1
|
Ribeiro Tomé LM, Quintanilha-Peixoto G, Costa-Rezende DH, Salvador-Montoya CA, Cardoso D, S Araújo D, Freitas JM, Bielefeld Nardoto G, Alves-Silva G, Drechsler-Santos ER, Góes-Neto A. Comparative genomics and stable isotope analysis reveal the saprotrophic-pathogenic lifestyle of a neotropical fungus. mBio 2024; 15:e0142324. [PMID: 39012152 PMCID: PMC11325261 DOI: 10.1128/mbio.01423-24] [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: 06/03/2024] [Accepted: 06/20/2024] [Indexed: 07/17/2024] Open
Abstract
In terrestrial forested ecosystems, fungi may interact with trees in at least three distinct ways: (i) associated with roots as symbionts; (ii) as pathogens in roots, trunks, leaves, flowers, and fruits; or (iii) decomposing dead tree tissues on soil or even on dead tissues in living trees. Distinguishing the latter two nutrition modes is rather difficult in Hymenochaetaceae (Basidiomycota) species. Herein, we have used an integrative approach of comparative genomics, stable isotopes, host tree association, and bioclimatic data to investigate the lifestyle ecology of the scarcely known neotropical genus Phellinotus, focusing on the unique species Phellinotus piptadeniae. This species is strongly associated with living Piptadenia gonoacantha (Fabaceae) trees in the Atlantic Forest domain on a relatively high precipitation gradient. Phylogenomics resolved P. piptadeniae in a clade that also includes both plant pathogens and typical wood saprotrophs. Furthermore, both genome-predicted Carbohydrate-Active Enzymes (CAZy) and stable isotopes (δ13C and δ15N) revealed a rather flexible lifestyle for the species. Altogether, our findings suggest that P. piptadeniae has been undergoing a pathotrophic specialization in a particular tree species while maintaining all the metabolic repertoire of a wood saprothroph. IMPORTANCE This is the first genomic description for Phellinotus piptadeniae. This basidiomycete is found across a broad range of climates and ecosystems in South America, including regions threatened by extensive agriculture. This fungus is also relevant considering its pathotrophic-saprotrophic association with Piptadenia goanocantha, which we began to understand with these new results that locate this species among biotrophic and necrotrophic fungi.
Collapse
Affiliation(s)
- Luiz Marcelo Ribeiro Tomé
- Department of Microbiology, Molecular and Computational Biology of Fungi Laboratory, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gabriel Quintanilha-Peixoto
- Department of Microbiology, Molecular and Computational Biology of Fungi Laboratory, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Diogo Henrique Costa-Rezende
- Departamento de Ciências Biológicas, Programa de Pós-graduação em Botânica, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Carlos A Salvador-Montoya
- MIND.Funga (Monitoring and Inventorying Neotropical Diversity of Fungi) - MICOLAB, Universidade Federal de Santa Catarina, Florianópolis, Brazil
- Fundación Miguel Lillo, Instituto Criptogámico-Sección Micología, San Miguel de Tucumán, Argentina
- Organización Juvenil "Hongos Perú", Cusco, Santiago, Peru
| | - Domingos Cardoso
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro (JBRJ), Rio de Janeiro, Brazil
- Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil
| | - Daniel S Araújo
- Program in Bioinformatics, Loyola University Chicago, Chicago, Illinois, USA
| | | | | | - Genivaldo Alves-Silva
- MIND.Funga (Monitoring and Inventorying Neotropical Diversity of Fungi) - MICOLAB, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Elisandro Ricardo Drechsler-Santos
- MIND.Funga (Monitoring and Inventorying Neotropical Diversity of Fungi) - MICOLAB, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Aristóteles Góes-Neto
- Department of Microbiology, Molecular and Computational Biology of Fungi Laboratory, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| |
Collapse
|
2
|
Rogers A, Jaiswal N, Roggenkamp E, Kim HS, MacCready JS, Chilvers MI, Scofield SR, Iyer-Pascuzzi AS, Helm M. Genome-Informed Trophic Classification and Functional Characterization of Virulence Proteins from the Maize Tar Spot Pathogen Phyllachora maydis. PHYTOPATHOLOGY 2024; 114:1940-1949. [PMID: 38717940 DOI: 10.1094/phyto-01-24-0037-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
Abstract
Phyllachora maydis is an ascomycete foliar fungal pathogen and the causal agent of tar spot in maize. Although P. maydis is considered an economically important foliar pathogen of maize, our general knowledge of the trophic lifestyle and functional role of effector proteins from this fungal pathogen remains limited. Here, we utilized a genome-informed approach to predict the trophic lifestyle of P. maydis and functionally characterized a subset of candidate effectors from this fungal pathogen. Leveraging the most recent P. maydis genome annotation and the CATAStrophy pipeline, we show that this fungal pathogen encodes a predicted carbohydrate-active enzymes (CAZymes) repertoire consistent with that of biotrophs. To investigate fungal pathogenicity, we selected 18 candidate effector proteins that were previously shown to be expressed during primary disease development. We assessed whether these putative effectors share predicted structural similarity with other characterized fungal effectors and determined whether any suppress plant immune responses. Using AlphaFold2 and Foldseek, we showed that one candidate effector, PM02_g1115, adopts a predicted protein structure similar to that of an effector from Verticillium dahlia. Furthermore, transient expression of candidate effector-fluorescent protein fusions in Nicotiana benthamiana revealed two putative effectors, PM02_g378 and PM02_g2610, accumulated predominantly in the cytosol, and three candidate effectors, PM02_g1115, PM02_g7882, and PM02_g8240, consistently attenuated chitin-mediated reactive oxygen species production. Collectively, the results presented herein provide insights into the predicted trophic lifestyle and putative functions of effectors from P. maydis and will likely stimulate continued research to elucidate the molecular mechanisms used by P. maydis to induce tar spot.
Collapse
Affiliation(s)
- Abigail Rogers
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Namrata Jaiswal
- Crop Production and Pest Control Research Unit, U.S. Department of Agriculture-Agricultural Research Service, West Lafayette, IN 47907
| | - Emily Roggenkamp
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Hye-Seon Kim
- U.S. Department of Agriculture-Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL 61604
| | - Joshua S MacCready
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Martin I Chilvers
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Steven R Scofield
- Crop Production and Pest Control Research Unit, U.S. Department of Agriculture-Agricultural Research Service, West Lafayette, IN 47907
| | | | - Matthew Helm
- Crop Production and Pest Control Research Unit, U.S. Department of Agriculture-Agricultural Research Service, West Lafayette, IN 47907
| |
Collapse
|
3
|
Khodadadi F, Luciano-Rosario D, Gottschalk C, Jurick WM, Aćimović SG. Unveiling the Arsenal of Apple Bitter Rot Fungi: Comparative Genomics Identifies Candidate Effectors, CAZymes, and Biosynthetic Gene Clusters in Colletotrichum Species. J Fungi (Basel) 2024; 10:493. [PMID: 39057378 PMCID: PMC11278308 DOI: 10.3390/jof10070493] [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: 05/29/2024] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
The bitter rot of apple is caused by Colletotrichum spp. and is a serious pre-harvest disease that can manifest in postharvest losses on harvested fruit. In this study, we obtained genome sequences from four different species, C. chrysophilum, C. noveboracense, C. nupharicola, and C. fioriniae, that infect apple and cause diseases on other fruits, vegetables, and flowers. Our genomic data were obtained from isolates/species that have not yet been sequenced and represent geographic-specific regions. Genome sequencing allowed for the construction of phylogenetic trees, which corroborated the overall concordance observed in prior MLST studies. Bioinformatic pipelines were used to discover CAZyme, effector, and secondary metabolic (SM) gene clusters in all nine Colletotrichum isolates. We found redundancy and a high level of similarity across species regarding CAZyme classes and predicted cytoplastic and apoplastic effectors. SM gene clusters displayed the most diversity in type and the most common cluster was one that encodes genes involved in the production of alternapyrone. Our study provides a solid platform to identify targets for functional studies that underpin pathogenicity, virulence, and/or quiescence that can be targeted for the development of new control strategies. With these new genomics resources, exploration via omics-based technologies using these isolates will help ascertain the biological underpinnings of their widespread success and observed geographic dominance in specific areas throughout the country.
Collapse
Affiliation(s)
- Fatemeh Khodadadi
- Department of Plant Pathology and Microbiology, University of California, Riverside, Riverside, CA 92521, USA;
| | - Dianiris Luciano-Rosario
- Food Quality Laboratory, U.S. Department of Agriculture, Agriculture Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA; (D.L.-R.)
| | - Christopher Gottschalk
- Appalachian Fruit Research Station, U.S. Department of Agriculture, Agriculture Research Service, Kearneysville, WV 25430, USA;
| | - Wayne M. Jurick
- Food Quality Laboratory, U.S. Department of Agriculture, Agriculture Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA; (D.L.-R.)
| | - Srđan G. Aćimović
- Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Winchester, VA 22602, USA
| |
Collapse
|
4
|
Díaz-Tapia KM, Zavala-Páramo MG, Villa-Rivera MG, Morelos-Martínez MI, López-Romero E, Simpson J, Bolaños-Rebolledo J, Cano-Camacho H. Differential Carbon Catabolite Repression and Hemicellulolytic Ability among Pathotypes of Colletotrichum lindemuthianum against Natural Plant Substrates. J Fungi (Basel) 2024; 10:406. [PMID: 38921392 PMCID: PMC11204554 DOI: 10.3390/jof10060406] [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: 05/08/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/27/2024] Open
Abstract
Colletotrichum lindemuthianum is a phytopathogenic fungus that causes anthracnose in common beans (Phaseolus vulgaris) and presents a great diversity of pathotypes with different levels of virulence against bean varieties worldwide. The purpose of this study was to establish whether pathotypic diversity is associated with differences in the mycelial growth and secretion of plant-cell-wall-degrading enzymes (PCWDEs). We evaluated growth, hemicellulase and cellulase activity, and PCWDE secretion in four pathotypes of C. lindemuthianum in cultures with glucose, bean hypocotyls and green beans of P. vulgaris, and water hyacinth (Eichhornia crassipes). The results showed differences in the mycelial growth, hemicellulolytic activity, and PCWDE secretion among the pathotypes. Glucose was not the preferred carbon source for the best mycelial growth in all pathotypes, each of which showed a unique PCWDE secretion profile, indicating different levels of carbon catabolite regulation (CCR). The pathotypes showed a high differential hemicellulolytic capacity to degrade host and water hyacinth tissues, suggesting CCR by pentoses and that there are differences in the absorption and metabolism of different monosaccharides and/or disaccharides. We propose that different levels of CCR could optimize growth in different host tissues and could allow for consortium behavior in interactions with bean crops.
Collapse
Affiliation(s)
- Karla Morelia Díaz-Tapia
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Km 9.5 Carretera Morelia-Zinapécuaro, Posta Veterinaria, Morelia 58000, Michoacán, Mexico; (K.M.D.-T.); (M.I.M.-M.); (J.B.-R.)
| | - María Guadalupe Zavala-Páramo
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Km 9.5 Carretera Morelia-Zinapécuaro, Posta Veterinaria, Morelia 58000, Michoacán, Mexico; (K.M.D.-T.); (M.I.M.-M.); (J.B.-R.)
| | - Maria Guadalupe Villa-Rivera
- Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Autónoma de México, Antigua Carretera a Pátzcuaro No. 8701, Morelia 58190, Michoacán, Mexico;
| | - Ma. Irene Morelos-Martínez
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Km 9.5 Carretera Morelia-Zinapécuaro, Posta Veterinaria, Morelia 58000, Michoacán, Mexico; (K.M.D.-T.); (M.I.M.-M.); (J.B.-R.)
| | - Everardo López-Romero
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta SN, Guanajuato 36030, Guanajuato, Mexico;
| | - June Simpson
- Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Km 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato 36821, Guanajuato, Mexico;
| | - Jeni Bolaños-Rebolledo
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Km 9.5 Carretera Morelia-Zinapécuaro, Posta Veterinaria, Morelia 58000, Michoacán, Mexico; (K.M.D.-T.); (M.I.M.-M.); (J.B.-R.)
| | - Horacio Cano-Camacho
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Km 9.5 Carretera Morelia-Zinapécuaro, Posta Veterinaria, Morelia 58000, Michoacán, Mexico; (K.M.D.-T.); (M.I.M.-M.); (J.B.-R.)
| |
Collapse
|
5
|
Zhan S, Wu W, Hu J, Liu F, Qiao X, Chen L, Zhou Y. The pathogenicity and regulatory function of temperature-sensitive proteins PscTSP in Pseudofabraea citricarpa under high temperature stress. Int J Biol Macromol 2024; 270:132017. [PMID: 38697438 DOI: 10.1016/j.ijbiomac.2024.132017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
Citrus fruit rich in beneficial health-promoting nutrients used for functional foods or dietary supplements production. However, its quality and yield were damaged by citrus target spot. Citrus target spot is a low-temperature fungal disease caused by Pseudofabraea citricarpa, resulting in citrus production reductions and economic losses. In this study, transcriptome and gene knockout mutant analyses were performed on the growth and pathogenicity of P. citricarpa under different temperature conditions to quantify the functions of temperature-sensitive proteins (PscTSP). The optimum growth temperature for P. citricarpa strain WZ1 was 20 °C, while it inhibited or stopped growth above 30 °C and stopped growth below 4 °C or above 30 °C. Certain PscTSP-key genes of P. citricarpa were identified under high temperature stress. qRT-PCR analysis confirmed the expression levels of PscTSPs under high temperature stress. PscTSPs were limited by temperature and deletion of the PscTSP-X gene leads to changes in the integrity of citrus cell walls, osmotic regulation, oxidative stress response, calcium regulation, chitin synthesis, and the pathogenicity of P. citricarpa. These results provide insight into the underlying mechanisms of temperature sensitivity and pathogenicity in P. citricarpa, providing a foundation for developing resistance strategies against citrus target spot disease.
Collapse
Affiliation(s)
- Shuang Zhan
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China
| | - Wang Wu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China
| | - Junhua Hu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China; Scientific Observing and Experimental Station of Fruit Tree Science (Southwest Region), Ministry of Agriculture, Chongqing 400712, China.
| | - Fengjiao Liu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China
| | - Xinghua Qiao
- Wanzhou District of Chongqing Plant Protection and Fruit Tree Technology Promotion Station, Wanzhou, 404000, China
| | - Li Chen
- Wanzhou District of Chongqing Plant Protection and Fruit Tree Technology Promotion Station, Wanzhou, 404000, China
| | - Yan Zhou
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China; Scientific Observing and Experimental Station of Fruit Tree Science (Southwest Region), Ministry of Agriculture, Chongqing 400712, China
| |
Collapse
|
6
|
Du S, Wang L, Yang H, Zhang Q. Tree phylogeny predicts more than litter chemical components in explaining enzyme activities in forest leaf litter decomposition. Microbiol Res 2024; 283:127658. [PMID: 38457993 DOI: 10.1016/j.micres.2024.127658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/15/2024] [Accepted: 02/18/2024] [Indexed: 03/10/2024]
Abstract
Litter decomposition is an important process in ecosystem and despite recent research elucidating the significant influence of plant phylogeny on plant-associated microbial communities, it remains uncertain whether a parallel correlation exists between plant phylogeny and the community of decomposers residing in forest litter. In this study, we conducted a controlled litterbag experiment using leaf litter from ten distinct tree species in a central subtropical forest ecosystem in a region characterized by subtropical humid monsoon climate in China. The litterbags were placed in situ using a random experimental design and were collected after 12 months of incubation. Then, the litter chemical properties, microbial community composition and activities of enzyme related to the decomposition of organic carbon (C) and nitrogen (N) were assessed. Across all ten tree species, Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were identified as the predominant bacterial classes, while the primary fungal classes were Dothideomycetes, Sordariomycetes and Eurotiomycetes. Mantel test revealed significant correlations between litter chemical component and microbial communities, as well as enzyme activities linked to N and C metabolism. However, after controlling for plant phylogenetic distance in partial Mantel test, the relationships between litter chemical component and microbial community structure and enzyme activities were not significant. Random forest and structural equation modeling indicated that plant phylogenetic distance exerted a more substantial influence than litter chemical components on microbial communities and enzyme activities associated with the decomposition of leaf litter. In summary, plant phylogenic divergence was found to be a more influential predictor of enzyme activity variations than microbial communities and litter traits, which were commonly considered reliable indicators of litter decomposition and ecosystem function, thereby highlighting the previously underestimated significance of plant phylogeny in shaping litter microbial communities and enzyme activities associated with degradation processes in forest litter.
Collapse
Affiliation(s)
- Shuhui Du
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi 030800, PR China
| | - Lujun Wang
- Anhui Academy of Forestry, No.618-1 Huangshan Road, Shushan District, Hefei 230031, PR China
| | - Haishui Yang
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Qian Zhang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China.
| |
Collapse
|
7
|
Baranda P, Islam S, Modi A, Mistry H, Al Obaid S, Ansari MJ, Yadav VK, Patel A, Joshi M, Sahoo DK, Bariya H. Whole-genome sequencing of marine water-derived Curvularia verruculosa KHW-7: a pioneering study. Front Microbiol 2024; 15:1363879. [PMID: 38846574 PMCID: PMC11155457 DOI: 10.3389/fmicb.2024.1363879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 05/06/2024] [Indexed: 06/09/2024] Open
Abstract
Marine microorganisms are renowned for being a rich source of new secondary metabolites that are significant to humans. The fungi strain KHW-7 was isolated from the seawater collected from the Gulf of Khambhat, India, and identified as Curvularia verruculosa KHW-7. On a next-generation sequencing platform, C. verruculosa KHW-7's whole-genome sequencing (WGS) and gene annotation were carried out using several bioinformatic methods. The 31.59 MB genome size, 52.3% GC, and 158 bp mean read length were discovered using WGS. This genome also contained 9,745 protein-coding genes, including 852 secreted proteins and 2048 transmembrane proteins. The antiSMASH algorithm used to analyze genomes found 25 secondary metabolite biosynthetic gene clusters (BGCs) that are abundant in terpene, non-ribosomal peptide synthetase (NRPS), and polyketides type 1 (T1PKS). To our knowledge, this is the first whole-genome sequence report of C. verruculosa. The WGS analysis of C. verruculosa KHW-7 indicated that this marine-derived fungus could be an efficient generator of bioactive secondary metabolites and an important industrial enzyme, both of which demand further investigation and development.
Collapse
Affiliation(s)
- Payal Baranda
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
| | - Shaikhul Islam
- Plant Pathology Division, Bangladesh Wheat and Maize Research Institute, Nashipur, Bangladesh
| | - Ashish Modi
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
| | - Harsh Mistry
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
| | - Sami Al Obaid
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Javed Ansari
- Department of Botany, Hindu College Moradabad (Mahatma Jyotiba Phule Rohilkhand University Bareilly), Uttar Pradesh, India
| | - Virendra Kumar Yadav
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
| | - Ashish Patel
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, India
| | - Dipak Kumar Sahoo
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Himanshu Bariya
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
| |
Collapse
|
8
|
Ruan Z, Jiao J, Zhao J, Liu J, Liang C, Yang X, Sun Y, Tang G, Li P. Genome sequencing and comparative genomics reveal insights into pathogenicity and evolution of Fusarium zanthoxyli, the causal agent of stem canker in prickly ash. BMC Genomics 2024; 25:502. [PMID: 38773367 PMCID: PMC11110190 DOI: 10.1186/s12864-024-10424-w] [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: 02/03/2024] [Accepted: 05/16/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Fusarium zanthoxyli is a destructive pathogen causing stem canker in prickly ash, an ecologically and economically important forest tree. However, the genome lack of F. zanthoxyli has hindered research on its interaction with prickly ash and the development of precise control strategies for stem canker. RESULTS In this study, we sequenced and annotated a relatively high-quality genome of F. zanthoxyli with a size of 43.39 Mb, encoding 11,316 putative genes. Pathogenicity-related factors are predicted, comprising 495 CAZymes, 217 effectors, 156 CYP450s, and 202 enzymes associated with secondary metabolism. Besides, a comparative genomics analysis revealed Fusarium and Colletotrichum diverged from a shared ancestor approximately 141.1 ~ 88.4 million years ago (MYA). Additionally, a phylogenomic investigation of 12 different phytopathogens within Fusarium indicated that F. zanthoxyli originated approximately 34.6 ~ 26.9 MYA, and events of gene expansion and contraction within them were also unveiled. Finally, utilizing conserved domain prediction, the results revealed that among the 59 unique genes, the most enriched domains were PnbA and ULP1. Among the 783 expanded genes, the most enriched domains were PKc_like kinases and those belonging to the APH_ChoK_Like family. CONCLUSION This study sheds light on the genetic basis of F. zanthoxyli's pathogenicity and evolution which provides valuable information for future research on its molecular interactions with prickly ash and the development of effective strategies to combat stem canker.
Collapse
Affiliation(s)
- Zhao Ruan
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jiahui Jiao
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Junchi Zhao
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jiaxue Liu
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Chaoqiong Liang
- Shaanxi Academy of Forestry, Xi'an, Shaanxi, 710082, People's Republic of China
| | - Xia Yang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yan Sun
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Guanghui Tang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Peiqin Li
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| |
Collapse
|
9
|
Gu X, Cao Z, Li Z, Yu H, Liu W. Plant immunity suppression by an β-1,3-glucanase of the maize anthracnose pathogen Colletotrichum graminicola. BMC PLANT BIOLOGY 2024; 24:339. [PMID: 38671375 PMCID: PMC11046878 DOI: 10.1186/s12870-024-05053-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND Many phytopathogens secrete a large number of cell wall degrading enzymes (CWDEs) to decompose host cell walls in order to penetrate the host, obtain nutrients and accelerate colonization. There is a wide variety of CWDEs produced by plant pathogens, including glycoside hydrolases (GHs), which determine the virulence, pathogenicity, and host specificity of phytopathogens. The specific molecular mechanisms by which pathogens suppress host immunity remain obscure. RESULT In this study, we found that CgEC124 encodes a glycosyl hydrolase with a signal peptide and a conserved Glyco_hydro_cc domain which belongs to glycoside hydrolase 128 family. The expression of CgEC124 was significantly induced in the early stage of Colletotrichum graminicola infection, especially at 12 hpi. Furthermore, CgEC124 positively regulated the pathogenicity, but it did not impact the vegetative growth of mycelia. Ecotopic transient expression of CgEC124 decreased the disease resistance and callose deposition in maize. Moreover, CgEC124 exhibited the β-1,3-glucanase activity and suppresses glucan-induced ROS burst in maize leaves. CONCLUSIONS Our results indicate that CgEC124 is required for full virulence of C. graminicola but not for vegetative growth. CgEC124 increases maize susceptibility by inhibiting host reactive oxygen species burst as well as callose deposition. Meanwhile, our data suggests that CgEC124 explores its β-1,3-glucanase activity to prevent induction of host defenses.
Collapse
Affiliation(s)
- Xiaoyu Gu
- College of Plant Protection, Hebei Agricultural University, Baoding, 071001, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhiyan Cao
- College of Plant Protection, Hebei Agricultural University, Baoding, 071001, China
| | - Zhiqiang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Haiyue Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| |
Collapse
|
10
|
Romero G, González S, Royero W, González A. Morphological and transcriptional analysis of Colletotrichum lindemuthianum race 7 during early stages of infection in common bean. Genet Mol Biol 2024; 47:e20220263. [PMID: 38593425 PMCID: PMC11003654 DOI: 10.1590/1678-4685-gmb-2022-0263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 01/26/2024] [Indexed: 04/11/2024] Open
Abstract
The infection process of the hemibiotrophic fungus Colletotrichum lindemuthianum has been independently studied at the microscopic and genomic levels. However, the relationship between the morphological changes and the pathogenicity mechanisms of the fungus at the early stages of the infection remains uncharacterized. Therefore, this study attempts to bridge this gap by integrating microscopic and transcriptional approaches to understand the infection process of C. lindemuthianum. Fungal structures were followed by fluorescence microscopy for 120 hours. Simultaneously, the transcriptomic profile was made using RNAseq. Morphological characterization shows that appressoria, infective vesicles, and secondary hypha formation occur before 72 hours. Additionally, we assembled 38,206 transcripts with lengths between 201 and 3,548 bp. The secretome annotation revealed the expression of 1,204 CAZymes, of which 17 exhibited secretion domains and were identified as chitinases and β-1,3-glucanases, 27 were effector candidates, and 30 were transport proteins mostly associated with ABC-type. Finally, we confirmed the presence and expression of CAC1 role during the appressoria formation of Clr7. This result represents the first report of adenylate cyclase expression evaluated under three different approaches. In conclusion, C. lindemuthianum colonizes the host through different infection structures complemented with the expression of multiple enzymes, where CAC1 favors disease development.
Collapse
Affiliation(s)
- German Romero
- Universidad Nacional de Colombia, Facultad de Ciencias Agrarias, Bogotá, Colombia
| | - Sandra González
- Universidad Nacional de Colombia, Instituto de Biotecnología, Bogotá, Colombia
| | - Wendy Royero
- Universidad Nacional de Colombia, Instituto de Biotecnología, Bogotá, Colombia
| | - Adriana González
- Universidad Nacional de Colombia, Facultad de Ciencias Agrarias, Bogotá, Colombia
| |
Collapse
|
11
|
Bradley JM, Butlin RK, Scholes JD. Comparative secretome analysis of Striga and Cuscuta species identifies candidate virulence factors for two evolutionarily independent parasitic plant lineages. BMC PLANT BIOLOGY 2024; 24:251. [PMID: 38582844 PMCID: PMC10998327 DOI: 10.1186/s12870-024-04935-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 03/20/2024] [Indexed: 04/08/2024]
Abstract
BACKGROUND Many parasitic plants of the genera Striga and Cuscuta inflict huge agricultural damage worldwide. To form and maintain a connection with a host plant, parasitic plants deploy virulence factors (VFs) that interact with host biology. They possess a secretome that represents the complement of proteins secreted from cells and like other plant parasites such as fungi, bacteria or nematodes, some secreted proteins represent VFs crucial to successful host colonisation. Understanding the genome-wide complement of putative secreted proteins from parasitic plants, and their expression during host invasion, will advance understanding of virulence mechanisms used by parasitic plants to suppress/evade host immune responses and to establish and maintain a parasite-host interaction. RESULTS We conducted a comparative analysis of the secretomes of root (Striga spp.) and shoot (Cuscuta spp.) parasitic plants, to enable prediction of candidate VFs. Using orthogroup clustering and protein domain analyses we identified gene families/functional annotations common to both Striga and Cuscuta species that were not present in their closest non-parasitic relatives (e.g. strictosidine synthase like enzymes), or specific to either the Striga or Cuscuta secretomes. For example, Striga secretomes were strongly associated with 'PAR1' protein domains. These were rare in the Cuscuta secretomes but an abundance of 'GMC oxidoreductase' domains were found, that were not present in the Striga secretomes. We then conducted transcriptional profiling of genes encoding putatively secreted proteins for the most agriculturally damaging root parasitic weed of cereals, S. hermonthica. A significant portion of the Striga-specific secretome set was differentially expressed during parasitism, which we probed further to identify genes following a 'wave-like' expression pattern peaking in the early penetration stage of infection. We identified 39 genes encoding putative VFs with functions such as cell wall modification, immune suppression, protease, kinase, or peroxidase activities, that are excellent candidates for future functional studies. CONCLUSIONS Our study represents a comprehensive secretome analysis among parasitic plants and revealed both similarities and differences in candidate VFs between Striga and Cuscuta species. This knowledge is crucial for the development of new management strategies and delaying the evolution of virulence in parasitic weeds.
Collapse
Affiliation(s)
- James M Bradley
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
- Present address: Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada.
| | - Roger K Butlin
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Department of Marine Sciences, University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Julie D Scholes
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| |
Collapse
|
12
|
Hallas-Mølle M, Burow M, Henrissat B, Johansen KS. Cryptococcus neoformans: plant-microbe interactions and ecology. Trends Microbiol 2024:S0966-842X(24)00059-3. [PMID: 38519353 DOI: 10.1016/j.tim.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/24/2024]
Abstract
While the opportunistic human pathogens Cryptococcus neoformans and Cryptococcus gattii are often isolated from plants and plant-related material, evidence suggests that these Cryptococcus species do not directly infect plants. Studies find that plants are important for Cryptococcus mating and dispersal. However, these studies have not provided enough detail about how plants and these fungi interact, especially in ways that could show the fungi are capable of causing disease. This review synthesizes recent findings from studies utilizing different plant models associated with the ecology of C. neoformans and C. gattii. Unanswered questions about their environmental role are highlighted. Overall, current research indicates that Cryptococcus utilizes plants as a substrate rather than harming them, arguing against Cryptococcus as a genuine plant pathogen. We hypothesize that plants represent reservoirs that aid dispersal, not hosts vulnerable to infection.
Collapse
Affiliation(s)
- Magnus Hallas-Mølle
- Department of Geoscience and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark
| | - Meike Burow
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kgs, Lyngby, Denmark
| | - Katja Salomon Johansen
- Department of Geoscience and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark.
| |
Collapse
|
13
|
Li Q, Feng Y, Li J, Hai Y, Si L, Tan C, Peng J, Hu Z, Li Z, Li C, Hao D, Tang W. Multi-omics approaches to understand pathogenicity during potato early blight disease caused by Alternaria solani. Front Microbiol 2024; 15:1357579. [PMID: 38529180 PMCID: PMC10961351 DOI: 10.3389/fmicb.2024.1357579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/14/2024] [Indexed: 03/27/2024] Open
Abstract
Potato early blight (PEB), a foliar disease of potato during the growing period, caused by Alternaria sp., is common in major potato-producing areas worldwide. Effective agents to control this disease or completely resistant potato varieties are absent. Large-scale use of fungicides is limited due to possibility of increase in pathogen resistance and the requirements of ecological agriculture. In this study, we focused on the composition and infection characteristics of early blight pathogens in Yunnan Province and screened candidate pathogenesis-related pathways and genes. We isolated 85 strains of Alternaria sp. fungi from typical early blight spots in three potato-growing regions in Yunnan Province from 2018 to 2022, and identified 35 strains of Alternaria solani and 50 strains of Alternaria alternata by morphological characterization and ITS sequence comparison, which were identified as the main and conditional pathogens causing early blight in potato, respectively. Scanning electron microscope analysis confirmed only A. solani producing appressorium at 4 h after inoculation successfully infected the leaf cells. Via genome assembly and annotation, combine transcriptome and proteomic analysis, the following pathogenicity-related unit, transcription factors and metabolic pathway were identified: (1) cell wall-degrading enzymes, such as pectinase, keratinase, and cellulase; (2) genes and pathways related to conidia germination and pathogenicity, such as ubiquitination and peroxisomes; and (3) transcription factors, such as Zn-clus, C2H2, bZIP, and bHLH. These elements were responsible for PEB epidemic in Yunnan.
Collapse
Affiliation(s)
- Qing Li
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, China
- School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Yan Feng
- School of Economics and Management, Yunnan Normal University, Kunming, China
| | - Jianmei Li
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, China
- School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Yang Hai
- Yunnan YinMore Modern Agriculture Co., Ltd., Kunming, China
| | - Liping Si
- Yunnan YinMore Modern Agriculture Co., Ltd., Kunming, China
| | - Chen Tan
- School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Jing Peng
- School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Zuo Hu
- Zhaotong Academy of Agricultural Sciences, Zhaotong, China
| | - Zhou Li
- Zhaotong Academy of Agricultural Sciences, Zhaotong, China
| | - Canhui Li
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, China
- School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Dahai Hao
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, China
- School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Wei Tang
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, China
- School of Life Sciences, Yunnan Normal University, Kunming, China
| |
Collapse
|
14
|
Wang X, Wei J, Liu Z, Wang Y, Yuan X, Wang D, Niu J, Yang Y, Zhou J. Comparative genomic analysis of Sanghuangporus sanghuang with other Hymenochaetaceae species. Braz J Microbiol 2024; 55:87-100. [PMID: 38099978 PMCID: PMC10920484 DOI: 10.1007/s42770-023-01212-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: 08/24/2023] [Accepted: 12/03/2023] [Indexed: 03/09/2024] Open
Abstract
Sanghuangporus sanghuang is a medicinal macrofungus with antioxidant and antitumor activities, and it is enriched with secondary metabolites such as polysaccharides, terpenes, polyphenols, and styrylpyrone compounds. To explore the putative core genes and gene clusters involved in sanghuang biosynthesis, we sequenced and assembled a 40.5-Mb genome of S. sanghuang (SH1 strain). Using antiSMASH, local BLAST, and NCBI comparison, 12 terpene synthases (TPSs), 1 non-ribosomal peptide synthase, and five polyketide synthases (PKSs) were identified in SH1. Combining the transcriptome analysis with liquid chromatography mass spectrometry-ion trap-time of flight analysis, we determined that ShPKS1, one phenylalanine aminolyase (ShPAL), and one P450 monooxygenase (ShC4H1) were associated with hispidin biosynthesis. Structural domain comparison indicated that ShPKS2 and ShPKS3 are involved in the biosynthesis of orsellinic acid and 2-hydroxy-6-methylbenzoic acid, respectively. Furthermore, comparative genomic analysis of SH1 with 14 other fungi from the Hymenochaetaceae family showed variation in the number of TPSs among different genomes, with Coniferiporia weirii exhibiting only 9 TPSs and Inonotus obliquus having 20. The number of TPSs also differed among the genomes of three strains of S. sanghuang, namely Kangneng (16), MS2 (9), and SH1 (12). The type and number of PKSs also varied among species and even strains, ranging from two PKSs in Pyrrhoderma noxium to five PKSs in S. sanghuang SH1. Among the three strains of S. sanghuang, both the structural domains and the number of PKSs in strains MS2 and SH1 were consistent, whereas strain Kangneng exhibited only four PKSs and lacked the PKS with the structural domain KS-AT-DH-KR-ACP. Additionally, Sanghuangporus species exhibited more similar PKSs to Inonotus, with higher gene similarity around five PKSs, while showing differences from those of other fungi in the same family, including Phellinus lamaoensis. This result supports the independent taxonomic significance of the genus Sanghuangporus to some extent.
Collapse
Affiliation(s)
- Xinyue Wang
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming, 650500, China
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
| | - Jiansheng Wei
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
- Haba Snow Mountain Provincial Nature Reserve Management and Protection Bureau, Diqing, 674402, China
| | - Zhenwen Liu
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
| | - Yi Wang
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China.
| | - Xiaolong Yuan
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
| | - Dong Wang
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
- College of Forestry, Southwest Forestry University, Kunming, 650224, Yunnan, China
| | - Junmei Niu
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming, 650500, China
| | - Yan Yang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Jing Zhou
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming, 650500, China.
| |
Collapse
|
15
|
Varrella S, Barone G, Corinaldesi C, Giorgetti A, Nomaki H, Nunoura T, Rastelli E, Tangherlini M, Danovaro R, Dell’Anno A. Fungal Abundance and Diversity in the Mariana Trench, the Deepest Ecosystem on Earth. J Fungi (Basel) 2024; 10:73. [PMID: 38248982 PMCID: PMC10820024 DOI: 10.3390/jof10010073] [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: 11/21/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
Hadal trenches host abundant and diversified benthic prokaryotic assemblages, but information on benthic fungi is still extremely limited. We investigated the fungal abundance and diversity in the Challenger Deep (at ca. 11,000 m depth) and the slope of the Mariana Trench in comparison with three sites of the adjacent abyssal plain. Our results indicate that trench sediments are a hotspot of fungal abundance in terms of the 18S rRNA gene copy number. The fungal diversity (as the number of amplicon sequence variants, ASVs) was relatively low at all sites (10-31 ASVs) but showed a high turnover diversity among stations due to the presence of exclusive fungal taxa belonging to Aspergillaceae, Trichosphaeriaceae, and Nectriaceae. Fungal abundance and diversity were closely linked to sediment organic matter content and composition (i.e., phytopigments and carbohydrates), suggesting a specialization of different fungal taxa for the exploitation of available resources. Overall, these findings provide new insights into the diversity of deep-sea fungi and the potential ecological role in trench sediments and pave the way for a better understanding of their relevance in one of the most extreme ecosystems on Earth.
Collapse
Affiliation(s)
- Stefano Varrella
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy; (G.B.); (A.G.); (R.D.)
- National Biodiversity Future Centre, 90133 Palermo, Italy;
| | - Giulio Barone
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy; (G.B.); (A.G.); (R.D.)
- Institute for Marine Biological Resources and Biotechnology, National Research Council, Largo Fiera della Pesca 2, 60125 Ancona, Italy
| | - Cinzia Corinaldesi
- National Biodiversity Future Centre, 90133 Palermo, Italy;
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Alessio Giorgetti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy; (G.B.); (A.G.); (R.D.)
| | - Hidetaka Nomaki
- X-Star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka 237-0061, Japan;
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), JAMSTEC, Yokosuka 237-0061, Japan
| | - Eugenio Rastelli
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy; (G.B.); (A.G.); (R.D.)
- National Biodiversity Future Centre, 90133 Palermo, Italy;
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy; (G.B.); (A.G.); (R.D.)
- National Biodiversity Future Centre, 90133 Palermo, Italy;
| |
Collapse
|
16
|
Datta R. Enzymatic degradation of cellulose in soil: A review. Heliyon 2024; 10:e24022. [PMID: 38234915 PMCID: PMC10792583 DOI: 10.1016/j.heliyon.2024.e24022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/13/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024] Open
Abstract
Cellulose degradation is a critical process in soil ecosystems, playing a vital role in nutrient cycling and organic matter decomposition. Enzymatic degradation of cellulosic biomass is the most sustainable and green method of producing liquid biofuel. It has gained intensive research interest with future perspective as the majority of terrestrial lignocellulose biomass has a great potential to be used as a source of bioenergy. However, the recalcitrant nature of lignocellulose limits its use as a source of energy. Noteworthy enough, enzymatic conversion of cellulose biomass could be a leading future technology. Fungal enzymes play a central role in cellulose degradation. Our understanding of fungal cellulases has substantially redirected in the past few years with the discovery of a new class of enzymes and Cellulosome. Efforts have been made from time to time to develop an economically viable method of cellulose degradation. This review provides insights into the current state of knowledge regarding cellulose degradation in soil and identifies areas where further research is needed.
Collapse
Affiliation(s)
- Rahul Datta
- Department of Geology and Pedology, Faculty of Forestry and Wood Technology. Mendel University In Brno, Czech Republic
| |
Collapse
|
17
|
Cheng H, Zhou X, Yang Y, Xu L, Ding Y, Yan T, Li Q. Environmental damages, cumulative exergy demand, and economic assessment of Panus giganteus farming with the application of solar technology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:168020. [PMID: 37898217 DOI: 10.1016/j.scitotenv.2023.168020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/06/2023] [Accepted: 10/20/2023] [Indexed: 10/30/2023]
Abstract
The use of photovoltaic (PV) technology in agricultural production can mitigate the environmental impacts of mushroom farming. However, changes in the environmental impacts and economic benefits of the application of PV technology are still unclear. Thus, we evaluated the environmental impacts, energy flow, and economic aspects of mushroom (Panus giganteus) farming systems without solar PV (WS) technology and with PV technology from the generation of substrate materials through harvesting. In addition to a 27 % increase in terrestrial ecotoxicity, P. giganteus farming with PV technology reduced all impact categories by 4-60 %, with a 60 % reduction in CO2 emissions and a 25 % reduction in land resources. These findings highlight the importance of combining PV technology with mushroom farming in agricultural carbon reduction and the efficient use of land resources. In terms of the climate change impact, the PV system reduced CO2 emissions by 2.94 kg CO2 eq./kg of mushrooms compared with the WS system, wherein the aspects of substrate transformation, spawn running, and cultivation were reduced by 78.27-89.91 %. The cumulative exergy demand (CExD) analysis showed that P. giganteus farming combined with PV technology reduced the total CExD by 48 %. With the application of PV technology, the top contributor to the total CExD of mushroom farming shifted from electricity to transportation throughout the supply chain. The PV system reduced costs by 22.09 % and increased the total revenue by 22 % and the cost-benefit ratio by 50 %. Halving the transportation distances of substrate materials and performing localized substitution of wood chips resulted in a 3-34 % reduction in the environmental impacts category and a 23-30 % reduction in nonrenewable fossil energy consumption. These results showed that improvements helped optimize the environmental performance in terms of carbon reduction and energy mixing. Thus, combining PV technology with greenhouse mushroom farming can improve trends in energy and environmental damage.
Collapse
Affiliation(s)
- Hanting Cheng
- Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou 57173, China
| | - Xiaohui Zhou
- Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; Key Laboratory of Low-carbon Green Agriculture in Tropical Region of China, Ministry of Agriculture and Rural Affairs, 571101, China
| | - Yang Yang
- Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; Hainan Provincial Key Laboratory of Tropical Eco-cycle Agriculture, Haikou, Hainan 571101, China
| | - Lin Xu
- Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; National Agricultural Experimental Station for Agricultural Environment, Danzhou 571737, Hainan, China
| | - Ye Ding
- Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; National Agricultural Experimental Station for Agricultural Environment, Danzhou 571737, Hainan, China
| | - Tingliang Yan
- Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; National Long-term Experimental Station for Agriculture Green Development, Danzhou 571737, Hainan, China
| | - Qinfen Li
- Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; Hainan Provincial Key Laboratory of Tropical Eco-cycle Agriculture, Haikou, Hainan 571101, China; National Agricultural Experimental Station for Agricultural Environment, Danzhou 571737, Hainan, China; National Long-term Experimental Station for Agriculture Green Development, Danzhou 571737, Hainan, China.
| |
Collapse
|
18
|
Scott CJR, Leadbeater DR, Oates NC, James SR, Newling K, Li Y, McGregor NGS, Bird S, Bruce NC. Whole genome structural predictions reveal hidden diversity in putative oxidative enzymes of the lignocellulose-degrading ascomycete Parascedosporium putredinis NO1. Microbiol Spectr 2023; 11:e0103523. [PMID: 37811978 PMCID: PMC10714830 DOI: 10.1128/spectrum.01035-23] [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: 03/31/2023] [Accepted: 08/22/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE An annotated reference genome has revealed P. putredinis NO1 as a useful resource for the identification of new lignocellulose-degrading enzymes for biorefining of woody plant biomass. Utilizing a "structure-omics"-based searching strategy, we identified new potentially lignocellulose-active sequences that would have been missed by traditional sequence searching methods. These new identifications, alongside the discovery of novel enzymatic functions from this underexplored lineage with the recent discovery of a new phenol oxidase that cleaves the main structural β-O-4 linkage in lignin from P. putredinis NO1, highlight the underexplored and poorly represented family Microascaceae as a particularly interesting candidate worthy of further exploration toward the valorization of high value biorenewable products.
Collapse
Affiliation(s)
- Conor J. R. Scott
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, United Kingdom
| | - Daniel R. Leadbeater
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, United Kingdom
| | - Nicola C. Oates
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, United Kingdom
| | - Sally R. James
- Department of Biology, Bioscience Technology Facility, University of York, York, United Kingdom
| | - Katherine Newling
- Department of Biology, Bioscience Technology Facility, University of York, York, United Kingdom
| | - Yi Li
- Department of Biology, Bioscience Technology Facility, University of York, York, United Kingdom
| | - Nicholas G. S. McGregor
- Department of Chemistry, York Structural Biology Laboratory, The University of York, York, United Kingdom
| | - Susannah Bird
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, United Kingdom
| | - Neil C. Bruce
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, United Kingdom
| |
Collapse
|
19
|
Gutiérrez-Sánchez A, Plasencia J, Monribot-Villanueva JL, Rodríguez-Haas B, Ruíz-May E, Guerrero-Analco JA, Sánchez-Rangel D. Virulence factors of the genus Fusarium with targets in plants. Microbiol Res 2023; 277:127506. [PMID: 37783182 DOI: 10.1016/j.micres.2023.127506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023]
Abstract
Fusarium spp. comprise various species of filamentous fungi that cause severe diseases in plant crops of both agricultural and forestry interest. These plant pathogens produce a wide range of molecules with diverse chemical structures and biological activities. Genetic functional analyses of some of these compounds have shown their role as virulence factors (VF). However, their mode of action and contributions to the infection process for many of these molecules are still unknown. This review aims to analyze the state of the art in Fusarium VF, emphasizing their biological targets on the plant hosts. It also addresses the current experimental approaches to improve our understanding of their role in virulence and suggests relevant research questions that remain to be answered with a greater focus on species of agroeconomic importance. In this review, a total of 37 confirmed VF are described, including 22 proteinaceous and 15 non-proteinaceous molecules, mainly from Fusarium oxysporum and Fusarium graminearum and, to a lesser extent, in Fusarium verticillioides and Fusarium solani.
Collapse
Affiliation(s)
- Angélica Gutiérrez-Sánchez
- Laboratorios de Fitopatología y Biología Molecular, Red de Estudios Moleculares Avanzados, Clúster BioMimic®, Instituto de Ecología, A. C. Xalapa, Veracruz 91073, Mexico; Laboratorio de Química de Productos Naturales, Red de Estudios Moleculares Avanzados, Clúster BioMimic®, Instituto de Ecología, A. C. Xalapa, Veracruz 91073, Mexico
| | - Javier Plasencia
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Juan L Monribot-Villanueva
- Laboratorio de Química de Productos Naturales, Red de Estudios Moleculares Avanzados, Clúster BioMimic®, Instituto de Ecología, A. C. Xalapa, Veracruz 91073, Mexico
| | - Benjamín Rodríguez-Haas
- Laboratorios de Fitopatología y Biología Molecular, Red de Estudios Moleculares Avanzados, Clúster BioMimic®, Instituto de Ecología, A. C. Xalapa, Veracruz 91073, Mexico
| | - Eliel Ruíz-May
- Laboratorio de Proteómica, Red de Estudios Moleculares Avanzados, Clúster BioMimic®, Instituto de Ecología, A. C. Xalapa, Veracruz 91073, Mexico
| | - José A Guerrero-Analco
- Laboratorio de Química de Productos Naturales, Red de Estudios Moleculares Avanzados, Clúster BioMimic®, Instituto de Ecología, A. C. Xalapa, Veracruz 91073, Mexico.
| | - Diana Sánchez-Rangel
- Laboratorios de Fitopatología y Biología Molecular, Red de Estudios Moleculares Avanzados, Clúster BioMimic®, Instituto de Ecología, A. C. Xalapa, Veracruz 91073, Mexico; Investigador por México - CONAHCyT en la Red de Estudios Moleculares Avanzados del Instituto de Ecología, A. C. (INECOL), Carretera antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico.
| |
Collapse
|
20
|
Yu J, Kong L, Fan S, Li M, Li J. Genomic Characterization of the Mycoparasite Pestalotiopsis sp. Strain cr013 from Cronartium ribicola. Pol J Microbiol 2023; 72:433-442. [PMID: 38095159 PMCID: PMC10725163 DOI: 10.33073/pjm-2023-041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/24/2023] [Indexed: 12/17/2023] Open
Abstract
The Pestalotiopsis sp. strain cr013 is a mycoparasite of Cronartium ribicola, a potential biocontrol fungus for Armand pine (Pinus armandii) blister rust. A previous study showed that the strain cr013 has great potential to produce new compounds. However, there has been no report of the whole-genome sequence of the mycoparasite Pestalotiopsis sp. In this study, the BGISEQ-500 and Oxford Nanopore GridION X5 sequencing platforms were used to sequence the strain cr013 isolates and assemble the reads to obtain the complete genome. We first report the whole-genome information of the mycoparasite Pestalotiopsis sp. strain cr013 (GenBank accession number: JACFXT010000000, BioProject ID: PRJNA647543, BioSample ID: SAMN15589943), and the genomic components and gene functions related to the mycoparasitism process were analyzed. This study provides a theoretical basis for understanding the lifestyle strategy of the mycoparasite Pestalotiopsis sp. and reveals the mechanisms underlying secondary metabolite diversity in the strain cr013.
Collapse
Affiliation(s)
- Jinde Yu
- College of Life Science, Southwest Forestry University, Kunming, People’s Republic of China
| | - Lei Kong
- College of Life Science, Southwest Forestry University, Kunming, People’s Republic of China
| | - Shichang Fan
- College of Life Science, Southwest Forestry University, Kunming, People’s Republic of China
| | - Mingjiao Li
- College of Life Science, Southwest Forestry University, Kunming, People’s Republic of China
| | - Jing Li
- College of Life Science, Southwest Forestry University, Kunming, People’s Republic of China
| |
Collapse
|
21
|
Li J, Zhang D, Du Y, Song J, Li R, Dai X, Chen J, Li G, Liu Z. Genome Sequence Resource of Cladosporium velox Strain C4 Causing Cotton Boll Disease in Xinjiang, China. PLANT DISEASE 2023; 107:4010-4015. [PMID: 37368501 DOI: 10.1094/pdis-11-22-2694-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Cladosporium spp., as one of the largest and most heterogeneous genera of hyphomycetes, are widely distributed worldwide. This genus is usually adaptable to a wide variety of extreme environments. However, only 11 genomes of Cladosporium genus have been publicly released. From 2017, we found for the first time that Cladosporium velox could cause cotton boll disease and lead to stiffness and cracking boll in Xinjiang, China. Herein, we provide a high-quality reference genome for the C. velox strain C4 isolated from cotton boll in Xinjiang, China. The genome size and encoding gene number of the C. velox strain C4 and C. cucumerinum strain CCNX2, which was recently released and caused the cucumber scab, showed minor differences. This resource will contribute to future research that aims to elucidate the genetic basis of C. velox pathogenicity and could expand our knowledge of Cladosporium spp. genomic characteristics that will be valuable for the development of Cladosporium disease control measures.
Collapse
Affiliation(s)
- Jingwen Li
- College of Agriculture/Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Dandan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Yejuan Du
- College of Agriculture/Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Jian Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Ran Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Xiaofeng Dai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jieyin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Guoying Li
- College of Agriculture/Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Zheng Liu
- College of Agriculture/Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang 832003, China
| |
Collapse
|
22
|
Ökmen B, Katzy P, Huang L, Wemhöner R, Doehlemann G. A conserved extracellular Ribo1 with broad-spectrum cytotoxic activity enables smut fungi to compete with host-associated bacteria. THE NEW PHYTOLOGIST 2023; 240:1976-1989. [PMID: 37680042 DOI: 10.1111/nph.19244] [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: 07/17/2023] [Accepted: 08/14/2023] [Indexed: 09/09/2023]
Abstract
Ribotoxins are secreted ribonucleases that specifically target and cleave the universally conserved sarcin-ricin loop sequence of rRNA, which leads to inhibition of protein biosynthesis and subsequently to cell death. We have identified and characterized a secreted Ribo1 protein of plant pathogenic smut fungi. Heterologous expression in different model systems showed that smut Ribo1 has cytotoxic activity against bacteria, yeast, host and nonhost plants. Recombinant expression of Ribo1 in Nicotiana benthamiana induced plant cell death; however, an active site mutant induced cell death only when expressed as a secreted protein. In the maize smut Ustilago maydis, transcription of Ribo1 is specifically induced in early infection stages. While a knockout mutant revealed that Ribo1 is dispensable for U. maydis virulence, the overexpression of Ribo1 in planta had a strong dominant negative effect on virulence and induced host defense responses including cell death. Our findings suggest a function of Ribo1 during the epiphytic development rather than for invasive colonization of the host. Accordingly, in the presence of the biocontrol bacteria Pantoea sp., which were isolated from maize leaves, the ribo1 knockout mutant was significantly impaired in virulence. Together, we conclude that Ribo1 enables smut fungi to compete with host-associated bacteria during epiphytic development.
Collapse
Affiliation(s)
- Bilal Ökmen
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Center for Molecular Biosciences, 50674, Cologne, Germany
- Department of Microbial Interactions, IMIT/ZMBP, University of Tübingen, 72076, Tübingen, Germany
| | - Philipp Katzy
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Center for Molecular Biosciences, 50674, Cologne, Germany
| | - Luyao Huang
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Center for Molecular Biosciences, 50674, Cologne, Germany
| | - Raphael Wemhöner
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Center for Molecular Biosciences, 50674, Cologne, Germany
| | - Gunther Doehlemann
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Center for Molecular Biosciences, 50674, Cologne, Germany
| |
Collapse
|
23
|
Rocha VDD, Dal'Sasso TCDS, Dal-Bianco M, Oliveira LOD. Genome-wide survey and evolutionary history of the pectin methylesterase (PME) gene family in the Dothideomycetes class of fungi. Fungal Genet Biol 2023; 169:103841. [PMID: 37797717 DOI: 10.1016/j.fgb.2023.103841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/06/2023] [Accepted: 10/03/2023] [Indexed: 10/07/2023]
Abstract
Once deposited in the plant cell wall, pectin undergoes demethylesterification by endogenous pectin methylesterases (PMEs), which play various roles in growth and development, including defense against pathogen attacks. Pathogen PMEs can alter pectin's methylesterification pattern, increasing its susceptibility to degradation by other fungal pectinases and thus playing a critical role as virulence factors during early infection stages. To investigate the evolutionary history of PMEs in the Dothideomycetes class of fungi, we obtained genomic data from 15 orders (79 species) and added genomic data from 61 isolates of Corynespora cassiicola. Our analyses involved maximum likelihood phylogenies, gene genealogies, and selection analyses. Additionally, we measured PME gene expression levels of C. cassiicola using soybean as a host through RT-qPCR assays. We recovered 145 putative effector PMEs and 57 putative non-effector PMEs from across the Dothideomycetes. The PME gene family exhibits a small size (up to 5 members per genome) and comprises three major clades. The evolutionary patterns of the PME1 and PME2 clades were largely shaped by duplications and recurring gene retention events, while biased gene loss characterized the small-sized PME3 clade. The presence of five members in the PME gene family of C. cassiicola suggests that the family may play a key role in the evolutionary success of C. cassiicola as a polyphagous plant pathogen. The haplogroups Cc_PME1.1 and Cc_PME1.2 exhibited an accelerated rate of evolution, whereas Cc_PME2.1, Cc_PME2.2, and Cc_PME2.3 seem to be under strong purifying selective constraints. All five PME genes were expressed during infection of soybean leaves, with the highest levels during from six to eight days post-inoculation. The highest relative expression level was measured for CC_29_g7533, a member of the Cc_PME2.3 clade, while the remaining four genes had relatively lower levels of expression.
Collapse
Affiliation(s)
| | | | - Maximiller Dal-Bianco
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Luiz Orlando de Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil.
| |
Collapse
|
24
|
Gurjar MS, Kumar TPJ, Shakouka MA, Saharan MS, Rawat L, Aggarwal R. Draft genome sequencing of Tilletia caries inciting common bunt of wheat provides pathogenicity-related genes. Front Microbiol 2023; 14:1283613. [PMID: 38033590 PMCID: PMC10684912 DOI: 10.3389/fmicb.2023.1283613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 10/05/2023] [Indexed: 12/02/2023] Open
Abstract
Common bunt of wheat caused by Tilletia caries is an important disease worldwide. The T. caries TC1_MSG genome was sequenced using the Illumina HiSeq 2500 and Nanopore ONT platforms. The Nanopore library was prepared using the ligation sequencing kit SQK-LSK110 to generate approximately 24 GB for sequencing. The assembly size of 38.18 Mb was generated with a GC content of 56.10%. The whole genome shotgun project was deposited at DDBJ/ENA/GenBank under the accession number JALUTQ000000000. Forty-six contigs were obtained with N50 of 1,798,756 bp. In total, 10,698 genes were predicted in the assembled genome. Out of 10,698 genes, 10,255 genes were predicted significantly in the genome. The repeat sequences made up approximately 1.57% of the genome. Molecular function, cellular components, and biological processes for predicted genes were mapped into the genome. In addition, repeat elements in the genome were assessed. In all, 0.89% of retroelements were observed, followed by long terminal repeat elements (0.86%) in the genome. In simple sequence repeat (SSR) analysis, 8,582 SSRs were found in the genome assembly. The trinucleotide SSR type (3,703) was the most abundant. Few putative secretory signal peptides and pathogenicity-related genes were predicted. The genomic information of T. caries will be valuable in understanding the pathogenesis mechanism as well as developing new methods for the management of the common bunt disease of wheat.
Collapse
Affiliation(s)
- Malkhan Singh Gurjar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Mohamad Ayham Shakouka
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Mahender Singh Saharan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Laxmi Rawat
- College of Hill Agriculture, VCSG Uttarakhand University of Horticulture and Forestry, Ranichauri, Uttarakhand, India
| | - Rashmi Aggarwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| |
Collapse
|
25
|
Chen X, Zou Y, Li Q, Wu C, Zhou P, Chen Z, Shi J, Zhao Z. Effect of Thermophilic Microbial Agents on Crude Fiber Content, Carbohydrate-Active Enzyme Genes, and Microbial Communities during Chinese Medicine Residue Composting. ACS OMEGA 2023; 8:39570-39582. [PMID: 37901486 PMCID: PMC10600912 DOI: 10.1021/acsomega.3c05442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/06/2023] [Indexed: 10/31/2023]
Abstract
The objective of this study was to investigate the impact of thermophilic bacteria on crude fiber content, carbohydrate-active enzyme (CAZyme) genes, and associated microbial communities during Chinese medicine residues composting. The study examines changes over 15 days of composting with (T) and without (CK) thermophilic microbial agents. Results show that the group T compost temperature reached a maximum of 71.0 °C and remained above 70 °C for 2 days, while the group CK maximum temperature was only 60.9 °C. On Day 15, the seed germination index (GI) of group T reached 98.7%, while the group CK GI was only 56.7%. After composting, the degradation rates of cellulose, hemicellulose, and lignin in group T increased by 5.1, 22.5, and 18.5%, respectively, compared to those in group CK. Thermophilic microbial agents changed the microbial communities related to CAZymes, increasing unclassified_o_Myxococcales and Sphaerobacter abundance and reducing Acinetobacter and Sphingobacterium abundance. Thermophilic microbial agents also increased the abundance of the GT4, GT2_Glycos_transf_2, and AA3 gene families. These results show that thermophilic microbial agents can increase composting temperature, accelerate compost maturation, and promote crude fiber degradation. Therefore, they have broad application potential.
Collapse
Affiliation(s)
- Xiaojia Chen
- Laboratory
of Biorefinery, Shanghai Advanced Research
Institute, Chinese Academy of Sciences, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Yijun Zou
- Laboratory
of Biorefinery, Shanghai Advanced Research
Institute, Chinese Academy of Sciences, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Qinyu Li
- Laboratory
of Biorefinery, Shanghai Advanced Research
Institute, Chinese Academy of Sciences, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengjian Wu
- Fuzhou
Kaijie Foodstuff Development Co., Ltd., Fuzhou 350003, China
| | - Peng Zhou
- School
of Health Science and Engineering, University
of Shanghai for Science and Technology, Shanghai 200093, China
| | - Zheng Chen
- School
of Health Science and Engineering, University
of Shanghai for Science and Technology, Shanghai 200093, China
| | - Jiping Shi
- Laboratory
of Biorefinery, Shanghai Advanced Research
Institute, Chinese Academy of Sciences, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijun Zhao
- Laboratory
of Biorefinery, Shanghai Advanced Research
Institute, Chinese Academy of Sciences, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
26
|
Dort EN, Layne E, Feau N, Butyaev A, Henrissat B, Martin FM, Haridas S, Salamov A, Grigoriev IV, Blanchette M, Hamelin RC. Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits. Sci Rep 2023; 13:17203. [PMID: 37821494 PMCID: PMC10567782 DOI: 10.1038/s41598-023-44005-w] [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: 04/04/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023] Open
Abstract
Invasive plant pathogenic fungi have a global impact, with devastating economic and environmental effects on crops and forests. Biosurveillance, a critical component of threat mitigation, requires risk prediction based on fungal lifestyles and traits. Recent studies have revealed distinct genomic patterns associated with specific groups of plant pathogenic fungi. We sought to establish whether these phytopathogenic genomic patterns hold across diverse taxonomic and ecological groups from the Ascomycota and Basidiomycota, and furthermore, if those patterns can be used in a predictive capacity for biosurveillance. Using a supervised machine learning approach that integrates phylogenetic and genomic data, we analyzed 387 fungal genomes to test a proof-of-concept for the use of genomic signatures in predicting fungal phytopathogenic lifestyles and traits during biosurveillance activities. Our machine learning feature sets were derived from genome annotation data of carbohydrate-active enzymes (CAZymes), peptidases, secondary metabolite clusters (SMCs), transporters, and transcription factors. We found that machine learning could successfully predict fungal lifestyles and traits across taxonomic groups, with the best predictive performance coming from feature sets comprising CAZyme, peptidase, and SMC data. While phylogeny was an important component in most predictions, the inclusion of genomic data improved prediction performance for every lifestyle and trait tested. Plant pathogenicity was one of the best-predicted traits, showing the promise of predictive genomics for biosurveillance applications. Furthermore, our machine learning approach revealed expansions in the number of genes from specific CAZyme and peptidase families in the genomes of plant pathogens compared to non-phytopathogenic genomes (saprotrophs, endo- and ectomycorrhizal fungi). Such genomic feature profiles give insight into the evolution of fungal phytopathogenicity and could be useful to predict the risks of unknown fungi in future biosurveillance activities.
Collapse
Affiliation(s)
- E N Dort
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
| | - E Layne
- School of Computer Science, McGill University, Montreal, QC, Canada
| | - N Feau
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, Victoria, BC, Canada
| | - A Butyaev
- School of Computer Science, McGill University, Montreal, QC, Canada
| | - B Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - F M Martin
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Unité Mixte de Recherche Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, Université de Lorraine, Champenoux, France
| | - S Haridas
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - A Salamov
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - I V Grigoriev
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - M Blanchette
- School of Computer Science, McGill University, Montreal, QC, Canada
| | - R C Hamelin
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.
- Département des Sciences du bois et de la Forêt, Faculté de Foresterie et Géographie, Université Laval, Québec, QC, Canada.
| |
Collapse
|
27
|
Mao H, Jiang C, Tang C, Nie X, Du L, Liu Y, Cheng P, Wu Y, Liu H, Kang Z, Wang X. Wheat adaptation to environmental stresses under climate change: Molecular basis and genetic improvement. MOLECULAR PLANT 2023; 16:1564-1589. [PMID: 37671604 DOI: 10.1016/j.molp.2023.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/19/2023] [Accepted: 09/01/2023] [Indexed: 09/07/2023]
Abstract
Wheat (Triticum aestivum) is a staple food for about 40% of the world's population. As the global population has grown and living standards improved, high yield and improved nutritional quality have become the main targets for wheat breeding. However, wheat production has been compromised by global warming through the more frequent occurrence of extreme temperature events, which have increased water scarcity, aggravated soil salinization, caused plants to be more vulnerable to diseases, and directly reduced plant fertility and suppressed yield. One promising option to address these challenges is the genetic improvement of wheat for enhanced resistance to environmental stress. Several decades of progress in genomics and genetic engineering has tremendously advanced our understanding of the molecular and genetic mechanisms underlying abiotic and biotic stress responses in wheat. These advances have heralded what might be considered a "golden age" of functional genomics for the genetic improvement of wheat. Here, we summarize the current knowledge on the molecular and genetic basis of wheat resistance to abiotic and biotic stresses, including the QTLs/genes involved, their functional and regulatory mechanisms, and strategies for genetic modification of wheat for improved stress resistance. In addition, we also provide perspectives on some key challenges that need to be addressed.
Collapse
Affiliation(s)
- Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cong Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chunlei Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Linying Du
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuling Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peng Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yunfeng Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
| |
Collapse
|
28
|
Ramos-Lizardo GN, Mucherino-Muñoz JJ, Aguiar ERGR, Pirovani CP, Corrêa RX. A repertoire of candidate effector proteins of the fungus Ceratocystis cacaofunesta. Sci Rep 2023; 13:16368. [PMID: 37773261 PMCID: PMC10542334 DOI: 10.1038/s41598-023-43117-7] [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: 01/31/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023] Open
Abstract
The genus Ceratocystis includes many phytopathogenic fungi that affect different plant species. One of these is Ceratocystis cacaofunesta, which is pathogenic to the cocoa tree and causes Ceratocystis wilt, a lethal disease for the crop. However, little is known about how this pathogen interacts with its host. The knowledge and identification of possible genes encoding effector proteins are essential to understanding this pathosystem. The present work aimed to predict genes that code effector proteins of C. cacaofunesta from a comparative analysis of the genomes of five Ceratocystis species available in databases. We performed a new genome annotation through an in-silico analysis. We analyzed the secretome and effectorome of C. cacaofunesta using the characteristics of the peptides, such as the presence of signal peptide for secretion, absence of transmembrane domain, and richness of cysteine residues. We identified 160 candidate effector proteins in the C. cacaofunesta proteome that could be classified as cytoplasmic (102) or apoplastic (58). Of the total number of candidate effector proteins, 146 were expressed, presenting an average of 206.56 transcripts per million. Our database was created using a robust bioinformatics strategy, followed by manual curation, generating information on pathogenicity-related genes involved in plant interactions, including CAZymes, hydrolases, lyases, and oxidoreductases. Comparing proteins already characterized as effectors in Sordariomycetes species revealed five groups of protein sequences homologous to C. cacaofunesta. These data provide a valuable resource for studying the infection mechanisms of these pathogens in their hosts.
Collapse
Affiliation(s)
- Gabriela N Ramos-Lizardo
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, BA, 45662-900, Brazil
| | - Jonathan J Mucherino-Muñoz
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, BA, 45662-900, Brazil
| | - Eric R G R Aguiar
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, BA, 45662-900, Brazil
| | - Carlos Priminho Pirovani
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, BA, 45662-900, Brazil
| | - Ronan Xavier Corrêa
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, BA, 45662-900, Brazil.
| |
Collapse
|
29
|
Jin P, Kong Y, Zhang Z, Zhang H, Dong Y, Lamour K, Yang Z, Zhou Y, Hu J. Comparative genomics and transcriptome analysis reveals potential pathogenic mechanisms of Microdochium paspali on seashore paspalum. Front Microbiol 2023; 14:1259241. [PMID: 37795300 PMCID: PMC10546424 DOI: 10.3389/fmicb.2023.1259241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023] Open
Abstract
The sparse leaf patch of seashore paspalum (Paspalum vaginatum Sw.) caused by Microdochium paspali seriously impacts the landscape value of turf and poses a challenge to the maintenance and management of golf courses. Little is known about the genome of M. paspali or the potential genes underlying pathogenicity. In this study, we present a high-quality genome assembly of M. paspali with 14 contigs using the Nanopore and Illumina platform. The M. paspali genome is roughly 37.32 Mb in size and contains 10,365 putative protein-coding genes. These encompass a total of 3,830 pathogen-host interactions (PHI) genes, 481 carbohydrate-active enzymes (CAZymes) coding genes, 105 effectors, and 50 secondary metabolite biosynthetic gene clusters (SMGCs) predicted to be associated with pathogenicity. Comparative genomic analysis suggests M. paspali has 672 species-specific genes (SSGs) compared to two previously sequenced non-pathogenic Microdochium species, including 24 species-specific gene clusters (SSGCs). Comparative transcriptomic analyses reveal that 739 PHIs, 198 CAZymes, 40 effectors, 21 SMGCs, 213 SSGs, and 4 SSGCs were significantly up-regulated during the process of infection. In conclusion, the study enriches the genomic resources of Microdochium species and provides a valuable resource to characterize the pathogenic mechanisms of M. paspali.
Collapse
Affiliation(s)
- Peiyuan Jin
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Yixuan Kong
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Ze Zhang
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Huangwei Zhang
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Yinglu Dong
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Zhimin Yang
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Yuxin Zhou
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Jian Hu
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
30
|
Dumigan CR, Maddock S, Bray-Stone D, Deyholos MK. Hybrid Genome Assembly of Berkeleyomyces rouxiae, an Emerging Cannabis Fungal Pathogen Causing Black Root Rot in an Aeroponic Facility. PLANT DISEASE 2023; 107:2679-2686. [PMID: 36774565 DOI: 10.1094/pdis-11-22-2690-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The resurged interest in cultivation of Cannabis sativa has presented an array of new challenges. Among them are the difficult-to-control pests and pathogens that infect cannabis plants. The limited methods for disease control available to cannabis growers necessitates early detection of plant pathogens, something that molecular techniques such as DNA sequencing has greatly improved. This study reports for the first time the fungal plant pathogen Berkeleyomyces rouxiae causing black root rot in high THC-containing cannabis. Aeroponically grown cannabis plants at a licenced production facility in Cranbrook BC, Canada, rapidly displayed root discoloration and rot symptoms despite testing negative for all commercially available pathogen tests. Developing sequencing-based disease diagnostics requires genomic information, so this study presents the first whole genome sequence of the multihost, widespread black root rot pathogen B. rouxiae. Hybrid genome assembly using Oxford Nanopore long-reads and Illumina short-reads yielded a genome size of 28.2 Mb represented over 404 contigs with an N50 of 267 kb. Genome annotation predicted 6,960 protein-coding genes with 59,477 functional annotations. The availability of this genome will assist in sequence-based diagnostic development, comparative genomics, and taxonomic resolution of this globally important plant pathogen.
Collapse
Affiliation(s)
- Christopher R Dumigan
- University of British Columbia Okanagan, Irving K. Barber Faculty of Science, Kelowna, British Columbia V1V 1V7, Canada
| | - Savanna Maddock
- University of British Columbia Okanagan, Irving K. Barber Faculty of Science, Kelowna, British Columbia V1V 1V7, Canada
| | | | - Michael K Deyholos
- University of British Columbia Okanagan, Irving K. Barber Faculty of Science, Kelowna, British Columbia V1V 1V7, Canada
| |
Collapse
|
31
|
MacCready JS, Roggenkamp EM, Gdanetz K, Chilvers MI. Elucidating the Obligate Nature and Biological Capacity of an Invasive Fungal Corn Pathogen. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:411-424. [PMID: 36853195 DOI: 10.1094/mpmi-10-22-0213-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Tar spot is a devasting corn disease caused by the obligate fungal pathogen Phyllachora maydis. Since its initial identification in the United States in 2015, P. maydis has become an increasing threat to corn production. Despite this, P. maydis has remained largely understudied at the molecular level, due to difficulties surrounding its obligate lifestyle. Here, we generated a significantly improved P. maydis nuclear and mitochondrial genome, using a combination of long- and short-read technologies, and also provide the first transcriptomic analysis of primary tar spot lesions. Our results show that P. maydis is deficient in inorganic nitrogen utilization, is likely heterothallic, and encodes for significantly more protein-coding genes, including secreted enzymes and effectors, than previous determined. Furthermore, our expression analysis suggests that, following primary tar spot lesion formation, P. maydis might reroute carbon flux away from DNA replication and cell division pathways and towards pathways previously implicated in having significant roles in pathogenicity, such as autophagy and secretion. Together, our results identified several highly expressed unique secreted factors that likely contribute to host recognition and subsequent infection, greatly increasing our knowledge of the biological capacity of P. maydis, which have much broader implications for mitigating tar spot of corn. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Joshua S MacCready
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Emily M Roggenkamp
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Kristi Gdanetz
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| |
Collapse
|
32
|
Advances in molecular interactions on the Rhizoctonia solani-sugar beet pathosystem. FUNGAL BIOL REV 2023. [DOI: 10.1016/j.fbr.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
33
|
Khanal S, Gaire SP, Zhou XG. Kernel Smut and False Smut: The Old-Emerging Diseases of Rice-A Review. PHYTOPATHOLOGY 2023; 113:931-944. [PMID: 36441871 DOI: 10.1094/phyto-06-22-0226-rvw] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Kernel smut, caused by Tilletia horrida, is a disease characterized by the replacement of rice grains with black sooty masses of teliospores or chlamydospores. Kernel smut differs from rice false smut, caused by Ustilaginoidea virens, in the color of chlamydospores. False smut is characterized by globose, velvety spore balls ranging from orangish yellow to greenish black in color. Both kernel smut and false smut have been persistent but are considered minor diseases in many countries since they were discovered in the late 1870s to the 1980s due to their sporadic outbreaks and limited economic impacts. In recent years, however, kernel smut and false smut have emerged as two of the most economically important diseases in rice, including organic rice, in many countries, especially in the United States. The increased use of susceptible rice cultivars, especially hybrids, excessive use of nitrogen fertilizer, and short crop rotations have resulted in an increase in kernel smut and false smut, causing significant losses in grain yield and quality. In this article, we provide a review of the distribution and economic importance of kernel smut; our current understanding of the taxonomy, biology, and epidemiology of kernel smut; and the genomics of the kernel smut fungus as compared with false smut and its causal agent. We also provide an update on the current management strategies of pathogen exclusion, cultivar resistance, fungicides, biological control, and cultural practices for kernel smut and false smut of rice.
Collapse
Affiliation(s)
- Sabin Khanal
- Texas A&M AgriLife Research Center, Beaumont, TX 77713
| | | | - Xin-Gen Zhou
- Texas A&M AgriLife Research Center, Beaumont, TX 77713
| |
Collapse
|
34
|
Chiba de Castro WA, Vaz GCDO, Silva Matos DMD, Vale AH, Bueno ACP, Fagundes LFG, Costa LD, Bonugli Santos RC. The Invasive Tradescantia zebrina Affects Litter Decomposition, but It Does Not Change the Lignocellulolytic Fungal Community in the Atlantic Forest, Brazil. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112162. [PMID: 37299140 DOI: 10.3390/plants12112162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023]
Abstract
Invasive plants affect ecosystems across various scales. In particular, they affect the quality and quantity of litter, which influences the composition of decomposing (lignocellulolytic) fungal communities. However, the relationship among the quality of invasive litter, lignocellulolytic cultivated fungal community composition, and litter decomposition rates under invasive conditions is still unknown. We evaluated whether the invasive herbaceous Tradescantia zebrina affects the litter decomposition in the Atlantic Forest and the lignocellulolytic cultivated fungal community composition. We placed litter bags with litter from the invader and native plants in invaded and non-invaded areas, as well as under controlled conditions. We evaluated the lignocellulolytic fungal communities by culture method and molecular identification. Litter from T. zebrina decomposed faster than litter from native species. However, the invasion of T. zebrina did not alter decomposition rates of either litter type. Although the lignocellulolytic fungal community composition changed over decomposition time, neither the invasion of T. zebrina nor litter type influenced lignocellulolytic fungal communities. We believe that the high plant richness in the Atlantic Forest enables a highly diversified and stable decomposing biota formed in conditions of high plant diversity. This diversified fungal community is capable of interacting with different litter types under different environmental conditions.
Collapse
Affiliation(s)
- Wagner Antonio Chiba de Castro
- Neotropical Biodiversity Graduate Program, Federal University of Latin American Integration, Foz do Iguaçu 85866-000, PR, Brazil
- Latin American Institute of Life and Nature Sciences, Federal University of Latin American Integration, Foz do Iguaçu 85866-000, PR, Brazil
| | - Giselle Cristina de Oliveira Vaz
- Neotropical Biodiversity Graduate Program, Federal University of Latin American Integration, Foz do Iguaçu 85866-000, PR, Brazil
| | - Dalva Maria da Silva Matos
- Neotropical Biodiversity Graduate Program, Federal University of Latin American Integration, Foz do Iguaçu 85866-000, PR, Brazil
- Department of Hydrobiology, Federal University of São Carlos, São Carlos 13600-970, SP, Brazil
| | - Alvaro Herrera Vale
- Latin American Institute of Life and Nature Sciences, Federal University of Latin American Integration, Foz do Iguaçu 85866-000, PR, Brazil
| | - Any Caroline Pantaleão Bueno
- Latin American Institute of Life and Nature Sciences, Federal University of Latin American Integration, Foz do Iguaçu 85866-000, PR, Brazil
| | - Luiz Fernando Grandi Fagundes
- Latin American Institute of Life and Nature Sciences, Federal University of Latin American Integration, Foz do Iguaçu 85866-000, PR, Brazil
| | - Letícia da Costa
- Neotropical Biodiversity Graduate Program, Federal University of Latin American Integration, Foz do Iguaçu 85866-000, PR, Brazil
| | - Rafaella Costa Bonugli Santos
- Neotropical Biodiversity Graduate Program, Federal University of Latin American Integration, Foz do Iguaçu 85866-000, PR, Brazil
- Latin American Institute of Life and Nature Sciences, Federal University of Latin American Integration, Foz do Iguaçu 85866-000, PR, Brazil
| |
Collapse
|
35
|
Hu L, Jia R, Sun Y, Chen J, Chen N, Zhang J, Wang Y. Streptomyces pratensis S10 Controls Fusarium Head Blight by Suppressing Different Stages of the Life Cycle and ATP Production. PLANT DISEASE 2023:PDIS09222063RE. [PMID: 36269586 DOI: 10.1094/pdis-09-22-2063-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Fusarium head blight (FHB) of wheat, predominately caused by Fusarium graminearum, is an economically important plant disease worldwide. With increased fungicide resistance, controlling this filamentous fungal disease has become an enormous challenge. Biocontrol agents alone or integrated with other methods could better manage FHB. Streptomyces pratensis S10 has strong antagonistic activity against FHB as reported in our previous study. We now have investigated S10 controls of FHB in more detail by combining microscope observations, biological assays, and transcriptome profiling. S10 culture filtrates (SCF) significantly inhibited essential stages of the life cycle of F. graminearum in the laboratory and under simulated natural conditions. SCF at different concentrations inhibited conidiation of F. graminearum with an inhibition of 57.49 to 83.83% in the medium and 64.04 to 85.89% in plants. Different concentrations of SCF reduced conidia germination by 47.33 to 67.67%. Two percent (vol/vol) SCF suppressed perithecia formation of F. graminearum by 84 and 81% in the laboratory and under simulated natural conditions, respectively. The S10 also reduced the pathogenicity and penetration ability of F. graminearum by suppressing ATP production. Collectively, these findings indicate that S. pratensis S10 should be explored further for efficacy at controlling FHB.
Collapse
Affiliation(s)
- Lifang Hu
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Ruimin Jia
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Yan Sun
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Jing Chen
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Na Chen
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Jing Zhang
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pest, Ministry of Education, College of Plant Protection, Hainan University, Haikou 570100, P.R. China
| | - Yang Wang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| |
Collapse
|
36
|
Rafiqi M, Kosawang C, Peers JA, Jelonek L, Yvanne H, McMullan M, Nielsen LR. Endophytic fungi related to the ash dieback causal agent encode signatures of pathogenicity on European ash. IMA Fungus 2023; 14:10. [PMID: 37170345 PMCID: PMC10176688 DOI: 10.1186/s43008-023-00115-8] [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: 01/19/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023] Open
Abstract
Tree diseases constitute a significant threat to biodiversity worldwide. Pathogen discovery in natural habitats is of vital importance to understanding current and future threats and prioritising efforts towards developing disease management strategies. Ash dieback is a fungal disease of major conservational concern that is infecting common ash trees, Fraxinus excelsior, in Europe. The disease is caused by a non-native fungal pathogen, Hymenoscyphus fraxineus. Other dieback causing-species have not previously been identified in the genus Hymenoscyphus. Here, we discover the pathogenicity potential of two newly identified related species of Asian origin, H. koreanus and H. occultus, and one Europe-native related species, H. albidus. We sequence the genomes of all three Hymenoscyphus species and compare them to that of H. fraxineus. Phylogenetic analysis of core eukaryotic genes identified H. albidus and H. koreanus as sister species, whilst H. occultus diverged prior to these and H. fraxineus. All four Hymenoscyphus genomes are of comparable size (55-62 Mbp) and GC contents (42-44%) and encode for polymorphic secretomes. Surprisingly, 1133 predicted secreted proteins are shared between the ash dieback pathogen H. fraxineus and the three related Hymenoscyphus endophytes. Amongst shared secreted proteins are cell death-inducing effector candidates, such as necrosis, and ethylene-inducing peptide 1-like proteins, Nep1-like proteins, that are upregulated during in planta growth of all Hymenoscyphus species. Indeed, pathogenicity tests showed that all four related Hymenoscyphus species develop pathogenic growth on European ash stems, with native H. albidus being the least virulent. Our results identify the threat Hymenoscypohus species pose to the survival of European ash trees, and highlight the importance of promoting pathogen surveillance in environmental landscapes. Identifying new pathogens and including them in the screening for durable immunity of common ash trees is key to the long-term survival of ash in Europe.
Collapse
Affiliation(s)
- Maryam Rafiqi
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK.
| | - Chatchai Kosawang
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark
| | - Jessica A Peers
- The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Lukas Jelonek
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Hélène Yvanne
- The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Mark McMullan
- The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Lene R Nielsen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark.
| |
Collapse
|
37
|
Long L, Wang W, Liu Z, Lin Y, Wang J, Lin Q, Ding S. Insights into the capability of the lignocellulolytic enzymes of Penicillium parvum 4-14 to saccharify corn bran after alkaline hydrogen peroxide pretreatment. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:79. [PMID: 37170321 PMCID: PMC10176746 DOI: 10.1186/s13068-023-02319-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/10/2023] [Indexed: 05/13/2023]
Abstract
BACKGROUND Corn bran is a major agro-industrial byproduct from corn starch processing. It contains abundant arabinoxylan that can be converted into value-added chemicals via biotechnology. Corn bran arabinoxylan (CBAX) is one of the most recalcitrant xylans for enzymatic degradation due to its particular heterogeneous nature. The present study aimed to investigate the capability of the filamentous fungus Penicillium parvum 4-14 to enzymatically saccharify CBAX and reveal the fungal carbohydrate-active enzyme (CAZyme) repertoire by genome sequencing and secretome analysis. RESULTS CBAX1 and CBAX2 with different branching degrees, together with corn bran residue (CBR) were generated from corn bran after alkaline hydrogen peroxide (AHP) pretreatment and graded ethanol precipitation. The protein blends E_CBAX1, E_CBAX2, and E_CBR were produced by the fungus grown on CBAX1, CBAX2, or CBR, respectively. Under the optimal conditions, E_CBAX1 released more than 80% xylose and arabinose from CBAX1 and CBAX2. Almost complete saccharification of the arabinoxylans was achieved by combining E_CBAX1 and a commercial enzyme cocktail Cellic®CTec3. Approximately 89% glucose, 64% xylose, and 64% arabinose were liberated from CBR by E_CBR. The combination of E_CBR with Cellic®CTec3 enhanced the saccharification of CBR, with conversion ratios of 97% for glucose, 81% for xylose, and 76% for arabinose. A total of 376 CAZymes including plentiful lignocellulolytic enzymes were predicted in P. parvum based on the fungal genomic sequence (25.8 Mb). Proteomic analysis indicated that the expression of CAZymes in P. parvum varied between CBAX1 and CBR, and the fungus produced complete cellulases, numerous hemicellulases, as well as high levels of glycosidases under the culture conditions. CONCLUSIONS This investigation disclosed the CAZyme repertoire of P. parvum at the genomic and proteomic levels, and elaborated on the promising potential of fungal lignocellulolytic enzymes upon saccharification of corn bran biomass after AHP pretreatment.
Collapse
Affiliation(s)
- Liangkun Long
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, Nanjing Forestry University, Nanjing, 210037, China
| | - Wei Wang
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhen Liu
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Yuanxin Lin
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Jing Wang
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Qunying Lin
- Nanjing Institute for the Comprehensive Utilization of Wild Plants, Nanjing, 211111, China
| | - Shaojun Ding
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China.
- Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, Nanjing Forestry University, Nanjing, 210037, China.
| |
Collapse
|
38
|
Zhong H, Zheng N, Wang J, Zhao S. Isolation and pan-genome analysis of Enterobacter hormaechei Z129, a ureolytic bacterium, from the rumen of dairy cow. Front Microbiol 2023; 14:1169973. [PMID: 37089548 PMCID: PMC10117971 DOI: 10.3389/fmicb.2023.1169973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 03/10/2023] [Indexed: 04/09/2023] Open
Abstract
IntroductionUrea is an important non-protein nitrogen source for ruminants. In the rumen, ureolytic bacteria play critical roles in urea-nitrogen metabolism, however, a few ureolytic strains have been isolated and genomically sequenced. The purpose of this study was to isolate a novel ureolytic bacterial strain from cattle rumen and characterize its genome and function.MethodsThe ureolytic bacterium was isolated using an anaerobic medium with urea and phenol red as a screening indicator from the rumen fluid of dairy cattle. The genome of isolates was sequenced, assembled, annotated, and comparatively analyzed. The pan-genome analysis was performed using IPGA and the biochemical activity was also analyzed by test kits.ResultsA gram-positive ureolytic strain was isolated. Its genome had a length of 4.52 Mbp and predicted genes of 4223. The 16S rRNA gene and genome GTDB-Tk taxonomic annotation showed that it was a novel strain of Enterobacter hormaechei, and it was named E. hormaechei Z129. The pan-genome analysis showed that Z129 had the highest identity to E. hormaechei ATCC 49162 with a genome average nucleotide identity of 98.69% and possessed 238 unique genes. Strain Z129 was the first E. hormaechei strain isolated from the rumen as we know. The functional annotation of the Z129 genome showed genes related to urea metabolism, including urea transport (urtA-urtE), nickel ion transport (ureJ, tonB, nixA, exbB, exbD, and rcnA), urease activation (ureA-ureG) and ammonia assimilation (gdhA, glnA, glnB, glnE, glnL, glsA, gltB, and gltD) were present. Genes involved in carbohydrate metabolism were also present, including starch hydrolysis (amyE), cellulose hydrolysis (celB and bglX), xylose transport (xylF-xylH) and glycolysis (pgi, pgk, fbaA, eno, pfkA, gap, pyk, gpmL). Biochemical activity analysis showed that Z129 was positive for alkaline phosphatase, leucine arylamidase, acid phosphatase, naphthol-AS-BI-phosphohydrolase, α-glucosidase, β-glucosidase, and pyrrolidone arylaminase, and had the ability to use D-ribose, L-arabinose, and D-lactose. Urea-nitrogen hydrolysis rate of Z129 reached 55.37% at 48 h of incubation.DiscussionTherefore, the isolated novel ureolytic strain E. hormaechei Z129 had diverse nitrogen and carbon metabolisms, and is a preferred model to study the urea hydrolysis mechanism in the rumen.
Collapse
|
39
|
Müller M, Kües U, Budde KB, Gailing O. Applying molecular and genetic methods to trees and their fungal communities. Appl Microbiol Biotechnol 2023; 107:2783-2830. [PMID: 36988668 PMCID: PMC10106355 DOI: 10.1007/s00253-023-12480-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.
Collapse
Affiliation(s)
- Markus Müller
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany.
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Katharina B Budde
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| |
Collapse
|
40
|
Li S, Wang Z, Gao M, Li T, Cui X, Zu J, Sang S, Fan W, Zhang H. Intraspecific Comparative Analysis Reveals Genomic Variation of Didymella arachidicola and Pathogenicity Factors Potentially Related to Lesion Phenotype. BIOLOGY 2023; 12:biology12030476. [PMID: 36979167 PMCID: PMC10045276 DOI: 10.3390/biology12030476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]
Abstract
Didymella arachidicola is one of the most important fungal pathogens, causing foliar disease and leading to severe yield losses of peanuts (Arachis hypogaea L.) in China. Two main lesion phenotypes of peanut web blotch have been identified as reticulation type (R type) and blotch type (B type). As no satisfactory reference genome is available, the genomic variations and pathogenicity factors of D. arachidicola remain to be revealed. In the present study, we collected 41 D. arachidicola isolates from 26 geographic locations across China (33 for R type and 8 for B type). The chromosome-scale genome of the most virulent isolate (YY187) was assembled as a reference using PacBio and Hi-C technologies. In addition, we re-sequenced 40 isolates from different sampling sites. Genome-wide alignments showed high similarity among the genomic sequences from the 40 isolates, with an average mapping rate of 97.38%. An average of 3242 SNPs and 315 InDels were identified in the genomic variation analysis, which revealed an intraspecific polymorphism in D. arachidicola. The comparative analysis of the most and least virulent isolates generated an integrated gene set containing 512 differential genes. Moreover, 225 genes individually or simultaneously harbored hits in CAZy-base, PHI-base, DFVF, etc. Compared with the R type reference, the differential gene sets from all B type isolates identified 13 shared genes potentially related to lesion phenotype. Our results reveal the intraspecific genomic variation of D. arachidicola isolates and pathogenicity factors potentially related to different lesion phenotypes. This work sets a genomic foundation for understanding the mechanisms behind genomic diversity driving different pathogenic phenotypes of D. arachidicola.
Collapse
Affiliation(s)
- Shaojian Li
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Zhenyu Wang
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Meng Gao
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Tong Li
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Xiaowei Cui
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Junhuai Zu
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Suling Sang
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Wanwan Fan
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Haiyan Zhang
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| |
Collapse
|
41
|
Caballero JRI, Lalande BM, Hanna JW, Klopfenstein NB, Kim MS, Stewart JE. Genomic Comparisons of Two Armillaria Species with Different Ecological Behaviors and Their Associated Soil Microbial Communities. MICROBIAL ECOLOGY 2023; 85:708-729. [PMID: 35312808 DOI: 10.1007/s00248-022-01989-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 03/06/2022] [Indexed: 06/14/2023]
Abstract
Armillaria species show considerable variation in ecological roles and virulence, from mycorrhizae and saprophytes to important root pathogens of trees and horticultural crops. We studied two Armillaria species that can be found in coniferous forests of northwestern USA and southwestern Canada. Armillaria altimontana not only is considered as a weak, opportunistic pathogen of coniferous trees, but it also appears to exhibit in situ biological control against A. solidipes, formerly North American A. ostoyae, which is considered a virulent pathogen of coniferous trees. Here, we describe their genome assemblies and present a functional annotation of the predicted genes and proteins for the two Armillaria species that exhibit contrasting ecological roles. In addition, the soil microbial communities were examined in association with the two Armillaria species within a 45-year-old plantation of western white pine (Pinus monticola) in northern Idaho, USA, where A. altimontana was associated with improved tree growth and survival, while A. solidipes was associated with reduced growth and survival. The results from this study reveal a high similarity between the genomes of the beneficial/non-pathogenic A. altimontana and pathogenic A. solidipes; however, many relatively small differences in gene content were identified that could contribute to differences in ecological lifestyles and interactions with woody hosts and soil microbial communities.
Collapse
Affiliation(s)
| | - Bradley M Lalande
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
- Forest Health Protection, USDA Forest Service, Gunnison, CO, 81230, USA
| | - John W Hanna
- Rocky Mountain Research Station, USDA Forest Service, Moscow, ID, 83843, USA
| | - Ned B Klopfenstein
- Rocky Mountain Research Station, USDA Forest Service, Moscow, ID, 83843, USA.
| | - Mee-Sook Kim
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, 97331, USA.
| | - Jane E Stewart
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| |
Collapse
|
42
|
Bi K, Liang Y, Mengiste T, Sharon A. Killing softly: a roadmap of Botrytis cinerea pathogenicity. TRENDS IN PLANT SCIENCE 2023; 28:211-222. [PMID: 36184487 DOI: 10.1016/j.tplants.2022.08.024] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/23/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
Botrytis cinerea, a widespread plant pathogen with a necrotrophic lifestyle, causes gray mold disease in many crops. Massive secretion of enzymes and toxins was long considered to be the main driver of infection, but recent studies have uncovered a rich toolbox for B. cinerea pathogenicity. The emerging picture is of a multilayered infection process governed by the exchange of factors that collectively contribute to disease development. No plant shows complete resistance against B. cinerea, but pattern-triggered plant immune responses have the potential to significantly reduce disease progression, opening new possibilities for producing B. cinerea-tolerant plants. We examine current B. cinerea infection models, highlight knowledge gaps, and suggest directions for future studies.
Collapse
Affiliation(s)
- Kai Bi
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan City, Hubei Province, China
| | - Yong Liang
- School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN 47907, USA
| | - Amir Sharon
- School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
| |
Collapse
|
43
|
Linking processes to community functions—insights into litter decomposition combining fungal metatranscriptomics and environmental NMR profiling. Mycol Prog 2023. [DOI: 10.1007/s11557-022-01859-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
AbstractIn forest ecosystems, decomposition is essential for carbon and nutrient cycling and therefore a key process for ecosystem functioning. During the decomposition process, litter chemistry, involved decomposer organisms, and enzymatic activity change interdependently. Chemical composition of the litter is the most complex and dynamic component in the decomposition process and therefore challenging to assess holistically. In this study, we aimed to characterize chemical shifts during decomposition and link them to changes in decomposer fungal activity. We characterized the chemical composition of freshly fallen autumn leaves of European beech (Fagus sylvatica) and the corresponding leaf litter after 1 year of decomposition by proton nuclear magnetic resonance spectroscopy. We further tested the applicability of spiking experiments for qualitative and quantitative characterization of leaves and litter chemistry. The composition and transcriptional activity of fungal communities was assessed by high-throughput Illumina sequencing in the same litter samples. We were able to distinguish freshly fallen leaves from 1-year-old litter based on their chemical composition. Chemical composition of leaves converged among regions with progressing decomposition. Fungal litter communities differed in composition among regions, but they were functionally redundant according to the expression of genes encoding litter degrading enzymes (CAZymes). Fungi of the saprotrophic genera Mycena and Chalara correlated with transcription of litter-degrading CAZymes in 1-year-old litter. Forestry measures influenced the diversity and transcription rate of the detected CAZymes transcripts in litter. Their expression was primarily predicted by composition of the soluble chemical fraction of the litter. Environmental NMR fingerprints thus proved valuable for inferring ecological contexts. We propose and discuss a holistic framework to link fungal activity, enzyme expression, and chemical composition.
Collapse
|
44
|
de Menezes TA, Aburjaile FF, Quintanilha-Peixoto G, Tomé LMR, Fonseca PLC, Mendes-Pereira T, Araújo DS, Melo TS, Kato RB, Delabie JHC, Ribeiro SP, Brenig B, Azevedo V, Drechsler-Santos ER, Andrade BS, Góes-Neto A. Unraveling the Secrets of a Double-Life Fungus by Genomics: Ophiocordyceps australis CCMB661 Displays Molecular Machinery for Both Parasitic and Endophytic Lifestyles. J Fungi (Basel) 2023; 9:jof9010110. [PMID: 36675931 PMCID: PMC9864599 DOI: 10.3390/jof9010110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/31/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Ophiocordyceps australis (Ascomycota, Hypocreales, Ophiocordycipitaceae) is a classic entomopathogenic fungus that parasitizes ants (Hymenoptera, Ponerinae, Ponerini). Nonetheless, according to our results, this fungal species also exhibits a complete set of genes coding for plant cell wall degrading Carbohydrate-Active enZymes (CAZymes), enabling a full endophytic stage and, consequently, its dual ability to both parasitize insects and live inside plant tissue. The main objective of our study was the sequencing and full characterization of the genome of the fungal strain of O. australis (CCMB661) and its predicted secretome. The assembled genome had a total length of 30.31 Mb, N50 of 92.624 bp, GC content of 46.36%, and 8,043 protein-coding genes, 175 of which encoded CAZymes. In addition, the primary genes encoding proteins and critical enzymes during the infection process and those responsible for the host-pathogen interaction have been identified, including proteases (Pr1, Pr4), aminopeptidases, chitinases (Cht2), adhesins, lectins, lipases, and behavioral manipulators, such as enterotoxins, Protein Tyrosine Phosphatases (PTPs), and Glycoside Hydrolases (GHs). Our findings indicate that the presence of genes coding for Mad2 and GHs in O. australis may facilitate the infection process in plants, suggesting interkingdom colonization. Furthermore, our study elucidated the pathogenicity mechanisms for this Ophiocordyceps species, which still is scarcely studied.
Collapse
Affiliation(s)
- Thaís Almeida de Menezes
- Department of Biological Sciences, Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Novo Horizonte, Feira de Santana 44036-900, BA, Brazil
| | - Flávia Figueira Aburjaile
- Laboratory of Integrative Bioinformatics, Preventive Veterinary Medicine Department, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Gabriel Quintanilha-Peixoto
- Laboratory of Molecular and Computational Biology of Fungi, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil
| | - Luiz Marcelo Ribeiro Tomé
- Laboratory of Molecular and Computational Biology of Fungi, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil
| | - Paula Luize Camargos Fonseca
- Laboratory of Molecular and Computational Biology of Fungi, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil
| | - Thairine Mendes-Pereira
- Laboratory of Molecular and Computational Biology of Fungi, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil
| | - Daniel Silva Araújo
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL 60660, USA
| | - Tarcisio Silva Melo
- Department of Biological Sciences, Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Novo Horizonte, Feira de Santana 44036-900, BA, Brazil
| | - Rodrigo Bentes Kato
- Laboratory of Molecular and Computational Biology of Fungi, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil
| | - Jacques Hubert Charles Delabie
- Laboratory of Myrmecology, Centro de Pesquisa do Cacau, Ilhéus 45600-000, BA, Brazil
- Department of Agricultural and Environmental Sciences, Universidade Estadual de Santa Cruz, Ilhéus 45600-970, BA, Brazil
| | - Sérvio Pontes Ribeiro
- Laboratory of Ecology of Diseases and Forests, Nucleus of Biological Science, Campus Morro do Cruzeiro, Universidade Federal de Ouro Preto, Ouro Preto 35402-163, MG, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, 37073 Göttingen, Germany
| | - Vasco Azevedo
- Laboratory of Cellular and Molecular Genetics, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | | | - Bruno Silva Andrade
- Department of Biological Sciences, Universidade Federal do Sudoeste da Bahia, Av. José Moreira Sobrinho, s/n, Jequiezinho, Jequié 45205-490, BA, Brazil
| | - Aristóteles Góes-Neto
- Laboratory of Molecular and Computational Biology of Fungi, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil
- Correspondence: ; Tel.: +55-31-3409-3050
| |
Collapse
|
45
|
Srivastava AK, Srivastava R, Yadav J, Singh AK, Tiwari PK, Srivastava AK, Sahu PK, Singh SM, Kashyap PL. Virulence and pathogenicity determinants in whole genome sequence of Fusarium udum causing wilt of pigeon pea. Front Microbiol 2023; 14:1066096. [PMID: 36876067 PMCID: PMC9981795 DOI: 10.3389/fmicb.2023.1066096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/23/2023] [Indexed: 02/19/2023] Open
Abstract
The present study deals with whole genome analysis of Fusarium udum, a wilt causing pathogen of pigeon pea. The de novo assembly identified a total of 16,179 protein-coding genes, of which 11,892 genes (73.50%) were annotated using BlastP and 8,928 genes (55.18%) from KOG annotation. In addition, 5,134 unique InterPro domains were detected in the annotated genes. Apart from this, we also analyzed genome sequence for key pathogenic genes involved in virulence, and identified 1,060 genes (6.55%) as virulence genes as per the PHI-BASE database. The secretome profiling of these virulence genes indicated the presence of 1,439 secretory proteins. Of those, an annotation of 506 predicted secretory proteins through CAZyme database indicated maximum abundance of Glycosyl hydrolase (GH, 45%) family proteins followed by auxiliary activity (AA) family proteins. Interestingly, the presence of effectors for cell wall degradation, pectin degradation, and host cell death was found. The genome comprised approximately 895,132 bp of repetitive elements, which includes 128 long terminal repeats (LTRs), and 4,921 simple sequence repeats (SSRs) of 80,875 bp length. The comparative mining of effector genes among different Fusarium species revealed five common and two specific effectors in F. udum that are related to host cell death. Furthermore, wet lab experiment validated the presence of effector genes like SIX (for Secreted in Xylem). We conclude that deciphering the whole genome of F. udum would be instrumental in understanding evolution, virulence determinants, host-pathogen interaction, possible control strategies, ecological behavior, and many other complexities of the pathogen.
Collapse
Affiliation(s)
- Alok K Srivastava
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, Uttar Pradesh, India
| | - Ruchi Srivastava
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, Uttar Pradesh, India
| | - Jagriti Yadav
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, Uttar Pradesh, India
| | - Alok K Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, Uttar Pradesh, India
| | - Praveen K Tiwari
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, Uttar Pradesh, India
| | - Anchal K Srivastava
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, Uttar Pradesh, India
| | - Pramod K Sahu
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, Uttar Pradesh, India
| | - Shiv M Singh
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Prem Lal Kashyap
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| |
Collapse
|
46
|
Kalntremtziou M, Papaioannou IA, Vangalis V, Polemis E, Pappas KM, Zervakis GI, Typas MA. Evaluation of the lignocellulose degradation potential of Mediterranean forests soil microbial communities through diversity and targeted functional metagenomics. Front Microbiol 2023; 14:1121993. [PMID: 36922966 PMCID: PMC10008878 DOI: 10.3389/fmicb.2023.1121993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/31/2023] [Indexed: 02/28/2023] Open
Abstract
The enzymatic arsenal of several soil microorganisms renders them particularly suitable for the degradation of lignocellulose, a process of distinct ecological significance with promising biotechnological implications. In this study, we investigated the spatiotemporal diversity and distribution of bacteria and fungi with 16S and Internally Trascribed Spacer (ITS) ribosomal RNA next-generation-sequencing (NGS), focusing on forest mainland Abies cephalonica and insular Quercus ilex habitats of Greece. We analyzed samples during winter and summer periods, from different soil depths, and we applied optimized and combined targeted meta-omics approaches aiming at the peroxidase-catalase family enzymes to gain insights into the lignocellulose degradation process at the soil microbial community level. The microbial communities recorded showed distinct patterns of response to season, soil depth and vegetation type. Overall, in both forests Proteobacteria, Actinobacteria, Acidobacteria were the most abundant bacteria phyla, while the other phyla and the super-kingdom of Archaea were detected in very low numbers. Members of the orders Agaricales, Russulales, Sebacinales, Gomphales, Geastrales, Hysterangiales, Thelephorales, and Trechisporales (Basidiomycota), and Pezizales, Sordariales, Eurotiales, Pleosporales, Helotiales, and Diaporthales (Ascomycota) were the most abundant for Fungi. By using optimized "universal" PCR primers that targeted the peroxidase-catalase enzyme family, we identified several known and novel sequences from various Basidiomycota, even from taxa appearing at low abundance. The majority of the sequences recovered were manganese peroxidases from several genera of Agaricales, Hysterangiales, Gomphales, Geastrales, Russulales, Hymenochaetales, and Trechisporales, while lignin -and versatile-peroxidases were limited to two to eight species, respectively. Comparisons of the obtained sequences with publicly available data allowed a detailed structural analysis of polymorphisms and functionally relevant amino-acid residues at phylogenetic level. The targeted metagenomics applied here revealed an important role in lignocellulose degradation of hitherto understudied orders of Basidiomycota, such as the Hysterangiales and Gomphales, while it also suggested the auxiliary activity of particular members of Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Gemmatimonadetes. The application of NGS-based metagenomics approaches allows a better understanding of the complex process of lignocellulolysis at the microbial community level as well as the identification of candidate taxa and genes for targeted functional investigations and genetic modifications.
Collapse
Affiliation(s)
- Maria Kalntremtziou
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis A Papaioannou
- Zentrum für Molekulare Biologie der Universität Heidelberg, ZMBH, University of Heidelberg, Heidelberg, Germany
| | - Vasileios Vangalis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Elias Polemis
- Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece
| | - Katherine M Pappas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios I Zervakis
- Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece
| | - Milton A Typas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| |
Collapse
|
47
|
Botrytis cinerea Transcription Factor BcXyr1 Regulates (Hemi-)Cellulase Production and Fungal Virulence. mSystems 2022; 7:e0104222. [PMID: 36468854 PMCID: PMC9765177 DOI: 10.1128/msystems.01042-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
Abstract
Botrytis cinerea is an agriculturally notorious plant-pathogenic fungus with a broad host range. During plant colonization, B. cinerea secretes a wide range of plant-cell-wall-degrading enzymes (PCWDEs) that help in macerating the plant tissue, but their role in pathogenicity has been unclear. Here, we report on the identification of a transcription factor, BcXyr1, that regulates the production of (hemi-)cellulases and is necessary for fungal virulence. Deletion of the bcxyr1 gene led to impaired spore germination and reduced fungal virulence and reactive oxygen species (ROS) production in planta. Secreted proteins collected from the bcxyr1 deletion strain displayed a weaker cell-death-inducing effect than the wild-type secretome when infiltrated to Nicotiana benthamiana leaves. Transcriptome sequencing (RNA-seq) analysis revealed 41 genes with reduced expression in the Δbcxyr1 mutant compared with those in the wild-type strain, of which half encode secreted proteins that are particularly enriched in carbohydrate-active enzyme (CAZyme)-encoding genes. Among them, we identified a novel putative expansin-like protein that was necessary for fungal virulence, supporting the involvement of BcXyr1 in the regulation of extracellular virulence factors. IMPORTANCE PCWDEs are considered important components of the virulence arsenal of necrotrophic plant pathogens. However, despite intensive research, the role of PCWDEs in the pathogenicity of necrotrophic phytopathogenic fungi remains ambiguous. Here, we demonstrate that the transcription factor BcXyr1 regulates the expression of a specific set of secreted PCWDE-encoding genes and that it is essential for fungal virulence. Furthermore, we identified a BcXyr1-regulated expansin-like gene that is required for fungal virulence. Our findings provide strong evidence for the importance of PCWDEs in the pathogenicity of B. cinerea and highlight specific PCWDEs that might be more important than others.
Collapse
|
48
|
Reveglia P, Billones-Baaijens R, Savocchia S. Phytotoxic Metabolites Produced by Fungi Involved in Grapevine Trunk Diseases: Progress, Challenges, and Opportunities. PLANTS (BASEL, SWITZERLAND) 2022; 11:3382. [PMID: 36501420 PMCID: PMC9736528 DOI: 10.3390/plants11233382] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Grapevine trunk diseases (GTDs), caused by fungal pathogens, are a serious threat to vineyards worldwide, causing significant yield and economic loss. To date, curative methods are not available for GTDs, and the relationship between the pathogen and symptom expression is poorly understood. Several plant pathologists, molecular biologists, and chemists have been investigating different aspects of the pathogenicity, biochemistry, and chemical ecology of the fungal species involved in GTDs. Many studies have been conducted to investigate virulence factors, including the chemical characterization of phytotoxic metabolites (PMs) that assist fungi in invading and colonizing crops such as grapevines. Moreover, multidisciplinary studies on their role in pathogenicity, symptom development, and plant-pathogen interactions have also been carried out. The aim of the present review is to provide an illustrative overview of the biological and chemical characterization of PMs produced by fungi involved in Eutypa dieback, Esca complex, and Botryosphaeria dieback. Moreover, multidisciplinary investigations on host-pathogen interactions, including those using cutting-edge Omics techniques, will also be reviewed and discussed. Finally, challenges and opportunities in the role of PMs for reliable field diagnosis and control of GTDs in vineyards will also be explored.
Collapse
Affiliation(s)
| | | | - Sandra Savocchia
- Gulbali Institute, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
| |
Collapse
|
49
|
The pan-genome of Aspergillus fumigatus provides a high-resolution view of its population structure revealing high levels of lineage-specific diversity driven by recombination. PLoS Biol 2022; 20:e3001890. [PMID: 36395320 PMCID: PMC9714929 DOI: 10.1371/journal.pbio.3001890] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 12/01/2022] [Accepted: 10/26/2022] [Indexed: 11/18/2022] Open
Abstract
Aspergillus fumigatus is a deadly agent of human fungal disease where virulence heterogeneity is thought to be at least partially structured by genetic variation between strains. While population genomic analyses based on reference genome alignments offer valuable insights into how gene variants are distributed across populations, these approaches fail to capture intraspecific variation in genes absent from the reference genome. Pan-genomic analyses based on de novo assemblies offer a promising alternative to reference-based genomics with the potential to address the full genetic repertoire of a species. Here, we evaluate 260 genome sequences of A. fumigatus including 62 newly sequenced strains, using a combination of population genomics, phylogenomics, and pan-genomics. Our results offer a high-resolution assessment of population structure and recombination frequency, phylogenetically structured gene presence-absence variation, evidence for metabolic specificity, and the distribution of putative antifungal resistance genes. Although A. fumigatus disperses primarily via asexual conidia, we identified extraordinarily high levels of recombination with the lowest linkage disequilibrium decay value reported for any fungal species to date. We provide evidence for 3 primary populations of A. fumigatus, with recombination occurring only rarely between populations and often within them. These 3 populations are structured by both gene variation and distinct patterns of gene presence-absence with unique suites of accessory genes present exclusively in each clade. Accessory genes displayed functional enrichment for nitrogen and carbohydrate metabolism suggesting that populations may be stratified by environmental niche specialization. Similarly, the distribution of antifungal resistance genes and resistance alleles were often structured by phylogeny. Altogether, the pan-genome of A. fumigatus represents one of the largest fungal pan-genomes reported to date including many genes unrepresented in the Af293 reference genome. These results highlight the inadequacy of relying on a single-reference genome-based approach for evaluating intraspecific variation and the power of combined genomic approaches to elucidate population structure, genetic diversity, and putative ecological drivers of clinically relevant fungi.
Collapse
|
50
|
Gourlie R, McDonald M, Hafez M, Ortega-Polo R, Low KE, Abbott DW, Strelkov SE, Daayf F, Aboukhaddour R. The pangenome of the wheat pathogen Pyrenophora tritici-repentis reveals novel transposons associated with necrotrophic effectors ToxA and ToxB. BMC Biol 2022; 20:239. [PMID: 36280878 PMCID: PMC9594970 DOI: 10.1186/s12915-022-01433-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In fungal plant pathogens, genome rearrangements followed by selection pressure for adaptive traits have facilitated the co-evolutionary arms race between hosts and their pathogens. Pyrenophora tritici-repentis (Ptr) has emerged recently as a foliar pathogen of wheat worldwide and its populations consist of isolates that vary in their ability to produce combinations of different necrotrophic effectors. These effectors play vital roles in disease development. Here, we sequenced the genomes of a global collection (40 isolates) of Ptr to gain insights into its gene content and genome rearrangements. RESULTS A comparative genome analysis revealed an open pangenome, with an abundance of accessory genes (~ 57%) reflecting Ptr's adaptability. A clear distinction between pathogenic and non-pathogenic genomes was observed in size, gene content, and phylogenetic relatedness. Chromosomal rearrangements and structural organization, specifically around effector coding genes, were detailed using long-read assemblies (PacBio RS II) generated in this work in addition to previously assembled genomes. We also discovered the involvement of large mobile elements associated with Ptr's effectors: ToxA, the gene encoding for the necrosis effector, was found as a single copy within a 143-kb 'Starship' transposon (dubbed 'Horizon') with a clearly defined target site and target site duplications. 'Horizon' was located on different chromosomes in different isolates, indicating mobility, and the previously described ToxhAT transposon (responsible for horizontal transfer of ToxA) was nested within this newly identified Starship. Additionally, ToxB, the gene encoding the chlorosis effector, was clustered as three copies on a 294-kb element, which is likely a different putative 'Starship' (dubbed 'Icarus') in a ToxB-producing isolate. ToxB and its putative transposon were missing from the ToxB non-coding reference isolate, but the homolog toxb and 'Icarus' were both present in a different non-coding isolate. This suggests that ToxB may have been mobile at some point during the evolution of the Ptr genome which is contradictory to the current assumption of ToxB vertical inheritance. Finally, the genome architecture of Ptr was defined as 'one-compartment' based on calculated gene distances and evolutionary rates. CONCLUSIONS These findings together reflect on the highly plastic nature of the Ptr genome which has likely helped to drive its worldwide adaptation and has illuminated the involvement of giant transposons in facilitating the evolution of virulence in Ptr.
Collapse
Affiliation(s)
- Ryan Gourlie
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, Lethbridge, AB Canada
| | - Megan McDonald
- grid.6572.60000 0004 1936 7486School of Biosciences, University of Birmingham, Institute of Microbiology and Infection, Edgbaston, Birmingham, UK
| | - Mohamed Hafez
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, Lethbridge, AB Canada
| | - Rodrigo Ortega-Polo
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, Lethbridge, AB Canada
| | - Kristin E. Low
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, Lethbridge, AB Canada
| | - D. Wade Abbott
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, Lethbridge, AB Canada
| | - Stephen E. Strelkov
- grid.17089.370000 0001 2190 316XFaculty of Agricultural, Life, and Environmental Sciences, University of Alberta, Edmonton, AB Canada
| | - Fouad Daayf
- grid.21613.370000 0004 1936 9609Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB Canada
| | - Reem Aboukhaddour
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, Lethbridge, AB Canada
| |
Collapse
|