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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Sessitsch A, Wakelin S, Schloter M, Maguin E, Cernava T, Champomier-Verges MC, Charles TC, Cotter PD, Ferrocino I, Kriaa A, Lebre P, Cowan D, Lange L, Kiran S, Markiewicz L, Meisner A, Olivares M, Sarand I, Schelkle B, Selvin J, Smidt H, van Overbeek L, Berg G, Cocolin L, Sanz Y, Fernandes WL, Liu SJ, Ryan M, Singh B, Kostic T. Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet. Microbiol Mol Biol Rev 2023; 87:e0021222. [PMID: 37367231 PMCID: PMC10521359 DOI: 10.1128/mmbr.00212-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial roles for the health of their hosts. Although we are starting to understand that microbiomes in different systems are interconnected, there is still a poor understanding of microbiome transfer and connectivity. In this review we show how microbiomes are connected within and transferred between different habitats and discuss the functional consequences of these connections. Microbiome transfer occurs between and within abiotic (e.g., air, soil, and water) and biotic environments, and can either be mediated through different vectors (e.g., insects or food) or direct interactions. Such transfer processes may also include the transmission of pathogens or antibiotic resistance genes. However, here, we highlight the fact that microbiome transmission can have positive effects on planetary and human health, where transmitted microorganisms potentially providing novel functions may be important for the adaptation of ecosystems.
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Affiliation(s)
| | | | | | - Emmanuelle Maguin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Tomislav Cernava
- University of Southampton, Faculty of Environmental and Life Sciences, Southampton, United Kingdom
| | | | | | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland and VistaMilk, Cork, Ireland
| | | | - Aicha Kriaa
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pedro Lebre
- University of Pretoria, Pretoria, South Africa
| | - Don Cowan
- University of Pretoria, Pretoria, South Africa
| | - Lene Lange
- LL-BioEconomy, Valby, Copenhagen, Denmark
| | | | - Lidia Markiewicz
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Department of Immunology and Food Microbiology, Olsztyn, Poland
| | - Annelein Meisner
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | - Marta Olivares
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Inga Sarand
- Tallinn University of Technology, Department of Chemistry and Biotechnology, Tallinn, Estonia
| | | | | | - Hauke Smidt
- Wageningen University and Research, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Leo van Overbeek
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | | | | | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | | | - S. J. Liu
- Chinese Academy of Sciences, Institute of Microbiology, Beijing, China
| | - Matthew Ryan
- Genetic Resources Collection, CABI, Egham, United Kingdom
| | - Brajesh Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Tanja Kostic
- AIT Austrian Institute of Technology GmbH, Tulln, Austria
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3
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Kumari M, Qureshi KA, Jaremko M, White J, Singh SK, Sharma VK, Singh KK, Santoyo G, Puopolo G, Kumar A. Deciphering the role of endophytic microbiome in postharvest diseases management of fruits: Opportunity areas in commercial up-scale production. Front Plant Sci 2022; 13:1026575. [PMID: 36466226 PMCID: PMC9716317 DOI: 10.3389/fpls.2022.1026575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
As endophytes are widely distributed in the plant's internal compartments and despite having enormous potential as a biocontrol agent against postharvest diseases of fruits, the fruit-endophyte-pathogen interactions have not been studied detail. Therefore, this review aims to briefly discuss the colonization patterns of endophytes and pathogens in the host tissue, the diversity and distribution patterns of endophytes in the carposphere of fruits, and host-endophyte-pathogen interactions and the molecular mechanism of the endophytic microbiome in postharvest disease management in fruits. Postharvest loss management is one of the major concerns of the current century. It is considered a critical challenge to food security for the rising global population. However, to manage the postharvest loss, still, a large population relies on chemical fungicides, which affect food quality and are hazardous to health and the surrounding environment. However, the scientific community has searched for alternatives for the last two decades. In this context, endophytic microorganisms have emerged as an economical, sustainable, and viable option to manage postharvest pathogens with integral colonization properties and eliciting a defense response against pathogens. This review extensively summarizes recent developments in endophytic interactions with harvested fruits and pathogens-the multiple biocontrol traits of endophytes and colonization and diversity patterns of endophytes. In addition, the upscale commercial production of endophytes for postharvest disease treatment is discussed.
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Affiliation(s)
- Madhuree Kumari
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Kamal A. Qureshi
- Department of Pharmaceutics, Unaizah College of Pharmacy, Qassim University, Unaizah, Saudi Arabia
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (R.S.R.C.), Division of Biological and Environmental Sciences and Engineering (B.E.S.E.), King Abdullah University of Science and Technology (K.A.U.S.T.), Thuwal, Saudi Arabia
| | - James White
- Department of Plant Biology, Rutgers University, The State University of New Jersey, New Brunswick, NJ, United States
| | - Sandeep Kumar Singh
- Division of Microbiology, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Vijay Kumar Sharma
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, India
| | | | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Gerardo Puopolo
- Center Agriculture Food Environment, University of Trento, Trentino, TN, Italy
| | - Ajay Kumar
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, India
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4
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Vaitiekūnaitė D, Bružaitė I, Snitka V. Endophytes from blueberry (Vaccinium sp.) fruit: Characterization of yeast and bacteria via label-free surface-enhanced Raman spectroscopy (SERS). Spectrochim Acta A Mol Biomol Spectrosc 2022; 275:121158. [PMID: 35334429 DOI: 10.1016/j.saa.2022.121158] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/06/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Blueberries (Vaccinium sp.) are consumed all around the globe, however, their endophytic community has not been thoroughly researched, specifically their fruit endophytes. We aimed to isolate and analyze easily cultivable blueberry fruit endophytes to help in future research, concerning probiotic microorganisms. Twelve strains were isolated in this pilot study, genetically homologous with Staphylococcus hominis, Staphylococcus cohnii, Salmonella enterica, Leuconostoc mesenteroides, and [Candida] santamariae. To determine the molecular composition of these isolates we used label-free surface-enhanced Raman spectroscopy (SERS). To our knowledge, this is the first time that SERS spectra for L. mesenteroides and C. santamariae are presented, as well as the first report of Candida yeast, isolated specifically from blueberry fruits. Our findings suggest that the differences in tested yeast and bacteria SERS spectra and subsequent differentiation are facilitated by minor shifts in spectral peak positions as well as their intensities. Moreover, we used principal component and discriminant function analyses to differentiate chemotypes within our isolate group, proving the sensitivity of the technique and its usefulness to recognize different strains in plant-associated microbe samples, which will aid to streamline future studies in biofertilizers and biocontrol agents.
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Affiliation(s)
- Dorotėja Vaitiekūnaitė
- Lithuanian Research Centre for Agriculture and Forestry, Laboratory of Forest Plant Biotechnology, Institute of Forestry, Liepu st. 1, LT-53101 Girionys, Lithuania.
| | - Ingrida Bružaitė
- Department of Chemistry and Bioengineering, Faculty of Fundamental Sciences, Vilnius Gediminas Technical University, Sauletekio av. 11, LT-10223 Vilnius, Lithuania.
| | - Valentinas Snitka
- Research Center for Microsystems and Nanotechnology, Kaunas University of Technology, Studentu str. 65, LT-51369 Kaunas, Lithuania.
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5
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Pereira AC, Tenreiro A, Cunha MV. When FLOW-FISH met FACS: Combining multiparametric, dynamic approaches for microbial single-cell research in the total environment. Sci Total Environ 2022; 806:150682. [PMID: 34600998 DOI: 10.1016/j.scitotenv.2021.150682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
In environmental microbiology, the ability to assess, in a high-throughput way, single-cells within microbial communities is key to understand their heterogeneity. Fluorescence in situ hybridization (FISH) uses fluorescently labeled oligonucleotide probes to detect, identify, and quantify single cells of specific taxonomic groups. The combination of Flow Cytometry (FLOW) with FISH (FLOW-FISH) enables high-throughput quantification of complex whole cell populations, which when associated with fluorescence-activated cell sorting (FACS) enables sorting of target microorganisms. These sorted cells may be investigated in many ways, for instance opening new avenues for cytomics at a single-cell scale. In this review, an overview of FISH and FLOW methodologies is provided, addressing conventional methods, signal amplification approaches, common fluorophores for cell physiology parameters evaluation, and model variation techniques as well. The coupling of FLOW-FISH-FACS is explored in the context of different downstream applications of sorted cells. Current and emerging applications in environmental microbiology to outline the interactions and processes of complex microbial communities within soil, water, animal microbiota, polymicrobial biofilms, and food samples, are described.
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Affiliation(s)
- André C Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Ana Tenreiro
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal.
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6
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Romero-Arguelles R, Romo-Sáenz CI, Morán-Santibáñez K, Tamez-Guerra P, Quintanilla-Licea R, Orozco-Flores AA, Ramírez-Villalobos JM, Tamez-Guerra R, Rodríguez-Padilla C, Gomez-Flores R. In Vitro Antitumor Activity of Endophytic and Rhizosphere Gram-Positive Bacteria from Ibervillea sonorae (S. Watson) Greene against L5178Y-R Lymphoma Cells. Int J Environ Res Public Health 2022; 19:894. [PMID: 35055716 DOI: 10.3390/ijerph19020894] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/31/2021] [Accepted: 01/12/2022] [Indexed: 12/17/2022]
Abstract
Plant-associated microorganisms represent a potential source of new antitumor compounds. The aim of the present study was to isolate endophytic and rhizosphere Gram-positive bacteria from Ibervillea sonorae and produce extracts with antitumor activity. Methanol and ethyl acetate extracts were obtained from 28 d bacterial fermentation, after which murine L5178Y-R lymphoma cells growth inhibition was evaluated at concentrations ranging from 15.62 µg/mL to 500 µg/mL by the 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide reduction colorimetric assay. IC50 and the selectivity index (SI) were calculated and compared with healthy control human peripheral blood mononuclear cells (PBMC). Identification of the isolated strains was performed using the 16S ribosomal gene and by MALDI-TOF MS mass spectrometry. The endophytic and rhizosphere bacterial extracts from strains ISE-B22, ISE-B26, ISE-B27, ISS-A01, ISS-A06, and ISS-A16 showed significant (p < 0.05) L5178Y-R cell growth inhibition, compared with an untreated control. The rhizosphere Micromonospora echinospora isolate ISS-A16 showed the highest (90.48%) percentage of lymphoma cells growth inhibition and SI (19.1) for PBMC, whereas the Bacillus subtilis ISE-B26 isolate caused significant (p < 0.01) growth inhibition (84.32%) and a SI of 5.2. Taken together, results of the present study evidenced antitumor effects by I. sonorae endophytic and rhizosphere bacteria culture extracts. Further research will involve the elucidation of the compounds that exert the antitumor activity and their evaluation in pre-clinical studies.
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7
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Franco-Frías E, Mercado-Guajardo V, Merino-Mascorro A, Pérez-Garza J, Heredia N, León JS, Jaykus LA, Dávila-Aviña J, García S. Analysis of Bacterial Communities by 16S rRNA Gene Sequencing in a Melon-Producing Agro-environment. Microb Ecol 2021; 82:613-622. [PMID: 33570667 DOI: 10.1007/s00248-021-01709-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Cantaloupe melons, which have been responsible of an increasing number of foodborne disease outbreaks, may become contaminated with microbial pathogens during production. However, little information is available on the microbial populations in the cantaloupe farm environment. The purpose of this work was to characterize the bacterial communities present on cantaloupe farms. Fruit, soil, and harvester hand rinsates were collected from two Mexican cantaloupe farms, each visited three times. Microbiome analysis was performed by sequencing 16sRNA and analyzed using qiime2 software. Correlations were determined between sample type and microbial populations. The α and β diversity analysis identified 2777 sequences across all samples. The soil samples had the highest number and diversity of unique species (from 130 to 1329 OTUs); cantaloupe (from 112 to 205 OTUs), and hands (from 67 to 151 OTUs) had similar diversity. Collectively, Proteobacteria was the most abundant phyla (from 42 to 95%), followed by Firmicutes (1-47%), Actinobacteria (< 1 to 23%), and Bacteroidetes (< 1 to 4.8%). The most abundant genera were Acinetobacter (20-58%), Pseudomonas (14.5%), Erwinia (13%), and Exiguobacterium (6.3%). Genera with potential to be pathogenic included Bacillus (4%), Salmonella (0.85%), Escherichia-Shigella (0.38%), Staphylococcus (0.32%), Listeria (0.29%), Clostridium (0.28%), and Cronobacter (0.27%), which were found at lower frequencies. This study provides information on the cantaloupe production microbiome, which can inform future research into critical food safety issues such as antimicrobial resistance, virulence, and genomic epidemiology.
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Affiliation(s)
- Eduardo Franco-Frías
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Victor Mercado-Guajardo
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Angel Merino-Mascorro
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Janeth Pérez-Garza
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Norma Heredia
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Juan S León
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Lee-Ann Jaykus
- Department of Food Science, North Carolina State University, Raleigh, NC, USA
| | - Jorge Dávila-Aviña
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Santos García
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México.
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8
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Nguyen MP, Lehosmaa K, Martz F, Koskimäki JJ, Pirttilä AM, Häggman H. Host species shape the community structure of culturable endophytes in fruits of wild berry species (Vaccinium myrtillus L., Empetrum nigrum L. and Vaccinium vitis-idaea L.). FEMS Microbiol Ecol 2021; 97:6319499. [PMID: 34251452 PMCID: PMC8292141 DOI: 10.1093/femsec/fiab097] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/08/2021] [Indexed: 11/12/2022] Open
Abstract
Wild berries are interesting research subjects due to their rich sources of health-beneficial phenolic compounds. However, the internal microbial communities, endophytes, associated with the wild berry fruits are currently unknown. Endophytes are bacteria or fungi inhabiting inside plant tissues, and their functions vary depending on the host species and environmental parameters. The present study aimed to examine community composition of fungal and bacterial endophytes in fruits of three wild berry species (bilberry Vaccinium myrtillus L., lingonberry Vaccinium vitis-idaea L. and crowberry Empetrum nigrum L.) and the effects of host plant species and their growth sites on shaping the endophytic communities. We found that the endophytic community structures differed between the berry species, and fungi were predominant over bacteria in the total endophytic taxa. We identified previously unknown endophytic fungal taxa including Angustimassarina, Dothidea, Fellozyma, Pseudohyphozyma, Hannaella coprosmae and Oberwinklerozyma straminea. A role of soluble phenolic compounds, the intracellular components in wild berry fruits, in shaping the endophytic communities is proposed. Overall, our study demonstrates that each berry species harbors a unique endophytic community of microbes.
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Affiliation(s)
- Minh-Phuong Nguyen
- Ecology and Genetics Research Unit, University of Oulu, FI-90014, P.O. Box 3000, Oulu, Finland
| | - Kaisa Lehosmaa
- Ecology and Genetics Research Unit, University of Oulu, FI-90014, P.O. Box 3000, Oulu, Finland
| | - Françoise Martz
- Natural Resources Institute Finland, Production Systems, Ounasjoentie 6, FI-96200, Rovaniemi, Finland
| | - Janne J Koskimäki
- Ecology and Genetics Research Unit, University of Oulu, FI-90014, P.O. Box 3000, Oulu, Finland
| | - Anna Maria Pirttilä
- Ecology and Genetics Research Unit, University of Oulu, FI-90014, P.O. Box 3000, Oulu, Finland
| | - Hely Häggman
- Ecology and Genetics Research Unit, University of Oulu, FI-90014, P.O. Box 3000, Oulu, Finland
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9
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Zhang H, Serwah Boateng NA, Ngolong Ngea GL, Shi Y, Lin H, Yang Q, Wang K, Zhang X, Zhao L, Droby S. Unravelling the fruit microbiome: The key for developing effective biological control strategies for postharvest diseases. Compr Rev Food Sci Food Saf 2021; 20:4906-4930. [PMID: 34190408 DOI: 10.1111/1541-4337.12783] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 12/15/2022]
Abstract
Fruit-based diets are recognized for their benefits to human health. The safety of fruit is a global concern for scientists. Fruit microbiome represents the whole microorganisms that are associated with a fruit. These microbes are either found on the surfaces (epiphytes) or in the tissues of the fruit (endophytes). The recent knowledge gained from these microbial communities is considered relevant to the field of biological control in prevention of postharvest fruit pathology. In this study, the importance of the microbiome of certain fruits and how it holds promise for solving the problems inherent in biocontrol and postharvest crop protection are summarized. Research needs on the fruit microbiome are highlighted. Data from DNA sequencing and "meta-omics" technologies very recently applied to the study of microbial communities of fruits in the postharvest context are also discussed. Various fruit parameters, management practices, and environmental conditions are the main determinants of the microbiome. Microbial communities can be classified according to their structure and function in fruit tissues. A critical mechanism of microbial biological control agents is to reshape and interact with the microbiome of the fruit. The ability to control the microbiome of any fruit is a great potential in postharvest management of fruits. Research on the fruit microbiome offers important opportunities to develop postharvest biocontrol strategies and products, as well as the health profile of the fruit.
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Affiliation(s)
- Hongyin Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | | | - Guillaume Legrand Ngolong Ngea
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China.,Institute of Fisheries Sciences, University of Douala, Douala, Cameroon
| | - Yu Shi
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Hetong Lin
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiya Yang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Kaili Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Xiaoyun Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Lina Zhao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Samir Droby
- Department of Postharvest Science, ARO, the Volcani Center, Rishon LeZion, Israel
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10
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Lei F, Liu X, Huang H, Fu S, Zou K, Zhang S, Zhou L, Zeng J, Liu H, Jiang L, Miao B, Liang Y. The Macleaya cordata Symbiont: Revealing the Effects of Plant Niches and Alkaloids on the Bacterial Community. Front Microbiol 2021; 12:681210. [PMID: 34177865 PMCID: PMC8219869 DOI: 10.3389/fmicb.2021.681210] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/07/2021] [Indexed: 11/13/2022] Open
Abstract
Endophytes are highly associated with plant growth and health. Exploring the variation of bacterial communities in different plant niches is essential for understanding microbe-plant interactions. In this study, high-throughput gene sequencing was used to analyze the composition and abundance of bacteria from the rhizospheric soil and different parts of the Macleaya cordata. The results indicated that the bacterial community structure varied widely among compartments. Bacterial diversity was observed to be the highest in the rhizospheric soil and the lowest in fruits. Proteobacteria, Actinobacteria, and Bacteroidetes were found as the dominant phyla. The genera Sphingomonas (∼47.77%) and Methylobacterium (∼45.25%) dominated in fruits and leaves, respectively. High-performance liquid chromatography (HPLC) was employed to measure the alkaloid content of different plant parts. Significant correlations were observed between endophytic bacteria and alkaloids. Especially, Sphingomonas showed a significant positive correlation with sanguinarine and chelerythrine. All four alkaloids were negatively correlated with the microbiota of stems. The predicted result of PICRUST2 revealed that the synthesis of plant alkaloids might lead to a higher abundance of endophytic microorganisms with genes related to alkaloid synthesis, further demonstrated the correlation between bacterial communities and alkaloids. This study provided the first insight into the bacterial community composition in different parts of Macleaya cordata and the correlation between the endophytic bacteria and alkaloids.
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Affiliation(s)
- Fangying Lei
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Haonan Huang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Shaodong Fu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Kai Zou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Shuangfei Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Li Zhou
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Jianguo Zeng
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Hongwei Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Luhua Jiang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Bo Miao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
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11
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Fort T, Pauvert C, Zanne AE, Ovaskainen O, Caignard T, Barret M, Compant S, Hampe A, Delzon S, Vacher C. Maternal effects shape the seed mycobiome in Quercus petraea. New Phytol 2021; 230:1594-1608. [PMID: 33341934 DOI: 10.1111/nph.17153] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
The tree seed mycobiome has received little attention despite its potential role in forest regeneration and health. The aim of the present study was to analyze the processes shaping the composition of seed fungal communities in natural forests as seeds transition from the mother plant to the ground for establishment. We used metabarcoding approaches and confocal microscopy to analyze the fungal communities of seeds collected in the canopy and on the ground in four natural populations of sessile oak (Quercus petraea). Ecological processes shaping the seed mycobiome were inferred using joint species distribution models. Fungi were present in seed internal tissues, including the embryo. The seed mycobiome differed among oak populations and trees within the same population. Its composition was largely influenced by the mother, with weak significant environmental influences. The models also revealed several probable interactions among fungal pathogens and mycoparasites. Our results demonstrate that maternal effects, environmental filtering and biotic interactions all shape the seed mycobiome of sessile oak. They provide a starting point for future research aimed at understanding how maternal genes and environments interact to control the vertical transmission of fungal species that could then influence seed dispersal and germination, and seedling recruitment.
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Affiliation(s)
- Tania Fort
- INRAE, BIOGECO, Univ. Bordeaux, Pessac, 33615, France
| | | | - Amy E Zanne
- Department of Biological Sciences, George Washington University, 800 22nd St., Washington, DC, 20052, USA
| | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, PO Box 65, Helsinki, 00014, Finland
- Center for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, 7491, Norway
| | | | - Matthieu Barret
- INRAE, IRHS, SFR 4207 QuaSaV, Institut Agro, Univ. Angers, Angers, 49000, France
| | - Stéphane Compant
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, Tulln, 3430, Austria
| | - Arndt Hampe
- INRAE, BIOGECO, Univ. Bordeaux, Pessac, 33615, France
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12
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Kumar A, Zhimo Y, Biasi A, Salim S, Feygenberg O, Wisniewski M, Droby S. Endophytic Microbiome in the Carposphere and Its Importance in Fruit Physiology and Pathology. Postharvest Pathology 2021. [DOI: 10.1007/978-3-030-56530-5_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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13
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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: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Thomas P, Shaik SP. Molecular Profiling on Surface-Disinfected Tomato Seeds Reveals High Diversity of Cultivation-Recalcitrant Endophytic Bacteria with Low Shares of Spore-Forming Firmicutes. Microb Ecol 2020; 79:910-924. [PMID: 31720799 DOI: 10.1007/s00248-019-01440-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
Seeds are known to harbor diverse microorganisms offering protective effects on them with the prospects of quick root colonization at germination, selective recruitment as endophytes, and possible vertical transmission. The study was undertaken to assess the gross seed-internal bacterial community in tomato and to confirm if spore-forming Firmicutes constituted major seed endophytes adopting cultivation versus molecular approach on surface-sterilized seeds. Testing the initial seed wash solutions of "Arka Vikas" and "Arka Abha" cultivars showed > 1000 bacterial cfu per dry seed, largely Bacillus spp. Tissue homogenates from surface-disinfected seeds did not show any cultivable bacteria on enriched media for 1-2 weeks, while 16S rRNA V3-V4 taxonomic profiling revealed a huge bacterial diversity (10-16 phyla per cultivar). Proteobacteria formed the dominant phylum (65.7-69.6% OTUs) followed by Firmicutes, Actinobacteria, Bacteroidetes, and a notable share of Euryarchaeota (1.1-3.1%). Five more phyla appeared common to both cultivars in minor shares (Acidobacteria, Planctomycetes, Chloroflexi, Spirochaetes, Verrucomicrobia) with the ten phyla together constituting 99.6-99.9% OTUs. Class level and family level, the cultivars displayed elevated bacterial diversity, but similar taxonomic profiles. Arka Vikas and Arka Abha showed 114 and 107 genera, respectively, with 63 common genera constituting 96-97% OTUs. Psychrobacter formed the dominant genus. Bacillus and related genera constituted only negligible OTU share (0.16-0.28%). KEGG functional analysis showed metabolism as the major bacterial community role. One-month-old in vitro seedlings showed the activation of some originally uncultivable bacteria uninfluenced by the OTU share. The study reveals a high diversity of cultivation-recalcitrant endophytic bacteria prevailing in tomato seeds with possible vertical transmission and significant roles in plant biology.
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Affiliation(s)
- Pious Thomas
- Division of Biotechnology, Endophytic and Molecular Microbiology Laboratory, ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake, Bengaluru, 560 089, India.
- Thomas Biotech & Cytobacts Centre for Biosciences, 318 Thalakavery Layout, Amruthahalli, Bengaluru, 560092, India.
| | - Sadiq Pasha Shaik
- Department of Biotechnology, Centre for Post-Graduate Studies, Jain University, Bengaluru, 560011, India
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15
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Sare AR, Stouvenakers G, Eck M, Lampens A, Goormachtig S, Jijakli MH, Massart S. Standardization of Plant Microbiome Studies: Which Proportion of the Microbiota is Really Harvested? Microorganisms 2020; 8:microorganisms8030342. [PMID: 32121205 PMCID: PMC7142977 DOI: 10.3390/microorganisms8030342] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/14/2020] [Accepted: 02/25/2020] [Indexed: 12/13/2022] Open
Abstract
Studies in plant-microbiome currently use diverse protocols, making their comparison difficult and biased. Research in human microbiome have faced similar challenges, but the scientific community proposed various recommendations which could also be applied to phytobiome studies. Here, we addressed the isolation of plant microbiota through apple carposphere and lettuce root microbiome. We demonstrated that the fraction of the culturable epiphytic microbiota harvested by a single wash might only represent one-third of the residing microbiota harvested after four successive washes. In addition, we observed important variability between the efficiency of washing protocols (up to 1.6-fold difference for apple and 1.9 for lettuce). QIIME2 analysis of 16S rRNA gene, showed a significant difference of the alpha and beta diversity between protocols in both cases. The abundance of 76 taxa was significantly different between protocols used for apple. In both cases, differences between protocols disappeared when sequences of the four washes were pooled. Hence, pooling the four successive washes increased the alpha diversity for apple in comparison to a single wash. These results underline the interest of repeated washing to leverage abundance of microbial cells harvested from plant epiphytic microbiota whatever the washing protocols, thus minimizing bias.
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Affiliation(s)
- Abdoul Razack Sare
- Laboratory of Integrated and Urban Phytopathology, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (G.S.); (M.E.); (M.H.J.); (S.M.)
- Correspondence:
| | - Gilles Stouvenakers
- Laboratory of Integrated and Urban Phytopathology, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (G.S.); (M.E.); (M.H.J.); (S.M.)
| | - Mathilde Eck
- Laboratory of Integrated and Urban Phytopathology, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (G.S.); (M.E.); (M.H.J.); (S.M.)
| | - Amber Lampens
- VIB-UGent Center of Plant Systems Biology, 9052 Ghent, Belgium; (A.L.); (S.G.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Sofie Goormachtig
- VIB-UGent Center of Plant Systems Biology, 9052 Ghent, Belgium; (A.L.); (S.G.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - M. Haïssam Jijakli
- Laboratory of Integrated and Urban Phytopathology, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (G.S.); (M.E.); (M.H.J.); (S.M.)
| | - Sebastien Massart
- Laboratory of Integrated and Urban Phytopathology, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (G.S.); (M.E.); (M.H.J.); (S.M.)
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16
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Mosquito S, Bertani I, Licastro D, Compant S, Myers MP, Hinarejos E, Levy A, Venturi V. In Planta Colonization and Role of T6SS in Two Rice Kosakonia Endophytes. Mol Plant Microbe Interact 2020; 33:349-363. [PMID: 31609645 DOI: 10.1094/mpmi-09-19-0256-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Endophytes live inside plants and are often beneficial. Kosakonia is a novel bacterial genus that includes many diazotrophic plant-associated isolates. Plant-bacteria studies on two rice endophytic Kosakonia beneficial strains were performed, including comparative genomics, secretome profiling, in planta tests, and a field release trial. The strains are efficient rhizoplane and root endosphere colonizers and localized in the root cortex. Secretomics revealed 144 putative secreted proteins, including type VI secretory system (T6SS) proteins. A Kosakonia T6SS genomic knock-out mutant showed a significant decrease in rhizoplane and endosphere colonization ability. A field trial using rice seed inoculated with Kosakonia spp. showed no effect on plant growth promotion upon nitrogen stress and microbiome studies revealed that Kosakonia spp. were significantly more present in the inoculated rice. Comparative genomics indicated that several protein domains were enriched in plant-associated Kosakonia spp. This study highlights that Kosakonia is an important, recently classified genus involved in plant-bacteria interaction.
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Affiliation(s)
- Susan Mosquito
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| | - Iris Bertani
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| | - Danilo Licastro
- CBM S.c.r.l., Area Science Park-Basovizza, 34149 Trieste, Italy
| | - Stéphane Compant
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, 3430 Tulln, Vienna, Austria
| | - Michael P Myers
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| | | | - Asaf Levy
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Vittorio Venturi
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
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17
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Buchholz F, Antonielli L, Kostić T, Sessitsch A, Mitter B. The bacterial community in potato is recruited from soil and partly inherited across generations. PLoS One 2019; 14:e0223691. [PMID: 31703062 PMCID: PMC6839881 DOI: 10.1371/journal.pone.0223691] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/25/2019] [Indexed: 01/18/2023] Open
Abstract
Strong efforts have been made to understand the bacterial communities in potato plants and the rhizosphere. Research has focused on the effect of the environment and plant genotype on bacterial community structures and dynamics, while little is known about the origin and assembly of the bacterial community, especially in potato tubers. The tuber microbiota, however, may be of special interest as it could play an important role in crop quality, such as storage stability. Here, we used 16S rRNA gene amplicon sequencing to study the bacterial communities that colonize tubers of different potato cultivars commonly used in Austrian potato production over three generations and grown in different soils. Statistical analysis of sequencing data showed that the bacterial community of potato tubers has changed over generations and has become more similar to the soil bacterial community, while the impact of the potato cultivar on the bacterial assemblage has lost significance over time. The communities in different tuber parts did not differ significantly, while the soil bacterial community showed significant differences to the tuber microbiota composition. Additionally, the presence of OTUs in subsequent tuber generation points to vertical transmission of a subset of the tuber microbiota. Four OTUs were common to all tuber generations and all potato varieties. In summary, we conclude that the microbiota of potato tubers is recruited from the soil largely independent from the plant variety. Furthermore, the bacterial assemblage in potato tubers consists of bacteria transmitted from one tuber generation to the next and bacteria recruited from the soil.
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Affiliation(s)
- Franziska Buchholz
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Livio Antonielli
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Tanja Kostić
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Angela Sessitsch
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Birgit Mitter
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln, Austria
- * E-mail:
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18
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Abstract
Allium species are popular vegetables in China and possess antifungal and antibacterial activities. This study aimed to compare the endophytic bacterial community in the four crucial Allium species in China, Chinese leek (CL), garlic (GA), onion (ON,) and Welsh onion (WO), using sequences of the V3–V4 region of the bacterial 16S rRNA gene. A total of 1,036,637 high-quality sequences and 719 operational taxonomic units (OTUs) were obtained across all libraries. A total of 20 phyla, 50 classes, 80 orders, 134 families, and 234 genera were identified. Among them, 18 OTUs and 19 genera were shared among the four Allium species. Proteobacteria (42.68%) and Bacteroidetes (20.18%) were the dominant phyla in CL, while one unclassified (>70%) was the dominant phyla in the other three Allium species. The alpha-diversity analysis showed the bacterial richness and diversity in CL were significantly higher than those in the other three Allium species. Principal coordinate analysis (PCA) showed endophytic bacterial communities in GA, WO, and ON were more similar than those in CL. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis revealed endophytic bacteria mostly enriched in Membrane Transport, Amino Acid Metabolism and Carbohydrate Metabolism pathway. 17 of the 23 Kyoto Encyclopedia of Genes and Genomes (KEGG) categories and 159 of the 206 lower-level KEGG pathways in CL were significantly higher than those in the other three Allium species. Pearson’s correlation indicated that KEGG pathways with significant differences among the Allium species were closely related to the bacterial genera with significant differences between the Allium species. The findings of our study provided insight into the complex endophytic microbial communities in Allium species.
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Fidan O, Zhan J. Discovery and engineering of an endophytic Pseudomonas strain from Taxus chinensis for efficient production of zeaxanthin diglucoside. J Biol Eng 2019; 13:66. [PMID: 31388354 PMCID: PMC6676639 DOI: 10.1186/s13036-019-0196-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 07/24/2019] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Endophytic microorganisms are a rich source of bioactive natural products. They are considered as promising biofertilizers and biocontrol agents due to their growth-promoting interactions with the host plants and their bioactive secondary metabolites that can help manage plant pathogens. Identification of new endophytes may lead to the discovery of novel molecules or provide new strains for production of valuable compounds. RESULTS In this study, we isolated an endophytic bacterium from the leaves of Taxus chinensis, which was identified as Pseudomonas sp. 102515 based on the 16S rRNA gene sequence and physiological characteristics. Analysis of its secondary metabolites revealed that this endophytic strain produces a major product zeaxanthin diglucoside, a promising antioxidant natural product that belongs to the family of carotenoids. A carotenoid (Pscrt) biosynthetic gene cluster was amplified from this strain, and the functions of PsCrtI and PsCrtY in the biosynthesis of zeaxanthin diglucoside were characterized in Escherichia coli BL21(DE3). The entire Pscrt biosynthetic gene cluster was successfully reconstituted in E. coli BL21(DE3) and Pseudomonas putida KT2440. The production of zeaxanthin diglucoside in Pseudomonas sp. 102515 was improved through the optimization of fermentation conditions such as medium, cultivation temperature and culture time. The highest yield under the optimized conditions reached 206 mg/L. The engineered strain of P. putida KT2440 produced zeaxanthin diglucoside at 121 mg/L in SOC medium supplemented with 0.5% glycerol at 18 °C, while the yield of zeaxanthin diglucoside in E. coli BL21(DE3) was only 2 mg/L. To further enhance the production, we introduced an expression plasmid harboring the Pscrt biosynthetic gene cluster into Pseudomonas sp. 102515. The yield in this engineered strain reached 380 mg/L, 85% higher than the wild type. Through PCR, we also discovered the presence of a turnerbactin biosynthetic gene cluster in Pseudomonas sp. 102515. Because turnerbactin is involved in nitrogen fixation, this endophytic strain might have a role in promoting growth of the host plant. CONCLUSIONS We isolated and identified an endophytic strain of Pseudomonas from T. chinensis. A zeaxanthin diglucoside biosynthetic gene cluster was discovered and characterized in this bacterium. Through fermentation and genetic engineering, the engineered strain produced zeaxanthin diglucoside at 380 ± 12 mg/L, representing a promising strain for the production of this antioxidant natural product. Additionally, Pseudomonas sp. 102515 might also be utilized as a plant-promoting strain for agricultural applications.
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Affiliation(s)
- Ozkan Fidan
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322-4105 USA
| | - Jixun Zhan
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322-4105 USA
- TCM and Ethnomedicine Innovation & Development Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan China
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20
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Singh K, Dwivedi GR, Sanket AS, Pati S. Therapeutic Potential of Endophytic Compounds: A Special Reference to Drug Transporter Inhibitors. Curr Top Med Chem 2019; 19:754-783. [DOI: 10.2174/1568026619666190412095105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/08/2019] [Accepted: 03/09/2019] [Indexed: 12/11/2022]
Abstract
From the discovery to the golden age of antibiotics (miracle), millions of lives have been saved. The era of negligence towards chemotherapeutic agents gave birth to drug resistance. Among all the regulators of drug resistance, drug transporters are considered to be the key regulators for multidrug resistance. These transporters are prevalent from prokaryotes to eukaryotes. Endophytes are one of the unexplored wealths of nature. Endophytes are a model mutualistic partner of plants. They are the reservoir of novel therapeutics. The present review deals with endophytes as novel drug resistance reversal agents by inhibiting the drug transporters across the genera. This review also focuses on drug transporters, and mutualistic chemical diversity, exploring drug transporter modulating potential of endophytes.
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Affiliation(s)
- Khusbu Singh
- Microbiology Department, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Gaurav Raj Dwivedi
- Microbiology Department, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - A. Swaroop Sanket
- Microbiology Department, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Sanghamitra Pati
- Microbiology Department, ICMR-Regional Medical Research Centre, Bhubaneswar, India
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21
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Abstract
The role of the plant microbiota in plant establishment, growth and health is well studied, but the dynamics of postharvest crop microbiota and its role in postharvest crop quality are largely unexplored, although food loss is an enormous issue worldwide. The microbiota might be especially important during crop storage by either preventing or favouring rots, or quality loss due to, for example, sprouting, saccharification, water loss or spoilage. We need more research on plant-microbe interactions in postharvest crops to be in future able to provide microbial solutions for plant production along the whole food chain from field to fork.
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Affiliation(s)
- Franziska Buchholz
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources, Konrad-Lorenz-Strasse 24, A-3430, Tulln, Austria
| | - Tanja Kostić
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources, Konrad-Lorenz-Strasse 24, A-3430, Tulln, Austria
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources, Konrad-Lorenz-Strasse 24, A-3430, Tulln, Austria
| | - Birgit Mitter
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources, Konrad-Lorenz-Strasse 24, A-3430, Tulln, Austria
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22
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Esteban-Cuesta I, Drees N, Ulrich S, Stauch P, Sperner B, Schwaiger K, Gareis M, Gottschalk C. Endogenous microbial contamination of melons (Cucumis melo) from international trade: an underestimated risk for the consumer? J Sci Food Agric 2018; 98:5074-5081. [PMID: 29604072 DOI: 10.1002/jsfa.9045] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/26/2018] [Accepted: 03/27/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Fruits and vegetables have increasingly been related to foodborne outbreaks. Besides surface contamination, a possible internalization of microorganisms into edible parts of plants during growth has already been observed. To examine an actual risk for the consumer, microbial contamination of the rind and pulp of 147 muskmelons from international trade was assessed using cultural and biochemical methods, polymerase chain reaction and matrix-assisted laser desorption/ionization-time of flight mass spectrometry. RESULTS One hundred percent of the rind samples [3.69-8.92 log colony forming units (CFU) g-1 ] and 89.8% of the pulp samples (maximum load 3.66 log CFU g-1 ) were microbiologically contaminated. Among the 432 pulp isolates, opportunistic and potentially pathogenic bacteria were identified, mainly Staphylococcus spp. (48.9%), Clostridium spp. (42.9%) and Enterobacteriaceae (27.9%). Salmonella spp., Escherichia coli and isolates of the Bacillus cereus group were found on the rind (1.4%, 0.7% and 42.9%, respectively) and in the pulp (0.7%, 1.4% and 4.7%). Clostridium perfringens was isolated from the rind of seven melons. CONCLUSION The present study revealed a regularly occurring internal contamination of melons. Possible health risks for consumers because of an occurrence of microorganisms in melon pulp should be considered in future food safety assessments. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Irene Esteban-Cuesta
- Food Safety, Veterinary Faculty, Ludwig-Maximilians-University Munich, Oberschleissheim, Germany
| | - Nathalie Drees
- Food Safety, Veterinary Faculty, Ludwig-Maximilians-University Munich, Oberschleissheim, Germany
| | - Sebastian Ulrich
- Food Safety, Veterinary Faculty, Ludwig-Maximilians-University Munich, Oberschleissheim, Germany
| | | | - Brigitte Sperner
- Food Safety, Veterinary Faculty, Ludwig-Maximilians-University Munich, Oberschleissheim, Germany
| | - Karin Schwaiger
- Food Safety, Veterinary Faculty, Ludwig-Maximilians-University Munich, Oberschleissheim, Germany
| | - Manfred Gareis
- Food Safety, Veterinary Faculty, Ludwig-Maximilians-University Munich, Oberschleissheim, Germany
| | - Christoph Gottschalk
- Food Safety, Veterinary Faculty, Ludwig-Maximilians-University Munich, Oberschleissheim, Germany
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Chaurasia A, Meena BR, Tripathi AN, Pandey KK, Rai AB, Singh B. Actinomycetes: an unexplored microorganisms for plant growth promotion and biocontrol in vegetable crops. World J Microbiol Biotechnol 2018; 34:132. [PMID: 30105532 DOI: 10.1007/s11274-018-2517-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 08/09/2018] [Indexed: 12/24/2022]
Abstract
Actinomycetes, a Gram positive bacteria, well reported as a source of antibiotics, also possess potential to control various plant pathogens, besides acting as plant growth promoting agent. Chemicals in different forms are extensively being used in vegetable farming, adversely affecting the environment and consumer health. Microbial agent like actinomycetes can substantially replace these harmful chemicals, and have now started finding a place as an important input in to farming practices. Only selected vegetable crops belonging to 11 different families have been explored with use of actinomycetes as biocontrol and plant growth promoting agent till now. It provides ample opportunities to vegetable researchers, to further explore with use of this very important group of microorganisms, in order to achieve even higher production level of safe vegetables. Mycostop and Actinovate are two actinomycetes based formulations globally available for use in vegetable farming as a substitute for chemical formulations. Present review article has summarized the literature available on use of actinomycetes in vegetable farming. Existing wide gap in knowledge, and potential thrust areas for future research have also been projected.
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Khalaf EM, Raizada MN. Bacterial Seed Endophytes of Domesticated Cucurbits Antagonize Fungal and Oomycete Pathogens Including Powdery Mildew. Front Microbiol 2018; 9:42. [PMID: 29459850 PMCID: PMC5807410 DOI: 10.3389/fmicb.2018.00042] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 01/09/2018] [Indexed: 01/28/2023] Open
Abstract
The cucurbit vegetables, including cucumbers, melons and pumpkins, have been cultivated for thousands of years without fungicides. However, their seed germination stage is prone to be infected by soil-borne fungal and oomycete pathogens. Endophytes are symbionts that reside inside plant tissues including seeds. Seed endophytes are founders of the juvenile plant microbiome and can promote host defense at seed germination and later stages. We previously isolated 169 bacterial endophytes associated with seeds of diverse cultivated cucurbits. We hypothesized that these endophytes can antagonize major fungal and oomycete pathogens. Here we tested the endophytes for in vitro antagonism (dual culture assays) against important soil-borne pathogens (Rhizoctonia solani, Fusarium graminearum, Phytophthora capsici, Pythium aphanideratum). The endophytes were also assayed in planta (leaf disk and detached leaf bioassays) for antagonism against a foliar pathogen of global importance, Podosphaera fuliginea, the causative agent of cucurbit powdery mildew. The endophytes were further tested in vitro for secretion of volatile organic compounds (VOCs) known to induce plant defense. Extracellular ribonuclease activity was also tested, as a subset of pathogenesis-related (PR) proteins of plant hosts implicated in suppression of fungal pathogens, displays ribonuclease activity. An unexpected majority of the endophytes (70%, 118/169) exhibited antagonism to the five phytopathogens, of which 68% (50/73) of in vitro antagonists belong to the genera Bacillus and Paenibacillus. All Lactococcus and Pantoea endophytes exhibited anti-oomycete activity. However, amongst the most effective inoculants against Podosphaera fuliginea were Pediococcus and Pantoea endophytes. Interestingly, 67% (113/169) of endophytes emitted host defense inducing VOCs (acetoin/diacetyl) and 62% (104/169) secreted extracellular ribonucleases in vitro, respectively. These results show that seeds of cultivated cucurbits package microbes with significant disease-suppression potential. As seeds can act as vectors for genetic transmission of endophytes across host generations, it is interesting to hypothesize whether humans, when selecting seeds of healthy hosts, may have inadvertently selected for disease-suppressing seed endophytes. As the majority of pathogen-suppressing endophytes belong to Bacillus and Paenibacillus, and since Bacilli are widely used as commercial biocontrol agents of vegetables, we propose that these agents are mimicking the ecological niche established by their endophytic cousins.
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Affiliation(s)
- Eman M. Khalaf
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
- Department of Microbiology and Immunology, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
| | - Manish N. Raizada
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
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Saminathan T, García M, Ghimire B, Lopez C, Bodunrin A, Nimmakayala P, Abburi VL, Levi A, Balagurusamy N, Reddy UK. Metagenomic and Metatranscriptomic Analyses of Diverse Watermelon Cultivars Reveal the Role of Fruit Associated Microbiome in Carbohydrate Metabolism and Ripening of Mature Fruits. Front Plant Sci 2018; 9:4. [PMID: 29403516 PMCID: PMC5780703 DOI: 10.3389/fpls.2018.00004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/03/2018] [Indexed: 05/06/2023]
Abstract
The plant microbiome is a key determinant of plant health and productivity, and changes in the plant microbiome can alter the tolerance to biotic and abiotic stresses and the quality of end produce. Little is known about the microbial diversity and its effect on carbohydrate metabolism in ripe fruits. In this study, we aimed to understand the diversity and function of microorganisms in relation to carbohydrate metabolism of ripe watermelon fruits. We used 16S metagenomics and RNAseq metatranscriptomics for analysis of red (PI459074, Congo, and SDRose) and yellow fruit-flesh cultivars (PI227202, PI435990, and JBush) of geographically and metabolically diverse watermelon cultivars. Metagenomics data showed that Proteobacteria were abundant in SDRose and PI227202, whereas Cyanobacteria were most abundant in Congo and PI4559074. In the case of metatranscriptome data, Proteobacteria was the most abundant in all cultivars. High expression of genes linked to infectious diseases and the expression of peptidoglycan hydrolases associated to pathogenicity of eukaryotic hosts was observed in SDRose, which could have resulted in low microbial diversity in this cultivar. The presence of GH28, associated with polygalacturonase activity in JBush and SDRose could be related to cell wall modifications including de-esterification and depolymerization, and consequent loss of galacturonic acid and neutral sugars. Moreover, based on the KEGG annotation of the expressed genes, nine α-galactosidase genes involved in key processes of galactosyl oligosaccharide metabolism, such as raffinose family were identified and galactose metabolism pathway was reconstructed. Results of this study underline the links between the host and fruit-associated microbiome in carbohydrate metabolism of the ripe fruits. The cultivar difference in watermelon reflects the quantum and diversity of the microbiome, which would benefit watermelon and other plant breeders aiming at the holobiont concept to incorporate associated microbiomes in breeding programs.
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Affiliation(s)
- Thangasamy Saminathan
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, United States
| | - Marleny García
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón, Mexico
| | - Bandana Ghimire
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, United States
| | - Carlos Lopez
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, United States
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón, Mexico
| | - Abiodun Bodunrin
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, United States
| | - Padma Nimmakayala
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, United States
| | - Venkata L. Abburi
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, United States
| | - Amnon Levi
- U.S. Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC, United States
| | - Nagamani Balagurusamy
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón, Mexico
| | - Umesh K. Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, United States
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Abstract
Plants are hosts to complex communities of endophytic bacteria that colonize the interior of both below- and aboveground tissues. Bacteria living inside plant tissues as endophytes can be horizontally acquired from the environment with each new generation, or vertically transmitted from generation to generation via seed. A better understanding of bacterial endophyte transmission routes and modes will benefit studies of plant–endophyte interactions in both agricultural and natural ecosystems. In this review, we provide an overview of the transmission routes that bacteria can take to colonize plants, including vertically via seeds and pollen, and horizontally via soil, atmosphere, and insects. We discuss both well-documented and understudied transmission routes, and identify gaps in our knowledge on how bacteria reach the inside of plants. Where little knowledge is available on endophytes, we draw from studies on bacterial plant pathogens to discuss potential transmission routes. Colonization of roots from soil is the best studied transmission route, and probably the most important, although more studies of transmission to aerial parts and stomatal colonization are needed, as are studies that conclusively confirm vertical transfer. While vertical transfer of bacterial endophytes likely occurs, obligate and strictly vertically transferred symbioses with bacteria are probably unusual in plants. Instead, plants appear to benefit from the ability to respond to a changing environment by acquiring its endophytic microbiome anew with each generation, and over the lifetime of individuals.
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Shen Z, Mustapha A, Lin M, Zheng G. Biocontrol of the internalization of Salmonella enterica and Enterohaemorrhagic Escherichia coli in mung bean sprouts with an endophytic Bacillus subtilis. Int J Food Microbiol 2017; 250:37-44. [DOI: 10.1016/j.ijfoodmicro.2017.03.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 03/07/2017] [Accepted: 03/22/2017] [Indexed: 01/09/2023]
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Abstract
“No plant is an island too…” Plants, though sessile, have developed a unique strategy to counter biotic and abiotic stresses by symbiotically co-evolving with microorganisms and tapping into their genome for this purpose. Soil is the bank of microbial diversity from which a plant selectively sources its microbiome to suit its needs. Besides soil, seeds, which carry the genetic blueprint of plants during trans-generational propagation, are home to diverse microbiota that acts as the principal source of microbial inoculum in crop cultivation. Overall, a plant is ensconced both on the outside and inside with a diverse assemblage of microbiota. Together, the plant genome and the genes of the microbiota that the plant harbors in different plant tissues, i.e., the ‘plant microbiome,’ form the holobiome which is now considered as unit of selection: ‘the holobiont.’ The ‘plant microbiome’ not only helps plants to remain fit but also offers critical genetic variability, hitherto, not employed in the breeding strategy by plant breeders, who traditionally have exploited the genetic variability of the host for developing high yielding or disease tolerant or drought resistant varieties. This fresh knowledge of the microbiome, particularly of the rhizosphere, offering genetic variability to plants, opens up new horizons for breeding that could usher in cultivation of next-generation crops depending less on inorganic inputs, resistant to insect pest and diseases and resilient to climatic perturbations. We surmise, from ever increasing evidences, that plants and their microbial symbionts need to be co-propagated as life-long partners in future strategies for plant breeding. In this perspective, we propose bottom–up approach to co-propagate the co-evolved, the plant along with the target microbiome, through – (i) reciprocal soil transplantation method, or (ii) artificial ecosystem selection method of synthetic microbiome inocula, or (iii) by exploration of microRNA transfer method – for realizing this next-generation plant breeding approach. Our aim, thus, is to bring closer the information accrued through the advanced nucleotide sequencing and bioinformatics in conjunction with conventional culture-dependent isolation method for practical application in plant breeding and overall agriculture.
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Affiliation(s)
- Murali Gopal
- Microbiology Section, ICAR-Central Plantation Crops Research Institute Kasaragod, India
| | - Alka Gupta
- Microbiology Section, ICAR-Central Plantation Crops Research Institute Kasaragod, India
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Aleti G, Lehner S, Bacher M, Compant S, Nikolic B, Plesko M, Schuhmacher R, Sessitsch A, Brader G. Surfactin variants mediate species-specific biofilm formation and root colonization in Bacillus. Environ Microbiol 2016; 18:2634-45. [PMID: 27306252 DOI: 10.1111/1462-2920.13405] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyclic lipopeptides (cLP) and especially surfactins produced by Bacillus spp. trigger biofilm formation and root colonization and are crucial for biocontrol activity and systemic resistance in plants. Bacillus atrophaeus 176s isolated from the moss Tortella tortuosa produces the cLP fengycins, iturins and surfactins, possesses antifungal activities and can protect tomato, lettuce and sugar beet against Rhizoctonia solani infection. In B. atrophaeus we identified for the first time the variant surfactin C, which differs from surfactin A produced by B. subtilis and B. amyloliquefaciens by an isoleucine instead of a leucine at position 7 of the lipopeptide backbone. The analysis of the complete surfactin gene clusters revealed that the dissimilarity is encoded in the adenylation domain of srfC and show that surfactin variations are distributed in a species-specific manner in bacilli. We demonstrate that the surfactin A and C with subtle structural differences have varying signal strengths on biofilm formation and root colonization and act specifically on the respective producing strain. This became evident as biofilm formation and root colonization but not swarming motility in surfactin biosynthesis mutants was restored differentially in the presence of exogenously supplemented cognate and non-cognate surfactin variants.
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Affiliation(s)
- Gajender Aleti
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse 24, Tulln, A-3430, Austria
| | - Sylvia Lehner
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences (BOKU), Konrad-Lorenz-Str. 20, 3430 Tulln, Austria
| | - Markus Bacher
- Department of Chemistry, University of Natural Resources and Life Sciences (BOKU), UFT Research Center Tulln, Konrad-Lorenz-Str. 24, Tulln, A-3430, Austria
| | - Stéphane Compant
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse 24, Tulln, A-3430, Austria
| | - Branislav Nikolic
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse 24, Tulln, A-3430, Austria
| | - Maja Plesko
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse 24, Tulln, A-3430, Austria
| | - Rainer Schuhmacher
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences (BOKU), Konrad-Lorenz-Str. 20, 3430 Tulln, Austria
| | - Angela Sessitsch
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse 24, Tulln, A-3430, Austria
| | - Günter Brader
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse 24, Tulln, A-3430, Austria
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30
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Abstract
BACKGROUND Endophytes are microbes that colonize plant internal tissues without causing disease. In particular, seed-associated endophytes may be vectors for founder microbes that establish the plant microbiome, which may subsequently contribute beneficial functions to their host plants including nutrient acquisition and promotion of plant growth. The Cucurbitaceae family of gourds (e.g., cucumbers, melons, pumpkin, squash), including its fruits and seeds, is widely consumed by humans. However, there is limited data concerning the taxonomy and functions of seed-associated endophytes across the Cucurbitaceae family. Here, bacteria from surface-sterilized seeds of 21 curcurbit varieties belonging to seven economically important species were cultured, classified using 16S rRNA gene sequencing, and subjected to eight in vitro functional tests. RESULTS In total, 169 unique seed-associated bacterial strains were cultured from selected cucurbit seeds. Interestingly, nearly all strains belonged to only two phyla (Firmicutes, Proteobacteria) and only one class within each phyla (Bacilli, γ-proteobacteria, respectively). Bacillus constituted 50 % of all strains and spanned all tested cucurbit species. Paenibacillus was the next most common genus, while strains of Enterobacteriaceae and lactic acid bacteria were also cultured. Phylogenetic trees showed limited taxonomic clustering of strains by host species. Surprisingly, 33 % of strains produced the plant hormone, indole-3-acetic acid (auxin), known to stimulate the growth of fruits/gourds and nutrient-acquiring roots. The next most common nutrient acquisition traits in vitro were (in rank order): nitrogen fixation/N-scavenging, phosphate solubilisation, siderophore secretion, and production of ACC deaminase. Secretion of extracellular enzymes required for nutrient acquisition, endophyte colonization and/or community establishment were observed. Bacillus strains had the potential to contribute all tested functional traits to their hosts. CONCLUSION The seeds of economically important cucurbits tested in this study have a culturable core microbiota consisting of Bacillus species with potential to contribute diverse nutrient acquisition and growth promotion activities to their hosts. These microbes may lead to novel seed inoculants to assist sustainable food production. Given that cucurbit seeds are consumed by traditional societies as a source of tryptophan, the precursor for auxin, we discuss the possibility that human selection inadvertently facilitated auxin-mediated increases in gourd size.
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Affiliation(s)
- Eman M Khalaf
- />Department of Plant Agriculture, University of Guelph, Guelph, N1G 2W1 ON Canada
- />Department of Microbiology and Immunology, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
| | - Manish N Raizada
- />Department of Plant Agriculture, University of Guelph, Guelph, N1G 2W1 ON Canada
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