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Nayak PK, Nayak AK, Panda BB, Senapati A, Panneerselvam P, Kumar A, Tripathi R, Poonam A, Shahid M, Mohapatra SD, Kaviraj M, Kumar U. Rice-based integrated farming system improves the soil quality, bacterial community structure and system productivity under sub-humid tropical condition. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:65. [PMID: 38321197 DOI: 10.1007/s10653-024-01863-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 01/07/2024] [Indexed: 02/08/2024]
Abstract
Rice-based integrated farming system improves the productivity and profitability by recycling resources efficiently. In the sub-humid tropics, rice production without sufficient nutrient replenishment often leads to soil health and fertility degradation. There has been very limited research on soil health and fertility after adopting a multi-enterprising rice-based integrated farming system (IFS), notably in the rice-fish-livestock and agroforestry system, when compared to a conventional farming system (CS). Therefore, the present study analyzed the dynamics of soil properties, soil bacterial community structure and their possible interaction mechanisms, as well as their effect on regulating soil quality and production in IFS, IFSw (water stagnant area of IFS) and CS. The results indicated that soil nutrient dynamics, bacterial diversity indices (Shannon index, Simpson index, Chao 1, ACE and Fisher index) and system productivity were higher in IFSw and IFS compared to CS. Moreover, relative operational taxonomic units of dominant bacterial genera (Chloroflexi, Acidobacteria, Verrucomicrobia, Planctomycetes, Cyanobacteria, Crenarchaeota and Gemmatimonadetes) were also higher in IFSw and IFS compared to CS. Mean soil quality index (SQI) was highest in IFSw (0.780 ± 0.201) followed by IFS (0.770 ± 0.080) and CS (0.595 ± 0.244). Moreover, rice equivalent yields (REY) and rice yields were well correlated with the higher levels of soil biological indices (SQIBiol) in IFS. Overall, our results revealed that rice-based IFS improved the soil health and fertility and ensuing crop productivity through positive interaction with soil bacterial communities and nutrient stoichiometry leading to agroecosystem sustainability.
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Affiliation(s)
| | - A K Nayak
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - B B Panda
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - A Senapati
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - P Panneerselvam
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - A Kumar
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - R Tripathi
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - A Poonam
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - M Shahid
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - S D Mohapatra
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Megha Kaviraj
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Upendra Kumar
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India.
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Zeeshan Ul Haq M, Yu J, Yao G, Yang H, Iqbal HA, Tahir H, Cui H, Liu Y, Wu Y. A Systematic Review on the Continuous Cropping Obstacles and Control Strategies in Medicinal Plants. Int J Mol Sci 2023; 24:12470. [PMID: 37569843 PMCID: PMC10419402 DOI: 10.3390/ijms241512470] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Continuous cropping (CC) is a common practice in agriculture, and usually causes serious economic losses due to soil degeneration, decreased crop yield and quality, and increased disease incidence, especially in medicinal plants. Continuous cropping obstacles (CCOs) are mainly due to changes in soil microbial communities, nutrient availability, and allelopathic effects. Recently, progressive studies have illustrated the molecular mechanisms of CCOs, and valid strategies to overcome them. Transcriptomic and metabolomics analyses revealed that identified DEGs (differently expressed genes) and metabolites involved in the response to CCOs are involved in various biological processes, including photosynthesis, carbon metabolism, secondary metabolite biosynthesis, and bioactive compounds. Soil improvement is an effective strategy to overcome this problem. Soil amendments can improve the microbial community by increasing the abundance of beneficial microorganisms, soil fertility, and nutrient availability. In this review, we sum up the recent status of the research on CCOs in medicinal plants, the combination of transcriptomic and metabolomics studies, and related control strategies, including uses of soil amendments, crop rotation, and intercropping. Finally, we propose future research trends for understanding CCOs, and strategies to overcome these obstacles and promote sustainable agriculture practices in medicinal plants.
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Affiliation(s)
| | | | | | | | | | | | | | - Ya Liu
- Sanya Nanfan Research Institute of Hainan University, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Yougen Wu
- Sanya Nanfan Research Institute of Hainan University, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
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Town JR, Dumonceaux T, Tidemann B, Helgason BL. Crop rotation significantly influences the composition of soil, rhizosphere, and root microbiota in canola (Brassica napus L.). ENVIRONMENTAL MICROBIOME 2023; 18:40. [PMID: 37161618 PMCID: PMC10169384 DOI: 10.1186/s40793-023-00495-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/19/2023] [Indexed: 05/11/2023]
Abstract
BACKGROUND Crop rotation is an agronomic practice that is known to enhance productivity and yield, and decrease pest and disease pressure. Economic and other factors have increased the frequency of certain crops, including canola, with unknown effects on the below ground microbial communities that impact plant health and performance. This study investigated the effect of 12 years of crop rotation including canola-wheat; canola-pea-barley; and unrotated canola across three geographic sites in Western Canada with diverse soil types and environmental conditions. To provide data on mature, established crop rotation strategies, root exudate profiles, soil nutrient fluxes, and bacterial and fungal microbial community profiles were determined at the flowering stage in the final two (canola) years of the 12-year rotations. RESULTS After 12 years of rotation, nutrient fluxes were affected in the soil in an inconsistent manner, with K, NO3, Mg, Ca, P, and Fe fluxes variably impacted by rotation depending on the year and site of sampling. As expected, rotation positively influenced yield and oil content, and decreased disease pressure from Leptosphaeria and Alternaria. In two of the three sites, root exudate profiles were significantly influenced by crop rotation. Bacterial soil, root, and rhizosphere communities were less impacted by crop rotation than the fungal communities. Fungal sequences that were associated with specific rotation strategies were identified in the bulk soil, and included known fungal pathogens in the canola-only strategy. Two closely related fungal sequences identified as Olpidium brassicae were extremely abundant at all sites in both years. One of these sequences was observed uniquely at a single site and was significantly associated with monocropped canola; moreover, its abundance correlated negatively with yield in both years. CONCLUSIONS Long-term canola monoculture affected root exudate profiles and soil nutrient fluxes differently in the three geographic locations. Bacterial communities were less impacted by rotation compared to the fungal communities, which consistently exhibited changes in composition in all ecological niches at all sites, in both years. Fungal sequences identified as O. brassicae were highly abundant at all sites, one of which was strongly associated with canola monoculture. Soil management decisions should include consideration of the effects on the microbial ecosystems associated with the plants in order to inform best management practices.
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Affiliation(s)
- Jennifer R Town
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK, Canada.
| | - Tim Dumonceaux
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK, Canada
| | - Breanne Tidemann
- Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, Lacombe, AB, Canada
| | - Bobbi L Helgason
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK, Canada
- Department of Soil Science, University of Saskatchewan, Saskatoon, SK, Canada
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Jayaweera DP, Ray RV. Yield Loss and Integrated Disease Control of Rhizoctonia solani AG2-1 Using Seed Treatment and Sowing Rate of Oilseed Rape. PLANT DISEASE 2023; 107:1159-1165. [PMID: 36194734 DOI: 10.1094/pdis-08-22-1817-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Rhizoctonia solani anastomosis group (AG) 2-1 is an ubiquitous soilborne pathogen causing severe damping-off of oilseed rape (OSR). In the absence of varietal resistance to AG2-1, there are limited methods for integrated disease management. The objectives of these field studies were to quantify yield losses due to AG2-1 and to determine the effectiveness of integrated control using sedaxane, fludioxonil, and metalaxyl-M applied as seed treatment on two OSR genotypes at a sowing rate of 40 (low) or 80 (high) seeds m-2. Crop assessments of green area index (GAI), vigor, and cabbage stem flea beetle (CSFB) Psylliodes chrysocephala damage were carried out at GS16, while pathogen DNA in soil was quantified using real-time PCR at GS32. Yield and seed weight losses of 41 and 18%, respectively, were associated with reduced establishment, GAI, vigor, and delayed development and flowering of OSR. Seed treatment reduced AG2-1 DNA in soil by 80%, resulting in a 94, 16, and 64% increase of establishment, thousand seed weight (TSW), and yield, respectively. Seed treatment also mitigated the effects of AG2-1 on delaying plant development, resulting in increased uniformity of crop flowering. OSR plants infected with AG2-1 suffered 27% more damage by the CSFB, indicating positive pathogen-pest interaction at the expense of the OSR host. Optimum control of AG2-1 infection was achieved by integrating low sowing rate and seed treatment. However, under dual pest and pathogen attack, high sowing rates should be combined with the use of seed treatment to mitigate seedling death and delayed development caused by AG2-1 and CSFB damage.
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Affiliation(s)
- Dasuni P Jayaweera
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, U.K
| | - Rumiana V Ray
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, U.K
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Wang Y, Teng Y, Zhang J, Zhang Z, Wang C, Wu X, Long X. Passion fruit plants alter the soil microbial community with continuous cropping and improve plant disease resistance by recruiting beneficial microorganisms. PLoS One 2023; 18:e0281854. [PMID: 36809377 PMCID: PMC9943001 DOI: 10.1371/journal.pone.0281854] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 02/02/2023] [Indexed: 02/23/2023] Open
Abstract
Passion fruit (Passiflora edulis) is widely grown in tropical and subtropical regions, showing high economic and ornamental value. Microorganisms are indicators for the stability and health of the soil ecosystem, which can affect the yield and quality of passion fruit under continuous cropping. High-throughput sequencing and interactive analysis were used to analyse the variation of microbial communities in the noncultivated soil (NCS), cultivated soil (CS), and the rhizosphere soil of purple passion fruit (Passiflora edulis f. edulis ×Passiflora edulis f. flavicarpa, RP) and yellow passion fruit (Passiflora edulis f. flavicarpa, RY). An average of 98,001 high-quality fungal internal transcribed spacer (ITS) sequences, mainly from Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota and Glomeromycota, as well as an average of 71,299 high-quality bacterial 16S rRNA sequences, mainly from Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Chloroflexi, were obtained per sample. It was found that the continuous cropping of passion fruit increased the richness but reduced the diversity of soil fungi, while it dramatically increased the richness and diversity of soil bacteria. In addition, during the continuous cropping, grafting different scions in the same rootstock contributed to the aggregation of differential rhizosphere microbial communities. Among fungal genera, Trichoderma showed higher abundance in RY than in RP and CS, while the opposite was observed in the pathogen Fusarium. Moreover, the co-occurrence network and potential function analyses also showed that the appearance of Trichoderma was related to Fusarium and its contribution to plant metabolism was significantly greater in RY than in RP and CS. In conclusion, the rhizosphere of yellow passion fruit may be beneficial for the enrichment of disease-resistant microbes, such as Trichoderma, which may be an important factor inducing stronger resistance to stem rot. It will help to form a potential strategy for overcoming the pathogen-mediated obstacles in passion fruit and improve its yield and quality.
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Affiliation(s)
- Ye Wang
- Guizhou Botanical Garden, Guizhou Academy of Sciences, Guiyang, Guizhou, China
- Institute of Mountain Resources of Guizhou Province, Guizhou Academy of Sciences, Guiyang, Guizhou, China
| | - Yao Teng
- Guizhou Botanical Garden, Guizhou Academy of Sciences, Guiyang, Guizhou, China
- Institute of Mountain Resources of Guizhou Province, Guizhou Academy of Sciences, Guiyang, Guizhou, China
| | - Jianli Zhang
- College of Eco-environmental Engineering, Guizhou Minzu University, Guiyang, Guizhou, China
| | - Zixiong Zhang
- Guizhou Botanical Garden, Guizhou Academy of Sciences, Guiyang, Guizhou, China
| | - Chen Wang
- Guizhou Botanical Garden, Guizhou Academy of Sciences, Guiyang, Guizhou, China
| | - Xiukun Wu
- Guizhou Botanical Garden, Guizhou Academy of Sciences, Guiyang, Guizhou, China
| | - Xiuqin Long
- Guizhou Botanical Garden, Guizhou Academy of Sciences, Guiyang, Guizhou, China
- * E-mail:
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Floc'h JB, Hamel C, Laterrière M, Tidemann B, St-Arnaud M, Hijri M. Inter-Kingdom Networks of Canola Microbiome Reveal Bradyrhizobium as Keystone Species and Underline the Importance of Bulk Soil in Microbial Studies to Enhance Canola Production. MICROBIAL ECOLOGY 2022; 84:1166-1181. [PMID: 34727198 DOI: 10.1007/s00248-021-01905-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
The subterranean microbiota of plants is of great importance for plant growth and health, as root-associated microbes can perform crucial ecological functions. As the microbial environment of roots is extremely diverse, identifying keystone microorganisms in plant roots, rhizosphere, and bulk soil is a necessary step towards understanding the network of influence within the microbial community associated with roots and enhancing its beneficial elements. To target these hot spots of microbial interaction, we used inter-kingdom network analysis on the canola growth phase of a long-term cropping system diversification experiment conducted at four locations in the Canadian Prairies. Our aims were to verify whether bacterial and fungal communities of canola roots, rhizosphere, and bulk soil are related and influenced by diversification of the crop rotation system; to determine whether there are common or specific core fungi and bacteria in the roots, rhizosphere, and bulk soil under canola grown in different environments and with different levels of cropping system diversification; and to identify hub taxa at the inter-kingdom level that could play an important ecological role in the microbiota of canola. Our results showed that fungi were influenced by crop diversification, which was not the case on bacteria. We found no core microbiota in canola roots but identified three core fungi in the rhizosphere, one core mycobiota in the bulk soil, and one core bacterium shared by the rhizosphere and bulk soil. We identified two bacterial and one fungal hub taxa in the inter-kingdom networks of the canola rhizosphere, and one bacterial and two fungal hub taxa in the bulk soil. Among these inter-kingdom hub taxa, Bradyrhizobium sp. and Mortierella sp. are particularly influential on the microbial community and the plant. To our knowledge, this is the first inter-kingdom network analysis utilized to identify hot spots of interaction in canola microbial communities.
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Affiliation(s)
- Jean-Baptiste Floc'h
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, 4101 East, Sherbrooke Street, Montréal, QC, H1X 2B2, Canada
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec City, QC, Canada
| | - Chantal Hamel
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, 4101 East, Sherbrooke Street, Montréal, QC, H1X 2B2, Canada
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec City, QC, Canada
| | - Mario Laterrière
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec City, QC, Canada
| | - Breanne Tidemann
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Marc St-Arnaud
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, 4101 East, Sherbrooke Street, Montréal, QC, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, 4101 East, Sherbrooke Street, Montréal, QC, H1X 2B2, Canada.
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, 43150, Ben Guerir, Morocco.
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Muscatt G, Hilton S, Raguideau S, Teakle G, Lidbury IDEA, Wellington EMH, Quince C, Millard A, Bending GD, Jameson E. Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere. MICROBIOME 2022; 10:181. [PMID: 36280853 PMCID: PMC9590211 DOI: 10.1186/s40168-022-01371-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/18/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND The rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-microbe interactions in the rhizosphere, remains undetermined. Given the impact of viruses on the ecology and evolution of their host communities, determining how soil viruses influence microbiome dynamics is crucial to build a holistic understanding of rhizosphere functions. RESULTS Here, we aimed to investigate the influence of crop management on the composition and activity of bulk soil, rhizosphere soil, and root viral communities. We combined viromics, metagenomics, and metatranscriptomics on soil samples collected from a 3-year crop rotation field trial of oilseed rape (Brassica napus L.). By recovering 1059 dsDNA viral populations and 16,541 ssRNA bacteriophage populations, we expanded the number of underexplored Leviviricetes genomes by > 5 times. Through detection of viral activity in metatranscriptomes, we uncovered evidence of "Kill-the-Winner" dynamics, implicating soil bacteriophages in driving bacterial community succession. Moreover, we found the activity of viruses increased with proximity to crop roots, and identified that soil viruses may influence plant-microbe interactions through the reprogramming of bacterial host metabolism. We have provided the first evidence of crop rotation-driven impacts on soil microbial communities extending to viruses. To this aim, we present the novel principal of "viral priming," which describes how the consecutive growth of the same crop species primes viral activity in the rhizosphere through local adaptation. CONCLUSIONS Overall, we reveal unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil, and bulk soil compartments. Our work demonstrates that the roles of soil viruses need greater consideration to exploit the rhizosphere microbiome for food security, food safety, and environmental sustainability. Video Abstract.
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Affiliation(s)
- George Muscatt
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Sebastien Raguideau
- School of Life Sciences, University of Warwick, Coventry, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Graham Teakle
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Ian D E A Lidbury
- School of Life Sciences, University of Warwick, Coventry, UK
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, UK
| | | | - Christopher Quince
- School of Life Sciences, University of Warwick, Coventry, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, UK.
- School of Natural Sciences, Bangor University, Bangor, UK.
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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.
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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.
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Orrù L, Canfora L, Trinchera A, Migliore M, Pennelli B, Marcucci A, Farina R, Pinzari F. How Tillage and Crop Rotation Change the Distribution Pattern of Fungi. Front Microbiol 2021; 12:634325. [PMID: 34220731 PMCID: PMC8247931 DOI: 10.3389/fmicb.2021.634325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 05/13/2021] [Indexed: 12/13/2022] Open
Abstract
Massive sequencing of fungal communities showed that climatic factors, followed by edaphic and spatial variables, are feasible predictors of fungal richness and community composition. This study, based on a long-term field experiment with tillage and no-tillage management since 1995 and with a crop rotation introduced in 2009, confirmed that tillage practices shape soil properties and impact soil fungal communities. Results highlighted higher biodiversity of saprotrophic fungi in soil sites with low disturbance and an inverse correlation between the biodiversity of ectomycorrhizal and saprotrophic fungi. We speculated how their mutual exclusion could be due to a substrate-mediated niche partitioning or by space segregation. Moreover, where the soil was ploughed, the species were evenly distributed. There was higher spatial variability in the absence of ploughing, with fungal taxa distributed according to a small-scale pattern, corresponding to micro-niches that probably remained undisturbed and heterogeneously distributed. Many differentially represented OTUs in all the conditions investigated were unidentified species or OTUs matching at high taxa level (i.e., phylum, class, order). Among the fungi with key roles in all the investigated conditions, there were several yeast species known to have pronounced endemism in soil and are also largely unidentified. In addition to yeasts, other fungal species emerged as either indicator of a kind of management or as strongly associated with a specific condition. Plant residues played a substantial role in defining the assortment of species.
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Affiliation(s)
- Luigi Orrù
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Loredana Canfora
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
| | - Alessandra Trinchera
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
| | - Melania Migliore
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
| | - Bruno Pennelli
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
| | - Andrea Marcucci
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
| | - Roberta Farina
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
| | - Flavia Pinzari
- National Research Council of Italy, Institute for Biological Systems, Rome, Italy
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Picot E, Hale CC, Hilton S, Teakle G, Schäfer H, Huang YJ, Perryman S, West JS, Bending GD. Contrasting Responses of Rhizosphere Bacterial, Fungal, Protist, and Nematode Communities to Nitrogen Fertilization and Crop Genotype in Field Grown Oilseed Rape (Brassica napus). FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.613269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The rhizosphere microbiome is considered to play a key role in determining crop health. However, current understanding of the factors which shape assembly and composition of the microbiome is heavily biased toward bacterial communities, and the relevance for other microbial groups is unclear. Furthermore, community assembly is determined by a variety of factors, including host genotype, environment and agricultural management practices, and their relative importance and interactions remain to be elucidated. We investigated the impact of nitrogen fertilization on rhizosphere bacterial, fungal, nematode and protist communities of 10 contrasting oilseed rape genotypes in a field experiment. We found significant differences in the composition of bacteria, fungi, protist and nematode communities between the rhizosphere and bulk soil. Nitrogen application had a significant but weak effect on fungal, bacterial, and protist community composition, and this was associated with increased relative abundance of a complex of fungal pathogens in the rhizosphere and soil, including Mycosphaerella sp. and Leptosphaeria sp. Network analysis showed that nitrogen application had different effects on microbial community connectivity in the soil and rhizosphere. Crop genotype significantly affected fungal community composition, with evidence for a degree of genotype specificity for a number of pathogens, including L. maculans, Alternaria sp., Pyrenopeziza brassicae, Olpidium brassicae, and L. biglobosa, and also potentially beneficial Heliotales root endophytes. Crop genotype had no significant effect on assembly of bacteria, protist or nematode communities. There was no relationship between genetic distance of crop genotypes and the extent of dissimilarity of rhizosphere microbial communities. Field disease assessment confirmed infection of crops by Leptosphaeria sp., P. brassicae, and Alternaria sp., indicating that rhizosphere microbiome sequencing was an effective indicator of plant health. We conclude that under field conditions soil and rhizosphere nutrient stoichiometry and crop genotype are key factors determining crop health by influencing the infection of roots by pathogenic and mutualistic fungal communities, and the connectivity and stability of rhizosphere microbiome interaction networks.
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11
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Bolaji AJ, Wan JC, Manchur CL, Lawley Y, de Kievit TR, Fernando WGD, Belmonte MF. Microbial Community Dynamics of Soybean ( Glycine max) Is Affected by Cropping Sequence. Front Microbiol 2021; 12:632280. [PMID: 33643263 PMCID: PMC7904696 DOI: 10.3389/fmicb.2021.632280] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 01/22/2021] [Indexed: 12/28/2022] Open
Abstract
The microbial composition of the rhizosphere soil could be an important determinant of crop yield, pathogen resistance, and other beneficial attributes in plants. However, little is known about the impact of cropping sequences on microbial community dynamics, especially in economically important species like soybean. Using 2-year crop sequences of corn-soybean, canola-soybean, and soybean-soybean, we investigated how crops from the previous growing season influenced the structure of the microbiome in both the bulk soil and soybean rhizosphere. A combination of marker-based Illumina sequencing and bioinformatics analyses was used to show that bacterial species richness and evenness in the soybean rhizosphere soil were similar following canola and soybean compared to a previous corn sequence. However, fungal species richness and evenness remained unaffected by crop sequence. In addition, bacterial and fungal species diversity in both the bulk and soybean rhizosphere soil were not influenced by crop sequence. Lastly, the corn-soybean sequence significantly differed in the relative abundance of certain bacterial and fungal classes in both the soybean rhizosphere and bulk soil. While canola-soybean and a continuous soybean sequence did not, suggesting that a preceding corn sequence may reduce the occurrence of overall bacterial and fungal community members. For the present study, crop sequence impacts bacterial diversity and richness in both the bulk soil and soybean rhizosphere soil whereas fungal diversity and richness are resilient to crop sequence practices. Together, these findings could help drive decision making for annual crop and soil management practices.
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Affiliation(s)
- Ayooluwa J Bolaji
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Joey C Wan
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | | | - Yvonne Lawley
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
| | - Teresa R de Kievit
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | | | - Mark F Belmonte
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
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12
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Hilton S, Picot E, Schreiter S, Bass D, Norman K, Oliver AE, Moore JD, Mauchline TH, Mills PR, Teakle GR, Clark IM, Hirsch PR, van der Gast CJ, Bending GD. Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale. MICROBIOME 2021; 9:19. [PMID: 33482913 PMCID: PMC7825223 DOI: 10.1186/s40168-020-00972-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 12/07/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND The plant microbiome plays a vital role in determining host health and productivity. However, we lack real-world comparative understanding of the factors which shape assembly of its diverse biota, and crucially relationships between microbiota composition and plant health. Here we investigated landscape scale rhizosphere microbial assembly processes in oilseed rape (OSR), the UK's third most cultivated crop by area and the world's third largest source of vegetable oil, which suffers from yield decline associated with the frequency it is grown in rotations. By including 37 conventional farmers' fields with varying OSR rotation frequencies, we present an innovative approach to identify microbial signatures characteristic of microbiomes which are beneficial and harmful to the host. RESULTS We show that OSR yield decline is linked to rotation frequency in real-world agricultural systems. We demonstrate fundamental differences in the environmental and agronomic drivers of protist, bacterial and fungal communities between root, rhizosphere soil and bulk soil compartments. We further discovered that the assembly of fungi, but neither bacteria nor protists, was influenced by OSR rotation frequency. However, there were individual abundant bacterial OTUs that correlated with either yield or rotation frequency. A variety of fungal and protist pathogens were detected in roots and rhizosphere soil of OSR, and several increased relative abundance in root or rhizosphere compartments as OSR rotation frequency increased. Importantly, the relative abundance of the fungal pathogen Olpidium brassicae both increased with short rotations and was significantly associated with low yield. In contrast, the root endophyte Tetracladium spp. showed the reverse associations with both rotation frequency and yield to O. brassicae, suggesting that they are signatures of a microbiome which benefits the host. We also identified a variety of novel protist and fungal clades which are highly connected within the microbiome and could play a role in determining microbiome composition. CONCLUSIONS We show that at the landscape scale, OSR crop yield is governed by interplay between complex communities of both pathogens and beneficial biota which is modulated by rotation frequency. Our comprehensive study has identified signatures of dysbiosis within the OSR microbiome, grown in real-world agricultural systems, which could be used in strategies to promote crop yield. Video abstract.
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Affiliation(s)
- Sally Hilton
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK.
| | - Emma Picot
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
| | | | - David Bass
- Department of Life Sciences, The Natural History Museum, London, SW7 5BD, UK
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, Dorset, DT4 8UB, UK
| | - Keith Norman
- Velcourt Group Ltd., The Veldt House, Much Marcle, Ledbury, Herefordshire, HR8 2LJ, UK
| | - Anna E Oliver
- Centre for Ecology and Hydrology, Wallingford, Oxfordshire, OX10 8BB, UK
| | | | | | | | - Graham R Teakle
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
| | | | | | | | - Gary D Bending
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK.
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13
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Floc'h JB, Hamel C, Harker KN, St-Arnaud M. Fungal Communities of the Canola Rhizosphere: Keystone Species and Substantial Between-Year Variation of the Rhizosphere Microbiome. MICROBIAL ECOLOGY 2020; 80:762-777. [PMID: 31897569 DOI: 10.1007/s00248-019-01475-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/16/2019] [Indexed: 05/25/2023]
Abstract
Rhizosphere microbes influence one another, forming extremely complex webs of interactions that may determine plant success. Identifying the key factors that structure the fungal microbiome of the plant rhizosphere is a necessary step in optimizing plant production. In a long-term field experiment conducted at three locations in the Canadian prairies, we tested the following hypotheses: (1) diversification of cropping systems influences the fungal microbiome of the canola (Brassica napus) rhizosphere; (2) the canola rhizosphere has a core fungal microbiome, i.e., a set of fungi always associated with canola; and (3) some taxa within the rhizosphere microbiome of canola are highly interrelated and fit the description of hub taxa. Our results show that crop diversification has a significant effect on the structure of the rhizosphere fungal community but not on fungal diversity. We also discovered and described a canola core microbiome made up of one zero-radius operational taxonomic unit (ZOTU), cf. Olpidium brassicae, and an eco-microbiome found only in 2013 consisting of 47 ZOTUs. Using network analysis, we identified four hub taxa in 2013: ZOTU14 (Acremonium sp.), ZOTU28 (Sordariomycetes sp.), ZOTU45 (Mortierella sp.) and ZOTU179 (cf. Ganoderma applanatum), and one hub taxon, ZOTU17 (cf. Mortierella gamsii) in 2016. None of these most interacting taxa belonged to the core microbiome or eco-microbiome for each year of sampling. This temporal variability puts into question the idea of a plant core fungal microbiome and its stability. Our results provide a basis for the development of ecological engineering strategies for the improvement of canola production systems in Canada.
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Affiliation(s)
- Jean-Baptiste Floc'h
- Institut de recherche en biologie végétale, ,Université de Montréal, 4101 East, Sherbrooke Street, Montréal, QC, H1X 2B2, Canada
- Jardin Botanique de Montréal, Montreal, Canada
- Québec Research and Development Centre of Quebec, Agriculture and Agri-Food Canada, Quebec City, QC, Canada
| | - Chantal Hamel
- Institut de recherche en biologie végétale, ,Université de Montréal, 4101 East, Sherbrooke Street, Montréal, QC, H1X 2B2, Canada
- Jardin Botanique de Montréal, Montreal, Canada
- Québec Research and Development Centre of Quebec, Agriculture and Agri-Food Canada, Quebec City, QC, Canada
| | - K Neil Harker
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Marc St-Arnaud
- Institut de recherche en biologie végétale, ,Université de Montréal, 4101 East, Sherbrooke Street, Montréal, QC, H1X 2B2, Canada.
- Jardin Botanique de Montréal, Montreal, Canada.
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14
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Song C, Zhu F, Carrión VJ, Cordovez V. Beyond Plant Microbiome Composition: Exploiting Microbial Functions and Plant Traits via Integrated Approaches. Front Bioeng Biotechnol 2020; 8:896. [PMID: 32850744 PMCID: PMC7426627 DOI: 10.3389/fbioe.2020.00896] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/13/2020] [Indexed: 12/12/2022] Open
Abstract
Plants recruit specific microorganisms to live inside and outside their roots that provide essential functions for plant growth and health. The study of the microbial communities living in close association with plants helps in understanding the mechanisms involved in these beneficial interactions. Currently, most of the research in this field has been focusing on the description of the taxonomic composition of the microbiome. Therefore, a focus on the plant-associated microbiome functions is pivotal for the development of novel agricultural practices which, in turn, will increase plant fitness. Recent advances in microbiome research using model plant species started to shed light on the functions of specific microorganisms and the underlying mechanisms of plant–microbial interaction. Here, we review (1) microbiome-mediated functions associated with plant growth and protection, (2) insights from native and agricultural habitats that can be used to improve soil health and crop productivity, (3) current -omics and new approaches for studying the plant microbiome, and (4) challenges and future perspectives for exploiting the plant microbiome for beneficial outcomes. We posit that integrated approaches will help in translating fundamental knowledge into agricultural practices.
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Affiliation(s)
- Chunxu Song
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China.,National Academy of Agriculture Green Development, China Agricultural University, Beijing, China.,Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Feng Zhu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Víctor J Carrión
- Institute of Biology, Leiden University, Leiden, Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Viviane Cordovez
- Institute of Biology, Leiden University, Leiden, Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
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15
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Rybakova D, Wikström M, Birch-Jensen F, Postma J, Ehlers RU, Schmuck M, Kollmann R, Köhl J, Berg G. Verticillium Wilt in Oilseed Rape-the Microbiome is Crucial for Disease Outbreaks as Well as for Efficient Suppression. PLANTS 2020; 9:plants9070866. [PMID: 32650549 PMCID: PMC7412322 DOI: 10.3390/plants9070866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 12/17/2022]
Abstract
Microbiome management is a promising way to suppress verticillium wilt, a severe disease in Brassica caused by Verticillium longisporum. In order to improve current biocontrol strategies, we compared bacterial Verticillium antagonists in different assays using a hierarchical selection and evaluation scheme, and we integrated outcomes of our previous studies. The result was strongly dependent on the assessment method chosen (in vitro, in vivo, in situ), on the growth conditions of the plants and their genotype. The most promising biocontrol candidate identified was a Brassica endophyte Serratia plymuthica F20. Positive results were confirmed in field trials and by microscopically visualizing the three-way interaction. Applying antagonists in seed treatment contributes to an exceptionally low ecological footprint, supporting efficient economic and ecological solutions to controlling verticillium wilt. Indigenous microbiome, especially soil and seed microbiome, has been identified as key to understanding disease outbreaks and suppression. We suggest that verticillium wilt is a microbiome-driven disease caused by a reduction in microbial diversity within seeds and in the soil surrounding them. We strongly recommend integrating microbiome data in the development of new biocontrol and breeding strategies and combining both strategies with the aim of designing healthy microbiomes, thus making plants more resilient toward soil-borne pathogens.
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Affiliation(s)
- Daria Rybakova
- Graz University of Technology, Environmental Biotechnology, Petersgasse 12, 8010 Graz, Austria; (D.R.); (M.S.)
| | - Mariann Wikström
- Agro Plantarum AB, Kärrarpsvägen 410, S-265 90 Åstorp, Sweden; (M.W.); (F.B.-J.)
| | - Fia Birch-Jensen
- Agro Plantarum AB, Kärrarpsvägen 410, S-265 90 Åstorp, Sweden; (M.W.); (F.B.-J.)
| | - Joeke Postma
- Wageningen University & Research, 6708 PB Wageningen, Netherlands; (J.P.); (J.K.)
| | - Ralf Udo Ehlers
- E-nema GmbH, Klausdorfer Str. 28–36, 24223 Schwentinental, Germany;
| | - Maria Schmuck
- Graz University of Technology, Environmental Biotechnology, Petersgasse 12, 8010 Graz, Austria; (D.R.); (M.S.)
| | - René Kollmann
- Strateco OG, Ruckerlberggasse 13, 8010 Graz, Austria;
- Sekem Energy GmbH, Steinberg 132, 8151 Hitzendorf, Austria
| | - Jürgen Köhl
- Wageningen University & Research, 6708 PB Wageningen, Netherlands; (J.P.); (J.K.)
| | - Gabriele Berg
- Graz University of Technology, Environmental Biotechnology, Petersgasse 12, 8010 Graz, Austria; (D.R.); (M.S.)
- Correspondence: ; Tel.: +43-316-873-8819
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16
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The Trichoderma viride F-00612 consortium tolerates 2-amino-3H-phenoxazin-3-one and degrades nitrated benzo[d]oxazol-2(3H)-one. CHEMOECOLOGY 2020. [DOI: 10.1007/s00049-020-00300-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
AbstractNumerous allelopathic plant secondary metabolites impact plant–microorganism interactions by injuring plant-associated beneficial bacteria and fungi. Fungi belonging to the genus Trichoderma positively influence crops, including benzoxazinone-containing maize. However, benzoxazinones and their downstream metabolites such as benzoxazolinone and phenoxazinones are often fungitoxic. Specimen Trichoderma viride F-00612 was found to be insensitive to 100-µM phenoxazinone and 500-µM benzoxazolinone. Screening of 46 additional specimens of ascomycetes revealed insensitivity to phenoxazinones among fungi that cause disease in benzoxazinone-producing cereal crops, whereas many other ascomycetes were highly sensitive. In contrast, most of the screened fungi were insensitive to benzoxazolinone. T. viride F-00612 was associated with bacteria and, thus, existed as a consortium. By contrast, Enterobacter species and Acinetobacter calcoaceticus were prominent in the original specimen, and Bacillus species predominated after antibiotic application. Prolonged cultivation of T. viride F-00612 in liquid medium and on Czapek agar in the presence of < 100 µM phenoxazinone and < 500 µM benzoxazolinone resulted in a massive loss of bacteria accompanied by impacted fungal growth in the presence of phenoxazinone. The original consortium was actively involved in implementing metabolic sequences for the degradation and detoxification of nitrated benzoxazolinone derivatives. The 2-aminophenol was rapidly converted into acetamidophenol, but benzoxazolinone, methoxylated benzoxazolinone, and picolinic acid remained unchanged. Excluding phenoxazinone, none of the tested compounds markedly impaired fungal growth in liquid culture. In conclusion, members of the T. viride F-00612 consortium may contribute to the ability to manage benzoxazinone downstream products and facilitate BOA-6-OH degradation via nitration.
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17
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Hansen JC, Schillinger WF, Sullivan TS, Paulitz TC. Soil Microbial Biomass and Fungi Reduced With Canola Introduced Into Long-Term Monoculture Wheat Rotations. Front Microbiol 2019; 10:1488. [PMID: 31354643 PMCID: PMC6637790 DOI: 10.3389/fmicb.2019.01488] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 06/14/2019] [Indexed: 01/29/2023] Open
Abstract
With increasing canola (Brassica napus L.) acreage in the Inland Pacific Northwest of the USA, we investigated the effect of this relatively new rotational crop on soil microbial communities and the performance of subsequent wheat (Triticum aestivum L.) crops. In a 6-year on-farm canola-wheat rotation study conducted near Davenport, WA, grain yields of spring wheat (SW) following winter canola (WC) were reduced an average of 17% compared to SW yields following winter wheat (WW). Using soil samples collected and analyzed every year from that study, the objective of this research was to determine the differences and similarities in the soil microbial communities associated with WC and WW, and if those differences were associated with SW yield response. Microbial biomass and community composition were determined using phospholipid fatty acid analysis (PLFA). The WC-associated microbial community contained significantly less fungi, mycorrhizae, and total microbial biomass than WW. Additionally, reduced fungal and mycorrhizal abundance in SW following WC suggests that the canola rotation effect can persist. A biocidal secondary metabolite of canola, isothiocyanate, may be a potential mechanism mediating the decline in soil microbial biomass. These results demonstrate the relationship between soil microbial community composition and crop productivity. Our data suggest that WC can have significant effects on soil microbial communities that ultimately drive microbially mediated soil processes.
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Affiliation(s)
- Jeremy C Hansen
- Northwest Sustainable Agroecosystems Research Unit, USDA-Agricultural Research Service, Washington State University, Pullman, WA, United States
| | - William F Schillinger
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Tarah S Sullivan
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Timothy C Paulitz
- Wheat Health, Genetics, and Quality Research Unit, USDA-Agricultural Research Service, Washington State University, Pullman, WA, United States
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18
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Bubici G, Kaushal M, Prigigallo MI, Gómez-Lama Cabanás C, Mercado-Blanco J. Biological Control Agents Against Fusarium Wilt of Banana. Front Microbiol 2019; 10:616. [PMID: 31024469 PMCID: PMC6459961 DOI: 10.3389/fmicb.2019.00616] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 03/11/2019] [Indexed: 11/13/2022] Open
Abstract
In the last century, the banana crop and industry experienced dramatic losses due to an epidemic of Fusarium wilt of banana (FWB), caused by Fusarium oxysporum f.sp. cubense (Foc) race 1. An even more dramatic menace is now feared due to the spread of Foc tropical race 4. Plant genetic resistance is generally considered as the most plausible strategy for controlling effectively such a devastating disease, as occurred for the first round of FWB epidemic. Nevertheless, with at least 182 articles published since 1970, biological control represents a large body of knowledge on FWB. Remarkably, many studies deal with biological control agents (BCAs) that reached the field-testing stage and even refer to high effectiveness. Some selected BCAs have been repeatedly assayed in independent trials, suggesting their promising value. Overall under field conditions, FWB has been controlled up to 79% by using Pseudomonas spp. strains, and up to 70% by several endophytes and Trichoderma spp. strains. Lower biocontrol efficacy (42-55%) has been obtained with arbuscular mycorrhizal fungi, Bacillus spp., and non-pathogenic Fusarium strains. Studies on Streptomyces spp. have been mostly limited to in vitro conditions so far, with very few pot-experiments, and none conducted in the field. The BCAs have been applied with diverse procedures (e.g., spore suspension, organic amendments, bioformulations, etc.) and at different stages of plant development (i.e., in vitro, nursery, at transplanting, post-transplanting), but there has been no evidence for a protocol better than another. Nonetheless, new bioformulation technologies (e.g., nanotechnology, formulation of microbial consortia and/or their metabolites, etc.) and tailor-made consortia of microbial strains should be encouraged. In conclusion, the literature offers many examples of promising BCAs, suggesting that biocontrol can greatly contribute to limit the damage caused by FWB. More efforts should be done to further validate the currently available outcomes, to deepen the knowledge on the most valuable BCAs, and to improve their efficacy by setting up effective formulations, application protocols, and integrated strategies.
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Affiliation(s)
- Giovanni Bubici
- Consiglio Nazionale delle Ricerche (CNR), Istituto per la Protezione Sostenibile delle Piante (IPSP), Bari, Italy
| | - Manoj Kaushal
- International Institute of Tropical Agriculture (IITA), Dar es Salaam, Tanzania
| | - Maria Isabella Prigigallo
- Consiglio Nazionale delle Ricerche (CNR), Istituto per la Protezione Sostenibile delle Piante (IPSP), Bari, Italy
| | | | - Jesús Mercado-Blanco
- Department of Crop Protection, Institute for Sustainable Agriculture (CSIC), Córdoba, Spain
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19
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He Z, Mao R, Dong JE, Liang Z, Zhang H, Liu L. Remediation of deterioration in microbial structure in continuous Pinellia ternata cropping soil by crop rotation. Can J Microbiol 2019; 65:282-295. [DOI: 10.1139/cjm-2018-0409] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pinellia ternata is a traditional Chinese herb that suffers from continuous cropping (CC), which significantly decreases both yield and quality. The influence of CC on the microbiome in P. ternata rhizosphere and the effects of remediation on microbiota by rotational cropping (CR) were assessed by Illumina high-throughput sequencing technology. CC tends to decrease the α-diversities as a function of cultivation time, whereas CR tends to increase them. Differentially abundant analysis showed that microbial structure was important in maintaining the health status of P. ternata rhizosphere. Results suggested that CC soils were mainly enriched for Pseudomonas, Rhizobium, and Streptophyta operational taxonomic units (OTUs), while the CR soils were mainly enriched for Rhizobium, Pseudomonas, Flavobacterium, Sphingomonas, Rhizobacter, and Arthrobacter OTUs. On the basis of the community dissimilarities, we grouped all sample replicates into three post hoc clusters in which soils were defined as healthy, health-suppressed, and health-depressed soils. The three soil types represented different soil physicochemical properties. The activities of the microbiome features, including ammonia oxidizer, sulfate reducer, nitrite reducer, dehalogenation, xylan degrader, sulfide oxidizer, nitrogen fixation, atrazine metabolism, chitin degradation, degraded aromatic hydrocarbons, and chlorophenol degradation, were also considerably different among the three soils.
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Affiliation(s)
- Zhigui He
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
- Institute of Food Science and Biological Engineering, Guilin Tourism University, Guilin 541006, P.R. China
| | - Renjun Mao
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
| | - Juan e Dong
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
| | - Zongsuo Liang
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
- School of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China
| | - Haihua Zhang
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
- School of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China
| | - Lin Liu
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
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20
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Assefa Y, Purcell LC, Salmeron M, Naeve S, Casteel SN, Kovács P, Archontoulis S, Licht M, Below F, Kandel H, Lindsey LE, Gaska J, Conley S, Shapiro C, Orlowski JM, Golden BR, Kaur G, Singh M, Thelen K, Laurenz R, Davidson D, Ciampitti IA. Assessing Variation in US Soybean Seed Composition (Protein and Oil). FRONTIERS IN PLANT SCIENCE 2019; 10:298. [PMID: 30915097 PMCID: PMC6421286 DOI: 10.3389/fpls.2019.00298] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/25/2019] [Indexed: 05/18/2023]
Abstract
Soybean [Glycine max (L.) Merr.] seed composition and yield are a function of genetics (G), environment (E), and management (M) practices, but contribution of each factor to seed composition and yield are not well understood. The goal of this synthesis-analysis was to identify the main effects of G, E, and M factors on seed composition (protein and oil concentration) and yield. The entire dataset (13,574 data points) consisted of 21 studies conducted across the United States (US) between 2002 and 2017 with varying treatments and all reporting seed yield and composition. Environment (E), defined as site-year, was the dominant factor accounting for more than 70% of the variation for both seed composition and yield. Of the crop management factors: (i) delayed planting date decreased oil concentration by 0.007 to 0.06% per delayed week (R 2∼0.70) and a 0.01 to 0.04 Mg ha-1 decline in seed yield per week, mainly in northern latitudes (40-45 N); (ii) crop rotation (corn-soybean) resulted in an overall positive impact for both seed composition and yield (1.60 Mg ha-1 positive yield difference relative to continuous soybean); and (iii) other management practices such as no-till, seed treatment, foliar nutrient application, and fungicide showed mixed results. Fertilizer N application in lower quantities (10-50 kg N ha-1) increased both oil and protein concentration, but seed yield was improved with rates above 100 kg N ha-1. At southern latitudes (30-35 N), trends of reduction in oil and increases in protein concentrations with later maturity groups (MG, from 3 to 7) was found. Continuing coordinated research is critical to advance our understanding of G × E × M interactions.
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Affiliation(s)
- Yared Assefa
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Larry C. Purcell
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Montse Salmeron
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Seth Naeve
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - Shaun N. Casteel
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Péter Kovács
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States
| | | | - Mark Licht
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Fred Below
- Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, IL, United States
| | - Herman Kandel
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Laura E. Lindsey
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
| | - John Gaska
- Department of Agronomy, University of Wisconsin–Madison, Madison, WI, United States
| | - Shawn Conley
- Department of Agronomy, University of Wisconsin–Madison, Madison, WI, United States
| | - Charles Shapiro
- Department of Agronomy and Horticulture, University of Nebraska System, Lincoln, NE, United States
| | - John M. Orlowski
- Delta Research and Extension Center, Mississippi State University, Stoneville, MS, United States
| | - Bobby R. Golden
- Delta Research and Extension Center, Mississippi State University, Stoneville, MS, United States
| | - Gurpreet Kaur
- Delta Research and Extension Center, Mississippi State University, Stoneville, MS, United States
| | - Maninderpal Singh
- Department of Plant, Soil and Microbial Sciences, Michigan State University, Allegan, MI, United States
| | - Kurt Thelen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, Allegan, MI, United States
| | - Randall Laurenz
- Department of Plant, Soil and Microbial Sciences, Michigan State University, Allegan, MI, United States
| | - Dan Davidson
- Illinois Soybean Association, Bloomington, IL, United States
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21
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Fabiańska I, Gerlach N, Almario J, Bucher M. Plant-mediated effects of soil phosphorus on the root-associated fungal microbiota in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2019; 221:2123-2137. [PMID: 30317641 PMCID: PMC6519159 DOI: 10.1111/nph.15538] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 09/19/2018] [Indexed: 05/22/2023]
Abstract
Plants respond to phosphorus (P) limitation through an array of morphological, physiological and metabolic changes which are part of the phosphate (Pi) starvation response (PSR). This response influences the establishment of the arbuscular mycorrhizal (AM) symbiosis in most land plants. It is, however, unknown to what extent available P and the PSR redefine plant interactions with the fungal microbiota in soil. Using amplicon sequencing of the fungal taxonomic marker ITS2, we examined the changes in root-associated fungal communities in the AM nonhost species Arabidopsis thaliana in response to soil amendment with P and to genetic perturbations in the plant PSR. We observed robust shifts in root-associated fungal communities of P-replete plants in comparison with their P-deprived counterparts, while bulk soil communities remained unaltered. Moreover, plants carrying mutations in the phosphate signaling network genes, phr1, phl1 and pho2, exhibited similarly altered root fungal communities characterized by the depletion of the chytridiomycete taxon Olpidium brassicae specifically under P-replete conditions. This study highlights the nutritional status and the underlying nutrient signaling network of an AM nonhost plant as previously unrecognized factors influencing the assembly of the plant fungal microbiota in response to P in nonsterile soil.
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Affiliation(s)
- Izabela Fabiańska
- Botanical InstituteCologne BiocenterUniversity of CologneCologne50931Germany
| | - Nina Gerlach
- Botanical InstituteCologne BiocenterUniversity of CologneCologne50931Germany
| | - Juliana Almario
- Botanical InstituteCologne BiocenterUniversity of CologneCologne50931Germany
- Cluster of Excellence on Plant Sciences (CEPLAS)University of CologneCologne50931Germany
- Present address:
Center for Plant Molecular BiologyUniversity of TübingenTübingen72074Germany
| | - Marcel Bucher
- Botanical InstituteCologne BiocenterUniversity of CologneCologne50931Germany
- Cluster of Excellence on Plant Sciences (CEPLAS)University of CologneCologne50931Germany
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22
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Lebreton L, Guillerm-Erckelboudt AY, Gazengel K, Linglin J, Ourry M, Glory P, Sarniguet A, Daval S, Manzanares-Dauleux MJ, Mougel C. Temporal dynamics of bacterial and fungal communities during the infection of Brassica rapa roots by the protist Plasmodiophora brassicae. PLoS One 2019; 14:e0204195. [PMID: 30802246 PMCID: PMC6388920 DOI: 10.1371/journal.pone.0204195] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 01/29/2019] [Indexed: 11/26/2022] Open
Abstract
The temporal dynamics of rhizosphere and root microbiota composition was compared between healthy and infected Chinese cabbage plants by the pathogen Plasmodiophora brassicae. When inoculated with P. brassicae, disease was measured at five sampling dates from early root hair infection to late gall development. The first symptoms of clubroot disease appeared 14 days after inoculation (DAI) and increased drastically between 14 and 35 DAI. The structure of microbial communities associated to rhizosphere soil and root from healthy and inoculated plants was characterized through high-throughput DNA sequencing of bacterial (16S) and fungal (18S) molecular markers and compared at each sampling date. In healthy plants, Proteobacteria and Bacteroidetes bacterial phyla dominated the rhizosphere and root microbiota of Chinese cabbage. Rhizosphere bacterial communities contained higher abundances of Actinobacteria and Firmicutes compared to the roots. Moreover, a drastic shift of fungal communities of healthy plants occurred between the two last sampling dates, especially in plant roots, where most of Ascomycota fungi dominated until they were replaced by a fungus assigned to the Chytridiomycota phylum. Parasitic invasion by P. brassicae disrupted the rhizosphere and root-associated community assembly at a late step during the root secondary cortical infection stage of clubroot disease. At this stage, Flavisolibacter and Streptomyces in the rhizosphere, and Bacillus in the roots, were drastically less abundant upon parasite invasion. Rhizosphere of plants colonized by P. brassicae was significantly more invaded by the Chytridiomycota fungus, which could reflect a mutualistic relationship in this compartment between these two microorganisms.
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Affiliation(s)
- Lionel Lebreton
- IGEPP, INRA, AGROCAMPUS OUEST, Université Rennes, Le Rheu, France
- * E-mail:
| | | | - Kévin Gazengel
- IGEPP, INRA, AGROCAMPUS OUEST, Université Rennes, Le Rheu, France
| | - Juliette Linglin
- IGEPP, INRA, AGROCAMPUS OUEST, Université Rennes, Le Rheu, France
| | - Morgane Ourry
- IGEPP, INRA, AGROCAMPUS OUEST, Université Rennes, Le Rheu, France
| | - Pascal Glory
- IGEPP, INRA, AGROCAMPUS OUEST, Université Rennes, Le Rheu, France
| | - Alain Sarniguet
- IGEPP, INRA, AGROCAMPUS OUEST, Université Rennes, Le Rheu, France
| | - Stéphanie Daval
- IGEPP, INRA, AGROCAMPUS OUEST, Université Rennes, Le Rheu, France
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23
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Wei Z, Yu D. Rhizosphere fungal community structure succession of Xinjiang continuously cropped cotton. Fungal Biol 2018; 123:42-50. [PMID: 30654956 DOI: 10.1016/j.funbio.2018.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 11/06/2018] [Indexed: 10/27/2022]
Abstract
The large-scale long-term plantation of cotton in the Xinjiang region has been accompanied by a regular and wide outbreak of soil-borne fungal diseases such as verticillium wilt, which significantly damaged the local cotton industry. High-throughput sequencing data showed that the cotton field cultivation management measures pose a significant influence upon the original ecological soil fungal community structure. During long-term continuous cropping of cotton, a new soil fungal community structure emerges after several repeated adjustments over five years. The number of verticillium wilt pathogens in the soil increased rapidly with prolonged continuous cropping time, reaching a maximum at around the 10th y; moreover, the abundance of the verticillium wilt pathogen only serves as one of numerous essential factors for disease occurrence. The fungal community structure and the abundance of verticillium wilt pathogens in local cotton fields are gradually formed under joint effects of year-long continuous cropping and supporting cultivation management measures.
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Affiliation(s)
- Zhang Wei
- Xinjiang Key Laboratory of Special Conservation and Regulatory Biology, School of Life Sciences, Xinjiang Normal University, Xinyi Road, Urumqi, 830046, China.
| | - Du Yu
- Xinjiang Key Laboratory of Special Conservation and Regulatory Biology, School of Life Sciences, Xinjiang Normal University, Xinyi Road, Urumqi, 830046, China
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24
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Siebers M, Rohr T, Ventura M, Schütz V, Thies S, Kovacic F, Jaeger KE, Berg M, Dörmann P, Schulz M. Disruption of microbial community composition and identification of plant growth promoting microorganisms after exposure of soil to rapeseed-derived glucosinolates. PLoS One 2018; 13:e0200160. [PMID: 29969500 PMCID: PMC6029813 DOI: 10.1371/journal.pone.0200160] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/20/2018] [Indexed: 12/17/2022] Open
Abstract
Land plants are engaged in intricate communities with soil bacteria and fungi indispensable for plant survival and growth. The plant-microbial interactions are largely governed by specific metabolites. We employed a combination of lipid-fingerprinting, enzyme activity assays, high-throughput DNA sequencing and isolation of cultivable microorganisms to uncover the dynamics of the bacterial and fungal community structures in the soil after exposure to isothiocyanates (ITC) obtained from rapeseed glucosinolates. Rapeseed-derived ITCs, including the cyclic, stable goitrin, are secondary metabolites with strong allelopathic affects against other plants, fungi and nematodes, and in addition can represent a health risk for human and animals. However, the effects of ITC application on the different bacterial and fungal organisms in soil are not known in detail. ITCs diminished the diversity of bacteria and fungi. After exposure, only few bacterial taxa of the Gammaproteobacteria, Bacteriodetes and Acidobacteria proliferated while Trichosporon (Zygomycota) dominated the fungal soil community. Many surviving microorganisms in ITC-treated soil where previously shown to harbor plant growth promoting properties. Cultivable fungi and bacteria were isolated from treated soils. A large number of cultivable microbial strains was capable of mobilizing soluble phosphate from insoluble calcium phosphate, and their application to Arabidopsis plants resulted in increased biomass production, thus revealing growth promoting activities. Therefore, inclusion of rapeseed-derived glucosinolates during biofumigation causes losses of microbiota, but also results in enrichment with ITC-tolerant plant microorganisms, a number of which show growth promoting activities, suggesting that Brassicaceae plants can shape soil microbiota community structure favoring bacteria and fungi beneficial for Brassica plants.
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Affiliation(s)
- Meike Siebers
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - Thomas Rohr
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - Marina Ventura
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - Vadim Schütz
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Martin Berg
- Institute for Organic Agriculture, University of Bonn, Bonn, Germany
- Experimental Farm Wiesengut of University of Bonn, Hennef, Germany
| | - Peter Dörmann
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - Margot Schulz
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
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25
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McMillan VE, Canning G, Moughan J, White RP, Gutteridge RJ, Hammond-Kosack KE. Exploring the resilience of wheat crops grown in short rotations through minimising the build-up of an important soil-borne fungal pathogen. Sci Rep 2018; 8:9550. [PMID: 29934522 PMCID: PMC6015077 DOI: 10.1038/s41598-018-25511-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 03/29/2018] [Indexed: 11/27/2022] Open
Abstract
Given the increasing demand for wheat which is forecast, cropping of wheat in short rotations will likely remain a common practice. However, in temperate wheat growing regions the soil-borne fungal pathogen Gaeumannomyces tritici becomes a major constraint on productivity. In cultivar rotation field experiments on the Rothamsted Farm (Hertfordshire, UK) we demonstrated a substantial reduction in take-all disease and grain yield increases of up to 2.4 tonnes/ha when a low take-all inoculum building wheat cultivar was grown in the first year of wheat cropping. Phenotyping of 71 modern elite wheat cultivars for the take-all inoculum build-up trait across six diverse trial sites identified a few cultivars which exhibited a consistent lowering of take-all inoculum build-up. However, there was also evidence of a significant interaction effect between trial site and cultivar when a pooled Residual Maximum Likelihood (REML) procedure was conducted. There was no evidence of an unusual rooting phenotype associated with take-all inoculum build-up in two independent field experiments and a sand column experiment. Together our results highlight the complex interactions between wheat genotype, environmental conditions and take-all inoculum build-up. Further work is required to determine the underlying genetic and mechanistic basis of this important phenomenon.
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Affiliation(s)
- V E McMillan
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - G Canning
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - J Moughan
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - R P White
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - R J Gutteridge
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - K E Hammond-Kosack
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
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26
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Lay CY, Bell TH, Hamel C, Harker KN, Mohr R, Greer CW, Yergeau É, St-Arnaud M. Canola Root-Associated Microbiomes in the Canadian Prairies. Front Microbiol 2018; 9:1188. [PMID: 29937756 PMCID: PMC6002653 DOI: 10.3389/fmicb.2018.01188] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/16/2018] [Indexed: 01/16/2023] Open
Abstract
Canola is one of the most economically important crops in Canada, and the root and rhizosphere microbiomes of a canola plant likely impact its growth and nutrient uptake. The aim of this study was to determine whether canola has a core root microbiome (i.e., set of microbes that are consistently selected in the root environment), and whether this is distinct from the core microbiomes of other crops that are commonly grown in the Canadian Prairies, pea, and wheat. We also assessed whether selected agronomic treatments can modify the canola microbiome, and whether this was associated to enhanced yield. We used a field experiment with a randomized complete block design, which was repeated at three locations across the canola-growing zone of Canada. Roots and rhizosphere soil were harvested at the flowering stage of canola. We separately isolated total extractable DNA from plant roots and from adjacent rhizosphere soil, and constructed MiSeq amplicon libraries for each of 60 samples, targeting bacterial, and archaeal 16S rRNA genes and the fungal ITS region. We determined that the microbiome of the roots and rhizosphere of canola was consistently different from those of wheat and pea. These microbiomes comprise several putative plant-growth-promoting rhizobacteria, including Amycolatopsis sp., Serratia proteamaculans, Pedobacter sp., Arthrobacter sp., Stenotrophomonas sp., Fusarium merismoides, and Fusicolla sp., which correlated positively with canola yield. Crop species had a significant influence on bacterial and fungal assemblages, especially within the roots, while higher nutrient input or seeding density did not significantly alter the global composition of bacterial, fungal, or archaeal assemblages associated with canola roots. However, the relative abundance of Olpidium brassicae, a known pathogen of members of the Brassicaceae, was significantly reduced in the roots of canola planted at higher seeding density. Our results suggest that seeding density and plant nutrition management modified the abundance of other bacterial and fungal taxa forming the core microbiomes of canola that are expected to impact crop growth. This work helps us to understand the microbial assemblages associated with canola grown under common agronomic practices and indicates microorganisms that can potentially benefit or reduce the yield of canola.
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Affiliation(s)
- Chih-Ying Lay
- Biodiversity Centre, Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montreal, QC, Canada
| | - Terrence H Bell
- Biodiversity Centre, Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montreal, QC, Canada.,Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, State College, PA, United States
| | - Chantal Hamel
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec City, QC, Canada
| | - K Neil Harker
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Ramona Mohr
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Charles W Greer
- Energy, Mining and Environment, National Research Council Canada, Montreal, QC, Canada
| | - Étienne Yergeau
- Energy, Mining and Environment, National Research Council Canada, Montreal, QC, Canada.,Centre INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Laval, QC, Canada
| | - Marc St-Arnaud
- Biodiversity Centre, Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montreal, QC, Canada
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27
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Taxonomy and pathogenicity of Olpidium brassicae and its allied species. Fungal Biol 2018; 122:837-846. [PMID: 30115317 DOI: 10.1016/j.funbio.2018.04.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 02/05/2023]
Abstract
The classification and physiology of the zoosporic plant-pathogen Olpidium brassicae and its relationships with the closely-related species are often confusing. This review focuses on these species and intends to differentiate them based on the literatures published since the discovery and establishment of the species by Woronin in 1878 under the name of Chytridium brassicae to current molecular era. The goal of this review is to help researchers better understand the taxonomy, the host range, and the potential role in plant health of O. brassicae-related species. To reach the goal, we reviewed the rationales behind the creation or reduction in synonymy of the different names for O. brassicae and its allied species in order to elucidate the evolution of the species concept on them based on the traditional morphological studies. Furthermore, the studies by molecular biology methods improve our knowledge and perspectives on O. brassicae and its host specificity. In particular, we clarify the differences between O. brassicae and Olpidium virulentus, and propose potential new research avenues. We therefore hope that this review will give a better perspective on Olpidium spp. and their potential role in the root microbiome of plants in natural environments and in agricultural settings.
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28
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Bass D, van der Gast C, Thomson S, Neuhauser S, Hilton S, Bending GD. Plant Rhizosphere Selection of Plasmodiophorid Lineages from Bulk Soil: The Importance of "Hidden" Diversity. Front Microbiol 2018; 9:168. [PMID: 29503632 PMCID: PMC5825890 DOI: 10.3389/fmicb.2018.00168] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 01/25/2018] [Indexed: 11/25/2022] Open
Abstract
Microbial communities closely associated with the rhizosphere can have strong positive and negative impacts on plant health and growth. We used a group-specific amplicon approach to investigate local scale drivers in the diversity and distribution of plasmodiophorids in rhizosphere/root and bulk soil samples from oilseed rape (OSR) and wheat agri-systems. Plasmodiophorids are plant- and stramenopile-associated protists including well known plant pathogens as well as symptomless endobiotic species. We detected 28 plasmodiophorid lineages (OTUs), many of them novel, and showed that plasmodiophorid communities were highly dissimilar and significantly divergent between wheat and OSR rhizospheres and between rhizosphere and bulk soil samples. Bulk soil communities were not significantly different between OSR and wheat systems. Wheat and OSR rhizospheres selected for different plasmodiophorid lineages. An OTU corresponding to Spongospora nasturtii was positively selected in the OSR rhizosphere, as were two genetically distinct OTUs. Two novel lineages related to Sorosphaerula veronicae were significantly associated with wheat rhizosphere samples, indicating unknown plant-protist relationships. We show that group-targeted eDNA approaches to microbial symbiont-host ecology reveal significant novel diversity and enable inference of differential activity and potential interactions between sequence types, as well as their presence.
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Affiliation(s)
- David Bass
- Department of Life Sciences, Natural History Museum, London, United Kingdom
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom
| | | | - Serena Thomson
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Sigrid Neuhauser
- Institute of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Gary D. Bending
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
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29
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Organic versus Conventional Cropping Sustainability: A Comparative System Analysis. SUSTAINABILITY 2018. [DOI: 10.3390/su10010272] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We are at a pivotal time in human history, as the agricultural sector undergoes consolidation coupled with increasing energy costs in the context of declining resource availability. Although organic systems are often thought of as more sustainable than conventional operations, the lack of concise and widely accepted means to measure sustainability makes coming to an agreement on this issue quite challenging. However, an accurate assessment of sustainability can be reached by dissecting the scientific underpinnings of opposing production practices and crop output between cropping systems. The purpose of this review is to provide an in-depth and comprehensive evaluation of modern global production practices and economics of organic cropping systems, as well as assess the sustainability of organic production practices through the clarification of information and analysis of recent research. Additionally, this review addresses areas where improvements can be made to help meet the needs of future organic producers, including organic-focused breeding programs and necessity of coming to a unified global stance on plant breeding technologies. By identifying management strategies that utilize practices with long-term environmental and resource efficiencies, a concerted global effort could guide the adoption of organic agriculture as a sustainable food production system.
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30
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Sergaki C, Lagunas B, Lidbury I, Gifford ML, Schäfer P. Challenges and Approaches in Microbiome Research: From Fundamental to Applied. FRONTIERS IN PLANT SCIENCE 2018; 9:1205. [PMID: 30174681 PMCID: PMC6107787 DOI: 10.3389/fpls.2018.01205] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/26/2018] [Indexed: 05/07/2023]
Abstract
We face major agricultural challenges that remain a threat for global food security. Soil microbes harbor enormous potentials to provide sustainable and economically favorable solutions that could introduce novel approaches to improve agricultural practices and, hence, crop productivity. In this review we give an overview regarding the current state-of-the-art of microbiome research by discussing new technologies and approaches. We also provide insights into fundamental microbiome research that aim to provide a deeper understanding of the dynamics within microbial communities, as well as their interactions with different plant hosts and the environment. We aim to connect all these approaches with potential applications and reflect how we can use microbial communities in modern agricultural systems to realize a more customized and sustainable use of valuable resources (e.g., soil).
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Affiliation(s)
- Chrysi Sergaki
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- *Correspondence: Chrysi Sergaki,
| | - Beatriz Lagunas
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ian Lidbury
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Miriam L. Gifford
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom
| | - Patrick Schäfer
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom
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Lally RD, Galbally P, Moreira AS, Spink J, Ryan D, Germaine KJ, Dowling DN. Application of Endophytic Pseudomonas fluorescens and a Bacterial Consortium to Brassica napus Can Increase Plant Height and Biomass under Greenhouse and Field Conditions. FRONTIERS IN PLANT SCIENCE 2017; 8:2193. [PMID: 29312422 PMCID: PMC5744461 DOI: 10.3389/fpls.2017.02193] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 12/12/2017] [Indexed: 05/26/2023]
Abstract
Plant associated bacteria with plant growth promotion (PGP) properties have been proposed for use as environmentally friendly biofertilizers for sustainable agriculture; however, analysis of their efficacy in the field is often limited. In this study, greenhouse and field trials were carried out using individual endophytic Pseudomonas fluorescens strains, the well characterized rhizospheric P. fluorescens F113 and an endophytic microbial consortium of 10 different strains. These bacteria had been previously characterized with respect to their PGP properties in vitro and had been shown to harbor a range of traits associated with PGP including siderophore production, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, and inorganic phosphate solubilization. In greenhouse experiments individual strains tagged with gfp and Kmr were applied to Brassica napus as a seed coat and were shown to effectively colonize the rhizosphere and root of B. napus and in addition they demonstrated a significant increase in plant biomass compared with the non-inoculated control. In the field experiment, the bacteria (individual and consortium) were spray inoculated to winter oilseed rape B. napus var. Compass which was grown under standard North Western European agronomic conditions. Analysis of the data provides evidence that the application of the live bacterial biofertilizers can enhance aspects of crop development in B. napus at field scale. The field data demonstrated statistically significant increases in crop height, stem/leaf, and pod biomass, particularly, in the case of the consortium inoculated treatment. However, although seed and oil yield were increased in the field in response to inoculation, these data were not statistically significant under the experimental conditions tested. Future field trials will investigate the effectiveness of the inoculants under different agronomic conditions.
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Affiliation(s)
- Richard D. Lally
- EnviroCORE, The Dargan Research and Innovation Centre, Department of Science and Health, Institute of Technology, Carlow, Carlow, Ireland
| | - Paul Galbally
- EnviroCORE, The Dargan Research and Innovation Centre, Department of Science and Health, Institute of Technology, Carlow, Carlow, Ireland
- Oak Park Crops Research Centre, Teagasc, Carlow, Ireland
| | - António S. Moreira
- EnviroCORE, The Dargan Research and Innovation Centre, Department of Science and Health, Institute of Technology, Carlow, Carlow, Ireland
- Dundalk Institute of Technology, Dundalk, Ireland
| | - John Spink
- Oak Park Crops Research Centre, Teagasc, Carlow, Ireland
| | - David Ryan
- EnviroCORE, The Dargan Research and Innovation Centre, Department of Science and Health, Institute of Technology, Carlow, Carlow, Ireland
| | - Kieran J. Germaine
- EnviroCORE, The Dargan Research and Innovation Centre, Department of Science and Health, Institute of Technology, Carlow, Carlow, Ireland
| | - David N. Dowling
- EnviroCORE, The Dargan Research and Innovation Centre, Department of Science and Health, Institute of Technology, Carlow, Carlow, Ireland
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Rathore R, Dowling DN, Forristal PD, Spink J, Cotter PD, Bulgarelli D, Germaine KJ. Crop Establishment Practices Are a Driver of the Plant Microbiota in Winter Oilseed Rape ( Brassica napus). Front Microbiol 2017; 8:1489. [PMID: 28848510 PMCID: PMC5553296 DOI: 10.3389/fmicb.2017.01489] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/24/2017] [Indexed: 02/01/2023] Open
Abstract
Gaining a greater understanding of the plant microbiota and its interactions with its host plant heralds a new era of scientific discovery in agriculture. Different agricultural management practices influence soil microbial populations by changing a soil's physical, chemical and biological properties. However, the impact of these practices on the microbiota associated with economically important crops such as oilseed rape, are still understudied. In this work we investigated the impact of two contrasting crop establishment practices, conventional (plow based) and conservation (strip-tillage) systems, on the microbiota inhabiting different plant microhabitats, namely rhizosphere, root and shoot, of winter oilseed rape under Irish agronomic conditions. Illumina 16S rRNA gene sequence profiling showed that the plant associated microhabitats (root and shoot), are dominated by members of the bacterial phyla Proteobacteria, Actinobacteria and Bacteroidetes. The root and shoot associated bacterial communities displayed markedly distinct profiles as a result of tillage practices. We observed a very limited 'rhizosphere effect' in the root zone of WOSR, i.e., there was little or no increase in bacterial community richness and abundance in the WOSR rhizosphere compared to the bulk soil. The two tillage systems investigated did not appear to lead to any major long term differences on the bulk soil or rhizosphere bacterial communities. Our data suggests that the WOSR root and shoot microbiota can be impacted by management practices and is an important mechanism that could allow us to understand how plants respond to different management practices and environments.
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Affiliation(s)
- Ridhdhi Rathore
- Envirocore, Dargan Research Centre, Institute of TechnologyCarlow, Ireland
| | - David N Dowling
- Envirocore, Dargan Research Centre, Institute of TechnologyCarlow, Ireland
| | | | - John Spink
- Teagasc Crops Research CentreCarlow, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, and the APC Microbiome InstituteCork, Ireland
| | - Davide Bulgarelli
- Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton InstituteInvergowrie, Scotland
| | - Kieran J Germaine
- Envirocore, Dargan Research Centre, Institute of TechnologyCarlow, Ireland
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Kowalczyk A, Price OR, van der Gast CJ, Finnegan CJ, van Egmond RA, Schäfer H, Bending GD. Spatial and temporal variability in the potential of river water biofilms to degrade p-nitrophenol. CHEMOSPHERE 2016; 164:355-362. [PMID: 27596822 DOI: 10.1016/j.chemosphere.2016.08.095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 08/14/2016] [Accepted: 08/20/2016] [Indexed: 06/06/2023]
Abstract
In order to predict the fate of chemicals in the environment, a range of regulatory tests are performed with microbial inocula collected from environmental compartments to investigate the potential for biodegradation. The abundance and distribution of microbes in the environment is affected by a range of variables, hence diversity and biomass of inocula used in biodegradation tests can be highly variable in space and time. The use of artificial or natural biofilms in regulatory tests could enable more consistent microbial communities be used as inocula, in order to increase test consistency. We investigated spatial and temporal variation in composition, biomass and chemical biodegradation potential of bacterial biofilms formed in river water. Sampling time and sampling location impacted the capacity of biofilms to degrade p-nitrophenol (PNP). Biofilm bacterial community structure varied across sampling times, but was not affected by sampling location. Degradation of PNP was associated with increased relative abundance of Pseudomonas syringae. Partitioning of the bacterial metacommunity into core and satellite taxa revealed that the P. syringae could be either a satellite or core member of the community across sampling times, but this had no impact on PNP degradation. Quantitative PCR analysis of the pnpA gene showed that it was present in all samples irrespective of their ability to degrade PNP. River biofilms showed seasonal variation in biomass, microbial community composition and PNP biodegradation potential, which resulted in inconsistent biodegradation test results. We discuss the results in the context of the mechanisms underlying variation in regulatory chemical degradation tests.
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Affiliation(s)
- Agnieszka Kowalczyk
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK.
| | - Oliver R Price
- Unilever, Safety and Environmental Assurance Centre, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Christopher J van der Gast
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK; NERC Centre for Ecology and Hydrology, Wallingford, OX10 8BB, UK
| | - Christopher J Finnegan
- Unilever, Safety and Environmental Assurance Centre, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Roger A van Egmond
- Unilever, Safety and Environmental Assurance Centre, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Hendrik Schäfer
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - Gary D Bending
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
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Barnes CJ, van der Gast CJ, Burns CA, McNamara NP, Bending GD. Temporally Variable Geographical Distance Effects Contribute to the Assembly of Root-Associated Fungal Communities. Front Microbiol 2016; 7:195. [PMID: 26941720 PMCID: PMC4766365 DOI: 10.3389/fmicb.2016.00195] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 12/05/2015] [Indexed: 11/16/2022] Open
Abstract
Root-associated fungi are key contributors to ecosystem functioning, however, the factors which determine community assembly are still relatively poorly understood. This study simultaneously quantified the roles of geographical distance, environmental heterogeneity and time in determining root-associated fungal community composition at the local scale within a short rotation coppice (SRC) willow plantation. Culture independent molecular analyses of the root-associated fungal community suggested a strong but temporally variable effect of geographical distance among fungal communities in terms of composition at the local geographical level. Whilst these distance effects were most prevalent on October communities, soil pH had an effect on structuring of the communities throughout the sampling period. Given the temporal variation in the effects of geographical distance and the environment for shaping root-associated fungal communities, there is clearly need for a temporal component to sampling strategies in future investigations of fungal ecology.
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Affiliation(s)
- Christopher J. Barnes
- School of Life Sciences, Gibbet Hill Campus, University of WarwickCoventry, UK
- Section of Evolutionary Genomics, National History Museum of Denmark, University of CopenhagenCopenhagen, Denmark
| | | | - Caitlin A. Burns
- School of Life Sciences, Gibbet Hill Campus, University of WarwickCoventry, UK
| | - Niall P. McNamara
- Natural Environment Research Council Centre for Ecology and Hydrology – Lancaster Environment CentreLancaster, UK
| | - Gary D. Bending
- School of Life Sciences, Gibbet Hill Campus, University of WarwickCoventry, UK
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Fonseca-García C, Coleman-Derr D, Garrido E, Visel A, Tringe SG, Partida-Martínez LP. The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity. Front Microbiol 2016; 7:150. [PMID: 26904020 PMCID: PMC4751269 DOI: 10.3389/fmicb.2016.00150] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/27/2016] [Indexed: 01/19/2023] Open
Abstract
Cactaceae represents one of the most species-rich families of succulent plants native to arid and semi-arid ecosystems, yet the associations Cacti establish with microorganisms and the rules governing microbial community assembly remain poorly understood. We analyzed the composition, diversity, and factors influencing above- and below-ground bacterial, archaeal, and fungal communities associated with two native and sympatric Cacti species: Myrtillocactus geometrizans and Opuntia robusta. Phylogenetic profiling showed that the composition and assembly of microbial communities associated with Cacti were primarily influenced by the plant compartment; plant species, site, and season played only a minor role. Remarkably, bacterial, and archaeal diversity was higher in the phyllosphere than in the rhizosphere of Cacti, while the opposite was true for fungi. Semi-arid soils exhibited the highest levels of microbial diversity whereas the stem endosphere the lowest. Despite their taxonomic distance, M. geometrizans and O. robusta shared most microbial taxa in all analyzed compartments. Influence of the plant host did only play a larger role in the fungal communities of the stem endosphere. These results suggest that fungi establish specific interactions with their host plant inside the stem, whereas microbial communities in the other plant compartments may play similar functional roles in these two species. Biochemical and molecular characterization of seed-borne bacteria of Cacti supports the idea that these microbial symbionts may be vertically inherited and could promote plant growth and drought tolerance for the fitness of the Cacti holobiont. We envision this knowledge will help improve and sustain agriculture in arid and semi-arid regions of the world.
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Affiliation(s)
- Citlali Fonseca-García
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados Irapuato, Mexico
| | - Devin Coleman-Derr
- Department of Energy Joint Genome InstituteWalnut Creek, CA, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA; Plant Gene Expression Center, United States Department of Agriculture-Agricultural Research ServiceAlbany, CA, USA
| | - Etzel Garrido
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados Irapuato, Mexico
| | - Axel Visel
- Department of Energy Joint Genome InstituteWalnut Creek, CA, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA; Molecular Cell Biology, School of Natural Sciences, University of California, MercedMerced, CA, USA
| | - Susannah G Tringe
- Department of Energy Joint Genome InstituteWalnut Creek, CA, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA; Molecular Cell Biology, School of Natural Sciences, University of California, MercedMerced, CA, USA
| | - Laila P Partida-Martínez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados Irapuato, Mexico
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Xiong W, Zhao Q, Xue C, Xun W, Zhao J, Wu H, Li R, Shen Q. Comparison of Fungal Community in Black Pepper-Vanilla and Vanilla Monoculture Systems Associated with Vanilla Fusarium Wilt Disease. Front Microbiol 2016; 7:117. [PMID: 26903995 PMCID: PMC4746283 DOI: 10.3389/fmicb.2016.00117] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 01/22/2016] [Indexed: 11/13/2022] Open
Abstract
Long-term vanilla monocropping often results in the occurrence of vanilla Fusarium wilt disease, seriously affecting its production all over the world. In the present study, vanilla exhibited significantly less Fusarium wilt disease in the soil of a long-term continuously cropped black pepper orchard. The entire fungal communities of bulk and rhizosphere soils between the black pepper-vanilla system (i.e., vanilla cropped in the soil of a continuously cropped black pepper orchard) and vanilla monoculture system were compared through the deep pyrosequencing. The results showed that the black pepper-vanilla system revealed a significantly higher fungal diversity than the vanilla monoculture system in both bulk and rhizosphere soils. The UniFrac-weighted PCoA analysis revealed significant differences in bulk soil fungal community structures between the two cropping systems, and fungal community structures were seriously affected by the vanilla root system. In summary, the black pepper-vanilla system harbored a lower abundance of Fusarium oxysporum in the vanilla rhizosphere soil and increased the putatively plant-beneficial fungal groups such as Trichoderma and Penicillium genus, which could explain the healthy growth of vanilla in the soil of the long-term continuously cropped black pepper field. Thus, cropping vanilla in the soil of continuously cropped black pepper fields for maintaining the vanilla industry is executable and meaningful as an agro-ecological system.
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Affiliation(s)
- Wu Xiong
- 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 UniversityNanjing, China
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural ScienceWanning, China
| | - Qingyun Zhao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural ScienceWanning, 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 UniversityNanjing, China
| | - Weibing Xun
- 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 UniversityNanjing, China
| | - Jun Zhao
- 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 UniversityNanjing, China
| | - Huasong Wu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural ScienceWanning, China
| | - 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 UniversityNanjing, China
| | - 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 UniversityNanjing, China
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Coleman‐Derr D, Desgarennes D, Fonseca‐Garcia C, Gross S, Clingenpeel S, Woyke T, North G, Visel A, Partida‐Martinez LP, Tringe SG. Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. THE NEW PHYTOLOGIST 2016; 209:798-811. [PMID: 26467257 PMCID: PMC5057366 DOI: 10.1111/nph.13697] [Citation(s) in RCA: 372] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 08/31/2015] [Indexed: 05/18/2023]
Abstract
Desert plants are hypothesized to survive the environmental stress inherent to these regions in part thanks to symbioses with microorganisms, and yet these microbial species, the communities they form, and the forces that influence them are poorly understood. Here we report the first comprehensive investigation of the microbial communities associated with species of Agave, which are native to semiarid and arid regions of Central and North America and are emerging as biofuel feedstocks. We examined prokaryotic and fungal communities in the rhizosphere, phyllosphere, leaf and root endosphere, as well as proximal and distal soil samples from cultivated and native agaves, through Illumina amplicon sequencing. Phylogenetic profiling revealed that the composition of prokaryotic communities was primarily determined by the plant compartment, whereas the composition of fungal communities was mainly influenced by the biogeography of the host species. Cultivated A. tequilana exhibited lower levels of prokaryotic diversity compared with native agaves, although no differences in microbial diversity were found in the endosphere. Agaves shared core prokaryotic and fungal taxa known to promote plant growth and confer tolerance to abiotic stress, which suggests common principles underpinning Agave-microbe interactions.
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Affiliation(s)
- Devin Coleman‐Derr
- Department of EnergyJoint Genome InstituteWalnut CreekCA94598USA
- Genomics DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
- Plant Gene Expression CenterUSDA‐ARSAlbanyCA94710USA
| | - Damaris Desgarennes
- Departamento de Ingeniería GenéticaCentro de Investigación y de Estudios AvanzadosIrapuato36821Mexico
| | - Citlali Fonseca‐Garcia
- Departamento de Ingeniería GenéticaCentro de Investigación y de Estudios AvanzadosIrapuato36821Mexico
| | - Stephen Gross
- Department of EnergyJoint Genome InstituteWalnut CreekCA94598USA
- Genomics DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Scott Clingenpeel
- Department of EnergyJoint Genome InstituteWalnut CreekCA94598USA
- Genomics DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Tanja Woyke
- Department of EnergyJoint Genome InstituteWalnut CreekCA94598USA
- Genomics DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Gretchen North
- Department of BiologyOccidental CollegeLos AngelesCA90041USA
| | - Axel Visel
- Department of EnergyJoint Genome InstituteWalnut CreekCA94598USA
- Genomics DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
- School of Natural SciencesUniversity of CaliforniaMercedCA95343USA
| | - Laila P. Partida‐Martinez
- Departamento de Ingeniería GenéticaCentro de Investigación y de Estudios AvanzadosIrapuato36821Mexico
| | - Susannah G. Tringe
- Department of EnergyJoint Genome InstituteWalnut CreekCA94598USA
- Genomics DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
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Tkacz A, Cheema J, Chandra G, Grant A, Poole PS. Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition. THE ISME JOURNAL 2015; 9:2349-59. [PMID: 25909975 PMCID: PMC4611498 DOI: 10.1038/ismej.2015.41] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 02/05/2015] [Accepted: 02/16/2015] [Indexed: 12/15/2022]
Abstract
We examined succession of the rhizosphere microbiota of three model plants (Arabidopsis, Medicago and Brachypodium) in compost and sand and three crops (Brassica, Pisum and Triticum) in compost alone. We used serial inoculation of 24 independent replicate microcosms over three plant generations for each plant/soil combination. Stochastic variation between replicates was surprisingly weak and by the third generation, replicate microcosms for each plant had communities that were very similar to each other but different to those of other plants or unplanted soil. Microbiota diversity remained high in compost, but declined drastically in sand, with bacterial opportunists and putative autotrophs becoming dominant. These dramatic differences indicate that many microbes cannot thrive on plant exudates alone and presumably also require carbon sources and/or nutrients from soil. Arabidopsis had the weakest influence on its microbiota and in compost replicate microcosms converged on three alternative community compositions rather than a single distinctive community. Organisms selected in rhizospheres can have positive or negative effects. Two abundant bacteria are shown to promote plant growth, but in Brassica the pathogen Olpidium brassicae came to dominate the fungal community. So plants exert strong selection on the rhizosphere microbiota but soil composition is critical to its stability. microbial succession/ plant-microbe interactions/rhizosphere microbiota/selection.
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Affiliation(s)
- Andrzej Tkacz
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
- Department of Plant Sciences, Oxford University, Oxford, UK
| | - Jitender Cheema
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Alastair Grant
- Earth and Life Systems Alliance, The School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Philip S Poole
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
- Department of Plant Sciences, Oxford University, Oxford, UK
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Characterization of para-Nitrophenol-Degrading Bacterial Communities in River Water by Using Functional Markers and Stable Isotope Probing. Appl Environ Microbiol 2015. [PMID: 26209677 DOI: 10.1128/aem.01794-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Microbial degradation is a major determinant of the fate of pollutants in the environment. para-Nitrophenol (PNP) is an EPA-listed priority pollutant with a wide environmental distribution, but little is known about the microorganisms that degrade it in the environment. We studied the diversity of active PNP-degrading bacterial populations in river water using a novel functional marker approach coupled with [(13)C6]PNP stable isotope probing (SIP). Culturing together with culture-independent terminal restriction fragment length polymorphism analysis of 16S rRNA gene amplicons identified Pseudomonas syringae to be the major driver of PNP degradation in river water microcosms. This was confirmed by SIP-pyrosequencing of amplified 16S rRNA. Similarly, functional gene analysis showed that degradation followed the Gram-negative bacterial pathway and involved pnpA from Pseudomonas spp. However, analysis of maleylacetate reductase (encoded by mar), an enzyme common to late stages of both Gram-negative and Gram-positive bacterial PNP degradation pathways, identified a diverse assemblage of bacteria associated with PNP degradation, suggesting that mar has limited use as a specific marker of PNP biodegradation. Both the pnpA and mar genes were detected in a PNP-degrading isolate, P. syringae AKHD2, which was isolated from river water. Our results suggest that PNP-degrading cultures of Pseudomonas spp. are representative of environmental PNP-degrading populations.
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40
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Tkacz A, Poole P. Role of root microbiota in plant productivity. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2167-75. [PMID: 25908654 PMCID: PMC4986727 DOI: 10.1093/jxb/erv157] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 03/09/2015] [Accepted: 03/12/2015] [Indexed: 05/19/2023]
Abstract
The growing human population requires increasing amounts of food, but modern agriculture has limited possibilities for increasing yields. New crop varieties may be bred to have increased yields and be more resistant to environmental stress and pests. However, they still require fertilization to supplement essential nutrients that are normally limited in the soil. Soil microorganisms present an opportunity to reduce the requirement for inorganic fertilization in agriculture. Microorganisms, due to their enormous genetic pool, are also a potential source of biochemical reactions that recycle essential nutrients for plant growth. Microbes that associate with plants can be considered to be part of the plant's pan-genome. Therefore, it is essential for us to understand microbial community structure and their 'metagenome' and how it is influenced by different soil types and crop varieties. In the future we may be able to modify and better utilize the soil microbiota potential for promoting plant growth.
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Affiliation(s)
- Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Philip Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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41
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Campisano A, Antonielli L, Pancher M, Yousaf S, Pindo M, Pertot I. Bacterial endophytic communities in the grapevine depend on pest management. PLoS One 2014; 9:e112763. [PMID: 25387008 PMCID: PMC4227848 DOI: 10.1371/journal.pone.0112763] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 10/16/2014] [Indexed: 01/26/2023] Open
Abstract
Microbial plant endophytes are receiving ever-increasing attention as a result of compelling evidence regarding functional interaction with the host plant. Microbial communities in plants were recently reported to be influenced by numerous environmental and anthropogenic factors, including soil and pest management. In this study we used automated ribosomal intergenic spacer analysis (ARISA) fingerprinting and pyrosequencing of 16S rDNA to assess the effect of organic production and integrated pest management (IPM) on bacterial endophytic communities in two widespread grapevines cultivars (Merlot and Chardonnay). High levels of the dominant Ralstonia, Burkholderia and Pseudomonas genera were detected in all the samples We found differences in the composition of endophytic communities in grapevines cultivated using organic production and IPM. Operational taxonomic units (OTUs) assigned to the Mesorhizobium, Caulobacter and Staphylococcus genera were relatively more abundant in plants from organic vineyards, while Ralstonia, Burkholderia and Stenotrophomonas were more abundant in grapevines from IPM vineyards. Minor differences in bacterial endophytic communities were also found in the grapevines of the two cultivars.
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Affiliation(s)
- Andrea Campisano
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), S. Michele all'Adige (TN), Italy
- * E-mail:
| | - Livio Antonielli
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), S. Michele all'Adige (TN), Italy
- Austrian Institute of Technology GmbH, Department of Health & Environment, Bioresources Unit, Tulln, Austria
| | - Michael Pancher
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), S. Michele all'Adige (TN), Italy
| | - Sohail Yousaf
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), S. Michele all'Adige (TN), Italy
- Department of Environmental Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), S. Michele all'Adige (TN), Italy
| | - Ilaria Pertot
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), S. Michele all'Adige (TN), Italy
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Impact of continuous Salvia miltiorrhiza cropping on rhizosphere actinomycetes and fungi communities. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0964-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Soil physicochemical and biological properties of paddy-upland rotation: a review. ScientificWorldJournal 2014; 2014:856352. [PMID: 24995366 PMCID: PMC4060577 DOI: 10.1155/2014/856352] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 04/26/2014] [Accepted: 05/16/2014] [Indexed: 12/03/2022] Open
Abstract
Paddy-upland rotation is an unavoidable cropping system for Asia to meet the increasing demand for food. The reduction in grain yields has increased the research interest on the soil properties of rice-based cropping systems. Paddy-upland rotation fields are unique from other wetland or upland soils, because they are associated with frequent cycling between wetting and drying under anaerobic and aerobic conditions; such rotations affect the soil C and N cycles, make the chemical speciation and biological effectiveness of soil nutrient elements varied with seasons, increase the diversity of soil organisms, and make the soil physical properties more difficult to analyze. Consequently, maintaining or improving soil quality at a desirable level has become a complicated issue. Therefore, fully understanding the soil characteristics of paddy-upland rotation is necessary for the sustainable development of the system. In this paper, we offer helpful insight into the effect of rice-upland combinations on the soil chemical, physical, and biological properties, which could provide guidance for reasonable cultivation management measures and contribute to the improvement of soil quality and crop yield.
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Liu X, Zhang J, Gu T, Zhang W, Shen Q, Yin S, Qiu H. Microbial community diversities and taxa abundances in soils along a seven-year gradient of potato monoculture using high throughput pyrosequencing approach. PLoS One 2014; 9:e86610. [PMID: 24497959 PMCID: PMC3907449 DOI: 10.1371/journal.pone.0086610] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Accepted: 12/11/2013] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Previous studies have focused on linking soil community structure, diversity, or specific taxa to disturbances. Relatively little attention has been directed to crop monoculture soils, particularly potato monoculture. Information about microbial community changes over time between monoculture and non-monoculture treatments is lacking. Furthermore, few studies have examined microbial communities in potato monoculture soils using a high throughput pyrosequencing approach. METHODOLOGY/PRINCIPAL FINDINGS Soils along a seven-year gradient of potato monoculture were collected and microbial communities were characterized using high throughput pyrosequencing approach. Principal findings are as follows. First, diversity (H(Shannon)) and richness (S(Chao1)) indices of bacterial community, but not of fungal community, were linearly decreased over time and corresponded to a decline of soil sustainability represented by yield decline and disease incidence increase. Second, Fusarium, the only soilborne pathogen-associated fungal genus substantially detected, was linearly increased over time in abundance and was closely associated with yield decline. Third, Fusarium abundance was negatively correlated with soil organic matter (OM) and total nitrogen (TN) but positively with electrical conductivity (EC). Fourth, Fusarium was correlated in abundances with 6 bacterial taxa over time. CONCLUSIONS Soil bacterial and fungal communities exhibited differential responses to the potato monoculture. The overall soil bacterial communities were shaped by potato monoculture. Fusarium was the only soilborne pathogen-associated genus associated with disease incidence increase and yield decline. The changes of soil OM, TN and EC were responsible for Fusarium enrichment, in addition to selections by the monoculture crop. Acidobacteria and Nitrospirae were linearly decreased over time in abundance, corresponding to the decrease of OM, suggesting their similar ecophysiologial trait. Correlations between abundance of Fusarium with several other bacterial taxa suggested their similar behaviors in responses to potato monoculture and/or soil variables, providing insights into the ecological behaviors of these taxa in the environment.
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Affiliation(s)
- Xing Liu
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, Gansu Province, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - Junlian Zhang
- College of Agronomy, Gansu Agricultural University, Lanzhou, Gansu Province, China
- Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Tianyu Gu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, Jaingsu Province, China
| | - Wenming Zhang
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, Gansu Province, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Shixue Yin
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, Jaingsu Province, China
| | - Huizhen Qiu
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, Gansu Province, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu Province, China
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Campos-Herrera R, Ali JG, Diaz BM, Duncan LW. Analyzing spatial patterns linked to the ecology of herbivores and their natural enemies in the soil. FRONTIERS IN PLANT SCIENCE 2013; 4:378. [PMID: 24137165 PMCID: PMC3786222 DOI: 10.3389/fpls.2013.00378] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 09/03/2013] [Indexed: 05/11/2023]
Abstract
Modern agricultural systems can benefit from the application of concepts and models from applied ecology. When understood, multitrophic interactions among plants, pests, diseases and their natural enemies can be exploited to increase crop production and reduce undesirable environmental impacts. Although the understanding of subterranean ecology is rudimentary compared to the perspective aboveground, technologies today vastly reduce traditional obstacles to studying cryptic communities. Here we emphasize advantages to integrating as much as possible the use of these methods in order to leverage the information gained from studying communities of soil organisms. PCR-based approaches to identify and quantify species (real time qPCR and next generation sequencing) greatly expand the ability to investigate food web interactions because there is less need for wide taxonomic expertise within research programs. Improved methods to capture and measure volatiles in the soil atmosphere in situ make it possible to detect and study chemical cues that are critical to communication across trophic levels. The application of SADIE to directly assess rather than infer spatial patterns in belowground agroecosystems has improved the ability to characterize relationships between organisms in space and time. We review selected methodology and use of these tools and describe some of the ways they were integrated to study soil food webs in Florida citrus orchards with the goal of developing new biocontrol approaches.
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Affiliation(s)
- R. Campos-Herrera
- Departamento de Contaminación Ambiental, Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones CientíficasMadrid, Spain
- Entomology and Nematology Department, Citrus Research and Education Center, University of FloridaLake Alfred, FL, USA
| | - J. G. Ali
- Entomology and Nematology Department, Citrus Research and Education Center, University of FloridaLake Alfred, FL, USA
- Department of Ecology and Evolutionary Biology, Cornell UniversityIthaca, NY, USA
| | - B. M. Diaz
- Departamento de Protección Vegetal, Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - L. W. Duncan
- Entomology and Nematology Department, Citrus Research and Education Center, University of FloridaLake Alfred, FL, USA
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Culture-Independent Molecular Tools for Soil and Rhizosphere Microbiology. DIVERSITY-BASEL 2013. [DOI: 10.3390/d5030581] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Davies LO, Schäfer H, Marshall S, Bramke I, Oliver RG, Bending GD. Light structures phototroph, bacterial and fungal communities at the soil surface. PLoS One 2013; 8:e69048. [PMID: 23894406 PMCID: PMC3716809 DOI: 10.1371/journal.pone.0069048] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 06/04/2013] [Indexed: 02/01/2023] Open
Abstract
The upper few millimeters of soil harbour photosynthetic microbial communities that are structurally distinct from those of underlying bulk soil due to the presence of light. Previous studies in arid zones have demonstrated functional importance of these communities in reducing soil erosion, and enhancing carbon and nitrogen fixation. Despite being widely distributed, comparative understanding of the biodiversity of the soil surface and underlying soil is lacking, particularly in temperate zones. We investigated the establishment of soil surface communities on pasture soil in microcosms exposed to light or dark conditions, focusing on changes in phototroph, bacterial and fungal communities at the soil surface (0–3 mm) and bulk soil (3–12 mm) using ribosomal marker gene analyses. Microbial community structure changed with time and structurally similar phototrophic communities were found at the soil surface and in bulk soil in the light exposed microcosms suggesting that light can influence phototroph community structure even in the underlying bulk soil. 454 pyrosequencing showed a significant selection for diazotrophic cyanobacteria such as Nostoc punctiforme and Anabaena spp., in addition to the green alga Scenedesmus obliquus. The soil surface also harboured distinct heterotrophic bacterial and fungal communities in the presence of light, in particular, the selection for the phylum Firmicutes. However, these light driven changes in bacterial community structure did not extend to the underlying soil suggesting a discrete zone of influence, analogous to the rhizosphere.
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Affiliation(s)
- Lawrence O Davies
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom.
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