1
|
Tagele SB, Gachomo EW. Evaluating the effects of mefenoxam on taxonomic and functional dynamics of nontarget fungal communities during carrot cultivation. Sci Rep 2024; 14:9867. [PMID: 38684826 PMCID: PMC11058253 DOI: 10.1038/s41598-024-59587-2] [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: 09/22/2023] [Accepted: 04/12/2024] [Indexed: 05/02/2024] Open
Abstract
Ridomil Gold SL (45.3% a.i. mefenoxam) is a widely used chemical fungicide for the control of oomycetes. However, its impact on fungal communities remains unexplored. Therefore, the goal of this study was to examine the effects of mefenoxam on the temporal dynamics of fungal taxonomic and functional diversities during carrot cultivation under four treatment groups: mefenoxam application with and without Pythium inoculation, and untreated control groups with and without Pythium inoculation. Our in vitro sensitivity assay showed that the maximum recommended concentration of mefenoxam, 0.24 ppm, did not suppress the mycelial growth of P. irregulare. At 100 ppm, mycelial growth was only reduced by 11.4%, indicating that the isolate was resistant to mefenoxam. MiSeq sequencing data revealed transient taxonomic variations among treatments 2 weeks post-treatment. Mortierella dominated the fungal community in the mefenoxam-Pythium combination treatment, as confirmed through PCR using our newly designed Mortierella-specific primers. Conversely, mefenoxam-Pythium combination had adverse effects on Penicillium, Trichoderma, and Fusarium, and decrease the overall alpha diversity. However, these compositional changes gradually reverted to those observed in the control by the 12th week. The predicted ecological functions of fungal communities in all Pythium and mefenoxam treatments shifted, leading to a decrease in symbiotrophs and plant pathogen functional groups. Moreover, the community-level physiological profiling approach, utilizing 96-well Biolog FF microplates, showed discernible variations in the utilization of 95 diverse carbon sources among the treatments. Notably, arbutin, L-arabinose, Tween 80, and succinamic acid demonstrated a strong positive association with Mortierella. Our findings demonstrate that a single application of mefenoxam at its recommended rate triggers substantial taxonomic and functional shifts in the soil fungal community. Considering this impact, the conventional agricultural practice of repeated mefenoxam application is likely to exert considerable shifts on the soil ecosystem that may affect agricultural sustainability.
Collapse
Affiliation(s)
- Setu Bazie Tagele
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, 92507, USA
| | - Emma W Gachomo
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, 92507, USA.
| |
Collapse
|
2
|
Jibola-Shittu MY, Heng Z, Keyhani NO, Dang Y, Chen R, Liu S, Lin Y, Lai P, Chen J, Yang C, Zhang W, Lv H, Wu Z, Huang S, Cao P, Tian L, Qiu Z, Zhang X, Guan X, Qiu J. Understanding and exploring the diversity of soil microorganisms in tea ( Camellia sinensis) gardens: toward sustainable tea production. Front Microbiol 2024; 15:1379879. [PMID: 38680916 PMCID: PMC11046421 DOI: 10.3389/fmicb.2024.1379879] [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: 01/31/2024] [Accepted: 04/03/2024] [Indexed: 05/01/2024] Open
Abstract
Leaves of Camellia sinensis plants are used to produce tea, one of the most consumed beverages worldwide, containing a wide variety of bioactive compounds that help to promote human health. Tea cultivation is economically important, and its sustainable production can have significant consequences in providing agricultural opportunities and lowering extreme poverty. Soil parameters are well known to affect the quality of the resultant leaves and consequently, the understanding of the diversity and functions of soil microorganisms in tea gardens will provide insight to harnessing soil microbial communities to improve tea yield and quality. Current analyses indicate that tea garden soils possess a rich composition of diverse microorganisms (bacteria and fungi) of which the bacterial Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Chloroflexi and fungal Ascomycota, Basidiomycota, Glomeromycota are the prominent groups. When optimized, these microbes' function in keeping garden soil ecosystems balanced by acting on nutrient cycling processes, biofertilizers, biocontrol of pests and pathogens, and bioremediation of persistent organic chemicals. Here, we summarize research on the activities of (tea garden) soil microorganisms as biofertilizers, biological control agents and as bioremediators to improve soil health and consequently, tea yield and quality, focusing mainly on bacterial and fungal members. Recent advances in molecular techniques that characterize the diverse microorganisms in tea gardens are examined. In terms of viruses there is a paucity of information regarding any beneficial functions of soil viruses in tea gardens, although in some instances insect pathogenic viruses have been used to control tea pests. The potential of soil microorganisms is reported here, as well as recent techniques used to study microbial diversity and their genetic manipulation, aimed at improving the yield and quality of tea plants for sustainable production.
Collapse
Affiliation(s)
- Motunrayo Y. Jibola-Shittu
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiang Heng
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Nemat O. Keyhani
- Department of Biological Sciences, University of Illinois, Chicago, IL, United States
| | - Yuxiao Dang
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ruiya Chen
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sen Liu
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongsheng Lin
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Pengyu Lai
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jinhui Chen
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chenjie Yang
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weibin Zhang
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huajun Lv
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ziyi Wu
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuaishuai Huang
- School of Ecology and Environment, Tibet University, Lhasa, China
| | - Pengxi Cao
- School of Ecology and Environment, Tibet University, Lhasa, China
| | - Lin Tian
- Tibet Plateau Institute of Biology, Lhasa, China
| | - Zhenxing Qiu
- Fuzhou Technology and Business University, Fuzhou, Fujian, China
| | - Xiaoyan Zhang
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiayu Guan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Junzhi Qiu
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
3
|
Jalloh AA, Khamis FM, Yusuf AA, Subramanian S, Mutyambai DM. Long-term push-pull cropping system shifts soil and maize-root microbiome diversity paving way to resilient farming system. BMC Microbiol 2024; 24:92. [PMID: 38500045 PMCID: PMC10946131 DOI: 10.1186/s12866-024-03238-z] [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: 10/05/2023] [Accepted: 02/26/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND The soil biota consists of a complex assembly of microbial communities and other organisms that vary significantly across farming systems, impacting soil health and plant productivity. Despite its importance, there has been limited exploration of how different cropping systems influence soil and plant root microbiomes. In this study, we investigated soil physicochemical properties, along with soil and maize-root microbiomes, in an agroecological cereal-legume companion cropping system known as push-pull technology (PPT). This system has been used in agriculture for over two decades for insect-pest management, soil health improvement, and weed control in sub-Saharan Africa. We compared the results with those obtained from maize-monoculture (Mono) cropping system. RESULTS The PPT cropping system changed the composition and diversity of soil and maize-root microbial communities, and led to notable improvements in soil physicochemical characteristics compared to that of the Mono cropping system. Distinct bacterial and fungal genera played a crucial role in influencing the variation in microbial diversity within these cropping systems. The relative abundance of fungal genera Trichoderma, Mortierella, and Bionectria and bacterial genera Streptomyces, RB41, and Nitrospira were more enriched in PPT. These microbial communities are associated with essential ecosystem services such as plant protection, decomposition, carbon utilization, bioinsecticides production, nitrogen fixation, nematode suppression, phytohormone production, and bioremediation. Conversely, pathogenic associated bacterial genus including Bryobacter were more enriched in Mono-root. Additionally, the Mono system exhibited a high relative abundance of fungal genera such as Gibberella, Neocosmospora, and Aspergillus, which are linked to plant diseases and food contamination. Significant differences were observed in the relative abundance of the inferred metabiome functional protein pathways including syringate degradation, L-methionine biosynthesis I, and inosine 5'-phosphate degradation. CONCLUSION Push-pull cropping system positively influences soil and maize-root microbiomes and enhances soil physicochemical properties. This highlights its potential for agricultural and environmental sustainability. These findings contribute to our understanding of the diverse ecosystem services offered by this cropping system where it is practiced regarding the system's resilience and functional redundancy. Future research should focus on whether PPT affects the soil and maize-root microbial communities through the release of plant metabolites from the intercrop root exudates or through the alteration of the soil's nutritional status, which affects microbial enzymatic activities.
Collapse
Affiliation(s)
- Abdul A Jalloh
- International Centre of Insect Physiology and Ecology, P.O. Box 30772-00100, Nairobi, Kenya
- Department of Zoology and Entomology, University of Pretoria, Private Bag x20 Hatfield, Pretoria, South Africa
| | - Fathiya Mbarak Khamis
- International Centre of Insect Physiology and Ecology, P.O. Box 30772-00100, Nairobi, Kenya
| | - Abdullahi Ahmed Yusuf
- Department of Zoology and Entomology, University of Pretoria, Private Bag x20 Hatfield, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag x20 Hatfield, Pretoria, South Africa
| | - Sevgan Subramanian
- International Centre of Insect Physiology and Ecology, P.O. Box 30772-00100, Nairobi, Kenya
| | - Daniel Munyao Mutyambai
- International Centre of Insect Physiology and Ecology, P.O. Box 30772-00100, Nairobi, Kenya.
- Department of Life Sciences, South Eastern Kenya University, P.O. Box 170-90200, Kitui, Kenya.
| |
Collapse
|
4
|
Muhammad M, Basit A, Ali K, Ahmad H, Li WJ, Khan A, Mohamed HI. A review on endophytic fungi: a potent reservoir of bioactive metabolites with special emphasis on blight disease management. Arch Microbiol 2024; 206:129. [PMID: 38416214 DOI: 10.1007/s00203-023-03828-x] [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: 11/15/2023] [Accepted: 12/30/2023] [Indexed: 02/29/2024]
Abstract
Phytopathogenic microorganisms have caused blight diseases that present significant challenges to global agriculture. These diseases result in substantial crop losses and have a significant economic impact. Due to the limitations of conventional chemical treatments in effectively and sustainably managing these diseases, there is an increasing interest in exploring alternative and environmentally friendly approaches for disease control. Using endophytic fungi as biocontrol agents has become a promising strategy in recent years. Endophytic fungi live inside plant tissues, forming mutually beneficial relationships, and have been discovered to produce a wide range of bioactive metabolites. These metabolites demonstrate significant potential for fighting blight diseases and provide a plentiful source of new biopesticides. In this review, we delve into the potential of endophytic fungi as a means of biocontrol against blight diseases. We specifically highlight their significance as a source of biologically active compounds. The review explores different mechanisms used by endophytic fungi to suppress phytopathogens. These mechanisms include competing for nutrients, producing antifungal compounds, and triggering plant defense responses. Furthermore, this review discusses the challenges of using endophytic fungi as biocontrol agents in commercial applications. It emphasizes the importance of conducting thorough research to enhance their effectiveness and stability in real-world environments. Therefore, bioactive metabolites from endophytic fungi have considerable potential for sustainable and eco-friendly blight disease control. Additional research on endophytes and their metabolites will promote biotechnology solutions.
Collapse
Affiliation(s)
- Murad Muhammad
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Abdul Basit
- Department of Horticultural Science, Kyungpook National University, Daegu, 41566, Korea
| | - Kashif Ali
- Center of Biotechnology and Microbiology, University of Peshawar, Peshawar, 25120, Pakistan
| | - Haris Ahmad
- Center of Biotechnology and Microbiology, University of Peshawar, Peshawar, 25120, Pakistan
| | - Wen-Jun Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ayesha Khan
- Department of Horticulture, Faculty of Crop Production Sciences, The University of Agriculture, Peshawar, 25120, Pakistan
| | - Heba I Mohamed
- Biological and Geological Sciences Department, Faculty of Education, Ain Shams University, Cairo, 11341, Egypt.
| |
Collapse
|
5
|
Viotti C, Chalot M, Kennedy PG, Maillard F, Santoni S, Blaudez D, Bertheau C. Primer pairs, PCR conditions, and peptide nucleic acid clamps affect fungal diversity assessment from plant root tissues. Mycology 2024; 15:255-271. [PMID: 38813472 PMCID: PMC11132971 DOI: 10.1080/21501203.2023.2301003] [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: 10/06/2023] [Accepted: 12/27/2023] [Indexed: 05/31/2024] Open
Abstract
High-throughput sequencing has become a prominent tool to assess plant-associated microbial diversity. Still, some technical challenges remain in characterising these communities, notably due to plant and fungal DNA co-amplification. Fungal-specific primers, Peptide Nucleic Acid (PNA) clamps, or adjusting PCR conditions are approaches to limit plant DNA contamination. However, a systematic comparison of these factors and their interactions, which could limit plant DNA contamination in the study of plant mycobiota, is still lacking. Here, three primers targeting the ITS2 region were evaluated alone or in combination with PNA clamps both on nettle (Urtica dioica) root DNA and a mock community. PNA clamps did not improve the richness or diversity of the fungal communities but increased the number of fungal reads. Among the tested factors, the most significant was the primer pair. Specifically, the 5.8S-Fun/ITS4-Fun pair exhibited a higher OTU richness but fewer fungal reads. Our study demonstrates that the choice of primers is critical for limiting plant and fungal DNA co-amplification. PNA clamps increase the number of fungal reads when ITS2 is targeted but do not result in higher fungal diversity recovery at high sequencing depth. At lower read depths, PNA clamps might enhance microbial diversity quantification for primer pairs lacking fungal specificity.
Collapse
Affiliation(s)
- Chloé Viotti
- CNRS, Chrono-environnement, Université de Franche-Comté, Montbéliard, France
| | - Michel Chalot
- CNRS, Chrono-environnement, Université de Franche-Comté, Montbéliard, France
- Faculté des Sciences et Technologies, Université de Lorraine, Nancy, France
| | - Peter G. Kennedy
- Department of Plant & Microbiology, University of Minnesota, St. Paul, MN, USA
| | - François Maillard
- Department of Plant & Microbiology, University of Minnesota, St. Paul, MN, USA
| | - Sylvain Santoni
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Coralie Bertheau
- CNRS, Chrono-environnement, Université de Franche-Comté, Montbéliard, France
| |
Collapse
|
6
|
Wu L, Ren C, Jiang H, Zhang W, Chen N, Zhao X, Wei G, Shu D. Land abandonment transforms soil microbiome stability and functional profiles in apple orchards of the Chinese Losses Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167556. [PMID: 37804979 DOI: 10.1016/j.scitotenv.2023.167556] [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: 08/01/2023] [Revised: 09/27/2023] [Accepted: 09/30/2023] [Indexed: 10/09/2023]
Abstract
Land abandonment is considered an effective strategy for ecological restoration on a global scale. However, few studies have focused on how environmental heterogeneity associated with the age of land abandonment affects the assembly and potential functions of the soil microbial community. In the present study, we investigated the community assembly of soil bacteria and fungi as well as the stability of soil networks and their potential functions in the chronosequence of abandoned apple orchards. We elucidated that the Shannon diversity of bacteria and the richness of fungi increased as land abandonment progressed. In addition, land abandonment destabilized the microbial network stability but increased network complexity. Soil available nitrogen, total carbon, and moisture are the potentially important factors in shaping the soil microbial assembly. Importantly, we showed that the microbial community diversity and functional diversity presented a synchronization effect in response to the different stages of land abandonment. Furthermore, specific bacterial taxa related to carbon fixation, dissimilatory nitrate reduction, and organic phosphorus mineralization were significantly enriched during the early abandonment stage. Collectively, these results indicate that land abandonment significantly transformed soil microbiome assembly and functional adaptation during the restoration process. These findings provide valuable insights into the influence of ecological restoration on soil microbiome and ecosystem functions in arable areas.
Collapse
Affiliation(s)
- Likun Wu
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Chengyao Ren
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Hai Jiang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wenyu Zhang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Ni Chen
- The Department of Agriculture and Rural Affairs of Shaanxi Province, Xi'an, Shaanxi 710000, China
| | - Xining Zhao
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, 712100 Yangling, Shaanxi Province, China; Institute of Soil and Water Conservation, Northwest A&F University, 712100 Yangling, Shaanxi Province, China
| | - Gehong Wei
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China.
| | - Duntao Shu
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China.
| |
Collapse
|
7
|
Costa LSAS, de Faria MR, Chiaramonte JB, Mendes LW, Sepo E, de Hollander M, Fernandes JMC, Carrión VJ, Bettiol W, Mauchline TH, Raaijmakers JM, Mendes R. Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness. ENVIRONMENTAL MICROBIOME 2023; 18:85. [PMID: 38053159 PMCID: PMC10696838 DOI: 10.1186/s40793-023-00529-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/19/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere microbiome. Here, we studied this remarkable phenomenon for Bipolaris sorokiniana in two wheat cultivars differing in resistance to this fungal root pathogen. RESULTS The results showed that repeated exposure of the susceptible wheat cultivar to the pathogen led to a significant reduction in disease severity after five successive growth cycles. Surprisingly, the resistant wheat cultivar, initially included as a control, showed the opposite pattern with an increase in disease severity after repeated pathogen exposure. Amplicon analyses revealed that the bacterial families Chitinophagaceae, Anaerolineaceae and Nitrosomonadaceae were associated with disease suppressiveness in the susceptible wheat cultivar; disease suppressiveness in the resistant wheat cultivar was also associated with Chitinophagaceae and a higher abundance of Comamonadaceae. Metagenome analysis led to the selection of 604 Biosynthetic Gene Clusters (BGCs), out of a total of 2,571 identified by AntiSMASH analysis, that were overrepresented when the soil entered the disease suppressive state. These BGCs are involved in the biosynthesis of terpenes, non-ribosomal peptides, polyketides, aryl polyenes and post-translationally modified peptides. CONCLUSION Combining taxonomic and functional profiling we identified key changes in the rhizosphere microbiome during disease suppression. This illustrates how the host plant relies on the rhizosphere microbiome as the first line of defense to fight soil-borne pathogens. Microbial taxa and functions identified here can be used in novel strategies to control soil-borne fungal pathogens.
Collapse
Affiliation(s)
- Lilian S Abreu Soares Costa
- Embrapa Environment, Jaguariúna, Brazil
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | | | | | - Lucas W Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Edis Sepo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | | | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Departamento de Microbiología y Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Málaga, Spain
| | | | - Tim H Mauchline
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, UK
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | | |
Collapse
|
8
|
Guzman Martinez M, Oliver JE, Severns PM. Evidence of Xylella fastidiosa Infection and Associated Thermal Signatures in Southern Highbush Blueberry ( Vaccinium corymbosum Interspecific Hybrids). PLANTS (BASEL, SWITZERLAND) 2023; 12:3562. [PMID: 37896024 PMCID: PMC10609813 DOI: 10.3390/plants12203562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023]
Abstract
Xylella fastidiosa, a gram-negative bacterium vectored to plants via feeding of infected insects, causes a number of notorious plant diseases throughout the world, such as Pierce's disease (grapes), olive quick decline syndrome, and coffee leaf scorch. Detection of Xf in infected plants can be challenging because the early foliar disease symptoms are subtle and may be attributed to multiple minor physiological stresses and/or borderline nutrient deficiencies. Furthermore, Xf may reside within an infected plant for one or more growing seasons before traditional visible diagnostic disease symptoms emerge. Any method that can identify infection during the latent period or pre-diagnostic disease progress state could substantially improve the outcome of disease control interventions. Because Xf locally and gradually impairs water movement through infected plant stems and leaves over time, infected plants may not be able to effectively dissipate heat through transpiration-assisted cooling, and this heat signature may be an important pre-diagnostic disease trait. Here, we report on the association between thermal imaging, the early stages of Xf infection, and disease development in blueberry plants, and discuss the benefits and limitations of using thermal imaging to detect bacterial leaf scorch of blueberries.
Collapse
Affiliation(s)
| | - Jonathan E. Oliver
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA
| | - Paul M. Severns
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
9
|
Brown JK. Editorial overview: Fungal diversity: Now for something completely different. Curr Opin Microbiol 2023; 73:102294. [PMID: 37018995 DOI: 10.1016/j.mib.2023.102294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- James Km Brown
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| |
Collapse
|