Plant pathogens present a major challenge to crop production, leading to decreased yield and quality during growth and storage. During long-term storage, healthy onions can develop diseases from latent pathogen infections. This poses a challenge for onion growers because infected bulbs without visible symptoms can lead to significant crop losses during the growing season. In this study, we aimed to isolate and identify Fusarium species from yellow onion bulbs (Allium cepa L.) that developed disease symptoms during storage. The aggressiveness of these strains against onion bulbs and seedlings was also evaluated. The isolated strains were further subjected to morphological and molecular differentiation. The results revealed that all 16 isolated strains belonged to the Fusarium complex species incarnatum-equiseti and Fusarium fujikuroi, namely, F. proliferatum (98%), F. oxysporum (1%), and Fusarium sp. (1%). Koch’s postulate analysis of isolated strains revealed varying aggressiveness on onion bulbs and plants depending on fungal species. Disease symptoms developed more slowly on plants than on onion bulb plants according to Koch’s postulates. Moreover, the results revealed that Fusarium strains that can infect onion plants were less pathogenic to onion bulbs and vice versa. In addition, three isolates were found to be non-pathogenic to onions. Furthermore, the in vitro control of Fusarium species through Bacillus velezensis KS04-AU and Streptomyces albidoflavus MGMM6 showed high potential for controlling the growth of these pathogenic fungi. These results may contribute to the development of environmentally friendly approaches for controlling onion spoilage caused by pathogens during storage.

Our study is the first to consider the changes in the entire set of matrix plant cell wall (PCW) polysaccharides in the course of a plant infectious disease. We compared the molecular weight distribution, monosaccharide content, and the epitope distribution of pectic compounds and cross-linking glycans in non-infected potato plants and plants infected with Pectobacterium atrosepticum at the initial and advanced stages of plant colonization by the pathogen. To predict the gene products involved in the modification of the PCW polysaccharide skeleton during the infection, the expression profiles of potato and P. atrosepticum PCW-related genes were analyzed by RNA-Seq along with phylogenetic analysis. The assemblage of P. atrosepticum biofilm-like structures—the bacterial emboli—and the accumulation of specific fragments of pectic compounds that prime the formation of these structures were demonstrated within potato plants (a natural host of P. atrosepticum). Collenchyma was shown to be the most “vulnerable” tissue to P. atrosepticum among the potato stem tissues. The infection caused by the representative of the Soft Rot Pectobacteriaceae was shown to affect not only pectic compounds but also cross-linking glycans; the content of the latter was increased in the infected plants compared to the non-infected ones.

Lignin is a complex aromatic polymer that constitutes a major fraction of plant biomass and represents a valuable renewable carbon resource. Naturally decaying wood serves as an environmental reservoir of microorganisms capable of degrading lignin. In this study, we isolated and characterized sixteen bacterial strains from decaying Tilia cordata wood using an enrichment culture technique with lignin as the sole carbon source. Taxonomic identification via 16S rRNA gene sequencing revealed microbial diversity spanning the genera Bacillus, Pseudomonas, Stenotrophomonas, and several members of the Enterobacteriaceae family, including Raoultella terrigena isolates. Metagenomic sequencing of the wood substrate revealed an exceptionally rich and balanced bacterial community (Shannon index H′ = 5.07), dominated by Streptomyces, Bradyrhizobium, Bacillus, and Pseudomonas, likely reflecting a specialized consortium adapted to lignin rich late-stage decay. Functional phenotyping demonstrated that all isolates possess ligninolytic potential, evidenced by peroxidase/laccase-type activity through methylene blue decolorization. Dynamic Light Scattering (DLS) and HPLC analyses showed that some isolates, such as Raoultella terrigena MGMM806, effectively depolymerized lignosulfonate into low molecular weight fragments (1.23 nm), while others accumulated intermediate metabolites or completely mineralized the substrate. Growth profiling on monolignol substrates revealed a broad spectrum of catabolic specialization in lignin monomer degradation. The results demonstrate a complex system of metabolic partitioning within a natural bacterial consortium. This collection represents a foundational genetic resource for developing engineered biocatalysts and synthetic microbial communities aimed at the efficient conversion of lignin into valuable aromatic compounds.

The studies were conducted to create new consortia of microorganisms obtained from wild plant species (hypericum, oregano, plantain and reed) and to test their ability to be maintained in the soil and rhizosphere. The properties of 216 bacterial isolates that are important for protecting and stimulating plant growth, both in laboratory and field conditions, were determined, namely, enzymatic activity, including phytase, protease, lipase, nitrogenase, cellulase and amylase. In addition, the antagonistic activity of the isolates to the phytopathogenic fungus Fusarium oxysporum was tested. Then isolates were identified by comparing the 16S rRNA gene sequences. Pathogenic bacteria were then screened out and the most promising bacterial isolates were selected based on their enzymatic activities, from which a consortium was assembled to test the possibility of its maintenance in the soil and rhizosphere of Universiade wheat plants. For this purpose, the seeds were treated with the consortium at a dose of ×107 CFU/ml in a 1% carboxymethylcellulose solution and the soil and roots of the control and test plants were washed after 14 days. The presence or absence of the strains under study was determined by polymerase chain reaction fingerprinting. The consortium of microorganisms was better preserved in the soil than on the roots of plants. Its use increased the shoot length of experimental plants, relative to the control, by 38.6% (from 10.6 cm to 14.7 cm), the length of the root system by 22.1% (from 12.2 cm to 14.9 cm) and seed germination by 3.0% (from 87% to 90%). The obtained data can be used for further experiments and practical application in agriculture.

Microorganisms are fundamental drivers of soil productivity, mediating nutrient cycling and pathogen suppression. In this study, we evaluated changes in the fungal community in the soil of barley (Hordeum vulgare L.) in a field experiment involving the application of a consortium of Paenibacillus pabuli, Priestia megaterium, Pseudomonas koreensis, and Pseudomonas orientalis. Seed pretreatment and seed pretreatment followed by rhizosphere drenching at different growth stages were implemented. Regarding fungal communities in bulk soil, the rhizospheres of untreated and treated plants were characterized based on full-length ribosomal RNA gene (18S-5.8S-28S) metabarcoding sequencing. Despite the compositional shifts, no statistical differences were observed among the alpha diversity metrics. Seed treatment resulted in long-term, targeted suppression of Fusarium graminearum, Fusarium fujikuroi, Fusarium musae, and Fusarium verticillioides from the booting through flowering and dough development stages, outperforming seed pretreatment followed by rhizosphere drenching. A low-modularity network was observed in the rhizosphere of untreated plants. Seed treatment fostered a highly interconnected and uniform network with low hub-betweenness scores. Rhizosphere drenching of pretreated seeds shifted the network topology toward higher hub-betweenness scores, reducing their connectivity by up to 10% in the rhizosphere and bulk soil. These findings provide a framework for optimizing the soil ecosystem for sustainable agriculture.

This study provides a comprehensive characterization of Streptomyces isolates associated with the rhizosphere of the centenarian Juniperus turcomanica. Screening for ligninolytic activity revealed that isolates—ATM9, ATM14, ATM15, ATM16, ATM18, and ATM19 synthesize enzymes capable of decolorizing methylene blue and modifying lignosulfonates. Isolates ATM16 and ATM18 demonstrated the highest efficiency in lignosulfonate decomposition, with lignosulfonate becoming undetectable in their culture broth. In the straw lignin degradation process, isolates ATM15 and ATM16 showed the most significant reductions in lignin content (44.2% and 54.8%, respectively), demonstrating promising biodegradation potential. Majority of isolates demonstrated antagonistic activity against fungal strains, while ATM19 completely inhibited the growth of all phytopathogenic fungi tested. Taxonomic identification based on 16S rRNA gene sequencing confirmed that all isolates belong to the genus Streptomyces, with species including S. shaanxiensis (ATM9), S. chryseus (ATM14), S. narbonensis (ATM15), S. venezuelae (ATM16), S. spiroverticillatus (ATM18), S. longhuiensis (ATM19), and Streptomyces sp. (ATM24). Considering our data, S. venezuelae ATM16 and S. spiroverticillatus ATM18 stand out as the most promising strains for biotechnological applications due to their ligninolytic and antagonistic activity against fungal phytopathogens. Furthermore, this study provides the first report on enzymatic and antifungal activities for the recently proposed species S. longhuiensis (ATM19) and S. shaanxiensis (ATM9).