CXR images (50 with lung nodules, 50 without), selected consecutively and based on inclusion and exclusion criteria, to evaluate the performance of all five AI-based solutions, participating in the Moscow Computer Vision Experiment and analyzing CXR. The evaluation was performed in 3 stages. In the first stage, the probability of a nodule in the lung obtained from AI services was compared with the Ground Truth (1-there is a nodule, 0-there is no nodule). In the second stage, 3 radiologists evaluated the segmentation of nodules performed by the AI services (1-nodule correctly segmented, 0-nodule incorrectly segmented or not segmented at all). In the third stage, the same radiologists additionally evaluated the classification of the nodules (1-nodule correctly segmented and classified, 0-all other cases). The results obtained in stages 2 and 3 were compared with Ground Truth, which was common to all three stages. For each stage, diagnostic accuracy metrics were calculated for each AI service. Results: Three software solutions (Celsus, Lunit INSIGHT CXR, and qXR) demonstrated diagnostic metrics that matched or surpassed the vendor specifications, and achieved the highest area under the receiver operating characteristic curve (AUC) of 0.956 [95% confidence interval (CI): 0.918 to 0.994]. However, when evaluated by three radiologists for accurate nodule segmentation and classification, all solutions performed below the vendor-declared metrics, with the highest AUC reaching 0.812 (95% CI: 0.744 to 0.879). Meanwhile, all AI services demonstrated 100% specificity at stages 2 and 3 of the study. Conclusions: To ensure the reliability and applicability of AI-based software, it is crucial to validate performance metrics using high-quality datasets and engage radiologists in the evaluation process. Developers are recommended to improve the accuracy of the underlying models before allowing the standalone use of the software for lung nodule detection. The dataset created during the study may be accessed at https://mosmed.ai/datasets/mosmeddatargogksnalichiemiotsutstviemlegochnihuzlovtipvii/.

Draft genome sequence of perfluorinated acids C7-C9 degrading bacterium Pseudomonas mosselii 5(3), isolated from soil contaminated with pesticides.

The Pseudomonas mosselii 5(3) strain is a potential degrader of persistent perfluorinated pollutants, particularly C7-C9 perfluorinated acids. The genome of the strain has been fully sequenced. It consists of a chromosome with a length of 5,676,241 base pairs and a G-C content of 64.38%.

Effects on Pseudomonas plecoglossicida 2,4-D and Humic Substances on the Growth, Pigment Indices and Concentration of Hormones in Wheat Seedlings Grown under Water Deficit.

The search for ways to increase plant productivity in drought conditions is of fundamental importance, since soil moisture deficiency is widespread and leads to critical crop losses. The aim of this study was to identify the effects of plant growth-promoting bacteria and humic substances on the growth, chlorophyll, flavonoids, nitrogen balance index, and concentration of cytokinins and abscisic acids in wheat plants grown in the laboratory under conditions of water deficit. An increase in the accumulation of plant mass was shown during the treatment of wheat plants with Pseudomonas plecoglossicida 2,4-D and humic substances in these conditions. It has been shown that stimulating plant growth is associated with increased root growth, which leads to an increase in the nitrogen balance index, chlorophyll, and flavonoid concentrations in treated plants. The detected increase in the concentration of chlorophyll in plants treated with P. plecoglossicida 2,4-D correlated with a decrease in the concentration of abscisic acid in plant shoots and, in plants treated with humates, with an increase in the concentration of cytokinins in shoots. The higher efficiency of treating plants with a combination of bacteria and humic substances than with any of them individually may be associated with the additive effect of these treatments on the hormonal balance.

Biodegradation Potential of C7-C10 Perfluorocarboxylic Acids and Data from the Genome of a New Strain of Pseudomonas mosselii 5(3).

The use of bacteria of the genus Pseudomonas-destructors of persistent pollutants for biotechnologies of environmental purification-is an interesting area of research. The aim of this work was to study the potential of Pseudomonas mosselii strain 5(3) isolated from pesticide-contaminated soil as a degrader of C7-C10 perfluorocarboxylic acids (PFCAs) and analyze its complete genome. The genome of the strain has been fully sequenced. It consists of a chromosome with a length of 5,676,241 b.p. and containing a total of 5134 genes, in particular, haloalkane dehalogenase gene (dhaA), haloacetate dehalogenase H-1 gene (dehH1), fluoride ion transporter gene (crcB) and alkanesulfonate monooxygenase gene (ssuE), responsible for the degradation of fluorinated compounds. The strain P. mosselii 5(3) for was cultivated for 7 days in a liquid medium with various C7-C10 PFCAs as the sole source of carbon and energy, and completely disposed of them. The results of LC-MS analysis showed that the transformation takes place due to perfluorohexanoic acid with the release of various levels of stoichiometry (depending on PFCA) of fluorine ion mineralization indicators determined by ion chromatography. Thus, Pseudomonas mosselii strain 5(3) demonstrates a genetically confirmed high potential for the decomposition of C7-C10 PFCA.

The Growth-Inhibitory Effect of Increased Planting Density Can Be Reduced by Abscisic Acid-Degrading Bacteria.

High-density planting can increase crop productivity per unit area of cultivated land. However, the application of this technology is limited by the inhibition of plant growth in the presence of neighbors, which is not only due to their competition for resources but is also caused by growth regulators. Specifically, the abscisic acid (ABA) accumulated in plants under increased density of planting has been shown to inhibit their growth. The goal of the present study was to test the hypothesis that bacteria capable of degrading ABA can reduce the growth inhibitory effect of competition among plants by reducing concentration of this hormone in plants and their environment. Lettuce plants were grown both individually and three per pot; the rhizosphere was inoculated with a strain of Pseudomonas plecoglossicida 2.4-D capable of degrading ABA. Plant growth was recorded in parallel with immunoassaying ABA concentration in the pots and plants. The presence of neighbors indeed inhibited the growth of non-inoculated lettuce plants. Bacterial inoculation positively affected the growth of grouped plants, reducing the negative effects of competition. The bacteria-induced increase in the mass of competing plants was greater than that in the single ones. ABA concentration was increased by the presence of neighbors both in soil and plant shoots associated with the inhibition of plant growth, but accumulation of this hormone as well as inhibition of the growth of grouped plants was prevented by bacteria. The results confirm the role of ABA in the response of plants to the presence of competitors as well as the possibility of reducing the negative effect of competition on plant productivity with the help of bacteria capable of degrading this hormone.

Clinical application of radiological AI for pulmonary nodule evaluation: Replicability and susceptibility to the population shift caused by the COVID-19 pandemic.

PURPOSE: replicability and generalizability of medical AI are the recognized challenges that hinder a broad AI deployment in clinical practice. Pulmonary nodes detection and characterization based on chest CT images is one of the demanded use cases for automatization by means of AI, and multiple AI solutions addressing this task are becoming available. Here, we evaluated and compared the performance of several commercially available radiological AI with the same clinical task on the same external datasets acquired before and during the pandemic of COVID-19. APPROACH: 5 commercially available AI models for pulmonary nodule detection were tested on two external datasets labelled by experts according to the intended clinical task. Dataset1 was acquired before the pandemic and did not contain radiological signs of COVID-19; dataset2 was collected during the pandemic and did contain radiological signs of COVID-19. ROC-analysis was applied separately for the dataset1 and dataset2 to select probability thresholds for each dataset separately. AUROC, sensitivity and specificity metrics were used to assess and compare the results of AI performance. RESULTS: Statistically significant differences in AUROC values were observed between the AI models for the dataset1. Whereas for the dataset2 the differences of AUROC values became statistically insignificant. Sensitivity and specificity differed statistically significantly between the AI models for the dataset1. This difference was insignificant for the dataset2 when we applied the probability threshold initially selected for the dataset1. An update of the probability threshold based on the dataset2 created statistically significant differences of sensitivity and specificity between AI models for the dataset2. For 3 out of 5 AI models, the update of the probability threshold was valuable to compensate for the degradation of AI model performances with the population shift caused by the pandemic. CONCLUSIONS: Population shift in the data is able to deteriorate differences of AI models performance. Update of the probability threshold together with the population shift seems to be valuable to preserve AI models performance without retraining them.

Changes in software as a medical device based on artificial intelligence technologies.

PURPOSE: to develop a procedure for registering changes, notifying users about changes made, unifying software as a medical device based on artificial intelligence technologies (SaMD-AI) changes, as well as requirements for testing and inspections-quality control before and after making changes. METHODS: The main types of changes, divided into two groups-major and minor. Major changes imply a subsequent change of a SaMD-AI version to improve efficiency and safety, to change the functionality, and to ensure the processing of new data types. Minor changes imply those that SaMD-AI developers can make due to errors in the program code. Three types of SaMD-AI testings are proposed to use: functional testing, calibration testing or control, and technical testing. RESULTS: The presented approaches for validation SaMD-AI changes were introduced. The unified requirements for the request for changes and forms of their submission made this procedure understandable for SaMD-AI developers, and also adjusted the workload for the Experiment experts who checked all the changes made to SaMD-AI. CONCLUSION: This article discusses the need to control changes in the module of SaMD-AI, as innovative products influencing medical decision making. It justifies the need to control a module operation of SaMD-AI after making changes. To streamline and optimize the necessary and sufficient control procedures, a systematization of possible changes in SaMD-AI and testing methods was carried out.

Effects of Humic Substances on the Growth of Pseudomonas plecoglossicida 2,4-D and Wheat Plants Inoculated with This Strain.

Both rhizosphere bacteria and humic substances (HSs) can promote plant growth when applied individually and even greater effects of their combination have been demonstrated. We aimed to elucidate the relative importance of the stimulating effects of HSs on bacterial growth and the effects of the combination of bacteria and HSs on plants themselves. The effects of humic (HA) and fulvic acids (FA) (components of humic substances) on the growth of Pseudomonas plecoglossicida 2,4-D in vitro were studied. We also studied the effects of this bacterial strain and HSs applied individually or in combination on the growth of wheat plants. Although the 2,4-D strain showed low ability to use HSs as the sole source of nutrition, the bacterial growth rate was increased by FA and HA, when other nutrients were available. HSs increased root colonization with bacteria, the effect being greater in the case of HA. The effects on roots and shoots increased when bacteria were associated with HSs. FA+ 2,4-D was more effective in stimulating shoot growth, while HA + 2,4-D was in the case of root growth. The latter effect is likely to be beneficial under edaphic stresses.

PGP-Bacterium Pseudomonas protegens Improves Bread Wheat Growth and Mitigates Herbicide and Drought Stress.

The reaction of plants to simultaneous stress action and treatment with biological stimulants still remains poorly studied. Laboratory and field experiments have been conducted to study the growth and yield of bread wheat (Triticum aestivum L.) of the variety Ekada 113; stress markers and quantitative ratios of phytohormones in plants under insufficient soil moisture; the effects of spraying with herbicide containing 2,4-D and dicamba and growth-stimulating bacterium Pseudomonas protegens DA1.2; and combinations of these factors. Under water shortage conditions, spraying plants with Chistalan reduced their growth compared to non-sprayed plants, which was associated with inhibition of root growth and a decrease in the content of endogenous auxins in the plants. Under conditions of combined stress, the treatment of plants with the strain P. protegens DA1.2 increased the IAA/ABA ratio and prevented inhibition of root growth by auxin-like herbicide, ensuring water absorption by the roots as well as increased transpiration. As a result, the content of malondialdehyde oxidative stress marker was reduced. Bacterization improved the water balance of wheat plants under arid field conditions. The addition of bacterium P. protegens DA1.2 to the herbicide Chistalan increased relative water content in wheat leaves by 11% compared to plants treated with herbicide alone. Application of the bacterial strain P. protegens DA1.2 increased the amount of harvested grain from 2.0-2.2 t/ha to 3.2-3.6 t/ha. Thus, auxin-like herbicide Chistalan and auxin-producing bacterium P. protegens DA1.2 may affect the balance of phytohormones in different ways. This could be the potential reason for the improvement in wheat plants' growth during dry periods when the bacterium P. protegens DA1.2 is included in mixtures for weed control.

Influence of Hydrocarbon-Oxidizing Bacteria on the Growth, Biochemical Characteristics, and Hormonal Status of Barley Plants and the Content of Petroleum Hydrocarbons in the Soil.

Much attention is paid to the relationship between bacteria and plants in the process of the bioremediation of oil-contaminated soils, but the effect of petroleum degrading bacteria that synthesize phytohormones on the content and distribution of these compounds in plants is poorly studied. The goal of the present field experiment was to study the effects of hydrocarbon-oxidizing bacteria that produce auxins on the growth, biochemical characteristics, and hormonal status of barley plants in the presence of oil, as well as assessing the effect of bacteria and plants separately and in association with the content of oil hydrocarbons in the soil. The treatment of plants with strains of Enterobacter sp. UOM 3 and Pseudomonas hunanensis IB C7 led to an increase in the length and mass of roots and shoots and the leaf surface index, and an improvement in some parameters of the elements of the crop structure, which were suppressed by the pollutant. The most noticeable effect of bacteria on the plant hormonal system was a decrease in the accumulation of abscisic acid. The data obtained indicate that the introduction of microorganisms weakened the negative effects on plants under abiotic stress caused by the presence of oil. Plant-bacteria associations were more effective in reducing the content of hydrocarbons in the soil and increasing its microbiological activity than when either organism was used individually.

Effects of Association of Barley Plants with Hydrocarbon-Degrading Bacteria on the Content of Soluble Organic Compounds in Clean and Oil-Contaminated Sand.

Plant-bacteria consortia are more effective in bioremediation of petroleum contaminated soil than when either organism is used individually. The reason for this is that plant root exudates promote growth and activity of oil degrading bacteria. However, insufficient attention has been paid to the ability of bacteria to influence root exudation. Therefore, the influence of barley plants and/or bacterial inoculation (Pseudomonas hunanensis IB C7 and Enterobacter sp. UOM 3) on the content of organic acids, sugars and plant hormones in the eluate from clean and oil-polluted sand was studied separately or in combination. These strains are capable of oxidizing hydrocarbons and synthesizing auxins. Concentrations of organic acids and sugars were determined using capillary electrophoresis, and hormones by enzyme-linked immunosorbent assays. In the absence of plants, no sugars were detected in the sand, confirming that root exudates are their main source. Introducing bacteria into the sand increased total contents of organic compounds both in the presence and absence of oil. This increase could be related to the increase in auxin amounts in the sand eluate, as well as in plants. The results indicate that bacteria are able to increase the level of root exudation. Since auxins can promote root exudation, bacterial production of this hormone is likely responsible for increased concentrations of soluble organic compounds in the sand. Bacterial mediation of root exudation by affecting plant hormonal status should be considered when choosing microorganisms for phytoremediation.

Capacity of Pseudomonas Strains to Degrade Hydrocarbons, Produce Auxins and Maintain Plant Growth under Normal Conditions and in the Presence of Petroleum Contaminants.

The phytoremediation of soil contaminated with petroleum oil products relies on co-operation between plants and rhizosphere bacteria, including the plant growth-promoting effect of the bacteria. We studied the capacity of strains of Pseudomonas, selected as oil degraders, to produce plant hormones and promote plant growth. Strains with intermediate auxin production were the most effective in stimulating the seedling growth of seven plant species under normal conditions. Bacterial seed treatment resulted in about a 1.6-fold increase in the weight of barley seedlings, with the increment being much lower in other plant species. The strains P. plecoglossicida 2.4-D and P. hunanensis IB C7, characterized by highly efficient oil degradation (about 70%) and stable intermediate in vitro auxin production in the presence of oil, were selected for further study with barley. These strains increased the seed germination percentage approximately two-fold under 5% oil concentration in the soil, while a positive effect on further seedling growth was significant when the oil concentration was raised to 8%. This resulted in a 1.3-1.7-fold increase in the seedling mass after 7 days of growth, depending on the bacterial strain. Thus, strains of oil-degrading bacteria selected for their intermediate and stable production of auxin were found to be effective ameliorators of plant growth inhibition resulting from petroleum stress.