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Roy M, Burragoni SG, Jeon J. Changes in Endophyte Communities across the Different Plant Compartments in Response to the Rice Blast Infection. THE PLANT PATHOLOGY JOURNAL 2024; 40:299-309. [PMID: 38835301 PMCID: PMC11162860 DOI: 10.5423/ppj.oa.12.2023.0175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/04/2024] [Accepted: 04/17/2024] [Indexed: 06/06/2024]
Abstract
The rice blast disease, caused by the fungal pathogen, Magnaporthe oryzae (syn. Pyricularia oryzae), poses a significant threat to the global rice production. Understanding how this disease impacts the plant's microbial communities is crucial for gaining insights into hostpathogen interactions. In this study, we investigated the changes in communities of bacterial and fungal endophytes inhabiting different compartments in healthy and diseased plants. We found that both alpha and beta diversities of endophytic communities do not change significantly by the pathogen infection. Rather, the type of plant compartment appeared to be the main driver of endophytic community structures. Although the overall structure seemed to be consistent between healthy and diseased plants, our analysis of differentially abundant taxa revealed the specific bacterial and fungal operational taxonomic units that exhibited enrichment in the root and leaf compartments of infected plants. These findings suggest that endophyte communities are robust to the changes at the early stage of pathogen infection, and that some of endophytes enriched in infected plants might have roles in the defense against the pathogen.
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Affiliation(s)
- Mehwish Roy
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea
| | | | - Junhyun Jeon
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea
- Plant Immunity Research Centre, Seoul National University, Seoul 08826, Korea
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2
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Guo JW, Mohamad OAA, Wang X, Egamberdieva D, Tian B. Editorial: Microbiome associated with plant pathogens, pathogenesis, and their applications in developing sustainable agriculture. Front Microbiol 2024; 15:1423961. [PMID: 38841068 PMCID: PMC11152044 DOI: 10.3389/fmicb.2024.1423961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 05/09/2024] [Indexed: 06/07/2024] Open
Affiliation(s)
- Jian-Wei Guo
- College of Agronomy and Life Sciences, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Osama Abdalla Abdelshafy Mohamad
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Department of Environmental Science, Institute of Environmental Studies, Arish University, El-Arish, Egypt
| | - Xiaolin Wang
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Dilfuza Egamberdieva
- Faculty of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
- Institute of Fundamental and Applied Research, National Research University TIIAME, Tashkent, Uzbekistan
| | - Baoyu Tian
- Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, China
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3
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Fouladvand S, Soltani J. Halophytic Bacterial Endophyte Microbiome from Coastal Desert-Adapted Wild Poaceae Alleviates Salinity Stress in the Common Wheat Triticum aestivum L. Curr Microbiol 2024; 81:132. [PMID: 38592497 DOI: 10.1007/s00284-024-03649-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 02/22/2024] [Indexed: 04/10/2024]
Abstract
Abiotic stresses threaten the strategic crops of Poaceae (Gramineae) worldwide. Habitat-adapted microbiome of wild plants has the potential to alleviate abiotic stresses in alternate hosts. Persian Gulf's coastal deserts are colonized by halophyte plants hosting habitat-adapted halophytic microbiota. Here, endophytic bacteria from wild Poaceae in coastal deserts of the north Persian Gulf at Hormozgan province, Iran, were isolated and screened for mitigating salinity stress in wheat. Accordingly, seven dominant species of wild Poaceae in the region, i.e., Aeloropus lagopoides, Aeloropus litiralis, Chrysopogon aucheri, Cymbopogon olivieri, Desmostachya sp., Halopayrum mucronatum, and Sporbuls arabicus, were explored. In total, 367 endophytic bacteria were isolated, 90 of which tolerated 2.5-M NaCl. Of these, 38 strains were selected based on their bioactivity and applied for in vitro wheat-interaction assays under 250-mM NaCl stress. Five superior strains promoted seed germination and growth indices in rain-fed winter wheat cv. Sardari, i.e., Bacillus subtilis B14, B19, & B27, Bacillus sp. B21, and Bacillus licheniformis Ba38. In planta assays in saline soil (2.7 dS m-1) using the superior strains indicated that Bacillus sp. B21 and Bacillus licheniformis Ba38 increased germination and root and shoot lengths and their dry and fresh weights in wheat seedlings. Moreover, phenolics and flavonoids contents of wheat seedlings were influenced by endophyte application. Thus, the coastal desert-adapted microbiome of wild Poaceae could alleviate abiotic stress and promote growth in cultivated species of Poaceae, such as wheat.
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Affiliation(s)
- Samaneh Fouladvand
- Phytopathology Section, Plant Protection Department, Bu-Ali Sina University, Hamedan, Iran
| | - Jalal Soltani
- Phytopathology Section, Plant Protection Department, Bu-Ali Sina University, Hamedan, Iran.
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Thomas VE, Antony-Babu S. Core hyphosphere microbiota of Fusarium oxysporum f. sp. niveum. ENVIRONMENTAL MICROBIOME 2024; 19:14. [PMID: 38461269 PMCID: PMC10924372 DOI: 10.1186/s40793-024-00558-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/22/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND Bacteria and fungi are dynamically interconnected, leading to beneficial or antagonistic relationships with plants. Within this interkingdom interaction, the microbial community directly associated with the pathogen make up the pathobiome. While the overall soil bacterial community associated with Fusarium wilt diseases has been widely examined, the specific bacterial populations that directly interact with the Fusarium wilt pathogens are yet to be discovered. In this study, we define the bacterial community associated with the hyphae of Fusarium oxysporum f. sp. niveum race 2 (FON2). Using the 16S rRNA gene metabarcoding, we describe the hyphosphere pathobiome of three isolates of FON2. RESULTS Our results show a core microbiome that is shared among the three tested hyphospheres. The core hyphosphere community was made up of 15 OTUs (Operational Taxonomic Units) that were associated with all three FON2 isolates. This core consisted of bacterial members of the families, Oxalobacteraceae, Propionibacteriaceae, Burkholderiaceae, Micrococcaceae, Bacillaceae, Comamonadaceae, Pseudomonadaceae and unclassified bacteria. The hyphosphere of FON2 was dominated by order Burkholderiales. While all three isolate hyphospheres were dominated by these taxa, the specific OTU differed. We also note that while the dominant OTU of one hyphosphere might not be the largest OTU for other hyphospheres, they were still present across all the three isolate hyphospheres. Additionally, in the correlation and co-occurrence analysis the most abundant OTU was negatively correlated with most of the other OTU populations within the hyphosphere. CONCLUSIONS The study indicates a core microbiota associated with FON2. These results provide insights into the microbe-microbe dynamic of the pathogen's success and its ability to recruit a core pathobiome. Our research promotes the concept of pathogens not being lone invaders but recruits from the established host microbiome to form a pathobiome.
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Affiliation(s)
- Vanessa E Thomas
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
| | - Sanjay Antony-Babu
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA.
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Jayasinghe H, Chang HX, Knobloch S, Yang SH, Hendalage DPB, Ariyawansa KGSU, Liu PY, Stadler M, Ariyawansa HA. Metagenomic insight to apprehend the fungal communities associated with leaf blight of Welsh onion in Taiwan. FRONTIERS IN PLANT SCIENCE 2024; 15:1352997. [PMID: 38495366 PMCID: PMC10941342 DOI: 10.3389/fpls.2024.1352997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 02/12/2024] [Indexed: 03/19/2024]
Abstract
Plants are associated with a large diversity of microbes, and these complex plant-associated microbial communities are critical for plant health. Welsh onion (Allium fistulosum L.) is one of the key and oldest vegetable crops cultivated in Taiwan. The leaf of the Welsh onion is one of the famous spices in Taiwanese cuisine, thus, it is crucial to control foliar diseases. In recent years, Welsh onion cultivation in Taiwan has been severely threatened by the occurrence of leaf blight disease, greatly affecting their yield and quality. However, the overall picture of microbiota associated with the Welsh onion plant is still not clear as most of the recent etiological investigations were heavily based on the isolation of microorganisms from diseased plants. Therefore, studying the diversity of fungal communities associated with the leaf blight symptoms of Welsh onion may provide information regarding key taxa possibly involved in the disease. Therefore, this investigation was mainly designed to understand the major fungal communities associated with leaf blight to identify key taxa potentially involved in the disease and further evaluate any shifts in both phyllosphere and rhizosphere mycobiome assembly due to foliar pathogen infection by amplicon sequencing targeting the Internal Transcribed Spacer (ITS) 1 region of the rRNA. The alpha and beta-diversity analyses were used to compare the fungal communities and significant fungal groups were recognized based on linear discriminant analyses. Based on the results of relative abundance data and co-occurrence networks in symptomatic plants we revealed that the leaf blight of Welsh onion in Sanxing, is a disease complex mainly involving Stemphylium and Colletotrichum taxa. In addition, genera such as Aspergillus, Athelia and Colletotrichum were abundantly found associated with the symptomatic rhizosphere. Alpha-diversity in some fields indicated a significant increase in species richness in the symptomatic phyllosphere compared to the asymptomatic phyllosphere. These results will broaden our knowledge of pathogens of Welsh onion associated with leaf blight symptoms and will assist in developing effective disease management strategies to control the progress of the disease.
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Affiliation(s)
- Himanshi Jayasinghe
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Hao-Xun Chang
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Stephen Knobloch
- Department of Food Technology, Fulda University of Applied Sciences, Fulda, Germany
| | - Shan-Hua Yang
- Institute of Fisheries Science, National Taiwan University, Taipei, Taiwan
| | - D. P. Bhagya Hendalage
- Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | | | - Po-Yu Liu
- School of Medicine, College of Medicine, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Braunschweig, Germany
| | - Hiran A. Ariyawansa
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
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6
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Waheed A, Haxim Y, Islam W, Ahmad M, Muhammad M, Alqahtani FM, Hashem M, Salih H, Zhang D. Climate change reshaping plant-fungal interaction. ENVIRONMENTAL RESEARCH 2023; 238:117282. [PMID: 37783329 DOI: 10.1016/j.envres.2023.117282] [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: 08/07/2023] [Revised: 09/13/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
Plant diseases pose a severe threat to modern agriculture, necessitating effective and lasting control solutions. Environmental factors significantly shape plant ecology. Human-induced greenhouse gas emissions have led to global temperature rise, impacting various aspects, including carbon dioxide (CO2) concentration, temperature, ozone (O3), and ultraviolet-B, all of which influence plant diseases. Altered pathogen ranges can accelerate disease transmission. This review explores environmental effects on plant diseases, with climate change affecting fungal biogeography, disease incidence, and severity, as well as agricultural production. Moreover, we have discussed how climate change influences pathogen development, host-fungal interactions, the emergence of new races of fungi, and the dissemination of emerging fungal diseases across the globe. The discussion about environment-mediated impact on pattern-triggered immunity (PTI), effector-triggered immunity (ETI), and RNA interference (RNAi) is also part of this review. In conclusion, the review underscores the critical importance of understanding how climate change is reshaping plant-fungal interactions. It highlights the need for continuous research efforts to elucidate the mechanisms driving these changes and their ecological consequences. As the global climate continues to evolve, it is imperative to develop innovative strategies for mitigating the adverse effects of fungal pathogens on plant health and food security.
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Affiliation(s)
- Abdul Waheed
- National Key Laboratory of Ecological Security and Resource Utilization in Arid Areas, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology & Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China
| | - Yakoopjan Haxim
- National Key Laboratory of Ecological Security and Resource Utilization in Arid Areas, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology & Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China
| | - Waqar Islam
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | | | - Murad Muhammad
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology & Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Fatmah M Alqahtani
- Department of Biology, College of Science, King Khalid University, Abha, 61413, Saudi Arabia
| | - Mohamed Hashem
- Department of Biology, College of Science, King Khalid University, Abha, 61413, Saudi Arabia
| | - Haron Salih
- National Key Laboratory of Ecological Security and Resource Utilization in Arid Areas, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology & Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China
| | - Daoyuan Zhang
- National Key Laboratory of Ecological Security and Resource Utilization in Arid Areas, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology & Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China.
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7
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Alleyne A, Mason S, Vallès Y. Characterization of the Cassava Mycobiome in Symptomatic Leaf Tissues Displaying Cassava Superelongation Disease. J Fungi (Basel) 2023; 9:1130. [PMID: 38132731 PMCID: PMC10743849 DOI: 10.3390/jof9121130] [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: 10/14/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Superelongation disease (SED) is a fungal disease that affects cassava in the Caribbean. The symptoms include the appearance of dry necrotic spots and lesions on the leaves, which may severely affect the plant yield. However, the primary causal pathogen is difficult to culture and isolate in the lab because of its slow growth and potential contamination from faster-growing organisms. In addition, the leaf symptoms can be confused with those caused by other pathogens that produce similar necrotic spots and scab-like lesions. There is also little or no information on the contribution of endophytes, if any, to disease symptoms in cassava, a plant where the disease is prevalent. Therefore, this study aimed to characterize the fungal communities in cassava associated with SED symptoms by analyzing gross fungal morphology and performing metagenomics profiling. First, several individual pathogenic fungi were isolated and cultured from diseased cassava leaf tissues from seven locations in Barbados (BB). Both culture isolation and molecular community analyses showed the presence of several other fungi in the disease microenvironment of symptomatic cassava leaves. These included Fusarium, Colletotrichum, and Alternaria species and the suspected species Elsinoë brasiliensis synonym Sphaceloma manihoticola. Additionally, a community analysis using ITS2 amplicon sequencing of 21 symptomatic leaf tissues from BB, St. Vincent and the Grenadines (SVG), Trinidad and Tobago (TT), and Jamaica (JA) revealed that the disease symptoms of superelongation may also result from the interactions of fungal communities in the mycobiome, including Elsinoë species and other fungi such as Colletotrichum, Cercospora, Alternaria, and Fusarium. Therefore, we suggest that examining the pathobiome concept in SED in the future is necessary.
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Affiliation(s)
- Angela Alleyne
- Faculty of Science and Technology, The University of the West Indies, Cave Hill Campus, Bridgetown BB11000, Barbados (Y.V.)
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8
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Mannaa M, Han G, Jung H, Park J, Kim JC, Park AR, Seo YS. Aureobasidium pullulans Treatment Mitigates Drought Stress in Abies koreana via Rhizosphere Microbiome Modulation. PLANTS (BASEL, SWITZERLAND) 2023; 12:3653. [PMID: 37896116 PMCID: PMC10610362 DOI: 10.3390/plants12203653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/20/2023] [Accepted: 10/22/2023] [Indexed: 10/29/2023]
Abstract
The Korean fir tree Abies koreana, an endangered species in Korea, faces threats primarily from climate change-induced stress and drought. This study proposed a sustainable method to enhance A. koreana drought tolerance using a black yeast-like fungus identified as Aureobasidium pullulans (AK10). The 16S/ITS metabarcoding analysis assessed the impact of drought and AK10 treatment on the seedlings' rhizosphere microbiome. Results revealed a profound drought influence on the microbiome, particularly affecting fungal mycobiota. Drought-stressed seedlings exhibited elevated Agaricaceae levels, opportunistic fungi generally associated with decomposition. AK10 treatment significantly mitigated this proliferation and increased the relative abundance of beneficial fungi like Cystofilobasidium and Mortierella, known biocontrol agents and phosphate solubilizers. A notable reduction in the phytopathogenic Fusarium levels was observed with AK10, alongside an increase in beneficial bacteria, including Azospirillum and Nitrospirillum. Furthermore, the conducted correlation analysis shed light on microbial interrelationships within the rhizosphere, elucidating potential co-associations and antagonisms. Taken together, the isolated A. pullulans AK10 identified in this study serves as a potential biostimulant, enhancing the drought tolerance in A. koreana through beneficial alterations in the rhizosphere microbiome. This approach presents a promising strategy for the conservation of this endangered species.
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Affiliation(s)
- Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (M.M.); (G.H.); (H.J.)
- Department of Plant Pathology, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Gil Han
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (M.M.); (G.H.); (H.J.)
| | - Hyejung Jung
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (M.M.); (G.H.); (H.J.)
| | - Jungwook Park
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea;
| | - Jin-Cheol Kim
- Division of Applied Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea; (J.-C.K.); (A.R.P.)
| | - Ae Ran Park
- Division of Applied Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea; (J.-C.K.); (A.R.P.)
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (M.M.); (G.H.); (H.J.)
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9
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Nemchinov LG, Irish BM, Uschapovsky IV, Grinstead S, Shao J, Postnikova OA. Composition of the alfalfa pathobiome in commercial fields. Front Microbiol 2023; 14:1225781. [PMID: 37692394 PMCID: PMC10491455 DOI: 10.3389/fmicb.2023.1225781] [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: 05/19/2023] [Accepted: 07/31/2023] [Indexed: 09/12/2023] Open
Abstract
Through the recent advances of modern high-throughput sequencing technologies, the "one microbe, one disease" dogma is being gradually replaced with the principle of the "pathobiome". Pathobiome is a comprehensive biotic environment that not only includes a diverse community of all disease-causing organisms within the plant but also defines their mutual interactions and resultant effect on plant health. To date, the concept of pathobiome as a major component in plant health and sustainable production of alfalfa (Medicago sativa L.), the most extensively cultivated forage legume in the world, is non-existent. Here, we approached this subject by characterizing the biodiversity of the alfalfa pathobiome using high-throughput sequencing technology. Our metagenomic study revealed a remarkable abundance of different pathogenic communities associated with alfalfa in the natural ecosystem. Profiling the alfalfa pathobiome is a starting point to assess known and identify new and emerging stress challenges in the context of plant disease management. In addition, it allows us to address the complexity of microbial interactions within the plant host and their impact on the development and evolution of pathogenesis.
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Affiliation(s)
- Lev G. Nemchinov
- Molecular Plant Pathology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Brian M. Irish
- Plant Germplasm Introduction and Testing Research Unit, Prosser, WA, United States
| | | | - Sam Grinstead
- Molecular Plant Pathology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Jonathan Shao
- United States Department of Agriculture, Agricultural Research Service, Office of The Area Director, Beltsville, MD, United States
| | - Olga A. Postnikova
- Molecular Plant Pathology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Center, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
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10
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Lv T, Zhan C, Pan Q, Xu H, Fang H, Wang M, Matsumoto H. Plant pathogenesis: Toward multidimensional understanding of the microbiome. IMETA 2023; 2:e129. [PMID: 38867927 PMCID: PMC10989765 DOI: 10.1002/imt2.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 06/14/2024]
Abstract
Single pathogen-targeted disease management measure has shown drawbacks in field efficacy under the scenario of global change. An in-depth understanding of plant pathogenesis will provide a promising solution but faces the challenges of the emerging paradigm involving the plant microbiome. While the beneficial impact of the plant microbiome is well characterized, their potential role in facilitating pathological processes has so far remained largely overlooked. To address these unsolved controversies and emerging challenges, we hereby highlight the pathobiome, the disease-assisting portion hidden in the plant microbiome, in the plant pathogenesis paradigm. We review the detrimental actions mediated by the pathobiome at multiple scales and further discuss how natural and human triggers result in the prevalence of the plant pathobiome, which would probably provide a clue to the mitigation of plant disease epidemics. Collectively, the article would advance the current insight into plant pathogenesis and also pave a new way to cope with the upward trends of plant disease by designing the pathobiome-targeted measure.
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Affiliation(s)
- Tianxing Lv
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Chengfang Zhan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Qianqian Pan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Haorong Xu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Hongda Fang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Mengcen Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- Global Education Program for AgriScience Frontiers, Graduate School of AgricultureHokkaido UniversitySapporoJapan
| | - Haruna Matsumoto
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
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11
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Chen W, Modi D, Picot A. Soil and Phytomicrobiome for Plant Disease Suppression and Management under Climate Change: A Review. PLANTS (BASEL, SWITZERLAND) 2023; 12:2736. [PMID: 37514350 PMCID: PMC10384710 DOI: 10.3390/plants12142736] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
The phytomicrobiome plays a crucial role in soil and ecosystem health, encompassing both beneficial members providing critical ecosystem goods and services and pathogens threatening food safety and security. The potential benefits of harnessing the power of the phytomicrobiome for plant disease suppression and management are indisputable and of interest in agriculture but also in forestry and landscaping. Indeed, plant diseases can be mitigated by in situ manipulations of resident microorganisms through agronomic practices (such as minimum tillage, crop rotation, cover cropping, organic mulching, etc.) as well as by applying microbial inoculants. However, numerous challenges, such as the lack of standardized methods for microbiome analysis and the difficulty in translating research findings into practical applications are at stake. Moreover, climate change is affecting the distribution, abundance, and virulence of many plant pathogens, while also altering the phytomicrobiome functioning, further compounding disease management strategies. Here, we will first review literature demonstrating how agricultural practices have been found effective in promoting soil health and enhancing disease suppressiveness and mitigation through a shift of the phytomicrobiome. Challenges and barriers to the identification and use of the phytomicrobiome for plant disease management will then be discussed before focusing on the potential impacts of climate change on the phytomicrobiome functioning and disease outcome.
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Affiliation(s)
- Wen Chen
- Ottawa Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Dixi Modi
- Ottawa Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Adeline Picot
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
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12
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Li L, Wang Y, Yu C, Li S, Lin T, Han S, Zhu T, Li S. Seasonal changes in the abundance Fusarium proliferatium, microbial endophytes and nutrient levels in the roots of hybrid bamboo Bambusa pervariabilis × Dendrocalamopsis grandis. FRONTIERS IN PLANT SCIENCE 2023; 14:1185449. [PMID: 37538062 PMCID: PMC10394707 DOI: 10.3389/fpls.2023.1185449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/04/2023] [Indexed: 08/05/2023]
Abstract
Plant root pathogens invade the soil around plant roots, disturbing the systemic balance, reducing plant defenses, and causing severe disease. At present, there are few studies on the severity of plant diseases caused by pathogen invasion in different seasons and how pathogens affect root microecology. In this study, we compared the levels of nutrients in the root tissues of the two groups of plants. We used 16S and ITS amplicon sequencing with Illumina NovaSeq 6000 to compare seasonal changes in the composition and structure of microbial communities from healthy roots of bamboo Bambusa pervariabilis × Dendrocalamopsis grandis and roots infected by the soilborne pathogen Fusarium proliferatum. We have found that the invasion of the pathogen led to a substantial decrease in nutrient elements in bamboo roots, except for nitrogen. The pathogen presence correlated with seasonal changes in the bamboo root microbiome and decreased bacterial richness in diseased plants. The root microbial community structure of healthy plants was more stable than that of their diseased counterparts. Furthermore, we identified the lesion area and relative abundance of F. proliferatum were significant predictors of disease progression. The potassium tissue content and the disease lesion area were identified as factors linked with the observed changes in the bamboo root microbiome. This study provides a theoretical foundation for understanding the seasonal dynamics F. proliferatum, an economically important soilborne pathogen of hybrid bamboo grown in Sichuan Province, China.
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Affiliation(s)
- Lin Li
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Yaxuan Wang
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Cailin Yu
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Shuying Li
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Tiantian Lin
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Shan Han
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Tianhui Zhu
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Shujiang Li
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Chengdu, China
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13
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Li Y, Lei S, Cheng Z, Jin L, Zhang T, Liang LM, Cheng L, Zhang Q, Xu X, Lan C, Lu C, Mo M, Zhang KQ, Xu J, Tian B. Microbiota and functional analyses of nitrogen-fixing bacteria in root-knot nematode parasitism of plants. MICROBIOME 2023; 11:48. [PMID: 36895023 PMCID: PMC9999639 DOI: 10.1186/s40168-023-01484-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Root-knot nematodes (RKN) are among the most important root-damaging plant-parasitic nematodes, causing severe crop losses worldwide. The plant rhizosphere and root endosphere contain rich and diverse bacterial communities. However, little is known about how RKN and root bacteria interact to impact parasitism and plant health. Determining the keystone microbial taxa and their functional contributions to plant health and RKN development is important for understanding RKN parasitism and developing efficient biological control strategies in agriculture. RESULTS The analyses of rhizosphere and root endosphere microbiota of plants with and without RKN showed that host species, developmental stage, ecological niche, and nematode parasitism, as well as most of their interactions, contributed significantly to variations in root-associated microbiota. Compared with healthy tomato plants at different developmental stages, significant enrichments of bacteria belonging to Rhizobiales, Betaproteobacteriales, and Rhodobacterales were observed in the endophytic microbiota of nematode-parasitized root samples. Functional pathways related to bacterial pathogenesis and biological nitrogen fixation were significantly enriched in nematode-parasitized plants. In addition, we observed significant enrichments of the nifH gene and NifH protein, the key gene/enzyme involved in biological nitrogen fixation, within nematode-parasitized roots, consistent with a potential functional contribution of nitrogen-fixing bacteria to nematode parasitism. Data from a further assay showed that soil nitrogen amendment could reduce both endophytic nitrogen-fixing bacteria and RKN prevalence and galling in tomato plants. CONCLUSIONS Results demonstrated that (1) community variation and assembly of root endophytic microbiota were significantly affected by RKN parasitism; (2) a taxonomic and functional association was found for endophytic nitrogen-fixing bacteria and nematode parasitism; and (3) the change of nitrogen-fixing bacterial communities through the addition of nitrogen fertilizers could affect the occurrence of RKN. Our results provide new insights into interactions among endophytic microbiota, RKN, and plants, contributing to the potential development of novel management strategies against RKN. Video Abstract.
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Affiliation(s)
- Ye Li
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, 350108, China
| | - Shaonan Lei
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, 350108, China
| | - Zhiqiang Cheng
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, 350108, China
| | - Lingyue Jin
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, 350108, China
| | - Ting Zhang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, 350108, China
| | - Lian-Ming Liang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China
| | - Linjie Cheng
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, 350108, China
| | - Qinyi Zhang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, 350108, China
| | - Xiaohong Xu
- Library, Fujian Normal University, Fuzhou, 350108, Fujian, China
| | - Canhua Lan
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, 350108, China
| | - Chaojun Lu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China
| | - Minghe Mo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada.
| | - Baoyu Tian
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, 350108, China.
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14
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Mansour A, Mannaa M, Hewedy O, Ali MG, Jung H, Seo YS. Versatile Roles of Microbes and Small RNAs in Rice and Planthopper Interactions. THE PLANT PATHOLOGY JOURNAL 2022; 38:432-448. [PMID: 36221916 PMCID: PMC9561162 DOI: 10.5423/ppj.rw.07.2022.0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 06/16/2023]
Abstract
Planthopper infestation in rice causes direct and indirect damage through feeding and viral transmission. Host microbes and small RNAs (sRNAs) play essential roles in regulating biological processes, such as metabolism, development, immunity, and stress responses in eukaryotic organisms, including plants and insects. Recently, advanced metagenomic approaches have facilitated investigations on microbial diversity and its function in insects and plants, highlighting the significance of microbiota in sustaining host life and regulating their interactions with the environment. Recent research has also suggested significant roles for sRNA-regulated genes during rice-planthopper interactions. The response and behavior of the rice plant to planthopper feeding are determined by changes in the host transcriptome, which might be regulated by sRNAs. In addition, the roles of microbial symbionts and sRNAs in the host response to viral infection are complex and involve defense-related changes in the host transcriptomic profile. This review reviews the structure and potential functions of microbes and sRNAs in rice and the associated planthopper species. In addition, the involvement of the microbiota and sRNAs in the rice-planthopper-virus interactions during planthopper infestation and viral infection are discussed.
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Affiliation(s)
- Abdelaziz Mansour
- Department of Integrated Biological Science, Pusan National University, Busan 46241,
Korea
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, Giza 12613,
Egypt
| | - Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan 46241,
Korea
- Department of Plant Pathology, Cairo University, Giza 12613,
Egypt
| | - Omar Hewedy
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1,
Canada
- Department of Genetics, Faculty of Agriculture, Menoufia University, Shibin El-Kom 32514,
Egypt
| | - Mostafa G. Ali
- Department of Botany and Microbiology, Faculty of Science, Benha University, Benha 13518,
Egypt
| | - Hyejung Jung
- Department of Integrated Biological Science, Pusan National University, Busan 46241,
Korea
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241,
Korea
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15
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Afridi MS, Fakhar A, Kumar A, Ali S, Medeiros FHV, Muneer MA, Ali H, Saleem M. Harnessing microbial multitrophic interactions for rhizosphere microbiome engineering. Microbiol Res 2022; 265:127199. [PMID: 36137486 DOI: 10.1016/j.micres.2022.127199] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 07/02/2022] [Accepted: 09/13/2022] [Indexed: 10/14/2022]
Abstract
The rhizosphere is a narrow and dynamic region of plant root-soil interfaces, and it's considered one of the most intricate and functionally active ecosystems on the Earth, which boosts plant health and alleviates the impact of biotic and abiotic stresses. Improving the key functions of the microbiome via engineering the rhizosphere microbiome is an emerging tool for improving plant growth, resilience, and soil-borne diseases. Recently, the advent of omics tools, gene-editing techniques, and sequencing technology has allowed us to unravel the entangled webs of plant-microbes interactions, enhancing plant fitness and tolerance to biotic and abiotic challenges. Plants secrete signaling compounds with low molecular weight into the rhizosphere, that engage various species to generate a massive deep complex array. The underlying principle governing the multitrophic interactions of the rhizosphere microbiome is yet unknown, however, some efforts have been made for disease management and agricultural sustainability. This review discussed the intra- and inter- microbe-microbe and microbe-animal interactions and their multifunctional roles in rhizosphere microbiome engineering for plant health and soil-borne disease management. Simultaneously, it investigates the significant impact of immunity utilizing PGPR and cover crop strategy in increasing rhizosphere microbiome functions for plant development and protection using omics techniques. The ecological engineering of rhizosphere plant interactions could be used as a potential alternative technology for plant growth improvement, sustainable disease control management, and increased production of economically significant crops.
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Affiliation(s)
- Muhammad Siddique Afridi
- Department of Plant Pathology, Federal University of Lavras, CP3037, 37200-900 Lavras, MG, Brazil.
| | - Ali Fakhar
- Division of Applied Science, Gyeongsang National University, South Korea
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, MP, India
| | - Sher Ali
- NMR Lab, Department of Chemistry, Federal University of Paraná, Curitiba 81530-900, PR, Brazil
| | - Flavio H V Medeiros
- Department of Plant Pathology, Federal University of Lavras, CP3037, 37200-900 Lavras, MG, Brazil
| | - Muhammad Atif Muneer
- International Magnesium Institute, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hina Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36104, USA
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16
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Hammami R, Oueslati M, Smiri M, Nefzi S, Ruissi M, Comitini F, Romanazzi G, Cacciola SO, Sadfi Zouaoui N. Epiphytic Yeasts and Bacteria as Candidate Biocontrol Agents of Green and Blue Molds of Citrus Fruits. J Fungi (Basel) 2022; 8:jof8080818. [PMID: 36012806 PMCID: PMC9410262 DOI: 10.3390/jof8080818] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/05/2022] [Accepted: 07/05/2022] [Indexed: 11/18/2022] Open
Abstract
Overall, 180 yeasts and bacteria isolated from the peel of citrus fruits were screened for their in vitro antagonistic activity against Penicillium digitatum and P. italicum, causative agents of green and blue mold of citrus fruits, respectively. Two yeast and three bacterial isolates were selected for their inhibitory activity on mycelium growth. Based on the phylogenetic analysis of 16S rDNA and ITS rDNA sequences, the yeast isolates were identified as Candida oleophila and Debaryomyces hansenii while the bacterial isolates were identified as Bacillus amyloliquefaciens, B. pumilus and B. subtilis. All five selected isolates significantly reduced the incidence of decay incited by P. digitatum and P. italicum on ‘Valencia’ orange and ‘Eureka’ lemon fruits. Moreover, they were effective in preventing natural infections of green and blue mold of fruits stored at 4 °C. Treatments with antagonistic yeasts and bacteria did not negatively affect the quality and shelf life of fruits. The antagonistic efficacy of the five isolates depended on multiple modes of action, including the ability to form biofilms and produce antifungal lipopeptides, lytic enzymes and volatile compounds. The selected isolates are promising as biocontrol agents of postharvest green and blue molds of citrus fruits.
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Affiliation(s)
- Rania Hammami
- Laboratoire de Mycologie, Pathologies et Biomarqueurs (LR16ES05), Département de Biologie, Université de Tunis-El Manar, Tunis 2092, Tunisia; (R.H.); (M.O.); (M.S.); (S.N.)
| | - Maroua Oueslati
- Laboratoire de Mycologie, Pathologies et Biomarqueurs (LR16ES05), Département de Biologie, Université de Tunis-El Manar, Tunis 2092, Tunisia; (R.H.); (M.O.); (M.S.); (S.N.)
| | - Marwa Smiri
- Laboratoire de Mycologie, Pathologies et Biomarqueurs (LR16ES05), Département de Biologie, Université de Tunis-El Manar, Tunis 2092, Tunisia; (R.H.); (M.O.); (M.S.); (S.N.)
| | - Souhaila Nefzi
- Laboratoire de Mycologie, Pathologies et Biomarqueurs (LR16ES05), Département de Biologie, Université de Tunis-El Manar, Tunis 2092, Tunisia; (R.H.); (M.O.); (M.S.); (S.N.)
| | - Mustapha Ruissi
- Laboratoire de Biotechnologie Appliquée à l’Agriculture, INRA Tunisie, Université de Carthage, Ariana 2049, Tunisia;
| | - Francesca Comitini
- Department of Life and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, 60131 Ancona, Italy;
| | - Gianfranco Romanazzi
- Plant Pathology, Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, 60131 Ancona, Italy;
| | - Santa Olga Cacciola
- Plant Pathology, Department of Agriculture, Food and Environment, University of Catania, V.S. Sofia, 100-95123 Catania, Italy;
| | - Najla Sadfi Zouaoui
- Laboratoire de Mycologie, Pathologies et Biomarqueurs (LR16ES05), Département de Biologie, Université de Tunis-El Manar, Tunis 2092, Tunisia; (R.H.); (M.O.); (M.S.); (S.N.)
- Correspondence:
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17
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Dastogeer KMG, Yasuda M, Okazaki S. Microbiome and pathobiome analyses reveal changes in community structure by foliar pathogen infection in rice. Front Microbiol 2022; 13:949152. [PMID: 35983324 PMCID: PMC9379101 DOI: 10.3389/fmicb.2022.949152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/12/2022] [Indexed: 12/11/2022] Open
Abstract
Increasing evidence suggests that the plant rhizosphere may recruit beneficial microbes to suppress soil-borne pathogens, but microbiome assembly due to foliar pathogen infection and ecological mechanisms that govern microbiome assembly and functions in the diseased host are not fully understood. To provide a comprehensive view of the rice-associated microbiome, we compared bacterial and fungal communities of healthy rice and those infected with Magnaporthe oryzae, the causal agent of blast disease. We found that the soil had a greater diversity of bacterial and fungal communities than plant endospheric communities. There was no significant dysbiosis of bacterial and fungal microbiome diversity due to disease, but it caused a substantial alteration of bacterial community structure in the root and rhizosphere compartments. The pathobiome analysis showed that the microbiome community structure of leaf and grain tissues was changed markedly at the pathogen infection site, although the alpha diversity did not change. Correspondingly, the relative abundances of some bacteria and fungi were clearly altered in symptomatic tissues. We noted an increase in Rhizobium bacteria and a decline of Tylospora, Clohesyomyces, and Penicillium fungi in the symptomatic leaf and grain tissues from both locations. According to the inferred microbial network, several direct interactions between M. oryzae and other microbes were identified. The majority of edges in the interaction network were positive in diseased samples; contrastingly, the number of edges was much lower in the healthy samples. With source tracking analysis, we observed a sharp contrast in the source of root endosphere bacteria due to Magnaporthe infection. Whereas the majority (71%) of healthy root bacteria could be tracked from the soil, only a very small portion (17%) could be tracked from the soil for diseased samples. These results advanced our understanding and provided potential ideas and a theoretical basis for studying pathobiome and exploiting the microbiome for sustainable agriculture.
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Affiliation(s)
- Khondoker M. G. Dastogeer
- Plant Microbiology Laboratory, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh, Bangladesh
- *Correspondence: Khondoker M. G. Dastogeer
| | - Michiko Yasuda
- Plant Microbiology Laboratory, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Shin Okazaki
- Plant Microbiology Laboratory, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Shin Okazaki
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18
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Metagenomic Analyses of the Soybean Root Mycobiome and Microbiome Reveal Signatures of the Healthy and Diseased Plants Affected by Taproot Decline. Microorganisms 2022; 10:microorganisms10050856. [PMID: 35630301 PMCID: PMC9143508 DOI: 10.3390/microorganisms10050856] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/14/2022] [Accepted: 04/18/2022] [Indexed: 11/17/2022] Open
Abstract
Invading pathogens interact with plant-associated microbial communities, which can be altered under the pressure of pathogen infection. Limited information exists on plant–microbe interactions occurring during natural outbreaks in agricultural fields. Taproot decline (TRD) of soybean is an emerging disease caused by Xylaria necrophora. TRD disease occurrence and yield loss associated with TRD are outstanding issues in soybean production. We applied nuclear ribosomal DNA Internal Transcribed Spacers and 16S rRNA gene taxonomic marker sequencing to define the composition of the fungal and bacterial communities associated with healthy and diseased soybean roots collected from the Mississippi Delta. The plant compartment was a significant factor regulating taxonomic diversity, followed by the disease status of the plant. TRD impacted the root endophytes, causing imbalances; at the intermediate and advanced stages of TRD, X. necrophora decreased mycobiome diversity, whereas it increased microbiome richness. Networks of significant co-occurrence and co-exclusion relationships revealed direct and indirect associations among taxa and identified hubs with potential roles in assembling healthy and TRD-affected soybean biomes. These studies advance the understanding of host–microbe interactions in TRD and the part of biomes in plant health and disease.
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19
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Olive Fungal Epiphytic Communities are Affected by Their Maturation Stage. Microorganisms 2022; 10:microorganisms10020376. [PMID: 35208831 PMCID: PMC8879224 DOI: 10.3390/microorganisms10020376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/29/2022] [Accepted: 02/03/2022] [Indexed: 02/04/2023] Open
Abstract
The phyllosphere comprises the aerial parts of plants and is colonized by a great diversity of microorganisms, either growing inside (as endophytes) or on the surface (as epiphytes) of plant tissues. The factors that structure the diversity of epiphytes and the importance of these microorganisms for host plant protection have been less studied when compared to the case of endophytes. In this work, the epiphytic fungal communities from fruits of the olive tree (olives) in different maturation stages (green and semi-ripened), obtained from different olive orchard managements (integrated and organic production) and from distinct cultivars displaying different susceptibilities to olive anthracnose (Cobrançosa and Madural), are compared by using a metabarcoding approach. We discuss whether such differences in host resistance against anthracnose depend on both the fungal taxa or fungal community composition. A total of 1565 amplicon sequence variants (ASVs) were obtained, mainly belonging to the Ascomycota phylum and Saccharomycetes class. Although significant differences on epiphytic fungal richness were observed among olives obtained in different production systems and maturation stages, these factors in addition to host cultivar did not influence the composition of the epiphytes. Despite these results, a co-inertia analysis showed that Aureobasidium spp. and Sporocadaceae spp. were positively associated with the green olives of the cv. Madural produced under integrated production, while Saccharomycetales spp. (Kluyveromyces, Candida, Kazachstania and Saccharomyces) were positively associated with the semi-ripened olives of the cv. Cobrançosa obtained from organic production. The discriminant power of these fungi, some of them recognized as biocontrol agents, suggest that they might be important in conferring differences on host plant susceptibility to anthracnose.
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20
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Degani O. A Review: Late Wilt of Maize-The Pathogen, the Disease, Current Status, and Future Perspective. J Fungi (Basel) 2021; 7:989. [PMID: 34829276 PMCID: PMC8621787 DOI: 10.3390/jof7110989] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/14/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022] Open
Abstract
Late wilt (LWD) is a vascular wilt disease that outbursts late in maize development, usually during or after flowering. The disease causal agent, the soil and seed-borne fungi, Magnaporthiopsis maydis, causes significant economic losses in Egypt, Israel, Spain, Portugal, and India. Since its discovery in the early 1960s in Egypt, the knowledge base of the disease was significantly expanded. This includes basic information on the pathogen and its mode of action, disease symptoms and damages, methods to study and monitor the pathogen, and above all, control strategies to restrain M. maydis and reduce its impact on commercial maize production. Three approaches stand out from the various control methods inspected. First, the traditional use of chemical pesticides was investigated extensively. This approach gained attention when, in 2018-2020, a feasible and economical treatment based on Azoxystrobin (alone or in combination with other fungicides) was proven to be effective even in severe cases of LWD. Second, the growing trend of replacing chemical treatments with eco-friendly biological and other green protocols has become increasingly important in recent years and has already made significant achievements. Last but not least, today's leading strategy to cope with LWD is to rely on resistant maize genotypes. The past two decades' introduction of molecular-based diagnostic methods to track and identify the pathogen marked significant progress in this global effort. Still, worldwide research efforts are progressing relatively slowly since the disease is considered exotic and unfamiliar in most parts of the world. The current review summarizes the accumulated knowledge on LWD, its causal agent, and the disease implications. An additional important aspect that will be addressed is a future perspective on risks and knowledge gaps.
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Affiliation(s)
- Ofir Degani
- Plant Sciences Department, Migal-Galilee Research Institute, Tarshish 2, Kiryat Shmona 11016, Israel;
- Faculty of Sciences, Tel-Hai College, Upper Galilee, Tel-Hai 12210, Israel
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21
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Bhalla K, Qu X, Kretschmer M, Kronstad JW. The phosphate language of fungi. Trends Microbiol 2021; 30:338-349. [PMID: 34479774 DOI: 10.1016/j.tim.2021.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 11/20/2022]
Abstract
Phosphate is an essential macronutrient for fungal proliferation as well as a key mediator of antagonistic, beneficial, and pathogenic interactions between fungi and other organisms. In this review, we summarize recent insights into the integration of phosphate metabolism with mechanisms of fungal adaptation that support growth and survival. In particular, we highlight aspects of phosphate sensing important for responses to stress and regulation of cell-surface changes with an impact on fungal pathogenesis, host immune responses, and disease outcomes. Additionally, new studies provide insights into the influence of phosphate availability on cooperative or antagonistic interactions between fungi and other microbes, the associations of mycorrhizal and endophytic fungi with plants, and connections with plant immunity. Overall, phosphate homeostasis is emerging as an integral part of fungal metabolism and communication to support diverse lifestyles.
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Affiliation(s)
- Kabir Bhalla
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Xianya Qu
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Matthias Kretschmer
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - James W Kronstad
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
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22
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Han G, Mannaa M, Kim N, Jeon HW, Jung H, Lee HH, Kim J, Park J, Park AR, Kim JC, Seo YS. Response of Pine Rhizosphere Microbiota to Foliar Treatment with Resistance-Inducing Bacteria against Pine Wilt Disease. Microorganisms 2021; 9:microorganisms9040688. [PMID: 33810444 PMCID: PMC8065550 DOI: 10.3390/microorganisms9040688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 11/19/2022] Open
Abstract
In this study, two bacterial strains, IRP7 and IRP8, were selected to induce resistance against pine wilt disease (PWD). Foliar application with these strains to nematode-inoculated pine seedlings significantly reduced PWD severity. The effect of nematode inoculation and bacterial treatment on the rhizosphere bacterial community was investigated. The results indicated that the rhizosphere of nematode-inoculated seedlings contained a lower relative abundance of beneficial microbes such as Paraburkholderia, Bradyrhizobium, Rhizobacter, Lysobacter, and Caballeronia. Bacterial treatment resulted in significant changes in the microbes that were represented in relatively low relative abundance. Treatment with IRP7 resulted in an increase in the relative abundance of Nitrospirillum, Bacillus, and Luteibacter, which might be useful for protection against infection. Treatment with IRP8 resulted in an increase in the relative abundance of obligate bacterial predators of the Bdellovibrio genus that were previously shown to control several bacterial phytopathogens and may have a role in the management of nematode-carried bacteria. The selected bacteria were identified as Pseudomonas koreensis IRP7 and Lysobacter enzymogenes IRP8 and are suggested as a potential treatment for induced resistance against PWD. To our knowledge, this is the first report on the effect of foliar treatment with resistance-inducing bacteria on the rhizosphere microbiota.
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Affiliation(s)
- Gil Han
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
| | - Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
- Department of Plant Pathology, Cairo University, Giza 12613, Egypt
| | - Namgyu Kim
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
| | - Hee Won Jeon
- Division of Applied Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea; (H.W.J.); (A.R.P.)
| | - Hyejung Jung
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
| | - Hyun-Hee Lee
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
| | - Junheon Kim
- Forest Insect Pests and Diseases Division, National Institute of Forest Science, Seoul 02455, Korea;
| | - Jungwook Park
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
- Environmental Microbiology Research Team, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju 37242, Korea
| | - Ae Ran Park
- Division of Applied Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea; (H.W.J.); (A.R.P.)
| | - Jin-Cheol Kim
- Division of Applied Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea; (H.W.J.); (A.R.P.)
- Correspondence: (J.-C.K.); (Y.-S.S.)
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
- Correspondence: (J.-C.K.); (Y.-S.S.)
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