Sexual compatibility in the Basidiomycota is governed by genetic identity at one or two loci, resulting in compatibility systems called bipolar and tetrapolar. The loci are known as HD and P/R, encoding homeodomain transcription factors and pheromone precursors and receptors, respectively. Bipolarity is known to evolve either by linkage of the two loci or by loss of mating-type determination of either the HD or the P/R locus. The ancestor to basidiomycete fungi is thought to have been tetrapolar, and many transitions to bipolarity have been described in different lineages. In the diverse genus Marasmius (Agaricales), both compatibility systems are found, and the system has been shown to follow the infrageneric sections of the genus, suggesting a single origin of bipolarity. Here, we tested this hypothesis using a comprehensive phylogenetic framework and investigated the mode by which bipolarity has evolved in this group. We utilized available genomic data and marker sequences to investigate evolution of sexual compatibility in Marasmius and allied genera. By generating a concatenated multilocus phylogeny, we found support for a single transition to known bipolarity within Marasmius. Furthermore, utilizing genomic data of the bipolar species Marasmius oreades, we found that the HD and P/R loci likely have remained unlinked through this transition. By comparing nucleotide diversity at the HD and P/R loci in Ma. oreades, we show that the HD locus has retained high diversity, and thus likely the function of determining sexual identity, as similarly in other bipolar mushroom-forming fungi. Finally, we describe the genomic architecture of the MAT loci of species of both sexual compatibility systems in Marasmiaceae and related families.
- Keywords
- Homeodomain, MAT, mating system, mating type, mushroom, pheromone receptor,
- MeSH
- Agaricales genetics classification MeSH
- Biological Evolution MeSH
- Genes, Mating Type, Fungal * genetics MeSH
- Phylogeny * MeSH
- Evolution, Molecular MeSH
- Receptors, Pheromone genetics MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- Receptors, Pheromone MeSH
Cryptosporidium mortiferum, a parasite transmitted by squirrels, is beginning to spread in Europe. C. mortiferum was detected in a symptomatic human. A 44-year-old man from the Czech Republic suffered from gastroenteritis characterized by abdominal pain, nausea, and loose stools. Molecular analyses confirmed the XIVaA20G2T1 subtype in the patient's stool. At the same time, the same subtype of C. mortiferum was detected in three red squirrels and two ground squirrels in the area where the patient lived. The intensity of the infection was significantly higher in the red squirrels that died, while the ground squirrels showed no symptoms. The results of the study indicate that red squirrels and ground squirrels are the reservoirs for the infection.
- Keywords
- Cryptosporidium mortiferum, human, infection, squirrels,
- MeSH
- Cryptosporidium * genetics isolation & purification classification MeSH
- Adult MeSH
- Feces parasitology MeSH
- Phylogeny MeSH
- Gastroenteritis parasitology MeSH
- Cryptosporidiosis * parasitology transmission epidemiology diagnosis MeSH
- Humans MeSH
- Sciuridae * parasitology MeSH
- Disease Reservoirs parasitology MeSH
- Zoonoses * parasitology transmission MeSH
- Animals MeSH
- Check Tag
- Adult MeSH
- Humans MeSH
- Male MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Case Reports MeSH
- Geographicals
- Czech Republic MeSH
- Europe MeSH
Tailocins are nano-scale phage tail-like protein complexes that can mediate antagonistic interactions between closely related bacterial species. While the capacity to produce R-type tailocin was found widely across Gammaproteobacteria, the production of F-type tailocins seems comparatively rare. In this study, we examined the freshwater isolate, Pragia fontium 24613, which can produce both R- and F-type tailocins. We investigated their inhibition spectrum, focusing on clinically relevant enterobacteria, and identified the associated tailocin gene cluster. Transmission electron microscopy confirmed that inactivation of the tape measure protein within the tailocin cluster disrupted R-tailocin production. Comparative analysis of Budviciaceae gene clusters showed high conservation of R-type tailocin genes, whereas F-type tailocin genes were found in only a few species, with little conservation. Our findings indicate a high prevalence of bacteriocin production among underexplored Enterobacteriales species. Detected tailocins showed potential as antimicrobials targeting clinically significant pathogens.
- Keywords
- Antibiotics, Antimicrobial agent, Enterobacteria, Fonticin, Phage tail-like particle, Yersinia enterocolitica,
- MeSH
- Anti-Bacterial Agents pharmacology biosynthesis MeSH
- Bacteriocins * genetics pharmacology MeSH
- Bacteriophages * genetics metabolism MeSH
- Enterobacteriaceae * genetics metabolism drug effects MeSH
- Phylogeny MeSH
- Multigene Family MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- Anti-Bacterial Agents MeSH
- Bacteriocins * MeSH
Sulfamethoxazole (SMX) and its residues exhibit high environmental persistence due to their resistance to conventional degradation processes. The bacterial strain Kocuria rhizophila SA117, isolated from polluted soils, was characterized biochemically, phylogenetically, and -omically. Herein, we describe a complete degradation pathway for SMX and determine two putative pathways: cleavage of the benzene ring and the degradation of the substituted isoxazole, leading to the formation of non-toxic Krebs cycle metabolites. Based on molecular structures containing 13C6-labeled carbons and 2H3 atoms, thirty metabolites were identified by high-resolution tandem mass spectrometry. Genomic and proteomic analysis of strain SA117 revealed its ability to perform a wide range of metabolic activities under sulfamethoxazole selective pressure. These activities include energy and sulfur metabolism, adaptation to stress conditions, and catabolism of aromatic compounds. This study has greatly enhanced the understanding of microbial sulfonamide degradation and highlighted the potential of the bacterium Kocuria in remediation strategies.
- Keywords
- Biodegradation, Genome sequencing, Metabolic profiling, Proteomics, Sulfonamide,
- MeSH
- Biodegradation, Environmental MeSH
- Phylogeny MeSH
- Catalysis MeSH
- Metabolic Networks and Pathways * MeSH
- Micrococcaceae * metabolism genetics MeSH
- Proteomics MeSH
- Sulfamethoxazole * metabolism MeSH
- Tandem Mass Spectrometry MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- Sulfamethoxazole * MeSH
Carnivorous plants secrete digestive enzymes for prey degradation. Although carnivorous plants have a polyphyletic origin and evolved several times independently, they surprisingly co-opted similar digestive enzymes during convergent evolution. However, despite having similar digestive enzymes, the mode of their regulation strongly differs across different phylogenetic lineages. But what factors are responsible for such diversity in their digestion? By combining phylogenetic relationships of digestive fluid proteins and biochemical data, the analyses showed that phylogeny seems to be a significant factor determining the regulation of digestion, but environment (water vs terrestrial) and type of trap do not affect regulation. The oldest carnivorous plant lineage, Caryophyllales, co-opted phytohormone jasmonic acid (JA) for regulation of digestive enzyme activity. However, the remaining orders of carnivorous plants do not accumulate JA in response to prey capture, and their digestive enzyme activity is not responsive to exogenous JA application. Instead, they use different modes of regulation, for example, development/senescence, osmotically induced and constitutive. These different modes of regulation can be explained by co-option, albeit of similar genes but different paralogs with different cis regulatory elements that have been fine-tuned during evolution.
- Keywords
- Venus flytrap, carnivorous plants, digestive enzymes, jasmonic acid, pitcher plant,
- MeSH
- Biological Evolution * MeSH
- Cyclopentanes metabolism MeSH
- Phylogeny MeSH
- Carnivorous Plant * physiology enzymology genetics MeSH
- Oxylipins metabolism MeSH
- Digestion * MeSH
- Publication type
- Journal Article MeSH
- Review MeSH
- Names of Substances
- Cyclopentanes MeSH
- jasmonic acid MeSH Browser
- Oxylipins MeSH
Microsporidia are disease-causing organisms that can infect invertebrate species. In apiculture, two microsporidians of importance are Vairimorpha (=Nosema) ceranae and Vairimorpha (=Nosema) apis. The taxonomy surrounding the genus assignment of these species has been heavily debated, due to molecular systematic and socio-economic reasons. We provide an update to this debate by developing a 508-gene concatenated protein phylogeny, and a 277-gene concatenated nucleotide phylogeny, to show that these parasites show strong phylogenetic positioning with the Vairimorpha genus and its type species Vairimorpha necatrix. Despite this assignment, we suggest that the terms 'nosema-disease', 'nosemosis' and 'nosematosis' should still be viable for use within apiculture, and be named after the family Nosematidae in which V. ceranae and V. apis sit, instead of the previous genus assignment: Nosema.
- Keywords
- Apiculture, Bee, Microsporidia, Nosematidae, Nosemosis, Taxonomy,
- MeSH
- Phylogeny MeSH
- Genomics MeSH
- Nosema * genetics classification MeSH
- Proteomics MeSH
- Bees microbiology MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
We examined the effect of light-induced heating of leaves in wild-type (Col-0) and tmm-1 Arabidopsis plants. The results showed that the tmm-1 mutant exhibits accelerated cooling of rosettes in response to changes in light intensity, as demonstrated by thermal imaging measurements. This is evident in the time constants determined for temperature kinetics, which were reduced during the transition from light to dark. Our findings indicate that these dynamics can be reliably assessed under various light conditions. Measurements of gas exchange showed that stomatal conductance, transpiration rate, and net CO2 assimilation rate were increased in the tmm-1 mutant. Furthermore, fluorescence analysis revealed that the tmm-1 mutant exhibited an increased ratio of total energy dissipation to the number of active reaction centers, as well as higher average absorption. We also observed that the performance index (PIABS) was reduced compared to Col-0. Nevertheless, the clustering of stomata did not affect the maximum quantum yield of PSII. Our results demonstrate that the maintenance of lower leaf temperatures and the greater cooling capacity in plants with clustered stomata positively affects overall photosynthetic performance.
- Keywords
- IR thermal imaging, Light-induced thermal kinetics, Photosynthesis, Stomatal patterning,
- MeSH
- Arabidopsis * physiology genetics radiation effects MeSH
- Photosynthesis physiology MeSH
- Plant Leaves * physiology radiation effects MeSH
- Mutation MeSH
- Carbon Dioxide metabolism MeSH
- Plant Stomata physiology MeSH
- Light MeSH
- Temperature MeSH
- Plant Transpiration physiology MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- Carbon Dioxide MeSH
BACKGROUND: Red wine is a common target of fraudulent acts considering its high market value and popularity. Although there has been much effort to assess the geographical and varietal origin of wine, this is not the case for wine vintage. Vintage is a crucial parameter for the market price, especially in the case of reputable wines. Considering the season-to-season variations affecting wine quality and the ever-occurring unstable climatological conditions due to climate change, developing analytical strategies to accurately assess wine vintage is topical and of high interest. RESULTS: In this study, we successfully employed ultraviolet-visible spectroscopy, fluorescence spectroscopy and mid-infrared spectroscopy to identify the vintage of a protected designation of origin red wine produced during four different vintages (n = 36). Class-based clustering and great discriminatory performance was achieved for the majority of the developed multivariate models and the impact of the applied spectral pre-processing was significant. Importantly, the tested scatter correction methods resulted in the best cross-validation parameters (goodness of fit, R2Y > 0.9 and goodness of prediction, Q2Y > 0.8) with calculated recognition and prediction abilities in the range 77-100% and 65-96%, respectively, when using partial least squares discriminant analysis. In addition, in the case of fluorescence spectroscopy, a batch effect was revealed, which was compensated by the spectral pre-processing methods. Spectral feature selection was performed in all cases to use only the analytically important spectral signals and omit model overfitting. CONCLUSIONS: The developed method is simple, cost-efficient and non-destructive, indicating its high potential for industrial applications as a rapid screening tool. © 2025 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
- Keywords
- absorption spectroscopy, attenuated total reflectance Fourier transform infrared spectroscopy, chemometrics, spectral pre‐processing, wine authenticity,
- MeSH
- Discriminant Analysis MeSH
- Spectrometry, Fluorescence methods MeSH
- Seasons MeSH
- Spectrum Analysis * methods MeSH
- Wine * analysis MeSH
- Vitis * chemistry growth & development MeSH
- Publication type
- Journal Article MeSH
- Evaluation Study MeSH
With increasing efforts to reuse wastewater treatment plant (WWTP) products in agriculture, assessing their impact on soil-plant systems is crucial, while the effects of accompanying antibiotic residues on soil microbial communities have not yet been adequately studied. This study focuses on clarithromycin (CLR), highly present in wastewater, and investigates the CLR-degradation potential of plant-associated microorganisms. Phaseolus vulgaris plants were grown in raised beds filled with Haplic Cambisol and amended with or without WWTP products (treated wastewater, biosolid, or composted biosolid), as a source of CLR residues. The rhizosphere microbiomes after biosolid amendments was significantly enriched by Pseudomonadaceae as assessed by 16S rRNA metagenomics and cultures enriched by CLR revealed dominance of Proteobacteria. However, no degradation of CLR by microbial consortia or enrichment cultures was observed, suggesting the multiplication of CLR-resistant bacteria with other resistance mechanisms. Cultivation-based approach combined with antibiotic modulation assays and subsequent LC-MS analysis confirmed the complete CLR removal by seven phylogenetic groups of actinomycetes in vitro. The proportion of isolates indicated that the rhizosphere is a natural reservoir for CLR-inactivating microorganisms; however, the amendment of soils with WWTP products can significantly increase their abundance and diversity.
- Keywords
- Streptomyces, Antimicrobial resistance, Biodegradation, Macrolides, Micropollutants, Soil microbiome,
- MeSH
- Anti-Bacterial Agents * pharmacology MeSH
- Phaseolus * microbiology drug effects growth & development MeSH
- Phylogeny MeSH
- Clarithromycin * pharmacology metabolism MeSH
- Microbiota drug effects MeSH
- Wastewater * chemistry MeSH
- Soil Microbiology MeSH
- Rhizosphere * MeSH
- RNA, Ribosomal, 16S genetics MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- Anti-Bacterial Agents * MeSH
- Clarithromycin * MeSH
- Wastewater * MeSH
- RNA, Ribosomal, 16S MeSH
Knowledge of Treponema pallidum subspecies pallidum (TPA) outer membrane protein (OMP) sequence variability is essential for understanding spirochete proliferation within endemic populations as well as the design of a globally effective syphilis vaccine. Our group has identified extracellular loops (ECLs) of TPA BamA (TP0326) and members of the FadL family (TP0548, TP0856, TP0858, TP0859, and TP0865) as potential components of a multivalent vaccine cocktail. As part of a consortium to explore TPA strain diversity, we mapped the variability of BamA and FadL orthologs in 186 TPA strains from Malawi, China, and Colombia onto predicted 3D structures. The 186 genomes fell into eight subclades (five Nichols- and three SS14-lineage) with substantial geographic restriction. Single nucleotide variants accounted for the large majority of proteoforms, with variability notably higher within the Nichols-lineage strains. Most mutations were in regions of the proteins predicted to be extracellular and harboring B cell epitopes. We observed a striking difference in the degree of variability between the six OMPs, suggesting that these proteins are following divergent evolutionary paths. Concatenation of OMP sequences recapitulated the phylogenetic structure of the TPA strains, effectively segregating within clades and largely clustering by subclades. Finally, we noted that BamA and FadL candidate ECL vaccinogens, previously shown to elicit antibodies that kill treponemes during in vitro cultivation, are well conserved. Taken as a whole, our study establishes a structural-phylogenetic approach for analyzing the forces shaping the host-pathogen interface in syphilis within endemic populations while informing the selection of vaccine targets.IMPORTANCESyphilis remains a major global health concern, reinforcing the need for a safe and effective vaccine. Understanding the variability of TPA OMPs is essential for tracking pathogen evolution and informing vaccine design. Here, we analyzed the variability of six TPA OMPs in 186 strains from Malawi, China, and Colombia, identifying protein-specific evolutionary patterns. Most mutations were localized in extracellular regions and, notably, appeared to correlate with the phylogenetic structure of TPA. Despite OMP heterogeneity, several candidate vaccinogens remained highly conserved, reinforcing their potential as globally effective vaccine targets. Our study establishes a structural-phylogenetic framework for dissecting the forces shaping the host-spirochete interface within endemic populations and provides a foundation for designing a globally effective syphilis vaccine.
- Keywords
- outer membrane proteins, protein variability, syphilis, vaccines, whole-genome sequencing,
- MeSH
- Bacterial Vaccines * genetics immunology MeSH
- Phylogeny MeSH
- Genetic Variation * MeSH
- Humans MeSH
- Evolution, Molecular * MeSH
- Bacterial Outer Membrane Proteins * genetics immunology chemistry MeSH
- Syphilis microbiology prevention & control MeSH
- Treponema pallidum * genetics immunology classification MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- China MeSH
- Colombia MeSH
- Malawi MeSH
- Names of Substances
- Bacterial Vaccines * MeSH
- Bacterial Outer Membrane Proteins * MeSH
