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This study presents comprehensive insights into the microbiological profile across all concentrated chicken broth processing stages, utilizing a combination of amplicon sequencing based on metataxonomic and culturing techniques. Samples were systematically collected throughout the production chain, with each batch yielding 10 samples per day across eight different dates. These samples underwent thorough analysis, including 16S rRNA and ITS sequencing (n = 30), culture-dependent microbiological tests (n = 40), and physical-chemical characterization (n = 10). Culturing analysis revealed the absence of Listeria monocytogenes and Salmonella spp. at any stage of processing, counts of various microorganisms such as molds, yeasts, Enterobacteria, and others remained below detection limits. Notably, spore counts of selected bacterial groups were observed post-processing, indicating the persistence of certain species, including Bacillus cereus and Clostridium perfringens, albeit in low counts. Furthermore, the study identified a diverse array of bacterial and fungal species throughout the processing chain, with notable occurrence of spore-forming bacteria. The presence of spore-forming bacteria in the final product, despite thermal processing, suggests the need for enhanced strategies to mitigate their introduction and persistence in the processing premises. Thus, this study offers valuable insights into microbial dynamics and diversity through processing concentrated chicken broth., 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.)

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.)

Fusarioid fungi, particularly Neocosmospora solani and Fusarium oxysporum, are emerging as significant human pathogens, causing infections ranging from localized mycoses to life-threatening systemic diseases. Accurate identification and preservation of these fungi in clinical laboratories remain challenging because of their diverse morphologies and specific growth requirements. This study evaluated a novel milk-honey and malt agar (MHM) against conventional media for cultivating and preserving 60 clinical fusarioid isolates, including Neocosmospora spp. (n = 47), Bisifusarium spp. (n = 5), and Fusarium spp. (n = 8). Compared with Sabouraud dextrose 2 % agar (SDA) and malt extract agar (ME2), MHM significantly increased conidia production (p < 0.0001, mean = 3.4 × 10 3 , standard deviation (SD) = ±1.3 × 10 3 ), with results similar to those of carnation leaf agar (CLA). MHM facilitated superior preservation of fusarioid viability for up to one year at room temperature on slant cultures and over two years on swabs in Amies gel with charcoal, outperforming current methods such as Castellani (water) or cryopreservation. Morphological characterization of fusarioid fungi grown on MHM revealed distinct growth patterns and conidial structures for Neocosmospora, Bisifusarium, and Fusarium species, aiding in identifying these genera. The superior performance of MHM in stimulating conidiation, maintaining viability, and preserving morphology underscore its potential as a reference medium for medically relevant fusarioid fungi, with broad implications for clinical mycology laboratories and resource-limited settings., 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. Published by Elsevier B.V.)

Background: Freshly extracted sugarcane juice is an ideal substrate for microbial fermentation and browning reactions. The present study is the first report on the potential of pulsed light (PL) processing in improving microbial stability with the retention of major bioactive. PL processing at different levels of voltage (2.1-2.7 kV) and number of pulses (100-200) was explored. The present study aimed to investigate the impact of PL processing on the quality of sugarcane juice, bioactive composition and microbial load., Results: The microbial load, such as aerobic mesophiles, yeast and mold, and total coliform, was reduced to below 1 log colony-forming units mL -1 in juice samples subjected to intense PL treatment at 2.7 kV. The maximum value of the total color difference of the sugarcane juice was below 4.0, even at extreme levels of PL process parameters. In comparison with the unprocessed juice, the reduction in total phenols (Folin ciocalteu reagent assay) and the total antioxidant capacity (2,2-diphenyl-1-picrylhydrazyl free radical scavenging assay) was limited to 6% and 16.7%, respectively, when treated at 2.7 kV/200 pulses. The pH and total soluble solids of the juice remained unaffected in all the processed samples. Among the process parameters considered, the treatment voltage was found to significantly affect the quality parameters and microbial load., Conclusion: PL processing at 2.1 kV/170 pulses gave an optimally processed juice with a microbial load below the permissible limit and desirability value of 0.77. The results suggest that the PL treatment is effective for enhancing the microbial stability and maintaining the bioactive components of the sugarcane juice. Furthermore, the outcomes from the present study are expected to pave the way for further in-depth investigation of the effect of PL treatment on the critical quality attributes and shelf life of sugarcane juice. The technology will be useful for adoption by different stakeholders, including manufacturers and retailers in the food processing sector. © 2024 Society of Chemical Industry., (© 2024 Society of Chemical Industry.)

Background: Chestnut fruit quality is affected by fungal contamination. The study of the patterns of contamination in the postharvest is crucial to individuate the critical phases and propose solutions. To understand how fungal colonization varies on fruits, the composition of mycobiota was investigated in postharvest handling and in between tissues (shell and kernel)., Results: Fungal sequences were clustered into 308 operational taxonomic units (OTUs). Biodiversity was higher in shell than kernel tissues. Results evidenced the risk of new contamination in specific phases such as the 'cold bath' and storage. Genera known as mycotoxin producers were detected in all phases. Specifically, 47 OTUs belonging to Penicillium, eight to Fusarium and two to Aspergillus genera were identified. While Fusarium spp. was sensitive to 'warm bath' phase, Penicillium spp. was largely insensitive and accumulated in storage conditions. Surprisingly, Aspergillus spp. was poorly represented. Aflatoxin, ochratoxin A, fumonisins and T-2/HT-2 detection was performed for shell and kernel, and process phases. Higher contamination was observed on shell than in kernel samples. While aflatoxins were within the European Union (EU) limits for dry fruits, Ochratoxin exceeded the EU limits. The present study represents the first report of fumonisins and T-2/HT-2 detection in chestnuts., Conclusion: Fungal contamination taxa is high in chestnut fruits following postharvest handling and storage. A parametrization of process phases such as the 'warm bath' is functional to reduce the risk for some taxa. For other spoilage and mycotoxigenic genera strict sanitation procedures of equipment and water must be individuated and implemented to reduce their impact. © 2024 The Author(s). Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry., (© 2024 The Author(s). Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.)

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.

A magnetic biochar nanomaterial derived from fungal hyphae was introduced into the sample preparation field. The magnetic fungal hyphae-derived biomass carbon (MFHBC) could be produced by a controllable hydrothermal method. In order to obtain the best sorbent for magnetic solid-phase extraction (MSPE), the reaction conditions containing temperature, time and the consumption of fungal hyphae were investigated. A series of MFHBC materials were characterized by vibrating sample magnetometers, X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, and transmission electron microscopy. A material with a satisfactory saturation magnetization (21.58 emu g-1) and largest surface area (88.06 m2 g-1) was selected as the sorbent to extract ten typical organochlorine pesticides (OCPs). The extraction conditions were optimized as 20 mL of sample solution with 70 mg of sorbent and 2.0 g of NaCl oscillated at 50 °C for 5.0 min. And the optimum desorption was performed by oscillating sorbent in 1.0 mL acetonitrile for 5.0 min. Then, the MFHBC-based MSPE-GC-MS/MS methods were established for different samples including water samples, tea beverages, and Chinese traditional medicines. The linearities were 10-2500 ng L -1 or 100-25,000 ng kg -1 , and the limits of detection were 0.3-13.9 ng L -1 for water sample, 0.1-9.7 ng L -1 for tea beverage samples, 0.1-21.4 ng L -1 for Shenqi Fuzheng injection samples, and 7.2-278.3 ng kg -1 for Astragali Radix decoction pieces. Except for satisfactory repeatability (RSDs ≤13.8%) in intra-day and inter-day tests (n = 3), the reproducibility (RSDs ≤13.5%, n = 3) of MFHBC was acceptable. The methods were applied in the determination of OCPs from above real samples, with the recoveries of 80.5-117.2% and the RSDs (n = 3) <8.9%. The methods were suitable in the sensitive determination of OCPs from simple to complex matrix samples., Competing Interests: Declaration of competing interest None., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Background: Saccharomyces cerevisiae CECA was a potential indigenous Chinese wine yeast that can produce aroma and flavor in Cabernet Sauvignon wines. High-throughput sequencing combined with metabolite analysis was applied to analyze the effects of CECA inoculation on the native microbial community interaction and metabolism during Cabernet Sauvignon wine fermentation., Results: Fermentations were performed with three different inoculant strategies: spontaneous fermentation without inoculation, inoculation with CECA after grape must sterilization, and direct inoculation of CECA. Results showed that the diversity of bacteria (P = 0.033) is more sensitive to CECA inoculation than fungi (P = 0.563). In addition, CECA inoculation altered the species composition of core microorganisms (relative abundance >1%) and the keystone species (accounting for the top 1% of the most important interactions), as well as of the biomarkers (linear discriminant analysis > 3.0, P < 0.05). Furthermore, the inoculation could change the cluster of metabolites, and these differential metabolite sets were correlated with four fungal taxa of Issatchenkia, Issatchenkia orientalis, Saccharomycetales, Saccharomycetes and two bacterial taxa of Pantoea, Tatumella ptyseos, were significantly correlated. Inoculated fermentation also altered the correlation between dominant microorganisms and aroma compounds, giving Cabernet Sauvignon wines more herbal, floral, fruity, and cheesy aromas., Conclusion: Saccharomyces cerevisiae CECA and dimethyl dicarbonate (DMDC) inhibition treatments significantly altered the microbial community structure of Cabernet Sauvignon wines, which in turn affected the microbial-metabolite correlation. These findings will help winemakers to control the microbial dynamics and functions during wine fermentation, and be more widely used in regional typical wine fermentations. © 2024 Society of Chemical Industry., (© 2024 Society of Chemical Industry.)

The Latin America region has a considerable extent of varied climate conditions: from tropical, subtropical, and warm temperate to temperate. Among the surface territory, different agricultural products are produced, making them an important food source for human consumption. Fungal species commonly colonize those important agricultural products and often contaminate them with mycotoxins that have a major impact on health, welfare, and productivity. Nowadays, special attention is paid to modified mycotoxins, which are those that cannot be detected by conventional analytical methods. However, little data about their natural occurrence in food and feed is available, especially in Latin American countries, where, among all the countries in this region, only a few of them are working on this subject. Thus, the present review summarizes the published information available in order to determine the possible human exposure risk to these toxins., (© 2024. The Author(s) under exclusive licence to Society for Mycotoxin (Research Gesellschaft für Mykotoxinforschung e.V.) and Springer-Verlag GmbH Germany, part of Springer Nature.)

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).)

Heavy metal (HM) contaminants are the emerging driving force for reshaping the microflora of plants by eradicating the non-tolerance and non-resistant microbes via their lethal effects. Seeds served as a prime source of ancestral microbial diversity hereditary transfer from generation to generation. However, the problem arises when they got exposed to metal contamination, does metal pollutant disrupt the delicate balance of microbial communities within seeds and lead to shifts in their microflora across generations. In this study, the endophytic community within Zea mays seeds was compared across three distinct regions in Yunnan province, China: a HM-contaminated site Ayika (AK), less-contaminated site Sanduoduo (SD), and a non-contaminated Site Dali (DL). High-throughput sequencing techniques were employed to analyze the microbial communities. A total of 492,177 high-quality reads for bacterial communities and 1,001,229 optimized sequences for fungal communities were obtained. These sequences were assigned to 502 and 239 operational taxonomic units (OTUs) for bacteria and fungi, respectively. A higher diversity was recorded in AK samples than in SD and DL. Microbial community structure analysis showed higher diversity and significant fluctuation in specific taxa abundance in the metal-polluted samples exhibiting higher response of microbial flora to HM. In AK samples, bacterial genera such as Gordonia and Burkholderia-Caballeronia-Paraburkholderia were dominant, while in SD Pseudomonas and Streptomyces were dominant. Among the fungal taxa, Fusarium, Saccharomycopsis, and Lecanicillium were prevalent in HM-contaminated sites. Our finding revealed the influential effect of HM contaminants on reshaping the seed microbiome of the Zea mays, showing both the resilience of certain important microbial taxa as well the shifts in the diversity in the contaminated and pristine conditions. The knowledge will benefit to develop effective soil remediation, reclamation, and crop management techniques, and eventually assisting in the extenuation of metal pollution's adverse effects on plant health and agricultural productivity., (© 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).)

This work focused on the physico-chemical, biochemical and microbiological characterization of a new organic fertilizer based on fermented forest litter (FFL) mixed with agro-industrial by-products, on the culture realized in airtight glass bottle. Under strict anaerobiosis (0% initial oxygen concentration (IOC)), after a 16-day batch culture, the bottle-headspace analysis showed that the specific CO 2 production rate was low (0.014 mL/h.g dry matter) compared to those reached under aerobic conditions (e.g. 0.464 mL/h.g dm at 21% IOC). Moreover, the culture displayed a slight fermented fruity odour, mainly due to ethanol and ethyl acetate detected in the headspace (335 µL and 58.6 µL accumulated, respectively). The FFL organic matter degradation followed by infrared spectroscopy and catabolic potential and diversity characterized by BIOLOG ® EcoPlates were poor and pH dropped to 4.54. The microbiome's metabolism was oriented toward lactic fermentation with medium acidification, enrichment in lactic acid bacteria (LAB), depletion in fungi and absence of pathogens. By increasing IOC from 0 to 21%, the respirometric activity, and the catabolic potential and diversity increased. However, some enterobacteria were detected above 5% IOC. Ethanol and ethyl acetate decreased strongly with IOC, and aromatics and proteins contained in the solid matrix remained in the culture. This study showed the importance of oxygen on the final product. A 2% IOC was found to ensure an optimal balance between LAB development, preservation of functional catabolic diversity and bio-product free of microbial pathogens., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

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.)

Over three-quarters of Earth's surface exhibits extreme environments where life thrives under harsh physicochemical conditions. While prokaryotes have often been investigated in these environments, only recent studies have revealed the remarkable adaptability of eukaryotes, in particular fungi. This study explored the mycobiota of two meromictic hypersaline lakes, Ursu and Fără Fund, in Transylvania (Romania). The intrinsic and extrinsic fungal diversity was assessed using amplicon sequencing of environmental DNA samples from sediments, water columns, surrounding soils, and an associated rivulet. The fungal communities, illustrated by the 18S rRNA gene and ITS2 region, exhibited contrasting patterns between the lakes. The ITS2 region assessed better than the 18S rRNA gene the fungal diversity. The ITS2 data showed that Ascomycota was the most abundant fungal group identified in both lakes, followed by Aphelidiomycota, Chytridiomycota, and Basidiomycota. Despite similar α-diversity levels, significant differences in fungal community structure were observed between the lakes, correlated with salinity, total organic carbon, total nitrogen, and ammonium. Taxonomic profiling revealed depth-specific variations, with Saccharomycetes prevalent in Ursu Lake's deeper layers and Lecanoromycetes prevalent in the Fără Fund Lake. The functional annotation using FungalTraits revealed diverse ecological roles within the fungal communities. Lichenized fungi were dominant in Fără Fund Lake, while saprotrophs were abundant in Ursu Lake. Additionally, wood and soil saprotrophs, along with plant pathogens, were more prevalent in the surrounding soils, rivulet, and surface water layers. A global overview of the trophic relations in each studied niche was impossible to establish due to the unconnected graphs corresponding to the trophic interactions of the analyzed fungi. Plotting the unweighted connected subgraphs at the genus level suggests that salinity made the studied niches similar for the identified taxa. This study shed light on the understudied fungal diversity, distribution, and ecological functions in hypersaline environments., (© 2024. The Author(s).)

Tillandsia recurvata is an epiphytic plant commonly found in tropical regions and colonizes tree trunks, fences, and power wires. This plant plays an important role in interacting with trees, sharing microorganisms, and performing specific functions in the process of tree colonization. The objective of this study was to evaluate and compare the microbiomes of T. recurvata collected from two different locations (trees and fences) and two plant tissues (leaves and roots). The hypothesis of this study was that the microbiome of T. recurvata is composed of microorganisms that would provide nutritional support to compensate for the lack of nutrients in a particular growth support. The results showed significant differences in microbial diversity between trees and fences, with trees exhibiting higher richness and more complex microbial networks. Proteobacteria was the most prevalent bacterial phylum, with Actinobacteria and Sphingomonas also playing key roles in nitrogen fixation and plant growth. Fungal communities were similar across locations, with Ascomycota and Basidiomycota being predominant, but Paraconiothyrium and Nigrospora showed significant differences in abundance between trees and fences. Functional analysis indicated similar metabolic profiles across leaf and root samples, with key functions for T. recurvata including carbohydrate and amino acid metabolism, stress control, and biofertilization., (© 2024. The Author(s).)

Chernozem soil is a valuable resource and contains a great diversity of microorganisms that play a global role in the process of soil formation, the species diversity of which has changed over the last five years under the influence of different agrotechnologies. For the first time, under the conditions of the Central Chernozem region, grain and fallow crop rotation, studies using the DNA-metabarcoding method were carried out to study the taxonomic structure of bacteria, fungi, cyanobacteria, and microalgae communities in the arable horizon of typical medium loamy chernozem under winter wheat cultivation. A comparative analysis of the composition of the genotypes showed significant differences in the presented level of mineral nutrition of the soil NPK (60) and NPK (100) compared with the control variant. After processing the 16S and 18S rRNA datasets, a similar trend of decreasing numbers of pro- and eukaryotic species was found from 6296 (control without MF) to 5310 with NPK (60) and to 4643 with NPK (100), respectively. The Chao1 index indicated that the expected diversity within the prokaryotic group was higher in the control without MF at 211, but decreased to 182 and 193 with NPK (60) and NPK (100) fertilizers, respectively. Analysis of the eukaryotic group revealed a 2.6- and 2.9-fold decrease in diversity by class and genus, respectively, depending on the nutritional levels in agrotechnologies, owing to the use of MF. In the prokaryotic community, Alphaproteobacteria microorganisms predominated at an amount of 14.20-14.46%, with Cyanophyceae accounting for 5.2-9.9%. The diversity of eukaryotes was smaller than the number of classes of prokaryotes; the main dominant were Zygnematophyceae 19.5-41%, Chlorophyceae occupied 10.4-15.8%. On the other hand, the doses of fertilizers used contributed to the emergence of dominant species adapted to high doses of mineral nutrients for plants., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

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.

Stormwater bioretention cells are green stormwater infrastructure systems that can help mitigate flooding and remove contaminants. Plants and bacteria improve nutrient removal and degrade organic contaminants; however, the roles of fungi in bioretention cells are less known. Although mycorrhizal fungi aid in plant growth/improve nutrient uptake, there is a notable lack of research investigating fungal diversity in bioretention cells. Other types of fungi could benefit bioretention cells ( e.g. , white rot fungi degrade recalcitrant contaminants). This study addresses the knowledge gap of fungal function and diversity within stormwater bioretention cells. We collected multiple soil samples from 27 different bioretention cells in temperate-climate eastern Iowa USA, characterized soil physicochemical parameters, sequenced the internal transcribed spacer (ITS) amplicon to identify fungal taxa from extracted DNA, and measured functional gene abundances for two fungal laccases ( Cu1 , Cu1A ) and a fungal nitrite reductase gene ( nirKf ). Fungal biodegradation functional genes were present in bioretention soils (mean copies per g: 7.4 × 10 5 nirKf , 3.2 × 10 6 Cu1 , 4.0 × 10 8 Cu1A ), with abundance of fungal laccase and fungal nitrite reductase genes significantly positively correlated with soil pH and organic matter (Pearson's R : >0.39; rho < 0.05). PERMANOVA analysis determined soil characteristics were not significant explanatory variables for community composition (beta diversity). In contrast, planting specifications significantly impacted fungal diversity; the presence/absence of a few planting types and predominant vegetation type in the cell explained 89% of variation in fungal diversity. These findings further emphasize the importance of plants and media as key design parameters for bioretention cells, with implications for fungal bioremediation of captured stormwater contaminants.

Background: Early diagnosis of invasive fungal disease is essential for optimizing management. Although the clinical utility of fungal polymerase chain reaction (PCR) testing on plasma and bronchoalveolar lavage (BAL) has been established, the role of follow-up testing remains unclear., Methods: This was a retrospective single-center study. The yield of follow-up PCR for Aspergillus species, Mucorales agents, Fusarium species, Scedosporium species, dimorphic fungi, Pneumocystis jirovecii, and Candida species on plasma and/or BAL was measured at intervals of 1, 2, 3, and 4 weeks following a negative result., Results: A total of 1389 follow-up tests on 406 plasma specimens from 264 patients and 983 BAL specimens from 431 patients were evaluated. Overall, the positivity rate at 1, 2, 3, and 4 weeks was 2.7% (4/148), 3.3% (4/123), 5.1% (4/78), and 3.5% (2/57), respectively, on plasma, and 0% (0/333), 0.3% (1/288), 0.4% (1/228), and 0.7% (1/134), respectively, on BAL. Conversions occurred with Aspergillus species, Mucorales agents, and Fusarium species PCR on plasma and Aspergillus species and P jirovecii PCR on BAL. All patients who converted were immunocompromised. Within 1 week of a prior negative test, 2 Aspergillus and 2 Mucorales PCRs were positive on plasma, and zero tests were positive on BAL. In week 1, only 1 Aspergillus species that was positive on day 7 was classified as probable fungal disease., Conclusions: Fungal PCR follow-up testing on plasma and BAL within 4 weeks of a prior negative result was of low yield and rarely generated a positive result considered clinically significant in the first week., Competing Interests: Potential conflicts of interest. The authors: No reported conflicts of interest. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed., (© The Author(s) 2024. Published by Oxford University Press on behalf of Infectious Diseases Society of America. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

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.

The biotechnological potential for agricultural applications in the soil in the thawing process on Whalers Bay, Deception Island, Antarctica was evaluated using a metagenomic approach through high-throughput sequencing. Approximately 22.70% of the sequences were affiliated to the phyla of the Bacteria dominion, followed by 0.26% to the Eukarya. Proteobacteria (Bacteria) and Ascomycota (Fungi) were the most abundant phyla. Thirty-two and thirty-six bacterial and fungal genera associated with agricultural biotechnological applications were observed. Streptomyces and Pythium were the most abundant genera related to the Bacteria and Oomycota, respectively. The main agricultural application associated with bacteria was nitrogen affixation; in contrast for fungi, was associated with phytopathogenic capabilities. The present study showed the need to use metagenomic technology to understand the dynamics and possible metabolic pathways associated with the microbial communities present in the soil sample in the process of thawing recovered from the Antarctic continent, which presented potential application in processes of agro-industrial interest., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

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.)

Objective: To investigate the pathogen species, composition, and distribution characteristics of infectious keratitis pathogens in Shandong Province and its surrounding areas. Methods: In this cross-sectional study, patients with keratitis who underwent corneal sampling and microbiological culture at the Shandong Eye Hospital from January 1, 2018 to December 31, 2022 were included. Under topical anesthesia, the edge of the lesion was scraped by an experienced physician. The samples were inoculated on blood agar and Sabouraud dextrose agar plates, separately for bacterial and fungal culture and identification. If necessary, the samples were inoculated on a non-nutrient agar medium with Escherichia coli for Acanthamoeba culture. Bacterial isolates were identified using Vitek 2 compact or matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Fungal isolates were identified based on morphological characteristics or sent to a company for sequencing in cases of difficult identification. The epidemiological data of the patients, pathogen species and number (counting as 1 strain if the same strain was isolated from multiple corneal specimens of the same patient), culture positivity rate, and seasonal distribution were recorded. Differences in pathogen positivity rates among different seasons were analyzed using the chi-square test. Results: Among the 4, 024 patients with infectious keratitis during the study period, there were 2 510 males (62.3%) and 1 514 females (37.6%), aged from 46 days to 94 years. Positive microbial culture results were achieved in 2, 363 patients (58.7%), including 906 cases (38.3%) with bacterial positivity, 1 231 cases (52.1%) with fungal positivity, 28 cases (1.2%) with Acanthamoeba positivity, and 198 cases (8.4%) with mixed fungal and bacterial infections. A total of 2 561 strains were isolated, including 1 104 bacterial strains. The most common bacteria were coagulase-negative Staphylococcus spp. (623/1 104, 56.4%), followed by Streptococcus spp. (131/1 104, 11.9%) and Pseudomonas aeruginosa (68/1 104, 6.2%). The most common fungi were Fusarium spp. (634/1 429, 44.4%), followed by Aspergillus spp. (279/1 429, 19.5%) and Alternaria spp. (229/1 429, 16.0%). Bacterial keratitis was more common in summer and autumn, while fungal keratitis was more common in autumn and winter. Conclusions: Among infectious keratitis cases in Shandong Eye Hospital, Fusarium species were predominant fungal pathogens, while coagulase-negative Staphylococcus predominated in bacterial pathogens. Both fungal and bacterial corneal infections showed seasonal variations.

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.)

Phyllosphere microorganisms are essential for plant growth and health. Although there are an increasing number of studies showing that the composition of phyllosphere communities varies among different plant species, it remains unclear whether and how their bacterial and fungal community composition predictably varies with plant traits and leaf age. In this study, we used high-throughput sequencing to explore the diversity and composition of phyllosphere communities in needles of different ages (originating from different cohorts) for three evergreen coniferous species (Pinus koraiensis, Picea koraiensis, and Abies nephrolepis). Our results indicated that Gammaproteobacteria (bacteria) and Dothideomycetes (fungi) were dominant in newly formed needles, whereas Actinobacteria (bacteria) and Eurotiomycetes (fungi) were dominant in perennial needles. Tree species identity and needle age were the main factors explaining the variations of the α diversity (species richness of phyllosphere communities) and β diversity (dissimilarity among phyllosphere communities). In particular, we found that leaf dry matter content, leaf mass per area, and total phosphorus content emerged as key predictors of composition and diversity of phyllosphere microbial communities, underscoring the major influence of tree species identity and needle age on phyllosphere communities through changes in plant functional traits. Finally, we found that the interaction between tree species identity and needle age also contributed significantly to explaining the diversity and composition of phyllosphere communities, probably because differences in plant functional traits or environmental conditions between new and perennial needles depend on tree growth rates and resource acquisition strategies. These findings provide new insights into the mechanisms of community assembly among different evergreen tree species and offer a better understanding of the interactions between plant traits and phyllosphere microorganisms during needle aging., (© 2024. The Author(s).)

To investigate the structure, diversity, and function of different paddy soil fungal communities and the factors affecting them in typical paddy cropping areas in China, five typical Chinese paddy soils were selected in this study, and the composition and diversity of soil fungal communities were comparatively analyzed using high-throughput sequencing technology and functionally predicted using the FUNGuild microecological tool. The results showed that： ① The fungal community diversity of soil samples from Heilongjiang （HLJ） was significantly lower than that of the other four regions （ P <0.05）； the highest fungal community richness was found in paddy soils from Yunnan （YN）, which was significantly higher than that of the other regions （ P <0.05）； and the soil samples from Hainan （HN）, Jiangxi （JX）, and Shandong （SD） were relatively close to each other. The highest average relative abundance at the level of the five typical paddy phyla was Ascomycota, and the genus with the highest average relative abundance was Tausonia . ② Fungi had the largest proportion of saprophytic trophic types, and their corresponding environmental functions were stronger. ③ The species abundance of soil fungi was highly significantly correlated with soil TP, EC, and BD （ P <0.01）, and redundancy analyses also showed that soil TP was the main driver of the fungal community as well as the saprophytic functional taxa. The above results showed that the soil fungal community diversity and structure varied greatly among samples, and the relative abundance of fungal genera was affected by soil physical and chemical properties and altered the fungal community structure in paddy fields. The development of this study will provide theoretical references for the sustainable management based on fungal diversity and function of paddy fields.

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).)

In macroscale ecosystems, such as rainforests or coral reefs, the spatial localization of organisms is the basis of our understanding of community ecology. In the microbial world, likewise, microscale ecosystems are far from a random and homogeneous mixture of organisms and habitats. Accessing the spatial distribution of microbes is fundamental for understanding the functioning and ecology of the microbiota, as cohabiting species are more likely to interact and influence each other's physiology. An interkingdom microbial ecosystem is at the core of fungus-growing ant colonies, which cultivate basidiomycete fungi as a nutritional resource. Attine ants forage for diverse substrates (mostly plant-based), metabolized by the cultivated fungus while forming a spongy structure, a "microbial garden" that acts as an external gut. The garden is an intertwined mesh of fungal hyphae growing by metabolizing the substrate, opening niches for a characteristic and adapted microbiota to establish. The microbiota is thought to be a contributor to substrate degradation and fungal growth, though its spatial organization is yet to be determined. Here, we describe how we employ Scanning Electron Microscopy (SEM) to investigate, with unprecedented detail, the microbiota and biofilm spatial organization across different fungiculture systems of fungus-growing ants. SEM imaging has provided a description of the microbiota spatial structure and organization. SEM revealed that microbiota commonly assemble in biofilms, a widespread structure of the microbial landscapes in fungiculture. We present the protocols employed to fix, dehydrate, dry, sputter coating, and image such a complex community. These protocols were optimized to deal with delicate and heterogeneous samples, comprising plant and fungal biomass, as well as the microbiota and the biofilm.

Aims: Hypogeal environments with cultural heritage interest pose a real challenge for their preservation and conservation. The ancient Etruscan Necropolis of Tarquinia, Italy, consists of 200 tombs decorated with extraordinary mural paintings, of great artistic and historical value. Since the beginning of the restoration campaign in 2016, a regular microbiological survey has been performed in the Tomba degli Scudi. The aim of this study was to investigate the nature of an expansion of black spots on the pictorial layers recently observed., Methods and Results: To determine the origin of the black spots in the atrium chamber of the Tomba degli Scudi, the fungal community was sampled using various techniques: cellulose discs, swabs, and nylon membranes and investigated by a multi-analytical approach. The obtained results suggest that the identified fungal strains (e.g. Gliomastix murorum and Pseudogymnoascus pannorum) are common to many subterranean environments around the world, such as Lascaux cave., Conclusions: The continuous and long-term monitoring made it possible to detect alterations at an early stage and assess the harmfulness of different fungal strains. This work is a demonstration of the effectiveness of prevention and monitoring actions within these fragile and valuable environments., (© The Author(s) 2024. Published by Oxford University Press on behalf of Applied Microbiology International.)

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.)

Soil and wastewater samples contaminated by petroleum-related industries were collected from various locations in Saudi Arabia, a country known for its vast oil reserves. The samples were analyzed for their physicochemical properties, including the presence of metals, petroleum hydrocarbons, and aromatic compounds. A total of 264 fungal isolates were analyzed and categorized into eight groups of Aspergillus (194 isolates) and four groups of Penicillium (70 isolates). The potential of these fungal groups to grow in oil or its derivatives was investigated. Two isolates, Aspergillus tubingensis FA-KSU5 and A. niger FU-KSU69, were utilized in two remediation experiments-one targeting wastewater and the other focusing on polluted soil. The FA-KSU5 strain demonstrated complete removal of Fe 3+ , As 3+ , Cr 6+ , Zn 2+ , Mn 2+ , Cu 2+ and Cd 2+ , with bioremediation efficiency for petroleum hydrocarbons in the wastewater from these sites ranging between 90.80 and 98.58%. Additionally, the FU-KSU69 strain achieved up to 100% reduction of Co 2+ , Ba 2+ , B 3+ , V + , Ni 2+ , Pb 2+ and Hg 2+ , with removal efficiency ranging from 93.17 to 96.02% for aromatic hydrocarbons after 180 min of wastewater treatment. After 21 days of soil incubation with Aspergillus tubingensis FA-KSU5, there was a 93.15% to 98.48% reduction in total petroleum hydrocarbons (TPHs) and an 88.11% to 97.31% decrease in polycyclic aromatic hydrocarbons (PAHs). This strain exhibited the highest removal rates for Cd 2+ and As 3+ followed by Fe 3+ , Zn 2+ , Cr 6+ , Se 4+ and Cu 2+ . Aspergillus niger FU-KSU69 achieved a 90.37% to 94.90% reduction in TPHs and a 95.13% to 98.15% decrease in PAHs, with significant removal of Ni 2+ , Pb 2+ and Hg 2+ , followed by Co 2+ , V + , Ba 2+ and B 3+ . The enzymatic activity in the treated soils increased by 1.54- to 3.57-fold compared to the polluted soil. Although the mixture of wastewater and polluted soil exhibited high cytotoxicity against normal human cell lines, following mycoremediation, all treated soils and effluents with the dead fungal biomass showed no toxicity against normal human cell lines at concentrations up to 500 µL/mL, with IC 50 values ≥ 1000 µL/mL. SEM and IR analysis revealed morphological and biochemical alterations in the biomass of A. tubingensis FA-KSU5 and A. niger FA-KSU69 when exposed to petroleum effluents. This study successfully introduces non-toxigenic and environmentally friendly fungal strains play a crucial role in the bioremediation of contaminated environments. Both strains serve as low-cost and effective adsorbents for bio-remediating petroleum wastewater and oil-contaminated soil. Heavy metals and hydrocarbons, the primary pollutants, were either completely removed or reduced to permissible levels according to international guidelines using the dead biomass of FA-KSU5 and FA-KSU69 fungi. Consequently, the environments associated with this globally significant industry are rendered biologically safe, particularly for humans, as evidenced by the absence of cytotoxicity in samples treated with A. tubingensis FA-KSU5 and A. niger FA-KSU69 on various human cell types., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

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).)

The toxicity of the contaminated powder contributed to toxic aflatoxins has been well-known in the literature. However, before this study, the specific fungal strain behind aflatoxin production remained unidentified. Our research aimed to isolate and identify fungi from the tainted sandwiches while also assessing the preservation of sandwiches in ambient conditions. The study pinpointed Aspergillus flavus as the fungus responsible for aflatoxin production. Analysis revealed that the sandwich samples contaminated with pure A. flavus exhibited a significant Aflatoxin B1 (AFB1) concentration of 55.2 ± 0.21 ng/g, accompanied by a spore count of 2 × 10 6 Colony-Forming Unit (CFU)/g after ten days. In contrast, sandwich samples contaminated with the unspecified fungi displayed a lower AFB1 content of 16.21 ± 0.42 ng/g, with a spore count of 2.2 × 10 2  CFU/g after the same duration. In the prevention study, the efficacy of the ethanol spray method for inhibiting aflatoxin from A. flavus was investigated. Results demonstrated that a 70 % ethanol concentration at a ratio of 2.0 % total weight of the sandwich proved highly effective, significantly impeding fungal growth. This method extended the preservation time by sevenfold compared to the control. Importantly, tests at 2.0 % ethanol of the sandwich weight did not detect aflatoxin presence., 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 Ltd. All rights reserved.)

Background: Children in the intensive care unit (ICU) who suffer from severe basic diseases and low immunity are usually in critical condition. It is crucial to assist clinicians in selecting the appropriate empirical antibiotic therapies for clinical infection control., Methods: We retrospectively analyzed data from 281 children with bloodstream infection (BSI). Comparisons of basic data, pathogenic information, and drug resistance of the main bacteria were conducted., Results: We detected 328 strains, including Gram-positive bacteria (223, 68%), mainly coagulase-negative Staphylococci (CoNS); Gram-negative bacteria (91, 27.7%); and fungi (14, 4.3%). The results of the binary logistic regression analysis showed that the main basic disease was an independent risk factor for death. Compared with Escherichia coli, Klebsiella pneumoniae exhibited a higher proportion of extended-spectrum β-lactamases (ESBLs), and its resistance to some β-lactamides and quinolones antibiotics were lower. Twenty-seven isolates of multidrug-resistant (MDR) bacteria were detected, of which carbapenem-resistant Acinetobacter baumannii (CRAB) accounted for the highest proportion (13, 48.2%)., Conclusions: CoNS was the principal pathogen causing BSI in children in the ICU of children, and Escherichia coli was the most common Gram-negative pathogen. The main basic disease was an independent risk factor for death. It is necessary to continuously monitor patients with positive blood cultures, pay special attention to detected MDR bacteria, and strengthen the management of antibiotics and prevention and control of nosocomial infections., (© 2024. The Author(s).)

Purpose: To evaluate microbiological cultures of cataract surgical devices and products that were reused for multiple cases., Setting: Aravind Eye Hospital, Pondicherry, Tamil Nadu, India., Design: Prospective cohort study., Methods: Samples from multiple surgical instruments and products that were reused for consecutive cataract surgeries underwent bacterial and fungal cultures and were monitored alongside positive controls for 7 days. This included instruments that were processed using immediate use steam sterilization (IUSS) between cases (eg, surgical cannulas, syringes, phacoemulsification and coaxial/bimanual irrigation/aspiration [I/A] tips, phacoemulsification and I/A sleeves) (Group 1), instruments that were used without sterilization between cases (eg, phacoemulsification tubing/handpieces, coaxial I/A handpieces) (Group 2), and the residual (unused) fluid from balanced salt solution bags after being used for multiple patients (Group 3)., Results: 3333 discrete samples were collected from all 3 product groups that were reused across multiple patients. In all collected samples, no bacterial or fungal growth was observed. Of the 3241 cataract surgeries that used reused and IUSS-sterilized instruments alongside instrument sets cultured on the same day and balanced salt solution bags shared across multiple patients, no eyes developed endophthalmitis over a 6-week follow-up period., Conclusions: Bacterial or fungal growth was not found in extensive microbiological cultures of IUSS-sterilized ophthalmic surgical instruments and cataract surgical products that were reused in multiple patients. This microbiological data complements clinical endophthalmitis data from 2 million consecutive cases at the Aravind Eye Hospital, suggesting that their instrument and surgical supply processing practices may allow for safe and sustainable ophthalmic care., (Copyright © 2024 Published by Wolters Kluwer on behalf of ASCRS and ESCRS.)

Accurate identification of the fungal community spontaneously colonizing food products, aged in natural and not controlled environments, provides information about potential mycotoxin risk associated with its consumption. Autochthonous mycobiota colonizing cheese aging in Dossena mines, was investigated and characterized by two approaches: microbial isolations and metabarcoding. Microbial isolations and metabarcoding analysis were conducted on cheese samples, obtained by four batches, produced in four different seasons of the year, aged for 90 and 180 days, by five dairy farms. The two approaches, with different taxonomical resolution power, highlighted Penicillium biforme among filamentous fungi, collected from 58 out of 68 cheeses, and Debaryomyces hansenii among yeasts, as the most abundant species (31 ÷ 65%), none representing a health risk for human cheese consumption. Shannon index showed that the richness of mycobiota increases after 180 days of maturation. Beta diversity analysis highlighted significant differences in composition of mycobiota of cheese produced by different dairy farms and aged for different durations. Weak negative growth interaction between P. biforme and Aspergillus westerdijkiae by in vitro analysis was observed leading to hypothesize that a reciprocal control is possible, also affected by natural environmental conditions, possibly disadvantageous for the last species., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Milena Brasca reports financial support was provided by CheeseMine project (201801063265), funded by Lombardy Region (Italy) within FEASR program. If there are other authors, they 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 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Background: New antifungal agents are required to mitigate against azole-resistant Aspergillus and drug-resistant non-Aspergillus moulds. The novel orotomide, olorofim (F2G, Manchester, UK), has potent fungicidal activity against Aspergillus including azole-resistant Aspergillus fumigatus, Lomentospora prolificans and Scedosporium spp. Development of olorofim-specific clinical breakpoints/epidemiological cut-off values requires reliable MIC data., Objectives: Determine the in vitro activity of olorofim compared with standard antifungals against mould pathogens at an Australian hospital., Materials and Methods: Olorofim MICs were determined for 507 clinical mould isolates using the CLSI M38-A3 standard. MICs of amphotericin B, anidulafungin, posaconazole, voriconazole and isavuconazole were obtained using Sensititre™ YeastOne YO10 and AUSNMRCI panels (Thermo-Fisher Scientific)., Results: A. fumigatus sensu stricto was the commonest species (33.3%) followed by L. prolificans (18.3%), Scedosporium (11.4%) and Fusarium (6%) species. Olorofim modal MICs were ≤0.25 mg/L (MIC90 0.25 mg/L) for all Aspergillus except Aspergillus Section Usti (1 mg/L); MICs for nine azole-resistant/non-wild-type A. fumigatus ranged from 0.008 to 0.125 mg/L. The MIC90 of olorofim for L. prolificans was 0.5 mg/L, 0.25-0.5 mg/L for Scedosporium spp. and 8 mg/L for the F. solani complex but with modal MICs of 0.25 and 0.008 mg/L for F. oxysporum and F. proliferatum complexes, respectively. For Verruconis gallopava (n = 10), the olorofim MIC90 was 0.06 mg/L (voriconazole MIC90 2 mg/L, isavuconazole MICs of 4->8 mg/L). Olorofim had little activity against other dematiaceous moulds including Exophiala species., Conclusions: Olorofim was highly active against Aspergillus spp. including azole-resistant A. fumigatus, L. prolificans, Scedosporium spp. and some Fusarium species with the new finding of potent activity against V. gallopava., (© The Author(s) 2024. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

The positive detection rate of blood metagenomic next-generation sequencing (mNGS) was still too low to meet clinical needs, while pus from the site of primary infection may be advantageous for identification of pathogens. To assess the value of mNGS using pus in patients with sepsis, thirty-five samples were collected. Pathogen identification and mixed infection diagnosis obtained by use of mNGS or cultivation methods were compared. Fifty-three aerobic or facultative anaerobes, 59 obligate anaerobes and 7 fungi were identified by the two methods. mNGS increased the accuracy rate of diagnosing aerobic or facultative anaerobic infections from 44.4% to 94.4%; mNGS also increased the sensitivity of diagnosing obligate anaerobic infections from 52.9% to 100.0%; however, mNGS did not show any advantage in terms of fungal infections. Culture and mNGS identified 1 and 24 patients with mixed infection, respectively. For obligate anaerobes, source of microorganisms was analyzed. The odontogenic bacteria all caused empyema (n = 7) or skin and soft tissue infections (n = 5), whereas the gut-derived microbes all caused intra-abdominal infections (n = 7). We also compared the clinical characteristics of non-obligate anaerobic and obligate anaerobic infection groups. The SOFA score [9.0 (7.5, 14.3) vs. 5.0 (3.0, 8.0), P = 0.005], procalcitonin value [4.7 (1.8, 39.9) vs. 2.50 (0.7, 8.0), P = 0.035], the proportion of septic shock (66.7% vs. 35.3%, P = 0.044) and acute liver injury (66.7% vs. 23.5%, P = 0.018) in the non-obligate anaerobic infection group were significantly higher than those in the obligate anaerobic infection group. In patients with sepsis caused by purulent infection, mNGS using pus from the primary lesion may yield more valuable microbiological information., (© 2024. The Author(s).)