Development of a novel mycobiome diagnostic for fungal infection

BACKGROUND

Amplicon-based mycobiome analysis has the potential to identify all fungal species within a sample and hence could provide a valuable diagnostic assay for use in clinical mycology settings. In the last decade, the mycobiome has been increasingly characterised by targeting the internal transcribed spacer (ITS) regions. Although ITS targets give broad coverage and high sensitivity, they fail to provide accurate quantitation as the copy number of ITS regions in fungal genomes is highly variable even within species. To address these issues, this study aimed to develop a novel NGS fungal diagnostic assay using an alternative amplicon target.

METHODS

Novel universal primers were designed to amplify a highly diverse single copy and uniformly sized DNA target (Tef1) to enable mycobiome analysis on the Illumina iSeq100 which is a low cost, small footprint and simple to use next-generation sequencing platform. To enable automated analysis and rapid results, a streamlined bioinformatics workflow and sequence database were also developed. Sequencing of mock fungal communities was performed to compare the Tef1 assay and established ITS1-based method. The assay was further evaluated using clinical respiratory samples and the feasibility of using internal spike-in quantitative controls was assessed.

RESULTS

The Tef1 assay successfully identified and quantified Aspergillus, Penicillium, Candida, Cryptococcus, Rhizopus, Fusarium and Lomentospora species from mock communities. The Tef1 assay was also capable of differentiating closely related species such as A. fumigatus and A. fischeri. In addition, it outperformed ITS1 at identifying A. fumigatus and other filamentous pathogens in mixed fungal communities (in the presence or absence of background human DNA). The assay could detect as few as 2 haploid genome equivalents of A. fumigatus from clinical respiratory samples. Lastly, spike-in controls were demonstrated to enable semi-quantitation of A. fumigatus load in clinical respiratory samples using sequencing data.

CONCLUSIONS

This study has developed and tested a novel metabarcoding target and found the assay outperforms ITS1 at identifying clinically relevant filamentous fungi. The assay is a promising diagnostic candidate that could provide affordable NGS analysis to clinical mycology laboratories.

Fungal microbiome (mycobiome) and virome of the lacrimal sac in patients with PANDO: the lacriome paper 5

PURPOSE

To study the fungal microbiome (mycobiome) and the virome of the lacrimal sacs in patients with primary acquired nasolacrimal duct obstruction (PANDO).

METHODS

A prospective study was performed on 10 consecutive samples of the lacrimal sac contents obtained from patients with PANDO. The samples were obtained from the lacrimal sacs under endoscopy guidance and immediately transported on ice to the laboratory. Following DNA extraction and library preparation, a whole shotgun metagenome sequencing was performed on the Illumina platform (NOVASEQ 6000). The fungal internal transcript spacer analysis was performed using the PIPITS v2.7 . The viral taxonomy profiling was performed using Kraken2 against the virus database.

RESULTS

The taxonomic hit distribution across the lacrimal sac samples showed rich fungal diversity (4 phyla, 12 classed, 21 families and 26 genera). The major phyla were Ascomycota and Basidiomycota, and the key genera identified were Alternaria, Hyphopichia, Malassezia, Aspergillus and Epicoccum. The virome analysis identified 13 phyla, 15 classes and 27 families. The viruses were commonly from the families Poxviridae, Retroviridae, Siphoviridae and Myoviridae, Poxviridae being the most prevalent family. The BeAn 58058 virus, a member of the Poxviridae family, was the most abundant in all the samples.

CONCLUSION

The present study is the first whole metagenome sequencing exclusively of the fungal microbiome and virome from the lacrimal sacs of patients with PANDO. The lacrimal sacs harbour diverse fungal and viral communities with distinct ecosystem dynamics. Further studies of their functions and interactions with the hosts would provide valuable insights.

Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients

BACKGROUND

The accuracy of internal-transcribed-spacer (ITS) and shotgun metagenomics has not been robustly evaluated, and the effect of diet on the composition and function of the bacterial and fungal gut microbiome in a longitudinal setting has been poorly investigated. Here we compared two approaches to study the fungal community (ITS and shotgun metagenomics), proposed an enrichment protocol to perform a reliable mycobiome analysis using a comprehensive in-house fungal database, and correlated dietary data with both bacterial and fungal communities.

RESULTS

We found that shotgun DNA sequencing after a new enrichment protocol combined with the most comprehensive and novel fungal databases provided a cost-effective approach to perform gut mycobiome profiling at the species level and to integrate bacterial and fungal community analyses in fecal samples. The mycobiome was significantly more variable than the bacterial community at the compositional and functional levels. Notably, we showed that microbial diversity, composition, and functions were associated with habitual diet composition instead of driven by global dietary changes. Our study indicates a potential competitive inter-kingdom interaction between bacteria and fungi for food foraging.

CONCLUSION

Together, our present work proposes an efficient workflow to study the human gut microbiome integrating robustly fungal, bacterial, and dietary data. These findings will further advance our knowledge of the interaction between gut bacteria and fungi and pave the way for future investigations in human mycobiome. Video Abstract.

Sapwood mycobiome varies across host, plant compartment and environments in Nothofagus forests from Northern Patagonia

Global forests are increasingly being threatened by altered climatic conditions and increased attacks by pests and pathogens. The complex ecological interactions among pathogens, microbial communities, tree hosts and the environment are important drivers of forest dynamics. Little is known about the ecology of forest pathology and related microbial communities in temperate forests of the southern hemisphere. In this study, we used next-generation sequencing to characterize sapwood-inhabiting fungal communities in North Patagonian Nothofagus forests and assessed patterns of diversity of taxa and ecological guilds across climatic, site and host variables (health condition and compartment) as a contribution to Nothofagus autecology. The diversity patterns inferred through the metabarcoding analysis were similar to those obtained through culture-dependent approaches. However, we detected additional heterogeneity and greater richness with culture-free methods. Host species was the strongest driver of fungal community structure and composition, while host health status was the weakest. The relative impacts of site, season, plant compartment and health status were different for each tree species; these differences can be interpreted as a matter of water availability. For Nothofagus dombeyi, which is distributed across a wide range of climatic conditions, site was the strongest driver of community composition. The microbiome of N. pumilio varied more with season and temperature, a relevant factor for forest conservation in the present climate change scenario. Both species carry a number of potential fungal pathogens in their sapwood, whether they exhibit symptoms or not. Our results provide insight into the diversity of fungi associated with the complex pathobiome of the dominant Nothofagus species in southern South America.

Nanopore sequencing of full rRNA operon improves resolution in mycobiome analysis and reveals high diversity in both human gut and environments

High-throughput sequencing has substantially improved our understanding of fungal diversity. However, the short read (<500 bp) length of current second-generation sequencing approaches provides limited taxonomic and phylogenetic resolution for species discrimination. Longer sequences containing more information are highly desired to provide greater taxonomic resolution. Here, we amplified full-length rRNA operons (~5.5 kb) and established a corresponding fungal rRNA operon database for ONT sequences (FRODO), which contains ONT sequences representing eight phyla, 41 classes, 109 orders, 256 families, 524 genera and 1116 species. We also benchmarked the optimal method for sequence classification and determined that the RDP classifier based on our FRODO database was capable of improving the classification of ONT reads, with an average of 98%-99% reads correctly classified at the genus or species level. We investigated the applicability of our approach in three representative mycobiomes, namely, the soil, marine and human gut mycobiomes, and found that the gut contains the largest number of unknown species (over 90%), followed by the marine (42%) and soil (33.8%) mycobiomes. We also observed a distinct difference in the composition of the marine and soil mycobiomes, with the highest richness and diversity detected in soils. Overall, our study provides a systematic approach for mycobiome studies and revealed that the previous methods might have underestimated the diversity of mycobiome species. Future application of this method will lead to a better understanding of the taxonomic and functional diversity of fungi in environmental and health-related mycobiomes.

Stable functional structure despite high taxonomic variability across fungal communities in soils of old-growth montane forests

BACKGROUND

Major advances over the past decade in molecular ecology are providing access to soil fungal diversity in forest ecosystems worldwide, but the diverse functions and metabolic capabilities of this microbial community remain largely elusive. We conducted a field survey in montane old-growth broadleaved and conifer forests, to investigate the relationship between soil fungal diversity and functional genetic traits. To assess the extent to which variation in community composition was associated with dominant tree species (oak, spruce, and fir) and environmental variations in the old-growth forests in the Jade Dragon Snow Mountain in Yunnan Province, we applied rDNA metabarcoding. We also assessed fungal gene expression in soil using mRNA sequencing and specifically assessed the expression of genes related to organic matter decomposition and nutrient acquisition in ectomycorrhizal and saprotrophic fungi.

RESULTS

Our taxonomic profiling revealed striking shifts in the composition of the saprotrophic and ectomycorrhizal guilds among the oak-, fir-, and spruce-dominated forests. The core fungal microbiome comprised only ~ 20% of the total OTUs across all soil samples, although the overlap between conifer-associated communities was substantial. In contrast, seasonality and soil layer explained only a small proportion of the variation in community structure. However, despite their highly variable taxonomic composition, fungal guilds exhibited remarkably similar functional traits for growth-related and core metabolic pathways across forest associations, suggesting ecological redundancy. However, we found that the expression profiles of genes related to polysaccharide and protein degradation and nutrient transport notably varied between and within the fungal guilds, suggesting niche adaptation.

CONCLUSIONS

Overall, our metatranscriptomic analyses revealed the functional potential of soil fungal communities in montane old-growth forests, including a suite of specialized genes and taxa involved in organic matter decomposition. By linking genes to ecological traits, this study provides insights into fungal adaptation strategies to biotic and environmental factors, and sheds light on the importance of understanding functional gene expression patterns in predicting ecosystem functioning. Video Abstract.

Quantifying the mycobiome and its major constituents on the skin of 20 normal dogs

OBJECTIVE

To report the density, and constituents, of the mycobiome on the skin surface of normal dogs.

ANIMALS

20 normal dogs were recruited for this study, with informed consent in all cases.

METHODS

Flocked swabs were used to sample the skin surface and to sample the skin surface after superficial scraping with a blunted scapula. Both samples were taken within a brass guide with an internal area of 3.5 cm-2. Next-generation DNA sequencing was used to identify and quantify components of the mycobiome.

RESULTS

The median density of the mycobiome was 1.1 X 105 cm-2 (IQR, 27,561, 409,572). Cladosporium spp and Vishniacozyma victoriae were found on all 20 dogs.

CLINICAL RELEVANCE

Knowledge of the density and the composition of the cutaneous mycobiome will increase our understanding of skin biology and may have relevance to future therapeutic trials.

Enterotypes of the human gut mycobiome

BACKGROUND

The fungal component of the human gut microbiome, also known as the mycobiome, plays a vital role in intestinal ecology and human health. However, the overall structure of the gut mycobiome as well as the inter-individual variations in fungal composition remains largely unknown. In this study, we collected a total of 3363 fungal sequencing samples from 16 cohorts across three continents, including 572 newly profiled samples from China.

RESULTS

We identify and characterize four mycobiome enterotypes using ITS profiling of 3363 samples from 16 cohorts. These enterotypes exhibit stability across populations and geographical locations and significant correlation with bacterial enterotypes. Particularly, we notice that fungal enterotypes have a strong age preference, where the enterotype dominated by Candida (i.e., Can_type enterotype) is enriched in the elderly population and confers an increased risk of multiple diseases associated with a compromised intestinal barrier. In addition, bidirectional mediation analysis reveals that the fungi-contributed aerobic respiration pathway associated with the Can_type enterotype might mediate the association between the compromised intestinal barrier and aging.

CONCLUSIONS

We show that the human gut mycobiome has stable compositional patterns across individuals and significantly correlates with multiple host factors, such as diseases and host age. Video Abstract.

Patterns and determinants of the global herbivorous mycobiome

Despite their role in host nutrition, the anaerobic gut fungal (AGF) component of the herbivorous gut microbiome remains poorly characterized. Here, to examine global patterns and determinants of AGF diversity, we generate and analyze an amplicon dataset from 661 fecal samples from 34 mammalian species, 9 families, and 6 continents. We identify 56 novel genera, greatly expanding AGF diversity beyond current estimates (31 genera and candidate genera). Community structure analysis indicates that host phylogenetic affiliation, not domestication status and biogeography, shapes the community rather than. Fungal-host associations are stronger and more specific in hindgut fermenters than in foregut fermenters. Transcriptomics-enabled phylogenomic and molecular clock analyses of 52 strains from 14 genera indicate that most genera with preferences for hindgut hosts evolved earlier (44-58 Mya) than those with preferences for foregut hosts (22-32 Mya). Our results greatly expand the documented scope of AGF diversity and provide an ecologically and evolutionary-grounded model to explain the observed patterns of AGF diversity in extant animal hosts.

Assessing the causes and consequences of gut mycobiome variation in a wild population of the Seychelles warbler

BACKGROUND

Considerable research has focussed on the importance of bacterial communities within the vertebrate gut microbiome (GM). However, studies investigating the significance of other microbial kingdoms, such as fungi, are notably lacking, despite their potential to influence host processes. Here, we characterise the fungal GM of individuals living in a natural population of Seychelles warblers (Acrocephalus sechellensis). We evaluate the extent to which fungal GM structure is shaped by environment and host factors, including genome-wide heterozygosity and variation at key immune genes (major histocompatibility complex (MHC) and Toll-like receptor (TLR)). Importantly, we also explore the relationship between fungal GM differences and subsequent host survival. To our knowledge, this is the first time that the genetic drivers and fitness consequences of fungal GM variation have been characterised for a wild vertebrate population.

RESULTS

Environmental factors, including season and territory quality, explain the largest proportion of variance in the fungal GM. In contrast, neither host age, sex, genome-wide heterozygosity, nor TLR3 genotype was associated with fungal GM differences in Seychelles warblers. However, the presence of four MHC-I alleles and one MHC-II allele was associated with changes in fungal GM alpha diversity. Changes in fungal richness ranged from between 1 and 10 sequencing variants lost or gained; in some cases, this accounted for 20% of the fungal variants carried by an individual. In addition to this, overall MHC-I allelic diversity was associated with small, but potentially important, changes in fungal GM composition. This is evidenced by the fact that fungal GM composition differed between individuals that survived or died within 7 months of being sampled.

CONCLUSIONS

Our results suggest that environmental factors play a primary role in shaping the fungal GM, but that components of the host immune system-specifically the MHC-may also contribute to the variation in fungal communities across individuals within wild populations. Furthermore, variation in the fungal GM can be associated with differential survival in the wild. Further work is needed to establish the causality of such relationships and, thus, the extent to which components of the GM may impact host evolution. Video Abstract.

Surface fungal diversity and several mycotoxin-related genes' expression profiles during the Lunar Palace 365 experiment

BACKGROUND

Chinese Lunar Palace 1 (LP1) is a ground-based bio-regenerative life support system (BLSS) test bed integrating highly efficient plant cultivation, animal protein production, urine nitrogen recycling, and bioconversion of solid waste. To date, there has been no molecular method-based detailed investigation of the fungal community and mycotoxin potential in BLSS habitats. To ensure safe BLSS design for actual space missions, we analyzed the LP1 surface mycobiome and mycotoxin potential during the Lunar Palace 365 project through internal transcribed spacer region 1 (ITS1) amplicon sequencing and quantitative polymerase chain reaction (qPCR) with primers specific for idh, ver1, nor1, tri5, and ITS1.

RESULTS

The LP1 system exhibited significant differences in fungal community diversity compared to other confined habitats, with higher fungal alpha diversity and different community structures. Significant differences existed in the surface fungal communities of the LP1 habitat due to the presence of different occupant groups. However, there was no significant difference between fungal communities in the plant cabin with various occupants. Source tracker analysis shows that most of the surface fungi in LP1 originated from plants. Regardless of differences in occupants or location, there were no significant differences in mycotoxin gene copy number.

CONCLUSIONS

Our study reveals that plants are the most crucial source of the surface fungal microbiome; however, occupant turnover can induce significant perturbations in the surface fungal community in a BLSS. Growing plants reduced fungal fluctuations, maintaining a healthy balance in the surface fungal microbiome and mycotoxin potential. Moreover, our study provides data important to (i) future risk considerations in crewed space missions with long-term residency, (ii) an optimized design and planning of a space mission that incorporates crew shifts and plant growth, and (iii) the expansion of our knowledge of indoor fungal communities with plant growth, which is essential to maintain safe working and living environments. Video Abstract.

The air mycobiome is decoupled from the soil mycobiome in the California San Joaquin Valley

Dispersal is a key force in the assembly of fungal communities and the air is the dominant route of dispersal for most fungi. Understanding the dynamics of airborne fungi is important for determining their source and for helping to prevent fungal disease. This understanding is important in the San Joaquin Valley of California, which is home to 4.2 million people and where the airborne fungus Coccidioides is responsible for the most important fungal disease of otherwise healthy humans, coccidioidomycosis. The San Joaquin Valley is the most productive agricultural region in the United States, with the principal crops grown therein susceptible to fungal pathogens. Here, we characterize the fungal community in soil and air on undeveloped and agricultural land in the San Joaquin Valley using metabarcoding of the internal transcribed spacer 2 variable region of fungal rDNA. Using 1,002 individual samples, we report one of the most extensive studies of fungi sampled simultaneously from air and soil using modern sequencing techniques. We find that the air mycobiome in the San Joaquin Valley is distinct from the soil mycobiome, and that the assemblages of airborne fungi from sites as far apart as 160 km are far more similar to one another than to the fungal communities in nearby soils. Additionally, we present evidence that airborne fungi in the San Joaquin Valley are subject to dispersal limitation and cyclical intra-annual patterns of community composition. Our findings are broadly applicable to understanding the dispersal of airborne fungi and the taxonomic structure of airborne fungal assemblages.

Multiple sclerosis patients have an altered gut mycobiome and increased fungal to bacterial richness

Trillions of microbes such as bacteria, fungi, and viruses exist in the healthy human gut microbiome. Although gut bacterial dysbiosis has been extensively studied in multiple sclerosis (MS), the significance of the fungal microbiome (mycobiome) is an understudied and neglected part of the intestinal microbiome in MS. The aim of this study was to characterize the gut mycobiome of patients with relapsing-remitting multiple sclerosis (RRMS), compare it to healthy controls, and examine its association with changes in the bacterial microbiome. We characterized and compared the mycobiome of 20 RRMS patients and 33 healthy controls (HC) using Internal Transcribed Spacer 2 (ITS2) and compared mycobiome interactions with the bacterial microbiome using 16S rRNA sequencing. Our results demonstrate an altered mycobiome in RRMS patients compared with HC. RRMS patients showed an increased abundance of Basidiomycota and decreased Ascomycota at the phylum level with an increased abundance of Candida and Epicoccum genera along with a decreased abundance of Saccharomyces compared to HC. We also observed an increased ITS2/16S ratio, altered fungal and bacterial associations, and altered fungal functional profiles in MS patients compared to HC. This study demonstrates that RRMS patients had a distinct mycobiome with associated changes in the bacterial microbiome compared to HC. There is an increased fungal to bacterial ratio as well as more diverse fungal-bacterial interactions in RRMS patients compared to HC. Our study is the first step towards future studies in delineating the mechanisms through which the fungal microbiome can influence MS disease.

Alterations in the Gut Fungal Community in a Mouse Model of Huntington's Disease

Huntington's disease (HD) is a neurodegenerative disorder caused by a trinucleotide expansion in the HTT gene, which is expressed throughout the brain and body, including the gut epithelium and enteric nervous system. Afflicted individuals suffer from progressive impairments in motor, psychiatric, and cognitive faculties, as well as peripheral deficits, including the alteration of the gut microbiome. However, studies characterizing the gut microbiome in HD have focused entirely on the bacterial component, while the fungal community (mycobiome) has been overlooked. The gut mycobiome has gained recognition for its role in host homeostasis and maintenance of the gut epithelial barrier. We aimed to characterize the gut mycobiome profile in HD using fecal samples collected from the R6/1 transgenic mouse model (and wild-type littermate controls) from 4 to 12 weeks of age, corresponding to presymptomatic through to early disease stages. Shotgun sequencing was performed on fecal DNA samples, followed by metagenomic analyses. The HD gut mycobiome beta diversity was significantly different from that of wild-type littermates at 12 weeks of age, while no genotype differences were observed at the earlier time points. Similarly, greater alpha diversity was observed in the HD mice by 12 weeks of age. Key taxa, including Malassezia restricta, Yarrowia lipolytica, and Aspergillus species, were identified as having a negative association with HD. Furthermore, integration of the bacterial and fungal data sets at 12 weeks of age identified negative correlations between the HD-associated fungal species and Lactobacillus reuteri. These findings provide new insights into gut microbiome alterations in HD and may help identify novel therapeutic targets. IMPORTANCE Huntington's disease (HD) is a fatal neurodegenerative disorder affecting both the mind and body. We have recently discovered that gut bacteria are disrupted in HD. The present study provides the first evidence of an altered gut fungal community (mycobiome) in HD. The genomes of many thousands of gut microbes were sequenced and used to assess "metagenomics" in particular the different types of fungal species in the HD versus control gut, in a mouse model. At an early disease stage, before the onset of symptoms, the overall gut mycobiome structure (array of fungi) in HD mice was distinct from that of their wild-type littermates. Alterations of multiple key fungi species were identified as being associated with the onset of disease symptoms, some of which showed strong correlations with the gut bacterial community. This study highlights the potential role of gut fungi in HD and may facilitate the development of novel therapeutic approaches.

Soil fungal communities affect the chemical quality of flue-cured tobacco leaves in Bijie, Southwest China

Soil microorganisms could affect the quality of tobacco leaves, however, little is known about the association of tobacco chemical components and soil fungal communities. In the present study, the relationship between soil fungi and tobacco quality based on chemical components in Bijie was investigated. The results showed that the total harmony scores (THS) of the analyzed tobacco leaves ranged from 46.55 ± 3.5 to 91.55 ± 2.25. Analyses of chemical components revealed that high contents of nicotine (≥ 1.06%) and sugar (total sugar: ≥ 22.96%, reducing sugar: ≥ 19.62%), as well as low potassium level (≤ 2.68%) were the main factors limiting the quality of flue-cured tobacco leaves. Pearson correlation analysis indicated that soil nitrate, available potassium/phosphorous, and organic matter significantly correlated with tobacco nicotine, potassium, and chloride levels (p < 0.05). Besides, the analysis of alpha- and beta-diversity of soil fungal communities implied that fungal structure rather than the richness affected the chemical quality of tobacco. In detail, the relative abundance of Humicola olivacea species in soils was positively correlated with the THS of tobaccos (r = 0.52, p < 0.05). Moreover, the species including Mortierella alpina, Mortierella hyalina, Tausonia pullulan, and Humicola olivacea were negatively correlated with tobacco sugar (r ≤  - 0.45, p < 0.05) while, Codinaea acaciae and Saitozyma podzolica species were negatively correlated with tobacco nicotine (r ≤  - 0.51, p < 0.05). The present study provides a preliminary basis for utilizing fungal species in soils to improve the chemical quality of tobacco in the studied area.

Fungal Dysbiosis in Children with Celiac Disease

BACKGROUND

Although intestinal fungi are known to interact with the immune system, the relationship between intestinal fungi and childhood celiac disease (CeD), an immune-mediated condition, has rarely been reported.

AIMS

The aim of this study was to describe gut fungal profiles in a cohort of children with new-onset CeD.

METHODS

Mucosal and fecal samples were collected from children with CeD and controls and subjected to metagenomics analysis of fungal microbiota communities. DNA libraries were sequenced using Illumina HiSeq platform 2 × 150 bp. Bioinformatic analysis was performed to quantify the relative abundance of fungi. Shannon alpha diversity metrics and beta diversity principal coordinate (PCo) analyses were calculated, and DESeq tests were performed between celiac and non-celiac groups.

RESULTS

Overall more abundant taxa in samples of children with CeD included Tricholomataceae, Saccharomycetaceae, Saccharomycetes Saccharomyces cerevisiae, and Candida, whereas less abundant taxa included Pichiaceae, Pichia kudriavzevii, Pneumocystis, and Pneumocystis jirovecii. Alpha diversity between CeD and control individuals did not differ significantly, and beta diversity PCo analysis showed overlap of samples from CeD and controls for both fecal or mucosal samples; however, there was a clear separation between mucosal and fecal overall samples CONCLUSIONS: We report fungal dysbiosis in children with CeD, suggesting a possible role in the pathogenesis of CeD. Further larger, controlled, prospective and longitudinal studies are needed to verify the results of this study and clarify the functional role of fungi in CeD.

Genetic determinants of endophytism in the Arabidopsis root mycobiome

The roots of Arabidopsis thaliana host diverse fungal communities that affect plant health and disease states. Here, we sequence the genomes of 41 fungal isolates representative of the A. thaliana root mycobiota for comparative analysis with other 79 plant-associated fungi. Our analyses indicate that root mycobiota members evolved from ancestors with diverse lifestyles and retain large repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. We identify a set of 84 gene families associated with endophytism, including genes encoding PCWDEs acting on xylan (family GH10) and cellulose (family AA9). Transcripts encoding these enzymes are also part of a conserved transcriptional program activated by phylogenetically-distant mycobiota members upon host contact. Recolonization experiments with individual fungi indicate that strains with detrimental effects in mono-association with the host colonize roots more aggressively than those with beneficial activities, and dominate in natural root samples. Furthermore, we show that the pectin-degrading enzyme family PL1_7 links aggressiveness of endophytic colonization to plant health.

An ancient antimicrobial protein co-opted by a fungal plant pathogen for in planta mycobiome manipulation

Microbes typically secrete a plethora of molecules to promote niche colonization. Soil-dwelling microbes are well-known producers of antimicrobials that are exploited to outcompete microbial coinhabitants. Also, plant pathogenic microbes secrete a diversity of molecules into their environment for niche establishment. Upon plant colonization, microbial pathogens secrete so-called effector proteins that promote disease development. While such effectors are typically considered to exclusively act through direct host manipulation, we recently reported that the soil-borne, fungal, xylem-colonizing vascular wilt pathogen Verticillium dahliae exploits effector proteins with antibacterial properties to promote host colonization through the manipulation of beneficial host microbiota. Since fungal evolution preceded land plant evolution, we now speculate that a subset of the pathogen effectors involved in host microbiota manipulation evolved from ancient antimicrobial proteins of terrestrial fungal ancestors that served in microbial competition prior to the evolution of plant pathogenicity. Here, we show that V. dahliae has co-opted an ancient antimicrobial protein as effector, named VdAMP3, for mycobiome manipulation in planta. We show that VdAMP3 is specifically expressed to ward off fungal niche competitors during resting structure formation in senescing mesophyll tissues. Our findings indicate that effector-mediated microbiome manipulation by plant pathogenic microbes extends beyond bacteria and also concerns eukaryotic members of the plant microbiome. Finally, we demonstrate that fungal pathogens can exploit plant microbiome-manipulating effectors in a life stage-specific manner and that a subset of these effectors has evolved from ancient antimicrobial proteins of fungal ancestors that likely originally functioned in manipulation of terrestrial biota.

Micronutrient supplements can promote disruptive protozoan and fungal communities in the developing infant gut

Supplementation with micronutrients, including vitamins, iron and zinc, is a key strategy to alleviate child malnutrition. However, association of gastrointestinal disorders with iron has led to ongoing debate over their administration. To better understand their impact on gut microbiota, we analyse the bacterial, protozoal, fungal and helminth communities of stool samples collected from a subset of 80 children at 12 and 24 months of age, previously enrolled into a large cluster randomized controlled trial of micronutrient supplementation in Pakistan (ClinicalTrials.gov identifier NCT00705445). We show that while bacterial diversity is reduced in supplemented children, vitamins and iron (as well as residence in a rural setting) may promote colonization with distinct protozoa and mucormycetes, whereas the addition of zinc appears to ameliorate this effect. We suggest that the risks and benefits of micronutrient interventions may depend on eukaryotic communities, potentially exacerbated by exposure to a rural setting. Larger studies are needed to evaluate the clinical significance of these findings and their impact on health outcomes.

Simulation and Prediction of Fungal Community Evolution Based on RBF Neural Network

Simulation and prediction of the scale change of fungal community. First, using the experimental data of a variety of fungal decomposition activities, a mathematical model of the decomposition rate and the relationship between the bacterial species was established, thereby revealing the internal mechanism of fungal decomposition activity in a complex environment. Second, based on the linear regression method and the principle of biodiversity, a model of fungal decomposition rate was constructed, and it was concluded that the interaction between mycelial elongation and moisture resistance could increase the fungal decomposition rate. Third, the differential equations are used to quantify the competitive relationship between different bacterial species, divide the boundaries of superior and inferior species, and simulate the long-term and short-term evolution trends of the community under the same initial environment. And an empirical analysis is made by taking the sudden change of the atmosphere affecting the evolution of the colony as an example. Finally, starting from summer, combining soil temperature, humidity, and fungal species data in five different environments such as arid and semiarid, a three-dimensional model and RBF neural network are introduced to predict community evolution. The study concluded that under given conditions, different strains are in short-term competition, and in the long-term, mutually beneficial symbiosis. Biodiversity is important for the biological regulation of nature.

Climate warming dominates over plant genotype in shaping the seasonal trajectory of foliar fungal communities on oak

Leaves interact with a wealth of microorganisms. Among these, fungi are highly diverse and are known to contribute to plant health, leaf senescence and early decomposition. However, patterns and drivers of the seasonal dynamics of foliar fungal communities are poorly understood. We used a multifactorial experiment to investigate the influence of warming and tree genotype on the foliar fungal community on the pedunculate oak Quercus robur across one growing season. Fungal species richness increased, evenness tended to decrease, and community composition strongly shifted during the growing season. Yeasts increased in relative abundance as the season progressed, while putative fungal pathogens decreased. Warming decreased species richness, reduced evenness and changed community composition, especially at the end of the growing season. Warming also negatively affected putative fungal pathogens. We only detected a minor imprint of tree genotype and warming × genotype interactions on species richness and community composition. Overall, our findings demonstrate that warming plays a larger role than plant genotype in shaping the seasonal dynamics of the foliar fungal community on oak. These warming-induced shifts in the foliar fungal community may have a pronounced impact on plant health, plant-fungal interactions and ecosystem functions.

Deciphering Trifolium pratense L. holobiont reveals a microbiome resilient to future climate changes

The plant microbiome supports plant growth, fitness, and resistance against climate change. Trifolium pratense (red clover), an important forage legume crop, positively contributes to ecosystem sustainability. However, T. pratense is known to have limited adaptive ability toward climate change. Here, the T. pratense microbiomes (including both bacteria and fungi) of the rhizosphere and the root, shoot, and flower endospheres were comparatively examined using metabarcoding in a field located in Central Germany that mimics the climate conditions projected for the next 50-70 years in comparison with the current climate conditions. Additionally, the ecological functions and metabolic genes of the microbial communities colonizing each plant compartment were predicted using FUNGuild, FAPROTAX, and Tax4Fun annotation tools. Our results showed that the individual plant compartments were colonized by specific microbes. The bacterial and fungal community compositions of the belowground plant compartments did not vary under future climate conditions. However, future climate conditions slightly altered the relative abundances of specific fungal classes of the aboveground compartments. We predicted several microbial functional genes of the T. pratense microbiome involved in plant growth processes, such as biofertilization (nitrogen fixation, phosphorus solubilization, and siderophore biosynthesis) and biostimulation (phytohormone and auxin production). Our findings indicated that T. pratense microbiomes show a degree of resilience to future climate changes. Additionally, microbes inhabiting T. pratense may not only contribute to plant growth promotion but also to ecosystem sustainability.

The bacterial and fungal community composition in time and space in the nest mounds of the ant Formica exsecta (Hymenoptera: Formicidae)

In a subarctic climate, the seasonal shifts in temperature, precipitation, and plant cover drive the temporal changes in the microbial communities in the topsoil, forcing soil microbes to adapt or decline. Many organisms, such as mound-building ants, survive the cold winter owing to the favorable microclimate in their nest mounds. We have previously shown that the microbial communities in the nest of the ant Formica exsecta are significantly different from those in the surrounding bulk soil. In the current study, we identified taxa, which were consistently present in the nests over a study period of three years. Some taxa were also significantly enriched in the nest samples compared with spatially corresponding reference soils. We show that the bacterial communities in ant nests are temporally stable across years, whereas the fungal communities show greater variation. It seems that the activities of the ants contribute to unique biochemical processes in the secluded nest environment, and create opportunities for symbiotic interactions between the ants and the microbes. Over time, the microbial communities may come to diverge, due to drift and selection, especially given the long lifespan (up to 30 years) of the ant colonies.

Untapping the potential of plant mycobiomes for applications in agriculture

Plant-fungal interactions are widespread in nature, and their multiple benefits for plant growth and health have been amply demonstrated. Endophytic and epiphytic fungi can significantly increase plant resilience, improving plant nutrition, stress tolerance and defence. Although some of these interactions have been known for decades, the relevance of the plant mycobiome within the plant microbiome has been largely underestimated. Our limited knowledge of fungal biology and their interactions with plants in the broader phytobiome context has hampered the development of optimal biotechnological applications in agrosystems and natural ecosystems. Exciting recent technical and knowledge advances in the context of molecular and systems biology open a plethora of opportunities for developing this field of research.

Caterpillar gut and host plant phylloplane mycobiomes differ: a new perspective on fungal involvement in insect guts

Compared with the highly diverse microbiota of leaves, herbivorous insects exhibit impoverished gut microbial communities. Research to date has focused on the bacterial component of these gut microbiomes, neglecting the fungal component. As caterpillar gut bacterial microbiomes are derived strongly from their diet, we hypothesized that their mycobiomes would reflect the host leaf mycobiomes. Using the ITS2 rDNA and V5-V6 16S rRNA gene regions for DNA metabarcoding of caterpillar gut and host leaf sample pairs we compared their mycobiome genus diversity and compositions and identified genera associated with caterpillar guts. Leaves and caterpillar guts harbored different mycobiomes with quite low qualitative similarity (Jaccard index = 38.03%). The fungal genera most significantly associated with the caterpillar gut included Penicillium, Mucor and unidentified Saccharomycetales, whereas leaf-associated genera included Holtermanniella, Gibberella (teleomorph of Fusarium) and Seimatosporium. Although caterpillar gut and leaf mycobiomes had similar genus richness overall, this indicator was not correlated for individual duplets. Moreover, as more samples entered the analysis, mycobiome richness increased more rapidly in caterpillar guts than in leaves. The results suggest that the mycobiota of the caterpillar gut differs from that of their feeding substrate; further, the mycobiomes appear to be richer than the well-studied bacterial microbiotas.

Straw retention efficiently improves fungal communities and functions in the fallow ecosystem

BACKGROUND

Straw retention is a substitute for chemical fertilizers, which effectively maintain organic matter and improve microbial communities on agricultural land. The purpose of this study was to provide sufficient information on soil fungal community networks and their functions in response to straw retention. Hence, we used quantitative real-time PCR (qRT-PCR), Illumina MiSeq (ITS rRNA) and FUNGuild to examine ITS rRNA gene populations, soil fungal succession and their functions under control (CK) and sugarcane straw retention (SR) treatments at different soil layers (0-10, 10-20, 20-30, and 30-40 cm) in fallow fields.

RESULT

The result showed that SR significantly enhanced ITS rRNA gene copy number and Shannon index at 0-10 cm soil depth. Fungi abundance, OTUs number and ACE index decreased with the increasing soil depth. The ANOSIM analysis revealed that the fungal community of SR significantly differed from that of CK. Similarly, significant difference was also observed between topsoil (0-20 cm) and subsoil (20-40 cm). Compared with CK, SR decreased the relative abundance of the pathogen, while increased the proportion of saprotroph. Regarding soil depth, pathogen relative abundance in topsoil was lower than that in subsoil. Besides, both sugarcane straw retention and soil depths (topsoil and subsoil) significantly altered the co-occurrence patterns and fungal keystone taxa closely related to straw decomposition. Furthermore, both SR and topsoil had higher average clustering coefficients (aveCC), negative edges and varied modularity.

CONCLUSIONS

Overall, straw retention improved α-diversity, network structure and fungal community, while reduced soil pathogenic microbes across the entire soil profile. Thus, retaining straw to improve fungal composition, community stability and their functions, in addition to reducing soil-borne pathogens, can be an essential agronomic practice in developing a sustainable agricultural system.

Soil properties, bacterial and fungal community compositions and the key factors after 5-year continuous monocropping of three minor crops

Minor grain crops are widely cultivated in northwest China and played important roles in local economic. Soil microbes play a central role in ecological function and biological stability and related to soil quality. In order to uncover the soil microbial composition differences and the factors under 5-year continuous monocropping of three minor crops (Proso millet, Common bean and Common buckwheat) in Guan-Zhong Plain, six soil nutrimental parameters, soil pH, soil moisture content, and four soil enzyme activities were analyzed and soil microbial composition were sequenced. The results showed that after 5-years of continuous monocropping, different cover crops influenced most of soil physicochemical properties, expect soil moisture content (P < 0.05), the available nutrients were significant higher in proso millet soil, and the pH was significantly higher in common buckwheat soil. soil ALP, catalase and urease activities were significantly different between soils (P< 0.01), in which soil catalase activities were significantly lower and soil ALP and urease activities were significantly higher than that of proso millet and common buckwheat. A total of 171439 sequences, 9468 OTUs and 29 phylum for bacteria, 128920 sequences, 544 OTUs and 27 phylum for fungi were obtained. In addition, no significantly difference obtained in diversity and richness between soils (P < 0.05). According to relative abundance, Proteobacteria, Chloroflexi, Gemmatimonadetes and Acidobacteria were the dominant bacterial phylum in all samples, moreover, the relative abundance of Caldiserica was significantly different between soils (P < 0.05). Ascomycota (79.04%-90.21%) was dominant phylum in fungal community and phylum Phragmoplastophyta (P < 0.01) and Glomeromycota (P < 0.05) were significantly different between soils. Redundancy analysis indicated that available nutrients Nitrogen and Potassium are the strongest predictors in both bacterial and fungal community. In conclusion, different cover crops influenced soil nutrient properties, soil pH and soil microbial composition, and continuous monocropping decreased soil fertility condition. Moreover, Common bean and Common buckwheat were more sensitive to monocropping treatment.

Comprehensive Fungal Community Analysis of House Dust Using Next-Generation Sequencing

Fungal community analyses in homes have been attracting attention because fungi are now generally considered to be allergens. Currently, these analyses are generally conducted using the culture method, although fungal communities in households often contain species that are difficult to culture. In contrast, next-generation sequencing (NGS) represents a comprehensive, labor- and time-saving approach that can facilitate species identification. However, the reliability of the NGS method has not been compared to that of the culture method. In this study, in an attempt to demonstrate the reliability of this application, we used the NGS method to target the internal transcribed spacer 1 (ITS1) in the fungal genome, conducted fungal community analyses for 18 house-dust samples and analyzed fungal community structures. The NGS method positively correlated with the culture method regarding the relative abundance of Aspergillus, Penicillium, Cladosporium and yeasts, which represent the major fungal components found in houses. Furthermore, several genera, such as Malassezia, could be sensitively detected. Our results imply that the reliability of the NGS method is comparable to that of the culture method and indicates that easily available databases may require modifications, including the removal of registrations that have not been sufficiently classified at the genus level.

Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota

BACKGROUND

From early life, children are exposed to a multitude of environmental exposures, which may be of crucial importance for healthy development. Here, the environmental microbiota may be of particular interest as it represents the interface between environmental factors and the child. As infants in modern societies spend a considerable amount of time indoors, we hypothesize that the indoor bed dust microbiota might be an important factor for the child and for the early colonization of the airway microbiome. To explore this hypothesis, we analyzed the influence of environmental exposures on 577 dust samples from the beds of infants together with 542 airway samples from the Copenhagen Prospective Studies on Asthma in Childhood₂₀₁₀ cohort.

RESULTS

Both bacterial and fungal community was profiled from the bed dust. Bacterial and fungal diversity in the bed dust was positively correlated with each other. Bacterial bed dust microbiota was influenced by multiple environmental factors, such as type of home (house or apartment), living environment (rural or urban), sex of siblings, and presence of pets (cat and/or dog), whereas fungal bed dust microbiota was majorly influenced by the type of home (house or apartment) and sampling season. We further observed minor correlation between bed dust and airway microbiota compositions among infants. We also analyzed the transfer of microbiota from bed dust to the airway, but we did not find evidence of transfer of individual taxa.

CONCLUSIONS

Current study explores the influence of environmental factors on bed dust microbiota (both bacterial and fungal) and its correlation with airway microbiota (bacterial) in early life using high-throughput sequencing. Our findings demonstrate that bed dust microbiota is influenced by multiple environmental exposures and could represent an interface between environment and child. Video Abstract.

Changes in plant function and root mycobiome caused by flood and drought in a riparian tree

Under increasingly harsh climatic conditions, conservation of threatened species requires integrative studies to understand stress tolerance. Riparian Ulmus minor Mill. populations have been massively reduced by Dutch Elm disease (DED). However, resistant genotypes were selected to restore lost populations. To understand the acclimation mechanisms to the succession of abiotic stresses, ramets of five DED-tolerant U. minor genotypes were subjected to flood and subsequently to drought. Physiological and biochemical responses were evaluated together with shifts in root-fungal assemblages. During both stresses, plants exhibited a decline in leaf net photosynthesis and an increase in percentage loss of stem hydraulic conductivity and in leaf and root proline content. Stomatal closure was produced by chemical signals during flood and hydraulic signals during drought. Despite broad similarities in plant response to both stresses, root-mycobiome shifts were markedly different. The five genotypes were similarly tolerant to moderate drought, however, flood tolerance varied between genotypes. In general, flood did not enhance drought susceptibility due to fast flood recovery, nevertheless, different responses to drought after flood were observed between genotypes. Associations were found between some fungal taxonomic groups and plant functional traits varying with flood and drought (e.g. proline, chlorophyll and starch content) indicating that the thriving of certain taxa depends on host responses to abiotic stress.

Metagenomics analysis of fungal communities associated with postharvest diseases in pear fruits under the effect of management practices

An amplicon metagenomic approach based on the ITS1 region of fungal rDNA was employed to identify the composition of fungal communities associated with diseases of pear fruits during postharvest storage. The sampled fruits were harvested at an orchard using routine management practices involving treatments with various chemical fungicides and were transferred to a storage packinghouse. Effective tags of reading sequences clustered into 53 OTUs whereas Ascomycota was the dominant phylum (83.4%) followed by Basidiomycota (15.8%). Our results revealed that four genera, Penicillium, Rhodotorula, Alternaria and Cladosporium were the most abundant representing 59-95% of the relative abundance per sample. The interruption of chemical treatments during the last month before harvest altered the structure of the fungal community of fruits among untreated and treated samples, mainly in cases of relative abundance of Penicillium and Rhodotorula genera. We hypothesize that various antagonistic interactions might occur on fruit surfaces among the detected fungal genera whose relative abundances were affected by fungicide treatments. Interestingly, some common pre- and postharvest pear fungal pathogens were either less present (such as Moniliana), or undetected (such as Aspergillus, Venturia and Septoria) in untreated and treated samples.

Fungal community composition change and heavy metal accumulation in response to the long-term application of anaerobically digested slurry in a paddy soil

Anaerobically digested slurry (ADS) has been widely used as a liquid fertilizer in agroecosystems. However, there is scant information on the effects of successive ADS applications on heavy metals (HMs) accumulation and fungal community composition in paddy soils. In this study, we conducted a field experiment over 10 years to assess the changes in soil HMs and fungal community composition under the long-term application of ADS in a paddy field. The four treatments were (1) no fertilizer (CK); (2) mineral fertilizer and 270 kg N ha^-1 from urea (MF); (3) 270 kg N ha^-1 from ADS (ADS1); and (4) 540 kg N ha^-1 from ADS (ADS2). The results revealed that ADS application improved paddy soil fertility compared to that under the MF treatment by increasing soil organic C (SOC), total N (TN) and available potassium (AK). Long-term application of ADS significantly increased soil total and available Zn (TZn and AZn) concentrations as compared to those under the MF treatment. However, there were no significant differences in the total and available Cu concentrations or the total Pb concentration between the ADS and MF treatments. Sequence analysis showed that application of ADS increased the fungal richness indexes (Chao1 and ACE) compared to MF treatment. Principal coordinate analysis (PCoA) showed that the soil fungal community compositions were significantly separated by high levels of ADS application. Long-term application of ADS increased the relative abundance of classes Sordariomycetes, Dothideomycetes and Agaricomycetes by 20.8-29.0%, 107.3-141.4% and 289.5-387.5%, respectively, but decreased that of Pezizomycetes by 14.0-33.0% compared to that under the MF treatment. At the genus level, compared to those under the MF treatment, the relative abundances of Pyrenochaetopsis and Myrothecium were significantly increased by the application of ADS, but those of Mrakia and Tetracladium were significantly decreased. Redundancy analysis (RDA) revealed that SOC, AZn and AP were the three most important factors affecting the fungal community composition of the paddy soil. Our findings suggested that fungal community composition could be affected by changes in the chemical properties and heavy metal contents of paddy soil under high application of ADS in the long term.

Biotic and abiotic factors shape arbuscular mycorrhizal fungal communities associated with the roots of the widespread fern Botrychium lunaria (Ophioglossaceae)

Arbuscular mycorrhizal fungi (AMF) play central roles in terrestrial ecosystems by interacting with both above and belowground communities as well as by influencing edaphic properties. The AMF communities associated with the roots of the fern Botrychium lunaria (Ophioglossaceae) were sampled in four transects at 2400 m a.s.l. in the Swiss Alps and analyzed using metabarcoding. Members of five Glomeromycota genera were identified across the 71 samples. Our analyses revealed the existence of a core microbiome composed of four abundant Glomus operational taxonomic units (OTUs), as well as a low OTU turnover between samples. The AMF communities were not spatially structured, which contrasts with most studies on AMF associated with angiosperms. pH, microbial connectivity and humus cover significantly shaped AMF beta diversity but only explained a minor fraction of variation in beta diversity. AMF OTUs associations were found to be significant by both cohesion and co-occurrence analyses, suggesting a role for fungus-fungus interactions in AMF community assembly. In particular, OTU co-occurrences were more frequent between different genera than among the same genus, rising the hypothesis of functional complementarity among the AMF associated to B. lunaria. Altogether, our results provide new insights into the ecology of fern symbionts in alpine grasslands.

Host plant phylogeny and geographic distance strongly structure Betulaceae-associated ectomycorrhizal fungal communities in Chinese secondary forest ecosystems

Environmental filtering and dispersal limitation are two of the primary drivers of community assembly in ecosystems, but their effects on ectomycorrhizal (EM) fungal communities associated with wide ranges of Betulaceae taxa at a large scale are poorly documented. In this study, we examined EM fungal communities associated with 23 species from four genera (Alnus, Betula, Carpinus and Corylus) of Betulaceae in Chinese secondary forest ecosystems, using Illumina MiSeq sequencing of the ITS2 region. Effects of host plant phylogeny, soil, climate and geographic distance on EM fungal community were explored. In total, we distinguished 1738 EM fungal operational taxonomic units (OTUs) at a 97% sequence similarity level. The EM fungal communities of Alnus had significantly lower OTU richness than those associated with the other three plant genera. The EM fungal OTU richness was significantly affected by geographic distance, host plant phylogeny, soil and climate. The EM fungal community composition was significantly influenced by host plant phylogeny (12.1% of variation explained in EM fungal community), geographic distance (7.7%), soil (4.6%) and climate (1.1%). This finding highlights that environmental filtering linked to host plant phylogeny and dispersal limitation strongly influence EM fungal communities associated with Betulaceae plants in Chinese secondary forest ecosystems.

Fungal diversity in canopy soil of silver beech, Nothofagus menziesii (Nothofagaceae)

Adventitious roots in canopy soils associated with silver beech (Nothofagus menziesii Hook.f. (Nothofagaceae)) form ectomycorrhizal associations. We investigated the extent to which canopy ectomycorrhizal communities contribute to overall diversity of ectomycorrhizal fungi associated with silver beech. Hyphal ingrowth bags were buried for 12 months in canopy and terrestrial soils of five trees at one site. We used amplicon sequencing of the nuclear ribosomal internal transcribed spacer 2 region (ITS2) to assess diversity of both ectomycorrhizal and non-ectomycorrhizal OTUs in hyphal ingrowth bags. There was a significant difference in ectomycorrhizal fungal community diversity between the terrestrial and canopy hyphal ingrowth bag communities. Ectomycorrhizal community composition of the terrestrial and canopy environments was also significantly different. Some ectomycorrhizal taxa were significantly differentially represented in either the terrestrial or canopy environment. The hyphal ingrowth bags also accumulated non-ectomycorrhizal species. The non-ectomycorrhizal fungi also had significantly different diversity and community composition between the canopy and terrestrial environments. Like the ectomycorrhizal community, some non-ectomycorrhizal taxa were significantly differentially represented in either the terrestrial or canopy environment. The canopy soil microhabitat provides a novel environment for growth of ectomycorrhizal adventitious roots and enables the spatial partitioning of ectomycorrhizal and non-ectomycorrhizal fungal diversity in the forest.

Dysfunction in the arbuscular mycorrhizal symbiosis has consistent but small effects on the establishment of the fungal microbiota in Lotus japonicus

Most land plants establish mutualistic interactions with arbuscular mycorrhizal (AM) fungi. Intracellular accommodation of AM fungal symbionts remodels important host traits like root morphology and nutrient acquisition. How mycorrhizal colonization impacts plant microbiota is unclear. To understand the impact of AM symbiosis on fungal microbiota, ten Lotus japonicus mutants impaired at different stages of AM formation were grown in non-sterile natural soil and their root-associated fungal communities were studied. Plant mutants lacking the capacity to form mature arbuscules (arb^- ) exhibited limited growth performance associated with altered phosphorus (P) acquisition and reduction-oxidation (redox) processes. Furthermore, arb^- plants assembled moderately but consistently different root-associated fungal microbiota, characterized by the depletion of Glomeromycota and the concomitant enrichment of Ascomycota, including Dactylonectria torresensis. Single and co-inoculation experiments showed a strong reduction of root colonization by D. torresensis in the presence of AM fungus Rhizophagus irregularis, particularly in arbuscule-forming plants. Our results suggest that impairment of central symbiotic functions in AM host plants leads to specific changes in root microbiomes and in tripartite interactions between the host plant, AM and non-AM fungi. This lays the foundation for mechanistic studies on microbe-microbe and microbe-host interactions in AM symbiosis of the model L. japonicus.

Species composition of arbuscular mycorrhizal communities changes with elevation in the Andes of South Ecuador

Arbuscular mycorrhizal fungi (AMF) are the most prominent mycobionts of plants in the tropics, yet little is known about their diversity, species compositions and factors driving AMF distribution patterns. To investigate whether elevation and associated vegetation type affect species composition, we sampled 646 mycorrhizal samples in locations between 1000 and 4000 m above sea level (masl) in the South of Ecuador. We estimated diversity, distribution and species compositions of AMF by cloning and Sanger sequencing the 18S rDNA (the section between AML1 and AML2) and subsequent derivation of fungal OTUs based on 99% sequence similarity. In addition, we analyzed the phylogenetic structure of the sites by computing the mean pairwise distance (MPD) and the mean nearest taxon difference (MNTD) for each elevation level. It revealed that AMF species compositions at 1000 and 2000 masl differ from 3000 and 4000 masl. Lower elevations (1000 and 2000 masl) were dominated by members of Glomeraceae, whereas Acaulosporaceae were more abundant in higher elevations (3000 and 4000 masl). Ordination of OTUs with respect to study sites revealed a correlation to elevation with a continuous turnover of species from lower to higher elevations. Most of the abundant OTUs are not endemic to South Ecuador. We also found a high proportion of rare OTUs at all elevations: 79-85% of OTUs occurred in less than 5% of the samples. Phylogenetic community analysis indicated clustering and evenness for most elevation levels indicating that both, stochastic processes and habitat filtering are driving factors of AMF community compositions.

Dynamics of fungal communities during Gastrodia elata growth

BACKGROUND

Gastrodia elata is a widely distributed achlorophyllous orchid and is highly valued as both medicine and food. Gastrodia elata produces dust-like seeds and relies on mycorrhizal fungi for its germination and growth. In its life cycle, G. elata is considered to switch from a specific single-fungus relationship (Mycena) to another single-fungus relationship (Armillaria). However, no studies have investigated the changes in the plant-fungus relationship during the growth of G. elata in the wild. In this study, high-throughput sequencing was used to characterize the fungal community of tubers in different growth phases as well as the soils surrounding G. elata.

RESULTS

The predominant fungi were Basidiomycota (60.44%) and Ascomycota (26.40%), which exhibited changes in abundance and diversity with the growth phases of G. elata. Diverse basidiomycetes in protocorms (phase P) were Hyphodontia, Sistotrema, Tricholoma, Mingxiaea, Russula, and Mycena, but the community changed from a large proportion of Resinicium bicolor (40%) in rice-like tubers (phase M) to an unidentified Agaricales operational taxonomic unit 1(OTU1,98.45%) in propagation vegetation tubers (phase B). The soil fungi primarily included Simocybe, Psathyrella, Conocybe, and Subulicystidium. Three Mycena OTUs obtained in this study were differentially distributed among the growth phases of G. elata, accounting for less than 1.0% of the total reads, and were phylogenetically close to Mycena epipterygia and M. alexandri.

CONCLUSIONS

Our data indicated that G. elata interacts with a broad range of fungi beyond the Mycena genus. These fungi changed with the growth phases of G. elata. In addition, these data suggested that the development of the fungal community during the growth of G. elata was more complex than previously assumed and that at least two different fungi could be involved in development before the arrival of Armillaria.

Vermicompost addition influences symbiotic fungi communities associated with leek cultivated in metal-rich soils

In the context of urban agriculture, where soils are frequently contaminated with metal(loid)s (TM), we studied the influence of vermicompost amendments on symbiotic fungal communities associated with plants grown in two metal-rich soils. Leek (Allium porrum L.) plants were grown with or without vermicompost in two metal-rich soils characterized by either geogenic or anthropogenic TM sources, to assess the influence of pollutant origin on soil-plant transfer. Fungal communities associated with the leek roots were identified by high throughput Illumina MiSeq and TM contents were measured using mass spectrometry. Vermicompost addition led to a dramatic change in the fungal community with a loss of diversity in the two tested soils. This effect could partially explain the changes in metal transfer at the soil-AMF-plant interface. Our results suggest being careful while using composts when growing edibles in contaminated soils. More generally, this study highlights the need for further research in the field of fungal communities to refine practical recommendations to gardeners. Graphical abstract.

A different suite: The assemblage of distinct fungal communities in water-damaged units of a poorly-maintained public housing building

Water-damaged housing has been associated with a number of negative health outcomes, principally respiratory disease and asthma. Much of what we know about fungi associated with water-damaged buildings has come from culture-based and immunochemical methods. Few studies have used high-throughput sequencing technologies to assess the impact of water-damage on microbial communities in residential buildings. In this study we used amplicon sequencing and quantitative-PCR to evaluate fungal communities on surfaces and in airborne dust in multiple units of a condemned public housing project located in the San Francisco Bay Area. We recruited 21 households to participate in this study and characterized their apartments as either a unit with visible mold or no visible mold. We sampled airborne fungi from dust settled over a month-long time period from the outdoors, in units with no visible mold, and units with visible mold. In units with visible mold we additionally sampled the visible fungal colonies from bathrooms, kitchens, bedrooms, and living rooms. We found that fungal biomass in settled dust was greater outdoors compared to indoors, but there was no significant difference of fungal biomass in units with visible mold and no visible mold. Interestingly, we found that fungal diversity was reduced in units with visible mold compared to units with no visible mold and the outdoors. Units with visible mold harbored fungal communities distinct from units with no visible mold and the outdoors. Units with visible mold had a greater abundance of taxa within the classes Eurotiomycetes, Saccharomycetes, and Wallemiomycetes. Colonies of fungi collected from units with visible mold were dominated by two Cladosporium species, C. sphaerospermum and C halotolerans. This study demonstrates that high-throughput sequencing of fungi indoors can be a useful strategy for distinguishing distinct microbial exposures in water-damaged homes with visible and nonvisible mold growth, and may provide a microbial means for identifying water damaged housing.

Plant-mediated effects of soil phosphorus on the root-associated fungal microbiota in Arabidopsis thaliana

Plants respond to phosphorus (P) limitation through an array of morphological, physiological and metabolic changes which are part of the phosphate (Pi) starvation response (PSR). This response influences the establishment of the arbuscular mycorrhizal (AM) symbiosis in most land plants. It is, however, unknown to what extent available P and the PSR redefine plant interactions with the fungal microbiota in soil. Using amplicon sequencing of the fungal taxonomic marker ITS2, we examined the changes in root-associated fungal communities in the AM nonhost species Arabidopsis thaliana in response to soil amendment with P and to genetic perturbations in the plant PSR. We observed robust shifts in root-associated fungal communities of P-replete plants in comparison with their P-deprived counterparts, while bulk soil communities remained unaltered. Moreover, plants carrying mutations in the phosphate signaling network genes, phr1, phl1 and pho2, exhibited similarly altered root fungal communities characterized by the depletion of the chytridiomycete taxon Olpidium brassicae specifically under P-replete conditions. This study highlights the nutritional status and the underlying nutrient signaling network of an AM nonhost plant as previously unrecognized factors influencing the assembly of the plant fungal microbiota in response to P in nonsterile soil.

Common garden experiments disentangle plant genetic and environmental contributions to ectomycorrhizal fungal community structure

The interactions among climate change, plant genetic variation and fungal mutualists are poorly understood, but probably important to plant survival under drought. We examined these interactions by studying the ectomycorrhizal fungal (EMF) communities of pinyon pine seedlings (Pinus edulis) planted in a wildland ecosystem experiencing two decades of climate change-related drought. We established a common garden containing P. edulis seedlings of known maternal lineages (drought tolerant, DT; drought intolerant, DI), manipulated soil moisture and measured EMF community structure and seedling growth. Three findings emerged: EMF community composition differed at the phylum level between DT and DI seedlings, and diversity was two-fold greater in DT than in DI seedlings. EMF communities of DT seedlings did not shift with water treatment and were dominated by an ascomycete, Geopora sp. By contrast, DI seedlings shifted to basidiomycete dominance with increased moisture, demonstrating a lineage by environment interaction. DT seedlings grew larger than DI seedlings in high (28%) and low (50%) watering treatments. These results show that inherited plant traits strongly influence microbial communities, interacting with drought to affect seedling performance. These interactions and their potential feedback effects may influence the success of trees, such as P. edulis, in future climates.

Different host factors are associated with patterns in bacterial and fungal gut microbiota in Slovenian healthy cohort

Gut microbiota in a healthy population is shaped by various geographic, demographic and lifestyle factors. Although the majority of research remains focused on the bacterial community, recent efforts to include the remaining microbial members like viruses, archaea and especially fungi revealed various functions they perform in the gut. Using the amplicon sequencing approach we analysed bacterial and fungal gut communities in a Slovenian cohort of 186 healthy volunteers. In the bacterial microbiome we detected 253 different genera. A core microbiome analysis revealed high consistency with previous studies, most prominently showing that genera Faecalibacterium, Bacteroides and Roseburia regularly comprise the core community. We detected a total of 195 fungal genera, but the majority of these showed low prevalence and are likely transient foodborne contaminations. The fungal community showed a low diversity per sample and a large interindividual variability. The most abundant fungi were Saccharomyces cerevisiae and Candida albicans. These, along with representatives from genera Penicillium and Debaryomyces, cover 82% of obtained reads. We report three significant questionnaire-based host covariates associated with microbiota composition. Bacterial community was associated with age and gender. More specifically, bacterial diversity was increased with age and was higher in the female population compared to male. The analysis of fungal community showed that more time dedicated to physical activity resulted in a higher fungal diversity and lower abundance of S. cerevisiae. This is likely dependent on different diets, which were reported by participants according to the respective rates of physical activity.

Contrasting dynamics of polychlorinated biphenyl dissipation and fungal community composition in low and high organic carbon soils with biochar amendment

Biochar amendment has been advocated as an effective method to remediate organic pollutant-contaminated soils through adsorption and stimulating microbial degradation. However, such effects can vary depending on soil properties and biochar physiochemical characteristics. The objective of this study was to compare the dynamic variations of polychlorinated biphenyls (PCBs) in low and high soil organic carbon (SOC) soils both amended with biochar and to investigate its linkage with fungal community composition. Two soils having the same texture and soil type but varying in SOC contents were contaminated with PCBs to a final concentration of 60 mg kg^-1 and amended with 2% bamboo biochar. Temporal changes of PCB remaining in soils and adsorbed on biochar particles were determined during a 2-month incubation. Diversity and composition of fungal communities in both low and high SOC soils were investigated with Illumina MiSeq sequencing. The results showed that the PCB concentrations in low SOC soil were significantly lower than those in high SOC soil during the incubation. In the low SOC soil, the biochar particle adsorbed higher amounts of PCB, tetra-, and penta-chlorobiphenyls (CBs) than those in high SOC soil, and stimulated the dissipation of di- and tri-CBs. The nonmetric multidimensional scaling profile showed significant (p < 0.05) differences in the fungal community composition between the low and high SOC soils. The relative abundances of Eurotiomycetes were gradually increased, whereas those of Sordariomycetes and Dothideomycetes were decreased with increasing incubation time in the low SOC soils. In contrast, the fungal communities in high SOC soils were relatively stable. The relative abundances of Eurotiomycetes and Sordariomycetes were positively correlated with PCB dissipation in low and high SOC content soils, respectively. Our results suggest that SOC content affects PCB dissipation and fungal community composition in biochar-amended soils, and biochars have a high remediation potential of PCB in soils with low SOC contents.

A multiscale study of fungal endophyte communities of the foliar endosphere of native rubber trees in Eastern Amazon

Hevea brasiliensis is a native hyperdiverse tree species in the Amazon basin with great economic importance since it produces the highest quality natural rubber. H. brasiliensis, in its natural habitat, may harbor fungal endophytes that help defend against phytopathogenic fungi. In this work, we investigated the fungal endophytic communities in two pristine areas in Eastern Amazon (Anavilhanas National Park - ANP and Caxiuanã National Forest - CNF) at different spatial scales: regional, local, individual (tree), and intra-individual (leaflet). Using a culture-based approach, 210 fungal endophytes were isolated from 240 sampling units and assigned to 46 distinct MOTUs based on sequencing of the nrITS DNA. The community compositions of the endophytomes are different at both regional and local scales, dominated by very few taxa and highly skewed toward rare taxa, with many endophytes infrequently isolated across hosts in sampled space. Colletotrichum sp. 1, a probably latent pathogen, was the most abundant endophytic putative species and was obtained from all individual host trees in both study areas. Although the second most abundant putative species differed between the two collection sites, Clonostachys sp. 1 and Trichoderma sp. 1, they are phylogenetically related (Hypocreales) mycoparasites. Thus, they probably exhibit the same ecological function in the foliar endosphere of rubber tree as antagonists of its fungal pathogens.

The response of dominant and rare taxa for fungal diversity within different root environments to the cultivation of Bt and conventional cotton varieties

BACKGROUND

Bacillus thuringiensis (Bt) crops have been cultivated at a large scale over the past several decades, which have raised concern about unintended effects on natural environments. Microbial communities typically contain numerous rare taxa that make up the majority of community populations. However, the response of dominant and rare taxa for fungal diversity to the different root environments of Bt plants remains unclear.

RESULTS

We quantified fungal population sizes and community composition via quantitative PCR of ITS genes and 18S rRNA gene sequencing of, respectively, that were associated with Bt and conventional cotton variety rhizosphere soils from different plant growth stages. qPCR analyses indicated that fungal abundances reached their peak at the seedling stage and that the taproots and lateral root rhizospheres of the Bt cotton SGK321 were significantly different. However, no significant differences in population sizes were detected between the same root zones from Bt and the conventional cotton varieties. The overall patterns of fungal genera abundances followed that of the dominant genera, whereas overall patterns of fungal genera richness followed those of the rare genera. These results suggest that the dominant and rare taxa play different roles in the maintenance of rhizosphere microhabitat ecosystems. Cluster analyses indicated a separation of fungal communities based on the lateral roots or taproots from the three cotton varieties at the seedling stage, suggesting that root microhabitats had marked effects on fungal community composition. Redundancy analyses indicated that pH was more correlated to soil fungal community composition than Bt protein content.

CONCLUSIONS

In conclusion, these results indicate that dominant and rare fungal taxa differentially contribute to community dynamics in different root microhabitats of both Bt and conventional cotton varieties. Moreover, these results showed that the rhizosphere fungal community of Bt cotton did not respond significantly to the presence of Bt protein when compared to the two conventional cotton varieties.

Mycobiome analysis of asymptomatic and symptomatic Norway spruce trees naturally infected by the conifer pathogens Heterobasidion spp

Plant microbiome plays an important role in maintaining the host fitness. Despite a significant progress in our understanding of the plant microbiome achieved in the recent years, very little is known about the effect of plant pathogens on composition of microbial communities associated with trees. In this study, we analysed the mycobiome of different anatomic parts of asymptomatic and symptomatic Norway spruce trees naturally infected by Heterobasidion spp. We also investigated the primary impact of the disease on the fungal communities, which are associated with Norway spruce trees. Our results demonstrate that the structure of fungal communities residing in the wood differed significantly among symptomatic and asymptomatic Heterobasidion-infected trees. However, no significant differences were found in the other anatomic regions of the trees. The results also show that not only each of individual tree tissues (wood, bark, needles and roots) harbours a unique fungal community, but also that symptomatic trees were more susceptible to co-infection by other wood-degrading fungi compared to the asymptomatic ones.