Impact of microbial-based biopreparations on soil quality, plant health, and fruit chemistry in raspberry cultivation.

Application of microbial-based biopreparations as a pre-harvest strategy offers a method to obtain sustainable agricultural practices and could be an important approach for advancing food science, promoting sustainability, and meeting global food market demands. The impact of a bacterial-fungal biopreparation mixture on soil-plant-microbe interactions, fruit chemical composition and yield of 7 raspberry clones was investigated by examining the structural and functional profiles of microbial communities within leaves, fruits, and soil. Biopreparation addition caused the enhancement of the microbiological utilization of specific compounds, such as d-mannitol, relevant in plant-pathogen interactions and overall plant health. The biopreparation treatment positively affected the nitrogen availability in soil (9-160%). The analysis of plant stress marker enzymes combined with the evaluation of fruit quality and chemical properties highlight changes inducted by the pre-harvest biopreparation application. Chemical analyses highlight biopreparations' role in soil and fruit quality improvement, promoting sustainable agriculture. This effect was dependent on tested clones, showing increase of soluble solid content in fruits, concentration of polyphenols or the sensory quality of the fruits. The results of the next-generation sequencing indicated increase in the effective number of bacterial species after biopreparation treatment. The network analysis showed stimulating effect of biopreparation on microbial communities by enhancing microbial interactions (increasing the number of network edges up to 260%) of and affecting the proportions of mutual relationships between both bacteria and fungi. These findings show the potential of microbial-based biopreparation in enhancing raspberry production whilst promoting sustainable practices and maintaining environmental homeostasis and giving inshght in holistic understanding of microbial-based approaches for advancing food science monitoring.

Airborne fungal communities are more susceptible to anthropogenic activities than bacteria.

Airborne microorganisms (AM) have significant environmental and health implications. Extensive studies have been conducted to investigate the factors influencing the composition and diversity of AM. However, the knowledge of AM with anthropogenic activities has not reach a consensus. In this study, we took advantage of the dramatic decline of outdoor anthropogenic activities resulting from COVID-19 lockdown to reveal their associations. We collected airborne particulate matter before and during the lockdown period in two cities. The results showed that it was fungal diversity and communities but not bacteria obviously different between pre-lockdown and lockdown samples, suggesting that airborne fungi were more susceptible to anthropogenic activities than bacteria. However, after the implementation of lockdown, the co-occurrence networks of both bacterial and fungal community became more complex, which might be due to the variation of microbial sources. Furthermore, Mantel test and correlation analysis showed that air pollutants also partly contributed to microbial alterations. Airborne fungal community was more affected by air pollutants than bacterial community. Notably, some human pathogens like Nigrospora and Arthrinium were negatively correlated with air pollutants. Overall, our study highlighted the more impacts of anthropogenic activities on airborne fungal community than bacterial community and advanced the understanding of associations between anthropogenic activities and AM.

Endophytic fungal diversity and bioactive potentials: investigating antimicrobial and antioxidant activities.

This study investigates the colonization of endophytic fungi in nettle leaf tissues and evaluates their antibacterial and antioxidant activities. Using an inverted optical microscope, extensive fungal colonization was observed in all leaf parts, with hyphae prevalent in epidermal cells, parenchyma cells, and vascular tissues. 144 endophytic fungal isolates were isolated from 800 leaf fragments, indicating an 18% retention rate. ANOVA analysis revealed significant differences (p < 0. 001) in colonization frequencies among 20 subjects, with subject 3 showing the highest frequency (40%) and subject 11 the lowest (2. 5%). Ethyl acetate extracts of the three most abundant endophytic fungi demonstrated notable antibacterial activity against both Gram-positive and Gram-negative bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). Inhibition zones ranged from 9. 5 to 15. 16 mm, with minimum inhibitory concentrations (MICs) between 0. 19 to 25 mg/mL. Alternaria sp. exhibited the highest antimicrobial activity against MRSA. Antioxidant activity was assessed using the DPPH radical scavenging test and FRAP method. All extracts showed substantial free radical scavenging properties, with IC50 values close to those of standards like BHT. Alternaria sp. had the highest antioxidant activity, followed by Epicocum sp. and Ulocladium sp. The FRAP method confirmed high reducing potential, with Alternaria sp. again exhibiting the highest activity. These findings highlight the potential of endophytic fungi in nettle leaves as sources of antimicrobial and antioxidant agents, with significant implications for pharmaceutical and biotechnological applications.

Effects of long-term continuous cultivation on the structure and function of soil bacterial and fungal communities of Fritillaria Cirrhosa on the Qinghai-Tibetan Plateau.

Fritillaria cirrhosa, an endangered medicinal plant in the Qinghai-Tibet Plateau, is facing resource scarcity. Artificial cultivation has been employed to address this issue, but problems related to continuous cultivation hinder successful transplantation. Imbalanced microbial communities are considered a potential cause, yet the overall changes in the microbial community under continuous cropping systems remain poorly understood. Here, we investigated the effects of varying durations of continuous cropping on the bacterial and fungal communities, as well as enzymatic activities, in the rhizospheric soil of F. cirrhosa. Our findings revealed that continuous cropping of F. cirrhosa resulted in soil acidification, nutrient imbalances, and increased enzyme activity. Specifically, after 10 years of continuous cropping, there was a notable shift in the abundance and diversity (e.g., Chao1 index) of soil bacteria and fungi. Moreover, microbial composition analyses revealed a significant accumulation of harmful microorganisms associated with soil-borne diseases (e.g., Luteimonas, Parastagonospora, Pseudogymnoascus) in successively cropped soils, in contrast to the significant reduction of beneficial microorganisms (e.g., Sphingomonas, Lysobacter, Cladosporium) that promote plant growth and development and protect against diseases such as Fusarium sp.These changes led to decreased connectivity and stability within the soil microbial community. Structural equation modeling and redundancy analysis revealed that alkaline hydrolytic nitrogen and available phosphorus directly influenced soil pH, which was identified as the primary driver of soil microbial community changes and subsequently contributed to soil health deterioration. Overall, our results highlight that soil acidification and imbalanced rhizosphere microbial communities are the primary challenges associated with continuous cropping of F. cirrhosa. These findings establish a theoretical foundation for standardized cultivation practices of F. cirrhosa and the bioremediation of continuously cultivated soils.

Structure and distribution of sensor histidine kinases in the fungal kingdom.

Two-component systems (TCSs) are diverse cell signaling pathways that play a significant role in coping with a wide range of environmental cues in both prokaryotic and eukaryotic organisms. These transduction circuitries are primarily governed by histidine kinases (HKs), which act as sensing proteins of a broad variety of stressors. To date, nineteen HK groups have been previously described in the fungal kingdom. However, the structure and distribution of these prominent sensing proteins were hitherto investigated in a limited number of fungal species. In this study, we took advantage of recent genomic resources in fungi to refine the fungal HK classification by deciphering the structural diversity and phylogenetic distribution of HKs across a large number of fungal clades. To this end, we browsed the genome of 91 species representative of different fungal clades, which yielded 726 predicted HK sequences. A domain organization analysis, coupled with a robust phylogenomic approach, led to an improved categorization of fungal HKs. While most of the compiled sequences were categorized into previously described fungal HK groups, some new groups were also defined. Overall, this study provides an improved overview of the structure, distribution, and evolution of HKs in the fungal kingdom.

A comprehensive review on microbial diversity and anticancer compounds derived from seaweed endophytes: a pharmacokinetic and pharmacodynamic approach.

Seaweed endophytes are a rich source of microbial diversity and bioactive compounds. This review provides a comprehensive analysis of the microbial diversity associated with seaweeds and their interaction between them. These diverse bacteria and fungi have distinct metabolic pathways, which result in the synthesis of bioactive compounds with potential applications in a variety of health fields. We examine many types of seaweed-associated microorganisms, their bioactive metabolites, and their potential role in cancer treatment using a comprehensive literature review. By incorporating recent findings, we hope to highlight the importance of seaweed endophytes as a prospective source of novel anticancer drugs and promote additional studies in this area. We also investigate the pharmacokinetic and pharmacodynamic profiles of these bioactive compounds because understanding their absorption, distribution, metabolism, excretion (ADMET), and toxicity profiles is critical for developing bioactive compounds with anticancer potential into effective cancer drugs. This knowledge ensures the safety and efficacy of proposed medications prior to clinical trials. This study not only provides promise for novel and more effective treatments for cancer with fewer side effects, but it also emphasizes the necessity of sustainable harvesting procedures and ethical considerations for protecting the delicate marine ecology during bioprospecting activities.

Evaluation of 1021Bp, a close relative of Pseudomonas eucalypticola, for potential of plant growth promotion, fungal pathogen suppression and boxwood blight control.

BACKGROUND: Pseudomonas eucalypticola, a new species of the P. fluorescens group that generates most Pseudomonas-based biocontrol agents, has not been found in any plants other than Eucalyptus dunnii leaves. Except for antagonism to the growth of a few fungi, its features in plant growth promotion and disease control have not been evaluated. Here, we identified a similar species of P. eucalypticola, 1021Bp, from endophyte cultures of healthy leaves of English boxwood (Buxus sempervirens 'Suffruticosa') and investigated its antifungal activity, plant growth promotion traits, and potential for boxwood blight control. RESULTS: Colorimetric or plate assays showed the properties of 1021Bp in nitrogen fixation, phosphate solubilization, and production of indole-3-acetic acid (IAA) and siderophores, as well as the growth suppression of all five plant fungal pathogens, including causal agents of widespread plant diseases, gray mold, and anthracnose. Boxwood plant leaves received 87.4% and 65.8% protection from infection when sprayed with cell-free cultural supernatant (CFS) but not the resuspended bacterial cells at 108-9/mL of 1021Bp at one and seven days before inoculation (dbi) with boxwood blight pathogen, Calonectria pseudonaviculata, at 5 × 104 spores/mL. They also received similarly high protection with the 1021Bp cell culture without separation of cells and CFS at 14 dbi (67.5%), suggesting a key role of 1021Bp metabolites in disease control. CONCLUSIONS: Given the features of plant growth and health and its similarity to P. eucalypticola with the P. fluorescens lineage, 1021Bp has great potential to be developed as a safe and environmentally friendly biofungicide and biofertilizer. However, its metabolites are the major contributors to 1021Bp activity for plant growth and health. Application with the bacterial cells alone, especially with nonionic surfactants, may result in poor performance unless survival conditions are present.

Genomic Insights into Pseudomonas protegens E1BL2 from Giant Jala Maize: A Novel Bioresource for Sustainable Agriculture and Efficient Management of Fungal Phytopathogens.

The relationships between plants and bacteria are essential in agroecosystems and bioinoculant development. The leaf endophytic Pseudomonas protegens E1BL2 was previously isolated from giant Jala maize, which is a native Zea mays landrace of Nayarit, Mexico. Using different Mexican maize landraces, this work evaluated the strain's plant growth promotion and biocontrol against eight phytopathogenic fungi in vitro and greenhouse conditions. Also, a plant field trial was conducted on irrigated fields using the hybrid maize Supremo. The grain productivity in this assay increased compared with the control treatment. The genome analysis of P. protegens E1BL2 showed putative genes involved in metabolite synthesis that facilitated its beneficial roles in plant health and environmental adaptation (bdhA, acoR, trpE, speE, potA); siderophores (ptaA, pchC); and extracellular enzymes relevant for PGPB mechanisms (cel3, chi14), protection against oxidative stress (hscA, htpG), nitrogen metabolism (nirD, nit1, hmpA), inductors of plant-induced systemic resistance (ISR) (flaA, flaG, rffA, rfaP), fungal biocontrol (phlD, prtD, prnD, hcnA-1), pest control (vgrG-1, higB-2, aprE, pslA, ppkA), and the establishment of plant-bacteria symbiosis (pgaA, pgaB, pgaC, exbD). Our findings suggest that P. protegens E1BL2 significantly promotes maize growth and offers biocontrol benefits, which highlights its potential as a bioinoculant.

Fungal Extracellular Vesicle Proteins with Potential in Biological Interaction.

Extracellular vesicles (EVs) are vesicle-like structures composed of lipid bilayers, which can be divided into apoptotic bodies, microbubbles and exosomes. They are nanoparticles used for the exchange of information between cells. EVs contains many substances, including protein. With the development of proteomics, we know more about the types and functions of protein in vesicles. The potential functions of proteins in the envelope are mainly discussed, including cell wall construction, fungal virulence transmission, signal transmission and redox reactions, which provides a new perspective for studying the interaction mechanism between fungi and other organisms. The fungal protein markers of EVs are also summarized, which provided an exploration tool for studying the mechanism of vesicles. In addition, the possible role of immune protein in the EVs in the treatment of human diseases is also discussed, which provides new ideas for vaccine development.

Microbial colonisation rewires the composition and content of poplar root exudates, root and shoot metabolomes.

BACKGROUND: Trees are associated with a broad range of microorganisms colonising the diverse tissues of their host. However, the early dynamics of the microbiota assembly microbiota from the root to shoot axis and how it is linked to root exudates and metabolite contents of tissues remain unclear. Here, we characterised how fungal and bacterial communities are altering root exudates as well as root and shoot metabolomes in parallel with their establishment in poplar cuttings (Populus tremula x tremuloides clone T89) over 30 days of growth. Sterile poplar cuttings were planted in natural or gamma irradiated soils. Bulk and rhizospheric soils, root and shoot tissues were collected from day 1 to day 30 to track the dynamic changes of fungal and bacterial communities in the different habitats by DNA metabarcoding. Root exudates and root and shoot metabolites were analysed in parallel by gas chromatography-mass spectrometry. RESULTS: Our study reveals that microbial colonisation triggered rapid and substantial alterations in both the composition and quantity of root exudates, with over 70 metabolites exclusively identified in remarkably high abundances in the absence of microorganisms. Noteworthy among these were lipid-related metabolites and defence compounds. The microbial colonisation of both roots and shoots exhibited a similar dynamic response, initially involving saprophytic microorganisms and later transitioning to endophytes and symbionts. Key constituents of the shoot microbiota were also discernible at earlier time points in the rhizosphere and roots, indicating that the soil constituted a primary source for shoot microbiota. Furthermore, the microbial colonisation of belowground and aerial compartments induced a reconfiguration of plant metabolism. Specifically, microbial colonisation predominantly instigated alterations in primary metabolism in roots, while in shoots, it primarily influenced defence metabolism. CONCLUSIONS: This study highlighted the profound impact of microbial interactions on metabolic pathways of plants, shedding light on the intricate interplay between plants and their associated microbial communities. Video Abstract.

A novel luciferase-based reporter tool to monitor the dynamics of carbon catabolite repression in filamentous fungi.

Filamentous fungi with their diverse inventory of carbohydrate-active enzymes promise a holistic usage of lignocellulosic residues. A major challenge for application is the inherent repression of enzyme production by carbon catabolite repression (CCR). In the presence of preferred carbon sources, the transcription factor CreA/CRE-1 binds to specific but conserved motifs in promoters of genes involved in sugar metabolism, but the status of CCR is notoriously difficult to quantify. To allow for a real-time evaluation of CreA/CRE-1-mediated CCR at the transcriptional level, we developed a luciferase-based construct, representing a dynamic, highly responsive reporter system that is inhibited by monosaccharides in a quantitative fashion. Using this tool, CreA/CRE-1-dependent CCR triggered by several monosaccharides could be measured in Neurospora crassa, Aspergillus niger and Aspergillus nidulans over the course of hours, demonstrating distinct and dynamic regulatory processes. Furthermore, we used the reporter to visualize the direct impacts of multiple CreA truncations on CCR induction. Our reporter thus offers a widely applicable quantitative approach to evaluate CreA/CRE-1-mediated CCR across diverse fungal species and will help to elucidate the multifaceted effects of CCR on fungal physiology for both basic research and industrial strain engineering endeavours.

Ridge planting increases the rhizosphere microbiome diversity and improves the yield of Pinellia ternata (Thunb.) Breit in North China.

Pinellia ternata (Thunb.) Breit is an important traditional Chinese medicine. In North China, conventional flat planting of P. ternate is prone to root rot during the rainy season, leading to severe yield loss. Variations in planting patterns (e.g., ridge planting) can effectively alleviate this situation. However, the relationship between planting patterns and the changes induced by rhizosphere microbiome still needs to be determined. In this study, we clarified the effect of ridge planting on the yield of P. ternata and rhizosphere microbial community using high-throughput amplicon sequencing of 16S rRNA. Field experiments showed that ridge planting could increase the yield of P. ternata by 72.69% compared with flat planting. The high-throughput sequencing results demonstrated that fungal and bacterial communities in rhizosphere siols of flat and ridge planting showed obvious difference in diversity, structure, relative abundance, and community composition. The fungal phyla Zygomycota, Basidiomycota, Glomeromycota, and the bacterial phyla Chlamydiae, Tenericutes, and Hydrogenedentes were present in a higher relative abundance in the rhizosphere of ridge planting. Adonis multivariate analysis of variance results showed that 29 bacterial genera were significantly up/down-regulated, and only 4 fungal genera were changed considerably in ridge planting soil, indicating that the bacterial community composition varied significantly between the two treatments. Correlation analysis revealed that the yield of P. ternata was positively correlated with fungal genera Emericellopsis while negatively correlated with bacterial genera Acetobacter, Iamia, and fungal genera Thielavia. Overall, this study showed that ridge cropping significantly impacts the diversity and composition of the rhizosphere microbiome. It creates an environment favorable for crop growth and can be an effective planting strategy for P. ternata in areas with irrigation and high monsoon rainfall in North China.

Fungal and bat diversities along a landscape gradient in central Mexico.

Species interactions between bats and fungi are poorly known. We documented the association between fungal and bat diversities along a landscape gradient. Ten, eight, and seven bat species were captured in conserved, semi-conserved, and urban sites, respectively. Eptesicus fuscus, Myotis ciliolabrum and Corynorhinus townsendii were the most abundant in conserved and semi-conserved sites. E. fuscus, Myotis velifer, and Lasiurus cinereus were abundant in urban sites. C. townsendii was the least abundant bat. A total of 15 cultivated fungi genera included the fungal diversity in bats, of which nine fungi genera were shared along the landscape gradient. Penicillium and Aspergillus were the most abundant genera, and Aureobasidium, Bispora, Stachybotrys, and Verticillium were only documented in the conserved sites. We observed a higher fungal diversity associated with bat species along this landscape gradient. The individual site-based accumulation curves of fungal diversity showed significant decreasing values along the conserved, semi-conserved, and urban sites, respectively. In conserved and urban sites, M. californicus and M. velifer showed the highest fungal diversity, respectively. E. fuscus was associated to the fungi genera Scopulariopsis, Alternaria, Penicillium and Beauveria; L. cinereus to Cladosporium and Aspergillus, and M. velifer to Alternaria sp1, Bispora and Trichoderma. Conserved sites showed both high bat and fungal diversities [species richness and abundance] compared to semi-conserved and urban sites. More studies associating bat and fungal diversities in other ecosystems are needed to corroborate this pattern.

A review on fungal-based biopesticides and biofertilizers production.

The escalating use of inorganic fertilizers and pesticides to boost crop production has led to the depletion of natural resources, contamination of water sources, and environmental crises. In response, the scientific community is exploring eco-friendly alternatives, such as fungal-based biofertilizers and biopesticides, which have proven effectiveness in enhancing plant health and growth while sustainably managing plant diseases and pests. This review article examines the production methodologies of these bioproducts, highlighting their role in sustainable agriculture and advancing our understanding of soil microorganisms. Despite their increasing demand, their global market presence remains limited compared to traditional chemical counterparts. The article addresses: 1) the production of biofertilizers and biopesticides, 2) their contribution to crop productivity, 3) their environmental impact and regulations, and 4) current production technologies. This comprehensive approach aims to promote the transition towards more sustainable agricultural practices.

Replicating biological 3D root and hyphal networks in transparent glass chips.

Replicating the complex 3D microvascular architectures found in biological systems is a critical challenge in tissue engineering and other fields requiring efficient mass transport. Conventional microfabrication techniques often face limitations in creating extensive hierarchical networks, especially within bulk materials. Here, we report a versatile bioinspired approach to generate optimized 3D microvascular networks within transparent glass matrix by transcribing the natural growth patterns of plants and fungi. Plant seeds or fungal spores are first cultivated on nanoparticle-based culture media. Subsequent heat treatment removes the biological species while sintering the surrounding compound into a solidified chip with replica root/hyphal architectures as open microchannels. A diverse range of architectures, including the hierarchical branching of plant roots and the intricate networks formed by fungal hyphae, can be faithfully replicated. The resultant glass microvascular networks exhibit high chemical and thermal stability, enabling applications under harsh conditions. Fluid flow experiments validate the functionalities of the fabricated channels. By co-cultivating plants and fungi, hierarchical multi-scale architectures mimicking natural vascular systems are achieved. This bioinspired manufacturing technique leverages autonomous biological growth for architectural optimization, offering a complementary approach to existing microfabrication methods. The transparent nature of the glass chips allows for direct optical inspection, potentially facilitating integration with imaging components. This versatile platform holds promise for various engineering applications, such as microreactors, heat exchangers, and advanced filtration systems.

Predicting how varying moisture conditions impact the microbiome of dust collected from the International Space Station.

BACKGROUND: The commercialization of space travel will soon lead to many more people living and working in unique built environments similar to the International Space Station, which is a specialized closed environment that contains its own indoor microbiome. Unintended microbial growth can occur in these environments as in buildings on Earth from elevated moisture, such as from a temporary ventilation system failure. This growth can drive negative health outcomes and degrade building materials. We need a predictive approach for modeling microbial growth in these critical indoor spaces. RESULTS: Here, we demonstrate that even short exposures to varying elevated relative humidity can facilitate rapid microbial growth and microbial community composition changes in dust from spacecraft. We modeled fungal growth in dust from the International Space Station using the time-of-wetness framework with activation and deactivation limited growth occurring at 85% and 100% relative humidity, respectively. Fungal concentrations ranged from an average of 4.4 × 106 spore equivalents per milligram of dust in original dust with no exposure to relative humidity to up to 2.1 × 1010 when exposed to 100% relative humidity for 2 weeks. As relative humidity and time-elevated increased, fungal diversity was significantly reduced for both alpha (Q < 0.05) and beta (R2 = 0.307, P = 0.001) diversity metrics. Bacteria were unable to be modeled using the time-of-wetness framework. However, bacterial communities did change based on constant relative humidity incubations for both beta (R2 = 0.22, P = 0.001) and alpha diversity decreasing with increasing moisture starting at 85% relative humidity (Q < 0.05). CONCLUSION: Our results demonstrate that moisture conditions can be used to develop and predict changes in fungal growth and composition onboard human-occupied spacecraft. This predictive model can be expanded upon to include other spacecraft environmental factors such as microgravity, elevated carbon dioxide conditions, and radiation exposure. Understanding microbial growth in spacecraft can help better protect astronaut health, fortify spacecraft integrity, and promote planetary protection as human activity increases in low-Earth orbit, the moon, Mars, and beyond. Video Abstract.

Metagenomics Applied to the Respiratory Mycobiome in Cystic Fibrosis.

Cystic fibrosis (CF) is a genetic disorder characterized by chronic microbial colonization and inflammation of the respiratory tract (RT), leading to pulmonary exacerbation (PEx) and lung damage. Although the lung bacterial microbiota has been extensively studied, the mycobiome remains understudied. However, its importance as a contributor to CF pathophysiology has been highlighted. The objective of this review is to provide an overview of the current state of knowledge regarding the mycobiome, as described through NGS-based studies, in patients with CF (pwCF).Several studies have demonstrated that the mycobiome in CF lungs is a dynamic entity, exhibiting a lower diversity and abundance than the bacterial microbiome. Nevertheless, the progression of lung damage is associated with a decrease in fungal and bacterial diversity. The core mycobiome of the RT in pwCFs is mainly composed of yeasts (Candida spp., Malassezia spp.) and molds with lower abundance. Some fungi (Aspergillus, Scedosporium/Pseudallescheria) have been demonstrated to play a role in PEx, while the involvement of others (Candida, Pneumocystis) remains uncertain. The "climax attack" ecological model has been proposed to explain the complexity and interplay of microbial populations in the RT, leading to PEx and lung damage. NGS-based studies also enable the detection of intra- and interkingdom correlations between fungi and bacteria. Further studies are required to ascertain the biological and pathophysiological relevance of these correlations. Finally, with the recent advent of CFTR modulators, our understanding of the pulmonary microbiome and mycobiome in pwCFs is about to change.

Cover crop species influences soil fungal species richness and community structure.

Despite the well documented link between cover cropping and soil microbiology, the influence of specific cover crop species on soil microbes remains poorly understood. We evaluated how soil fungal communities in a no till system respond to four cover crop treatments: no cover crop (REF), cereal ryegrass (CRYE), wild pennycress (WPEN), and a mix of pea, clover, radish, and oat (PCRO). Soil samples were collected from experimental plots following termination of cover crops from depths of 0-2 cm and 2-4 cm where cover crops had significantly increased soil organic matter. There was no significant interaction between soil depth and cover crop treatment on either alpha diversity or beta diversity. All cover crop treatments (CRYE, PCRO, and WPEN) enhanced soil fungal richness but only CRYE enhanced soil fungal diversity and altered the fungal community structure. Soil depth altered the fungal community structure but had no effect on fungal diversity and richness. Genus Fusarium which includes some of the most economically destructive pathogens was more abundant in REF and PCRO treatments compared to CRYE and WPEN. In contrast, genus Mortierella which is known to promote plant health was more abundant in all cover crop treatments relative to the REF. These findings demonstrate that cover cropping can increase soil fungal species richness and alter fungal community structure, potentially promoting the abundance of beneficial fungi and reducing the abundance of some plant pathogens within the genus Fusarium. These effects are dependent on cover crop species, a factor that should be considered when selecting appropriate cover crops for a particular cropping system.

Drivers of diversification in fungal pathogen populations.

To manage and treat chronic fungal diseases effectively, we require an improved understanding of their complexity. There is an increasing appreciation that chronic infection populations are often heterogeneous due to diversification and drift, even within a single microbial species. Genetically diverse populations can contribute to persistence and resistance to treatment by maintaining cells with different phenotypes capable of thriving in these dynamic environments. In chronic infections, fungal pathogens undergo prolonged challenges that can drive trait selection to convergent adapted states through restricted access to critical nutrients, assault by immune effectors, competition with other species, and antifungal drugs. This review first highlights the various genetic and epigenetic mechanisms that promote diversity in pathogenic fungal populations and provide an additional barrier to assessing the actual heterogeneity of fungal infections. We then review existing studies of evolution and genetic heterogeneity in fungal populations from lung infections associated with the genetic disease cystic fibrosis. We conclude with a discussion of open research questions that, once answered, may aid in diagnosing and treating chronic fungal infections.

Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses.

Thermophily is a trait scattered across the fungal tree of life, with its highest prevalence within three fungal families (Chaetomiaceae, Thermoascaceae, and Trichocomaceae), as well as some members of the phylum Mucoromycota. We examined 37 thermophilic and thermotolerant species and 42 mesophilic species for this study and identified thermophily as the ancestral state of all three prominent families of thermophilic fungi. Thermophilic fungal genomes were found to encode various thermostable enzymes, including carbohydrate-active enzymes such as endoxylanases, which are useful for many industrial applications. At the same time, the overall gene counts, especially in gene families responsible for microbial defense such as secondary metabolism, are reduced in thermophiles compared to mesophiles. We also found a reduction in the core genome size of thermophiles in both the Chaetomiaceae family and the Eurotiomycetes class. The Gene Ontology terms lost in thermophilic fungi include primary metabolism, transporters, UV response, and O-methyltransferases. Comparative genomics analysis also revealed higher GC content in the third base of codons (GC3) and a lower effective number of codons in fungal thermophiles than in both thermotolerant and mesophilic fungi. Furthermore, using the Support Vector Machine classifier, we identified several Pfam domains capable of discriminating between genomes of thermophiles and mesophiles with 94% accuracy. Using AlphaFold2 to predict protein structures of endoxylanases (GH10), we built a similarity network based on the structures. We found that the number of disulfide bonds appears important for protein structure, and the network clusters based on protein structures correlate with the optimal activity temperature. Thus, comparative genomics offers new insights into the biology, adaptation, and evolutionary history of thermophilic fungi while providing a parts list for bioengineering applications.