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Surfactins are lipopeptide-type biosurfactants produced mainly by Bacillus species, consisting of a peptide loop of seven amino acids and a hydrophobic fatty acid chain (C12–C16). These molecules have been proven to exhibit various biological activities; thus, their therapeutic and environmental applications are considered. Within the surfactin lipopeptide family, there is a wide spectrum of different homologues and isomers; to date, more than 30 variants have been described. Since the newest members of these lipopeptides were described recently, there is no information that is available on their characteristic features, e.g., the dependence of their production from different cultivation parameters. This study examined the effects of both the different carbon sources and various metal ions on the surfactin production of a selected B. subtilis strain. Among the applied carbon sources, fructose and xylose had the highest impacts on the ratio of the different variants, regarding both the peptide sequences and the lengths of the fatty acids. Furthermore, the application of metal ions Mn2+, Cu2+ and Ni2+ in the media completely changed the surfactin variant compositions of the fermenting broths leading to the appearance of methyl esterified surfactin forms, and resulted in the appearance of novel surfactin variants with fatty acid chains containing no more than 11 carbon atoms.

Armillaria species are both devastating forest pathogens and some of the largest terrestrial organisms on Earth. They forage for hosts and achieve immense colony sizes via rhizomorphs, root-like multicellular structures of clonal dispersal. Here, we sequenced and analysed the genomes of four Armillaria species and performed RNA sequencing and quantitative proteomic analysis on the invasive and reproductive developmental stages of A. ostoyae . Comparison with 22 related fungi revealed a significant genome expansion in Armillaria , affecting several pathogenicity-related genes, lignocellulose-degrading enzymes and lineage-specific genes expressed during rhizomorph development. Rhizomorphs express an evolutionarily young transcriptome that shares features with the transcriptomes of both fruiting bodies and vegetative mycelia. Several genes show concomitant upregulation in rhizomorphs and fruiting bodies and share cis -regulatory signatures in their promoters, providing genetic and regulatory insights into complex multicellularity in fungi. Our results suggest that the evolution of the unique dispersal and pathogenicity mechanisms of Armillaria might have drawn upon ancestral genetic toolkits for wood-decay, morphogenesis and complex multicellularity. Fungi of the genus Armillaria include devastating forest pathogens that cause root rot disease in many plants. Sequencing genomes and transcriptomes of several species, the authors reveal the genetic basis of dispersal, multicellular development and pathogenic mechanisms in Armillaria .

Surfactins are cyclic lipopeptides consisting of a β-hydroxy fatty acid of various chain length and a peptide ring of seven amino acids linked together by a lactone bridge, forming the cyclic structure of the peptide chain. These compounds are produced mainly by Bacillus species and possess numerous biological effects such as antimicrobial (antiviral, antibacterial, and antifungal) activities. A mixture of surfactins extracted from Bacillus subtilis strain SZMC 6179J was examined by HPLC-ESI-IT-MS technique, enhancing their separation to reveal novel lipopeptide varieties with higher masses and to characterize their structures. During the MS2 spectra analyses of their sodiated molecular ions [M + Na]+, a previously rarely encountered group of surfactins was detected and two novel types of the group were discovered containing methyl esterified aspartic acid residue in their fifth amino acid position. The relative amounts of these monomethyl isoforms exceeded 35% of the produced surfactin in total. In the m/z value of 1114, all the detected isoforms possessed aspartic acid 4-methyl ester residue in their fifth amino acid position (C17-[Lxx4, AME5], C18-[AME5]), offering an opportunity to separate a pure fraction of the compound and to study its biological activities in the future.

Armillarioids, including the genera Armillaria, Desarmillaria and Guyanagaster, represent white-rot specific fungal saprotrophs with soilborne pathogenic potentials on woody hosts. They propagate in the soil by root-like rhizomorphs, connecting between susceptible root sections of their hosts, and often forming extended colonies in native forests. Pathogenic abilities of Armillaria and Desarmillaria genets can readily manifest in compromised hosts, or hosts with full vigour can be invaded by virulent mycelia when exposed to a larger number of newly formed genets. Armillaria root rot-related symptoms are indicators of ecological imbalances in native forests and plantations at the rhizosphere levels, often related to abiotic environmental threats, and most likely unfavourable changes in the microbiome compositions in the interactive zone of the roots. The less-studied biotic impacts that contribute to armillarioid host infection include fungi and insects, as well as forest conditions. On the other hand, negative biotic impactors, like bacterial communities, antagonistic fungi, nematodes and plant-derived substances may find applications in the environment-friendly, biological control of armillarioid root diseases, which can be used instead of, or in combination with the classical, but frequently problematic silvicultural and chemical control measures.

A composite soil bioinoculant containing beneficial bacteria and fungi was developed for biocontrol of plant pathogens, phosphorous mobilization, stem degradation, humification, and nitrogen fixation. A Trichoderma asperellum isolate with outstanding in vitro antagonistic abilities toward a series of plant pathogenic fungi was included as a potential biocontrol component. The selected strain was also shown to promote growth and increase photosynthetic activity of tomato plants. For phosphorous mobilization and stem degradation, a Trichoderma atrobrunneum strain was selected, which produced cellulose-degrading enzymes even in the absence of stem residues, while this ability increased 10–15-fold in the presence of ground maize stem. The strain was also shown to produce large amounts of enzymes liberating organically bound phosphorous, as well as cellulase and xylanase activities in solid-state fermentation on various plant residues. A Streptomyces albus strain with excellent peroxidase-producing abilities was selected as a potential humus-producing component, while an Azotobacter vinelandii strain with the potential to provide excess nitrogen for crops was included for nitrogen fixation. The assembled soil bioinoculant had positive effect on the uptake of certain important macro- and microelements (potassium, sodium, and manganese) from the soil by field-grown tomato plants. The applied screening strategy proved to be applicable for the assembly of a composite soil bioinoculant with notable application potentials.

Several Bacillus strains are used as biocontrol agents, as they frequently have strong antagonistic effects against microbial plant pathogens. Bacillus strain SZMC 6179J, isolated from tomato rhizosphere, was previously shown to have excellent in vitro antagonistic properties against the most important fungal pathogens of tomato (Alternaria solani, Botrytis cinerea, Phytophthora infestans and Sclerotinia sclerotiorum) as well as several Fusarium species. Taxonomic investigations revealed that it is a member of the B. subtilis subsp. subtilis group and very closely related with the reference type strain B. subtilis subsp. subtilis 168. The sequenced genome of strain SZMC 6179J contains the genes responsible for the synthesis of the extracellular antibiotics surfactin, fengycin and bacilysin. Compared to strain 168, a prophage-like region is missing from the genome of SZMC 6179J, while there are 106 single nucleotide polymorphisms and 23 deletion-insertion polymorphisms. The high biocontrol potential of strain SZMC 6179J may results from a single base deletion in the sfp gene encoding the transcription factor of the surfactin and fengycin operons. Hypermutated regions reflecting short-time evolutionary processes could be detected in SZMC 6179J. The deletion-insertion polymorphism in the sfp gene and the detected hypermutations can be suggested as genetic determinants of biocontrol features in B. subtilis.Graphical Abstract

Research Highlights: A large scale effort to screen, characterize, and select Trichoderma strains with the potential to antagonize Armillaria species revealed promising candidates for field applications. Background and Objectives: Armillaria species are among the economically most relevant soilborne tree pathogens causing devastating root diseases worldwide. Biocontrol agents are environment-friendly alternatives to chemicals in restraining the spread of Armillaria in forest soils. Trichoderma species may efficiently employ diverse antagonistic mechanisms against fungal plant pathogens. The aim of this paper is to isolate indigenous Trichoderma strains from healthy and Armillaria-damaged forests, characterize them, screen their biocontrol properties, and test selected strains under field conditions. Materials and Methods: Armillaria and Trichoderma isolates were collected from soil samples of a damaged Hungarian oak and healthy Austrian spruce forests and identified to the species level. In vitro antagonism experiments were performed to determine the potential of the Trichoderma isolates to control Armillaria species. Selected biocontrol candidates were screened for extracellular enzyme production and plant growth-promoting traits. A field experiment was carried out by applying two selected Trichoderma strains on two-year-old European Turkey oak seedlings planted in a forest area heavily overtaken by the rhizomorphs of numerous Armillaria colonies. Results: Although A. cepistipes and A. ostoyae were found in the Austrian spruce forests, A. mellea and A. gallica clones dominated the Hungarian oak stand. A total of 64 Trichoderma isolates belonging to 14 species were recovered. Several Trichoderma strains exhibited in vitro antagonistic abilities towards Armillaria species and produced siderophores and indole-3-acetic acid. Oak seedlings treated with T. virens and T. atrobrunneum displayed better survival under harsh soil conditions than the untreated controls. Conclusions: Selected native Trichoderma strains, associated with Armillaria rhizomorphs, which may also have plant growth promoting properties, are potential antagonists of Armillaria spp., and such abilities can be exploited in the biological control of Armillaria root rot.

In the version of this Article originally published, it was incorrectly stated that “16,687 protein-coding genes were inferred for the most recent common ancestor (MRCA) of Armillaria ”; the value was incorrect and it should have read “15,787”. This has now been corrected.

In this study, more than 150 bacteria showing antagonistic properties against bacterial and fungal pathogens of the tomato plant were isolated and characterized. The most efficient agents against these phytopathogenic microorganisms belong to the genus Bacillus: the best biocontrol isolates were representatives of Bacillus subtilis, B. mojavensis and B. amyloliquefaciens species. They intensively produced fengycin or/and surfactin depsipeptide antibiotics and also proved to be excellent protease secretors. It was proved, that the selected strains were able to use ethylenethiourea (ETU) as sole nitrogen source. These antagonistic and ETU-degrading Bacillus strains can be applied as biocontrol and also as bioremediation agents.

A good antibiotic-producing Bacillus subtilis and an elevated extracellular enzyme-secreting Bacillus amyloliquefaciens biocontrol strain were investigated. The B. subtilis strain produces non-ribosomal oligopeptides: iturin, surfactin and fengycin. These cyclic lipopeptides have antifungal and antibacterial effects. The B. amyloliquefaciens strain secrets many extracellular enzymes (proteases, chitinases, cellulases and lipases); these have great significance in the antagonism. Kurosawa and co-workers reported elevated protease and P-amylase secretion from streptomycin-resistant B. subtilis mutants. We isolated twenty spontaneous streptomycin resistant mutants from our B. subtilis strain and four spontaneous streptomycin resistant mutants from the B. amyloliquefaciens strain. We investigated the extracellular enzyme and antibiotic production of the mutants. Some of the mutants showed elevated enzyme and antibiotic secretion. The rpsL gene in theses spontaneous streptomycin resistant mutants, were sequenced and point mutations were detected in it, so very likely the changes of the structure of the rpsL protein is responsible in some cases for the elevated enzyme and depsipeptide production.