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Accelerating the pace of microbiome science to enhance crop productivity and agroecosystem health will require transdisciplinary studies, comparisons among datasets, and synthetic analyses of research from diverse crop management contexts. However, despite the widespread availability of crop-associated microbiome data, variation in field sampling and laboratory processing methodologies, as well as metadata collection and reporting, significantly constrains the potential for integrative and comparative analyses. Here we discuss the need for agriculture-specific metadata standards for microbiome research, and propose a list of “required” and “desirable” metadata categories and ontologies essential to be included in a future minimum information metadata standards checklist for describing agricultural microbiome studies. We begin by briefly reviewing existing metadata standards relevant to agricultural microbiome research, and describe ongoing efforts to enhance the potential for integration of data across research studies. Our goal is not to delineate a fixed list of metadata requirements. Instead, we hope to advance the field by providing a starting point for discussion, and inspire researchers to adopt standardized procedures for collecting and reporting consistent and well-annotated metadata for agricultural microbiome research.

The present study aims to verify the autumn effect in the gold market, first presented 10 years ago by Dirk Baur in the paper “The autumn effect of gold” and to investigate the calendar effects occurring for other precious metals. This empirical research is presented in a way to place the results obtained in the context of the Efficient Market Hypothesis (EMH) and the more current Adaptive Market Hypothesis (AMH). The study was conducted as an extended reproduction of the Baur study. The main conclusion is that, the autumn effect on the gold market has been reversed and replaced by the winter effect, which is linked to the AMH. An equally interesting calendar effect was observed for silver. Platinum and palladium saw an increase in prices in January, but given the patterns in the gold market, it is very likely that this phenomenon will also change over time.

The study aims to empirically analyze the reaction of stock prices to the information about the conclusion and acceptance of a debtor–creditor arrangement under restructuring proceedings of companies listed on the stock exchange in Poland. The following main research hypothesis was verified: public disclosure of information about an arrangement conclusion and acceptance in restructuring proceedings results in above-average rates of return due to investments in the stocks of these entities in the short term. Three events were assessed: the public disclosure of information about the conclusion of a debtor–creditor arrangement (Event 1), its approval by a court (Event 2), and the decision becoming final (Event 3). The research method applied was the event study. Event 1 and Event 3 leads to an above-average and statistically significant increase in stock prices on the day of the event. In contrast, no statistically significant above-average rates of return accompanied Event 2.

Background: Gut microbiota generates a series of bioactive metabolites that can be converted into uremic toxins such as trimethylamine-N-oxide (TMAO), p-cresyl sulfate (pCS), and indoxyl sulfate (IS). The aim of the study was to examine the association between diet and the concentrations of the mentioned gut microbiota-derived uremic toxins., Methods: An observational cross-sectional study was conducted involving 210 participants: 84 hemodialysis (HD) patients, 44 peritoneal dialysis (PD) patients, 52 kidney transplant recipients (KTR), and 30 healthy controls. Dietary intake was assessed using a 3-day food diary and a food frequency questionnaire with 6 answers (FFQ-6). The alternate Mediterranean diet (aMED) score was calculated based on data obtained from the 3-day food diary and FFQ-6. Blood samples were analyzed for TMAO, pCS, and IS concentrations using liquid chromatography-mass spectrometry (LC-MS/MS)., Results: Significant differences in TMAO, pCS, and IS concentrations were observed among the study groups. HD and PD patients exhibited higher levels of these metabolites compared to KTR and healthy controls. The median aMED score was 4 (3-5) points in the HD group, 4.5 (4-6) points in the PD group, 5 (4-6) points in the KTRs, and 6 (5-7) points in the control group. Higher adherence to the Mediterranean diet (aMED score) was associated with lower pCS levels in dialysis patients. Vegetable intake several times a day was found to mitigate the effects of phenylalanine and tyrosine intake on pCS concentration among dialysis patients., Conclusions: The diet of patients undergoing kidney replacement therapy (KRT) significantly affects the concentrations of gut microbiota-derived uremic toxins. These findings highlight the importance of dietary management in mitigating the adverse effects of these toxins in patients with chronic kidney disease (CKD)., Competing Interests: Conflict of interest The authors declare no conflict of interest., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

In light of growing concerns about climate change and environmental issues, investor interest has surged in the new green economy market. However, the existing literature is limited regarding potential price bubbles and co-bubbles within this new domain. This study examines price bubbles and co-bubbles in the new green economy market, covering 31 indexes classified into three groups: the green economy market and its components, geographical regions, and sectors. Using daily data from August 31, 2005, to May 31, 2024, a test procedure is first applied to detect periods of price bubble in the various indexes, then logistic regressions are employed to examine price co-bubble behaviours. The results show evidence of price bubbles in the green economy market, particularly in solar and wind indexes, with peaks during the COVID-19 pandemic and Russia-Ukraine conflict, whereas the water index is the least prone to price bubbles. Regarding geographical region, the USA market exhibits a higher tendency for price bubbles than the Asian or European markets. Several sectors are resistant to price bubbles. The co-bubble analysis reveals a strong reliance of wind index on price bubbles in the solar and water indexes. Price bubbles in Asia significantly influence price bubbles in Europe and the USA. These findings have implications for investment portfolio management and risk management strategies in the new green economy market., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Chronic kidney disease (CKD) is linked to an elevated risk of malnutrition and sarcopenia, contributing to the intricate network of CKD-related metabolic disorders. Adipokines and myokines are markers and effectors of sarcopenia and nutritional status. The aim of this study was to assess whether the adipokine-myokine signature in patients on kidney replacement therapy could help identify malnutrition and sarcopenia. The study involved three groups: 84 hemodialysis (HD) patients, 44 peritoneal dialysis (PD) patients, and 52 kidney transplant recipients (KTR). Mean age was 56.1 ± 16.3 years. Malnutrition was defined using the 7-Point Subjective Global Assessment (SGA) and the Malnutrition-Inflammation Score (MIS). Sarcopenia was diagnosed based on reduced handgrip strength (HGS) and diminished muscle mass. Concentrations of adipokines and myokines were determined using the enzyme-linked immunosorbent assay (ELISA). 32.8% of all study participants were identified as malnourished and 20.6% had sarcopenia. For malnutrition, assessed using the 7-Point SGA, in ROC analysis albumin (area under the curve (AUC) 0.67 was the best single biomarker identified. In dialysis patients, myostatin (AUC 0.79) and IL-6 (AUC 0.67) had a high discrimination value for sarcopenia, and we were able to develop a prediction model for sarcopenia, including age, albumin, adiponectin, and myostatin levels, with an AUC of 0.806 (95% CI: 0.721-0.891). Adipokines and myokines appear to be useful laboratory markers for assessing malnutrition and sarcopenia. The formula we propose could contribute to a better understanding of sarcopenia and potentially lead to more effective interventions and management strategies for dialysis patients.

Emerging evidence suggests that microbiota plays a crucial role in the development, progression, and therapeutic options in obesity and its comorbidities. This study assessed preoperative probiotic therapy's impact on bariatric treatment outcomes. A 12-week randomized, double-blind, placebo-controlled trial with 48 patients undergoing bariatric surgery was conducted. Participants received probiotics-Sanprobi Barrier-which contained nine strains of bacteria: Bifidobacterium bifidum W23, Bifidobacterium lactis W51 and W52, Lactobacillus acidophilus W37, Levilactobacillus brevis W63, Lacticaseibacillus casei W56, Ligilactobacillus salivarius W24, Lactococcus lactis W19, and Lactococcus lactis W58. Primary outcomes included excess body weight loss, body weight loss, and excess body mass index loss, with secondary objectives focusing on metabolic profiles. Surgical treatment of obesity significantly improved anthropometric and metabolic parameters. No significant differences were observed in primary outcomes or in secondary outcomes between groups at any time point post-surgery. Preoperative probiotics administration did not affect clinical outcomes 1, 3, or 6 months following bariatric surgery.

Depositing plastic waste has long been a prevalent method of utilization, persisting today. Plastic waste within municipal waste landfills (MWL) undergoes diverse (bio-)degradation processes, which may be a potential source of chemicals and microorganisms harmful to the environment and human health. Soil and air samples were collected from modern MWL to identify environmental contamination caused by 5 years of plastic (bio-)degradation. The pH of soil samples was higher than in the reference area (RA), which was possibly caused by alterations in soil anionic composition detected with ion chromatography. The presence of plastic additives with a toxic potential was detected in soil samples by gas chromatography coupled with tandem mass spectrometry (GC-MS/MS). With the use of thermal desorption and GC - MS, hazardous substances (phthalic anhydride, phenylmaleic anhydride, ethylbenzene, xylene) with a known impact on the human endocrine system were also detected. The number of microorganisms, both fungi, and bacteria, was highly increased in soil and air in the MWL as compared to the RA. The soil collected in the MWL area appeared to be phytotoxic, and inhibited seed germination (Phytotoxkit FTM bioassay), while acute toxicity Microtox® bioassay showed a hormetic effect towards Aliivibrio fischeri. Obtained results exhibited massive soil and air contamination, with both chemical substances and microorganisms while plastic waste undergoes (bio-)degradation. It may contribute to serious environmental contamination and pose a threat to human health., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this publication., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Poultry farming is one of the most efficient animal husbandry methods and it provides nutritional security to a significant number of the world population. Using modern intensive farming techniques, global production has reached 133.4 mil. t in 2020, with a steady growth each year. Such intensive growth methods however lead to a significant environmental footprint. Waste materials such as poultry litter and manure can pose a serious threat to environmental and human health, and need to be managed properly. Poultry production and waste by-products are linked to NH 3 , N 2 O and CH 4 emissions, and have an impact on global greenhouse gas emissions, as well as animal and human health. Litter and manure can contain pesticide residues, microorganisms, pathogens, pharmaceuticals (antibiotics), hormones, metals, macronutrients (at improper ratios) and other pollutants which can lead to air, soil and water contamination as well as formation of antimicrobial/multidrug resistant strains of pathogens. Dust emitted from intensive poultry production operations contains feather and skin fragments, faeces, feed particles, microorganisms and other pollutants, which can adversely impact poultry health as well as the health of farm workers and nearby inhabitants. Fastidious odours are another problem that can have an adverse impact on health and quality of life of workers and surrounding population. This study discusses the current knowledge on the impact of intensive poultry farming on environmental and human health, as well as taking a look at solutions for a sustainable future., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

Morbid obesity is considered a civilization disease of the 21st century. Not only does obesity increase mortality, but it is also the most important cause of the shortening life expectancy in the modern world. Obesity is associated with many metabolic abnormalities: dyslipidemia, hyperglycemia, cardiovascular diseases, and others. An increasing number of patients diagnosed with chronic kidney disease (CKD) are obese. Numerous additional disorders associated with impaired kidney function make it difficult to conduct slimming therapy and may also be associated with a greater number of complications than in people with normal kidney function. Currently available treatments for obesity include lifestyle modification, pharmacotherapy, and bariatric surgery (BS). There are no precise recommendations on how to reduce excess body weight in patients with CKD treated conservatively, undergoing chronic dialysis, or after kidney transplantation. The aim of this study was to analyze studies on the bariatric treatment of obesity in this group of people, as well as to compare the recommendations typical for bariatrics and CKD.

Hemodialysis (HD) patients are characterized by malnutrition, which adversely affects their survival. The development of malnutrition is influenced, among other factors, by improper diet and the advanced age of patients. The study aimed to assess the nutritional status and adherence to dietary recommendations among older patients. The multicenter study included 179 stable HD patients. The nutritional status was assessed by a 7-point Subjective Global Assessment (SGA). Anthropometry and body composition was analyzed. The diet was assessed based on the 3-day food diary and the Food Frequency Questionnaire with 6 answers (FFQ-6). Blood laboratory tests were performed. Based on the 7-point SGA, malnutrition was diagnosed in 38.5% of HD patients. The decreased content of the muscle tissue (LTI < 14 kg/m2) was observed in 70.4% of the examined patients and the decreased concentration of s-albumin was observed in 44.1% of patients. Older patients had significantly lower LTI. 26% of patients consumed less than 25 kcal/kg body weight and less than 0.8 g protein/kg body weight. Older patients’ diets contained significantly fewer calories. There were significant differences between nutrient intake on a weekday with dialysis, a weekday without dialysis, and a weekend day without dialysis. The lowest intake of nutrients was observed on the day of dialysis. Nutritional education and the determination of whether food is permitted during hemodialysis are necessary to improve patients’ nutrition.

Coastal and transitional waters are often used as bathing waters. In many regions, such activities play an important economic role. According to the European Union Bathing Water Directive (2006/7/EC) (BWD) the concentration of Escherichia coli in bathing water exceeding 500 CFU·100 mL -1 poses a high risk for bathers' health. In order to safeguard public health, microbiological environmental monitoring is carried out, which has recently been supported or replaced by mathematical models detailing the spread of sanitary contamination. This study focuses on the problems and limitations that can be encountered in the process of constructing a mathematical model describing the spread of biological contamination by E. coli bacteria in coastal seawater. This and other studies point to the following problems occurring during the process of building and validating a model: the lack of data on loads of sanitary contamination (often connected with multiple sources of biological contamination inflow) makes the model more complex; E. coli concentrations higher than 250 CFU·100 mL -1 (low hazard for health) are observed very rarely, and are associated with great uncertainty; the impossibility of predicting the time and intensity of precipitation as well as stronger winds and rougher sea, which may be a significant source of E. coli . However, there is universal agreement that such models will be useful in managing bathing water quality and protecting public health, especially during big failures of the wastewater network.

The prevalence of cephalosporine-resistant (3GC-R) strains among United States community-related research samples ranged from 5.6 to 10.8%, while, in the European countries, it was 1.2% to 10.1%. Several studies suggest that meat of animal origin could be one of the reservoirs of 3GC-R bacteria. Here, 86 raw meat samples (turkey, pork, chicken and beef) were collected randomly and verified for the presence of 3GC-R bacteria. The 3GC-R bacteria were isolated, identified and characterized phenotypically (antibiotic resistance, motility and biofilm) and genotypically (repetitive-sequence-based rep-PCR) to elucidate any correlations with principal component analysis (PCA). From 28 3GC-R positive samples, 41 strains were isolated, from which the majority belonged to Serratia fonticola (39%), followed by Escherichia coli (19.5%), Enterobacter cloacae (17.1%) and Klebsiella pneumoniae (14.6%). The isolates of E. coli and S. fonticola presented diverse profiles in rep-PCR. Generally, 3GC-R strains were more resistant to antibiotics used in veterinary medicine than in human medicine. PCA derived from antibiotic resistance, motility and biofilm formation of S. fonticola and E. coli strains showed that resistance to beta-lactams was separated from the resistance to other antibiotic classes. Moreover, for the S. fonticola , E. coli and En. cloacae , the type of meat can create a specific tendency towards antibiotic resistance and phenotypic characteristics for S. fonticola , while these relationships were not found for other tested species.

Obesity is a disease which leads to the development of many other disorders. Excessive accumulation of lipids in adipose tissue (AT) leads to metabolic changes, including hypertrophy of adipocytes, macrophage migration, changes in the composition of immune cells, and impaired secretion of adipokines. Adipokines are cytokines produced by AT and greatly influence human health. Obesity and the pro-inflammatory profile of adipokines lead to the development of chronic kidney disease (CKD) through different mechanisms. In obesity and adipokine profile, there are gender differences that characterize the male gender as more susceptible to metabolic disorders accompanying obesity, including impaired renal function. The relationship between impaired adipokine secretion and renal disease is two-sided. In the developed CKD, the concentration of adipokines in the serum is additionally disturbed due to their insufficient excretion by the excretory system caused by renal pathology. Increased levels of adipokines affect the nutritional status and cardiovascular risk (CVR) of patients with CKD. This article aims to systematize the current knowledge on the influence of obesity, AT, and adipokine secretion disorders on the pathogenesis of CKD and their influence on nutritional status and CVR in patients with CKD.

The gut microbiota is a crucial factor in maintaining homeostasis. The presence of commensal microorganisms leads to the stimulation of the immune system and its maturation. In turn, dysbiosis with an impaired intestinal barrier leads to accelerated contact of microbiota with the host's immune cells. Microbial structural parts, i.e., pathogen-associated molecular patterns (PAMPs), such as flagellin (FLG), peptidoglycan (PGN), lipoteichoic acid (LTA), and lipopolysaccharide (LPS), induce inflammation via activation of pattern recognition receptors. Microbial metabolites can also develop chronic low-grade inflammation, which is the cause of many metabolic diseases. This article aims to systematize information on the influence of microbiota on chronic inflammation and the benefits of microbiota modification through dietary changes, prebiotics, and probiotic intake. Scientific research indicates that the modification of the microbiota in various disease states can reduce inflammation and improve the metabolic profile. However, since there is no pattern for a healthy microbiota, there is no optimal way to modify it. The methods of influencing microbiota should be adapted to the type of dysbiosis. Although there are studies on the microbiota and its effects on inflammation, this subject is still relatively unknown, and more research is needed in this area.

Despite the fact that cephalosporins are rarely used in medical or veterinary treatment, the presence of Enterobacterales strains resistant to this group of anti-bacterial drugs (ESBL) is an important issue that requires attention. Between 2019 and 2021, 14 retention reservoirs, 12 streams, 3 rivers and 1 lake situated in the Tricity area (in northern Poland) were sampled for the presence of ESBL strains. Out of 40 water samples, characteristic growth (E. coli and the KESC group) on Chromagar ESBL plates was observed for 33 samples. The average number of ESBL E. coli was 42±132 CFU/100 ml, while the KESC group was 73±147 CFU/100 ml. Out of 33 positive samples, 57 ESBL Enterobacterales strains were isolated, of which the most abundant species were E. coli (13 isolates) and S. fonticola (23 isolates). The E. coli ESBL isolates not only showed resistance to third generation cephalosporins but also to antibiotics from other groups, such as fluoroquinolones, aminoglycosides and sulfonamides. The S. fonticola ESBL isolates were also found to be mainly resistant to the third generation cephalosporins, with the exception of 5 imipenem and 2 ertapenem-resistant strains. These strains presented highly diverse fingerprinting profiles, as well as significant differences in phenotypic traits helpful for survival in the environment, such as biofilm formation and motility. Moreover, biofilm formation and the swimming ability were species and temperature dependent. We confirmed the presence of highly diverse ESBL strains with multiple drug resistance patterns in the Tricity water reservoirs. This could possibly pose a threat to human health and create a suitable ground for acquiring antibiotics resistance in the natural environment.

Coumarins belong to a group of secondary metabolites well known for their high biological activities including antibacterial and antifungal properties. Recently, an important role of coumarins in plant resistance to pathogens and their release into the rhizosphere upon pathogen infection was discovered. It is also well documented that coumarins play a crucial role in the Arabidopsis thaliana growth under Fe-limited conditions. However, the mechanisms underlying interplay between plant resistance, accumulation of coumarins and Fe status, remain largely unknown. In this work, we investigated the effect of both mentioned factors on the disease severity using the model system of Arabidopsis/ Dickeya spp. molecular interactions. We evaluated the disease symptoms in Arabidopsis plants, wild-type Col-0 and its mutants defective in coumarin accumulation, grown in hydroponic cultures with contrasting Fe regimes and in soil mixes. Under all tested conditions, Arabidopsis plants inoculated with Dickeya solani IFB0099 strain developed more severe disease symptoms compared to lines inoculated with Dickeya dadantii 3937. We also showed that the expression of genes encoding plant stress markers were strongly affected by D. solani IFB0099 infection. Interestingly, the response of plants to D. dadantii 3937 infection was genotype-dependent in Fe-deficient hydroponic solution.

Up to 25% of plastic waste in Europe is still disposed of in landfills, despite recycling efforts. The plastic waste in the landfill plot may be exposed both to abiotic and biotic degradation processes, although it is thought that most of the plastic materials tend to be resistant to biodegradation or biodeterioration even after a long time. To verify if polypropylene (PP) can undergo the process of short-term biodegradation and how this process is manifested in a municipal waste landfill, we collected a plastic sample from an already closed landfill plot estimating its age at approximately 5 years. Fourier-Transform Infrared Spectroscopy led to sample identification as PP as well as showed additional bands which are not specific to polymer structure but rather result from microbial metabolism. Differential Scanning Calorimetry was performed to examine the influence of the environmental degradation process on the degree of crystallisation of the tested PP. Moreover, significant changes on the surface of an old PP packaging were observed with Scanning Electron Microscopy (SEM) showing clear signs of PP delamination which resulted in microplastic particles formation (smaller than 5 μm in diameter). Additionally, several round and oval shaped structures were observed with SEM leading to the suspicion of biofilm formation on the PP surface. Indeed, the microorganisms were present in a vast amount on the old PP surface and possibly formed a viable biofilm as it was confirmed with fluorescence microscopy. These data show that plastic waste can be inhabited by microorganisms from the ambient environment which may probably lead to its faster degradation. However, this process should be investigated in more detail in order to shed light upon the possible risk factors of plastic biodegradation in waste landfills to the environment and human health. Even after five years, polypropylene can undergo deterioration/biodegradation in a waste landfill with viable microbial cells on its surface, possibly involved in its degradation., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020. Published by Elsevier B.V.)

The Lon protein is a protease implicated in the virulence of many pathogenic bacteria, including some plant pathogens. However, little is known about the role of Lon in bacteria from genus Dickeya . This group of bacteria includes important potato pathogens, with the most aggressive species, D. solani . To determine the importance of Lon for pathogenicity and response to stress conditions of bacteria, we constructed a D. solani Δlon strain. The mutant bacteria showed increased sensitivity to certain stress conditions, in particular osmotic and high-temperature stresses. Furthermore, qPCR analysis showed an increased expression of the lon gene in D. solani under these conditions. The deletion of the lon gene resulted in decreased motility, lower activity of secreted pectinolytic enzymes and finally delayed onset of blackleg symptoms in the potato plants. In the Δlon cells, the altered levels of several proteins, including virulence factors and proteins associated with virulence, were detected by means of Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) analysis. These included components of the type III secretion system and proteins involved in bacterial motility. Our results indicate that Lon protease is important for D. solani to withstand stressful conditions and effectively invade the potato plant.

Global warming may shortly increase the risk of disease development on plants. Significant differences in the metabolic activity screened with Phenotype Microarray at 22°C and 28°C were observed between D. solani strains with high and low virulence level. Highly virulent D. solani was characterized by a higher number of metabolized compounds and a faster metabolism and was more tolerant to non-favorable pH and osmolarity. Metabolic phenotyping showed for the first time that the mutation in pecT gene, which encodes a global repressor of virulence, affects several pathways of the basic cell metabolism. PecT mutants had a higher maceration capacity of potato tissue and showed a higher pectinolytic activity than the wild-type strains. On the contrary, mutation in expI gene, which encoded the signaling molecules synthase crucial for quorum sensing, had an insignificant effect on the cell metabolism, although it slightly reduced the potato tissue maceration. The ability to utilize most of the tested compounds was higher at 28°C, while the survival at non-favorable pH and osmolarity was higher at 22°C. These results proved that the temperature of incubation had the most significant impact on the D. solani metabolic profiles., (© FEMS 2020.)

Industrial poultry breeding is associated with the need to increase productivity while maintaining low meat prices. Little is known about its impact on the environment of soil pollution by pharmaceuticals. Breeders routinely use veterinary pharmaceuticals for therapeutic and preventive purposes. The aim of this work was to determine the influence of mass breeding of hens on the soil contamination with 26 pharmaceuticals and caffeine. During two seasons-winter and summer 2019-15 soil samples were collected. Liquid extraction was used to isolate analytes from samples. Extracts were analyzed using ultra-high performance liquid chromatography coupled with tandem mass spectrometry detection (UPLC-MS/MS). The results showed the seasonal changes in pharmaceutical presence in analyzed soil samples. Ten pharmaceuticals (metoclopramide, sulphanilamide, salicic acid, metoprolol, sulphamethazine, nimesulide, carbamazepine, trimethoprim, propranolol, and paracetamol) and caffeine were determined in soil samples collected in March, and five pharmaceuticals (metoclopramide, sulphanilamide, sulphamethazine, carbamazepine, sulfanilamid) in soil samples collected in July. The highest concentrations were observed for sulphanilamide, in a range from 746.57 ± 15.61 ng/g d.w to 3518.22 ± 146.05 ng/g d.w. The level of bacterial resistance to antibiotics did not differ between samples coming from intensive breeding farm surroundings and the reference area, based on antibiotic resistance of 85 random bacterial isolates.

Bacteria belonging to the genera Dickeya and Pectobacterium are responsible for significant economic losses in a wide variety of crops and ornamentals. During last years, increasing losses in potato production have been attributed to the appearance of Dickeya solani . The D. solani strains investigated so far share genetic homogeneity, although different virulence levels were observed among strains of various origins. The purpose of this study was to investigate the genetic traits possibly related to the diverse virulence levels by means of comparative genomics. First, we developed a new genome assembly pipeline which allowed us to complete the D. solani genomes. Four de novo sequenced and ten publicly available genomes were used to identify the structure of the D. solani pangenome, in which 74.8 and 25.2% of genes were grouped into the core and dispensable genome, respectively. For D. solani panregulon analysis, we performed a binding site prediction for four transcription factors, namely CRP, KdgR, PecS and Fur, to detect the regulons of these virulence regulators. Most of the D. solani potential virulence factors were predicted to belong to the accessory regulons of CRP, KdgR, and PecS. Thus, some differences in gene expression could exist between D. solani strains. The comparison between a highly and a low virulent strain, IFB0099 and IFB0223, respectively, disclosed only small differences between their genomes but significant differences in the production of virulence factors like pectinases, cellulases and proteases, and in their mobility. The D. solani strains also diverge in the number and size of prophages present in their genomes. Another relevant difference is the disruption of the adhesin gene fhaB2 in the highly virulent strain. Strain IFB0223, which has a complete adhesin gene, is less mobile and less aggressive than IFB0099. This suggests that in this case, mobility rather than adherence is needed in order to trigger disease symptoms. This study highlights the utility of comparative genomics in predicting D. solani traits involved in the aggressiveness of this emerging plant pathogen.

Bacteria from the genus Dickeya cause severe symptoms on numerous economically important plants. Dickeya solani is the Dickeya species most frequently found on infected potato plants in Europe. D. solani strains from different countries show high genetic homogeneity, but significant differences in their virulence level. Dickeya species possess two quorum sensing (QS) mechanisms: the Exp system based on classic N-acyl-homoserine lactone (AHL) signals and a specific system depending on the production and perception of a molecule of unknown structure, Virulence Factor Modulating (VFM). To study the interplay between these two QS systems, five D. solani strains exhibiting different virulence levels were selected. Mutants were constructed by inactivating genes coding for each QS system. Double mutants were obtained by simultaneous inactivation of genes coding for both QS systems. Most of the D. solani mutants showed an attenuation of chicory maceration and a decreased production of plant cell wall-degrading enzymes (PCWDEs) and motility, but to different degrees depending on the strain. The VFM-QS system seems to regulate virulence in both D. solani and Dickeya dadantii, but the AHL-QS system has greater effects in D. solani than in D. dadantii. The inactivation of both QS systems in D. solani did not reveal any additive effect on the tested features. The inactivation of vfm genes generally has a more dominant effect relative to that of exp genes. Thus, VFM- and AHL-QS systems do not work in synergy to modulate the production of diverse virulence factors and the ability to macerate plant tissue., (© 2017 BSPP AND JOHN WILEY & SONS LTD.)

Bacteria from the genera Dickeya (formerly Erwinia chrysanthemi) and Pectobacterium (formerly E. carotovora) are the agents of blackleg and soft rot on many important crops. In 2005, Dickeya solani was isolated for the first time in Poland from a symptomatic potato plant. To establish the presence and diversity of Dickeya spp. in Poland, we surveyed potato fields and water sources, including surface waters near potato fields and water from potato-processing facilities and sewage plants. Only D. dianthicola and D. solani were isolated from symptomatic potato, and only D. zeae and D. chrysanthemi were isolated from water sources. The Dickeya spp. isolated from potato formed a relatively homogenous group, while those from water sources were more diverse. To our knowledge, this is the first comprehensive characterization of Dickeya spp. isolated during several years from regions with a temperate climate in Central Europe.

Bacteria from the genus Dickeya (formerly Erwinia chrysanthemi) are plant pathogens causing severe diseases in many economically important crops. A majority of the strains responsible for potato disease in Europe belong to a newly identified Dickeya solani species. Although some ecological and epidemiological studies have been carried out, little is known about the regulation of D. solani virulence. The characterization of four D. solani strains indicates significant differences in their virulence on potato although they are genetically similar based on genomic fingerprinting profiles. A phenotypic examination included an analysis of virulence on potato, growth rate in culture, motility, Fe 3+ chelation, and pectate lyase, cellulase, protease, biosurfactant and blue pigment production. Mutants of four D. solani strains were constructed by inactivating the genes coding either for one of the main negative regulators of D. dadantii virulence (kdgR, pecS and pecT) or for the synthesis and perception of signaling molecules (expI and expR). Analysis of these mutants indicated that PecS, PecT and KdgR play a similar role in both species, repressing to different degrees the synthesis of virulence factors. The thermoregulator PecT seems to be a major regulator of D. solani virulence. This work also reveals the role of quorum sensing mediated by ExpI and ExpR in D. solani virulence on potato.