1
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Pawlowska TE. Symbioses between fungi and bacteria: from mechanisms to impacts on biodiversity. Curr Opin Microbiol 2024; 80:102496. [PMID: 38875733 DOI: 10.1016/j.mib.2024.102496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/16/2024]
Abstract
Symbiotic interactions between fungi and bacteria range from positive to negative. They are ubiquitous in free-living as well as host-associated microbial communities worldwide. Yet, the impact of fungal-bacterial symbioses on the organization and dynamics of microbial communities is uncertain. There are two reasons for this uncertainty: (1) knowledge gaps in the understanding of the genetic mechanisms underpinning fungal-bacterial symbioses and (2) prevailing interpretations of ecological theory that favor antagonistic interactions as drivers stabilizing biological communities despite the existence of models emphasizing contributions of positive interactions. This review synthesizes information on fungal-bacterial symbioses common in the free-living microbial communities of the soil as well as in host-associated polymicrobial biofilms. The interdomain partnerships are considered in the context of the relevant community ecology models, which are discussed critically.
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Affiliation(s)
- Teresa E Pawlowska
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
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2
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Tanwar M, Singh A, Singh TP, Sharma S, Sharma P. Comprehensive Review on the Virulence Factors and Therapeutic Strategies with the Aid of Artificial Intelligence against Mucormycosis. ACS Infect Dis 2024; 10:1431-1457. [PMID: 38682683 DOI: 10.1021/acsinfecdis.4c00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Mucormycosis, a rare but deadly fungal infection, was an epidemic during the COVID-19 pandemic. The rise in cases (COVID-19-associated mucormycosis, CAM) is attributed to excessive steroid and antibiotic use, poor hospital hygiene, and crowded settings. Major contributing factors include diabetes and weakened immune systems. The main manifesting forms of CAM─cutaneous, pulmonary, and the deadliest, rhinocerebral─and disseminated infections elevated mortality rates to 85%. Recent focus lies on small-molecule inhibitors due to their advantages over standard treatments like surgery and liposomal amphotericin B (which carry several long-term adverse effects), offering potential central nervous system penetration, diverse targets, and simpler dosing owing to their small size, rendering the ability to traverse the blood-brain barrier via passive diffusion facilitated by the phospholipid membrane. Adaptation and versatility in mucormycosis are facilitated by a multitude of virulence factors, enabling the pathogen to dynamically respond to various environmental stressors. A comprehensive understanding of these virulence mechanisms is imperative for devising effective therapeutic interventions against this highly opportunistic pathogen that thrives in immunocompromised individuals through its angio-invasive nature. Hence, this Review delineates the principal virulence factors of mucormycosis, the mechanisms it employs to persist in challenging host environments, and the current progress in developing small-molecule inhibitors against them.
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Affiliation(s)
- Mansi Tanwar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Anamika Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Tej Pal Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Sujata Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110029, India
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3
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Lax C, Nicolás FE, Navarro E, Garre V. Molecular mechanisms that govern infection and antifungal resistance in Mucorales. Microbiol Mol Biol Rev 2024; 88:e0018822. [PMID: 38445820 PMCID: PMC10966947 DOI: 10.1128/mmbr.00188-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Abstract
SUMMARYThe World Health Organization has established a fungal priority pathogens list that includes species critical or highly important to human health. Among them is the order Mucorales, a fungal group comprising at least 39 species responsible for the life-threatening infection known as mucormycosis. Despite the continuous rise in cases and the poor prognosis due to innate resistance to most antifungal drugs used in the clinic, Mucorales has received limited attention, partly because of the difficulties in performing genetic manipulations. The COVID-19 pandemic has further escalated cases, with some patients experiencing the COVID-19-associated mucormycosis, highlighting the urgent need to increase knowledge about these fungi. This review addresses significant challenges in treating the disease, including delayed and poor diagnosis, the lack of accurate global incidence estimation, and the limited treatment options. Furthermore, it focuses on the most recent discoveries regarding the mechanisms and genes involved in the development of the disease, antifungal resistance, and the host defense response. Substantial advancements have been made in identifying key fungal genes responsible for invasion and tissue damage, host receptors exploited by the fungus to invade tissues, and mechanisms of antifungal resistance. This knowledge is expected to pave the way for the development of new antifungals to combat mucormycosis. In addition, we anticipate significant progress in characterizing Mucorales biology, particularly the mechanisms involved in pathogenesis and antifungal resistance, with the possibilities offered by CRISPR-Cas9 technology for genetic manipulation of the previously intractable Mucorales species.
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Affiliation(s)
- Carlos Lax
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Francisco E. Nicolás
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Eusebio Navarro
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Victoriano Garre
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
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4
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Roberts K, Osme A, De Salvo C, Zoli E, Herrada J, McCormick TS, Ghannoum M, Cominelli F, Di Martino L. Candida tropicalis Affects Candida albicans Virulence by Limiting Its Capacity to Adhere to the Host Intestinal Surface, Leading to Decreased Susceptibility to Colitis in Mice. J Fungi (Basel) 2024; 10:245. [PMID: 38667916 PMCID: PMC11051055 DOI: 10.3390/jof10040245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/15/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Candida (C.) infections represent a serious health risk for people affected by inflammatory bowel disease. An important fungal virulence factor is the capacity of the fungus to form biofilms on the colonized surface of the host. This research study aimed to determine the effect of a C. tropicalis and C. albicans co-infection on dextran sodium sulfate (DSS)-induced colitis in mice. The colitis severity was evaluated using histology and a colonoscopy. The mice were mono-inoculated with C. albicans or C. tropicalis or co-challenged with both species. The mice were administered 3% DSS to induce acute colitis. The biofilm activity was assessed using (2-methoxy-4-nitro-5-sulfophenyl)-5-[(phenylamino)carbonyl] 2H-tetrazoliumhydroxide (XTT) and dry-weight assays. The abundance of C. albicans in the colon tissues was assessed by immunohistochemistry. The co-challenged mice showed a decreased colitis severity compared to the mono-inoculated mice. The dry-weight assay demonstrated a marked decrease in C. albicans biofilm production in a C. albicans culture incubated with C. tropicalis supernatant. Immunohistochemical staining showed that C. albicans was more abundant in the mucosa of C. albicans mono-inoculated mice compared to the co-inoculated group. These data indicate an antagonistic microbial interaction between the two Candida species, where C. tropicalis may produce molecules capable of limiting the ability of C. albicans to adhere to the host intestinal surface, leading to a reduction in biofilm formation.
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Affiliation(s)
- Kyle Roberts
- Center for Medical Mycology and Integrated Microbiome Core, Department of Dermatology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH 44106, USA; (K.R.); (J.H.); (T.S.M.); (M.G.)
| | - Abdullah Osme
- Department of Anatomic Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Carlo De Salvo
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (C.D.S.); (F.C.)
| | - Eleonora Zoli
- Case Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA;
- Department of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Janet Herrada
- Center for Medical Mycology and Integrated Microbiome Core, Department of Dermatology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH 44106, USA; (K.R.); (J.H.); (T.S.M.); (M.G.)
| | - Thomas S. McCormick
- Center for Medical Mycology and Integrated Microbiome Core, Department of Dermatology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH 44106, USA; (K.R.); (J.H.); (T.S.M.); (M.G.)
| | - Mahmoud Ghannoum
- Center for Medical Mycology and Integrated Microbiome Core, Department of Dermatology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH 44106, USA; (K.R.); (J.H.); (T.S.M.); (M.G.)
| | - Fabio Cominelli
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (C.D.S.); (F.C.)
- Case Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA;
- Department of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Luca Di Martino
- Case Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA;
- Department of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
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5
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Liu XL, Zhao H, Wang YX, Liu XY, Jiang Y, Tao MF, Liu XY. Detecting and characterizing new endofungal bacteria in new hosts: Pandoraea sputorum and Mycetohabitans endofungorum in Rhizopus arrhizus. Front Microbiol 2024; 15:1346252. [PMID: 38486702 PMCID: PMC10939042 DOI: 10.3389/fmicb.2024.1346252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024] Open
Abstract
The fungus Rhizopus arrhizus (=R. oryzae) is commonly saprotrophic, exhibiting a nature of decomposing organic matter. Additionally, it serves as a crucial starter in food fermentation and can act as a pathogen causing mucormycosis in humans and animals. In this study, two distinct endofungal bacteria (EFBs), associated with individual strains of R. arrhizus, were identified using live/dead staining, fluorescence in situ hybridization, transmission electron microscopy, and 16S rDNA sequencing. The roles of these bacteria were elucidated through antibiotic treatment, pure cultivation, and comparative genomics. The bacterial endosymbionts, Pandoraea sputorum EFB03792 and Mycetohabitans endofungorum EFB03829, were purified from the host fungal strains R. arrhizus XY03792 and XY03829, respectively. Notably, this study marks the first report of Pandoraea as an EFB genus. Compared to its free-living counterparts, P. sputorum EFB03792 exhibited 28 specific virulence factor-related genes, six specific CE10 family genes, and 74 genes associated with type III secretion system (T3SS), emphasizing its pivotal role in invasion and colonization. Furthermore, this study introduces R. arrhizus as a new host for EFB M. endofungorum, with EFB contributing to host sporulation. Despite a visibly reduced genome, M. endofungorum EFB03829 displayed a substantial number of virulence factor-related genes, CE10 family genes, T3SS genes, mobile elements, and significant gene rearrangement. While EFBs have been previously identified in R. arrhizus, their toxin-producing potential in food fermentation has not been explored until this study. The discovery of these two new EFBs highlights their potential for toxin production within R. arrhizus, laying the groundwork for identifying suitable R. arrhizus strains for fermentation processes.
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Affiliation(s)
- Xiao-Ling Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Heng Zhao
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yi-Xin Wang
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xin-Ye Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Yang Jiang
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Meng-Fei Tao
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xiao-Yong Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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6
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Scheler J, Binder U. Alternative in-vivo models of mucormycosis. Front Cell Infect Microbiol 2024; 14:1343834. [PMID: 38362495 PMCID: PMC10867140 DOI: 10.3389/fcimb.2024.1343834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/16/2024] [Indexed: 02/17/2024] Open
Abstract
Mucormycosis is still regarded a rare fungal infection, but the high incidences of COVID-associated cases in India and other countries have shown its potential threat to large patient cohorts. In addition, infections by these fast-growing fungi are often fatal and cause disfigurement, badly affecting patients' lives. In advancing our understanding of pathogenicity factors involved in this disease, to enhance the diagnostic toolset and to evaluate novel treatment regimes, animal models are indispensable. As ethical and practical considerations typically favor the use of alternative model systems, this review provides an overview of alternative animal models employed for mucormycosis and discusses advantages and limitations of the respective model.
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Affiliation(s)
| | - Ulrike Binder
- Department of Hygiene, Microbiology and Public Health, Division of Hygiene and Medical Microbiology, Medical University Innsbruck, Innsbruck, Tirol, Austria
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7
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Amses K, Desiró A, Bryson A, Grigoriev I, Mondo S, Lipzen A, LaButti K, Riley R, Singan V, Salazar-Hamm P, King J, Ballou E, Pawlowska T, Adeleke R, Bonito G, Uehling J. Convergent reductive evolution and host adaptation in Mycoavidus bacterial endosymbionts of Mortierellaceae fungi. Fungal Genet Biol 2023; 169:103838. [PMID: 37716699 DOI: 10.1016/j.fgb.2023.103838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/18/2023]
Abstract
Intimate associations between fungi and intracellular bacterial endosymbionts are becoming increasingly well understood. Phylogenetic analyses demonstrate that bacterial endosymbionts of Mucoromycota fungi are related either to free-living Burkholderia or Mollicutes species. The so-called Burkholderia-related endosymbionts or BRE comprise Mycoavidus, Mycetohabitans and Candidatus Glomeribacter gigasporarum. These endosymbionts are marked by genome contraction thought to be associated with intracellular selection. However, the conclusions drawn thus far are based on a very small subset of endosymbiont genomes, and the mechanisms leading to genome streamlining are not well understood. The purpose of this study was to better understand how intracellular existence shapes Mycoavidus and BRE functionally at the genome level. To this end we generated and analyzed 14 novel draft genomes for Mycoavidus living within the hyphae of Mortierellomycotina fungi. We found that our novel Mycoavidus genomes were significantly reduced compared to free-living Burkholderiales relatives. Using a genome-scale phylogenetic approach including the novel and available existing genomes of Mycoavidus, we show that the genus is an assemblage composed of two independently derived lineages including three well supported clades of Mycoavidus. Using a comparative genomic approach, we shed light on the functional implications of genome reduction, documenting shared and unique gene loss patterns between the three Mycoavidus clades. We found that many endosymbiont isolates demonstrate patterns of vertical transmission and host-specificity, but others are present in phylogenetically disparate hosts. We discuss how reductive evolution and host specificity reflect convergent adaptation to the intrahyphal selective landscape, and commonalities of eukaryotic endosymbiont genome evolution.
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Affiliation(s)
- Kevin Amses
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97333, USA
| | - Alessandro Desiró
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing MI 48824, USA
| | - Abigail Bryson
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing MI 48824, USA
| | - Igor Grigoriev
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Stephen Mondo
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Anna Lipzen
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kurt LaButti
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert Riley
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Vasanth Singan
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Paris Salazar-Hamm
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97333, USA
| | - Jason King
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Elizabeth Ballou
- School of Biosciences, University of Sheffield, Western Bank S10 2TN, UK
| | - Teresa Pawlowska
- MRC Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD, UK
| | - Rasheed Adeleke
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853-5904, USA; Unit for Environmental Sciences and Management, North-West University, Potchefstroom, Private bag X6001, 2520, South Africa
| | - Gregory Bonito
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing MI 48824, USA
| | - Jessie Uehling
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97333, USA.
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8
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Takashima Y, Yamamoto K, Degawa Y, Guo Y, Nishizawa T, Ohta H, Narisawa K. Detection and isolation of a new member of Burkholderiaceae-related endofungal bacteria from Saksenaea boninensis sp. nov., a new thermotolerant fungus in Mucorales. IMA Fungus 2023; 14:24. [PMID: 37996922 PMCID: PMC10666400 DOI: 10.1186/s43008-023-00129-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 11/05/2023] [Indexed: 11/25/2023] Open
Abstract
Thermotolerance in Mucorales (Mucoromycotina) is one of the factors to be opportunistic pathogens, causing mucormycosis. Among thermotolerant mucoralean fungi, Burkholderiaceae-related endobacteria (BRE) are rarely found and the known range of hosts is limited to Rhizopus spp. The phylogenetic divergence of BRE has recently expanded in other fungal groups such as Mortierellaceae spp. (Mortierellomycotina); however, it remains unexplored in Mucorales. Here, we found a thermotolerant mucoralean fungus obtained from a litter sample collected from Haha-jima Island in the Ogasawara (Bonin) Islands, Japan. The fungus was morphologically, phylogenetically, and physiologically characterized and proposed as a new species, Saksenaea boninensis sp. nov. Besides the fungal taxonomy, we also found the presence of BRE in isolates of this species by diagnostic PCR amplification of the 16S rRNA gene from mycelia, fluorescence microscopic observations, and isolation of the bacterium in pure culture. Phylogenetic analysis of the 16S rRNA gene of BRE revealed that it is distinct from all known BRE. The discovery of a culturable BRE lineage in the genus Saksenaea will add new insight into the evolutional origin of mucoralean fungus-BRE associations and emphasize the need to pay more attention to endofungal bacteria potentially associated with isolates of thermotolerant mucoralean fungi causing mucormycosis.
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Affiliation(s)
- Yusuke Takashima
- Genetic Resources Center, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
- Mountain Science Center, Sugadaira Research Station, University of Tsukuba, Sugadaira-kogen 1278-294, Nagano, 386-2204, Japan.
- Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami-machi, Ibaraki, 300-0393, Japan.
| | - Kohei Yamamoto
- Tochigi Prefectural Museum, 2-2 Mutsumi-cho, Utsunomiya, Tochigi, 320-0865, Japan
| | - Yousuke Degawa
- Mountain Science Center, Sugadaira Research Station, University of Tsukuba, Sugadaira-kogen 1278-294, Nagano, 386-2204, Japan
| | - Yong Guo
- Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami-machi, Ibaraki, 300-0393, Japan
- Institute for Plant Protection, National Agriculture and Food Research Organization, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Tomoyasu Nishizawa
- Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami-machi, Ibaraki, 300-0393, Japan
| | - Hiroyuki Ohta
- Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki, 310-8512, Japan
| | - Kazuhiko Narisawa
- Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami-machi, Ibaraki, 300-0393, Japan
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9
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Ingersoll JG. Thermophilic Fungi as the Microbial Agents of Choice for the Industrial Co-Fermentation of Wood Wastes and Nitrogen-Rich Organic Wastes to Bio-Methane. Microorganisms 2023; 11:2600. [PMID: 37894258 PMCID: PMC10609292 DOI: 10.3390/microorganisms11102600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
The novel industrial approach of co-fermenting wood wastes with agricultural wastes that are rich in nitrogen such as animal manures to produce bio-methane (renewable natural gas) fuel via thermophilic anaerobic digestion mimics an analogous process occurring in lower termites, but it relies instead on thermophilic fungi along with other thermophilic microorganisms comprising suitable bacteria and archaea. Wood microbial hydrolysis under thermophilic temperatures (range of 55 °C to 70 °C) and aerobic or micro-aerobic conditions constitutes the first step of the two-step (hydrolysis and fermentation) dry thermophilic anaerobic digestion industrial process, designated as "W2M3+2", that relies on thermophilic fungi species, most of which grow naturally in wood piles. Eleven thermophilic fungi have been identified as likely agents of the industrial process, and their known growth habitats and conditions have been reviewed. Future research is proposed such that the optimal growth temperature of these thermophilic fungi could be increased to the higher thermophilic range approaching 70 °C, and a tolerance to partial anaerobic conditions can be obtained by modifying the fungal microbiome via a symbiotic existence with bacteria and/or viruses.
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Affiliation(s)
- John G Ingersoll
- ECOCORP INC., 1211 South Eads Street, Suite 803, Arlington, VA 22202, USA
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10
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Alonso MF, Bain JM, Erwig LP, Brown AJP, Gow NAR. Fungal spore swelling and germination are restricted by the macrophage phagolysosome. Fungal Biol 2023; 127:1291-1297. [PMID: 37821151 PMCID: PMC10849972 DOI: 10.1016/j.funbio.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/05/2023] [Accepted: 08/08/2023] [Indexed: 10/13/2023]
Abstract
Many species of medically important fungi are prolific in the formation of asexual spores. Spores undergo a process of active swelling and cell wall remodelling before a germ tube is formed and filamentous growth ensues. Highly elongated germ tubes are known to be difficult to phagocytose and pose particular challenges for immune phagocytes. However, the significance of the earliest stages of spore germination during immune cell interactions has not been investigated and yet this is likely to be important for defence against sporogenous fungal pathogens. We show here that macrophages restrict the early phases of the spore germination process of Aspergillus fumigatus and Mucor circinelloides including the initial phase of spore swelling, spore germination and early polarised growth. Macrophages are therefore adept at retarding germination as well as subsequent vegetative growth which is likely to be critical for immune surveillance and protection against sporulating fungi.
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Affiliation(s)
- María Fernanda Alonso
- Aberdeen Fungal Group, School of Medicine, Medical Sciences & Nutrition, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
| | - Judith M Bain
- Aberdeen Fungal Group, School of Medicine, Medical Sciences & Nutrition, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
| | - Lars P Erwig
- Aberdeen Fungal Group, School of Medicine, Medical Sciences & Nutrition, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
| | - Alistair J P Brown
- Aberdeen Fungal Group, School of Medicine, Medical Sciences & Nutrition, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK; Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
| | - Neil A R Gow
- Aberdeen Fungal Group, School of Medicine, Medical Sciences & Nutrition, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK; Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
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11
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Corzo-León DE, Uehling JK, Ballou ER. Rhizopus arrhizus. Trends Microbiol 2023; 31:985-987. [PMID: 37062623 DOI: 10.1016/j.tim.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 04/18/2023]
Affiliation(s)
| | - Jessie K Uehling
- Department of Botany and Plant Pathology, Oregon State University, OR, USA
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12
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Kelliher JM, Robinson AJ, Longley R, Johnson LYD, Hanson BT, Morales DP, Cailleau G, Junier P, Bonito G, Chain PSG. The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research. MICROBIOME 2023; 11:192. [PMID: 37626434 PMCID: PMC10463477 DOI: 10.1186/s40168-023-01634-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/29/2023] [Indexed: 08/27/2023]
Abstract
As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), mycoviruses, other fungi, and whole algal cells within their hyphae. Constituents of this complex endohyphal microbiome have been interrogated using multi-omic approaches. However, a lack of tools, techniques, and standardization for integrative multi-omics for small-scale microbiomes (e.g., intracellular microbiomes) has limited progress towards investigating and understanding the total diversity of the endohyphal microbiome and its functional impacts on fungal hosts. Understanding microbiome impacts on fungal hosts will advance explorations of how "microbiomes within microbiomes" affect broader microbial community dynamics and ecological functions. Progress to date as well as ongoing challenges of performing integrative multi-omics on the endohyphal microbiome is discussed herein. Addressing the challenges associated with the sample extraction, sample preparation, multi-omic data generation, and multi-omic data analysis and integration will help advance current knowledge of the endohyphal microbiome and provide a road map for shrinking microbiome investigations to smaller scales. Video Abstract.
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Affiliation(s)
| | | | - Reid Longley
- Los Alamos National Laboratory, Los Alamos, NM, USA
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13
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Njovu IK, Nalumaga PP, Ampaire L, Nuwagira E, Mwesigye J, Musinguzi B, Kassaza K, Taseera K, Kiguli Mukasa J, Bazira J, Iramiot JS, Baguma A, Bongomin F, Kwizera R, Achan B, Cox MJ, King JS, May R, Ballou ER, Itabangi H. Investigating Metabolic and Molecular Ecological Evolution of Opportunistic Pulmonary Fungal Coinfections: Protocol for a Laboratory-Based Cross-Sectional Study. JMIR Res Protoc 2023; 12:e48014. [PMID: 37581914 PMCID: PMC10466149 DOI: 10.2196/48014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Fungal-bacterial cocolonization and coinfections pose an emerging challenge among patients suspected of having pulmonary tuberculosis (PTB); however, the underlying pathogenic mechanisms and microbiome interactions are poorly understood. Understanding how environmental microbes, such as fungi and bacteria, coevolve and develop traits to evade host immune responses and resist treatment is critical to controlling opportunistic pulmonary fungal coinfections. In this project, we propose to study the coexistence of fungal and bacterial microbial communities during chronic pulmonary diseases, with a keen interest in underpinning fungal etiological evolution and the predominating interactions that may exist between fungi and bacteria. OBJECTIVE This is a protocol for a study aimed at investigating the metabolic and molecular ecological evolution of opportunistic pulmonary fungal coinfections through determining and characterizing the burden, etiological profiles, microbial communities, and interactions established between fungi and bacteria as implicated among patients with presumptive PTB. METHODS This will be a laboratory-based cross-sectional study, with a sample size of 406 participants. From each participant, 2 sputa samples (one on-spot and one early morning) will be collected. These samples will then be analyzed for both fungal and bacterial etiology using conventional metabolic and molecular (intergenic transcribed spacer and 16S ribosomal DNA-based polymerase chain reaction) approaches. We will also attempt to design a genome-scale metabolic model for pulmonary microbial communities to analyze the composition of the entire microbiome (ie, fungi and bacteria) and investigate host-microbial interactions under different patient conditions. This analysis will be based on the interplays of genes (identified by metagenomics) and inferred from amplicon data and metabolites (identified by metabolomics) by analyzing the full data set and using specific computational tools. We will also collect baseline data, including demographic and clinical history, using a patient-reported questionnaire. Altogether, this approach will contribute to a diagnostic-based observational study. The primary outcome will be the overall fungal and bacterial diagnostic profile of the study participants. Other diagnostic factors associated with the etiological profile, such as incidence and prevalence, will also be analyzed using univariate and multivariate schemes. Odds ratios with 95% CIs will be presented with a statistical significance set at P<.05. RESULTS The study has been approved by the Mbarara University Research Ethic Committee (MUREC1/7-07/09/20) and the Uganda National Council of Science and Technology (HS1233ES). Following careful scrutiny, the protocol was designed to enable patient enrollment, which began in March 2022 at Mbarara University Teaching Hospital. Data collection is ongoing and is expected to be completed by August 2023, and manuscripts will be submitted for publication thereafter. CONCLUSIONS Through this protocol, we will explore the metabolic and molecular ecological evolution of opportunistic pulmonary fungal coinfections among patients with presumptive PTB. Establishing key fungal-bacterial cross-kingdom synergistic relationships is crucial for instituting fungal bacterial coinfecting etiology. TRIAL REGISTRATION ISRCTN Registry ISRCTN33572982; https://tinyurl.com/caa2nw69. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/48014.
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Affiliation(s)
- Israel Kiiza Njovu
- Medical Mycology Unit, Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Pauline Petra Nalumaga
- Medical Mycology Unit, Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Lucas Ampaire
- Department of Medical Laboratory Sciences, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Edwin Nuwagira
- Department of Internal Medicine, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - James Mwesigye
- Medical Mycology Unit, Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Benson Musinguzi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Muni University, Arua, Uganda
| | - Kennedy Kassaza
- Medical Mycology Unit, Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Kabanda Taseera
- Medical Mycology Unit, Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - James Kiguli Mukasa
- Department of Microbiology and Immunology, School of Health Sciences, Soroti University, Soroti, Uganda
| | - Joel Bazira
- Medical Mycology Unit, Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Jacob Stanley Iramiot
- Mycology Unit, Department of Microbiology and Immunology, Busitema University, Mbale, Uganda
| | - Andrew Baguma
- Department of Microbiology, School of Medicine, Kabale University, Kabale, Uganda
| | - Felix Bongomin
- Department of Microbiology and Immunology, Faculty of Medicine, Gulu University, Gulu, Uganda
| | - Richard Kwizera
- Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Beatrice Achan
- Department of Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Michael J Cox
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Jason S King
- School of Biosciences, Sheffield University, Sheffield, United Kingdom
| | - Robin May
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Elizabeth R Ballou
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Herbert Itabangi
- Medical Mycology Unit, Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
- Mycology Unit, Department of Microbiology and Immunology, Busitema University, Mbale, Uganda
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Gryganskyi AP, Golan J, Muszewska A, Idnurm A, Dolatabadi S, Mondo SJ, Kutovenko VB, Kutovenko VO, Gajdeczka MT, Anishchenko IM, Pawlowska J, Tran NV, Ebersberger I, Voigt K, Wang Y, Chang Y, Pawlowska TE, Heitman J, Vilgalys R, Bonito G, Benny GL, Smith ME, Reynolds N, James TY, Grigoriev IV, Spatafora JW, Stajich JE. Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned? Microorganisms 2023; 11:1830. [PMID: 37513002 PMCID: PMC10386755 DOI: 10.3390/microorganisms11071830] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/13/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
The first genome sequenced of a eukaryotic organism was for Saccharomyces cerevisiae, as reported in 1996, but it was more than 10 years before any of the zygomycete fungi, which are the early-diverging terrestrial fungi currently placed in the phyla Mucoromycota and Zoopagomycota, were sequenced. The genome for Rhizopus delemar was completed in 2008; currently, more than 1000 zygomycete genomes have been sequenced. Genomic data from these early-diverging terrestrial fungi revealed deep phylogenetic separation of the two major clades-primarily plant-associated saprotrophic and mycorrhizal Mucoromycota versus the primarily mycoparasitic or animal-associated parasites and commensals in the Zoopagomycota. Genomic studies provide many valuable insights into how these fungi evolved in response to the challenges of living on land, including adaptations to sensing light and gravity, development of hyphal growth, and co-existence with the first terrestrial plants. Genome sequence data have facilitated studies of genome architecture, including a history of genome duplications and horizontal gene transfer events, distribution and organization of mating type loci, rDNA genes and transposable elements, methylation processes, and genes useful for various industrial applications. Pathogenicity genes and specialized secondary metabolites have also been detected in soil saprobes and pathogenic fungi. Novel endosymbiotic bacteria and viruses have been discovered during several zygomycete genome projects. Overall, genomic information has helped to resolve a plethora of research questions, from the placement of zygomycetes on the evolutionary tree of life and in natural ecosystems, to the applied biotechnological and medical questions.
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Affiliation(s)
- Andrii P. Gryganskyi
- Division of Biological & Nanoscale Technologies, UES, Inc., Dayton, OH 45432, USA
| | - Jacob Golan
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Anna Muszewska
- Institute of Biochemistry & Biophysics, Polish Academy of Sciences, 01-224 Warsaw, Poland;
| | - Alexander Idnurm
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia;
| | - Somayeh Dolatabadi
- Biology Department, Hakim Sabzevari University, Sabzevar 96179-76487, Iran;
| | - Stephen J. Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.J.M.); (I.V.G.)
| | - Vira B. Kutovenko
- Department of Agrobiology, National University of Life & Environmental Sciences, 03041 Kyiv, Ukraine; (V.B.K.)
| | - Volodymyr O. Kutovenko
- Department of Agrobiology, National University of Life & Environmental Sciences, 03041 Kyiv, Ukraine; (V.B.K.)
| | | | - Iryna M. Anishchenko
- MG Kholodny Institute of Botany, National Academy of Sciences, 01030 Kyiv, Ukraine;
| | - Julia Pawlowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological & Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland;
| | - Ngoc Vinh Tran
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Ingo Ebersberger
- Leibniz Institute for Natural Product Research & Infection Biology, 07745 Jena, Germany; (I.E.); (K.V.)
| | - Kerstin Voigt
- Leibniz Institute for Natural Product Research & Infection Biology, 07745 Jena, Germany; (I.E.); (K.V.)
| | - Yan Wang
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 1A1, Canada;
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
| | - Ying Chang
- Department of Biological Sciences, National University of Singapore, Singapore 119077, Singapore;
| | - Teresa E. Pawlowska
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA; (T.E.P.); (N.R.)
| | - Joseph Heitman
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC 27710, USA;
| | - Rytas Vilgalys
- Biology Department, Duke University, Durham, NC 27708, USA;
| | - Gregory Bonito
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA;
| | - Gerald L. Benny
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Matthew E. Smith
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Nicole Reynolds
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA; (T.E.P.); (N.R.)
| | - Timothy Y. James
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.J.M.); (I.V.G.)
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Joseph W. Spatafora
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
| | - Jason E. Stajich
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA 93106, USA;
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Cánovas-Márquez JT, Lax C, Tahiri G, Navarro E, Nicolás FE, Garre V. Advances in understanding infections caused by the basal fungus Mucor. PLoS Pathog 2023; 19:e1011394. [PMID: 37262085 DOI: 10.1371/journal.ppat.1011394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Affiliation(s)
- José T Cánovas-Márquez
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Carlos Lax
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Ghizlane Tahiri
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Eusebio Navarro
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Francisco E Nicolás
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Victoriano Garre
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
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16
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Mucorales and Mucormycosis: Recent Insights and Future Prospects. J Fungi (Basel) 2023; 9:jof9030335. [PMID: 36983503 PMCID: PMC10058716 DOI: 10.3390/jof9030335] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/28/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023] Open
Abstract
The classification of Mucorales encompasses a collection of basal fungi that have traditionally demonstrated an aversion to modern genetic manipulation techniques. This aversion led to a scarcity of knowledge regarding their biology compared to other fungal groups. However, the emergence of mucormycosis, a fungal disease caused by Mucorales, has attracted the attention of the clinical field, mainly because available therapies are ineffective for decreasing the fatal outcome associated with the disease. This revitalized curiosity about Mucorales and mucormycosis, also encouraged by the recent COVID-19 pandemic, has spurred a significant and productive effort to uncover their mysteries in recent years. Here, we elaborate on the most remarkable breakthroughs related to the recently discovered genetic advances in Mucorales and mucormycosis. The utilization of a few genetic study models has enabled the identification of virulence factors in Mucorales that were previously described in other pathogens. More notably, recent investigations have identified novel genes and mechanisms controlling the pathogenic potential of Mucorales and their interactions with the host, providing fresh avenues to devise new strategies against mucormycosis. Finally, new study models are allowing virulence studies that were previously hampered in Mucorales, predicting a prolific future for the field.
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17
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Cabrera-Rangel JF, Mendoza-Servín JV, Córdova-López G, Alcalde-Vázquez R, García-Estrada RS, Winkler R, Partida-Martínez LP. Symbiotic and toxinogenic Rhizopus spp. isolated from soils of different papaya producing regions in Mexico. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:893700. [PMID: 37746220 PMCID: PMC10512248 DOI: 10.3389/ffunb.2022.893700] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 10/10/2022] [Indexed: 09/26/2023]
Abstract
Mucoralean fungi from the genus Rhizopus are common inhabitants of terrestrial ecosystems, being some pathogens of animals and plants. In this study, we analyzed the symbiotic and toxinogenic potential of Rhizopus species derived from agricultural soils dedicated to the production of papaya (Carica papaya L.) in Mexico. Four representative strains of soil-derived Rhizopus spp. were analyzed employing molecular, microscopic, and metabolic methods. The ITS phylogenies identified the fungi as Rhizopus microsporus HP499, Rhizopus delemar HP475 and HP479, and Rhizopus homothallicus HP487. We discovered that R. microsporus HP499 and R. delemar HP475 harbor similar endofungal bacterial symbionts that belong to the genus Mycetohabitans (Burkholderia sensu lato) and that none of the four fungi were associated with Narnavirus RmNV-20S and RmNV-23S. Intriguingly, the interaction between R. delemar - Mycetohabitans showed different phenotypes from known R. microsporus - Mycetohabitans symbioses. Elimination of bacteria in R. delemar HP475 did not cause a detrimental effect on fungal growth or asexual reproduction. Moreover, metabolic and molecular analyses confirmed that, unlike symbiotic R. microsporus HP499, R. delemar HP475 does not produce rhizoxin, one of the best-characterized toxins produced by Mycetohabitans spp. The rhizoxin (rhi) biosynthetic gene cluster seems absent in this symbiotic bacterium. Our study highlights that the symbioses between Rhizopus and Mycetohabitans are more diverse than anticipated. Our findings contribute to expanding our understanding of the role bacterial symbionts have in the pathogenicity, biology and evolution of Mucorales.
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Affiliation(s)
| | | | - Gonzalo Córdova-López
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | - Raúl Alcalde-Vázquez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | | | - Robert Winkler
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | - Laila P. Partida-Martínez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
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18
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Abstract
The fungus Rhizopus microsporus harbors a bacterial endosymbiont (Mycetohabitans rhizoxinica) for the production of the antimitotic toxin rhizoxin. Although rhizoxin is the causative agent of rice seedling blight, the toxinogenic bacterial-fungal alliance is, not restricted to the plant disease. It has been detected in numerous environmental isolates from geographically distinct sites covering all five continents, thus raising questions regarding the ecological role of rhizoxin beyond rice seedling blight. Here, we show that rhizoxin serves the fungal host in fending off protozoan and metazoan predators. Fluorescence microscopy and coculture experiments with the fungivorous amoeba Protostelium aurantium revealed that ingestion of R. microsporus spores is toxic to P. aurantium. This amoebicidal effect is caused by the dominant bacterial rhizoxin congener rhizoxin S2, which is also lethal toward the model nematode Caenorhabditis elegans. By combining stereomicroscopy, automated image analysis, and quantification of nematode movement, we show that the fungivorous nematode Aphelenchus avenae actively feeds on R. microsporus that is lacking endosymbionts, whereas worms coincubated with symbiotic R. microsporus are significantly less lively. This study uncovers an unexpected ecological role of rhizoxin as shield against micropredators. This finding suggests that predators may function as an evolutionary driving force to maintain toxin-producing endosymbionts in nonpathogenic fungi.
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19
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Snelders NC, Rovenich H, Thomma BPHJ. Microbiota manipulation through the secretion of effector proteins is fundamental to the wealth of lifestyles in the fungal kingdom. FEMS Microbiol Rev 2022; 46:6590816. [PMID: 35604874 PMCID: PMC9438471 DOI: 10.1093/femsre/fuac022] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Fungi are well-known decomposers of organic matter that thrive in virtually any environment on earth where they encounter wealths of other microbes. Some fungi evolved symbiotic lifestyles, including pathogens and mutualists, that have mostly been studied in binary interactions with their hosts. However, we now appreciate that such interactions are greatly influenced by the ecological context in which they take place. While establishing their symbioses, fungi not only interact with their hosts, but also with the host-associated microbiota. Thus, they target the host and its associated microbiota as a single holobiont. Recent studies have shown that fungal pathogens manipulate the host microbiota by means of secreted effector proteins with selective antimicrobial activity to stimulate disease development. In this review we discuss the ecological contexts in which such effector-mediated microbiota manipulation is relevant for the fungal lifestyle and argue that this is not only relevant for pathogens of plants and animals, but beneficial in virtually any niche where fungi occur. Moreover, we reason that effector-mediated microbiota manipulation likely evolved already in fungal ancestors that encountered microbial competition long before symbiosis with land plants and mammalian animals evolved. Thus, we claim that effector-mediated microbiota manipulation is fundamental to fungal biology.
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Affiliation(s)
- Nick C Snelders
- Institute for Plant Sciences, University of Cologne, Cologne, Germany.,Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Hanna Rovenich
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Bart P H J Thomma
- Institute for Plant Sciences, University of Cologne, Cologne, Germany.,Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, CologneGermany
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Villada JC, Schulz F. The endosymbiotic box of protective tricks. Nat Rev Microbiol 2022; 20:255. [PMID: 35352029 DOI: 10.1038/s41579-022-00727-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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