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The rhizosphere soil properties and microbial communities of Lilium tsingtauense , an endangered wild plant, have not been examined in previous studies. Here, we characterized spatial variation in soil properties and microbial communities in the rhizosphere of L. tsingtauense . We measured the abundance of L. tsingtauense at different altitudes and collected rhizosphere and bulk soils at three representative altitudes. The results showed that L. tsingtauense was more abundant, and the rhizosphere soil was richer in nitrogen, phosphorus, potassium, water content, and organic matter and more acidic at high altitudes than at lower altitudes. The diversity and richness of rhizosphere bacteria and fungi increased with altitude and were higher in rhizosphere soil than in bulk soil. In addition, ectomycorrhizal fungi, endophytic fungi, and nitrogen-fixing bacteria were more abundant, and plant-pathogenic fungi were less abundant at high altitudes. Co-occurrence network analysis identified four key phyla (Bacteroidota, Proteobacteria, Ascomycota, and Basidiomycota) in the microbial communities. We identified a series of microbial taxa (Acidobacteriales, Xanthobacteraceae, and Chaetomiaceae) and rhizosphere soil metabolites (phosphatidylcholine and phosphatidylserine) that are crucial for the survival of L. tsingtauense . Correlation analysis and random forest analysis showed that some environmental factors were closely related to the rhizosphere soil microbial community and played an important role in predicting the distribution and growth status of L. tsingtauense . In sum, the results of this study revealed altitudinal variation in the rhizosphere microbial communities of L. tsingtauense and the factors driving this variation. Our findings also have implications for habitat restoration and the conservation of this species., Importance: Our study highlighted the importance of the rhizosphere microbial community of the endangered plant L. tsingtauense . We found that soil pH plays an important role in the survival of L. tsingtauense . Our results demonstrated that a series of microbial taxa (Acidobacteriales, Xanthobacteraceae, Aspergillaceae, and Chaetomiaceae) and soil metabolites (phosphatidylcholine and phosphatidylserine) could be essential indicators for L. tsingtauense habitat. We also found that some environmental factors play an important role in shaping rhizosphere microbial community structure. Collectively, these results provided new insights into the altitudinal distribution of L. tsingtauense and highlight the importance of microbial communities in their growth., Competing Interests: The authors declare no conflict of interest.

Mycotoxin-producing fungi are widespread and their adverse effects on mammals have been investigated; however, their impacts on soil invertebrates are not fully understood. Folsomia candida is a model soil arthropod that represents an important part of the soil invertebrate community. This study investigated the consequences of F. candida grazing on mycotoxin-producing fungi Fusarium verticillioides , F. graminearum , Aspergillus ochraceus , and A. nidulans . Consuming mycotoxin-producing fungi affected the body size and reproductive ability of F. candida , and altered the gut bacterial composition, with decreased Proteobacteria and increased Actinobacteria ( Microbacterium ) abundances. Notably, the abundance of foodborne fungi can be detected. Furthermore, certain bacteria isolated from F. candida 's gut inhibited the growth of corresponding mycotoxin-producing fungi. The gut bacteria that inhibited mycotoxin-producing fungi growth in Aspergillus groups were also associated with poor fitness parameters and larger disruption in gut microbiota. Importantly, switching back to yeast diets reversed both the fitness parameters and gut bacterial composition. Together, our study demonstrated that grazing of mycotoxin-producing fungi by F. candida resulted in reduced physiological parameters and disturbed the gut bacterial community, and those changes can be restored by switching back to yeast diets, which indicates a strong resilience of springtails to mycotoxin-producing fungi., Importance: Mycotoxin-producing fungi are widespread in nature and raise concerns for human and livestock health. Although they share the same ecosystem, interactions between mycotoxin-producing fungi and soil arthropods are not well understood. In this study, we report an unexpected finding that the soil arthropod Folsomia candida is rather tolerant to these mycotoxin-producing fungi. F. candida can survive solely on mycotoxin-producing fungi as a food source with reduced physiological parameters. Moreover, the gut microbial community is disturbed by mycotoxin-producing fungi, and some of the bacteria isolated from F. candida 's gut can inhibit the growth of corresponding fungi. Notably, the altered physiological parameters and gut microbiota are restored when a normal diet is reintroduced, suggesting F. candida 's resilience to mycotoxin-producing fungi. These findings clarify the impact of toxin-producing diets on F. candida , shedding light on how organisms can build resilience to environmental stimuli., Competing Interests: The authors declare no conflict of interest.

Abdominal aortic aneurysm (AAA) is a large-vessel disease with high mortality, characterized by complex pathogenic mechanisms. Current therapeutic approaches remain insufficient to halt its progression. Fungi are important members of the gut microbiota. However, their characteristic alterations and roles in AAA remain unclear. This study investigated the role of gut fungal communities in the development of AAA through metagenomic sequencing of fecal samples from 31 healthy individuals and 33 AAA patients. We observed significant dysbiosis in the gut mycobiomes of AAA patients compared to healthy individuals, characterized by an increase in pathogenic fungi like Candida species and a decrease in beneficial yeasts such as Saccharomyces cerevisiae . The changes in fungal populations correlated strongly with clinical indicators of AAA, highlighting their potential for diagnosing and predicting AAA progression. Furthermore, our animal experiments demonstrated that Saccharomyces cerevisiae significantly ameliorated pathological alterations in AAA mice, suggesting a protective role for specific yeast strains against AAA development. These findings underscore the significant impact of gut mycobiomes on AAA and suggest that modulating these fungal communities could offer a novel therapeutic approach. Our research advances the understanding of the influence of gut microbiome on vascular diseases and suggests potential non-surgical approaches for managing AAA. By elucidating the diagnostic and therapeutic potential of gut fungi in AAA, this study provided important clues for future clinical strategies and therapeutic developments in the field of vascular medicine., Importance: Our research highlights the crucial role of gut fungi in abdominal aortic aneurysm (AAA) development. By analyzing fecal samples from AAA patients and healthy controls, we discovered significant dysbiosis in gut fungal communities, characterized by an increase in harmful Candida species and a decrease in beneficial yeasts like Saccharomyces cerevisiae . This dysbiosis was correlated with the severity of AAA. Importantly, in animal experiments, supplementing with Saccharomyces cerevisiae significantly slowed AAA progression. These findings suggest that modulating gut fungi may offer a novel, non-surgical approach to the diagnosis and treatment of AAA, potentially reducing the need for invasive procedures., Competing Interests: The authors declare no conflict of interest.

The endophyte is closely related to medicinal plant growth and development, stress resistance, and active ingredients' accumulation. However, a seasonal succession of endophytes and the association with active ingredients is still unclear. In this study, we used high-throughput sequencing methods to compare the endophyte diversity of Rheum palmatum under different seasons and analyze the association between endophytes and five active ingredients. The results show that the diversity of endophytic fungi increased and then decreased, while bacterial diversity increased with the change of season. Community composition showed that the dominant genera of endophytic fungi were different under the different seasons, while the dominant genera of endophytic bacteria were Delftia . Analysis of co-occurrence network maps showed that the connectivity and complexity of endophytic fungi and bacterial networks decreased with the change of season. Spearman analysis indicated that the active ingredients of R. palmatum were significantly positive correlation with genera of endophytic fungi ( Chalara ). FUNGuild and PICRUSt predictive analysis indicated that the function of endophytic fungi and bacteria, respectively, were symbiotroph and metabolism, and relative abundances were different under the different seasons. Our results help elucidate the mechanism of medicinal plant-endophyte interaction., Importance: Through the investigation of the seasonal succession of endophytes and the association with active ingredients in Rheum palmatum , we found that the diversity and composition of endophytes in R. palmatum exhibited seasonal dynamics, and the active ingredients of R. palmatum showed a significantly positive correlation with the genus of endophytic fungi ( Chalara ). Our results may lay a foundation for understanding the interaction mechanism of endophyte and medicinal plant, and can also provide a theoretical basis for sustainable production of medicinal plants., Competing Interests: The authors declare no conflict of interest.

Background/objective: Abortions in livestock herds are a major contributor to economic losses. The incidence of fungal aetiology has been reported thus far. The purpose of this study is to investigate the prevalence of abortions due to fungi in referred cases to the Center of Excellence in Ruminant Abortion and Neonatal Mortality, Veterinary Hospital of Ferdowsi University of Mashhad, Mashhad, Iran, from different provinces of Iran., Methods: A total of 200 calves were referred between 2018 and 2022. Samples were taken from the lungs, liver, spleen and abomasum. The fungi present in the cultures were analysed microscopically and morphologically., Results: There were varying contamination levels in the liver, spleen and lungs, with prevalence ranging from 15% to 17%. Abdomasum had a 1% prevalence rate. Different fungal species, including Cryptococcus neoformans (C. neoformans), Aspergillus spp., Rhodotorula spp., Trichosporon spp., Candida spp., Geotrichum spp., Penicillium spp. and Mucor spp., were identified, indicating a diverse range of pathogens affecting calves. The specificity of fungal contaminants in certain organs, such as C. neoformans, Rhodotorula spp. and Trichosporon spp., highlighted the organ's microenvironment as a potential factor influencing fungal growth., Conclusion: As fungi are emerging as a significant cause of morbidity and mortality in animals, the growing role of fungi in livestock abortions should be investigated. As clinical signs are not pathognomonic, laboratory help is imperative to confirm fungal abortion diagnosis., (© 2024 The Author(s). Veterinary Medicine and Science published by John Wiley & Sons Ltd.)

Diet is an important component to influence microbiota, there are less data available about the microbiome of Suffolk cross with Tibetan (SCT) animals with different fodders. The current study was conducted for comparing the fungi microbiota in SCT sheep fed with different forages. Sequencing of ileum samples from sheep groups of AH (alfalfa and oat grass), BH (mixture of grass and concentrated feeds), CH (concentrated feed I), DH (concentrated feed II) and EH (concentrated feed III) achieved 3,171,271 raw and 2,719,649 filtered sequences. Concentrated feeds changed fungi microbiota in SCT sheep with three phyla and 47 genera significantly different among the groups. Genera include positive genus of Scytalidium and negative fungi of Sarocladium , Kazachstania , Gibberella , Scytalidium , Candida , Wickerhamomyces . The findings of our study will contribute to efficient feeding of SCT sheep at cold plateau areas.

Background: Extensive research on the diversity and functional roles of the microorganisms associated with reef-building corals has been promoted as a consequence of the rapid global decline of coral reefs attributed to climate change. Several studies have highlighted the importance of coral-associated algae (Symbiodinium) and bacteria and their potential roles in promoting coral host fitness and survival. However, the complex coral holobiont extends beyond these components to encompass other entities such as protists, fungi, and viruses. While each constituent has been individually investigated in corals, a comprehensive understanding of their collective roles is imperative for a holistic comprehension of coral health and resilience., Results: The metagenomic analysis of the microbiome of the coral Oculina patagonica has revealed that fungi of the genera Aspergillus, Fusarium, and Rhizofagus together with the prokaryotic genera Streptomyces, Pseudomonas, and Bacillus were abundant members of the coral holobiont. This study also assessed changes in microeukaryotic, prokaryotic, and viral communities under three stress conditions: aquaria confinement, heat stress, and Vibrio infections. In general, stress conditions led to an increase in Rhodobacteraceae, Flavobacteraceae, and Vibrionaceae families, accompanied by a decrease in Streptomycetaceae. Concurrently, there was a significant decline in both the abundance and richness of microeukaryotic species and a reduction in genes associated with antimicrobial compound production by the coral itself, as well as by Symbiodinium and fungi., Conclusion: Our findings suggest that the interplay between microeukaryotic and prokaryotic components of the coral holobiont may be disrupted by stress conditions, such as confinement, increase of seawater temperature, or Vibrio infection, leading to a dysbiosis in the global microbial community that may increase coral susceptibility to diseases. Further, microeukaryotic community seems to exert influence on the prokaryotic community dynamics, possibly through predation or the production of secondary metabolites with anti-bacterial activity. Video Abstract., (© 2024. The Author(s).)

Bats are known reservoirs for a wide range of pathogenic microorganisms, including viruses, bacteria, fungi, helminths, and protozoa, which can be transmitted and infect other zoonotic organisms. Various studies have utilised next-generation sequencing (NGS) to describe the pathogens associated with bats. Although most have characterised microbial communities in specific body fluids, few have analysed the composition and diversity of these microbial communities across different body fluids at the individual level. In this study, we employed two next-generation sequencing techniques: amplicon-based sequencing of the V4 hypervariable region of the 16S- and 18S-rRNA genes and viral metagenomics, to describe the prokaryotic, eukaryotic, and viral communities present in blood, faeces, and oral swab samples collected from two genera of bats (Carollia and Phyllostomus) in the department of Casanare, eastern Colombia. A total of 60 samples corresponding to the three bodily fluids were processed and analysed. The results indicated that the microbial communities across the body fluids were mainly composed of bacteria, fungi, protozoa, and various DNA and RNA viruses, showing a variability of microbial genera and species. The abundances, diversity metrics, and correlations of these microorganisms displayed patterns associated with bat genus and body fluids, suggesting that the ecological characteristics of these microbial communities may be influenced by the ecological and physiological traits of the bats. Additionally, we found similar community compositions of bacteria, some fungal genera, and viruses in the three body fluids, indicating a possible circulation of these microbes within the same bat. This could be due to microbial movement from the gut microbiota to other physiological systems or transmission via blood-feeding vectors. Furthermore, our results revealed the presence of various microbes of public health concern, including Bartonella spp., Mannheimia haemolytica, Rhodotorula spp., Piroplasmida spp., Toxoplasma gondii, Alphacoronavirus spp., and Bat circovirus. The abundance of these pathogenic microbial species across the three bodily fluids suggests potential transmission routes from bats to other organisms, which may contribute to the emergence of zoonotic disease outbreaks. These findings highlight the variability of microorganisms present within the same bat and the different pathogen-host interactions that may regulate the presence and transmission of these zoonotic microbes. Further research is required to elucidate the genomic features, ecological interactions, and biological activities of these microbial communities in bats., (© 2024. The Author(s).)

Biodiversity, the source of origin, and ecological roles of fungi in groundwater are to this day a largely neglected field in fungal and freshwater ecology. We used DNA-based Illumina high-throughput sequence analysis of both fungal gene markers 5.8S and internal transcribed spacers region 2 (ITS2), improving taxonomic classification. This study focused on the groundwater and river mycobiome along an altitudinal and longitudinal transect of a pre-alpine valley in Austria in two seasons. Using Bayesian network modeling approaches, we identified patterns in fungal community assemblages that were mostly shaped by differences in landscape (climatic, topological, and geological) and environmental conditions. While river fungi were comparatively more diverse, unique fungal assemblages could be recovered from groundwater, including typical aquatic lineages such as Rozellomycota and Olpidiomycota. The most specious assemblages in groundwater were not linked to the input of organic material from the surface, and as such, seem to be sustained by characteristic groundwater conditions. Based on what is known from closely related fungi, our results suggest that the present fungal communities potentially contribute to mineral weathering, carbon cycling, and denitrification in groundwater. Furthermore, we were able to observe the effects of varying land cover due to agricultural practices on fungal biodiversity in groundwater ecosystems. This study contributes to improving our understanding of fungi in the subsurface aquatic biogeosphere., (© The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.)

Mt. Erebus, Antarctica, is the southernmost active volcano in the world and harbors diverse geothermally unique ecosystems, including "Subglacial" and "Exposed" features, surrounded by a vast desert of ice and snow. Previous studies, while limited in scope, have highlighted the unique and potentially endemic biota of Mt. Erebus. Here, we provide an amplicon-based biodiversity study across all domains of life and all types of geothermal features, with physicochemical and biological data from 48 samples (39 Exposed and 9 Subglacial) collected through various field seasons. We found potentially high taxonomic novelty among prokaryotes and fungi, supporting past hypotheses of high endemism due to the distinctive and isolated environment; in particular, the large number of taxonomically divergent fungal sequences was surprising. We found that different site types had unique physicochemistry and biota; Exposed sites were warmer than Subglacial (median: 40°C versus 10°C for Exposed and Subglacial, respectively) and tended to have more photosynthetic organisms (Cyanobacteria and Chlorophyta). Subglacial sites had more Actinobacteriota, correlated with greater concentrations of Ca and Mg present. Our results also suggest potential human impacts on these remote, highly significant sites, finding evidence for fungal taxa normally associated with wood decay. In this study, we provide a blueprint for future work aimed at better understanding the novel biota of Mt. Erebus., (© The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.)

Paphiopedilum armeniacum, Paphiopedilum wenshanense and Paphiopedilum emersonii are critically endangered wild orchids. Their populations are under severe threat, with a dramatic decline in the number of their natural distribution sites. Ex situ conservation and artificial breeding are the keys to maintaining the population to ensure the success of ex situ conservation and field return in the future. The habitat characteristics and soil nutrient information of the last remaining wild distribution sites of the three species were studied. ITS high-throughput sequencing was used to reveal the composition and structure of the soil fungal community, analyze its diversity and functional characteristics, and reveal its relationship with soil nutrients. The three species preferred to grow on low-lying, ventilated and shaded declivities with good water drainage. There were significant differences in soil alkali-hydrolyzed nitrogen and available phosphorus among the three species. There were 336 fungal species detected in the samples. On average, there were different dominant groups in the soil fungal communities of the three species. The functional groups of soil fungi within their habitats were dominated by saprophytic fungi and ectomycorrhizae, with significant differences in diversity and structure. The co-occurrence network of habitat soil fungi was mainly positive. Soil pH significantly affected soil fungal diversity within their habitats of the three paphiopedilum species. The study confirmed that the dominant groups of soil fungi were significantly correlated with soil nutrients. The three species exhibit comparable habitat inclinations, yet they display substantial variations in the composition, structure, and diversity of soil fungi. The fungal functional group is characterized by a rich presence of saprophytic fungi, a proliferation of ectomycorrhizae, and a modest occurrence of orchid mycorrhizae. The symbiotic interactions among the soil fungi associated with these three species are well-coordinated, enhancing their resilience against challenging environmental conditions. There is a significant correlation between soil environmental factors and the composition of soil fungal communities, with pH emerging as a pivotal factor regulating fungal diversity. Our research into the habitat traits and soil fungal ecosystems of the three wild Paphiopedilum species has established a cornerstone for prospective ex situ conservation measures and the eventual reestablishment of these species in their native landscapes., (© 2024. The Author(s).)

To understand the microbial diversity and community composition within the main constructive tree species, Picea crassifolia, Betula platyphylla, and Pinus tabuliformis, in Helan Mountain and their response to changes in soil physicochemical factors, a high throughput sequencing technology was used to analyze the bacterial and fungal diversity and community structure. RDA (Redundancy Analysis) and Pearson correlation analysis were used to explore the influence of soil physicochemical factors on microbial community construction, and co-occurrence network analysis was conducted on the microbial communities. The results showed that the fungal and bacterial diversity was highest in B. platyphylla, and lowest in P. crassifolia. Additionally, the fungal/bacterial richness was greatest in the rhizosphere soils of P. tabuliformis and B. platyphylla. RDA and Pearson correlation analysis revealed that NN (nitrate nitrogen) and AP (available phosphorus) were the main determining factors of the bacterial community, while NN and SOC (soil water content) were the main determining factors of the fungal community. Pearson correlation analysis between soil physicochemical factors and the alpha diversity of the microbial communities revealed a significant positive correlation between pH and the bacterial and fungal diversity, while SOC, TN (total nitrogen), AP, and AN (available nitrogen) were significantly negatively correlated with the bacterial and fungal diversity. Co-occurrence network analysis revealed that the soil bacterial communities exhibit richer network nodes, edges, greater diversity, and greater network connectivity. Indicating that bacterial communities exhibit more complex and stable interaction patterns in soil. This study reveals the complex interactive relationship between microbial communities and soil physicochemical factors in forest ecosystems. By analyzing the response of rhizosphere microbial communities of major tree species in Helan Mountain to nutrient dynamics and pH changes, we can deepen our understanding of the role of microorganisms in regulating ecosystem functions and provide theoretical basis for soil improvement and ecological restoration strategies., (© 2024. The Author(s).)

Background: While substantial research has explored rhizosphere and phyllosphere microbiomes, knowledge on flower microbiome, particularly in wild plants remains limited. This study explores into the diversity, abundance, and composition of bacterial and fungal communities on leaves and flowers of wild flowering plants in their natural alpine habitat, considering the influence of environmental factors., Methods: We investigated 50 wild flowering plants representing 22 families across seven locations in Austria. Sampling sites encompassed varied soil types (carbonate/silicate) and altitudes (450-2760 m). Amplicon sequencing to characterize bacterial and fungal communities and quantitative PCR to assess microbial abundance was applied, and the influence of biotic and abiotic factors assessed., Results: Our study revealed distinct bacterial and fungal communities on leaves and flowers, with higher diversity and richness on leaves (228 fungal and 91 bacterial ASVs) than on flowers (163 fungal and 55 bacterial ASVs). In addition, Gammaproteobacteria on flowers and Alphaproteobacteria on leaves suggests niche specialization for plant compartments. Location significantly shaped both community composition and fungal diversity on both plant parts. Notably, soil type influenced community composition but not diversity. Altitude was associated with increased fungal species diversity on leaves and flowers. Furthermore, significant effects of plant family identity emerged within a subset of seven families, impacting bacterial and fungal abundance, fungal Shannon diversity, and bacterial species richness, particularly on flowers., Conclusion: This study provides novel insights into the specific microbiome of wild flowering plants, highlighting adaptations to local environments and plant-microbe coevolution. The observed specificity indicates a potential role in plant health and resilience, which is crucial for predicting how microbiomes respond to changing environments, ultimately aiding in the conservation of natural ecosystems facing climate change pressures., (© 2024. The Author(s).)

Background: Studies have shown that changes in the frequency of oral microorganisms may play a key role in the development of Alzheimer's disease (AD). However, no research has been conducted on the oral fungal composition in AD-patients. The present study aimed to investigate the changes in the frequency of oral fungal composition, the antifungal susceptibility, and the enzymatic profiles of oral fungal composition in patients suffering from AD compared to non-AD individuals., Materials and Methods: In the present analytical cross-sectional study during 12 months, 76 hospitalized patients with AD were matched with 76 individuals without AD. A sterile serum physiology-moistened cotton-tipped swab was used to sample the mouth area. All swabs were cultured on Sabouraud Chloramphenicol Agar. Fungal identified were confirmed through the PCR-sequencing techniques. Enzyme activity index (EAI) for important pathogenic factors including proteinase, esterase and hemolysin was measured using relevant protocols. The susceptibility to 8 antifungal agents (nystatin, voriconazole, itraconazole, fluconazole, posaconazole, amphotericin B, 5-fluorocytosine, and caspofungin) against fungal strains obtained from AD-patients was evaluated according to the Clinical and Laboratory Standards Institute (CLSI) guidelines, document M38-A2 for filamentous fungi, and document M27-A4 for yeasts., Results: The results showed that compared to the non-AD individuals, the prevalence of oral fungal composition in AD group was 1.6 times higher. Candida albicans was the most common fungal species isolated from oral swab samples of AD group (n=53, 80%) and non-AD group (n=28, 40%), and the diversity of the oral fungal composition in AD-patients were lower than non-AD individuals. Among the 3 investigated virulence factors, a statistically significant difference was shown in terms of hemolysin activity level between the two studied groups ( p <0.05) and the activity level of esterase and proteinase enzymes did not show a significant difference in the two studied groups ( p >0.05). The results showed that almost all of the tested isolates were susceptible to nystatin, the most widely prescribed antifungal to treat superficial infections, and only 1.69 % (2/118) of the Candida isolates were resistant to this antifungal drug., Conclusion: Understanding the changes in the frequency of oral fungal composition the antifungal susceptibility, and the enzymatic profiles of oral fungal composition in patients suffering from AD compared to non-AD individuals makes it possible to better understand the etiology of this disease., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Golipoor, Rafat, Saberi, Roostaei and Shabanpour.)

Introduction: In "Do-It-Yourself" (DIY) stores, workers from the wood department are considered woodworkers. Given the health risks associated with woodworking, particularly from fungi and their metabolites, this study aims to assess microbial contamination and health risks for both workers and customers., Methods: The study was developed in 13 DIY stores in Lisbon Metropolitan Area, Portugal. It employed a comprehensive sampling approach combining active (MAS-100, Andersen six-stage, Coriolis μ , and SKC Button Aerosol Sampler) and passive (electrostatic dust collectors, surface swabs, e-cloths, settled dust, filters from vacuumed dust, filtering respiratory protection devices, and mechanical protection gloves) methods to assess microbial contamination. A Lighthouse Handheld Particle Counter HH3016- IAQ was used to monitor the particulate matter size, temperature, and humidity., Results: The wood exhibition area presented the highest fungal load, while the payment area exhibited the highest bacterial load. MAS-100 detected the highest fungal load, and surface swabs had the highest bacterial load. Penicillium sp. was the most frequently observed fungal species, followed by Aspergillus sp. Mycotoxins, namely mycophenolic acid, griseofulvin, and aflatoxin G1, were detected in settled dust samples and one filter from the vacuum cleaner from the wood exhibition area. Cytotoxicity evaluation indicates the wood-cutting area has the highest cytotoxic potential. Correlation analysis highlights relationships between fungal contamination and particle size and biodiversity differences among sampling methods., Discussion: The comprehensive approach applied, integrating numerous sampling methods and laboratory assays, facilitated a thorough holistic analysis of this specific environment, enabling Occupational and Public Health Services to prioritize interventions for accurate exposure assessment and detailed risk management., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Dias, Gomes, Pena, Cervantes, Gonçalves, Carolino, Twarużek, Kosicki, Ałtyn, Caetano, Viegas and Viegas.)

Background: Fungi are common opportunistic pathogens that pose a significant threat to immunocompromised patients, particularly when late detection occurs., Methods: In this study a multiplex real-time PCR has been developed for simultaneous detection of common fungal pathogens associated with invasive mycoses in a diagnostic setting., Results: The specificity of the assay was rigorously tested on 40 types of organisms ( n = 65), demonstrating 100% specificity. The limit of detection was determined to be 100 pg/μl (10 6 copies/μl), achievable within a rapid 3-h timeframe. The PCR assay efficiency exhibited a range between 89.77% and 104.30% for each target organism, with linearity falling between 0.9780 and 0.9983., Conclusion: This multiplex real-time PCR assay holds promise for enhancing the timely and accurate diagnosis of invasive mycoses, particularly in immunocompromised patient populations., Competing Interests: The authors declare that they have no competing interests., (© 2024 Ismadi et al.)

Host-associated microbiota form complex microbial communities that are increasingly associated with host behavior and disease. While these microbes include bacterial, archaeal, viral, and eukaryotic constituents, most studies have focused on bacteria due to their dominance in the human host and available tools for investigation. Accumulating evidence suggests microbial eukaryotes in the microbiome play pivotal roles in host health, but our understandings of these interactions are limited to a few readily identifiable taxa because of technical limitations in unbiased eukaryote exploration. Here, we combined cell sorting, optimized eukaryotic cell lysis, and shotgun sequencing to accelerate metagenomic discovery and analysis of host-associated microbial eukaryotes. Using synthetic communities with a 1% microbial eukaryote representation, the eukaryote-optimized cell lysis and DNA recovery method alone yielded a 38-fold increase in eukaryotic DNA. Automated sorting of eukaryotic cells from stool samples of healthy adults increased the number of microbial eukaryote reads in metagenomic pools by up to 28-fold compared to commercial kits. Read frequencies for identified fungi increased by 10,000× on average compared to the Human Microbiome Project and allowed for the identification of novel taxa, de novo assembly of contigs from previously unknown microbial eukaryotes, and gene prediction from recovered genomic segments. These advances pave the way for the unbiased inclusion of microbial eukaryotes in deciphering determinants of health and disease in the host-associated microbiome.IMPORTANCEMicrobial eukaryotes are common constituents of the human gut where they can contribute to local ecology and host health, but they are often overlooked in microbiome studies. The lack of attention is due to current technical limitations that are heavily biased or poorly recovered DNA from microbial eukaryotes. We developed a method to increase the representation of these eukaryotes in metagenomic sequencing of microbiome samples that allows to improve their detection compared to prior methods and allows for the identification of new species. Application of the technique to gut microbiome samples improved detection of fungi, protists, and helminths. New eukaryotic taxa and their encoded genes could be identified by sequencing a small number of samples. This approach can improve the inclusion of eukaryotes into microbiome research., Competing Interests: M.Z.A. is a board member of the Native BioData Consortium.

Quinoa is an Andean pseudo-cereal crop that is mainly cultivated for its energy and protein-rich, gluten-free seeds. Quinoa is currently being popularized in Burkina Faso, but manifestations of fungal diseases have been observed on the plants. The aim of this study was to establish a causal relationship between the observed symptoms and the associated fungal pathogens. Samples of symptomatic organs were collected from the three agro-ecological zones and examined for fungal pathogen species via isolation on media. A total of six (6) diseases and twenty-nine (29) fungal species were described and identified in the collected organs. The diseases were present in the following proportions: (i) panicle browning followed by complete plant drying (45.36%), (ii) brown crown rot (41.20%), (iii) brown stalk rot (27.31%), (iv) damping-off (22.68%), (v) chlorosis with necrotic brown leaf spots (19.33%), and (vi) plant wilting (13.88%). The essential epidemiological factors of these pathologies are discussed., (© 2024. The Author(s).)

To investigate the dynamic changes and potential correlations between microbial diversity and volatile organic compounds (VOCs) during Chinese medium-temperature Daqu (MTD) manufacturing at different key stages, in this study, high-throughput sequencing (HTS) and gas chromatography-ion mobility spectrometry (GC-IMS) were employed to analyze the microbial diversity and VOCs of MTD, respectively. The results showed that Weissella , Staphylococcus , Thermoactinomyces , Kroppenstedtia , and Lactobacillus were the dominant bacterial genera, while Aspergillus , Alternaria , Thermoascus , Thermomyces , Wickerhamomyces , and Saccharomyces were the dominant fungal genera. A total of 61 VOCs were detected by GC-IMS, among which, 13 differential VOCs (VIP > 1) were identified, that could be used as potential biomarkers to judge the fermentation stage of MTD. Kroppenstedtia and Saccharopolyspora were positively correlated with 3-methyl-2-butenal and 2,2,4,6,6-pentamethylheptane-D, respectively, and both of these were positively correlated with butanal-D. Acetobacter , Streptomyces , and lactic acid bacteria (LAB) including Leuconostoc , Pediococcus , Weissella , and Lactobacillus were negatively correlated with their associated VOCs, while fungi were generally positively correlated with VOCs. Wickerhamomyces , Saccharomyces , and Candida were positively correlated with butan-2-one-M. This study provides a theoretical basis for explaining the mechanisms of MTD flavor formation and screening functional microorganisms to improve the quality of MTD.

Microbial succession has been suggested to supplement established postmortem interval (PMI) estimation methods for human remains. Due to limitations of entomological and morphological PMI methods, microbes are an intriguing target for forensic applications as they are present at all stages of decomposition. Previous machine learning models from soil necrobiome data have produced PMI error rates from two and a half to six days; however, these models are built solely on amplicon sequencing of biomarkers (e.g., 16S, 18S rRNA genes) and do not consider environmental factors that influence the presence and abundance of microbial decomposers. This study builds upon current research by evaluating the inclusion of environmental data on microbial-based PMI estimates from decomposition soil samples. Random forest regression models were built to predict PMI using relative taxon abundances obtained from different biological markers (bacterial 16S, fungal ITS, 16S-ITS combined) and taxonomic levels (phylum, class, order, OTU), both with and without environmental predictors (ambient temperature, soil pH, soil conductivity, and enzyme activities) from 19 deceased human individuals that decomposed on the soil surface (Tennessee, USA). Model performance was evaluated by calculating the mean absolute error (MAE). MAE ranged from 804 to 997 accumulated degree hours (ADH) across all models. 16S models outperformed ITS models (p = 0.006), while combining 16S and ITS did not improve upon 16S models alone (p = 0.47). Inclusion of environmental data in PMI prediction models had varied effects on MAE depending on the biological marker and taxonomic level conserved. Specifically, inclusion of the measured environmental features reduced MAE for all ITS models, but improved 16S models at higher taxonomic levels (phylum and class). Overall, we demonstrated some level of predictability in soil microbial succession during human decomposition, however error rates were high when considering a moderate population of donors., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Mason et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Mixed tree plantations containing nitrogen (N2)-fixing species have the potential to enhance C sequestration, soil biodiversity and forest productivity. Here, we investigated the impact of Acacia mangium and Eucalyptus urophilla x E. grandis mixed plantations in the Congolese coastal plains on soil mycobiota community structure and diversity by ITS metabarcoding sequencing and bioinformatic analysis. Higher Faith's phylogenetic diversity and Evenness' was found in Eucalyptus monoculture relative to stands containing Acacia. Differences in beta diversity were found among Eucalyptus and Acacia monoculture, and mixed-species stands highlight the effects of plant species on fungal community structure. Ascomycota, Basidiomycota and Rozellomycota phyla were predominant in all stands, with both Dikarya (Ascomycota and Basidiomycota) accounting for more than 70% in all stands. Correlation analysis revealed that sulfur (S) was the most correlated soil attribute with the three predominant phyla but also with Mucoromycota and Calcarisporiellomycota phyla, although mostly negatively correlated (4 out of 5). Phosphorus was mostly positively correlated to soil attributes (3 out of 4) and nitrogen was correlated twice, positively and negatively. Distance-based redundancy analysis revealed a positive correlation of nitrogen (p-value = 0.0019, contribution = 22%) and phosphorus (p-value = 0.0017, contribution = 19%) with soil mycobiota. A high prevalence of generalists (28% to 38%) than specialists (9% to 24%) were found among the different sites. In stands containing Acacia (pure and mixed species) the soil mycobiota harbor the prevalence of generalist strategies with the potential to withstand environmental stresses and utilize a higher number of resources against specialists in Eucalyptus stands. Stronger positive correlation between soil attributes and main fungal taxa, higher generalists' strategies and lower Faith's phylogenetic diversity and Evenness were reported in stands containing Acacia. This highlights the potential of mixed-species in preserving community stability following environmental disturbances and increasing the number of resources confirming their important ecological role in boosting the resilience of the forest ecosystems to climate and land-use (plant species as shown by PCA analysis) changes., Competing Interests: The authors have read the journal’s policy and have the following competing interests: the authors received funding from Moët Hennessy, France. This does not alter our adherence to PLOS ONE policies on sharing data and materials., (Copyright: © 2024 Koutika et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: Disinfection has a fundamental role in the control of pathogens in the hospital environment. This study was designed to assess the efficacy and functional impact of disinfectants in reducing pathogens related to healthcare associated infections (HAIs) in hospitals., Methods: This observation study was conducted at three university hospitals in Gorgan, Iran, from May to Oct 2023. The data including used disinfectants and microbiological examination were obtained from the infection control unit of each hospital., Results: The results showed that a variety of disinfectants from intermediate to high levels were employed in accordance with the World Health Organization (WHO) protocols. The microbial result revealed that 31.6% (286 out of 906) of the sample had at least one microorganism. Among identified organisms, Bacillus spp. were the predominant species followed by Staphylococcus epidermis, fungus genera, Enterobacter spp., Enterococcus spp., Pseudomonas spp., Escherichia coli, Alcaligenes spp., Staphylococcus aureus, Citrobacter spp., Corynebacterium spp., Klebsiella spp., Acinetobacter spp., Micrococcus spp., Staphylococcus saprophyticus, and Serratias spp. The highest prevalence rates of microorganisms were observed in the wards of ICU, emergency, internal medicine, and women's ward. The chi-square test revealed a significant relationship between the presence of organisms and hospital wards (P < 0.05)., Conclusion: The presence of pathogens indicates a defect in the disinfection process, probably due to both little attention to disinfection protocols and multidrug resistance. It is not yet possible to eliminate pathogens from the hospital environment, but it can be minimized by education intervention, standardizing disinfecting processes, and monitoring by the infection control committee., (© 2024. The Author(s).)

Continuous cropping is a common cultivation practice in lavender cultivation, and the structure of the soil microbial community is one of the main reasons affecting the continuous cropping disorder in lavender; however, the relationship between the number of years of cultivation and inter-root microbial composition has not yet been investigated; using Illumina high-throughput sequencing we detected fungal community structure of rhizosphere soil under 1 (L1), 3 (L3), 5 (L5) and 0 (L0) years' of lavender cultivation in Yili, Xinjiang China. The results showed that with the extension of planting years, the physical-chemical characteristics of the soil shifted, and the diversity of the fungal communities shrank, the abundance and richness of species decreased and then increased, and the phylogenetic diversity increased, The structure of the soil fungal communities varied greatly. At phylum level, dominant fungal phyla were Ascomycetes, Basidiomycetes, etc. At genus level, dominant genera were Gibberella, Mortierella, etc, whose absolute abundance all increased with increasing planting years (P < 0.05); redundancy analysis showed that thesoil physicochemical characteristics significantly correlated with dominant bacterial genera. The FUN Guild prediction showed that six groups of plant pathogens and plant saprotrophs changed significantly (P < 0.05), the amount of harmful bacteria in the soil increased while the amount of arbuscular mycorrhizal fungui (AMF) decreased, leading to a continuous cropping obstacle of lavender. The findings of this study provida theoretical foundation for the management of continuous cropping and the prevention fungus-related diseases in lavender., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Deng et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, little is known about the difference in rhizosphere microbes in dioecious plants. In this study, we used amplicon sequencing to analyze the differences in rhizosphere microbial diversity and community composition of males and females of dioecious Hippophae tibetana at different habitats, and their key factors in driving the differences were investigated. The results showed that there were differences in the diversity, community composition, and connectivity and complexity of the co-occurrence network of rhizosphere microbes between females and males of the dioecious H. tibetana at different habitats. Zoopagomycota is a unique phylum of rhizosphere fungi in the males of the dioecious H. tibetana , while Dependentiae is a unique phylum of rhizosphere bacteria in the females of the dioecious H. tibetana . Linear discriminant analysis effect size (LEfSe) analysis indicated significant enrichment of species at different levels, suggesting that these species could be potential biomarkers for females and males of H. tibetana . Spearman's analysis showed that the dominant genera of rhizosphere fungi were significantly positively correlated with soil physicochemical properties (total nitrogen and phosphorus; organic matter; available phosphorus, potassium and nitrogen; salt content; water content). PICRUSt and FUNGuild predictive analysis indicated that the function of rhizosphere fungi was different between females and males of the dioecious H. tibetana at different habitats, while metabolites were the dominant functions of rhizosphere bacteria in all samples. These results highlighted the sexual discrimination of rhizosphere microbes on the dioecious plants and provided important knowledge for females and males of the dioecious plant-microbe interaction.IMPORTANCEThis study explores the differences in rhizosphere microbes of dioecious Hippophae tibetana at different habitats and their key factors in driving the differences. Through employing amplicon sequencing techniques, we found that rhizosphere microbial communities and diversity were different between females and males of the dioecious H. tibetana at different habitats, and there notably existed unique phylum and potential biomarkers of rhizosphere microbes between females and males of the dioecious H. tibetana . Rhizosphere fungi were significantly positively correlated with soil physicochemical properties. This study reveals the differences in rhizosphere microbes of dioecious H. tibetana at different habitats and driving factors; it also contributes to our understanding of the dioecious plant-microbe interaction., Competing Interests: The authors declare no conflict of interest.

Below-ground microorganisms, particularly endophytes, are pivotal for plant establishment and functioning through nutrient acquisition and enhancing resistance to abiotic and biotic stresses. The impact of host plant origin within a species on the composition and interaction networks of root endophytic fungi and bacteria has been less explored compared with plant phylogeny and biological distance. This study investigates the effect of geographic origin on the fungal and bacterial microbiomes of Pinus sylvestris L. root endophytes. Roots from plants grown in a common garden, originating from six locations, were harvested in two distinct seasons. Fungal and bacterial microbiomes were analyzed using Illumina MiSeq sequencing. The operational taxonomic unit (OTU) richness of endophytic fungi and bacteria showed no significant variation due to tree origin or season. However, the Shannon diversity index for endophytic fungi was seasonally influenced. The composition of endophytic fungal and bacterial communities was affected by both tree origin and season, correlating with host root biochemical parameters, such as starch, total non-structural carbohydrates, carbon, nitrogen, and climatic factors, such as mean annual precipitation and temperature. Moreover, the abundance of specific endophytic fungi and bacteria varied across different P. sylvestris origins, depending on the season. The complexity of the co-occurrence networks of fungal and bacterial endophytes within P. sylvestris also differed by geographical origin and season. This study highlights the significant role of biochemical and climatic factors associated with tree origin in shaping interactions with endophytic communities, potentially affecting plant health and adaptability across diverse environments., Importance: This study advances our understanding of how plant ecotype and seasonal changes influence root endophytic communities in Scots pine ( Pinus sylvestris ). By examining trees from various origins grown in a common garden, it highlights the role of tree origin and season in shaping fungal and bacterial community and co-occurrence networks. Importantly, this research demonstrates that tree origin impacts the composition and interaction networks of root endophytes and depends on the season. The study's findings suggest that root biochemical traits and climatic conditions (e.g., temperature, precipitation) associated with tree origin are crucial in determining the assembly of endophytic communities. This understanding could lead to innovative strategies for enhancing plant health and adaptability across different environments, contributing to forestry and conservation efforts. The research underscores the complexity of plant-microbe interactions and the need for a comprehensive approach to studying them, highlighting the interplay between tree origin and microbial ecology in forest ecosystems., Competing Interests: The authors declare no conflict of interest.

The seed serves as the primary source for establishing microbial populations in plants across subsequent generations, influencing plant growth and overall health. Cropping conditions, especially farming practices, can influence the composition and functionality of the seed microbiome. Very little is known about the differences in seed microbiome between organic and conventional production systems. In this study, we characterized the endophytic microbial populations in seeds of rice grown under organic and conventional management practices through culture-dependent and -independent analyses. The V4 region of 16S rRNA was used for bacterial taxa identification, and the ITS1 region was used for the identification of fungal taxa. Our results revealed significantly higher Shannon and Simpson indices for bacterial diversity in the conventional farming system, whereas the fungal diversity was higher for observed, Shannon, and Simpson indices in the organic farming system. The cultivable endophytic bacteria were isolated and identified using the full-length 16S rRNA gene. There was no difference in culturable endophytic bacterial isolates in rice seeds grown under both conventional and organic farming systems. Among 33 unique isolates tested in vitro , three bacteria- Bacillus sp. ST24, Burkholderia sp. OR5, and Pantoea sp. ST25-showed antagonistic activities against Marasmius graminum, Rhizoctonia solani AG4, and R. solani AG11, the fungal pathogens causing seedling blight in rice., Importance: In this paper, we studied the differences in the endophytic microbial composition of rice seeds grown in conventional and organic farming systems. Our results demonstrate a greater bacterial diversity in conventional farming, while organic farming showcases a higher fungal diversity. Additionally, our research reveals the ability of seed bacterial endophytes to inhibit the growth of three fungal pathogens responsible for causing seedling blight in rice. This study provides valuable insights into the potential use of beneficial seed microbial endophytes for developing a novel microbiome-based strategy in the management of rice diseases. Such an approach has the potential to enhance overall plant health and improve crop productivity., Competing Interests: The authors declare no conflict of interest.

Pinewood nematodes (PWN, Bursaphelenchus xylophilus ) are destructive plant parasitic nematodes that cause pine wilt disease (PWD) by attacking the vascular systems of pine trees, resulting in widespread tree mortality. Research has shown that there are connections between nematode-associated microbes and PWD. Yet the variations in microbial communities across different geographic regions are not well-understood. In this study, we examined the bacterial and fungal communities associated with nematodes and infested wood collected from 34 sites across three vegetation zones in China, as well as samples from the United States, using 16S rRNA and internal transcribed spacer (ITS) gene amplicon sequencing. The predominant genera Pseudomonas and Rhodococcus were found in nematodes, and Acinetobacter was present in the wood of PWD-infected pine trees across China. Network analysis revealed that core bacterial taxa belonged to the Pseudomonadota and Actinomycetota phyla for the nematodes, whereas the Pseudomonadota and Bacteroidota phyla were dominant in the infested wood. Identification of enriched key microbial taxa in nematodes and infested wood across vegetation zones indicates distinct biogeographic microbial community structures and key bacterial species. Although the nematode-associated bacterial community showed consistency across geographic distances, the similarity of the PWD pine trees' bacterial community decreased with distance, suggesting a spatial correlation with environmental variables. Our findings enhance our understanding of the microbiota associated with pinewood nematode (PWN) and offer valuable insights into PWD management., Importance: Our research uncovered specific bacteria and fungi linked to pinewood nematode (PWN) and infested wood in three different vegetation zones in China, as well as samples from the United States. This sheds light on the critical roles of certain microbial groups, such as Pseudomonas, Acinetobacter , and Stenotrophomonas , in influencing PWN fitness. Understanding these patterns provides valuable insights into the dynamics of PWN-associated microbiomes, offering potential strategies for managing pine wilt disease (PWD). We found significant correlations between geographic distance and similarity in bacterial communities in the infested wood, indicating a spatial influence on wood-associated microbial communities due to limited dispersal and localized environmental conditions. Further investigations of these spatial patterns and driving forces are crucial for understanding the ecological processes that shape microbial communities in complex ecosystems and, ultimately, for mitigating the transmission of PWN in forests., Competing Interests: The authors declare no conflict of interest.

The use of rock phosphate (RP) instead of soluble phosphate fertilizers is preferred for the development of more sustainable agriculture. However, the impact of high concentrations in RP on bacterial and fungal communities remains poorly documented. Thus, next-generation sequencing was used to characterize bacterial and fungal communities in the soils and roots of four plant species growing naturally in a self-restored ecosystem, on former open-pit phosphate mines where past exploitation generated locally a substantial phosphate enrichment of the soil. Our results show that bacterial communities are dominated by Actinobacteria and Proteobacteria phyla, while the Ascomycota and Basidiomycota phyla predominate in the fungal community. The alpha and beta diversities of both bacterial and fungal communities differ significantly between the root and soil compartments but are not significantly affected by RP inputs. However, Amplicon Sequence Variants (ASVs) indicative of RP-enriched soils have been identified; among them are bacteria representative of Streptomyces, Bacillus, Mycobacterium or Agromyces. Implications of these results open new ways of reflection to understand the microbial response following RP-inputs and long-term soil restoration, as well as to formulate microbial-based bioinoculants for sustainable agriculture applications based on microorganisms better adapted to high concentrations of RP., (© 2024 The Author(s). Environmental Microbiology Reports published by John Wiley & Sons Ltd.)

The microbiota of medicinal plants is known to be highly specific and can contribute to medicinal activity. However, the majority of plant species have not yet been studied. Here, we investigated the phyllosphere composition of two common Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii, by a polyphasic approach combining analyses of metagenomic DNA and isolates. Microbial abundance estimated via qPCR using specific marker gene primers showed that all leaf samples were densely colonized, with up to 10 8 per gram of leaf, with higher bacterial and fungal abundance than Archaea. While no statistically significant differences between both plant species were found for abundance, amplicon sequencing of 16S rRNA and ITS genes revealed distinct microbiota compositions. Only seven of the 27 genera isolated were represented on both plants, e.g. dominant Sphingomonas spp., and numerous members of Xanthomonadaceae and Enterobacteriaceae. The most dominant fungal families on both plants were Cladosporiaceae, Mycosphaerellaceae and Trichosphaeriaceae. In addition, 225 plant-specific isolates were identified, with Pseudomonadota and Enterobacteriaceae being dominant. Interestingly, 29 isolates are likely species previously unknown, and 14 of these belong to Burkholderiales. However, a high proportion, 56% and 40% of the isolates from E. lateriflora and F. thonningii, respectively, were characterized as various Escherichia coli. The growth of most of the bacterial isolates was not influenced by extractable secondary metabolites of plants. Our results suggest that a specific and diverse microbial community inhabits the leaves of both E. lateriflora and F. thonningii, including potentially new species and producers of antimicrobials., (© 2024. The Author(s).)

Background: The plant microbiome is one of the key determinants of healthy plant growth. However, the complexity of microbial diversity in plant microenvironments in different regions, especially the relationship between subsurface and aboveground microorganisms, is not fully understood. The present study investigated the diversity of soil microorganisms in different regions and the diversity of microorganisms within different ecological niches, and compared soil microorganisms and endophytic microorganisms., Methods: 16 S and ITS sequencing was used to sequence the soil and endophytes microbiome of honeysuckle. Alpha diversity analysis and principal component analysis (PCoA) were used to study the soil and endophyte microbial communities, and the function of endophyte bacteria and fungi was predicted based on the PICRUST2 process and FUNGuild., Results: In total, there were 382 common bacterial genera and 139 common fungal genera in the soil of different producing areas of honeysuckle. There were 398 common bacterial genera and 157 common fungal genera in rhizosphere soil. More beneficial bacteria were enriched in rhizosphere soil. Endophytic bacteria were classified into 34 phyla and 770 genera. Endophytic fungi were classified into 11 phyla and 581 genera, among which there were significant differences in the dominant genera of roots, stems, leaves, and flowers, as well as in community diversity and richness. Endophytic fungal functions were mainly dominated by genes related to saprophytes, functional genes that could fight microorganisms were also found in KEGG secondary functional genes., Conclusion: More beneficial bacteria were enriched in rhizosphere soil of honeysuckle, and the microbial network of the rhizosphere is more complex than that of the soil. Among the tissues of honeysuckle, the flowers have the richest diversity of endophytes. The endogenous dominant core bacteria in each part of honeysuckle plant have a high degree of overlap with the dominant bacteria in soil. Functional prediction suggested that some dominant core bacteria have antibacterial effects, providing a reference for further exploring the strains with antibacterial function of honeysuckle. Understanding the interaction between honeysuckle and microorganisms lays a foundation for the study of growth promotion, quality improvement, and disease and pests control of honeysuckle from the perspective of microorganisms., (© 2024. The Author(s).)

Endophytic fungi have been shown to synthesize bioactive secondary metabolites, some of which promote plant growth through various mechanisms. In our previous study, endophytic fungi were isolated from mango trees ( Mangifera indica L.). The present study examined fifty endophytic fungal isolates for mineral solubilization activity, ammonia production, and siderophore production. It was shown that these isolates could produce phytohormones indole-3-acetic acid and gibberellic acid, as well as inhibit plant pathogens, specifically Colletotrichum gloeosporioides and Lasiodiplodia theobromae . The results showed that all the isolated fungal endophytes exhibited various activities. Based on the findings, two fungal endophytes- Aureobasidium pullulans CY.OS 13 and Aspergillus tamarii CY.OS 144-were selected for dual inoculation in chili plants under pot-scale conditions to investigate their potential to improve growth-related traits such as seed germination, shoot and root length, biomass, and chlorophyll content. Seed treated with A. pullulans CY.OS 13 and/or A. tamarii CY.OS 144 showed a significant ( p < 0.05) increase in seed germination and growth parameters of chili plants grown under pot-scale conditions. Particularly, chili plants whose seeds were injected with a combination of the two selected endophytic fungi showed the highest plant development traits. Therefore, the selected endophytic fungi have the potential to be used as biofertilizers, especially when combined. They could eventually replace chemical fertilizers because they are environmentally friendly, beneficial to humans, and can even promote sustainable agriculture.

Nanopore sequencing technology has enabled the rapid, on-site taxonomic identification of samples from anything and anywhere. However, sequencing errors, inadequate databases, as well as the need for bioinformatic expertise and powerful computing resources, have hampered the widespread use of the technology for pathogen identification in the agricultural sector. Here we present RAPiD, a lightweight and accurate real-time taxonomic profiling pipeline. Compared to other metagenomic profilers, RAPiD had a higher classification precision achieved through the use of a curated, non-redundant database of common agricultural pathogens and extensive quality filtering of alignments. On a fungal, bacterial and mixed mock community RAPiD was the only pipeline to detect all members of the communities. We also present a protocol for in-field sample processing enabling pathogen identification from plant sample to sequence within 3 h using low-cost equipment. With sequencing costs continuing to decrease and more high-quality reference genomes becoming available, nanopore sequencing provides a viable method for rapid and accurate pathogen identification in the field. A web implementation of the RAPiD pipeline for real-time analysis is available at https://agrifuture.senckenberg.de., Competing Interests: The authors declare that they have no competing interests., (© 2024 Knobloch et al.)

Leaf litter decomposition, a crucial component of the global carbon cycle, relies on the pivotal role played by microorganisms. However, despite their ecological importance, leaf-litter-decomposing microorganism taxonomic and functional diversity needs additional study. This study explores the taxonomic composition, dynamics, and functional role of microbial communities that decompose leaf litter of forest-forming tree species in two ecologically unique regions of Europe. Twenty-nine microbial metagenomes isolated from the leaf litter of eight forest-forming species of woody plants were investigated by Illumina technology using read- and assembly-based approaches of sequences analysis. The taxonomic structure of the microbial community varies depending on the stage of litter decomposition; however, the community's core is formed by Pseudomonas , Sphingomonas , Stenotrophomonas , and Pedobacter genera of Bacteria and by Aureobasidium , Penicillium , Venturia genera of Fungi. A comparative analysis of the taxonomic structure and composition of the microbial communities revealed that in both regions, seasonal changes in structure take place; however, there is no clear pattern in its dynamics. Functional gene analysis of MAGs revealed numerous metabolic profiles associated with leaf litter degradation. This highlights the diverse metabolic capabilities of microbial communities and their implications for ecosystem processes, including the production of volatile organic compounds (VOCs) during organic matter decomposition. This study provides important advances in understanding of ecosystem processes and the carbon cycle, underscoring the need to unravel the intricacies of microbial communities within these contexts., Competing Interests: The authors declare there are no competing interests., (©2024 Khomutovska et al.)

Until recently, the data on the diversity of the entire microbial community from the Baltic Sea were relatively rare and very scarce. However, modern molecular methods have provided new insights into this field with interesting results. They can be summarized as follows. (i) Although low salinity causes a reduction in the biodiversity of multicellular species relative to the populations of the North-East Atlantic, no such reduction occurs in bacterial diversity. (ii) Among cyanobacteria, the picocyanobacterial group dominates when considering gene abundance, while filamentous cyanobacteria dominate in means of biomass. (iii) The diversity of diatoms and dinoflagellates is significantly larger than described a few decades ago; however, molecular studies on these groups are still scarce. (iv) Knowledge gaps in other protistan communities are evident. (v) Salinity is the main limiting parameter of pelagic fungal community composition, while the benthic fungal diversity is shaped by water depth, salinity, and sediment C and N availability. (vi) Bacteriophages are the predominant group of viruses, while among viruses infecting eukaryotic hosts, Phycodnaviridae are the most abundant; the Baltic Sea virome is contaminated with viruses originating from urban and/or industrial habitats. These features make the Baltic Sea microbiome specific and unique among other marine environments., (© The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.)

Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.

Background: The epidemiology of fungi identified via next-generation sequencing in bronchoalveolar lavage fluid among patients with COVID-19 is unknown., Methods: De-identified information, including age, SARS-CoV-2 reads and fungi from bronchoalveolar lavage fluid, were used to analysis., Results: A total of 960 patients with COVID-19 were included. Gender was unknown in 38 patients, and 648 (70.3%) of the rest patients were male. For 876 patients with information on age, their mean ± standard age was 63.4 ± 21.3 years, with the minimum being 0.2 years and the maximum being 101 years. For all the patients, their median [interquartile range] SARS-CoV-2 reads were 26,038 [4421.5, 44,641.5]. The Aspergilli were identified in 159 (16.6%) patients, with Aspergillus fumigatus, Aspergillus flavus and Aspergillus niger in 103 (10.7%), 81 (8.4%) and 17 (1.8%), respectively. The Mucoraceae were identified in 14 (1.5%) patients. Pneumocystis jirovecii was identified in 65 (6.8%) patients, among whom 12 (18.5%) patients also had Aspergilli. The Cryptococcaceae and the Dematiaceae were also identified in some patients, including Cryptococcus in 11 (1.1%) patients., Conclusions: In bronchoalveolar lavage fluid among patients with COVID-19, the Aspergilli were very commonly identified, as were the Mucoraceae, Pneumocystis jirovecii and Cryptococcus via next-generation sequencing., (© 2024. The Author(s).)

Elemental profiling of fungal species as a phenotyping tool is an understudied topic and is typically performed to examine plant tissue or non-biological materials. Traditional analytical techniques such as inductively coupled plasma-optical emission spectroscopy (ICP-OES) and inductively coupled plasma-mass spectrometry (ICP-MS) have been used to identify elemental profiles of fungi; however, these techniques can be cumbersome due to the difficulty of preparing samples. Additionally, the instruments used for these techniques can be expensive to procure and operate. Laser-induced breakdown spectroscopy (LIBS) is an alternative elemental analytical technique-one that is sensitive across the periodic table, easy to use on various sample types, and is cost-effective in both procurement and operation. LIBS has not been used on axenic filamentous fungal isolates grown in substrate media. In this work, as a proof of concept, we used LIBS on two genetically distinct fungal species grown on a nutrient-rich and nutrient-poor substrate media to determine whether robust elemental profiles can be detected and whether differences between the fungal isolates can be identified. Our results demonstrate a distinct correlation between fungal species and their elemental profile, regardless of the substrate media, as the same strains shared a similar uptake of carbon, zinc, phosphorus, manganese, and magnesium, which could play a vital role in their survival and propagation. Independently, each fungal species exhibited a unique elemental profile. This work demonstrates a unique and valuable approach to rapidly phenotype fungi through optical spectroscopy, and this approach can be critical in understanding these fungi's behavior and interactions with the environment., Importance: Historically, ionomics, the elemental profiling of an organism or materials, has been used to understand the elemental composition in waste materials to identify and recycle heavy metals or rare earth elements, identify the soil composition in space exploration on the moon or Mars, or understand human disorders or disease. To our knowledge, ionomic profiling of microbes, particularly fungi, has not been investigated to answer applied and fundamental biological questions. The reason is that current ionomic analytical techniques can be laborious in sample preparation, fail to measure all potential elements accurately, are cost-prohibitive, or provide inconsistent results across replications. In our previous efforts, we explored whether laser-induced breakdown spectroscopy (LIBS) could be used in determining the elemental profiles of poplar tissue, which was successful. In this proof-of-concept endeavor, we undertook a transdisciplinary effort between applied and fundamental mycology and elemental analytical techniques to address the biological question of how LIBS can used for fungi grown axenically in a nutrient-rich and nutrient-poor environment., Competing Interests: The authors declare no conflict of interest.

The diversity of endophytes and their ecological relationships with the endangered conifer Araucaria angustifolia (a critically endangered species) are unrevealed. This study aimed to characterize the diversity of endophytic fungi associated with A. angustifolia. To this end, we analyzed 90 fragments from five individuals collected from a mixed localized fragment in Guarapuava-PR, Brazil. The total DNA of 61 morphotypes was extracted and the Internal Transcribed Spacer (ITS) region was amplified and sequenced. The sequence analysis allowed the identification of 37 genera belonging to the phylum Ascomycota and the classes Eurotiomycetes, Dothideomycetes, and Sordariomycetes, divided into 11 orders and 13 families. Most of the isolated fungi belonged to the Sordariomycetes class (40%) and to the Xylaria genus (14%), while Eurotiomycetes was the minority class within the community. Our results reveal the high endophytic richness supporting the life cycle of A. angustifolia and reinforce the necessity for the conservation of this conifer, as many genetic resources can be lost owing to its irrational exploration.

Pinellia ternata (Thunb.) Breit is an important traditional Chinese medicine. In North China, conventional flat planting of P. ternate is prone to root rot during the rainy season, leading to severe yield loss. Variations in planting patterns (e.g., ridge planting) can effectively alleviate this situation. However, the relationship between planting patterns and the changes induced by rhizosphere microbiome still needs to be determined. In this study, we clarified the effect of ridge planting on the yield of P. ternata and rhizosphere microbial community using high-throughput amplicon sequencing of 16S rRNA. Field experiments showed that ridge planting could increase the yield of P. ternata by 72.69% compared with flat planting. The high-throughput sequencing results demonstrated that fungal and bacterial communities in rhizosphere siols of flat and ridge planting showed obvious difference in diversity, structure, relative abundance, and community composition. The fungal phyla Zygomycota, Basidiomycota, Glomeromycota, and the bacterial phyla Chlamydiae, Tenericutes, and Hydrogenedentes were present in a higher relative abundance in the rhizosphere of ridge planting. Adonis multivariate analysis of variance results showed that 29 bacterial genera were significantly up/down-regulated, and only 4 fungal genera were changed considerably in ridge planting soil, indicating that the bacterial community composition varied significantly between the two treatments. Correlation analysis revealed that the yield of P. ternata was positively correlated with fungal genera Emericellopsis while negatively correlated with bacterial genera Acetobacter, Iamia, and fungal genera Thielavia. Overall, this study showed that ridge cropping significantly impacts the diversity and composition of the rhizosphere microbiome. It creates an environment favorable for crop growth and can be an effective planting strategy for P. ternata in areas with irrigation and high monsoon rainfall in North China., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Li et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: Accurate identification of infectious diseases using molecular techniques, such as PCR and NGS, is well-established. This study aims to assess the utility of Bactfast and Fungifast in diagnosing bloodstream infections in ICU settings, comparing them against traditional culture methods. The objectives include evaluating sensitivity and specificity and identifying a wide range of pathogens, including non-culturable species., Methods: We collected 500 non-duplicate blood samples from ICU patients between January 2023 and December 2023. Specimens underwent traditional culture, MALDI-TOF, VITEK ® 2 compact system, and NGS-based Bactfast and Fungifast analyses., Results: Out of the 500 samples, 26.8% (n=134) showed bacterial growth via traditional culture methods, while 4.8% (n=24) were positive for fungal growth. MALDI-TOF and VITEK ® 2 compact system yielded comparable results, identifying 26.4% (n=132) of specimens with bacterial growth. NGS-based Bactfast detected bacterial presence in 38.2% (n=191) of samples, including non-culturable bacteria missed by traditional methods. However, NGS-based Fungifast showed concordant fungal detection rates with culture methods. Among identified pathogens by culture method included Klebsiella pneumoniae 20.89% (n=28), Enterococcus faecalis 18.65% (n=25), Escherichia coli 15.67% (n=21), Pseudomonas aeruginosa 12.68% (n=17), Acinetobacter baumannii 10.44% (n=14), various Streptococcus species 7.46% (n=10), Mycobacterium tuberculosis 6.71% (n=9), Mycobacterium abscessus 4.47% (n=6), and Salmonella spp 2.98% (n=4). Non-culture-based NGS identified additional (n=33) pathogens, including Klebsiella pneumoniae 27.27% (n=9), Bacteroides fragilis 21.21% (n=7), Aerococcus viridans 15.15% (n=5), Elizabethkingia anopheles 12.12% (n=4), Aeromonas salmonicida 9% (n=3), Clostridium 9% (n=3), and Bacteroides vulgatus 6% (n=2). Candida albicans was reported in 5% (n=24) of samples by both methods., Conclusion: NGS-based Bactfast and Fungifast demonstrate high sensitivity in identifying a wide array of bacterial and fungal pathogens in ICU patients, outperforming traditional culture methods in detecting non-culturable organisms. These molecular assays offer rapid and comprehensive diagnostic capabilities, potentially improving clinical outcomes through timely and accurate pathogen identification., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Wang, Chauhan, Luo, Sharma, Li and Chen.)

Background: Cutaneous infectious granulomas (CIG) are localized and chronic skin infection caused by a variety of pathogens such as protozoans, bacteria, worms, viruses and fungi. The diagnosis of CIG is difficult because microbiological examination shows low sensitivity and the histomorphological findings of CIG caused by different pathogens are commonly difficult to be distinguished., Objective: The objective of this study is to explore the application of mNGS in tissue sample testing for CIG cases, and to compare mNGS with traditional microbiological methods by evaluating sensitivity and specificity., Methods: We conducted a retrospective study at the Department of Dermatology of Sun Yat-sen Memorial Hospital, Sun Yat-sen University from January 1st, 2020, to May 31st, 2024. Specimens from CIG patients with a clinical presentation of cutaneous infection that was supported by histological examination were retrospectively enrolled. Specimens were delivered to be tested for microbiological examinations and mNGS., Results: Our data show that mNGS detected Non-tuberculosis mycobacteria, Mycobacterium tuberculosis, fungi and bacteria in CIG. Compared to culture, mNGS showed a higher positive rate (80.77% vs. 57.7%) with high sensitivity rate (100%) and negative predictive value (100%). In addition, mNGS can detect more pathogens in one sample and can be used to detect variable samples including the samples of paraffin-embedded tissue with shorter detective time. Of the 21 patients who showed clinical improvement within a 30-day follow-up, eighteen had their treatments adjusted, including fifteen who continued treatment based on the results of mNGS., Conclusions: mNGS could provide a potentially rapid and effective alternative detection method for diagnosis of cutaneous infectious granulomas and mNGS results may affect the clinical prognosis resulting from enabling the patients to initiate timely treatment., (© 2024. The Author(s).)

Background: The commercialization of space travel will soon lead to many more people living and working in unique built environments similar to the International Space Station, which is a specialized closed environment that contains its own indoor microbiome. Unintended microbial growth can occur in these environments as in buildings on Earth from elevated moisture, such as from a temporary ventilation system failure. This growth can drive negative health outcomes and degrade building materials. We need a predictive approach for modeling microbial growth in these critical indoor spaces., Results: Here, we demonstrate that even short exposures to varying elevated relative humidity can facilitate rapid microbial growth and microbial community composition changes in dust from spacecraft. We modeled fungal growth in dust from the International Space Station using the time-of-wetness framework with activation and deactivation limited growth occurring at 85% and 100% relative humidity, respectively. Fungal concentrations ranged from an average of 4.4 × 10 6 spore equivalents per milligram of dust in original dust with no exposure to relative humidity to up to 2.1 × 10 10 when exposed to 100% relative humidity for 2 weeks. As relative humidity and time-elevated increased, fungal diversity was significantly reduced for both alpha (Q < 0.05) and beta (R 2  = 0.307, P = 0.001) diversity metrics. Bacteria were unable to be modeled using the time-of-wetness framework. However, bacterial communities did change based on constant relative humidity incubations for both beta (R 2  = 0.22, P = 0.001) and alpha diversity decreasing with increasing moisture starting at 85% relative humidity (Q < 0.05)., Conclusion: Our results demonstrate that moisture conditions can be used to develop and predict changes in fungal growth and composition onboard human-occupied spacecraft. This predictive model can be expanded upon to include other spacecraft environmental factors such as microgravity, elevated carbon dioxide conditions, and radiation exposure. Understanding microbial growth in spacecraft can help better protect astronaut health, fortify spacecraft integrity, and promote planetary protection as human activity increases in low-Earth orbit, the moon, Mars, and beyond. Video Abstract., (© 2024. The Author(s).)

Species interactions between bats and fungi are poorly known. We documented the association between fungal and bat diversities along a landscape gradient. Ten, eight, and seven bat species were captured in conserved, semi-conserved, and urban sites, respectively. Eptesicus fuscus, Myotis ciliolabrum and Corynorhinus townsendii were the most abundant in conserved and semi-conserved sites. E. fuscus, Myotis velifer, and Lasiurus cinereus were abundant in urban sites. C. townsendii was the least abundant bat. A total of 15 cultivated fungi genera included the fungal diversity in bats, of which nine fungi genera were shared along the landscape gradient. Penicillium and Aspergillus were the most abundant genera, and Aureobasidium, Bispora, Stachybotrys, and Verticillium were only documented in the conserved sites. We observed a higher fungal diversity associated with bat species along this landscape gradient. The individual site-based accumulation curves of fungal diversity showed significant decreasing values along the conserved, semi-conserved, and urban sites, respectively. In conserved and urban sites, M. californicus and M. velifer showed the highest fungal diversity, respectively. E. fuscus was associated to the fungi genera Scopulariopsis, Alternaria, Penicillium and Beauveria; L. cinereus to Cladosporium and Aspergillus, and M. velifer to Alternaria sp1, Bispora and Trichoderma. Conserved sites showed both high bat and fungal diversities [species richness and abundance] compared to semi-conserved and urban sites. More studies associating bat and fungal diversities in other ecosystems are needed to corroborate this pattern., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Gutiérrez-Granados et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: Plant-associated microorganisms can be found in various plant niches and collectively comprise the plant microbiome. The plant microbiome assemblages have been extensively studied, primarily in model species. However, a deep understanding of the microbiome assembly associated with plant health is still needed. Ginger rhizome rot has been variously attributed to multiple individual causal agents. Due to its global relevance, we used ginger and rhizome rot as a model to elucidate the metabolome-driven microbiome assembly associated with plant health., Results: Our study thoroughly examined the biodiversity of soilborne and endophytic microbiota in healthy and diseased ginger plants, highlighting the impact of bacterial and fungal microbes on plant health and the specific metabolites contributing to a healthy microbial community. Metabarcoding allowed for an in-depth analysis of the associated microbial community. Dominant genera represented each microbial taxon at the niche level. According to linear discriminant analysis effect size, bacterial species belonging to Sphingomonas, Quadrisphaera, Methylobacterium-Methylorubrum, Bacillus, as well as the fungal genera Pseudaleuria, Lophotrichus, Pseudogymnoascus, Gymnoascus, Mortierella, and Eleutherascus were associated with plant health. Bacterial dysbiosis related to rhizome rot was due to the relative enrichment of Pectobacterium, Alcaligenes, Klebsiella, and Enterobacter. Similarly, an imbalance in the fungal community was caused by the enrichment of Gibellulopsis, Pyxidiophorales, and Plectosphaerella. Untargeted metabolomics analysis revealed several metabolites that drive microbiome assembly closely related to plant health in diverse microbial niches. At the same time, 6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)oxane-2,3,4,5-tetrol was present at the level of the entire healthy ginger plant. Lipids and lipid-like molecules were the most significant proportion of highly abundant metabolites associated with ginger plant health versus rhizome rot disease., Conclusions: Our research significantly improves our understanding of metabolome-driven microbiome structure to address crop protection impacts. The microbiome assembly rather than a particular microbe's occurrence drove ginger plant health. Most microbial species and metabolites have yet to be previously identified in ginger plants. The indigenous microbial communities and metabolites described can support future strategies to induce plant disease resistance. They provide a foundation for further exploring pathogens, biocontrol agents, and plant growth promoters associated with economically important crops. Video Abstract., (© 2024. The Author(s).)

The presence of fungi in tracheal wash (TW) of horses was recently linked to mild-moderate equine asthma, indicating a possible causal role; however, increased numbers of fungi may also stem from asthma-related alteration of tracheal mucus clearance or from environmental exposure. Our objective was to elucidate the association between the presence of fungi in TW and asthma status while controlling for relevant confounders. We conducted a retrospective case-control study involving 73 horses, including 34 controls and 39 asthmatic cases. Each asthmatic horse was matched with a control from the same barn to account for the influence of environmental exposure. All horses underwent respiratory clinical scoring, endoscopy, TW, and bronchoalveolar lavage (BAL). The association between asthma status and presence of TW fungi was tested with multivariable logistic regression modelling, accounting for selected management factors, tracheal mucus accumulation, and selected TW and BAL cytological characteristics, including multinucleated giant cells (MGCs) in the TW. Given the variability in MGC definitions in the literature, particularly concerning their morphology and number of nuclei, we constructed two distinct models for each outcome (asthma status or presence of fungi in TW): one considering MGCs as cells with ≥ 3 nuclei, and another using a criterion of ≥ 10 nuclei. Horses with a tracheal mucus score ≥ 2 exhibited 3.6 to 4.3 higher odds of being asthmatic, depending on the MGC definition. None of the other variables examined were associated with either asthma status or TW fungi detection. Notably, the presence of fungal elements in the TW was not associated with equine asthma., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Dély et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Due to its nutritional value and health benefits, the date palm (Phoenix dactylifera L.) is an essential dietary food crop throughout Middle Eastern and African countries. Consumers are concerned about the possible microbial contamination of dates, especially since most dates arriving in local markets are unprocessed. The absence of processing increases the possibility of microbial contamination, which raises the probability of microbial contamination. This study aims to analyze and evaluate the variability of fungal and bacterial microbiota identified in the most popular date palm fruits in Saudi Arabia. The study assessed ten date variety fruits from the most popular date palm varieties for consumption in Saudi Arabia and analyzed the microbial count. Morphological and molecular characterization and comparison of nuclear ribosomal DNA internal transcribed spacer (ITS) sequences identified 78 fungi, including 36 distinct species across 15 fungal genera. Alternaria, Fusarium, Curvilaria, Aspergillus, and Penicillium were the most frequent genera among the ten fruit cultivars studied, according to ITS-rDNA sequence analysis. Furthermore, 36 bacterial isolates were obtained from ten date varieties studied, each with a unique colony morphology. These isolates were identified based on sequence alignment and comparison of their 16S rDNA internal spacer regions to those available in public databases. The results showed that the bacterial isolates included 15 species from five bacterial genera. The results suggested that Bacillus, Stenotrophomonas, and Brucella were the prevailing genera among the ten tested fruit varieties. Some bacterial genera, such as Brucella, Achromobacter, and Stenotrophomonas, are well-known potential human pathogens. Chaetomium globosum was also recognized as air pollution causing adverse health effects such as allergies and as the causal agent of human fungal infections among the tested date varieties; the Rashodiah type exhibited the highest fungal contamination, whereas the Sagai variety displayed the lowest fungal contamination. Conversely, the Sukkari, Barhi, and Mejdool varieties were the most contaminated with bacteria among the ten tested varieties, while the Khalas variety showed the least bacterial contamination. To the best of the authors' knowledge, this study provides the initial comprehensive account of the molecular and morphological identification of all fungal and bacterial genera associated with date palm (P. dactylifera) fruits., (© 2024. The Author(s).)

Type 2 diabetes mellitus (T2DM) is globally recognized as a significant health concern, with diabetic foot (DF) identified as a severe long-term complication that can lead to tissue death or amputation. The discovery of the impact of mycobiota, a diverse group of multicellular eukaryotes in the gut microbiome, on the onset of endocrine disorders holds great significance. Therefore, this research aimed to examine variations in fungal mycobiome and identify potential biomarkers for T2DM and T2DM-DF. Fecal and blood samples were collected from 33 individuals with T2DM, 32 individuals with T2DM-DF, and 32 healthy individuals without any health conditions (HC). Blood samples were used for laboratory parameters analysis, while total DNA was extracted from fecal samples and sequenced using Illumina 18s rRNA. Bioinformatics tools were employed to analyze fungal abundance and diversity, revealing differentially expressed fungal species and signature fungi that distinguished between T2DM, T2DM-DF, and HC groups. Firstly, significant alterations in some laboratory parameters were observed among the three groups, which also differed between T2DM and T2DM-DF. The diversity of gut fungi in T2DM and T2DM-DF significantly differed from that of the HC group; however, more pronounced changes were observed in T2DM-DF. Additionally, two significantly altered phyla, Ascomycota and Basidiomycota, were identified with higher Ascomycota abundance but lower Basidiomycota abundance in both the T2DM and T2DM-DF compared to the HC group. Furthermore, the top 15 fungi showing significant changes at the species level included a notable decrease in Rhodotorula&#95;mucilaginosa abundance in patients with T2DM compared to HC and a substantial increase in unclassified&#95;g&#95;Candida abundance specifically seen only among patients with T2DM-DF, but not among those diagnosed with T2DM or HC. Thirdly, KEGG was employed to analyze enzyme expression across the three groups, revealing a more pronounced alteration in gut fungal function within T2DM-DF compared to T2DM. Subsequently, to accurately identify signature fungi in each group, a random forest was utilized to rank the top 15 significant fungi. Notably, 11 fungi were identified as potential biomarkers for distinguishing T2DM or T2DM-DF from HC, while eight fungi could discriminate between T2DM and T2DM-DF. Furthermore, receiver operating characteristic curve (ROC) analysis demonstrated enhanced accuracy of predicted outcomes. These findings suggest that changes in fungal mycobiome are closely associated with the progression and complications of T2DM and DF, offering promising prospects for diagnosis and treatment., (© 2024. The Author(s).)

Filamentous fungi present significant health hazards to immunocompromised individuals globally; however, the prompt and precise identification of them during infection remains challenging. In this study, a TaqMan probe-based multiplex real-time PCR (M-qPCR) assay was developed to detect simultaneously the target genes of four important pathogenic filamentous fungi: ANXC4 gene of Aspergillus fumigatus, EF1-α gene of Fusarium spp . , mitochondrial rnl gene of Mucorales, and hcp100 gene of Histoplasma capsulatum . In this M-qPCR assay, the limit of detection (LoD) to all four kinds of fungi was 100 copies and the correlation coefficients (R 2 ) were above 0.99. The specificity of this assay is 100%, and the minimum detection limit is 100 copies/reaction. In conclusion, an M-qPCR detection assay was well established with high specificity and sensitivity for rapid and simultaneous detection on four important filamentous fungi in the clinic., Importance: World Health Organization developed the first fungal priority pathogens list (WHO FPPL) in 2022. Aspergillus fumigatus , Mucorales, Fusarium spp., and Histoplasma spp. are the four types of pathogenic fungi with filamentous morphology in the critical priority group and high priority group of WHO FPPL. These four filamentous fungal infections have become more common and severe in immunocompromised patients with the increase in susceptible populations in recent decades, which resulted in a substantial burden on the public health system. However, prompt and precise identification of them during infection remains challenging. Our study established successfully a TaqMan probe-based multiplex real-time qPCR assay for four clinically important filamentous fungi, A. fumigatus , Fusarium spp., Mucorales, and Histoplasma capsulatum, with high sensitivity and specificity, which shows promising potential for prompt and precise diagnosis against fungal infection., Competing Interests: The authors declare no conflict of interest.

While fungal infections cause considerable morbidity and mortality, the performance of the current diagnostic tests for fungal infection is low. Even though fungal metagenomics or targeted next-generation sequencing have been investigated for various clinical samples, the real-time clinical utility of these methods still needs to be elucidated. In this study, we used internal transcribed spacer (ITS) and D1-D3 ribosomal DNA nanopore amplicon metagenomic sequencing to assess its utility in patients with fungal infections. Eighty-four samples from seventy-three patients were included and categorized into 'Fungal infection,' 'Fungal colonization,' and 'Fungal contamination' groups based on the judgement of infectious disease specialists. In the 'Fungal infection' group, forty-seven initial samples were obtained from forty-seven patients. Three fungal cases detected not by the sequencing but by conventional fungal assays were excluded from the analysis. In the remaining cases, the conventional fungal assay-negative/sequencing-positive group (n=11) and conventional fungal assay-positive/sequencing-positive group (n=33) were compared. Non-Candida and non-Aspergillus fungi infections were more frequent in the conventional-negative/sequencing-positive group (p-value = 0.031). We demonstrated the presence of rare human pathogens, such as Trichosporon asahii and Phycomyces blakesleeanus. In the 'Fungal infection' group and 'Fungal colonization' group, sequencing was faster than culturing (mean difference = 4.92 days, p-value < 0.001/ mean difference = 4.67, p-value <0.001). Compared to the conventional diagnostic methods including culture, nanopore amplicon sequencing showed a shorter turnaround time and a higher detection rate for uncommon fungal pathogens., Competing Interests: Conflicts of interest The authors declare that they have no competing interests., (Copyright © 2024 The Authors. Published by Elsevier GmbH.. All rights reserved.)

The contamination of mycotoxins is a serious problem around the world. It has detrimental effects on human beings and leads to tremendous economic loss. It is essential to develop a rapid and non-destructive method for contamination recognition particularly for early alarm. In this study, the whole-cell biosensor array was constructed and employed for rapid recognition of wheat contamination by combining with machine learning algorithms. Seven key VOCs were explored through univariate coupling to multivariate analysis of orthogonal partial least squares-discrimination analysis (OPLS-DA) models. The promoters of dnaK, katG, oxyR, soxS obtained from the stress-responsive of key VOCs were fused to the bacterial operon and fabricated on the whole-cell biosensor. The constructed whole-cell biosensor array was consisted with four kinds of sensors and 18 sensor unit. The bioluminescent intensity combined with linear machine learning algorithm of partial least squares discriminant analysis (PLS-DA) and non-linear algorithms of back propagating artificial neural network (BP-ANN) and least square support vector machine (LS-SVM) were employed to establish discrimination models for mold contamination especially for early warning. The Monte-Carlo strategy was performed to generate thirty subsets for modeling to give more reliable results. As a result, the whole-cell biosensor combined with non-linear algorithm of LS-SVM was practicable for detecting mold identification for wheat early-warning with the accuracy of 97.24%. Additionally, this study provides practical and effective methods not only for wheat quality guarantee and supervision but also for other foodstuffs., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)