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Vergine M, Vita F, Casati P, Passera A, Ricciardi L, Pavan S, Aprile A, Sabella E, De Bellis L, Luvisi A. Characterization of the olive endophytic community in genotypes displaying a contrasting response to Xylella fastidiosa. BMC PLANT BIOLOGY 2024; 24:337. [PMID: 38664617 PMCID: PMC11044560 DOI: 10.1186/s12870-024-04980-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 04/03/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND Endophytes mediate the interactions between plants and other microorganisms, and the functional aspects of interactions between endophytes and their host that support plant-growth promotion and tolerance to stresses signify the ecological relevance of the endosphere microbiome. In this work, we studied the bacterial and fungal endophytic communities of olive tree (Olea europaea L.) asymptomatic or low symptomatic genotypes sampled in groves heavily compromised by Xylella fastidiosa subsp. pauca, aiming to characterize microbiota in genotypes displaying differential response to the pathogen. RESULTS The relationships between bacterial and fungal genera were analyzed both separately and together, in order to investigate the intricate correlations between the identified Operational Taxonomic Units (OTUs). Results suggested a dominant role of the fungal endophytic community compared to the bacterial one, and highlighted specific microbial taxa only associated with asymptomatic or low symptomatic genotypes. In addition, they indicated the occurrence of well-adapted genetic resources surviving after years of pathogen pressure in association with microorganisms such as Burkholderia, Quambalaria, Phaffia and Rhodotorula. CONCLUSIONS This is the first study to overview endophytic communities associated with several putatively resistant olive genotypes in areas under high X. fastidiosa inoculum pressure. Identifying these negatively correlated genera can offer valuable insights into the potential antagonistic microbial resources and their possible development as biocontrol agents.
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Affiliation(s)
- Marzia Vergine
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Federico Vita
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy.
| | - Paola Casati
- Department of Agricultural and Environmental Sciences, Production, Landscape, Agroenergy, University of Milan, Milano, Italy
| | - Alessandro Passera
- Department of Agricultural and Environmental Sciences, Production, Landscape, Agroenergy, University of Milan, Milano, Italy
| | - Luigi Ricciardi
- Department of Soil, Plant and Food Science, University of Bari "Aldo Moro", Bari, Italy
| | - Stefano Pavan
- Department of Soil, Plant and Food Science, University of Bari "Aldo Moro", Bari, Italy
| | - Alessio Aprile
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Erika Sabella
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Luigi De Bellis
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Andrea Luvisi
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
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Dos Reis JBA, Lorenzi AS, Pinho DB, Cortelo PC, do Vale HMM. The hidden treasures in endophytic fungi: a comprehensive review on the diversity of fungal bioactive metabolites, usual analytical methodologies, and applications. Arch Microbiol 2024; 206:185. [PMID: 38506928 DOI: 10.1007/s00203-024-03911-x] [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: 01/25/2024] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024]
Abstract
This review provides a comprehensive overview of the key aspects of the natural metabolite production by endophytic fungi, which has attracted significant attention due to its diverse biological activities and wide range of applications. Synthesized by various fungal species, these metabolites encompass compounds with therapeutic, agricultural, and commercial significance. We delved into strategies and advancements aimed at optimizing fungal metabolite production. Fungal cultivation, especially by Aspergillus, Penicillium, and Fusarium, plays a pivotal role in metabolite biosynthesis, and researchers have explored both submerged and solid-state cultivation processes to harness the full potential of fungal species. Nutrient optimization, pH, and temperature control are critical factors in ensuring high yields of the targeted bioactive metabolites especially for scaling up processes. Analytical methods that includes High-Performance Liquid Chromatography (HPLC), Liquid Chromatography-Mass Spectrometry (LC-MS), Gas Chromatography-Mass Spectrometry (GC-MS), Nuclear Magnetic Resonance (NMR), and Mass Spectrometry (MS), are indispensable for the identification and quantification of the compounds. Moreover, genetic engineering and metabolic pathway manipulation have emerged as powerful tools to enhance metabolite production and develop novel fungal strains with increased yields. Regulation and control mechanisms at the genetic, epigenetic, and metabolic levels are explored to fine-tune the biosynthesis of fungal metabolites. Ongoing research aims to overcome the complexity of the steps involved to ensure the efficient production and utilization of fungal metabolites.
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Affiliation(s)
| | - Adriana Sturion Lorenzi
- Department of Cellular Biology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, DF, Brazil
| | - Danilo Batista Pinho
- Department of Phytopathology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, DF, Brazil
| | | | - Helson Mario Martins do Vale
- Department of Phytopathology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, DF, Brazil
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Lane DM, Valentine DL, Peng X. Genomic analysis of the marine yeast Rhodotorula sphaerocarpa ETNP2018 reveals adaptation to the open ocean. BMC Genomics 2023; 24:695. [PMID: 37986036 PMCID: PMC10662464 DOI: 10.1186/s12864-023-09791-7] [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: 06/29/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Despite a rising interest in the diversity and ecology of fungi in marine environments, there are few published genomes of fungi isolated from the ocean. The basidiomycetous yeast (unicellular fungus) genus Rhodotorula are prevalent and abundant in the open ocean, and they have been isolated from a wide range of other environments. Many of these environments are nutrient poor, such as the Antarctica and the Atacama deserts, raising the question as to how Rhodotorula yeasts may have adapted their metabolic strategies to optimize survival under low nutrient conditions. In order to understand their adaptive strategies in the ocean, the genome of R. sphaerocarpa ETNP2018 was compared to that of fourteen representative Rhodotorula yeasts, isolated from a variety of environments. RESULTS Rhodotorula sphaerocarpa ETNP2018, a strain isolated from the oligotrophic part of the eastern tropical North Pacific (ETNP) oxygen minimum zone (OMZ), hosts the smallest of the fifteen genomes and yet the number of protein-coding genes it possesses is on par with the other strains. Its genome exhibits a distinct reduction in genes dedicated to Major Facilitator Superfamily transporters as well as biosynthetic enzymes. However, its core metabolic pathways are fully conserved. Our research indicates that the selective pressures of the ETNP OMZ favor a streamlined genome with reduced overall biosynthetic potential balanced by a stable set of core metabolisms and an expansion of mechanisms for nutrient acquisition. CONCLUSIONS In summary, this study offers insights into the adaptation of fungi to the oligotrophic ocean and provides valuable information for understanding the ecological roles of fungi in the ocean.
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Affiliation(s)
- Dylan M Lane
- School of Earth, Ocean, and Environment, University of South Carolina, Columbia, SC, USA
| | - David L Valentine
- Marine Science Institute, University of California, Santa Barbara, CA, USA
- Department of Earth Science, University of California, Santa Barbara, CA, USA
| | - Xuefeng Peng
- School of Earth, Ocean, and Environment, University of South Carolina, Columbia, SC, USA.
- Marine Science Institute, University of California, Santa Barbara, CA, USA.
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Mano J, Sushida H, Tanaka T, Naito K, Ono H, Ike M, Tokuyasu K, Kitaoka M. Extracellular oil production by Rhodotorula paludigena BS15 for biorefinery without complex downstream processes. Appl Microbiol Biotechnol 2023; 107:6799-6809. [PMID: 37725141 DOI: 10.1007/s00253-023-12762-3] [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: 04/04/2023] [Revised: 07/12/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023]
Abstract
To realize biomass refinery without complex downstream processes, we extensively screened for microbial strains that efficiently produce extracellular oil from sugars. Rhodotorula paludigena (formerly Rhodosporidium paludigenum) BS15 was found to efficiently produce polyol esters of fatty acids (PEFAs), which mainly comprised of 3-acetoxypalmitic acid and partially acetylated mannitol/arabinitol. To evaluate the performance of this strain, fed-batch fermentation was demonstrated on a flask scale, and 110 g/L PEFA and 103 g/L dry cells were produced in 12 days. To the best of our knowledge, the strain BS15 exhibited the highest PEFA titer (g/L) ever to be reported so far. Because the PEFA precipitated at the bottom of the culture broth, it could be easily recovered by simply discarding the upper phase. Various carbon sources can be utilized for cell growth and/or PEFA production, which signifies the potential for converting diverse biomass sources. Two different types of next-generation sequencers, Illumina HiSeq and Oxford Nanopore PromethION, were used to analyze the whole-genome sequence of the strain BS15. The integrative data analysis generated a high-quality and reliable reference genome for PEFA-producing R. paludigena. The 22.5-M base genome sequence and the estimated genes were registered in Genbank (accession numbers BQKY01000001-BQKY01000019). KEY POINTS: • R. paludigena BS15 was isolated after an extensive screening of extracellular oil producers from natural sources. • Fed-batch fermentation of R. paludigena BS15 yielded 110 g/L of PEFA, which is the highest titer ever reported to date. • Combined analysis using Illumina and Oxford Nanopore sequencers produced the near-complete genome sequence.
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Affiliation(s)
- Junichi Mano
- Institute of Food Research, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan.
| | - Hirotoshi Sushida
- Institute of Food Research, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
| | - Tsuyoshi Tanaka
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Ken Naito
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Hiroshi Ono
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Masakazu Ike
- Institute of Food Research, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
| | - Ken Tokuyasu
- Institute of Food Research, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
| | - Motomitsu Kitaoka
- Institute of Food Research, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
- Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan
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Tian Y, Liu Y, Uwaremwe C, Zhao X, Yue L, Zhou Q, Wang Y, Tran LSP, Li W, Chen G, Sha Y, Wang R. Characterization of three new plant growth-promoting microbes and effects of the interkingdom interactions on plant growth and disease prevention. PLANT CELL REPORTS 2023; 42:1757-1776. [PMID: 37674059 DOI: 10.1007/s00299-023-03060-3] [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: 06/04/2023] [Accepted: 08/12/2023] [Indexed: 09/08/2023]
Abstract
KEY MESSAGE The novel interkingdom PGPM consortia enhanced the ability of plant growth promotion and disease resistance, which would be beneficial to improve plant growth in sustainable agriculture through engineering microbiome. Plant growth-promoting microbes (PGPMs) play important roles in promoting plant growth and bio-controlling of pathogens. Much information reveals that the plant growth-promoting ability of individual PGPM affects plant growth. However, the effects of the PGPM consortia properties on plant growth remain largely unexplored. Here, we characterized three new PGPM strains including Rhodotorula graminis JJ10.1 (termed as J), Pseudomonas psychrotolerans YY7 (termed as Y) and P. chlororaphis T8 (termed as T), and assessed their effects in combination with Bacillus amyloliquefaciens FZB42 (termed as F) on plant growth promotion and disease prevention in Arabidopsis thaliana and tomato (Solanum lycopersicum) plants by investigating morphological changes, whole-genome sequencing and plant growth promoting (PGP) characterization. Results revealed that the three new strains R. graminis JJ10.1, P. psychrotolerans YY7 and P. chlororaphis T8 had the potential for being combined with B. amyloliquefaciens FZB42 to form interkingdom PGPM consortia. The combinations of R. graminis JJ10.1, B. amyloliquefaciens FZB42, and P. psychrotolerans YY7, i. e. JF and JYF, exhibited the strongest ability of synergetic biofilm production. Furthermore, the growth-promotion abilities of the consortia were significantly enhanced compared with those of individual strains under both inoculation and volatile organic compounds (VOCs) treatment. Importantly, the consortia showed stronger abilities of in planta disease prevention than individual strains. Findings of our study may provide future guidance for engineering the minimal microbiome communities to improve plant growth and/or disease resistance in sustainable agriculture.
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Affiliation(s)
- Yuan Tian
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yang Liu
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Constantine Uwaremwe
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xia Zhao
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Liang Yue
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Qin Zhou
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yun Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Weiqiang Li
- Jilin Da'an Agro-Ecosystem National Observation Research Station, Changchun Jingyuetan Remote Sensing Experiment Station, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Changchun, 130102, People's Republic of China
| | - Gaofeng Chen
- Gansu Shangnong Biotechnology Co. Ltd, Baiyin, 730900, People's Republic of China
| | - Yuexia Sha
- Institute of Plant Protection, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, People's Republic of China
| | - Ruoyu Wang
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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Wang K, Wen Z, Asiegbu FO. The dark septate endophyte Phialocephala sphaeroides suppresses conifer pathogen transcripts and promotes root growth of Norway spruce. TREE PHYSIOLOGY 2022; 42:2627-2639. [PMID: 35878416 PMCID: PMC9743008 DOI: 10.1093/treephys/tpac089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Plant-associated microbes including dark septate endophytes (DSEs) of forest trees play diverse functional roles in host fitness including growth promotion and increased defence. However, little is known about the impact on the fungal transcriptome and metabolites during tripartite interaction involving plant host, endophyte and pathogen. To understand the transcriptional regulation of endophyte and pathogen during co-infection, Norway spruce (Picea abies) seedlings were infected with DSE Phialocephala sphaeroides, or conifer root-rot pathogen Heterobasidion parviporum, or both. Phialocephala sphaeroides showed low but stable transcripts abundance (a decrease of 40%) during interaction with Norway spruce and conifer pathogen. By contrast, H. parviporum transcripts were significantly reduced (92%) during co-infection. With RNA sequencing analysis, P. sphaeroides experienced a shift from cell growth to anti-stress and antagonistic responses, while it repressed the ability of H. parviporum to access carbohydrate nutrients by suppressing its carbohydrate/polysaccharide-degrading enzyme machinery. The pathogen on the other hand secreted cysteine peptidase to restrict free growth of P. sphaeroides. The expression of both DSE P. sphaeroides and pathogen H. parviporum genes encoding plant growth promotion products were equally detected in both dual and tripartite interaction systems. This was further supported by the presence of tryptophan-dependent indolic compound in liquid culture of P. sphaeroides. Norway spruce and Arabidopsis seedlings treated with P. sphaeroides culture filtrate exhibited auxin-like phenotypes, such as enhanced root hairs, and primary root elongation at low concentration but shortened primary root at high concentration. The results suggested that the presence of the endophyte had strong repressive or suppressive effect on H. parviporum transcripts encoding genes involved in nutrient acquisition.
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Affiliation(s)
- Kai Wang
- Corresponding authors: K.Wang (; ) and F.Asiegbu ()
| | - Zilan Wen
- Department of Forest Sciences, University of Helsinki, PO Box 27, Helsinki FIN-00014, Finland
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Bo S, Ni X, Guo J, Liu Z, Wang X, Sheng Y, Zhang G, Yang J. Carotenoid Biosynthesis: Genome-Wide Profiling, Pathway Identification in Rhodotorula glutinis X-20, and High-Level Production. Front Nutr 2022; 9:918240. [PMID: 35782944 PMCID: PMC9247606 DOI: 10.3389/fnut.2022.918240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/13/2022] [Indexed: 01/04/2023] Open
Abstract
Rhodotorula glutinis, as a member of the family Sporidiobolaceae, is of great value in the field of biotechnology. However, the evolutionary relationship of R. glutinis X-20 with Rhodosporidiobolus, Sporobolomyces, and Rhodotorula are not well understood, and its metabolic pathways such as carotenoid biosynthesis are not well resolved. Here, genome sequencing and comparative genome techniques were employed to improve the understanding of R. glutinis X-20. Phytoene desaturase (crtI) and 15-cis-phytoene synthase/lycopene beta-cyclase (crtYB), key enzymes in carotenoid pathway from R. glutinis X-20 were more efficiently expressed in S. cerevisiae INVSc1 than in S. cerevisiae CEN.PK2-1C. High yielding engineered strains were obtained by using synthetic biology technology constructing carotenoid pathway in S. cerevisiae and optimizing the precursor supply after fed-batch fermentation with palmitic acid supplementation. Genome sequencing analysis and metabolite identification has enhanced the understanding of evolutionary relationships and metabolic pathways in R. glutinis X-20, while heterologous construction of carotenoid pathway has facilitated its industrial application.
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Xia Y, Liu J, Chen C, Mo X, Tan Q, He Y, Wang Z, Yin J, Zhou G. The Multifunctions and Future Prospects of Endophytes and Their Metabolites in Plant Disease Management. Microorganisms 2022; 10:microorganisms10051072. [PMID: 35630514 PMCID: PMC9146654 DOI: 10.3390/microorganisms10051072] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/19/2022] [Accepted: 05/21/2022] [Indexed: 01/27/2023] Open
Abstract
Endophytes represent a ubiquitous and magical world in plants. Almost all plant species studied by different researchers have been found to harbor one or more endophytes, which protect host plants from pathogen invasion and from adverse environmental conditions. They produce various metabolites that can directly inhibit the growth of pathogens and even promote the growth and development of the host plants. In this review, we focus on the biological control of plant diseases, aiming to elucidate the contribution and key roles of endophytes and their metabolites in this field with the latest research information. Metabolites synthesized by endophytes are part of plant disease management, and the application of endophyte metabolites to induce plant resistance is very promising. Furthermore, multi-omics should be more fully utilized in plant–microbe research, especially in mining novel bioactive metabolites. We believe that the utilization of endophytes and their metabolites for plant disease management is a meaningful and promising research direction that can lead to new breakthroughs in the development of more effective and ecosystem-friendly insecticides and fungicides in modern agriculture.
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Affiliation(s)
- Yandong Xia
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
| | - Junang Liu
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
| | - Cang Chen
- College of Life Science, Hunan Normal University, Changsha 410081, China;
| | - Xiuli Mo
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
| | - Qian Tan
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
| | - Yuan He
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
| | - Zhikai Wang
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
| | - Jia Yin
- College of Life Science, Hunan Normal University, Changsha 410081, China;
- Correspondence: (J.Y.); (G.Z.)
| | - Guoying Zhou
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
- Correspondence: (J.Y.); (G.Z.)
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Belaouni HA, Compant S, Antonielli L, Nikolic B, Zitouni A, Sessitsch A. In-depth genome analysis of Bacillus sp. BH32, a salt stress-tolerant endophyte obtained from a halophyte in a semiarid region. Appl Microbiol Biotechnol 2022; 106:3113-3137. [PMID: 35435457 DOI: 10.1007/s00253-022-11907-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/16/2022] [Accepted: 03/26/2022] [Indexed: 11/02/2022]
Abstract
Endophytic strains belonging to the Bacillus cereus group were isolated from the halophytes Atriplex halimus L. (Amaranthaceae) and Tamarix aphylla L. (Tamaricaceae) from costal and continental regions in Algeria. Based on their salt tolerance (up to 5%), the strains were tested for their ability to alleviate salt stress in tomato and wheat. Bacillus sp. strain BH32 showed the highest potential to reduce salinity stress (up to + 50% and + 58% of dry weight improvement, in tomato and wheat, respectively, compared to the control). To determine putative mechanisms involved in salt tolerance and plant growth promotion, the whole genome of Bacillus sp. BH32 was sequenced, annotated, and used for comparative genomics against the genomes of closely related strains. The pangenome of Bacillus sp. BH32 and its closest relative was further analyzed. The phylogenomic analyses confirmed its taxonomic position, a member of the Bacillus cereus group, with intergenomic distances (GBDP analysis) pinpointing to a new taxon (digital DNA-DNA hybridization, dDDH < 70%). Genome mining unveiled several genes involved in stress tolerance, production of anti-oxidants and genes involved in plant growth promotion as well as in the production of secondary metabolites. KEY POINTS : • Bacillus sp. BH32 and other bacterial endophytes were isolated from halophytes, to be tested on tomato and wheat and to limit salt stress adverse effects. • The strain with the highest potential was then studied at the genomic level to highlight numerous genes linked to plant growth promotion and stress tolerance. • Pangenome approaches suggest that the strain belongs to a new taxon within the Bacillus cereus group.
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Affiliation(s)
- Hadj Ahmed Belaouni
- Laboratoire de Biologie Des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
| | - Stéphane Compant
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Bioresources Unit, 3430, Tulln, Austria.
| | - Livio Antonielli
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Bioresources Unit, 3430, Tulln, Austria
| | - Branislav Nikolic
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Bioresources Unit, 3430, Tulln, Austria
| | - Abdelghani Zitouni
- Laboratoire de Biologie Des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Bioresources Unit, 3430, Tulln, Austria
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Zhou X, Yu D, Cao Z. Convergence Analysis of Rust Fungi and Anther Smuts Reveals Their Common Molecular Adaptation to a Phytoparasitic Lifestyle. Front Genet 2022; 13:863617. [PMID: 35464858 PMCID: PMC9023891 DOI: 10.3389/fgene.2022.863617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/25/2022] [Indexed: 11/28/2022] Open
Abstract
Convergent evolution between distantly related taxa often mirrors adaptation to similar environments. Rust fungi and anther smuts, which belong to different classes in Pucciniomycotina, have independently evolved a phytoparasitic lifestyle, representing an example of convergent evolution in the fungal kingdom. To investigate their adaptations and the genetic bases underlying their phytoparasitic lifestyles, we performed genome-wide convergence analysis of amino acid substitutions, evolutionary rates, and gene gains and losses. Convergent substitutions were detected in ATPeV0D and RP-S27Ae, two genes important for the generation of turgor pressure and ribosomal biosynthesis, respectively. A total of 51 positively selected genes were identified, including eight genes associated with translation and three genes related to the secretion pathway. In addition, rust fungi and anther smuts contained more proteins associated with oligopeptide transporters and vacuolar proteases than did other fungi. For rust fungi and anther smuts, these forms of convergence suggest four adaptive mechanisms for a phytoparasitic lifestyle: 1) reducing the metabolic demand for hyphal growth and penetration at the pre-penetration stage, 2) maintaining the efficiency of protein synthesis during colonization, 3) ensuring the normal secretion of rapidly evolving secreted proteins, and 4) improving the capacity for oligopeptide metabolism. Our results are the first to shed light on the genetic convergence mechanisms and molecular adaptation underlying phytoparasitic lifestyles in fungi.
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Affiliation(s)
| | | | - Zhimin Cao
- College of Forestry, Northwest A&F University, Yangling, China
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11
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Near Chromosome-Level Genome Assembly and Annotation of Rhodotorula babjevae Strains Reveals High Intraspecific Divergence. J Fungi (Basel) 2022; 8:jof8040323. [PMID: 35448555 PMCID: PMC9027234 DOI: 10.3390/jof8040323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/16/2022] [Accepted: 03/19/2022] [Indexed: 02/04/2023] Open
Abstract
The genus Rhodotorula includes basidiomycetous oleaginous yeast species. Rhodotorula babjevae can produce compounds of biotechnological interest such as lipids, carotenoids, and biosurfactants from low value substrates such as lignocellulose hydrolysate. High-quality genome assemblies are needed to develop genetic tools and to understand fungal evolution and genetics. Here, we combined short- and long-read sequencing to resolve the genomes of two R. babjevae strains, CBS 7808 (type strain) and DBVPG 8058, at chromosomal level. Both genomes are 21 Mbp in size and have a GC content of 68.2%. Allele frequency analysis indicates that both strains are tetraploid. The genomes consist of a maximum of 21 chromosomes with a size of 0.4 to 2.4 Mbp. In both assemblies, the mitochondrial genome was recovered in a single contig, that shared 97% pairwise identity. Pairwise identity between most chromosomes ranges from 82 to 87%. We also found indications for strain-specific extrachromosomal endogenous DNA. A total of 7591 and 7481 protein-coding genes were annotated in CBS 7808 and DBVPG 8058, respectively. CBS 7808 accumulated a higher number of tandem duplications than DBVPG 8058. We identified large translocation events between putative chromosomes. Genome divergence values between the two strains indicate that they may belong to different species.
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12
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Petkova M, Petrova S, Spasova-Apostolova V, Naydenov M. Tobacco Plant Growth-Promoting and Antifungal Activities of Three Endophytic Yeast Strains. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11060751. [PMID: 35336632 PMCID: PMC8953121 DOI: 10.3390/plants11060751] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 05/10/2023]
Abstract
In this research, the biosynthetic and biocontrol potential of endophytic yeast to improve the growth and development of tobacco has been elucidated. Three yeast strains were enriched and isolated from different plant tissues. Partial sequence analysis of ITS5-5.8-ITS4 region of the nuclear ribosomal DNA with universal primers identified YD5, YE1, and YSW1 as Saccharomyces cerevisiae (S. cerevisiae), Zygosaccharomyces bailii (Z. bailii), and Saccharomyces kudriavzevii (S. kudriavzevii), respectively. When cultivated in a medium supplemented with 0.1% L-tryptophan, isolated yeast strains produced indole-3-acetic acid (IAA). The capacities of those strains to improve the mobility of phosphorus and synthesize siderophores has been proven. Their antimicrobial activities against several Solanaceae plant pathogenic fungi (Alternaria solani pathovar. tobacco, Rhizoctonia solani, and Fusarium solani pathovar. phaseoli) were determined. S. cerevisiae YD5, Z. bailii YE1, and S. kudriavzevii YSW1 inhibited the growth of all tested pathogens. Yeast strains were tested for endophytic colonization of tobacco by two different inoculation methods: soil drench (SD) and leaf spraying (LS). To establish colonization in the various tissues of tested tobacco (Nicotiana tabaccum L.) plants, samples were taken on the seventh, fourteenth, and twenty-first days after treatment (DAT), and explants were inoculated on yeast malt agar (YMA). Both techniques of inoculation showed a high frequency of colonization from 83.33% to 100%. To determine the effectiveness of the microbial endophytes, their effect on some physiological processes in the plant were analyzed, such as photosynthesis, stomatal conductivity, and transpiration intensity. The effect of single and double treatment with yeast inoculum on the development and biochemical parameters of tobacco was reported. Plants have the ability of structural and functional adaptation to stress effects of different natures. All treated plants had a higher content of photosynthetic pigments compared to the control. Photosynthesis is probably more intense, and growth stimulation has been observed. The chlorophyll a/b ratio remained similar, and the total chlorophyll/carotenoid ratio slightly increased as a result of elevated chlorophyll levels. The most significant stimulating effect was recorded in tobacco plants treated by foliar spraying with Z. bailii YE1 and S. cerevisiae YD5. In contrast, S. kudriavzevii YSW1 had a better effect when applied as a soil drench. Thus, S. cerevisiae YD5, Z. bailii YE1, and S. kudriavzevii YSW1 have a high potential to be used as a biocontrol agents in organic agriculture.
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Affiliation(s)
- Mariana Petkova
- Department of Microbiology and Environmental Biotechnology, Agricultural University of Plovdiv, 4000 Plovdiv, Bulgaria; (S.P.); (V.S.-A.); (M.N.)
- Correspondence:
| | - Slaveya Petrova
- Department of Microbiology and Environmental Biotechnology, Agricultural University of Plovdiv, 4000 Plovdiv, Bulgaria; (S.P.); (V.S.-A.); (M.N.)
- Department of Ecology and Environmental Conservation, Plovdiv University Paisii Hilendarski, 4000 Plovdiv, Bulgaria
| | - Velichka Spasova-Apostolova
- Department of Microbiology and Environmental Biotechnology, Agricultural University of Plovdiv, 4000 Plovdiv, Bulgaria; (S.P.); (V.S.-A.); (M.N.)
- Agricultural Academy, Tobacco and Tobacco Products Institute, 4108 Markovo, Bulgaria
| | - Mladen Naydenov
- Department of Microbiology and Environmental Biotechnology, Agricultural University of Plovdiv, 4000 Plovdiv, Bulgaria; (S.P.); (V.S.-A.); (M.N.)
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13
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Amelioration in traditional farming system by exploring the different plant growth-promoting attributes of endophytes for sustainable agriculture. Arch Microbiol 2022; 204:151. [DOI: 10.1007/s00203-021-02637-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 11/23/2021] [Accepted: 12/06/2021] [Indexed: 11/25/2022]
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14
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Xiang JY, Chi YY, Han JX, Kong P, Liang Z, Wang D, Xiang H, Xie Q. Litchi chinensis seed prevents obesity and modulates the gut microbiota and mycobiota compositions in high-fat diet-induced obese zebrafish. Food Funct 2022; 13:2832-2845. [DOI: 10.1039/d1fo03991a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Obesity continues to be a global public health challenge. Litchi chinensis seed is rich in bioactive ingredients with pharmacological effects, such as hypoglycemic activity and anti-oxidation. This study aimed to...
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15
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Cui X, Stolzer M, Durand D. Evidence for exon shuffling is sensitive to model choice. J Bioinform Comput Biol 2021; 19:2140013. [PMID: 34806953 DOI: 10.1142/s0219720021400138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The exon shuffling theory posits that intronic recombination creates new domain combinations, facilitating the evolution of novel protein function. This theory predicts that introns will be preferentially situated near domain boundaries. Many studies have sought evidence for exon shuffling by testing the correspondence between introns and domain boundaries against chance intron positioning. Here, we present an empirical investigation of how the choice of null model influences significance. Although genome-wide studies have used a uniform null model, exclusively, more realistic null models have been proposed for single gene studies. We extended these models for genome-wide analyses and applied them to 21 metazoan and fungal genomes. Our results show that compared with the other two models, the uniform model does not recapitulate genuine exon lengths, dramatically underestimates the probability of chance agreement, and overestimates the significance of intron-domain correspondence by as much as 100 orders of magnitude. Model choice had much greater impact on the assessment of exon shuffling in fungal genomes than in metazoa, leading to different evolutionary conclusions in seven of the 16 fungal genomes tested. Genome-wide studies that use this overly permissive null model may exaggerate the importance of exon shuffling as a general mechanism of multidomain evolution.
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Affiliation(s)
- Xiaoyue Cui
- Department of Computational Biology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Maureen Stolzer
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Dannie Durand
- Departments of Biological Sciences and Computational Biology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
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16
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Olivieri L, Saville RJ, Gange AC, Xu X. Apple endophyte community in relation to location, scion and rootstock genotypes and susceptibility to European canker. FEMS Microbiol Ecol 2021; 97:fiab131. [PMID: 34601593 PMCID: PMC8497447 DOI: 10.1093/femsec/fiab131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 09/24/2021] [Indexed: 12/30/2022] Open
Abstract
European apple canker, caused by Neonectria ditissima, is a severe disease of apple. Achieving effective control is difficult with the currently available pesticides. Specific apple endophytes associated with cultivars may partially contribute to the cultivar response to the pathogen and thus could be used for disease management. We sought to determine whether the overall endophyte community differed among cultivars differing in their susceptibility to N. ditissima and to identify specific microbial groups associated with the susceptibility. Using Illumina MiSeq meta-barcoding, we profiled apple tree endophytes in 16 scion-rootstock combinations at two locations and quantified the relative contribution of scion, rootstock and location to the observed variability in the endophyte communities. Endophyte diversity was primarily affected by the orchard location (accounting for 29.4% and 85.9% of the total variation in the PC1 for bacteria and fungi, respectively), followed by the scion genotype (24.3% and 19.5% of PC2), whereas rootstock effects were small (<3% of PC1 and PC2). There were significant differences in the endophyte community between canker-resistant and -susceptible cultivars. Several bacterial and fungal endophyte groups had different relative abundance between susceptible and resistant cultivars. These endophyte groups included putative pathogen antagonists as well as plant pathogens. Their possible ecological roles in the N. ditissima pathosystem are discussed.
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Affiliation(s)
- Leone Olivieri
- NIAB EMR, New Road, East Malling, Kent ME19 6BJ, UK
- Department of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - Robert J Saville
- NIAB EMR, New Road, East Malling, Kent ME19 6BJ, UK
- Agriculture & Horticulture Development Board, Stoneleigh Park, Kenilworth, Warwickshire CV8 2TL, UK
| | - Alan C Gange
- Department of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - Xiangming Xu
- NIAB EMR, New Road, East Malling, Kent ME19 6BJ, UK
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17
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Mycobiota in the Carposphere of Sour and Sweet Cherries and Antagonistic Features of Potential Biocontrol Yeasts. Microorganisms 2021; 9:microorganisms9071423. [PMID: 34209423 PMCID: PMC8307871 DOI: 10.3390/microorganisms9071423] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/27/2021] [Accepted: 06/28/2021] [Indexed: 01/04/2023] Open
Abstract
Sour cherries (Prunus cerasus L.) and sweet cherries (P. avium L.) are economically important fruits with high potential in the food industry and medicine. In this study, we analyzed fungal communities associated with the carposphere of sour and sweet cherries that were freshly harvested from private plantations and purchased in a food store. Following DNA isolation, a DNA fragment of the ITS2 rRNA gene region of each sample was individually amplified and subjected to high-throughput NGS sequencing. Analysis of 168,933 high-quality reads showed the presence of 690 fungal taxa. Investigation of microbial ASVs diversity revealed plant-dependent and postharvest handling-affected fungal assemblages. Among the microorganisms inhabiting tested berries, potentially beneficial or pathogenic fungi were documented. Numerous cultivable yeasts were isolated from the surface of tested berries and characterized by their antagonistic activity. Some of the isolates, identified as Aureobasidium pullulans, Metschnikowia fructicola, and M. pulcherrima, displayed pronounced activity against potential fungal pathogens and showed attractiveness for disease control.
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18
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Hage H, Rosso MN, Tarrago L. Distribution of methionine sulfoxide reductases in fungi and conservation of the free-methionine-R-sulfoxide reductase in multicellular eukaryotes. Free Radic Biol Med 2021; 169:187-215. [PMID: 33865960 DOI: 10.1016/j.freeradbiomed.2021.04.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022]
Abstract
Methionine, either as a free amino acid or included in proteins, can be oxidized into methionine sulfoxide (MetO), which exists as R and S diastereomers. Almost all characterized organisms possess thiol-oxidoreductases named methionine sulfoxide reductase (Msr) enzymes to reduce MetO back to Met. MsrA and MsrB reduce the S and R diastereomers of MetO, respectively, with strict stereospecificity and are found in almost all organisms. Another type of thiol-oxidoreductase, the free-methionine-R-sulfoxide reductase (fRMsr), identified so far in prokaryotes and a few unicellular eukaryotes, reduces the R MetO diastereomer of the free amino acid. Moreover, some bacteria possess molybdenum-containing enzymes that reduce MetO, either in the free or protein-bound forms. All these Msrs play important roles in the protection of organisms against oxidative stress. Fungi are heterotrophic eukaryotes that colonize all niches on Earth and play fundamental functions, in organic matter recycling, as symbionts, or as pathogens of numerous organisms. However, our knowledge on fungal Msrs is still limited. Here, we performed a survey of msr genes in almost 700 genomes across the fungal kingdom. We show that most fungi possess one gene coding for each type of methionine sulfoxide reductase: MsrA, MsrB, and fRMsr. However, several fungi living in anaerobic environments or as obligate intracellular parasites were devoid of msr genes. Sequence inspection and phylogenetic analyses allowed us to identify non-canonical sequences with potentially novel enzymatic properties. Finaly, we identified several ocurences of msr horizontal gene transfer from bacteria to fungi.
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Affiliation(s)
- Hayat Hage
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Marie-Noëlle Rosso
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Lionel Tarrago
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France.
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19
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Genome Sequence Analysis of the Oleaginous Yeast, Rhodotorula diobovata, and Comparison of the Carotenogenic and Oleaginous Pathway Genes and Gene Products with Other Oleaginous Yeasts. J Fungi (Basel) 2021; 7:jof7040320. [PMID: 33924147 PMCID: PMC8074367 DOI: 10.3390/jof7040320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/18/2022] Open
Abstract
Rhodotorula diobovata is an oleaginous and carotenogenic yeast, useful for diverse biotechnological applications. To understand the molecular basis of its potential applications, the genome was sequenced using the Illumina MiSeq and Ion Torrent platforms, assembled by AbySS, and annotated using the JGI annotation pipeline. The genome size, 21.1 MB, was similar to that of the biotechnological “workhorse”, R. toruloides. Comparative analyses of the R. diobovata genome sequence with those of other Rhodotorula species, Yarrowia lipolytica, Phaffia rhodozyma, Lipomyces starkeyi, and Sporidiobolus salmonicolor, were conducted, with emphasis on the carotenoid and neutral lipid biosynthesis pathways. Amino acid sequence alignments of key enzymes in the lipid biosynthesis pathway revealed why the activity of malic enzyme and ATP-citrate lyase may be ambiguous in Y. lipolytica and L. starkeyi. Phylogenetic analysis showed a close relationship between R. diobovata and R. graminis WP1. Dot-plot analysis of the coding sequences of the genes crtYB and ME1 corroborated sequence homologies between sequences from R. diobovata and R. graminis. There was, however, nonsequential alignment between crtYB CDS sequences from R. diobovata and those from X. dendrorhous. This research presents the first genome analysis of R. diobovata with a focus on its biotechnological potential as a lipid and carotenoid producer.
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20
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Sagita R, Quax WJ, Haslinger K. Current State and Future Directions of Genetics and Genomics of Endophytic Fungi for Bioprospecting Efforts. Front Bioeng Biotechnol 2021; 9:649906. [PMID: 33791289 PMCID: PMC8005728 DOI: 10.3389/fbioe.2021.649906] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/16/2021] [Indexed: 12/16/2022] Open
Abstract
The bioprospecting of secondary metabolites from endophytic fungi received great attention in the 1990s and 2000s, when the controversy around taxol production from Taxus spp. endophytes was at its height. Since then, hundreds of reports have described the isolation and characterization of putative secondary metabolites from endophytic fungi. However, only very few studies also report the genetic basis for these phenotypic observations. With low sequencing cost and fast sample turnaround, genetics- and genomics-based approaches have risen to become comprehensive approaches to study natural products from a wide-range of organisms, especially to elucidate underlying biosynthetic pathways. However, in the field of fungal endophyte biology, elucidation of biosynthetic pathways is still a major challenge. As a relatively poorly investigated group of microorganisms, even in the light of recent efforts to sequence more fungal genomes, such as the 1000 Fungal Genomes Project at the Joint Genome Institute (JGI), the basis for bioprospecting of enzymes and pathways from endophytic fungi is still rather slim. In this review we want to discuss the current approaches and tools used to associate phenotype and genotype to elucidate biosynthetic pathways of secondary metabolites in endophytic fungi through the lens of bioprospecting. This review will point out the reported successes and shortcomings, and discuss future directions in sampling, and genetics and genomics of endophytic fungi. Identifying responsible biosynthetic genes for the numerous secondary metabolites isolated from endophytic fungi opens the opportunity to explore the genetic potential of producer strains to discover novel secondary metabolites and enhance secondary metabolite production by metabolic engineering resulting in novel and more affordable medicines and food additives.
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Affiliation(s)
| | | | - Kristina Haslinger
- Groningen Institute of Pharmacy, Chemical and Pharmaceutical Biology, University of Groningen, Groningen, Netherlands
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21
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Burragoni SG, Jeon J. Applications of endophytic microbes in agriculture, biotechnology, medicine, and beyond. Microbiol Res 2021; 245:126691. [PMID: 33508761 DOI: 10.1016/j.micres.2020.126691] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/14/2020] [Accepted: 12/30/2020] [Indexed: 12/26/2022]
Abstract
Endophytes are emerging as integral components of plant microbiomes. Some of them play pivotal roles in plant development and plant responses to pathogens and abiotic stresses, whereas others produce useful and/or interesting secondary metabolites. The appreciation of their abilities to affect plant phenotypes and produce useful compounds via genetic and molecular interactions has paved the way for these abilities to be exploited for health and welfare of plants, humans and ecosystems. Here we comprehensively review current and potential applications of endophytes in the agricultural, pharmaceutical, and industrial sectors. In addition, we briefly discuss the research objectives that should be focused upon in the coming years in order for endophytes and their metabolites to be fully harnessed for potential use in diverse areas.
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Affiliation(s)
- Sravanthi Goud Burragoni
- Department of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
| | - Junhyun Jeon
- Department of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
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Genomics- and Metabolomics-Based Investigation of the Deep-Sea Sediment-Derived Yeast, Rhodotorula mucilaginosa 50-3-19/20B. Mar Drugs 2020; 19:md19010014. [PMID: 33396687 PMCID: PMC7823890 DOI: 10.3390/md19010014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/14/2020] [Accepted: 12/24/2020] [Indexed: 01/10/2023] Open
Abstract
Red yeasts of the genus Rhodotorula are of great interest to the biotechnological industry due to their ability to produce valuable natural products, such as lipids and carotenoids with potential applications as surfactants, food additives, and pharmaceuticals. Herein, we explored the biosynthetic potential of R. mucilaginosa 50-3-19/20B collected from the Mid-Atlantic Ridge using modern genomics and untargeted metabolomics tools. R. mucilaginosa 50-3-19/20B exhibited anticancer activity when grown on PDA medium, while antimicrobial activity was observed when cultured on WSP-30 medium. Applying the bioactive molecular networking approach, the anticancer activity was linked to glycolipids, namely polyol esters of fatty acid (PEFA) derivatives. We purified four PEFAs (1–4) and the known methyl-2-hydroxy-3-(1H-indol-2-yl)propanoate (5). Their structures were deduced from NMR and HR-MS/MS spectra, but 1–5 showed no anticancer activity in their pure form. Illumina-based genome sequencing, de novo assembly and standard biosynthetic gene cluster (BGC) analyses were used to illustrate key components of the PEFA biosynthetic pathway. The fatty acid producing BGC3 was identified to be capable of producing precursors of PEFAs. Some Rhodotorula strains are able to convert inulin into high-yielding PEFA and cell lipid using a native exo-inulinase enzyme. The genomic locus for an exo-inulinase enzyme (g1629.t1), which plays an instrumental role in the PEFA production via the mannitol biosynthesis pathway, was identified. This is the first untargeted metabolomics study on R. mucilaginosa providing new genomic insights into PEFA biosynthesis.
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Genomics and lipidomics analysis of the biotechnologically important oleaginous red yeast Rhodotorula glutinis ZHK provides new insights into its lipid and carotenoid metabolism. BMC Genomics 2020; 21:834. [PMID: 33243144 PMCID: PMC7690147 DOI: 10.1186/s12864-020-07244-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 11/18/2020] [Indexed: 11/26/2022] Open
Abstract
Background Rhodotorula glutinis is recognized as a biotechnologically important oleaginous red yeast, which synthesizes numerous meritorious compounds with wide industrial usages. One of the most notable properties of R. glutinis is the formation of intracellular lipid droplets full of carotenoids. However, the basic genomic features that underlie the biosynthesis of these valuable compounds in R. glutinis have not been fully documented. To reveal the biotechnological potential of R. glutinis, the genomics and lipidomics analysis was performed through the Next-Generation Sequencing and HPLC-MS-based metabolomics technologies. Results Here, we firstly assemble the genome of R. glutinis ZHK into 21.8 Mb, containing 30 scaffolds and 6774 predicted genes with a N50 length of 14, 66,672 bp and GC content of 67.8%. Genome completeness assessment (BUSCO alignment: 95.3%) indicated the genome assembly with a high-quality features. According to the functional annotation of the genome, we predicted several key genes involved in lipids and carotenoids metabolism as well as certain industrial enzymes biosynthesis. Comparative genomics results suggested that most of orthologous genes have underwent the strong purifying selection within the five Rhodotorula species, especially genes responsible for carotenoids biosynthesis. Furthermore, a total of 982 lipids were identified using the lipidomics approaches, mainly including triacylglycerols, diacylglyceryltrimethylhomo-ser and phosphatidylethanolamine. Conclusion Using whole genome shotgun sequencing, we comprehensively analyzed the genome of R. glutinis and predicted several key genes involved in lipids and carotenoids metabolism. By performing comparative genomic analysis, we show that most of the ortholog genes have undergone strong purifying selection within the five Rhodotorula species. Furthermore, we identified 982 lipid species using lipidomic approaches. These results provided valuable resources to further advance biotechnological applications of R .glutinis. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07244-z.
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Chen QL, Cai L, Wang HC, Cai LT, Goodwin P, Ma J, Wang F, Li Z. Fungal Composition and Diversity of the Tobacco Leaf Phyllosphere During Curing of Leaves. Front Microbiol 2020; 11:554051. [PMID: 33013785 PMCID: PMC7499341 DOI: 10.3389/fmicb.2020.554051] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/12/2020] [Indexed: 11/16/2022] Open
Abstract
Rhizopus oryzae causes tobacco pole rot in China during tobacco flue-curing. Flue-curing is a post-harvest process done to prepare tobacco leaves and involves three different stages: the yellowing stage has the lowest temperatures and highest humidity, then the color-fixing stage has higher temperatures and medium humidity, and finally the stem-drying stage has the highest temperatures and lowest humidity. In this study, fungal culturing and IonS5XL high-throughput sequencing techniques were used to reveal the fungal community of the petioles and lamina of tobacco leaves infected with pole rot during flue-curing. A total of 108 fungal isolates belonging to 6 genera were isolated on media. The most common fungal species isolated was the pathogen, R. oryzae, that was most often found equally on petioles and laminas in the color-fixing stage, followed by saprotrophs, mostly Aspergillus spp. High-throughput sequencing revealed saprotrophs with Alternaria being the most abundant genus, followed by Phoma, Cercospora, and Aspergillus, whereas Rhizopus was the tenth most abundant genus, which was mostly found on petioles at the yellowing stage. Both culturable fungal diversity and fungal sequence diversity was higher at stem-drying stage than the yellowing and color-fixing stages, and diversity was higher with leaf lamina than petioles revealing that the changes in fungal composition and diversity during the curing process were similar with both methods. This study demonstrates that the curing process affects the leaf microbiome of tobacco during the curing process, and future work could examine if any of these saprotrophic fungi detected during the curing of tobacco leaves may be potential biocontrol agents for with pole rot in curing chambers.
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Affiliation(s)
- Qian-Li Chen
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, China
- College of Agriculture, Guizhou University, Guiyang, China
| | - Lin Cai
- College of Plant Protection, Southwest University, Chongqing, China
| | - Han-Cheng Wang
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Liu-Ti Cai
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Paul Goodwin
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Jun Ma
- Qianxinan Branch of Guizhou Tobacco Company, Guiyang, China
| | - Feng Wang
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Zhong Li
- College of Agriculture, Guizhou University, Guiyang, China
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25
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Elmassry MM, Ray N, Sorge S, Webster J, Merry K, Caserio A, Vecellio DJ, Kruczek C, Dowd S, Ardon-Dryer K, Vanos J, San Francisco MJ. Investigating the culturable atmospheric fungal and bacterial microbiome in West Texas: implication of dust storms and origins of the air parcels. FEMS MICROBES 2020; 1:xtaa009. [PMID: 37333960 PMCID: PMC10117434 DOI: 10.1093/femsmc/xtaa009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/21/2020] [Indexed: 11/10/2023] Open
Abstract
Individuals often experience ailments such as allergies, asthma and respiratory tract infections throughout the year. Weather reports often include estimations of common allergens that can affect these individuals. To describe the local 'atmospheric microbiome' in Lubbock, Texas, USA, we examined the culturable fungal and bacterial microbiome present in the air on calm and dust storm days using internal transcribed spacer (ITS)-1 and 16S rRNA amplicon sequencing, respectively. While some types of airborne fungi were frequently present throughout the year, distinct differences were also observed between calm and dust storm days. We also observed the influence of the origin of air parcels and wind elevation of the air trajectory. The most abundant genera of fungi identified during the study period were Cryptococcus, Aureobasidium, Alternaria, Cladosporium and Filobasidium. This observation was not surprising considering the agricultural intensive environment of West Texas. Interestingly, Cladosporium, a common allergenic mold, was increased during days with dust storm events. The predominant bacterial genera observed were Bacillus, Pseudomonas, Psychrobacter, Massilia and Exiguobacterium. The relative abundance of the psychrophiles, Psychrobacter and Exiguobacterium, was surprising, given the semi-aridity of West Texas. Coupling our observations with back trajectories of the wind (Hybrid Single-Particle Lagrangian Integrated Trajectory models) demonstrated that dust storms, regional anthropogenic activity and origin of air parcels are important influences on the diversity and temporal presence of the atmospheric microbiome.
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Affiliation(s)
- Moamen M Elmassry
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Nandini Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Sara Sorge
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Jennifer Webster
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Kyle Merry
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Angelica Caserio
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Daniel J Vecellio
- Department of Geography, Texas A&M University, College Station, TX 77843, USA
| | - Cassandra Kruczek
- Department of Medical Education, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Scot Dowd
- Molecular Research LP, Clovis Road, Shallowater, TX 79363, USA
| | - Karin Ardon-Dryer
- Department of Geosciences, Atmospheric Science Group, Texas Tech University, Lubbock, TX 79409, USA
| | - Jennifer Vanos
- School of Sustainability, Arizona State University, Tempe, AZ 85281, USA
| | - Michael J San Francisco
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
- Honors College, Texas Tech University, Lubbock, TX 79410, USA
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26
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Geetha Thanuja K, Annadurai B, Thankappan S, Uthandi S. Non-rhizobial endophytic (NRE) yeasts assist nodulation of Rhizobium in root nodules of blackgram (Vigna mungo L.). Arch Microbiol 2020; 202:2739-2749. [PMID: 32737540 DOI: 10.1007/s00203-020-01983-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/25/2020] [Accepted: 07/14/2020] [Indexed: 10/23/2022]
Abstract
The signal orchestration between legumes and the rhizobia attribute to symbiotic nitrogen fixation through nodule formation. Root nodules serve as a nutrient-rich reservoir and harbor diverse microbial communities. However, the existence of non-rhizobial endophytes (NRE) and their role inside the root nodules are being explored; there is no evidence on yeast microflora inhabiting nodule niche. This study focused on unraveling the presence of yeast in the root nodules and their possible function in either nodulation or signal exchange. From the root nodules of blackgram, two yeast strains were isolated and identified as Candida glabrata VYP1 and Candida tropicalis VYW1 based on 18S rRNA gene sequencing and phylogeny. These strains possessed plant growth-promoting traits viz., IAA, ACC deaminase, siderophore, ammonia, and polyamine production. The functional capacity of endophytic yeast strains, and their interaction with Rhizobium sp. was further unveiled via profiling volatile organic compounds (VOC). Among the VOCs, α-glucopyranoside and pyrroloquinoline pitches a pivotal role in activating lectin pathways and phosphorous metabolism. Further, lectin pathways are crucial for nodulating bacterium, and our study showed that these endophytic yeasts assist nodulation by Rhizobium sp. via activating the nod factors. The plant growth-promoting traits of NRE yeast strains coupled with their metabolite production, could recruit them as potential drivers in the plant-microbe interaction.
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Affiliation(s)
- Kalyanasundaram Geetha Thanuja
- Biocatalysts Laboratory, Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India
| | - Brundha Annadurai
- Biocatalysts Laboratory, Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India
| | - Sugitha Thankappan
- Biocatalysts Laboratory, Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India
| | - Sivakumar Uthandi
- Biocatalysts Laboratory, Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India.
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Queiroz CBD, Santana MF. Prediction of the secretomes of endophytic and nonendophytic fungi reveals similarities in host plant infection and colonization strategies. Mycologia 2020; 112:491-503. [PMID: 32286912 DOI: 10.1080/00275514.2020.1716566] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Endophytic fungi are microorganisms that inhabit internal plant tissues without causing apparent damage. During the infection process, both endophytic and phytopathogenic fungi secrete proteins to resist or supplant the plant's defense mechanisms. This study analyzed the predicted secretomes of six species of endophytic fungi and compared them with predicted secretomes of eight fungal species with different lifestyles: saprophytic, necrotrophic, hemibiotrophic, and biotrophic. The sizes of the predicted secretomes varied from 260 to 1640 proteins, and the predicted secretomes have a wide diversity of CAZymes, proteases, and conserved domains. Regarding the CAZymes in the secretomes of the analyzed fungi, the most abundant CAZyme families were glycosyl hydrolase and serine proteases. Several predicted proteins have characteristics similar to those found in small, secreted proteins with effector characteristics (SSPEC). The most abundant conserved domains, besides those found in the SSPEC, have oxidation activities, indicating that these proteins can protect the fungus against oxidative stress, against domains with protease activity, which may be involved in the mechanisms of nutrition, or against lytic enzymes secreted by the host plant. This study demonstrates that secretomes of endophytic and nonendophytic fungi share an arsenal of proteins important in the process of infection and colonization of host plants.
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Affiliation(s)
- Casley Borges de Queiroz
- Laboratório de Biologia Molecular, Embrapa Amazônia Ocidental , Rodovia AM 10, km 29, s/n, CEP: 69010-970, Manaus, Amazonas, Brazil
| | - Mateus Ferreira Santana
- Departamento de Microbiologia (BIOAGRO), Universidade Federal de Viçosa , CEP: 36570-900, Viçosa, Minas Gerais, Brazil
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28
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Gupta S, Chaturvedi P, Kulkarni MG, Van Staden J. A critical review on exploiting the pharmaceutical potential of plant endophytic fungi. Biotechnol Adv 2020; 39:107462. [DOI: 10.1016/j.biotechadv.2019.107462] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 09/22/2019] [Accepted: 10/22/2019] [Indexed: 02/08/2023]
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29
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Sui Y, Wisniewski M, Droby S, Piombo E, Wu X, Yue J. Genome Sequence, Assembly, and Characterization of the Antagonistic Yeast Candida oleophila Used as a Biocontrol Agent Against Post-harvest Diseases. Front Microbiol 2020; 11:295. [PMID: 32158440 PMCID: PMC7052047 DOI: 10.3389/fmicb.2020.00295] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/10/2020] [Indexed: 11/29/2022] Open
Abstract
Candida oleophila is an effective biocontrol agent used to control post-harvest diseases of fruits and vegetables. C. oleophila I-182 was the active agent used in the first-generation yeast-based commercial product, Aspire®, for post-harvest disease management. Several action modes, like competition for nutrients and space, induction of pathogenesis-related genes in host tissues, and production of extracellular lytic enzymes, have been demonstrated for the biological control activity exhibited by C. oleophila through which it inhibits post-harvest pathogens. In the present study, the whole genome of C. oleophila I-182 was sequenced using PacBio and Illumina shotgun sequencing technologies, yielding an estimated genome size of 14.73 Mb. The genome size is similar in length to that of the model yeast strain Saccharomyces cerevisiae S288c. Based on the assembled genome, protein-coding sequences were identified and annotated. The predicted genes were further assigned with gene ontology terms and clustered in special functional groups. A comparative analysis of C. oleophila proteome with the proteomes of 11 representative yeasts revealed 2 unique and 124 expanded families of proteins in C. oleophila. Availability of the genome sequence will facilitate a better understanding the properties of biocontrol yeasts at the molecular level.
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Affiliation(s)
- Yuan Sui
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, College of Forestry and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, China
| | - Michael Wisniewski
- U.S. Department of Agriculture-Agricultural Research Service, Kearneysville, WV, United States
| | - Samir Droby
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
| | - Edoardo Piombo
- Department of Agricultural, Forestry and Food Sciences, University of Turin, Turin, Italy
| | - Xuehong Wu
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Junyang Yue
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
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30
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Paul K, Saha C, Nag M, Mandal D, Naiya H, Sen D, Mitra S, Kumar M, Bose D, Mukherjee G, Naskar N, Lahiri S, Das Ghosh U, Tripathi S, Sarkar MP, Banerjee M, Kleinert A, Valentine AJ, Tripathy S, Sinharoy S, Seal A. A Tripartite Interaction among the Basidiomycete Rhodotorula mucilaginosa, N 2-Fixing Endobacteria, and Rice Improves Plant Nitrogen Nutrition. THE PLANT CELL 2020; 32:486-507. [PMID: 31757927 PMCID: PMC7008492 DOI: 10.1105/tpc.19.00385] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 10/25/2019] [Accepted: 11/19/2019] [Indexed: 05/21/2023]
Abstract
Nitrogen (N) limits crop yield, and improvement of N nutrition remains a key goal for crop research; one approach to improve N nutrition is identifying plant-interacting, N2-fixing microbes. Rhodotorula mucilaginosa JGTA-S1 is a basidiomycetous yeast endophyte of narrowleaf cattail (Typha angustifolia). JGTA-S1 could not convert nitrate or nitrite to ammonium but harbors diazotrophic (N2-fixing) endobacteria (Pseudomonas stutzeri) that allow JGTA-S1 to fix N2 and grow in a N-free environment; moreover, P. stutzeri dinitrogen reductase was transcribed in JGTA-S1 even under adequate N. Endobacteria-deficient JGTA-S1 had reduced fitness, which was restored by reintroducing P. stutzeri JGTA-S1 colonizes rice (Oryza sativa), significantly improving its growth, N content, and relative N-use efficiency. Endofungal P. stutzeri plays a significant role in increasing the biomass and ammonium content of rice treated with JGTA-S1; also, JGTA-S1 has better N2-fixing ability than free-living P. stutzeri and provides fixed N to the plant. Genes involved in N metabolism, N transporters, and NODULE INCEPTION-like transcription factors were upregulated in rice roots within 24 h of JGTA-S1 treatment. In association with rice, JGTA-S1 has a filamentous phase and P. stutzeri only penetrated filamentous JGTA-S1. Together, these results demonstrate an interkingdom interaction that improves rice N nutrition.
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Affiliation(s)
- Karnelia Paul
- Department of Biotechnology and Dr. B.C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata 700019, India
| | - Chinmay Saha
- Department of Biotechnology and Dr. B.C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata 700019, India
- Department of Endocrinology & Metabolism, Institute of Post Graduate Medical Education & Research and SSKM Hospital, Kolkata 700020, West Bengal, India
| | - Mayurakshi Nag
- Department of Biotechnology and Dr. B.C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata 700019, India
| | - Drishti Mandal
- National Institute of Plant Genome Research, New Delhi 110067, India
| | - Haraprasad Naiya
- Department of Biotechnology and Dr. B.C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata 700019, India
- ICAR-Indian Institute of Natural Resins and Gums Namkum, Ranchi 834010, Jharkhand, India
| | - Diya Sen
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Stockholm, SE 75007, Sweden
- Computational Genomics Laboratory, Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Souvik Mitra
- Department of Botany, Darjeeling Government College, Darjeeling 734101, India
| | - Mohit Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Dipayan Bose
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata 700064, India
| | - Gairik Mukherjee
- Department of Biotechnology and Dr. B.C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata 700019, India
| | - Nabanita Naskar
- Saha Institute of Nuclear Physics, Kolkata 700064, India
- Department of Environmental Science, University of Calcutta, Kolkata 700019, India
| | - Susanta Lahiri
- Saha Institute of Nuclear Physics, Kolkata 700064, India
| | - Upal Das Ghosh
- P.G. Department of Botany, Bidhannagar College, Kolkata 700026, India
| | - Sudipta Tripathi
- Agricultural Experimental Farm, Institute of Agricultural Science, University of Calcutta, Kolkata 700144, India
| | | | - Manidipa Banerjee
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Aleysia Kleinert
- Botany & Zoology Department, University of Stellenbosch Private Bag X1 Matieland 7602 South Africa
| | - Alexander J Valentine
- Botany & Zoology Department, University of Stellenbosch Private Bag X1 Matieland 7602 South Africa
| | - Sucheta Tripathy
- Computational Genomics Laboratory, Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Senjuti Sinharoy
- National Institute of Plant Genome Research, New Delhi 110067, India
| | - Anindita Seal
- Department of Biotechnology and Dr. B.C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata 700019, India
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31
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Long XE, Yao H. Phosphorus Input Alters the Assembly of Rice (Oryza sativa L.) Root-Associated Communities. MICROBIAL ECOLOGY 2020; 79:357-366. [PMID: 31342100 DOI: 10.1007/s00248-019-01407-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
Rice root-associated microbial community play an important role in plant nutrient acquisition, biomass production, and stress tolerance. Herein, root-associated community assembly was investigated under different phosphate input levels in phosphorus (P)-deficient paddy soil. Rice was grown in a long-term P-depleted paddy soil with 0 (P0), 50 (PL), or 200 (PH) mg P2O5 kg-1 application. DNA from root endophytes was isolated after 46 days, and PCR amplicons from archaea, bacteria, and fungi were sequenced by an Illumina Miseq PE300 platform, respectively. P application had no significant effect on rice root endophytic archaea, which were dominated by ammonia-oxidizing Candidatus Nitrososphaera. By contrast, rice root endophytic community structure of the bacteria and fungi was affected by soil P. Low P input increased endophytic bacterial diversity, whereas high P input increased rhizosphere fungi diversity. Bacillus and Pleosporales, associated with phosphate solubilization and P uptake, dominated in P0 and PH treatments, and Pseudomonas were more abundant in the PL treatment than in the P0 and PH treatments. Co-occurrence network analysis revealed a close interaction between endophytic bacteria and fungi. Soil P application affected both the rice root endosphere and soil rhizosphere microbial community and interaction between rice root endophytic bacteria, and fungi, especially species related to P cycling.
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Affiliation(s)
- Xi-En Long
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen, 361021, China
- School of Geographic Sciences, Nantong University, No. 999 Tongjing Road, Nantong, 226007, China
| | - Huaiying Yao
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen, 361021, China.
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, 206 Guanggu 1st Road, Wuhan, 430205, China.
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32
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Su X, Zhou M, Hu P, Xiao Y, Wang Z, Mei R, Hashmi MZ, Lin H, Chen J, Sun F. Whole-genome sequencing of an acidophilic Rhodotorula sp. ZM1 and its phenol-degrading capability under acidic conditions. CHEMOSPHERE 2019; 232:76-86. [PMID: 31152906 DOI: 10.1016/j.chemosphere.2019.05.195] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 04/09/2019] [Accepted: 05/22/2019] [Indexed: 05/16/2023]
Abstract
The goal of this work was to investigate the genetics of an acidophilic phenol-degrading yeast strain using whole-genome sequencing (WGS), characterize the growth of the strain and phenol degradation capability as well as degradation pathway under extremely acidic conditions. The result showed that the strain ZM1 isolated from an acid mine drainage (AMD) belongs to basidiomycetous yeast Rhodotorula sp., which possesses some unique genes compared to other four closely related Rhodotorula species. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested that ZM1 possessed the degradation potentials for aromatic compounds. ZM1 was acidophilic with the optimum growth at the initial pH of 3.0. It could adjust pH to desired levels probably by acid production during the cultivation. Notably, at pH 3.0, the strain ZM1 showed a high phenol-degrading capability that almost completely degraded 1100 mg/L of phenol in 120 h with the highest degradation rate of 0.074 g/(g cell dry weight h). Under the same pH, the strain could completely degrade 500 mg/L phenol within 48 h at NaCl concentration up to 10 g/L. The identification of the gene catA by the KEGG analysis, together with the presence of metabolic intermediate of cis, cis-muconic acid detected by gas chromatography-mass spectrometry, confirmed that the strain ZM1 degraded phenol via ortho-cleavage pathway. These findings suggest that the indigenous yeasts strain ZM1 could be exploited as an important member for in-situ biodegradation of aromatic compounds in the extremely acidic environments.
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Affiliation(s)
- Xiaomei Su
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Meng Zhou
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Pin Hu
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Yeyuan Xiao
- Department of Civil and Environmental Engineering, Shantou University, Shantou, Guangdong, 515063, China
| | - Zhen Wang
- Environmental Science Research and Design Institute of Zhejiang Province, Hangzhou, 310007, China
| | - Rongwu Mei
- Environmental Science Research and Design Institute of Zhejiang Province, Hangzhou, 310007, China
| | | | - Hongjun Lin
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Jianrong Chen
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Faqian Sun
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China.
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33
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Weitemier K, Straub SC, Fishbein M, Bailey CD, Cronn RC, Liston A. A draft genome and transcriptome of common milkweed ( Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae. PeerJ 2019; 7:e7649. [PMID: 31579586 PMCID: PMC6756140 DOI: 10.7717/peerj.7649] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/09/2019] [Indexed: 02/06/2023] Open
Abstract
Milkweeds (Asclepias) are used in wide-ranging studies including floral development, pollination biology, plant-insect interactions and co-evolution, secondary metabolite chemistry, and rapid diversification. We present a transcriptome and draft nuclear genome assembly of the common milkweed, Asclepias syriaca. This reconstruction of the nuclear genome is augmented by linkage group information, adding to existing chloroplast and mitochondrial genomic resources for this member of the Apocynaceae subfamily Asclepiadoideae. The genome was sequenced to 80.4× depth and the draft assembly contains 54,266 scaffolds ≥1 kbp, with N50 = 3,415 bp, representing 37% (156.6 Mbp) of the estimated 420 Mbp genome. A total of 14,474 protein-coding genes were identified based on transcript evidence, closely related proteins, and ab initio models, and 95% of genes were annotated. A large proportion of gene space is represented in the assembly, with 96.7% of Asclepias transcripts, 88.4% of transcripts from the related genus Calotropis, and 90.6% of proteins from Coffea mapping to the assembly. Scaffolds covering 75 Mbp of the Asclepias assembly formed 11 linkage groups. Comparisons of these groups with pseudochromosomes in Coffea found that six chromosomes show consistent stability in gene content, while one may have a long history of fragmentation and rearrangement. The progesterone 5β-reductase gene family, a key component of cardenolide production, is likely reduced in Asclepias relative to other Apocynaceae. The genome and transcriptome of common milkweed provide a rich resource for future studies of the ecology and evolution of a charismatic plant family.
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Affiliation(s)
- Kevin Weitemier
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | | | - Mark Fishbein
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK, USA
| | - C. Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Richard C. Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, USA
| | - Aaron Liston
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, USA
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34
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Sen D, Paul K, Saha C, Mukherjee G, Nag M, Ghosh S, Das A, Seal A, Tripathy S. A unique life-strategy of an endophytic yeast Rhodotorula mucilaginosa JGTA-S1-a comparative genomics viewpoint. DNA Res 2019; 26:131-146. [PMID: 30615101 PMCID: PMC6476726 DOI: 10.1093/dnares/dsy044] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 12/05/2018] [Indexed: 01/30/2023] Open
Abstract
Endophytic yeasts of genus Rhodotorula are gaining importance for their ability to improve plant growth. The nature of their interaction with plants, however, remains unknown. Rhodotorula mucilaginosa JGTA-S1 was isolated as an endophyte of Typha angustifolia and promoted growth in the host. To investigate the life-strategy of the yeast from a genomics perspective, we used Illumina and Oxford Nanopore reads to generate a high-quality annotated draft assembly of JGTA-S1 and compared its genome to three other Rhodotorula yeasts and the close relative Rhodosporidium toruloides. JGTA-S1 is a haploid yeast possessing several genes potentially facilitating its endophytic lifestyle such as those responsible for solubilizing phosphate and producing phytohormones. An intact mating-locus in JGTA-S1 raised the possibility of a yet unknown sexual reproductive cycle in Rhodotorula yeasts. Additionally, JGTA-S1 had functional anti-freezing genes and was also unique in lacking a functional nitrate-assimilation pathway—a feature that is associated with obligate biotrophs. Nitrogen-fixing endobacteria were found within JGTA-S1 that may circumvent this defective N-metabolism. JGTA-S1 genome data coupled with experimental evidence give us an insight into the nature of its beneficial interaction with plants.
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Affiliation(s)
- Diya Sen
- Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India
| | - Karnelia Paul
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
| | - Chinmay Saha
- Department of Endocrinology & Metabolism, Institute of Post Graduate Medical Education & Research and SSKM Hospital, Kolkata, West Bengal, India
| | - Gairik Mukherjee
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
| | - Mayurakshi Nag
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
| | - Samrat Ghosh
- Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research, New Delhi, India
| | - Abhishek Das
- Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research, New Delhi, India
| | - Anindita Seal
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
| | - Sucheta Tripathy
- Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research, New Delhi, India
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35
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Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: major ecological adaptations and evolutionary transitions. Biol Rev Camb Philos Soc 2019; 94:1443-1476. [PMID: 31021528 PMCID: PMC6850671 DOI: 10.1111/brv.12510] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 12/13/2022]
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). Throughout this review we use an evolutionary and comparative-genomics perspective to understand fungal ecological diversity. Finally, we highlight the importance of genome-enabled inferences to envision plausible narratives and scenarios for important transitions.
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Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
| | - Toni Gabaldón
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF)08003BarcelonaSpain
- ICREA, Pg. Lluís Companys 2308010BarcelonaSpain
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36
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Correia K, Yu SM, Mahadevan R. AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019; 2019:5403499. [PMID: 30893420 PMCID: PMC6425859 DOI: 10.1093/database/baz022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/17/2019] [Accepted: 01/28/2019] [Indexed: 12/14/2022]
Abstract
Budding yeasts inhabit a range of environments by exploiting various metabolic traits. The genetic bases for these traits are mostly unknown, preventing their addition or removal in a chassis organism for metabolic engineering. Insight into the evolution of orthologs, paralogs and xenologs in the yeast pan-genome can help bridge these genotypes; however, existing phylogenomic databases do not span diverse yeasts, and sometimes cannot distinguish between these homologs. To help understand the molecular evolution of these traits in yeasts, we created Analyzing Yeasts by Reconstructing Ancestry of Homologs (AYbRAH), an open-source database of predicted and manually curated ortholog groups for 33 diverse fungi and yeasts in Dikarya, spanning 600 million years of evolution. OrthoMCL and OrthoDB were used to cluster protein sequence into ortholog and homolog groups, respectively; MAFFT and PhyML reconstructed the phylogeny of all homolog groups. Ortholog assignments for enzymes and small metabolite transporters were compared to their phylogenetic reconstruction, and curated to resolve any discrepancies. Information on homolog and ortholog groups can be viewed in the AYbRAH web portal (https://lmse.github.io/aybrah/), including functional annotations, predictions for mitochondrial localization and transmembrane domains, literature references and phylogenetic reconstructions. Ortholog assignments in AYbRAH were compared to HOGENOM, KEGG Orthology, OMA, eggNOG and PANTHER. PANTHER and OMA had the most congruent ortholog groups with AYbRAH, while the other phylogenomic databases had greater amounts of under-clustering, over-clustering or no ortholog annotations for proteins. Future plans are discussed for AYbRAH, and recommendations are made for other research communities seeking to create curated ortholog databases.
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Affiliation(s)
- Kevin Correia
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, College Street, Toronto, ON, Canada
| | - Shi M Yu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, College Street, Toronto, ON, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, College Street, Toronto, ON, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, College Street, Toronto, ON, Canada
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Identification of Novel Endophytic Yeast Strains from Tangerine Peel. Curr Microbiol 2019; 76:1066-1072. [DOI: 10.1007/s00284-019-01721-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/19/2019] [Indexed: 01/14/2023]
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38
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Aghai MM, Khan Z, Joseph MR, Stoda AM, Sher AW, Ettl GJ, Doty SL. The Effect of Microbial Endophyte Consortia on Pseudotsuga menziesii and Thuja plicata Survival, Growth, and Physiology Across Edaphic Gradients. Front Microbiol 2019; 10:1353. [PMID: 31275276 PMCID: PMC6591459 DOI: 10.3389/fmicb.2019.01353] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/31/2019] [Indexed: 11/17/2022] Open
Abstract
Increased frequency of droughts and degraded edaphic conditions decreases the success of many reforestation efforts in the Pacific Northwest. Microbial endophyte consortia have been demonstrated to contribute to plant growth promotion and protection from abiotic and biotic stresses – specifically drought conditions – across a number of food crops but for limited tree species. Our research aimed to investigate the potential to improve establishment of economically and ecologically important conifers through a series of in situ field trials and ex situ simulations. Microbial endophyte consortia from Salicaceae, previously shown to confer drought tolerance, and conifer endophyte strains with potentially symbiotic traits were selected for trials with Douglas-fir (Pseudotsuga menziesii) and western redcedar (Thuja plicata). Reductive experimentation was used to subject seedlings to a spectrum of simulated drought levels or presence/absence of fertilizer, testing hypotheses that endophyte consortia impart improved drought resistance and growth promotion, respectively. Inoculation from Salicaceae consortia significantly (p ≤ 0.05) improved survival among seedlings of both species subject to increasing drought stress, with T. plicata seedlings surviving at twofold higher rates in extreme drought conditions. Both species demonstrated improved growth 540 days after inoculation of seed with conifer derived consortia. In the carefully controlled greenhouse experiments with both species, seedling Fv/Fm and SPAD values remained significantly (p ≤ 0.05) more stable in inoculated treatment groups as stress increased. Our findings confirm that multi-strain consortia may be applied as seed or field amendment to conifers, and the approach is efficient in garnering a positive growth response and can mitigate abiotic stressors.
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Affiliation(s)
- Matthew M Aghai
- UW Center for Sustainable Forestry at Pack Forest, Eatonville, WA, United States.,School of Environmental and Forest Sciences, University of Washington, Seattle, WA, United States
| | - Zareen Khan
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, United States
| | - Matthew R Joseph
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, United States
| | - Aubrey M Stoda
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, United States
| | - Andrew W Sher
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, United States
| | - Gregory J Ettl
- UW Center for Sustainable Forestry at Pack Forest, Eatonville, WA, United States.,School of Environmental and Forest Sciences, University of Washington, Seattle, WA, United States
| | - Sharon L Doty
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, United States
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39
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Bergeron MJ, Feau N, Stewart D, Tanguay P, Hamelin RC. Genome-enhanced detection and identification of fungal pathogens responsible for pine and poplar rust diseases. PLoS One 2019; 14:e0210952. [PMID: 30726264 PMCID: PMC6364900 DOI: 10.1371/journal.pone.0210952] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/06/2019] [Indexed: 01/19/2023] Open
Abstract
Biosurveillance is a proactive approach that may help to limit the spread of invasive fungal pathogens of trees, such as rust fungi which have caused some of the world's most damaging diseases of pines and poplars. Most of these fungi have a complex life cycle, with up to five spore stages, which is completed on two different hosts. They have a biotrophic lifestyle and may be propagated by asymptomatic plant material, complicating their detection and identification. A bioinformatics approach, based on whole genome comparison, was used to identify genome regions that are unique to the white pine blister rust fungus, Cronartium ribicola, the poplar leaf rust fungi Melampsora medusae and Melampsora larici-populina or to members of either the Cronartium and Melampsora genera. Species- and genus-specific real-time PCR assays, targeting these unique regions, were designed with the aim of detecting each of these five taxonomic groups. In total, twelve assays were developed and tested over a wide range of samples, including different spore types, different infected plant parts on the pycnio-aecial or uredinio-telial host, and captured insect vectors. One hundred percent detection accuracy was achieved for the three targeted species and two genera with either a single assay or a combination of two assays. This proof of concept experiment on pine and poplar leaf rust fungi demonstrates that the genome-enhanced detection and identification approach can be translated into effective real-time PCR assays to monitor tree fungal pathogens.
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Affiliation(s)
- Marie-Josée Bergeron
- Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, Québec, Québec, Canada
| | - Nicolas Feau
- Forest Sciences Centre, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Don Stewart
- Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, Québec, Québec, Canada
| | - Philippe Tanguay
- Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, Québec, Québec, Canada
| | - Richard C. Hamelin
- Forest Sciences Centre, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Institut de Biologie Intégrative des Systèmes, Université Laval, Québec, Québec, Canada
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40
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Exploring the Benefits of Endophytic Fungi via Omics. ADVANCES IN ENDOPHYTIC FUNGAL RESEARCH 2019. [DOI: 10.1007/978-3-030-03589-1_4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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41
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Camiolo S, Toome-Heller M, Aime MC, Haridas S, Grigoriev IV, Porceddu A, Mannazzu I. An analysis of codon bias in six red yeast species. Yeast 2018; 36:53-64. [PMID: 30264407 DOI: 10.1002/yea.3359] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 09/10/2018] [Accepted: 09/23/2018] [Indexed: 11/11/2022] Open
Abstract
Red yeasts, primarily species of Rhodotorula, Sporobolomyces, and other genera of Pucciniomycotina, are traditionally considered proficient systems for lipid and terpene production, and only recently have also gained consideration for the production of a wider range of molecules of biotechnological potential. Improvements of transgene delivery protocols and regulated gene expression systems have been proposed, but a dearth of information on compositional and/or structural features of genes has prevented transgene sequence optimization efforts for high expression levels. Here, the codon compositional features of genes in six red yeast species were characterized, and the impact that evolutionary forces may have played in shaping this compositional bias was dissected by using several computational approaches. Results obtained are compatible with the hypothesis that mutational bias, although playing a significant role, cannot alone explain synonymous codon usage bias of genes. Nevertheless, several lines of evidences indicated a role for translational selection in driving the synonymous codons that allow high expression efficiency. These optimal synonymous codons are identified for each of the six species analyzed. Moreover, the presence of intragenic patterns of codon usage, which are thought to facilitate polyribosome formation, was highlighted. The information presented should be taken into consideration for transgene design for optimal expression in red yeast species.
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Affiliation(s)
- Salvatore Camiolo
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Merje Toome-Heller
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - Sajeet Haridas
- US Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Andrea Porceddu
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Ilaria Mannazzu
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
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42
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Mukherjee G, Saha C, Naskar N, Mukherjee A, Mukherjee A, Lahiri S, Majumder AL, Seal A. An Endophytic Bacterial Consortium modulates multiple strategies to improve Arsenic Phytoremediation Efficacy in Solanum nigrum. Sci Rep 2018; 8:6979. [PMID: 29725058 PMCID: PMC5934359 DOI: 10.1038/s41598-018-25306-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 04/16/2018] [Indexed: 12/31/2022] Open
Abstract
Endophytic microbes isolated from plants growing in contaminated habitats possess specialized properties that help their host detoxify the contaminant/s. The possibility of using microbe-assisted phytoremediation for the clean-up of Arsenic (As) contaminated soils of the Ganga-Brahmaputra delta of India, was explored using As-tolerant endophytic microbes from an As-tolerant plant Lantana camara collected from the contaminated site and an intermediate As-accumulator plant Solanum nigrum. Endophytes from L. camara established within S. nigrum as a surrogate host. The microbes most effectively improved plant growth besides increasing bioaccumulation and root-to-shoot transport of As when applied as a consortium. Better phosphate nutrition, photosynthetic performance, and elevated glutathione levels were observed in consortium-treated plants particularly under As-stress. The consortium maintained heightened ROS levels in the plant without any deleterious effect and concomitantly boosted distinct antioxidant defense mechanisms in the shoot and root of As-treated plants. Increased consortium-mediated As(V) to As(III) conversion appeared to be a crucial step in As-detoxification/translocation. Four aquaporins were differentially regulated by the endophytes and/or As. The most interesting finding was the strong upregulation of an MRP transporter in the root by the As + endophytes, which suggested a major alteration of As-detoxification/accumulation pattern upon endophyte treatment that improved As-phytoremediation.
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Affiliation(s)
- Gairik Mukherjee
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Chinmay Saha
- Department of Endocrinology & Metabolism, Institute Of Post Graduate Medical Education & Research and SSKM Hospital, Room No. 9A, 4th Floor, Ronald Ross Building, 244, AJC Bose Road, Kolkata, 700020, India
| | - Nabanita Naskar
- Department of Environmental Science, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
- Saha Institute of Nuclear Physics, Sector - 1, Block - AF Bidhannagar, Kolkata, 700064, India
| | - Abhishek Mukherjee
- Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Arghya Mukherjee
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Susanta Lahiri
- Saha Institute of Nuclear Physics, Sector - 1, Block - AF Bidhannagar, Kolkata, 700064, India
- Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Arun Lahiri Majumder
- Division of Plant Biology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Anindita Seal
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
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43
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Kot AM, Błażejak S, Gientka I, Kieliszek M, Bryś J. Torulene and torularhodin: "new" fungal carotenoids for industry? Microb Cell Fact 2018; 17:49. [PMID: 29587755 PMCID: PMC5870927 DOI: 10.1186/s12934-018-0893-z] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 03/17/2018] [Indexed: 03/11/2023] Open
Abstract
Torulene and torularhodin represent the group of carotenoids and are synthesized by yeasts and fungi. The most important producers of these two compounds include yeasts of Rhodotorula and Sporobolomyces genera. The first reports confirming the presence of torulene and torularhodin in the cells of microorganisms date to the 1930s and 1940s; however, only in the past few years, the number of works describing the properties of these compounds increased. These compounds have strong anti-oxidative and anti-microbial properties, and thus may be successfully used as food, feedstock, and cosmetics additives. In addition, tests performed on rats and mice showed that both torulene and torularhodin have anti-cancerous properties. In order to commercialize the production of these two carotenoids, it is necessary to obtain highly efficient yeast strains, for example, via mutagenization and optimization of cultivation conditions. Further studies on the activity of torulene and torularhodin on the human body are also needed.
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Affiliation(s)
- Anna M Kot
- Department of Biotechnology, Microbiology and Food Evaluation, Faculty of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159C, 02-776, Warsaw, Poland.
| | - Stanisław Błażejak
- Department of Biotechnology, Microbiology and Food Evaluation, Faculty of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159C, 02-776, Warsaw, Poland
| | - Iwona Gientka
- Department of Biotechnology, Microbiology and Food Evaluation, Faculty of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159C, 02-776, Warsaw, Poland
| | - Marek Kieliszek
- Department of Biotechnology, Microbiology and Food Evaluation, Faculty of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159C, 02-776, Warsaw, Poland
| | - Joanna Bryś
- Department of Chemistry, Faculty of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159C, 02-776, Warsaw, Poland
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Nguyen H, Das U, Wang B, Xie J. The matrices and constraints of GT/AG splice sites of more than 1000 species/lineages. Gene 2018; 660:92-101. [PMID: 29588184 DOI: 10.1016/j.gene.2018.03.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 03/08/2018] [Accepted: 03/12/2018] [Indexed: 12/11/2022]
Abstract
To provide a resource for the splice sites (SS) of different species, we calculated the matrices of nucleotide compositions of about 38 million splice sites from >1000 species/lineages. The matrices are enriched of aGGTAAGT (5'SS) or (Y)6N(C/t)AG(g/a)t (3'SS) overall; however, they are quite diverse among hundreds of species. The diverse matrices remain prominent even under sequence selection pressures, suggesting the existence of diverse constraints as well as U snRNAs and other spliceosomal factors and/or their interactions with the splice sites. Using an algorithm to measure and compare the splice site constraints across all species, we demonstrate their distinct differences quantitatively. As an example of the resource's application to answering specific questions, we confirm that high constraints of particular positions are significantly associated with transcriptome-wide, increased occurrences of alternative splicing when uncommon nucleotides are present. More interestingly, the abundance of alternative splicing in 16 species correlates with the average constraint index of splice sites in a bell curve. This resource will allow users to assess specific sequences/splice sites against the consensus of every Ensembl-annotated species, and to explore the evolutionary changes or relationship to alternative splicing and transcriptome diversity. Web-search or update features are also included.
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Affiliation(s)
- Hai Nguyen
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; University of Winnipeg, Winnipeg, MB R3B 2E9, Canada
| | - Urmi Das
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Benjamin Wang
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; University of Illinois Urbana-Champaign, IL, USA
| | - Jiuyong Xie
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
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45
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Tkavc R, Matrosova VY, Grichenko OE, Gostinčar C, Volpe RP, Klimenkova P, Gaidamakova EK, Zhou CE, Stewart BJ, Lyman MG, Malfatti SA, Rubinfeld B, Courtot M, Singh J, Dalgard CL, Hamilton T, Frey KG, Gunde-Cimerman N, Dugan L, Daly MJ. Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149. Front Microbiol 2018; 8:2528. [PMID: 29375494 PMCID: PMC5766836 DOI: 10.3389/fmicb.2017.02528] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/05/2017] [Indexed: 02/03/2023] Open
Abstract
Highly concentrated radionuclide waste produced during the Cold War era is stored at US Department of Energy (DOE) production sites. This radioactive waste was often highly acidic and mixed with heavy metals, and has been leaking into the environment since the 1950s. Because of the danger and expense of cleanup of such radioactive sites by physicochemical processes, in situ bioremediation methods are being developed for cleanup of contaminated ground and groundwater. To date, the most developed microbial treatment proposed for high-level radioactive sites employs the radiation-resistant bacterium Deinococcus radiodurans. However, the use of Deinococcus spp. and other bacteria is limited by their sensitivity to low pH. We report the characterization of 27 diverse environmental yeasts for their resistance to ionizing radiation (chronic and acute), heavy metals, pH minima, temperature maxima and optima, and their ability to form biofilms. Remarkably, many yeasts are extremely resistant to ionizing radiation and heavy metals. They also excrete carboxylic acids and are exceptionally tolerant to low pH. A special focus is placed on Rhodotorula taiwanensis MD1149, which was the most resistant to acid and gamma radiation. MD1149 is capable of growing under 66 Gy/h at pH 2.3 and in the presence of high concentrations of mercury and chromium compounds, and forming biofilms under high-level chronic radiation and low pH. We present the whole genome sequence and annotation of R. taiwanensis strain MD1149, with a comparison to other Rhodotorula species. This survey elevates yeasts to the frontier of biology's most radiation-resistant representatives, presenting a strong rationale for a role of fungi in bioremediation of acidic radioactive waste sites.
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Affiliation(s)
- Rok Tkavc
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Vera Y Matrosova
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Olga E Grichenko
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Robert P Volpe
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Polina Klimenkova
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Elena K Gaidamakova
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Carol E Zhou
- Lawrence Livermore National Laboratory, Computing Applications and Research Department, Livermore, CA, United States
| | - Benjamin J Stewart
- Biosciences and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Mathew G Lyman
- Biosciences and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Stephanie A Malfatti
- Biosciences and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Bonnee Rubinfeld
- Biosciences and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Melanie Courtot
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Jatinder Singh
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Clifton L Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,The American Genome Center, Bethesda, MD, United States
| | - Theron Hamilton
- Biological Defense Research Directorate, Naval Medical Research Center, Fredrick, MD, United States
| | - Kenneth G Frey
- Biological Defense Research Directorate, Naval Medical Research Center, Fredrick, MD, United States
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Lawrence Dugan
- Biosciences and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Michael J Daly
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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Landolfo S, Ianiri G, Camiolo S, Porceddu A, Mulas G, Chessa R, Zara G, Mannazzu I. CAR gene cluster and transcript levels of carotenogenic genes in Rhodotorula mucilaginosa. Microbiology (Reading) 2018; 164:78-87. [DOI: 10.1099/mic.0.000588] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sara Landolfo
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Giuseppe Ianiri
- Department of Agricultural, Environmental and Food Sciences, Università degli Studi del Molise, Via Francesco de Sanctis, 86100 Campobasso, Italy
- Present address: Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Salvatore Camiolo
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Andrea Porceddu
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Giuliana Mulas
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Rossella Chessa
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Giacomo Zara
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Ilaria Mannazzu
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
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Dupont PY, Cox MP. Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi. G3 (BETHESDA, MD.) 2017; 7:1301-1314. [PMID: 28235827 PMCID: PMC5386878 DOI: 10.1534/g3.116.038448] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/17/2017] [Indexed: 12/26/2022]
Abstract
Lateral gene transfer (LGT, also known as horizontal gene transfer), an atypical mechanism of transferring genes between species, has almost become the default explanation for genes that display an unexpected composition or phylogeny. Numerous methods of detecting LGT events all rely on two fundamental strategies: primary structure composition or gene tree/species tree comparisons. Discouragingly, the results of these different approaches rarely coincide. With the wealth of genome data now available, detection of laterally transferred genes is increasingly being attempted in large uncurated eukaryotic datasets. However, detection methods depend greatly on the quality of the underlying genomic data, which are typically complex for eukaryotes. Furthermore, given the automated nature of genomic data collection, it is typically impractical to manually verify all protein or gene models, orthology predictions, and multiple sequence alignments, requiring researchers to accept a substantial margin of error in their datasets. Using a test case comprising plant-associated genomes across the fungal kingdom, this study reveals that composition- and phylogeny-based methods have little statistical power to detect laterally transferred genes. In particular, phylogenetic methods reveal extreme levels of topological variation in fungal gene trees, the vast majority of which show departures from the canonical species tree. Therefore, it is inherently challenging to detect LGT events in typical eukaryotic genomes. This finding is in striking contrast to the large number of claims for laterally transferred genes in eukaryotic species that routinely appear in the literature, and questions how many of these proposed examples are statistically well supported.
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Affiliation(s)
- Pierre-Yves Dupont
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
- the Bio-Protection Research Centre, Massey University, Palmerston North 4442, New Zealand
| | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
- the Bio-Protection Research Centre, Massey University, Palmerston North 4442, New Zealand
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Castanera R, Borgognone A, Pisabarro AG, Ramírez L. Biology, dynamics, and applications of transposable elements in basidiomycete fungi. Appl Microbiol Biotechnol 2017; 101:1337-1350. [PMID: 28074220 DOI: 10.1007/s00253-017-8097-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 12/20/2016] [Accepted: 01/02/2017] [Indexed: 11/25/2022]
Abstract
The phylum Basidiomycota includes filamentous fungi and yeast species with different ecological and genomic characteristics. Transposable elements (TEs) are abundant components of most eukaryotic genomes, and their transition from being genomic parasites to key drivers of genomic architecture, functionality, and evolution is a subject receiving much attention. In light of the abundant genomic information released during the last decade, the aims of this mini-review are to discuss the dynamics and impact of TEs in basidiomycete fungi. To do this, we surveyed and explored data from 75 genomes, which encompass the phylogenetic diversity of the phylum Basidiomycota. We describe annotation approaches and analyze TE distribution in the context of species phylogeny and genome size. Further, we review the most relevant literature about the role of TEs in species lifestyle, their impact on genome architecture and functionality, and the defense mechanisms evolved to control their proliferation. Finally, we discuss potential applications of TEs that can drive future innovations in fungal research.
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Affiliation(s)
- Raúl Castanera
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006, Pamplona, Spain
| | - Alessandra Borgognone
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006, Pamplona, Spain
| | - Antonio G Pisabarro
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006, Pamplona, Spain
| | - Lucía Ramírez
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006, Pamplona, Spain.
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Phylogenetics and Phylogenomics of Rust Fungi. FUNGAL PHYLOGENETICS AND PHYLOGENOMICS 2017; 100:267-307. [DOI: 10.1016/bs.adgen.2017.09.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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