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Maestro-Gaitán I, Redondo-Nieto M, González-Bodí S, Rodríguez-Casillas L, Matías J, Bolaños L, Reguera M. Insights into quinoa endophytes: core bacterial communities reveal high stability to water stress and genotypic variation. ENVIRONMENTAL MICROBIOME 2025; 20:16. [PMID: 39901227 PMCID: PMC11789408 DOI: 10.1186/s40793-025-00673-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Accepted: 01/13/2025] [Indexed: 02/05/2025]
Abstract
BACKGROUND Plant endophytes, comprising non-pathogenic bacteria, fungi, and archaea, inhabit various plant parts, including roots, stems, leaves, and seeds. These microorganisms play a crucial role in plant development by enhancing germination, growth, and stress resilience. Seed endophytes, in particular, represent the most adapted and conserved segment of plant microbiota, significantly influencing the initial stages of plant growth and microbial community establishment. This study investigates the impact of environmental and genotypic factors on the endophytic communities of Chenopodium quinoa Willd. (quinoa), a crop notable for its adaptability and nutritional value. RESULTS We aimed to characterize the core endophytic communities in quinoa seeds and roots from two distinct genotypes under well-watered (WW) and water-deficit (WD) conditions, utilizing various soil infusions as inoculants to explore potential changes in these endophytes. Our findings reveal distinct changes with quinoa seeds exhibiting a high degree of conservation in their endophytic microbiome, even between maternal and offspring seeds, with specific bacterial taxa showing only minor differences. Tissue specificity emerged as a key factor, with seeds maintaining a stable microbial community, while roots exhibited more pronounced shifts, highlighting the tissue-dependent patterns of microbial enrichment. CONCLUSIONS The results highlight the stability and conservation of endophytic communities in quinoa seeds, even under varying water conditions and across different genotypes, emphasizing the role of tissue specificity in shaping microbial associations. These findings suggest that quinoa-associated endophytes, particularly those conserved in seeds, may play a crucial role in enhancing drought resilience. Understanding the dynamics of plant-microbe interactions in quinoa is vital for developing stress-resilient crop varieties, supporting sustainable agricultural practices, and ensuring food security in the face of climate change and environmental challenges.
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Affiliation(s)
- Isaac Maestro-Gaitán
- Departamento de Biología, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, 28049, Spain
| | - Miguel Redondo-Nieto
- Departamento de Biología, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, 28049, Spain
| | - Sara González-Bodí
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, Madrid, Spain
| | - Laura Rodríguez-Casillas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, Spain
| | - Javier Matías
- Centro de Investigaciones Científicas y Tecnológicas de Extremadura (CICYTEX), Instituto de Investigaciones Agrarias Finca La Orden, Área de Cultivos Extensivos, A5 km372, Badajoz, 06187, Spain
| | - Luis Bolaños
- Departamento de Biología, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, 28049, Spain
| | - María Reguera
- Departamento de Biología, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, 28049, Spain.
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Kou Z, Liu J, Tohti G, Zhu X, Zheng B, Zhu Y, Zhang W. Distinct Bacterial Communities Within the Nonrhizosphere, Rhizosphere, and Endosphere of Ammodendron bifolium Under Winter Condition in the Takeermohuer Desert. MICROBIAL ECOLOGY 2024; 87:151. [PMID: 39611982 DOI: 10.1007/s00248-024-02462-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 11/10/2024] [Indexed: 11/30/2024]
Abstract
Due to human activities and severe climatic conditions, the population of Ammodendron bifolium, an excellent sand-fixing plant, has gradually decreased in the Takeermohuer Desert. The plant-associated bacteria community can enhance its survival in harsh environments. However, the understanding of A. bifolium-associated bacterial community is still unclear during the harsh winter. We investigated the bacterial community structure from the A. bifolium rhizosphere and nonrhizosphere at different depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) and from endosphere (i.e., root endosphere and stem endosphere) in winter. At the same time, we analyzed the impact of different compartments and soil factors on the bacterial community structure. Studies have shown that the A. bifolium rhizosphere exhibits higher levels of SOM (soil organic matter), SOC (soil organic carbon), SAN (soil alkaline nitrogen), and SAK (soil available potassium) compared with the nonrhizosphere. The dominant bacterial phyla were Proteobacteria (19.6%), Cyanobacteria (15.9%), Actinobacteria (13.6%), Acidobacteria (9.0%), and Planctomycetota (5.7%) in the desert. Proteobacteria (24.0-30.2%) had the highest relative abundance in rhizosphere, Actinobacteria (18.3-22.6%) had the highest relative abundance in nonrhizosphere, and Cyanobacteria had the highest relative abundance in endosphere. At the genus level, the relative abundance of Pseudomonas (1.2%) in the root endosphere was the highest and the other genera were mostly unclassified. The Chao1 and PD_whole_tree indices showed that the diversity of the bacterial communities decreased from nonrhizosphere, rhizosphere, root endosphere to stem endosphere. Co-occurrence network analyses identified Proteobacteria and Actinobacteria as key species across the three compartments. Additionally, unique keystone species like Cyanobacteria, Verrucomicrobiota, and Desulfobacterota were found only in the endosphere. The bacterial community in the rhizosphere was influenced by factors such as EC (electrical conductivity), STC (soil total carbon), SOM, SOC, STN (soil total nitrogen), SAN, STP (soil total phosphorus), and SAK, while that of the nonrhizosphere was mainly influenced by pH, C/N (STC/STN), SAP, and distance. The study highlighted differences in bacterial community composition, diversity, and influencing factors across the three compartments, which can provide a better understanding of the association/interactions between A. bifolium and bacterial communities and lay a foundation for revealing its adaptability in winter.
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Affiliation(s)
- Zhining Kou
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Special Environment Biodiversity Application and Regulation in Xinjiang, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China
| | - Jiaqin Liu
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Special Environment Biodiversity Application and Regulation in Xinjiang, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China
| | - Gulpiye Tohti
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Special Environment Biodiversity Application and Regulation in Xinjiang, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China
| | - Xiaoying Zhu
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Special Environment Biodiversity Application and Regulation in Xinjiang, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China
| | - Bei Zheng
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Special Environment Biodiversity Application and Regulation in Xinjiang, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China
| | - Yanlei Zhu
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China.
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Special Environment Biodiversity Application and Regulation in Xinjiang, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China.
| | - Wei Zhang
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China.
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Special Environment Biodiversity Application and Regulation in Xinjiang, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China.
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Daraz U, Erhunmwunse AS, Dubeux JCB, Mackowiak C, Liao HL, Wang XB. Soil fungal community structure and function response to rhizoma perennial peanut cultivars. BMC PLANT BIOLOGY 2024; 24:582. [PMID: 38898415 PMCID: PMC11186081 DOI: 10.1186/s12870-024-05209-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Crop-associated microorganisms play a crucial role in soil nutrient cycling, and crop growth, and health. Fine-scale patterns in soil microbial community diversity and composition are commonly regulated by plant species or genotype. Despite extensive reports in different crop or its cultivar effects on the microbial community, it is uncertain how rhizoma peanut (RP, Arachis glabrata Benth.), a perennial warm-season legume forage that is well-adapted in the southern USA, affects soil microbial community across different cultivars. RESULTS This study explored the influence of seven different RP cultivars on the taxonomic composition, diversity, and functional groups of soil fungal communities through a field trial in Marianna, Florida, Southern USA, using next-generation sequencing technique. Our results showed that the taxonomic diversity and composition of the fungal community differed significantly across RP cultivars. Alpha diversity (Shannon, Simpson, and Pielou's evenness) was significantly higher in Ecoturf but lower in UF_Peace and Florigraze compared to other cultivars (p < 0.001). Phylogenetic diversity (Faith's PD) was lowest in Latitude compared to other cultivars (p < 0.0001). The dominant phyla were Ascomycota (13.34%), Mortierellomycota (3.82%), and Basidiomycota (2.99%), which were significantly greater in Florigraze, UF_Peace, and Ecoturf, respectively. The relative abundance of Neocosmospora was markedly high (21.45%) in UF_Tito and showed large variations across cultivars. The relative abundance of the dominant genera was significantly greater in Arbrook than in other cultivars. There were also significant differences in the co-occurrence network, showing different keystone taxa and more positive correlations than the negative correlations across cultivars. FUNGuild analysis showed that the relative abundance of functional guilds including pathogenic, saprotrophic, endophytic, mycorrhizal and parasitic fungi significantly differed among cultivars. Ecoturf had the greatest relative abundance of mycorrhizal fungal group (5.10 ± 0.44), whereas UF_Peace had the greatest relative abundance of endophytic (4.52 ± 0.56) and parasitic fungi (1.67 ± 0.30) compared to other cultivars. CONCLUSIONS Our findings provide evidence of crop cultivar's effect in shaping fine-scale fungal community patterns in legume-based forage systems.
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Affiliation(s)
- Umar Daraz
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral, Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou, China
| | | | - José C B Dubeux
- North Florida Research and Education Center, University of Florida, Marianna, FL, USA
| | - Cheryl Mackowiak
- North Florida Research and Education Center, University of Florida, Quincy, FL, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy, FL, USA
| | - Xiao-Bo Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral, Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou, China.
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Brescia F, Sillo F, Balestrini R, Sbrana C, Zampieri E. Characterization of endophytic bacteria isolated from root nodules of lentil in intercropping with durum wheat. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 5:100205. [PMID: 38077268 PMCID: PMC10697992 DOI: 10.1016/j.crmicr.2023.100205] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2025] Open
Abstract
Legumes improve soil fertility by interacting symbiotically with nitrogen-fixing rhizobia allocated in root nodules. Some bacterial endophytes can coexist with rhizobia in nodules and might help legumes by enhancing stress tolerance, producing hormones stimulating plant growth, and increasing plant nutrient intake. Twenty-six bacterial endophytes from Lens culinaris root nodules cultivated in intercropping with Triticum durum were identified and characterized molecularly and biochemically. Potential plant growth-promoting strains have been selected according to the indole acetic acid and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase production, and for their inorganic phosphate solubilization ability. The presence of genes associated to ACC deaminase and nitrogenase was evaluated. Six selected strains were grown with varying NaCl and polyethylene glycol concentrations to test their salt and osmotic stress tolerance. Priestia megaterium 11NL3 and Priestia aryabhattai 19NL1, resulted to be tolerant to salinity and osmotic stress, were tested on four genotypes of T. durum seeds in different stress conditions. The effect of strain inoculation on seed germination, vigor, and root-to-shoot ratio varied depending on the type of stress and on the durum wheat genotypes. For future research, it will be necessary to test the selected bacterial strains at different plant phenological stages and to clarify the mechanisms involved in the different outcomes of plant-microbe interactions.
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Affiliation(s)
| | - Fabiano Sillo
- CNR-IPSP, Strada delle Cacce 73, Torino 10135, Italy
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Daraz U, Erhunmwunse AS, Dubeux JCB, Mackowiak C, Guerra VA, Hsu CM, Ma J, Li Y, Yang X, Liao HL, Wang XB. Soil Bacterial Communities Across Seven Rhizoma Peanut Cultivars (Arachis glabrata Benth.) Respond to Seasonal Variation. MICROBIAL ECOLOGY 2023; 86:2703-2715. [PMID: 37507489 DOI: 10.1007/s00248-023-02277-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/24/2023] [Indexed: 07/30/2023]
Abstract
Soil microorganisms play key roles in soil nutrient transformations and have a notable effect on plant growth and health. Different plant genotypes can shape soil microbial patterns via the secretion of root exudates and volatiles, but it is uncertain how a difference in soil microorganisms induced by crop cultivars will respond to short-term seasonal variations. A field experiment was conducted to assess the changes in soil bacterial communities of seven rhizoma peanut (Arachis glabrata Benth, RP) cultivars across two growing seasons, April (Spring season) and October (Fall season). Soils' bacterial communities were targeted using 16S rRNA gene amplicon sequencing. Bacterial community diversity and taxonomic composition among rhizoma peanut cultivars were significantly affected by seasons, cultivars, and their interactions (p < 0.05). Alpha diversity, as estimated by the OTU richness and Simpson index, was around onefold decrease in October than in April across most of the RP cultivars, while the soils from Arblick and Latitude had around one time higher alpha diversity in both seasons compared with other cultivars. Beta diversity differed significantly in April (R = 0.073, p < 0.01) and October (R = 0.084, p < 0.01) across seven cultivars. Bacterial dominant taxa (at phylum and genus level) were strongly affected by seasons and varied towards more dominant groups that have functional potentials involved in nutrient cycling from April to October. A large shift in water availability induced by season variations in addition to host cultivar's effects can explain the observed patterns in diversity, composition, and co-occurrence of bacterial taxa. Overall, our results demonstrate an overriding effect of short-term seasonal variations on soil bacterial communities associated with different crop cultivars. The findings suggest that season-induced shifts in environmental conditions could exert stronger impacts on soil microorganisms than the finer-scale rhizosphere effect from crop cultivars, and consequently influence largely microbe-mediated soil processes and crop health in agricultural ecosystems.
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Affiliation(s)
- Umar Daraz
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral, Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou, China
| | | | - José C B Dubeux
- North Florida Research and Education Center, University of Florida, Marianna, FL, USA
| | - Cheryl Mackowiak
- North Florida Research and Education Center, University of Florida, Quincy, FL, USA
| | - Victor A Guerra
- North Florida Research and Education Center, University of Florida, Quincy, FL, USA
| | - Chih-Ming Hsu
- North Florida Research and Education Center, University of Florida, Quincy, FL, USA
| | - Jianguo Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral, Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou, China
| | - Yuman Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral, Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou, China
| | - Xiaoqian Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral, Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou, China
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy, FL, USA
| | - Xiao-Bo Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral, Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou, China.
- Erguna Forest-Steppe Ecotone Research Station, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China.
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Kumar A, Rithesh L, Kumar V, Raghuvanshi N, Chaudhary K, Abhineet, Pandey AK. Stenotrophomonas in diversified cropping systems: friend or foe? Front Microbiol 2023; 14:1214680. [PMID: 37601357 PMCID: PMC10437078 DOI: 10.3389/fmicb.2023.1214680] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/21/2023] [Indexed: 08/22/2023] Open
Abstract
In the current scenario, the use of synthetic fertilizers is at its peak, which is an expensive affair, possesses harmful effects to the environment, negatively affecting soil fertility and beneficial soil microfauna as well as human health. Because of this, the demand for natural, chemical-free, and organic foods is increasing day by day. Therefore, in the present circumstances use of biofertilizers for plant growth-promotion and microbe-based biopesticides against biotic stresses are alternative options to reduce the risk of both synthetic fertilizers and pesticides. The plant growth promoting rhizobacteria (PGPR) and microbial biocontrol agents are ecologically safe and effective. Owning their beneficial properties on plant systems without harming the ecosystem, they are catching the widespread interest of researchers, agriculturists, and industrialists. In this context, the genus Stenotrophomonas is an emerging potential source of both biofertilizer and biopesticide. This genus is particularly known for producing osmoprotective substances which play a key role in cellular functions, i.e., DNA replication, DNA-protein interactions, and cellular metabolism to regulate the osmotic balance, and also acts as effective stabilizers of enzymes. Moreover, few species of this genus are disease causing agents in humans that is why; it has become an emerging field of research in the present scenario. In the past, many studies were conducted on exploring the different applications of Stenotrophomonas in various fields, however, further researches are required to explore the various functions of Stenotrophomonas in plant growth promotion and management of pests and diseases under diverse growth conditions and to demonstrate its interaction with plant and soil systems. The present review discusses various plant growth and biocontrol attributes of the genus Stenotrophomonas in various food crops along with knowledge gaps. Additionally, the potential risks and challenges associated with the use of Stenotrophomonas in agriculture systems have also been discussed along with a call for further research in this area.
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Affiliation(s)
- Abhishek Kumar
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
- Department of Agriculture, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, India
| | - Lellapalli Rithesh
- Department of Plant Pathology, Kerala Agricultural University, Thiruvananthapuram, Kerala, India
| | - Vikash Kumar
- Faculty of Agricultural Sciences, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh, India
| | - Nikhil Raghuvanshi
- Department of Agronomy, Institute of Agriculture and Natural Science, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh, India
| | - Kautilya Chaudhary
- Department of Agronomy, Chaudhary Charan Singh Haryana Agricultural University Hisar, Hisar, Haryana, India
| | - Abhineet
- Department of Agriculture, Integral Institute of Agricultural Sciences & Technology, Integral University, Lucknow, Uttar Pradesh, India
| | - Abhay K. Pandey
- Department of Mycology & Microbiology, Tea Research Association, North Bengal Regional R&D Center, Nagrakata, West Bengal, India
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Valente J, Gerin F, Mini A, Richard R, Le Gouis J, Prigent-Combaret C, Moënne-Loccoz Y. Symbiotic Variations among Wheat Genotypes and Detection of Quantitative Trait Loci for Molecular Interaction with Auxin-Producing Azospirillum PGPR. Microorganisms 2023; 11:1615. [PMID: 37375117 DOI: 10.3390/microorganisms11061615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/13/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023] Open
Abstract
Crop varieties differ in their ability to interact with Plant Growth-Promoting Rhizobacteria (PGPR), but the genetic basis for these differences is unknown. This issue was addressed with the PGPR Azospirillum baldaniorum Sp245, using 187 wheat accessions. We screened the accessions based on the seedling colonization by the PGPR and the expression of the phenylpyruvate decarboxylase gene ppdC (for synthesis of the auxin indole-3-acetic acid), using gusA fusions. Then, the effects of the PGPR on the selected accessions stimulating Sp245 (or not) were compared in soil under stress. Finally, a genome-wide association approach was implemented to identify the quantitative trait loci (QTL) associated with PGPR interaction. Overall, the ancient genotypes were more effective than the modern genotypes for Azospirillum root colonization and ppdC expression. In non-sterile soil, A. baldaniorum Sp245 improved wheat performance for three of the four PGPR-stimulating genotypes and none of the four non-PGPR-stimulating genotypes. The genome-wide association did not identify any region for root colonization but revealed 22 regions spread on 11 wheat chromosomes for ppdC expression and/or ppdC induction rate. This is the first QTL study focusing on molecular interaction with PGPR bacteria. The molecular markers identified provide the possibility to improve the capacity of modern wheat genotypes to interact with Sp245, as well as, potentially, other Azospirillum strains.
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Affiliation(s)
- Jordan Valente
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne, France
| | - Florence Gerin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne, France
| | - Agathe Mini
- GDEC, INRAE, UCA, F-63000 Clermont-Ferrand, France
| | | | | | - Claire Prigent-Combaret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne, France
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8
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Quiza L, Tremblay J, Pagé AP, Greer CW, Pozniak CJ, Li R, Haug B, Hemmingsen SM, St-Arnaud M, Yergeau E. The effect of wheat genotype on the microbiome is more evident in roots and varies through time. ISME COMMUNICATIONS 2023; 3:32. [PMID: 37076737 PMCID: PMC10115884 DOI: 10.1038/s43705-023-00238-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 03/27/2023] [Accepted: 04/04/2023] [Indexed: 04/21/2023]
Abstract
Crop breeding has traditionally ignored the plant-associated microbial communities. Considering the interactions between plant genotype and associated microbiota is of value since different genotypes of the same crop often harbor distinct microbial communities which can influence the plant phenotype. However, recent studies have reported contrasting results, which led us to hypothesize that the effect of genotype is constrained by growth stages, sampling year and plant compartment. To test this hypothesis, we sampled bulk soil, rhizosphere soil and roots of 10 field-grown wheat genotypes, twice per year, for 4 years. DNA was extracted and regions of the bacterial 16 S rRNA and CPN60 genes and the fungal ITS region were amplified and sequenced. The effect of genotype was highly contingent on the time of sampling and on the plant compartment sampled. Only for a few sampling dates, were the microbial communities significantly different across genotypes. The effect of genotype was most often significant for root microbial communities. The three marker genes used provided a highly coherent picture of the effect of genotype. Taken together, our results confirm that microbial communities in the plant environment strongly vary across compartments, growth stages, and years, and that this can mask the effect of genotype.
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Affiliation(s)
- Liliana Quiza
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, QC, Canada
| | - Julien Tremblay
- Energy, Mining, and Environment Research Centre, National Research Council Canada, Montréal, QC, Canada
| | - Antoine P Pagé
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Charles W Greer
- Energy, Mining, and Environment Research Centre, National Research Council Canada, Montréal, QC, Canada
| | | | - Rong Li
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Brenda Haug
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Sean M Hemmingsen
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Marc St-Arnaud
- Institut de recherche en biologie végétale, Université de Montréal and Jardin botanique de Montréal, 4101 rue Sherbrooke E., Montréal, QC, Canada
| | - Etienne Yergeau
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, QC, Canada.
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Wolfgang A, Temme N, Tilcher R, Berg G. Understanding the sugar beet holobiont for sustainable agriculture. Front Microbiol 2023; 14:1151052. [PMID: 37138624 PMCID: PMC10149816 DOI: 10.3389/fmicb.2023.1151052] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023] Open
Abstract
The importance of crop-associated microbiomes for the health and field performance of plants has been demonstrated in the last decades. Sugar beet is the most important source of sucrose in temperate climates, and-as a root crop-yield heavily depends on genetics as well as on the soil and rhizosphere microbiomes. Bacteria, fungi, and archaea are found in all organs and life stages of the plant, and research on sugar beet microbiomes contributed to our understanding of the plant microbiome in general, especially of microbiome-based control strategies against phytopathogens. Attempts to make sugar beet cultivation more sustainable are increasing, raising the interest in biocontrol of plant pathogens and pests, biofertilization and -stimulation as well as microbiome-assisted breeding. This review first summarizes already achieved results on sugar beet-associated microbiomes and their unique traits, correlating to their physical, chemical, and biological peculiarities. Temporal and spatial microbiome dynamics during sugar beet ontogenesis are discussed, emphasizing the rhizosphere formation and highlighting knowledge gaps. Secondly, potential or already tested biocontrol agents and application strategies are discussed, providing an overview of how microbiome-based sugar beet farming could be performed in the future. Thus, this review is intended as a reference and baseline for further sugar beet-microbiome research, aiming to promote investigations in rhizosphere modulation-based biocontrol options.
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Affiliation(s)
- Adrian Wolfgang
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Nora Temme
- KWS SAAT SE & Co. KGaA, Einbeck, Germany
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Microbiome Biotechnology Department, Leibniz-Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- *Correspondence: Gabriele Berg
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10
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Aswini K, Suman A, Sharma P, Singh PK, Gond S, Pathak D. Seed endophytic bacterial profiling from wheat varieties of contrasting heat sensitivity. FRONTIERS IN PLANT SCIENCE 2023; 14:1101818. [PMID: 37089648 PMCID: PMC10117849 DOI: 10.3389/fpls.2023.1101818] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/10/2023] [Indexed: 05/03/2023]
Abstract
Wheat yield can be limited by many biotic and abiotic factors. Heat stress at the grain filling stage is a factor that reduces wheat production tremendously. The potential role of endophytic microorganisms in mitigating plant stress through various biomolecules like enzymes and growth hormones and also by improving plant nutrition has led to a more in-depth exploration of the plant microbiome for such functions. Hence, we devised this study to investigate the abundance and diversity of wheat seed endophytic bacteria (WSEB) from heatS (heat susceptible, GW322) and heatT (heat tolerant, HD3298 and HD3271) varieties by culturable and unculturable approaches. The results evidenced that the culturable diversity was higher in the heatS variety than in the heatT variety and Bacillus was found to be dominant among the 10 different bacterial genera identified. Though the WSEB population was higher in the heatS variety, a greater number of isolates from the heatT variety showed tolerance to higher temperatures (up to 55°C) along with PGP activities such as indole acetic acid (IAA) production and nutrient acquisition. Additionally, the metagenomic analysis of seed microbiota unveiled higher bacterial diversity, with a predominance of the phyla Proteobacteria covering >50% of OTUs, followed by Firmicutes and Actinobacteria. There were considerable variations in the abundance and diversity between heat sensitivity contrasting varieties, where notably more thermophilic bacterial OTUs were observed in the heatT samples, which could be attributed to conferring tolerance against heat stress. Furthermore, exploring the functional characteristics of culturable and unculturable microbiomes would provide more comprehensive information on improving plant growth and productivity for sustainable agriculture.
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Affiliation(s)
- Krishnan Aswini
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Archna Suman
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Archna Suman,
| | - Pushpendra Sharma
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pradeep Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shrikant Gond
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Devashish Pathak
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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11
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Antoszewski M, Mierek-Adamska A, Dąbrowska GB. The Importance of Microorganisms for Sustainable Agriculture-A Review. Metabolites 2022; 12:1100. [PMID: 36422239 PMCID: PMC9694901 DOI: 10.3390/metabo12111100] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 08/27/2023] Open
Abstract
In the face of climate change, progressive degradation of the environment, including agricultural land negatively affecting plant growth and development, endangers plant productivity. Seeking efficient and sustainable agricultural techniques to replace agricultural chemicals is one of the most important challenges nowadays. The use of plant growth-promoting microorganisms is among the most promising approaches; however, molecular mechanisms underneath plant-microbe interactions are still poorly understood. In this review, we summarized the knowledge on plant-microbe interactions, highlighting the role of microbial and plant proteins and metabolites in the formation of symbiotic relationships. This review covers rhizosphere and phyllosphere microbiomes, the role of root exudates in plant-microorganism interactions, the functioning of the plant's immune system during the plant-microorganism interactions. We also emphasized the possible role of the stringent response and the evolutionarily conserved mechanism during the established interaction between plants and microorganisms. As a case study, we discussed fungi belonging to the genus Trichoderma. Our review aims to summarize the existing knowledge about plant-microorganism interactions and to highlight molecular pathways that need further investigation.
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Affiliation(s)
| | - Agnieszka Mierek-Adamska
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland
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12
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Sun Y, Huang Z, Chen S, Yang D, Lin X, Liu W, Yang S. Higher-Quality Pumpkin Cultivars Need to Recruit More Abundant Soil Microbes in Rhizospheres. Microorganisms 2022; 10:2219. [PMID: 36363811 PMCID: PMC9698040 DOI: 10.3390/microorganisms10112219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 08/17/2023] Open
Abstract
Two different qualities of pumpkin, cultivars G1519 and G1511, were grown in the same environment under identical management. However, their qualities, such as the contents of total soluble solids, starch, protein, and vitamin C, were significantly different. Do rhizospheric microbes contribute to pumpkin quality? To answer this question, this study investigated the soil microbial compositions in the rhizospheres of different quality pumpkin cultivars to determine the differences in these soil microbial compositions and thus determine how soil microbes may affect pumpkin quality. Firstly, a randomized complete block design with two pumpkin cultivars and three replications was performed in this study. The soil microbial compositions and structures in the rhizospheres of the two pumpkin cultivars were analyzed using a high-throughput sequencing technique. In comparison with the low-quality pumpkin cultivar (G1519), higher microbial diversity and richness could be found in the rhizospheres of the high-quality pumpkin cultivar (G1511). The results showed that there were significant differences in the soil bacterial and fungal community compositions in the rhizospheres of the high- and low-quality pumpkin cultivars. Although the compositions and proportions of microorganisms were similar in the rhizospheres of the two pumpkin cultivars, the proportions of Basidiomycota and Micropsalliota in the G1519 rhizosphere were much higher than those in the G1511 rhizosphere. Furthermore, the fungal phylum and genus Rozellomycota and Unclassified_p__Rozellomycota were unique in the rhizosphere of the high-quality pumpkin cultivar (G1511). All the above results indicate that soil microbes were enriched differentially in the rhizospheres of the low- and high-quality pumpkin cultivars. In other words, more abundant soil microbes were recruited in the rhizosphere of the high-quality pumpkin cultivar as compared to that of the low-quality cultivar. Rozellomycota and Unclassified_p__Rozellomycota may be functional microorganisms relating to pumpkin quality.
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Affiliation(s)
- Yan Sun
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, Nanning 530004, China
| | - Ziyue Huang
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, Nanning 530004, China
| | - Siyu Chen
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, Nanning 530004, China
| | - Da Yang
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, Nanning 530004, China
| | - Xinru Lin
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, Nanning 530004, China
| | - Wenjun Liu
- Vegetable Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Shangdong Yang
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, Nanning 530004, China
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13
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Cappelli SL, Domeignoz-Horta LA, Loaiza V, Laine AL. Plant biodiversity promotes sustainable agriculture directly and via belowground effects. TRENDS IN PLANT SCIENCE 2022; 27:674-687. [PMID: 35279365 DOI: 10.1016/j.tplants.2022.02.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/10/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
While the positive relationship between plant biodiversity and ecosystem functioning (BEF) is well established, the extent to which this is mediated via belowground microbial processes is poorly understood. Growing evidence suggests that plant community structure influences soil microbial diversity, which in turn promotes functions desired for sustainable agriculture. Here, we outline the 'plant-directed' and soil microbe-mediated mechanisms expected to promote positive BEF. We identify how this knowledge can be utilized in plant diversification schemes to maximize ecosystem functioning in agroecosystems, which are typically species poor and sensitive to biotic and abiotic stressors. In the face of resource overexploitation and global change, bridging the gaps between biodiversity science and agricultural practices is crucial to meet food security in the Anthropocene.
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Affiliation(s)
- Seraina L Cappelli
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
| | - Luiz A Domeignoz-Horta
- Department of Evolutionary Biology and Environmental Sciences, University of Zürich, Zürich, Switzerland
| | - Viviana Loaiza
- Department of Evolutionary Biology and Environmental Sciences, University of Zürich, Zürich, Switzerland
| | - Anna-Liisa Laine
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland; Department of Evolutionary Biology and Environmental Sciences, University of Zürich, Zürich, Switzerland
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14
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Differential Response of Wheat Rhizosphere Bacterial Community to Plant Variety and Fertilization. Int J Mol Sci 2022; 23:ijms23073616. [PMID: 35408978 PMCID: PMC8998456 DOI: 10.3390/ijms23073616] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/17/2022] [Accepted: 03/23/2022] [Indexed: 02/01/2023] Open
Abstract
The taxonomic assemblage and functions of the plant bacterial community are strongly influenced by soil and host plant genotype. Crop breeding, especially after the massive use of nitrogen fertilizers which led to varieties responding better to nitrogen fertilization, has implicitly modified the ability of the plant root to recruit an effective bacterial community. Among the priorities for harnessing the plant bacterial community, plant genotype-by-microbiome interactions are stirring attention. Here, we analyzed the effect of plant variety and fertilization on the rhizosphere bacterial community. In particular, we clarified the presence in the bacterial community of a varietal effect of N and P fertilization treatment. 16S rRNA gene amplicon sequence analysis of rhizospheric soil, collected from four wheat varieties grown under four N-P fertilization regimes, and quantification of functional bacterial genes involved in the nitrogen cycle (nifH; amoA; nirK and nosZ) were performed. Results showed that variety played the most important role and that treatments did not affect either bacterial community diversity or bacterial phyla abundance. Variety-specific response of rhizosphere bacterial community was detected, both in relation to taxa (Nitrospira) and metabolic functions. In particular, the changes related to amino acid and aerobic metabolism and abundance of genes involved in the nitrogen cycle (amoA and nosZ), suggested that plant variety may lead to functional changes in the cycling of the plant-assimilable nitrogen.
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15
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Gholizadeh S, Mohammadi SA, Salekdeh GH. Changes in root microbiome during wheat evolution. BMC Microbiol 2022; 22:64. [PMID: 35219318 PMCID: PMC8881823 DOI: 10.1186/s12866-022-02467-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 02/08/2022] [Indexed: 12/20/2022] Open
Abstract
Abstract
Background
Although coevolutionary signatures of host-microbe interactions are considered to engineer the healthy microbiome of humans, little is known about the changes in root-microbiome during plant evolution. To understand how the composition of the wheat and its ancestral species microbiome have changed over the evolutionary processes, we performed a 16S rRNA metagenomic analysis on rhizobacterial communities associated with a phylogenetic framework of four Triticum species T. urartu, T. turgidum, T. durum, and T. aestivum along with their ancestral species Aegilops speltoides, and Ae. tauschii during vegetative and reproductive stages.
Results
In this study, we illustrated that the genome contents of wild species Aegilops speltoides and Ae. tauschii can be significant factors determining the composition of root-associated bacterial communities in domesticated bread wheat. Although it was found that domestication and modern breeding practices might have had a significant impact on microbiome-plant interactions especially at the reproductive stage, we observed an extensive and selective control by wheat genotypes on associated rhizobacterial communities at the same time. Our data also showed a strong genotypic variation within species of T. aestivum and Ae. tauschii, suggesting potential breeding targets for plants surveyed.
Conclusions
This study performed with different genotypes of Triticum and Aegilops species is the first study showing that the genome contents of Ae. speltoides and Ae. tauschii along with domestication-related changes can be significant factors determining the composition of root-associated bacterial communities in bread wheat. It is also indirect evidence that shows a very extensive range of host traits and genes are probably involved in host-microbe interactions. Therefore, understanding the wheat root-associated microbiome needs to take into consideration of its polygenetic mosaic nature.
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16
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Gruet C, Muller D, Moënne-Loccoz Y. Significance of the Diversification of Wheat Species for the Assembly and Functioning of the Root-Associated Microbiome. Front Microbiol 2022; 12:782135. [PMID: 35058901 PMCID: PMC8764353 DOI: 10.3389/fmicb.2021.782135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/30/2021] [Indexed: 12/15/2022] Open
Abstract
Wheat, one of the major crops in the world, has had a complex history that includes genomic hybridizations between Triticum and Aegilops species and several domestication events, which resulted in various wild and domesticated species (especially Triticum aestivum and Triticum durum), many of them still existing today. The large body of information available on wheat-microbe interactions, however, was mostly obtained without considering the importance of wheat evolutionary history and its consequences for wheat microbial ecology. This review addresses our current understanding of the microbiome of wheat root and rhizosphere in light of the information available on pre- and post-domestication wheat history, including differences between wild and domesticated wheats, ancient and modern types of cultivars as well as individual cultivars within a given wheat species. This analysis highlighted two major trends. First, most data deal with the taxonomic diversity rather than the microbial functioning of root-associated wheat microbiota, with so far a bias toward bacteria and mycorrhizal fungi that will progressively attenuate thanks to the inclusion of markers encompassing other micro-eukaryotes and archaea. Second, the comparison of wheat genotypes has mostly focused on the comparison of T. aestivum cultivars, sometimes with little consideration for their particular genetic and physiological traits. It is expected that the development of current sequencing technologies will enable to revisit the diversity of the wheat microbiome. This will provide a renewed opportunity to better understand the significance of wheat evolutionary history, and also to obtain the baseline information needed to develop microbiome-based breeding strategies for sustainable wheat farming.
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Affiliation(s)
| | | | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), VetAgro Sup, UMR 5557 Ecologie Microbienne, Villeurbanne, France
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17
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Tayyab M, Islam W, Noman A, Pang Z, Li S, Lin S, Wenxiong L, Hua Z. Sugarcane cultivars manipulate rhizosphere bacterial communities' structure and composition of agriculturally important keystone taxa. 3 Biotech 2022; 12:32. [PMID: 35070622 PMCID: PMC8724486 DOI: 10.1007/s13205-021-03091-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 12/09/2021] [Indexed: 01/03/2023] Open
Abstract
Different sugarcane cultivars are grown to produce renewable energy and sugar in China. However, we have a limited awareness of the interactive influence of varying sugarcane cultivars on rhizosphere bacterial structure and diversity. Assessing cultivar choice impact on soil bacterial communities is vital since bacterial taxa are frequently impacted by planting performance. Employing high-throughput Illumina sequencing, we examined bacterial communities' assemblage in the rhizosphere of six Chinese sugarcane cultivars (Regan14-62, Guitang 08-120, Haizhe 22, Guitang 08-1180, Taitang 22 and Liucheng 05-136). Our results indicated that different sugarcane cultivars have no significant influence on the Shannon index; however, their impact on richness was substantial. There was a difference in the bacterial community structure that is also associated with a change in the community composition, as determined by the DESeq2 results, suggesting that "Haizhe 22 (HZ22)" had a completely different beta diversity as compared to other five cultivars by enriching abundance of Firmicutes, Proteobacteria, Gemmatimonadetes, Saccharibacteria and Bacteroidetes and reducing the quantity of Actinobacteria, Chloroflexi, Acidobacteria, and Planctomycetes, respectively. The HZ22 rhizosphere significantly enriched six genera (e.g., Devosia, Mizugakiibacter, Mycobacterium, Nakamurella, Rhizomicrobium, and Virgibacillus) relative to other varieties, suggesting an important role in plant disease tolerance and growth development, including soil nutrient cycling and bioremediation. Analysis of similarity (ANOSIM) and correlation analysis revealed that cultivars, soil organic matter, pH and soil moisture were central factors influencing bacterial composition. These findings may help in selection of plant cultivars capable of supporting highly abundant specific beneficial microbial groups, improving plant disease resistance, growth stimulation, and soil bioremediation capabilities, further leading to improvements in breeding strategies. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03091-1.
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Affiliation(s)
- Muhammad Tayyab
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Waqar Islam
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ali Noman
- Department of Botany, Govt. College University Faisalabad, Faisalabad, Pakistan
| | - Ziqin Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Shiyan Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Sheng Lin
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lin Wenxiong
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhang Hua
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Hu M, Li C, Xue Y, Hu A, Chen S, Chen Y, Lu G, Zhou X, Zhou J. Isolation, Characterization, and Genomic Investigation of a Phytopathogenic Strain of Stenotrophomonas maltophilia. PHYTOPATHOLOGY 2021; 111:2088-2099. [PMID: 33759550 DOI: 10.1094/phyto-11-20-0501-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Stenotrophomonas maltophilia is ubiquitous in diverse environmental habitats. It merits significant concern because of its increasing incidence of nosocomial and community-acquired infection in immunocompromised patients and multiple drug resistance. It is rarely reported as a phytopathogen except in causing white stripe disease of rice in India and postharvest fruit rot of Lanzhou lily. For this study, Dickeya zeae and S. maltophilia strains were simultaneously isolated from soft rot leaves of Clivia miniata in Guangzhou, China, and were both demonstrated to be pathogenic to the host. Compared with the D. zeae strains, S. maltophilia strains propagated faster for greater growth in lysogeny broth medium and produced no cellulases or polygalacturonases, but did produce more proteases and fewer extracellular polysaccharides. Furthermore, S. maltophilia strains swam and swarmed dramatically less on semisolid media, but formed a great many more biofilms. Both D. zeae and S. maltophilia strains isolated from clivia caused rot symptoms on other monocot hosts, but not on dicots. Similar to previously reported S. maltophilia strains isolated from other sources, the strain JZL8 survived under many antibiotic stresses. The complete genome sequence of S. maltophilia strain JZL8 consists of a chromosome of 4,635,432 bp without a plasmid. Pan-genome analysis of JZL8 and 180 other S. maltophilia strains identified 50 genes that are unique to JZL8, seven of which implicate JZL8 as the potential pathogen contributor in plants. JZL8 also contains three copies of Type I Secretion System machinery; this is likely responsible for its greater production of proteases. Findings from this study extend our knowledge on the host range of S. maltophilia and provide insight into the phenotypic and genetic features underlying the plant pathogenicity of JZL8.
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Affiliation(s)
- Ming Hu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Chuhao Li
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Yang Xue
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Anqun Hu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Shanshan Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Yufan Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Guangtao Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Jianuan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
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Quiza L, Tremblay J, Greer CW, Hemmingsen SM, St-Arnaud M, Pozniak CJ, Yergeau E. Rhizosphere shotgun metagenomic analyses fail to show differences between ancestral and modern wheat genotypes grown under low fertilizer inputs. FEMS Microbiol Ecol 2021; 97:6279035. [PMID: 34014265 DOI: 10.1093/femsec/fiab071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/17/2021] [Indexed: 12/13/2022] Open
Abstract
It is thought that modern wheat genotypes have lost their capacity to associate with soil microbes that would help them acquire nutrients from the soil. To test this hypothesis, ten ancestral and modern wheat genotypes were seeded in a field experiment under low fertilization conditions. The rhizosphere soil was collected, its DNA extracted and submitted to shotgun metagenomic sequencing. In contrast to our hypothesis, there was no significant difference in the global rhizosphere metagenomes of the different genotypes, and this held true when focusing the analyses on specific taxonomic or functional categories of genes. Some genes were significantly more abundant in the rhizosphere of one genotype or another, but they comprised only a small portion of the total genes identified and did not affect the global rhizosphere metagenomes. Our study shows for the first time that the rhizosphere metagenome of wheat is stable across a wide variety of genotypes when growing under nutrient poor conditions.
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Affiliation(s)
- Liliana Quiza
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Julien Tremblay
- Energy, Mining, and Environment, National Research Council Canada, 6100 Royalmount Ave., Montréal, QC, H4P 2R2, Canada
| | - Charles W Greer
- Energy, Mining, and Environment, National Research Council Canada, 6100 Royalmount Ave., Montréal, QC, H4P 2R2, Canada
| | - Sean M Hemmingsen
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place Saskatoon, SK, S7N 0W9, Canada
| | - Marc St-Arnaud
- Institut de recherche en biologie végétale, Université de Montréal and Jardin botanique de Montréal, 4101 Sherbrooke East, Montréal, QC, H1X 2B2, Canada
| | - Curtis J Pozniak
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Etienne Yergeau
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 boul. des Prairies, Laval, QC, H7V 1B7, Canada
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Prudence SMM, Newitt† JT, Worsley SF, Macey MC, Murrell JC, Lehtovirta-Morley LE, Hutchings MI. Soil, senescence and exudate utilisation: characterisation of the Paragon var. spring bread wheat root microbiome. ENVIRONMENTAL MICROBIOME 2021; 16:12. [PMID: 34154664 PMCID: PMC8215762 DOI: 10.1186/s40793-021-00381-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 05/13/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND Conventional methods of agricultural pest control and crop fertilisation are unsustainable. To meet growing demand, we must find ecologically responsible means to control disease and promote crop yields. The root-associated microbiome can aid plants with disease suppression, abiotic stress relief, and nutrient bioavailability. The aim of the present work was to profile the community of bacteria, fungi, and archaea associated with the wheat rhizosphere and root endosphere in different conditions. We also aimed to use 13CO2 stable isotope probing (SIP) to identify microbes within the root compartments that were capable of utilising host-derived carbon. RESULTS Metabarcoding revealed that community composition shifted significantly for bacteria, fungi, and archaea across compartments. This shift was most pronounced for bacteria and fungi, while we observed weaker selection on the ammonia oxidising archaea-dominated archaeal community. Across multiple soil types we found that soil inoculum was a significant driver of endosphere community composition, however, several bacterial families were identified as core enriched taxa in all soil conditions. The most abundant of these were Streptomycetaceae and Burkholderiaceae. Moreover, as the plants senesce, both families were reduced in abundance, indicating that input from the living plant was required to maintain their abundance in the endosphere. Stable isotope probing showed that bacterial taxa within the Burkholderiaceae family, among other core enriched taxa such as Pseudomonadaceae, were able to use root exudates, but Streptomycetaceae were not. CONCLUSIONS The consistent enrichment of Streptomycetaceae and Burkholderiaceae within the endosphere, and their reduced abundance after developmental senescence, indicated a significant role for these families within the wheat root microbiome. While Streptomycetaceae did not utilise root exudates in the rhizosphere, we provide evidence that Pseudomonadaceae and Burkholderiaceae family taxa are recruited to the wheat root community via root exudates. This deeper understanding crop microbiome formation will enable researchers to characterise these interactions further, and possibly contribute to ecologically responsible methods for yield improvement and biocontrol in the future.
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Affiliation(s)
- Samuel MM. Prudence
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jake T. Newitt†
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Sarah F. Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - Michael C. Macey
- School of Environment, Earth & Ecosystem Sciences, The Open University, Milton Keynes, MK7 6AA UK
| | - J. Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | | | - Matthew I. Hutchings
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
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Kinnunen-Grubb M, Sapkota R, Vignola M, Nunes IM, Nicolaisen M. Breeding selection imposed a differential selective pressure on the wheat root-associated microbiome. FEMS Microbiol Ecol 2021; 96:5911094. [PMID: 32970821 DOI: 10.1093/femsec/fiaa196] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/22/2020] [Indexed: 12/22/2022] Open
Abstract
Plants-microbiome associations are the result of millions of years of co-evolution. Due to breeding-accelerated plant evolution in non-native and highly managed soil, plant-microbe links could have been lost. We hypothesized that post-domestication breeding of wheat changed the root-associated microbiome. To test this, we analyzed root-associated fungal and bacterial communities shortly after emergence of seedlings representing a transect of wheat evolution including modern wheat, landraces and ancestors. Numbers of observed microbial taxa were highest in landraces bred in low-input agricultural systems, and lowest in ancestors that had evolved in native soils. The microbial communities of modern cultivars were different from those of landraces and ancestors. Old wheat accessions enriched Acidobacteria and Actinobacteria, while modern cultivars enriched OTUs from Candidatus Saccharibacteria, Verrucomicrobia and Firmicutes. The fungal pathogens Fusarium, Neoascochyta and Microdochium enriched in modern cultivars. Both bacterial and fungal communities followed a neutral assembly model when bulk soil was considered as the source community, but accessions of the ancient Triticum turgidum and T. monococcum created a more isolated environment in their roots. In conclusion, wheat root-associated microbiomes have dramatically changed through a transect of breeding history.
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Affiliation(s)
- Marta Kinnunen-Grubb
- Novozymes A/S, Microbiomics and Microbe Discovery Denmark, Biologiens Vej 2, 2800 Kgs. Lyngby, Denmark
| | - Rumakanta Sapkota
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Marta Vignola
- School of Engineering, University of Glasgow, 78 Oakfield Ave, Glasgow G12 8LS, United Kingdom
| | - Inês Marques Nunes
- Novozymes A/S, Microbiomics and Microbe Discovery Denmark, Biologiens Vej 2, 2800 Kgs. Lyngby, Denmark
| | - Mogens Nicolaisen
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
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Sandhu N, Sethi M, Kumar A, Dang D, Singh J, Chhuneja P. Biochemical and Genetic Approaches Improving Nitrogen Use Efficiency in Cereal Crops: A Review. FRONTIERS IN PLANT SCIENCE 2021; 12:657629. [PMID: 34149755 PMCID: PMC8213353 DOI: 10.3389/fpls.2021.657629] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/06/2021] [Indexed: 05/22/2023]
Abstract
Nitrogen is an essential nutrient required in large quantities for the proper growth and development of plants. Nitrogen is the most limiting macronutrient for crop production in most of the world's agricultural areas. The dynamic nature of nitrogen and its tendency to lose soil and environment systems create a unique and challenging environment for its proper management. Exploiting genetic diversity, developing nutrient efficient novel varieties with better agronomy and crop management practices combined with improved crop genetics have been significant factors behind increased crop production. In this review, we highlight the various biochemical, genetic factors and the regulatory mechanisms controlling the plant nitrogen economy necessary for reducing fertilizer cost and improving nitrogen use efficiency while maintaining an acceptable grain yield.
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Domestication affects the composition, diversity, and co-occurrence of the cereal seed microbiota. J Adv Res 2020; 31:75-86. [PMID: 34194833 PMCID: PMC8240117 DOI: 10.1016/j.jare.2020.12.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/14/2020] [Indexed: 12/15/2022] Open
Abstract
Introduction The seed-associated microbiome has a strong influence on plant ecology, fitness, and productivity. Plant microbiota could be exploited for a more responsible crop management in sustainable agriculture. However, the relationships between seed microbiota and hosts related to the changes from ancestor species to breeded crops still remain poor understood. Objectives Our aims were i) to understand the effect of cereal domestication on seed endophytes in terms of diversity, structure and co-occurrence, by comparing four cereal crops and the respective ancestor species; ii) to test the phylogenetic coherence between cereals and their seed microbiota (clue of co-evolution). Methods We investigated the seed microbiota of four cereal crops (Triticum aestivum, Triticum monococcum, Triticum durum, and Hordeum vulgare), along with their respective ancestors (Aegilops tauschii, Triticum baeoticum, Triticum dicoccoides, and Hordeum spontaneum, respectively) using 16S rRNA gene metabarcoding, Randomly Amplified Polymorphic DNA (RAPD) profiling of host plants and co-evolution analysis. Results The diversity of seed microbiota was generally higher in cultivated cereals than in wild ancestors, suggesting that domestication lead to a bacterial diversification. On the other hand, more microbe-microbe interactions were detected in wild species, indicating a better-structured, mature community. Typical human-associated taxa, such as Cutibacterium, dominated in cultivated cereals, suggesting an interkingdom transfers of microbes from human to plants during domestication. Co-evolution analysis revealed a significant phylogenetic congruence between seed endophytes and host plants, indicating clues of co-evolution between hosts and seed-associated microbes during domestication. Conclusion This study demonstrates a diversification of the seed microbiome as a consequence of domestication, and provides clues of co-evolution between cereals and their seed microbiota. This knowledge is useful to develop effective strategies of microbiome exploitation for sustainable agriculture.
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24
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Wen T, Yuan J, He X, Lin Y, Huang Q, Shen Q. Enrichment of beneficial cucumber rhizosphere microbes mediated by organic acid secretion. HORTICULTURE RESEARCH 2020; 7:154. [PMID: 33082961 PMCID: PMC7527982 DOI: 10.1038/s41438-020-00380-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/05/2020] [Accepted: 07/10/2020] [Indexed: 05/16/2023]
Abstract
Resistant cultivars have played important roles in controlling Fusarium wilt disease, but the roles of rhizosphere interactions among different levels of resistant cultivars are still unknown. Here, two phenotypes of cucumber, one resistant and one with increased susceptibility to Fusarium oxysporum f.sp. cucumerinum (Foc), were grown in the soil and hydroponically, and then 16S rRNA gene sequencing and nontargeted metabolomics techniques were used to investigate rhizosphere microflora and root exudate profiles. Relatively high microbial community evenness for the Foc-susceptible cultivar was detected, and the relative abundances of Comamonadaceae and Xanthomonadaceae were higher for the Foc-susceptible cultivar than for the other cultivar. FishTaco analysis revealed that specific functional traits, such as protein synthesis and secretion, bacterial chemotaxis, and small organic acid metabolism pathways, were significantly upregulated in the rhizobacterial community of the Foc-susceptible cultivar. A machine-learning approach in conjunction with FishTaco plus metabolic pathway analysis revealed that four organic acids (citric acid, pyruvate acid, succinic acid, and fumarate) were released at higher abundance by the Foc-susceptible cultivar compared with the resistant cultivar, which may be responsible for the recruitment of Comamonadaceae, a potential beneficial microbial group. Further validation demonstrated that Comamonadaceae can be "cultured" by these organic acids. Together, compared with the resistant cultivar, the susceptible cucumber tends to assemble beneficial microbes by secreting more organic acids.
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Affiliation(s)
- Tao Wen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jun Yuan
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, 210095 Nanjing, China
| | - Xiaoming He
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong, China
| | - Yue Lin
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong, China
| | - Qiwei Huang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, 210095 Nanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, 210095 Nanjing, China
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25
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Martínez-Romero E, Aguirre-Noyola JL, Taco-Taype N, Martínez-Romero J, Zuñiga-Dávila D. Plant microbiota modified by plant domestication. Syst Appl Microbiol 2020; 43:126106. [PMID: 32847781 DOI: 10.1016/j.syapm.2020.126106] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 12/19/2022]
Abstract
Human life became largely dependent on agricultural products after distinct crop-domestication events occurred around 10,000 years ago in different geographical sites. Domestication selected suitable plants for human agricultural practices with unexpected consequences on plant microbiota, which has notable effects on plant growth and health. Among other traits, domestication has changed root architecture, exudation, or defense responses that could have modified plant microbiota. Here we present the comparison of reported data on the microbiota from widely consumed cereals and legumes and their ancestors showing that different bacteria were found in domesticated and wild plant microbiomes in some cases. Considering the large variability in plant microbiota, adequate sampling efforts and function-based approaches are needed to further support differences between the microbiota from wild and domesticated plants. The study of wild plant microbiomes could provide a valuable resource of unexploited beneficial bacteria for crops.
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Affiliation(s)
| | | | - Nataly Taco-Taype
- Laboratorio de Ecología Microbiana, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
| | | | - Doris Zuñiga-Dávila
- Laboratorio de Ecología Microbiana, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
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26
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Glaeser SP, Gabur I, Haghighi H, Bartz JO, Kämpfer P, Snowdon R, Obermeier C. Endophytic bacterial communities of oilseed rape associate with genotype-specific resistance against Verticillium longisporum. FEMS Microbiol Ecol 2020; 96:5643882. [PMID: 31769797 DOI: 10.1093/femsec/fiz188] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/25/2019] [Indexed: 01/23/2023] Open
Abstract
Associations of endophytic bacterial community composition of oilseed rape (Brassica napus L.) with quantitative resistance against the soil-borne fungal pathogen Verticillium longisporum was assessed by 16S rRNA gene amplicon sequencing in roots and hypocotyls of four plant lines with contrasting genetic composition in regard to quantitative resistance reactions. The plant compartment was found to be the dominating driving factor for the specificity of bacterial communities in healthy plants. Furthermore, V. longisporum infection triggered a stabilization of phylogenetic group abundance in replicated samples suggesting a host genotype-specific selection. Genotype-specific associations with bacterial phylogenetic group abundance were identified by comparison of plant genotype groups (resistant versus susceptible) and treatment groups (healthy versus V. longisporum-infected) allowing dissection into constitutive and induced directional association patterns. Relative abundance of Flavobacteria, Pseudomonas, Rhizobium and Cellvibrio was associated with resistance/susceptibility. Relative abundance of Flavobacteria and Cellvibrio was increased in resistant genotypes according to their known ecological functions. In contrast, a higher relative abundance of Pseudomonas and Rhizobium, which are known to harbor many species with antagonistic properties to fungal pathogens, was found to be associated with susceptibility, indicating that these groups do not play a major role in genetically controlled resistance of oilseed rape against V. longisporum.
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Affiliation(s)
- Stefanie P Glaeser
- Department of Applied Microbiology, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Iulian Gabur
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Hossein Haghighi
- Department of Applied Microbiology, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.,Department of Life Sciences, University of Modena and Reggio Emilia, Via Kenedy 17/I, 42124 Reggio Emilia, Italy
| | - Jens-Ole Bartz
- Department of Applied Microbiology, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Peter Kämpfer
- Department of Applied Microbiology, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Rod Snowdon
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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27
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Shi Q, Jin J, Liu Y, Zhang Y, Cai Z, Ma Q, Cheng Y, Wen R, Nian H, Lian T. High Aluminum Drives Different Rhizobacterial Communities Between Aluminum-Tolerant and Aluminum-Sensitive Wild Soybean. Front Microbiol 2020; 11:1996. [PMID: 32973720 PMCID: PMC7466775 DOI: 10.3389/fmicb.2020.01996] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 07/28/2020] [Indexed: 11/18/2022] Open
Abstract
Aluminum (Al)-resistant plant cultivars can recruit beneficial microbes to alleviate the stresses. However, the mechanism of how rhizobacterial communities strengthen Al tolerance of wild soybean has not been addressed. The aim of this study was to investigate the bacterial community structure in the rhizosphere of Al-tolerant (BW69) and Al-sensitive (W270) wild soybean germplasm subjected to three Al concentrations. We analyzed the rhizobacterial communities of the two genotypes by high-throughput sequencing of 16S rRNA genes. The results showed that high Al stress recruited different rhizobacterial communities between two genotypes. In total, 49 OTUs, such as OTU15 (Gammaproteobacteria_KF-JG30-C25_norank), OTU23 (Mizugakiibacter), and OTU93 (Alkanibacter), were enriched in the rhizosphere of BW69 at the low and high Al concentrations. Moreover, bacterial community in the rhizosphere of BW69 had a more complex co-occurrence network than did W270 at the high Al concentration. Overall, our findings highlighted that high Al concentration magnified the difference in rhizobacterial community structure between two genotypes. However, the lower modularity of the co-occurrence network in rhizosphere of BW69 than W270 under Al stress may cause the rhizobacterial community to be less resistant and more influenced by disturbance. This study emphasizes the possibility of using rhizobacteria as an improved crop breeding or gene to produce crops that are more resistant to the toxicity of heavy metal.
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Affiliation(s)
- Qihan Shi
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Jing Jin
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yuantai Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yafeng Zhang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Qibin Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yanbo Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Ronghui Wen
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
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28
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Ma L, Luo S, Xu S, Chang C, Tian L, Zhang J, Zhou X, Shi S, Tian C. Different Effects of Wild and Cultivated Soybean on Rhizosphere Bacteria. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261719060109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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29
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Kavamura VN, Robinson RJ, Hughes D, Clark I, Rossmann M, Melo ISD, Hirsch PR, Mendes R, Mauchline TH. Wheat dwarfing influences selection of the rhizosphere microbiome. Sci Rep 2020; 10:1452. [PMID: 31996781 PMCID: PMC6989667 DOI: 10.1038/s41598-020-58402-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/14/2020] [Indexed: 12/23/2022] Open
Abstract
The development of dwarf wheat cultivars combined with high levels of agrochemical inputs during the green revolution resulted in high yielding cropping systems. However, changes in wheat cultivars were made without considering impacts on plant and soil microbe interactions. We studied the effect of these changes on root traits and on the assembly of rhizosphere bacterial communities by comparing eight wheat cultivars ranging from tall to semi-dwarf plants grown under field conditions. Wheat breeding influenced root diameter and specific root length (SRL). Rhizosphere bacterial communities from tall cultivars were distinct from those associated with semi-dwarf cultivars, with higher differential abundance of Actinobacteria, Bacteroidetes and Proteobacteria in tall cultivars, compared with a higher differential abundance of Verrucomicrobia, Planctomycetes and Acidobacteria in semi-dwarf cultivars. Predicted microbial functions were also impacted and network analysis revealed a greater level of connectedness between microbial communities in the tall cultivars relative to semi-dwarf cultivars. Taken together, results suggest that the development of semi-dwarf plants might have affected the ability of plants to recruit and sustain a complex bacterial community network in the rhizosphere.
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Affiliation(s)
- Vanessa N Kavamura
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Rebekah J Robinson
- Plant Pathology Laboratory, Royal Horticultural Society, RHS Garden Wisley, Woking, Surrey, GU23 6QB, United Kingdom
| | - David Hughes
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Ian Clark
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Maike Rossmann
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna-SP, Brazil
| | - Itamar Soares de Melo
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna-SP, Brazil
| | - Penny R Hirsch
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna-SP, Brazil
| | - Tim H Mauchline
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom.
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30
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Valente J, Gerin F, Le Gouis J, Moënne-Loccoz Y, Prigent-Combaret C. Ancient wheat varieties have a higher ability to interact with plant growth-promoting rhizobacteria. PLANT, CELL & ENVIRONMENT 2020; 43:246-260. [PMID: 31509886 DOI: 10.1111/pce.13652] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 05/27/2023]
Abstract
Plant interactions with plant growth-promoting rhizobacteria (PGPR) are highly dependent on plant genotype. Modern plant breeding has largely sought to improve crop performance but with little focus on the optimization of plant × PGPR interactions. The interactions of the model PGPR strain Pseudomonas kilonensis F113 were therefore compared in 199 ancient and modern wheat genotypes. A reporter system, in which F113 colonization and expression of 2,4-diacetylphloroglucinol biosynthetic genes (phl) were measured on roots was used to quantify F113 × wheat interactions under gnotobiotic conditions. Thereafter, eight wheat accessions that differed in their ability to interact with F113 were inoculated with F113 and grown in greenhouse in the absence or presence of stress. F113 colonization was linked to improved stress tolerance. Moreover, F113 colonization and phl expression were higher overall on ancient genotypes than modern genotypes. F113 colonization improved wheat performance in the four genotypes that showed the highest level of phl expression compared with the four genotypes in which phl expression was lowest. Taken together, these data suggest that recent wheat breeding strategies have had a negative impact on the ability of the plants to interact with PGPR.
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Affiliation(s)
- Jordan Valente
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Florence Gerin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622 Villeurbanne, France
| | | | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Claire Prigent-Combaret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622 Villeurbanne, France
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31
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Wang X, Hsu C, Dubeux JCB, Mackowiak C, Blount A, Han X, Liao H. Effects of rhizoma peanut cultivars ( Arachis glabrata Benth.) on the soil bacterial diversity and predicted function in nitrogen fixation. Ecol Evol 2019; 9:12676-12687. [PMID: 31788206 PMCID: PMC6875664 DOI: 10.1002/ece3.5735] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/25/2022] Open
Abstract
There is a growing awareness of the importance of soil microorganisms in agricultural management practices. Currently, much less is known about whether different crop cultivar has an effect on the taxonomic structure and diversity, and specific functions of soil bacterial communities. Here, we examined the changes of the diversity and composition and enzyme-encoding nitrogenase genes in a long-term field experiment with seven different rhizoma peanut cultivars in southeastern USA, coupling high-throughput 16S rRNA gene sequencing and the sequence-based function prediction with Tax4Fun. Of the 32 phyla detected (Proteobacteria class), 13 were dominant: Acidobacteria, Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Deltaproteobacteria, Gemmatimonadetes, Firmicutes, Nitrospirae, Chloroflexi, and Planctomycetes (relative abundance >1%). We found no evidence that the diversity and composition of bacterial communities were significantly different among different cultivars, but the abundance of some dominant bacterial groups that have N-fixation potentials (at broad or fine taxonomic level) and predicted abundances of some enzyme-encoding nitrogenase genes showed significant across-cultivar differences. The nitrogenase genes were notably abundant in Florigraze and Latitude soils while remarkably lower in Arbook and UF_TITO soils when compared with other cultivars, indicating different nitrogen fixation potentials among different cultivars. The findings also suggest that the abundance of certain bacterial taxa and the specific function bacteria perform in ecosystems can have an inherent association. Our study is helpful to understand how microbiological responses and feedback to different plant genotypes through the variation in structure and function of their communities in the rhizosphere.
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Affiliation(s)
- Xiao‐Bo Wang
- North Florida Research and Education CenterUniversity of FloridaQuincyFLUSA
- Erguna Forest‐Steppe Ecotone Research StationInstitute of Applied EcologyChinese Academy of SciencesShenyangChina
- Key Laboratory of Vegetation EcologyMinistry of EducationNortheast Normal UniversityChangchunChina
| | - Chih‐Ming Hsu
- North Florida Research and Education CenterUniversity of FloridaQuincyFLUSA
| | - José C. B. Dubeux
- North Florida Research and Education CenterUniversity of FloridaMariannaFLUSA
| | - Cheryl Mackowiak
- North Florida Research and Education CenterUniversity of FloridaQuincyFLUSA
| | - Ann Blount
- North Florida Research and Education CenterUniversity of FloridaMariannaFLUSA
| | - Xing‐Guo Han
- Erguna Forest‐Steppe Ecotone Research StationInstitute of Applied EcologyChinese Academy of SciencesShenyangChina
- Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Hui‐Ling Liao
- North Florida Research and Education CenterUniversity of FloridaQuincyFLUSA
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Cordero J, de Freitas JR, Germida JJ. Bacterial microbiome associated with the rhizosphere and root interior of crops in Saskatchewan, Canada. Can J Microbiol 2019; 66:71-85. [PMID: 31658427 DOI: 10.1139/cjm-2019-0330] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rhizosphere and root associated bacteria are key components of plant microbiomes and influence crop production. In sustainable agriculture, it is important to investigate bacteria diversity in various plant species and how edaphic factors influence the bacterial microbiome. In this study, we used high-throughput sequencing to assess bacterial communities associated with the rhizosphere and root interior of canola, wheat, field pea, and lentil grown at four locations in Saskatchewan, Canada. Rhizosphere bacteria communities exhibited distinct profiles among crops and sampling locations. However, each crop was associated with distinct root endophytic bacterial communities, suggesting that crop species may influence the selection of root bacterial microbiome. Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla in the root interior, whereas Gemmatimonadetes, Firmicutes, and Acidobacteria were prevalent in the rhizosphere soil. Pseudomonas and Stenotrophomonas were predominant in the rhizosphere and root interior, whereas Acinetobacter, Arthrobacter, Rhizobium, Streptomyces, Variovorax, and Xanthomonas were dominant in the root interior of all crops. The relative abundance of specific bacterial groups in the rhizosphere correlated with soil pH and silt and organic matter contents; however, there was no correlation between root endophytes and analyzed soil properties. These results suggest that the root microbiome may be modulated by plant factors rather than soil characteristics.
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Affiliation(s)
- Jorge Cordero
- Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada.,Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - J Renato de Freitas
- Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada.,Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - James J Germida
- Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
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Wassermann B, Cernava T, Müller H, Berg C, Berg G. Seeds of native alpine plants host unique microbial communities embedded in cross-kingdom networks. MICROBIOME 2019; 7:108. [PMID: 31340847 PMCID: PMC6651914 DOI: 10.1186/s40168-019-0723-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/16/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND The plant microbiota is crucial for plant health and growth. Recently, vertical transmission of a beneficial core microbiota was identified for crop seeds, but for native plants, complementary mechanisms are almost completely unknown. METHODS We studied the seeds of eight native plant species growing together for centuries under the same environmental conditions in Alpine meadows (Austria) by qPCR, FISH-CLSM, and amplicon sequencing targeting bacteria, archaea, and fungi. RESULTS Bacteria and fungi were determined with approx. 1010 gene copy numbers g-1 seed as abundant inhabitants. Archaea, which were newly discovered as seed endophytes, are less and represent only 1.1% of the signatures. The seed microbiome was highly diversified, and all seeds showed a species-specific, highly unique microbial signature, sharing an exceptionally small core microbiome. The plant genotype (species) was clearly identified as the main driver, while different life cycles (annual/perennial) had less impact on the microbiota composition, and fruit morphology (capsule/achene) had no significant impact. A network analysis revealed significant co-occurrence patterns for bacteria and archaea, contrasting with an independent fungal network that was dominated by mutual exclusions. CONCLUSIONS These novel insights into the native seed microbiome contribute to a deeper understanding of seed microbial diversity and phytopathological processes for plant health, and beyond that for ecosystem plasticity and diversification within plant-specific microbiota.
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Affiliation(s)
- Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Christian Berg
- Institute of Biology, Department of Plant Sciences, NAWI Graz, University of Graz, 8010 Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
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Sendek A, Karakoç C, Wagg C, Domínguez-Begines J, do Couto GM, van der Heijden MGA, Naz AA, Lochner A, Chatzinotas A, Klotz S, Gómez-Aparicio L, Eisenhauer N. Drought modulates interactions between arbuscular mycorrhizal fungal diversity and barley genotype diversity. Sci Rep 2019; 9:9650. [PMID: 31273222 PMCID: PMC6609766 DOI: 10.1038/s41598-019-45702-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/07/2019] [Indexed: 01/31/2023] Open
Abstract
Droughts associated with climate change alter ecosystem functions, especially in systems characterized by low biodiversity, such as agricultural fields. Management strategies aimed at buffering climate change effects include the enhancement of intraspecific crop diversity as well as the diversity of beneficial interactions with soil biota, such as arbuscular mycorrhizal fungi (AMF). However, little is known about reciprocal relations of crop and AMF diversity under drought conditions. To explore the interactive effects of plant genotype richness and AMF richness on plant yield under ambient and drought conditions, we established fully crossed diversity gradients in experimental microcosms. We expected highest crop yield and drought tolerance at both high barley and AMF diversity. While barley richness and AMF richness altered the performance of both barley and AMF, they did not mitigate detrimental drought effects on the plant and AMF. Root biomass increased with mycorrhiza colonization rate at high AMF richness and low barley richness. AMF performance increased under higher richness of both barley and AMF. Our findings indicate that antagonistic interactions between barley and AMF may occur under drought conditions, particularly so at higher AMF richness. These results suggest that unexpected alterations of plant-soil biotic interactions could occur under climate change.
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Affiliation(s)
- Agnieszka Sendek
- Systematic Botany and Functional Biodiversity, Institute of Biology, Leipzig University, Johannisallee 21-23, 04103, Leipzig, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Strasse 4, 06120, Halle, Germany.
- Department of Geobotany and Botanical Garden, Martin Luther University of Halle-Wittenberg, Am Kirchweg 2, 06108, Halle, Germany.
| | - Canan Karakoç
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Cameron Wagg
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstr. 190, Zürich, CH-8057, Switzerland
- Fredericton Research and Development Center, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - Jara Domínguez-Begines
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Institute of Natural Resources and Agrobiology of Seville (IRNAS), CSIC, LINCGlobal, Avenida Reina Mercedes, 10, 41012, Sevilla, Spain
| | - Gabriela Martucci do Couto
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Marcel G A van der Heijden
- Plant-Soil-Interactions, Department of Agroecology and Environment, Agroscope, Reckenholzstrasse 191, 8046, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Ali Ahmad Naz
- Crop Genetics and Biotechnology Unit, Institute of Crop Science and Resource Conservation, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Alfred Lochner
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Antonis Chatzinotas
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Stefan Klotz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Strasse 4, 06120, Halle, Germany
| | - Lorena Gómez-Aparicio
- Institute of Natural Resources and Agrobiology of Seville (IRNAS), CSIC, LINCGlobal, Avenida Reina Mercedes, 10, 41012, Sevilla, Spain
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103, Leipzig, Germany
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Wong JWH, Plett JM. Root renovation: how an improved understanding of basic root biology could inform the development of elite crops that foster sustainable soil health. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:597-612. [PMID: 31029179 DOI: 10.1071/fp18200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 03/08/2019] [Indexed: 05/24/2023]
Abstract
A major goal in agricultural research is to develop 'elite' crops with stronger, resilient root systems. Within this context, breeding practices have focussed on developing plant varieties that are, primarily, able to withstand pathogen attack and, secondarily, able to maximise plant productivity. Although great strides towards breeding disease-tolerant or -resistant root stocks have been made, this has come at a cost. Emerging studies in certain crop species suggest that domestication of crops, together with soil management practices aimed at improving plant yield, may hinder beneficial soil microbial association or reduce microbial diversity in soil. To achieve more sustainable management of agricultural lands, we must not only shift our soil management practices but also our breeding strategy to include contributions from beneficial microbes. For this latter point, we need to advance our understanding of how plants communicate with, and are able to differentiate between, microbes of different lifestyles. Here, we present a review of the key findings on belowground plant-microbial interactions that have been made over the past decade, with a specific focus on how plants and microbes communicate. We also discuss the currently unresolved questions in this area, and propose plausible ways to use currently available research and integrate fast-emerging '-omics' technologies to tackle these questions. Combining past and developing research will enable the development of new crop varieties that will have new, value-added phenotypes belowground.
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Affiliation(s)
- Johanna W-H Wong
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia
| | - Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia; and Corresponding author.
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36
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Beule L, Chen KH, Hsu CM, Mackowiak C, Dubeux Jr. JC, Blount A, Liao HL. Soil bacterial and fungal communities of six bahiagrass cultivars. PeerJ 2019; 7:e7014. [PMID: 31179193 PMCID: PMC6545100 DOI: 10.7717/peerj.7014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/19/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Cultivars of bahiagrass (Paspalum notatum Flüggé) are widely used for pasture in the Southeastern USA. Soil microbial communities are unexplored in bahiagrass and they may be cultivar-dependent, as previously proven for other grass species. Understanding the influence of cultivar selection on soil microbial communities is crucial as microbiome taxa have repeatedly been shown to be directly linked to plant performance. OBJECTIVES This study aimed to determine whether different bahiagrass cultivars interactively influence soil bacterial and fungal communities. METHODS Six bahiagrass cultivars ('Argentine', 'Pensacola', 'Sand Mountain', 'Tifton 9', 'TifQuik', and 'UF-Riata') were grown in a randomized complete block design with four replicate plots of 4.6 × 1.8 m per cultivar in a Rhodic Kandiudults soil in Northwest Florida, USA. Three soil subsamples per replicate plot were randomly collected. Soil DNA was extracted and bacterial 16S ribosomal RNA and fungal ribosomal internal transcribed spacer 1 genes were amplified and sequenced with one Illumina Miseq Nano. RESULTS The soil bacterial and fungal community across bahiagrass cultivars showed similarities with communities recovered from other grassland ecosystems. Few differences in community composition and diversity of soil bacteria among cultivars were detected; none were detected for soil fungi. The relative abundance of sequences assigned to nitrite-oxidizing Nitrospira was greater under 'Sand Mountain' than 'UF-Riata'. Indicator species analysis revealed that several bacterial and fungal indicators associated with either a single cultivar or a combination of cultivars are likely to be plant pathogens or antagonists. CONCLUSIONS Our results suggest a low impact of plant cultivar choice on the soil bacterial community composition, whereas the soil fungal community was unaffected. Shifts in the relative abundance of Nitrospira members in response to cultivar choice may have implications for soil N dynamics. The cultivars associated with presumptive plant pathogens or antagonists indicates that the ability of bahiagrass to control plant pathogens may be cultivar-dependent, however, physiological studies on plant-microbe interactions are required to confirm this presumption. We therefore suggest that future studies should explore the potential of different bahiagrass cultivars on plant pathogen control, particularly in sod-based crop rotation.
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Affiliation(s)
- Lukas Beule
- Molecular Phytopathology and Mycotoxin Research, Georg-August Universität Göttingen, Goettingen, Germany
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States of America
| | - Ko-Hsuan Chen
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States of America
| | - Chih-Ming Hsu
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States of America
| | - Cheryl Mackowiak
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States of America
| | - Jose C.B. Dubeux Jr.
- North Florida Research and Education Center, University of Florida, Marianna, FL, United States of America
| | - Ann Blount
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States of America
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States of America
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Cultivar and phosphorus effects on switchgrass yield and rhizosphere microbial diversity. Appl Microbiol Biotechnol 2018; 103:1973-1987. [PMID: 30535577 DOI: 10.1007/s00253-018-9535-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/10/2018] [Accepted: 11/18/2018] [Indexed: 01/16/2023]
Abstract
Switchgrass (Panicum virgatum L.) is a native perennial grass identified as a promising biofuel crop for production on marginal agricultural lands. As such, research into switchgrass fertility and the switchgrass rhizosphere microbiome has been ongoing in an effort to increase production sustainability. We examined the effects of cultivar and phosphorus (P) fertilization on biomass yield, P removal, and rhizosphere bacterial and fungal community structure in three switchgrass cultivars: Sunburst, Shawnee, and Liberty. The Liberty cv. is the first lowland-type bioenergy switchgrass adapted to USDA hardiness zones 4, 5, and 6. On a medium soil test P clay loam soil, biomass yield response to applied P was linear, increasing 135 kg ha-1 for every kilogram of P applied prior to establishment. Average post-frost biomass yield was 9.6 Mg ha-1 year-1 when unfertilized, and maximum biomass yield was 10.3 Mg ha-1 year-1 when fertilized at 58.6 kg ha-1 P, suggesting that P application on medium soil test P soils is beneficial for switchgrass establishment and early growth. Switchgrass cv. Shawnee was more productive than cvs. Liberty or Sunburst (11.3, 10.2, and 8.6 Mg ha-1 year-1, respectively). Both bacterial and fungal communities were significantly shaped by cultivar. These shifts, while inconsistent between year and cultivar, may reflect a selection of the microbial community from that present in soil to maximize total nutrient uptake, regardless of additional P amendments. Phosphorus fertilization did not affect microbial community structure. Results of this study suggest that the cultivar-associated selection of particular microbial taxa may have implications for increased productivity.
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Chaluvadi S, Bennetzen JL. Species-Associated Differences in the Below-Ground Microbiomes of Wild and Domesticated Setaria. FRONTIERS IN PLANT SCIENCE 2018; 9:1183. [PMID: 30186294 PMCID: PMC6111228 DOI: 10.3389/fpls.2018.01183] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 07/24/2018] [Indexed: 05/08/2023]
Abstract
The rhizosphere microbiome is known to play a crucial role in promoting plant growth, partly by countering soil-borne phytoparasites and by improving nutrient uptake. The abundance and composition of the rhizosphere and root-associated microbiota are influenced by several factors, including plant species and genotype. We hypothesize that crop domestication might influence the composition and diversity of plant-associated microbiomes. We tested the contribution of domestication to the bacterial and archaeal root and soil composition associated with six genotypes of domesticated Setaria italica and four genotypes of its wild ancestor, S. viridis. The bacterial microbiome in the rhizoplane and root endophyte compartments, and the archaea in the endophyte compartment, showed major composition differences. For instance, members of the Betaproteobacteria and Firmicutes were overrepresented in S. italica root samples compared to S. viridis. Metagenomic analysis of samples that contained both root surface-bound (rhizoplane) and inside-root (endophytic) bacteria defined two unique microbial communities only associated with S. italica roots and one only associated with S. viridis roots. Root endophytic bacteria were found in six discernible communities, of which four were primarily on S. italica and two primarily on S. viridis. Among archaea, Methanobacteria, and Methanomicrobia exhibited species-associated differences in the rhizosphere and root compartments, but most detected archaea were not classified more specifically than at the level of phylum. These results indicate a host genetic contribution to the microbial composition in Setaria, and suggest that domestication has selected for specific associations in the root and in the rhizosphere.
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39
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Saving seed microbiomes. ISME JOURNAL 2018; 12:1167-1170. [PMID: 29335636 DOI: 10.1038/s41396-017-0028-2] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 10/10/2017] [Accepted: 11/09/2017] [Indexed: 01/18/2023]
Abstract
Plant seeds are home to diverse microbial communities whose composition is determined by plant genotype, environment, and management practices. Plant domestication is now recognized as an important driver of plant-associated microbial diversity. To what extent and how domestication affects seed microbiomes is less well studied. Here we propose a 'back-to-the-future' approach to harness seed microbiomes of wild relatives of crop cultivars to save and re-instate missing beneficial seed microbes for improved plant tolerance to biotic and abiotic stress.
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Berg G, Köberl M, Rybakova D, Müller H, Grosch R, Smalla K. Plant microbial diversity is suggested as the key to future biocontrol and health trends. FEMS Microbiol Ecol 2017; 93:3744313. [PMID: 28430944 DOI: 10.1093/femsec/fix050] [Citation(s) in RCA: 225] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/18/2017] [Indexed: 12/16/2022] Open
Abstract
The microbiome of plants plays a crucial role in both plant and ecosystem health. Rapid advances in multi-omics tools are dramatically increasing access to the plant microbiome and consequently to the identification of its links with diseases and to the control of those diseases. Recent insights reveal a close, often symbiotic relationship between microorganisms and plants. Microorganisms can stimulate germination and plant growth, prevent diseases, and promote stress resistance and general fitness. Plants and their associated microorganisms form a holobiont and have to be considered as co-evolved species assemblages consisting of bacterial, archaeal and diverse eukaryotic species. The beneficial interplay of the host and its microbiome is responsible for maintaining the health of the holobiont, while diseases are often correlated with microbial dysbioses. Microbial diversity was identified as a key factor in preventing diseases and can be implemented as a biomarker in plant protection strategies. Targeted and predictive biocontrol approaches are possible by developing microbiome-based solutions. Moreover, combined breeding and biocontrol strategies maintaining diversity and ecosystem health are required. The analysis of plant microbiome data has brought about a paradigm shift in our understanding of its role in health and disease and has substantial consequences for biocontrol and health issues.
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Affiliation(s)
- Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria.,Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14, 8010 Graz, Austria
| | - Martina Köberl
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Daria Rybakova
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Henry Müller
- BioTenzz, Plüddemanngasse 39, 8010 Graz, Austria
| | - Rita Grosch
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Kornelia Smalla
- Julius Kühn-Institut (JKI), Messeweg 11-12, 38104 Braunschweig, Germany
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Khan MS, Sadat SU, Jan A, Munir I. Impact of Transgenic Brassica napus Harboring the Antifungal Synthetic Chitinase (NiC) Gene on Rhizosphere Microbial Diversity and Enzyme Activities. FRONTIERS IN PLANT SCIENCE 2017; 8:1307. [PMID: 28791039 PMCID: PMC5524829 DOI: 10.3389/fpls.2017.01307] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/12/2017] [Indexed: 06/07/2023]
Abstract
Transgenic Brassica napus harboring the synthetic chitinase (NiC) gene exhibits broad-spectrum antifungal resistance. As the rhizosphere microorganisms play an important role in element cycling and nutrient transformation, therefore, biosafety assessment of NiC containing transgenic plants on soil ecosystem is a regulatory requirement. The current study is designed to evaluate the impact of NiC gene on the rhizosphere enzyme activities and microbial community structure. The transgenic lines with the synthetic chitinase gene (NiC) showed resistance to Alternaria brassicicola, a common disease causing fungal pathogen. The rhizosphere enzyme analysis showed no significant difference in the activities of fivesoil enzymes: alkalyine phosphomonoestarase, arylsulphatase, β-glucosidase, urease and sucrase between the transgenic and non-transgenic lines of B. napus varieties, Durr-e-NIFA (DN) and Abasyne-95 (AB-95). However, varietal differences were observed based on the analysis of molecular variance. Some individual enzymes were significantly different in the transgenic lines from those of non-transgenic but the results were not reproducible in the second trail and thus were considered as environmental effect. Genotypic diversity of soil microbes through 16S-23S rRNA intergenic spacer region amplification was conducted to evaluate the potential impact of the transgene. No significant diversity (4% for bacteria and 12% for fungal) between soil microbes of NiC B. napus and the non-transgenic lines was found. However, significant varietal differences were observed between DN and AB-95 with 79% for bacterial and 54% for fungal diversity. We conclude that the NiC B. napus lines may not affect the microbial enzyme activities and community structure of the rhizosphere soil. Varietal differences might be responsible for minor changes in the tested parameters.
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Affiliation(s)
- Mohammad S. Khan
- Genomics and Bioinformatics Laboratory, Institute of Biotechnology and Genetic Engineering (IBGE), Faculty of Crop Production Sciences, University of AgriculturePeshawar, Pakistan
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Di Benedetto NA, Corbo MR, Campaniello D, Cataldi MP, Bevilacqua A, Sinigaglia M, Flagella Z. The role of Plant Growth Promoting Bacteria in improving nitrogen use efficiency for sustainable crop production: a focus on wheat. AIMS Microbiol 2017; 3:413-434. [PMID: 31294169 PMCID: PMC6604983 DOI: 10.3934/microbiol.2017.3.413] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/25/2017] [Indexed: 11/28/2022] Open
Abstract
Due to the increase in both human population growth and environmental pressure, it is necessary to raise agricultural productivity without enhancing environmental footprint. Within this context, soil inoculation with PGPB (Plant Growth Promoting Bacteria) may be considered a promising tool of integrated management systems. In particular, PGPB may improve plant growth either directly, by facilitating resource use or modulating plant hormone levels, or indirectly by decreasing the inhibitory effects of various pathogenic agents. PGPB comprise different functional and taxonomic groups of bacteria like Pseudomonas, Bacillus, Rhizobium and others. Their ability to either mobilize mineral or organic bound nutrients from the pedosphere or to fix atmospheric N2 and make it available to the plants, is a crucial feature in their application. In literature some data are available on the use of commercial PGPB, while less efforts have been made on the study of the effect of autochthonous PGPB isolated from soils on sustainability of cropping systems; thus a literature survey on these aspects was carried out with special focus on wheat, a staple food for a large part of world population. In particular, the main topic of this review is the potential of PGPB to enhance use efficiency of agro-environmental resources focusing on the interaction PGPB-wheat for improving nitrogen use efficiency.
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Affiliation(s)
- Nilde Antonella Di Benedetto
- Laboratory of Nutritional and Healthy Quality of Herbaceous Crop, Department of the Science of Agriculture, Food and Environment (SAFE) University of Foggia, Foggia, Italy
| | - Maria Rosaria Corbo
- Laboratory of Predictive Microbiology, Department of the Science of Agriculture, Food and Environment (SAFE), University of Foggia, Foggia, Italy
| | - Daniela Campaniello
- Laboratory of Predictive Microbiology, Department of the Science of Agriculture, Food and Environment (SAFE), University of Foggia, Foggia, Italy
| | - Mariagrazia Pia Cataldi
- Laboratory of Nutritional and Healthy Quality of Herbaceous Crop, Department of the Science of Agriculture, Food and Environment (SAFE) University of Foggia, Foggia, Italy
| | - Antonio Bevilacqua
- Laboratory of Predictive Microbiology, Department of the Science of Agriculture, Food and Environment (SAFE), University of Foggia, Foggia, Italy
| | - Milena Sinigaglia
- Laboratory of Predictive Microbiology, Department of the Science of Agriculture, Food and Environment (SAFE), University of Foggia, Foggia, Italy
| | - Zina Flagella
- Laboratory of Nutritional and Healthy Quality of Herbaceous Crop, Department of the Science of Agriculture, Food and Environment (SAFE) University of Foggia, Foggia, Italy
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Zhang R, Vivanco JM, Shen Q. The unseen rhizosphere root-soil-microbe interactions for crop production. Curr Opin Microbiol 2017; 37:8-14. [PMID: 28433932 DOI: 10.1016/j.mib.2017.03.008] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/22/2017] [Indexed: 02/03/2023]
Abstract
The underground root-soil-microbe interactions are extremely complex, but vitally important for aboveground plant growth, health and fitness. The pressure to reduce our reliance on agrochemicals, and sustainable efforts to develop agriculture makes rhizosphere interactions' research a hotspot. Recent advances provide new insights about the signals, pathways, functions and mechanisms of these interactions. In this review, we provide an overview about recent progress in rhizosphere interaction networks in crops. We also discuss a holistic view of the root-soil-rhizomicrobiome interactions achieved through the advances of omics and bioinformatics technologies, and the potential strategies to manage the complex rhizosphere interactions for enhancing crop production.
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Affiliation(s)
- Ruifu Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Jorge M Vivanco
- Department of Horticulture and Landscape Architecture and Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO 80523, United States
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China.
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44
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Leff JW, Lynch RC, Kane NC, Fierer N. Plant domestication and the assembly of bacterial and fungal communities associated with strains of the common sunflower, Helianthus annuus. THE NEW PHYTOLOGIST 2017; 214:412-423. [PMID: 27879004 DOI: 10.1111/nph.14323] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/09/2016] [Indexed: 05/21/2023]
Abstract
Root and rhizosphere microbial communities can affect plant health, but it remains undetermined how plant domestication may influence these bacterial and fungal communities. We grew 33 sunflower (Helianthus annuus) strains (n = 5) that varied in their extent of domestication and assessed rhizosphere and root endosphere bacterial and fungal communities. We also assessed fungal communities in the sunflower seeds to investigate the degree to which root and rhizosphere communities were influenced by vertical transmission of the microbiome through seeds. Neither root nor rhizosphere bacterial communities were affected by the extent of sunflower domestication, but domestication did affect the composition of rhizosphere fungal communities. In particular, more modern sunflower strains had lower relative abundances of putative fungal pathogens. Seed-associated fungal communities strongly differed across strains, but several lines of evidence suggest that there is minimal vertical transmission of fungi from seeds to the adult plants. Our results indicate that plant-associated fungal communities are more strongly influenced by host genetic factors and plant breeding than bacterial communities, a finding that could influence strategies for optimizing microbial communities to improve crop yields.
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Affiliation(s)
- Jonathan W Leff
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, 80309-0216, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Ryan C Lynch
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
- Medicinal Genomics, 12 Gill St, Woburn, MA, 01801, USA
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, 80309-0216, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
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Lee S, An R, Grewal P, Yu Z, Borherova Z, Lee J. High-Performing Windowfarm Hydroponic System: Transcriptomes of Fresh Produce and Microbial Communities in Response to Beneficial Bacterial Treatment. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:965-976. [PMID: 28035839 DOI: 10.1094/mpmi-08-16-0162-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Beneficial microorganisms play an important role in enhancing plant health, especially by promoting resistance to plant pathogen infection. The purpose of this study was to gain an understanding of such protection by i) examining the responses of fresh produce (lettuce) to beneficial treatments in their transcriptomes, ii) comparing biological (bacteria, fungi, and oomycete) communities and their diversity when treated with Pseudomonas chlororaphis (beneficial bacterium) in windowfarm hydroponic systems, and iii) identifying the microorganisms in root areas and water. P. chlororaphis treatment was for increasing plant growth and fighting for Pythium ultimum infection. In addition, two more treatments were conducted: i) adding supporting media for increasing bacterial colonizing areas around roots and ii) UV irradiation in water for controlling nuisance biofilm buildup. Changes in gene regulation and expression in lettuce in response to these treatments were investigated. Comparisons of microbial profiles among the treatments and microbial identification were conducted using samples of supporting media (around roots) and water. The results demonstrated that i) P. chlororaphis enhanced lettuce growth, ii) P. chlororaphis-treated lettuce showed dominantly expressed genes for membrane, catalytic activity, cellular process, and metabolic process categories, iii) P. chlororaphis treatment induced genes related to growth promotion and defense pathways, and iv) the microbial community of the root area was affected significantly by P. chlororaphis treatment and microbial diversity in water was significantly changed by UV irradiation. This study provided insight into how beneficial treatments affects the fresh produce growth in root areas and water in a vertical hydroponic system.
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Affiliation(s)
- Seungjun Lee
- 1 Environmental Sciences Graduate Program, The Ohio State University, Columbus, U.S.A
| | - Ruisheng An
- 2 Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, U.S.A
| | - Parwinder Grewal
- 2 Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, U.S.A
| | - Zhongtang Yu
- 1 Environmental Sciences Graduate Program, The Ohio State University, Columbus, U.S.A
- 3 Department of Animal Sciences
| | | | - Jiyoung Lee
- 1 Environmental Sciences Graduate Program, The Ohio State University, Columbus, U.S.A
- 5 Department of Food Science and Technology, and
- 6 College of Public Health, Division of Environmental Health Sciences, The Ohio State University
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do Amaral FP, Pankievicz VCS, Arisi ACM, de Souza EM, Pedrosa F, Stacey G. Differential growth responses of Brachypodium distachyon genotypes to inoculation with plant growth promoting rhizobacteria. PLANT MOLECULAR BIOLOGY 2016; 90:689-697. [PMID: 26873699 DOI: 10.1007/s11103-016-0449-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 02/05/2016] [Indexed: 06/05/2023]
Abstract
Plant growth promoting rhizobacteria (PGPR) can associate and enhance the growth of important crop grasses. However, in most cases, the molecular mechanisms responsible for growth promotion are not known. Such research could benefit by the adoption of a grass model species that showed a positive response to bacterial inoculation and was amenable to genetic and molecular research methods. In this work we inoculated different genotypes of the model grass Brachypodium distachyon with two, well-characterized PGPR bacteria, Azospirillum brasilense and Herbaspirillum seropedicae, and evaluated the growth response. Plants were grown in soil under no nitrogen or with low nitrogen (i.e., 0.5 mM KNO3). A variety of growth parameters (e.g., shoot height, root length, number of lateral roots, fresh and dry weight) were measured 35 days after inoculation. The data indicate that plant genotype plays a very important role in determining the plant response to PGPR inoculation. A positive growth response was observed with only four genotypes grown under no nitrogen and three genotypes tested under low nitrogen. However, in contrast, relatively good root colonization was seen with most genotypes, as measured by drop plate counting and direct, microscopic examination of roots. In particular, the endophytic bacteria H. seropedicae showed strong epiphytic and endophytic colonization of roots.
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Affiliation(s)
- Fernanda P do Amaral
- Divisions of Plant Science and Biochemistry, C. S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | - Vânia C S Pankievicz
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, 81531-980, Brazil
| | - Ana Carolina M Arisi
- Department of Food Science and Technology, Federal University of Santa Catarina, Florianópolis, 88034-001, Brazil
| | - Emanuel M de Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, 81531-980, Brazil
| | - Fabio Pedrosa
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, 81531-980, Brazil
| | - Gary Stacey
- Divisions of Plant Science and Biochemistry, C. S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA.
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Pérez-Jaramillo JE, Mendes R, Raaijmakers JM. Impact of plant domestication on rhizosphere microbiome assembly and functions. PLANT MOLECULAR BIOLOGY 2016; 90:635-44. [PMID: 26085172 PMCID: PMC4819786 DOI: 10.1007/s11103-015-0337-7] [Citation(s) in RCA: 326] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/04/2015] [Indexed: 05/18/2023]
Abstract
The rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. Plants can actively recruit members of the soil microbial community for positive feedbacks, but the underlying mechanisms and plant traits that drive microbiome assembly and functions are largely unknown. Domestication of plant species has substantially contributed to human civilization, but also caused a strong decrease in the genetic diversity of modern crop cultivars that may have affected the ability of plants to establish beneficial associations with rhizosphere microbes. Here, we review how plants shape the rhizosphere microbiome and how domestication may have impacted rhizosphere microbiome assembly and functions via habitat expansion and via changes in crop management practices, root exudation, root architecture, and plant litter quality. We also propose a "back to the roots" framework that comprises the exploration of the microbiome of indigenous plants and their native habitats for the identification of plant and microbial traits with the ultimate goal to reinstate beneficial associations that may have been undermined during plant domestication.
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Affiliation(s)
- Juan E Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands
- Sylvius Laboratories, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, Embrapa Environment, Rodovia SP 340 - km 127.5, Jaguariúna, 13820-000, Brazil
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands.
- Sylvius Laboratories, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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Zachow C, Berg C, Müller H, Monk J, Berg G. Endemic plants harbour specific Trichoderma communities with an exceptional potential for biocontrol of phytopathogens. J Biotechnol 2016; 235:162-70. [PMID: 27039271 DOI: 10.1016/j.jbiotec.2016.03.049] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/26/2016] [Accepted: 03/29/2016] [Indexed: 10/22/2022]
Abstract
Trichoderma strains exhibit enormous potential for applications in biotechnology, in particular as biocontrol agents against pathogens. However, little is known about the diversity of plant-associated Trichoderma communities at a global scale and their antagonistic spectrum. In order to gather information about structure and function, we compared Trichoderma biomes of endemic (Aeonium, Diospyros, Hebe, Rhododendron) and cosmopolitan plants (Zea mays) in a global study encompassing the area Northwest Africa to New Zealand via the European Alps and Madagascar. At the quantitative level we found no differences between cosmopolitan and endemic plants. Statistically significant differences were detected at the qualitative level: Trichoderma populations of endemic plants were highly specific and diverse with hot spots appearing in Madagascar and New Zealand. By contrast, maize plants from all sites shared the majority of Trichoderma species (65.5%). Interestingly, the high above ground biodiversity in ecosystems containing endemic plants was confirmed by a high below ground Trichoderma diversity. Despite the differences, we found a global Trichoderma core community shared by all analysed plants, which was dominated by T. koningii and T. koningiopsis. Amplicon-based network analyses revealed a high similarity between maize Trichoderma grown world-wide and distinct populations of endemic plants. Furthermore, Trichoderma strains from endemic plants showed a higher antagonistic activity against fungal pathogens compared to maize-associated strains. Our results showed that endemic plants are associated with a specific Trichoderma microbiome which possesses a high antagonistic activity indicating that it has potential to be used for biocontrol purposes.
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Affiliation(s)
- Christin Zachow
- Graz University of Technology, Institute of Environmental Biotechnology, Petersgasse 12, 8010 Graz, Austria; Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14, 8010 Graz, Austria.
| | - Christian Berg
- Karl-Franzens-University of Graz, Institute of Plant Sciences, Holteigasse 6, 8010 Graz, Austria
| | - Henry Müller
- Graz University of Technology, Institute of Environmental Biotechnology, Petersgasse 12, 8010 Graz, Austria
| | - Jana Monk
- AgResearch Limited, 4749 Private Bag, 8140 Christchurch, New Zealand
| | - Gabriele Berg
- Graz University of Technology, Institute of Environmental Biotechnology, Petersgasse 12, 8010 Graz, Austria
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49
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Moreira FDS, Costa PBD, Souza RD, Beneduzi A, Lisboa BB, Vargas LK, Passaglia LMP. Functional abilities of cultivable plant growth promoting bacteria associated with wheat (Triticum aestivum L.) crops. Genet Mol Biol 2016; 39:111-21. [PMID: 27007904 PMCID: PMC4807380 DOI: 10.1590/1678-4685-gmb-2015-0140] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/24/2015] [Indexed: 12/15/2022] Open
Abstract
In the pursuit of sustainable agriculture, bioinoculants usage as providers of a
crop's needs is a method to limit environmental damage. In this study, a
collection of cultivable putative plant growth promoting (PGP) bacteria
associated with wheat crops was obtained and this bacterial sample was
characterized in relation to the functional diversity of certain PGP features.
The isolates were obtained through classical cultivation methods, identified by
partial 16S rRNA gene sequencing and characterized for PGP traits of interest.
Functional diversity characterization was performed using Categorical Principal
Component Analysis (CatPCA) and Multiple Correspondence Analysis (MCA). The most
abundant genera found among the 346 isolates were Pseudomonas,
Burkholderia, and Enterobacter. Occurrence of PGP
traits was affected by genus, niche, and sampling site. A large number of genera
grouped together with the ability to produce indolic compounds; phosphate
solubilization and siderophores production formed a second group related to
fewer genera, in which the genus Burkholderia has a great
importance. The results obtained may help future studies aiming prospection of
putative plant growth promoting bacteria regarding the desired organism and PGP
trait.
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Affiliation(s)
- Fernanda da S Moreira
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Pedro B da Costa
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Rocheli de Souza
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Anelise Beneduzi
- Fundação Estadual de Pesquisa Agropecuária, Porto Alegre, RS, Brazil
| | - Bruno B Lisboa
- Fundação Estadual de Pesquisa Agropecuária, Porto Alegre, RS, Brazil
| | - Luciano K Vargas
- Fundação Estadual de Pesquisa Agropecuária, Porto Alegre, RS, Brazil
| | - Luciane M P Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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50
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Dessaux Y, Grandclément C, Faure D. Engineering the Rhizosphere. TRENDS IN PLANT SCIENCE 2016; 21:266-278. [PMID: 26818718 DOI: 10.1016/j.tplants.2016.01.002] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 12/14/2015] [Accepted: 01/04/2016] [Indexed: 05/25/2023]
Abstract
All components of the rhizosphere can be engineered to promote plant health and growth, two features that strongly depend upon the interactions of living organisms with their environment. This review describes the progress in plant and microbial molecular genetics and ecology that has led to a wealth of potential applications. Recent efforts especially deal with the plant defense machinery that is instrumental in engineering plant resistance to biotic stresses. Another approach involves microbial population engineering rather than single strain engineering. More generally, the plants (and the associated microbes) are no longer seen as 'individual' but rather as a holobiont, in other words a unit of selection in evolution, a concept that holds great promise for future plant breeding programs.
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Affiliation(s)
- Yves Dessaux
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette CEDEX, France.
| | - Catherine Grandclément
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette CEDEX, France
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette CEDEX, France
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