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Kumari R, Kumar V, Arukha AP, Rabbee MF, Ameen F, Koul B. Screening of the Biocontrol Efficacy of Potent Trichoderma Strains against Fusarium oxysporum f.sp. ciceri and Scelrotium rolfsii Causing Wilt and Collar Rot in Chickpea. Microorganisms 2024; 12:1280. [PMID: 39065049 PMCID: PMC11278996 DOI: 10.3390/microorganisms12071280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
Chickpeas contribute to half of the pulses produced in India and are an excellent source of protein, fibers, carbohydrates, minerals, and vitamins. However, the combination of the wilt and root rot diseases drastically lowers its yield. The use of antagonist microbes that restrict the growth of other phytopathogens is an ecofriendly approach to combat the serious threats raised by the plant pathogens. Trichoderma spp. are well known as biocontrol agents, especially against soil- and seed-borne phytopathogens. In this study, 21 Trichoderma isolates that were collected from different rhizospheric soils were evaluated against two notorious soil-borne pathogens, such as Fusarium oxysproum f.sp. ciceri and Sclerotium rolfsii. The maximum percentage of inhibition against the tested pathogens was observed in Trichoderma isolate PBT13 (72.97%, 61.1%) followed by PBT3 (72.23%, 59.3%). The mycelial extension rate method, dual culture (antagonism), production of cell-wall degrading enzymes (CWDs), and antifungal metabolites (by GC-MS) were used as selection criteria for potent Trichoderma isolates. Among the 21 isolates, PBT3, PBT4, PBT9, and PBT13 exhibited high antagonistic activity, production of antifungal metabolites, and chitinase and β-1,3-glucanase activity. These four species were subjected to molecular characterization using an internal transcribed spacer (ITS 1 and ITS4). The results of molecular characterization identified the four species as T. virnes, T. asperellum, T. lixii, and T. harzianum. Moreover, significant chitinase and β-1,3-glucanase activities of all Trichoderma isolates were recorded in the growth medium. Trichoderma harzianum (isolate PBT13) was found to exhibit the highest chitinase activity in terms of zone formation (4.40 ± 0.17 cm), whereas Trichoderma virens (isolate PBT3) exhibited the highest β-1,3-glucanase activity1.511 μmole/min. A GC-MS analysis of ethyl extracts from two isolates of Trichoderma (PBT9, PBT13) revealed the presence of 28 VOCs. Overall, this study suggests that these four Trichoderma strains are promising biological control agents (BCAs) and could be developed as bio-pesticides after stringent field trials for the management of soil-borne diseases of chickpeas.
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Affiliation(s)
- Ranjna Kumari
- Department of Botany, Lovely Professional University, Phagwara 144411, Punjab, India;
| | - Vipul Kumar
- Department of Plant Pathology, School of Agriculture, Lovely Professional University, Phagwara 144411, Punjab, India;
| | - Ananta Prasad Arukha
- Department of Nephrology and Hypertension, Mayo Medical Sciences, Rochester, MN 55902, USA;
| | - Muhammad Fazle Rabbee
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Fuad Ameen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Bhupendra Koul
- Department of Botany, Lovely Professional University, Phagwara 144411, Punjab, India;
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Sanchez Barrios A, Lundberg D, de Lorenzo L, Amos BK, Nair M, Hunt A, DeBolt S. Bacterial Spermosphere Inoculants Alter N. benthamiana-Plant Physiology and Host Bacterial Microbiome. PLANTS (BASEL, SWITZERLAND) 2024; 13:1677. [PMID: 38931109 PMCID: PMC11207711 DOI: 10.3390/plants13121677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/15/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024]
Abstract
In this study, we investigated the interplay between the spermosphere inoculum, host plant physiology, and endophytic compartment (EC) microbial community. Using 16S ribosomal RNA gene sequencing of root, stem, and leaf endophytic compartment communities, we established a baseline microbiome for Nicotiana sp. Phenotypic differences were observed due to the addition of some bacterial inoculants, correlated with endogenous auxin loads using transgenic plants expressing the auxin reporter pB-GFP::P87. When applied as spermosphere inoculants, select bacteria were found to create reproducible variation within the root EC microbiome and, more systematically, the host plant physiology. Our findings support the assertion that the spermosphere of plants is a zone that can influence the EC microbiome when applied in a greenhouse setting.
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Affiliation(s)
| | - Derek Lundberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
| | - Laura de Lorenzo
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA
| | - B Kirtley Amos
- Department of Horticulture, University of Kentucky, Lexington, KY 40546, USA; (A.S.B.)
| | - Meera Nair
- Department of Horticulture, University of Kentucky, Lexington, KY 40546, USA; (A.S.B.)
| | - Arthur Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA
| | - Seth DeBolt
- Department of Horticulture, University of Kentucky, Lexington, KY 40546, USA; (A.S.B.)
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Bamba M, Akyol TY, Azuma Y, Quilbe J, Andersen SU, Sato S. Synergistic effects of plant genotype and soil microbiome on growth in Lotus japonicus. FEMS Microbiol Ecol 2024; 100:fiae056. [PMID: 38678008 PMCID: PMC11068475 DOI: 10.1093/femsec/fiae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/25/2024] [Accepted: 04/10/2024] [Indexed: 04/29/2024] Open
Abstract
The biological interactions between plants and their root microbiomes are essential for plant growth, and even though plant genotype (G), soil microbiome (M), and growth conditions (environment; E) are the core factors shaping root microbiome, their relationships remain unclear. In this study, we investigated the effects of G, M, and E and their interactions on the Lotus root microbiome and plant growth using an in vitro cross-inoculation approach, which reconstructed the interactions between nine Lotus accessions and four soil microbiomes under two different environmental conditions. Results suggested that a large proportion of the root microbiome composition is determined by M and E, while G-related (G, G × M, and G × E) effects were significant but small. In contrast, the interaction between G and M had a more pronounced effect on plant shoot growth than M alone. Our findings also indicated that most microbiome variations controlled by M have little effect on plant phenotypes, whereas G × M interactions have more significant effects. Plant genotype-dependent interactions with soil microbes warrant more attention to optimize crop yield and resilience.
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Affiliation(s)
- Masaru Bamba
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
| | - Turgut Yigit Akyol
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Yusuke Azuma
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
| | - Johan Quilbe
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Stig Uggerhøj Andersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
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Fan Y, He X, Dai J, Yang N, Jiang Q, Xu Z, Tang X, Yu Y, Xiao M. Induced Resistance Mechanism of Bacillus velezensis S3-1 Against Pepper Wilt. Curr Microbiol 2023; 80:367. [PMID: 37819393 DOI: 10.1007/s00284-023-03470-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 09/02/2023] [Indexed: 10/13/2023]
Abstract
In recent years, pepper wilt has emerged as a pivotal constraint on pepper yield augmentation. Bacillus velezensis S3-1, with a wide array of hosts, can be used as both a biocontrol agent and biofertilizer. Nonetheless, the precise mechanisms underpinning its employment in combating pepper wilt remain cloaked in ambiguity. In our study, we found that B. velezensis S3-1 could significantly inhibit Fusarium sp. F1T that caused pepper wilt. S3-1 could effectively inhibit both the growth and germination of F1T conidia, leading to a reduction in the spore germination percentage from 83.2 to 37.1% in vitro experiments. Additionally, leaf detachment experiments revealed that the volatile compounds produced by S3-1 could inhibit the spread of pepper leaf spot area. Moreover, we observed a significant decrease in the content of malondialdehyde (MDA) in pepper treated with S3-1, along with a significant increase in the content of soluble protein, polyphenol oxidase (PPO), peroxidase (POD), and phenylalanine ammonia-lyase (PAL) in pepper. Furthermore, RT-PCR analysis showed that the expression of the defense genes CaPR 1 and CaPIN II in pepper after treatment with S3-1 was significantly upregulated, suggesting that S3-1 had the potential to induce systemic resistance in pepper, thereby enhancing its disease resistance. Hence, our findings suggest that S3-1 can be a promising biocontrol agent for managing pepper wilt in modern agriculture.
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Affiliation(s)
- Yongjie Fan
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Xingjie He
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Jiawei Dai
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Ning Yang
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Qiuyan Jiang
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Zhaofeng Xu
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Xiaorong Tang
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Yating Yu
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Ming Xiao
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, People's Republic of China.
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Behr JH, Kampouris ID, Babin D, Sommermann L, Francioli D, Kuhl-Nagel T, Chowdhury SP, Geistlinger J, Smalla K, Neumann G, Grosch R. Beneficial microbial consortium improves winter rye performance by modulating bacterial communities in the rhizosphere and enhancing plant nutrient acquisition. FRONTIERS IN PLANT SCIENCE 2023; 14:1232288. [PMID: 37711285 PMCID: PMC10498285 DOI: 10.3389/fpls.2023.1232288] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/03/2023] [Indexed: 09/16/2023]
Abstract
The beneficial effect of microbial consortium application on plants is strongly affected by soil conditions, which are influenced by farming practices. The establishment of microbial inoculants in the rhizosphere is a prerequisite for successful plant-microorganism interactions. This study investigated whether a consortium of beneficial microorganisms establishes in the rhizosphere of a winter crop during the vegetation period, including the winter growing season. In addition, we aimed for a better understanding of its effect on plant performance under different farming practices. Winter rye plants grown in a long-time field trial under conventional or organic farming practices were inoculated after plant emergence in autumn with a microbial consortium containing Pseudomonas sp. (RU47), Bacillus atrophaeus (ABi03) and Trichoderma harzianum (OMG16). The density of the microbial inoculants in the rhizosphere and root-associated soil was quantified in autumn and the following spring. Furthermore, the influence of the consortium on plant performance and on the rhizosphere bacterial community assembly was investigated using a multidisciplinary approach. Selective plating showed a high colonization density of individual microorganisms of the consortium in the rhizosphere and root-associated soil of winter rye throughout its early growth cycle. 16S rRNA gene amplicon sequencing showed that the farming practice affected mainly the rhizosphere bacterial communities in autumn and spring. However, the microbial consortium inoculated altered also the bacterial community composition at each sampling time point, especially at the beginning of the new growing season in spring. Inoculation of winter rye with the microbial consortium significantly improved the plant nutrient status and performance especially under organic farming. In summary, the microbial consortium showed sufficient efficacy throughout vegetation dormancy when inoculated in autumn and contributed to better plant performance, indicating the potential of microbe-based solutions in organic farming where nutrient availability is limited.
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Affiliation(s)
- Jan Helge Behr
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Großbeeren, Germany
| | - Ioannis D. Kampouris
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Doreen Babin
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Loreen Sommermann
- Department of Agriculture, Ecotrophology and Landscape Development, Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Germany
| | - Davide Francioli
- Department of Nutritional Crop Physiology, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
- Department of Soil Science and Plant Nutrition, Hochschule Geisenheim University, Geisenheim, Germany
| | - Theresa Kuhl-Nagel
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Großbeeren, Germany
| | - Soumitra Paul Chowdhury
- Institute for Network Biology, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Joerg Geistlinger
- Department of Agriculture, Ecotrophology and Landscape Development, Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Germany
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Günter Neumann
- Department of Nutritional Crop Physiology, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Rita Grosch
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Großbeeren, Germany
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Dela Cruz TEE, Behr JH, Geistlinger J, Grosch R, Witzel K. Monitoring of an Applied Beneficial Trichoderma Strain in Root-Associated Soil of Field-Grown Maize by MALDI-TOF MS. Microorganisms 2023; 11:1655. [PMID: 37512828 PMCID: PMC10384135 DOI: 10.3390/microorganisms11071655] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/08/2023] [Accepted: 06/16/2023] [Indexed: 07/30/2023] Open
Abstract
The persistence of beneficial microorganisms in the rhizosphere or surrounding soil following their application is a prerequisite for the effective interaction with the plant or indigenous microbial communities in the respective habitats. The goal of the study was to analyze the establishment and persistence of the applied beneficial Trichoderma harzianum (OMG16) strain in the maize root-associated soil depending on agricultural practice (soil management practice, N-fertilizer intensity) in a field experiment. A rapid identification of the inoculated strain OMG16 is essential for its monitoring. We used a culture-based approach coupled to matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis for the rapid identification of the inoculated Trichoderma strain as part of the beneficial microbe consortium (BMc). We isolated 428 fungal isolates from eight treatments of the field experiment. Forty eight percent of the isolated fungi equivalent to 205 fungal isolates were identified as Trichoderma, of which 87% (=179 isolates) were obtained from the fields inoculated with BMc. Gene sequence analysis showed a high similarity of the MALDI-TOF MS-identified Trichoderma, with that of the inoculated Trichoderma harzianum OMG16 confirming the re-isolation of the added beneficial fungus. This study highlighted the use of MALDI-TOF MS analysis as a quick, cost-effective detection and efficient monitoring tool for microbial-based bioinoculants in the field.
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Affiliation(s)
- Thomas Edison E Dela Cruz
- Department of Biological Sciences, College of Science, University of Santo Tomas (UST), España Blvd., Manila 1015, Philippines
| | - Jan Helge Behr
- Department of Plant-Microbes Systems, Leibniz Institute of Vegetables and Ornamental Crops (IGZ), Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
| | - Joerg Geistlinger
- Department of Agriculture, Landscape Development and Ecotrophology, Anhalt University of Applied Sciences (AUAS), Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Rita Grosch
- Department of Plant-Microbes Systems, Leibniz Institute of Vegetables and Ornamental Crops (IGZ), Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
| | - Katja Witzel
- Department of Plant-Microbes Systems, Leibniz Institute of Vegetables and Ornamental Crops (IGZ), Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
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Cardoni M, Fernández-González AJ, Valverde-Corredor A, Fernández-López M, Mercado-Blanco J. Co-occurrence network analysis unveils the actual differential impact on the olive root microbiota by two Verticillium wilt biocontrol rhizobacteria. ENVIRONMENTAL MICROBIOME 2023; 18:21. [PMID: 36949520 PMCID: PMC10035242 DOI: 10.1186/s40793-023-00480-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Verticillium wilt of olive (VWO), caused by Verticillium dahliae Kleb, is one of the most threatening diseases affecting olive cultivation. An integrated disease management strategy is recommended for the effective control of VWO. Within this framework, the use of biological control agents (BCAs) is a sustainable and environmentally friendly approach. No studies are available on the impact that the introduction of BCAs has on the resident microbiota of olive roots. Pseudomonas simiae PICF7 and Paenibacillus polymyxa PIC73 are two BCAs effective against VWO. We examined the effects of the introduction of these BCAs on the structure, composition and co-occurrence networks of the olive (cv. Picual) root-associated microbial communities. The consequences of the subsequent inoculation with V. dahliae on BCA-treated plants were also assessed. RESULTS Inoculation with any of the BCAs did not produce significant changes in the structure or the taxonomic composition of the 'Picual' root-associated microbiota. However, significant and distinctive alterations were observed in the topologies of the co-occurrence networks. The introduction of PIC73 provoked a diminution of positive interactions within the 'Picual' microbial community; instead, PICF7 inoculation increased the microbiota's compartmentalization. Upon pathogen inoculation, the network of PIC73-treated plants decreased the number of interactions and showed a switch of keystone species, including taxa belonging to minor abundant phyla (Chloroflexi and Planctomycetes). Conversely, the inoculation of V. dahliae in PICF7-treated plants significantly increased the complexity of the network and the number of links among their modules, suggestive of a more stable network. No changes in their keystone taxa were detected. CONCLUSION The absence of significant modifications on the structure and composition of the 'Picual' belowground microbiota due to the introduction of the tested BCAs underlines the low/null environmental impact of these rhizobacteria. These findings may have important practical consequences regarding future field applications of these BCAs. Furthermore, each BCA altered the interactions among the components of the olive belowground microbiota in idiosyncratic ways (i.e. PIC73 strongly modified the number of positive relations in the 'Picual' microbiota whereas PICF7 mostly affected the network stability). These modifications may provide clues on the biocontrol strategies used by these BCAs.
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Affiliation(s)
- Martina Cardoni
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas [CSIC], Córdoba, Spain
| | | | - Antonio Valverde-Corredor
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas [CSIC], Córdoba, Spain
| | - Manuel Fernández-López
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Jesús Mercado-Blanco
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas [CSIC], Córdoba, Spain.
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, CSIC, Granada, Spain.
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Dumack K, Feng K, Flues S, Sapp M, Schreiter S, Grosch R, Rose LE, Deng Y, Smalla K, Bonkowski M. What Drives the Assembly of Plant-associated Protist Microbiomes? Investigating the Effects of Crop Species, Soil Type and Bacterial Microbiomes. Protist 2022; 173:125913. [PMID: 36257252 DOI: 10.1016/j.protis.2022.125913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/24/2022] [Accepted: 09/22/2022] [Indexed: 12/30/2022]
Abstract
In a field experiment we investigated the influence of the environmental filters soil type (i.e. three contrasting soils) and plant species (i.e. lettuce and potato) identity on rhizosphere community assembly of Cercozoa, a dominant group of mostly bacterivorous soil protists. Plant species (14%) and rhizosphere origin (vs bulk soil) with 13%, together explained four times more variation in cercozoan beta diversity than the three soil types (7% explained variation). Our results clearly confirm the existence of plant species-specific protist communities. Network analyses of bacteria-Cercozoa rhizosphere communities identified scale-free small world topologies, indicating mechanisms of self-organization. While the assembly of rhizosphere bacterial communities is bottom-up controlled through the resource supply from root (secondary) metabolites, our results support the hypothesis that the net effect may depend on the strength of top-down control by protist grazers. Since grazing of protists has a strong impact on the composition and functioning of bacteria communities, protists expand the repertoire of plant genes by functional traits, and should be considered as 'protist microbiomes' in analogy to 'bacterial microbiomes'.
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Affiliation(s)
- Kenneth Dumack
- University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Str. 47b, 50674 Köln, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany.
| | - Kai Feng
- University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Str. 47b, 50674 Köln, Germany; CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Sebastian Flues
- University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Str. 47b, 50674 Köln, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany
| | - Melanie Sapp
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Population Genetics, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Susanne Schreiter
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany; Helmholtz Centre for Environmental Research GmbH (UFZ), Deptartment Soil System Science, Theodor-Lieser-Str.4, 06120 Halle, Germany
| | - Rita Grosch
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Laura E Rose
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Population Genetics, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Kornelia Smalla
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Michael Bonkowski
- University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Str. 47b, 50674 Köln, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany
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Windisch S, Walter A, Moradtalab N, Walker F, Höglinger B, El-Hasan A, Ludewig U, Neumann G, Grosch R. Role of Benzoic Acid and Lettucenin A in the Defense Response of Lettuce against Soil-Borne Pathogens. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112336. [PMID: 34834699 PMCID: PMC8618419 DOI: 10.3390/plants10112336] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/16/2021] [Accepted: 10/25/2021] [Indexed: 05/28/2023]
Abstract
Soil-borne pathogens can severely limit plant productivity. Induced defense responses are plant strategies to counteract pathogen-related damage and yield loss. In this study, we hypothesized that benzoic acid and lettucenin A are involved as defense compounds against Rhizoctonia solani and Olpidium virulentus in lettuce. To address this hypothesis, we conducted growth chamber experiments using hydroponics, peat culture substrate and soil culture in pots and minirhizotrons. Benzoic acid was identified as root exudate released from lettuce plants upon pathogen infection, with pre-accumulation of benzoic acid esters in the root tissue. The amounts were sufficient to inhibit hyphal growth of R. solani in vitro (30%), to mitigate growth retardation (51%) and damage of fine roots (130%) in lettuce plants caused by R. solani, but were not able to overcome plant growth suppression induced by Olpidium infection. Additionally, lettucenin A was identified as major phytoalexin, with local accumulation in affected plant tissues upon infection with pathogens or chemical elicitation (CuSO4) and detected in trace amounts in root exudates. The results suggest a two-stage defense mechanism with pathogen-induced benzoic acid exudation initially located in the rhizosphere followed by accumulation of lettucenin A locally restricted to affected root and leaf tissues.
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Affiliation(s)
- Saskia Windisch
- Department of Nutritional Crop Physiology, Institute of Crop Sciences, University of Hohenheim, 70599 Stuttgart, Germany; (A.W.); (N.M.); (U.L.); (G.N.)
| | - Anja Walter
- Department of Nutritional Crop Physiology, Institute of Crop Sciences, University of Hohenheim, 70599 Stuttgart, Germany; (A.W.); (N.M.); (U.L.); (G.N.)
| | - Narges Moradtalab
- Department of Nutritional Crop Physiology, Institute of Crop Sciences, University of Hohenheim, 70599 Stuttgart, Germany; (A.W.); (N.M.); (U.L.); (G.N.)
| | - Frank Walker
- Central Chemical-Analytical Laboratory, Institute of Phytomedicine, University of Hohenheim, 70599 Stuttgart, Germany; (F.W.); (B.H.)
| | - Birgit Höglinger
- Central Chemical-Analytical Laboratory, Institute of Phytomedicine, University of Hohenheim, 70599 Stuttgart, Germany; (F.W.); (B.H.)
| | - Abbas El-Hasan
- Department of Phytopathology, Institute of Phytomedicine, University of Hohenheim, 70599 Stuttgart, Germany;
| | - Uwe Ludewig
- Department of Nutritional Crop Physiology, Institute of Crop Sciences, University of Hohenheim, 70599 Stuttgart, Germany; (A.W.); (N.M.); (U.L.); (G.N.)
| | - Günter Neumann
- Department of Nutritional Crop Physiology, Institute of Crop Sciences, University of Hohenheim, 70599 Stuttgart, Germany; (A.W.); (N.M.); (U.L.); (G.N.)
| | - Rita Grosch
- Programme Area Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V., 14979 Großbeeren, Germany;
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10
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Carles L, Martin-Laurent F, Devers M, Spor A, Rouard N, Beguet J, Besse-Hoggan P, Batisson I. Potential of preventive bioremediation to reduce environmental contamination by pesticides in an agricultural context: A case study with the herbicide 2,4-D. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125740. [PMID: 33848793 DOI: 10.1016/j.jhazmat.2021.125740] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/01/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
One of the major problems with pesticides is linked to the non-negligible proportion of the sprayed active ingredient that does not reach its intended target and contaminates environmental compartments. Here, we have implemented and provided new insights to the preventive bioremediation process based on the simultaneous application of the pesticide with pesticide-degrading microorganisms to reduce the risk of leaching into the environment. This study pioneers such a practice, in an actual farming context. The 2,4-dichlorophenoxyacetic acid herbicide (2,4-D) and one of its bacterial mineralizing-strains (Cupriavidus necator JMP134) were used as models. The 2,4-D biodegradation was studied in soil microcosms planted with sensitive (mustard) and insensitive (wheat) plants. Simultaneous application of a 2,4-D commercial formulation (DAM®) at agricultural recommended doses with 105 cells.g-1 dw of soil of the JMP134 strain considerably accelerated mineralization of the herbicide since its persistence was reduced threefold for soil supplemented with the mineralizing bacterium without reducing the herbicide efficiency. Furthermore, the inoculation of the Cupriavidus necator strain did not significantly affect the α- and β-diversity of the bacterial community. By tackling the contamination immediately at source, the preventive bioremediation process proves to be an effective and promising way to reduce environmental contamination by agricultural pesticides.
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Affiliation(s)
- Louis Carles
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement (LMGE), F-63000 Clermont-Ferrand, France; Université Clermont Auvergne, CNRS, Sigma Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France.
| | - Fabrice Martin-Laurent
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ., Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Marion Devers
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ., Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Aymé Spor
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ., Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Nadine Rouard
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ., Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Jérémie Beguet
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ., Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Pascale Besse-Hoggan
- Université Clermont Auvergne, CNRS, Sigma Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Isabelle Batisson
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement (LMGE), F-63000 Clermont-Ferrand, France
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11
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Berg G, Kusstatscher P, Abdelfattah A, Cernava T, Smalla K. Microbiome Modulation-Toward a Better Understanding of Plant Microbiome Response to Microbial Inoculants. Front Microbiol 2021; 12:650610. [PMID: 33897663 PMCID: PMC8060476 DOI: 10.3389/fmicb.2021.650610] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/19/2021] [Indexed: 12/31/2022] Open
Abstract
Plant-associated microorganisms are involved in important functions related to growth, performance and health of their hosts. Understanding their modes of action is important for the design of promising microbial inoculants for sustainable agriculture. Plant-associated microorganisms are able to interact with their hosts and often exert specific functions toward potential pathogens; the underlying in vitro interactions are well studied. In contrast, in situ effects of inoculants, and especially their impact on the plant indigenous microbiome was mostly neglected so far. Recently, microbiome research has revolutionized our understanding of plants as coevolved holobionts but also of indigenous microbiome-inoculant interactions. Here we disentangle the effects of microbial inoculants on the indigenous plant microbiome and point out the following types of plant microbiome modulations: (i) transient microbiome shifts, (ii) stabilization or increase of microbial diversity, (iii) stabilization or increase of plant microbiome evenness, (iv) restoration of a dysbiosis/compensation or reduction of a pathogen-induced shift, (v) targeted shifts toward plant beneficial members of the indigenous microbiota, and (vi) suppression of potential pathogens. Therefore, we suggest microbiome modulations as novel and efficient mode of action for microbial inoculants that can also be mediated via the plant.
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Affiliation(s)
- Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
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12
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Babin D, Sommermann L, Chowdhury SP, Behr JH, Sandmann M, Neumann G, Nesme J, Sørensen SJ, Schellenberg I, Rothballer M, Geistlinger J, Smalla K, Grosch R. Distinct rhizomicrobiota assemblages and plant performance in lettuce grown in soils with different agricultural management histories. FEMS Microbiol Ecol 2021; 97:fiab027. [PMID: 33571366 DOI: 10.1093/femsec/fiab027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/09/2021] [Indexed: 12/21/2022] Open
Abstract
A better understanding of factors shaping the rhizosphere microbiota is important for sustainable crop production. We hypothesized that the effect of agricultural management on the soil microbiota is reflected in the assemblage of the rhizosphere microbiota with implications for plant performance. We designed a growth chamber experiment growing the model plant lettuce under controlled conditions in soils of a long-term field experiment with contrasting histories of tillage (mouldboard plough vs cultivator tillage), fertilization intensity (intensive standard nitrogen (N) + pesticides/growth regulators vs extensive reduced N without fungicides/growth regulators), and last standing field crop (rapeseed vs winter wheat). High-throughput sequencing of bacterial and archaeal 16S rRNA genes and fungal ITS2 regions amplified from total community DNA showed that these factors shaped the soil and rhizosphere microbiota of lettuce, however, to different extents among the microbial domains. Pseudomonas and Olpidium were identified as major indicators for agricultural management in the rhizosphere of lettuce. Long-term extensive fertilization history of soils resulted in higher lettuce growth and increased expression of genes involved in plant stress responses compared to intensive fertilization. Our work adds to the increasing knowledge on how soil microbiota can be manipulated by agricultural management practices which could be harnessed for sustainable crop production.
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Affiliation(s)
- Doreen Babin
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Loreen Sommermann
- Anhalt University of Applied Sciences, Department of Agriculture, Ecotrophology and Landscape Development, Institute of Bioanalytical Sciences (IBAS), Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Soumitra Paul Chowdhury
- Institute of Network Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Jan H Behr
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Martin Sandmann
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Günter Neumann
- University of Hohenheim, Institute of Crop Science, Department of Nutritional Crop Physiology, Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Joseph Nesme
- University of Copenhagen, Department of Biology, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- University of Copenhagen, Department of Biology, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Ingo Schellenberg
- Anhalt University of Applied Sciences, Department of Agriculture, Ecotrophology and Landscape Development, Institute of Bioanalytical Sciences (IBAS), Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Michael Rothballer
- Institute of Network Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Joerg Geistlinger
- Anhalt University of Applied Sciences, Department of Agriculture, Ecotrophology and Landscape Development, Institute of Bioanalytical Sciences (IBAS), Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Rita Grosch
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
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13
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Bonkowski M, Tarkka M, Razavi BS, Schmidt H, Blagodatskaya E, Koller R, Yu P, Knief C, Hochholdinger F, Vetterlein D. Spatiotemporal Dynamics of Maize ( Zea mays L.) Root Growth and Its Potential Consequences for the Assembly of the Rhizosphere Microbiota. Front Microbiol 2021; 12:619499. [PMID: 33815308 PMCID: PMC8010349 DOI: 10.3389/fmicb.2021.619499] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
Abstract
Numerous studies have shown that plants selectively recruit microbes from the soil to establish a complex, yet stable and quite predictable microbial community on their roots – their “microbiome.” Microbiome assembly is considered as a key process in the self-organization of root systems. A fundamental question for understanding plant-microbe relationships is where a predictable microbiome is formed along the root axis and through which microbial dynamics the stable formation of a microbiome is challenged. Using maize as a model species for which numerous data on dynamic root traits are available, this mini-review aims to give an integrative overview on the dynamic nature of root growth and its consequences for microbiome assembly based on theoretical considerations from microbial community ecology.
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Affiliation(s)
- Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Mika Tarkka
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Bahar S Razavi
- Department of Soil and Plant Microbiome, Christian-Albrecht University of Kiel, Kiel, Germany
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Evgenia Blagodatskaya
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany
| | - Robert Koller
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Peng Yu
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation - Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Frank Hochholdinger
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Doris Vetterlein
- Department of Soil System Science, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany.,Soil Science, Martin-Luther-University Halle-Wittenberg, Halle, Germany
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14
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Munoz‐Ucros J, Zwetsloot MJ, Cuellar‐Gempeler C, Bauerle TL. Spatiotemporal patterns of rhizosphere microbiome assembly: From ecological theory to agricultural application. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.13850] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Juana Munoz‐Ucros
- School of Integrative Plant Science Cornell University Ithaca NY USA
| | | | | | - Taryn L. Bauerle
- School of Integrative Plant Science Cornell University Ithaca NY USA
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15
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Galitskaya P, Biktasheva L, Blagodatsky S, Selivanovskaya S. Response of bacterial and fungal communities to high petroleum pollution in different soils. Sci Rep 2021; 11:164. [PMID: 33420266 PMCID: PMC7794381 DOI: 10.1038/s41598-020-80631-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 12/21/2020] [Indexed: 01/29/2023] Open
Abstract
Petroleum pollution of soils is a major environmental problem. Soil microorganisms can decompose a significant fraction of petroleum hydrocarbons in soil at low concentrations (1-5%). This characteristic can be used for soil remediation after oil pollution. Microbial community dynamics and functions are well studied in cases of moderate petroleum pollution, while cases with heavy soil pollution have received much less attention. We studied bacterial and fungal successions in three different soils with high petroleum contents (6 and 25%) in a laboratory experiment. The proportion of aliphatic and aromatic compounds decreased by 4-7% in samples with 6% pollution after 120 days of incubation but remained unchanged in samples with 25% hydrocarbons. The composition of the microbial community changed significantly in all cases. Oil pollution led to an increase in the relative abundance of bacteria such as Actinobacteria and the candidate TM7 phylum (Saccaribacteria) and to a decrease in that of Bacteroidetes. The gene abundance (number of OTUs) of oil-degrading bacteria (Rhodococcus sp., candidate class TM7-3 representative) became dominant in all soil samples, irrespective of the petroleum pollution level and soil type. The fungal communities in unpolluted soil samples differed more significantly than the bacterial communities. Nonmetric multidimensional scaling revealed that in the polluted soil, successions of fungal communities differed between soils, in contrast to bacterial communities. However, these successions showed similar trends: fungi capable of lignin and cellulose decomposition, e.g., from the genera Fusarium and Mortierella, were dominant during the incubation period.
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Affiliation(s)
- Polina Galitskaya
- grid.77268.3c0000 0004 0543 9688Institute of Environmental Sciences, Kazan Federal University, Kazan, 420008 Russia
| | - Liliya Biktasheva
- grid.77268.3c0000 0004 0543 9688Institute of Environmental Sciences, Kazan Federal University, Kazan, 420008 Russia
| | - Sergey Blagodatsky
- grid.9464.f0000 0001 2290 1502Institute of Plant Production and Agroecology in the Tropics and Subtropics, University of Hohenheim, 70599 Stuttgart, Germany ,grid.451005.5Institute of Physico-Chemical and Biological Problems of Soil Science, Pushchino, 142290 Russia
| | - Svetlana Selivanovskaya
- grid.77268.3c0000 0004 0543 9688Institute of Environmental Sciences, Kazan Federal University, Kazan, 420008 Russia
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16
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Ray P, Lakshmanan V, Labbé JL, Craven KD. Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture. Front Microbiol 2020; 11:622926. [PMID: 33408712 PMCID: PMC7779556 DOI: 10.3389/fmicb.2020.622926] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/02/2020] [Indexed: 12/14/2022] Open
Abstract
Light, water and healthy soil are three essential natural resources required for agricultural productivity. Industrialization of agriculture has resulted in intensification of cropping practices using enormous amounts of chemical pesticides and fertilizers that damage these natural resources. Therefore, there is a need to embrace agriculture practices that do not depend on greater use of fertilizers and water to meet the growing demand of global food requirements. Plants and soil harbor millions of microorganisms, which collectively form a microbial community known as the microbiome. An effective microbiome can offer benefits to its host, including plant growth promotion, nutrient use efficiency, and control of pests and phytopathogens. Therefore, there is an immediate need to bring functional potential of plant-associated microbiome and its innovation into crop production. In addition to that, new scientific methodologies that can track the nutrient flux through the plant, its resident microbiome and surrounding soil, will offer new opportunities for the design of more efficient microbial consortia design. It is now increasingly acknowledged that the diversity of a microbial inoculum is as important as its plant growth promoting ability. Not surprisingly, outcomes from such plant and soil microbiome studies have resulted in a paradigm shift away from single, specific soil microbes to a more holistic microbiome approach for enhancing crop productivity and the restoration of soil health. Herein, we have reviewed this paradigm shift and discussed various aspects of benign microbiome-based approaches for sustainable agriculture.
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Affiliation(s)
- Prasun Ray
- Noble Research Institute, LLC, Ardmore, OK, United States
| | | | - Jessy L. Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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17
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Oni FE, Geudens N, Onyeka JT, Olorunleke OF, Salami AE, Omoboye OO, Arias AA, Adiobo A, De Neve S, Ongena M, Martins JC, Höfte M. Cyclic lipopeptide-producing Pseudomonas koreensis group strains dominate the cocoyam rhizosphere of a Pythium root rot suppressive soil contrasting with P. putida prominence in conducive soils. Environ Microbiol 2020; 22:5137-5155. [PMID: 32524747 DOI: 10.1111/1462-2920.15127] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/31/2020] [Accepted: 06/08/2020] [Indexed: 11/29/2022]
Abstract
Pseudomonas isolates from tropical environments have been underexplored and may form an untapped reservoir of interesting secondary metabolites. In this study, we compared Pseudomonas and cyclic lipopeptide (CLP) diversity in the rhizosphere of a cocoyam root rot disease (CRRD) suppressive soil in Boteva, Cameroon with those from four conducive soils in Cameroon and Nigeria. Compared with other soils, Boteva andosols were characterized by high silt, organic matter, nitrogen and calcium. Besides, the cocoyam rhizosphere at Boteva was characterized by strains belonging mainly to the P. koreensis and P. putida (sub)groups, with representations in the P. fluorescens, P. chlororaphis, P. jessenii and P. asplenii (sub)groups. In contrast, P. putida isolates were prominent in conducive soils. Regarding CLP diversity, Boteva was characterized by strains producing 11 different CLP types with cocoyamide A producers, belonging to the P. koreensis group, being the most abundant. However, putisolvin III-V producers were the most dominant in the rhizosphere of conducive soils in both Cameroon and Nigeria. Furthermore, we elucidated the chemical structure of putisolvin derivatives-putisolvin III-V, and described its biosynthetic gene cluster. We show that high Pseudomonas and metabolic diversity may be driven by microbial competition, which likely contributes to soil suppressiveness to CRRD.
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Affiliation(s)
- Feyisara Eyiwumi Oni
- Phytopathology Laboratory, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.,Unit for Environmental Sciences and Management, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa
| | - Niels Geudens
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, Ghent, Belgium
| | - Joseph T Onyeka
- Plant Pathology Unit, National Root Crops Research Institute (NRCRI), Umudike, Abia, Nigeria
| | - Oluwatoyin Faith Olorunleke
- Phytopathology Laboratory, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Ayodeji Ekundayo Salami
- Department of Crop, Horticulture and Landscape Design, Faculty of Agricultural Sciences, Ekiti State University (EKSU), Ado-Ekiti, Nigeria
| | - Olumide Owolabi Omoboye
- Phytopathology Laboratory, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Anthony Arguelles Arias
- Microbial Processes and Interactions Unit, Faculty of Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Amayana Adiobo
- Institute for Agricultural Research for Development (IRAD), Ekona, Cameroon
| | - Stefaan De Neve
- Research Group of Soil Fertility and Nutrient Management, Department of Environment, Ghent University, Ghent, Belgium
| | - Marc Ongena
- Microbial Processes and Interactions Unit, Faculty of Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - José C Martins
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, Ghent, Belgium
| | - Monica Höfte
- Phytopathology Laboratory, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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18
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Munir S, Li Y, He P, Huang M, He P, He P, Cui W, Wu Y, He Y. Core endophyte communities of different citrus varieties from citrus growing regions in China. Sci Rep 2020; 10:3648. [PMID: 32108149 PMCID: PMC7046616 DOI: 10.1038/s41598-020-60350-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 02/11/2020] [Indexed: 02/07/2023] Open
Abstract
The native microbiomes of citrus trees play important roles in plant health, with good communication between the native microbiome and the host plant. Here, we report on the native endophytes in 24 citrus varieties in nine citrus growing regions in China; some of the trees were healthy and others had asymptomatic or symptomatic huanglongbing, which is caused by the pathogen Candidatus Liberibacter asiaticus (CLas). We used culture-dependent analysis and characterized the isolates by partial 16S rRNA gene sequencing. The endophytes were compared between different citrus varieties, regions, and disease states (healthy, asymptomatic, and symptomatic). The total number of endophytes isolated from most of the citrus varieties was 104-106 CFU/g of leaves, but it differed significantly by disease state, with the highest numbers in the healthy leaves and the lowest in the symptomatic leaves (p < 0.05). Among the citrus varieties, the Valencia variety had the maximum number of endophyte species (22). The most dominant endophytes were Bacillus subtilis, B. velezensis, Curtobacterium luteum, and Microbacterium testaceum. The higher frequency of B. subtilis in the healthy/asymptomatic plants compared to the symptomatic plants suggests that it has a role in huanglongbing resistance. Native endophyte communities in various citrus varieties could be used to improve citrus growth and combat CLas.
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Affiliation(s)
- Shahzad Munir
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Yongmei Li
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Pengfei He
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Min Huang
- Agriculture College and Urban Modern Agriculture Engineering Research Center, Kunming University, Kunming, 650214, Yunnan, China
| | - Pengbo He
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Pengjie He
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Wenyan Cui
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Yixin Wu
- National and Local Joint Engineering Research Center for Screening and Application of Microbial Strains, Kunming, 650217, Yunnan, China
- Faculty of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Yueqiu He
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
- National and Local Joint Engineering Research Center for Screening and Application of Microbial Strains, Kunming, 650217, Yunnan, China.
- Faculty of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
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19
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Dutta S, Yu SM, Jeong SC, Lee YH. High-throughput analysis of genes involved in biocontrol performance of Pseudomonas fluorescens NBC275 against Gray mold. J Appl Microbiol 2019; 128:265-279. [PMID: 31574191 DOI: 10.1111/jam.14475] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 09/01/2019] [Accepted: 09/17/2019] [Indexed: 01/16/2023]
Abstract
AIMS Many physiological and microbial characteristics influence the biocontrol performance of the biological control agents (BCAs) in agricultural fields. To implement effective biocontrol, the contribution of specific genes, mechanisms and traits to the biocontrol performance of BCAs need to be characterized and explored in greater detail. METHODS AND RESULTS In this study, a transposon (Tn) mutant library using the BCA Pseudomonas fluorescens NBC275 (Pf275) was generated to explore genes and bacterial characteristics involved in antifungal activity and biocontrol performance. Among the Tn mutants, 205 strains showing variations in antifungal activity compared to wild-type (WT) were selected and further analysed for biocontrol efficacy against gray mold in pepper fruits. The genes involved in pyoverdine biosynthesis (pvdI and pvdD) and chitin-binding protein (gbpA) played essential roles in the antifungal activity and biocontrol capacity of Pf275. In addition, a mutation in phlD completely abolished the antifungal activity and significantly suppressed the biocontrol ability of the strain. Genes affecting antifungal activity of Pf275 significantly influenced swimming motility, which was identified as an important trait for the biocontrol ability of the bacterial strain. CONCLUSIONS Overall, our results suggest that antifungal compound production, siderophore biosynthesis and swimming motility synergistically contribute to Pf275 biocontrol performance. The utility of this library was demonstrated by identifying genes for antagonism and biocontrol ability in this BCA strain. The functional roles of many genes identified as contributing to antagonism and in vivo biocontrol activity require further study. SIGNIFICANCE AND IMPACT OF THIS STUDY Genes contributing to antifungal activity and biocontrol performance of P. fluorescens were identified and highlighted by Tn mutagenesis, which will give insight to improve the biocontrol performance of this BCA.
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Affiliation(s)
- S Dutta
- Division of Biotechnology, Chonbuk National University, Iksan-si, Jeollabuk-do, Republic of Korea
| | - S-M Yu
- Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, Sangju-si, Gyeongsangbuk-do, Republic of Korea
| | - S C Jeong
- Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, Sangju-si, Gyeongsangbuk-do, Republic of Korea
| | - Y H Lee
- Division of Biotechnology, Chonbuk National University, Iksan-si, Jeollabuk-do, Republic of Korea.,Advanced Institute of Environment and Bioscience, Plant Medical Research Center, and Institute of Bio-industry, Chonbuk National University, Ikansi-si, Jeollabuk-do, Republic of Korea
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Ciancio A, Pieterse CMJ, Mercado-Blanco J. Editorial: Harnessing Useful Rhizosphere Microorganisms for Pathogen and Pest Biocontrol - Second Edition. Front Microbiol 2019; 10:1935. [PMID: 31555222 PMCID: PMC6724568 DOI: 10.3389/fmicb.2019.01935] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/06/2019] [Indexed: 01/22/2023] Open
Affiliation(s)
- Aurelio Ciancio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Corné M J Pieterse
- Department of Biology, Science4Life, Utrecht University, Utrecht, Netherlands
| | - Jesús Mercado-Blanco
- Instituto de Agricultura Sostenible, Agencia Estatal Consejo Superior de Investigaciones Científicas, Córdoba, Spain
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Hassani MA, Özkurt E, Seybold H, Dagan T, Stukenbrock EH. Interactions and Coadaptation in Plant Metaorganisms. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:483-503. [PMID: 31348865 DOI: 10.1146/annurev-phyto-082718-100008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Plants associate with a wide diversity of microorganisms. Some microorganisms engage in intimate associations with the plant host, collectively forming a metaorganism. Such close coexistence with plants requires specific adaptations that allow microorganisms to overcome plant defenses and inhabit plant tissues during growth and reproduction. New data suggest that the plant immune system has a broader role beyond pathogen recognition and also plays an important role in the community assembly of the associated microorganism. We propose that core microorganisms undergo coadaptation with their plant host, notably in response to the plant immune system allowing them to persist and propagate in their host. Microorganisms, which are vertically transmitted from generation to generation via plant seeds, putatively compose highly adapted species and may have plant-beneficial functions. The extent to which plant domestication has impacted the underlying genetics of plant-microbe associations remains poorly understood. We propose that the ability of domesticated plants to select and maintain advantageous microbial partners may have been affected. In this review, we discuss factors that impact plant metaorganism assembly and function. We underline the importance of microbe-microbe interactions in plant tissues, as they are still poorly studied but may have a great impact on plant health.
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Affiliation(s)
- M Amine Hassani
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany;
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Ezgi Özkurt
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany;
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Heike Seybold
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany;
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Tal Dagan
- Institute of Microbiology, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Eva H Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany;
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
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Eltlbany N, Baklawa M, Ding GC, Nassal D, Weber N, Kandeler E, Neumann G, Ludewig U, van Overbeek L, Smalla K. Enhanced tomato plant growth in soil under reduced P supply through microbial inoculants and microbiome shifts. FEMS Microbiol Ecol 2019; 95:5544364. [DOI: 10.1093/femsec/fiz124] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 08/05/2019] [Indexed: 12/20/2022] Open
Abstract
ABSTRACTSoil microbial communities interact with roots, affecting plant growth and nutrient acquisition. In the present study, we aimed to decipher the effects of the inoculants Trichoderma harzianum T-22, Pseudomonas sp. DSMZ 13134, Bacillus amyloliquefaciens FZB42 or Pseudomonas sp. RU47 on the rhizosphere microbial community and their beneficial effects on tomato plants grown in moderately low phosphorous soil under greenhouse conditions. We analyzed the plant mass, inoculant colony forming units and rhizosphere communities on 15, 22, 29 and 43 days after sowing. Selective plating showed that the bacterial inoculants had a good rhizocompetence and accelerated shoot and root growth and nutrient accumulation. 16S rRNA gene fingerprints indicated changes in the rhizosphere bacterial community composition. Amplicon sequencing revealed that rhizosphere bacterial communities from plants treated with bacterial inoculants were more similar to each other and distinct from those of the control and the Trichoderma inoculated plants at harvest time, and numerous dynamic taxa were identified. In conclusion, likely both, inoculants and the rhizosphere microbiome shifts, stimulated early plant growth mainly by improved spatial acquisition of available nutrients via root growth promotion. At harvest, all tomato plants were P-deficient, suggesting a limited contribution of inoculants and the microbiome shifts to the solubilization of sparingly soluble soil P.
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Affiliation(s)
- Namis Eltlbany
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Messweg 11-12, 38104 Braunschweig, Germany
- Faculty of Agriculture, Suez Canal University, 4.5 Km the Ring Road, 41522 Ismailia, Egypt
| | - Mohamed Baklawa
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Messweg 11-12, 38104 Braunschweig, Germany
- Faculty of Agriculture, Suez Canal University, 4.5 Km the Ring Road, 41522 Ismailia, Egypt
| | - Guo-Chun Ding
- College of Resources and Environmental Science, China Agricultural University, 100193 Beijing, People's Republic of China
- Organic recycling institute (Suzhou), China agricultural university, 215128 Wuzhong, Jiangsu Province, People's Republic of China
| | - Dinah Nassal
- Institute of Soil Science and Land Evaluation, University of Hohenheim, Emil-Wolff Strasse 27, 70593 Stuttgart, Germany
| | - Nino Weber
- Nutritional Crop Physiology (340h), Institute of Crop Science, University of Hohenheim, Emil-Wolff Strasse 27, 70593 Stuttgart, Germany
| | - Ellen Kandeler
- Institute of Soil Science and Land Evaluation, University of Hohenheim, Emil-Wolff Strasse 27, 70593 Stuttgart, Germany
| | - Günter Neumann
- Nutritional Crop Physiology (340h), Institute of Crop Science, University of Hohenheim, Emil-Wolff Strasse 27, 70593 Stuttgart, Germany
| | - Uwe Ludewig
- Nutritional Crop Physiology (340h), Institute of Crop Science, University of Hohenheim, Emil-Wolff Strasse 27, 70593 Stuttgart, Germany
| | - Leo van Overbeek
- Wageningen Plant Research, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Messweg 11-12, 38104 Braunschweig, Germany
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23
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Analysis of the genome sequence of plant beneficial strain Pseudomonas sp. RU47. J Biotechnol 2018; 281:183-192. [DOI: 10.1016/j.jbiotec.2018.07.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 11/22/2022]
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Soil Properties Related to the Occurrence of Rock Phosphate-Solubilizing Bacteria in the Rhizosphere Soil of Faba Bean (Vicia faba L.) in Morocco. SOIL SYSTEMS 2018. [DOI: 10.3390/soilsystems2020031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Schreiter S, Babin D, Smalla K, Grosch R. Rhizosphere Competence and Biocontrol Effect of Pseudomonas sp. RU47 Independent from Plant Species and Soil Type at the Field Scale. Front Microbiol 2018; 9:97. [PMID: 29449832 PMCID: PMC5799239 DOI: 10.3389/fmicb.2018.00097] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/16/2018] [Indexed: 12/20/2022] Open
Abstract
Biocontrol inoculants often show inconsistency in their efficacy at field scale and the reason for this remains often unclear. A high rhizosphere competence of inoculant strains is assumed to be a key factor for successful biocontrol effects as the biocontrol strain has to compete with the indigenous microbial community in the rhizosphere. It is known that many factors, among them plant species and soil type shape the rhizosphere microbial community composition. However, microbial community composition in the rhizosphere can also be influenced by the presence of a pathogen. We hypothesized that plant species, soil type, and a pathogen affect the rhizosphere competence of a biocontrol strain and its biocontrol effect against a soil-borne pathogen. To test the hypothesis, we used an experimental plot system with three soil types (diluvial sand, alluvial loam, loess loam) kept under similar agricultural management at the same field site for 12 years. We investigate the rhizosphere competence of Pseudomonas sp. RU47 in two plant species (potato and lettuce) and its biocontrol effect against Rhizoctonia diseases. The colonization density of a rifampicin resistant mutant of RU47 in the rhizosphere of both crops was evaluated by plate counts. Bacterial community compositions were analyzed by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments amplified from total community DNA. The inoculant RU47 was able to colonize the rhizosphere of both model crops in a sufficient density and to reduce disease severity of black scurf on potato and bottom rot on lettuce in all three soils. DGGE indicated that RU47 affected the bacterial community composition stronger in the rhizosphere of lettuce than in the potato rhizosphere. In contrast, the effect of the pathogen Rhizoctonia solani on the bacterial community was much stronger in the rhizosphere of potato than in the lettuce rhizosphere. A significant effect of RU47 on the Pseudomonas-specific gacA fingerprints of the rhizosphere was only observed in lettuce in alluvial soil. The soil type and plant species independent biocontrol effects of RU47 and its minor influence on the indigenous bacterial community composition might be important criteria for the registration and use of RU47 as biocontrol strain.
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Affiliation(s)
- Susanne Schreiter
- Institute for Epidemiology and Pathogen Diagnostics, Federal Research Centre for Cultivated Plants, Julius Kühn-Institut (JKI), Braunschweig, Germany
| | - Doreen Babin
- Institute for Epidemiology and Pathogen Diagnostics, Federal Research Centre for Cultivated Plants, Julius Kühn-Institut (JKI), Braunschweig, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Federal Research Centre for Cultivated Plants, Julius Kühn-Institut (JKI), Braunschweig, Germany
| | - Rita Grosch
- Department Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
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Molina-Romero D, Baez A, Quintero-Hernández V, Castañeda-Lucio M, Fuentes-Ramírez LE, Bustillos-Cristales MDR, Rodríguez-Andrade O, Morales-García YE, Munive A, Muñoz-Rojas J. Compatible bacterial mixture, tolerant to desiccation, improves maize plant growth. PLoS One 2017; 12:e0187913. [PMID: 29117218 PMCID: PMC5678714 DOI: 10.1371/journal.pone.0187913] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/27/2017] [Indexed: 11/18/2022] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) increase plant growth and crop productivity. The inoculation of plants with a bacterial mixture (consortium) apparently provides greater benefits to plant growth than inoculation with a single bacterial strain. In the present work, a bacterial consortium was formulated containing four compatible and desiccation-tolerant strains with potential as PGPR. The formulation had one moderately (Pseudomonas putida KT2440) and three highly desiccation-tolerant (Sphingomonas sp. OF178, Azospirillum brasilense Sp7 and Acinetobacter sp. EMM02) strains. The four bacterial strains were able to adhere to seeds and colonize the rhizosphere of plants when applied in both mono-inoculation and multi-inoculation treatments, showing that they can also coexist without antagonistic effects in association with plants. The effects of the bacterial consortium on the growth of blue maize were evaluated. Seeds inoculated with either individual bacterial strains or the bacterial consortium were subjected to two experimental conditions before sowing: normal hydration or desiccation. In general, inoculation with the bacterial consortium increased the shoot and root dry weight, plant height and plant diameter compared to the non-inoculated control or mono-inoculation treatments. The bacterial consortium formulated in this work had greater benefits for blue maize plants even when the inoculated seeds underwent desiccation stress before germination, making this formulation attractive for future field applications.
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Affiliation(s)
- Dalia Molina-Romero
- Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Edificio IC11, Ciudad Universitaria, Colonia Jardines de San Manuel, Puebla, Puebla, México
- Laboratorio de Biología Molecular y Microbiología, Facultad de Ciencias Biológicas, BUAP, Edificio 112-A, Ciudad Universitaria, Colonia Jardines de San Manuel, Puebla, Puebla, México
| | - Antonino Baez
- Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Edificio IC11, Ciudad Universitaria, Colonia Jardines de San Manuel, Puebla, Puebla, México
| | - Verónica Quintero-Hernández
- CONACYT, LEMM, CICM, IC-BUAP, Edificio IC11, Ciudad Universitaria, Colonia Jardines de San Manuel, Puebla, Puebla, México
| | - Miguel Castañeda-Lucio
- Genética Molecular Microbiana, CICM, IC-BUAP, Edificio IC11, Ciudad Universitaria, Colonia Jardines de San Manuel, Puebla, Puebla, México
| | - Luis Ernesto Fuentes-Ramírez
- Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Edificio IC11, Ciudad Universitaria, Colonia Jardines de San Manuel, Puebla, Puebla, México
| | - María del Rocío Bustillos-Cristales
- Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Edificio IC11, Ciudad Universitaria, Colonia Jardines de San Manuel, Puebla, Puebla, México
| | - Osvaldo Rodríguez-Andrade
- Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Edificio IC11, Ciudad Universitaria, Colonia Jardines de San Manuel, Puebla, Puebla, México
| | - Yolanda Elizabeth Morales-García
- Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Edificio IC11, Ciudad Universitaria, Colonia Jardines de San Manuel, Puebla, Puebla, México
- Laboratorio de Biología Molecular y Microbiología, Facultad de Ciencias Biológicas, BUAP, Edificio 112-A, Ciudad Universitaria, Colonia Jardines de San Manuel, Puebla, Puebla, México
| | - Antonio Munive
- Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Edificio IC11, Ciudad Universitaria, Colonia Jardines de San Manuel, Puebla, Puebla, México
| | - Jesús Muñoz-Rojas
- Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Edificio IC11, Ciudad Universitaria, Colonia Jardines de San Manuel, Puebla, Puebla, México
- * E-mail:
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Finkel OM, Castrillo G, Herrera Paredes S, Salas González I, Dangl JL. Understanding and exploiting plant beneficial microbes. CURRENT OPINION IN PLANT BIOLOGY 2017; 38:155-163. [PMID: 28622659 PMCID: PMC5561662 DOI: 10.1016/j.pbi.2017.04.018] [Citation(s) in RCA: 286] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/25/2017] [Indexed: 05/18/2023]
Abstract
After a century of incremental research, technological advances, coupled with a need for sustainable crop yield increases, have reinvigorated the study of beneficial plant-microbe interactions with attention focused on how microbiomes alter plant phenotypes. We review recent advances in plant microbiome research, and describe potential applications for increasing crop productivity. The phylogenetic diversity of plant microbiomes is increasingly well characterized, and their functional diversity is becoming more accessible. Large culture collections are available for controlled experimentation, with more to come. Genetic resources are being brought to bear on questions of microbiome function. We expect that microbial amendments of varying complexities will expose rules governing beneficial plant-microbe interactions contributing to plant growth promotion and disease resistance, enabling more sustainable agriculture.
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Affiliation(s)
- Omri M Finkel
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599-3280, USA.
| | - Gabriel Castrillo
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Sur Herrera Paredes
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Isai Salas González
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
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Defining the Core Citrus Leaf- and Root-Associated Microbiota: Factors Associated with Community Structure and Implications for Managing Huanglongbing (Citrus Greening) Disease. Appl Environ Microbiol 2017; 83:AEM.00210-17. [PMID: 28341678 DOI: 10.1128/aem.00210-17] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/09/2017] [Indexed: 12/22/2022] Open
Abstract
Stable associations between plants and microbes are critical to promoting host health and productivity. The objective of this work was to test the hypothesis that restructuring of the core microbiota may be associated with the progression of huanglongbing (HLB), the devastating citrus disease caused by Liberibacter asiaticus, Liberibacter americanus, and Liberibacter africanus The microbial communities of leaves (n = 94) and roots (n = 79) from citrus trees that varied by HLB symptom severity, cultivar, location, and season/time were characterized with Illumina sequencing of 16S rRNA genes. The taxonomically rich communities contained abundant core members (i.e., detected in at least 95% of the respective leaf or root samples), some overrepresented site-specific members, and a diverse community of low-abundance variable taxa. The composition and diversity of the leaf and root microbiota were strongly associated with HLB symptom severity and location; there was also an association with host cultivar. The relative abundance of Liberibacter spp. among leaf microbiota positively correlated with HLB symptom severity and negatively correlated with alpha diversity, suggesting that community diversity decreases as symptoms progress. Network analysis of the microbial community time series identified a mutually exclusive relationship between Liberibacter spp. and members of the Burkholderiaceae, Micromonosporaceae, and Xanthomonadaceae This work confirmed several previously described plant disease-associated bacteria, as well as identified new potential implications for biological control. Our findings advance the understanding of (i) plant microbiota selection across multiple variables and (ii) changes in (core) community structure that may be a precondition to disease establishment and/or may be associated with symptom progression.IMPORTANCE This study provides a comprehensive overview of the core microbial community within the microbiomes of plant hosts that vary in extent of disease symptom progression. With 16S Illumina sequencing analyses, we not only confirmed previously described bacterial associations with plant health (e.g., potentially beneficial bacteria) but also identified new associations and potential interactions between certain bacteria and an economically important phytopathogen. The importance of core taxa within broader plant-associated microbial communities is discussed.
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Antweiler K, Schreiter S, Keilwagen J, Baldrian P, Kropf S, Smalla K, Grosch R, Heuer H. Statistical test for tolerability of effects of an antifungal biocontrol strain on fungal communities in three arable soils. Microb Biotechnol 2017; 10:434-449. [PMID: 28111906 PMCID: PMC5328832 DOI: 10.1111/1751-7915.12595] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/12/2016] [Accepted: 12/14/2016] [Indexed: 11/23/2022] Open
Abstract
A statistical method was developed to test for equivalence of microbial communities analysed by next-generation sequencing of amplicons. The test uses Bray-Curtis distances between the microbial community structures and is based on a two-sample jackknife procedure. This approach was applied to investigate putative effects of the antifungal biocontrol strain RU47 on fungal communities in three arable soils which were analysed by high-throughput ITS amplicon sequencing. Two contrasting workflows to produce abundance tables of operational taxonomic units from sequence data were applied. For both, the developed test indicated highly significant equivalence of the fungal communities with or without previous exposure to RU47 for all soil types, with reference to fungal community differences in conjunction with field site or cropping history. However, minor effects of RU47 on fungal communities were statistically significant using highly sensitive multivariate tests. Nearly all fungal taxa responding to RU47 increased in relative abundance indicating the absence of ecotoxicological effects. Use of the developed equivalence test is not restricted to evaluate effects on soil microbial communities by inoculants for biocontrol, bioremediation or other purposes, but could also be applied for biosafety assessment of compounds like pesticides, or genetically engineered plants.
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Affiliation(s)
- Kai Antweiler
- Department for Biometry and Medical InformaticsOtto‐von‐Guericke University MagdeburgMagdeburgGermany
| | - Susanne Schreiter
- Department of Epidemiology and Pathogen DiagnosticsJulius Kühn‐Institut – Federal Research Centre for Cultivated PlantsBraunschweigGermany
- Present address: Department of AgroEcologyRothamsted ResearchWest Common, Harpenden, HertfordshireAL5 2JQUK
| | - Jens Keilwagen
- Department of Biosafety in Plant BiotechnologyJulius Kühn‐Institut – Federal Research Centre for Cultivated PlantsQuedlinburgGermany
| | - Petr Baldrian
- Laboratory of Environmental MicrobiologyInstitute of Microbiology of the CASPragueCzech Republic
| | - Siegfried Kropf
- Department for Biometry and Medical InformaticsOtto‐von‐Guericke University MagdeburgMagdeburgGermany
| | - Kornelia Smalla
- Department of Epidemiology and Pathogen DiagnosticsJulius Kühn‐Institut – Federal Research Centre for Cultivated PlantsBraunschweigGermany
| | - Rita Grosch
- Leibniz Institute of Vegetable and Ornamental CropsGrossbeerenGermany
| | - Holger Heuer
- Department of Epidemiology and Pathogen DiagnosticsJulius Kühn‐Institut – Federal Research Centre for Cultivated PlantsBraunschweigGermany
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30
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Hilber-Bodmer M, Schmid M, Ahrens CH, Freimoser FM. Competition assays and physiological experiments of soil and phyllosphere yeasts identify Candida subhashii as a novel antagonist of filamentous fungi. BMC Microbiol 2017; 17:4. [PMID: 28056814 PMCID: PMC5216558 DOI: 10.1186/s12866-016-0908-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While recent advances in next generation sequencing technologies have enabled researchers to readily identify countless microbial species in soil, rhizosphere, and phyllosphere microbiomes, the biological functions of the majority of these species are unknown. Functional studies are therefore urgently needed in order to characterize the plethora of microorganisms that are being identified and to point out species that may be used for biotechnology or plant protection. Here, we used a dual culture assay and growth analyses to characterise yeasts (40 different isolates) and their antagonistic effect on 16 filamentous fungi; comprising plant pathogens, antagonists, and saprophytes. RESULTS Overall, this competition screen of 640 pairwise combinations revealed a broad range of outcomes, ranging from small stimulatory effects of some yeasts up to a growth inhibition of more than 80% by individual species. On average, yeasts isolated from soil suppressed filamentous fungi more strongly than phyllosphere yeasts and the antagonistic activity was a species-/isolate-specific property and not dependent on the filamentous fungus a yeast was interacting with. The isolates with the strongest antagonistic activity were Metschnikowia pulcherrima, Hanseniaspora sp., Cyberlindnera sargentensis, Aureobasidium pullulans, Candida subhashii, and Pichia kluyveri. Among these, the soil yeasts (C. sargentensis, A. pullulans, C. subhashii) assimilated and/or oxidized more di-, tri- and tetrasaccharides and organic acids than yeasts from the phyllosphere. Only the two yeasts C. subhashii and M. pulcherrima were able to grow with N-acetyl-glucosamine as carbon source. CONCLUSIONS The competition assays and physiological experiments described here identified known antagonists that have been implicated in the biological control of plant pathogenic fungi in the past, but also little characterised species such as C. subhashii. Overall, soil yeasts were more antagonistic and metabolically versatile than yeasts from the phyllosphere. Noteworthy was the strong antagonistic activity of the soil yeast C. subhashii, which had so far only been described from a clinical sample and not been studied with respect to biocontrol. Based on binary competition assays and growth analyses (e.g., on different carbon sources, growth in root exudates), C. subhashii was identified as a competitive and antagonistic soil yeast with potential as a novel biocontrol agent against plant pathogenic fungi.
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Affiliation(s)
- Maja Hilber-Bodmer
- Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.B., 8820, Wädenswil, Switzerland
| | - Michael Schmid
- Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.B., 8820, Wädenswil, Switzerland.,SIB, Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Christian H Ahrens
- Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.B., 8820, Wädenswil, Switzerland.,SIB, Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Florian M Freimoser
- Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.B., 8820, Wädenswil, Switzerland.
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31
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Cipriano MAP, Lupatini M, Lopes-Santos L, da Silva MJ, Roesch LFW, Destéfano SAL, Freitas SS, Kuramae EE. Lettuce and rhizosphere microbiome responses to growth promoting Pseudomonas species under field conditions. FEMS Microbiol Ecol 2016; 92:fiw197. [PMID: 27660605 DOI: 10.1093/femsec/fiw197] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2016] [Indexed: 11/13/2022] Open
Abstract
Plant growth promoting rhizobacteria are well described and recommended for several crops worldwide. However, one of the most common problems in research into them is the difficulty in obtaining reproducible results. Furthermore, few studies have evaluated plant growth promotion and soil microbial community composition resulting from bacterial inoculation under field conditions. Here we evaluated the effect of 54 Pseudomonas strains on lettuce (Lactuca sativa) growth. The 12 most promising strains were phylogenetically and physiologically characterized for plant growth-promoting traits, including phosphate solubilization, hormone production and antagonism to pathogen compounds, and their effect on plant growth under farm field conditions. Additionally, the impact of beneficial strains on the rhizospheric bacterial community was evaluated for inoculated plants. The strains IAC-RBcr4 and IAC-RBru1, with different plant growth promoting traits, improved lettuce plant biomass yields up to 30%. These two strains also impacted rhizosphere bacterial groups including Isosphaera and Pirellula (phylum Planctomycetes) and Acidothermus, Pseudolabrys and Singusphaera (phylum Actinobacteria). This is the first study to demonstrate consistent results for the effects of Pseudomonas strains on lettuce growth promotion for seedlings and plants grown under tropical field conditions.
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Affiliation(s)
- Matheus A P Cipriano
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Agronomic Institute of Campinas (IAC), Campinas, São Paulo, Brazil
| | - Manoeli Lupatini
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | | | | | - Luiz F W Roesch
- Federal University of Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | | | - Sueli S Freitas
- Agronomic Institute of Campinas (IAC), Campinas, São Paulo, Brazil
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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32
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Chen X, Pizzatti C, Bonaldi M, Saracchi M, Erlacher A, Kunova A, Berg G, Cortesi P. Biological Control of Lettuce Drop and Host Plant Colonization by Rhizospheric and Endophytic Streptomycetes. Front Microbiol 2016; 7:714. [PMID: 27242735 PMCID: PMC4874062 DOI: 10.3389/fmicb.2016.00714] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 04/29/2016] [Indexed: 12/17/2022] Open
Abstract
Lettuce drop, caused by the soil borne pathogen Sclerotinia sclerotiorum, is one of the most common and serious diseases of lettuce worldwide. Increased concerns about the side effects of chemical pesticides have resulted in greater interest in developing biocontrol strategies against S. sclerotiorum. However, relatively little is known about the mechanisms of Streptomyces spp. as biological control agents against S. sclerotiorum on lettuce. Two Streptomyces isolates, S. exfoliatus FT05W and S. cyaneus ZEA17I, inhibit mycelial growth of Sclerotinia sclerotiorum by more than 75% in vitro. We evaluated their biocontrol activity against S. sclerotiorum in vivo, and compared them to Streptomyces lydicus WYEC 108, isolated from Actinovate®. When Streptomyces spp. (10(6) CFU/mL) were applied to S. sclerotiorum inoculated substrate in a growth chamber 1 week prior lettuce sowing, they significantly reduced the risk of lettuce drop disease, compared to the inoculated control. Interestingly, under field conditions, S. exfoliatus FT05W and S. cyaneus ZEA17I protected lettuce from drop by 40 and 10% respectively, whereas S. lydicus WYEC 108 did not show any protection. We further labeled S. exfoliatus FT05W and S. cyaneus ZEA17I with the enhanced GFP (EGFP) marker to investigate their rhizosphere competence and ability to colonize lettuce roots using confocal laser scanning microscopy (CLSM). The abundant colonization of young lettuce seedlings by both strains demonstrated Streptomyces' capability to interact with the host from early stages of seed germination and root development. Moreover, the two strains were detected also on 2-week-old roots, indicating their potential of long-term interactions with lettuce. Additionally, scanning electron microscopy (SEM) observations showed EGFP-S. exfoliatus FT05W endophytic colonization of lettuce root cortex tissues. Finally, we determined its viability and persistence in the rhizosphere and endorhiza up to 3 weeks by quantifying its concentration in these compartments. Based on these results we conclude that S. exfoliatus FT05W has high potential to be exploited in agriculture for managing soil borne diseases barely controlled by available plant protection products.
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Affiliation(s)
- Xiaoyulong Chen
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Cristina Pizzatti
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Maria Bonaldi
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Marco Saracchi
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Armin Erlacher
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, Austria
| | - Andrea Kunova
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, Austria
| | - Paolo Cortesi
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
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33
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Debnath R, Yadav A, Gupta VK, Singh BP, Handique PJ, Saikia R. Rhizospheric Bacterial Community of Endemic Rhododendron arboreum Sm. Ssp. delavayi along Eastern Himalayan Slope in Tawang. FRONTIERS IN PLANT SCIENCE 2016; 7:1345. [PMID: 27642287 PMCID: PMC5009118 DOI: 10.3389/fpls.2016.01345] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/22/2016] [Indexed: 05/15/2023]
Abstract
Information on rhizosphere microbiome of endemic plants from high mountain ecosystems against those of cultivated plantations is inadequate. Comparative bacterial profiles of endemic medicinal plant Rhododendron arboreum Sm. subsp. delavayi rhizosphere pertaining to four altitudinal zonation Pankang Thang (PTSO), Nagula, Y-junction and Bum La (Indo-China border; in triplicates each) along cold adapted Eastern slope of Himalayan Tawang region, India is described here. Significant differences in DGGE profile between below ground bulk vs. rhizospheric community profile associated with the plant was identified. Tagged 16S amplicon sequencing from PTSO (3912 m) to Bum La (4509 m), revealed that soil pH, total nitrogen (TN), organic matter (OM) significantly influenced the underlying bacterial community structure at different altitudes. The relative abundance of Acidobacteria was inversely related to pH, as opposed to TN which was positively correlated to Acidobacteria and Proteobacteria abundance. TN was also the significant predictor for less abundant taxonomic groups Chloroflexi, Gemmatimonadetes, and Nitrospirae. Bum La soil harbored less bacterial diversity compared to other sites at lower altitudes. The most abundant phyla at 3% genetic difference were Acidobacteria, Actinobacteria, and Proteobacteria amongst others. Analysis of similarity indicated greater similarity within lower altitudinal than higher altitudinal group (ANOSIM, R = 0.287, p = 0.02). Constraining the ordination with the edaphic factor explained 83.13% of variation. Unique phylotypes of Bradyrhizobium and uncultured Rhizobiales were found in significant proportions at the four regions. With over 1% relative abundance Actinobacteria (42.6%), Acidobacteria (24.02%), Proteobacteria (16.00%), AD3 (9.23%), WPS-2 (5.1%), and Chloroflexi (1.48%) dominated the core microbiome.
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Affiliation(s)
- Rajal Debnath
- Microbial Biotechnology Group, Biological Science and Technology Division, Council of Scientific and Industrial Research-North East Institute of Science and TechnologyJorhat, India
| | - Archana Yadav
- Microbial Biotechnology Group, Biological Science and Technology Division, Council of Scientific and Industrial Research-North East Institute of Science and TechnologyJorhat, India
| | - Vijai K. Gupta
- Molecular Glycobiotechnology Group, Discipline of Biochemistry, National University of Ireland GalwayGalway, Ireland
| | - Bhim P. Singh
- Molecular Microbiology and Systematics Laboratory, Department of Biotechnology, Mizoram UniversityAizawl, India
| | | | - Ratul Saikia
- Microbial Biotechnology Group, Biological Science and Technology Division, Council of Scientific and Industrial Research-North East Institute of Science and TechnologyJorhat, India
- *Correspondence: Ratul Saikia,
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34
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Shakeel M, Rais A, Hassan MN, Hafeez FY. Root Associated Bacillus sp. Improves Growth, Yield and Zinc Translocation for Basmati Rice (Oryza sativa) Varieties. Front Microbiol 2015; 6:1286. [PMID: 26635754 PMCID: PMC4649038 DOI: 10.3389/fmicb.2015.01286] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/03/2015] [Indexed: 11/17/2022] Open
Abstract
Plant associated rhizobacteria prevailing in different agro-ecosystems exhibit multiple traits which could be utilized in various aspect of sustainable agriculture. Two hundred thirty four isolates were obtained from the roots of basmati-385 and basmati super rice varieties growing in clay loam and saline soil at different locations of Punjab (Pakistan). Out of 234 isolates, 27 were able to solubilize zinc (Zn) from different Zn ores like zinc phosphate [Zn3 (PO4)2], zinc carbonate (ZnCO3) and zinc oxide (ZnO). The strain SH-10 with maximum Zn solubilization zone of 24 mm on Zn3 (PO4)2ore and strain SH-17 with maximum Zn solubilization zone of 14–15 mm on ZnO and ZnCO3ores were selected for further studies. These two strains solubilized phosphorous (P) and potassium (K) in vitro with a solubilization zone of 38–46 mm and 47–55 mm respectively. The strains also suppressed economically important rice pathogens Pyricularia oryzae and Fusarium moniliforme by 22–29% and produced various biocontrol determinants in vitro. The strains enhanced Zn translocation toward grains and increased yield of basmati-385 and super basmati rice varieties by 22–49% and 18–47% respectively. The Zn solubilizing strains were identified as Bacillus sp. and Bacillus cereus by 16S rRNA gene analysis.
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Affiliation(s)
- Muhammad Shakeel
- Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Pakistan
| | - Afroz Rais
- Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Pakistan
| | - Muhammad Nadeem Hassan
- Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Pakistan
| | - Fauzia Yusuf Hafeez
- Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Pakistan
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35
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Schreiter S, Ding GC, Grosch R, Kropf S, Antweiler K, Smalla K. Soil type-dependent effects of a potential biocontrol inoculant on indigenous bacterial communities in the rhizosphere of field-grown lettuce. FEMS Microbiol Ecol 2014; 90:718-30. [PMID: 25244497 DOI: 10.1111/1574-6941.12430] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/09/2014] [Accepted: 09/14/2014] [Indexed: 11/30/2022] Open
Abstract
Bacterial biocontrol strains used as an alternative to chemical fungicides may influence bacterial communities in the rhizosphere and effects might differ depending on the soil type. Here we present baseline data on the effects of Pseudomonas jessenii RU47 on the bacterial community composition in the rhizosphere of lettuce grown in diluvial sand, alluvial loam and loess loam at the same field site. 16S rRNA gene fragments amplified from total community DNA were analyzed by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. DGGE fingerprints revealed that in three consecutive years (2010-2012) RU47 had a slight but statistically significant effect on the bacterial community composition in one (2010), two (2011) or all the three soils (2012). However, these effects were much less pronounced compared with the influence of soil types. Additional pyrosequence analysis of samples from 2011 showed that significant changes in bacterial community compositions in response to RU47 inoculation occurred only in alluvial loam. Different taxonomic groups responded to the RU47 application depending on the soil type. Most remarkable was the increased relative abundance of OTUs belonging to the genera Bacillus and Paenibacillus in alluvial loam. Pyrosequencing allowed side-effects of the application of bacterial inoculants into the rhizosphere to be identified.
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Affiliation(s)
- Susanne Schreiter
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; Department Plant Health, Leibniz Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V., Großbeeren, Germany
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