Changes in Microbial Community Structure in Response to Gummosis in Peach Tree Bark
Abstract
1. Introduction
2. Results
2.1. Biodiversity in Bark and Soil
2.2. Extensive Profiling of Taxonomic Composition
2.3. Biomarker-Mining for Gummosis Diagnosis
2.4. Network Analysis
3. Discussion
4. Materials and Methods
4.1. Rhizosphere Soil and Bark Sample Collection
4.2. Microbial DNA Extraction
4.3. Library Preparation and High-throughput Sequencing
4.4. Bioinformatical Analysis
4.5. Computational and Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Reilly, C.C.; Okie, W.R. Distribution in the Southeastern United States of peach tree fungal gummosis caused by Botryosphaeria dothidea. Plant Dis. 1982, 66, 158–161. [Google Scholar] [CrossRef]
- Biggs, A.R.; Britton, K.O. Presymptom histopathology of peach trees inoculated with Botryosphaeria obtusa and B. dothidea. Phytopathology 1988, 78, 1109–1118. [Google Scholar] [CrossRef]
- Daniell, J.W.; Chandler, W.A. Field resistance of peach cultivars to gummosis disease. HortScience 1982, 17, 375–376. [Google Scholar] [CrossRef]
- Weaver, D. A gummosis disease of peach trees caused by Botryosphaeria dothidea. Phytopathology 1974, 64, 1429–1432. [Google Scholar] [CrossRef]
- Li, H.-Y.; Cao, R.-B.; Mu, Y.-T. In vitro inhibition of Botryosphaeria dothidea and Lasiodiplodia theobromae, and chemical control of gummosis disease of Japanese apricot and peach trees in Zhejiang Province, China. J. Crop Prot. 1995, 14, 187–191. [Google Scholar] [CrossRef]
- Verma, L.; Sharma, R. Diseases of Horticultural Crops: Fruits; Indus Publishing: New Delhi, India, 1999. [Google Scholar]
- Britton, K.; Hendrix, F. Three species of Botryosphaeria cause peach tree gummosis in Georgia. Plant Dis. 1982, 66, 1120–1121. [Google Scholar] [CrossRef]
- Ko, Y.; Sun, S.-K. Peach gummosis disease caused by Botryosphaeria dothidea in Taiwan. Plant Pathol.Bull. 1992, 1, 70–78. [Google Scholar]
- Pusey, P. Role of Botryosphaeria species in peach tree gummosis on the basis of differential isolation from outer and inner bark. Plant Dis. 1993, 77, 170–174. [Google Scholar] [CrossRef]
- Wang, F.; Zhao, L.; Li, G.; Huang, J.; Hsiang, T. Identification and characterization of Botryosphaeria spp. causing gummosis of peach trees in Hubei Province, Central China. Plant Dis. 2011, 95, 1378–1384. [Google Scholar] [CrossRef]
- Konavko, D.; Moročko-Bičevska, I.; Bankina, B. Pseudomonas syringae as important pathogen of fruit trees with emphasis on plum and cherry. Res. Rural. Dev. 2014, 1, 19–25. [Google Scholar]
- Saniewski, M.; Ueda, J.; Miyamoto, K.; Horbowicz, M.; Puchalski, J. Hormonal control of gummosis in Rosaceae. J. Fruit Ornam. Plant Res. 2006, 14, 137. [Google Scholar]
- Wilson, M.B.; Spivak, M.; Hegeman, A.D.; Rendahl, A.; Cohen, J.D. Metabolomics reveals the origins of antimicrobial plant resins collected by honey bees. PLoS ONE 2013, 8, e77512. [Google Scholar] [CrossRef] [PubMed]
- Zeneli, G.; Krokene, P.; Christiansen, E.; Krekling, T.; Gershenzon, J. Methyl jasmonate treatment of mature Norway spruce (Picea abies) trees increases the accumulation of terpenoid resin components and protects against infection by Ceratocystis polonica, a bark beetle-associated fungus. Tree Physiol. 2006, 26, 977–988. [Google Scholar] [CrossRef] [PubMed]
- Langenheim, J.H. Plant resins. Am. Sci. 1990, 78, 16–24. [Google Scholar]
- Chapuisat, M.; Oppliger, A.; Magliano, P.; Christe, P. Wood ants use resin to protect themselves against pathogens. Proc. R. Soc. B Boil. Sci. 2007, 274, 2013–2017. [Google Scholar] [CrossRef]
- Khanzada, M.A.; Lodhi, A.M.; Shahzad, S. Chemical control of Lasiodiplodia theobromae, the causal agent of mango decline in Sindh. Pak. J. Bot. 2005, 37, 1023. [Google Scholar]
- Beckman, T.; Pusey, P.; Bertrand, P. Impact of fungal gummosis on peach trees. HortScience 2003, 38, 1141–1143. [Google Scholar] [CrossRef]
- Ma, Z.; Luo, Y.; Michailides, T.J. Resistance of Botryosphaeria dothidea from pistachio to iprodione. Plant Dis. 2001, 85, 183–188. [Google Scholar] [CrossRef]
- Trivedi, P.; Mattupalli, C.; Eversole, K.; Leach, J.E. Enabling sustainable agriculture through understanding and enhancement of microbiomes. New Phytol. 2021, 230, 2129–2147. [Google Scholar] [CrossRef]
- Qu, Q.; Zhang, Z.; Peijnenburg, W.J.G.M.; Liu, W.; Lu, T.; Hu, B.; Chen, J.-M.; Chen, J.; Lin, Z.; Qian, H. Rhizosphere microbiome assembly and its impact on plant growth. J. Agric. Food Chem. 2020, 68, 5024–5038. [Google Scholar] [CrossRef]
- Noman, M.; Ahmed, T.; Ijaz, U.; Shahid, M.; Azizullah; Li, D.; Manzoor, I.; Song, F. Plant–Microbiome crosstalk: Dawning from composition and assembly of microbial community to improvement of disease resilience in plants. Int. J. Mol. Sci. 2021, 22, 6852. [Google Scholar] [CrossRef] [PubMed]
- Berens, M.L.; Wolinska, K.W.; Spaepen, S.; Ziegler, J.; Nobori, T.; Nair, A.; Krüler, V.; Winkelmüller, T.M.; Wang, Y.; Mine, A.; et al. Balancing trade-offs between biotic and abiotic stress responses through leaf age-dependent variation in stress hormone cross-talk. Proc. Natl. Acad. Sci. USA 2019, 116, 2364–2373. [Google Scholar] [CrossRef] [PubMed]
- Caddell, D.F.; Deng, S.; Coleman-Derr, D.; Verman, S.; White, J.J. Seed Endophytes; Springer: Berlin/Heidelberg, Germany, 2019. [Google Scholar]
- Cheng, Y.T.; Zhang, L.; He, S.Y. Plant-microbe interactions facing environmental challenge. Cell Host Microbe 2019, 26, 183–192. [Google Scholar] [CrossRef]
- Hiruma, K. Roles of plant-derived secondary metabolites during interactions with pathogenic and beneficial microbes under conditions of environmental stress. Microorganisms 2019, 7, 362. [Google Scholar] [CrossRef]
- Jo, Y.; Back, C.-G.; Choi, H.; Cho, W.K. Comparative microbiome study of mummified peach fruits by metagenomics and metatranscriptomics. Plants 2020, 9, 1052. [Google Scholar] [CrossRef] [PubMed]
- Li, K.; DiLegge, M.J.; Minas, I.S.; Hamm, A.; Manter, D.; Vivanco, J.M. Soil sterilization leads to re-colonization of a healthier rhizosphere microbiome. Rhizosphere 2019, 12, 100176. [Google Scholar] [CrossRef]
- Liu, J.; Zhang, X.; Tian, J.; Li, Y.; Liu, Q.; Chen, X.; Feng, F.; Yu, X.; Yang, C. Multiomics analysis reveals that peach gum colouring reflects plant defense responses against pathogenic fungi. Food Chem. 2022, 383, 132424. [Google Scholar] [CrossRef]
- Pervaiz, Z.H.; Contreras, J.; Hupp, B.M.; Lindenberger, J.H.; Chen, D.; Zhang, Q.; Wang, C.; Twigg, P.; Saleem, M. Root microbiome changes with root branching order and root chemistry in peach rhizosphere soil. Rhizosphere 2020, 16, 100249. [Google Scholar] [CrossRef]
- Pirttilä, A.; Tabas, H.M.P.; Baruah, N.; Koskimäki, J. Biofertilizers and biocontrol agents for agriculture: How to identify and develop new potent microbial strains and traits. Microorganisms 2021, 9, 817. [Google Scholar] [CrossRef]
- Mazzola, M.; Hewavitharana, S.S. Advances in understanding tree fruit-rhizosphere microbiome relationships for enhanced plant health. In Achieving Sustainable Cultivation of Temperate Zone Tree Fruits and Berries; Burleigh Dodds Science Publishing: Cambridge, UK, 2019; pp. 3–30. [Google Scholar]
- Mendes, R.; Kruijt, M.; de Bruijn, I.; Dekkers, E.; Van Der Voort, M.; Schneider, J.H.; Piceno, Y.M.; DeSantis, T.Z.; Andersen, G.L.; Bakker, P.A.; et al. Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 2011, 332, 1097–1100. [Google Scholar] [CrossRef]
- Chapelle, E.; Mendes, R.; Bakker, P.A.H.M.; Raaijmakers, J.M. Fungal invasion of the rhizosphere microbiome. ISME J. 2016, 10, 265–268. [Google Scholar] [CrossRef] [PubMed]
- Fu, L.; Penton, C.R.; Ruan, Y.; Shen, Z.; Xue, C.; Li, R.; Shen, Q. Inducing the rhizosphere microbiome by biofertilizer application to suppress banana Fusarium wilt disease. Soil Biol. Biochem. 2017, 104, 39–48. [Google Scholar] [CrossRef]
- Li, Q.; Guo, R.; Li, Y.; Hartman, W.H.; Li, S.; Zhang, Z.; Tringe, S.G.; Wang, H. Insight into the bacterial endophytic communities of peach cultivars related to crown gall disease resistance. Appl. Environ. Microb. 2019, 85, e02931-18. [Google Scholar] [CrossRef] [PubMed]
- Chaparro, J.M.; Badri, D.V.; Vivanco, J.M. Rhizosphere microbiome assemblage is affected by plant development. ISME J. 2014, 8, 790–803. [Google Scholar] [CrossRef]
- Geng, L.-L.; Shao, G.-X.; Raymond, B.; Wang, M.-L.; Sun, X.-X.; Shu, C.-L.; Zhang, J. Subterranean infestation by Holotrichia parallela larvae is associated with changes in the peanut (Arachis hypogaea L.) rhizosphere microbiome. Microbiol. Res. 2018, 211, 13–20. [Google Scholar] [CrossRef]
- Rolli, E.; Vergani, L.; Ghitti, E.; Patania, G.; Mapelli, F.; Borin, S. ‘Cry-for-help’in contaminated soil: A dialogue among plants and soil microbiome to survive in hostile conditions. Environ. Microbiol. 2021, 23, 5690–5703. [Google Scholar] [CrossRef]
- Liu, H.; Brettell, L.E.; Qiu, Z.; Singh, B.K. Microbiome-mediated stress resistance in plants. Trends Plant Sci. 2020, 25, 733–743. [Google Scholar] [CrossRef]
- Yuan, J.; Wen, T.; Zhang, H.; Zhao, M.; Penton, C.R.; Thomashow, L.S.; Shen, Q. Predicting disease occurrence with high accuracy based on soil macroecological patterns of Fusarium wilt. ISME J. 2020, 14, 2936–2950. [Google Scholar] [CrossRef]
- Liu, L.; Chen, S.; Zhao, J.; Zhou, X.; Wang, B.; Li, Y.; Zheng, G.; Zhang, J.; Cai, Z.; Huang, X. Watermelon planting is capable to restructure the soil microbiome that regulated by reductive soil disinfestation. Appl. Soil Ecol. 2018, 129, 52–60. [Google Scholar] [CrossRef]
- Huang, H.; Lin, J.; Wang, W.; Li, S. Biopolymers Produced by Sphingomonas Strains and Their Potential Applications in Petroleum Production. Polymers 2022, 14, 1920. [Google Scholar] [CrossRef]
- Franklin, M.J.; Nivens, D.E.; Weadge, J.T.; Howell, P.L. Biosynthesis of the Pseudomonas aeruginosa extracellular polysaccharides, alginate, Pel, and Psl. Front. Microbiol. 2011, 2, 167. [Google Scholar] [CrossRef] [PubMed]
- Maszenan, A.M.; Seviour, R.J.; Patel, B.K.C.; Schumann, P.; Burghardt, J.; Webb, R.I.; Soddell, J.A.; Rees, G.N. Friedmanniella spumicola sp. nov. and Friedmanniella capsulata sp. nov. from activated sludge foam: Gram-positive cocci that grow in aggregates of repeating groups of cocci. Int. J. Syst. Evol. 1999, 49, 1667–1680. [Google Scholar] [CrossRef] [PubMed]
- Kim, S.-Y.; Kim, J.-H.; Kim, C.-J.; Oh, D.-K. Metal adsorption of the polysaccharide produced from Methylobacterium organophilum. Biotechnol. Lett. 1996, 18, 1161–1164. [Google Scholar] [CrossRef]
- Yarnell, E. Plant chemistry in veterinary medicine: Medicinal constituents and their mechanisms of action. In Veterinary Herbal Medicine; Mosby: Maryland Heights, MO, USA, 2007; pp. 159–182. [Google Scholar]
- Ares, A.; Pereira, J.; Garcia, E.; Costa, J.; Tiago, I. The leaf bacterial microbiota of female and male kiwifruit plants in distinct seasons: Assessing the impact of Pseudomonas syringae pv. actinidiae. Phytobiomes J. 2021, 5, 275–287. [Google Scholar] [CrossRef]
- Park, T.; Kim, H.-J.; Myeong, N.R.; Lee, H.G.; Kwack, I.; Lee, J.; Kim, B.J.; Sul, W.J.; An, S. Collapse of human scalp microbiome network in dandruff and seborrhoeic dermatitis. Exp. Dermatol. 2017, 26, 835–838. [Google Scholar] [CrossRef]
- Ibal, J.-C.; Park, M.-K.; Park, G.-S.; Jung, B.-K.; Park, T.-H.; Kim, M.-S.; Kang, G.-U.; Park, Y.-J.; Shin, J.-H. Use of acyl-homoserine lactones leads to improved growth of ginseng seedlings and shifts in soil microbiome structure. Agronomy 2021, 11, 2177. [Google Scholar] [CrossRef]
- Bolyen, E.; Rideout, J.R.; Dillon, M.R.; Bokulich, N.A.; Abnet, C.C.; Al-Ghalith, G.A.; Alexander, H.; Alm, E.J.; Arumugam, M.; Asnicar, F.; et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 2019, 37, 852–857. [Google Scholar] [CrossRef]
- Callahan, B.J.; Mcmurdie, P.J.; Rosen, M.J.; Han, A.W.; Johnson, A.J.A.; Holmes, S.P. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods. 2016, 13, 581–583. [Google Scholar] [CrossRef]
- Bokulich, N.A.; Kaehler, B.D.; Rideout, J.R.; Dillon, M.; Bolyen, E.; Knight, R.; Huttley, G.A.; Gregory Caporaso, J. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2′s q2-feature-classifier plugin. Microbiome 2018, 6, 90. [Google Scholar] [CrossRef]
- McMurdie, P.J.; Holmes, S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 2013, 8, e61217. [Google Scholar] [CrossRef]
- Dixon, P. VEGAN, a package of R functions for community ecology. J. Veg. Sci. 2003, 14, 927–930. [Google Scholar] [CrossRef]
- Csárdi, G.; Nepusz, T. The igraph software package for complex network research. Int. J. Complex Syst. 2006, 1695, 1–9. [Google Scholar]
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. |
© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Jo, Y.; Jung, D.-R.; Park, T.-H.; Lee, D.; Park, M.-K.; Lim, K.; Shin, J.-H. Changes in Microbial Community Structure in Response to Gummosis in Peach Tree Bark. Plants 2022, 11, 2834. https://doi.org/10.3390/plants11212834
Jo Y, Jung D-R, Park T-H, Lee D, Park M-K, Lim K, Shin J-H. Changes in Microbial Community Structure in Response to Gummosis in Peach Tree Bark. Plants. 2022; 11(21):2834. https://doi.org/10.3390/plants11212834
Chicago/Turabian StyleJo, YoungJae, Da-Ryung Jung, Tae-Hyung Park, Dokyung Lee, Min-Kyu Park, Kyeongmo Lim, and Jae-Ho Shin. 2022. "Changes in Microbial Community Structure in Response to Gummosis in Peach Tree Bark" Plants 11, no. 21: 2834. https://doi.org/10.3390/plants11212834
APA StyleJo, Y., Jung, D.-R., Park, T.-H., Lee, D., Park, M.-K., Lim, K., & Shin, J.-H. (2022). Changes in Microbial Community Structure in Response to Gummosis in Peach Tree Bark. Plants, 11(21), 2834. https://doi.org/10.3390/plants11212834