Fungal Amplicon Sequence Variants Research Articles

Temporal Dynamics of Fungal Communities in Alkali-Treated Round Bamboo Deterioration under Natural Weathering.

Microbes naturally inhabit bamboo-based materials in outdoor environments, sequentially contributing to their deterioration. Fungi play a significant role in deterioration, especially in environments with abundant water and favorable temperatures. Alkali treatment is often employed in the pretreatment of round bamboo to change its natural elastic and aesthetic behaviors. However, little research has investigated the structure and dynamics of fungal communities on alkali-treated round bamboo during natural deterioration. In this work, high-throughput sequencing and multiple characterization methods were used to disclose the fungal community succession and characteristic alterations of alkali-treated round bamboo in both roofed and unroofed habitats throughout a 13-week deterioration period. In total, 192 fungal amplicon sequence variants (ASVs) from six phyla were identified. The fungal community richness of roofed bamboo samples declined, whereas that of unroofed bamboo samples increased during deterioration. The phyla Ascomycota and Basidiomycota exhibited dominance during the entire deterioration process in two distinct environments, and the relative abundance of them combined was more than 99%. A distinct shift in fungal communities from Basidiomycota dominant in the early stage to Ascomycota dominant in the late stage was observed, which may be attributed to the increase of moisture and temperature during succession and the effect of alkali treatment. Among all environmental factors, temperature contributed most to the variation in the fungal community. The surface of round bamboo underwent continuous destruction from fungi and environmental factors. The total amount of cell wall components in bamboo epidermis in both roofed and unroofed conditions presented a descending trend. The content of hemicellulose declined sharply by 8.3% and 11.1% under roofed and unroofed environments after 9 weeks of deterioration. In addition, the contact angle was reduced throughout the deterioration process in both roofed and unroofed samples, which might be attributed to wax layer removal and lignin degradation. This study provides theoretical support for the protection of round bamboo under natural weathering.

Comparative metabarcoding and biodiversity of gut-associated fungal assemblages of Dendroctonus species (Curculionidae: Scolytinae).

The genus Dendroctonus is a Holarctic taxon composed of 21 nominal species; some of these species are well known in the world as disturbance agents of forest ecosystems. Under the bark of the host tree, these insects are involved in complex and dynamic associations with phoretic ectosymbiotic and endosymbiotic communities. Unlike filamentous fungi and bacteria, the ecological role of yeasts in the bark beetle holobiont is poorly understood, though yeasts were the first group to be recorded as microbial symbionts of these beetles. Our aim was characterize and compare the gut fungal assemblages associated to 14 species of Dendroctonus using the internal transcribed spacer 2 (ITS2) region. A total of 615,542 sequences were recovered yielding 248 fungal amplicon sequence variants (ASVs). The fungal diversity was represented by 4 phyla, 16 classes, 34 orders, 54 families, and 71 genera with different relative abundances among Dendroctonus species. The α-diversity consisted of 32 genera of yeasts and 39 genera of filamentous fungi. An analysis of β-diversity indicated differences in the composition of the gut fungal assemblages among bark beetle species, with differences in species and phylogenetic diversity. A common core mycobiome was recognized at the genus level, integrated mainly by Candida present in all bark beetles, Nakazawaea, Cladosporium, Ogataea, and Yamadazyma. The bipartite networks confirmed that these fungal genera showed a strong association between beetle species and dominant fungi, which are key to maintaining the structure and stability of the fungal community. The functional variation in the trophic structure was identified among libraries and species, with pathotroph-saprotroph-symbiotroph represented at the highest frequency, followed by saprotroph-symbiotroph, and saprotroph only. The overall network suggested that yeast and fungal ASVs in the gut of these beetles showed positive and negative associations among them. This study outlines a mycobiome associated with Dendroctonus nutrition and provides a starting point for future in vitro and omics approaches addressing potential ecological functions and interactions among fungal assemblages and beetle hosts.

Exploring the diversity, bioactivity of endophytes, and metabolome in Synsepalum dulcificum.

Synsepalum dulcificum exhibits high edible and medicinal value; however, there have been no reports on the exploration of its endophyte resources. Here, we conducted analyses encompassing plant metabolomics, microbial diversity, and the biological activities of endophytic metabolites in S. dulcificum. High-throughput sequencing identified 4,913 endophytic fungal amplicon sequence variants (ASVs) and 1,703 endophytic bacterial ASVs from the roots, stems, leaves, flowers, and fruits of S. dulcificum. Fungi were classified into 5 phyla, 24 classes, 75 orders, 170 families, and 313 genera, while bacteria belonged to 21 phyla, 47 classes, 93 orders, 145 families, and 232 genera. Furthermore, there were significant differences in the composition and content of metabolites in different tissues of S. dulcificum. Spearman's correlation analysis of the differential metabolites and endophytes revealed that the community composition of the endophytes correlated with plant-rich metabolites. The internal transcribed spacer sequences of 105 isolates were determined, and phylogenetic analyses revealed that these fungi were distributed into three phyla (Ascomycota, Basidiomycota, and Mucoromycota) and 20 genera. Moreover, 16S rDNA sequencing of 46 bacteria revealed they were distributed in 16 genera in three phyla: Actinobacteria, Proteobacteria, and Firmicutes. The antimicrobial activities (filter paper method) and antioxidant activity (DPPH and ABTS assays) of crude extracts obtained from 68 fungal and 20 bacterial strains cultured in different media were evaluated. Additionally, the α-glucosidase inhibitory activity of the fungal extracts was examined. The results showed that 88.6% of the strains exhibited antimicrobial activity, 55.7% exhibited antioxidant activity, and 85% of the fungi exhibited α-glucosidase inhibitory activity. The research suggested that the endophytes of S. dulcificum are highly diverse and have the potential to produce bioactive metabolites, providing abundant species resources for developing antibiotics, antioxidants and hypoglycemic drugs.

The Diverse Mycorrizal Morphology of Rhododendron dauricum, the Fungal Communities Structure and Dynamics from the Mycorrhizosphere.

It is generally believed that mycorrhiza is a microecosystem composed of mycorrhizal fungi, host plants and other microscopic organisms. The mycorrhiza of Rhododendron dauricum is more complex and the diverse morphology of our investigated results displays both typical ericoid mycorrhizal characteristics and ectomycorrhizal traits. The characteristics of ectendoomycorrhiza, where mycelial invade from the outside into the root cells, have also been observed. In order to further clarify the mycorrhizal fungi members and other fungal communities of R. dauricum mycorrhiza, and explore the effects of vegetation and soil biological factors on their community structure, we selected two woodlands in the northeast of China as samples-one is a mixed forest of R. dauricum and Quercus mongolica, and the other a mixed forest of R. dauricum, Q. mongolica, and Pinus densiflor. The sampling time was during the local growing season, from June to September. High-throughput sequencing yielded a total of 3020 fungal amplicon sequence variants (ASVs), which were based on sequencing of the internal transcribed spacer ribosomal RNA (ITS rRNA) via the Illumina NovaSeq platform. In the different habitats of R. dauricum, there are differences in the diversity of fungi obtained from mycorrhizal niches, and specifically the mycorrhizal fungal community structure in the complex vegetation of mixed forests, where R. dauricum is found, exhibits greater stability, with relatively minor changes over time. Soil fungi are identified as the primary source of fungi within the mycorrhizal niche, and the abundance of mycorrhizal fungi from mycorrhizal niches in R. dauricum is significantly influenced by soil pH, organic matter, and available nitrogen. The relationship between soil fungi and mycorrhizal fungi from mycorrhizal niches is simultaneously found to be intricate, while the genus Hydnellum emerges as a central genus among mycorrhizal fungi from mycorrhizal niches. However, there is currently a substantial gap in the foundational research of this genus, including the fact that mycorrhizal fungi from mycorrhizal niches have, compared to fungi present in the soil, proven to be more sensitive to changes in soil moisture.

Microbial biomarkers of tree water status for next-generation biomonitoring of forest ecosystems.

Next-generation biomonitoring proposes to combine machine-learning algorithms with environmental DNA data to automate the monitoring of the Earth's major ecosystems. In the present study, we searched for molecular biomarkers of tree water status to develop next-generation biomonitoring of forest ecosystems. Because phyllosphere microbial communities respond to both tree physiology and climate change, we investigated whether environmental DNA data from tree phyllosphere could be used as molecular biomarkers of tree water status in forest ecosystems. Using an amplicon sequencing approach, we analysed phyllosphere microbial communities of four tree species (Quercus ilex, Quercus robur, Pinus pinaster and Betula pendula) in a forest experiment composed of irrigated and non-irrigated plots. We used these microbial community data to train a machine-learning algorithm (Random Forest) to classify irrigated and non-irrigated trees. The Random Forest algorithm detected tree water status from phyllosphere microbial community composition with more than 90% accuracy for oak species, and more than 75% for pine and birch. Phyllosphere fungal communities were more informative than phyllosphere bacterial communities in all tree species. Seven fungal amplicon sequence variants were identified as candidates for the development of molecular biomarkers of water status in oak trees. Altogether, our results show that microbial community data from tree phyllosphere provides information on tree water status in forest ecosystems and could be included in next-generation biomonitoring programmes that would use in situ, real-time sequencing of environmental DNA to help monitor the health of European temperate forest ecosystems.

Dynamics of the Gut Mycobiome in Patients With Ulcerative Colitis

Intestinal fungi have been implicated in the pathogenesis of ulcerative colitis (UC). However, it remains unclear if fungal composition is altered during active versus quiescent disease. We analyzed clinical and metagenomic data from the Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease (SPARC IBD), available via the IBD Plexus Program of the Crohn's & Colitis Foundation. We evaluated the fungal composition of fecal samples from 421 patients with UC during clinical activity and remission. Within a longitudinal subcohort (n= 52), we assessed for dynamic taxonomic changes across alterations in clinical activity over time. We examined if fungal amplicon sequence variants and fungal-bacterial relationships were altered during activity versus remission. Finally, we classified activity in UC using a supervised machine learning random forest model trained on fungal abundance data. During clinical activity, the relative abundance of genus Candida was increased 3.5-fold (P-adj < 1× 10-4) compared with during remission. Patients with longitudinal reductions in clinical activity demonstrated parallel reductions in Candida relative abundance (P < .05). Candida relative abundance correlated with Parabacteroides diastonis, Faecalibacterium prausnitzii, and Bacteroides dorei relative abundance (P < .05) during remission; however, these correlations were disrupted during activity. Fungal abundance data successfully classified patients with active or quiescent UC (area under the curve ∼0.80), with Candida relative abundance critical to the success of the model. Clinical activity in UC is associated with an increased relative abundance of Candida, cross-sectionally and dynamically over time. The role of fecal Candida as a target for therapeutics in UC should be evaluated.

Metagenomic Analysis of the Composition of Microbial Consortia Involved in Spruce Degradation over Time in Białowieża Natural Forest.

Deadwood plays an important role in forest ecology; its degradation and, therefore, carbon assimilation is carried out by fungi and bacteria. To quantify the abundance and distribution of microbial taxa inhabiting dead spruce logs fallen over a span of 50 years and the soil beneath, we used taxonomic profiling with NGS sequencing of hypervariable DNA fragments of ITS1 and 16S V3-V4, respectively. The analysis of sequencing data revealed a high level of diversity in microbial communities participating in the degradation of spruce logs. Differences in the relative abundance of microbial taxa between the samples of the wood that died in 1974 and 2014, and of the soil in its immediate vicinity, were visible, especially at the genus level. Based on the Lefse analysis significantly higher numbers of classified bacterial taxa were observed in the wood and soil samples from 2014 (wood: 1974-18 and 2014-28 taxa; soil: 1974-8 and 2014-41 taxa) while the number of classified fungal taxa was significantly higher in the wood and soil samples from 1974 (wood: 1974-17 and 2014-9 taxa; soil: 1974-57 and 2014-28 taxa). Most of the bacterial and fungal amplicon sequence variants (ASVs) unique to wood were found in the samples from 1974, while those unique to soil were detected in the samples from 2014. The ATR-FTIR method supported by CHN analysis revealed physicochemical changes in deadwood induced by the activity of fungal and bacterial organisms.

Phyllosphere microbial diversity and specific taxa mediate within-cultivar resistance to Phytophthora palmivora in cacao.

The oomycete pathogen Phytophthora palmivora, which causes black pod rot (BPR) on cacao (Theobroma cacao L.), is responsible for devastating yield losses worldwide. Genetic variation in resistance to Phytophthora spp. is well documented among cacao cultivars, but variation has also been observed in the incidence of BPR even among trees of the same cultivar. In light of evidence that the naturally occurring phyllosphere microbiome can influence foliar disease resistance in other host-pathogen systems, it was hypothesized that differences in the phyllosphere microbiome between two field accessions of the cultivar Gainesville II 164 could be responsible for their contrasting resistance to P. palmivora. Bacterial alpha diversity was higher but fungal alpha diversity was lower in the more resistant accession MITC-331, and the accessions harbored phyllosphere microbiomes with distinct community compositions. Six bacterial and 82 fungal amplicon sequence variants (ASVs) differed in relative abundance between MITC-333 and MITC-331, including bacterial putative biocontrol agents and a high proportion of fungal pathogens, and nine fungal ASVs were correlated with increased lesion development. The roles of contrasting light availability and host mineral nutrition, particularly potassium, are also discussed. Results of this preliminary study can be used to guide research into microbiome-informed integrated pest management strategies effective against Phytophthora spp. in cacao. IMPORTANCE Up to 40% of the world's cacao is lost each year to diseases, the most devastating of which is black pod rot, caused by Phytophthora palmivora. Though disease resistance is often attributed to cacao genotypes (i.e., disease-resistant rootstocks), this study highlights the role of the microbiome in contributing to differences in resistance even among accessions of the same cacao cultivar. Future studies of plant-pathogen interactions may need to account for variation in the host microbiome, and optimizing the cacao phyllosphere microbiome could be a promising new direction for P. palmivora resistance research.

Effects of postharvest chitosan and potassium sorbate coating on the storage quality and fungal community of fresh jujube

Fresh jujube fruit are confronted with serious quality deterioration after harvest. This study explored the effects of chitosan and potassium sorbate coatings on the physicochemical quality and fungal community of jujube during cold storage. Microscopic observation showed that chitosan can uniformly distribute potassium sorbate on the surface of jujube. Chitosan coating inhibited the increase in respiration rate and total soluble solids and the decrease in titratable acidity and firmness. Jujube fruit treated with chitosan and potassium sorbate showed the lowest decay rate (2.67%) after 35 d of storage. High-throughput sequencing analysis indicated that the largest number of fungal amplicon sequence variants (ASVs) was detected in jujube treated with chitosan and potassium sorbate, exhibiting higher Chao1, Shannon and Simpson diversity indices. Treatment with chitosan or potassium sorbate alone reduced the relative abundance of Cladosporium in jujube fruit. Jujube treated with chitosan and potassium sorbate had the lowest total relative abundance of all potential pathogenic fungi (Cladosporium, Alternaria and Diaporthe). FUNGuild analysis showed that chitosan and potassium sorbate treatment could inhibit the relative abundance of plant pathogenic fungi. As a result, chitosan maintained the physicochemical properties of jujube by inhibiting the respiration rate, and the combination of chitosan and potassium sorbate reduced the decay rate of jujube by inhibiting pathogenic fungi. Therefore, chitosan and potassium sorbate coating is a promising approach to improve the storage quality and delay the decay of jujube fruit after harvest.

Alterations in the Fungal Microbiome in Ulcerative Colitis.

Although gut fungi have been implicated in the immunopathogenesis of inflammatory bowel disease, the fungal microbiome has not been deeply explored across endohistologic activity and treatment exposure in ulcerative colitis. We analyzed data from the SPARC IBD (Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease) registry. We evaluated the fungal composition of fecal samples from 98 patients with ulcerative colitis across endoscopic activity (n = 43), endohistologic activity (n = 41), and biologic exposure (n = 82). Across all subgroups, we assessed fungal diversity and differential abundance of taxonomic groups. We identified 500 unique fungal amplicon sequence variants across the cohort of 82 patients, dominated by phylum Ascomycota. Compared with endoscopic remission, patients with endoscopic activity had increased Saccharomyces (log2 fold change = 4.54; adjusted P < 5 × 10-5) and increased Candida (log2 fold change = 2.56; adjusted P < .03). After adjusting for age, sex, and biologic exposure among patients with endoscopic activity, Saccharomyces (log2 fold change = 7.76; adjusted P < 1 × 10-15) and Candida (log2 fold change = 7.28; adjusted P< 1 × 10-8) remained enriched during endoscopic activity compared with quiescence. Endoscopic inflammation in ulcerative colitis is associated with an expansion of Saccharomyces and Candida compared with remission. The role of these fungal taxa as potential biomarkers and targets for personalized approaches to therapeutics in ulcerative colitis should be evaluated.

The distinct plastisphere microbiome in the terrestrial-marine ecotone is a reservoir for putative degraders of petroleum-based polymers

Research into plastic-degrading bacteria and fungi is important for understanding how microorganisms can be used to address the problem of plastic pollution and for developing new approaches to sustainable waste management and bioplastic production. In the present study, we isolated 55 bacterial and 184 fungal strains degrading polycaprolactone (PCL) in plastic waste samples from Dafeng coastal salt marshes, Jiangsu, China. Of these, Jonesia and Streptomyces bacteria also showed potential to degrade other types of petroleum-based polymers. The metabarcoding results proved the existence of plastisphere as a distinct ecological niche regardless of the plastic types where 27 bacterial and 29 fungal amplicon sequence variants (ASVs) were found to be significantly (p < 0.05) enriched, including some belonging to Alternaria (Ascomycota, Fungi) and Pseudomonas (Gammaproteobacteria, Bacteria) that were also mined out by the method of cultivation. Further assembly analyses demonstrated the importance of deterministic processes especially the environmental filtering effect of carbon content and pH on bacteria as well as the carbon and cation content on fungi in shaping the plastisphere communities in this ecosystem. Thus, the unique microbiome of the plastisphere in the terrestrial-marine ecotone is enriched with microorganisms that are potentially capable of utilizing petroleum-based polymers, making it a valuable resource for screening plastic biodegraders.

384 Alterations in the fungal microbiome in ulcerative colitis

OBJECTIVES/GOALS: Although gut fungi have been implicated in the immunopathogenesis of inflammatory bowel disease, the fungal microbiome has not been deeply explored across endo-histologic activity and treatment-exposure in ulcerative colitis. METHODS/STUDY POPULATION: Our retrospective cohort was derived from the Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease. We evaluated the fungal composition of fecal samples from 98 ulcerative colitis patients across endoscopic activity (n=43), endo-histologic activity (n=41), and biologic-exposure (n=98). Across all subgroups, we assessed fungal diversity and differential abundance of specific taxonomic groups. RESULTS/ANTICIPATED RESULTS: We identified 504 unique fungal amplicon sequence variants across the cohort of 98 patients, dominated by phylum Ascomycota. Compared to endoscopic remission, patients with endoscopic activity had an increased global fungus load (p DISCUSSION/SIGNIFICANCE: Endoscopic inflammation in ulcerative colitis is associated with altered fungal diversity driven by expansion of Saccharomyces and Candida compared to remission. The role of these fungal taxa as potential biomarkers and targets for personalized approaches to therapeutics in ulcerative colitis should be evaluated.

Habitat and tree species identity shape aboveground and belowground fungal communities in central European forests.

Trees interact with fungi in mutualistic, saprotrophic, and pathogenic relationships. With their extensive aboveground and belowground structures, trees provide diverse habitats for fungi. Thus, tree species identity is an important driver of fungal community composition in forests. Here we investigate how forest habitat (bark surface vs. soil) and tree species identity (deciduous vs. coniferous) affect fungal communities in two Central European forests. We assess differences and interactions between fungal communities associated with bark surfaces and soil, in forest plots dominated either by Fagus sylvatica, Picea abies, or Pinus sylvestris in two study regions in southwestern and northeastern Germany. ITS metabarcoding yielded 3,357 fungal amplicon sequence variants (ASVs) in the northern and 6,088 in the southern region. Overall, soil communities were 4.7 times more diverse than bark communities. Habitat type explained 48-69% of the variation in alpha diversity, while tree species identity explained >1-3%. NMDS ordinations showed that habitat type and host tree species structured the fungal communities. Overall, few fungal taxa were shared between habitats, or between tree species, but the shared taxa were highly abundant. Network analyses, based on co-occurrence patterns, indicate that aboveground and belowground communities form distinct subnetworks. Our study suggests that habitat (bark versus soil) and tree species identity are important factors structuring fungal communities in temperate European forests. The aboveground (bark-associated) fungal community is currently poorly known, including a high proportion of reads assigned to "unknown Ascomycota" or "unknown Dothideomycetes." The role of bark as a habitat and reservoir of unique fungal diversity in forests has been underestimated.

DIFFERENTIAL ABUNDANCE OF THE FUNGAL MYCOBIOME IN PATIENTS WITH ULCERATIVE COLITIS

Abstract BACKGROUND The fungal mycobiome has been increasingly implicated in the pathogenesis of inflammatory bowel disease (IBD). Circulating antibodies to Saccharomyces antibodies are detected in 60-70% of Crohn’s disease and in 10-15% of patients with ulcerative colitis (UC). Specific fungal species, including Candida albicans, are increased in active IBD compared to healthy controls. Recently, UC patients with high fecal Candida prior to fecal microbial transplantation (FMT) were more likely to demonstrate robust treatment responses to transplant, with low Candida levels post-FMT predicting ameliorated inflammation in the recipient. Despite the accumulation of findings supporting the role of fungi in IBD, the mycobiome remains poorly characterized in UC. Few studies have examined changes in the UC mycobiome with respect to validated endoscopic indices or histologic parameters; furthermore, the effects of treatment exposure, including biologic medications, on fungal communities in UC are unknown. AIMS In this study, we aim to characterize the fungal mycobiome in UC patients with varying levels of endoscopic activity, endo-histologic activity, and treatment exposure. METHODS We performed a secondary analysis using the data extracted from the Crohn’s and Colitis Foundation’s Study of a Prospective Adult Research Cohort with IBD, which contains clinical, endoscopic, histologic, and metagenomic data. Using Internal Transcribed Spacer based deep sequencing of fungal rDNA from fecal samples, we classified sequences utilizing the UNITE fungal database and a fitted classifier. The R package DESeq2 was used to calculate the log-2 fold change of differential abundance. RESULTS We identified 504 unique fungal amplicon sequence variants across the cohort of 98 patients, belonging to phylum Ascomycota (71.5%), Basidiomycota (11%), Mucoromycota (0.16%), or unidentified (17.2%). Compared to endoscopic remission, patients with endoscopic activity (n=25) were enriched with Saccharomyces (4.31, p&amp;lt; 5 x 10-5) and Candida (2.53, p&amp;lt; 1 x 10-3). Similarly, compared to endo-histologic remission, patients with endo-histologic activity (n=19) were also enriched for Saccharomyces (2.71, p&amp;lt;0.05) and Candida (2.07, p=0.05). Biologic exposure favored the growth of Candida (p-adj &amp;lt; 1 x10-4). After adjusting for age, gender, and biologic exposure among patients with endoscopic activity, Saccharomyces (p-adj &amp;lt; 5 x 10-12) and Candida (p-adj&amp;lt; 1 x 10-8) remained enriched. CONCLUSION These data demonstrate that endoscopic and histologic inflammation in UC is associated with expansion of Saccharomyces and Candida compared to remission, even after controlling for exposure to biologic exposure. These findings are recapitulated during endo-histologic activity. The role of these fungal taxa as potential biomarkers and targets for personalized approaches to therapeutics in UC should be evaluated.

Microbiome analysis of raw honey reveals important factors influencing the bacterial and fungal communities.

Raw honeys contain diverse microbial communities. Previous studies have focused on isolating bacteria and fungi that are culturable, while missing a large proportion of the microbial community due to culture-based constraints. This study utilized next-generation sequencing (NGS) to analyze the composition of microorganisms in raw honey; these data can reveal environmental and physicochemical variables that are associated with different microbial communities. To examine the microbial composition (bacteria and fungi) of raw honey and analyze its association with physicochemical properties, four types of honey (monofloral, wildflower, manuka, and feral; n total = 36) were analyzed via amplicon metagenomics. The analyzed honey samples had relatively similar bacterial communities but more distinct and diverse fungal communities. Honey type was determined as a significant factor influencing alpha and beta diversity metrics of bacterial and fungal communities. For the bacterial communities, titratable acidity (TA) was associated with community richness and diversity. For the fungal communities, Brix, TA, and color were associated with community richness, while water activity and color were associated with community diversity. Additionally, important bacterial and fungal amplicon sequence variants (ASVs) that influenced the overall community were identified. Results from this study provide important insights into the microbial communities associated with different types of raw honey, which could improve our understanding of microbial dynamics in beehives, improve honey production, and prevent honeybee disease.

Large-diameter trees and deadwood correspond with belowground ectomycorrhizal fungal richness

BackgroundLarge-diameter trees have an outsized influence on aboveground forest dynamics, composition, and structure. Although their influence on aboveground processes is well studied, their role in shaping belowground fungal communities is largely unknown. We sought to test if (i) fungal community spatial structure matched aboveground forest structure; (ii) fungal functional guilds exhibited differential associations to aboveground trees, snags, and deadwood; and (iii) that large-diameter trees and snags have a larger influence on fungal community richness than smaller-diameter trees. We used MiSeq sequencing of fungal communities collected from soils in a spatially intensive survey in a portion of Cedar Breaks National Monument, Utah, USA. We used random forest models to explore the spatial structure of fungal communities as they relate to explicitly mapped trees and deadwood distributed across 1.15 ha of a 15.32-ha mapped subalpine forest.ResultsWe found 6,177 fungal amplicon sequence variants across 117 sequenced samples. Tree diameter, deadwood presence, and tree species identity explained more than twice as much variation (38.7% vs. 10.4%) for ectomycorrhizal composition and diversity than for the total or saprotrophic fungal communities. Species identity and distance to the nearest large-diameter tree (≥ 40.2 cm) were better predictors of fungal richness than were the identity and distance to the nearest tree. Soil nutrients, topography, and tree species differentially influenced the composition and diversity of each fungal guild. Locally rare tree species had an outsized influence on fungal community richness.ConclusionsThese results highlight that fungal guilds are differentially associated with the location, size, and species of aboveground trees. Large-diameter trees are implicated as drivers of belowground fungal diversity, particularly for ectomycorrhizal fungi.

Fungal and fungal-like diversity in marine sediments from the maritime Antarctic assessed using DNA metabarcoding

We assessed the fungal and fungal-like sequence diversity present in marine sediments obtained in the vicinity of the South Shetland Islands (Southern Ocean) using DNA metabarcoding through high-throughput sequencing (HTS). A total of 193,436 DNA reads were detected in sediment obtained from three locations: Walker Bay (Livingston Island) at 52 m depth (48,112 reads), Whalers Bay (Deception Island) at 151 m (104,704) and English Strait at 404 m (40,620). The DNA sequence reads were assigned to 133 distinct fungal amplicon sequence variants (ASVs) representing the phyla Ascomycota, Basidiomycota, Mortierellomycota, Chytridiomycota, Glomeromycota, Monoblepharomycota, Mucoromycota and Rozellomycota and the fungal-like Straminopila. Thelebolus balaustiformis, Pseudogymnoascus sp., Fungi sp. 1, Ciliophora sp., Agaricomycetes sp. and Chaetoceros sp. were the dominant assigned taxa. Thirty-eight fungal ASVs could only be assigned to higher taxonomic levels, and may represent taxa not currently included in the available databases or represent new taxa and/or new records for Antarctica. The total fungal community displayed high indices of diversity, richness and moderate to low dominance. However, diversity and taxa distribution varied across the three sampling sites. In Walker Bay, unidentified fungi were dominant in the sequence assemblage. Whalers Bay sediment was dominated by Antarctic endemic and cold-adapted taxa. Sediment from English Strait was dominated by Ciliophora sp. and Chaetoceros sp. These fungal assemblages were dominated by saprotrophic, plant and animal pathogenic and symbiotic taxa. The detection of an apparently rich and diverse fungal community in these marine sediments reinforces the need for further studies to characterize their richness, functional ecology and potential biotechnological applications.

Cryptic fungal diversity revealed by DNA metabarcoding in historic wooden structures at Whalers Bay, Deception Island, maritime Antarctic.

We provide the first assessment of fungal diversity associated with historic wooden structures at Whalers Bay (Heritage Monument 71), Deception Island, maritime Antarctic, using DNA metabarcoding. We detected a total of 177 fungal amplicon sequence variants (ASVs) dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota, Chytridiomycota, Monoblepharomycota, Rozellomycota, and Zoopagomycota. The assemblages were dominated by Helotiales sp. 1 and Herpotrichiellaceae sp. 1. Functional assignments indicated that the taxa detected were dominated by saprotrophic, plant and animal pathogenic, and symbiotic taxa. Metabarcoding revealed the presence of a rich and complex fungal community, which may be due to the wooden structures acting as baits attracting taxa to niches sheltered against extreme conditions, generating a hotspot for fungi in Antarctica. The sequences assigned included both cosmopolitan and endemic taxa, as well as potentially unreported diversity. The detection of DNA assigned to taxa of human and animal opportunistic pathogens raises a potential concern asWhalers Bay is one of the most popular visitor sites in Antarctica. The use of metabarcoding to detect DNA present in environmental samples does not confirm the presence of viable or metabolically active fungi and further studies using different culturing conditions and media, different growth temperatures and incubation periods, in combination with further molecular approaches such as shotgun sequencing are now required to clarify the functional ecology of these fungi.

Drought Tolerance Traits in Neotropical Trees Correlate with the Composition of Phyllosphere Fungal Communities

Plant-associated microorganisms have been shown to aid plants in coping with drought. However, the underlying mechanisms are poorly understood and there is uncertainty regarding which microbial taxa and functions are mostly involved. We explored these issues in Neotropical rainforests and identified foliar microorganisms that may play a role in drought tolerance of trees. Our objectives were to (i) test the relationship between drought tolerance traits in Neotropical trees and the diversity and composition of their foliar fungal and bacterial communities and (ii) identify leaf microbial taxa positively or negatively associated with drought tolerance traits. Our results showed that the composition of leaf fungal communities but not bacterial communities was related to drought tolerance. We identified 27 fungal amplicon sequence variants whose relative abundance covaried with drought tolerance traits. Most variants were assigned to fungal clades often described as plant pathogens and increased in abundance with drought susceptibility. This greater relative abundance of leaf pathogens in the most drought-susceptible trees might increase their vulnerability to climate change. Moreover, we identified the Strelitziana and Ochroconis fungal genera as potential candidates for future culture-dependent studies aimed at understanding and improving drought tolerance in Neotropical forests. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Wild Panax plants adapt to their thermal environment by harboring abundant beneficial seed endophytic bacteria

The seed microbiome of crop wild relatives is a potential reservoir of beneficial traits that potentially improve their host plant resilience to fluctuating environments and pathogenic threats. Herein, we studied the seed microbiome of three species of the medicinal genus Panax (P. vietnamensis, P. japonicas, and P. stipuleanatus) collected from seven locations in Southwest China. We used qPCR and metabarcoding high-throughput sequencing to target both endophytic bacteria and fungi. Seed bacterial absolute abundance (1.1 × 109∼1.0 × 107 gene copy numbers per gram seed) was substantially higher than that of fungi (7.6 × 105∼3.7 × 102). Host plant genotype was the main driver of seed microbiome composition for both bacteria and fungi. Panax growing hypothermal environments significantly shaped their seed endophytic bacterial but not fungal microbiota. The three Panax species’ seeds harbored unique microbes [averaged ∼150 amplicon sequence variants (ASVs)], sharing only 12 bacterial ASVs (half affiliated to Halomonas) and four fungal ASVs. Network analysis showed that the Panax seed endophytic bacteria tend to form inter-weaved functional modules that are majorly connected by core members from the genus Halomonas, Pseudomonas, and Pantoea. These genera have been associated with nutrient cycling, plant, disease suppression, and tolerance to environmental fluctuation. Together, these novel insights may shade light on the ecological strategies of wild Panax plants adaptation to their thermal environment by possessing abundant beneficial seed endophytic bacteria.