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Robinson JM, Barnes AD, Fickling N, Costin S, Sun X, Breed MF. Food webs in food webs: the micro-macro interplay of multilayered networks. Trends Ecol Evol 2024; 39:913-922. [PMID: 38960756 DOI: 10.1016/j.tree.2024.06.006] [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: 01/21/2024] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 07/05/2024]
Abstract
Food webs are typically defined as being macro-organism-based (e.g., plants, mammals, birds) or microbial (e.g., bacteria, fungi, viruses). However, these characterizations have limits. We propose a multilayered food web conceptual model where microbial food webs are nested within food webs composed of macro-organisms. Nesting occurs through host-microbe interactions, which influence the health and behavior of host macro-organisms, such that host microbiomes likely alter population dynamics of interacting macro-organisms and vice versa. Here, we explore the theoretical underpinnings of multilayered food webs and the implications of this new conceptual model on food web ecology. Our framework opens avenues for new empirical investigations into complex ecological networks and provides a new lens through which to view a network's response to ecosystem changes.
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Affiliation(s)
- Jake M Robinson
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia; The Aerobiome Innovation and Research Hub, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia.
| | - Andrew D Barnes
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Nicole Fickling
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia; The Aerobiome Innovation and Research Hub, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Sofie Costin
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Xin Sun
- The Aerobiome Innovation and Research Hub, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia; Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia; The Aerobiome Innovation and Research Hub, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia.
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Liu Y, Lai J, Sun X, Huang L, Sheng Y, Zhang Q, Zeng H, Zhang Y, Ye P, Wei S. Comparative Metagenomic Analysis Reveals Rhizosphere Microbiome Assembly and Functional Adaptation Changes Caused by Clubroot Disease in Chinese Cabbage. Microorganisms 2024; 12:1370. [PMID: 39065138 PMCID: PMC11278620 DOI: 10.3390/microorganisms12071370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Clubroot is a major disease and severe threat to Chinese cabbage, and it is caused by the pathogen Plasmodiophora brassicae Woron. This pathogen is an obligate biotrophic protist and can persist in soil in the form of resting spores for more than 18 years, which can easily be transmitted through a number of agents, resulting in significant economic losses to global Chinese cabbage production. Rhizosphere microbiomes play fundamental roles in the occurrence and development of plant diseases. The changes in the rhizosphere microorganisms could reveal the severity of plant diseases and provide the basis for their control. Here, we studied the rhizosphere microbiota after clubroot disease infections with different severities by employing metagenomic sequencing, with the aim of exploring the relationships between plant health, rhizosphere microbial communities, and soil environments; then, we identified potential biomarker microbes of clubroot disease. The results showed that clubroot disease severity significantly affected the microbial community composition and structure of the rhizosphere soil, and microbial functions were also dramatically influenced by it. Four different microbes that had great potential in the biocontrol of clubroot disease were identified from the obtained results; they were the genera Pseudomonas, Gemmatimonas, Sphingomonas, and Nocardioides. Soil pH, organic matter contents, total nitrogen, and cation exchange capacity were the major environmental factors modulating plant microbiome assembly. In addition, microbial environmental information processing was extremely strengthened when the plant was subjected to pathogen invasion, but weakened when the disease became serious. In particular, oxidative phosphorylation and glycerol-1-phosphatase might have critical functions in enhancing Chinese cabbage's resistance to clubroot disease. This work revealed the interactions and potential mechanisms among Chinese cabbage, soil environmental factors, clubroot disease, and microbial community structure and functions, which may provide a novel foundation for further studies using microbiological or metabolic methods to develop disease-resistant cultivation technologies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Pengsheng Ye
- Industrial Crops Research Institute, Sichuan Academy of Agricultural Sciences/The Key Laboratory of Vegetable Germplasm and Variety Innovation in Sichuan Province, Chengdu 610300, China; (Y.L.); (J.L.); (X.S.); (L.H.); (Y.S.); (Q.Z.); (H.Z.); (Y.Z.)
| | - Shugu Wei
- Industrial Crops Research Institute, Sichuan Academy of Agricultural Sciences/The Key Laboratory of Vegetable Germplasm and Variety Innovation in Sichuan Province, Chengdu 610300, China; (Y.L.); (J.L.); (X.S.); (L.H.); (Y.S.); (Q.Z.); (H.Z.); (Y.Z.)
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Hauschild K, Orth N, Liu B, Giongo A, Gschwendtner S, Beerhues L, Schloter M, Vetterlein D, Winkelmann T, Smalla K. Rhizosphere competent inoculants modulate the apple root-associated microbiome and plant phytoalexins. Appl Microbiol Biotechnol 2024; 108:344. [PMID: 38801472 PMCID: PMC11129989 DOI: 10.1007/s00253-024-13181-8] [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: 12/18/2023] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
Modulating the soil microbiome by applying microbial inoculants has gained increasing attention as eco-friendly option to improve soil disease suppressiveness. Currently, studies unraveling the interplay of inoculants, root-associated microbiome, and plant response are lacking for apple trees. Here, we provide insights into the ability of Bacillus velezensis FZB42 or Pseudomonas sp. RU47 to colonize apple root-associated microhabitats and to modulate their microbiome. We applied the two strains to apple plants grown in soils from the same site either affected by apple replant disease (ARD) or not (grass), screened their establishment by selective plating, and measured phytoalexins in roots 3, 16, and 28 days post inoculation (dpi). Sequencing of 16S rRNA gene and ITS fragments amplified from DNA extracted 28 dpi from different microhabitat samples revealed significant inoculation effects on fungal β-diversity in root-affected soil and rhizoplane. Interestingly, only in ARD soil, most abundant bacterial amplicon sequence variants (ASVs) changed significantly in relative abundance. Relative abundances of ASVs affiliated with Enterobacteriaceae were higher in rhizoplane of apple grown in ARD soil and reduced by both inoculants. Bacterial communities in the root endosphere were not affected by the inoculants but their presence was indicated. Interestingly and previously unobserved, apple plants responded to the inoculants with increased phytoalexin content in roots, more pronounced in grass than ARD soil. Altogether, our results indicate that FZB42 and RU47 were rhizosphere competent, modulated the root-associated microbiome, and were perceived by the apple plants, which could make them interesting candidates for an eco-friendly mitigation strategy of ARD. KEY POINTS: • Rhizosphere competent inoculants modulated the microbiome (mainly fungi) • Inoculants reduced relative abundance of Enterobacteriaceae in the ARD rhizoplane • Inoculants increased phytoalexin content in roots, stronger in grass than ARD soil.
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Affiliation(s)
- Kristin Hauschild
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Nils Orth
- Institute of Horticultural Production Systems, Leibniz University Hannover, Hannover, Germany
| | - Benye Liu
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Adriana Giongo
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Silvia Gschwendtner
- Research Unit Comparative Microbiome Analysis, Helmholtz Centre Munich, Munich, Germany
| | - Ludger Beerhues
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Centre Munich, Munich, Germany
| | - Doris Vetterlein
- Department of Soil System Science, Helmholtz Centre for Environmental Research, Halle/Saale, Germany
| | - Traud Winkelmann
- Institute of Horticultural Production Systems, Leibniz University Hannover, Hannover, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Braunschweig, Germany.
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Benning S, Pritsch K, Radl V, Siani R, Wang Z, Schloter M. (Pan)genomic analysis of two Rhodococcus isolates and their role in phenolic compound degradation. Microbiol Spectr 2024; 12:e0378323. [PMID: 38376357 PMCID: PMC10986565 DOI: 10.1128/spectrum.03783-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/25/2024] [Indexed: 02/21/2024] Open
Abstract
The genus Rhodococcus is recognized for its potential to degrade a large range of aromatic substances, including plant-derived phenolic compounds. We used comparative genomics in the context of the broader Rhodococcus pan-genome to study genomic traits of two newly described Rhodococcus strains (type-strain Rhodococcus pseudokoreensis R79T and Rhodococcus koreensis R85) isolated from apple rhizosphere. Of particular interest was their ability to degrade phenolic compounds as part of an integrated approach to treat apple replant disease (ARD) syndrome. The pan-genome of the genus Rhodococcus based on 109 high-quality genomes was open with a small core (1.3%) consisting of genes assigned to basic cell functioning. The range of genome sizes in Rhodococcus was high, from 3.7 to 10.9 Mbp. Genomes from host-associated strains were generally smaller compared to environmental isolates which were characterized by exceptionally large genome sizes. Due to large genomic differences, we propose the reclassification of distinct groups of rhodococci like the Rhodococcus equi cluster to new genera. Taxonomic species affiliation was the most important factor in predicting genetic content and clustering of the genomes. Additionally, we found genes that discriminated between the strains based on habitat. All members of the genus Rhodococcus had at least one gene involved in the pathway for the degradation of benzoate, while biphenyl degradation was mainly restricted to strains in close phylogenetic relationships with our isolates. The ~40% of genes still unclassified in larger Rhodococcus genomes, particularly those of environmental isolates, need more research to explore the metabolic potential of this genus.IMPORTANCERhodococcus is a diverse, metabolically powerful genus, with high potential to adapt to different habitats due to the linear plasmids and large genome sizes. The analysis of its pan-genome allowed us to separate host-associated from environmental strains, supporting taxonomic reclassification. It was shown which genes contribute to the differentiation of the genomes based on habitat, which can possibly be used for targeted isolation and screening for desired traits. With respect to apple replant disease (ARD), our isolates showed genome traits that suggest potential for application in reducing plant-derived phenolic substances in soil, which makes them good candidates for further testing against ARD.
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Affiliation(s)
- Sarah Benning
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Karin Pritsch
- Research Unit for Environmental Simulations, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Viviane Radl
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Roberto Siani
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Zhongjie Wang
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Chair for Environmental Microbiology, TUM School of Life Sciences, Technical University Munich, Munich, Germany
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Darriaut R, Marzari T, Lailheugue V, Tran J, Martins G, Marguerit E, Masneuf-Pomarède I, Lauvergeat V. Microbial dysbiosis in roots and rhizosphere of grapevines experiencing decline is associated with active metabolic functions. FRONTIERS IN PLANT SCIENCE 2024; 15:1358213. [PMID: 38628369 PMCID: PMC11018932 DOI: 10.3389/fpls.2024.1358213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024]
Abstract
When grapevine decline, characterized by a premature decrease in vigor and yield and sometimes plant death, cannot be explained by pathological or physiological diseases, one may inquire whether the microbiological status of the soil is responsible. Previous studies have shown that the composition and structure of bacterial and fungal microbial communities in inter-row soil are affected in areas displaying vine decline, compared to areas with non-declining vines within the same plot. A more comprehensive analysis was conducted in one such plot. Although soil chemical parameters could not directly explain these differences, the declining vines presented lower vigor, yield, berry quality, and petiole mineral content than those in non-declining vines. The bacterial and fungal microbiome of the root endosphere, rhizosphere, and different horizons of the bulk soil were explored through enzymatic, metabolic diversity, and metabarcoding analysis in both areas. Despite the lower microbial diversity and richness in symptomatic roots and soil, higher microbial activity and enrichment of potentially both beneficial bacteria and pathogenic fungi were found in the declining area. Path modeling analysis linked the root microbial activity to berry quality, suggesting a determinant role of root microbiome in the berry mineral content. Furthermore, certain fungal and bacterial taxa were correlated with predicted metabolic pathways and metabolic processes assessed with Eco-Plates. These results unexpectedly revealed active microbial profiles in the belowground compartments associated with stressed vines, highlighting the interest of exploring the functional microbiota of plants, and more specifically roots and rhizosphere, under stressed conditions.
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Affiliation(s)
- Romain Darriaut
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Tania Marzari
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Vincent Lailheugue
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Joseph Tran
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Guilherme Martins
- Université de Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, UMR Œnologie 1366, ISVV, Villenave d’Ornon, France
- Bordeaux Sciences Agro, 1 cours du Général de Gaulle, Gradignan, France
| | - Elisa Marguerit
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Isabelle Masneuf-Pomarède
- Université de Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, UMR Œnologie 1366, ISVV, Villenave d’Ornon, France
- Bordeaux Sciences Agro, 1 cours du Général de Gaulle, Gradignan, France
| | - Virginie Lauvergeat
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
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Busnena BA, Beerhues L, Liu B. Biphenyls and dibenzofurans of the rosaceous subtribe Malinae and their role as phytoalexins. PLANTA 2023; 258:78. [PMID: 37689618 PMCID: PMC10492887 DOI: 10.1007/s00425-023-04228-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/23/2023] [Indexed: 09/11/2023]
Abstract
MAIN CONCLUSION Biphenyl and dibenzofuran phytoalexins are differentially distributed among species of the rosaceous subtribe Malinae, which includes apple and pear, and exhibit varying inhibitory activity against phytopathogenic microorganisms. Biphenyls and dibenzofurans are specialized metabolites, which are formed in species of the rosaceous subtribe Malinae upon elicitation by biotic and abiotic inducers. The subtribe Malinae (previously Pyrinae) comprises approximately 1000 species, which include economically important fruit trees such as apple and pear. The present review summarizes the current status of knowledge of biphenyls and dibenzofurans in the Malinae, mainly focusing on their role as phytoalexins. To date, 46 biphenyls and 41 dibenzofurans have been detected in 44 Malinae species. Structurally, 54 simple molecules, 23 glycosidic compounds and 10 miscellaneous structures were identified. Functionally, 21 biphenyls and 21 dibenzofurans were demonstrated to be phytoalexins. Furthermore, their distribution in species of the Malinae, inhibitory activities against phytopathogens, and structure-activity relationships were studied. The most widely distributed phytoalexins of the Malinae are the three biphenyls aucuparin (3), 2'-methoxyaucuparin (7), and 4'-methoxyaucuparin (9) and the three dibenzofurans α-cotonefuran (47), γ-cotonefuran (49), and eriobofuran (53). The formation of biphenyl and dibenzofuran phytoalexins appears to be an essential defense weapon of the Malinae against various stresses. Manipulating phytoalexin formation may enhance the disease resistance in economically important fruit trees. However, this approach requires an extensive understanding of how the compounds are formed. Although the biosynthesis of biphenyls was partially elucidated, formation of dibenzofurans remains largely unclear. Thus, further efforts have to be made to gain deeper insight into the distribution, function, and metabolism of biphenyls and dibenzofurans in the Malinae.
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Affiliation(s)
- Belnaser A Busnena
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106, Braunschweig, Germany
| | - Ludger Beerhues
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106, Braunschweig, Germany
| | - Benye Liu
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106, Braunschweig, Germany.
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Li X, Skillman V, Dung J, Frost K. Legacy effects of fumigation on soil bacterial and fungal communities and their response to metam sodium application. ENVIRONMENTAL MICROBIOME 2022; 17:59. [PMID: 36461097 PMCID: PMC9719244 DOI: 10.1186/s40793-022-00454-w] [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: 08/13/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Soil microorganisms are integral to maintaining soil health and crop productivity, but fumigation used to suppress soilborne diseases may affect soil microbiota. Currently, little is known about the legacy effects of soil fumigation on soil microbial communities and their response to fumigation at the production scale. Here, 16S rRNA gene and internal transcribed spacer amplicon sequencing was used to characterize the bacterial and fungal communities in soils from intensively managed crop fields with and without previous exposure to metam sodium (MS) fumigation. The effect of fumigation history, soil series, and rotation crop diversity on microbial community variation was estimated and the response of the soil microbiome to MS application in an open microcosm system was documented. RESULTS We found that previous MS fumigation reduced soil bacterial diversity but did not affect microbial richness and fungal diversity. Fumigation history, soil series, and rotation crop diversity were the main contributors to the variation in microbial β-diversity. Between fumigated and non-fumigated soils, predominant bacterial and fungal taxa were similar; however, their relative abundance varied with fumigation history. In particular, the abundance of Basidiomycete yeasts was decreased in fumigated soils. MS fumigation also altered soil bacterial and fungal co-occurrence network structure and associations. In microcosms, application of MS reduced soil microbial richness and bacterial diversity. Soil microbial β-diversity was also affected but microbial communities of the microcosm soils were always similar to that of the field soils used to establish the microcosms. MS application also induced changes in relative abundance of several predominant bacterial and fungal genera based on a soil's previous fumigation exposure. CONCLUSIONS The legacy effects of MS fumigation are more pronounced on soil bacterial diversity, β-diversity and networks. Repeated fumigant applications shift soil microbial compositions and may contribute to differential MS sensitivity among soil microorganisms. Following MS application, microbial richness and bacterial diversity decreases, but microbial β-diversity was similar to that of the field soils used to establish the microcosms in the short-term (< 6 weeks). The responses of soil microbiome to MS fumigation are context dependent and rely on abiotic, biotic, and agricultural management practices.
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Affiliation(s)
- Xiaoping Li
- Virginia Tech, Hampton Roads Agricultural Research and Extension Center, Virginia Beach, VA, 23455, USA
| | - Victoria Skillman
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, 97838, USA
| | - Jeremiah Dung
- Central Oregon Agricultural Research and Extension Center, Oregon State University, Madras, OR, 97741, USA
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97333, USA
| | - Kenneth Frost
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, 97838, USA.
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97333, USA.
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Liu Y, Liu Q, Li X, Tang Z, Zhang Z, Gao H, Ma F, Li C. Exogenous Dopamine and MdTyDC Overexpression Enhance Apple Resistance to Fusarium solani. PHYTOPATHOLOGY 2022; 112:2503-2513. [PMID: 35801852 DOI: 10.1094/phyto-04-22-0142-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Fusarium solani, one of the main pathogenic fungi involved in apple replant disease (ARD), is a serious threat to apple growth and development. Dopamine and tyrosine decarboxylase (TyDC), a key enzyme in the dopamine synthesis pathway, have been reported to play an active role in plant responses to biotic and abiotic stresses, but little is known about the functions of dopamine and Malus domestica TyDC (MdTyDC) in the interaction between F. solani and apple roots. In this study, seedlings treated with exogenous dopamine and apple plants overexpressing MdTyDC were inoculated with F. solani; both treatments reduced the root system damage caused by F. solani. After inoculation with F. solani, exogenous dopamine increased dopamine content in the seedlings; alleviated the inhibition of biomass accumulation; increased root metabolic activity, photosynthetic efficiency, and antioxidant enzyme activities; reduced reactive oxygen species accumulation; and upregulated the expression of genes encoding chitinase, β-1,3-glucanase, and pathogenesis-related proteins. Similar results were observed in MdTyDC-overexpressing apple plants. In addition, the overexpression of MdTyDC increased tyramine content and the deposition of cell wall-bound amines in roots. Overall, our results reveal that exogenous dopamine and overexpression of MdTyDC enhance apple resistance to F. solani, which is an important application for the prevention of ARD.
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Affiliation(s)
- Yusong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Qianwei Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Xuewen Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Zhongwen Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Zhijun Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Hanbing Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Chao Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, China
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Wu H, Fang C, Malacrinò A, Winkelmann T, Xiong W. Editorial: Rhizosphere conversation among the plant-plant microbiome-soil under consecutive monoculture regimes. Front Microbiol 2022; 13:1061427. [DOI: 10.3389/fmicb.2022.1061427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 10/11/2022] [Indexed: 11/13/2022] Open
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10
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Ni H, Zong R, Sun J, Wu Y, Yu L, Liu Y, Liu J, Ju R, Sun X, Zheng Y, Tan L, Liu L, Dong Y, Li T, Zhang Y, Tu Q. Response of Bacterial Community to the Occurrence of Clubroot Disease in Chinese Cabbage. Front Microbiol 2022; 13:922660. [PMID: 35875525 PMCID: PMC9298529 DOI: 10.3389/fmicb.2022.922660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Clubroot disease is a common soilborne disease caused by Plasmodiophora brassicas Wor. and widely occurs in Chinese cabbage. Soil microorganisms play vital roles in the occurrence and development of plant diseases. The changes in the soil bacterial community could indicate the severity of plant disease and provide the basis for its control. This study focused on the bacterial community of the clubroot disease-infected soil-root system with different severity aiming to reveal the composition and structure of soil bacteria and identified potential biomarker bacteria of the clubroot disease. In the clubroot disease-infected soil, the bacterial community is mainly composed of Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Bacilli, Thermolrophilia, Bacteroidia, Gemmatimonadetes, Subgroup_6, Deltaproteobacteria, KD4-96, and some other classes, while the major bacterial classes in the infected roots were Oxyphotobacteria, Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, Bacilli, Bacteroidia, Saccharimonadia, Thermoleophilia, Clostridia, Chloroflexia, and some other classes. The severe clubroot disease soil-root system was found to possess a poorer bacterial richness, evenness, and better coverage. Additionally, a significant difference was observed in the structure of the bacterial community between the high-severity (HR) and healthy (LR) soil-root system. Bacillus asahii and Noccaea caerulescens were identified as the differential bacteria between the LR and HR soil and roots, respectively. pH was demonstrated as a vital factor that was significantly associated with the abundance of B. asahii and N. caerulescens. This study provides novel insight into the relationship between soil bacteria and the pathogen of clubroot disease in Chinese cabbage. The identification of resistant species provides candidates for the monitoring and biocontrol of the clubroot disease.
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Affiliation(s)
- Haiping Ni
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, China.,Qingdao Hexie Biotechnology Co., Ltd., Qingdao, China
| | - Rui Zong
- Qingdao Hexie Biotechnology Co., Ltd., Qingdao, China
| | - Jianjun Sun
- Qingdao Hexie Biotechnology Co., Ltd., Qingdao, China
| | - Yuxia Wu
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, China.,Shandong Agricultural Technology Extension Center, Jinan, China
| | - Lei Yu
- Shandong Agricultural Technology Extension Center, Jinan, China
| | - Yuanyuan Liu
- Qingdao Hexie Biotechnology Co., Ltd., Qingdao, China
| | - Jin Liu
- Qingdao Hexie Biotechnology Co., Ltd., Qingdao, China
| | - Ruicheng Ju
- Qingdao Hexie Biotechnology Co., Ltd., Qingdao, China
| | - Xianli Sun
- Qingdao Hexie Biotechnology Co., Ltd., Qingdao, China
| | - Yulian Zheng
- Qingdao Hexie Biotechnology Co., Ltd., Qingdao, China
| | - Lekun Tan
- Qingdao Hexie Biotechnology Co., Ltd., Qingdao, China
| | - Lumin Liu
- Qingdao Hexie Biotechnology Co., Ltd., Qingdao, China
| | - Yachao Dong
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Tao Li
- Shandong Agricultural Technology Extension Center, Jinan, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, China.,Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Qiang Tu
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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11
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Somera TS, Mazzola M. Toward a holistic view of orchard ecosystem dynamics: A comprehensive review of the multiple factors governing development or suppression of apple replant disease. Front Microbiol 2022; 13:949404. [PMID: 35958152 PMCID: PMC9358454 DOI: 10.3389/fmicb.2022.949404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Replant diseases are a common occurrence in perennial cropping systems. In apple, progress toward the development of a universally effective disease management strategy, beyond the use of broad-spectrum soil fumigants, is impeded by inconsistencies in defining replant disease etiology. A preponderance of evidence attributes apple replant disease to plant-induced changes in the soil microbiome including the proliferation of soilborne plant pathogens. Findings from alternative studies suggest that the contribution of abiotic factors, such as the accumulation of phenolic detritus from previous orchard plantings, may play a part as well. Engineering of the resident soil microbiome using resource-based strategies is demonstrating potential to limit activity of replant pathogens and improve productivity in newly established orchards. An understanding of factors promoting the assembly of a disease-suppressive soil microbiome along with consideration of host factors that confer disease tolerance or resistance is imperative to the developing a more holistic view of orchard ecosystem dynamics. Here, we review the literature concerning the transition of orchard soil from a healthy state to a replant disease-conducive state. Included in the scope of this review are studies on the influence of soil type and geography on the apple replant pathogen complex. Furthermore, several tolerance and innate resistance mechanisms that have been described in apple to date, including the role of root chemistry/exudates are discussed. Finally, the interplay between apple rootstock genotype and key resource-based strategies which have been shown to “reshape” the plant holobiont in favor of a more prophylactic or disease-suppressive state is highlighted.
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Affiliation(s)
- Tracey S. Somera
- USDA, Agricultural Research Service, Wenatchee, WA, United States
- *Correspondence: Tracey S. Somera,
| | - Mark Mazzola
- USDA, Agricultural Research Service, Wenatchee, WA, United States
- Department of Plant Pathology, Stellenbosch University, Stellenbosch, South Africa
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12
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Peixoto RS, Voolstra CR, Sweet M, Duarte CM, Carvalho S, Villela H, Lunshof JE, Gram L, Woodhams DC, Walter J, Roik A, Hentschel U, Thurber RV, Daisley B, Ushijima B, Daffonchio D, Costa R, Keller-Costa T, Bowman JS, Rosado AS, Reid G, Mason CE, Walke JB, Thomas T, Berg G. Harnessing the microbiome to prevent global biodiversity loss. Nat Microbiol 2022; 7:1726-1735. [PMID: 35864220 DOI: 10.1038/s41564-022-01173-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 06/14/2022] [Indexed: 01/21/2023]
Abstract
Global biodiversity loss and mass extinction of species are two of the most critical environmental issues the world is currently facing, resulting in the disruption of various ecosystems central to environmental functions and human health. Microbiome-targeted interventions, such as probiotics and microbiome transplants, are emerging as potential options to reverse deterioration of biodiversity and increase the resilience of wildlife and ecosystems. However, the implementation of these interventions is urgently needed. We summarize the current concepts, bottlenecks and ethical aspects encompassing the careful and responsible management of ecosystem resources using the microbiome (termed microbiome stewardship) to rehabilitate organisms and ecosystem functions. We propose a real-world application framework to guide environmental and wildlife probiotic applications. This framework details steps that must be taken in the upscaling process while weighing risks against the high toll of inaction. In doing so, we draw parallels with other aspects of contemporary science moving swiftly in the face of urgent global challenges.
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Affiliation(s)
- Raquel S Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Christian R Voolstra
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, UK
| | - Carlos M Duarte
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Helena Villela
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jeantine E Lunshof
- Department of Global Health and Social Medicine, Center for Bioethics, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Douglas C Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - Jens Walter
- APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork, Cork, Ireland
| | - Anna Roik
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany
| | - Ute Hentschel
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | - Brendan Daisley
- Lawson Health Research Institute, University of Western Ontario, London, Ontario, Canada
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Tina Keller-Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Jeff S Bowman
- Scripps Institution of Oceanography, University of California San Diego, San Diego, CA, USA
| | - Alexandre S Rosado
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Gregor Reid
- Lawson Health Research Institute, University of Western Ontario, London, Ontario, Canada
| | | | - Jenifer B Walke
- Department of Biology, Eastern Washington University, Cheney, WA, USA
| | - Torsten Thomas
- Centre for Marine Science and Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.,University of Postdam and Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
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13
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Mahnkopp-Dirks F, Radl V, Kublik S, Gschwendtner S, Schloter M, Winkelmann T. Dynamics of Bacterial Root Endophytes of Malus domestica Plants Grown in Field Soils Affected by Apple Replant Disease. Front Microbiol 2022; 13:841558. [PMID: 35401446 PMCID: PMC8993231 DOI: 10.3389/fmicb.2022.841558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/14/2022] [Indexed: 01/04/2023] Open
Abstract
Apple replant disease (ARD) is a worldwide problem for tree nurseries and orchards leading to reduced plant growth and fruit quality. The etiology of this complex phenomenon is poorly understood, but shifts of the bulk soil and rhizosphere microbiome seem to play an important role. Since roots are colonized by microbes from the rhizosphere, studies of the endophytic microbiome in relation to ARD are meaningful. In this study, culture-independent and culture-dependent approaches were used in order to unravel the endophytic root microbiome of apple plants 3, 7, and 12 months after planting in ARD-affected soil and ARD-unaffected control soil at two different field sites. Next to a high diversity of Pseudomonas in roots from all soils, molecular barcoding approaches revealed an increase in relative abundance of endophytic Actinobacteria over time in plants grown in ARD and control plots. Furthermore, several amplicon sequence variants (ASVs) linked to Streptomyces, which had been shown in a previous greenhouse ARD biotest to be negatively correlated to shoot length and fresh mass, were also detected in roots from both field sites. Especially in roots of apple plants from control soil, these Streptomyces ASVs increased in their relative abundance over time. The isolation of 150 bacterial strains in the culture-dependent approach revealed a high diversity of members of the genus Pseudomonas, confirming the data of the molecular barcoding approach. However, only partial overlaps were found between the two approaches, underlining the importance of combining these methods in order to better understand this complex disease and develop possible countermeasures. Overall, this study suggests a key role of Streptomyces in the etiology of ARD in the field.
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Affiliation(s)
- Felix Mahnkopp-Dirks
- Section Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hanover, Germany
| | - Viviane Radl
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Silvia Gschwendtner
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Traud Winkelmann
- Section Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hanover, Germany
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14
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Duan Y, Zhao L, Jiang W, Chen R, Zhang R, Chen X, Yin C, Mao Z. The Phlorizin-Degrading Bacillus licheniformis XNRB-3 Mediates Soil Microorganisms to Alleviate Apple Replant Disease. Front Microbiol 2022; 13:839484. [PMID: 35308362 PMCID: PMC8927668 DOI: 10.3389/fmicb.2022.839484] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/24/2022] [Indexed: 11/25/2022] Open
Abstract
In this study, an endophytic phlorizin-degrading Bacillus licheniformis XNRB-3 was isolated from the root tissue of healthy apple trees, and its control effect on apple replant disease (ARD) and how it alleviates the pathogen pressure via changes in soil microbiomes were studied. The addition of strain XNRB-3 in Fusarium infested soils significantly reduced the number of pathogens in the soil, thus resulting in a lower disease incidence, and the relative control effect on Fusarium oxysporum reached the highest of 66.11%. The fermentation broth can also protect the roots of the plants from Fusarium oxysporum, Fusarium moniliforme, Fusarium proliferatum, and Fusarium solani infection. These antagonistic effects were further validated using an in vitro assay in which the pathogen control was related to growth and spore germination inhibition via directly secreted antimicrobial substances and indirectly affecting the growth of pathogens. The secreted antimicrobial substances were identified using gas chromatography-mass spectrometry (GC-MS) technology. Among them, alpha-bisabolol and 2,4-di-tert-butylphenol had significant inhibitory effects on many planted pathogenic fungi. Butanedioic acid, monomethyl ester, and dibutyl phthalate promoted root development of Arabidopsis plants. Strain XNRB-3 has multifarious plant growth promoting traits and antagonistic potential. In pot and field experiments, the addition of strain XNRB-3 significantly promoted the growth of plants, and the activity of enzymes related to disease resistance [superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)] was also significantly enhanced. It also reduced the abundance of four species of Fusarium and the content of phenolic acids in the rhizosphere soil, improved soil microbial community structure and nutritional conditions, and increased soil microbial diversity and activity, as well as the soil enzyme activity. The above results indicated that B. licheniformis XNRB-3 could be developed into a promising biocontrol and plant-growth-promoting agent.
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Affiliation(s)
| | | | | | | | | | | | - Chengmiao Yin
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong, China
| | - Zhiquan Mao
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong, China
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15
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Effects of Bacillus amyloliquefaciens QSB-6 on the Growth of Replanted Apple Trees and the Soil Microbial Environment. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8010083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Apple replant disease (ARD), caused largely by soil-borne fungal pathogens, has seriously hindered the development of the apple industry. The use of antagonistic microorganisms has been confirmed as a low-cost and environmentally friendly means of controlling ARD. In the present study, we assessed the effects of Bacillus amyloliquefaciens QSB-6 on the growth of replanted apple saplings and the soil microbial environment under field conditions, thus providing a theoretical basis for the successful use of microbial biocontrol agents. Four treatments were implemented in three apple orchards: untreated replant soil (CK1), methyl bromide fumigation (CK2), blank carrier treatment (T1), and QSB-6 bacterial fertilizer treatment (T2). The plant height, ground diameter, and branch length of apple saplings treated with T2 in three replanted apple orchards were significantly higher than that of the CK1 treatment. Compared with the other treatments, T2 significantly increased the number of soil bacteria, the proportion of actinomycetes, and the activities of soil enzymes. By contrast, compared with the CK1 treatments, the phenolic acid content, the number of fungi, and the abundance of Fusarium oxysporum, Fusarium moniliforme, Fusarium proliferatum, and Fusarium solani in the soil were significantly reduced. PCoA and cluster analysis showed that soil inoculation with strain QSB-6 significantly decreased the Mcintosh and Brillouin index of soil fungi and increased the diversity of soil bacteria in T2 relative to CK1. The soil bacterial community structure in T2 was different from the other treatments, and the soil fungal communities of T2 and CK2 were similar. In summary, QSB-6 bacterial fertilizer shows promise as a potential bio-inoculum for the control of ARD.
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16
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Busnena BA, Beuerle T, Mahnkopp-Dirks F, Winkelmann T, Beerhues L, Liu B. Formation and exudation of biphenyl and dibenzofuran phytoalexins by roots of the apple rootstock M26 grown in apple replant disease soil. PHYTOCHEMISTRY 2021; 192:112972. [PMID: 34624729 DOI: 10.1016/j.phytochem.2021.112972] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/21/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
Apple replant disease (ARD) is a severe soil-borne disease frequently observed in apple tree nurseries and orchards worldwide. One of the responses of apple trees to ARD is the formation of biphenyl and dibenzofuran phytoalexins in their roots. However, there is no information on whether or not these phytoalexins are exuded into the soil. To answer this open question, a model system was established using the ARD-sensitive apple rootstock M26 (Malus × domestica Borkh. Rosaceae) and GC-MS analysis in combination with an in-house GC-MS database including retention indices. We have detected a total of 35 phytoalexins, i.e. 10 biphenyls and 25 dibenzofurans in root samples, thereby adding eight compounds to the previously reported 27 phytoalexins of Malinae species. When in vitro cultured M26 plantlets were treated with yeast extract, all the 35 phytoalexins were formed in the roots and 85.2% of the total phytoalexin amount was exuded into the culture medium. In roots of M26 plants grown in ARD soil in pot, 26 phytoalexins were detected and their exudation was demonstrated using two independent approaches of collecting root exudates. In a modified dipping experiment and a soil-hydroponic hybrid setup, the exudation rate was 39.5% and 20.6%, respectively. The exudation rates for individual phytoalexins differed, indicating controlled exudation processes. The exuded phytoalexins may play an important role in shaping the soil microbiome, which appears to greatly influence the development and severity of ARD.
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Affiliation(s)
- Belnaser A Busnena
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106, Braunschweig, Germany.
| | - Till Beuerle
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106, Braunschweig, Germany.
| | - Felix Mahnkopp-Dirks
- Institute of Horticultural Production Systems, Woody Plant and Propagation Physiology Section, Gottfried Wilhelm Leibniz Universität Hannover, Herrenhäuser Straße 2, 30419, Hanover, Germany.
| | - Traud Winkelmann
- Institute of Horticultural Production Systems, Woody Plant and Propagation Physiology Section, Gottfried Wilhelm Leibniz Universität Hannover, Herrenhäuser Straße 2, 30419, Hanover, Germany.
| | - Ludger Beerhues
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106, Braunschweig, Germany.
| | - Benye Liu
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106, Braunschweig, Germany.
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17
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Wang X, Yao Y, Wang G, Ma J, Yin C, Chen X, Mao Z. Comprehensive Analysis of the Influence of Fulvic Acid from Paper Mill Effluent on Soil Properties, Soil Microbiome, and Growth of Malus hupehensis Rehd. Seedlings under Replant Conditions. ACS OMEGA 2021; 6:24027-24038. [PMID: 34568681 PMCID: PMC8459433 DOI: 10.1021/acsomega.1c03201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Indexed: 06/13/2023]
Abstract
In this study, the potential regulatory effects of fulvic acid extracted from paper mill effluent (PFA) in apple replant disease (ARD) were investigated through a comprehensive experimental evaluation of the effects of PFA on soil properties, growth inhibition of apple replant pathogens, and growth of replanted Malus hupehensis Rehd. seedlings. PFA with a relatively lower molecular weight was mainly composed of carbohydrates, lignin derivatives, and polysaccharides and was rich in functional groups such as carboxyl and phenolic hydroxyl groups. Treatment with PFA dosages ranging from 2 to 3 g/pot significantly increased available phosphorus (P) in soil by 47.5 to 57.5% when compared with the control without PFA, indicating that PFA had a positive effect in activating P. In addition, PFA stimulated the growth of replanted seedlings by promoting root elongation, enhancing leaf photosynthesis, and increasing the activity of root antioxidant enzymes including superoxide dismutase, peroxidase, and catalase. However, no convincing evidence was found that application of different dosages of PFA had remarkable effects on soil pH, inorganic nitrogen, available potassium, organic matter, and the numbers of bacteria and fungi. Notably, PFA had no effect on the copy number of the main pathogenic fungi causing ARD, including Fusarium oxysporum, Fusarium solani, Fusarium proliferatum, and Fusarium moniliforme. Overall, PFA can alleviate ARD to a certain extent mainly through its effects on improving the resilience of replanted young seedlings rather than by affecting soil microorganisms or providing nutrients.
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Affiliation(s)
- Xiaoqi Wang
- College
of Horticulture Science and Engineering, State Key Laboratory of Crop
Biology, Shandong Agricultural University, Tai’an 271018, China
- National
Engineering Laboratory for Efficient Utilization of Soil and Fertilizer
Resources, College of Recourses and Environment, Shandong Agricultural University, Tai’an 271018, China
| | - Yuanyuan Yao
- National
Engineering Laboratory for Efficient Utilization of Soil and Fertilizer
Resources, College of Recourses and Environment, Shandong Agricultural University, Tai’an 271018, China
| | - Guiwei Wang
- College
of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Jinzhao Ma
- Shandong
Provincial Key Laboratory of Eco-Environmental Science for Yellow
River Delta, Binzhou University, Binzhou 256603, China
| | - Chengmiao Yin
- College
of Horticulture Science and Engineering, State Key Laboratory of Crop
Biology, Shandong Agricultural University, Tai’an 271018, China
| | - Xuesen Chen
- College
of Horticulture Science and Engineering, State Key Laboratory of Crop
Biology, Shandong Agricultural University, Tai’an 271018, China
| | - Zhiquan Mao
- College
of Horticulture Science and Engineering, State Key Laboratory of Crop
Biology, Shandong Agricultural University, Tai’an 271018, China
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18
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Babin D, Leoni C, Neal AL, Sessitsch A, Smalla K. Editorial to the Thematic Topic "Towards a more sustainable agriculture through managing soil microbiomes". FEMS Microbiol Ecol 2021; 97:6321563. [PMID: 34263312 DOI: 10.1093/femsec/fiab094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 06/22/2021] [Indexed: 11/15/2022] Open
Affiliation(s)
- Doreen Babin
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Carolina Leoni
- Instituto Nacional de Investigación Agropecuaria (INIA), Programa de Producción y Sustentabilidad Ambiental, Estación Experimental INIA Las Brujas, Ruta 48 Km 10, 90200 Rincón del Colorado, Canelones, Uruguay
| | - Andrew L Neal
- Department of Sustainable Agriculture Sciences, Rothamsted Research, North Wyke, Devon EX20 2SB, United Kingdom
| | - Angela Sessitsch
- AIT Austrian Institute of Technology, Center for Health and Bioresources, Bioresources Unit, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
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