Internal Transcribed Spacer Amplicon Sequencing Research Articles

A Pilot Study Characterization of the Scalp Microbiome in Central Centrifugal Cicatricial Alopecia Shows Shift in <i>Corynebacterium</i>

<b><i>Introduction:</i></b> Aberrant fibrosis in central centrifugal cicatricial alopecia (CCCA) is thought to be driven by persistent low-grade inflammation, but the source of inflammation is unclear. Alterations in the scalp microbiota may contribute to inflammation and thus provide a target for therapeutic intervention. We sought to compare the bacterial and fungal cutaneous scalp microbiota in patients with CCCA versus controls. <b><i>Methods:</i></b> Six patients with CCCA and seven controls were sampled at the vertex scalp. 16S rRNA sequencing of V3-V4 region and internal transcribed spacer amplicon sequencing was used to compare bacterial and fungal microbiomes. <b><i>Results:</i></b> A significantly higher relative abundance of <i>Corynebacterium</i> was noted in patients with CCCA versus controls. No significant difference in scalp fungal or bacterial microbiota composition was observed. <b><i>Limitations:</i></b> V3-V4 sequencing can be limited in detection of major skin bacterial species. <b><i>Conclusion:</i></b> CCCA is characterized by a distinct bacterial microbiome community and high relative abundances of <i>Corynebacterium</i>. Future studies should characterize the relationship between <i>Corynebacterium</i> and scalp inflammation and the role it may play in the progression of CCCA.

Host- and Fusarium-Adapted Bacterial Consortia Alter Microbial Community Structures in Arabidopsis Roots and Suppress Fusarium oxysporum

The plant-associated microbiota confers beneficial traits to the plant host by promoting growth and preventing disease. However, it is not fully understood how the host and its associated microbiota interact with pathogens. In this work, we studied how the host plant modulates its associated microbiome to suppress disease. For this, we used two Arabidopsis thaliana lines with different host responses to Fusarium oxysporum f. sp. mathioli (FOM). We isolated bacterial consortia (BCs) from FOM-infected or healthy host plants of the two lines of Arabidopsis and studied their effect on the root-associated microbiota and FOM progression in the following generations of Arabidopsis plants. Root bacterial and fungal communities were profiled using 16S ribosomal RNA and internal transcribed spacer amplicon sequencing, respectively, while quantitative PCR was used for assessment of FOM quantities in shoots of Arabidopsis. Host- or pathogen-adapted BCs significantly reduced FOM quantities in shoots of both the resistant Col-0 and the susceptible Ler-0 Arabidopsis lines. Several bacterial taxa, including Chthoniobacter, Bacillus, Chryseobacterium and Actinoplanes negatively correlated with FOM, suggestive of an antagonistic effect. Furthermore, both host- and pathogen-adapted BCs significantly affected community composition with distinct differentially abundant taxa and co-occurrence network structures. Taken together, our findings suggest that using a subcommunity selection approach is a potential route for exploiting plant-associated rhizosphere microbiomes for engineering disease resilient microbiomes. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Features of combined gut bacteria and fungi from a Chinese cohort of colorectal cancer, colorectal adenoma, and post-operative patients.

Colorectal cancer (CRC) accounts for the third highest morbidity burden among malignant tumors worldwide. Previous studies investigated gut microbiome changes that occur during colorectal adenomas (CRA) progression to overt CRC, thus highlighting the importance of the gut microbiome in carcinogenesis. However, few studies have examined gut microbiome characteristics across the entire spectrum, from CRC development to treatment. The study used 16S ribosomal ribonucleic acid and internal transcribed spacer amplicon sequencing to compare the composition of gut bacteria and fungi in a Chinese cohort of healthy controls (HC), CRC patients, CRA patients, and CRC postoperative patients (PP). Our analysis showed that beta diversity was significantly different among the four groups based on the gut bacterial and fungal data. A total of 51 species of bacteria and 8 species of fungi were identified in the HC, CRA, CRC, and PP groups. Correlation networks for both the gut bacteria and fungi in HC vs. CRA, HC vs. CRC, and HC vs. PP indicated some hub bacterial and fungal genera in each model, and the correlation between bacterial and fungal data indicated that a highly significant negative correlation exists among groups. Quantitative polymerase chain reaction (qPCR) analysis in a large cohort of HC, CRC, CRA, and PP patients demonstrated a significantly increasing trend of Fusobacterium nucleatum, Bifidobacterium bifidum, Candida albicans, and Saccharomyces cerevisiae in the feces of CRC patients than that of HC patients (p < 0.01). However, the abundance levels of CRA and PP were significantly lower in HC patients than those in CRC patients. Further studies are required to identify the functional consequences of the altered bacterial/fungal composition on metabolism and CRC tumorigenesis in the host.

Cadmium inhibits powdery mildew colonization and reconstructs microbial community in leaves of the hyperaccumulator plant Sedum alfredii

Understanding the influence of the heavy metal cadmium (Cd) on the phyllosphere microbiome of hyperaccumulator plants is crucial for enhancing phytoremediation. The characteristics of the phyllosphere of Sedum alfredii Hance, a hyperaccumulator plant, were investigated using 16S rRNA and internal transcribed spacer amplicon sequencing of powdery mildew-infected leaves treated or untreated with Cd. The results showed that the colonization of powdery mildew caused severe chlorosis and necrosis in S. alfredii leaves, and the relative abundance of Leotiomycetes in infected leaves increased dramatically and significantly decreased phyllosphere microbiome diversity. However, S. alfredii preferentially accumulated higher concentrations of Cd in the leaves of infected plants than in uninfected plants by powdery mildew, which in turn significantly inhibited powdery mildew colonization in leaves; the relative abundance of the fungal class Leotiomycetes in infected leaves decreased, and alpha and beta diversities of the phyllosphere microbiome significantly increased with Cd treatment in the infected plants. In addition, the inter-kingdom networks in the microbiota of the infected leaves treated with Cd presented many nodes and edges, and the highest inter-kingdom modularity compared to the untreated infected leaves, indicating a highly connected microbial community. These results suggest that Cd significantly inhibits powdery mildew colonization by altering the composition of the phyllosphere microbiome in S. alfredii leaves, paving the way for efficient heavy metal phytoremediation and providing a new perspective on defense strategies against heavy metals.

Sour Orange Microbiome Is Affected by Infections of Plenodomus tracheiphilus Causal Agent of Citrus Mal Secco Disease

Mal secco is a severe vascular citrus disease (MSD) caused by the mitosporic fungus Plenodomus tracheiphilus (Pt). The pathogen enters through wounds on the above- and below-ground parts of the tree. The susceptible species sour orange (Citrus aurantium) is the most commonly used rootstock for lemon trees in Italy. In this study, sour orange seedlings were wound-inoculated with P. tracheiphilus in leaves or roots. Six months post-inoculation, the microbial communities of rhizosphere, endorhizosphere, and xylem endosphere samples from inoculated and healthy plants were analyzed by 16S rRNA and ITS (internal transcribed spacer) amplicon sequencing. The DNA of Pt was quantified by real-time PCR in the three compartments. According to our results, the endorhizosphere of root-inoculated plants showed the highest concentration of the pathogen DNA. Bacterial populations of potentially beneficial taxa (e.g., Pseudomonas and Burkholderia) were depleted in the rhizosphere of the inoculated plants. Infection through leaves and roots also produced a network-wide rewiring of microbial associations in sour orange roots. Overall, our findings revealed community-level changes induced by Pt infection in the sour orange root and xylem microbiome, providing further insights into the beneficial multispecies interactions in Citrus-associated microbial communities.

Legacy effects of fumigation on soil bacterial and fungal communities and their response to metam sodium application

BackgroundSoil microorganisms are integral to maintaining soil health and crop productivity, but fumigation used to suppress soilborne diseases may affect soil microbiota. Currently, little is known about the legacy effects of soil fumigation on soil microbial communities and their response to fumigation at the production scale. Here, 16S rRNA gene and internal transcribed spacer amplicon sequencing was used to characterize the bacterial and fungal communities in soils from intensively managed crop fields with and without previous exposure to metam sodium (MS) fumigation. The effect of fumigation history, soil series, and rotation crop diversity on microbial community variation was estimated and the response of the soil microbiome to MS application in an open microcosm system was documented.ResultsWe found that previous MS fumigation reduced soil bacterial diversity but did not affect microbial richness and fungal diversity. Fumigation history, soil series, and rotation crop diversity were the main contributors to the variation in microbial β-diversity. Between fumigated and non-fumigated soils, predominant bacterial and fungal taxa were similar; however, their relative abundance varied with fumigation history. In particular, the abundance of Basidiomycete yeasts was decreased in fumigated soils. MS fumigation also altered soil bacterial and fungal co-occurrence network structure and associations. In microcosms, application of MS reduced soil microbial richness and bacterial diversity. Soil microbial β-diversity was also affected but microbial communities of the microcosm soils were always similar to that of the field soils used to establish the microcosms. MS application also induced changes in relative abundance of several predominant bacterial and fungal genera based on a soil’s previous fumigation exposure.ConclusionsThe legacy effects of MS fumigation are more pronounced on soil bacterial diversity, β-diversity and networks. Repeated fumigant applications shift soil microbial compositions and may contribute to differential MS sensitivity among soil microorganisms. Following MS application, microbial richness and bacterial diversity decreases, but microbial β-diversity was similar to that of the field soils used to establish the microcosms in the short-term (< 6 weeks). The responses of soil microbiome to MS fumigation are context dependent and rely on abiotic, biotic, and agricultural management practices.

Profiling the Fungal Microbiome after Fecal Microbiota Transplantation for Graft-versus-Host Disease: Insights from a Phase 1 Interventional Study

Disruption of the intestinal bacterial microbiota is frequently observed in the context of allogeneic hematopoietic cell transplantation (HCT) and is particularly pronounced in patients who develop graft-versus-host disease (GVHD). Donor fecal microbiota transplantation (FMT) restores gut microbial diversity and reduces GVHD in HCT recipients. The composition of the intestinal fungal community in patients with GVHD, and whether fungal taxa are transferred during FMT are currently unknown. We performed a secondary analysis of our clinical trial of FMT in patients with steroid-refractory GVHD with a focus on the mycobiota. We characterized the fecal mycobiota of 17 patients and healthy FMT donors using internal transcribed spacer amplicon sequencing. The donor who provided the majority of FMT material in our study represents an n-of-one study of the intestinal flora over time. In this donor, mycobiota composition fluctuated over time while the bacterial microbiota remained stable over 16 months. Fungal DNA was detected more frequently in baseline stool samples from patients with steroid-refractory GVHD than in patients with steroid-dependent GVHD. We could detect fungal taxa in the majority of samples but did not see evidence of mycobiota transfer from donor to recipient. Our study demonstrates the feasibility of profiling the mycobiota alongside the more traditional bacterial microbiota, establishes the methodology, and provides a first insight into the mycobiota composition of patients with GVHD.

Stem traits, compartments and tree species affect fungal communities on decaying wood.

SummaryDead wood quantity and quality is important for forest biodiversity, by determining wood‐inhabiting fungal assemblages. We therefore evaluated how fungal communities were regulated by stem traits and compartments (i.e. bark, outer‐ and inner wood) of 14 common temperate tree species. Fresh logs were incubated in a common garden experiment in a forest site in the Netherlands. After 1 and 4 years of decay, the fungal composition of different compartments was assessed using Internal Transcribed Spacer amplicon sequencing. We found that fungal alpha diversity differed significantly across tree species and stem compartments, with bark showing significantly higher fungal diversity than wood. Gymnosperms and Angiosperms hold different fungal communities, and distinct fungi were found between inner wood and other compartments. Stem traits showed significant afterlife effects on fungal communities; traits associated with accessibility (e.g. conduit diameter), stem chemistry (e.g. C, N, lignin) and physical defence (e.g. density) were important factors shaping fungal community structure in decaying stems. Overall, stem traits vary substantially across stem compartments and tree species, thus regulating fungal communities and the long‐term carbon dynamics of dead trees.

Advances in understanding the enzymatic potential and production of ochratoxin A of filamentous fungi isolated from cocoa fermented beans

In this work, we determined the degree of filamentous fungi contamination in cocoa fermented seeds and the fungal potential to produce enzymes that could contribute to the cocoa quality. Internal transcribed spacer amplicon sequencing (ITS) showed 11 different species with Byssochlamys spectabilis, Aspergillus niger, Aspergillus flavus, Aspergillus carbonarius, Circinella muscae and Penicillium citrinum as the most abundant species. Our results evidenced intra and inter-species differences in the enzymes production. Cellulases, β-glucosidase, ornithine decarboxylase and phenylalanine decarboxylase were the most diffused enzymes expressed in the 53 strains here studied. Moreover, A. niger (6/12), A. carbonarius (2/3), and P. citrinum (3/3) showed high pectinolytic activity. Remarkable was the amino decarboxylase activity of P. citrinum, and A. flavus strains. For the first time we reported the presence of B. spectabilis in cocoa fermented beans, which could play an important role in the biogenic amines formation. In addition, we explored the capability of the Aspergillus section Nigri strains, to produce ochratoxin A (OTA) in a cacao model system (CPMS) and in malt extract medium (MEL). We observed that CPMS, but not MEL, stimulated the OTA production in 6 out 15 strains of Aspergillus section Nigri, reaching values ranging between 1.70 and 4995 μg OTA kg−1 dry mycelium.

Focused Microbiome Shifts in Reconstructed Wetlands Correlated with Elevated Copper Concentrations Originating from Micronized Copper Azole-Treated Wood.

Micronized copper (Cu) azole (MCA) wood preservative formulations include Cu in nano form, and relatively little is known about longer term effects of Cu leached from MCA into wetland ecosystems. We tested the hypothesis that changes in soil microbiomes within reconstructed freshwater wetlands will be associated with exposure to elevated Cu concentrations originating from immersed MCA-treated wood stakes. Eight replicate communities were assembled with Willamette Valley (OR, USA) flood plain soil and clonally propagated wetland plants within mesocosms. Inundated communities were equilibrated for 5 months before installation of MCA or control southern yellow pine stakes (n = 4 communities/experimental group). Soil samples were collected for 16S and internal transcribed spacer amplicon sequencing to quantify responses in prokaryotes and eukaryotes, respectively, at 15 time points, spanning two simulated seasonal dry downs, for up to 678 days. Physiochemical properties of water and soil were monitored at 20 and 12 time points respectively, over the same period. For both taxonomic groups of organisms, phylogenetic diversity increased and was positively correlated with elapsed days. Furthermore, there was significant divergence among eukaryotes during the second year based on experimental group. Although the composition of taxa underwent succession over time, there was significantly reduced relative abundance of sequence variants from Gomphonema diatoms and Scutellinia fungi in communities where MCA wood stakes were present compared with the controls. These focused microbiome shifts were positively correlated with surface water Cu and soil Cu concentrations, which were significantly elevated in treated communities. The reconstructed communities were effective systems for assessing potential impacts to wetland microbiomes after exposure to released copper. The results further inform postcommercialization risk assessments on MCA-treated wood. Environ Toxicol Chem 2021;40:3351-3368.Published 2021. This article is a U.S. Government work and is in the public domain in the USA.

Detection of Pathogenic and Beneficial Microbes for Roselle Wilt Disease.

Wilt disease of roselle (Hibiscus sabdariffa L.) is common in Taiwan; however, the causative agent remains unknown. The stems of wilted roselle are browned, slightly constricted, and covered by white aerial hyphae, suggesting that potential pathogens may originate from soil. To identify the potential pathogens, we conducted a rhizosphere microbiota survey in phenotypically healthy and diseased plants through fungal internal transcribed spacer (ITS) and bacterial 16S rRNA amplicon sequencing for uncovering the microbial compositions in the roselle rhizosphere. The fungal family Nectriaceae exhibited significantly higher abundance in diseased rhizospheres than in healthy rhizospheres, and this bacterial community was more specific to geography (i.e., plot-dependent) than to rhizosphere disease status. However, a few bacterial groups such as Bacilli were associated with the healthy rhizosphere. Fusarium species were the most dominant species of Nectriaceae in the survey and became the main target for potential pathogen isolation. We successfully isolated 119 strains from diseased plants in roselle fields. Koch’s postulates were used to evaluate the pathogenicity of these strains; our results indicated that Fusarium solani K1 (FsK1) can cause wilting and a rotted pith in roselles, which was consistent with observations in the fields. This is the first demonstration that F. solani can cause roselle wilt in Taiwan. Furthermore, these newly isolated strains are the most dominant operational taxonomic units detected in ITS amplicon sequencing in diseased rhizospheres, which serves as further evidence that F. solani is the main pathogen causing the roselle wilt disease. Administration of Bacillus velezensis SOI-3374, a strain isolated from a healthy roselle rhizosphere, caused considerable anti-FsK1 activity, and it can serve as a potential biocontrol agent against roselle wilt disease.

Large-Scale Characterization of the Soil Microbiome in Ancient Tea Plantations Using High-Throughput 16S rRNA and Internal Transcribed Spacer Amplicon Sequencing.

There is a special interaction between the environment, soil microorganisms, and tea plants, which constitute the ecosystem of tea plantations. Influenced by environmental factors and human management, the changes in soil microbial community affected the growth, quality, and yield of tea plants. However, little is known about the composition and structure of soil bacterial and fungal communities in 100-year-old tea plantations and the mechanisms by which they are affected. In this regard, we characterized the microbiome of tea plantation soils by considering the bacterial and fungal communities in 448 soil samples from 101 ancient tea plantations in eight counties of Lincang city, which is one of the tea domestication centers in the world. 16S and Internal Transcribed Spacer (ITS) rRNA high-throughput amplicon sequencing techniques were applied in this study. The results showed that the abundance, diversity, and composition of the bacterial and fungal communities have different sensitivity with varying pH, altitude, and latitude. pH and altitude affect soil microbial communities, and bacterial communities are more sensitive than fungi in terms of abundance and diversity to pH. The highest α-diversity of bacterial communities is shown in the pH 4.50–5.00 and 2,200-m group, and fungi peaked in the pH 5.00–5.50 and 900-m group. Because of environmental and geographical factors, all microbes are similarly changing, and further correlations showed that the composition and structure of bacterial communities are more sensitive than fungal communities, which were affected by latitude and altitude. In conclusion, the interference of anthropogenic activities plays a more important role in governing fungal community selection than environmental or geographical factors, whereas for the bacterial community, it is more selective to environment adaptation than to adaptation to human activities.

Microbiomes of Field-Grown Maize and Soybean in Southeastern and Central Brazil Inferred by High-Throughput 16S and Internal Transcribed Spacer Amplicon Sequencing.

ABSTRACTWe report the microbial 16S rRNA gene and internal transcribed spacer (ITS) sequencing data of maize and soybean plants and field soil from eight locations in Brazil. Enterobacter and Pseudomonas were among the most abundant genera. The data suggest the presence of several species that have not been documented for Brazil.

Organic mulching alters the composition, but not the diversity, of rhizosphere bacterial and fungal communities

Organic mulching is an effective forest management technique that provides carbon and nutrient sources to soil ecosystems, thereby improving the soil environment and promoting plant growth. Although the importance of rhizosphere microbiomes in plant and soil ecosystem functions has been widely recognised, the effect of organic mulching on rhizosphere microorganisms and the underlying mechanisms are unclear. We performed a field experiment in a 15-year-old Ligustrum lucidum forest of urban green space. The diversity and composition of the rhizosphere bacterial and fungal communities following organic mulching were assessed by combining 16S ribosomal RNA and internal transcribed spacer amplicon sequencing. The correlations between microbial diversity, composition, and fine-root traits, as well as rhizosphere soil properties, were also analysed. The results showed that organic mulching did not significantly affect the diversity of the rhizosphere bacterial or fungal communities on the whole, but it increased the bacterial diversity after 6 months, with a 20-cm-thick mulch layer showing a greater effect than 5- or 10-cm layers. Organic mulching significantly altered the rhizosphere bacterial and fungal community composition; after 6 months of mulching, the community compositions were significantly associated with fine-root traits (specific root length, nitrogen, and phosphorus concentration) and enzyme (urease and dehydrogenase) activity. Moreover, alterations in the bacterial and fungal communities occurred at the order level within each mulching stage. Bacterial diversity is affected by fungal diversity and rhizosphere soil properties (water content and organic carbon) in time-dependent manners. Hence, organic mulching appears to directly affect the fungal composition while indirectly affecting the bacterial composition via influencing rhizosphere soil properties (dissolved organic carbon and peroxidase activity). Our study suggests that organic mulching affects the rhizosphere bacterial and fungal community composition through different pathways; however, the underlying mechanisms, including the effects of time and soil layers, require further exploration combined with multi-index measurements and long-term dynamic monitoring.

Temporal differences in microbial composition of Époisses cheese rinds during ripening and storage

Époisses is a protected designation of origin smear-ripened cheese from the Burgundy region in France. It has an orange color and a strong flavor, both of which are generated by surface microorganisms. The objective of the present study was to investigate the microbial dynamics at the surface of Époisses cheese during ripening and postmanufacturing storage at low temperatures. Rind samples were analyzed by enumeration on agar plates and by 16S rRNA gene and internal transcribed spacer amplicon sequencing. During most of the ripening process, the counts of yeasts, which corresponded to the species Debaryomyces hansenii and Geotrichum candidum, were higher than those of the aerobic acid-sensitive bacteria. Debaryomyces hansenii reached a level of about 3 × 108 cfu/cm2, and its viability strongly decreased in the late stage of ripening and during storage at 4°C. Two of the inoculated bacterial species, Brevibacterium aurantiacum and Staphylococcus xylosus, did not establish themselves at the cheese surface. At the end of ripening, among the 18 most abundant bacterial species detected by amplicon sequencing, 14 were gram-negative, mainly from genera Psychrobacter, Vibrio, Halomonas, and Mesonia. It was hypothesized that the high moisture level of the Époisses rinds, due the humid atmosphere of the ripening rooms and to the frequent washings of the curds, favored growth of these gram-negative species. These species may be of interest for the development of efficient ripening cultures. In addition, because the orange color of Époisses cheeses could not be attributed to the growth of Brevibacterium, it would be interesting to investigate the type and origin of the pigments that confer color to this cheese.

Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce.

ABSTRACTThe health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species Picea abies (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus Cortinarius.IMPORTANCE A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. Typically, gene expression studies focus on the plant component or, in a limited number of studies, expression in one or more associated organisms. However, metatranscriptomic data are rarely used for taxonomic profiling, which is currently performed using amplicon approaches. We created an assembly-based, reproducible, and hardware-agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data. While we identified some limitations and caveats, we show that functional, taxonomic, and compositional insights can all be obtained from RNA-Seq data. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response, and effect between host plants and their associated microbial communities.

Fungal community succession and volatile compound dynamics in Harbin dry sausage during fermentation

This study investigated the fungal community succession and volatile compound dynamics of Harbin dry sausage during a twelve-day fermentation using high-throughput internal transcribed spacer amplicon sequencing and headspace solid-phase microextraction gas chromatography-mass spectrometry. Aspergillus pseudoglaucus was found to be the primary species in the sausages during fermentation, whereas Lasiodiplodia theobromae, Alternaria alternata, Aspergillus caesiellus, and Trichosporon asahii were also prevalent. Additionally, a total of 72 volatile compounds were identified in the dry sausages, of which 24 key compounds (odor activity value > 1) dominated flavor development, including 3 aldehydes, 1 ketone, 4 alcohols, 9 esters, 4 alkenes, and 3 other compounds. Furthermore, correlation analysis suggested that most of the core fungi were positively correlated with the key volatile compounds, particularly A. pseudoglaucus, Aspergillus gracilis, Trichosporon caseorum, Debaryomyces hansenii, and T. asahii. Our findings provide novel insights into the fungal ecology and flavor development of Harbin dry sausages.

The Structure of Rhizosphere Fungal Communities of Wild and Domesticated Rice: Changes in Diversity and Co-occurrence Patterns.

The rhizosphere fungal community affects the ability of crops to acquire nutrients and their susceptibility to pathogen invasion. However, the effects of rice domestication on the diversity and interactions of rhizosphere fungal community still remain largely unknown. Here, internal transcribed spacer amplicon sequencing was used to systematically analyze the structure of rhizosphere fungal communities of wild and domesticated rice. The results showed that domestication increased the alpha diversity indices of the rice rhizosphere fungal community. The changes of alpha diversity index may be associated with the enrichment of Acremonium, Lecythophora, and other specific rare taxa in the rhizosphere of domesticated rice. The co-occurrence network showed that the complexity of wild rice rhizosphere fungal community was higher than that of the domesticated rice rhizosphere fungal community. Arbuscular mycorrhizal fungi (AMF) and soilborne fungi were positively and negatively correlated with more fungi in the wild rice rhizosphere, respectively. For restructuring the rhizomicrobial community of domesticated crops, we hypothesize that microbes that hold positive connections with AMF and negative connections with soilborne fungi can be used as potential sources for bio-inoculation. Our findings provide a scientific basis for reshaping the structure of rhizomicrobial community and furthermore create potential for novel intelligent and sustainable agricultural solutions.

Sequential presence of heavy metal resistant fungal communities influenced by biochar amendment in the poultry manure composting process

In this study, we investigated the influence of coconut shell biochar (CSB) on heavy metal resistance fungi (HMRF) during poultry manure (PM) composting by 18 S rDNA Internal Transcribed Spacer Amplicon Sequencing analysis. Five different concentrations of CSB (2.5%, 5%, 7.5%, and 10% dry weights basis) were applied with a mixture of PM and wheat straw (5:1 ratio dry weight basis) and without CSB (CK) was used as control. The results showed that sequence number rose along with increasing CSB concentration but total relative abundance (RA) of HMRF decreased 56.33%, 74.65% in T4 and T5, respectively. However, greater RA of HMRF was found in T1 or without biochar applied treatment. The phylum of Basidiomycota was the dominant fungal community accounting for 61.14%, 6.16%, 32.18%, 74.65%, and 73.73% from T1 to T5 of the total fungi abundance, with wide presence of the Wallemiomycetes and Eurotiomycetes classes. The Wallemia and Aspergillus were the richest genus and species. Wallemia_sebi , Altemaria_alternata and Aspergillus_amoenus were detected having greater abundance among all treatments. Besides this, the network correlation pattern confirmed that the relative greater percentage of correlation among dominant HMRF community with bio-available HM and other physicochemical factors increased with the addition of biochar. There was reasonable infer that the biochar amendment in composting could constitute favorable habitat for an active fungal population. • Biochar has positive effect to reduce heavy metal resistant fungal diversity by 56.33%–74.65%. • The superior fungi were Basidiomycota with relative abundance of 6.16–73.73%. • The 7.5% biochar can be efficiently altered the heavy metals resistant fungal diversity. • Coconut shell biochar remarkably effective to improve the poultry manure composting. • Biochar amendment in composting provided favorable habitat for an active fungal population.

Amplicon Sequencing Reveals Extensive Coinfections of Foliar Pathogens in Soybean.

Soybean (Glycine max) is one of the most economically important crops grown in North America and in other regions worldwide. However, the plant is susceptible to a variety of foliar pathogenic microorganisms, some of which are a significant threat to production. Several molecular and serological approaches are currently available to diagnose plant pathogens, but all have limitations including their capability to accurately detect coinfections of individual plants. We therefore used 16S and internal transcribed spacer amplicon sequencing to identify the suite of bacterial and fungal organisms infecting 96 soybean leaf samples collected throughout southern Manitoba, Canada, at two growth stages (V2/3 and R6). We were able to confirm the presence of pathogens previously known to our sampling regions, such as Septoria glycines, Alternaria alternata, and Pseudomonas spp. Importantly, we found that most of plants were infected by more than one putative pathogen, with 64% of V2/3 and 26% of R6 plants infected by three or more pathogens. Amplicon sequencing also indicated the presence of residual pathogens that infect crops other than soybean, as well as nonfoliar pathogens and nonpathogenic microorganisms. We discuss some of the benefits and drawbacks of using amplicon sequencing to detect foliar pathogens of soybean.