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Life
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Advances in Fungal -Omics
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Advances in Fungal -Omics

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: closed (16 October 2020) | Viewed by 33054

Special Issue Editors

Dr. Laura Selbmann

E-Mail Website
Guest Editor
Department of Ecological and BiologicalSciences (DEB), University of Tuscia, Largo dell'Università snc, 01100 Viterbo, Italy
Interests: fungi from extreme environments
Special Issues, Collections and Topics in MDPI journals
Dr. Claudia Coleine

E-Mail Website
Co-Guest Editor
Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy
Interests: extreme environments; extremophiles; fungi; drylands; climate change; astrobiology; metagenomics

Special Issue Information

Dear Colleagues,

Fungi are stunning organisms displaying astonishing ecological, biological, and morphological plasticity. They can shift across different growth forms according to the variation of physic or chemical conditions, adapting and exploiting virtually all environments, including extremes normally precluded among most life-forms. They also may adopt different lifestyles, acting as saprotrophs, symbionts, or parasites, and shift from one kind of interaction to another depending on the timeline of their life-cycle. Due to their tremendous metabolic possibilities, they act as major decomposers, recycling organic matter and favoring nutrient uptake, being crucial for the balance and functioning of any kind of ecosystem. Due the potential of -omics sciences (genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics) applied to fungi, information is rapidly growing and is providing unprecedented insight into the complexity of fungal biological processes from species to community levels. This includes physiology, stress tolerance, adaptation, evolution, communications, pathogen–host interactions, biodiversity, and community composition/functioning and interactions.

This Special Issue will merge the most recent studies dealing with all aspects of fungal -omics, spanning biodiversity, community composition and interactions, fungal evolution, pathogenicity, ecology, biotechnology, and beyond. We also welcome papers focussed on the developments of new bioinformatic tools for high-throughput -omic data analysis. All this will give a complete and up to date overview of the most recent advances in this promising and rapidly growing area of research.

Dr. Laura Selbmann
Dr. Claudia Coleine
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • NGS
  • bioinformatics
  • fungal genomics
  • fungal metabolomics
  • fungal phylogenomics
  • fungal proteomics
  • fungal transcriptomics
  • metagenomics

Published Papers (7 papers)

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Research

Jump to: Review

13 pages, 1704 KiB  
Article
Metabolomics of Dry Versus Reanimated Antarctic Lichen-Dominated Endolithic Communities
by Giuseppina Fanelli, Claudia Coleine, Federica Gevi, Silvano Onofri, Laura Selbmann and Anna Maria Timperio
Life 2021, 11(2), 96; https://doi.org/10.3390/life11020096 - 27 Jan 2021
Cited by 4 | Viewed by 2335
Abstract
Cryptoendolithic communities are almost the sole life form in the ice-free areas of the Antarctic desert, encompassing among the most extreme-tolerant organisms known on Earth that still assure ecosystems functioning, regulating nutrient and biogeochemical cycles under conditions accounted as incompatible with active life. [...] Read more.
Cryptoendolithic communities are almost the sole life form in the ice-free areas of the Antarctic desert, encompassing among the most extreme-tolerant organisms known on Earth that still assure ecosystems functioning, regulating nutrient and biogeochemical cycles under conditions accounted as incompatible with active life. If high-throughput sequencing based studies are unravelling prokaryotic and eukaryotic diversity, they are not yet characterized in terms of stress adaptations and responses, despite their paramount ecological importance. In this study, we compared the responses of Antarctic endolithic communities, with special focus on fungi, both under dry conditions (i.e., when dormant), and after reanimation by wetting, light, and optimal temperature (15 °C). We found that several metabolites were differently expressed in reanimated opposite sun exposed communities, suggesting a critical role in their success. In particular, the saccharopine pathway was up-regulated in the north surface, while the spermine/spermidine pathway was significantly down-regulated in the shaded exposed communities. The carnitine-dependent pathway is up-regulated in south-exposed reanimated samples, indicating the preferential involvement of the B-oxidation for the functioning of TCA cycle. The role of these metabolites in the performance of the communities is discussed herein. Full article
(This article belongs to the Special Issue Advances in Fungal -Omics)
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13 pages, 3042 KiB  
Communication
Shed Light in the DaRk LineagES of the Fungal Tree of Life—STRES
by Laura Selbmann, Zsigmond Benkő, Claudia Coleine, Sybren de Hoog, Claudio Donati, Irina Druzhinina, Tamás Emri, Cassie L. Ettinger, Amy S. Gladfelter, Anna A. Gorbushina, Igor V. Grigoriev, Martin Grube, Nina Gunde-Cimerman, Zsolt Ákos Karányi, Beatrix Kocsis, Tania Kubressoian, Ida Miklós, Márton Miskei, Lucia Muggia, Trent Northen, Monika Novak-Babič, Christa Pennacchio, Walter P. Pfliegler, Istvàn Pòcsi, Valeria Prigione, Meritxell Riquelme, Nicola Segata, Julia Schumacher, Ekaterina Shelest, Katja Sterflinger, Donatella Tesei, Jana M. U’Ren, Giovanna C. Varese, Xabier Vázquez-Campos, Vania A. Vicente, Emanuel M. Souza, Polona Zalar, Allison K. Walker and Jason E. Stajichadd Show full author list remove Hide full author list
Life 2020, 10(12), 362; https://doi.org/10.3390/life10120362 - 19 Dec 2020
Cited by 16 | Viewed by 5621
Abstract
The polyphyletic group of black fungi within the Ascomycota (Arthoniomycetes, Dothideomycetes, and Eurotiomycetes) is ubiquitous in natural and anthropogenic habitats. Partly because of their dark, melanin-based pigmentation, black fungi are resistant to stresses including UV- and ionizing-radiation, heat and desiccation, toxic metals, and [...] Read more.
The polyphyletic group of black fungi within the Ascomycota (Arthoniomycetes, Dothideomycetes, and Eurotiomycetes) is ubiquitous in natural and anthropogenic habitats. Partly because of their dark, melanin-based pigmentation, black fungi are resistant to stresses including UV- and ionizing-radiation, heat and desiccation, toxic metals, and organic pollutants. Consequently, they are amongst the most stunning extremophiles and poly-extreme-tolerant organisms on Earth. Even though ca. 60 black fungal genomes have been sequenced to date, [mostly in the family Herpotrichiellaceae (Eurotiomycetes)], the class Dothideomycetes that hosts the largest majority of extremophiles has only been sparsely sampled. By sequencing up to 92 species that will become reference genomes, the “Shed light in The daRk lineagES of the fungal tree of life” (STRES) project will cover a broad collection of black fungal diversity spread throughout the Fungal Tree of Life. Interestingly, the STRES project will focus on mostly unsampled genera that display different ecologies and life-styles (e.g., ant- and lichen-associated fungi, rock-inhabiting fungi, etc.). With a resequencing strategy of 10- to 15-fold depth coverage of up to ~550 strains, numerous new reference genomes will be established. To identify metabolites and functional processes, these new genomic resources will be enriched with metabolomics analyses coupled with transcriptomics experiments on selected species under various stress conditions (salinity, dryness, UV radiation, oligotrophy). The data acquired will serve as a reference and foundation for establishing an encyclopedic database for fungal metagenomics as well as the biology, evolution, and ecology of the fungi in extreme environments. Full article
(This article belongs to the Special Issue Advances in Fungal -Omics)
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12 pages, 834 KiB  
Article
Whole Genome Sequencing and Comparative Genome Analysis of the Halotolerant Deep Sea Black Yeast Hortaea werneckii
by Orazio Romeo, Alessia Marchetta, Domenico Giosa, Letterio Giuffrè, Clara Urzì and Filomena De Leo
Life 2020, 10(10), 229; https://doi.org/10.3390/life10100229 - 02 Oct 2020
Cited by 9 | Viewed by 3378
Abstract
Hortaea werneckii, an extreme halotolerant black yeast in the order of Capnodiales, was recently isolated from different stations and depths in the Mediterranean Sea, where it was shown to be the dominant fungal species. In order to explore the genome characteristics of [...] Read more.
Hortaea werneckii, an extreme halotolerant black yeast in the order of Capnodiales, was recently isolated from different stations and depths in the Mediterranean Sea, where it was shown to be the dominant fungal species. In order to explore the genome characteristics of these Mediterranean isolates, we carried out a de-novo sequencing of the genome of one strain isolated at a depth of 3400 m (MC873) and a re-sequencing of one strain taken from a depth of 2500 m (MC848), whose genome was previously sequenced but was highly fragmented. A comparative phylogenomic analysis with other published H. werneckii genomes was also carried out to investigate the evolution of the strains from the deep sea in this environment. A high level of genome completeness was obtained for both genomes, for which genome duplication and an extensive level of heterozygosity (~4.6%) were observed, supporting the recent hypothesis that a genome duplication caused by intraspecific hybridization occurred in most H. werneckii strains. Phylogenetic analyses showed environmental and/or geographical specificity, suggesting a possible evolutionary adaptation of marine H. werneckii strains to the deep sea environment. We release high-quality genome assemblies from marine H. werneckii strains, which provides additional data for further genomics analysis, including niche adaptation, fitness and evolution studies. Full article
(This article belongs to the Special Issue Advances in Fungal -Omics)
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Review

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77 pages, 3594 KiB  
Review
An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota
by Lucia Muggia, Claudio G. Ametrano, Katja Sterflinger and Donatella Tesei
Life 2020, 10(12), 356; https://doi.org/10.3390/life10120356 - 17 Dec 2020
Cited by 13 | Viewed by 6869
Abstract
Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary [...] Read more.
Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi. Full article
(This article belongs to the Special Issue Advances in Fungal -Omics)
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16 pages, 565 KiB  
Review
Cross-Disciplinary Genomics Approaches to Studying Emerging Fungal Infections
by Pria N. Ghosh, Lola M. Brookes, Hannah M. Edwards, Matthew C. Fisher, Phillip Jervis, Dana Kappel, Thomas R. Sewell, Jennifer M.G. Shelton, Emily Skelly and Johanna L. Rhodes
Life 2020, 10(12), 315; https://doi.org/10.3390/life10120315 - 28 Nov 2020
Cited by 3 | Viewed by 3383
Abstract
Emerging fungal pathogens pose a serious, global and growing threat to food supply systems, wild ecosystems, and human health. However, historic chronic underinvestment in their research has resulted in a limited understanding of their epidemiology relative to bacterial and viral pathogens. Therefore, the [...] Read more.
Emerging fungal pathogens pose a serious, global and growing threat to food supply systems, wild ecosystems, and human health. However, historic chronic underinvestment in their research has resulted in a limited understanding of their epidemiology relative to bacterial and viral pathogens. Therefore, the untargeted nature of genomics and, more widely, -omics approaches is particularly attractive in addressing the threats posed by and illuminating the biology of these pathogens. Typically, research into plant, human and wildlife mycoses have been largely separated, with limited dialogue between disciplines. However, many serious mycoses facing the world today have common traits irrespective of host species, such as plastic genomes; wide host ranges; large population sizes and an ability to persist outside the host. These commonalities mean that -omics approaches that have been productively applied in one sphere and may also provide important insights in others, where these approaches may have historically been underutilised. In this review, we consider the advances made with genomics approaches in the fields of plant pathology, human medicine and wildlife health and the progress made in linking genomes to other -omics datatypes and sets; we identify the current barriers to linking -omics approaches and how these are being underutilised in each field; and we consider how and which -omics methodologies it is most crucial to build capacity for in the near future. Full article
(This article belongs to the Special Issue Advances in Fungal -Omics)
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18 pages, 1149 KiB  
Review
The Mycobiota of the Deep Sea: What Omics Can Offer
by Lluvia Vargas-Gastélum and Meritxell Riquelme
Life 2020, 10(11), 292; https://doi.org/10.3390/life10110292 - 19 Nov 2020
Cited by 22 | Viewed by 5839
Abstract
The deep sea (>1000 m below sea level) represents one of the most extreme environments of the ocean. Despite exhibiting harsh abiotic conditions such as low temperatures, high hydrostatic pressure, high salinity concentrations, a low input of organic matter, and absence of light, [...] Read more.
The deep sea (>1000 m below sea level) represents one of the most extreme environments of the ocean. Despite exhibiting harsh abiotic conditions such as low temperatures, high hydrostatic pressure, high salinity concentrations, a low input of organic matter, and absence of light, the deep sea encompasses a great fungal diversity. For decades, most knowledge on the fungal diversity of the deep sea was obtained through culture-dependent techniques. More recently, with the latest advances of high-throughput next generation sequencing platforms, there has been a rapid increment in the number of studies using culture-independent techniques. This review brings into the spotlight the progress of the techniques used to assess the diversity and ecological role of the deep-sea mycobiota and provides an overview on how the omics technologies have contributed to gaining knowledge about fungi and their activity in poorly explored marine environments. Finally, current challenges and suggested coordinated efforts to overcome them are discussed. Full article
(This article belongs to the Special Issue Advances in Fungal -Omics)
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22 pages, 1250 KiB  
Review
Mass Spectrometry: A Rosetta Stone to Learn How Fungi Interact and Talk
by Erika Calla-Quispe, Hammerly Lino Fuentes-Rivera, Pablo Ramírez, Carlos Martel and Alfredo J. Ibañez
Life 2020, 10(6), 89; https://doi.org/10.3390/life10060089 - 20 Jun 2020
Cited by 9 | Viewed by 4752
Abstract
Fungi are a highly diverse group of heterotrophic organisms that play an important role in diverse ecological interactions, many of which are chemically mediated. Fungi have a very versatile metabolism, which allows them to synthesize a large number of still little-known chemical compounds, [...] Read more.
Fungi are a highly diverse group of heterotrophic organisms that play an important role in diverse ecological interactions, many of which are chemically mediated. Fungi have a very versatile metabolism, which allows them to synthesize a large number of still little-known chemical compounds, such as soluble compounds that are secreted into the medium and volatile compounds that are chemical mediators over short and long distances. Mass spectrometry (MS) is currently playing a dominant role in mycological studies, mainly due to its inherent sensitivity and rapid identification capabilities of different metabolites. Furthermore, MS has also been used as a reliable and accurate tool for fungi identification (i.e., biotyping). Here, we introduce the readers about fungal specialized metabolites, their role in ecological interactions and provide an overview on the MS-based techniques used in fungal studies. We particularly present the importance of sampling techniques, strategies to reduce false-positive identification and new MS-based analytical strategies that can be used in mycological studies, further expanding the use of MS in broader applications. Therefore, we foresee a bright future for mass spectrometry-based research in the field of mycology. Full article
(This article belongs to the Special Issue Advances in Fungal -Omics)
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