Estimating the Quality of Eukaryotic Genomes Recovered from Metagenomic Analysis
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Calcium Affects Polyphosphate and Lipid Accumulation in Mucoromycota Fungi
Journal of Fungi Article Calcium Affects Polyphosphate and Lipid Accumulation in Mucoromycota Fungi Simona Dzurendova 1,*, Boris Zimmermann 1 , Achim Kohler 1, Kasper Reitzel 2 , Ulla Gro Nielsen 3 , Benjamin Xavier Dupuy--Galet 1 , Shaun Leivers 4 , Svein Jarle Horn 4 and Volha Shapaval 1 1 Faculty of Science and Technology, Norwegian University of Life Sciences, Drøbakveien 31, 1433 Ås, Norway; [email protected] (B.Z.); [email protected] (A.K.); [email protected] (B.X.D.–G.); [email protected] (V.S.) 2 Department of Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; [email protected] 3 Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; [email protected] 4 Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Christian Magnus Falsens vei 1, 1433 Ås, Norway; [email protected] (S.L.); [email protected] (S.J.H.) * Correspondence: [email protected] or [email protected] Abstract: Calcium controls important processes in fungal metabolism, such as hyphae growth, cell wall synthesis, and stress tolerance. Recently, it was reported that calcium affects polyphosphate and lipid accumulation in fungi. The purpose of this study was to assess the effect of calcium on the accumulation of lipids and polyphosphate for six oleaginous Mucoromycota fungi grown under different phosphorus/pH conditions. A Duetz microtiter plate system (Duetz MTPS) was used for the cultivation. The compositional profile of the microbial biomass was recorded using Fourier-transform infrared spectroscopy, the high throughput screening extension (FTIR-HTS). -
Characterization of Two Undescribed Mucoralean Species with Specific
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 26 March 2018 doi:10.20944/preprints201803.0204.v1 1 Article 2 Characterization of Two Undescribed Mucoralean 3 Species with Specific Habitats in Korea 4 Seo Hee Lee, Thuong T. T. Nguyen and Hyang Burm Lee* 5 Division of Food Technology, Biotechnology and Agrochemistry, College of Agriculture and Life Sciences, 6 Chonnam National University, Gwangju 61186, Korea; [email protected] (S.H.L.); 7 [email protected] (T.T.T.N.) 8 * Correspondence: [email protected]; Tel.: +82-(0)62-530-2136 9 10 Abstract: The order Mucorales, the largest in number of species within the Mucoromycotina, 11 comprises typically fast-growing saprotrophic fungi. During a study of the fungal diversity of 12 undiscovered taxa in Korea, two mucoralean strains, CNUFC-GWD3-9 and CNUFC-EGF1-4, were 13 isolated from specific habitats including freshwater and fecal samples, respectively, in Korea. The 14 strains were analyzed both for morphology and phylogeny based on the internal transcribed 15 spacer (ITS) and large subunit (LSU) of 28S ribosomal DNA regions. On the basis of their 16 morphological characteristics and sequence analyses, isolates CNUFC-GWD3-9 and CNUFC- 17 EGF1-4 were confirmed to be Gilbertella persicaria and Pilobolus crystallinus, respectively.To the 18 best of our knowledge, there are no published literature records of these two genera in Korea. 19 Keywords: Gilbertella persicaria; Pilobolus crystallinus; mucoralean fungi; phylogeny; morphology; 20 undiscovered taxa 21 22 1. Introduction 23 Previously, taxa of the former phylum Zygomycota were distributed among the phylum 24 Glomeromycota and four subphyla incertae sedis, including Mucoromycotina, Kickxellomycotina, 25 Zoopagomycotina, and Entomophthoromycotina [1]. -
Fungal Evolution: Major Ecological Adaptations and Evolutionary Transitions
Biol. Rev. (2019), pp. 000–000. 1 doi: 10.1111/brv.12510 Fungal evolution: major ecological adaptations and evolutionary transitions Miguel A. Naranjo-Ortiz1 and Toni Gabaldon´ 1,2,3∗ 1Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain 2 Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain 3ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain ABSTRACT Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts). -
Study of Soil Fungi in the Territory of Kapan City and Its Surrounding
PROCEEDINGS OF THE YEREVAN STATE UNIVERSITY C h e m i s t r y a n d B i o l o g y 2018, 52(3), p. 193–197 Bi o l o g y STUDY OF SOIL FUNGI IN THE TERRITORY OF KAPAN CITY AND ITS SURROUNDING R. E. MATEVOSYAN , S. G. NANAGULYAN **, I. M. ELOYAN, T. A. YESAYAN Chair of Botany and Mycology YSU, Armenia During the studies of micromycetes-decomposers of Kapan City and its surrounding, 32 species of fungi were detected, 8 of which belong to Zygomycetes and 24 belong to Ascomycetes classes. In the studied soils there were widespread species of genus Penicillium (9), Aspergillus (8) and representatives of mucoral fungi (8 species). Keywords: soil fungi, micromycetes, dilution method, contaminated territory. Introduction. Fungi are very important organisms in terrestrial ecosystem function. Micromycetes-decomposers, which are found in the soil, in a large number, and diverse species are active components of biogenocenosis. The negative impact on the environment of Armenia is extended by air emission of a number of industrial enterprises, the technological processes of which where developed out of the view of their conservation. As a result, various toxic chemicals settle on the soil. The mycelium of soil fungi absorbs nutrients from the roots it has colonized, surface organic matter or from the soil. From this point of view, it is of great interest to conduct mycological analysis of soils on the territories or surroundings of industrial factories with the aim of studying the effect of industrial wastes and emissions on the changes of the soil mycobiota. -
Genome-Resolved Metagenomics of Eukaryotic Populations During Early Colonization of Premature Infants and in Hospital Rooms Matthew R
Olm et al. Microbiome (2019) 7:26 https://doi.org/10.1186/s40168-019-0638-1 RESEARCH Open Access Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms Matthew R. Olm1†, Patrick T. West1†, Brandon Brooks1,8, Brian A. Firek2, Robyn Baker3, Michael J. Morowitz2 and Jillian F. Banfield4,5,6,7* Abstract Background: Fungal infections are a significant cause of mortality and morbidity in hospitalized preterm infants, yet little is known about eukaryotic colonization of infants and of the neonatal intensive care unit as a possible source of colonizing strains. This is partly because microbiome studies often utilize bacterial 16S rRNA marker gene sequencing, a technique that is blind to eukaryotic organisms. Knowledge gaps exist regarding the phylogeny and microdiversity of eukaryotes that colonize hospitalized infants, as well as potential reservoirs of eukaryotes in the hospital room built environment. Results: Genome-resolved analysis of 1174 time-series fecal metagenomes from 161 premature infants revealed fungal colonization of 10 infants. Relative abundance levels reached as high as 97% and were significantly higher in the first weeks of life (p = 0.004). When fungal colonization occurred, multiple species were present more often than expected by random chance (p = 0.008). Twenty-four metagenomic samples were analyzed from hospital rooms of six different infants. Compared to floor and surface samples, hospital sinks hosted diverse and highly variable communities containing genomically novel species, including from Diptera (fly) and Rhabditida (worm) for which genomes were assembled. With the exception of Diptera and two other organisms, zygosity of the newly assembled diploid eukaryote genomes was low. -
Gut Mycobiota Alterations in Patients with COVID-19 and H1N1 Infections
ARTICLE https://doi.org/10.1038/s42003-021-02036-x OPEN Gut mycobiota alterations in patients with COVID- 19 and H1N1 infections and their associations with clinical features Longxian Lv1,3, Silan Gu1,3, Huiyong Jiang1,3, Ren Yan1,3, Yanfei Chen1,3, Yunbo Chen1, Rui Luo1, Chenjie Huang1, ✉ Haifeng Lu1, Beiwen Zheng1, Hua Zhang1, Jiafeng Xia1, Lingling Tang2, Guoping Sheng2 & Lanjuan Li 1 The relationship between gut microbes and COVID-19 or H1N1 infections is not fully understood. Here, we compared the gut mycobiota of 67 COVID-19 patients, 35 H1N1- infected patients and 48 healthy controls (HCs) using internal transcribed spacer (ITS) 3- 1234567890():,; ITS4 sequencing and analysed their associations with clinical features and the bacterial microbiota. Compared to HCs, the fungal burden was higher. Fungal mycobiota dysbiosis in both COVID-19 and H1N1-infected patients was mainly characterized by the depletion of fungi such as Aspergillus and Penicillium, but several fungi, including Candida glabrata, were enriched in H1N1-infected patients. The gut mycobiota profiles in COVID-19 patients with mild and severe symptoms were similar. Hospitalization had no apparent additional effects. In COVID-19 patients, Mucoromycota was positively correlated with Fusicatenibacter, Aspergillus niger was positively correlated with diarrhoea, and Penicillium citrinum was negatively corre- lated with C-reactive protein (CRP). In H1N1-infected patients, Aspergillus penicilloides was positively correlated with Lachnospiraceae members, Aspergillus was positively correlated with CRP, and Mucoromycota was negatively correlated with procalcitonin. Therefore, gut mycobiota dysbiosis occurs in both COVID-19 patients and H1N1-infected patients and does not improve until the patients are discharged and no longer require medical attention. -
Microbial Community Structure in Rice, Crops, and Pastures Rotation Systems with Different Intensification Levels in the Temperate Region of Uruguay
Supplementary Material Microbial community structure in rice, crops, and pastures rotation systems with different intensification levels in the temperate region of Uruguay Sebastián Martínez Table S1. Relative abundance of the 20 most abundant bacterial taxa of classified sequences. Relative Taxa Phylum abundance 4,90 _Bacillus Firmicutes 3,21 _Bacillus aryabhattai Firmicutes 2,76 _uncultured Prosthecobacter sp. Verrucomicrobia 2,75 _uncultured Conexibacteraceae bacterium Actinobacteria 2,64 _uncultured Conexibacter sp. Actinobacteria 2,14 _Nocardioides sp. Actinobacteria 2,13 _Acidothermus Actinobacteria 1,50 _Bradyrhizobium Proteobacteria 1,23 _Bacillus Firmicutes 1,10 _Pseudolabrys_uncultured bacterium Proteobacteria 1,03 _Bacillus Firmicutes 1,02 _Nocardioidaceae Actinobacteria 0,99 _Candidatus Solibacter Acidobacteria 0,97 _uncultured Sphingomonadaceae bacterium Proteobacteria 0,94 _Streptomyces Actinobacteria 0,91 _Terrabacter_uncultured bacterium Actinobacteria 0,81 _Mycobacterium Actinobacteria 0,81 _uncultured Rubrobacteria Actinobacteria 0,77 _Xanthobacteraceae_uncultured forest soil bacterium Proteobacteria 0,76 _Streptomyces Actinobacteria Table S2. Relative abundance of the 20 most abundant fungal taxa of classified sequences. Relative Taxa Orden abundance. 20,99 _Fusarium oxysporum Ascomycota 11,97 _Aspergillaceae Ascomycota 11,14 _Chaetomium globosum Ascomycota 10,03 _Fungi 5,40 _Cucurbitariaceae; uncultured fungus Ascomycota 5,29 _Talaromyces purpureogenus Ascomycota 3,87 _Neophaeosphaeria; uncultured fungus Ascomycota -
Fungal Pathogenesis in Humans the Growing Threat
Fungal Pathogenesis in Humans The Growing Threat Edited by Fernando Leal Printed Edition of the Special Issue Published in Genes www.mdpi.com/journal/genes Fungal Pathogenesis in Humans Fungal Pathogenesis in Humans The Growing Threat Special Issue Editor Fernando Leal MDPI • Basel • Beijing • Wuhan • Barcelona • Belgrade Special Issue Editor Fernando Leal Instituto de Biolog´ıa Funcional y Genomica/Universidad´ de Salamanca Spain Editorial Office MDPI St. Alban-Anlage 66 4052 Basel, Switzerland This is a reprint of articles from the Special Issue published online in the open access journal Genes (ISSN 2073-4425) from 2018 to 2019 (available at: https://www.mdpi.com/journal/genes/special issues/Fungal Pathogenesis Humans Growing Threat). For citation purposes, cite each article independently as indicated on the article page online and as indicated below: LastName, A.A.; LastName, B.B.; LastName, C.C. Article Title. Journal Name Year, Article Number, Page Range. ISBN 978-3-03897-900-5 (Pbk) ISBN 978-3-03897-901-2 (PDF) Cover image courtesy of Fernando Leal. c 2019 by the authors. Articles in this book are Open Access and distributed under the Creative Commons Attribution (CC BY) license, which allows users to download, copy and build upon published articles, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. The book as a whole is distributed by MDPI under the terms and conditions of the Creative Commons license CC BY-NC-ND. Contents About the Special Issue Editor ...................................... vii Fernando Leal Special Issue: Fungal Pathogenesis in Humans: The Growing Threat Reprinted from: Genes 2019, 10, 136, doi:10.3390/genes10020136 .................. -
Genomic and Fossil Windows Into the Secret Lives of the Most Ancient Fungi
REVIEWS Genomic and fossil windows into the secret lives of the most ancient fungi Mary L. Berbee 1 ✉ , Christine Strullu- Derrien 2,3, Pierre- Marc Delaux 4, Paul K. Strother5, Paul Kenrick 2, Marc- André Selosse 3,6 and John W. Taylor 7 Abstract | Fungi have crucial roles in modern ecosystems as decomposers and pathogens, and they engage in various mutualistic associations with other organisms, especially plants. They have a lengthy geological history, and there is an emerging understanding of their impact on the evolution of Earth systems on a large scale. In this Review, we focus on the roles of fungi in the establishment and early evolution of land and freshwater ecosystems. Today, questions of evolution over deep time are informed by discoveries of new fossils and evolutionary analysis of new genomes. Inferences can be drawn from evolutionary analysis by comparing the genes and genomes of fungi with the biochemistry and development of their plant and algal hosts. We then contrast this emerging picture against evidence from the fossil record to develop a new, integrated perspective on the origin and early evolution of fungi. Fungi are crucial for thriving land plant communities as enzymes surely kept pace3,16,17. Comparative analy- mycorrhizal symbionts1,2 and decomposers3. For perhaps sis of genomes of land plants18 and their closest algal 500 million years4,5, fungi have been supplying land plants relatives19,20 reveals the evolutionary origins of constitu- with phosphorus and other minerals, thereby speeding ents of plant immune systems that are fundamental both up photosynthesis and contributing to the drawdown for defence against fungal parasites and for the evolution 6–8 mycorrhizae21 1Department of Botany, of atmospheric carbon dioxide . -
A Taxonomic Revision of the Genus
A peer-reviewed open-access journal MycoKeys 66: 55–81 (2020) Revision of the genus Conidiobolus 55 doi: 10.3897/mycokeys.66.46575 RESEARCH ARTICLE MycoKeys http://mycokeys.pensoft.net Launched to accelerate biodiversity research A taxonomic revision of the genus Conidiobolus (Ancylistaceae, Entomophthorales): four clades including three new genera Yong Nie1,2, De-Shui Yu1, Cheng-Fang Wang1, Xiao-Yong Liu3, Bo Huang1 1 Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei 230036, China 2 School of Civil Engineering and Architecture, Anhui University of Technology, Ma’anshan 243002, China 3 State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China Corresponding author: Xiao-Yong Liu ([email protected]), Bo Huang ([email protected]) Academic editor: M. Stadler | Received 14 September 2019 | Accepted 13 March 2020 | Published 30 March 2020 Citation: Nie Y, Yu D-S, Wang C-F, Liu X-Y, Huang B (2020) A taxonomic revision of the genus Conidiobolus (Ancylistaceae, Entomophthorales): four clades including three new genera. MycoKeys 66: 55–81. https://doi. org/10.3897/mycokeys.66.46575 Abstract The genus Conidiobolus is an important group in entomophthoroid fungi and is considered to be poly- phyletic in recent molecular phylogenies. To re-evaluate and delimit this genus, multi-locus phylogenetic analyses were performed using the large and small subunits of nuclear ribosomal DNA (nucLSU and nuc- SSU), the small subunit of the mitochondrial ribosomal DNA (mtSSU) and the translation elongation factor 1-alpha (EF-1α). The results indicated that the Conidiobolus is not monophyletic, being grouped into a paraphyletic grade with four clades. -
Discovery of New Mycoviral Genomes Within Publicly Available Fungal Transcriptomic Datasets
bioRxiv preprint doi: https://doi.org/10.1101/510404; this version posted January 3, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Discovery of new mycoviral genomes within publicly available fungal transcriptomic datasets 1 1 1,2 1 Kerrigan B. Gilbert , Emily E. Holcomb , Robyn L. Allscheid , James C. Carrington * 1 Donald Danforth Plant Science Center, Saint Louis, Missouri, USA 2 Current address: National Corn Growers Association, Chesterfield, Missouri, USA * Address correspondence to James C. Carrington E-mail: [email protected] Short title: Virus discovery from RNA-seq data bioRxiv preprint doi: https://doi.org/10.1101/510404; this version posted January 3, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract The distribution and diversity of RNA viruses in fungi is incompletely understood due to the often cryptic nature of mycoviral infections and the focused study of primarily pathogenic and/or economically important fungi. As most viruses that are known to infect fungi possess either single-stranded or double-stranded RNA genomes, transcriptomic data provides the opportunity to query for viruses in diverse fungal samples without any a priori knowledge of virus infection. Here we describe a systematic survey of all transcriptomic datasets from fungi belonging to the subphylum Pezizomycotina. -
Architecture [Version 1; Peer Review: 2 Approved] Shelby J
F1000Research 2020, 9(Faculty Rev):776 Last updated: 27 JUL 2020 REVIEW Advances in understanding the evolution of fungal genome architecture [version 1; peer review: 2 approved] Shelby J. Priest, Vikas Yadav, Joseph Heitman Department of Molecular Genetics and Microbiology, Duke University Medical Centre, Durham, NC, USA First published: 27 Jul 2020, 9(Faculty Rev):776 Open Peer Review v1 https://doi.org/10.12688/f1000research.25424.1 Latest published: 27 Jul 2020, 9(Faculty Rev):776 https://doi.org/10.12688/f1000research.25424.1 Reviewer Status Abstract Invited Reviewers Diversity within the fungal kingdom is evident from the wide range of 1 2 morphologies fungi display as well as the various ecological roles and industrial purposes they serve. Technological advances, particularly in version 1 long-read sequencing, coupled with the increasing efficiency and 27 Jul 2020 decreasing costs across sequencing platforms have enabled robust characterization of fungal genomes. These sequencing efforts continue to reveal the rampant diversity in fungi at the genome level. Here, we discuss studies that have furthered our understanding of fungal genetic diversity Faculty Reviews are review articles written by the and genomic evolution. These studies revealed the presence of both prestigious Members of Faculty Opinions. The small-scale and large-scale genomic changes. In fungi, research has articles are commissioned and peer reviewed before recently focused on many small-scale changes, such as how hypermutation publication to ensure that the final, published version and allelic transmission impact genome evolution as well as how and why a few specific genomic regions are more susceptible to rapid evolution than is comprehensive and accessible.