Linking meta-omics and biogeochemistry approaches in soils has remained challenging. This study evaluates the use of an internal RNA extraction standard and its potential for making quantitative estimates of a given microbial community size (biomass) in soil metatranscriptomics. We evaluate commonly used laboratory protocols for RNA processing, metatranscriptomic sequencing and quantitative reverse transcription polymerase chain reaction (qRT-PCR). Metatranscriptomic profiles from soil samples were generated using two library preparation protocols and prepared in triplicates. RNA extracted from pure cultures of Saccharolobus solfataricus was added to the samples as an internal nucleic acid extraction standard (NAEstd). RNA reads originating from NAEstd were identified with a 99.9% accuracy. A remarkable replication consistency between triplicates was seen (average Bray-Curtis dissimilarity 0.03 ± 0.02), in addition to a clear library preparation bias. Nevertheless, the between-sample pattern was not affected by library type. Estimates of 16S rRNA transcript abundance derived from qRT-PCR experiments, NAEstd and a previously published quantification method of metatranscriptomics (hereafter qMeTra) were compared with microbial biomass carbon (MBC) and nitrogen (MBN) extracts. The derived biomass estimates differed by orders of magnitude. While most estimates were significantly correlated with each other, no correlation was observed between NAEstd and MBC extracts. We discuss how simultaneous changes in community size and the soils nucleic acid retention strength might hamper accurate biomass estimation. Adding NAEstd has the potential to shed important light on nucleic acid retention in the substance matrix (e.g., soil) during extraction.

• Keywords
• RNA, biomass estimates, extraction standard, metatranscriptomics, quantitative transcriptomics,
• MeSH
• Bacteria * genetics   classification   MeSH
• Metagenomics * methods   MeSH
• Microbiota * MeSH
• Soil chemistry   MeSH
• Soil Microbiology * MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Gene Expression Profiling * methods   MeSH
• Transcriptome MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Soil MeSH
• RNA, Ribosomal, 16S MeSH

Molasses stillage, with its high organic content and nutrient-rich composition, represents a promising feedstock for biogas production. This study systematically evaluated its biochemical methane potential (BMP) using two inocula (wastewater treatment plant vs agricultural biogas plant) across three temperatures (40, 50, 60 °C) and initial substrate load (ISL: 2, 5, 10 g·Lincolum -1). The wastewater inoculum achieved superior methane yields (0.262-0.477 N m3·kgvs -1), peaking at 50 °C with a 22% increase over agricultural systems (0.192-0.378 N m3·kgvs -1). 16S rRNA sequencing revealed the wastewater treatment plant inoculum's superior functional diversity, dominated by syntrophic Chloroflexota and Acidobacteriota alongside methanogenic Methanobacterium (52-61% relative abundance) and acetoclastic Methanothrix (18-23%). In contrast, agricultural biogas plant inocula showed specialized thermophilic communities dominated by Bacillota (68-72%) and hydrogenotrophic Methanoculleus (29-34%). Both systems exhibited inhibition at 60 °C/ISL10 (yields reduced by 34-42%), correlating with declining diversity and Methanofastidiosum proliferation. These findings provide two key operational insights: wastewater inocula offer greater process stability due to microbial diversity, and 50 °C represents the thermal optimum for stillage codigestion, balancing yield and community resilience.

• Publication type
• Journal Article MeSH

Edible insects, particularly Tenebrio molitor (Linnaeus) (mealworm) and Zophobas morio (Fabricius) (superworm), have drawn increasing attention as alternative protein sources. This study aims to develop an accurate molecular detection method for T. molitor, an EU-approved food species, and to differentiate it from Z. morio, which remains unapproved for human consumption in the EU. The process enables precise and sensitive identification methods by optimizing singleplex and duplex PCR techniques targeting 16S rRNA and COI gene regions. The DNA of T. molitor was detected in various food matrices, including pastries, chocolate, and porridge, while avoiding cross-reactivity with Z. morio, Gryllus asimilis, and Locusta migratoria. The detection limit for both singleplex and duplex PCR was 10 pg of DNA, ensuring robustness against inhibitory effects from complex food matrices. The developed approach ensures reliable detection and compliance with EU regulations regarding insect-based foods, providing a critical tool for food authentication and preventing adulteration. The key advancements of this approach lie in its improved specificity and sensitivity, allowing for the ability to detect complex food matrices. An applied perspective was evaluated using real commercial food products.

• Keywords
• edible insects, molecular detection, novel food,
• Publication type
• Journal Article MeSH

The biogenesis of the mitoribosomal small subunit involves a dynamic network of assembly factors. Conserved methyltransferases Mettl15 and Mettl17 act on the solvent-exposed surface of rRNA. Binding of Mettl17 is associated with the early assembly stage, whereas Mettl15 is involved in the late stage. Here, we integrate structural data from Trypanosoma brucei with mammalian homologs and molecular dynamics simulations. We reveal how the interplay of Mettl15 and Mettl17 in intermediate steps links the distinct stages of small subunit assembly. The analysis suggests a model wherein Mettl17 acts as a platform for Mettl15 recruitment. Subsequent release of Mettl17 allows a conformational change of Mettl15 for substrate recognition. Upon methylation, Mettl15 adopts a loosely bound state which leads to its replacement by initiation factors, concluding the assembly. Together, our results indicate that assembly factors Mettl15 and Mettl17 cooperate to regulate the biogenesis process.

• Keywords
• Trypanosoma, biogenesis, cryo-EM, methyltransferase, mitochondria, mitoribosome, molecular dynamics, ribosome assembly, translation,
• Publication type
• Journal Article MeSH

The recovery of the soil ecosystem after severe disturbances, such as coal-mining activities, depends on both abiotic and biotic improvements. This study assessed the influence of arbuscular mycorrhizal (AM) fungal consortia on microbial community dynamics across two stages of soil recovery - 2 years (2Y) and 15 years (15Y) post-disturbance - using a secondary succession forest (SSR) as a reference. We analyzed bacterial community composition via 16 S rRNA gene amplicon sequencing and evaluated key soil quality indicators. While inoculation with AM fungal consortia had minimal effects on most soil parameters, significant differences were observed between recovery stages. The 15Y recovery site exhibited improved soil structure, microbial activity, and aggregate stability compared to the 2Y site, highlighting the importance of long-term restoration. However, potential overlap in ecological roles among native microorganisms likely mitigates the impact of AMF inoculation. These findings suggest that AM fungal consortia alone may not drive immediate improvements in soil quality but can contribute to microbial interactions and recovery processes over time. This study highlights the complexity of soil restoration and emphasizes the need for strategies that integrate plant cover with microbial community development to enhance long-term ecosystem stability. Further research should explore the specific roles of AM fungi and native soil microbes in promoting soil structure and accelerating recovery.

• Keywords
• AM fungal consortia, Combined inoculation, Glomeromycota, Microbiome, Simplified community,
• MeSH
• Bacteria classification   genetics   isolation & purification   MeSH
• Ecosystem MeSH
• Microbiota * MeSH
• Mycorrhizae * physiology   MeSH
• Soil chemistry   MeSH
• Soil Microbiology * MeSH
• Coal Mining MeSH
• Coal MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Soil MeSH
• Coal MeSH

BACKGROUND: The perinatal period has been linked with higher vulnerability to stress and symptoms of depression and anxiety, as well as with dynamic changes in the composition of maternal gut microbiota. While recent studies indicated significant associations between stress, depression, or anxiety, and alterations in gut microbiota in pregnant women, research in this avenue is still emerging, with existing studies often being limited by small sample sizes. METHOD: We conducted a prospective longitudinal study of 171 women, collecting gut microbiota samples in each trimester of pregnancy and in the early postpartum, questionnaire data (perceived stress via the Perceived Stress Scale, symptoms of depression via the Edinburgh Postnatal Depression Scale, and anxiety via the 6-item State-Trait Anxiety Inventory) twice in each trimester and twice in the early postpartum period, and blood samples for cortisol levels analysis in the first and third pregnancy trimesters. Gut microbiota samples were analyzed by amplicon sequencing of 16S rRNA gene. RESULTS: Perceived stress and symptoms of depression and anxiety showed moderate temporal changes and a high consistency at the individual level over the study period. Cortisol levels rose significantly from the first to the third trimester. There were significant temporal changes in microbiota composition between the first and second trimesters, and between the first and third trimesters. After controlling for false positive findings due to multiple testing, we found no significant associations between stress-related variables (perceived stress, cortisol levels, symptoms of depression and anxiety) and gut microbiota diversity, microbial community composition, or relative abundances of individual bacterial taxa. CONCLUSIONS: The present study results contradict previous research that indicated significant associations between emotions and gut microbiota in the perinatal period. Although we cannot provide an ultimate explanation for this discrepancy, we propose it can lie in insufficient control for false positives in the differential abundance analyses in most previous studies.

• Keywords
• Anxiety, Cortisol, Depression, Dysbiosis, Gut-brain axis, Metagenome, Microbiome, Prenatal stress,
• MeSH
• Bacteria * classification   genetics   isolation & purification   MeSH
• Depression microbiology   MeSH
• Adult MeSH
• Hydrocortisone blood   MeSH
• Humans MeSH
• Longitudinal Studies MeSH
• Young Adult MeSH
• Postpartum Period MeSH
• Prospective Studies MeSH
• Surveys and Questionnaires MeSH
• Stress, Psychological * microbiology   MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Gastrointestinal Microbiome * MeSH
• Pregnancy MeSH
• Pregnant People psychology   MeSH
• Anxiety microbiology   MeSH
• Check Tag
• Adult MeSH
• Humans MeSH
• Young Adult MeSH
• Pregnancy MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Hydrocortisone MeSH
• RNA, Ribosomal, 16S MeSH

Numerous cyanobacterial strains previously identified as Scytonema hyalinum were determined to be phylogenetically distant from the type species of Scytonema, S. hofmannii. Morphological and molecular evidence suggests this distinct clade necessitates placement in a new genus, and we have described Kalymmatonema gen. nov. herein. Kalymmatonema has been demonstrated to exhibit five ribosomal operons, all of which differed in both sequence and secondary structure of conserved helical domains in the 16S-23S internal transcribed spacer rRNA region. Four of these operon copies were highly similar in 16S and 23S rRNA gene sequences, whereas the divergent fifth copy is thought to represent a whole-operon horizontal gene transfer event. Through in-depth analysis, we were able to recognize seven species new to science, the type species K. desertorum sp. nov., K. arcangelii comb. nov., K. chimaera sp. nov., K. ethiopiense sp. nov., K. gypsitolerans sp. nov., K. mateoae sp. nov., and K. oahuense sp. nov. We also created the new combination, K. hyalinum comb. nov., in order to include the original Scytonema hyalinum in this new genus based upon the common morphological feature of a mucilaginous apical cap on the trichomes. Kalymmatonema displays a complex evolution of its ribosomal operons, with evidence not only of horizontal gene transfer but also of internal rearrangements and mobile genetic elements that have transposed the tRNA-containing region of the ITS rRNA region among the four similar operons. Additional investigation of the evolutionary history of this interesting genus will likely lead to a better understanding of the processes shaping ribosomal evolution in cyanobacteria.

• Keywords
• Kalymmatonema, Scytonema, ITS, Scytonemataceae, biological soil crust, cyanobacteria, ribosomal operons,
• Publication type
• Journal Article MeSH

Aquatic ecosystems suffer disproportionately from plastic pollution given that they integrate material from terrestrial watersheds. Most studies on microbial colonisation and degradation of plastics have focused on marine environments, leaving a knowledge gap for freshwaters. Our study explores the possible degradation and the role of bacterial community composition of plastics in Lake Geneva. We exposed polyethylene terephthalate (PET) and low-density polyethylene (LDPE) for 45 weeks to environmental lake gradients that change with depth and season. The substrates were suspended at 2 and 30 m depth, resulting in strikingly different environmental conditions for biofilm development, including light (PAR), temperature, and nutrient availability. We monitored the bacterial colonisation using 16S rRNA sequencing and assessed the abundance of the alkane hydrolase gene (alkB) to evaluate the potential ability of the biofilm to degrade PET and LDPE. Additionally, we analysed plastic surface modifications through spectroscopy, contact angle measurements and microscopy. We found that the PET surface showed no degradation after 45 weeks in the lake, at either depth. The LDPE surface at 2 m exhibited a decrease in hydrophobicity, but no evidence of oxidation or degradation was found. In contrast, the LDPE surface at 30 m displayed oxidation, a decrease in hydrophobicity, and porous cavities. In addition, we observed an increase in the alkane alkB gene abundance in the biofilm, with the development of plastic-degrading taxa in the community. Our results underline the complexity of plastic degradation in aquatic ecosystems; not only does the type of plastic have an effect, so do the spatio-temporal variable environmental lake conditions and the biofilm community. The multifactorial nature of these processes complicates predictions on the fate of plastics in the environment.

• Keywords
• Biofilm, Degradation, Freshwater, Plastics, Weathering,
• MeSH
• Bacteria metabolism   MeSH
• Biodegradation, Environmental MeSH
• Biofilms MeSH
• Water Pollutants, Chemical * metabolism   analysis   MeSH
• Lakes * microbiology   chemistry   MeSH
• Microbiota MeSH
• Environmental Monitoring MeSH
• Plastics * metabolism   analysis   MeSH
• Polyethylene Terephthalates MeSH
• Seasons MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Water Pollutants, Chemical * MeSH
• Plastics * MeSH
• Polyethylene Terephthalates MeSH

In this study, we investigated the behavior of rDNA loci in senescent MCF-7 mammary cancer cells induced by gamma irradiation. To analyze changes in nucleolar structure we used rDNA-FISH and immunohistochemical staining with fibrillarin and UBF transcription factor. The expression levels of rDNAs and nucleolar proteins were determined by RNA-seq of total and poly-A libraries. The cytological and molecular parameters of nucleoli were monitored throughout the 7-day interval following irradiation. Senescent cells exhibited a higher proportion of smaller nucleoli as compared to cycling cells, indicating nucleolar fragmentation. The rDNA copy number and expression of rDNA variants remained stable in cycling and senescent cells. However, the levels of polyadenylated rRNA species derived from external (5'ETS) and internal (ITS1) rDNA spacers tend to increase (c.2 fold) following irradiation. At the protein level, senescent cells showed decreased levels of fibrillarin and UBF transcription factor while localization of both proteins in the nucleolus was not impaired. We conclude that withdrawal from cell cycle does not change expression patterns of rDNA variants. However, defects in rRNA processing may lead to fragmentation of nucleoli in senescent cells.

• Keywords
• Cancer cell, Irradiation, Nucleolus, Senescence, rDNA,
• Publication type
• Journal Article MeSH

Spodoptera frugiperda (fall armyworm) poses a substantial risk to crops worldwide, resulting in considerable economic damage. The gut microbiota of insects plays crucial roles in digestion, nutrition, immunity, growth and, sometimes, the degradation of insecticides. The current study examines the effect of synthetic insecticides on the gut microbiome of third instar S. frugiperda larvae using both culture-dependent techniques and 16S rRNA gene sequencing for bacterial community profiling and diversity analysis. In untreated larvae, the sequencing approach revealed a diverse microbiome dominated by the phyla Firmicutes, Proteobacteria and Bacteroidota, with key genera including Bacteroides, Faecalibacterium and Pelomonas. In parallel, 323 bacterial strains were isolated and assigned to the orders Bacillales, Burkholderiales, Enterobacterales, Flavobacteriales, Lactobacillales, Micrococcales, Neisseriaies, Pseudomonadales, Sphingobacteriales and Xanthomonadales. The prevailing culturable species included Serratia marcescens, Klebsiella variicola and Enterobacter quasiroggenkampii. Treatment with sublethal concentrations of three insecticides (broflanilide, spinosad and indoxacarb) caused significant changes in gut microbiome diversity and composition. Treated larvae showed a shift towards increased Proteobacteria abundance and decreased Firmicutes. Specifically, Acinetobacter and Rhodococcus were dominant in treated samples. Functional predictions highlighted significant metabolic versatility involving nutrient processing, immune response, detoxification, xenobiotic metabolism, and stress response, suggesting microbial adaptation to insecticide exposure. Network correlation analysis highlighted disrupted microbial interactions and altered community structures under insecticide treatment. These findings enhance our understanding of how insecticides impact the gut microbiota in S. frugiperda and may inform future strategies for managing pest resistance through microbiome-based approaches.

• Keywords
• bacterial communities, gut microbiome, insect microbiome, insecticide toxicity, microbial diversity, microbial interactions, pest management, synthetic insecticides,
• MeSH
• Bacteria * drug effects   genetics   classification   metabolism   isolation & purification   MeSH
• Insecticides * pharmacology   MeSH
• Larva microbiology   drug effects   growth & development   MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Spodoptera * microbiology   growth & development   drug effects   MeSH
• Gastrointestinal Microbiome * drug effects   MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Insecticides * MeSH
• RNA, Ribosomal, 16S MeSH