1
|
Du YC, Yuan CS, Song YQ, Yang Y, Zheng QS, Hou Q, Wang D, Wang L. Enhancing soil health and strawberry disease resistance: the impact of calcium cyanamide treatment on soil microbiota and physicochemical properties. Front Microbiol 2024; 15:1366814. [PMID: 38577678 PMCID: PMC10991749 DOI: 10.3389/fmicb.2024.1366814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 02/23/2024] [Indexed: 04/06/2024] Open
Abstract
Introduction Continuous strawberry cropping often causes soil-borne diseases, with 20 calcium cyanamide being an effective soil fumigant, pig manure can often be used as soil organic fertilizer. Its impact on soil microorganisms structure, however, remains unclear. Methods This study investigated the effectiveness of calcium cyanamide and pig manure in treating strawberry soil, specifically against strawberry anthracnose. We examined the physical and chemical properties of the soil and the rhizosphere microbiome and performed a network analysis. Results Results showed that calcium cyanamide treatment significantly reduces the mortality rate of strawberry in seedling stage by reducing pathogen abundance, while increasing actinomycetes and Alphaproteobacteria during the harvest period. This treatment also enhanced bacterial network connectivity, measured by the average connectivity of each Operational Taxonomic Unit (OTU), surpassing other treatments. Moreover, calcium cyanamide notably raised the levels of organic matter, available potassium, and phosphorus in the soil-key factors for strawberry disease resistance and yield. Discussion Overall, applying calcium cyanamide to soil used for continuous strawberry cultivation can effectively decrease anthracnose incidence. It may be by changing soil physical and chemical properties and enhancing bacterial network stability, thereby reducing the copy of anthracnose. This study highlights the dual benefit of calcium cyanamide in both disease control and soil nutrient enhancement, suggesting its potential as a valuable tool in sustainable strawberry farming.
Collapse
Affiliation(s)
- Ying-chun Du
- College of Rural Revitalization, Jiangsu Open University, Nanjing, China
| | - Can-sheng Yuan
- College of Rural Revitalization, Jiangsu Open University, Nanjing, China
| | - Yu-qi Song
- College of Rural Revitalization, Jiangsu Open University, Nanjing, China
| | - Ying Yang
- College of Rural Revitalization, Jiangsu Open University, Nanjing, China
| | - Qing-song Zheng
- Sanya Research Institute, Nanjing Agricultural University, Sanya, Hainan, China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Qiong Hou
- College of Rural Revitalization, Jiangsu Open University, Nanjing, China
| | - Di Wang
- Sanya Research Institute, Nanjing Agricultural University, Sanya, Hainan, China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Lin Wang
- College of Rural Revitalization, Jiangsu Open University, Nanjing, China
| |
Collapse
|
2
|
Guaschino M, Garello M, Nari L, Zhimo YV, Droby S, Spadaro D. Soil, rhizosphere, and root microbiome in kiwifruit vine decline, an emerging multifactorial disease. Front Microbiol 2024; 15:1330865. [PMID: 38577679 PMCID: PMC10991698 DOI: 10.3389/fmicb.2024.1330865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/14/2024] [Indexed: 04/06/2024] Open
Abstract
Kiwifruit vine decline syndrome (KVDS) is characterized by severe root system impairment, which leads to irreversible wilting of the canopy. Plants usually collapse rapidly from the appearance of the first aboveground symptoms, without recovery even in the following seasons. The syndrome has been negatively impacting kiwifruit yield in different areas of Italy, the main producing European country, since its first outbreak in 2012. To date, a unique, common causal factor has yet to be found, and the syndrome is referred to as multifactorial. In this article, we investigated the whole biotic community (fungi, bacteria, and oomycetes) associated with the development of KVDS in three different belowground matrices/compartments (soil, rhizosphere, and root). Sampling was performed at both healthy and affected sites located in the main kiwifruit-producing area of Northwestern Italy. To address the multifactorial nature of the syndrome and to investigate the potential roles of abiotic factors in shaping these communities, a physicochemical analysis of soils was also performed. This study investigates the associations among taxonomic groups composing the microbiome and also between biotic and abiotic factors. Dysbiosis was considered as a driving event in shaping KVDS microbial communities. The results obtained from this study highlight the role of the oomycete genus Phytopythium, which resulted predominantly in the oomycete community composition of diseased matrices, though it was also present in healthy ones. Both bacterial and fungal communities resulted in a high richness of genera and were highly correlated to the sampling site and matrix, underlining the importance of multiple location sampling both geographically and spatially. The rhizosphere community associated with KVDS was driven by a dysbiotic process. In addition, analysis of the association network in the diseased rhizosphere revealed the presence of potential cross-kingdom competition for plant-derived carbon between saprobes, oomycetes, and bacteria.
Collapse
Affiliation(s)
- Micol Guaschino
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Grugliasco, Italy
- Interdepartmental Centre for Innovation in Agro-environmental Sector – AGROINNOVA, University of Turin, Grugliasco, Italy
| | - Marco Garello
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Grugliasco, Italy
- Interdepartmental Centre for Innovation in Agro-environmental Sector – AGROINNOVA, University of Turin, Grugliasco, Italy
| | | | - Yeka V. Zhimo
- Department of Postharvest Science, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Samir Droby
- Department of Postharvest Science, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Davide Spadaro
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Grugliasco, Italy
- Interdepartmental Centre for Innovation in Agro-environmental Sector – AGROINNOVA, University of Turin, Grugliasco, Italy
| |
Collapse
|
3
|
Fang M, Long W, Sun J, Wang A, Chen L, Cui Y, Huang Z, Li J, Ruan W, Rasmann S, Wei X. Toxicity of fungal-derived volatile organic compounds against root-knot nematodes. PEST MANAGEMENT SCIENCE 2023; 79:5162-5172. [PMID: 37574969 DOI: 10.1002/ps.7719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 08/15/2023]
Abstract
BACKGROUND Root-knot nematodes (RKNs), including Meloidogyne species, are among the most destructive plant-parasites worldwide. Recent evidence suggests that entomopathogenic fungi (EPF) can antagonize RKNs. Such antagonistic effects are likely mediated by toxic metabolites, including volatile organic compounds (VOCs), produced by the fungi. However, how widespread these effects are across EPF species, and which VOCs mediate negative interactions between EPF and RKNs needs to be further elucidated. RESULTS First, we evaluated the nematicidal effect of VOCs emitted by 46 EPF isolates against Meloidogyne incognita and found variable toxicity depending on the isolate. Second, we measured the nematicidal effect of highly toxic isolates, including species in the genus Talaromyces, Aspergillus, Clonostachys, and Purpureocillium and, third, we analyzed the nematicidal effect of major VOCs, including 2-methyl-1-propanol, 3-methyl-1-butanol, isopropyl alcohol and 2-methyl-3-pentanone. The mortality of M. incognita juveniles (J2s) was generally high (50%) either via airborne or in-solution contact with VOCs. Moreover, the tested VOCs significantly inhibited egg hatching, and repelled J2s away from the VOCs. CONCLUSION This study not only provides insights into the ecological function of VOCs in the rhizosphere, but also provides new approaches for developing environmentally friendly control methods of RKNs in agroecosystems. © 2023 Society of Chemical Industry.
Collapse
Affiliation(s)
- Ming Fang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Wenxin Long
- School of Mathematical Sciences and LPMC, Nankai University, Tianjin, China
| | - Jie Sun
- College of Life Sciences, Nankai University, Tianjin, China
| | - Ailing Wang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Lei Chen
- College of Life Sciences, Nankai University, Tianjin, China
| | | | | | | | - Weibin Ruan
- College of Life Sciences, Nankai University, Tianjin, China
| | - Sergio Rasmann
- Laboratory of Functional Ecology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Xianqin Wei
- College of Life Sciences, Nankai University, Tianjin, China
| |
Collapse
|
4
|
Luo S, Tian C, Zhang H, Yao Z, Guan Z, Li Y, Zhang J, Song Y. Isolation and Identification of Biocontrol Bacteria against Atractylodes Chinensis Root Rot and Their Effects. Microorganisms 2023; 11:2384. [PMID: 37894042 PMCID: PMC10609459 DOI: 10.3390/microorganisms11102384] [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: 08/11/2023] [Revised: 09/11/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
Fusarium root rot (FRR) seriously affects the growth and productivity of A. chinensis. Therefore, protecting A. chinensis from FRR has become an important task, especially for increasing A. chinensis production. The purpose of this study was to screen FRR control strains from the A. chinensis rhizosphere soil. Eighty-four bacterial strains and seven fungal strains were isolated, and five strains were identified with high inhibitory effects against Fusarium oxysporum (FO): Trichoderma harzianum (MH), Bacillus amyloliquefaciens (CJ5, CJ7, and CJ8), and Bacillus subtilis (CJ9). All five strains had high antagonistic effects in vitro. Results showed that MH and CJ5, as biological control agents, had high control potential, with antagonistic rates of 86.01% and 82.78%, respectively. In the pot experiment, the growth levels of roots and stems of A. chinensis seedlings treated with MH+CJ were significantly higher than those of control plants. The total nitrogen, total phosphorus, total potassium, indoleacetic acid, and chlorophyll contents in A. chinensis leaves were also significantly increased. In the biocontrol test, the combined MH + CJ application significantly decreased the malondialdehyde content in A. chinensis roots and significantly increased the polyphenol oxidase, phenylalanine ammonolyase, and peroxidase ability, indicating a high biocontrol effect. In addition, the application of Bacillus spp. and T. harzianum increased the abundance and diversity of the soil fungal population, improved the soil microbial community structure, and significantly increased the abundance of beneficial strains, such as Holtermanniella and Metarhizium. The abundance of Fusarium, Volutella, and other pathogenic strains was significantly reduced, and the biocontrol potential of A. chinensis root rot was increased. Thus, Bacillus spp. and T. harzianum complex bacteria can be considered potential future biocontrol agents for FRR.
Collapse
Affiliation(s)
- Shouyang Luo
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Hengfei Zhang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil, Conservation College of Life Science, The Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Zongmu Yao
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Zhihui Guan
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yingxin Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Jianfeng Zhang
- Key Laboratory of Straw Comprehensive Utilization and Black Soil, Conservation College of Life Science, The Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Yanyu Song
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| |
Collapse
|
5
|
Lawrence BT, Melgar JC. Annual compost amendments can replace synthetic fertilizer, improve soil moisture, and ensure tree performance during peach orchard establishment in a humid subtropical climate. FRONTIERS IN PLANT SCIENCE 2023; 14:1172038. [PMID: 37223805 PMCID: PMC10200951 DOI: 10.3389/fpls.2023.1172038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/13/2023] [Indexed: 05/25/2023]
Abstract
The application of organic matter (OM) to peach orchards is currently uncommon in commercial operations but could potentially replace synthetic fertilizers and improve long-term orchard sustainability. The purpose of the study was to monitor how annual applications of compost to replace synthetic fertilizer would change soil quality, peach tree nutrient and water status, and tree performance during the first four years of orchard establishment within a subtropical climate. Food waste compost was incorporated before planting and added annually over four years with the following treatments: 1) 1x rate, applied as dry weight at 22,417 kg ha-1 (10 tons acre-1) incorporated during the first year and 11,208 kg ha-1 (5 tons acre-1) applied topically each year after; 2) 2x rate, applied as dry weight at 44,834 kg ha-1 (20 tons acre-1) incorporated during the first year and 22,417 kg ha-1 (10 tons acre-1) applied topically each year after; and 3) control, with no compost added. Treatments were applied to a virgin orchard location, where peach trees had never previously been grown, and to a replant location, where peach trees had been grown previously for more than 20 years. Synthetic fertilizer was reduced in the 1x and 2x rates by 80 and 100% during the spring and all treatments received the summer application according to standard practice. Soil OM, phosphorus and sodium all increased with the addition of 2x compost in the replant location at 15 cm depth, but not within the virgin location compared to the control treatment. The 2x rate of compost improved soil moisture during the growing season, but tree water status was similar between treatments. Tree growth was similar between treatments in the replant location, but the 2x treatment had larger trees compared to the control by the third year. Foliar nutrients were similar between treatments over the four years, while 2x compost rate increased fruit yield in the virgin location compared to the control the second year of harvest. The 2x food waste compost rate could be considered as a replacement for synthetic fertilizers and to potentially increase tree growth during orchard establishment.
Collapse
|
6
|
Jara-Servin A, Silva A, Barajas H, Cruz-Ortega R, Tinoco-Ojanguren C, Alcaraz LD. Root microbiome diversity and structure of the Sonoran desert buffelgrass (Pennisetum ciliare L.). PLoS One 2023; 18:e0285978. [PMID: 37205698 DOI: 10.1371/journal.pone.0285978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/28/2023] [Indexed: 05/21/2023] Open
Abstract
Buffelgrass (Pennisetum ciliare) is an invasive plant introduced into Mexico's Sonoran desert for cattle grazing and has converted large areas of native thorn scrub. One of the invasion mechanisms buffelgrass uses to invade is allelopathy, which consists of the production and secretion of allelochemicals that exert adverse effects on other plants' growth. The plant microbiome also plays a vital role in establishing invasive plants and host growth and development. However, little is known about the buffelgrass root-associated bacteria and the effects of allelochemicals on the microbiome. We used 16S rRNA gene amplicon sequencing to obtain the microbiome of buffelgrass and compare it between samples treated with root exacknudates and aqueous leachates as allelochemical exposure and samples without allelopathic exposure in two different periods. The Shannon diversity values were between H' = 5.1811-5.5709, with 2,164 reported bacterial Amplicon Sequence Variants (ASVs). A total of 24 phyla were found in the buffelgrass microbiome, predominantly Actinobacteria, Proteobacteria, and Acidobacteria. At the genus level, 30 different genera comprised the buffelgrass core microbiome. Our results show that buffelgrass recruits microorganisms capable of thriving under allelochemical conditions and may be able to metabolize them (e.g., Planctomicrobium, Aurantimonas, and Tellurimicrobium). We also found that the community composition of the microbiome changes depending on the developmental state of buffelgrass (p = 0.0366; ANOSIM). These findings provide new insights into the role of the microbiome in the establishment of invasive plant species and offer potential targets for developing strategies to control buffelgrass invasion.
Collapse
Affiliation(s)
- Angélica Jara-Servin
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Adán Silva
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, Sonora, Mexico
| | - Hugo Barajas
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rocío Cruz-Ortega
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Clara Tinoco-Ojanguren
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, Sonora, Mexico
| | - Luis D Alcaraz
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
7
|
Zhang D, Lei M, Wan X, Guo G, Zhao X, Liu Y. Responses of diversity and arsenic-transforming functional genes of soil microorganisms to arsenic hyperaccumulator (Pteris vittata L.)/pomegranate (Punica granatum L.) intercropping. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:157767. [PMID: 35926620 DOI: 10.1016/j.scitotenv.2022.157767] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/28/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Intercropping of arsenic (As) hyperaccumulator (Pteris vittata L.) with crops can reduce the As concentration in soil and the resulting ecological and health risks, while maintaining certain economic benefits. However, it is still unclear how As-transforming functional bacteria and dominant bacteria in the rhizosphere of P. vittata affect the microbial properties of crop rhizosphere soil, as well as how As concentration and speciation change in crop rhizosphere soil under intercropping. This is of great significance for understanding the biogeochemical cycle of As in soil and crops. This study aimed to use high-throughput sequencing and quantitative polymerase chain reaction (qPCR) to analyze the effects of different rhizosphere isolation patterns on the bacterial diversity and the copy number of As-transforming functional genes in pomegranate (Punica granatum L.) rhizosphere soil. The results showed that the abundance of bacteria in the rhizosphere soil of pomegranate increased by 16.3 %, and the soil bacterial community structure significantly changed. C_Alphaproteobacteria and o_Rhizobiales bacteria significantly accumulated in the rhizosphere of pomegranate. The copy number of As methylation (arsM) gene in pomegranate rhizosphere soil significantly increased by 63.37 %. The concentrations of nonspecifically sorbed As (F1), As associated with amorphous Fe (hydr)oxides (F3), and the total As (FT) decreased; the proportion of As (III) in pomegranate rhizosphere soil decreased; and the proportion of As (V) increased in pomegranate rhizosphere soil. c_Alphaproteobacteria and o_Rhizobiales accumulated in crop rhizosphere soil under the intercropping of P. vittata with crops. Also, the copy number of As methylation functional genes in crop rhizosphere soil significantly increased, which could reduce As (III) proportion in crop rhizosphere soil. These changes favored simultaneous agricultural production and soil remediation. The results provided the theoretical basis and practical guidance for the safe utilization of As-contaminated soil in the intercropping of As-hyperaccumulator and cash crops.
Collapse
Affiliation(s)
- Degang Zhang
- Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; HongHe University, Mengzi 661100, Yunnan, China
| | - Mei Lei
- Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiaoming Wan
- Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guanghui Guo
- Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaofeng Zhao
- Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanhong Liu
- HongHe University, Mengzi 661100, Yunnan, China
| |
Collapse
|
8
|
Divergent Changes in Bacterial Functionality as Affected by Root-Zone Ecological Restoration in an Aged Peach Orchard. Microorganisms 2022; 10:microorganisms10112127. [DOI: 10.3390/microorganisms10112127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022] Open
Abstract
Soil restoration is a crucial approach to improving plant productivity in orchards with soil degradation, yield reduction, and fruit quality declination in China. A self-invented root-zone ecological restoration practice (RERP) with soil conditioner, or organic fertilizer, was employed in a degraded peach orchard in Beijing in 2020 to investigate the consequent impacts on soil bacterial composition and functionality at soil depths of 0–20 cm and 20–40 cm. Bacterial diversity was sensitive to RERP, especially in subsurface soil. RERP with soil conditioner significantly increased bacterial diversity, and affected abundances of certain genera, such as a significantly increased amount of Bacillus in surface soil and Blastococcus, Microvirga, Nocardioides, and Sphingomonas in subsurface soil. It also significantly affected abundances of bacterial functions related to metabolism in subsurface soil, particularly those with low abundance such as decreased transcription abundance and increased amino acid metabolism abundance. Soil bacterial functions were observably affected by bacterial diversity and composition, particularly in the deep soil layer. RERP affected bacterial functionality via responses of soil bacteria and bacteria-mediated alterations to the changed soil property. Correlation analysis between soil properties, bacterial taxonomy, and bacterial functions revealed that RERP affected bacterial functionality by altering the soil microenvironment with ample nutrients and water supply in root zone. Consequently, shifted bacterial functionality could have a potential in orchard ecosystem services in view of fruit yield and quality. Taken together, RERP had notably positive impacts on soil bacterial diversity and functions, and a prospect of increased plant productivity in the degrade orchard ecosystem.
Collapse
|
9
|
Khan AR, Wicaksono WA, Ott NJ, Poret-Peterson AT, Browne GT. Random forest analysis reveals taxa predictive of Prunus replant disease in peach root microbiomes. PLoS One 2022; 17:e0275587. [PMID: 36227955 PMCID: PMC9560047 DOI: 10.1371/journal.pone.0275587] [Citation(s) in RCA: 2] [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: 10/12/2021] [Accepted: 09/20/2022] [Indexed: 11/06/2022] Open
Abstract
Successive plantings of Prunus species produce suboptimal growth and yield in many California soils due to a poorly understood soilborne disease complex, Prunus replant disease (PRD). We explored the hypothesis that PRD is mediated by microbial taxa in roots of Nemaguard peach, a rootstock for almond and other stone fruits. In a greenhouse bioassay, portions of 10 replant soils were treated with fumigation or pasteurization or left untreated as a control before being planted with peach seedlings. Ten weeks after planting, seedlings were considered PRD-affected if their top fresh weights in the control were significantly reduced, compared to the weights in pasteurization and fumigation treatments; plants with equivalent top weights in all treatments were considered to be non-affected. The roots were washed from the soil, frozen, extracted for total DNA, and used for metabarcoding of rRNA gene amplicons from bacteria, fungi, and oomycetes. High-throughput amplicon sequencing revealed that root microbial community shifts resulted from preplant treatments, and specific taxa were associated with PRD induction among controls. Random forest (RF) analysis discriminated effectively between PRD-affected and non-affected root communities. Among the 30 RF top-ranked amplicon sequence variant (ASV) predictors, 26 were bacteria, two were oomycetes, and two were fungi. Among them, only Streptomyces scabiei, Steroidobacter denitrificans, Streptomyces bobili, and Pythium mamillatum had root abundances ≥5% that were either associated positively (former two ASVs) or negatively (latter two) with PRD. Thus, our findings were consistent with microbial mediation of PRD in roots and suggested taxa that may be involved in the mediation.
Collapse
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
- * E-mail:
| |
Collapse
|
10
|
Chen P, Li HQ, Li XY, Zhou XH, Zhang XX, Zhang AS, Liu QZ. Transcriptomic analysis provides insight into defensive strategies in response to continuous cropping in strawberry (Fragaria × ananassa Duch.) plants. BMC PLANT BIOLOGY 2022; 22:476. [PMID: 36203126 PMCID: PMC9540695 DOI: 10.1186/s12870-022-03857-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Strawberries are an important economic fruit crop world-wide. In strawberry cultivation, continuous cropping (CC) can seriously threaten yield and quality. However, our understanding of the gene expression changes in response to CC and during subsequent defense processes is limited. In this study, we analyzed the impact of CC on the transcriptome of strawberry roots using RNA-Seq technology to elucidate the effect of CC and the subsequent molecular changes. RESULTS We found that CC significantly affects the growth of strawberry plants. The transcriptome analysis identified 136 differentially expressed genes (DEGs), including 49 up-regulated and 87 down-regulated DEGs. A Gene Ontology (GO) analysis indicated that the up-regulated DEGs were mainly assigned to defense-related GO terms, and most down-regulated DEGs were assigned to nutrient-related GO terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the responsive DEGs were classified in a large number of important biological pathways, such as phenylalanine metabolism, starch and sucrose metabolism, phenylpropanoid biosynthesis, glutathione metabolism and plant-pathogen interaction. We also found that four WRKY transcription factors and three peroxidase genes involved in plant defense pathways were up-regulated in the roots of strawberry plants subjected to CC. CONCLUSION Several unigenes involved in plant defense processes, such as CNGCs, WRKY transcription factors, PR1, and peroxidase genes with highly variable expression levels between non-CC and CC treatments may be involved in the regulation of CC in strawberry. These results indicate that strawberry roots reallocate development resources to defense mechanisms in response to CC. This study will further deepen our understanding of the fundamental regulatory mechanisms of strawberry resource reallocation in response to CC.
Collapse
Affiliation(s)
- Peng Chen
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Shandong Provincial Engineering Technology Research Center on Biocontrol of Crop Diseases and Insect Pest, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, 250100 Jinan, China
- Laboratory of Entomology and Nematology, College of Plant Protection, China Agricultural University, 100193 Beijing, China
| | - He-qin Li
- Shandong Provincial Key Laboratory of Dryland Technology, College of Agronomy, Qingdao Agricultural University, 266109 Qingdao, China
| | - Xing-yue Li
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, 610066 Chengdu, China
| | - Xian-hong Zhou
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Shandong Provincial Engineering Technology Research Center on Biocontrol of Crop Diseases and Insect Pest, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, 250100 Jinan, China
| | - Xiu-xia Zhang
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Shandong Provincial Engineering Technology Research Center on Biocontrol of Crop Diseases and Insect Pest, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, 250100 Jinan, China
| | - An-sheng Zhang
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Shandong Provincial Engineering Technology Research Center on Biocontrol of Crop Diseases and Insect Pest, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, 250100 Jinan, China
| | - Qi-zhi Liu
- Laboratory of Entomology and Nematology, College of Plant Protection, China Agricultural University, 100193 Beijing, China
| |
Collapse
|
11
|
Xin A, Jin H, Yang X, Guan J, Hui H, Liu H, Cui Z, Dun Z, Qin B. Allelochemicals from the Rhizosphere Soil of Potato ( Solanum tuberosum L.) and Their Interactions with the Soilborne Pathogens. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11151934. [PMID: 35893638 PMCID: PMC9331876 DOI: 10.3390/plants11151934] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/09/2022] [Accepted: 07/14/2022] [Indexed: 05/13/2023]
Abstract
To reveal the allelopathic effects of potato, seven compounds were isolated from the rhizosphere soil: 7-methoxycoumarin (1), palmitic acid (2), caffeic acid (3), chlorogenic acid (4), quercetin dehydrate (5), quercitrin (6), and rutin (7). Bioassays showed that compounds 1, 2, 4, and 6 had inhibitory effects on the growth of L. sativa and tissue culture seedlings of potato. The existence of the allelochemicals was confirmed by HPLC, and their contents were quantified with a total concentration of 9.02 μg/g in the rhizosphere soil of replanted potato. Approaches on the interactions of the allelochemicals and pathogens of potato including A. solani, B. cinerea, F. solani, F. oxysporum, C. coccodes, and V. dahlia revealed that compound 1 had inhibitory effects but compounds 2-4 promoted the colony growth of the pathogens. These findings demonstrated that the autotoxic allelopathy and enhancement of the pathogens caused by the accumulation of the allelochemicals in the continuously cropped soil should be one of the main reasons for the replant problems of potato.
Collapse
Affiliation(s)
- Aiyi Xin
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; (A.X.); (H.J.); (X.Y.); (H.H.); (H.L.)
- School of Chemistry and Chemical Engineering, Mianyang Normal University, Mianyang 621000, China
| | - Hui Jin
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; (A.X.); (H.J.); (X.Y.); (H.H.); (H.L.)
| | - Xiaoyan Yang
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; (A.X.); (H.J.); (X.Y.); (H.H.); (H.L.)
| | - Jinfeng Guan
- Institute for Food and Drug Control, Tongliao City, Inner Mongolia Autonomous Region, Tongliao 028000, China;
| | - Heping Hui
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; (A.X.); (H.J.); (X.Y.); (H.H.); (H.L.)
| | - Haoyue Liu
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; (A.X.); (H.J.); (X.Y.); (H.H.); (H.L.)
| | - Zengtuan Cui
- Cultivated Land Quality Construction and Management Station of Gansu Province, Lanzhou 730030, China; (Z.C.); (Z.D.)
| | - Zhiheng Dun
- Cultivated Land Quality Construction and Management Station of Gansu Province, Lanzhou 730030, China; (Z.C.); (Z.D.)
| | - Bo Qin
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; (A.X.); (H.J.); (X.Y.); (H.H.); (H.L.)
- Correspondence: ; Tel.: +86-931-4968371; Fax: +86-931-4968019
| |
Collapse
|
12
|
Zhang B, Ma L, Zhang Y, Qi K, Li C, Qi J. Impact of ozonated water disinfestation on soil fungal community composition in continuous ginger field. PLoS One 2022; 17:e0266619. [PMID: 35390087 PMCID: PMC8989316 DOI: 10.1371/journal.pone.0266619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 03/23/2022] [Indexed: 12/04/2022] Open
Abstract
This study aimed to explore the impact of ozonated water (OW) disinfestation on soil fungal community composition in continuous ginger field. All soil samples were collected in continuous ginger field. There were two groups and 5 time points (0, 1, 3, 5, 9 day) in our study, including OW disinfestation treatment group (O3 group) and control group (CK group). Via internal transcribed spacer (ITS) sequencing and further analysis, the changes of fungal community composition were determined. As a result, at 0 and 9 days after aeration, the operational taxonomic units (OTUs) in O3 group were significantly higher than that in CK group. Compared with the CK group, in O3 group: the ACE and Chao1 index significantly increased on day 1, and the Shannon index significantly decreased while Simpson index significantly increased on day 0 after aeration. In O3 group, there were dynamic changes of top 10 abundance fungi from the genus-level and the growth of Trichoderma and Rhodotorula had been promoted while Hannaella was inhibited. In conclusion, OW disinfestation had complicated impacts on fungal communities in continuous ginger fields. The growth of Trichoderma and Rhodotorula has been promoted during disinfestation, which provided more reference information for soil OW disinfestation research.
Collapse
Affiliation(s)
- Bo Zhang
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences/Shandong Province Key Laboratory of Plant Virology, Jinan, Shandong, P. R. China
| | - Liguo Ma
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences/Shandong Province Key Laboratory of Plant Virology, Jinan, Shandong, P. R. China
| | - Yueli Zhang
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences/Shandong Province Key Laboratory of Plant Virology, Jinan, Shandong, P. R. China
| | - Kai Qi
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences/Shandong Province Key Laboratory of Plant Virology, Jinan, Shandong, P. R. China
| | - Changsong Li
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences/Shandong Province Key Laboratory of Plant Virology, Jinan, Shandong, P. R. China
| | - Junshan Qi
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences/Shandong Province Key Laboratory of Plant Virology, Jinan, Shandong, P. R. China
| |
Collapse
|
13
|
Zhao L, Jiang W, Chen R, Wang H, Duan Y, Chen X, Shen X, Yin C, Mao Z. Quicklime and Superphosphate Alleviating Apple Replant Disease by Improving Acidified Soil. ACS OMEGA 2022; 7:7920-7930. [PMID: 35284737 PMCID: PMC8908487 DOI: 10.1021/acsomega.1c06876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
A two-year field experiment was carried out in order to study the effect of different soil modifiers on alleviating apple replant disease (ARD) in the apple orchards. Four treatments were as follows: replanted apple orchard soil (CK), replanted apple orchard soil treated with quicklime 1.0 g·kg-1 (T1), replanted apple orchard soil treated with 1.0 g·kg-1 quicklime and 1.0 g·kg-1 superphosphate (T2), and replanted apple orchard soil treated with 1.0 g·kg-1 plant ash (T3). Soil pH, plant biomass, soil bacteria, soil fungi, Fusarium oxysporum, soil enzymes, plant chlorophyll, and photosynthetic parameters were measured to detect the improvement effects of different soil amendments on acidified soil and to alleviate the ARD. The three treatments stably raised the pH of acidified soil and improved the conditions of the plant rhizosphere environment. Compared with the control, T1, T2, and T3 treatments significantly increased growth and plant biomass indexes, such as plant height and ground diameter, as well as photosynthetic parameters. Among the three treatments, T2 had the strongest effects. In July 2018 and July 2019, the number of bacteria was 151.3 and 190.5% higher in T2-treated soil than in control soil, and the number of soil fungi was 53.6 and 53.3% lower. In 2018 and 2019, the copy number of Fusarium solani was 63.6 and 58.6% lower and that of F. oxysporum was 51.8 and 55.7% lower. The T1, T2, and T3 treatments significantly increased soil enzyme activity and leaf chlorophyll content, and their effects were generally ranked T2 > T1 > T3. In conclusion, a combination of 1.0 g·kg-1 quicklime and 1.0 g·kg-1 superphosphate added to acidified replant soil increased the soil pH, improved the soil environment, increased the number of bacteria, reduced the number of fungi, increased soil enzyme activity, and improved plant photosynthetic capacity, thereby promoting the growth of replanted seedlings and effectively reducing ARD.
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Poveda J, Martínez-Gómez Á, Fenoll C, Escobar C. The Use of Biochar for Plant Pathogen Control. PHYTOPATHOLOGY 2021; 111:1490-1499. [PMID: 33529050 DOI: 10.1094/phyto-06-20-0248-rvw] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
To support the search for alternative, nonchemical plant disease control strategies, we present a review of the pathogen-suppressive effects of biochar, a product derived from agricultural and other organic wastes, used as a soil amendment. A wide range of biochar effects contribute to the control of root or foliar fungal pathogens through modification of root exudates, soil properties, and nutrient availability, which influence the growth of antagonist microorganisms. The induction of systemic plant defenses by biochar in the roots to reduce foliar pathogenic fungi, the activation of stress-hormone responses, as well as changes in active oxygen species are indicative of a coordinated hormonal signaling within the plant. Although scarce data are available for oomycetes and bacterial pathogens, reports indicate that biochar promotes changes in the soil microbiota influencing pathogen motility and colonization, and the induction of plant systemic defenses, both contributing to disease suppression. Biochar also suppresses nematode and insect pests. For plant-parasitic nematodes, the primary modes of action are changes in soil microbial community diversity, the release of nematicidal compounds, and the induction of plant defenses. Use of biochar-based soil amendments is a promising strategy compatible with a circular economy, based on zero waste, as part of integrated pathogen and pest management. Since biochars exert complex and distinct modes of action for the control of plant pathogens, its nature and application regimes should be designed for particular pathogens and its effects studied locally.
Collapse
Affiliation(s)
- Jorge Poveda
- Biological Mission of Galicia (MBG-CSIC), Pontevedra, Spain
| | - Ángela Martínez-Gómez
- Facultad de Ciencias Ambientales y Bioquímica, Área de Fisiología Vegetal, Universidad de Castilla-La Mancha, Avda. Carlos III, s/n, 45071 Toledo, Spain
| | - Carmen Fenoll
- Facultad de Ciencias Ambientales y Bioquímica, Área de Fisiología Vegetal, Universidad de Castilla-La Mancha, Avda. Carlos III, s/n, 45071 Toledo, Spain
| | - Carolina Escobar
- Facultad de Ciencias Ambientales y Bioquímica, Área de Fisiología Vegetal, Universidad de Castilla-La Mancha, Avda. Carlos III, s/n, 45071 Toledo, Spain
- International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, Kumamoto 860-8555, Japan
| |
Collapse
|
16
|
Sun K, Fu L, Song Y, Yuan L, Zhang H, Wen D, Yang N, Wang X, Yue Y, Li X, Wang K. Effects of continuous cucumber cropping on crop quality and soil fungal community. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 193:436. [PMID: 34155596 DOI: 10.1007/s10661-021-09136-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 05/17/2021] [Indexed: 06/13/2023]
Abstract
Long-term continuous cropping is a common practice in facility vegetable production, which has an adverse effect on cucumber yield and quality. Soil fungi are of great significance for creating a normal soil ecological environment. However, the impact of continuous cropping on cucumber quality and soil fungal community has yet to be understood. In this study, we evaluated the effects of continuous cropping on cucumber using high-throughput sequencing technology. The results showed that the extension of continuous cropping would increase nitrate and total acidity of cucumber, while the contents of vitamin C (VC), soluble sugar, and protein were decreased. The increase of continuous cropping duration also reduced the fungal diversity of the cucumber soil. For example, the activity of three dominant fungal phylums, Ascomycota, Aphelidiomycota, and Basidiomycota, decreased with the extension of planting years. The relative abundance of the two fungi species (Remersonia_thermophila, Mortierella_oligospora) was negatively correlated with the contents of available phosphorus and available potassium (P < 0.05). Redundancy analysis (RDA) found that soil electrical conductivity (EC), available phosphorus (AP), and pH accounted for the top three major factors of fungal community structure changes. The soil fungal community was changed during the continuous cucumber cultivation, which might be the result of the combined cultivation period of cucumber and excessive application of chemical fertilizers (nitrogen fertilizer, phosphate fertilizer, etc.). Our study provides a theoretical basis for the understanding of the impact of continuous cropping in cucumber facilities.
Collapse
Affiliation(s)
- Kaining Sun
- Institute of Vegetables and FlowersShandong Branch of National Improvement Center for VegetablesShandong Key Laboratory of Greenhouse Vegetable Biology, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Huang-Huai-Hai Region Scientific Observation and Experimental Station of Vegetables, Jinan, Shandong, 250100, People's Republic of China
| | - Longyun Fu
- Institute of Agricultural Resource and Environment, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250100, People's Republic of China
| | - Yang Song
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, 71 East Beijing Road, Nanjing, Jiangsu, 210008, People's Republic of China
| | - Liang Yuan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Haoran Zhang
- College of Horticulture, Qingdao Agricultural University, Qingdao, Shandong, 266109, People's Republic of China
| | - Dan Wen
- Institute of Vegetables and FlowersShandong Branch of National Improvement Center for VegetablesShandong Key Laboratory of Greenhouse Vegetable Biology, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Huang-Huai-Hai Region Scientific Observation and Experimental Station of Vegetables, Jinan, Shandong, 250100, People's Republic of China
| | - Ning Yang
- Institute of Vegetables and FlowersShandong Branch of National Improvement Center for VegetablesShandong Key Laboratory of Greenhouse Vegetable Biology, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Huang-Huai-Hai Region Scientific Observation and Experimental Station of Vegetables, Jinan, Shandong, 250100, People's Republic of China
| | - Xiao Wang
- Institute of Vegetables and FlowersShandong Branch of National Improvement Center for VegetablesShandong Key Laboratory of Greenhouse Vegetable Biology, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Huang-Huai-Hai Region Scientific Observation and Experimental Station of Vegetables, Jinan, Shandong, 250100, People's Republic of China
| | - Yaoquan Yue
- College of Horticulture, Qingdao Agricultural University, Qingdao, Shandong, 266109, People's Republic of China
| | - Xuhua Li
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong, 271018, People's Republic of China.
| | - Kean Wang
- Institute of Vegetables and FlowersShandong Branch of National Improvement Center for VegetablesShandong Key Laboratory of Greenhouse Vegetable Biology, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Huang-Huai-Hai Region Scientific Observation and Experimental Station of Vegetables, Jinan, Shandong, 250100, People's Republic of China.
| |
Collapse
|
17
|
Xi H, Zhang X, Qu Z, Yang D, Alariqi M, Yang Z, Nie X, Zhu L. Effects of cotton-maize rotation on soil microbiome structure. MOLECULAR PLANT PATHOLOGY 2021; 22:673-682. [PMID: 33774915 PMCID: PMC8126184 DOI: 10.1111/mpp.13053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 12/08/2020] [Accepted: 02/25/2021] [Indexed: 05/13/2023]
Abstract
Verticillium wilt is a disastrous disease in cotton-growing regions in China. As a common management method, cotton rotation with cereal crops is used to minimize the loss caused by Verticillium dahliae. However, the correlation between soil microbiome and the control of Verticillium wilt under a crop rotation system is unclear. Therefore, three cropping systems (fallow, cotton continuous cropping, and cotton-maize rotation) were designed and applied for three generations under greenhouse conditions to investigate the different responses of the soil microbial community. The soil used in this study was taken from a long-term cotton continuous cropping field and inoculated with V. dahliae before use. Our results showed that the diversity of the soil bacterial community was increased under cotton-maize rotation, while the diversity of the fungal community was obviously decreased. Meanwhile, the structure and composition of the bacterial communities were similar even under the different cropping systems, but they differed in the soil fungal communities. Through microbial network interaction analysis, we found that Verticillium interacted with 17 bacterial genera, among which Terrabacter had the highest correlation with Verticillium. Furthermore, eight fungal and eight bacterial species were significantly correlated with V. dahliae. Collectively, this work aimed to study the interactions among V. dahliae, the soil microbiome, and plant hosts, and elucidate the relationship between crop rotation and soil microbiome, providing a new theoretical basis to screen the biological agents that may contribute to Verticillium wilt control.
Collapse
Affiliation(s)
- Hui Xi
- College of AgricultureShihezi UniversityShiheziChina
| | - Xuekun Zhang
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
| | - Zheng Qu
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
| | - Dingyi Yang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Muna Alariqi
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | | | - Xinhui Nie
- College of AgricultureShihezi UniversityShiheziChina
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| |
Collapse
|
18
|
Shi Y, Xiao Y, Li Z, Zhang X, Liu T, Li Y, Pan Y, Yan W. Microorganism structure variation in urban soil microenvironment upon ZnO nanoparticles contamination. CHEMOSPHERE 2021; 273:128565. [PMID: 33087259 DOI: 10.1016/j.chemosphere.2020.128565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/28/2020] [Accepted: 10/03/2020] [Indexed: 06/11/2023]
Abstract
Nanoparticles (NPs) sink into the soil via agricultural spreading, surface water, atmospheric deposition, and industrial emission, which affects plant growth and soil microenvironment. To understand how NPs influence urban soil microenvironment, the effect of typical nano-pollutants zinc oxide nanoparticles (ZnONPs) was investigated in urban solid-waste land. Pokeweed (Phytolacca Americana L.) soil samples from solid-waste land were collected and exposed to 200, 500, and 1000 mg kg-1 ZnONPs. The physiological characteristics of pokeweed, soil bacterial community composition, and soil physiochemical properties and enzymatic activities were determined. Our results show that pokeweed growth was slightly inhibited, and soil acid-base homeostasis was affected in ZnONPs-contaminated samples. Meanwhile, enzymatic activities related to soil C cycle were enhanced, and bacterial community structure at the phylum and genus levels was altered. Specifically, the abundance of hydrocarbon-degrading taxa reduced substantially upon ZnONPs exposure. The phenoloxidase (PPO) activity and the refractory hydrocarbon-degrading bacteria Bacteroidetes was adversely affected by ZnONPs exposure. In addition, Subgroup_10 of Acidobacteria was identified as an indicator of soil ZnONPs contamination. Our study detected changes in plant growth, soil environmental factors, and soil microbe community composition in urban solid-waste land treated by ZnONPs. The results of this research provide evidence for ZnONPs toxicology on urban soil microenvironment.
Collapse
Affiliation(s)
- Yang Shi
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan, 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan, 410004, China
| | - Yunmu Xiao
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan, 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan, 410004, China
| | - Ziqian Li
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan, 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan, 410004, China
| | - Xuyuan Zhang
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan, 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan, 410004, China
| | - Ting Liu
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan, 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan, 410004, China
| | - Yong Li
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan, 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan, 410004, China.
| | - Yuliang Pan
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan, 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan, 410004, China
| | - Wende Yan
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan, 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan, 410004, China.
| |
Collapse
|
19
|
Guo S, Xiong W, Hang X, Gao Z, Jiao Z, Liu H, Mo Y, Zhang N, Kowalchuk GA, Li R, Shen Q, Geisen S. Protists as main indicators and determinants of plant performance. MICROBIOME 2021; 9:64. [PMID: 33743825 PMCID: PMC7981826 DOI: 10.1186/s40168-021-01025-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 02/04/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND Microbiomes play vital roles in plant health and performance, and the development of plant beneficial microbiomes can be steered by organic fertilizer inputs. Especially well-studied are fertilizer-induced changes on bacteria and fungi and how changes in these groups alter plant performance. However, impacts on protist communities, including their trophic interactions within the microbiome and consequences on plant performance remain largely unknown. Here, we tracked the entire microbiome, including bacteria, fungi, and protists, over six growing seasons of cucumber under different fertilization regimes (conventional, organic, and Trichoderma bio-organic fertilization) and linked microbial data to plant yield to identify plant growth-promoting microbes. RESULTS Yields were higher in the (bio-)organic fertilization treatments. Soil abiotic conditions were altered by the fertilization regime, with the prominent effects coming from the (bio-)organic fertilization treatments. Those treatments also led to the pronounced shifts in protistan communities, especially microbivorous cercozoan protists. We found positive correlations of these protists with plant yield and the density of potentially plant-beneficial microorganisms. We further explored the mechanistic ramifications of these relationships via greenhouse experiments, showing that cercozoan protists can positively impact plant growth, potentially via interactions with plant-beneficial microorganisms including Trichoderma, the biological agent delivered by the bio-fertilizer. CONCLUSIONS We show that protists may play central roles in stimulating plant performance through microbiome interactions. Future agricultural practices might aim to specifically enhance plant beneficial protists or apply those protists as novel, sustainable biofertilizers. Video abstract.
Collapse
Affiliation(s)
- Sai Guo
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, PR China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, PR China
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Xinnan Hang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Zhilei Gao
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Zixuan Jiao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, PR China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Hongjun Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yani Mo
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, PR China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Nan Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, PR China.
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, PR China.
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, PR China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, Wageningen, 6700 AA, The Netherlands
- Netherlands Department of Terrestrial Ecology, Netherlands Institute for Ecology, (NIOO-KNAW), Wageningen, 6708 PB, The Netherlands
| |
Collapse
|
20
|
Ji L, Tian L, Nasir F, Chang J, Chang C, Zhang J, Li X, Tian C. Impacts of replanting American ginseng on fungal assembly and abundance in response to disease outbreaks. Arch Microbiol 2021; 203:2157-2170. [PMID: 33616683 PMCID: PMC8205870 DOI: 10.1007/s00203-021-02196-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 12/24/2020] [Accepted: 02/04/2021] [Indexed: 11/29/2022]
Abstract
Soil physicochemical properties and fungal communities are pivotal factors for continuous cropping of American ginseng (Panax quinquefolium L.). However, the response of soil physicochemical properties and fungal communities to replant disease of American ginseng has not yet been studied. High-throughput sequencing and soil physicochemical analyses were undertaken to investigate the difference of soil fungal communities and environmental driver factors in new and old ginseng fields; the extent of replant disease in old ginseng fields closely related to changes in soil properties and fungal communities was also determined. Results indicated that fungal communities in an old ginseng field were more sensitive to the soil environment than those in a new ginseng field, and fungal communities were mainly driven by soil organic matter (SOM), soil available phosphorus (AP), and available potassium (AK). Notably, healthy ginseng plants in new and old ginseng fields may influence fungal communities by actively recruiting potential disease suppressive fungal agents such as Amphinema, Cladophialophora, Cadophora, Mortierella, and Wilcoxina. When these key groups and members were depleted, suppressive agents in the soil possibly declined, increasing the abundance of pathogens. Soil used to grow American ginseng in the old ginseng field contained a variety of fungal pathogens, including Alternaria, Armillaria, Aphanoascus, Aspergillus, Setophoma, and Rhexocercosporidium. Additionally, micro-ecological factors affecting disease outbreaks in the old ginseng field included a strengthening in competition relationships, a weakening in cooperation relationships, and a change of trophic strategies among fungal communities.
Collapse
Affiliation(s)
- Li Ji
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Fahad Nasir
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Jingjing Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunling Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Jianfeng Zhang
- Key Laboratory of Straw Biology and Utilization of the Ministry of Education, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Xiujun Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China. .,Key Laboratory of Straw Biology and Utilization of the Ministry of Education, Jilin Agricultural University, Changchun, 130118, Jilin, China.
| |
Collapse
|
21
|
ITRAQ-based quantitative proteomic analysis of Fusarium moniliforme (Fusarium verticillioides) in response to Phloridzin inducers. Proteome Sci 2021; 19:2. [PMID: 33446211 PMCID: PMC7807804 DOI: 10.1186/s12953-021-00170-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 01/02/2021] [Indexed: 11/13/2022] Open
Abstract
Background Apple replant disease (ARD) has been reported from all major fruit-growing regions of the world, and is often caused by biotic factors (pathogen fungi) and abiotic factors (phenolic compounds). In order to clarify the proteomic differences of Fusarium moniliforme under the action of phloridzin, and to explore the potential mechanism of F. moniliforme as the pathogen of ARD, the role of Fusarium spp. in ARD was further clarified. Methods In this paper, the quantitative proteomics method iTRAQ analysis technology was used to analyze the proteomic differences of F. moniliforme before and after phloridzin treatment. The differentially expressed protein was validated by qRT-PCR analysis. Results A total of 4535 proteins were detected, and 293 proteins were found with more than 1.2 times (P< 0.05) differences. In-depth data analysis revealed that 59 proteins were found with more than 1.5 times (P< 0.05) differences, and most proteins were consistent with the result of qRT-PCR. Differentially expressed proteins were influenced a variety of cellular processes, particularly metabolic processes. Among these metabolic pathways, a total of 8 significantly enriched KEGG pathways were identified with at least 2 affiliated proteins with different abundance in conidia and mycelium. Functional pathway analysis indicated that up-regulated proteins were mainly distributed in amino sugar, nucleotide sugar metabolism, glycolysis/ gluconeogenesis and phagosome pathways. Conclusions This study is the first to perform quantitative proteomic investigation by iTRAQ labeling and LC-MS/MS to identify differentially expressed proteins in F. moniliforme under phloridzin conditions. The results confirmed that F. moniliforme presented a unique protein profile that indicated the adaptive mechanisms of this species to phloridzin environments. The results deepened our understanding of the proteome in F. moniliforme in response to phloridzin inducers and provide a basis for further exploration for improving the efficiency of the fungi as biocontrol agents to control ARD. Supplementary Information The online version contains supplementary material available at 10.1186/s12953-021-00170-2.
Collapse
|
22
|
Grunewaldt-Stöcker G, Popp C, Baumann A, Fricke S, Menssen M, Winkelmann T, Maiss E. Observations on early fungal infections with relevance for replant disease in fine roots of the rose rootstock Rosa corymbifera 'Laxa'. Sci Rep 2020; 10:22410. [PMID: 33376252 PMCID: PMC7772344 DOI: 10.1038/s41598-020-79878-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 12/14/2020] [Indexed: 11/09/2022] Open
Abstract
Replant disease is a worldwide phenomenon affecting various woody plant genera and species, especially within the Rosaceae. Compared to decades of intensive studies regarding replant disease of apple (ARD), the replant disease of roses (RRD) has hardly been investigated. The etiology of RRD is also still unclear and a remedy desperately needed. In greenhouse pot trials with seedlings of the RRD-sensitive rootstock Rosa corymbifera ‘Laxa’ cultured in replant disease affected soils from two different locations, early RRD symptom development was studied in fine roots. In microscopic analyses we found similarities to ARD symptoms with regards to structural damages, impairment in the root hair status, and necroses and blackening in the cortex tissue. Examinations of both whole mounts and thin sections of fine root segments revealed frequent conspicuous fungal infections in association with the cellular disorders. Particularly striking were fungal intracellular structures with pathogenic characteristics that are described for the first time. Isolated fungi from these tissue areas were identified by means of ITS primers, and many of them were members of the Nectriaceae. In a next step, 35 of these isolates were subjected to a multi-locus sequence analysis and the results revealed that several genera and species were involved in the development of RRD within a single rose plant. Inoculations with selected single isolates (Rugonectria rugulosa and Ilyonectria robusta) in a Perlite assay confirmed their pathogenic relationship to early necrotic host plant reactions, and symptoms were similar to those exhibited in ARD.
Collapse
Affiliation(s)
- G Grunewaldt-Stöcker
- Institute of Horticultural Production Systems, Section Phytomedicine, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - C Popp
- Institute of Horticultural Production Systems, Section Phytomedicine, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - A Baumann
- Institute of Horticultural Production Systems, Section of Woody Plant and Propagation Physiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - S Fricke
- Institute of Horticultural Production Systems, Section Phytomedicine, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - M Menssen
- Department of Biostatistics, Institute of Cell Biology and Biophysics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - T Winkelmann
- Institute of Horticultural Production Systems, Section of Woody Plant and Propagation Physiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany.
| | - E Maiss
- Institute of Horticultural Production Systems, Section Phytomedicine, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| |
Collapse
|
23
|
Abstract
The continuous cropping (CC) of major agricultural, horticultural, and industrial crops is an established practice worldwide, though it has significant soil health-related concerns. However, a combined review of the effects of CC on soil health indicators, in particular omics ones, remains missing. The CC may negatively impact multiple biotic and abiotic indicators of soil health, fertility, and crop yield. It could potentially alter the soil biotic indicators, which include but are not limited to the composition, abundance, diversity, and functioning of soil micro- and macro-organisms, microbial networks, enzyme activities, and soil food web interactions. Moreover, it could also alter various soil abiotic (physicochemical) properties. For instance, it could increase the accumulation of toxic metabolites, salts, and acids, reduce soil aggregation and alter the composition of soil aggregate-size classes, decrease mineralization, soil organic matter, active carbon, and nutrient contents. All these alterations could accelerate soil degradation. Meanwhile, there is still a great need to develop quantitative ranges in soil health indicators to mechanistically predict the impact of CC on soil health and crop yield gaps. Following ecological principles, we strongly highlight the significance of inter-, mixture-, and rotation-cropping with cover crops to sustain soil health and agricultural production.
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Wang Y, Xu X, Liu T, Wang H, Yang Y, Chen X, Zhu S. Analysis of bacterial and fungal communities in continuous-cropping ramie (Boehmeria nivea L. Gaud) fields in different areas in China. Sci Rep 2020; 10:3264. [PMID: 32094349 PMCID: PMC7039886 DOI: 10.1038/s41598-020-58608-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/16/2020] [Indexed: 11/09/2022] Open
Abstract
Ramie (Boehmeria nivea L. Gaud) suffers from long-term continuous cropping. Here, using Illumina high-throughput sequencing technology, we aimed to identify bacteria and fungi associated with continuous cropping in ramie fields in Yuanjiang, Xianning, Sichuan, and Jiangxi. The rarefaction results showed that Jiangxi had significantly lower bacterial α-diversity than that of the other areas. Firmicutes, Proteobacteria, and Acidobacteria were the dominant bacterial phyla, and Ascomycota, Basidiomycota, and Zygomycota were the dominant fungal phyla. In Jiangxi, Firmicutes accounted for 79.03% of all valid reads, which could have significant decreased microbial diversity and negative effects of continuous ramie cropping. We used traditional methods to examine soil nutrients. Sichuan had a relatively high pH and available P and K, but low total N; opposite findings were recorded in Jiangxi. The redundancy analysis revealed that the urease activity, PH, available K, and total N significantly correlated with bacterial community abundance, whereas only total N significantly correlated with fungal community abundance (P < 0.01). Overall, the effect of soil environmental factors on the bacterial diversity of continuous ramie cropping was greater than that on fungal diversity. In the future, we will focus on the effect of rhizosphere bacteria to solve the obstacle in continuous ramie cropping.
Collapse
Affiliation(s)
- Yanzhou Wang
- Institute of bast fiber crops, Chinese Academy of Agricultrial Sciences, Changsha Hunan, 410205, P.R. China
| | - Xiaomin Xu
- Institute of bast fiber crops, Chinese Academy of Agricultrial Sciences, Changsha Hunan, 410205, P.R. China
| | - Touming Liu
- Institute of bast fiber crops, Chinese Academy of Agricultrial Sciences, Changsha Hunan, 410205, P.R. China
| | - Hongwu Wang
- Xianning Agriculture Academy of sciences, Hubei, China
| | - Yan Yang
- Dazhou Agriculture Academy of sciences, Sichuan, China
| | - Xiaorong Chen
- Yichun Institute of Agricultural Sciences, Jiangxi, China
| | - Siyuan Zhu
- Institute of bast fiber crops, Chinese Academy of Agricultrial Sciences, Changsha Hunan, 410205, P.R. China.
| |
Collapse
|
26
|
Xi H, Shen J, Qu Z, Yang D, Liu S, Nie X, Zhu L. Effects of Long-term Cotton Continuous Cropping on Soil Microbiome. Sci Rep 2019; 9:18297. [PMID: 31797982 PMCID: PMC6892916 DOI: 10.1038/s41598-019-54771-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/18/2019] [Indexed: 11/24/2022] Open
Abstract
Verticillium wilt is a severe disease of cotton crops in Xinjiang and affecting yields and quality, due to the continuous cotton cropping in the past decades. The relationship between continuous cropping and the changes induced on soil microbiome remains unclear to date. In this study, the culture types of 15 isolates from Bole (5F), Kuitun (7F), and Shihezi (8F) of north Xinjiang were sclerotium type. Only isolates from field 5F belonged to nondefoliating pathotype, the others belonged to defoliating pathotype. The isolates showed pathogenicity differentiation in cotton. Fungal and bacterial communities in soils had some difference in alpha-diversity, relative abundance, structure and taxonomic composition, but microbial groups showed similarity in the same habitat, despite different sampling sites. The fungal phyla Ascomycota, and the bacterial phyla Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria and Gemmatimonadetes were strongly enriched. Verticillium abundance was significantly and positively correlated with AN, but negatively correlated with soil OM, AK and pH. Moreover, Verticillium was correlated in abundances with 5 fungal and 6 bacterial genera. Overall, we demonstrate that soil microbiome communities have similar responses to long-term continuous cotton cropping, providing new insights into the effects of continuous cotton cropping on soil microbial communities.
Collapse
Affiliation(s)
- Hui Xi
- College of Agronomy, Shihezi University, Shihezi, 832000, P.R. China
| | - Jili Shen
- College of Agronomy, Shihezi University, Shihezi, 832000, P.R. China
| | - Zheng Qu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, P.R. China
| | - Dingyi Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, P.R. China
| | - Shiming Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, P.R. China
| | - Xinhui Nie
- College of Agronomy, Shihezi University, Shihezi, 832000, P.R. China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, P.R. China.
| |
Collapse
|
27
|
Chen A, Gu L, Xu N, Feng F, Chen D, Yang C, Zhang B, Li M, Zhang Z. NB-LRRs Not Responding Consecutively to Fusarium oxysporum Proliferation Caused Replant Disease Formation of Rehmannia glutinosa. Int J Mol Sci 2019; 20:ijms20133203. [PMID: 31261891 PMCID: PMC6651281 DOI: 10.3390/ijms20133203] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 06/19/2019] [Accepted: 06/25/2019] [Indexed: 12/15/2022] Open
Abstract
Consecutive monoculture practice facilitates enrichment of rhizosphere pathogenic microorganisms and eventually leads to the emergence of replant disease. However, little is known about the interaction relationship among pathogens enriched in rhizosphere soils, Nucleotide binding-leucine-rich repeats (NB-LRR) receptors that specifically recognize pathogens in effector-triggered immunity (ETI) and physiological indicators under replant disease stress in Rehmannia glutinosa. In this study, a controlled experiment was performed using different kinds of soils from sites never planted R. glutinosa (NP), replanted R. glutinosa (TP) and mixed by different ration of TP soils (1/3TP and 2/3TP), respectively. As a result, different levels of TP significantly promoted the proliferation of Fusarium oxysporum f.sp. R.glutinosa (FO). Simultaneously, a comparison between FO numbers and NB-LRR expressions indicated that NB-LRRs were not consecutively responsive to the FO proliferation at transcriptional levels. Further analysis found that NB-LRRs responded to FO invasion with a typical phenomenon of “promotion in low concentration and suppression in high concentration”, and 6 NB-LRRs were identified as candidates for responding R. glutinosa replant disease. Furthermore, four critical hormones of salicylic acid (SA), jasmonic acid (JA), ethylene (ET) and abscisic acid (ABA) had higher levels in 1/3TP, 2/3TP and TP than those in NP. Additionally, increasing extents of SA contents have significantly negative trends with FO changes, which implied that SA might be inhibited by FO in replanted R. glutinosa. Concomitantly, the physiological indexes reacted alters of cellular process regulated by NB-LRR were affected by complex replant disease stresses and exhibited strong fluctuations, leading to the death of R. glutinosa. These findings provide important insights and clues into further revealing the mechanism of R. glutinosa replant disease.
Collapse
Affiliation(s)
- Aiguo Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Tobacco Research, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Li Gu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Na Xu
- Institute of Tobacco Research, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Fajie Feng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dexin Chen
- Institute of Tobacco Research, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Chuyun Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Bao Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mingjie Li
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zhongyi Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| |
Collapse
|
28
|
Jiao XL, Zhang XS, Lu XH, Qin R, Bi YM, Gao WW. Effects of maize rotation on the physicochemical properties and microbial communities of American ginseng cultivated soil. Sci Rep 2019; 9:8615. [PMID: 31197229 PMCID: PMC6565631 DOI: 10.1038/s41598-019-44530-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 05/13/2019] [Indexed: 11/26/2022] Open
Abstract
The production of American ginseng (Panax quinquefolius L.) is severely limited by the replant disorders in China. Crop rotation with maize might reduce the replant problems, but little information is available on the effect of maize rotation on soil cultivated with ginseng. In this study, we analyzed nutrients, phenolic acids, and microbial communities in soils from the fields with continuous maize, mono-culture ginseng, and 1-, 3-, and 5-year maize rotation after ginseng. Pot experiments were also conducted to evaluate the performance of replanting ginseng in these soils. The results showed that Mn, Cu, and 5 phenolic acids in ginseng-cultivated soil were significantly decreased by maize rotation. A 5-year maize rotation significantly increased the relative abundance of beneficial soil bacteria, such as Arthrobacter, rather than decreasing the abundances of potential pathogenic genera. Clustering analysis revealed that the physicochemical properties and microbial communities of 3- and 5-year maize rotation soil were more similar to CM than to G soil. The biomass of replanted ginseng root was improved, and root disease was reduced over 3 years of maize rotation. Overall, the results showed that at least a 3-year maize rotation is needed to overcome the replant failure of American ginseng.
Collapse
Affiliation(s)
- Xiao-Lin Jiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Xue-Song Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Xiao-Hong Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ruijun Qin
- Oregon State University-Hermiston Agricultural Research and Extension Center, Hermiston, OR, 97838, USA
| | - Yan-Meng Bi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Wei-Wei Gao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China.
| |
Collapse
|
29
|
Stringlis IA, Yu K, Feussner K, de Jonge R, Van Bentum S, Van Verk MC, Berendsen RL, Bakker PAHM, Feussner I, Pieterse CMJ. MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health. Proc Natl Acad Sci U S A 2018; 115:E5213-E5222. [PMID: 29686086 DOI: 10.1094/pbiomes-11-18-0050-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Abstract
Plant roots nurture a tremendous diversity of microbes via exudation of photosynthetically fixed carbon sources. In turn, probiotic members of the root microbiome promote plant growth and protect the host plant against pathogens and pests. In the Arabidopsis thaliana-Pseudomonas simiae WCS417 model system the root-specific transcription factor MYB72 and the MYB72-controlled β-glucosidase BGLU42 emerged as important regulators of beneficial rhizobacteria-induced systemic resistance (ISR) and iron-uptake responses. MYB72 regulates the biosynthesis of iron-mobilizing fluorescent phenolic compounds, after which BGLU42 activity is required for their excretion into the rhizosphere. Metabolite fingerprinting revealed the antimicrobial coumarin scopoletin as a dominant metabolite that is produced in the roots and excreted into the rhizosphere in a MYB72- and BGLU42-dependent manner. Shotgun-metagenome sequencing of root-associated microbiota of Col-0, myb72, and the scopoletin biosynthesis mutant f6'h1 showed that scopoletin selectively impacts the assembly of the microbial community in the rhizosphere. We show that scopoletin selectively inhibits the soil-borne fungal pathogens Fusarium oxysporum and Verticillium dahliae, while the growth-promoting and ISR-inducing rhizobacteria P. simiae WCS417 and Pseudomonas capeferrum WCS358 are highly tolerant of the antimicrobial effect of scopoletin. Collectively, our results demonstrate a role for coumarins in microbiome assembly and point to a scenario in which plants and probiotic rhizobacteria join forces to trigger MYB72/BGLU42-dependent scopolin production and scopoletin excretion, resulting in improved niche establishment for the microbial partner and growth and immunity benefits for the host plant.
Collapse
Affiliation(s)
- Ioannis A Stringlis
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Ke Yu
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Kirstin Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, 37077 Göttingen, Germany
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Sietske Van Bentum
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Marcel C Van Verk
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Roeland L Berendsen
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Peter A H M Bakker
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, 37077 Göttingen, Germany
- Department of Plant Biochemistry, Göttingen Center for Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands;
| |
Collapse
|
30
|
Browne G, Ott N, Poret-Peterson A, Gouran H, Lampinen B. Efficacy of Anaerobic Soil Disinfestation for Control of Prunus Replant Disease. PLANT DISEASE 2018; 102:209-219. [PMID: 30673462 DOI: 10.1094/pdis-09-16-1392-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Prunus replant disease (PRD) is an important soilborne complex that suppresses growth and productivity of replanted stone fruit and nut orchards. It is effectively managed with preplant soil fumigation but, due to regulatory challenges, nonfumigant-based control strategies for PRD and other soilborne disease problems may become increasingly important, especially in California. We examined the potential of preplant anaerobic soil disinfestation (ASD) for control of PRD in four repeated orchard replant trials on sandy loam soil near Parlier, CA. After removal of the old orchard trees, alternative ASD treatments, all using rice bran as the main carbon source, were implemented, starting in late September. The alternative treatments incorporated rice bran at (i) 20 t ha-1, alone, in 3.0-m-wide row strips; (ii) 20 t ha-1, preceded by incorporation of a sudangrass cover crop and followed by drip application of molasses (10 t ha-1), in 3.0-m-wide row strips; (iii) 20 t ha-1, alone, in 1.8-m-wide strips; or (iv) 12 t ha-1, alone, in 1.8-m-wide strips. All ASD-treated areas were covered with clear tarp and drip irrigated with 25 cm of water. Tarps remained for 6 weeks, during which the soil moisture level was kept at or above field capacity by drip irrigation. All trials included nontreated control and fumigated standard treatments. ASD raised temperature and reduced redox potential in soil at 15- and 46-cm depths for 6 weeks. Fumigation and ASD treatments both nearly eradicated bioassay inoculum of Pythium ultimum in the soil before almond trees were replanted and significantly affected almond tree root communities of fungi and oomycetes after planting. Fumigation treatments and ASD treatments with rice bran at 20 t ha-1 in 3.0-m strips increased tree growth significantly and by similar magnitudes. Among repeated experiments, mean increases in trunk cross-sectional area growth due to fumigation ranged from 137 to 264%, while the increases due to ASD at 20 t ha-1 in 3.0-m strips ranged from 148 to 214%, compared with controls. ASD offers effective control of PRD and is worthy of further optimization and testing for management of PRD and additional orchard replant problems.
Collapse
Affiliation(s)
- G Browne
- United States Department of Agriculture-Agricultural Research Service Crops Pathology and Genetics Research Unit, Department of Plant Pathology, University of California, Davis
| | - N Ott
- United States Department of Agriculture-Agricultural Research Service Crops Pathology and Genetics Research Unit, Department of Plant Pathology, University of California, Davis
| | - A Poret-Peterson
- United States Department of Agriculture-Agricultural Research Service Crops Pathology and Genetics Research Unit, Department of Plant Pathology, University of California, Davis
| | - H Gouran
- United States Department of Agriculture-Agricultural Research Service Crops Pathology and Genetics Research Unit, Department of Plant Pathology, University of California, Davis
| | - B Lampinen
- Department of Plant Sciences, University of California, Davis
| |
Collapse
|
31
|
She S, Niu J, Zhang C, Xiao Y, Chen W, Dai L, Liu X, Yin H. Significant relationship between soil bacterial community structure and incidence of bacterial wilt disease under continuous cropping system. Arch Microbiol 2017; 199:267-275. [PMID: 27699437 DOI: 10.1007/s00203-016-1301-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/22/2016] [Accepted: 09/28/2016] [Indexed: 10/20/2022]
Abstract
Soil bacteria are very important in biogeochemical cycles and play significant role in soil-borne disease suppression. Although continuous cropping is responsible for soil-borne disease enrichment, its effect on tobacco plant health and how soil bacterial communities change are yet to be elucidated. In this study, soil bacterial communities across tobacco continuous cropping time-series fields were investigated through high-throughput sequencing of 16S ribosomal RNA genes. The results showed that long-term continuous cropping could significantly alter soil microbial communities. Bacterial diversity indices and evenness indices decreased over the monoculture span and obvious variations for community structures across the three time-scale tobacco fields were detected. Compared with the first year, the abundances of Arthrobacter and Lysobacter showed a significant decrease. Besides, the abundance of the pathogen Ralstonia spp. accumulated over the monoculture span and was significantly correlated with tobacco bacterial wilt disease rate. Moreover, Pearson's correlation demonstrated that the abundance of Arthrobacter and Lysobacter, which are considered to be beneficial bacteria had significant negative correlation with tobacco bacterial wilt disease. Therefore, after long-term continuous cropping, tobacco bacterial wilt disease could be ascribed to the alteration of the composition as well as the structure of the soil microbial community.
Collapse
Affiliation(s)
- Siyuan She
- School of Minerals Processing and Bioengineering, Central South University, No. 932, South Lushan Road, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Jiaojiao Niu
- School of Minerals Processing and Bioengineering, Central South University, No. 932, South Lushan Road, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Chao Zhang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Yunhua Xiao
- School of Minerals Processing and Bioengineering, Central South University, No. 932, South Lushan Road, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Wu Chen
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Linjian Dai
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, No. 932, South Lushan Road, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, No. 932, South Lushan Road, Changsha, 410083, China.
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China.
| |
Collapse
|
32
|
Yamaguchi M, Narimatsu M, Fujita T, Kawai M, Kobayashi H, Ohta A, Yamada A, Matsushita N, Neda H, Shimokawa T, Murata H. A qPCR assay that specifically quantifies Tricholoma matsutake biomass in natural soil. MYCORRHIZA 2016; 26:847-861. [PMID: 27371100 DOI: 10.1007/s00572-016-0718-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/23/2016] [Indexed: 06/06/2023]
Abstract
Tricholoma matsutake is an ectomycorrhizal basidiomycete that produces prized, yet uncultivable, "matsutake" mushrooms along densely developed mycelia, called "shiro," in the rhizosphere of coniferous forests. Pinus densiflora is a major host of this fungus in Japan. Measuring T. matsutake biomass in soil allows us to determine the kinetics of fungal growth before and after fruiting, which is useful for analyzing the conditions of the shiro and its surrounding mycorrhizosphere, predicting fruiting timing, and managing forests to obtain better crop yields. Here, we document a novel method to quantify T. matsutake mycelia in soil by quantifying a single-copy DNA element that is uniquely conserved within T. matsutake but is absent from other fungal species, including close relatives and a wide range of ectomycorrhizal associates of P. densiflora. The targeted DNA region was amplified quantitatively in cultured mycelia that were mixed with other fungal species and soil, as well as in an in vitro co-culture system with P. densiflora seedlings. Using this method, we quantified T. matsutake mycelia not only from shiro in natural environments but also from the surrounding soil in which T. matsutake mycelia could not be observed by visual examination or distinguished by other means. It was demonstrated that the core of the shiro and its underlying area in the B horizon are predominantly composed of fungal mycelia. The fungal mass in the A or A0 horizon was much lower, although many white mycelia were observed at the A horizon. Additionally, the rhizospheric fungal biomass peaked during the fruiting season.
Collapse
Affiliation(s)
- Muneyoshi Yamaguchi
- Department of Applied Microbiology and Mushroom Science, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan.
| | - Maki Narimatsu
- Iwate Prefectural Forestry Technology Center, Kemuyama, Yahaba, Iwate, 028-3623, Japan
| | - Toru Fujita
- Kyoto Prefectural Forestry Technology Center, 1 Tsuchiya Honjo, Kyotanba, Kyoto, 629-1121, Japan
| | - Masataka Kawai
- Nara Forest Research Institute, Takatori, Nara, 635-0133, Japan
| | - Hisayasu Kobayashi
- Ibaraki Prefectural Forestry Research Institute, Naka, Ibaraki, 311-0122, Japan
| | - Akira Ohta
- Shiga Forest Research Center, Yasu, Shiga, 520-2321, Japan
| | - Akiyoshi Yamada
- Faculty of Agriculture, Shinshu University, Minami-minowa, Nagano, 399-4598, Japan
| | - Norihisa Matsushita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hitoshi Neda
- Department of Applied Microbiology and Mushroom Science, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| | - Tomoko Shimokawa
- Department of Applied Microbiology and Mushroom Science, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| | - Hitoshi Murata
- Department of Applied Microbiology and Mushroom Science, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| |
Collapse
|
33
|
Hamidat M, Barakat M, Ortet P, Chanéac C, Rose J, Bottero JY, Heulin T, Achouak W, Santaella C. Design Defines the Effects of Nanoceria at a Low Dose on Soil Microbiota and the Potentiation of Impacts by the Canola Plant. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:6892-6901. [PMID: 27243334 DOI: 10.1021/acs.est.6b01056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Soils act as nanoceria sinks via agricultural spreading and surface waters. Canola plants were grown for one month in soil spiked with nanoceria (1 mg·kg(-1)). To define the role of nanomaterials design on environmental impacts, we studied nanoceria with different sizes (3.5 or 31 nm) and coating (citrate). We measured microbial activities involved in C, N, and P cycling in the rhizosphere and unplanted soil. Bacterial community structure was analyzed in unplanted soil, rhizosphere, and plant roots by 454-pyrosequencing of the 16S rRNA gene. This revealed an impact gradient dependent on nanomaterials design, ranging from decreased microbial enzymatic activities in planted soil to alterations in bacterial community structure in roots. Particle size/aggregation was a key parameter in modulating nanoceria effects on root communities. Citrate coating lowered the impact on microbial enzymatic activities but triggered variability in the bacterial community structure near the plant root. Some nanoceria favored taxa whose closest relatives are hydrocarbon-degrading bacteria and disadvantaged taxa frequently associated in consortia with disease-suppressive activity toward plant pathogens. This work provides a basis to determine outcomes of nanoceria in soil, at a dose close to predicted environmental concentrations, and to design them to minimize these impacts.
Collapse
Affiliation(s)
- Mohamed Hamidat
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| | - Mohamed Barakat
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| | - Philippe Ortet
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| | - Corinne Chanéac
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
- Chimie de la Matière Condensée, UMR7574, Collège de France, Université de Jussieu , Paris F-75231, France
| | - Jérome Rose
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
- CNRS, Aix-Marseille Université, IRD, CEREGE UM34, F-13545 Aix en Provence, France
| | - Jean-Yves Bottero
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
- CNRS, Aix-Marseille Université, IRD, CEREGE UM34, F-13545 Aix en Provence, France
| | - Thierry Heulin
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| | - Wafa Achouak
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| | - Catherine Santaella
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| |
Collapse
|
34
|
Xiong W, Li Z, Liu H, Xue C, Zhang R, Wu H, Li R, Shen Q. The Effect of Long-Term Continuous Cropping of Black Pepper on Soil Bacterial Communities as Determined by 454 Pyrosequencing. PLoS One 2015; 10:e0136946. [PMID: 26317364 PMCID: PMC4552827 DOI: 10.1371/journal.pone.0136946] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 08/11/2015] [Indexed: 11/18/2022] Open
Abstract
In the present study, 3 replanted black pepper orchards with continuously cropping histories for 10, 21, and 55 years in tropical China, were selected for investigating the effect of monoculture on soil physiochemical properties, enzyme activities, bacterial abundance, and bacterial community structures. Results showed long-term continuous cropping led to a significant decline in soil pH, organic matter contents, enzymatic activities, and resulted in a decrease in soil bacterial abundance. 454 pyrosequencing analysis of 16S rRNA genes revealed that the Acidobacteria and Proteobacteria were the main phyla in the replanted black pepper orchard soils, comprising up to 73.82% of the total sequences; the relative abundances of Bacteroidetes and Firmicutes phyla decreased with long-term continuous cropping; and at genus level, the Pseudomonas abundance significantly depleted after 21 years continuous cropping. In addition, bacterial diversity significantly decreased after 55 years black pepper continuous cropping; obvious variations for community structures across the 3 time-scale replanted black pepper orchards were observed, suggesting monoculture duration was the major determinant for bacterial community structure. Overall, continuous cropping during black pepper cultivation led to a significant decline in soil pH, organic matter contents, enzymatic activities, resulted a decrease in soil bacterial abundance, and altered soil microbial community membership and structure, which in turn resulted in black pepper poor growth in the continuous cropping system.
Collapse
Affiliation(s)
- Wu Xiong
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Science, Wanning, Hainan 571533, China
- National Engineering Research Center for Organic-based Fertilizers, Jiangsu Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhigang Li
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Science, Wanning, Hainan 571533, China
| | - Hongjun Liu
- National Engineering Research Center for Organic-based Fertilizers, Jiangsu Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 210095, Nanjing, China
| | - Chao Xue
- National Engineering Research Center for Organic-based Fertilizers, Jiangsu Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 210095, Nanjing, China
| | - Ruifu Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Huasong Wu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Science, Wanning, Hainan 571533, China
- * E-mail: (RL); (HW)
| | - Rong Li
- National Engineering Research Center for Organic-based Fertilizers, Jiangsu Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 210095, Nanjing, China
- * E-mail: (RL); (HW)
| | - Qirong Shen
- National Engineering Research Center for Organic-based Fertilizers, Jiangsu Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 210095, Nanjing, China
| |
Collapse
|
35
|
Sun J, Zhang Q, Zhou J, Wei Q. Illumina amplicon sequencing of 16S rRNA tag reveals bacterial community development in the rhizosphere of apple nurseries at a replant disease site and a new planting site. PLoS One 2014; 9:e111744. [PMID: 25360786 PMCID: PMC4216118 DOI: 10.1371/journal.pone.0111744] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 10/03/2014] [Indexed: 11/24/2022] Open
Abstract
We used a next-generation, Illumina-based sequencing approach to characterize the bacterial community development of apple rhizosphere soil in a replant site (RePlant) and a new planting site (NewPlant) in Beijing. Dwarfing apple nurseries of 'Fuji'/SH6/Pingyitiancha trees were planted in the spring of 2013. Before planting, soil from the apple rhizosphere of the replant site (ReSoil) and from the new planting site (NewSoil) was sampled for analysis on the Illumina MiSeq platform. In late September, the rhizosphere soil from both sites was resampled (RePlant and NewPlant). More than 16,000 valid reads were obtained for each replicate, and the community was composed of five dominant groups (Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes and Actinobacteria). The bacterial diversity decreased after apple planting. Principal component analyses revealed that the rhizosphere samples were significantly different among treatments. Apple nursery planting showed a large impact on the soil bacterial community, and the community development was significantly different between the replanted and newly planted soils. Verrucomicrobia were less abundant in RePlant soil, while Pseudomonas and Lysobacter were increased in RePlant compared with ReSoil and NewPlant. Both RePlant and ReSoil showed relatively higher invertase and cellulase activities than NewPlant and NewSoil, but only NewPlant soil showed higher urease activity, and this soil also had the higher plant growth. Our experimental results suggest that planting apple nurseries has a significant impact on soil bacterial community development at both replant and new planting sites, and planting on new site resulted in significantly higher soil urease activity and a different bacterial community composition.
Collapse
Affiliation(s)
- Jian Sun
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Qiang Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jia Zhou
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Qinping Wei
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| |
Collapse
|
36
|
PRISE2: software for designing sequence-selective PCR primers and probes. BMC Bioinformatics 2014; 15:317. [PMID: 25252611 PMCID: PMC4261892 DOI: 10.1186/1471-2105-15-317] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 09/20/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND PRISE2 is a new software tool for designing sequence-selective PCR primers and probes. To achieve high level of selectivity, PRISE2 allows the user to specify a collection of target sequences that the primers are supposed to amplify, as well as non-target sequences that should not be amplified. The program emphasizes primer selectivity on the 3' end, which is crucial for selective amplification of conserved sequences such as rRNA genes. In PRISE2, users can specify desired properties of primers, including length, GC content, and others. They can interactively manipulate the list of candidate primers, to choose primer pairs that are best suited for their needs. A similar process is used to add probes to selected primer pairs. More advanced features include, for example, the capability to define a custom mismatch penalty function. PRISE2 is equipped with a graphical, user-friendly interface, and it runs on Windows, Macintosh or Linux machines. RESULTS PRISE2 has been tested on two very similar strains of the fungus Dactylella oviparasitica, and it was able to create highly selective primers and probes for each of them, demonstrating the ability to create useful sequence-selective assays. CONCLUSIONS PRISE2 is a user-friendly, interactive software package that can be used to design high-quality selective primers for PCR experiments. In addition to choosing primers, users have an option to add a probe to any selected primer pair, enabling design of Taqman and other primer-probe based assays. PRISE2 can also be used to design probes for FISH and other hybridization-based assays.
Collapse
|
37
|
Almario J, Muller D, Défago G, Moënne-Loccoz Y. Rhizosphere ecology and phytoprotection in soils naturally suppressive to Thielaviopsis black root rot of tobacco. Environ Microbiol 2014; 16:1949-60. [PMID: 24650207 DOI: 10.1111/1462-2920.12459] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Accepted: 03/16/2014] [Indexed: 11/27/2022]
Abstract
Soil suppressiveness to disease is an intriguing emerging property in agroecosystems, with important implications because it enables significant protection of susceptible plants from soil-borne pathogens. Unlike many soils where disease suppressiveness requires crop monoculture to establish, certain soils are naturally suppressive to disease, and this type of specific disease suppressiveness is maintained despite crop rotation. Soils naturally suppressive to Thielaviopsis basicola-mediated black root rot of tobacco and other crops occur in Morens region (Switzerland) and have been studied for over 30 years. In Morens, vermiculite-rich suppressive soils formed on morainic deposits while illite-rich conducive soils developed on sandstone, but suppressiveness is of microbial origin. Antagonistic pseudomonads play a role in black root rot suppressiveness, including Pseudomonas protegens (formerly P. fluorescens) CHA0, a major model strain for research. However, other types of rhizobacterial taxa may differ in prevalence between suppressive and conducive soils, suggesting that the microbial basis of black root rot suppressiveness could be far more complex than solely a Pseudomonas property. This first review on black root rot suppressive soils covers early findings on these soils, the significance of recent results, and compares them with other types of suppressive soils in terms of rhizosphere ecology and plant protection mechanisms.
Collapse
Affiliation(s)
- Juliana Almario
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
| | | | | | | |
Collapse
|
38
|
A method to detect and quantify Phaeomoniella chlamydospora and Phaeoacremonium aleophilum DNA in grapevine-wood samples. Appl Microbiol Biotechnol 2013; 97:10163-75. [PMID: 24136470 DOI: 10.1007/s00253-013-5299-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/26/2013] [Accepted: 09/27/2013] [Indexed: 10/26/2022]
Abstract
Grapevines are sensitive to a wide range of fungal pathogens, including agents such as Phaeomoniella chlamydospora and Phaeoacremonium aleophilum that cause tracheomycosis. In the present study, a procedure for DNA extraction from grapevine woody tissue is first evaluated and shown to be suitable for quantitative analysis. Next, a multiplex real-time PCR method targeting the β-tubulin gene of the pathogens and the actin gene of plant material is developed and its quantitative capability is verified. This protocol was evaluated in inoculated grapevine-wood samples and in young vines from a nursery and was found to be reliable and highly specific. Results obtained from inoculated cuttings show that the fungal colonization process must be considered regardless of the wood phenotype. An analysis of samples of young vines from the nursery shows that a high rate of contamination occurs at the basis of plants and that this contamination is associated with low quantitative values. This finding provides evidence that in vine nurseries, these fungi may be efficient soil-borne pathogens.
Collapse
|