Fungal Microbiome Research Articles

Fungal microbiome shifts on avocado fruit associated with a combination of postharvest chemical and physical interventions.

The aim was to characterize the baseline microbial population of the avocado carposphere and understand shifts in community structure from the harvest to ready-to-eat stages. The changes in surface or stem-end (SE) fungal microbiomes at the postharvest stage of avocado fruit were studied using next-generation sequencing of the internal transcribed spacer region. Avocado fructoplane and SE pulp fungal richness differed significantly between postharvest stages with a decline following prochloraz dip treatments. Known postharvest decay-causing genera, Colletotrichum, Fusarium, Alternaria, Epicoccum, Penicillium and Neofusicoccum were detected, with Papiliotrema, Meyerozyma and Aureobasidium confirmed as the most dominant potentially beneficial genera. Postharvest interventions such as prochloraz had a negative non-target effect on the presence of Papiliotrema flavescens on the avocado fructoplane. Our findings reveal a core community of beneficial and pathogenic taxa in the avocado fructoplane and further highlight the reduction of pathogenic fungi as a consequence of fungicide use. The current study provides important baseline data for further exploration of fungal population shifts in avocado fruit driven by chemical (fungicide) as well as physical (cold storage) interventions.

Airborne fungal and bacterial microbiome in classrooms of elementary schools during the COVID-19 pandemic period: Effects of school disinfection and other environmental factors.

The aim of the study was to examine the effects of environmental factors including disinfection on airborne microbiome during the coronavirus disease 2019 pandemic, we evaluated indoor and outdoor air collected from 19 classrooms regularly disinfected. Extracted bacterial and fungal DNA samples were sequenced using the Illumina MiSeq™ platform. Using bacterial DNA copy number concentrations from qPCR analysis, multiple linear regressions including environmental factors as predictors were performed. Microbial diversity and community composition were evaluated. Classrooms disinfected with spray ≤1 week before sampling had lower bacterial DNA concentration (3116 DNA copies/m3) than those >1 week (5003 copies/m3) (p‐values = 0.06). The bacterial DNA copy number concentration increased with temperature and was higher in classrooms in coastal than inland cities (p‐values <0.01). Bacterial diversity in outdoor air was higher in coastal than inland cities while outdoor fungal diversity was higher in inland than coastal cities. These outdoor microbiomes affected classroom microbial diversity but bacterial community composition at the genus level in occupied classrooms were similar between coastal and inland cities. Our findings emphasize that environmental conditions including disinfection, climate, and school location are important factors in shaping classroom microbiota. Yet, further research is needed to understand the effects of modified microbiome by disinfection on occupants' health.

Performance and mechanisms of enhanced hydrolysis acidification by adding different iron scraps: Microbial characteristics and fate of iron scraps.

HA, as one of low-carbon pre-treatment technology could be enhanced by packing of iron or iron oxide powder for enhancing the transformation of large molecular weight to generate volatile fatty acids (VFAs) for fuel production. However, the controversy of iron strengthening the HA and inherent drawbacks of iron oxide, such as poor mass transfer, and difficult recovery, limit this pretreatment technology. Clean and rusty iron scraps were packed into an HA system to address these issues while focusing on the system performance and the response of core bacterial and fungal microbiomes to iron scrap exposure. Results showed that clean and rusty iron scraps can significantly improve the HA performance while considering hydrolysis efficiency (HE), acidification efficiency (AE) and VFAs production, given that VFAs ratios (Cacetate: Cpropionate: Cbutyrate) were changed from the 14:5:1 to 14:2:1 and 29:4:1, respectively, and the obtained VFAs ratios in iron scraps addition systems were more closely to the optimal VFAs ratio for lipids production. Redundant and molecular ecological network analyses indicated that iron scraps promote the system stability and acidogenesis capacity by boosting the complexity of microbes’ networks and enriching core functional microbes that show a positive response to HA performance, among which the relative abundance of related bacterial genera was promoted by 19.71 and 17.25% for RRusty and RClean systems. Moreover, except for the differences between the control and iron scraps addition systems, the findings confirmed that the RRusty system is slightly different from the RClean one, which was perhaps driven by the behavior of 6.20% of DIRB in RRusty system and only 1.16% of homoacetogens in RClean system when considering the microbial community and fate of iron scraps. Totally, the observed results highlight the application potential of the iron scrap-coupled HA process for the generation of VFAs and provide new insights into the response of different iron scraps in microbes communities.

Characterization of the Intestinal Fungal Microbiome in HIV and HCV Mono-Infected or Co-Infected Patients.

Intestinal mycobiome dysbiosis plays an important role in the advancement of HIV- and HCV-infected patients. Co-infection with HCV is an important risk factor for exacerbating immune activation in HIV-infected patients, and gut fungal microbial dysbiosis plays an important role. However, no systematic study has been conducted on the intestinal fungal microbiome of HIV/HCV co-infected patients to date. Patients infected with HIV and HCV, either alone or in combination, and healthy volunteers were included. Stool samples were collected for fungal ITS sequencing and for further mycobiome statistical analysis. We found that the abundance of fungal species significantly decreased in the HIV/HCV co-infection group compared to in the healthy control group, while no significant differences were found in the mono-infection groups. Low-CD4 + T-cell patients in the HIV group and high-ALT-level patients in the HCV group were discovered to have a more chaotic fungal community. Furthermore, the opportunistic pathogenic fungal profiles and fungal inter-correlations in the co-infection group became less characteristic but more complicated than those in the mono-infection groups. Intestinal fungal dysregulation occurs in HIV- and HCV-infected patients, and this dysregulation is further complicated in HIV/HCV co-infected patients.

Fungal diversity in the gut microbiome of young South African children

BackgroundThe fungal microbiome, or mycobiome, is a poorly described component of the gut ecosystem and little is known about its structure and development in children. In South Africa, there have been no culture-independent evaluations of the child gut mycobiota. This study aimed to characterise the gut mycobiota and explore the relationships between fungi and bacteria in the gut microbiome of children from Cape Town communities.MethodsStool samples were collected from children enrolled in the TB-CHAMP clinical trial. Internal transcribed spacer 1 (ITS1) gene sequencing was performed on a total of 115 stool samples using the Illumina MiSeq platform. Differences in fungal diversity and composition in relation to demographic, clinical, and environmental factors were investigated, and correlations between fungi and previously described bacterial populations in the same samples were described.ResultsTaxa from the genera Candida and Saccharomyces were detected in all participants. Differential abundance analysis showed that Candida spp. were significantly more abundant in children younger than 2 years compared to older children. The gut mycobiota was less diverse than the bacterial microbiota of the same participants, consistent with the findings of other human microbiome studies. The variation in richness and evenness of fungi was substantial, even between individuals of the same age. There was significant association between vitamin A supplementation and higher fungal alpha diversity (p = 0.047), and girls were shown to have lower fungal alpha diversity (p = 0.003). Co-occurrence between several bacterial taxa and Candida albicans was observed.ConclusionsThe dominant fungal taxa in our study population were similar to those reported in other paediatric studies; however, it remains difficult to identify the true core gut mycobiota due to the challenges set by the low abundance of gut fungi and the lack of true gut colonising species. The connection between the microbiota, vitamin A supplementation, and growth and immunity warrants exploration, especially in populations at risk for micronutrient deficiencies. While we were able to provide insight into the gut mycobiota of young South African children, further functional studies are necessary to explain the role of the mycobiota and the correlations between bacteria and fungi in human health.

The changing influence of host genetics on the leaf fungal microbiome throughout plant development.

Host genetics and the environment influence which fungal microbes colonize a plant. A new study in PLOS Biology finds that the relative influence of these factors changes throughout the development of the biofuel crop switchgrass growing in field settings.

Host genotype controls ecological change in the leaf fungal microbiome.

Leaf fungal microbiomes can be fundamental drivers of host plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass (Panicum virgatum). We also sampled a replicated subset of genotypes across 3 additional sites to compare the importance of time, space, ecology, and genetics. We found a strong successional pattern in the microbiome shaped both by host genetics and environmental factors. Further, we used genome-wide association (GWA) mapping and RNA sequencing to show that 3 cysteine-rich receptor-like kinases (crRLKs) were linked to a genetic locus associated with microbiome structure. We confirmed GWAS results in an independent set of genotypes for both the internal transcribed spacer (ITS) and large subunit (LSU) ribosomal DNA markers. Fungal pathogens were central to microbial covariance networks, and genotypes susceptible to pathogens differed in their expression of the 3 crRLKs, suggesting that host immune genes are a principal means of controlling the entire leaf microbiome.

Host Plant Selection Imprints Structure and Assembly of Fungal Community along the Soil-Root Continuum.

ABSTRACTThe soil fungal community plays pivotal roles in soil nutrient cycling and plant health and productivity in agricultural ecosystems. However, the differential adaptability of soil fungi to different microenvironments (niches) is a bottleneck limiting their application in agriculture. Hence, the understanding of ecological processes that drive fungal microbiome assembly along the soil-root continuum is fundamental to harnessing the plant-associated microbiome for sustainable agriculture. Here, we investigated the factors that shape fungal community structure and assembly in three compartment niches (the bulk soil, rhizosphere, and rhizoplane) associated with tobacco (Nicotiana tabacum L.), with four soil types tested under controlled greenhouse conditions. Our results demonstrate that fungal community assembly along the soil-root continuum is governed by host plant rather than soil type and that soil chemical properties exert a negligible effect on the fungal community assembly in the rhizoplane. Fungal diversity and network complexity decreased in the order bulk soil > rhizosphere > rhizoplane, with a dramatic decrease in Ascomycota species number and abundance along the soil-root continuum. However, facilitations (positive interactions) were enhanced among fungal taxa in the rhizoplane niche. The rhizoplane supported species specialization with enrichment of some rare species, contributing to assimilative community assembly in the rhizoplane in all soil types. Mortierella and Pyrenochaetopsis were identified as important indicator genera of the soil-root microbiome continuum and good predictors of plant agronomic traits. The findings provide empirical evidence for host plant selection and enrichment/depletion processes of fungal microbiome assembly along the soil-root continuum.IMPORTANCE Fungal community assembly along the soil-root continuum is shaped largely by the host plant rather than the soil type. This finding facilitates the implementations of fungi-associated biocontrol and growth-promoting for specific plants in agriculture practice, regardless of the impacts from variations in geographical environments. Furthermore, the depletion of complex ecological associations in the fungal community along the soil-root continuum and the enhancement of facilitations among rhizoplane-associated fungal taxa provide empirical evidence for the potential of community simplification as an approach to target the plant rhizoplane for specific applications. The identified indicators Mortierella and Pyrenochaetopsis along the soil-root microbiome continuum are good predictors of tobacco plant agronomic traits, which should be given attention when manipulating the root-associated microbiome.

Critical roles of sepsis-reshaped fecal virota in attenuating sepsis severity.

Because studies on all fecal organisms (bacteria, fungi, and viruses) in sepsis are rare and bacteriophages during sepsis might have adapted against gut bacteria with possible pathogenicity, cecal ligation and puncture (CLP; a sepsis mouse model) was evaluated. In fecal bacteriome, sepsis increased Bacteroides and Proteobacteria but decreased Firmicutes, while fecal virome demonstrated increased Podoviridae when compared with sham feces. There was no difference in the fungal microbiome (predominant Ascomycota in both sham and CLP mice) and the abundance of all organisms between sepsis and control groups. Interestingly, the transfers of feces from CLP mice worsened sepsis severity when compared with sham fecal transplantation, as evaluated by mortality, renal injury (serum creatinine and histology), liver damage (liver enzyme and histology), spleen apoptosis, serum cytokines, endotoxemia, and bacteremia. In contrast, the transfers of fecal viral particles from sepsis mice, but not from sham mice, attenuated inflammation in CLP sepsis possibly through the decrease in several fecal pathogenic bacteria (such as Proteobacteria, Gammaproteobacteria, and Prevotellaceae) as evaluated by fecal microbiome analysis. Perhaps the isolation of favorable bacteriophages in sepsis feces and increased abundance ex vivo before oral treatment in a high concentration are beneficial.

Microbiome and pathobiome analyses reveal changes in community structure by foliar pathogen infection in rice.

Increasing evidence suggests that the plant rhizosphere may recruit beneficial microbes to suppress soil-borne pathogens, but microbiome assembly due to foliar pathogen infection and ecological mechanisms that govern microbiome assembly and functions in the diseased host are not fully understood. To provide a comprehensive view of the rice-associated microbiome, we compared bacterial and fungal communities of healthy rice and those infected with Magnaporthe oryzae, the causal agent of blast disease. We found that the soil had a greater diversity of bacterial and fungal communities than plant endospheric communities. There was no significant dysbiosis of bacterial and fungal microbiome diversity due to disease, but it caused a substantial alteration of bacterial community structure in the root and rhizosphere compartments. The pathobiome analysis showed that the microbiome community structure of leaf and grain tissues was changed markedly at the pathogen infection site, although the alpha diversity did not change. Correspondingly, the relative abundances of some bacteria and fungi were clearly altered in symptomatic tissues. We noted an increase in Rhizobium bacteria and a decline of Tylospora, Clohesyomyces, and Penicillium fungi in the symptomatic leaf and grain tissues from both locations. According to the inferred microbial network, several direct interactions between M. oryzae and other microbes were identified. The majority of edges in the interaction network were positive in diseased samples; contrastingly, the number of edges was much lower in the healthy samples. With source tracking analysis, we observed a sharp contrast in the source of root endosphere bacteria due to Magnaporthe infection. Whereas the majority (71%) of healthy root bacteria could be tracked from the soil, only a very small portion (17%) could be tracked from the soil for diseased samples. These results advanced our understanding and provided potential ideas and a theoretical basis for studying pathobiome and exploiting the microbiome for sustainable agriculture.

Community structure and environmental determinants of the bacterial and fungal gut microflora in Hainan gibbons (Nomascus hainanus)

High-throughput sequencing technology was used to establish the OTU (Operational Taxonomic Units) composition and diversity of bacteria and fungi in the gut of three family groups of Hainan gibbons ( Nomascus hainanus ) in the Bawangling National Nature Reserve on Hainan Island, southern China. Firmicutes (47.23%) and Bacteroidetes (36.54%) predominated at the phylum level, while the predominant genera were Prevotella-7 (15.30%), Lachnospiraceae_NK3A20_group (12.49%), and uncultured_bacterium_f_Erysipelotrichaceae (11.79%). At the phylum level, the dominant fungi were Ascomycota (66.41%), as well as Hanseniaspora (23.33%), Schwanniomyces (13.44%), and Pichia (5.43%) at the genus level. We found significant differences in the bacterial OTU diversity (Shannon index) between family groups living in Tropical Lowland or Tropical Montane Rain Forest, compared to those inhabiting Tropical Montane Evergreen Forest at higher altitudes. Bacterial OTU community composition also differed between family groups, unraveling significant differences among the 30 most dominant bacterial core taxa. Furthermore, we unraveled a significant difference of OTU richness in the fungal microbiome (Chao 1) between family groups living at lower altitudes, i.e., Tropical Lowland or Tropical Montane Rain Forest and those inhabiting the Tropical Montane Evergreen Forest. Our analysis further indicated significant differences in the fungal OTU community composition between the three family groups, especially regarding the three most dominant fungal core taxa. Subsequently, two habitat factors, and nine environmental and anthropogenic variables were used to explore possible causes of disparity in the microbial flora of gibbon groups. A factor reduction procedure resulted into three principal components which were correlated to bacterial and fungal OTU richness and diversity using Spearman's rank-order correlations. Bacterial and fungal OTU diversity was high in areas of high altitude, steep slopes, high tree density, but low tree height, while high fungal OTU richness corresponded to high altitude habitats, i.e., in the Tropical Montane Evergreen Forest. Distance to human settlements and to the next water body showed no significant relation with bacterial and fungal richness and diversity.

The bacterial and fungal microbiomes of ectomycorrhizal roots from stone oaks and Yunnan pines in the subtropical forests of the Ailao Mountains of Yunnan.

Ectomycorrhizal (ECM) symbioses play an important role in tree biology and forest ecology. However, little is known on the composition of bacterial and fungal communities associated to ECM roots. In the present study, we surveyed the bacterial and fungal microbiome of ECM roots from stone oaks (Lithocarpus spp.) and Yunnan pines (Pinus yunnanensis) in the subtropical forests of the Ailao Mountains (Yunnan, China). The bacterial community was dominated by species pertaining to Rhizobiales and Acidobacteriales, whereas the fungal community was mainly composed of species belonging to the Russulales and Thelephorales. While the bacterial microbiome hosted by ECM roots from stone oaks and Yunnan pines was very similar, the mycobiome of these host trees was strikingly distinct. The microbial networks for bacterial and fungal communities showed a higher complexity in Lithocarpus ECM roots compared to Pinus ECM roots, but their modularity was higher in Pinus ECM roots. Seasonality also significantly influenced the fungal diversity and their co-occurrence network complexity. Our findings thus suggest that the community structure of fungi establishing and colonizing ECM roots can be influenced by the local soil/host tree environment and seasonality. These results expand our knowledge of the ECM root microbiome and its diversity in subtropical forest ecosystems.

Autotoxin affects the rhizosphere microbial community structure by influencing the secretory characteristics of grapevine roots.

Autotoxins secreted by roots into the soil can trigger rhizosphere microecological imbalances and affect root secretory properties resulting in conditions such as replanting disease. However, information on the effect of autotoxins on root secretion characteristics and regulation of the composition of rhizosphere microorganisms by altered root exudates is limited. In this study, autotoxin ρ-hydroxybenzoic acid (4-HBA) was added to the soil of potted grapevine seedlings, CO2 pulse-labeling, and DNA stable isotope probing were used to track the rhizosphere microbiome that assimilates root exudates. Bacterial and fungal microbiomes that assimilated plant-derived carbon were identified by high-throughput sequencing. Results showed that 4-HBA treatment altered bacterial and fungal communities in 13C-labeled organisms, with a lower abundance of beneficial bacteria (e.g., Gemmatimonas, Streptomyces, and Bacillus) and a higher abundance of potential pathogen fungi (e.g., Fusarium, Neocosmospora, Gibberella, and Fusicolla) by changing the composition of root exudates. The exogenous addition of upregulated compound mixtures of root exudates reduced the abundance of beneficial bacterial Bacillus and increased the abundance of potential pathogen fungi Gibberella. These results suggest that 4-HBA can alter root secretion properties and altered root exudates may enrich certain potential pathogens and reduce certain beneficial bacteria, thereby unbalancing the structure of the rhizosphere microbial community.

Vestibulodynia and the Vaginal Microbiome: A Case-Control Study

BackgroundRecent studies of the vaginal microbiome have led to a better understanding of the microbiota and interactions with the host environment, however the role of the vaginal microbiome in vestibulodynia remains unclear. AimThis study aims to investigate and examine differences in the bacterial and fungal microbiome among patients with vestibulodynia and healthy controls. MethodsA case-control study was conducted examining the vaginal microbiome of 29 patients with vestibulodynia and 26 controls through Stony Brook University Obstetrics and Gynecology ambulatory clinic. Exclusion criteria included a diagnosis of vaginal infection at the time of presentation, a prior diagnosis of vulvodynia or receipt of treatment, immunosuppression, and receipt of steroid or antibiotic therapy. Vaginal swab samples were obtained from participants. DNA was extracted and sent for diversity assay of 16S rRNA for prokaryotic species and internal transcribed spacers (ITS) for fungi. Demographic characteristics for both cases and controls were obtained through a retrospective chart review. Outcome MeasurePrincipal component analysis (PCA) and linear discriminant analysis effect size (LefSe) were used to identify differences in relative abundance of operational taxonomic units (OTUs) for the vaginal microbiome between vestibulodynia patients and controls. ResultsLactobacillus species were dominant amongst both cases and controls. PCA of 16S and ITS OTUs did not show significant differences in microbiome composition between vestibulodynia patients and controls. LefSe demonstrated higher abundance of Bifidobacterium longum, the Genus Sneathia, and the Family Leptotrichiaceae, in controls compared to vestibulodynia samples. For ITS, Aspergillus spp. was significantly more prevalent in controls than in vestibulodynia cases. Clinical ImplicationsAdditional studies are needed to further assess the clinical significance of these findings. Strengths and LimitationsStrengths of this study include ITS amplicon sequence analysis for fungal species diversity. Limitations of this study include small sample size and lack of racial diversity. ConclusionsOur study did not find significant differences in composition or diversity between the vaginal microbiomes of cases of vestibulodynia and controls; however, the data suggests differences in abundance of biota requiring further research for biological and clinical significance.Panzarella DA, Peresleni T, Collier JL, et al. Vestibulodynia and the Vaginal Microbiome: A Case-Control Study. J Sex Med 2022;19:1451–1462.

Camel milk microbiota: A culture-independent assessment

Camel milk is renowned for its nutritional value and its therapeutic properties. It is considered a promising alternative to bovine milk due to its higher nutritional benefits, hypoallergenic characteristics and greater digestibility in the human gastrointestinal system. This study reports camel milk's bacterial and fungal microbiota, and the effect of geographical location and season on its bacterial community. We sequenced the V3-V4 regions of the16S rRNA gene for bacteria and the internal transcribed spacer (ITS) for fungi. A total of 134 samples of dromedary raw camel milk were collected from south, north and middle Kuwait during two seasons. Raw camel milk showed a diversified bacterial community, with 1196 genera belonging to 33 phyla. The four most predominant phyla of bacteria were Proteobacteria, Firmicutes, Actinobacteria and Bacteroidota. The core microbiota of raw camel milk, represented by the dominant genera shared by the majority of samples, was constituted by the genera Schlegelella, Paenibacillus, Lactobacillus, unclassified Comamonadaceae, Pediococcus, Moraxella, Acinetobacter, Staphylococcus, Enterococcus, Pseudomonas, Streptococcus, unclassified Micrococcaceae, Rothia, unclassified Sphingomonadaceae, unclassified Neisseriaceae and Sphingomonas. The fungal population was assessed in 14 raw camel milk samples, and comprised 87 genera belonging to 3 phyla. The genera Penicillium, Cladosporium, Candida, Aspergillus, Alternaria and Fusarium, dominated the fungal community. These findings shed light on raw camel milk's core bacterial and fungal microbiome. The geographical location and the season had a significant impact on the diversity and composition of camel milk microbiome.

Gut Fungal Microbiome Responses to Natural Cryptosporidium Infection in Horses.

It is critical to characterize changes in the structure and composition of the host fungal community in natural Cryptosporidium infection, because it gives the possible overview of gut microbiome in host homeostasis and disease progression. A total of 168 rectal fecal samples were collected and examined using nPCR. The positive samples were double-checked using 18S rDNA high-throughput sequencing. After confirmation, ITS high-throughput sequencing was utilized to investigate the fungal community’s response to natural Cryptosporidium infection. Results showed that a total of three positive samples (1.79%) were identified with an increased abundance of fungi associated with health hazards, such as class Dothideomycetes, families, i.e., Cladosporiaceae, Glomerellaceae, and genera, i.e., Wickerhamomyces, Talaromyces, Cladosporium, Dactylonectria, and Colletotrichum. On the contrary, taxa associated with favorable physiological effects on the host were shown to have the reverse impact, such as families, i.e., Psathyrellaceae, Pseudeurotiaceae and genera (Beauveria, Nigrospora, and Diversispora). For the first time, we evaluated the condition of natural Cryptosporidium infection in horses in Wuhan, China, and discovered distinct variations in the fungal microbiome in response to natural infection. It might prompt a therapy or prevention strategy to apply specific fungal microorganisms that are probably responsible for decreased susceptibility or increased resistance to infection.

The interplay of fungal and bacterial microbiomes on rainforest frogs following a disease outbreak

AbstractEmerging infectious diseases are a serious threat to wildlife populations, and there is growing evidence that host microbiomes play important roles in infection dynamics, possibly even mitigating diseases. Nevertheless, most research on this topic has focused only on bacterial microbiomes, while fungal microbiomes have been largely neglected. To help fill this gap in our knowledge, we examined both the bacterial and fungal microbiomes of four sympatric Australian frog species, which had different population‐level responses to the emergence of chytridiomycosis, a widespread disease caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd). We sequenced 16,884 fungal amplicon sequence variants (ASVs) and 41,774 bacterial ASVs. Bacterial communities had higher richness and were less variable within frog species than were fungal communities. Nevertheless, both communities were correlated for both ASV richness and beta diversity (i.e., frogs with similar bacterial richness and community composition tended to also have similar fungal richness and community composition). This suggests that either one microbial community was having a large impact on the other or that they were both being driven by similar environmental factors. For both microbial taxa, we found little evidence of associations between Bd (prevalence or intensity) and either individuals' ASVs or beta diversity. However, there was mixed evidence of associations between richness (both bacterial and fungal) and Bd, with high richness potentially providing a protective effect. Surprisingly, the relative abundance of bacteria that have previously been shown to inhibit Bd was also positively associated with Bd infection intensity, suggesting that a high relative abundance of those bacteria provides poor protection against infection.

Altered skin fungal and bacterial community compositions in tinea capitis.

Tinea capitis is an infection of the scalp and hair shaft caused by dermatophytes that predominantly occurs in children. Skin fungal infections have been found to be associated with alterations in the overall bacterial and fungal communities. However, the scalp microbiome in tinea capitis have not been fully investigated. To investigate and compare the scalp bacterial and fungal microbiomes between children with tinea capitis and healthy children and between children and adults. Skin samples were collected from the scalp. Bacterial and fungal community compositions were analysed by amplification sequencing of the V3-V4 of 16S rDNA and ITS1-5F, respectively. The predominant fungi detected using amplicon sequencing were consistent with the culture- or real-time PCR-positive pathogens in most samples. Children with tinea capitis had lower fungal and higher bacterial Shannon diversity than healthy children. A higher relative abundance of pathogenic fungi and significant alterations in the bacterial community in the lesional sites of tinea capitis than healthy scalps. Compared with adults, healthy children were characterised by higher Shannon diversities with significantly lower relative abundances of Malassezia and Cutibacterium and higher relative abundances of Candida and Streptococcus. We demonstrated that tinea capitis was characterised by significant alterations in both fungal and bacterial communities and amplicon sequencing could be a complementary method for pathogen identification.

The relative abundances of yeasts attractive to Drosophila suzukii differ between fruit types and are greatest on raspberries

Fungal metabolic volatiles attract Drosophila suzukii which oviposits in ripening fruits, but there are few data describing the fungal microbiomes of commercial fruits susceptible to this insect pest. We tested the hypothesis that fruit type and ripening stage have a significant effect on fruit surface fungal communities using DNA metabarcoding approaches and found strong support for differences in all three fungal community biodiversity metrics analysed (numbers, types, and abundances of taxa). There was an average fivefold greater difference in fungal communities between sites with different fruit types (strawberry, cherry, raspberry, and blueberry) than across fruit developmental stages, demonstrating site and/or fruit type is the greater factor defining fungal community assemblage. The addition of a fungal internal standard (Plectosphaerella cucumerina) showed cherry had relatively static fungal populations across ripening. Raspberry had a greater prevalence of Saccharomycetales yeasts attractive to D. suzukii, including Hanseniaspora uvarum, which aligns with reports that raspberry is among the fruits with greatest susceptibility and attraction to D. suzukii. Greater knowledge of how yeast communities change during fruit maturation and between species or sites may be valuable for developing methods to manipulate fruit microbiomes for use in integrated pest management strategies to control D. suzukii.

Identification of fungal taxa with pathogenic potential in soil samples from Perunika Glacier’s newly formed forefields - Livingston Island, Antarctica

Antarctica peninsula periphery islands undergo one of the most dramatic ecological changes due to ongoing global warming. The front fields of the Antarctic glaciers are extreme environments and pioneering sites for ecological succession. Rising temperatures lead to deglaciation in the Antarctic habitats, and the new terrain is subjected to the process of soil formation and microbial colonization. In the present study, we investigated the formation of pathogenic fungal soil microbiomes as an effect of forefield deglaciation. Soil samples were taken from two different forefields, one formed several years ago and the other freshly uncovered. Both habitats were in the vicinity of the Perunika Glacier situated in the northeastern direction of Hurd Peninsula, Livingston Island, the second largest island from the South Shetland Archipelago, about 100 km north of the Antarctic Peninsula. Total DNA was extracted and targeted ITS amplicon sequencing was applied. The ITS marker sequences were then taxonomically identified. The abundance of the fungal taxa was calculated. Alpha and Beta diversity analyses to obtain fungal richness in samples were performed. Our results showed that soil habitat formation, initiated by deglaciation, was such that: In the newly deglaciated forefield, there was almost no fungal DNA, which prevented further analysis; At older drier fields metagenome content was much higher; Further analysis showed that the most abundant genera were Pseudogymnoascus, Simplicillium, Hanseniaspora, Mycothermus, and Malassezia. In the newly deglaciated forefield, there was almost no fungal DNA, which prevented further analysis; At older drier fields metagenome content was much higher; Further analysis showed that the most abundant genera were Pseudogymnoascus, Simplicillium, Hanseniaspora, Mycothermus, and Malassezia. It is known that Pseudogymnoascus and Malassezia species have pathogenic keratinolytic activity. In conclusion, the phylum Ascomycota, which dominated the core microbiome showed much higher ecological diversity and abundance, i.e. potential for colonization of the glacier forefields. In contrast, the phylum Basidiomycota appeared to be less fit for these conditions.