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Guha T, Mandal Biswas S. Recent progress in the role of seed endophytic bacteria as plant growth-promoting microorganisms and biocontrol agents. World J Microbiol Biotechnol 2024; 40:218. [PMID: 38806849 DOI: 10.1007/s11274-024-04031-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/21/2024] [Indexed: 05/30/2024]
Abstract
The importance of microorganisms residing within the host plant for their growth and health is increasingly acknowledged, yet the significance of microbes associated with seeds, particularly seed endophytic bacteria, remains underestimated. Seeds harbor a wide range of bacteria that can boost the growth and resilience of their host plants against environmental challenges. These endophytic associations also offer advantages for germination and seedling establishment, as seed endophytic bacteria are present during the initial stages of plant growth and development. Furthermore, plants can selectively choose bacteria possessing beneficial traits, which are subsequently transmitted through seeds to confer benefits to future generations. Interestingly, even with the ongoing discovery of endophytes in seeds through high-throughput sequencing methods, certain endophytes remain challenging to isolate and culture from seeds, despite their high abundance. These challenges pose difficulties in studying seed endophytes, making many of their effects on plants unclear. In this article, a framework for understanding the assembly and function of seed endophytes, including their sources and colonization processes was outlined in detail and available research on bacterial endophytes discovered within the seeds of various plant species has also been explored. Thus, this current review aims to provide valuable insights into the mechanism of underlying seed endophytic bacteria-host plant interactions and offers significant recommendations for utilizing the seed endophytic bacteria in sustainable agriculture as plant growth promoters and enhancers of environmental stress tolerance.
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Affiliation(s)
- Titir Guha
- Agricultural & Ecological Research Unit, Biological Sciences Division, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700 108, India
| | - Suparna Mandal Biswas
- Agricultural & Ecological Research Unit, Biological Sciences Division, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700 108, India.
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2
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Hauschild K, Orth N, Liu B, Giongo A, Gschwendtner S, Beerhues L, Schloter M, Vetterlein D, Winkelmann T, Smalla K. Rhizosphere competent inoculants modulate the apple root-associated microbiome and plant phytoalexins. Appl Microbiol Biotechnol 2024; 108:344. [PMID: 38801472 PMCID: PMC11129989 DOI: 10.1007/s00253-024-13181-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
Modulating the soil microbiome by applying microbial inoculants has gained increasing attention as eco-friendly option to improve soil disease suppressiveness. Currently, studies unraveling the interplay of inoculants, root-associated microbiome, and plant response are lacking for apple trees. Here, we provide insights into the ability of Bacillus velezensis FZB42 or Pseudomonas sp. RU47 to colonize apple root-associated microhabitats and to modulate their microbiome. We applied the two strains to apple plants grown in soils from the same site either affected by apple replant disease (ARD) or not (grass), screened their establishment by selective plating, and measured phytoalexins in roots 3, 16, and 28 days post inoculation (dpi). Sequencing of 16S rRNA gene and ITS fragments amplified from DNA extracted 28 dpi from different microhabitat samples revealed significant inoculation effects on fungal β-diversity in root-affected soil and rhizoplane. Interestingly, only in ARD soil, most abundant bacterial amplicon sequence variants (ASVs) changed significantly in relative abundance. Relative abundances of ASVs affiliated with Enterobacteriaceae were higher in rhizoplane of apple grown in ARD soil and reduced by both inoculants. Bacterial communities in the root endosphere were not affected by the inoculants but their presence was indicated. Interestingly and previously unobserved, apple plants responded to the inoculants with increased phytoalexin content in roots, more pronounced in grass than ARD soil. Altogether, our results indicate that FZB42 and RU47 were rhizosphere competent, modulated the root-associated microbiome, and were perceived by the apple plants, which could make them interesting candidates for an eco-friendly mitigation strategy of ARD. KEY POINTS: • Rhizosphere competent inoculants modulated the microbiome (mainly fungi) • Inoculants reduced relative abundance of Enterobacteriaceae in the ARD rhizoplane • Inoculants increased phytoalexin content in roots, stronger in grass than ARD soil.
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Affiliation(s)
- Kristin Hauschild
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Nils Orth
- Institute of Horticultural Production Systems, Leibniz University Hannover, Hannover, Germany
| | - Benye Liu
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Adriana Giongo
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Silvia Gschwendtner
- Research Unit Comparative Microbiome Analysis, Helmholtz Centre Munich, Munich, Germany
| | - Ludger Beerhues
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Centre Munich, Munich, Germany
| | - Doris Vetterlein
- Department of Soil System Science, Helmholtz Centre for Environmental Research, Halle/Saale, Germany
| | - Traud Winkelmann
- Institute of Horticultural Production Systems, Leibniz University Hannover, Hannover, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Braunschweig, Germany.
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3
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Liu Y, Zhao K, Stirling E, Wang X, Gao Z, Ma B, Xu C, Chen S, Chu G, Zhang X, Wang D. Heterosis of endophytic microbiomes in hybrid rice varieties improves seed germination. mSystems 2024; 9:e0000424. [PMID: 38591897 PMCID: PMC11097635 DOI: 10.1128/msystems.00004-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 02/27/2024] [Indexed: 04/10/2024] Open
Abstract
Seed endophytic microbiomes are shaped by host and environmental factors and play a crucial role in their host growth and health. Studies have demonstrated that host genotype, including hybridization, affects seed microbiomes. Heterosis features are also observed in root-associated microbiomes. It remains unclear, however, whether heterosis exists in seed endophytic microbiomes and whether hybrid microbiota provide noticeable advantages to host plant growth, especially to seed germination. Here, we investigated the structure of seed endophytic bacterial and fungal communities from three hybrid rice varieties and their respective parents using amplicon sequencing targeting 16S rRNA and ITS2 genes. Heterosis was found in diversity and composition of seed endophytic microbiomes in hybrids, which hosted more diverse communities and significantly higher abundances of plant growth-promoting taxa, such as Pseudomonas and Rhizobium genera compared with their parental lines. Co-occurrence network analysis revealed that there are potentially tighter microbial interactions in the hybrid seeds compared with their parent seeds. Finally, inoculation of seed-cultivable endophytes, isolated from hybrids, resulted in a greater promotion of seed germination compared with those isolated from parent lines. These findings suggest that heterosis exists not only in plant traits but also in seed endophytic microbiota, the latter in turn promotes seed germination, which offers valuable guidance for microbiome-assisted rice breeding.IMPORTANCEGenetic and physiological changes associated with plant hybridization have been studied for many crop species. Still, little is known about the impact of hybridization on the seed microbiota. In this study, we indicate that hybridization has a significant impact on the endophytic bacterial and fungal communities in rice seeds. The seed endophytic microbiomes of hybrids displayed distinct characteristics from those of their parental lines and exhibited potential heterosis features. Furthermore, the inoculation of seed-cultivable endophytes isolated from hybrids exhibited a greater promotion effect on seed germination compared with those isolated from the parents. Our findings make a valuable contribution to the emerging field of microbiome-assisted plant breeding, highlighting the potential for a targeted approach that aims to achieve not only desired plant traits but also plant-beneficial microbial communities on the seeds.
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Affiliation(s)
- Yuanhui Liu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Kankan Zhao
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Erinne Stirling
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Adelaide, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Xiaolin Wang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Bin Ma
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chunmei Xu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Song Chen
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Guang Chu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Xiufu Zhang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Danying Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang, China
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Yang J, Xie J, Chen H, Zhu S, Hou X, Zhang Z. Diversity and Biological Characteristics of Seed-Borne Bacteria of Achnatherum splendens. Microorganisms 2024; 12:339. [PMID: 38399743 PMCID: PMC10892246 DOI: 10.3390/microorganisms12020339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
As a high-quality plant resource for ecological restoration, Achnatherum splendens has strong adaptability and wide distribution. It is a constructive species of alkaline grassland in Northwest China. The close relationship between seed-borne bacteria and seeds causes a specific co-evolutionary effect which can enhance the tolerance of plants under various stresses. In this study, 272 bacterial isolates were isolated from the seeds of Achnatherum splendens in 6 different provinces of China. In total, 41 dominant strains were identified, and their motility, biofilm formation ability and antibiotic resistance were analyzed. The results showed that the bacteria of Achnatherum splendens belonged to 3 phyla and 14 genera, of which Firmicutes was the dominant phylum and Bacillus was the dominant genus. The motility and biofilm formation ability of the isolated strains were studied. It was found that there were six strains with a moving diameter greater than 8 cm. There were 16 strains with strong biofilm formation ability, among which Bacillus with biofilm formation ability was the most common, accounting for 37.5%. The analysis of antibiotic resistance showed that sulfonamides had stronger antibacterial ability to strains. Correlation analysis showed that the resistance of strains to aminoglycosides (kanamycin, amikacin, and gentamicin) was significantly positively correlated with their biofilm formation ability. This study provides fungal resources for improving the tolerance of plants under different stresses. In addition, this is the first report on the biological characteristics of bacteria in Achnatherum splendens.
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Affiliation(s)
| | | | | | | | | | - Zhenfen Zhang
- Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural College, Gansu Agricultural University, Lanzhou 730070, China; (J.Y.); (J.X.); (H.C.); (S.Z.); (X.H.)
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Kumar A, Solanki MK, Wang Z, Solanki AC, Singh VK, Divvela PK. Revealing the seed microbiome: Navigating sequencing tools, microbial assembly, and functions to amplify plant fitness. Microbiol Res 2024; 279:127549. [PMID: 38056172 DOI: 10.1016/j.micres.2023.127549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 12/08/2023]
Abstract
Microbial communities within seeds play a vital role in transmitting themselves to the next generation of plants. These microorganisms significantly impact seed vigor and early seedling growth, for successful crop establishment. Previous studies reported on seed-associated microbial communities and their influence on processes like dormancy release, germination, and disease protection. Modern sequencing and conventional methods reveal microbial community structures and environmental impacts, these information helps in microbial selection and manipulation. These studies form the foundation for using seed microbiomes to enhance crop resilience and productivity. While existing research has primarily focused on characterizing microbiota in dried mature seeds, a significant gap exists in understanding how these microbial communities assemble during seed development. The review also discusses applying seed-associated microorganisms to improve crops in the context of climate change. However, limited knowledge is available about the microbial assembly pattern on seeds, and their impact on plant growth. The review provides insight into microbial composition, functions, and significance for plant health, particularly regarding growth promotion and pest control.
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Affiliation(s)
- Ajay Kumar
- Amity Institute of Biotechnology, Amity University, Sector-125, Noida, Uttar Pradesh 201313, India
| | - Manoj Kumar Solanki
- Department of Life Sciences and Biological Sciences, IES University, Bhopal, Madhya Pradesh, India; Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland.
| | - Zhen Wang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin 537000, China
| | - Anjali Chandrol Solanki
- Department of Agriculture, Mansarover Global University, Bhopal, Madhya Pradesh 462042, India
| | - Vipin Kumar Singh
- Department of Botany, K.S. Saket P.G. College, Ayodhya 224123, Uttar Pradesh, India
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Li N, Zheng N, Pan J, An Q, Li X, Sun S, Chen C, Zhu H, Li Z, Ji Y. Distribution and major driving elements of antibiotic resistance genes in the soil-vegetable system under microplastic stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167619. [PMID: 37806594 DOI: 10.1016/j.scitotenv.2023.167619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/05/2023] [Accepted: 10/04/2023] [Indexed: 10/10/2023]
Abstract
Microplastics (MPs) and antibiotic resistance genes (ARGs) are both enriched in soil-vegetable systems as a consequence of the prolonged use of agricultural mulches. MPs can form unique bacterial communities and provide potential hosts for ARGs. Therefore, MPs stress may promote the spread of ARGs from soil to crops. Increasing ARGs pollution in soil-vegetable system. In our research, we investigated the distribution and major driving elements of antibiotic resistance genes in the soil-vegetable system under microplastic stress. The results showed that MPs treatment decreased the relative abundance of ARGs in non-rhizosphere soil. High concentrations of MPs promoted the enrichment of tetracycline antibiotic resistance genes in rhizosphere soil. MPs treatment promoted the enrichment of ARGs and mobile genetic elements (MGEs) in lettuce tissues, and the overall abundance of ARGs in root after 0.5 %, 1 %, and 2 % (w/w, dry weight) polyethylene (PE) administration was considerably higher compared to that in the untreated group (p < 0.05). At the same time, high PE concentrations promoted the spread of sulfa ARGs from root to leaf. MPs also impacted the bacterial communities in the soil-plant system, and the changes in ARGs as well as MGEs in each part of the soil-vegetable system were significantly correlated with the bacterial diversity index (p < 0.05). Correlation analysis and network analysis showed that bacterial communities and MGEs were the main drivers of ARGs variation in soil-lettuce systems.
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Affiliation(s)
- Ning Li
- College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Na Zheng
- College of New Energy and Environment, Jilin University, Changchun 130012, China; Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130012, China.
| | - Jiamin Pan
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Qirui An
- College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Xiaoqian Li
- College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Siyu Sun
- College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Changcheng Chen
- College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Huicheng Zhu
- College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Zimeng Li
- College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Yining Ji
- College of New Energy and Environment, Jilin University, Changchun 130012, China
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Gonçalves AC, Sánchez-Juanes F, Meirinho S, Silva LR, Alves G, Flores-Félix JD. Insight into the Taxonomic and Functional Diversity of Bacterial Communities Inhabiting Blueberries in Portugal. Microorganisms 2022; 10:2193. [PMID: 36363783 PMCID: PMC9695653 DOI: 10.3390/microorganisms10112193] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 10/15/2023] Open
Abstract
Vaccinium myrtillus is a dwarf shrub of the Ericaceae family with a Palearctic distribution, associated with temperate and cold humid climates. It is widespread on the European continent; on the Iberian Peninsula it is located on Atlantic climate mountains and glacial relicts. In Portugal, we find scattered and interesting populations; however, the majority of them are threatened by climate change and wildfires. Given that, the objective of this study is to determine the rhizospheric and root bacterial communities of this plant in the southernmost regions, and, consequently, its potential range and ability to be used as a biofertilizer. In this work, metabarcoding of 16S rRNA gene showed that the endophytic bacterial diversity is dependent on the plant and selected by it according to the observed alpha and beta diversity. Moreover, a culturomic approach allowed 142 different strains to be isolated, some of them being putative new species. Additionally, some strains belonging to the genera Bacillus, Paenibacillus, Pseudomonas, Paraburkholderia, and Caballeronia showed significant potential to be applied as multifunctional biofertilizers since they present good plant growth-promoting (PGP) mechanisms, high colonization capacities, and an increase in vegetative parameters in blueberry and tomato plants.
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Affiliation(s)
- Ana C. Gonçalves
- CICS–UBI—Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
- CIBIT—Coimbra Institute for Biomedical Imaging and Translational Research, University of Coimbra, 3000-540 Coimbra, Portugal
| | - Fernando Sánchez-Juanes
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Sara Meirinho
- CICS–UBI—Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
| | - Luís R. Silva
- CICS–UBI—Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
- CPIRN-UDI/IPG—Center of Potential and Innovation of Natural Resources, Research Unit for Inland Development (UDI), Polytechnic Institute of Guarda, 6300-559 Guarda, Portugal
| | - Gilberto Alves
- CICS–UBI—Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
| | - José David Flores-Félix
- CICS–UBI—Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
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Gerna D, Clara D, Antonielli L, Mitter B, Roach T. Seed Imbibition and Metabolism Contribute Differentially to Initial Assembly of the Soybean Holobiont. PHYTOBIOMES JOURNAL 2022; 8:21-33. [PMID: 38818306 PMCID: PMC7616048 DOI: 10.1094/pbiomes-03-23-0019-mf] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Seed germination critically determines successful plant establishment and agricultural productivity. In the plant holobiont's life cycle, seeds are hubs for microbial communities' assembly, but what exactly shapes the holobiont during germination remains unknown. Here, 16S rRNA gene amplicon sequencing characterized the bacterial communities in embryonic compartments (cotyledons and axes) and on seed coats pre- and post-germination of four soybean (Glycine max) cultivars, in the presence or absence of exogenous abscisic acid (ABA), which prevented germination and associated metabolism of seeds that had imbibed. Embryonic compartments were metabolically profiled during germination to design minimal media mimicking the seed endosphere for bacterial growth assays. The distinction between embryonic and seed coat bacterial microbiomes of dry seeds weakened during germination, resulting in the plumule, radicle, cotyledon, and seed coat all hosting the same most abundant and structurally influential genera in germinated seeds of every cultivar. Treatment with ABA prevented the increase of bacterial microbiomes' richness, but not taxonomic homogenization across seed compartments. Growth assays on minimal media containing the most abundant metabolites that accumulated in germinated seeds revealed that seed reserve mobilization promoted enrichment of copiotrophic bacteria. Our data show that seed imbibition enabled distribution of seed-coat-derived epiphytes into embryos irrespective of germination, while germinative metabolism promoted proliferation of copiotrophic taxa, which predominated in germinated seeds.
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Affiliation(s)
- Davide Gerna
- Department of Botany and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria
| | - David Clara
- Department of Botany and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria
| | - Livio Antonielli
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, 3430 Tulln, Austria Accepted for publication 17 August 2023
| | - Birgit Mitter
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, 3430 Tulln, Austria Accepted for publication 17 August 2023
| | - Thomas Roach
- Department of Botany and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria
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Gerna D, Clara D, Allwardt D, Mitter B, Roach T. Tailored Media Are Key to Unlocking the Diversity of Endophytic Bacteria in Distinct Compartments of Germinating Seeds. Microbiol Spectr 2022; 10:e0017222. [PMID: 35867396 PMCID: PMC9431621 DOI: 10.1128/spectrum.00172-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 07/01/2022] [Indexed: 11/24/2022] Open
Abstract
Seeds offer an internal microbial niche, termed the endosphere, colonized by communities of endophytic bacteria. To elucidate the functions of seed endophytes during germination and early plant growth, studies with culturable isolates are essential. Conventional growth media favor few fast-growing taxa, while micro organisms with restricted nutrient requirements are usually outcompeted prior to isolation. Consequently, current knowledge of the interaction between seeds and their endophytes remains limited to only few bacterial taxa, despite a "black box" of unculturable isolates colonizing the endosphere. Here, we designed various solid media to mimic the endosphere of germinating soybean (Glycine max L.) seeds and assessed their effect on the diversity of culturable endophytic bacteria. The embryonic axis (i.e., the future plant) possessed higher richness and harbored more unique genera (i.e., Brevundimonas, Methylobacterium, Microbacterium, Pseudoclavibacter, and Rathayibacter) than cotyledons (i.e., seed storage organs). Overall, media containing germinating and ground seeds enabled culturing and isolation of the broadest diversity of endophytic bacteria, viewed through the molecular identification of 246 isolates. The use of multiple tailored media helped uncover trophic adaptation of the core taxa. Furthermore, comparison of seeds from four lots of distinct cultivars and origin revealed few overlapping taxa, indicating that the parental environment, including soil and fertilization regime, influenced seed endophytic diversity. Extended diversity of native seed endophytic bacteria revealed the functional relevance of unique Arthrobacter, Bacillus, and Curtobacterium strains to seed germination under salt stress, exemplifying the importance of enhanced culturing approaches to elucidate the role of microbiota in seed germination. IMPORTANCE Plant growth-promoting endophytic isolates that appear to advance seed germination are often obtained from plant niches other than the seed endosphere. Isolating pure cultures of native endophytes from seeds during germination is crucial to investigate their function during early plant growth. Here, the diversity of endophytic bacteria isolated from seeds during soybean germination was enhanced by combining media tailored to the nutritional composition of the seed endosphere, including pregerminated seeds themselves. Our results show that isolation from distinct soybean seed compartments affected such diversity, with the embryonic axis harboring more unique taxa while displaying higher endophytic richness. Furthermore, using pools of seeds from separate lots, each corresponding to a certain cultivar and field site, supported isolation of further unique strains that often unveiled substantial effects on germination performance. Such findings are relevant to assist studies on the interactions between seeds and their native endophytic bacteria.
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Affiliation(s)
- Davide Gerna
- Department of Botany and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - David Clara
- Department of Botany and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Dorothee Allwardt
- Bioresources Unit, Austrian Institute of Technology GmbH, Tulln, Austria
| | - Birgit Mitter
- Bioresources Unit, Austrian Institute of Technology GmbH, Tulln, Austria
| | - Thomas Roach
- Department of Botany and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
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Olmo R, Wetzels SU, Armanhi JSL, Arruda P, Berg G, Cernava T, Cotter PD, Araujo SC, de Souza RSC, Ferrocino I, Frisvad JC, Georgalaki M, Hansen HH, Kazou M, Kiran GS, Kostic T, Krauss-Etschmann S, Kriaa A, Lange L, Maguin E, Mitter B, Nielsen MO, Olivares M, Quijada NM, Romaní-Pérez M, Sanz Y, Schloter M, Schmitt-Kopplin P, Seaton SC, Selvin J, Sessitsch A, Wang M, Zwirzitz B, Selberherr E, Wagner M. Microbiome Research as an Effective Driver of Success Stories in Agrifood Systems – A Selection of Case Studies. Front Microbiol 2022; 13:834622. [PMID: 35903477 PMCID: PMC9315449 DOI: 10.3389/fmicb.2022.834622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/24/2022] [Indexed: 12/14/2022] Open
Abstract
Increasing knowledge of the microbiome has led to significant advancements in the agrifood system. Case studies based on microbiome applications have been reported worldwide and, in this review, we have selected 14 success stories that showcase the importance of microbiome research in advancing the agrifood system. The selected case studies describe products, methodologies, applications, tools, and processes that created an economic and societal impact. Additionally, they cover a broad range of fields within the agrifood chain: the management of diseases and putative pathogens; the use of microorganism as soil fertilizers and plant strengtheners; the investigation of the microbial dynamics occurring during food fermentation; the presence of microorganisms and/or genes associated with hazards for animal and human health (e.g., mycotoxins, spoilage agents, or pathogens) in feeds, foods, and their processing environments; applications to improve HACCP systems; and the identification of novel probiotics and prebiotics to improve the animal gut microbiome or to prevent chronic non-communicable diseases in humans (e.g., obesity complications). The microbiomes of soil, plants, and animals are pivotal for ensuring human and environmental health and this review highlights the impact that microbiome applications have with this regard.
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Affiliation(s)
- Rocío Olmo
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
- *Correspondence: Rocío Olmo,
| | - Stefanie Urimare Wetzels
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Jaderson Silveira Leite Armanhi
- Symbiomics Microbiome Solutions, Florianópolis, Brazil
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, Campinas, Brazil
| | - Paulo Arruda
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Paul D. Cotter
- Food Bioscience, Teagasc Food Research Centre Moorepark, Fermoy, Ireland
- APC Microbiome Ireland and VistaMilk, Cork, Ireland
| | - Solon Cordeiro Araujo
- SCA, Consultoria em Microbiologia Agrícola, Campinas, Brazil
- Brazil National Association of Inoculant Producers and Importers (ANPII), Campinas, Brazil
| | - Rafael Soares Correa de Souza
- Symbiomics Microbiome Solutions, Florianópolis, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Ilario Ferrocino
- Department of Agricultural, Forest and Food Science, University of Torino, Torino, Italy
| | - Jens C. Frisvad
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Marina Georgalaki
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Hanne Helene Hansen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Maria Kazou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | | | - Tanja Kostic
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Susanne Krauss-Etschmann
- Research Center Borstel, Leibniz Lung Center, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
- Institute for Experimental Medicine, Christian Albrechts University, Kiel, Germany
| | - Aicha Kriaa
- Microbiota Interaction With Human and Animal Team (MIHA), Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Lene Lange
- BioEconomy, Research & Advisory, Copenhagen, Denmark
| | - Emmanuelle Maguin
- Microbiota Interaction With Human and Animal Team (MIHA), Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Birgit Mitter
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Mette Olaf Nielsen
- Department of Animal Science, Faculty of Technical Sciences, Aarhus University, Tjele, Denmark
| | - Marta Olivares
- Microbial Ecology, Nutrition and Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Narciso Martín Quijada
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Marina Romaní-Pérez
- Microbial Ecology, Nutrition and Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Yolanda Sanz
- Microbial Ecology, Nutrition and Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Center Munich, Neuherberg, Germany
| | | | | | - Joseph Selvin
- School of Life Sciences, Pondicherry University, Puducherry, India
| | - Angela Sessitsch
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Mengcen Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Benjamin Zwirzitz
- Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Evelyne Selberherr
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Martin Wagner
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
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11
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Abdelfattah A, Tack AJM, Wasserman B, Liu J, Berg G, Norelli J, Droby S, Wisniewski M. Evidence for host-microbiome co-evolution in apple. THE NEW PHYTOLOGIST 2022; 234:2088-2100. [PMID: 34823272 PMCID: PMC9299473 DOI: 10.1111/nph.17820] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 10/18/2021] [Indexed: 05/07/2023]
Abstract
Plants evolved in association with a diverse community of microorganisms. The effect of plant phylogeny and domestication on host-microbiome co-evolutionary dynamics are poorly understood. Here we examined the effect of domestication and plant lineage on the composition of the endophytic microbiome of 11 Malus species, representing three major groups: domesticated apple (M. domestica), wild apple progenitors, and wild Malus species. The endophytic community of M. domestica and its wild progenitors showed higher microbial diversity and abundance than wild Malus species. Heirloom and modern cultivars harbored a distinct community composition, though the difference was not significant. A community-wide Bayesian model revealed that the endophytic microbiome of domesticated apple is an admixture of its wild progenitors, with clear evidence for microbiome introgression, especially for the bacterial community. We observed a significant correlation between the evolutionary distance of Malus species and their microbiome. This study supports co-evolution between Malus species and their microbiome during domestication. This finding has major implications for future breeding programs and our understanding of the evolution of plants and their microbiomes.
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Affiliation(s)
- Ahmed Abdelfattah
- Institute of Environmental BiotechnologyGraz University of TechnologyPetersgasse 12Graz8010Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB)Max‐Eyth Allee 10014469PotsdamGermany
| | - Ayco J. M. Tack
- Department of Ecology, Environment and Plant SciencesStockholm UniversitySvante Arrhenius väg 20AStockholmSE‐106 91Sweden
| | - Birgit Wasserman
- Institute of Environmental BiotechnologyGraz University of TechnologyPetersgasse 12Graz8010Austria
| | - Jia Liu
- Chongqing Key Laboratory of Economic Plant BiotechnologyCollege of Landscape Architecture and Life SciencesChongqing University of Arts and SciencesYongchuanChongquing402160China
| | - Gabriele Berg
- Institute of Environmental BiotechnologyGraz University of TechnologyPetersgasse 12Graz8010Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB)Max‐Eyth Allee 10014469PotsdamGermany
- Institute for Biochemistry and BiologyUniversity of Postdam14476Potsdam OT GolmGermany
| | - John Norelli
- Appalachian Fruit Research StationUnited States Department of Agriculture – Agricultural Research ServiceKearneysvilleWV25430USA
| | - Samir Droby
- Department of Postharvest ScienceAgricultural Research OrganizationThe Volcani InstitutePO Box 15159Rishon LeZion7505101Israel
| | - Michael Wisniewski
- Department of Biological SciencesVirginia Polytechnic Institute and State University220 Ag Quad LnBlacksburgVA24061USA
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12
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Simonin M, Briand M, Chesneau G, Rochefort A, Marais C, Sarniguet A, Barret M. Seed microbiota revealed by a large-scale meta-analysis including 50 plant species. THE NEW PHYTOLOGIST 2022; 234:1448-1463. [PMID: 35175621 DOI: 10.1111/nph.18037] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/03/2022] [Indexed: 05/15/2023]
Abstract
Seed microbiota constitutes a primary inoculum for plants that is gaining attention owing to its role for plant health and productivity. Here, we performed a meta-analysis on 63 seed microbiota studies covering 50 plant species to synthesize knowledge on the diversity of this habitat. Seed microbiota are diverse and extremely variable, with taxa richness varying from one to thousands of taxa. Hence, seed microbiota presents a variable (i.e. flexible) microbial fraction but we also identified a stable (i.e. core) fraction across samples. Around 30 bacterial and fungal taxa are present in most plant species and in samples from all over the world. Core taxa, such as Pantoea agglomerans, Pseudomonas viridiflava, P. fluorescens, Cladosporium perangustum and Alternaria sp., are dominant seed taxa. The characterization of the core and flexible seed microbiota provided here will help uncover seed microbiota roles for plant health and design effective microbiome engineering.
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Affiliation(s)
- Marie Simonin
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, F-49000, Angers, France
| | - Martial Briand
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, F-49000, Angers, France
| | - Guillaume Chesneau
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, F-49000, Angers, France
| | - Aude Rochefort
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, F-49000, Angers, France
| | - Coralie Marais
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, F-49000, Angers, France
| | - Alain Sarniguet
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, F-49000, Angers, France
| | - Matthieu Barret
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, F-49000, Angers, France
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13
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Tamošiūnė I, Andriūnaitė E, Vinskienė J, Stanys V, Rugienius R, Baniulis D. Enduring Effect of Antibiotic Timentin Treatment on Tobacco In Vitro Shoot Growth and Microbiome Diversity. PLANTS (BASEL, SWITZERLAND) 2022; 11:832. [PMID: 35336713 PMCID: PMC8954828 DOI: 10.3390/plants11060832] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Plant in vitro cultures initiated from surface-sterilized explants often harbor complex microbial communities. Antibiotics are commonly used to decontaminate plant tissue culture or during genetic transformation; however, the effect of antibiotic treatment on the diversity of indigenous microbial populations and the consequences on the performance of tissue culture is not completely understood. Therefore, the aim of this study was to assess the effect of antibiotic treatment on the growth and stress level of tobacco (Nicotiana tabacum L.) shoots in vitro as well as the composition of the plant-associated microbiome. The study revealed that shoot cultivation on a medium supplemented with 250 mg L-1 timentin resulted in 29 ± 4% reduced biomass accumulation and a 1.2-1.6-fold higher level of oxidative stress injury compared to the control samples. Moreover, the growth properties of shoots were only partially restored after transfer to a medium without the antibiotic. Microbiome analysis of the shoot samples using multivariable region-based 16S rRNA gene sequencing revealed a diverse microbial community in the control tobacco shoots, including 59 bacterial families; however, it was largely dominated by Mycobacteriaceae. Antibiotic treatment resulted in a decline in microbial diversity (the number of families was reduced 4.5-fold) and increased domination by the Mycobacteriaceae family. These results imply that the diversity of the plant-associated microbiome might represent a significant factor contributing to the efficient propagation of in vitro tissue culture.
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14
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Moreira ZPM, Helgason BL, Germida JJ. Assembly and potential transmission of the lens culinaris seed microbiome. FEMS Microbiol Ecol 2021; 97:6484792. [PMID: 34958355 DOI: 10.1093/femsec/fiab166] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/22/2021] [Indexed: 11/12/2022] Open
Abstract
Soil is an important source of bacteria and fungi for the plant, but seeds can also provide microbial inocula through heritable or stochastic assembly. Seed-associated microbial communities can potentially interact with the host plant through multiple generations. Here, we assessed the impact of two different soil types on the seed microbiome assembly of seven lentil (Lens culinaris) genotypes under environmentally controlled conditions and examined the vertical transmission of bacterial communities from seed to seed across two generations. Bulk soil microbiomes and seed microbiomes were characterized using high-throughput amplicon sequencing of the bacterial 16S rRNA gene. Our results revealed that bacterial communities in the two soils differed significantly and that bacterial communities associated with seeds were significantly impacted by genotype (15%) in one of the soils. Co-occurrence of amplicon sequence variants (ASVs) between generations suggests members of the genera Cutibacterium, Methylobacterium, Sphingomonas, Streptococcus, and Tepidimonas are transmitted and preserved in lentil genotypes irrespective of the soil in which they were grown. Increasing our knowledge of how microbial communities carried by seeds are assembled, transmitted, and preserved offers a promising way for future breeding programs to consider microbial communities when selecting for more resilient and productive cultivars.
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Affiliation(s)
- Zayda P Morales Moreira
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Bobbi L Helgason
- Department of Soil Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - James J Germida
- Department of Soil Science, University of Saskatchewan, Saskatoon, SK, Canada
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15
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Thomas P, Sahu PK. Vertical Transmission of Diverse Cultivation-Recalcitrant Endophytic Bacteria Elucidated Using Watermelon Seed Embryos. Front Microbiol 2021; 12:635810. [PMID: 34867834 PMCID: PMC8634838 DOI: 10.3389/fmicb.2021.635810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 09/27/2021] [Indexed: 11/16/2022] Open
Abstract
Seed transmission of endophytic microorganisms is a growing research area in plant biology and microbiology. We employed cultivation versus cultivation-independent approaches on excised embryos from watermelon seeds (6-12 months in storage) and on embryo-derived in vitro seedlings (EIVS) to assess the vertical transmission of endophytic bacteria. Surface-disinfected watermelon seeds bore abundant residual bacteria in the testa and perisperm tissues, predominantly Bacillus spp. propounding the essentiality of excluding all non-embryonic tissues for vertical transmission studies. Tissue homogenates from re-disinfected seed embryos displayed no cultivable bacteria during the 1-week monitoring. Bright-field live microscopy revealed abundant bacteria in tissue homogenates and in embryo sections as intracellular motile particles. Confocal imaging on embryo sections after SYTO-9 staining and eubacterial fluorescent in situ hybridization (FISH) endorsed enormous bacterial colonization. Quantitative Insights Into Microbial Ecology (QIIME)-based 16S rRNA V3-V4 taxonomic profiling excluding the preponderant chloroplast and mitochondrial sequences revealed a high bacterial diversity in watermelon seed embryos mainly Firmicutes barring spore formers followed by Proteobacteria, Bacteroidetes, and Actinobacteria, and other minor phyla. Embryo-base (comprising the radicle plus plumule parts) and embryo-cotyledon parts differed in bacterial profiles with the abundance of Firmicutes in the former and Proteobacteria dominance in the latter. EIVS displayed a higher bacterial diversity over seed embryos indicating the activation from the dormant stage of more organisms in seedlings or their better amenability to DNA techniques. It also indicated embryo-to-seedling bacterial transmission, varying taxonomic abundances for seed embryos and seedlings, and differing phylogenic profiles for root, hypocotyl, and cotyledon/shoot-tip tissues. Investigations on different watermelon cultivars confirmed the embryo transmission of diverse cultivation recalcitrant endophytic bacteria. Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes formed the core phyla across different cultivars with 80-90% similarity at genus to phylum levels. Conversely, freshly harvested seeds displayed a dominance of Proteobacteria. The findings revealed that dicot seeds such as in different watermelon cultivars come packaged with abundant and diverse vertical and seedling-transmissible cultivation recalcitrant endophytic bacteria with significant implications for plant biology.
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Affiliation(s)
- Pious Thomas
- Thomas Biotech & Cytobacts Centre for Biosciences, Bengaluru, India
- Division of Biotechnology, ICAR-Indian Institute of Horticultural Research, Bengaluru, India
| | - Pramod Kumar Sahu
- ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
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16
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Chen X, Krug L, Yang M, Berg G, Cernava T. The Himalayan Onion (Allium wallichii Kunth) Harbors Unique Spatially Organized Bacterial Communities. MICROBIAL ECOLOGY 2021; 82:909-918. [PMID: 33723621 PMCID: PMC8551121 DOI: 10.1007/s00248-021-01728-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
Plant-associated microorganisms are known to contribute with various beneficial functions to the health and productivity of their hosts, yet the microbiome of most plants remains unexplored. This especially applies to wild relatives of cultivated plants, which might harbor beneficial microorganisms that were lost during intensive breeding. We studied bacterial communities of the Himalayan onion (Allium wallichii Kunth), a wild relative of onion native to mountains in East Asia. The bacterial community structure was assessed in different plant microhabitats (rhizosphere, endosphere, anthosphere) by sequencing of 16S rRNA gene fragment amplicons. Targeted bioinformatic analyses were implemented in order to identify unique features in each habitat and to map the overall community in the first representative of the Amaryllidaceae plant family. The highest bacterial diversity was found for bulk soil (Shannon index, H' 9.3) at the high-altitude sampling location. It was followed by the plant rhizosphere (H' 8.9) while communities colonizing flowers (H' 6.1) and the endosphere (H' 6.5 and 5.6) where less diverse. Interestingly, we observed a non-significant rhizosphere effect. Another specificity of the microbiome was its high evenness in taxonomic distribution, which was so far not observed in plant microbiomes. Pseudomonas was identified among additional 10 bacterial genera as a plant-specific signature. The first insights into the microbiome of a plant in the widespread Allium genus will facilitate upcoming comparisons with its domesticated relatives while additionally providing a detailed microbiome mapping of the plant's microhabitats to facilitate bioresource mining.
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Affiliation(s)
- Xiaoyulong Chen
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China
- College of Tobacco Science, Guizhou University, Guiyang, 550025, China
- Key Laboratory of Agricultural Microbiology, Guizhou University, Guiyang, 550025, China
- College of Science, Tibet University, Lhasa, 850012, China
| | - Lisa Krug
- Institute of Environmental Biotechnology, Graz University of Technology, 8010, Graz, Austria
| | - Maofa Yang
- College of Tobacco Science, Guizhou University, Guiyang, 550025, China
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, 8010, Graz, Austria
| | - Tomislav Cernava
- College of Tobacco Science, Guizhou University, Guiyang, 550025, China.
- Institute of Environmental Biotechnology, Graz University of Technology, 8010, Graz, Austria.
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17
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Bziuk N, Maccario L, Straube B, Wehner G, Sørensen SJ, Schikora A, Smalla K. The treasure inside barley seeds: microbial diversity and plant beneficial bacteria. ENVIRONMENTAL MICROBIOME 2021; 16:20. [PMID: 34711269 PMCID: PMC8554914 DOI: 10.1186/s40793-021-00389-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/04/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND Bacteria associated with plants can enhance the plants' growth and resistance against phytopathogens. Today, growers aim to reduce the use of mineral fertilizers and pesticides. Since phytopathogens cause severe yield losses in crop production systems, biological alternatives gain more attention. Plant and also seed endophytes have the potential to influence the plant, especially seed-borne bacteria may express their beneficiary impact at initial plant developmental stages. In the current study, we assessed the endophytic seed microbiome of seven genetically diverse barley accessions by 16S rRNA gene amplicon sequencing and verified the in vitro plant beneficial potential of isolated seed endophytes. Furthermore, we investigated the impact of the barley genotype and its seed microbiome on the rhizosphere microbiome at an early growth stage by 16S rRNA gene amplicon sequencing. RESULTS The plant genotype displayed a significant impact on the microbiota in both barley seed and rhizosphere. Consequently, the microbial alpha- and beta-diversity of the endophytic seed microbiome was highly influenced by the genotype. Interestingly, no correlation was observed between the endophytic seed microbiome and the single nucleotide polymorphisms of the seven genotypes. Unclassified members of Enterobacteriaceae were by far most dominant. Other abundant genera in the seed microbiome belonged to Curtobacterium, Paenibacillus, Pantoea, Sanguibacter and Saccharibacillus. Endophytes isolated from barley seeds were affiliated to dominant genera of the core seed microbiome, based on their 16S rRNA gene sequence. Most of these endophytic isolates produced in vitro plant beneficial secondary metabolites known to induce plant resistance. CONCLUSION Although barley accessions representing high genetic diversity displayed a genotype-dependent endophytic seed microbiome, a core seed microbiome with high relative abundances was identified. Endophytic isolates were affiliated to members of the core seed microbiome and many of them showed plant beneficial properties. We propose therefore that new breeding strategies should consider genotypes with high abundance of beneficial microbes.
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Affiliation(s)
- Nina Bziuk
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Lorrie Maccario
- Section of Microbiology, Copenhagen University, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Benjamin Straube
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Gwendolin Wehner
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Søren J. Sørensen
- Section of Microbiology, Copenhagen University, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Adam Schikora
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104 Braunschweig, Germany
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18
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Tarquinio F, Attlan O, Vanderklift MA, Berry O, Bissett A. Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds. Front Microbiol 2021; 12:703014. [PMID: 34621247 PMCID: PMC8491609 DOI: 10.3389/fmicb.2021.703014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Seagrasses are marine angiosperms that can live completely or partially submerged in water and perform a variety of significant ecosystem services. Like terrestrial angiosperms, seagrasses can reproduce sexually and, the pollinated female flower develop into fruits and seeds, which represent a critical stage in the life of plants. Seed microbiomes include endophytic microorganisms that in terrestrial plants can affect seed germination and seedling health through phytohormone production, enhanced nutrient availability and defence against pathogens. However, the characteristics and origins of the seagrass seed microbiomes is unknown. Here, we examined the endophytic bacterial community of six microenvironments (flowers, fruits, and seeds, together with leaves, roots, and rhizospheric sediment) of the seagrass Halophila ovalis collected from the Swan Estuary, in southwestern Australia. An amplicon sequencing approach (16S rRNA) was used to characterize the diversity and composition of H. ovalis bacterial microbiomes and identify core microbiome bacteria that were conserved across microenvironments. Distinct communities of bacteria were observed within specific seagrass microenvironments, including the reproductive tissues (flowers, fruits, and seeds). In particular, bacteria previously associated with plant growth promoting characteristics were mainly found within reproductive tissues. Seagrass seed-borne bacteria that exhibit growth promoting traits, the ability to fix nitrogen and anti-pathogenic potential activity, may play a pivotal role in seed survival, as is common for terrestrial plants. We present the endophytic community of the seagrass seeds as foundation for the identification of potential beneficial bacteria and their selection in order to improve seagrass restoration.
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Affiliation(s)
- Flavia Tarquinio
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia.,Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Océane Attlan
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia.,Sciences et Technologies, Université de la Réunion, Saint-Denis, France
| | - Mathew A Vanderklift
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Oliver Berry
- Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Hobart, TAS, Australia
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19
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Bergmann GE, Busby PE. The core seed mycobiome of Pseudotsuga menziesii var. menziesii across provenances of the Pacific Northwest, USA. Mycologia 2021; 113:1169-1180. [PMID: 34543153 DOI: 10.1080/00275514.2021.1952830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Fungal symbionts occur in all plant tissues, and many aid their host plants with critical functions, including nutrient acquisition, defense against pathogens, and tolerance of abiotic stress. "Core" taxa in the plant mycobiome, defined as fungi present across individuals, populations, or time, may be particularly crucial to plant survival during the challenging seedling stage. However, studies on core seed fungi are limited to individual sampling sites, raising the question of whether core taxa exist across large geographic scales. We addressed this question using both culture-based and culture-free techniques to identify the fungi found in individual seeds collected from nine provenances across the range of coastal Douglas-fir (Pseudotsuga menziesii var. menziesii), a foundation tree species in the Pacific Northwest and a globally important timber crop that is propagated commercially by seed. Two key findings emerged: (i) Seed mycobiome composition differed among seed provenances. (ii) Despite variation in the seed mycobiome, we detected four core members, none of which is a known pathogen of Douglas-fir: Trichoderma spp., Hormonema macrosporum, Mucor plumbeus, and Talaromyces rugulosus. Our results support the concept of a core seed microbiome, yet additional work is needed to determine the functional consequences of core taxa for seedling germination, growth, survival, and competition.
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Affiliation(s)
- Gillian E Bergmann
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331.,Bio-Protection Research Centre, Lincoln University, Lincoln, Canterbury, New Zealand
| | - Posy E Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
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20
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Zhang N, He J, Shen X, Sun C, Muhammad A, Shao Y. Contribution of sample processing to gut microbiome analysis in the model Lepidoptera, silkworm Bombyx mori. Comput Struct Biotechnol J 2021; 19:4658-4668. [PMID: 34504661 PMCID: PMC8390955 DOI: 10.1016/j.csbj.2021.08.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 11/23/2022] Open
Abstract
Microbes that live inside insects play various roles in host biology, ranging from nutrient supplementation to host defense. Although Lepidoptera (butterflies and moths) are one of the most diverse insect taxa and important in natural ecosystems, their microbiotas are little-studied, and to understand their structure and function, it is necessary to identify potential factors that affect microbiome analysis. Using a model organism, the silkworm Bombyx mori, we investigated the effects of different sample types (whole gut, gut content, gut tissue, starvation, or frass) and metagenomic DNA extraction methodologies (small-scale versus large-scale) on the composition and diversity of the caterpillar gut microbial communities. High-throughput 16S rRNA gene sequencing and computational analysis of the resulting data unraveled that DNA extraction has a large effect on the outcome of metagenomic analysis: significant biases were observed in estimates of community diversity and in the ratio between Gram-positive and Gram-negative bacteria. Furthermore, bacterial communities differed significantly among sample types. The gut content and whole gut samples differed least, both had a higher percentage of Enterococcus and Acinetobacter species; whereas the frass and starvation samples differed substantially from the whole gut and were poor representatives of the gut microbiome. Thus, we recommend a small-scale DNA extraction methodology for sampling the whole gut under normal insect rearing conditions whenever possible, as this approach provides the most accurate assessment of the gut microbiome. Our study highlights that evaluation of the optimal sample-processing approach should be the first step taken to confidently assess the contributions of microbiota to Lepidoptera.
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Affiliation(s)
- Nan Zhang
- Max Planck Partner Group, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Jintao He
- Max Planck Partner Group, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Xiaoqiang Shen
- Max Planck Partner Group, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Chao Sun
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Abrar Muhammad
- Max Planck Partner Group, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yongqi Shao
- Max Planck Partner Group, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory for Molecular Animal Nutrition, Ministry of Education, China
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21
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Andriūnaitė E, Tamošiūnė I, Aleksandravičiūtė M, Gelvonauskienė D, Vinskienė J, Rugienius R, Baniulis D. Stimulation of Nicotiana tabacum L. In Vitro Shoot Growth by Endophytic Bacillus cereus Group Bacteria. Microorganisms 2021; 9:1893. [PMID: 34576789 PMCID: PMC8470653 DOI: 10.3390/microorganisms9091893] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 11/16/2022] Open
Abstract
In vitro plant tissue cultures face various unfavorable conditions, such as mechanical damage, osmotic shock, and phytohormone imbalance, which can be detrimental to culture viability, growth efficiency, and genetic stability. Recent studies have revealed a presence of diverse endophytic bacteria, suggesting that engineering of the endophytic microbiome of in vitro plant tissues has the potential to improve their acclimatization and growth. Therefore, the aim of this study was to identify cultivated tobacco (Nicotiana tabacum L.) endophytic bacteria isolates that are capable of promoting the biomass accumulation of in vitro tobacco shoots. Forty-five endophytic bacteria isolates were obtained from greenhouse-grown tobacco plant leaves and were assigned to seven Bacillus spp. and one Pseudomonas sp. based on 16S rRNA or genome sequence data. To evaluate the bacterial effect on in vitro plant growth, tobacco shoots were inoculated with 22 isolates selected from distinct taxonomic groups. Four isolates of Bacillus cereus group species B. toyonensis, B. wiedmannii and B. mycoides promoted shoot growth by 11-21%. Furthermore, a contrasting effect on shoot growth was found among several isolates of the same species, suggesting the presence of strain-specific interaction with the plant host. Comparative analysis of genome assemblies was performed on the two closely related B. toyonensis isolates with contrasting plant growth-modulating properties. This revealed distinct structures of the genomic regions, including a putative enzyme cluster involved in the biosynthesis of linear azol(in)e-containing peptides and polysaccharides. However, the function of these clusters and their significance in plant-promoting activity remains elusive, and the observed contrasting effects on shoot growth are more likely to result from genomic sequence variations leading to differences in metabolic or gene expression activity. The Bacillus spp. isolates with shoot-growth-promoting properties have a potential application in improving the growth of plant tissue cultures in vitro.
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Affiliation(s)
| | | | | | | | | | | | - Danas Baniulis
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas str. 30, Babtai, 54333 Kaunas reg., Lithuania; (E.A.); (I.T.); (M.A.); (D.G.); (J.V.); (R.R.)
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22
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Chesneau G, Torres-Cortes G, Briand M, Darrasse A, Preveaux A, Marais C, Jacques MA, Shade A, Barret M. Temporal dynamics of bacterial communities during seed development and maturation. FEMS Microbiol Ecol 2021; 96:5910485. [PMID: 32966572 DOI: 10.1093/femsec/fiaa190] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 09/17/2020] [Indexed: 12/20/2022] Open
Abstract
Seed microbiota acts as a starting point for the assembly of the plant microbiota and contributes to successful plant establishment. To date, the order and timing of microbial taxa immigration during seed development and maturation remained unknown. We investigated the temporal dynamics of seed bacterial communities in bean and radish. A high phylogenetic turnover was observed for both plant species with few taxa associated with all seed developmental stages. Greater heterogeneity in communities structure within each stage was observed for radish. While, about one-third of radish seed bacterial taxa were detected in buds, flowers and fruits, very few taxa seem to be transmitted by the floral route in bean. In the latter species, bacterial populations belonging to the P. fluorescens species complex were found either in buds, flowers and fruits or in seeds. The relative phylogenetic proximity of these bacterial populations combined with their habitat specificity led us to explore the genetic determinants involved in successful seed transmission in bean. Comparative genomic analyses of representatives bacterial strains revealed dozens of coding sequences specifically associated with seed-transmitted strains. This study provided a first glimpse on processes involved in seed microbiota assembly, which could be used for designing plant-beneficial microbial consortia.
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Affiliation(s)
- Guillaume Chesneau
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Gloria Torres-Cortes
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Martial Briand
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Armelle Darrasse
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Anne Preveaux
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Coralie Marais
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Marie-Agnès Jacques
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Program in Ecology, Evolutionary Biology, and Behavior, The DOE Great Lakes Bioenergy Research Center, and The Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Matthieu Barret
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
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23
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Wang P, Kong X, Chen H, Xiao Y, Liu H, Li X, Zhang Z, Tan X, Wang D, Jin D, Deng Y, Cernava T. Exploration of Intrinsic Microbial Community Modulators in the Rice Endosphere Indicates a Key Role of Distinct Bacterial Taxa Across Different Cultivars. Front Microbiol 2021; 12:629852. [PMID: 33664718 PMCID: PMC7920960 DOI: 10.3389/fmicb.2021.629852] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/20/2021] [Indexed: 11/22/2022] Open
Abstract
Microbial communities associated with the plant phyllosphere and endosphere can have both beneficial as well as detrimental effects on their hosts. There is an ongoing debate to which extend the phyllosphere and endosphere microbiome assembly is controlled by the host plant how pronounced cultivar effects are. We investigated the bacterial and fungal communities from the phyllosphere and endosphere of 10 different rice cultivars grown under identical environmental conditions in the frame of a targeted approach to identify drivers of community assembly. The results indicated that the endophytic bacterial communities were clearly separated into two groups. The α-diversity and microbial network complexity within Group I were significantly lower than in Group II. Moreover, the genera Nocardioides, Microvirga, and Gaiella were significantly more abundant in Group II and only present in the interaction networks of this group. These three genera were significantly correlated with α- and β-diversity of the endophytic bacterial community and thus identified as major drivers of the endosphere community. We have identified keystone taxa that shape endophytic bacterial communities of different rice cultivars. Our overall findings provide new insights into plant-microbe interactions, and may contribute to targeted improvements of rice varieties in the future.
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Affiliation(s)
- Pei Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xiao Kong
- School of Public Health, Qingdao University, Qingdao, China
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Hongsong Chen
- Guangxi Key Laboratory for Biology of Crop Diseases and Insect Pests, Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Youlun Xiao
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Huijun Liu
- Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing University of Agriculture, Beijing, China
| | - Xiaojuan Li
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Zhuo Zhang
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xinqiu Tan
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Diandong Wang
- College of Life Science and Technology, Yangtze Normal University, Chongqing, China
| | - Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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24
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Abdelfattah A, Wisniewski M, Schena L, Tack AJM. Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root. Environ Microbiol 2021; 23:2199-2214. [PMID: 33427409 DOI: 10.1111/1462-2920.15392] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/26/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022]
Abstract
While the environment is considered the primary origin of the plant microbiome, the potential role of seeds as a source of transmitting microorganisms has not received much attention. Here we tested the hypothesis that the plant microbiome is partially inherited through vertical transmission. An experimental culturing device was constructed to grow oak seedlings in a microbe-free environment while keeping belowground and aboveground tissues separated. The microbial communities associated with the acorn's embryo and pericarp and the developing seeding's phyllosphere and root systems were analysed using amplicon sequencing of fungal ITS and bacterial 16S rDNA. Results showed that the seed microbiome is diverse and non-randomly distributed within an acorn. The microbial composition of the phyllosphere was diverse and strongly resembled the composition found in the embryo, whereas the roots and pericarp each had a less diverse and distinct microbial community. Our findings demonstrate a high level of microbial diversity and spatial partitioning of the fungal and bacterial community within both seed and seedling, indicating inheritance, niche differentiation and divergent transmission routes for the establishment of root and phyllosphere communities.
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Affiliation(s)
- Ahmed Abdelfattah
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Michael Wisniewski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Kearneysville, West Virginia, USA
| | - Leonardo Schena
- Dipartimento di Agraria, Università Mediterranea, Reggio Calabria, Italy.,Department of Biological Sciences, Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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25
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Chen X, Wicaksono WA, Berg G, Cernava T. Bacterial communities in the plant phyllosphere harbour distinct responders to a broad-spectrum pesticide. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:141799. [PMID: 32889475 DOI: 10.1016/j.scitotenv.2020.141799] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/29/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Pesticide application can be accompanied by harmful non-target effects that affect humans, animals, as well as whole ecosystems. However, such effects remain mainly unaddressed in connection with microorganisms, and especially bacteria therein, which are essential for ecosystem functioning and host health. We analysed bacterial communities by sequencing 16S rRNA gene fragment amplicons following spray application of a broad-spectrum fungicide based on the active ingredient N-(3,5-dichlorophenyl) succinimide on Nicotiana tabacum L. leaves. The plant's phyllosphere was predominantly colonized by Proteobacteria, with Alphaproteobacteria accounting for up to 33.8% of the indigenous bacterial community. Bioinformatic analyses indicated that pesticide applications had an effect on the core microbiome as well as the rare microbiome. Moreover, the interference of the pesticide with phyllosphere bacteria was found to be selective. We have identified four positive responders including an ASV assigned to the genus Acinetobacter and 12 negative responders mainly assigned to bacterial genera known for beneficial plant-microbe interactions, including Stenotrophomonas, Sphingomonas, Flavobacterium and Serratia. Complementary inference of bacterial functioning on community level indicated that microbes with distinct stress response systems were likely enriched in the conducted treatments. The overall findings confirmed that pesticide treatments can induce measureable shifts in non-target bacterial communities colonizing the plant phyllosphere. They also indicate that potentially beneficial bacteria, which are known for their intrinsic association with plants, are among the most sensitive responders to the employed fungicide and thus highlight the importance of off-target studies in the context of the plant microbiome.
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Affiliation(s)
- Xiaoyulong Chen
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, 550025 Guiyang, China; College of Tobacco Science, Guizhou University, 550025 Guiyang, China; Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, 550025 Guiyang, China
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria.
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria.
| | - Tomislav Cernava
- College of Tobacco Science, Guizhou University, 550025 Guiyang, China; Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, 550025 Guiyang, China; Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria.
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26
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Kusstatscher P, Adam E, Wicaksono WA, Bernhart M, Olimi E, Müller H, Berg G. Microbiome-Assisted Breeding to Understand Cultivar-Dependent Assembly in Cucurbita pepo. FRONTIERS IN PLANT SCIENCE 2021; 12:642027. [PMID: 33897731 PMCID: PMC8063107 DOI: 10.3389/fpls.2021.642027] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/08/2021] [Indexed: 05/14/2023]
Abstract
Recently, it was shown that long-term plant breeding does not only shape plant characteristics but also impacts plant-associated microbiota substantially. This requires a microbiome-integrative breeding approach, which was not yet shown. Here we investigate this for the Styrian oil pumpkin (Cucurbita pepo L. subsp. pepo var. styriaca Greb.) by analyzing the microbiome of six genotypes (the complete pedigree of a three-way cross-hybrid, consisting of three inbred lines and one open pollinating cultivar) in the seed and rhizosphere as well as the progeny seeds. Using high-throughput amplicon sequencing targeting the 16S rRNA and the ITS1 genes, the bacterial and fungal microbiomes were accessed. Seeds were found to generally carry a significantly lower microbial diversity compared to the rhizosphere and soil as well as a different microbial composition, with an especially high fraction of Enterobacteriaceae (40-83%). Additionally, potential plant-beneficial bacterial taxa, including Bacillaceae, Burkholderiaceae, and Pseudomonadaceae, were found to be enriched in progeny seeds. Between genotypes, more substantial changes can be observed for seed microbiomes compared to the rhizosphere. Moreover, rhizosphere communities were assembled for the most part from soil. Interestingly, bacterial signatures are mainly linked from seed to seed, while fungal communities are shaped by the soil and rhizosphere. Our findings provide a deep look into the rhizosphere and seed microbiome assembly of pumpkin-associated communities and represent the first steps into microbiome-driven breeding for plant-beneficial microbes.
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Affiliation(s)
- Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- *Correspondence: Peter Kusstatscher,
| | - Eveline Adam
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Saatzucht Gleisdorf GmbH, Gleisdorf, Austria
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Expedito Olimi
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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27
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Compant S, Cambon MC, Vacher C, Mitter B, Samad A, Sessitsch A. The plant endosphere world - bacterial life within plants. Environ Microbiol 2020; 23:1812-1829. [PMID: 32955144 DOI: 10.1111/1462-2920.15240] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/11/2020] [Accepted: 09/16/2020] [Indexed: 12/23/2022]
Abstract
The plant endosphere is colonized by complex microbial communities and microorganisms, which colonize the plant interior at least part of their lifetime and are termed endophytes. Their functions range from mutualism to pathogenicity. All plant organs and tissues are generally colonized by bacterial endophytes and their diversity and composition depend on the plant, the plant organ and its physiological conditions, the plant growth stage as well as on the environment. Plant-associated microorganisms, and in particular endophytes, have lately received high attention, because of the increasing awareness of the importance of host-associated microbiota for the functioning and performance of their host. Some endophyte functions are known from mostly lab assays, genome prediction and few metagenome analyses; however, we have limited understanding on in planta activities, particularly considering the diversity of micro-environments and the dynamics of conditions. In our review, we present recent findings on endosphere environments, their physiological conditions and endophyte colonization. Furthermore, we discuss microbial functions, the interaction between endophytes and plants as well as methodological limitations of endophyte research. We also provide an outlook on needs of future research to improve our understanding on the role of microbiota colonizing the endosphere on plant traits and ecosystem functioning.
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Affiliation(s)
- Stéphane Compant
- Center for Health and Bioresources, Bioresources Unit, Konrad Lorenz Straße 24, AIT Austrian Institute of Technology, Tulln, A-3430, Austria
| | | | | | - Birgit Mitter
- Center for Health and Bioresources, Bioresources Unit, Konrad Lorenz Straße 24, AIT Austrian Institute of Technology, Tulln, A-3430, Austria
| | - Abdul Samad
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, G1V4C7, Canada
| | - Angela Sessitsch
- Center for Health and Bioresources, Bioresources Unit, Konrad Lorenz Straße 24, AIT Austrian Institute of Technology, Tulln, A-3430, Austria
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28
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Dubey A, Malla MA, Kumar A, Dayanandan S, Khan ML. Plants endophytes: unveiling hidden agenda for bioprospecting toward sustainable agriculture. Crit Rev Biotechnol 2020; 40:1210-1231. [PMID: 32862700 DOI: 10.1080/07388551.2020.1808584] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Endophytic microbes are present in nearly all of the plant species known to date but how they enter and flourish inside a host plant and display multiple benefits like plant growth promotion (PGP), biodegradation, and stress alleviation are still unexplored. Until now, the majority of the research has been conducted assuming that the host-endophyte interaction is analogous to the PGP microbes, although, studies related to the mechanisms of their infection, colonization as well as conferring important traits to the plants are limited. It would be fascinating to explore the role of these endophytic microbes in host gene expression, metabolism, and the modulation of phenotypic traits, under abiotic and biotic stress conditions. In this review, we critically focused on the following areas: (i) endophytic lifestyle and the mechanism of their entry into plant tissues, (ii) how endophytes modulate the immune system of plants and affect the genotypic and phenotypic expression of host plants under abiotic and biotic stress condition, and (iii) the role of omics and other integrated genomic approaches in unraveling complex host-endophyte signaling crosstalk. Furthermore, we discussed their role in phytoremediation of heavy metal stress and whole genomic analysis based on an understanding of different metabolic pathways these endophytes utilize to combat stress.
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Affiliation(s)
- Anamika Dubey
- Department of Botany, Metagenomics and Secretomics Research Laboratory, Dr. Harisingh Gour University (A Central University), Sagar, India
| | - Muneer Ahmad Malla
- Department of Zoology, Dr. Harisingh Gour University (A Central University), Sagar, India
| | - Ashwani Kumar
- Department of Botany, Metagenomics and Secretomics Research Laboratory, Dr. Harisingh Gour University (A Central University), Sagar, India
| | - Selvadurai Dayanandan
- Department of Zoology, Dr. Harisingh Gour University (A Central University), Sagar, India.,Biology Department, Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Mohammad Latif Khan
- Department of Botany, Metagenomics and Secretomics Research Laboratory, Dr. Harisingh Gour University (A Central University), Sagar, India
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