scholarly journals Giant Starship elements mobilize accessory genes in fungal genomes

2021 ◽  
Author(s):  
Emile Gluck-Thaler ◽  
Timothy Ralston ◽  
Zachary Konkel ◽  
Cristhian Grabowski Ocampos ◽  
Veena Devi Ganeshan ◽  
...  
Keyword(s):  
Genome Structure ◽  
5S Rdna ◽  
Macrophomina Phaseolina ◽  
Fungal Species ◽  
Mobile Elements ◽  
Integrative And Conjugative Elements ◽  
Standing Variation ◽  
Accessory Genes ◽  
Fungal Genomes ◽  
The Impact

Accessory genes are variably present among members of a species and are a reservoir of adaptive functions. In bacteria, differences in gene distributions among individuals largely result from mobile elements that acquire and disperse accessory genes as cargo. In contrast, the impact of cargo-carrying elements on eukaryotic evolution remains largely unknown. Here, we show that variation in genome content within multiple fungal species is facilitated by Starships, a novel group of massive mobile elements that are 110 kb long on average, share conserved components, and carry diverse arrays of accessory genes. We identified hundreds of Starship-like regions across every major class of filamentous Ascomycetes, including 28 distinct Starships that range from 27-393 kb and last shared a common ancestor ca. 400 mya. Using new long-read assemblies of the plant pathogen Macrophomina phaseolina, we characterize 4 additional Starships whose past and ongoing activities contribute to standing variation in genome structure and content. One of these elements, Voyager, inserts into 5S rDNA and contains a candidate virulence factor whose increasing copy number has contrasting associations with pathogenic and saprophytic growth, suggesting Voyager activity underlies an ecological trade-off. We propose that Starships are eukaryotic analogs of bacterial integrative and conjugative elements based on parallels between their conserved components and may therefore represent the first known agents of active gene transfer in eukaryotes. Our results suggest that Starships have shaped the content and structure of fungal genomes for millions of years and reveal a new concerted route for evolution throughout an entire eukaryotic phylum.

scholarly journals Core genes can have higher recombination rates than accessory genes within global microbial populations

2021 ◽  
Author(s):  
Asher Preska Steinberg ◽  
Mingzhi Lin ◽  
Edo Kussell
Keyword(s):  
Homologous Recombination ◽  
Antigenic Variation ◽  
Genome Structure ◽  
Microbial Evolution ◽  
Gene Pools ◽  
Recombination Rates ◽  
Accessory Genes ◽  
Efficiency Of Selection ◽  
The Impact ◽  
Core Genes

Recombination is essential to microbial evolution, and is involved in the spread of antibiotic resistance, antigenic variation, and adaptation to the host niche. Yet quantifying the impact of homologous recombination on different gene classes, which is critical to understanding how selection acts on variation to shape species diversity and genome structure, remains challenging. This is largely due to the dynamic nature of bacterial genomes, whose high intraspecies genome content diversity and complex phylogenetic relationships present difficulties for inferring rates of recombination, particularly for rare genes. In this work, we apply a computationally efficient, non-phylogenetic approach to measure homologous recombination rates in the core and accessory genome (genes present in all strains and only a subset of strains, respectively) using >100,000 whole genome sequences from 12 microbial species. Our analysis suggests that even well-resolved sequence clusters sampled from global populations interact with overlapping gene pools, which has implications for the role of population structure in genome evolution. We show that in a majority of species, core genes have shorter coalescence times and higher recombination rates than accessory genes, and that gene frequency is often positively correlated with increased recombination. Our results provide a new line of population genomic evidence supporting the hypothesis that core genes are under strong, purifying selection, and indicate that homologous recombination may play a key role in increasing the efficiency of selection in those parts of the genome most conserved within each species.

scholarly journals Metabolomic Analysis of The Chemical Diversity of South Africa Leaf Litter Fungal Species Using an Epigenetic Culture-Based Approach

Molecules ◽  
2021 ◽  
Vol 26 (14) ◽  
pp. 4262
Author(s):  
Rachel Serrano ◽  
Víctor González-Menéndez ◽  
Germán Martínez ◽  
Clara Toro ◽  
Jesús Martín ◽  
...  
Keyword(s):  
South Africa ◽  
Genome Mining ◽  
Fungal Species ◽  
Chemical Diversity ◽  
Fermentation Conditions ◽  
Metabolite Profiles ◽  
Different Populations ◽  
Fungal Genomes ◽  
Microbial Natural Products ◽  
Fermentation Media

Microbial natural products are an invaluable resource for the biotechnological industry. Genome mining studies have highlighted the huge biosynthetic potential of fungi, which is underexploited by standard fermentation conditions. Epigenetic effectors and/or cultivation-based approaches have successfully been applied to activate cryptic biosynthetic pathways in order to produce the chemical diversity suggested in available fungal genomes. The addition of Suberoylanilide Hydroxamic Acid to fermentation processes was evaluated to assess its effect on the metabolomic diversity of a taxonomically diverse fungal population. Here, metabolomic methodologies were implemented to identify changes in secondary metabolite profiles to determine the best fermentation conditions. The results confirmed previously described effects of the epigenetic modifier on the metabolism of a population of 232 wide diverse South Africa fungal strains cultured in different fermentation media where the induction of differential metabolites was observed. Furthermore, one solid-state fermentation (BRFT medium), two classic successful liquid fermentation media (LSFM and YES) and two new liquid media formulations (MCKX and SMK-II) were compared to identify the most productive conditions for the different populations of taxonomic subgroups.

scholarly journals New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences

2021 ◽  
Vol 7 (3) ◽  
pp. 207
Author(s):  
Lene Lange ◽  
Kristian Barrett ◽  
Anne S. Meyer
Keyword(s):  
Fungal Species ◽  
Fungal Genome ◽  
Sequencing Data ◽  
Carbohydrate Active Enzymes ◽  
New Approach ◽  
Fungal Enzyme ◽  
Biomass Processing ◽  
Fungal Genomes ◽  
Robust Prediction ◽  
Fungal Kingdom

Fungal genome sequencing data represent an enormous pool of information for enzyme discovery. Here, we report a new approach to identify and quantitatively compare biomass-degrading capacity and diversity of fungal genomes via integrated function-family annotation of carbohydrate-active enzymes (CAZymes) encoded by the genomes. Based on analyses of 1932 fungal genomes the most potent hotspots of fungal biomass processing CAZymes are identified and ranked according to substrate degradation capacity. The analysis is achieved by a new bioinformatics approach, Conserved Unique Peptide Patterns (CUPP), providing for CAZyme-family annotation and robust prediction of molecular function followed by conversion of the CUPP output to lists of integrated “Function;Family” (e.g., EC 3.2.1.4;GH5) enzyme observations. An EC-function found in several protein families counts as different observations. Summing up such observations allows for ranking of all analyzed genome sequenced fungal species according to richness in CAZyme function diversity and degrading capacity. Identifying fungal CAZyme hotspots provides for identification of fungal species richest in cellulolytic, xylanolytic, pectinolytic, and lignin modifying enzymes. The fungal enzyme hotspots are found in fungi having very different lifestyle, ecology, physiology and substrate/host affinity. Surprisingly, most CAZyme hotspots are found in enzymatically understudied and unexploited species. In contrast, the most well-known fungal enzyme producers, from where many industrially exploited enzymes are derived, are ranking unexpectedly low. The results contribute to elucidating the evolution of fungal substrate-digestive CAZyme profiles, ecophysiology, and habitat adaptations, and expand the knowledge base for novel and improved biomass resource utilization.

scholarly journals Mycoflora associated with two species of Liliaceae in Bangladesh

2013 ◽  
Vol 22 (1) ◽  
pp. 39-46
Author(s):  
Shamim Shamsi ◽  
Najmun Naher
Keyword(s):  
Fusarium Solani ◽  
Alternaria Alternata ◽  
New Record ◽  
Macrophomina Phaseolina ◽  
Fungal Species ◽  
Colletotrichum Orbiculare ◽  
Lasiodiplodia Theobromae ◽  
Colletotrichum Capsici ◽  
Colletotrichum Dematium

A total of nine fungi were isolated from two ornamental angiosperms, namely Hemerocallis fulva L. and Pancratium verecundum Ant. belong to Liliaceae. Three species of fungi were found to be associated with the leaf of Hemerocallis fulva. The fungi were Colletotrichum capsici, (Syd.) Bull. & Bisby, Colletotrichum dematium (Pers. Ex Fr.) and Glomerella montana (Sacc.)v Arx & E. Muller. Six species of fungi, namely Alternaria alternata (Fries) Keissler, Colletotrichum orbiculare (Berk & Mont.) Arex., Curvularia clavata Jain, Fusarium solani (Mort.) Sacc., Lasiodiplodia theobromae (Pat.) Griffon and Maubol and Macrophomina phaseolina (Tassi) Goid were found to be associated with P. verecundum. Among the fungal species Glomerella montana is new record for Bangladesh. Dhaka Univ. J. Biol. Sci. 22(1): 39-46, 2013 (January)

scholarly journals Impact of selected antagonistic fungi on Fusarium species – toxigenic cereal pathogens

2013 ◽  
Vol 43 (1) ◽  
pp. 29-40 ◽  
Author(s):  
Delfina Popiel ◽  
Hanna Kwaśny ◽  
Jerzy Chełkowski ◽  
Łukasz Stępień ◽  
Magdalena Laskowska
Keyword(s):  
Fusarium Species ◽  
Fungal Species ◽  
Antagonistic Activity ◽  
Antagonistic Effect ◽  
Fusarium Avenaceum ◽  
Dual Culture ◽  
Ear Blight ◽  
Yield And Quality ◽  
Significant Yield ◽  
The Impact

<em>Fusarium</em>-ear blight is a destructive disease in various cereal-growing regions and leads to significant yield and quality losses for farmers and to contamination of cereal grains with mycotoxins, mainly deoxynivalenol and derivatives, zearalenone and moniliformin. <em>Fusarium</em> pathogens grow well and produce significant inoculum on crop resiudues. Reduction of mycotoxins production and pathogen sporulation may be influenced by saprophytic fungi, exhibiting antagonistic effect. Dual culture bioassays were used to examine the impact of 92 isolates (belonging to 29 fungal species) against three toxigenic species, i.e. <em>Fusarium avenaceum</em> (Corda) Saccardo, <em>F. culmorum</em> (W.G.Smith) Saccardo and <em>F. graminearum</em> Schwabe. Both <em>F.culmorum</em> and <em>F. graminearum</em> isolates produce trichothecene mycotoxins and mycohormone zearalenone and are considered to be the most important cereal pathogens worldwide. Infection with those pathogens leads to accumulation of mycotoxins: deoxynivalenol (DON) and zearalenone (ZEA) in grains. <em>Fusarium avenaceum</em> isolates are producers of moniliformin (MON) and enniatins. Isolates of <em>Trichoderma</em> sp. were found to be the most effective ones to control the growth of examined <em>Fusarium</em> species. The response of <em>Fusarium</em> isolates to antagonistic activity of <em>Trichoderma</em> isolates varied and also the isolates of <em>Trichoderma</em> differed in their antagonistic activity against <em>Fusarium</em> isolates. The production of MON by two isolates of F. avenaceum in dual culture on rice was reduced by 95% to 100% by <em>T. atroviride</em> isolate AN 35. The same antagonist reduced the amount of moniliformin from 100 μg/g to 6.5 μg/g when inoculated to rice culture contaminated with MON, which suggests the possible decomposition of this mycotoxin.

scholarly journals Dry root rot of chickpea: A disease favored by drought

Plant Disease ◽  
2021 ◽  
Author(s):  
Avanish Rai ◽  
Vadivelmurugan Irulappan ◽  
Muthappa Senthil-Kumar
Keyword(s):  
Root Rot ◽  
Management Practices ◽  
Lateral Roots ◽  
Research Priorities ◽  
Macrophomina Phaseolina ◽  
Emerging Diseases ◽  
Research Progress ◽  
Initial Symptoms ◽  
New Research ◽  
The Impact

Chickpea is an essential crop for protein nutrition and is grown around the world in rain-fed conditions. However, chickpea cultivation is under threat due to emerging diseases favored by drought stress. Dry root rot (DRR), an economically devastating disease, is an example. Chickpea-specific strains of a necrotic fungal phytopathogen, Macrophomina phaseolina, cause DRR. Microsclerotia of this fungus, which are capable of withstanding harsh environmental conditions, serve as primary inoculum. Initial symptoms are scattered necrotic spots in roots, progressing to rotting and withering lateral roots, accompanied by prematurely dried, straw-colored foliage. The recent rise in global temperature and worsening of drought spells have aggravated DRR outbreaks in chickpea. To date, DRR epidemiology has not been clarified in detail. Also, the literature lacks clarity on M. phaseolina taxonomy, morphology, disease progression, and diagnosis. In this article, research progress on patterns of DRR occurrence in the field and belowground and above-ground symptoms are clarified. In addition, the current understanding of taxonomy and management practices is elaborated. We also summarize knowledge of the impact of drought and high temperature on DRR severity. Further, we provide future perspectives on the importance of host resistance, QTL identification, genotype screening for the identification of resistant genotypes. The article proposes new research priorities and a corresponding plan for the mitigation of DRR.

Fungal richness does not buffer the effects of streams salinization on litter decomposition

2021 ◽  
Vol 57 ◽  
pp. 5
Author(s):  
Janine Pereira da Silva ◽  
Aingeru Martínez ◽  
Ana Lúcia Gonçalves ◽  
Felix Bärlocher ◽  
Cristina Canhoto
Keyword(s):  
Mass Loss ◽  
Litter Decomposition ◽  
Fungal Biomass ◽  
Fungal Species ◽  
Aquatic Hyphomycetes ◽  
Negative Effects ◽  
Stream Functioning ◽  
Induced Changes ◽  
Sporulation Rate ◽  
The Impact

Freshwater salinization is a world-wide phenomenon threatening stream communities and ecosystem functioning. In these systems, litter decomposition is a main ecosystem-level process where fungi (aquatic hyphomycetes) play a central role linking basal resource and higher levels of food-web. The current study evaluated the impact of aquatic hyphomycete richness on leaf litter decomposition when subjected to salinization. In a microcosm study, we analysed leaf mass loss, fungal biomass, respiration and sporulation rate by fungal assemblages at three levels of species richness (1, 4, 8 species) and three levels of salinity (0, 8, 16 g NaCl L‑1). Mass loss and sporulation rate were depressed at 8 and 16 g NaCl L‑1, while fungal biomass and respiration were only negatively affected at 16 g L‑1. A richness effect was only observed on sporulation rates, with the maximum values found in assemblages of 4 species. In all cases, the negative effects of high levels of salinization on the four tested variables superimposed the potential buffer capacity of fungal richness. The study suggests functional redundancy among the fungal species even at elevated salt stress conditions which may guarantee stream functioning at extreme levels of salinity. Nonetheless, it also points to the possible importance of salt induced changes on fungal diversity and identity in salinized streams able to induce bottom-up effects in the food webs.

scholarly journals Systemic anti-commensal response to fungi analyzed by flow cytometry is related to gut mycobiome ecology

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Alicia Moreno-Sabater ◽  
Gaelle Autaa ◽  
Delphine Sterlin ◽  
Amenie Jerbi ◽  
Remy Villette ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Alpha Diversity ◽  
Fungal Species ◽  
Individual Variability ◽  
Humoral Immune ◽  
Healthy Donors ◽  
Significant Difference ◽  
Genus Richness ◽  
Humoral Responses ◽  
The Impact

Abstract Background Interest for the study of gut mycobiota in relation with human health and immune homeostasis has increased in the last years. From this perspective, new tools to study the immune/fungal interface are warranted. Systemic humoral immune responses could reflect the dynamic relationships between gut mycobiota and immunity. Using a novel flow cytometry technology (Fungi-Flow) to determine immunoglobulin (Ig) responses to fungi, we studied the relationships between gut mycobiota and systemic humoral anti-commensal immunity. Results The Fungi-Flow method allows a sensitive and specific measurement of systemic IgG responses against 17 commensal and environmental fungi from the two main divisions; Ascomycota and Basidiomycota. IgG responses exhibited a high inter-individual variability. Anti-commensal IgG responses were contrasted with the relative abundance, alpha-diversity, and intra-genus richness of fungal species in gut mycobiota of twenty healthy donors. Categorization of gut mycobiota composition revealed two differentiated fungal ecosystems. Significant difference of anti-Saccharomyces systemic IgG responses were observed in healthy donors stratified according to the fungal ecosystem colonizing their gut. A positive and significant correlation was observed between the variety of IgG responses against fungal commensals and intestinal alpha-diversity. At the level of intra-genus species richness, intense IgG responses were associated with a low intra-genus richness for known pathobionts, but not commensals. Conclusions Fungi-Flow allows an easy and reliable measure of personalized humoral responses against commensal fungi. Combining sequencing technology with our novel Fungi-Flow immunological method, we propose that there are at least two defined ecosystems in the human gut mycobiome associated with systemic humoral responses. Fungi-Flow opens new opportunities to improve our knowledge about the impact of mycobiota in humoral anti-commensal immunity and homeostasis.

scholarly journals 1737. Impact of Therapeutic Drug Monitoring (TDM) of Azole Prophylaxis in Lung Transplant Recipients on the Development of Positive Fungal Events

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S636-S636
Author(s):  
Anooj Shah ◽  
Carly D’Agostino ◽  
Kathleen Cunningham ◽  
Clare Kane ◽  
Michael G Ison ◽  
...  
Keyword(s):  
Therapeutic Drug Monitoring ◽  
Drug Monitoring ◽  
Lung Transplant ◽  
Study Groups ◽  
Fungal Species ◽  
Therapeutic Drug ◽  
Transplant Recipients ◽  
Lung Transplant Recipients ◽  
Index Value ◽  
The Impact

Abstract Background The utility and clinical impact of therapeutic drug monitoring (TDM) of prophylactic azole antifungals in lung transplant recipients is not well described. The objective of this study was to investigate the impact of TDM of azole prophylaxis in lung transplant recipients on the development of positive fungal events. Methods A retrospective analysis was performed on 47 lung transplant recipients between 2013 and 2018 at Northwestern Memorial Hospital. A positive fungal event was defined as fungal species on BAL culture and/or positive BAL Aspergillus galactomannan (GM) with an index value ≥1.0. Study groups were defined based on attainment of therapeutic trough levels after initiation of oral therapy (therapeutic if posaconazole level ≥0.7 μg/mL or voriconazole ≥1–5.5 μg/mL, subtherapeutic if ≥2 consecutive levels of posaconazole <0.7 μg/mL or voriconazole <1 μg/mL after initial dose increase). Results There were no differences in baseline characteristics (Figure 1). There were a total of 11 fungal events with 3 (12.0%) occurring in the therapeutic cohort and 8 (36.4%) in those subtherapeutic (P = 0.08). In the 5 patients with a positive GM, the mean index was 2.02 ± 0.95. 7/30 (23.3%) of patients on posaconazole had a fungal event, with 2/7 (28.6%) requiring treatment at the time of event. For patients on voriconazole, 4/17 (23.5%) had a fungal event, with 1/4 (25.0%) requiring treatment. Mean time to fungal event was 164.5 ± 8.9 days vs. 135.9 ± 13.7 days in the therapeutic and subtherapeutic group, respectively (P = 0.05). All patients on posaconazole suspension who experienced a fungal event were subtherapeutic (3/3, 100%) compared with the majority of patients on posaconazole delayed release (DR) tablets who achieved therapeutic levels (17/22, 77.3%). Mean posaconazole trough level observed in the patients receiving DR tablet was 2.15 ± 0.95 μg/mL. Conclusion There was an association between two consecutive subtherapeutic azole prophylaxis levels and positive fungal events indicating a role for TDM in lung transplant recipients. Time to fungal event post-transplant was shorter in subtherapeutic patients. As anticipated, the use of posaconazole suspension resulted in subtherapeutic levels. This study presents an opportunity for further research of the impact of TDM on clinical outcomes to optimize patient care. Disclosures All authors: No reported disclosures.

scholarly journals Early Stage Root-Associated Fungi Show a High Temporal Turnover, but Are Independent of Beech Progeny

2020 ◽  
Vol 8 (2) ◽  
pp. 210 ◽  
Author(s):  
Kezia Goldmann ◽  
Silke Ammerschubert ◽  
Rodica Pena ◽  
Andrea Polle ◽  
Bin-Wei Wu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Early Stage ◽  
European Beech ◽  
Fungal Species ◽  
Fungal Communities ◽  
Transplant Experiment ◽  
Fungal Community Structure ◽  
Temporal Turnover ◽  
One Year ◽  
The Impact

The relationship between trees and root-associated fungal communities is complex. By specific root deposits and other signal cues, different tree species are able to attract divergent sets of fungal species. Plant intraspecific differences can lead to variable fungal patterns in the root’s proximity. Therefore, within the Beech Transplant Experiment, we analyzed the impact of three different European beech ecotypes on the fungal communities in roots and the surrounding rhizosphere soil at two time points. Beech nuts were collected in three German sites in 2011. After one year, seedlings of the different progenies were out-planted on one site and eventually re-sampled in 2014 and 2017. We applied high-throughput sequencing of the fungal ITS2 to determine the correlation between tree progeny, a possible home-field advantage, plant development and root-associated fungal guilds under field conditions. Our result showed no effect of beech progeny on either fungal OTU richness or fungal community structure. However, over time the fungal OTU richness in roots increased and the fungal communities changed significantly, also in rhizosphere. In both plant compartments, the fungal communities displayed a high temporal turnover, indicating a permanent development and functional adaption of the root mycobiome of young beeches.

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