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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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2
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Topalović O, Geisen S. Nematodes as suppressors and facilitators of plant performance. THE NEW PHYTOLOGIST 2023; 238:2305-2312. [PMID: 37010088 DOI: 10.1111/nph.18925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/26/2023] [Indexed: 05/19/2023]
Abstract
Plant-nematode interactions are mainly considered from the negative aspect with a focus on plant-parasitic nematodes (PPNs), which is justified considering the agronomic losses caused by PPNs. Despite the fact that PPNs are outnumbered by nonparasitic free-living nematodes (FLNs), the functional importance of FLNs, especially with regard to plant performance, remains largely unknown. Here, we provide a comprehensive overview and most recent insights into soil nematodes by showing direct and indirect links of both PPNs and FLNs with plant performance. We especially emphasize the knowledge gaps and potential of FLNs as important indirect players in driving plant performance such as stimulating the resistance to pests via improving the disease suppressive activity of the rhizobiome. Together, we present a holistic view of soil nematodes as positive and negative contributors to plant performance, accentuating the positive but underexplored role of FLNs.
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Affiliation(s)
- Olivera Topalović
- Section of Terrestrial Ecology, University of Copenhagen, Copenhagen, DK-2100, Denmark
- Department of Nematology, Wageningen University and Research, Wageningen, 6708PB, the Netherlands
| | - Stefan Geisen
- Department of Nematology, Wageningen University and Research, Wageningen, 6708PB, the Netherlands
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3
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Ajeethan N, Ali S, Fuller KD, Abbey L, Yurgel SN. Apple Root Microbiome as Indicator of Plant Adaptation to Apple Replant Diseased Soils. Microorganisms 2023; 11:1372. [PMID: 37374874 DOI: 10.3390/microorganisms11061372] [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: 03/12/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 06/29/2023] Open
Abstract
The tree fruit industry in Nova Scotia, Canada, is dominated by the apple (Malus domestica) sector. However, the sector is faced with numerous challenges, including apple replant disease (ARD), which is a well-known problem in areas with intensive apple cultivation. A study was performed using 16S rRNA/18S rRNA and 16S rRNA/ITS2 amplicon sequencing to assess soil- and root-associated microbiomes, respectively, from mature apple orchards and soil microbiomes alone from uncultivated soil. The results indicated significant (p < 0.05) differences in soil microbial community structure and composition between uncultivated soil and cultivated apple orchard soil. We identified an increase in the number of potential pathogens in the orchard soil compared to uncultivated soil. At the same time, we detected a significant (p < 0.05) increase in relative abundances of several potential plant-growth-promoting or biocontrol microorganisms and non-fungal eukaryotes capable of promoting the proliferation of bacterial biocontrol agents in orchard soils. Additionally, the apple roots accumulated several potential PGP bacteria from Proteobacteria and Actinobacteria phyla, while the relative abundances of fungal taxa with the potential to contribute to ARD, such as Nectriaceae and plant pathogenic Fusarium spp., were decreased in the apple root microbiome compared to the soil microbiome. The results suggest that the health of a mature apple tree can be ascribed to a complex interaction between potential pathogenic and plant growth-promoting microorganisms in the soil and on apple roots.
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Affiliation(s)
- Nivethika Ajeethan
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro NS B2N 5E3, Canada
- Department of Biosystems Technology, Faculty of Technology, University of Jaffna, Kilinochchi 44000, Sri Lanka
| | - Shawkat Ali
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville NS B4N 1J5, Canada
| | - Keith D Fuller
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville NS B4N 1J5, Canada
| | - Lord Abbey
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro NS B2N 5E3, Canada
| | - Svetlana N Yurgel
- USDA, ARS, Grain Legume Genetics and Physiology Research Unit, Prosser, WA 99350, USA
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Duan YN, Jiang WT, Zhang R, Chen R, Chen XS, Yin CM, Mao ZQ. Discovery of Fusarium proliferatum f. sp. malus domestica Causing Apple Replant Disease in China. PLANT DISEASE 2022; 106:2958-2966. [PMID: 35306841 DOI: 10.1094/pdis-12-21-2802-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Apple replant disease (ARD) is the most serious threat facing the apple industry globally. ARD is mainly manifested as decreased plant growth, serious root rot disease, and considerable yield loss. Microbial factors are the dominant factors leading to the occurrence of ARD. Research on soil-borne pathogenic fungi leading to the occurrence of ARD in China is limited. In the present study, we selected 16 replanting orchards from the Northwest Loess region and around the Bohai Gulf. Diseased roots and rhizosphere soil from healthy apple trees and trees showing ARD symptoms were sampled at random. High-throughput sequencing was used to study the fungal communities in the rhizosphere soil, which showed that the composition of the rhizosphere soil fungal community of ARD-symptomatic and healthy apple trees was different. Nectriaceae at the family level and Fusarium at the genus level dominated the rhizosphere soil fungal community in the two regions, while for healthy apple trees, the relative abundance of Mortierella, Minimedusa, Tetracladium, and Chaetomium was higher. Tissue separation and serial dilution were used to separate fungi, and a total of 89 genera and 219 species were obtained, most of which were Fusarium. Fusarium was further confirmed to be the most abundant pathogen species leading to the occurrence of ARD in China through pathogenicity assays. A pathogenicity assay was carried out by the dip-and-cut technique using different host plants. It was found that Fusarium MR5 showed strong aggressiveness to apple rootstocks. Diseased seedlings specifically exhibited chlorosis of the leaves, browning from the edge of the leaf, followed by rolling and yellowing of the leaves, resulting in wilting and eventually death. Strain MR5 was preliminarily identified as F. proliferatum according to the morphological and cultural characteristics. A maximum likelihood analysis of identities based on six gene sequence (ITS, TUB2, IGS, mtSSU, RPB2, and the TEF gene) alignments between the MR5 strain and other strains showed 99 to 100% homology with F. proliferatum. Based on our test results, strain MR5 was identified as F. proliferatum f. sp. malus domestica, which is of great significance for finding new measures to control ARD in China.
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Affiliation(s)
- Y N Duan
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong 271018, China
| | - W T Jiang
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong 271018, China
| | - R Zhang
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong 271018, China
| | - R Chen
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong 271018, China
| | - X S Chen
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong 271018, China
| | - C M Yin
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong 271018, China
| | - Z Q Mao
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong 271018, China
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Meloidogyne incognita Management Using Fumigant and Non-fumigant Nematicides on Sweet Potato. J Nematol 2022; 54:20220026. [PMID: 35975221 PMCID: PMC9338709 DOI: 10.2478/jofnem-2022-0026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Indexed: 11/20/2022] Open
Abstract
Abstract
Southern root-knot nematode (SRKN, Meloidogyne incognita) is a major pest of sweet potato, and nematicides are needed to manage this nematode. The objectives of this study were to assess the efficacy of fluazaindolizine, a new non-fumigant nematicide, in comparison with the fumigant nematicide 1,3-dichloropropene (1,3-D) and non-fumigant nematicides fluopyram and oxamyl for (1) SRKN management, (2) impacts on free-living nematodes, and (3) sweet potato yield in field trials. Among all nematicides, 1,3-D at 84 kg/ha most consistently (2 of 3 years) managed SRKN soil populations and improved yield. Fluazaindolizine at 2.24 kg/ha and fluazindolizine at 1.12 kg/ha plus oxamyl at 2.14 kg/ha managed SRKN populations and improved yield in 1 of 3 years, whereas fluazaindolizine alone at 1.12 kg/ha only decreased SRKN populations. Fluopyram at 238 g/ha did not affect SRKN or yield. Nematicide application also had non-target effects on free-living nematodes with 1,3-D reducing abundances relative to untreated most frequently (2018 and 2020), but other nematicides also reducing free-living nematode abundances in 2020. In summary, 1,3-D is the most consistent option for SRKN control on sweet potato, but fluazaindolizine, oxamyl or combinations of the two products can also be effective.
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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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7
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Reim S, Winkelmann T, Cestaro A, Rohr AD, Flachowsky H. Identification of Candidate Genes Associated With Tolerance to Apple Replant Disease by Genome-Wide Transcriptome Analysis. Front Microbiol 2022; 13:888908. [PMID: 35615498 PMCID: PMC9125221 DOI: 10.3389/fmicb.2022.888908] [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: 03/03/2022] [Accepted: 03/29/2022] [Indexed: 12/03/2022] Open
Abstract
Apple replant disease (ARD) is a worldwide economic risk in apple cultivation for fruit tree nurseries and fruit growers. Several studies on the reaction of apple plants to ARD are documented but less is known about the genetic mechanisms behind this symptomatology. RNA-seq analysis is a powerful tool for revealing candidate genes that are involved in the molecular responses to biotic stresses in plants. The aim of our work was to find differentially expressed genes in response to ARD in Malus. For this, we compared transcriptome data of the rootstock ‘M9’ (susceptible) and the wild apple genotype M. ×robusta 5 (Mr5, tolerant) after cultivation in ARD soil and disinfected ARD soil, respectively. When comparing apple plantlets grown in ARD soil to those grown in disinfected ARD soil, 1,206 differentially expressed genes (DEGs) were identified based on a log2 fold change, (LFC) ≥ 1 for up– and ≤ −1 for downregulation (p < 0.05). Subsequent validation revealed a highly significant positive correlation (r = 0.91; p < 0.0001) between RNA-seq and RT-qPCR results indicating a high reliability of the RNA-seq data. PageMan analysis showed that transcripts of genes involved in gibberellic acid (GA) biosynthesis were significantly enriched in the DEG dataset. Most of these GA biosynthesis genes were associated with functions in cell wall stabilization. Further genes were related to detoxification processes. Genes of both groups were expressed significantly higher in Mr5, suggesting that the lower susceptibility to ARD in Mr5 is not due to a single mechanism. These findings contribute to a better insight into ARD response in susceptible and tolerant apple genotypes. However, future research is needed to identify the defense mechanisms, which are most effective for the plant to overcome ARD.
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Affiliation(s)
- Stefanie Reim
- Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Dresden, Germany
- *Correspondence: Stefanie Reim,
| | - Traud Winkelmann
- Woody Plant and Propagation Physiology Section, Institute of Horticultural Production Systems, Leibniz University Hannover, Hanover, Germany
| | - Alessandro Cestaro
- Computational Biology Unit, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Annmarie-Deetja Rohr
- Woody Plant and Propagation Physiology Section, Institute of Horticultural Production Systems, Leibniz University Hannover, Hanover, Germany
| | - Henryk Flachowsky
- Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Dresden, Germany
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8
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Wang L, Wang Y, Xiu W, Tan B, Li G, Zhao J, Yang D, Zhang G, Zhang Y. Responses of Soil Microbial and Nematode Communities to Various Cover Crop Patterns in a Tea Garden of China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19052695. [PMID: 35270386 PMCID: PMC8910492 DOI: 10.3390/ijerph19052695] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 02/13/2022] [Indexed: 01/27/2023]
Abstract
As one of the typical farmland ecosystems, tea gardens are of vital importance in China. The purpose of this study was to quantify the dynamic of soil properties, soil microbial diversity, and nematodes, as affected by various cover crop patterns in a Tanjiawan tea garden in Hubei Province, China. Four cover crop patterns were established as following: naturally covered of bare land and mixed planting with two species, four species, and eight species. The results revealed that soil organic matter, pH, and total phosphorous content were significantly related to cover crop patterns. The number of nematodes increased with cover crop diversity, and the percentage of plant parasitic nematodes in cover crop treatments was lower than in naturally covered bare land. A higher diversity of cover crops increased the number of bacterivores and fungivores, thereby enhancing the bacterial decomposition pathway of soil organic matter. Both soil nematodes and microbial communities showed significant seasonal changes under different cover crop patterns. The soil food webs were more stable and mature under cover crops with two species and four species. Combined with the results of a structural equation model, we found that soil properties, characterized by the total nitrogen, available phosphorus, NO3--N, and soil organic matter, were significantly correlated with soil nematodes and microbial communities. In addition, acterivores and plant parasites were significantly negatively correlated with omnivores/predators. Our results implied that soil properties and seasonal changes influence the relationships between cover crops, soil nematodes, and microbial communities. These findings provide a theoretical basis for future studies on interactions between soil properties, soil microorganisms, and nematodes in tea gardens.
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Affiliation(s)
- Lili Wang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; (Y.W.); (W.X.); (B.T.); (G.L.); (J.Z.); (D.Y.); (G.Z.); (Y.Z.)
- Key Laboratory of Original Agro-environment Pollution Prevention and Control of Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
- Correspondence: ; Tel.: +86-22-23611803
| | - Yang Wang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; (Y.W.); (W.X.); (B.T.); (G.L.); (J.Z.); (D.Y.); (G.Z.); (Y.Z.)
- Key Laboratory of Original Agro-environment Pollution Prevention and Control of Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Weiming Xiu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; (Y.W.); (W.X.); (B.T.); (G.L.); (J.Z.); (D.Y.); (G.Z.); (Y.Z.)
- Key Laboratory of Original Agro-environment Pollution Prevention and Control of Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Bingchang Tan
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; (Y.W.); (W.X.); (B.T.); (G.L.); (J.Z.); (D.Y.); (G.Z.); (Y.Z.)
- Key Laboratory of Original Agro-environment Pollution Prevention and Control of Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Gang Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; (Y.W.); (W.X.); (B.T.); (G.L.); (J.Z.); (D.Y.); (G.Z.); (Y.Z.)
- Key Laboratory of Original Agro-environment Pollution Prevention and Control of Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Jianning Zhao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; (Y.W.); (W.X.); (B.T.); (G.L.); (J.Z.); (D.Y.); (G.Z.); (Y.Z.)
- Key Laboratory of Original Agro-environment Pollution Prevention and Control of Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Dianlin Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; (Y.W.); (W.X.); (B.T.); (G.L.); (J.Z.); (D.Y.); (G.Z.); (Y.Z.)
- Key Laboratory of Original Agro-environment Pollution Prevention and Control of Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Guilong Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; (Y.W.); (W.X.); (B.T.); (G.L.); (J.Z.); (D.Y.); (G.Z.); (Y.Z.)
- Key Laboratory of Original Agro-environment Pollution Prevention and Control of Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Yanjun Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; (Y.W.); (W.X.); (B.T.); (G.L.); (J.Z.); (D.Y.); (G.Z.); (Y.Z.)
- Key Laboratory of Original Agro-environment Pollution Prevention and Control of Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
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Kanfra X, Wrede A, Moll J, Heuer H. Nematode-Microbe Complexes in Soils Replanted with Apple. Microorganisms 2022; 10:microorganisms10010157. [PMID: 35056606 PMCID: PMC8780120 DOI: 10.3390/microorganisms10010157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 02/01/2023] Open
Abstract
Apple replant disease is a severe problem in orchards and tree nurseries. Evidence for the involvement of a nematode–microbe disease complex was reported. To search for this complex, plots with a history of apple replanting, and control plots cultivated for the first time with apple were sampled in two fields in two years. Shoot weight drastically decreased with each replanting. Amplicon sequencing of the nematode community and co-extracted fungal and bacterial communities revealed significant differences between replanted and control plots. Free-living nematodes of the genera Aphelenchus and Cephalenchus and an unidentified Dorylaimida were associated with replanted plots, as indicated by linear discriminant analysis effect size. Among the co-extracted fungi and bacteria, Mortierella and Methylotenera were most indicative of replanting. Some genera, mostly Rhabditis, Streptomyces and a fungus belonging to the Chaetomiaceae indicated healthy control plots. Isolating and investigating the putative disease complexes will help to understand and alleviate stress-induced root damage of apple in replanted soil.
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Affiliation(s)
- Xorla Kanfra
- Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany;
| | - Andreas Wrede
- Department of Horticulture, Landwirtschaftskammer Schleswig-Holstein, 25373 Ellerhoop, Germany;
| | - Julia Moll
- Helmholtz Centre for Environmental Research—UFZ, Department of Soil Ecology, 06120 Halle (Saale), Germany;
| | - Holger Heuer
- Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany;
- Correspondence:
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10
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Chen L, Li J, Zhu Y, Guo L, Ji R, Miao Y, Guo L, Du H, Liu D. Caffeic Acid, an Allelochemical in Artemisia argyi, Inhibits Weed Growth via Suppression of Mitogen-Activated Protein Kinase Signaling Pathway and the Biosynthesis of Gibberellin and Phytoalexin. FRONTIERS IN PLANT SCIENCE 2022; 12:802198. [PMID: 35069660 PMCID: PMC8770944 DOI: 10.3389/fpls.2021.802198] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
Artemisia argyi is widely distributed in Asia, and it often becomes the dominant population in the field because of its strong ecological niche competitiveness. Allelochemicals secreted by plants are generally considered an important reason for their dominance in ecological competition. In this study, the allelochemicals in A. argyi were screened by a series of experiments and their mechanisms were explored via transcriptomics. First, the inhibitory effects of A. argyi on Echinochloa crusgalli, Setaria viridis, Portulaca oleracea and Amaranthus retroflexus were evaluated. Then, we carried out a qualitative and quantitative analysis of the chemical composition of the aqueous extract of A. argyi to screen for potential allelochemicals that can inhibit weed growth. Four potential allelochemicals were quantified: neochlorogenic acid (5-CQA), chlorogenic acid (3-CQA), cryptochlorogenic acid (4-CQA), and caffeic acid (CA). Coincidentally, their allelopathic effects on weeds seemed to be identical to their content, in the order CA>4-CQA>5-CQA>3-CQA. These findings suggested that CA might be the main allelopathic compound in the aqueous extract of A. argyi. Subsequently, the allelopathic effect and molecular mechanism of CA on S. viridis leaves were investigated. The physiological results showed that CA significantly induced reactive oxygen species (ROS) production, led to malondialdehyde (MDA) accumulation, and disrupted enzyme activities (POD, SOD, CAT) in S. viridis leaves. Moreover, transcriptome results revealed that CA inhibited S. viridis growth by downregulating multiple genes involved in gibberellin (GA) and phytoalexin biosynthesis and Mitogen-activated protein kinase (MAPK) signaling pathways. In addition, differentially expressed genes (DEGs) related to the biosynthesis and signaling pathways of phytohormones were verified by Quantitative Real-Time PCR (RT-qPCR). Taken together, this study may be the first to identify allelochemicals and explore their molecular mechanism about A. argyi. Importantly, the ecological advantages of A. argyi could be applied to ecological regulation and the development of botanical herbicides.
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Affiliation(s)
- Le Chen
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan, China
| | - Jinxin Li
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan, China
| | - Yunyun Zhu
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan, China
| | - Lujuan Guo
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan, China
| | - Rongsheng Ji
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan, China
| | - Yuhuan Miao
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Hongzhi Du
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan, China
| | - Dahui Liu
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan, China
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11
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Khan AR, Wicaksono WA, Ott NJ, Poret-Peterson AT, Browne GT. Characterization of soils conducive and non-conducive to Prunus replant disease. PLoS One 2021; 16:e0260394. [PMID: 34890412 PMCID: PMC8664177 DOI: 10.1371/journal.pone.0260394] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/09/2021] [Indexed: 01/04/2023] Open
Abstract
Successive orchard plantings of almond and other Prunus species exhibit reduced growth and yield in many California soils. This phenomenon, known as Prunus replant disease (PRD), can be prevented by preplant soil fumigation or anaerobic soil disinfestation, but its etiology is poorly understood and its incidence and severity are hard to predict. We report here on relationships among physicochemical variables, microbial community structure, and PRD induction in 25 diverse replant soils from California. In a greenhouse bioassay, soil was considered to be "PRD-inducing" when growth of peach seedlings in it was significantly increased by preplant fumigation and pasteurization, compared to an untreated control. PRD was induced in 18 of the 25 soils, and PRD severity correlated positively with soil exchangeable-K, pH, %clay, total %N, and electrical conductivity. The structure of bacterial, fungal, and oomycete communities differed significantly between the PRD-inducing and non-inducing soils, based on PERMANOVA of Bray Curtis dissimilarities. Bacterial class MB-A2-108 of phylum Actinobacteria had high relative abundances among PRD-inducing soils, while Bacteroidia were relatively abundant among non-inducing soils. Among fungi, many ASVs classified only to kingdom level were relatively abundant among PRD-inducing soils whereas ASVs of Trichoderma were relatively abundant among non-inducing soils. Random forest classification effectively discriminated between PRD-inducing and non-inducing soils, revealing many bacterial ASVs with high explanatory values. Random forest regression effectively accounted for PRD severity, with soil exchangeable-K and pH having high predictive value. Our work revealed several biotic and abiotic variables worthy of further examination in PRD etiology.
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Affiliation(s)
- Abdur R. Khan
- Department of Plant Pathology, University of California, Davis, California, United States of America
| | - Wisnu A. Wicaksono
- Department of Plant Pathology, University of California, Davis, California, United States of America
| | - Natalia J. Ott
- USDA-ARS Crops Pathology and Genetics Research Unit, Davis, California, United States of America
| | - Amisha T. Poret-Peterson
- USDA-ARS Crops Pathology and Genetics Research Unit, Davis, California, United States of America
| | - Greg T. Browne
- USDA-ARS Crops Pathology and Genetics Research Unit, Davis, California, United States of America
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12
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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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13
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Alleviation of Nematode-Mediated Apple Replant Disease by Pre-Cultivation of Tagetes. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7110433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Apple replant disease (ARD) is a severe problem in orchards and tree nurseries caused by yet unknown soil biota that accumulate over replanting cycles. This study tested the contribution of nematodes to ARD, and cultivation of Tagetes as a control option. In a pot experiment, Tagetes patula or Tagetes tenuifolia were grown in ARD soil, incorporated or removed. Nematodes extracted from untreated ARD soil and washed on 20-µm sieves induced ARD symptoms when inoculated to apple plantlets growing in a sterile substrate. In contrast, nematodes from Tagetes treated ARD soil did not reduce root growth compared to uninoculated plants, irrespective of Tagetes species and incorporation. In plots of five apple tree nurseries or orchards, either Tagetes or grass was grown on ARD soil. Nematodes extracted from the grass plots and inoculated to apple plantlets significantly reduced plant growth compared to nematodes from Tagetes plots for all five farms. Apple rootstocks showed overall a significantly higher increase in shoot base diameter when grown on Tagetes-treated plots compared to grass plots, while this effect differed among farms. Plant-parasitic nematodes were too low in abundance to explain plant damage. In conclusion, Tagetes alleviated ARD by changing the nematode community in soil.
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14
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Balbín-Suárez A, Lucas M, Vetterlein D, Sørensen SJ, Winkelmann T, Smalla K, Jacquiod S. Exploring microbial determinants of apple replant disease (ARD): a microhabitat approach under split-root design. FEMS Microbiol Ecol 2021; 96:5921174. [PMID: 33045057 DOI: 10.1093/femsec/fiaa211] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/09/2020] [Indexed: 12/13/2022] Open
Abstract
Apple replant disease (ARD) occurs worldwide in apple orchards and nurseries and leads to a severe growth and productivity decline. Despite research on the topic, its causality remains unclear. In a split-root experiment, we grew ARD-susceptible 'M26' apple rootstocks in different substrate combinations (+ARD: ARD soil; -ARD: gamma-irradiated ARD soil; and Control: soil with no apple history). We investigated the microbial community composition by 16S rRNA gene amplicon sequencing (bacteria and archaea) along the soil-root continuum (bulk soil, rhizosphere and rhizoplane). Significant differences in microbial community composition and structure were found between +ARD and -ARD or +ARD and Control along the soil-root continuum, even for plants exposed simultaneously to two different substrates (-ARD/+ARD and Control/+ARD). The substrates in the respective split-root compartment defined the assembly of root-associated microbial communities, being hardly influenced by the type of substrate in the respective neighbor compartment. Root-associated representatives from Actinobacteria were the most dynamic taxa in response to the treatments, suggesting a pivotal role in ARD. Altogether, we evidenced an altered state of the microbial community in the +ARD soil, displaying altered alpha- and beta-diversity, which in turn will also impact the normal development of apple rhizosphere and rhizoplane microbiota (dysbiosis), concurring with symptom appearance.
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Affiliation(s)
- Alicia Balbín-Suárez
- Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
| | - Maik Lucas
- Department of Soil System Science, Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Str. 4, 06120 Halle/Saale, Germany.,Soil Science, Martin-Luther-University Halle-Wittenberg, Von-Seckendorff-Platz 3, 06120 Halle/Saale, Germany
| | - Doris Vetterlein
- Department of Soil System Science, Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Str. 4, 06120 Halle/Saale, Germany.,Soil Science, Martin-Luther-University Halle-Wittenberg, Von-Seckendorff-Platz 3, 06120 Halle/Saale, Germany
| | - Søren J Sørensen
- University of Copenhagen, Department of Biology, Section of Microbiology, Copenhagen, Denmark
| | - Traud Winkelmann
- Institute of Horticultural Production Systems, Section Woody Plant and Propagation Physiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Kornelia Smalla
- Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
| | - Samuel Jacquiod
- University of Copenhagen, Department of Biology, Section of Microbiology, Copenhagen, Denmark.,Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne Franche-Comté, Dijon, France
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15
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Bacterial profiling of Haemonchus contortus gut microbiome infecting Dohne Merino sheep in South Africa. Sci Rep 2021; 11:5905. [PMID: 33723324 PMCID: PMC7961046 DOI: 10.1038/s41598-021-85282-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/26/2021] [Indexed: 11/09/2022] Open
Abstract
A metagenomic approach was used to study the gut microbiome of Haemonchus contortus field strains and that of its predilection site, the abomasum of Dohne Merino sheep. The abomasum contents and H. contortus were collected from 10 naturally infected Dohne Merino sheep. The H. contortus specimens were classified and sexually differentiated using morphometric characters and was further confirmed through molecular identification. We investigated differences and similarities between the bacterial composition of the adult male and female H. contortus gut microbiomes, which were both dominated by bacteria from the Escherichia, Shigella, Vibrio and Halomonas genera. Major abundance variations were identified between the shared adult male and female H. contortus microbiomes. The results also revealed that Succiniclasticum, Rikenellaceae RC9 gut group and Candidatus Saccharimonas were the predominant genera in the Dohne Merino abomasum. This study provides insight into the highly diverse bacterial composition of the H. contortus gut microbiome and the Dohne Merino abomasum which needs to be studied further to explore the complex interactions of different gastrointestinal nematode microbiomes with the host.
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16
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Functional Diversity of Soil Nematodes in Relation to the Impact of Agriculture—A Review. DIVERSITY 2021. [DOI: 10.3390/d13020064] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The analysis of the functional diversity of soil nematodes requires detailed knowledge on theoretical aspects of the biodiversity–ecosystem functioning relationship in natural and managed terrestrial ecosystems. Basic approaches applied are reviewed, focusing on the impact and value of soil nematode diversity in crop production and on the most consistent external drivers affecting their stability. The role of nematode trophic guilds in two intensively cultivated crops are examined in more detail, as representative of agriculture from tropical/subtropical (banana) and temperate (apple) climates. The multiple facets of nematode network analysis, for management of multitrophic interactions and restoration purposes, represent complex tasks that require the integration of different interdisciplinary expertise. Understanding the evolutionary basis of nematode diversity at the field level, and its response to current changes, will help to explain the observed community shifts. Integrating approaches based on evolutionary biology, population genetics and ecology can quantify the contribution of nematode fauna to fundamental soil functions. These include carbon transformation, nutrient cycling, pest control and disease transmission. In conclusion, different facets of nematode diversity such as trophic groups, life history traits, variability in body size and/or taxa identities in combination with DNA-based techniques are needed in order to disclose nematode–soil–ecosystem functioning relationships. Further experimental studies are required to define locally adapted and sustainable management practices, through ecosystem-based approaches and nature-based solutions.
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17
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Shi G, Sun H, Calderón-Urrea A, Jia X, Yang H, Su G. Soil Fungal Diversity Loss and Appearance of Specific Fungal Pathogenic Communities Associated With the Consecutive Replant Problem (CRP) in Lily. Front Microbiol 2020; 11:1649. [PMID: 32760386 PMCID: PMC7373732 DOI: 10.3389/fmicb.2020.01649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 06/25/2020] [Indexed: 02/03/2023] Open
Abstract
Edible lily (Lilium davidii var. unicolor) has economic value in China, particularly in Gansu Province, due to its uses as food and in gardening. Edible lily is usually cultivated in a long-term continuous monoculture resulting in the so-called consecutive replant problem (CRP), which is associated with severe soil degradation and significant yield and quality losses. This study was conducted to investigate the fungal community structure and specific fungal members related to lily's CRPs using metabarcoding analysis. Fungal diversity of rhizosphere soil was analyzed by high-throughput DNA sequencing (Miseq) of samples collected in fields at 0, 3, 6, and 9 replant years (L0, L3, L6, and L9, respectively). The results show that long-term replanting significantly decreased both soil fungal diversity and abundance at the OTUs levels. Furthermore, replanting altered the soil microbial communities, where 4 to 5 years of replanting is a key transition period for substantial change of fungal community structure, resulting in new fungal community structures in L6 and L9 compared to in L0 and L3. The fungal diversity loss and fungal community structure simplification contributes to the negative effect of replanting in lily, and after 6 years of replanting, accumulation of highly abundant pathogenic fungal genera and depletion of the putative plant-beneficial fungal genera exacerbate the lily CRP. In addition, changes in the soil physiochemical properties strongly contributes to the new structure of fungal communities, and the genera Cryptococcus and Guehomyces could be regarded as potential indicators to monitor and manage sustainable soil health in the lily cropping system.
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Affiliation(s)
- Guiying Shi
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Hongqiang Sun
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Alejandro Calderón-Urrea
- College of Plant Protection, Gansu Agricultural University, Lanzhou, China
- Department of Biology, College of Science and Mathematics, California State University, Fresno, Fresno, CA, United States
| | - Xixia Jia
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Hongyu Yang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Guoli Su
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
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18
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Abstract
Replant disease is a soil (micro-) biome-based, harmfully-disturbed physiological and morphological reaction of plants to replanting similar cultures on the same sites by demonstrating growth retardation and leading to economic losses especially in Rosaceae plant production. Commonly, replant disease is overcome by soil fumigation with toxic chemicals. With chemical soil fumigation being restricted in many countries, other strategies are needed. Biofumigation, which is characterized by the incorporation of Brassicaceae plant materials into soil, is a promising method. We review the potential of biofumigation in the fight against replant disease. Biofumigation using optimized Brassicaceae seed meal compositions in combination with replant disease tolerant plant genotypes shows promising results, but the efficacy is still soil and site-dependent. Therefore, future studies should address the optimal timing as well as amount and type of incorporated plant material and environmental conditions during incubation in dependence of the soil physical and chemical characteristics.
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19
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Radl V, Winkler JB, Kublik S, Yang L, Winkelmann T, Vestergaard G, Schröder P, Schloter M. Reduced microbial potential for the degradation of phenolic compounds in the rhizosphere of apple plantlets grown in soils affected by replant disease. ENVIRONMENTAL MICROBIOME 2019; 14:8. [PMID: 33902732 PMCID: PMC8204438 DOI: 10.1186/s40793-019-0346-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/07/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Apple replant disease (ARD) is a syndrome that occurs in areas where apple plants or closely related species have been previously cultivated. Even though ARD is a well-known phenomenon, which has been observed in different regions worldwide and occurs independent of the soil type, its causes still remain unclear. RESULTS As expected, the biomass of plants grown in replant soil was significantly lower compared to those grown in control (virgin) soil. A shotgun metagenome analysis showed a clear differentiation between the rhizosphere and bulk soil compartments independent from the soil used. However, significant differences associated with apple replant disease were only observed in the rhizosphere compartment, for which we detected changes in the abundance of major bacterial genera. Interestingly, reads assigned to Actinobacteria were significantly reduced in relative abundance in rhizosphere samples of the soil affected by replant disease. Even though reads assigned to pathogenic fungi were detected, their relative abundance was low and did not differ significantly between the two different soils. Differences in microbiome structure also resulted in shifts in functional pattern. We observed an increase in genes related to stress sensing in the rhizosphere of soils affected by replant disease, whereas genes linked to nutrient sensing and uptake dominated in control soils. Moreover, we observed a lower abundance of genes coding for enzymes which trigger the degradation of aromatic compounds in rhizosphere of soils affected by replant disease, which is probably connected with higher concentration of phenolic compounds, generally associated with disease progression. CONCLUSIONS Our study shows, for the first time, how apple replanting affects soil functioning by altering the soil microbiome. Particularly, the decrease in the abundance of genes which code for enzymes catalyzing the degradation of aromatic compounds, observed in the rhizosphere of plants grown in soil affected by apple replant disease, is of interest. Apple rootstocks are known to synthetize many phenolic compounds, including defense related phytoalexins, which have been considered for long to be connected with the emergence of replant disease. The knowledge gained in this study might help to develop targeted strategies to overcome or at least reduce the effects of ARD symptoms.
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Affiliation(s)
- Viviane Radl
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Jana Barbro Winkler
- Research Unit Environmental Simulations, Helmholtz Zentrum München, Munich, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Luhua Yang
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Traud Winkelmann
- Woody Plant and Propagation Physiology Section, Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hanover, Germany
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | - Peter Schröder
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
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20
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Reim S, Rohr AD, Winkelmann T, Weiß S, Liu B, Beerhues L, Schmitz M, Hanke MV, Flachowsky H. Genes Involved in Stress Response and Especially in Phytoalexin Biosynthesis Are Upregulated in Four Malus Genotypes in Response to Apple Replant Disease. FRONTIERS IN PLANT SCIENCE 2019; 10:1724. [PMID: 32180775 PMCID: PMC7059805 DOI: 10.3389/fpls.2019.01724] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 12/09/2019] [Indexed: 05/17/2023]
Abstract
Apple replant disease (ARD) is a soil-borne disease, which is of particular importance for fruit tree nurseries and fruit growers. The disease manifests by a poor vegetative development, stunted growth, and reduced yield in terms of quantity and quality, if apple plants (usually rootstocks) are replanted several times at the same site. Genotype-specific differences in the reaction of apple plants to ARD are documented, but less is known about the genetic mechanisms behind this symptomatology. Recent transcriptome analyses resulted in a number of candidate genes possibly involved in the plant response. In the present study, the expression of 108 selected candidate genes was investigated in root and leaf tissue of four different apple genotypes grown in untreated ARD soil and ARD soil disinfected by γ-irradiation originating from two different sites in Germany. Thirty-nine out of the 108 candidate genes were differentially expressed in roots by taking a p-value of < 0.05 and a fold change of > 1.5 as cutoff. Sixteen genes were more than 4.5-fold upregulated in roots of plants grown in ARD soil. The four genes MNL2 (putative mannosidase); ALF5 (multi antimicrobial extrusion protein); UGT73B4 (uridine diphosphate (UDP)-glycosyltransferase 73B4), and ECHI (chitin-binding) were significantly upregulated in roots. These genes seem to be related to the host plant response to ARD, although they have never been described in this context before. Six of the highly upregulated genes belong to the phytoalexin biosynthesis pathway. Their genotype-specific gene expression pattern was consistent with the phytoalexin content measured in roots. The biphenyl synthase (BIS) genes were found to be useful as early biomarkers for ARD, because their expression pattern correlated well with the phenotypic reaction of the Malus genotypes investigated.
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Affiliation(s)
- Stefanie Reim
- Institute for Breeding Research on Fruit Crops, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Dresden, Germany
| | - Annmarie-Deetja Rohr
- Institute of Horticultural Production Systems, Woody Plant and Propagation Physiology Section, Gottfried Wilhelm Leibniz University Hannover, Hanover, Germany
| | - Traud Winkelmann
- Institute of Horticultural Production Systems, Woody Plant and Propagation Physiology Section, Gottfried Wilhelm Leibniz University Hannover, Hanover, Germany
- *Correspondence: Traud Winkelmann,
| | - Stefan Weiß
- Institute of Horticultural Production Systems, Woody Plant and Propagation Physiology Section, Gottfried Wilhelm Leibniz University Hannover, Hanover, Germany
| | - Benye Liu
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Ludger Beerhues
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michaela Schmitz
- Department of Natural Sciences, Hochschule Bonn-Rhein-Sieg, Rheinbach, Germany
| | - Magda-Viola Hanke
- Institute for Breeding Research on Fruit Crops, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Dresden, Germany
| | - Henryk Flachowsky
- Institute for Breeding Research on Fruit Crops, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Dresden, Germany
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