Individual Microorganisms Research Articles

Assessed correlation between biological diversity of oropharyngeal microbiota and atopic dermatitis severity and exacerbations

Atopic dermatitis (AtD) is a multifactorial inflammatory skin disease characterized by itching, chronic recurrent course and age-related features of lesions. AtD pathogenesis has not been fully elucidated yet. An important factor for AtD emergence and progression is the imbalance in symbiotic microbiota. The research publications provide a few studies about a role for oropharyngeal microorganisms in AtD immunopathogenesis. The aim of the study is to analyze biological diversity of oropharyngeal microbial communities in varying AtD severity. 97 male patients, aged from 16 to 19 years, with different AtD severity were included in the study. Culture study of oropharyngeal discharge was also performed. Biological material was seeded on the expanded list of growth media and incubated for 5 days at the 37°С. To assess the biological diversity of the oropharyngeal microbiota, the coefficient of constancy (C) was used, in order to classify individual microorganisms as permanent, additional or transient. Statistical data processing was performed using the Stat Tech software (version 4.0.0, Stattech LLC, Russia). While examining biological diversity of the oropharyngeal microbiota in AtD patients, 58 microbial species were isolated and identified. After statistical analysis the significant differences in frequency of isolation, depending on different AtD severity were observed for microbes such asStreptococcus vestibularisandRothia dentocariosa. WhenR. dentocariosais isolated from the oropharynx, the chances of AtD exacerbation emergence decreased by 6 times, whereas in case ofS. vestibularis, on the contrary, it increased by 5 times. Therefore, identification of transitions of individual microbes from transient to additional and permanent microbiota and vice versa, depending on the AtD stage and severity, allows to analyze an influence of specific microorganisms in AtD pathological processes and to establish definite new microbiological predictors of AtD exacerbation and remission.

PlasmidScope: a comprehensive plasmid database with rich annotations and online analytical tools.

Plasmids are extrachromosomal genetic molecules that replicate independent of chromosomes in bacteria, archaea, and eukaryotic organisms. They contain diverse functional elements and are capable of horizontal gene transfer among hosts. While existing plasmid databases have archived plasmid sequences isolated from individual microorganisms or natural environments, there is a need for a comprehensive, standardized, and annotated plasmid database to address the vast accumulation of plasmid sequences. Here, we propose PlasmidScope (https://plasmid.deepomics.org/), a plasmid database offering comprehensive annotations, automated online analysis, and interactive visualization. PlasmidScope harbors a substantial collection of 852 600 plasmids curated from 10 repositories. Along with consolidated background information, PlasmidScope utilizes 12 state-of-the-art tools and provides comprehensive annotations for the curated plasmids, covering genome completeness, topological structure, mobility, host source, tRNA, tmRNA, signal peptides, transmembrane proteins and CRISPR/Cas systems. PlasmidScope offers diverse functional annotations for its 25 231 059 predicted genes from 9 databases as well as corresponding protein structures predicted by ESMFold. In addition, PlasmidScope integrates online analytical modules and interactive visualization, empowering researchers to delve into the complexities of plasmids.

Enhancing the Shelf Life of Sous-Vide Red Deer Meat with Piper nigrum Essential Oil: A Study on Antimicrobial Efficacy against Listeria monocytogenes.

Using sous-vide technology in combination with essential oils offers the potential to extend the preservation of food items while preserving their original quality. This method aligns with the growing consumer demand for safer and healthier food production practices. This study aimed to assess the suitability of minimal processing of game meat and the effectiveness of vacuum packaging in combination with Piper nigrum essential oil (PNEO) treatment to preserve red deer meat samples inoculated with Listeria monocytogenes. Microbial analyses, including total viable count (TVC) for 48 h at 30 °C, coliform bacteria (CB) for 24 h at 37 °C, and L. monocytogenes count for 24 h at 37 °C, were conducted. The cooking temperature of the sous-vide was from 50 to 65 °C and the cooking time from 5 to 20 min. Additionally, the study monitored the representation of microorganism species identified through mass spectrometry. The microbiological quality of red deer meat processed using the sous-vide method was monitored over 14 days of storage at 4 °C. The results indicated that the TVC, CB, and L. monocytogenes counts decreased with the temperature and processing time of the sous-vide method. The lowest counts of individual microorganism groups were observed in samples treated with 1% PNEO. The analysis revealed that PNEO, in combination with the sous-vide method, effectively reduced L. monocytogenes counts and extended the shelf life of red deer meat. Kocuria salsicia, Pseudomonas taetrolens, and Pseudomonas fragi were the most frequently isolated microorganism species during the 14-day period of red deer meat storage prepared using the sous-vide method.

A novel hierarchical network-based approach to unveil the complexity of functional microbial genome

Biological networks serve a crucial role in elucidating intricate biological processes. While interspecies environmental interactions have been extensively studied, the exploration of gene interactions within species, particularly among individual microorganisms, is less developed. The increasing amount of microbiome genomic data necessitates a more nuanced analysis of microbial genome structures and functions. In this context, we introduce a complex structure using higher-order network theory, “Solid Motif Structures (SMS)”, via a hierarchical biological network analysis of genomes within the same genus, effectively linking microbial genome structure with its function. Leveraging 162 high-quality genomes of Microcystis, a key freshwater cyanobacterium within microbial ecosystems, we established a genome structure network. Employing deep learning techniques, such as adaptive graph encoder, we uncovered 27 critical functional subnetworks and their associated SMSs. Incorporating metagenomic data from seven geographically distinct lakes, we conducted an investigation into Microcystis’ functional stability under varying environmental conditions, unveiling unique functional interaction models for each lake. Our work compiles these insights into an extensive resource repository, providing novel perspectives on the functional dynamics within Microcystis. This research offers a hierarchical network analysis framework for understanding interactions between microbial genome structures and functions within the same genus.

Antagonistic activity of monocultures and consortia of lactobacilli against multidrug-resistant isolates of opportunistic bacteria as a screening of their probiotic potential

Background. In recent years, special attention has been paid to the studying the consortia of probiotic bacteria. In these associations, the properties of individual microorganisms can be enhanced, in particular, their antagonistic activity which is an effective indicator for screening of probiotic potential. The development of probiotics based on such consortia with antibacterial properties is critical in the light of the growing problem of drug resistance in microorganisms.The aim of the work. To study the antagonistic activity of monocultures and consortia of lactobacilli against multidrug-resistant isolates of opportunistic bacteria. Materials and methods. The antagonistic activity of lactobacilli monocultures and their consortia was assessed simultaneously by two methods: the cross streak method and the well diffusion method.Results. All strains of lactobacilli and their consortia, depending on the research method, had varying degrees of antagonistic activity. Five consortia had stronger antagonism to test cultures as compared to monocultures, while in one consortium, the effect of antagonistic activity was reduced compared to monocultures. The results of studying the antagonistic activity of two consortia (Limosilactobacillus fermentum 44/1 and Lacticaseibacillus rhamnosus 12L, Latilactobacillus curvatus LCR-111-1 and Lactiplantibacillus plantarum 8PAZ) contradict data on the biocompatibility of strains in these consortia. Differences in the degree of antagonistic effects of lactobacilli on gram-positive and gram-negative species of opportunistic bacteria were revealed.Conclusion. The study showed that both the biocompatibility of the probiotic strains and the antagonistic activity of the consortium are the important requirements for creating a probiotic consortium with effective probiotic potential. To study the antagonistic properties of lactobacilli, the number of isolates of target gram-positive and gram-negative bacteria and normobiota should be increased. This will allow us to determine effective strategies for using probiotics in conditions of the spread of drug resistance of microorganisms.

Comparative analysis of the microbiota of prostate secretion in patients with chronic abacterial prostatitis of categories IIIa and IIIb

Numerous studies have established that chronic prostatitis/ chronic pelvic pain syndrome ( CP/CPPS) is the focus of attention of the global medical community, because it is the most common type of disease, the treatment of which has largely unsatisfactory results.Purpose of the work: to conduct a comparative analysis of the microbiota of prostate secretions in patients with CP/CPPS IIIa and IIIb using mass spectrometry of microbial markers (MSMM).Material and methods. A prospective comparative study was conducted from 2018 to 2023 at the SM-Clinic medical center. 205 patients with prostatitis-like symptoms and 70 males who applied for a screening examination with no complaints at the age of 25 to 50 years were selected. The subjects were divided into three groups: group 1 – patients with CP/CPPS category IIIa, group 2 ( n = 85) patients with CP/CPPS category IIIb with clinical manifestations of chronic prostatitis and group 3 ( n = 70) – without clinical manifestations prostatitis/control group. A study of the microbiota of prostate secretions was carried out using gas chromatograph mass spectrometer "Maestro" (LLC "Interlab", Russia).Results. The results of statistical analysis showed that the level of cocci and bacilli, anaerobes, actinobacteria, fungi and yeasts, as well as total viruses in patients with CP/CPPS IIIa, compared with patients with CP/CPPS IIIb and the control group, was significantly higher ( p = 0.0020 ; p < 0.0001; p < 0.0001; p = 0.0254; p = 0.0254). It was revealed that in patients with CP/CPPS IIIa, compared with patients with CP/CPPS IIIb and healthy people, there was a significant increase in the total load of cocci and bacilli, anaerobes, actinobacteria, fungi and yeasts, as well as total viruses . When analyzing the relationship between the absolute number of microorganisms, it was revealed that an increase in the level of many microorganisms is associated with an increase in the probability of detecting a leukocyte level 10. An analysis of the relationship between the occurrence of individual microorganisms and leukocyte values in prostate secretions ≥10 showed that an increase in the indicators of many microorganisms, compared with the control group, increased the chances of having a leukocyte level ≥10 several times.Conclusion. Identification of microbial associations in prostate secretions using the MSMM method and an increase in the total load of microorganisms in patients with CP/CPPS IIIa, compared with CP/CPPS IIIa and the control group, suggests the role of infection in a certain part of patients with CP/CPPS IIIa, which dictates the need to change the view of the urologist in the diagnosis and treatment strategy of these patients.

Multivariate comparison of taxonomic, chemical and operational data from 80 different full-scale anaerobic digester-related systems

BackgroundThe holistic characterization of different microbiomes in anaerobic digestion (AD) systems can contribute to a better understanding of these systems and provide starting points for bioengineering. The present study investigates the microbiome of 80 European full-scale AD systems. Operational, chemical and taxonomic data were thoroughly collected, analysed and correlated to identify the main drivers of AD processes.ResultsThe present study describes chemical and operational parameters for a broad spectrum of different AD systems. With this data, Spearman correlation and differential abundance analyses were applied to narrow down the role of the individual microorganisms detected. The authors succeeded in further limiting the number of microorganisms in the core microbiome for a broad range of AD systems. Based on 16S rRNA gene amplicon sequencing, MBA03, Proteiniphilum, a member of the family Dethiobacteraceae, the genus Caldicoprobacter and the methanogen Methanosarcina were the most prevalent and abundant organisms identified in all digesters analysed. High ratios for Methanoculleus are often described for agricultural co-digesters. Therefore, it is remarkable that Methanosarcina was surprisingly high in several digesters reaching ratios up to 47.2%. The various statistical analyses revealed that the microorganisms grouped according to different patterns. A purely taxonomic correlation enabled a distinction between an acetoclastic cluster and a hydrogenotrophic one. However, in the multivariate analysis with chemical parameters, the main clusters corresponded to hydrolytic and acidogenic microorganisms, with SAOB bacteria being particularly important in the second group. Including operational parameters resulted in digester-type specific grouping of microbes. Those with separate acidification stood out among the many reactor types due to their unexpected behaviour. Despite maximizing the organic loading rate in the hydrolytic pretreatments, these stages turned into extremely robust methane production units.ConclusionsFrom 80 different AD systems, one of the most holistic data sets is provided. A very distinct formation of microbial clusters was discovered, depending on whether taxonomic, chemical or operational parameters were combined. The microorganisms in the individual clusters were strongly dependent on the respective reference parameters.Graphical

PSVI-6 Metabolic potential of three novel rumen bacterial species from sheep characterized by utilizing a metagenomic-based approach

Abstract The sheep rumen microbiome contains a vast wealth of known and unknown members, whose metabolic processes impact nutrient acquisition as well as gut and overall health of the animal. Based on previous research from our group on investigating the impact of a change in diet on the composition of the rumen microbiome in lambs, further insights into the metabolic functions of novel bacterial species represented by three Operational Taxonomic Units (OTUs) were pursued. The rumen fluid samples with the greatest abundance of OTUs RA1-01223, RA1-00032, and RA1-04216 were, respectively, used as representatives for metagenomic investigations to assemble the genomes of their corresponding bacterial species. Purified microbial genomic DNA was used as a template for ‘shotgun’ sequencing with an Illumina Miseq (2 x 250) platform. Raw datasets were filtered for quality then used for contig assembly with an in-house developed set of Perl scripts, generating 64 contigs for RA1-01223 [combined total length: 2,046,349 base pairs (bp)], 118 contigs for RA1-00032 (combined total length: 3,704,255 bp), and 119 contigs for RA1-04216 (combined total length: 8,884,743 bp). After building, coding sequences were identified and annotated using RAST, with metabolic pathways of predicted enzymes constructed for each OTU of interest using KEGG pathways as a model reference. Annotated coding sequences were also screened by blastp to assign contig sets to each OTU based on their respective taxonomic affiliation; both OTU RA1-01223 and OTU RA1-00032 were found to be most closely related to Ruminococcus bili (94.8% and 86.8%, respectively), while RA1-04216 was affiliated to Succinivibrio dextrinsolvens (96.9%). As RA1-01223 and RA1-00032 were found to possess enzymes responsible for lactate metabolism, they could potentially affect susceptibility to acidosis by acting as modulators of ruminal pH or by producing lactate from starch degradation. Distinguishing features between these two OTUS included the pathway for vitamin B5 synthesis, using uracil or L-aspartate as precursors (RA1-01223), and the ability to produce ethanol as an end product of ruminal fermentation (RA1-00032). Distinguishing metabolic activities of interest for RA1-04216 included synthesis of chorismate and prephenate, which are precursors for tryptophan and phenylalanine, respectively. Together, these results contribute to a better understanding of the metabolic roles of individual microorganisms in the rumen, providing information that is crucial for creating a healthy and proactive environment that benefits the host.

The Role of the Gut Microbiota in the Development of Colorectal Cancer

Colorectal cancer (CRC) is one of the most common malignant tumours, which development significantly depends on the role of gut microbiota. Here we discuss the possibilities of using individual microorganisms as biomarkers for CRC screening. During the tumorigenesis, a complex interaction is established between the gut microbiome, the tumor microenvironment and the immune system. The composition of the fecal microbiome in patients with CRC is characterized by reduced numbers of protective microorganisms (Clostridiales, Roseburia, Feacalibacterium) and increased diversity of potentially carcinogenic taxa (Bacteroides, Fusobacterium, Campylobacter, Escherichia, Porphyromonas, Prevotella nigrescens, Thermanaerovibrio acidaminovorans). Recent metagenomic studies of stool samples and tumor biopsies indicate an increased representation of oral pathogenic bacteria in the intestinal microbiome in patients with CRC as compared to the control group, suggesting their potential causative role in CRC. The detection of the abovementioned taxa can be used to differentiate individuals with CRC from healthy individuals. Prospects for further research are associated with the identification of microbial CRC markers in prospective epidemiological studies and their applications for non-invasive screening of CRC.

Influence of yeast size on the kinetics of cell disruption in an ultrasonic homogenizer

The results of studies on the disintegration kinetics of the yeast Saccharomyces cerevisiae are presented. The process was carried out in a 500 W ultrasonic homogenizer equipped with a spherical working chamber with a volume of 100 cm 3. The concentration of the suspension of microorganisms was 0.05 g d.m./cm 3. The continuous phase was water solution containing 0.15 M NaCl and 4 mM K 2HPO 4. The kinetics of cell disruption were studied by the direct method. The theory of random transformation of dispersed matter was used to analyze the process. There was significant variation in the size of yeast cells. The range of changes in the values of parameters describing the size of microorganisms was divided into size classes. The kinetics of cell disruption in individual classes was described by a first-order linear differential equation. During the implosion of cavitation bubbles, the transformation volume of individual microorganisms is generated. It has been shown that as the volume of cells in subsequent size classes increases, their transformation volumes do not increase significantly. The safe volume for cells remains unchanged. As the size of the microorganisms increased, there was no increase in the constant rate of cell disruption.

Metagenomic Analysis of Antarctic Ocean near the King Sejong Station Reveals the Diversity of Carotenoid Biosynthetic Genes.

Carotenoids, biotechnologically significant pigments, play crucial biological roles in marine microorganisms. While various environments have been explored to understand the diversity of carotenoids and their biosynthesis, the Antarctic Ocean remains relatively under-investigated. This study conducted a metagenomic analysis of seawater from two depths (16 and 25 m) near the King Sejong Station in the Antarctic Ocean. The analysis revealed a rich genetic diversity underlying C40 (astaxanthin, myxol, okenone, spheroidene, and spirilloxanthin), C30 (diaponeurosporene, diapolycopene, and staphyloxanthin), and C50 (C.p. 450) carotenoid biosynthesis in marine microorganisms, with notable differential gene abundances between depth locations. Exploring carotenoid pathway genes offers the potential for discovering diverse carotenoid structures of biotechnological value and better understanding their roles in individual microorganisms and broader ecosystems.

Trophic relationships between protists and bacteria and fungi drive the biogeography of rhizosphere soil microbial community and impact plant physiological and ecological functions

Rhizosphere microorganisms play a vital role in enhancing plant health, productivity, and the accumulation of secondary metabolites. Currently, there is a limited understanding of the ecological processes that control the assembly of community. To address the role of microbial interactions in assembly and for functioning of the rhizosphere soil microbiota, we collected rhizosphere soil samples from Anisodus tanguticus on the Tibetan Plateau spanning 1500 kilometers, and sequenced the bacteria, fungi, archaea, and protist communities. We observed a significant but weak distance-decay relationship in the microbial communities of rhizosphere soil. Our comprehensive analysis of spatial, abiotic, and biotic factors showed that trophic relationships between protists and bacteria and fungi predominantly influenced the alpha and beta diversity of bacterial, fungal, and protistan communities, while abiotic factors had a greater impact on archaeal communities, including soil pH, available phosphorus, total phosphorus and mean annual temperature. Importantly, microbial interactions had a more significant influence on Anisodus tanguticus physiological and ecological functions compared to individual microorganisms. Network analyses revealed that bacteria occupy a central position of the co-occurrence network and play a crucial role of connector within this community. The addition of protists increased the stability of bacterial, fungal, and archaeal networks. Overall, our findings indicate that trophic relationships play an important role in assembly and for functioning of the rhizosphere soil microbiota. Bacterial communities serve as a crucial link between different kingdoms of microorganisms in the rhizosphere community. These findings help us to fully harness the beneficial functions of rhizosphere microorganisms for plants and achieve sustainable use of biological resources.

Assessment of species diversity of anaerobic intestinal microbiota in children and adolescents with exogenous constitutional obesity

The problem of the increasing obesity among children and adolescents is urgent. One of the most interesting and promising directions in this area is to study the correlation of individual microorganisms with the presence and absence of obesity. The aim of the study was to assess the correlation between the isolation frequency of individual microorganisms and the presence of obesity in children and adolescents and to identify possible associations between different groups of microorganisms in obese patients. Material and methods. 156 male and female patients aged from 7 to 17 years were included in the study. The patients were divided into a control group (n=23) (healthy patients), a group of children with exogenous constitutional obesity without complications (n=25), a group of children who had one or more complications of obesity (n=108). For all patients body mass index (BMI) was calculated. Additional examination included a cultural study of the intestinal microbiota. Fecal samples of patients were used as the material. Preparation of the material for inoculation, inoculation and subsequent incubation of the Petri plates were carried out under anaerobic conditions. The isolated microorganisms were identified using the MALDI-ToF mass spectrometry method. Results. When analyzing the correlation between obesity and individual taxa, statistically significant differences were obtained only for Bifidobacterium spp. (p=0.045). The analysis of the correlation between obesity and the isolation of individual microorganisms has shown that Bifidobacterium pseudocatenulatum (p=0.012), Candida albicans (p=0.012), Streptococcus salivarius (p=0.016), Bifidobacterium breve (p=0.003), Veillonella parvula (p=0.013), Haemophilus parainfluenzae (p=0.003), Streptococcus oralis (p=0.001), Weissella confusa (p=0.036), Enterococcus mundtii (p=0.036) were isolated less often in patients with obesity than in control group. Conclusion. The results of the study has demonstrated that only one taxon, Bifidobacterium spp., had a significant correlation with the absence of obesity. At the same time, a reliable correlation with the absence of obesity was also established for individual microorganisms, including several microorganisms from Bifidobacterium spp. and Streptococcus spp., which may enable to establish certain microbiological predictors of obesity and its complications.

The influence of antagonistic microorganisms on limiting the development of Fusarium fungi and the development of winter wheat seedlings

The study aimed to assess the impact of Trichoderma harzianum, Trichoderma atroviride, Sarocladium strictum, Wickerhamomyces anomalus and Bacillus spp. on the growth inhibition of Fusarium spp. colonies, and on the health and development of winter wheat va¬rietas Euforia seedlings. In the laboratory conditions, the presence of T. atroviride and T. harzianum the most strongly limited the growth of the colonies of Fusarium culmorum, Fusarium graminearum and Fusarium avenaceum. Well-developed growth inhibition zones were observed in the bicultures containing strains of Bacillus spp. and W. anomalus. The development of wheat seedlings in the presence of antagonistic and pathogenic fungi was varied, but W. anomalus provided the best protection against damping off caused by F. culmorum and F. graminearum. The influence of individual antagonistic microorganisms in variants with inoculation with pathogenic microorgan¬isms on the green mass of wheat seedlings was variable. The best results were achieved with T. atroviride, S. strictum and Bacillus spp.

Сравнительный анализ микробиоты секрета простаты у больных хроническим абактериальным простатитом категории IIIа и IIIб

Numerous studies have established that chronic prostatitis/ chronic pelvic pain syndrome ( CP/CPPS) is the focus of attention of the global medical community, because it is the most common type of disease, the treatment of which has largely unsatisfactory results. Purpose of the work: to conduct a comparative analysis of the microbiota of prostate secretions in patients with CP/CPPS IIIa and IIIb using mass spectrometry of microbial markers (MSMM). Material and methods. A prospective comparative study was conducted from 2018 to 2023 at the SM-Clinic medical center. 205 patients with prostatitis-like symptoms and 70 males who applied for a screening examination with no complaints at the age of 25 to 50 years were selected. The subjects were divided into three groups: group 1 – patients with CP/CPPS category IIIa, group 2 ( n = 85) patients with CP/CPPS category IIIb with clinical manifestations of chronic prostatitis and group 3 ( n = 70) – without clinical manifestations prostatitis/control group. A study of the microbiota of prostate secretions was carried out using gas chromatograph mass spectrometer "Maestro" (LLC "Interlab", Russia). Results. The results of statistical analysis showed that the level of cocci and bacilli, anaerobes, actinobacteria, fungi and yeasts, as well as total viruses in patients with CP/CPPS IIIa, compared with patients with CP/CPPS IIIb and the control group, was significantly higher ( p = 0.0020 ; p < 0.0001; p < 0.0001; p = 0.0254; p = 0.0254). It was revealed that in patients with CP/CPPS IIIa, compared with patients with CP/CPPS IIIb and healthy people, there was a significant increase in the total load of cocci and bacilli, anaerobes, actinobacteria, fungi and yeasts, as well as total viruses . When analyzing the relationship between the absolute number of microorganisms, it was revealed that an increase in the level of many microorganisms is associated with an increase in the probability of detecting a leukocyte level ≥10. An analysis of the relationship between the occurrence of individual microorganisms and leukocyte values in prostate secretions ≥10 showed that an increase in the indicators of many microorganisms, compared with the control group, increased the chances of having a leukocyte level ≥10 several times. Conclusion. Identification of microbial associations in prostate secretions using the MSMM method and an increase in the total load of microorganisms in patients with CP/CPPS IIIa, compared with CP/CPPS IIIa and the control group, suggests the role of infection in a certain part of patients with CP/CPPS IIIa, which dictates the need to change the view of the urologist in the diagnosis and treatment strategy of these patients

Horizontal metaproteomics and CAZymes analysis oflignocellulolytic microbial consortia selectively enriched from cow rumen and termitegut

Selectively enriched microbial consortia are potentially useful for theconversion of lignocellulose (LC) into biofuels and commodity chemicals. Consortiaare also of interest to elucidate the roles of individual microorganisms and thedynamics of enzymes involved in LC deconstruction. Using metaproteomics, 16 S rRNAgene amplicon sequencing and multivariate discriminant analysis, we revealed thetemporal dynamics of microbial species and their proteins during anaerobicconversion of LC by microbial consortia derived from cow rumen (RWS) and termite gut(TWS) microbiomes. Bacteroidetes (Bacteroidota), Firmicutes (Bacillota) andProteobacteria (Pseudomonadota) phyla were dominant, irrespective the inoculumorigin, displaying functional complementarities. We identified a large variety ofcarbohydrate-active enzymes, distributed in 94 CAZy families, involved in biomassdeconstruction. Additionally, proteins involved in short chain fatty acidsbiosynthesis were detected. Multivariate analysis clearly differentiates RWS and TWSmetaproteomes, with differences originating in the initial inoculates. Furthersupervised discriminant analysis of the temporal succession of CAZymes revealed thatboth consortia consume easily accessible oligosaccharides during the early stage ofincubation, degrading more complex hemicellulose and cellulose fractions at laterstages, an action that pursues throughout the incubation period. Our results providenew insights regarding the functional roles and complementarities existing inlignocellulolytic consortia and highlight their potential for biorefineryapplications.

Антагонистическая активность экстремофильных микроорганизмов в отношении фитопатогенов сельскохозяйственных культур

Wheat is a vital agricultural crop whose phytopathogens include fungi of the genera Fusarium and Alternaria. Synthetic pesticides, which are used to combat them, have a negative impact on the environment. Therefore, there is a need for developing safe and effective biopesticides. We aimed to create a consortium of extremophilic microorganisms isolated from natural sources to protect wheat from the diseases caused by Alternaria and Fusarium fungi.
 Ten isolates of extremophilic microorganisms were tested for their antimicrobial activity against Escherichia coli and their antagonistic activity against phytopathogens. Based on the results, we developed microbial consortia and evaluated their effectiveness in protecting wheat from phytopathogens.
 Five of the strains under study showed the highest activity, three of which were biocompatible, namely Leclercia sp., Sphingomonas paucimobilis, and Lactobacillus plantarum. Four consortia were created from these microorganisms, of which consortium B (with a 2:1:1 ratio of the strains, respectively) proved the most effective. In particular, it increased the area free from the phytopathogen by 4.2% compared to the average values of its individual microorganisms. Also, the consortium had a phytostimulating effect on wheat seedlings (germination of 73.2–99.6%) and protected the seeds infected with phytopathogens from morphometric changes.
 The resulting consortium can be used as a biopesticide since it is highly effective in protecting wheat from Alternaria and Fusarium pathogens.

Resource partitioning and amino acid assimilation in a terrestrial geothermal spring.

High-temperature geothermal springs host simplified microbial communities; however, the activities of individual microorganisms and their roles in the carbon cycle in nature are not well understood. Here, quantitative stable isotope probing (qSIP) was used to track the assimilation of 13C-acetate and 13C-aspartate into DNA in 74 °C sediments in Gongxiaoshe Hot Spring, Tengchong, China. This revealed a community-wide preference for aspartate and a tight coupling between aspartate incorporation into DNA and the proliferation of aspartate utilizers during labeling. Both 13C incorporation into DNA and changes in the abundance of taxa during incubations indicated strong resource partitioning and a significant phylogenetic signal for aspartate incorporation. Of the active amplicon sequence variants (ASVs) identified by qSIP, most could be matched with genomes from Gongxiaoshe Hot Spring or nearby springs with an average nucleotide similarity of 99.4%. Genomes corresponding to aspartate primary utilizers were smaller, near-universally encoded polar amino acid ABC transporters, and had codon preferences indicative of faster growth rates. The most active ASVs assimilating both substrates were not abundant, suggesting an important role for the rare biosphere in the community response to organic carbon addition. The broad incorporation of aspartate into DNA over acetate by the hot spring community may reflect dynamic cycling of cell lysis products in situ or substrates delivered during monsoon rains and may reflect N limitation.

Degradation and decolorization of textile azo dyes by effective fungal-bacterial consortium.

Synthetic dyes are one of the main pollutants in the textile industry and bioremediation is considered as an environmentally friendly method to degrade them. Soil microbial consortia (MCs) are reported having the potential of decolorizing most of textile dyes. This study aimed at evaluating dye-degrading ability of MCs developed from fungi and bacteria. Fungi and bacteria were isolated from the soil samples obtained from textile waste dumping site at Horana industrial zone, Sri Lanka and were screened for crystal violet (CV) and congo red (CR) dyes to develop MCs. Decolorization assay was performed for MCs along with individual isolates under variable pH levels. Metabolized products were characterized to confirm the biodegradation. A. tamari (F5) and P. putida (B3) significantly (P < 0.05) decolorized both dyes. All the MCs showed higher decolorization percentages over the individual microorganisms. Neutral pH (pH 7) was the optimum pH for the decolorization of both dyes by individual isolates and the percentages were significantly changed under the acidic and basic pH levels. However, decolorization ability by all MCs was not significantly changed with pH. Consortium with A. tamari - P. putida significantly (P < 0.05) decolourized both dyes under optimum pH 7. All MCs showed better pH tolerance in degrading CV and CR. Thus, it can be concluded that the selected MC with A. tamari - P. putida can degrade CV and CR textile dyes efficiently into non-toxic compounds against plants under neutral pH. Degradation and decolorization of textile azo dyes by effective fungal-bacterial consortium.

Beneficial microbial consortium improves winter rye performance by modulating bacterial communities in the rhizosphere and enhancing plant nutrient acquisition.

The beneficial effect of microbial consortium application on plants is strongly affected by soil conditions, which are influenced by farming practices. The establishment of microbial inoculants in the rhizosphere is a prerequisite for successful plant-microorganism interactions. This study investigated whether a consortium of beneficial microorganisms establishes in the rhizosphere of a winter crop during the vegetation period, including the winter growing season. In addition, we aimed for a better understanding of its effect on plant performance under different farming practices. Winter rye plants grown in a long-time field trial under conventional or organic farming practices were inoculated after plant emergence in autumn with a microbial consortium containing Pseudomonas sp. (RU47), Bacillus atrophaeus (ABi03) and Trichoderma harzianum (OMG16). The density of the microbial inoculants in the rhizosphere and root-associated soil was quantified in autumn and the following spring. Furthermore, the influence of the consortium on plant performance and on the rhizosphere bacterial community assembly was investigated using a multidisciplinary approach. Selective plating showed a high colonization density of individual microorganisms of the consortium in the rhizosphere and root-associated soil of winter rye throughout its early growth cycle. 16S rRNA gene amplicon sequencing showed that the farming practice affected mainly the rhizosphere bacterial communities in autumn and spring. However, the microbial consortium inoculated altered also the bacterial community composition at each sampling time point, especially at the beginning of the new growing season in spring. Inoculation of winter rye with the microbial consortium significantly improved the plant nutrient status and performance especially under organic farming. In summary, the microbial consortium showed sufficient efficacy throughout vegetation dormancy when inoculated in autumn and contributed to better plant performance, indicating the potential of microbe-based solutions in organic farming where nutrient availability is limited.