The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

Spinach seed microbiome characteristics linked to suppressiveness against Globisporangium ultimum damping-off

Recently we demonstrated that the seed microbiome of certain spinach (Spinacia oleracea) seed lots can confer disease suppression against Globisporangium ultimum damping-off (previously known as Pythium ultimum). We hypothesized that differences in the microbial community composition of spinach seed lots correlate with the levels of damping-off suppressiveness of each seed lot. Here, we show that a large proportion of variance in seed-associated bacterial (16S) and fungal (Internal Transcribed Spacer 1) amplicon sequences was explained by seed lot identity, while 9.8% of bacterial and 7.1% of fungal community variance correlated with disease suppression. More specifically, a higher relative abundance of basidiomycetous dimorphic yeasts such as Vishniacozyma, Filobasidium, and Papiliotrema and of the bacterial genus Massilia was a key feature of suppressive seed microbiomes. We suggest that the abundance of these genera is indicative of seed lot suppressive potential. Seed processing and treatment can become more targeted with indicator taxa being used to evaluate the presence of beneficial seed-associated microbial functions. This process, in turn, could contribute to the sustainable management of seedling diseases. Finally, this study highlights the ubiquity of yeasts in spinach seed microbiota and their potential beneficial roles for seed health.

Fungal communities in boreal soils are influenced by land use, agricultural soil management, and depth

Land use and agricultural soil management affect soil fungal communities that ultimately influence soil health. Subsoils harbor nutrient reservoir for plants and can play a significant role in plant growth and soil carbon sequestration. Typically, microbial analyses are restricted to topsoil (0-30 cm) leaving subsoil fungal communities underexplored. To address this knowledge gap, we analyzed fungal communities in the vertical profile of four boreal soil treatments: long-term (24 years) organic and conventional crop rotation, meadow, and forest. Internal transcribed spacer (ITS2) amplicon sequencing revealed soil-layer-specific land use or agricultural soil management effects on fungal communities down to the deepest measured soil layer (40-80 cm). Compared to other treatments, higher proportion of symbiotrophs, saprotrophs, and pathotrophs + plant pathogens were found in forest, meadow and crop rotations, respectively. The proportion of arbuscular mycorrhizal fungi was higher in deeper (>20 cm) soil than in topsoil. Forest soil below 20 cm was dominated by fungal functional groups with proposed interactions with plants or other soil biota, whether symbiotrophic or pathotrophic. Ferrous oxide was an important factor shaping fungal communities throughout the vertical profile of meadow and cropping systems. Our results emphasize the importance of including subsoil in microbial community analyses in differently managed soils.

Gut Microbiome Diversity in European Honeybees (Apis mellifera L.) from La Union, Northern Luzon, Philippines

Insects often rely on symbiotic bacteria and fungi for various physiological processes, developmental stages, and defenses against parasites and diseases. Despite their significance, the associations between bacterial and fungal symbionts in Apis mellifera are not well studied, particularly in the Philippines. In this study, we collected A. mellifera from two different sites in the Municipality of Bacnotan, La Union, Philippines. A gut microbiome analysis was conducted using next-generation sequencing with the Illumina MiSeq platform. Bacterial and fungal community compositions were assessed using 16S rRNA and ITS gene sequences, respectively. Our findings confirm that adult worker bees of A. mellifera from the two locations possess distinct but comparably proportioned bacterial and fungal microbiomes. Key bacterial symbionts, including Lactobacillus, Bombilactobacillus, Bifidobacterium, Gilliamella, Snodgrassella, and Frischella, were identified. The fungal community was dominated by the yeasts Zygosaccharomyces and Priceomyces. Using the ENZYME nomenclature database and PICRUSt2 software version 2.5.2, a predicted functional enzyme analysis revealed the presence of β-glucosidase, catalase, glucose-6-phosphate dehydrogenase, glutathione transferase, and superoxide dismutase, which are involved in host defense, carbohydrate metabolism, and energy support. Additionally, we identified notable bacterial enzymes, including acetyl-CoA carboxylase and AMPs nucleosidase. Interestingly, the key bee symbionts were observed to have a negative correlation with other microbiota. These results provide a detailed characterization of the gut microbiota associated with A. mellifera in the Philippines and lay a foundation for further metagenomic studies of microbiomes in native or indigenous bee species in the region.

Metagenomic insights into the development of microbial communities of straw and leaf composts

Introduction

Soil microbiome is a major source of physiologically active microorganisms, which can be potentially mobilized by adding various nutrients. To study this process, a long-term experiment was conducted on the decomposition of oat straw and leaf litter using soil as a microbial inoculum.

Methods

Combined analyses of enzymatic activity and NGS data for 16S rRNA gene amplicon and full metagenome sequencing were applied to study taxonomic, carbohydrate-active enzyme (CAZy), and polysaccharide utilization loci (PULs) composition of microbial communities at different stages of decomposition between substrates.

Results

In straw degradation, the microbial community demonstrated higher amylase, protease, catalase, and cellulase activities, while peroxidase, invertase, and polyphenol oxidase were more active in leaf litter. Consistent with this, the metagenome analysis showed that the microbiome of straw compost was enriched in genes for metabolic pathways of simpler compounds. At the same time, there were more genes for aromatic compound degradation pathways in leaf litter compost. We identified nine metagenome-assembled genomes (MAGs) as the most promising prokaryotic decomposers due to their abnormally high quantity of PULs for their genome sizes, which were confirmed by 16S rRNA gene amplicon sequencing to constitute the bulk of the community at all stages of substrate degradation. MAGs from Bacteroidota (Chitinophaga and Ohtaekwangia) and Actinomycetota (Streptomyces) were found in both composts, while those from Bacillota (Pristimantibacillus) were specific for leaf litter. The most frequently identified PULs were specialized on xylans and pectins, but not cellulose, suggesting that PUL databases may be underrepresented in clusters for complex substrates.

Discussion

Our study explores microbial communities from natural ecosystems, such as soil and lignocellulosic waste, which are capable of decomposing lignocellulosic substrates. Using a comprehensive approach with chemical analyses of the substrates, amplicon, and full metagenome sequencing data, we have shown that such communities may be a source of identifying the highly effective decomposing species with novel PULs.

Intercropping of Saccharum spp. with Dictyophora indusiata: effects on microbial communities and metabolite profiles during bagasse degradation

Background

Intercropping Saccharum spp. (sugarcane) with the fungus Dictyophora indusiata together with bagasse amendment represents an innovative circular agriculture method that can enhance soil health, boost sugarcane yields, and increase farm profitability. Understanding the process by which D. indusiata degrades bagasse is key to optimizing this method.

Aims

This study aims to clarify the microbial and metabolic processes involved in bagasse degradation by D. indusiata in the sugarcane intercropping system.

Methods

Chemical composition analysis, metabarcoding sequencing, and metabolomic profiling were conducted on D. indusiata-degraded bagasse (DIBA) and naturally degraded bagasse (BA).

Results

Analysis of chemical composition revealed that only acid detergent fiber (ADF) and crude protein content differed significantly between the DIBA and BA treatments. Metabarcoding sequencing showed that DIBA significantly altered the bacterial and fungal communities, reducing microbial diversity. Metabolomic analysis indicated an enhancement of biological metabolism, particularly carbohydrate breakdown, in the DIBA treatment. Key metabolites, such as glucose, cellobiose, and D-mannose, were more abundant in DIBA samples. In addition, unique metabolites such as L-alanine, serine, and oxaloacetate were detected in the DIBA treatment, suggesting more efficient bagasse degradation compared with natural processes.

Conclusion

The use of macrofungi such as D. indusiata can play a pivotal role in circular agriculture by transforming agricultural waste into valuable soil amendments. Future research should focus on the long-term impact of this system on soil quality and crop yield, as well as the underlying mechanisms, to further optimize intercropping systems and the use of fungi in agricultural waste management.

Optimizing Bioaugmentation for Pharmaceutical Stabilization of Sewage Sludge: A Study on Short-Term Composting Under Real Conditions

A significant concentration of pharmaceuticals has been detected within composted sewage sludge. Their uncomplete removal and lack of monitoring during composting neglects their potentially toxic effects when used as a soil organic amendment. Previously, we successfully implemented a bioaugmentation-composting system focused on toxicity and pharmaceuticals' concentration reduction. This method, however, comprised a long inoculant-acclimatization period, making it an unprofitable technology. Hence, this work aimed to explore a shorter and yet effective composting process by simultaneously implementing the inoculation of a native microbial consortium and the fungus Penicillium oxalicum XD 3.1 in composting piles of sewage sludge and olive prunings. All the piles were subjected to frequent inoculation, windrow turning, and monitoring of the physicochemical and biological parameters. Additionally, both the bioaugmentation stability and pharmaceuticals degradation were evaluated through different analysis and removal rates calculations. One hundred days earlier than previous attempts, both bioaugmentation treatments achieved adequate composting conditions, maintained core native populations while improving the degrading microbial diversity, and achieved around 70-72% of pharmaceutical remotion. Nevertheless, only Penicillium inoculation produced favorable toxicity results ideal for organic amendments (acute microtoxicity and phytotoxicity). Thus, a shorter but equally stable and effective degrading bioaugmentation-composting with P. oxalicum was achieved here.

Characterizing the microbiome recruited by the endangered plant Firmiana danxiaensis in phosphorus-deficient acidic soil

Phosphorus (P)-deficient soils serve as crucial habitats for endangered plant species. Microbiomes play pivotal roles in soil element cycling and in determining a plant's adaptability to the environment. However, the relationship between the endangered plant, microbiome, and soil stoichiometric traits, and how it affects plant adaption to P-deficient habitats remain largely unexplored. In this study, we investigated the microbiome (bacteria and fungi) in the rhizosphere of Firmiana danxiaensis, an endangered plant species growing exclusively in P-deficient acidic soils on Mt. Danxia, South China; the non-endangered coexisting tree species Pinus massoniana was used as a reference. Our results showed that soil traits in the rhizosphere of F. danxiaensis differed significantly from that of P. massoniana, including higher soil pH, lower C:N, and higher N:P. The rhizosphere of F. danxiaensis harbors higher microbial diversity and different microbial communities from P. massoniana. Using the machine learning approach, we characterized 76 bacterial and 20 fungal phylotypes dominated in F. danxiaensis rhizosphere, most of which had strong impacts on microbial ecological network structure (they accounted for only 0.33% node numbers but linked 21.2% of the nodes in the network); specifically, Udaeobacter spp., a highly abundant (constituting 4.07% of the total bacterial community) member of Verrucomicrobiota exclusively accumulated in the rhizosphere of F. danxiaensis but not P. massoniana, demonstrated a pronounced ecological prefers toward F. danxiaensis rhizosphere habitat (high pH, low C:N and high N:P) and potential antagonistic indication. In contrast, P. massoniana rhizosphere harbored more Subgroup2 of Acidobacteria and Gammaproteobacterial N-fixer. Taken together, this study provided novel evidence that endangered plants recruited a unique microbiome characterized by Udaeobacter spp. favoring high N habitat. It contributes not only to our understanding of microbiome recruitment by plants in P-deficient acidic soils, but also underscores the importance of microbiome in the conservation and population restoration of endangered plants.

Correlation Between Cryptococcus Infection and the Nasal Mycobiota in a Population of Free-Ranging Koalas (Phascolarctos cinereus) in New South Wales, Australia

Cryptococcosis is a fungal disease in humans and animals, caused by the Cryptococcus neoformans and Cryptococcus gattii species complexes. Clinical cryptococcosis primarily manifests as upper respiratory tract disease; however, dissemination to other organs, particularly the brain, can occur. Nasal colonisation and subclinical cryptococcosis are common in koalas (Phascolarctos cinereus) due to their shared environmental niche with Cryptococcus: Eucalyptus trees. However, for reasons that remain unclear, the prevalence of clinical disease is low in koalas. Interactions between respiratory pathogens and the nasal mycobiome are thought to play a role in the development and progression of numerous respiratory diseases. As such, this study aimed to characterise the mycobiome of the nasal vestibule in koalas with and without evidence of cryptococcal colonisation and subclinical disease via the next-generation sequencing (NGS) of the ITS1 region of the fungal internal transcribed spacer (ITS) gene. Samples were collected from 47 koalas from a population of free-ranging koalas in the Liverpool Plains, NSW, Australia, with a known history of Cryptococcus exposure and nasal colonisation. Of the 47 animals tested, 6.4% were culture-positive only, 4.3% were seropositive only, and 2.1% were culture- and seropositive. C. gattii was detected in four samples via NGS. C. neoformans was not detected via NGS. There were no significant differences in the nasal mycobiomes of Cryptococcus-positive and -negative animals; thus, we could not establish a definitive association between the mycobiome and infection outcomes. We identified a number of fungal genera that were significantly more abundant in samples from Cryptococcus-positive animals, but there was no apparent relationship between these genera and the development of cryptococcosis. This study represents the first investigation of the nasal mycobiota of wild koalas. Further studies involving koalas with clinical disease are necessary to determine the role of the nasal mycobiota in the development of cryptococcosis.

Microbial generalists as keystone species: constructing core network modules in the anthosphere of twelve diverse wild plant species

BACKGROUND

The anthosphere, also known as the floral microbiome, is a crucial component of the plant reproductive system. Therefore, understanding the anthospheric microbiome is essential to explore the diversity, interactions, and functions of wildflowers that coexist in natural habitats. We aimed to explore microbial interaction mechanisms and key drivers of microbial community structures using 144 flower samples from 12 different wild plant species inhabiting the same natural environment in South Korea.

RESULTS

The microbial diversity of the anthosphere showed plant dependence, with the highest diversity observed in Forsythia koreana, indicating microbial dynamics in relation to plant species. Caulobacter, Sphingomonas, Achromobacter, Epicoccum, Cladosporium, and Alternaria were anthosphere generalists, suggesting that the local plant anthosphere had a similar microbial composition. Ecological network analysis revealed that anthosphere generalists were tightly coupled to each other and constructed core modules in the anthosphere. Functions associated with parasites and pathogens were commonly observed in the anthosphere, particularly in Capsella bursa-pastoris and Brassica juncea.

CONCLUSION

Overall, the anthosphere depends on the plant species and microbial generalists function as keystone species to support and connect the anthospheric microbiome in natural habitats.

The microbiota of cork and yellow stain as a model for a new route for the synthesis of chlorophenols and chloroanisoles from the microbial degradation of suberin and/or lignin

BACKGROUND

The main application of cork is the production of stoppers for wine bottles. Cork sometimes contains 2,4,6-trichloroanisole, a compound that, at a concentration of ng/L, produces an unpleasant musty odor that destroys the organoleptic properties of wine and results in enormous economic losses for wineries and cork industries. Cork can exhibit a defect known as yellow stain, which is associated with high levels of 2,4,6-trichloroanisole. We describe how the microbiota of cork and yellow stain define a novel mechanism that explains the formation of chlorophenols and chloroanisoles (including 2,4,6-trichloroanisole) from p-hydroxybenzoate produced during lignin and/or suberin breakdown.

RESULTS

Electron microscopy revealed that cork affected by yellow stain exhibited significant structural degradation. This deterioration was attributed to the presence of higher microbial populations compared to those found in standard cork. Cork microbiota is rich in filamentous fungi able to metabolize lignin. A metataxonomic analysis confirmed that yellow stain contained significantly greater populations of fungal species belonging to Absidia, Geomyces, Mortierella, Mucor, Penicillium, Pseudogymnoascus, Talaromyces, and Umbelopsis. It also contained significantly greater amounts of bacteria belonging to Enterobacterales, Streptosporangiales, Tepidisphaerales, Pseudomonas, and several members of Burkholderiaceae, particularly species of the Burkholderia-Caballeronia-Paraburkholderia group. The extraction of aromatic compounds from cork samples allowed the identification of several compounds typically observed following lignin depolymerization. Notably, p-hydroxybenzoic acid and phenol were detected. Two strains of the genus Streptomyces isolated from yellow stain were able to biotransform p-hydroxybenzoate into phenol in resting cell assays. Phenol could be efficiently chlorinated in vitro to produce 2,4,6-trichlorophenol by a fungal chloroperoxidase, an enzymatic activity commonly found in filamentous fungi isolated from cork. Finally, as has been widely demonstrated before, 2,4,6-trichlorophenol can be efficiently O-methylated to 2,4,6-trichloroanisole by many of fungi that inhabit cork.

CONCLUSIONS

Chlorophenols and chloroanisoles can be produced de novo in cork from p-hydroxybenzoate generated by the microbial biodegradation of lignin and/or suberin through the participation of different types of microorganisms present in cork. The natural origin of these compounds, which are of great interest for the chlorine cycle and represent a new source of environmental contamination that differs from that caused by human activity, is described. Video Abstract.

Bacterial wilt disease alters the structure and function of fungal communities around plant roots

BACKGROUND

Fungal communities around plant roots play crucial roles in maintaining plant health. Nonetheless, the responses of fungal communities to bacterial wilt disease remain poorly understood. Here, the structure and function of fungal communities across four consecutive compartments (bulk soil, rhizosphere, rhizoplane and root endosphere) were investigated under the influence of bacterial wilt disease.

RESULTS

The results showed that bacterial wilt disease caused different assembly patterns of fungal communities in the bulk soil, rhizosphere, rhizoplane and endosphere. Under the influence of bacterial wilt disease, a decreased fungal diversity was observed in the rhizoplane and endosphere, and completely different kinds of fungal genera were enriched in the four compartments. The complexity and stability of fungal networks were less affected, but the number of key fungal members in networks were significantly reduced in diseased samples. Functional predictions based on FUNGuild suggested that with the pathogen infection, saprotrophic fungi were increased in the bulk soil, but pathotrophic fungi (potential plant and animal pathogens) were increased in the rhizosphere, rhizoplane and endosphere.

CONCLUSION

This work provides a deep insight into the effects of bacterial wilt disease on fungal communities along the soil-root continuum, and is helpful to identify plant-associated beneficial fungi to resist plant disease.

CLINICAL TRIAL NUMBER

Not applicable.

The impact of spray-induced gene silencing on cereal phyllosphere microbiota

BACKGROUND

Fusarium head blight (FHB) is a major disease affecting cereal crops including wheat, barley, rye, oats and maize. Its predominant causal agent is the ascomycete fungus Fusarium graminearum, which infects the spikes and thereby reduces grain yield and quality. The frequency and severity of FHB epidemics has increased in recent years, threatening global food security. Spray-induced gene silencing (SIGS) is an alternative technique for tackling this devastating disease through foliar spraying with exogenous double-stranded RNA (dsRNA) to silence specific pathogen genes via RNA interference. This has the advantage of avoiding transgenic approaches, but several aspects of the technology require further development to make it a viable field-level management tool. One such existing knowledge gap is how dsRNA spraying affects the microbiota of the host plants.

RESULTS

We found that the diversity, structure and composition of the bacterial microbiota are subject to changes depending on dsRNA targeted and host studied, while the fungal microbiota in the phyllosphere remained relatively unchanged upon spraying with dsRNA. Analyses of fungal co-occurrence patterns also showed that F. graminearum established itself among the fungal communities through negative interactions with neighbouring fungi. Through these analyses, we have also found bacterial and fungal genera ubiquitous in the phyllosphere, irrespective of dsRNA treatment. These results suggest that although rarer and less abundant microbial species change upon dsRNA spray, the ubiquitous bacterial and fungal components of the phyllosphere in wheat and barley remain unchanged.

CONCLUSION

We show for the first time the effects of exogenous dsRNA spraying on bacterial and fungal communities in the wheat and barley phyllospheres using a high-throughput amplicon sequencing approach. The results obtained further validate the safety and target-specificity of SIGS and emphasize its potential as an environmentally friendly option for managing Fusarium head blight in wheat and barley.

Isolation and characterization of a new Leptobacillium species promoting tomato plant growth

Endophytes can be a promising alternative for sustainable agronomic practices. In this study, we report for the first time a root-colonizing fungal strain (Sl27) of the genus Leptobacillium as a tomato (Solanum lycopersicum) endophyte, with no clear homology to any known species. Performed analyses and assays, including morphological and physiological characterization of the fungal isolate, provided insights into the ecological niche and potential agronomical and industrial applications of the fungal isolate. The ability of Sl27 to establish a symbiotic relationship with the host plant was assessed through experiments under controlled conditions in the growth chamber and greenhouse. Seed-inoculation showed no detrimental effects in the three tomato genotypes studied (TH-30, ADX2, MO-10). The influence of Sl27 on growth parameters of the host plant was dependent on the tomato genotype, with TH-30 showing the most prominent improved phenotype. Moreover, chlorophyll and lycopene content in fruits were enhanced. These findings provide a basis for further studies on the potential application of this new isolate for improving crop performance.

Diversity of Soil Microbial Communities in the Bulk and Rhizosphere Soils of Acanthopanax senticosus in Different Habitats

Comprehending the interplay between the microbial communities of bulk soil (BS) and rhizosphere soil (RS) holds crucial significance in maintaining soil health and fertility, as well as enhancing crop quality. Our research focused on examining these microbial communities in BS and RS of Acanthopanax senticosus, along with their correlation with soil nutrients, across three distinct habitats in Yichun, Heilongjiang Province. To achieve this, we employed high-throughput sequencing technology, specifically targeting the 16S and amplicon regions. The results showed that there were significant differences in soil nutrients, microbial diversity and composition between BS and RS in different habitats. Available phosphorus (AP), total nitrogen (TN), ammonium-nitrogen (NH4+-N) and available potassium (AK) content in RS were higher than that in BS, but TP content was opposite. The Mantel experiment's findings revealed that the soil physicochemical attributes exerted a more significant impact on the microbial community present in RS compared to its influence in BS. Redundancy analysis (RDA) indicated that the bacterial community of BS was affected by SMC and TP. The fungal structure of BS was affected by soil moisture content (SMC), AP, AK (P < 0.01) and TN (P < 0.05). The fungal structure of RS was affected by soil organic carbon (SOC), AP and AK. A noteworthy inverse relationship was observed between Actinomycetes and SMC as well as AP. In conclusion, these results extend the understanding of soil microbial community of A. senticosus and provide a preliminary understanding of the effects of habitat changes caused by human activities on A. senticosus.

Impact of Improved Sanitation Standard Operating Procedures on Microbial Populations at Three Tree Fruit Packing Facilities

Cleaning and sanitizing are of vital importance to control Listeria monocytogenes in food processing facilities. Here, we evaluated the effect of four cleaning and sanitation standard operating procedures (SSOPs; T1, T2, T3, T4) on the reduction of total aerobic mesophilic microorganisms, the occurrence of L. monocytogenes, and the microbiota composition in three tree fruit packing facilities (F1, F2, and F3) over two packing seasons (Y1 and Y2). Environmental samples were collected from non-food contact surfaces before and after the application of SSOPs. Total aerobic bacteria were quantified using a standard plate count method, and Listeria spp. and L. monocytogenes concentration was quantified using a Most Probable Number method. Amplicon sequencing was used to determine bacterial and fungal microbiota composition, and Nanopore sequencing was used to detect functional elements in the microbiota that could promote the survival and persistence of L. monocytogenes in the studied environments. The use of SSOPs reduced the total bacterial load by 0.27-2.48 log10 CFU/swab (p ≤ 0.001). Among the treatments tested, the inclusion of a biofilm remover in T4 was most effective in significantly reducing the total Listeria spp. concentration by 1.57-1.27 log10 MPN/swab (p < 0.02) and the frequency of L. monocytogenes, although the latter was not statistically significant. We observed inconsistent changes in the bacterial and fungal microbiota composition due to the application of cleaning and sanitizing SSOPs, which may be due to the presence of dead DNA after the treatment. Using Nanopore sequencing, we detected functional elements related to biofilm formation and stress resistance in the microbiomes of the studied environments. Overall, our study shows that the implementation of SSOPs improved the sanitation outcomes in tree fruit packing facilities. There is a need for the future work to focus on optimizing and validating the standard operating procedures, especially in the areas in which SSOPs were less effective, such as those covered with wax residues.

Differential impacts of water diversion and environmental factors on bacterial, archaeal, and fungal communities in the eastern route of the South-to-North water diversion project

Water diversion projects effectively mitigate the uneven distribution of water resources but can also influence aquatic biodiversity and ecosystem functions. Despite their importance, the impacts of such projects on multi-domain microbial community dynamics and the underlying mechanisms remain poorly understood. Utilizing high-throughput sequencing, we investigated bacterial, archaeal, and fungal community dynamics along the eastern route of the South-to-North water diversion project during both non-water diversion period (NWDP) and water diversion period (WDP). Our findings revealed competitive exclusion effects among bacterial and archaeal communities during the WDP, characterized by decreased species richness and increased biomass, while fungal biomass significantly declined. Distance-decay relationships suggested microbial homogenization during the WDP. Robustness analyses revealed reduced community stability during the WDP, with water diversion primarily influencing bacterial stability, while environmental factors had a greater impact on archaeal and fungal communities. Stochastic processes, primarily homogenizing dispersal and drift, intensified for bacterial and fungal communities during the WDP. Notably, only bacterial functional diversity decreased during the WDP, with increased relative abundance of chemoheterotrophic and organic compound catabolic bacteria and declined photoautotrophic bacteria. PLS-PM indicated that water diversion primarily shaped bacterial assembly processes and functional guilds, whereas environmental factors had a greater influence on archaeal communities. This study enhances our understanding of microbial dynamics during the WDP and underscores the importance of assessing both direct impacts and resulting environmental fluctuations.

Melatonin reprograms soil microbial community, creates friendly soil environments, and promotes peanut growth

Melatonin helps to regulate various physiological processes in plants, including growth, seed germination, and stress responses. However, the mechanism of how melatonin treatments affect soil microbe diversity and ecology, and plant growth needs to be better understood. Here, we report that melatonin coordinates interactions between soil microorganisms and root exudates to create a friendly soil environment for peanut growth under a controlled environment. Interestingly, the results showed that melatonin was capable of regulating the structure of the soil microbial community, improving its relative abundance of beneficial microorganisms (such as Sphingomonas, Trichoderma, and Penicillium) in the soil. Furthermore, melatonin could also change the composition of soil metabolites and nutrients. These altered soil profiles reflected a healthy environment for peanuts created by melatonin. Furthermore, the favorable growing environment increased photosynthetic performance, biomass, and peanut yield. Collectively, our findings will help us better understand the role of melatonin as a bioregulator in maintaining a healthy plant growth environment. SYNOPSIS: Melatonin treatments improved soil microbe biodiversity and enhanced plant growth and development and sustainable agricultural development.

Marine fungi degrade plastic and can be conditioned to do it faster

Plastics are a prevalent and persistent pollutant in the environment. As plastic production increases, finding ways to degrade these recalcitrant polymers is paramount. Many terrestrial fungi, across the kingdom, degrade various types of plastic. Plastics are the fastest-growing habitat in the oceans, and we hypothesized that fungi isolated from the ocean would demonstrate high success rates in degrading polyurethane (PU). To test this, visual degradation assays were performed by inoculating 1% PU medium with 68 different fungal strains cultured from marine habitats. The area of clearance of the fungus was measured periodically, to determine a relative degradation rate. Of the 68 fungal strains, 42 demonstrated the ability to degrade PU. We conditioned the nine fastest PU degraders through serial inoculations into liquid media with increasing concentrations of PU, starting at 1% and going up to 12%. The growth rates of the original and conditioned fungi were then compared in new inoculation trials, and results show that three of the nine conditioned fungi demonstrate higher PU degradation rates than their unconditioned counterparts. Marine fungi, coupled with conditioning, show promise for developing novel mycoremediation technologies.

Field Reduction of Ectomycorrhizal Fungi Has Cascading Effects on Soil Microbial Communities and Reduces the Abundance of Ectomycorrhizal Symbiotic Bacteria

Specific interactions between bacteria and ectomycorrhizal fungi (EcMF) can benefit plant health, and saprotrophic soil fungi represent a potentially antagonistic guild to these mutualisms. Yet there is little field-derived experimental evidence showing how the relationship among these three organismal groups manifests across time. To bridge this knowledge gap, we experimentally reduced EcMF in forest soils and monitored both bacterial and fungal soil communities over the course of a year. Our analyses demonstrate that soil trenching shifts the community composition of fungal communities towards a greater abundance of taxa with saprotrophic traits, and this shift is linked to a decrease in both EcMF and a common ectomycorrhizal helper bacterial genus, Burkholderia, in a time-dependent manner. These results not only reveal the temporal nature of a widespread tripartite symbiosis between bacteria, EcMF and a shared host tree, but they also refine our understanding of the commonly referenced 'Gadgil effect' by illustrating the cascading effects of EcMF suppression and implicating soil saprotrophic fungi as potential antagonists on bacterial-EcMF interactions.

Facade eluates affect active and total soil microbiome

The application of biocides in building materials has become a prevalent practice to mitigate the growth of microorganisms such as algae, fungi, and bacteria on the façades. These can leach out from the material and reach the nearby soil environment. This study aimed to characterize the effect of façade eluates generated within different leaching experiments on total and metabolic active soil microbial community composition and functions. Façade eluates were produced by immersion testing DIN EN 16105 and a natural weathering experiment. Afterward, soil microcosms were treated with the respective façade eluate and incubated for 29 days. Subsequently, the active and total soil microbial community compositions were investigated. Fungal internal transcribed spacer region gene and bacterial 16S rRNA gene were sequenced for active (bromodeoxyuridine labeled DNA) microbial community and total community. Façade eluates reduced total bacterial and fungal gene copy numbers. Overall, active bacterial and fungal richness was reduced and altered in community composition in comparison to the total richness and composition, respectively. Façade eluates retrieved of façade samples without biocides did alter the soil microbial communities to the same extent as façade eluates with biocides. Additionally, members of the active microbiome that benefit from the presence of façade eluates and omitted ones could be identified. Our result demonstrated that façade eluates affect active and total soil microbial community composition and function regardless of the leaching procedure and biocides addition.

The Ribosomal Operon Database: A Full-Length rDNA Operon Database Derived From Genome Assemblies

Current rDNA reference sequence databases are tailored towards shorter DNA markers, such as parts of the 16/18S marker or the internally transcribed spacer (ITS) region. However, due to advances in long-read DNA sequencing technologies, longer stretches of the rDNA operon are increasingly used in environmental sequencing studies to increase the phylogenetic resolution. There is, therefore, a growing need for longer rDNA reference sequences. Here, we present the ribosomal operon database (ROD), which includes eukaryotic full-length rDNA operons fished from publicly available genome assemblies. Full-length operons were detected in 34.1% of the 34,701 examined eukaryotic genome assemblies from NCBI. In most cases (53.1%), more than one operon variant was detected, which can be due to intragenomic operon copy variability, allelic variation in non-haploid genomes, or technical errors from the sequencing and assembly process. The highest copy number found was 5947 in Zea mays. In total, 453,697 unique operons were detected, with 69,480 operon variant clusters remaining after intragenomic clustering at 99% sequence identity. The operon length varied extensively across eukaryotes, ranging from 4136 to 16,463 bp, which will lead to considerable polymerase chain reaction (PCR) bias during amplification of the entire operon. Clustering the full-length operons revealed that the different parts (i.e., 18S, 28S, and the hypervariable regions V4 and V9 of 18S) provide divergent taxonomic resolution, with 18S, the V4 and V9 regions being the most conserved. The ROD will be updated regularly to provide an increasing number of full-length rDNA operons to the scientific community.

Assembly and network of Rhei Radix et Rhizoma surface microbiome shaped by processing methods and sampling locations

Objective

Rhei Radix et Rhizoma has five types of products, namely, raw rhubarb (RR), wine rhubarb (WR), vinegar rhubarb (VR), cooked rhubarb (CR), and rhubarb charcoal (RC). However, Rhei Radix et Rhizoma is easily contaminated with fungi and mycotoxins if not harvested or processed properly. Here, we intend to analyze how microbiome assemblies and co-occurrence patterns are influenced by sampling locations and processing methods.

Methods

High-throughput sequencing and internal transcribed spacer 2 (ITS2) were carried out to study the diversities (α- and β-diversity), composition (dominant taxa and potential biomarkers), and network complexitity of surface fungi on RR, WR, VR, CR, and RC collected from Gansu and Sichuan provinces, China.

Results

The phyla Ascomycota and Basidiomycota; the genera Kazachstania, Malassezia, and Asterotremella; and the species Kazachstania exigua, Asterotremella pseudolonga, and Malassezia restricta were the dominant fungi and exhibited differences in the two provinces and the five processed products. The α-diversity and network complexity were strongly dependent on processing methods. Chao 1, the Shannon index, and network complexity and connectivity were highest in the CR group. The α-diversity and network complexity were influenced by sampling locations. Chao 1 and network complexity and connectivity were highest in the Gansu Province.

Conclusion

The assembly and network of the surface microbiome on Rhei Radix et Rhizoma were shaped by processing methods and sampling locations. This paper offers a comprehensive understanding of microorganisms, which can provide early warning for potential mycotoxins and ensure the safety of drugs and consumers.

Elevated CO2 Increased Antibiotic Resistomes in Seed Endophytes: Evidence from a Free-Air CO2 Enrichment (FACE) Experiment

Climate warming affects antibiotic resistance genes (ARGs) in soil and the plant microbiome, including seed endophytes. Seeds act as vectors for ARG dissemination in the soil-plant system, but the impact of elevated CO2 on seed resistomes remains poorly understood. Here, a free-air CO2 enrichment system was used to examine the impact of elevated CO2 on seed-associated ARGs and seed endophytic bacteria and fungi. Results indicated that elevated CO2 levels significantly increased the relative abundance of seed ARGs and mobile genetic elements (MGEs), especially those related to beta-lactam resistance and MGEs. Increased CO2 levels also influenced the composition of seed bacterial and fungal communities and the complexity of bacteria-fungi interactions. Fungi were more sensitive to changes in the CO2 level than bacteria, with deterministic processes playing a greater role in fungal community assembly. Co-occurrence network analysis revealed a stronger correlation between fungi and ARGs compared to bacteria. The structure equation model (SEM) showed that elevated CO2 directly influenced seed resistomes by altering bacterial composition and indirectly through bacteria-fungi interactions. Together, our work offers new insights into the effects of elevated CO2 on antibiotic resistomes in the seed endosphere, highlighting their increased dissemination potential within soil-plant systems and the associated health risks in a changing environment.

Effect of exogenous treatment with zaxinone and its mimics on rice root microbiota across different growth stages

Enhancing crops productivity to ensure food security is one of the major challenges encountering agriculture today. A promising solution is the use of biostimulants, which encompass molecules that enhance plant fitness, growth, and productivity. The regulatory metabolite zaxinone and its mimics (MiZax3 and MiZax5) showed promising results in improving the growth and yield of several crops. Here, the impact of their exogenous application on soil and rice root microbiota was investigated. Plants grown in native paddy soil were treated with zaxinone, MiZax3, and MiZax5 and the composition of bacterial and fungal communities in soil, rhizosphere, and endosphere at the tillering and the milky stage was assessed. Furthermore, shoot metabolome profile and nutrient content of the seeds were evaluated. Results show that treatment with zaxinone and its mimics predominantly influenced the root endosphere prokaryotic community, causing a partial depletion of plant-beneficial microbes at the tillering stage, followed by a recovery of the prokaryotic community structure during the milky stage. Our study provides new insights into the role of zaxinone and MiZax in the interplay between rice and its root-associated microbiota and paves the way for their practical application in the field as ecologically friendly biostimulants to enhance crop productivity.

Metagenome-validated combined amplicon sequencing and text mining-based annotations for simultaneous profiling of bacteria and fungi: vaginal microbiota and mycobiota in healthy women

BACKGROUND

Amplicon sequencing of kingdom-specific tags such as 16S rRNA gene for bacteria and internal transcribed spacer (ITS) region for fungi are widely used for investigating microbial communities. So far most human studies have focused on bacteria while studies on host-associated fungi in health and disease have only recently started to accumulate. To enable cost-effective parallel analysis of bacterial and fungal communities in human and environmental samples, we developed a method where 16S rRNA gene and ITS1 amplicons were pooled together for a single Illumina MiSeq or HiSeq run and analysed after primer-based segregation. Taxonomic assignments were performed with Blast in combination with an iterative text-extraction-based filtration approach, which uses extensive literature records from public databases to select the most probable hits that were further validated by shotgun metagenomic sequencing.

RESULTS

Using 50 vaginal samples, we show that the combined run provides comparable results on bacterial composition and diversity to conventional 16S rRNA gene amplicon sequencing. The text-extraction-based taxonomic assignment-guided tool provided ecosystem-specific bacterial annotations that were confirmed by shotgun metagenomic sequencing (VIRGO, MetaPhlAn, Kraken2). Fungi were identified in 39/50 samples with ITS sequencing while in the metagenome data fungi largely remained undetected due to their low abundance and database issues. Co-abundance analysis of bacteria and fungi did not show strong between-kingdom correlations within the vaginal ecosystem of healthy women.

CONCLUSION

Combined amplicon sequencing for bacteria and fungi provides a simple and cost-effective method for simultaneous analysis of microbiota and mycobiota within the same samples. Conventional metagenomic sequencing does not provide sufficient fungal genome coverage for their reliable detection in vaginal samples. Text extraction-based annotation tool facilitates ecosystem-specific characterization and interpretation of microbial communities by coupling sequence homology to microbe metadata readily available through public databases. Video Abstract.

Temporal dynamics in the composition of metabolically active bacteria and fungi in the ileo-cecal lymph nodes of suckling and newly weaned piglets

The early microbial colonization of the porcine gut is an important priming factor for gut and immune development. Nevertheless, little is known about the composition of microbes that translocate into the ileo-cecal lymph nodes (ICLN) in the neonatal phase. This study aimed to characterize age- and nutrition-related changes in the metabolically active bacterial and fungal composition of the ICLN in suckling and newly weaned piglets. Ten litters received only sow milk, while ten litters had access to creep feed from day of life (DoL) 10. Weaning occurred on DoL28. The ICLN were collected from 10 piglets/feeding group on each sampling day (DoL7, 14, 21, 28, 31 and 35) for RNA isolation, transcription into complementary DNA for 16 S rRNA and ITS2 amplicon sequencing. Age and weaning influenced the microbiome in the ICLN more than the nutrition during the suckling phase. Species richness and alpha-diversity of the bacterial but not fungal communities were increased on DoL7 and postweaning. Potential modes of action may have been linked to gut permeability at these ages and selective sampling by immune cells. Potential selective transfer of microbes may explain the dominance of Lactobacillus and Limosilactobacillus in the ICLN. Piglets that only drank sow milk comprised more Bacteroides in their ICLN on DoL35 compared to the creep fed piglets. Especially the role of fungi in the ICLN, including their mechanisms for translocation survival, needs further attention, as we detected metabolically active mold fungi and plant pathogens (e.g., Fusarium, Alternaria and Blumeria) in the ICLN.

Airborne DNA: State of the art - Established methods and missing pieces in the molecular genetic detection of airborne microorganisms, viruses and plant particles

Bioaerosol is composed of different particles, originating from organisms, or their fragments with different origin, shape, and size. Sampling, analysing, identification and describing this airborne diversity has been carried out for over 100 years, and more recently the use of molecular genetic tools has been implemented. However, up to now there are no established protocols or standards for detecting airborne diversity of bacteria, fungi, viruses, pollen, and plant particles. In this review we evaluated commonalities of methods used in molecular genetic based studies in the last 23 years, to give an overview of applicable methods as well as knowledge gaps in diversity assessment. Various sampling techniques show different levels of effectiveness in detecting airborne particles based on their DNA. The storage and processing of samples, as well as DNA processing, influences the outcome of sampling campaigns. Moreover, the decisions on barcode selection, method of analysis, reference database as well as negative and positive controls may severely impact the results obtained. To date, the chain of decisions, methodological biases and error propagation have hindered DNA based molecular sequencing from offering a holistic picture of the airborne biodiversity. Reviewing the available studies, revealed a great diversity in used methodology and many publications didn't state all used methods in detail, making comparisons with other studies difficult or impossible. To overcome these limitations and ensure genuine comparability across studies, it is crucial to standardize protocols. Publications need to include all necessary information to enable comparison among different studies and to evaluate how methodological choices can impacts the results. Besides standardization, implementing of automatic tools and combining of different analytical techniques, such as real-time evaluation combined with sampling and molecular genetic analysis, could assist in achieving the goal of accurately assessing the actual airborne biodiversity.

Dynamic response of soil microbial communities and network to hymexazol exposure

Fungicides are an essential component of current agricultural practices, but their extensive use has raised concerns about their effects on non-target soil microorganisms, which carry out essential ecosystem functions. However, despite the complexity of microbial communities, many studies investigating their response to fungicides focus only on bacteria or fungi at one point in time. In this study, we used amplicon sequencing to assess the effect of the fungicide hymexazol on the diversity, composition, and co-occurrence network of soil bacteria, fungi, and protists at 7, 21, and 60 days after application. We found that hymexazol had very little effect on microbial alpha-diversity, but that microbial community composition and OTU differential abundance were altered over the duration of the experiment, even after hymexazol concentrations were undetectable. The co-occurrence patterns within and between microbial kingdoms were affected by hymexazol dose, suggesting that indirect effects may play a role in the microbial community response. Nitrogen cycling was also affected, with a transient hymexazol-associated increase in the abundance of ammonia-oxidizing microorganisms and soil nitrate concentration. These findings highlight that the effects of fungicides on soil microorganisms are dynamic and extensive, spanning several taxonomic kingdoms.

Assessing the health of climate-sensitive trees in a subalpine ecosystem through microbial community dynamics

Climate change has significantly affected the subalpine ecosystems, leading to mass die-offs of the Korean fir tree, a key climate-sensitive species in these environments. Proactive analysis of the phenotypic responses of these trees to climate change or the establishment of preemptive strategies for trees to adapt to these environmental changes remains a challenge. The current study aimed to investigate the impact of climate change on the health of Korean fir (Abies koreana) in the subalpine ecosystem of Jirisan Mountain, South Korea. We integrated soil physicochemical analyses, microbial community dynamics, neutral community model, and network analyses to examine the relationships between tree health and microbial communities. Our findings revealed significant changes in soil chemical properties, including pH and nutrient concentrations, across the various health statuses of trees. Microbial community analysis demonstrated shifts in bacterial and fungal communities corresponding to the health continuum of the trees, with decreased diversity and altered composition in the declining trees. A remarkable increase in modularity of the microbial network and a clear transition from stochastic to deterministic microbial community assembly processes were observed as the trees progressed from a healthy to a dead stage. Two bacterial genera, Bradyrhizobium and Burkholderia, along with an unclassified fungal group from Basidiomycota, were identified as key microbial indicators of good tree health. This study highlighted the importance of microbial communities as bioindicators for assessing the health of subalpine ecosystem and its resilience to climate change, offering valuable insights into the conservation and management strategies for subalpine ecosystems.

Microbial landscapes in Trinervitermes trinervoides termite colonies are affected by mound compartments and soil properties but not by symbiotic Podaxis fungi

Termites are important ecosystem engineers and play key roles in modulating microbial communities within and outside their mounds. Microbial diversity within termite mounds is generally lower than surrounding soils, due to termite-associated antimicrobial compounds and active sanitary behaviours. Microbial symbionts of termites can also influence the microbial landscape, by inhibiting or out-competing other microbes. Certain members of the arid habitat fungal genus Podaxis (Agaricomycetes; Agaricaceae) are symbiotic with savannah specialist grass-cutting termites, and have the potential to influence mound-associated microbiomes. To test this, we characterized fungal (ITS2) and bacterial (16S rRNA) communities within and outside 49 Trinervitermes trinervoides mounds with and without Podaxis fruiting bodies across a 1000 km transect in South Africa. We predicted that Podaxis would be a dominant member of the fungal communities in mounds and negatively impact microbial diversity. Further, we explored how environmental variables shaped microbial communities, including whether soil elemental composition affected Podaxis presence. As expected, we observed less diverse fungal communities, but not bacterial communities, within than outside mounds, while microbial communities differed by sampling regions and mound compartments. Podaxis sequences were present in 48 out of 49 mounds in low relative abundances, and neither fruiting body presence nor sequence abundance were associated with microbial diversity or composition. There was, however, an overall association between the presence of Podaxis fruiting bodies and elemental composition, with different elements displaying varying associations depending on geographic region. Both environmental variables and soil elements were associated with fungal and bacterial taxa, indicating that they are key drivers of microbial community composition. Taken together, our findings suggest that microbial landscapes in termite mounds are not strongly influenced by Podaxis but mainly driven by termite filtering and regional abiotic variables and elemental compositions.

Microbial consortia driving (ligno)cellulose transformation in agricultural woodchip bioreactors

Freshwater ecosystems can be largely affected by neighboring agriculture fields where potential fertilizer nitrate run-off may leach into surrounding water bodies. To counteract this eutrophic driver, farmers in certain areas are utilizing denitrifying woodchip bioreactors (WBRs) in which a consortium of microorganisms convert the nitrate into nitrogen gases in anoxia, fueled by the degradation of lignocellulose. Polysaccharide-degrading strategies have been well described for various aerobic and anaerobic systems, including the use of carbohydrate-active enzymes, utilization of lytic polysaccharide monooxygenases (LPMOs) and other redox enzymes, as well as the use of cellulosomes and polysaccharide utilization loci (PULs). However, for denitrifying microorganisms, the lignocellulose-degrading strategies remain largely unknown. Here, we have applied a combination of enrichment techniques, gas measurements, multi-omics approaches, and amplicon sequencing of fungal ITS and procaryotic 16S rRNA genes to identify microbial drivers for lignocellulose transformation in woodchip bioreactors and their active enzymes. Our findings highlight a microbial community enriched for (ligno)cellulose-degrading denitrifiers with key players from the taxa Giesbergeria, Cellulomonas, Azonexus, and UBA5070 (Fibrobacterota). A wide substrate specificity is observed among the many expressed carbohydrate-active enzymes (CAZymes) including PULs from Bacteroidetes. This suggests a broad degradation of lignocellulose subfractions, including enzymes with auxiliary activities whose functionality is still puzzling under strict anaerobic conditions.

IMPORTANCE

Freshwater ecosystems face significant threats from agricultural runoff, which can lead to eutrophication and subsequent degradation of water quality. One solution to mitigate this issue is using denitrifying woodchip bioreactors (WBRs), where microorganisms convert nitrate into nitrogen gases utilizing lignocellulose as a carbon source. Despite the well-documented polysaccharide-degrading strategies in various systems, the mechanisms employed by denitrifying microorganisms in WBRs remain largely unexplored. This study fills a critical knowledge gap by revealing the degrading strategies of denitrifying microbial communities in WBRs. By integrating state-of-the-art techniques, we have identified key microbial drivers including Giesbergeria, Cellulomonas, Azonexus, and UBA5070 (Fibrobacterota) playing significant roles in lignocellulose transformation and showcasing a broad substrate specificity and complex metabolic capability. Our findings advance the understanding of microbial ecology in WBRs and by revealing the enzymatic activities, this research may inform efforts to improve water quality, protect aquatic ecosystems, and reduce greenhouse gas emissions from WBRs.

Decay experiments and microbial community analysis of water lily leaf biofilms: Sediment effects on leaf preservation potential

Understanding the intricate dynamics of sediment-mediated microbial interactions and their impact on plant tissue preservation is crucial for unraveling the complexities of leaf decay and preservation processes. To elucidate the earliest stages of leaf preservation, a series of decay experiments was carried out for three months on Nymphaea water lily leaves in aquariums with pond water and one of three distinctly different, sterilized, fine-grained substrates-commercially purchased kaolinite clay or fine sand, or natural pond mud. One aquarium contained only pond water as a control. We use 16S and ITS rRNA gene amplicon sequencing to identify and characterize the complex composition of the bacterial and fungal communities on leaves. Our results reveal that the pond mud substrate produces a unique community composition in the biofilms compared to other substrates. The mud substrate significantly influences microbial communities, as shown by the correlation between high concentrations of minerals in the water and bacterial abundance. Furthermore, more biofilm formers are observed on the leaves exposed to mud after two months, contrasting with declines on other substrates. The mud substrate also enhanced leaf tissue preservation compared to the other sediment types, providing insight into the role of sediment and biofilms in fossilization processes. Notably, leaves on kaolinite clay have the fewest biofilm formers by the end of the experiment. We also identify key biofilm-forming microbes associated with each substrate. The organic-rich mud substrate emerges as a hotspot for biofilm formers, showing that it promotes biofilm formation on leaves and may increase the preservation potential of leaves better than other substrates. The mud's chemical composition, rich in minerals such as silica, iron, aluminum, and phosphate, may slow or suspend decay and facilitate biomineralization, thus paving the way toward leaf preservation. Our study bridges the information gap between biofilms observed on modern leaves and the mineral encrustation on fossil leaves by analyzing the microbial response in biofilms to substrate types in which fossil leaves are commonly found.

The nasal mycobiome of individuals with allergic rhinitis and asthma differs from that of healthy controls in composition, structure and function

Allergic rhinitis (AR) and asthma (AS) are two of the most common chronic respiratory diseases and a major public health concern. Multiple studies have demonstrated the role of the nasal bacteriome in AR and AS, but little is known about the airway mycobiome and its potential association to airway inflammatory diseases. Here we used the internal transcriber spacers (ITS) 1 and 2 and high-throughput sequencing to characterize the nasal mycobiome of 339 individuals with AR, AR with asthma (ARAS), AS and healthy controls (CT). Seven to ten of the 14 most abundant fungal genera (Malassezia, Alternaria, Cladosporium, Penicillium, Wallemia, Rhodotorula, Sporobolomyces, Naganishia, Vishniacozyma, and Filobasidium) in the nasal cavity differed significantly (p ≤ 0.049) between AS, AR or ARAS, and CT. However, none of the same genera varied significantly between the three respiratory disease groups. The nasal mycobiomes of AR and ARAS patients showed the highest intra-group diversity, while CT showed the lowest. Alpha-diversity indices of microbial richness and evenness only varied significantly (p ≤ 0.024) between AR or ARAS and CT, while all disease groups showed significant differences (p ≤ 0.0004) in microbial structure (i.e., beta-diversity indices) when compared to CT samples. Thirty metabolic pathways (PICRUSt2) were differentially abundant (Wald's test) between AR or ARAS and CT patients, but only three of them associated with 5-aminoimidazole ribonucleotide (AIR) biosynthesis were over abundant (log2 Fold Change >0.75) in the ARAS group. AIR has been associated to fungal pathogenesis in plants. Spiec-Easi fungal networks varied among groups, but AR and ARAS showed more similar interactions among their members than with those in the CT mycobiome; this suggests chronic respiratory allergic diseases may disrupt fungal connectivity in the nasal cavity. This study contributes valuable fungal data and results to understand the relationships between the nasal mycobiome and allergy-related conditions. It demonstrates for the first time that the nasal mycobiota varies during health and allergic rhinitis (with and without comorbid asthma) and reveals specific taxa, metabolic pathways and fungal interactions that may relate to chronic airway disease.

Gut Mycobiota of Three Rhinopithecus Species Provide New Insights Into the Association Between Diet and Environment

Gut mycobiota are part of the gut microbiome, typically derived from the host diet and living environment. In this study, we examined the gut mycobiota of three snub-nosed monkeys: Rhinopithecus roxellana, R. bieti, and R. strykeri using next-generation amplicon sequencing targeting the fungal internal transcribed spacer. The alpha diversity indexes of gut mycobiota in R. bieti were significantly higher than R. roxellana and R. strykeri, the beta diversity indicated that R. roxellana and R. bieti had more similar feeding habits. Core mycobiota demonstrated commonalities among the three species and potentially associated with feeding habits. Mycobiota displaying significant differences exhibited the respective characteristics of the host, likely associated with the hosts' living environment. Among them, animal and plant pathogenic fungi and lichen parasites are potential threats to the survival of snub-nosed monkeys for their pathogenicity to both monkeys and their food plants. Functionally, fungal trophic modes and functional guilds revealed a strong association between gut mycobiota and host diet. We found a higher abundance and more significant correlations with lichen parasitic fungi in R. strykeri than the other two species, indicating potential threats to their foods. Accordingly, this study revealed the basic structures of gut mycobiota of three wild Rhinopithecus species and highlighted the associations between gut mycobiota and their feeding habits and living environments. Furthermore, due to the close connection between fungi and the environment, animals could ingest fungi from their diet; thus, we speculate that gut mycobiota may serve a role in environmental monitoring for wildlife.

Understanding the influence of plant genetic factors on rhizosphere microbiome assembly in Panax notoginseng

Introduction

Functional rhizosphere microbiomes (FRM) are critical for plant health and yield. However, the ecological succession of FRM and their links to plant genetic factors across the life cycle of perennial plants remain poorly understood.

Methods

This study profiled FRM, including plant-beneficial bacteria (PBB) and fungal plant pathogens (FPP), across different developmental stages of Panax notoginseng.

Results

The biodiversity of both PBB and FPP were significantly higher in rhizosphere compared with farmland soil, and exhibited different succession patterns with plant growth. The relative abundance of PBB, but not FPP, decreased after plant cultivation. There were significantly negative correlations between FPP and PBB, particularly the biocontrol subgroup (ρ = -0.56, p < 0.001). The antagonistic effects of biocontrol bacteria against fungal pathogens were further validated by in vitro assays. The fitting of neutral community model indicated that the deterministic assembly of PBB, especially the biocontrol subgroup, was the strongest at the 3rd-year root growth stage of P. notoginseng. Plant genes involved in protein export, biosynthesis of alkaloids and amino acids were identified as drivers of the deterministic assembly of biocontrol subcommunity by RNA-Seq analysis. Additionally, a total of 13 transcription factors potentially regulating the expression of these biosynthesis genes were identified through co-expression network. In summary, this study unveils the succession patterns of FRM throughout the life cycle of P. notoginseng and the underlying plant genetic mechanisms, providing valuable insights for developing new plant disease management strategies by manipulating microbes.

Enhancing chickpea growth through arbuscular mycorrhizal fungus inoculation: facilitating nutrient uptake and shifting potential pathogenic fungal communities

Arbuscular mycorrhizal fungi (AMF) are the most widespread plant symbionts associated with plant roots, and theyperform numerous functions that contribute to plants' health and physiology. However, there are many knowledge gaps in how the interactions between AMF and root mycobiomes influence the performance of the host plants. To this end, we inoculated a local chickpea cultivar grown in agricultural soil under semi-controlled conditions with Rhizophagus irregularis. In addition to examining mycorrhizal colonization, plant biomass, and mineral nutrition, we sequenced the ITS region of the rDNA to assess the chickpea mycobiome and identify key fungal taxa potentially responding to R. irregularis inoculation. Our results showed that inoculation had a positive effect on chickpea biomass and mineral nutrition, especially the total aboveground phosphorus, potassium and sodium contents. Fusarium, Sporomia, Alternaria, and unknown Pleosporales were the most abundant taxa in the roots, while Stachybotris, Penicillum, Fusarium, Ascobolus, an unknown Pleosporales and Acrophialophora were the most abundant in the rhizosphere. Among the ASVs that either were enriched or depleted in the rhizosphere and roots are potential plant pathogens from the genera Didymella, Fusarium, Neocosmospora, and Stagonosporopsis. This study highlights the relevance of AMF inoculation not only for enhancing chickpea growth and mineral nutrition in semi-arid conditions but also for influencing the composition of the plants' fungal community which contributes to improved plant performance and resilience against biotic and abiotic stress.

Soil Plastisphere Reinforces the Adverse Effect of Combined Pollutant Exposure on the Microfood Web

Microbial interactions form microfood webs, crucial for ecological functions. The steady state of these webs, shaped by cooperation and competition among trophic levels, prevents pathogen proliferation and invasion, maintaining soil health. Combined pollutants pose a widespread environmental issue, exerting significant pressure on microfood webs. However, understanding how these webs respond to combined pollutants in soil plastispheres, an emerging niche, remains limited. This study explores trophic interactions among bacteria, fungi, and protists, examining their effects on potential pathogens in three soil types amended with Cu or disinfectant, along with their plastispheres, using a microcosm experiment. Pollutant exposure disrupts trophic-level interactions through bottom-up and top-down regulation in soils and plastispheres, respectively. Microfood web network topology parameters prove more sensitive to pollutant stress than indicators from a single trophic-level community composition. Combined exposure causes greater disruption to the microfood web than exposure to a single pollutant (Cu or didecyl dimethylammonium chloride (DDAC)). Plastisphere reinforces negative impacts of combined pollutant exposure on the microfood web network, escalating potential pathogenic bacteria. Overall, this study deepens our understanding of microfood web responses under pollutant pressure in soil plastispheres and provides valuable insights for health risk assessments of soil combined pollutants.

Temperature governs the community assembly of root-associated ectomycorrhizal fungi in alpine forests on the Qinghai-Tibetan Plateau

Unraveling the assembly processes of ectomycorrhizal (ECM) fungal communities in changing environments is crucial for forecasting the impacts of climate change on forests. However, the assembly processes and key drivers of root-associated ECM fungal communities in alpine coniferous forests remain poorly understood. To address this knowledge gap, we conducted sampling in 65 monodominant alpine coniferous forests, which encompass 11 plant species belonging to three genera (Abies, Pinus, and Picea) within the Pinaceae family, all located on the Qinghai-Tibetan Plateau. We employed a combination of null model and multivariate analyses to elucidate the drivers and assembly processes of ECM fungal communities. Our results revealed significant variation in the composition and diversity of root-associated ECM fungal communities among Abies, Pinus, and Picea, indicating specific preferences for ECM fungi among Pinaceae genera. Importantly, mean annual temperature (MAT) emerged as the primary driver of these variations and regulated the assembly processes within the community of root-associated ECM fungi. As MAT temperature, the α-diversity of these fungi significantly decreased, suggesting that increased temperature may reduce the species diversity of root-associated ECM fungi in alpine forests. Furthermore, stochastic processes, such as dispersal limitation and drift, became more influential as MAT increased. Conversely, the role of deterministic processes, particularly heterogeneous selection, in shaping the ECM fungal community assembly weakened with increasing MAT. This study provides novel theoretical insights into the processes of ECM fungal community assembly in alpine forests, emphasizing the pivotal role of temperature in regulating the assembly processes and compositional dynamics of root-associated ECM fungal communities in these unique environments.

Zonation of the Vitis vinifera microbiome in Vino Nobile di Montepulciano PDO production area

The microbial dimension of the terroir is crucial for wine quality, as microbiomes contribute to plant biofertilization, stress tolerance and pathogen suppression. While microbial terroir can act as a biological signature at large scale, data for local contexts is lacking, hindering the characterization of regional microbial diversity in vineyards. Here, we define the microbial terroir of vineyards across the 12 sub-areas (Additional Geographic Units -AGUs) of the "Consorzio del Vino Nobile di Montepulciano DOCG" PDO area (Italy), a world-renowned wine-producing region. Rhizospheres of Vitis vinifera cultivar Sangiovese and soil samples were collected throughout the 2022 viticultural season and analyzed through an integrated metabarcoding/shotgun metagenomic approach, targeting bacteria and fungi. Wine metabolomics was also perfomed, projecting compositional and functional variations of the microbial terroir at the AGUs level into a corresponding variation in the product metabolic profile. Our findings reveal a unique taxonomic configuration of the Vino Nobile di Montepulciano terroir compared to other vineyards, with microbiomes being "AGU-specific" in taxonomic abundances and plant growth-promoting functions, confirming the potential relevance of characterizing and preserving the microbial terroir to safeguard high-quality traditional wines.

Mycobiome analysis of leaf, root, and soil of symptomatic oil palm trees (Elaeis guineensis Jacq.) affected by leaf spot disease

Recently, attention has been shifting toward the perspective of the existence of plants and microbes as a functioning ecological unit. However, studies highlighting the impacts of the microbial community on plant health are still limited. In this study, fungal community (mycobiome) of leaf, root, and soil of symptomatic leaf-spot diseased (SS) oil palm were compared against asymptomatic (AS) trees using ITS2 rRNA gene metabarcoding. A total of 3,435,417 high-quality sequences were obtained from 29 samples investigated. Out of the 14 phyla identified, Ascomycota and Basidiomycota were the most dominant accounting for 94.2 and 4.7% of the total counts in AS, and 75 and 21.2% in SS, respectively. Neopestalotiopsis is the most abundant genus for AS representing 8.0% of the identified amplicons compared to 2.0% in SS while Peniophora is the most abundant with 8.6% of the identified amplicons for SS compared to 0.1% in AS. The biomarker discovery algorithm LEfSe revealed different taxa signatures for the sample categories, particularly soil samples from asymptomatic trees, which were the most enriched. Network analysis revealed high modularity across all groups, except in root samples. Additionally, a large proportion of the identified keystone species consisted of rare taxa, suggesting potential role in ecosystem functions. Surprisingly both AS and SS leaf samples shared taxa previously associated with oil palm leaf spot disease. The significant abundance of Trichoderma asperellum in the asymptomatic root samples could be further explored as a potential biocontrol agent against oil palm disease.

Gut microbiota and metabolic responses to a 12-week caloric restriction combined with strength and HIIT training in patients with obesity: a randomized trial

BACKGROUND

Nowadays, obesity has become a major health issue. In addition to negatively affecting body composition and metabolic health, recent evidence shows unfavorable shifts in gut microbiota in individuals with obesity. However, the effects of weight loss on gut microbes and metabolites remain controversial. Therefore, the purpose of this study was to investigate the effects of a 12-week program on gut microbiota and metabolic health in patients with obesity.

METHODS

We conducted a controlled trial in 23 male and female patients with obesity. Twelve participants completed a 12-week program of caloric restriction combined with strength and HIIT training (INT, pre-BMI 37.33 ± 6.57 kg/m2), and eleven participants were designated as non-intervention controls (pre-BMI 38.65 ± 8.07 kg/m2). Metagenomic sequencing of the V3-V4 region of the 16S rDNA gene from fecal samples allowed for gut microbiota classification. Nuclear magnetic resonance spectroscopy characterized selected serum and fecal metabolite concentrations.

RESULTS

Within INT, we observed a significant improvement in body composition; a significant decrease in liver enzymes (AST, ALT, and GMT); a significant increase in the relative abundance of the commensal bacteria (e.g., Akkermansia muciniphila, Parabacteroides merdae, and Phocaeicola vulgatus); and a significant decrease in the relative abundance of SCFA-producing bacteria (e.g., the genera Butyrivibrio, Coprococcus, and Blautia). In addition, significant correlations were found between gut microbes, body composition, metabolic health biomarkers, and SCFAs. Notably, the Random Forest Machine Learning analysis identified predictors (Butyrivibrio fibrisolvens, Blautia caecimuris, Coprococcus comes, and waist circumference) with a moderate ability to discriminate between INT subjects pre- and post-intervention.

CONCLUSIONS

Our results indicate that a 12-week caloric restriction combined with strength and HIIT training positively influences body composition, metabolic health biomarkers, gut microbiota, and microbial metabolites, demonstrating significant correlations among these variables. We observed a significant increase in the relative abundance of bacteria linked to obesity, e.g., Akkermansia muciniphila. Additionally, our study contributes to the ongoing debate about the role of SCFAs in obesity, as we observed a significant decrease in SCFA producers after a 12-week program.

TRIAL REGISTRATION

The trial was registered on [05/12/2014] with ClinicalTrials.gov (No: NCT02325804).

Fungal microbiome in gut of systemic lupus erythematosus (SLE)-prone mice (pristane and FCGRIIb deficiency), a possible impact of fungi in lupus

The gut mycobiota (fungal microbiota) plays a crucial role in the immune system, potentially impacting autoimmune diseases such as systemic lupus erythematosus (SLE). Despite growing interest, data on intestinal fungi in SLE remain limited. This study thereby investigated the human-mimicked (mice) gut mycobiome and quantitative gut mycobiome analyses using universal fungal internal transcribed spacer 2 (ITS2) DNA next generation sequencing and real-time PCR, tracking time-series dynamics from preclinical to established SLE conditions in two SLE-prone mouse models. These models included pristane -induced mice, representing an environmental cause of SLE, and Fc gamma receptor RIIb (FcgRIIb) deficiency mice, representing a genetic factor. Fecal samples and different intestinal sections from mice aged 2-10 months were analyzed, including samples from 4-month-old and 11-month-old mice, which represented preclinical lupus (negative for anti-dsDNA) and established SLE conditions (positive for anti-dsDNA with proteinuria), respectively, alongside age-matched healthy controls. Results showed increased fungal diversity, specific changes in gut fungal species (i.e. increased Candida spp.), and an elevated Basidiomycota-to-Ascomycota (Basidiomycota/Ascomycota) ratio, which correlated with lupus activity in both lupus models. Linear discriminant analysis Effect Size (LEfSe; a possible representative organism) helped identify specific fungal difference between the lupus models. Our findings revealed that active lupus states may elevate gut fungal populations and alter fungal components in both the pristane and genetically susceptible SLE-prone mice, as indicated by mycobiota and quantitative mycobiota analyses. These changes could, in turn, influence disease activity. This research is essential for a deeper understand of the SLE-gut microbiome association, as the gut microbiome comprises both bacterial and fungal symbiosis. Manipulating fungal communities could present a potential therapeutic avenue for influencing disease outcomes in lupus. Further studies are crucial to clarify the direct role of gut fungi in lupus disease progression.

Root microbiome of Panax ginseng in comparison with three other medicinal plants in the families of Araliaceae and Apiaceae

The intricate interplay between endophytic microorganisms and plants in the upkeep of biodiversity, the stability of communities, and the operation of ecosystems needs to be more adequately extensive. Although root-associated microbial communities of plants have been revealed for the last decade, the understanding of bacterial and fungal communities associated with the roots of medicinal plants remains elusive. To highlight the importance of Panax ginseng Meyer (PG) in our research, we investigated the root endophytic bacterial and fungal communities of Panax ginseng Meyer (PG), alongside Aralia cordata (AC), Angelica gigas (AG), and Peucedanum japonicum (PJ), utilizing amplicon-based community profiling and advanced bioinformatic methodologies. The study aimed to investigate the root-endophytic microbiota of ginseng and three other medicinal plants and identify similarities in microbiome composition across different plant species and families. Results revealed that root-endophytic bacterial and fungal communities were influenced by plant species and phylogenetic differences at the family level. Differential abundance tests and random forest models showed microbial features within the same plant family. PG had a distinctive microbial profile with significant B1653_o_Enterobacterales and F8_o_Helotiales. PG had a core microbiome, B10_Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, and a more evenly distributed microbial network compared to AG, PJ, and AC. Our research reveals the intricate endophytic microbial communities within the roots of medicinal plants, pinpointing specific taxa that may be pivotal to their medicinal qualities and overall plant health. These insights carry notable implications for future studies, particularly those focused on the endophytes of PG and their secondary metabolites, as they deepen our understanding of plant-microbe interactions and their role in enhancing the plants' therapeutic potential.

Local signal from Trichoderma afroharzianum T22 induces host transcriptome and endophytic microbiome leading to growth promotion in sorghum

Trichoderma, a highly abundant soil fungus, may benefit plants, yet it remains understudied in sorghum (Sorghum bicolor). In this study, sorghum plants were grown for 5 weeks in pots of soil with or without inoculation of T. afroharzianum T22. Inoculation with T. afroharzianum T22 significantly increased growth parameters and nutrient levels, demonstrating its beneficial role in sorghum. A split-root assay demonstrated that T. afroharzianum T22 is essential in both compartments of the pot for promoting plant growth, suggesting that local signals from this fungus drive symbiotic benefits in sorghum. RNA-seq analysis revealed that inoculation with T. afroharzianum T22 induced genes responsible for mineral transport (such as nitrate and aquaporin transporters), auxin response, sugar assimilation (hexokinase), and disease resistance (thaumatin) in sorghum roots. Microbial community analysis further unveiled the positive role of T. afroharzianum T22 in enriching Penicillium and Streptomyces while reducing disease-causing Fusarium in the roots. The microbial consortium, consisting of enriched microbiomes from bacterial and fungal communities, showed disrupted morphological features in plants inoculated with T. afroharzianum T22 in the absence of Streptomyces griseus. However, this disruption was not observed in the absence of Penicillium chrysogenum. These results indicate that S. griseus acts as a helper microbe in close association with T. afroharzianum T22 in the sorghum endosphere. This study provides the first comprehensive explanation of how T. afroharzianum T22 modulates host molecular determinants and endophytic helper microbes, thereby collectively promoting sorghum growth. These findings may facilitate the formulation of synthetic microbial inoculants dominated by T. afroharzianum T22 to enhance growth and stress resilience in sorghum and similar crops.

Soil eDNA biomonitoring reveals changes in multitrophic biodiversity and ecological health of agroecosystems

Soil health is integral to sustainable agroecosystem management. Current monitoring and assessment practices primarily focus on soil physicochemical properties, yet the perspective of multitrophic biodiversity remains underexplored. Here we used environmental DNA (eDNA) technology to monitor multitrophic biodiversity in four typical agroecosystems, and analyzed the species composition and diversity changes in fungi, bacteria and metazoan, and combined with the traditional physicochemical variables to establish a soil health assessment framework centered on biodiversity data. First, eDNA technology detected rich multitrophic biodiversity in four agroecosystems, including 100 phyla, 273 classes, 611 orders, 1026 families, 1668 genera and 1146 species with annotated classification, and the relative sequence abundance of dominant taxa fluctuates tens of times across agroecosystems. Second, significant differences in soil physicochemical variables such as organic matter (OM), total nitrogen (TN) and available phosphorus (AP) were observed among different agroecosystems, nutrients were higher in cropland and rice paddies, while heavy metals were higher in fish ponds and lotus ponds. Third, biodiversity metrics, including α and β diversity, also showed significant changes across agroecosystems, the soil biota was generally more sensitive to nutrients (e.g., OM, TN or AP), while the fungal communities were mainly affected by heavy metals in October (e.g., Cu and Cr). Finally, we screened 48 sensitive organismal indicators and found significant positive consistency between the developed eDNA indices and the traditional soil quality index (SQI, reaching up to R2 = 0.58). In general, this study demonstrated the potential of eDNA technology in soil health assessment and underscored the importance of a multitrophic perspective for efficient monitoring and managing agroecosystems.

Environmental concentrations of the fungicide tebuconazole alter microbial biodiversity and trigger biofilm-released transformation products

Freshwater microbial communities are integral components of riverine biodiversity. The ecological effects of toxic chemical pollutants, such as fungicides (e.g., tebuconazole), on microbial abundance and diversity are needed for risk assessment and regulation. The emergence of RNA metabarcoding approaches allow us to describe at unprecedented resolution the microbial diversity of the active part of a microbial community. Our study assesses the ecotoxicological impact of chronic and acute tebuconazole exposures on fungal, bacterial, and algal biomass and biodiversity of aquatic fungi and bacteria in stream biofilms using an RNA metabarcoding approach. In addition, the study uses HPLC-MS to evaluate the capability of biofilms to metabolize tebuconazole. Natural biofilm communities from a Swedish stream were exposed chronically (24 days) and acutely (96 h) to environmental concentrations of tebuconazole (10 and 100 μg/L) in microcosms conditions. The diversity and community structure of fungi and bacteria was assessed by ITS2 and 16S cDNA amplicon-sequencing, respectively. Biofilms chronically exposed to tebuconazole produced and released unidentified transformation products into the water column, suggesting a biotransformation capability following 24 days of uninterrupted exposure. The fungal biomass markedly decreased by a biomass loss of 40% when chronically exposed to 10 μg/L, and 60% when chronically exposed to 100 μg/L. Bacterial and algal biomass remained comparable with the controls in all tebuconazole treatments. Fungal and bacterial alpha diversity metrics were not significantly impacted, although a decreasing trend in fungal richness was observed with the treatments. However, beta diversity was significantly impacted in both fungal and bacterial compartments. Chronic exposures resulted in a shift in community composition, where taxa potentially more tolerant to tebuconazole (i.e. Lecanoromycetes) replaced more sensitive taxa (i.e. Malasseziomycetes). This study indicates that tebuconazole at environmental concentrations might pose a risk to freshwater systems, mainly due to its high toxicity to fungi.

Prevalent arbuscular mycorrhizae in roots and highly variable mycobiome in leaves of epiphytic subtropical fern Ophioderma pendulum

PREMISE

Endophytic and mycorrhizal fungi are crucial in facilitating plant nutrition acquisition and stress tolerance. In epiphytic habitats, plants face nutrition and water stress, but their roots are mostly nonmycorrhizal and especially lacking in arbuscular mycorrhizal associations. Ophioderma pendulum is an epiphytic fern with a partially mycoheterotrophic lifestyle, likely heavily reliant on symbiotic fungi. To characterize fungal associations in the sporophyte of O. pendulum, we focused on leaves and roots of O. pendulum, seeking to reveal the fungal communities in these organs.

METHODS

Roots and leaves from O. pendulum in a subtropical forest were examined microscopically to observe the morphology of fungal structures and determine the percentage of various fungal structures in host tissues. Fungal composition was profiled using metabarcoding techniques that targeted ITS2 of the nuclear ribosomal DNA.

RESULTS

Roots were consistently colonized by arbuscular mycorrhizal fungi (Glomeromycota), especially Acaulospora. Unlike previous findings on epiphytic ferns, dark septate endophytes were rare in O. pendulum roots. Leaves were predominantly colonized by Ascomycota fungi, specifically the classes Dothideomycetes (46.88%), Eurotiomycetes (11.51%), Sordariomycetes (6.23%), and Leotiomycetes (6.14%). Across sampling sites, fungal community compositions were similar in the roots but differed significantly in the leaves.

CONCLUSIONS

Ophioderma pendulum maintains stable, single-taxon-dominant communities in the roots, primarily featuring arbuscular mycorrhizal fungi, whereas the leaves may harbor opportunistic fungal colonizers. Our study underlines the significance of mycorrhizal fungi in the adaptation of epiphytic ferns.

Dryland fungi are spatially heterogeneous and resistant to global change drivers

Fungi are considered particularly important in regulating the structure and function of dryland ecosystems, yet the response of dryland fungal communities to global change remains notably understudied. Without a clear understanding of how fungi respond to global change drivers, mitigation plans-required for biodiversity and ecosystem service conservation and restoration-are impossible to develop. In this study we asked the following: (1) how does the fungal community respond to the individual and interactive effects of physical disturbance and drought in a heterogeneous dryland landscape comprised of drought-adapted shrubs separated by adjacent open areas of soil, and (2) what are the larger scale impacts of this response? We assessed fungal communities (using fungal-specific DNA metabarcoding analyses) of surface soil samples in an in situ global change experiment that included disturbance and drought in a full factorial design in the northern extent of the Chihuahuan Desert. We found that the fungal community was spatially heterogenous and remarkably resistant to disturbance and drought. We also show that dryland soils harbor high shares of facultative pathogenic and obligately pathogenic fungal taxa, with several concerning taxa reaching high relative abundances under drought. Our results suggest that the fungal community is highly influenced by microclimatic conditions associated with the presence or absence of vegetation. Moreover, our results imply that the fungal community in our experiment was already adapted to the magnitude of stress imposed by two years of experimental disturbance and drought treatments. Overall, our study shows that the fungal community is spatially heterogeneous, resistant to global change drivers, and houses many fungal species known for being stress tolerant and pathogenic.

Exogenous ketones exert antiseizure effects and modulate the gut microbiome and mycobiome in a clinically relevant murine model of epilepsy

OBJECTIVE

Despite growing interest in the potential use of exogenous ketones for the treatment of epilepsy, their impact on seizures and the gut microbiome and mycobiome remain unclear.

METHODS

Here, we examined the effects of both oral gavage and subcutaneous (SC) injection of a ketone ester (KE) in spontaneously epileptic Kcna1-null (KO) mice that model seminal aspects of human temporal lobe epilepsy. Electroencephalographic recordings and biochemical analyses were performed in KE-treated KO mice. Fecal microbial and fungal communities were profiled to determine whether the antiseizure activity of KE involves changes in the gut microbiome.

RESULTS

We found that exogenous KE administration by SC injection was more effective than oral gavage in terms of rendering antiseizure effects while generating similar degrees of ketonemia. However, reductions in mean daily seizure counts were accompanied by overall alterations in the fecal bacterial microbiome. Either oral or SC injection imposed a greater impact on the microbiome in male than female mice. In males, oral KE decreased Bacteroidota phylum and genera of Ligilactobacillus and Muribaculaceae, whereas SC injection decreased Bacteroides, Lactobacillus, and Lachnospiraceae. The fecal mycobiome was affected by KE injection to a greater degree than by oral gavage, and more in females than in males, as reflected by an increase in Ascomycota and Saccharomyces. Correlation analysis between microbiome and seizure counts revealed that in mice receiving KE injection, the seizure count was positively correlated with an amplicon sequencing variant of Lactobacillus (Spearman rho = .64, p = .03) and tended toward a negative correlation with Saccharomyces (Spearman rho = -.57, p = .057).

SIGNIFICANCE

Our findings demonstrate that exogenous ketone administration alone can induce antiseizure effects equally via different routes of administration, and that they induce differential shifts in both the bacterial microbiome and mycobiome.

Wise Roles and Future Visionary Endeavors of Current Emperor: Advancing Dynamic Methods for Longitudinal Microbiome Meta-Omics Data in Personalized and Precision Medicine

Understanding the etiological complexity of diseases requires identifying biomarkers longitudinally associated with specific phenotypes. Advanced sequencing tools generate dynamic microbiome data, providing insights into microbial community functions and their impact on health. This review aims to explore the current roles and future visionary endeavors of dynamic methods for integrating longitudinal microbiome multi-omics data in personalized and precision medicine. This work seeks to synthesize existing research, propose best practices, and highlight innovative techniques. The development and application of advanced dynamic methods, including the unified analytical frameworks and deep learning tools in artificial intelligence, are critically examined. Aggregating data on microbes, metabolites, genes, and other entities offers profound insights into the interactions among microorganisms, host physiology, and external stimuli. Despite progress, the absence of gold standards for validating analytical protocols and data resources of various longitudinal multi-omics studies remains a significant challenge. The interdependence of workflow steps critically affects overall outcomes. This work provides a comprehensive roadmap for best practices, addressing current challenges with advanced dynamic methods. The review underscores the biological effects of clinical, experimental, and analytical protocol settings on outcomes. Establishing consensus on dynamic microbiome inter-studies and advancing reliable analytical protocols are pivotal for the future of personalized and precision medicine.