Antimicrobial resistance (AMR) in aquaculture environments has become an increasing concern due to the dissemination of antibiotic-resistant bacteria in aquatic ecosystems. This study investigated the occurrence of presumptive antimicrobial-resistant bacteria in commercial fish farms in Hajdú-Bihar county, Hungary. Between 2023 and 2024, water samples were collected from fishponds from Hajdúszoboszló, Biharugra, and Debrecen, followed by membrane filtration with 0.45 µm pore size mixed cellulose ester membrane filters, bacterial isolation using selective media including vancomycin-resistant enterococci (VRE) agar, Eosin Methylene Blue (EMB) agar, and Endo’s medium. The phenotypic characterization revealed the presence of diverse bacterial populations that could be associated with potential antimicrobial resistance. Bacterial identification using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) showed several bacterial genera, predominantly Acinetobacter, Pseudomonas, Enterococcus, Bacillus, and Escherichia. A total of 16 presumptive antimicrobial-resistant bacterial isolates recovered from selective media were identified using MALDI-TOF MS. Several detected species, including Acinetobacter baumannii, Pseudomonas aeruginosa, Enterococcus faecium, and Enterococcus faecalis, are recognized as opportunistic bacteria associated with antimicrobial resistance dissemination. The findings demonstrate that aquaculture waters in Hajdú-Bihar county may serve as reservoirs of antimicrobial-resistant bacteria.

Black locust (Robinia pseudoacacia L.) has exceptional growth capacity in nutrient-poor environments and is therefore widely used for afforestation and land reclamation on degraded soils. However, drought stress can restrict sapling growth, which undermines the success of their establishment. The effect of a product containing two endophytic strains (Trichoderma afroharzianum P. Chaverri, F.B. Rocha, Degenkolb & Druzhinina TR04 and Trichoderma simmonsii P. Chaverri, F.B. Rocha, Degenkolb & Druzhinina TR05) was studied on a black locust sapling stand under severe drought in eastern Hungary. The two-year-old saplings were root-soaked before planting in sandy soil. The growth of Trichoderma-treated plants improved by late spring. Compared to the control trees, average height increased by 25.75%, and root collar diameter was 21.96% larger. Treated plants also showed 9.1% higher chlorophyll content and 11.1% Normalized Difference Vegetation Index (NDVI). The reduced intercellular CO2 concentration, together with slightly lower stomatal conductance and increased transpiration rate, suggests tighter stomatal regulation and altered water-use dynamics under drought conditions. These responses indicate improved short-term drought acclimation rather than enhanced carbon assimilation capacity. Pre-planting inoculation with endophytic Trichoderma strains provides a sustainable method to enhance the early establishment and drought resilience of black locust, thereby increasing the efficacy of forest restoration by improving the survival of black locust on challenging degraded sites.

Aquaculture is a key food production sector responsible for meeting the nutritional needs of a rapidly growing global population. However, the emergence of disease outbreaks has become a major challenge for the aquaculture industry, resulting in significant economic losses. The use of costly and toxic antibiotics for treatment has a negative impact on the aquatic environment. Consequently, there has been a growing interest in probiotics as a non-antibiotic approach to manage disease outbreaks and improve fish performance. The use of the yeast Saccharomyces cerevisiae (SC) has shown remarkable benefits in aquaculture. In February 2025, a systematic search was conducted based on the Web of Science (WoS) database for the period 2015–2025 to identify relevant studies investigating the beneficial effects of SC in aquaculture. After searching on WoS, 466 documents were found and analyzed using R-bibliometric package for comprehensive analysis to identify research gap, trends, and distribution of global literature that focuses on SC in aquaculture. The most relevant and recent articles were reviewed, summarized and discussed. The yeast SC have shown a wide range of benefits, including improved growth performance, feed efficiency, enhanced diversity of the gut microbiome and immune response. The implementation of SC is becoming a recent trend and its efficacy in aquatic environments has been thoroughly investigated. This review aims to provide a valuable insight into SC as one of the most important aquaculture probiotics. It also emphasizes the need for further research to fully understand its benefits and the way it works.

Mabroom dates (Phoenix dactylifera L.) are recognized as one of the most important crops in Qatar. Fresh fruit dates are susceptible to mould and post-harvest spoilage, resulting in a significant financial loss. Octanoic fatty acid (OFA) has been shown to regulate the growth of mould-causing organisms such as fungi and bacteria. It is known to have antibacterial properties. The objective of the current study was to evaluate the in vitro effect of OFA on the post-harvest pathogens of Mabroom fruits. Fresh, apparently healthy, and fully ripe Mabroom dates were obtained from the National Agriculture and Food Corporation (NAFCO). The chosen fruits were packed in sterile, well-ventilated plastic boxes and transported to the lab under controlled conditions. The fruits were distributed into five groups (G1 to G5). The groups G1, G2, and G3 received 1%, 2%, and 3.5% OFA, respectively, while G4 was left untreated and G5 was washed only with tap water as a positive control treatment. Each group contained 200 g of fresh and healthy semi-soft dates. The samples were then dried and incubated in a humidity chamber at 25 °C ± 2 for seven days. The signs and symptoms of decay were monitored and recorded. The presence of pathogens was confirmed via phenotypic and microscopic-based methods. The results showed a significant difference (p ≤ 0.05) among the groups. OFA at 3.5% had the strongest inhibitory action against post-harvest pathogens, followed by OFA2%. However, there were no differences (p ≤ 0.05) between OFA1% and the control groups. Aspergillus spp., Penicillium spp., Rhizopus spp., and Botrytis spp. were most abundant in the control group, followed by OFA2% and OFA1%, respectively. In conclusion, octanoic fatty acid at 3.5% may improve the quality of date fruits through its high antimicrobial activity, reduce the effect of post-harvest decay, minimize the loss of date fruits during storage, and improve the sustainability of date fruits. Further experiments are necessary to confirm the effectiveness of OFA as a green solution for sustainable date fruit production.

Antibiotic resistance in aquaculture has emerged as a global crisis, representing a serious threat to the health of aquatic animals, environment, and human. The extensive use of antibiotics in aquaculture has led to rapid development of resistant bacterial strains, resulting in environmental contamination and the dissemination of resistant genes. Understanding of the research trends, key contributors, and thematic evolution of this field is essential for guiding future studies and policy interventions. The study aimed to conduct a bibliometric analysis of research on antibiotic resistance development in aquaculture, identifying key areas of research, leading contributors, emerging challenges, and alternative solutions. Data were extracted from the Web of Science (WoS) database covering the period from 2000 to 2025. A systematic search strategy was employed, utilizing terms including “antibiotic resistance” AND “bacteria,” AND “aquaculture”. Relevant publications were extracted from the WoS using these keywords. R-tool was then used to analyze the obtained metadata including keywords, citation patterns, and co-authored country. The analysis revealed a remarkable increase in publications over the past 25 years, with key contributions from China, India, and the USA. The most significant articles focused on the presence of multidrug resistant bacteria in the aquatic environments and, antibiotic-resistant genes, and horizontal gene transfer. Probiotics are the alternative solution to overcome the antibiotic resistance and enhance aquaculture sustainability. Future research should focus on the interdisciplinary collaboration, novel antimicrobial alternatives, and global monitoring approaches.

Walnut (Juglans regia L.) fruit rot significantly impacts yield and quality, yet the pathogens responsible for it remain insufficiently characterized. In this study, we identified several fungi associated with the disease and characterized their morphology and physiology. Pathogenicity tests at two developmental stages of the walnut fruit were performed for the newly described pathogen. Among the Botrytis, Alternaria, and Penicillium species, Botrytis cinerea sensu lato stands out as a newly identified pathogen of the cultivated walnut. Growth assessments revealed variability in B. cinerea strains, with consistent patterns found across different temperatures. Pathogenicity of the isolated B. cinerea strains differed: one strain caused husk necrosis, three strains caused kernel necrosis in younger fruits, while two strains induced kernel necrosis in the later developmental stages. Additionally, we evaluated the biocontrol potential of Trichoderma strains against B. cinerea and demonstrated their efficiency in suppressing each isolated B. cinerea strain (76–100% inhibition), highlighting their potential in sustainable disease management in walnut production.

The aim of this study was to determine the levels of deoxynivalenol (DON) and fumonisin mycotoxins in tillage and no-till systems in 2020 and 2021. Additionally, we sought to establish the levels of internal Fusarium infection in different tillage systems. We examined four tillage systems for two years (conventional tillage (plowing), conservation tillage, reduced tillage, and strip-till). The results indicate that toxin levels varied between the two years, with fumonisin production dominant in 2021, while DON toxin production was dominant in 2020. Regarding internal Fusarium infection, the lowest levels were observed in the plowing system in 2020, whereas in 2021, the lowest levels were measured in the reduced tillage system. Like the low DON levels in 2020, the plowing-based tillage system resulted in the lowest fumonisin levels in 2021. Throughout our experiment, the toxin levels were below the permissible limits for unprocessed corn, with DON levels under 1750 μg kg-1 and combined fumonisin B1 and B2 levels under 4000 μg kg-1. However, in areas where toxin contamination is typically problematic, considering the beneficial impact of plowing on reducing toxin contamination might be advisable when planning tillage.

Sour cherry is a non-climacteric fruit that quickly loses its quality after harvest, so effective storage and packaging are essential to minimize postharvest decay. Our study aimed to (i) evaluate fruit decay incidence during shelf-life for both freshly harvested and six-week-cold-stored sour cherry fruits, comparing normal atmospheric conditions with modified atmosphere packaging across three sour cherry cultivars (‘Érdi bőtermő’, ‘Újfehértói fürtös’, and ‘Petri’); and (ii) assess postharvest fruit decay incidence across the following three production systems: conventional, integrated pest management (IPM), and reduced IPM, for the cultivar ‘Érdi bőtermő’. The results showed that modified atmosphere packaging effectively preserved or slightly increased fruit firmness (ranging from 27.1 to 46%) compared to control fruits across all cultivars. Fruit weight loss (ranging from 1.18 to 26.1%) was also significantly reduced under modified atmosphere packaging compared to normal atmospheric storage. Over a 14-day period, the decay incidence of harvested fruits consistently increased, with major losses from day 6 onward (ranging from 17.7 to 77.0% at shelf-life day 14) across all cultivars and years. After six weeks of normal atmospheric cold storage, decay incidence remained low (ranging from 0 to 9.4%) and was comparable across all cultivars. Both normal atmospheric and modified atmosphere packaging storage maintained sour cherry quality during cold storage, but the shelf-life of the fruits was significantly shorter at room temperature, regardless of the storage methods. Fruit decay incidence at harvest was highest in the reduced IPM system (ranging from 3.2 to 6.4%), significantly exceeding those observed in the conventional and IPM systems. In post-MAP cold storage, decay incidence followed the following order: conventional < IPM < reduced IPM, with significant differences observed only between the conventional and reduced IPM systems. In conclusion, our results suggest that sour cherries produced under conventional or IPM systems and stored in modified atmosphere packaging offer an effective postharvest strategy for preserving fruit quality.

AbstractThe acreage of English walnut (Juglans regia L.) is constantly expanding in Hungary, due to the favorable climatic conditions and economic importance. Last years, serious damage was reported from several orchards with high percentage of rotted, moldy kernels. The aim of this research was to identify the pathogens at different growth stages. Fungi were cultured from the spotty, shriveled and rotted kernels, and monosporic isolates were identified based on morphological characters and molecular markers (ITS region and tef1 locus sequences). Botryosphaeria dothidea and Diaporthe eres were identified in high proportion from symptomatic kernels. These species were also isolated from different parts of walnut trees in different seasons. D. eres was detected in a high proportion from asymptomatic buds in March, while the presence of both species was observed in symptomatic husks with Overnight Freezing-Incubation Technique (ONFIT) in June. Their optimal growth temperature defined to be between 20–25 °C, and the growth of D. eres isolates was completely inhibited at 35 °C.

Walnut (Juglans regia L.) production is a developing sector in Hungarian horticulture, where preharvest fruit rot increasingly causes economic losses. Previously, fungi from the Diaporthaceae and Botryosphaeriaceae families were isolated with a high incidence from rotten fruits. Here, we identify these pathogens from different plant parts (twigs, buds, and shoots) in orchards in the north-east of Hungary, and test their pathogenicity on immature nuts. Diaporthe eres Nitschke and Diplodia seriata De Notaris were identified in isolates from different symptomatic and asymptomatic plant parts based on their ITS (nuclear ribosomal internal transcribed spacer) and tef1 (translation elongation factor EF-1-alpha gene) DNA sequences. Purified monocultures caused rot of immature nuts following in vitro inoculation. Our results suggest that D. eres Nitschke and D. seriata De Notaris lingering on buds and overwintering woody parts may affect the seasonal nuts through wound infection. Infection by Diaporthe and Botryosphaeriaceae species present on woody plant parts, as well as on/in buds has been reported in Mediterranean countries. This is the first report of such stepwise aetiology from a region with continental weather. Climate change, associated weather patterns and the limitations of fungicide use in the European Union, among other factors, could be responsible for the increasing number of infections and economic damage caused by these pathogens.

In the first part of this two-piece publication, the isolation, identification and in vitro characterization of ten endophytic Trichoderma isolates were reported. Here we report the ability of two different mixes of some of these isolates (Trichoderma simmonsii, Trichoderma orientale and Trichoderma gamsii as well as of Trichoderma afroharzianum and T. simmonsii) to colonize and stimulate the growth of grapevines. Two commercial vineyards about 400 km away from the site of isolation were used as experimental fields, from which the strains of three Trichoderma species were re-isolated up to four years after rootstock soaking treatment with conidiospores, performed before planting. The treatments decreased the overall percentage of lost plants of about 30%, although a low number of lost plants (about 5%) were observed also in the control plot. For all cultivars and clones, the Trichoderma treatments significantly increased both the bud burst ratio and bud burst vigor index. In addition, the grape must parameters such as the Brix degrees, as well as the extract, the D-glucose and the D-fructose concentrations all appeared to be improved, suggesting a potentially higher ethanol content of the produced wine. We conclude that grapevine-endophytic Trichoderma isolates promote plant growth, which could be a useful feature for sustainable agriculture in general and integrated plant production in particular.

This paper reports on the identification and in vitro characterization of several Trichoderma strains isolated from the Tokaj Wine Region in North-East Hungary. Ten isolates were analyzed and found to consist of six individual species—T. gamsii, T. orientale, T. simmonsii, T. afroharzianum, T. atrobrunneum and T. harzianum sensu stricto. The growth potential of the strains was assessed at a range of temperatures. We also report here on the in vitro biocontrol properties and fungicide tolerance of the most promising strains.

In this research, our aim was to assess the occurrence of Staphylococcus aureus in a Hungarian large-scale dairy farm during the S. aureus control program conducted in the course of our studies. Furthermore, the phenotypic and genotypic properties of the isolates (type of haemolysis, antibiotic susceptibility, staphylococcal enterotoxin (SE) gene carrying ability and spa type) were determined. S. aureus was detected in all bulk tank milk samples collected during this study. Two different spa types were identified among the 17 strains isolated in the farm. A total of 14 of the 17 studied strains (82%) showed β-haemolysis on blood agar, 2/17 strains (12%) expressed double zone and 1/17 strains (6%) showed weak β-haemolysis. All strains were susceptible to most antibiotics tested (cefoxitin, chloramphenicol, clindamycin, erythromycin, gentamicin, tetracycline and trimethoprim/sulphamethoxazole), but all strains were resistant to penicillin G. A total of 11 of the 17 strains (65%) were found to harbour seg, sei, selm, seln, selo genes; 4/17 strains (24%) harboured sei, selm, seln, selo genes and 2/17 strains (11%) harboured sei gene. Since the new SEs/SEls can also cause foodborne outbreaks potentially and all strains were found to be resistant to penicillin G, it is essential to decrease and keep the prevalence of S. aureus low in the dairy farm and the implementation of the S. aureus control program is also highly justified. The results showed that the S. aureus count decreased by the end of our studies, so the control program was proved to be effective.

DNA extraction from minute fungal samples is challenging in all genetic studies. Identification of genetic groups and population biology mostly rely on the laborious production of single conidium isolates or on field samples, including infected plant materials. This paper reports a simple and cost-effective protocol for DNA extraction from individual chasmothecia of Erysiphe necator for subsequent applications. It is a less laborious alternative for genotyping purposes than production and analysis of single conidium isolates or analysis of infected plant material from the field. Using the protocols described here for 186 E. necator samples tested, genetic groups A and B were assigned. Based on CYP51 sequences, all the samples belonged to group B, while TUB2 sequences exhibited SNPs also diagnostic for group A. Additionally, a quantitative real-time PCR detection method of single nucleotide polymorphism in the CYP51 gene associated with DMI fungicide resistance was applied. The A495T marker, associated with DMI resistance, and here reported for the first time from Hungary, was detected by quantitative real-time PCR assays and direct sequencing of CYP51. The methods developed in this study can be applied as routine tests to monitor powdery mildew populations for fungicide resistance and other genetic characteristics.

Sexual reproduction is a general feature in higher eukaryotes, although the genetic machinery to produce sexually derived offspring can be very different. Contrary to the megabase-sized sexual chromosomes of animals, fungal genomes harbour much shorter sequences located at the MAT locus which governs the mating processes. For heterothallic fungi, the two mating-types are characterised by the presence of either of the two idiomorphs of the MAT locus, MAT-1 or MAT-2, while homothallic species may contain both MAT idiomorphs. The black mould Aspergillus niger is known as an asexual species, but some related presumed asexual species have recently been shown to have a cryptic sexual cycle. The scope of this work was to screen for and compare mating and meiosis related genes in the two sequenced A. niger genomes and to compare them to those in related Aspergilli. The MAT-1 mating type gene was found in both sequenced A. niger strains, a MAT-2 homologue was not detected in either, indicating that this species is either heterothallic or truly asexual. In comparison, the sequenced homothallic A. nidulans genome contains both MAT genes on different chromosomes, whereas the A. fumigatus, A. oryzae, and A. terreus genomes contain one MAT gene per sequenced genome. Many of the proteins known from Saccharomyces cerevisiae to be involved in meiosis proved well conserved in all five tested sexual and presumed asexual Aspergillus species. The Aspergilli also proved to have very similar sets of pheromone processing and response pathway proteins. Comparison of the two A. niger genomes for their gene sets show that many of these proteins may have essential pleiotropic functions next to mating and meiosis.

Heterokaryon incompatibility among Aspergillus niger strains is a widespread phenomenon that is observed as the inability to form stable heterokaryons. The genetic basis of heterokaryon incompatibility reactions is well established in some sexual filamentous fungi but largely unknown in presumed asexual species, such as A. niger. To test whether the genes that determine heterokaryon incompatibility in Neurospora crassa, such as het-c, vib-1 and pin-c, have a similar function in A. niger, we performed a short in silico search for homologues of these genes in the A. niger and several related genomes. For het-c, pin-c and vib-1 we did indeed identify putative orthologues. We then screened a genetically diverse worldwide collection of incompatible black Aspergilli for polymorphisms in the het-c orthologue. No size variation was observed in the variable het-c indel region that determines the specificity in N. crassa. Sequence comparison showed only minor variation in the number of glutamine coding triplets. However, introduction of one of the three N. crassa alleles (het-c2) in A. niger by transformation resulted in an abortive phenotype, reminiscent of the heterokaryon incompatibility in N. crassa. We conclude that although the genes required are present and the het-c homologue could potentially function as a heterokaryon incompatibility gene, het-c has no direct function in heterokaryon incompatibility in A. niger because the necessary allelic variation is absent.

Herman J Pel1, Johannes H de Winde1,2, David B Archer3, Paul S Dyer3, Gerald Hofmann4, Peter J Schaap5, Geoffrey Turner6, Ronald P de Vries7, Richard Albang8, Kaj Albermann8, Mikael R Andersen4, Jannick D Bendtsen9, Jacques A E Benen5, Marco van den Berg10, Stefaan Breestraat1, Mark X Caddick11, Roland Contreras12, Michael Cornell13, Pedro M Coutinho14, Etienne G J Danchin14, Alfons J M Debets15, Peter Dekker1, Piet W M van Dijck1, Alard van Dijk1, Lubbert Dijkhuizen16,17, Arnold J M Driessen17, Christophe d’Enfert18, Steven Geysens12, Coenie Goosen16,17, Gert S P Groot1, Piet W J de Groot19, Thomas Guillemette20, Bernard Henrissat14, Marga Herweijer1, Johannes P T W van den Hombergh1, Cees A M J J van den Hondel21, Rene T J M van der Heijden22, Rachel M van der Kaaij16,17, Frans M Klis19, Harrie J Kools5, Christian P Kubicek23, Patricia A van Kuyk21, Jürgen Lauber24, Xin Lu25, Marc J E C van der Maarel16, Rogier Meulenberg1, Hildegard Menke1, Martin A Mortimer11, Jens Nielsen4, Stephen G Oliver13, Maurien Olsthoorn1, Karoly Pal15,26, Noël N M E van Peij1, Arthur F J Ram21, Ursula Rinas25, Johannes A Roubos1, Cees M J Sagt1, Monika Schmoll23, Jibin Sun25, David Ussery27, Janos Varga26,28, Wouter Vervecken12, Peter J J van de Vondervoort21, Holger Wedler24, Han A B Wösten7, An-Ping Zeng25, Albert J J van Ooyen1, Jaap Visser29 & Hein Stam1

The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis.

Fungal polyketide synthases are responsible for the biosynthesis of several mycotoxins and other secondary metabolites. The aim of our work was to investigate the diversity of polyketide synthases in Aspergillus species using two approaches: PCR amplification using oligonucleotide primers, and bioinformatics. Ketosynthase domain probes amplified DNA fragments of about 700 bp in each examined isolate. Sequences of these domains were aligned and analyzed by phylogenetic methods. The ketosynthase domain sequences were highly diverse indicating that they most probably represent polyketide synthases responsible for different functions. A. albertensis and A. niger ketosynthase domain sequences clustered together with sequences of genes required for pigment biosynthesis (wA) in A. nidulans and P. patulum, while the ketosynthase domain sequence of A. muricatus was most closely related to an A. parasiticus wA type domain sequence, and those of the A. ochraceus isolates formed a distinct clade on the tree. These sequences were highly homologous to an A. terreus naphthopyrone synthase gene. An Aspergillus fumigatus genomic database was also searched for ketosynthase domain sequences, which have been included in the phylogenetic analysis. Altogether 14 putative ketosynthase domain sequences were identified. Clustering of the ketosynthase domain sequences correlated well with the type of metabolites produced by the corresponding polyketide synthases. At least 8 clusters with putative ketosynthase domain sequences of unknown function have been identified. Further studies are in progress to clarify the role of some of the identified polyketide synthase genes.