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Dendooven L, Pérez-Hernández V, Navarro-Pérez G, Tlalmis-Corona J, Navarro-Noya YE. Spatial and Temporal Shifts of Endophytic Bacteria in Conifer Seedlings of Abies religiosa (Kunth) Schltdl. & Cham. MICROBIAL ECOLOGY 2024; 87:90. [PMID: 38958675 PMCID: PMC11222277 DOI: 10.1007/s00248-024-02398-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/09/2024] [Indexed: 07/04/2024]
Abstract
Endophytes play an important role in plant development, survival, and establishment, but their temporal dynamics in young conifer plants are still largely unknown. In this study, the bacterial community was determined by metabarcoding of the 16S rRNA gene in the rhizoplane, roots, and aerial parts of 1- and 5-month-old seedlings of natural populations of Abies religiosa (Kunth) Schltdl. & Cham. In 1-month-old seedlings, Pseudomonas dominated aerial parts (relative abundance 71.6%) and roots (37.9%). However, the roots exhibited significantly higher bacterial species richness than the aerial parts, with the dissimilarity between these plant sections mostly explained by the loss of bacterial amplification sequence variants. After 5 months, Mucilaginibacter dominated in the rhizoplane (9.0%), Streptomyces in the roots (12.2%), and Pseudomonas in the aerial parts (18.1%). The bacterial richness and community structure differed significantly between the plant sections, and these variations were explained mostly by 1-for-1 substitution. The relative abundance of putative metabolic pathways significantly differed between the plant sections at both 1 and 5 months. All the dominant bacterial genera (e.g., Pseudomonas and Burkholderia-Caballeronia-Paraburkholderia) have been reported to have plant growth-promoting capacities and/or antagonism against pathogens, but what defines their role for plant development has still to be determined. This investigation improves our understanding of the early plant-bacteria interactions essential for natural regeneration of A. religiosa forest.
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Affiliation(s)
- Luc Dendooven
- Laboratory of Soil Ecology, Cinvestav, Mexico City, Mexico.
| | | | | | - Juanita Tlalmis-Corona
- Laboratorio de Interacciones Bióticas, Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, San Felipe Ixtacuixtla, Mexico
| | - Yendi E Navarro-Noya
- Laboratorio de Interacciones Bióticas, Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, San Felipe Ixtacuixtla, Mexico.
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2
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Emitaro WO, Kawaka F, Musyimi DM, Adienge A. Diversity of endophytic bacteria isolated from leguminous agroforestry trees in western Kenya. AMB Express 2024; 14:18. [PMID: 38329624 PMCID: PMC10853127 DOI: 10.1186/s13568-024-01676-6] [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: 11/25/2022] [Accepted: 01/31/2024] [Indexed: 02/09/2024] Open
Abstract
Plants have diverse and vast niches colonized by endophytic microorganisms that promote the wellbeing of host plant. These microbes inhabit internal plant tissues with no signs of ill health. Bacterial endophytes from many plants have been isolated and characterized due to their beneficial roles however their diversity in leguminous plants still remain unexploited. Diversity of bacterial endophytes isolated from Sesbania sesban, Leucaena diversifolia and Calliandra calothyrsus was assessed using morphological and molecular characteristics. A total of 27 pure isolates were recovered from C. Calothyrsus, L. diversifolia and S. sesban constituting 44.4%, 33.3% and 22.2% from the leaves, stems and roots respectively. The isolates differentiated into Gram positive and negative with rods and spherical shapes. Analysis of 16S rRNA gene sequences revealed 8 closely related bacterial genera that consisted of Bacillus (33.3%), Staphylococcus (22.2%), Alcaligens (11.1%), Pantoea (11.1%), Xanthomonas,and Sphingomonas (7.4%) each. Others included Acinetobacter, and Pseudomonas at 3.7% each. Bacterial endophytes of genus bacillus were isolated from all the three plants. These results indicate the presence of high diversity of endophytic bacteria associated with the different parts of L. diversifolia, S. sesban and C. salothyrsus growing in western Kenya.
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Affiliation(s)
- William Omuketi Emitaro
- Department of Biological Sciences, Jaramogi Oginga Odinga University of Science and Technology, 210, Bondo, 40601, Kenya.
| | - Fanuel Kawaka
- Department of Biological Sciences, Jaramogi Oginga Odinga University of Science and Technology, 210, Bondo, 40601, Kenya
| | | | - Asenath Adienge
- Department of Biotechnology, Kenya Forestry Research Institute, 20412-00200, Nairobi, Kenya
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Negi R, Sharma B, Kumar S, Chaubey KK, Kaur T, Devi R, Yadav A, Kour D, Yadav AN. Plant endophytes: unveiling hidden applications toward agro-environment sustainability. Folia Microbiol (Praha) 2024; 69:181-206. [PMID: 37747637 DOI: 10.1007/s12223-023-01092-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/04/2023] [Indexed: 09/26/2023]
Abstract
Endophytic microbes are plant-associated microorganisms that reside in the interior tissue of plants without causing damage to the host plant. Endophytic microbes can boost the availability of nutrient for plant by using a variety of mechanisms such as fixing nitrogen, solubilizing phosphorus, potassium, and zinc, and producing siderophores, ammonia, hydrogen cyanide, and phytohormones that help plant for growth and protection against various abiotic and biotic stresses. The microbial endophytes have attained the mechanism of producing various hydrolytic enzymes such as cellulase, pectinase, xylanase, amylase, gelatinase, and bioactive compounds for plant growth promotion and protection. The efficient plant growth promoting endophytic microbes could be used as an alternative of chemical fertilizers for agro-environmental sustainability. Endophytic microbes belong to different phyla including Euryarchaeota, Ascomycota, Basidiomycota, Mucoromycota, Firmicutes, Proteobacteria, and Actinobacteria. The most pre-dominant group of bacteria belongs to Proteobacteria including α-, β-, γ-, and δ-Proteobacteria. The least diversity of the endophytic microbes have been revealed from Bacteroidetes, Deinococcus-Thermus, and Acidobacteria. Among reported genera, Achromobacter, Burkholderia, Bacillus, Enterobacter, Herbaspirillum, Pseudomonas, Pantoea, Rhizobium, and Streptomyces were dominant in most host plants. The present review deals with plant endophytic diversity, mechanisms of plant growth promotion, protection, and their role for agro-environmental sustainability. In the future, application of endophytic microbes have potential role in enhancement of crop productivity and maintaining the soil health in sustainable manner.
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Affiliation(s)
- Rajeshwari Negi
- Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, 173101, Himachal Pradesh, India
| | - Babita Sharma
- Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Sirmour, 173101, Himachal Pradesh, India
| | - Sanjeev Kumar
- Faculty of Agricultural Sciences, GLA University, Mathura, 281406, Uttar Pradesh, India
| | - Kundan Kumar Chaubey
- Division of Research and Innovation, School of Applied and Life Sciences, Uttaranchal University, Premnagar, Dehradun, 248007, Uttarakhand, India
| | - Tanvir Kaur
- Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, 173101, Himachal Pradesh, India
| | - Rubee Devi
- Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, 173101, Himachal Pradesh, India
| | - Ashok Yadav
- Department of Botany, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Divjot Kour
- Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Sirmour, 173101, Himachal Pradesh, India
| | - Ajar Nath Yadav
- Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, 173101, Himachal Pradesh, India.
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4
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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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Acuña JJ, Hu J, Inostroza NG, Valenzuela T, Perez P, Epstein S, Sessitsch A, Zhang Q, Jorquera MA. Endophytic bacterial communities in ungerminated and germinated seeds of commercial vegetables. Sci Rep 2023; 13:19829. [PMID: 37963999 PMCID: PMC10645892 DOI: 10.1038/s41598-023-47099-4] [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: 07/26/2023] [Accepted: 11/09/2023] [Indexed: 11/16/2023] Open
Abstract
Chile is a prominent seed exporter globally, but the seed microbiome of vegetables (46% of seeds) and its role in the early stages of plant growth have remained largely unexplored. Here, we employed DNA metabarcoding analysis to investigate the composition and putative functions of endophytic bacterial communities in ungerminated and germinated seeds of the commercial vegetables Apiaceae (parsley and carrot), Asteraceae (lettuce), Brassicaceae (cabbage and broccoli), and Solanaceae (tomato). Bacterial quantification showed 104 to 108 copies of the 16S rRNA gene per gram of ungerminated and germinated seeds. Alpha diversity analysis (e.g., Chao1, Shannon, and Simpson indices) did not indicate significant differences (Kruskal-Wallis test) between ungerminated and germinated seeds, except for Solanaceae. However, beta diversity (PCoA) analysis showed distinctions (Adonis test) between ungerminated and germinated seeds, except Apiaceae. Pseudomonadota and Bacillota were identified as the dominant and specialist taxa in both ungerminated and germinated seed samples. Chemoheterotrophy and fermentation were predicted as the main microbial functional groups in the endophytic bacterial community. Notably, a considerable number of the 143 isolated endophytic strains displayed plant growth-promoting traits (10 to 64%) and biocontrol activity (74% to 82%) against plant pathogens (Xanthomonas and Pseudomonas). This study revealed the high variability in the abundance, diversity, composition, and functionality of endophytic bacteria between ungerminated and germinated seeds in globally commercialized vegetables. Furthermore, potential beneficial endophytic bacteria contained in their seed microbiomes that may contribute to the microbiome of the early stages, development, growth and progeny of vegetables were found.
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Affiliation(s)
- Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Millennium Institute Center for Genome Regulation (MI-CGR), Valenzuela Puelma 10207, 7800003, Santiago, La Reina, Chile
| | - Jingming Hu
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, 361102, China
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Nitza G Inostroza
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Tamara Valenzuela
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Pablo Perez
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Slava Epstein
- College of Science, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, USA
| | - Angela Sessitsch
- Health & Bioresources, AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430, Tulln, Austria
| | - Qian Zhang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, 361102, China.
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China.
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile.
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile.
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Prodhan MY, Rahman MB, Rahman A, Akbor MA, Ghosh S, Nahar MNEN, Simo, Shamsuzzoha M, Cho KM, Haque MA. Characterization of Growth-Promoting Activities of Consortia of Chlorpyrifos Mineralizing Endophytic Bacteria Naturally Harboring in Rice Plants-A Potential Bio-Stimulant to Develop a Safe and Sustainable Agriculture. Microorganisms 2023; 11:1821. [PMID: 37512993 PMCID: PMC10385066 DOI: 10.3390/microorganisms11071821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/03/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Eighteen pesticide-degrading endophytic bacteria were isolated from the roots, stems, and leaves of healthy rice plants and identified through 16S rRNA gene sequencing. Furthermore, biochemical properties, including enzyme production, dye degradation, anti-bacterial activities, plant-growth-promoting traits, including N-fixation, P-solubilization, auxin production, and ACC-deaminase activities of these naturally occurring endophytic bacteria along with their four consortia, were characterized. Enterobacter cloacae HSTU-ABk39 and Enterobacter sp. HSTU-ABk36 displayed inhibition zones of 41.5 ± 1.5 mm, and 29 ± 09 mm against multidrug-resistant human pathogenic bacteria Staphylococcus aureus and Staphylococcus epidermidis, respectively. FT-IR analysis revealed that all eighteen isolates were able to degrade chlorpyrifos pesticide. Our study confirms that pesticide-degrading endophytic bacteria from rice plants play a key role in enhancing plant growth. Notably, rice plants grown in pots containing reduced urea (30%) mixed with either endophytic bacterial consortium-1, consortium-2, consortium-3, or consortia-4 demonstrated an increase of 17.3%, 38.6%, 18.2%, and 39.1% yields, respectively, compared to the control plants grown in pots containing 100% fertilizer. GC-MS/MS analysis confirmed that consortia treatment caused the degradation of chlorpyrifos into different non-toxic metabolites, including 2-Hydroxy-3,5,6 trichloropyridine, Diethyl methane phosphonate, Phorate sulfoxide, and Carbonochloridic. Thus, these isolates could be deployed as bio-stimulants to improve crop production by creating a sustainable biological system.
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Affiliation(s)
- Md Yeasin Prodhan
- Department of Biochemistry and Molecular Biology, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Md Bokhtiar Rahman
- Department of Biochemistry and Molecular Biology, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Aminur Rahman
- Department of Biomedical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Md Ahedul Akbor
- Institute of National Analytical Research and Services (INARS), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka 1205, Bangladesh
| | - Sibdas Ghosh
- Department of Biological Sciences, College of Arts and Sciences, Carlow University, 3333 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Mst Nur-E-Nazmun Nahar
- Department of Biochemistry and Molecular Biology, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Simo
- Department of Biochemistry and Molecular Biology, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Md Shamsuzzoha
- Department of Chemistry, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Kye Man Cho
- Department of Green Bio Science and Agri-Food Bio Convergence Institute, Gyeongsang National University, Jinju 52725, Republic of Korea
| | - Md Azizul Haque
- Department of Biochemistry and Molecular Biology, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
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Sinha S, Thakuria D, Chaliha C, Uzir P, Hazarika S, Dutta P, Singh AK, Laloo B. Plant growth-promoting traits of culturable seed microbiome of citrus species from Purvanchal Himalaya. FRONTIERS IN PLANT SCIENCE 2023; 14:1104927. [PMID: 37492766 PMCID: PMC10365123 DOI: 10.3389/fpls.2023.1104927] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/30/2023] [Indexed: 07/27/2023]
Abstract
Despite Northeastern India being "Treasure House of Citrus Genetic Wealth," genetic erosion of citrus diversity poses severe concern with a corresponding loss in seed microbial diversity. The seed microbiome of citrus species unique to the Purvanchal Himalaya is seldom explored for their use in sustainable orchard management. Isolation and characterization of culturable seed microbiomes of eight citrus species, namely, Citrus reticulata Blanco, C. grandis (L.) Osbeck, C. latipes Tanaka, C. megaloxycarpa Lushaigton, C. jambhiri Lush, C. sinensis (L.) Osbeck, C. macroptera Montr, and C. indica Tanaka collected from NE India were carried out. The isolates were then screened for an array of plant growth-promoting (PGP) traits [indole acetic acid (IAA) production, N2 fixation, phosphate and zinc complex dissolution, siderophores, and Hydrogen Cyanide (HCN) production]. The pure culture isolates of seed microbiomes were capable of dissolving insoluble Ca3(PO4)2 (1.31-4.84 µg Pi ml-1 h-1), Zn3(PO4)2 (2.44-3.16 µg Pi ml-1 h-1), AlPO4 (1.74-3.61 µg Pi ml-1 h-1), and FePO4 (1.54-4.61µg Pi ml-1 h-1), mineralized phytate (12.17-18.00 µg Pi ml-1 h-1) and produced IAA-like substances (4.8-187.29 µg ml-1 h-1). A few isolates of the seed microbiome were also able to fix nitrogen, secrete siderophore-like compounds and HCN, and dissolve ZnSO4 and ZnO. The 16S ribosomal Ribonucleic Acid (rRNA)-based taxonomic findings revealed that Bacillus was the most dominant genus among the isolates across citrus species. Isolates CG2-1, CME6-1, CME6-4, CME6-5, CME6-9, CJ7-1, CMA10-1, CI11-3, and CI11-4 were identified as promising bioinoculants for development of microbial consortium having multifaceted PGP traits for nutritional benefits of nitrogen, phosphorus and zinc, and IAA hormonal benefits to citrus crops for better fitness in acid soils.
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Affiliation(s)
- Sakshi Sinha
- School of Natural Resource Management, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Dwipendra Thakuria
- School of Natural Resource Management, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Chayanika Chaliha
- School of Natural Resource Management, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Panchali Uzir
- School of Natural Resource Management, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Samarendra Hazarika
- Division of System Research and Engineering, Indian Council of Agricultural Research (ICAR) Research Complex for North Eastern Hill Region, Umiam, Meghalaya, India
| | - Pranab Dutta
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - A. K. Singh
- School of Natural Resource Management, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Bingiala Laloo
- School of Crop Improvement, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
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Muratova A, Golubev S, Romanova V, Sungurtseva I, Nurzhanova A. Effect of Heavy-Metal-Resistant PGPR Inoculants on Growth, Rhizosphere Microbiome and Remediation Potential of Miscanthus × giganteus in Zinc-Contaminated Soil. Microorganisms 2023; 11:1516. [PMID: 37375018 DOI: 10.3390/microorganisms11061516] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Microbial-assisted phytoremediation is considered a more effective approach to soil rehabilitation than the sole use of plants. Mycolicibacterium sp. Pb113 and Chitinophaga sp. Zn19, heavy-metal-resistant PGPR strains originally isolated from the rhizosphere of Miscanthus × giganteus, were used as inoculants of the host plant grown in control and zinc-contaminated (1650 mg/kg) soil in a 4-month pot experiment. The diversity and taxonomic structure of the rhizosphere microbiomes, assessed with metagenomic analysis of rhizosphere samples for the 16S rRNA gene, were studied. Principal coordinate analysis showed differences in the formation of the microbiomes, which was affected by zinc rather than by the inoculants. Bacterial taxa affected by zinc and the inoculants, and the taxa potentially involved in the promotion of plant growth as well as in assisted phytoremediation, were identified. Both inoculants promoted miscanthus growth, but only Chitinophaga sp. Zn19 contributed to significant Zn accumulation in the aboveground part of the plant. In this study, the positive effect of miscanthus inoculation with Mycolicibacterium spp. and Chitinophaga spp. was demonstrated for the first time. On the basis of our data, the bacterial strains studied may be recommended to improve the efficiency of M. × giganteus phytoremediation of zinc-contaminated soil.
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Affiliation(s)
- Anna Muratova
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
| | - Sergey Golubev
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
| | - Valeria Romanova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420021 Kazan, Russia
| | - Irina Sungurtseva
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
| | - Asil Nurzhanova
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
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War AF, Bashir I, Reshi ZA, Kardol P, Rashid I. Insights into the seed microbiome and its ecological significance in plant life. Microbiol Res 2023; 269:127318. [PMID: 36753851 DOI: 10.1016/j.micres.2023.127318] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/12/2022] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
In recent years, the microbiome has attracted much attention because of the multiple roles and functions that microbes play in plants, animals, and human beings. Seed-associated microbes are of particular interest in being the initial microbial inoculum that affects the critical early life stages of a plant. The seed-microbe interactions are also known to improve nutrient acquisition, resilience against pathogens, and resistance against abiotic stresses. Despite these diverse roles, the seed microbiome has received little attention in plant ecology. Thus, we review the current knowledge on seed microbial diversity, community structure, and functions obtained through culture-dependent and culture-independent approaches. Furthermore, we present a comprehensive synthesis of the ecological literature on seed-microbe interactions to better understand the impact of these interactions on plant health and productivity. We suggest that future research should focus on the role of the seed microbiome in the establishment, colonization and spread of plant species in their native and non-native ranges as it may provide new insights into conservation biology and invasion ecology.
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Affiliation(s)
- Aadil Farooq War
- Department of Botany, University of Kashmir, Srinagar 190006, Jammu and Kashmir, India.
| | - Iqra Bashir
- Department of Botany, University of Kashmir, Srinagar 190006, Jammu and Kashmir, India
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Srinagar 190006, Jammu and Kashmir, India
| | - Paul Kardol
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, S 901 83 Umeå, Sweden
| | - Irfan Rashid
- Department of Botany, University of Kashmir, Srinagar 190006, Jammu and Kashmir, India
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Shirazi K, Ketabchi S, Kargar M. Screening of endophytic bacteria from potato tubers and their antagonistic activity against soil-borne potato pathogens. JOURNAL OF BIOLOGICAL RESEARCH - BOLLETTINO DELLA SOCIETÀ ITALIANA DI BIOLOGIA SPERIMENTALE 2022. [DOI: 10.4081/jbr.2023.10625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In order to appraise the bacterial endophyte communities that help resist disease in potato tuber, the separation, the population density, biodiversity and the antagonistic activity of endophytic bacteria, from the tuber peel of potato cultivars (Fontan90, Agria, Sante’a and Jeli89), were examined in the Fars province in Iran. In this study, the bacterial endophyte Colony Forming Units (CFU) were counted based on the most suitable dilution in petri dishes and expressed per g of wet weight of tuber tissue. The presence of bacteria was found mostly in the outer layer. A wide variety of endophyte species biodiversity was in Agria cultivar. To estimate the antagonistic effect of potato associated endophytic bacteria, 115 bacterial isolates were evaluated by dual culture method against main soil-borne potato pathogens Fusarium oxysporum, Rhizoctonia solani, Verticillium dahliae, Streptomyces scabies and Ralstonia solanacearum. Endophyte strains were identified based on physiological, morphological and chemical characteristics and the 16S rRNA gene sequence analysis. The highest degree of the inhibitory activity in all layers of potato cultivars was related to Bacillus subtilis, Bacillus mojavensis and Klebsiella variicola. Antagonistic activity of endophytic bacteria against the pathogens was significantly higher (p<0.01) in the examined strains from the outermost layer of tuber peel and decreased progressively toward the center of the tuber. In this research, Klebsiella variicola was reported as endophyte bacteria in the four commercial potatocultivars mentioned above, for the first time.
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Mataranyika PN, Chimwamurombe PM, Venturi V, Uzabakiriho JD. Bacterial bioinoculants adapted for sustainable plant health and soil fertility enhancement in Namibia. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.1002797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The increase in dryland agriculture elicits the need to develop sustainable practices that improve crop yield and protect soil fertility. The use of biofertilisers adapted to nutrient deficient soils and arid climates would help achieve this. In this review, the use of plant growth-promoting bacteria is explored as a possible solution to the current state of dryland agriculture and climate change threats to agriculture. Plant microbe interactions form the basis of this review as evidence has shown that these interactions often exist to improve the health of plants. This is achieved by the production of important biochemicals and enzymes like indole acetic acid and amino cyclopropane-1-carboxylate deaminase while also actively protecting plants from pathogens including fungal pathogens. Research, therefore, has shown that these plant-growth promoting bacteria may be exploited and developed into biofertilisers. These biofertilisers are both economically and environmentally sustainable while improving soil quality and crop yield. The literature presented in this review is in context of the Namibian climate and soil profiles.
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12
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Francioli D, Cid G, Hajirezaei MR, Kolb S. Leaf bacterial microbiota response to flooding is controlled by plant phenology in wheat (Triticum aestivum L.). Sci Rep 2022; 12:11197. [PMID: 35778470 PMCID: PMC9249782 DOI: 10.1038/s41598-022-15133-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/20/2022] [Indexed: 11/09/2022] Open
Abstract
Leaf microbiota mediates foliar functional traits, influences plant fitness, and contributes to various ecosystem functions, including nutrient and water cycling. Plant phenology and harsh environmental conditions have been described as the main determinants of leaf microbiota assembly. How climate change may modulate the leaf microbiota is unresolved and thus, we have a limited understanding on how environmental stresses associated with climate change driven weather events affect composition and functions of the microbes inhabiting the phyllosphere. Thus, we conducted a pot experiment to determine the effects of flooding stress on the wheat leaf microbiota. Since plant phenology might be an important factor in the response to hydrological stress, flooding was induced at different plant growth stages (tillering, booting and flowering). Using a metabarcoding approach, we monitored the response of leaf bacteria to flooding, while key soil and plant traits were measured to correlate physiological plant and edaphic factor changes with shifts in the bacterial leaf microbiota assembly. In our study, plant growth stage represented the main driver in leaf microbiota composition, as early and late plants showed distinct bacterial communities. Overall, flooding had a differential effect on leaf microbiota dynamics depending at which developmental stage it was induced, as a more pronounced disruption in community assembly was observed in younger plants.
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Affiliation(s)
- Davide Francioli
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research E.V. (ZALF), Müncheberg, Germany.
| | - Geeisy Cid
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mohammad-Reza Hajirezaei
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research E.V. (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
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13
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Broccanello C, Ravi S, Deb S, Bolton M, Secor G, Richards C, Maretto L, Lucia MCD, Bertoldo G, Orsini E, Ronquillo-López MG, Concheri G, Campagna G, Squartini A, Stevanato P. Bacterial endophytes as indicators of susceptibility to Cercospora Leaf Spot (CLS) disease in Beta vulgaris L. Sci Rep 2022; 12:10719. [PMID: 35739218 PMCID: PMC9226160 DOI: 10.1038/s41598-022-14769-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 06/13/2022] [Indexed: 12/03/2022] Open
Abstract
The fungus Cercospora beticola causes Cercospora Leaf Spot (CLS) of sugar beet (Beta vulgaris L.). Despite the global importance of this disease, durable resistance to CLS has still not been obtained. Therefore, the breeding of tolerant hybrids is a major goal for the sugar beet sector. Although recent studies have suggested that the leaf microbiome composition can offer useful predictors to assist plant breeders, this is an untapped resource in sugar beet breeding efforts. Using Ion GeneStudio S5 technology to sequence amplicons from seven 16S rRNA hypervariable regions, the most recurring endophytes discriminating CLS-symptomatic and symptomless sea beets (Beta vulgaris L.ssp. maritima) were identified. This allowed the design of taxon-specific primer pairs to quantify the abundance of the most representative endophytic species in large naturally occurring populations of sea beet and subsequently in sugar beet breeding genotypes under either CLS symptomless or infection stages using qPCR. Among the screened bacterial genera, Methylobacterium and Mucilaginibacter were found to be significantly (p < 0.05) more abundant in symptomatic sea beets with respect to symptomless. In cultivated sugar beet material under CLS infection, the comparison between resistant and susceptible genotypes confirmed that the susceptible genotypes hosted higher contents of the above-mentioned bacterial genera. These results suggest that the abundance of these species can be correlated with increased sensitivity to CLS disease. This evidence can further prompt novel protocols to assist plant breeding of sugar beet in the pursuit of improved pathogen resistance.
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Affiliation(s)
- Chiara Broccanello
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Viale Dell'Università, Legnaro, PD, Italy
| | - Samathmika Ravi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Viale Dell'Università, Legnaro, PD, Italy
| | - Saptarathi Deb
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Viale Dell'Università, Legnaro, PD, Italy
| | - Melvin Bolton
- Northern Crop Science Laboratory, U.S. Dept. Agriculture, Fargo, ND, USA
| | - Gary Secor
- Plant Pathology Department, North Dakota State University, Fargo, ND, USA
| | | | - Laura Maretto
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Viale Dell'Università, Legnaro, PD, Italy
| | - Maria Cristina Della Lucia
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Viale Dell'Università, Legnaro, PD, Italy
| | - Giovanni Bertoldo
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Viale Dell'Università, Legnaro, PD, Italy
| | - Elena Orsini
- Strube Research GmbH & Co. KG, Söllingen, Germany
| | | | - Giuseppe Concheri
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Viale Dell'Università, Legnaro, PD, Italy
| | | | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Viale Dell'Università, Legnaro, PD, Italy
| | - Piergiorgio Stevanato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Viale Dell'Università, Legnaro, PD, Italy.
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14
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Ahmad T, Farooq S, Mirza DN, Kumar A, Mir RA, Riyaz-Ul-Hassan S. Insights into the Endophytic Bacterial Microbiome of Crocus sativus: Functional Characterization Leads to Potential Agents that Enhance the Plant Growth, Productivity, and Key Metabolite Content. MICROBIAL ECOLOGY 2022; 83:669-688. [PMID: 34241654 DOI: 10.1007/s00248-021-01810-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
The study was undertaken to unravel the culturable endophytic bacterial microbiome of Crocus sativus L. (saffron crocus) and consequently obtain potential leads to develop plant growth-promoting and biocontrol agents for increased productivity and sustainable cultivation. The endophytes formed 47 different operational taxonomic units (OTUs), spanning over 28 genera. The host was preferentially colonized by the genus Bacillus, followed by Burkholderia and Pantoea, respectively. Several endophytes possessed potential plant growth-promoting properties and inhibitory activities against the specific fungal pathogens of saffron. The endophytes, except for Microbacterium oxydans, did not cause any disease symptoms in the pot experiments. The selected cultures, Burkholderia gladioli, Streptomyces achromogenes, and three species of Bacillus, enhanced the host plant growth significantly. Based on the pot experiment results, two isolates, Bacillus mojavensis CS4EB32 and Burkholderia gladioli E39CS3, were selected for the field experiments. We obtained an increase of 67.5%, 69.8%, and 68.3% in the production of flowers with the individual and collective treatments, respectively. The treatments also enhanced the biomass of the plant and the length and weight of stigmas significantly. The endophyte treatments induced the expression of the pathway genes, resulting in a marked increase in the concentration of apocarotenoids. The study indicates that the dominant endophytes support plant growth and development in nature and present an opportunity for developing microbial formulations for the sustainability of saffron cultivation.
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Affiliation(s)
- Tanveer Ahmad
- Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, 190005, J&K, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, UP, India
| | - Sadaqat Farooq
- Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, 190005, J&K, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, UP, India
| | - Dania Nazir Mirza
- Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, 190005, J&K, India
| | - Amit Kumar
- Quality Management and Instrumentation Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, J&K, India
| | - Raouf Ahmad Mir
- Research and Development Division, GloBiLs Agri and Food Enterprises, IGC Lassipora, Pulwama, 192305, J&K, India
| | - Syed Riyaz-Ul-Hassan
- Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, 190005, J&K, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, UP, India.
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15
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Ntemafack A, Ahmed S, Kumar A, Chouhan R, Kapoor N, Bharate SB, Hassan QP, Gandhi SG. Plant growth promoting potential of butyl isobutyl phthalate and Streptomyces sp. from Rumex dentatus on rice. Appl Microbiol Biotechnol 2022; 106:2603-2617. [PMID: 35262787 DOI: 10.1007/s00253-022-11862-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/19/2022] [Accepted: 02/26/2022] [Indexed: 11/25/2022]
Abstract
Rice (Oryza sativa L.) is one of the most important staple foods consumed in many countries of the world. It is mostly consumed in developing countries where different chemical fertilizers are used to improve the productivity of the crop plant. In the present study, endophytic actinomycetes isolated from Rumex dentatus were identified morphologically and by scanning electron microscopy. Butyl isobutyl phthalate (BIBP) was isolated from the root endophyte Streptomyces sp. JR9 using column chromatography and HPLC methods. The compound was tested for its effect on rice seed germination. BIBP, extracts, and isolates were evaluated for their plant growth effect on rice in a growth chamber. Isolates were also screened in vitro for phosphate solubilization activity and enzyme production. Indole-3-acetic acid (IAA) and BIBP produced in extracts were quantified and detected using high performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS) methods, respectively. BIBP was found to increase the germination of rice seeds by 6 to 12% in treated samples and displayed potent effect at lowest concentration (0.437 µM). Both the compound and the extract depicted significant increases in almost all growth parameters at lowest concentration of 0.125 µg/mL and 62.5 µg/mL, respectively. BIBP also increased significantly shoot length, fresh root, fresh shoot, and dried shoot weight at high concentrations and was more potent than the standard phytohormone IAA. HPLC quantification showed 7.952 µg/mg and 0.371 µg/mg of IAA in extracts of Streptomyces sp. JR9 and the stem endophyte Streptomyces sp. KS3, respectively. IAA containing extract of JR9 increased significantly most growth parameters at lowest concentration (125 µg/mL). The extract of KS3 depicted significant increases in almost all growth parameters at high concentration (500 µg/mL). Our investigation showed that streptomycetes isolated from R. dentatus and BIBP are potent growth promoting agents and can be used in agriculture as bio-fertilizer to improve the growth and productivity of rice. KEY POINTS: • Butyl isobutyl phthalate (BIBP) isolated from endophytic Streptomyces sp. JR9 is a potent rice seed germination activator and promotes significantly the growth of rice • Isolated endophytes showed the ability to produce enzymes and phytohormone IAA • Isolates enhanced significantly the growth of rice.
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Affiliation(s)
- Augustin Ntemafack
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India. .,Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.
| | - Sajad Ahmed
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Amit Kumar
- Instrumentation Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Rekha Chouhan
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Nitika Kapoor
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India.,Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Sandip B Bharate
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Qazi Parvaiz Hassan
- Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, India.
| | - Sumit G Gandhi
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.
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16
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Kumar K, Verma A, Pal G, Anubha, White JF, Verma SK. Seed Endophytic Bacteria of Pearl Millet ( Pennisetum glaucum L.) Promote Seedling Development and Defend Against a Fungal Phytopathogen. Front Microbiol 2021; 12:774293. [PMID: 34956137 PMCID: PMC8696672 DOI: 10.3389/fmicb.2021.774293] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 11/08/2021] [Indexed: 12/02/2022] Open
Abstract
Seed endophytic bacteria (SEB) are primary symbionts that play crucial roles in plant growth and development. The present study reports the isolation of seven culturable SEB including Kosakonia cowanii (KAS1), Bacillus subtilis (KAS2), Bacillus tequilensis (KAS3), Pantoea stewartii (KAS4), Paenibacillus dendritiformis (KAS5), Pseudomonas aeruginosa (KAS6), and Bacillus velezensis (KAS7) in pearl millet seeds. All the isolates were characterized for their plant growth promoting activities. Most of the SEB also inhibited the growth of tested fungal phytopathogens in dual plate culture. Removal of these SEB from seeds compromised the growth and development of seedlings, however, re-inoculation with the SEB (Kosakonia cowanii, Pantoea stewartii, and Pseudomonas aeruginosa) restored the growth and development of seedlings significantly. Fluorescence microscopy showed inter and intracellular colonization of SEB in root parenchyma and root hair cells. Lipopeptides were extracted from all three Bacillus spp. which showed strong antifungal activity against tested fungal pathogens. Antifungal lipopeptide genes were also screened in Bacillus spp. After lipopeptide treatment, live-dead staining with fluorescence microscopy along with bright-field and scanning electron microscopy (SEM) revealed structural deformation and cell death in Fusarium mycelia and spores. Furthermore, the development of pores in the membrane and leakages of protoplasmic substances from cells and ultimately death of hyphae and spores were also confirmed. In microcosm assays, treatment of seeds with Bacillus subtilis or application of its lipopeptide alone significantly protected seedlings from Fusarium sp. infection.
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Affiliation(s)
- Kanchan Kumar
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Anand Verma
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Gaurav Pal
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Anubha
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - James F White
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, United States
| | - Satish K Verma
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
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17
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Chandel A, Mann R, Kaur J, Norton S, Edwards J, Spangenberg G, Sawbridge T. Implications of Seed Vault Storage Strategies for Conservation of Seed Bacterial Microbiomes. Front Microbiol 2021; 12:784796. [PMID: 34925291 PMCID: PMC8678515 DOI: 10.3389/fmicb.2021.784796] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/25/2021] [Indexed: 12/20/2022] Open
Abstract
Global seed vaults are important, as they conserve plant genetic resources for future breeding to improve crop yield and quality and to overcome biotic and abiotic stresses. However, little is known about the impact of standard storage procedures, such as seed drying and cold storage on the seed bacterial community, and the ability to recover seed-associated bacteria after storage. In this study, soybean [Glycine max (L.) Merr.] seeds were analyzed to characterize changes in the bacterial community composition and culturability under varying storage conditions. The G. max bacterial microbiome was analyzed from undried seed, dried seed, and seed stored for 0, 3, 6, and 14months. Storage temperatures consisted of −20°C, 4°C, and room temperature (RT), with −20°C being commonly used in seed storage vaults globally. The seed microbiome of G. max was dominated by Gammaproteobacteria under all conditions. Undried seed was dominated by Pantoea (33.9%) and Pseudomonas (51.1%); however, following drying, the abundance of Pseudomonas declined significantly (0.9%), Pantoea increased significantly (73.6%), and four genera previously identified including Pajaroellobacter, Nesterenkonia, env.OPS_17, and Acidibacter were undetectable. Subsequent storage at RT, 4, or −20°C maintained high-abundance Genera at the majority of time points, although RT caused greater fluctuations in abundances. For many of the low-abundance Genera, storage at −20°C resulted in their gradual disappearance, whereas storage at 4°C or RT resulted in their more rapid disappearance. The changes in seed bacterial composition were reflected by cultured bacterial taxa obtained from the stored G. max seed. The main taxa were largely culturable and had similar relative abundance, while many, but not all, of the low-abundance taxa were also culturable. Overall, these results indicate that the initial seed drying affects the seed bacterial composition, suggesting that microbial isolation prior to seed drying is recommended to conserve these microbes. The standard seed storage condition of −20°C is most suitable for conservation of the bacterial seed microbiome, as this storage temperature slows down the loss of seed bacterial diversity over longer time periods, particularly low-abundance taxa.
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Affiliation(s)
- Ankush Chandel
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Ross Mann
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Jatinder Kaur
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Sally Norton
- Agriculture Victoria Research, Australian Grains Genebank, Horsham, VIC, Australia
| | - Jacqueline Edwards
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - German Spangenberg
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Timothy Sawbridge
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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18
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Francioli D, Cid G, Kanukollu S, Ulrich A, Hajirezaei MR, Kolb S. Flooding Causes Dramatic Compositional Shifts and Depletion of Putative Beneficial Bacteria on the Spring Wheat Microbiota. Front Microbiol 2021; 12:773116. [PMID: 34803993 PMCID: PMC8602104 DOI: 10.3389/fmicb.2021.773116] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/13/2021] [Indexed: 01/04/2023] Open
Abstract
Flooding affects both above- and below-ground ecosystem processes, and it represents a substantial threat for crop and cereal productivity under climate change. Plant-associated microbiota play a crucial role in plant growth and fitness, but we still have a limited understanding of the response of the crop-microbiota complex under extreme weather events, such as flooding. Soil microbes are highly sensitive to abiotic disturbance, and shifts in microbial community composition, structure and functions are expected when soil conditions are altered due to flooding events (e.g., anoxia, pH alteration, changes in nutrient concentration). Here, we established a pot experiment to determine the effects of flooding stress on the spring wheat-microbiota complex. Since plant phenology could be an important factor in the response to hydrological stress, flooding was induced only once and at different plant growth stages (PGSs), such as tillering, booting and flowering. After each flooding event, we measured in the control and flooded pots several edaphic and plant properties and characterized the bacterial community associated to the rhizosphere and roots of wheat plant using a metabarcoding approach. In our study, flooding caused a significant reduction in plant development and we observed dramatic shifts in bacterial community composition at each PGS in which the hydrological stress was induced. However, a more pronounced disruption in community assembly was always shown in younger plants. Generally, flooding caused a (i) significant increase of bacterial taxa with anaerobic respiratory capabilities, such as members of Firmicutes and Desulfobacterota, (ii) a significant reduction in Actinobacteria and Proteobacteria, (iii) depletion of several putative plant-beneficial taxa, and (iv) increases of the abundance of potential detrimental bacteria. These significant differences in community composition between flooded and control samples were correlated with changes in soil conditions and plant properties caused by the hydrological stress, with pH and total N as the soil, and S, Na, Mn, and Ca concentrations as the root properties most influencing microbial assemblage in the wheat mircobiota under flooding stress. Collectively, our findings demonstrated the role of flooding on restructuring the spring wheat microbiota, and highlighted the detrimental effect of this hydrological stress on plant fitness and performance.
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Affiliation(s)
- Davide Francioli
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Geeisy Cid
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Saranya Kanukollu
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Andreas Ulrich
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Mohammad-Reza Hajirezaei
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany.,Faculty of Life Sciences, Thaer Institute, Humboldt University of Berlin, Berlin, Germany
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19
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Tayyab M, Yang Z, Zhang C, Islam W, Lin W, Zhang H. Sugarcane monoculture drives microbial community composition, activity and abundance of agricultural-related microorganisms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:48080-48096. [PMID: 33904129 DOI: 10.1007/s11356-021-14033-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/16/2021] [Indexed: 05/28/2023]
Abstract
Sugarcane monoculture (SM) often leads to soil problems, like soil acidification, degradation, and soil-borne diseases, which ultimately pose a negative impact on agricultural productivity and sustainability. Understanding the change in microbial communities' composition, activities, and functional microbial taxa associated with the plant and soil under SM is unclear. Using multidisciplinary approaches such as Illumina sequencing, measurements of soil properties, and enzyme activities, we analyzed soil samples from three sugarcane fields with different monoculture histories (1-, 2-, and 4-year cultivation times, respectively). We observed that SM induced soil acidity and had adverse effects on soil fertility, i.e., soil organic matter (OM), total nitrogen (TN), total carbon (TC), and available potassium (AK), as well as enzyme activities indicative for carbon, phosphorus, and nitrogen cycles. Non-metric multidimensional scaling (NMDS) analysis showed that SM time greatly affected soil attribute patterns. We observed strong correlation among soil enzymes activities and soil physiochemical properties (soil pH, OM, and TC). Alpha diversity analysis showed a varying response of the microbes to SM time. Bacterial diversity increased with increasing oligotrophs (e.g., Acidobacteria and Chloroflexi), while fungal diversity decreased with reducing copiotrophs (e.g., Ascomycota). β-Diversity analysis showed that SM time had a great influence on soil microbial structure and soil properties, which led to the changes in major components of microbial structure (soil pH, OM, TC, bacteria and soil pH; TC, fungi). Additionally, SM time significantly stimulated (four bacterial and ten fungal) and depleted (12 bacterial and three fungal) agriculturally and ecologically important microbial genera that were strongly and considerably correlated with soil characteristics (soil pH, OM, TC, and AK). In conclusion, SM induces soil acidity, reduces soil fertility, shifts microbial structure, and reduces its activity. Furthermore, most beneficial bacterial genera decreased significantly due to SM, while beneficial fungal genera showed a reverse trend. Therefore, mitigating soil acidity, improving soil fertility, and soil enzymatic activities, including improved microbial structure with beneficial service to plants and soil, can be an effective measure to develop a sustainable sugarcane cropping system.
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Affiliation(s)
- Muhammad Tayyab
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agro-ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, 35002, China
| | - Ziqi Yang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Caifang Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Waqar Islam
- College of Geography, Fujian Normal University, Fuzhou, 350007, China
| | - Wenxiong Lin
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Fujian Provincial Key Laboratory of Agro-ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, 35002, China.
| | - Hua Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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20
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Liang D, Guo J, Hou F, Bowatte S. High level of conservation and diversity among the endophytic seed bacteriome in eight alpine grassland species growing at the Qinghai Tibetan Plateau. FEMS Microbiol Ecol 2021; 97:6246421. [PMID: 33885767 DOI: 10.1093/femsec/fiab060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
Seed borne microorganisms play an important role in plant biology. Concerns have recently been raised about loss of seed microbial diversity by seed treatments, crop domestication and plant breeding. Information on the seed microbiomes of native plants growing in natural ecosystems is beneficial as they provide the best settings to detect indigenous plant microbe interactions. Here, we characterized the seed bacterial community of 8 native alpine grassland plants. First, seed bacterial diversity was examined using Illumina DNA sequencing, then 28 cultivable bacteria were isolated and potential functions were explored. Across 8 plant species, 343 different bacterial genera were identified as seed endophytes, 31 of those were found in all plant species, indicating a high level of conservation. Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Chloroflexi were the top five dominant phyla. Plant species identity was a key determinant shaping the seed endophytic bacteriome. ACC deaminase activity, siderophores production and secretion of lytic enzymes were common functions shown by isolated bacteria. Our results demonstrate that highly diverse and beneficial bacterial populations are hosted by seeds of alpine grassland species to ensure the establishment of best bacterial symbionts for the next generation. This information is useful for crop improvement by reinstating beneficial seed microbial diversities for high-quality forage and crop seeds.
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Affiliation(s)
- Danni Liang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Jiayuguan West Roadd 768, Lanzhou, Gansu, 730020, China
| | - Jianxiu Guo
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Jiayuguan West Roadd 768, Lanzhou, Gansu, 730020, China
| | - Fujiang Hou
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Jiayuguan West Roadd 768, Lanzhou, Gansu, 730020, China
| | - Saman Bowatte
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Jiayuguan West Roadd 768, Lanzhou, Gansu, 730020, China.,AgResearch Limited, Grasslands Research Center, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
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21
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Comprehensive Review of Endophytic Flora from African Medicinal Plants. Curr Microbiol 2021; 78:2860-2898. [PMID: 34184112 DOI: 10.1007/s00284-021-02566-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 06/04/2021] [Indexed: 12/15/2022]
Abstract
Many people in different African countries are suffering from different diseases many of which result in serious life threat and public health problems with high risk of infection and mortality. Due to less accessibility and high cost of modern drugs, people of this continent often depend on traditional medicine using medicinal plants to manage the diseases. Africa has large tropical rain forests, which are very rich in medicinal plants. Many of them have been scientifically proven for their medicinal values. These medicinal plants which constitute a large repertoire of endophytes have not been significantly explored for the isolation of these microorganisms and their bioactive secondary metabolites. This review summarizes the research on endophytes isolated from medicinal plants of Africa, their pharmacological potential and some of their biotechnological aspects. Novel compounds reported from endophytes from Africa with their biological activities have also been reviewed. Information documented in this review might serve as starting point for future researches on endophytes in different African countries.
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22
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Invasive Lactuca serriola seeds contain endophytic bacteria that contribute to drought tolerance. Sci Rep 2021; 11:13307. [PMID: 34172799 PMCID: PMC8233371 DOI: 10.1038/s41598-021-92706-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023] Open
Abstract
The mutualistic relationship between alien plant species and microorganisms is proposed to facilitate or hinder invasive success, depending on whether plants can form novel associations with microorganisms in the introduced habitats. However, this hypothesis has not considered seed endophytes that would move together with plant propagules. Little information is available on the seed endophytic bacteria of invasive species and their effects on plant performance. We isolated the seed endophytic bacteria of a xerophytic invasive plant, Lactuca serriola, and examined their plant growth-promoting traits. In addition, we assessed whether these seed endophytes contributed to plant drought tolerance. Forty-two bacterial species were isolated from seeds, and all of them exhibited at least one plant growth-promoting trait. Kosakonia cowanii occurred in all four tested plant populations and produced a high concentration of exopolysaccharides in media with a highly negative water potential. Notably, applying K. cowanii GG1 to Arabidopsis thaliana stimulated plant growth under drought conditions. It also reduced soil water loss under drought conditions, suggesting bacterial production of exopolysaccharides might contribute to the maintenance of soil water content. These results imply that invasive plants can disperse along with beneficial bacterial symbionts, which potentially improve plant fitness and help to establish alien plant species.
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23
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Sharma A, Kaushik N, Sharma A, Bajaj A, Rasane M, Shouche YS, Marzouk T, Djébali N. Screening of Tomato Seed Bacterial Endophytes for Antifungal Activity Reveals Lipopeptide Producing Bacillus siamensis Strain NKIT9 as a Potential Bio-Control Agent. Front Microbiol 2021; 12:609482. [PMID: 34177819 PMCID: PMC8222588 DOI: 10.3389/fmicb.2021.609482] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/23/2021] [Indexed: 11/13/2022] Open
Abstract
The current study investigates the diversity pattern and fungicidal potential of bacterial endophytes isolated from two different organic varieties of tomato plants (V1 and V2). A total of seventy-five bacterial isolates identified by 16S rRNA gene sequencing revealed a majority of genus as Bacillus and one Planococcus, which were grouped into eight different species. The Shannon diversity H' (1.56), Simpson's index of diversity (0.93), Magalef' index (2.23), Evenness (0.96), and Species richness (7) indicated the high endophytic bacterial diversity in the V1 variety of the tomato. Bacterial endophytes isolated from both of the varieties were screened for their antifungal activity against five economically critical fungal pathogens (viz., Botrytis cinerea, Rhizoctonia solani, Fusarium solani, Verticillium lateritium, and Alternaria solani) of tomato crop through dual culture assay. The data revealed B. siamensis strain NKIT9 as the most potent antagonist, significantly (p < 0.05) inhibiting the mycelial growth between 75 to 90% against selected fungal pathogens. High bioactivity of lipopeptide extract of strain NKIT9 was recorded against R. solani with minimum IC50 value of 230 μg/ml. The Ultra Performance Liquid Chromatography-High Definition Mass Spectrometry (UPLC-HDMS) analysis of this lipopeptide extract revealed the presence of Surfactin and Bacillomycin D. Furthermore, in-vitro results showed that the selected bacterial strain significantly minimized the disease incidence in damping-off assay which makes this strain a promising antifungal bio-control agent. Moreover, in the pot experiment the NKIT9 increased the fruit yield by 59.2% compared with the untreated R. solani infested control.
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Affiliation(s)
- Ayushi Sharma
- Amity Food and Agriculture Foundation, Amity University Uttar Pradesh, Noida, India.,Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida, India
| | - Nutan Kaushik
- Amity Food and Agriculture Foundation, Amity University Uttar Pradesh, Noida, India
| | - Abhishek Sharma
- Amity Food and Agriculture Foundation, Amity University Uttar Pradesh, Noida, India
| | - Abhay Bajaj
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Mandar Rasane
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Yogesh S Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Takwa Marzouk
- Centre of Biotechnology of Borj Cedria, Laboratory of Bioactive Substances, Hammam-lif, Tunisia
| | - Naceur Djébali
- Centre of Biotechnology of Borj Cedria, Laboratory of Bioactive Substances, Hammam-lif, Tunisia
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24
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Mishra S, Goyal D, Phurailatpam L. Targeted 16S rRNA gene and ITS2 amplicon sequencing of leaf and spike tissues of Piper longum identifies new candidates for bioprospecting of bioactive compounds. Arch Microbiol 2021; 203:3851-3867. [PMID: 34013420 DOI: 10.1007/s00203-021-02356-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/27/2021] [Accepted: 05/03/2021] [Indexed: 12/19/2022]
Abstract
Piper longum (also known as Indian long pepper) is widely used in Ayurvedic, Siddha and Unani medicine systems. The principle bioactive compound of this plant is piperine, which mainly accumulates in the fruits called spikes. The report of piperine production by endophytic microbes isolated from Piper sp., motivated us to investigate the endophytic microbial diversity associated with the spikes vis-à-vis leaves (which contain negligible levels of piperine). This is the first report to use metagenomics approach to unravel the endophytic microbial diversity in P. longum. Our results indicate that 2, 56, 631 bacterial OTUs and 1090 fungal OTUs were picked cumulatively from both the tissues. Although bacterial and fungal endophytes occupy the same niche, remarkable differences exist in their diversity and abundance. For instance, the most abundant bacterial genera in spikes were Nocardioides and Pseudonocardia (Phylum Actinobacteria; reported to produce bioactive compounds); while, in leaves were Larkinella and Hymenobacter (Phylum Bacteriodetes). Likewise, the fungal endophytes, Periconia, Cladosporium and Coniothyrium (which have been earlier reported to produce commercially important metabolites including piperine), were also present in high abundance in spikes, in comparison to leaves. Further, the results of PICRUSt analysis reveal the high metabolic potential of spike-associated bacteria for secondary metabolism, namely biosynthesis of alkaloids (including pyridine/piperidine), terpenes, flavonoids and antibiotics. Therefore, our findings indicate that the endophytes abundant or unique in spikes could be explored for bioprospecting of novel/commercially important metabolites; an approach that has both ecological and economical benefits.
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Affiliation(s)
- Sushma Mishra
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed-to-be-University), Agra, Uttar Pradesh, India.
| | - Deepika Goyal
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed-to-be-University), Agra, Uttar Pradesh, India
| | - Laccy Phurailatpam
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed-to-be-University), Agra, Uttar Pradesh, India
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25
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Cardinale M, Viola M, Miceli E, Faddetta T, Puglia AM, Maggini V, Tani C, Firenzuoli F, Schiff S, Bogani P, Fani R, Papini A. The cypsela (achene) of Echinacea purpurea as a diffusion unit of a community of microorganisms. Appl Microbiol Biotechnol 2021; 105:2951-2965. [PMID: 33687502 PMCID: PMC8007504 DOI: 10.1007/s00253-021-11212-2] [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: 11/22/2020] [Revised: 02/15/2021] [Accepted: 02/28/2021] [Indexed: 11/30/2022]
Abstract
Echinacea purpurea is a plant cultivated worldwide for its pharmaceutical properties, mainly related to the stimulation of the immune system in the treatment of respiratory infections. The cypselas (fruits) of E. purpurea were examined in order to investigate the presence, localization and potential function(s) of endophytic microorganisms. Electron and confocal microscopy observations showed that three different components of microorganisms were associated to cypselas of E. purpurea: (i) one endocellular bacterial component in the cotyledons, enclosed within the host membrane; (ii) another more generic bacterial component adhering to the external side of the perianth; and (iii) a fungal component inside the porous layer of the perianth, the woody and porous modified residual of the flower, in the form of numerous hyphae able to cross the wall between adjacent cells. Isolated bacteria were affiliated to the genera Paenibacillus, Pantoea, and Sanguibacter. Plate tests showed a general resistance to six different antibiotics and also to an antimicrobial-producing Rheinheimera sp. test strain. Finally, microbiome-deprived E. purpurea seeds showed a reduced ability to germinate, suggesting an active role of the microbiome in the plant vitality. Our results suggest that the endophytic bacterial community of E. purpurea, previously found in roots and stem/leaves, might be already carried at the seed stage, hosted by the cotyledons. A further microbial fungal component is transported together with the seed in the perianth of the cypsela, whose remarkable structure may be considered as an adaptation for fungal transportation, and could influence the capability of the seed to germinate in the soil.Key Points• The fruit of Echinacea purpurea contains fungi not causing any damage to the plant.• The seed cotyledons contain endocellular bacteria.• Seed/fruit deprived of the microbiome showed a reduced ability to germinate.
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Affiliation(s)
- Massimiliano Cardinale
- Department of Biological and Environmental Sciences and Technologies, University of Salento, P.le Lecce-Monteroni, 73100, Lecce, Italy
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Marian Viola
- Laboratory of Biomorphologies, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Italy
| | - Elisangela Miceli
- Laboratory of Microbial and Molecular evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Italy
| | - Teresa Faddetta
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, Viale delle Scienze Ed. 16, 90128, Palermo, Italy
| | - Anna Maria Puglia
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, Viale delle Scienze Ed. 16, 90128, Palermo, Italy
| | - Valentina Maggini
- Referring Center for Phytotherapy, Tuscany Region, Careggi University Hospital, Largo Brambilla 3, 50134, Florence, Italy
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134, Florence, Italy
| | - Corrado Tani
- Laboratory of Biomorphologies, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Italy
| | - Fabio Firenzuoli
- Referring Center for Phytotherapy, Tuscany Region, Careggi University Hospital, Largo Brambilla 3, 50134, Florence, Italy
| | - Silvia Schiff
- Laboratory of Biomorphologies, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Italy
| | - Patrizia Bogani
- Laboratory of Plant Genetics, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Italy
| | - Renato Fani
- Laboratory of Microbial and Molecular evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Italy.
| | - Alessio Papini
- Laboratory of Biomorphologies, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Italy.
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26
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Kavamura VN, Mendes R, Bargaz A, Mauchline TH. Defining the wheat microbiome: Towards microbiome-facilitated crop production. Comput Struct Biotechnol J 2021; 19:1200-1213. [PMID: 33680361 PMCID: PMC7902804 DOI: 10.1016/j.csbj.2021.01.045] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 12/17/2022] Open
Abstract
Wheat is one of the world's most important crops, but its production relies heavily on agrochemical inputs which can be harmful to the environment when used excessively. It is well known that a multitude of microbes interact with eukaryotic organisms, including plants, and the sum of microbes and their functions associated with a given host is termed the microbiome. Plant-microbe interactions can be beneficial, neutral or harmful to the host plant. Over the last decade, with the development of next generation DNA sequencing technology, our understanding of the plant microbiome structure has dramatically increased. Considering that defining the wheat microbiome is key to leverage crop production in a sustainable way, here we describe how different factors drive microbiome assembly in wheat, including crop management, edaphic-environmental conditions and host selection. In addition, we highlight the benefits to take a multidisciplinary approach to define and explore the wheat core microbiome to generate solutions based on microbial (synthetic) communities or single inoculants. Advances in plant microbiome research will facilitate the development of microbial strategies to guarantee a sustainable intensification of crop production.
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Affiliation(s)
- Vanessa N. Kavamura
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna, SP, Brazil
| | - Adnane Bargaz
- Agrobiosciences, Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Tim H. Mauchline
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, UK
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27
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Definition of Core Bacterial Taxa in Different Root Compartments of Dactylis glomerata, Grown in Soil under Different Levels of Land Use Intensity. DIVERSITY 2020. [DOI: 10.3390/d12100392] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Plant-associated bacterial assemblages are critical for plant fitness. Thus, identifying a consistent plant-associated core microbiome is important for predicting community responses to environmental changes. Our target was to identify the core bacterial microbiome of orchard grass Dactylis glomerata L. and to assess the part that is most sensitive to land management. Dactylis glomerata L. samples were collected from grassland sites with contrasting land use intensities but comparable soil properties at three different timepoints. To assess the plant-associated bacterial community structure in the compartments rhizosphere, bulk soil and endosphere, a molecular barcoding approach based on high throughput 16S rRNA amplicon sequencing was used. A distinct composition of plant-associated core bacterial communities independent of land use intensity was identified. Pseudomonas, Rhizobium and Bradyrhizobium were ubiquitously found in the root bacterial core microbiome. In the rhizosphere, the majority of assigned genera were Rhodoplanes, Methylibium, Kaistobacter and Bradyrhizobium. Due to the frequent occurrence of plant-promoting abilities in the genera found in the plant-associated core bacterial communities, our study helps to identify “healthy” plant-associated bacterial core communities. The variable part of the plant-associated microbiome, represented by the fluctuation of taxa at the different sampling timepoints, was increased under low land use intensity. This higher compositional variation in samples from plots with low land use intensity indicates a more selective recruitment of bacteria with traits required at different timepoints of plant development compared to samples from plots with high land use intensity.
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28
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Wang Z, Zhu Y, Jing R, Wu X, Li N, Liu H, Zhang X, Wang W, Liu Y. High-throughput sequencing-based analysis of the composition and diversity of endophytic bacterial community in seeds of upland rice. Arch Microbiol 2020; 203:609-620. [PMID: 32995980 DOI: 10.1007/s00203-020-02058-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/17/2020] [Accepted: 09/19/2020] [Indexed: 01/07/2023]
Abstract
Upland rice is an ecotype crop resulting from the long-term domestication and evolution of rice in dry land without a water layer. Generally, the stems and leaves are thick and luxuriant, while the leaves also typically broad and light. The root system is developed with abundant root hair, and the osmotic pressure of the root and cell juice concentration in the leaves is high, while this plant is drought-resistant, heat-resistant, and water absorbent. This study aims to reveal the "core flora" of the endophytes in upland rice seeds by examining their diversity and community structures. It further intends to reveal the impact of the soil environment on the formation of endophyte community structures in upland rice seeds by comparing the environmental soil microorganisms in upland rice habitats. In this study, high-throughput sequencing technology based on the Illumina Hiseq 2500 platform was used to investigate the structure and diversity of endophytic bacterial communities using upland rice varieties collected from different locations and soil samples from unified planting sites as materials. Here, 42 endophytic OTUs were found to coexist in the 14 samples. At the phylum level, the first dominant phyla in all the samples were Proteobacteria (93.81-99.99%). At the genus level, Pantoea (8.77-87.77%), Pseudomonas (1.15-61.58%), Methylobacterium (0.40-4.64%), Sphingomonas (0.26-3.85%), Microbacterium (0.01-4.67%) and Aurantimonas (0.04-4.34%), which represent the core microflora in upland rice seeds, served as the dominant genera that coexisted in all the upland rice seeds tested. This study significant for the isolation, screening, functional evaluation, and re-action of various functional microorganisms in upland rice to improve its agronomic traits. It also provides a specific reference for the interaction between microorganisms and plants.
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Affiliation(s)
- Zhishan Wang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yongqiang Zhu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center At Shanghai, Shanghai, 201203, China
| | - Ruixue Jing
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xianyu Wu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Ni Li
- State Key Laboratory of Hybrid Rice (Hunan Hybrid Rice Research Center), Changsha, 410125, China
| | - Hai Liu
- State Key Laboratory of Hybrid Rice (Hunan Hybrid Rice Research Center), Changsha, 410125, China
| | - Xiaoxia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Weiping Wang
- State Key Laboratory of Hybrid Rice (Hunan Hybrid Rice Research Center), Changsha, 410125, China.
| | - Yang Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
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29
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Romano I, Ventorino V, Ambrosino P, Testa A, Chouyia FE, Pepe O. Development and Application of Low-Cost and Eco-Sustainable Bio-Stimulant Containing a New Plant Growth-Promoting Strain Kosakonia pseudosacchari TL13. Front Microbiol 2020; 11:2044. [PMID: 33013749 PMCID: PMC7461993 DOI: 10.3389/fmicb.2020.02044] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/03/2020] [Indexed: 01/26/2023] Open
Abstract
The use of beneficial microbes as inoculants able to improve fitness, growth and health of plants also in stress conditions is an attractive low-cost and eco-friendly alternative strategy to harmful chemical inputs. Thirteen potential plant growth-promoting bacteria were isolated from the rhizosphere of wheat plants cultivated under drought stress and nitrogen deficiency. Among these, the two isolates TL8 and TL13 showed multiple plant growth promotion activities as production of indole-3-acetic acid (IAA), siderophores, ammonia, and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase production, the ability to solubilize phosphate as well as exerted antimicrobial activity against plant pathogens as Botrytis spp. and Phytophthora spp. The two selected strains were identified as Kosakonia pseudosacchari by sequencing of 16S rRNA gene. They resulted also tolerant to abiotic stress and were able to efficiently colonize plant roots as observed in vitro assay under fluorescence microscope. Based on the best PGP properties, the strain K. pseudosacchari TL13 was selected to develop a new microbial based formulate. A sustainable and environmentally friendly process for inoculant production was developed using agro-industrial by-products for microbial growth. Moreover, the application of K. pseudosacchari TL13- based formulates in pot experiment improved growth performance of maize plants.
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Affiliation(s)
- Ida Romano
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Valeria Ventorino
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Patrizia Ambrosino
- Agriges S.r.l. - Nutrizione Speciale per L'Agricoltura Biologica e Integrata, San Salvatore Telesino, Italy
| | - Antonino Testa
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Fatima Ezzahra Chouyia
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy.,Department of Biology, Faculty of Sciences and Techniques, Hassan II University of Casablanca, Casablanca, Morocco
| | - Olimpia Pepe
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
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30
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Alsharif W, Saad MM, Hirt H. Desert Microbes for Boosting Sustainable Agriculture in Extreme Environments. Front Microbiol 2020; 11:1666. [PMID: 32793155 PMCID: PMC7387410 DOI: 10.3389/fmicb.2020.01666] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 06/25/2020] [Indexed: 11/13/2022] Open
Abstract
A large portion of the earth's surface consists of arid, semi-arid and hyper-arid lands. Life in these regions is profoundly challenged by harsh environmental conditions of water limitation, high levels of solar radiation and temperature fluctuations, along with soil salinity and nutrient deficiency, which have serious consequences on plant growth and survival. In recent years, plants that grow in such extreme environments and their naturally associated beneficial microbes have attracted increased interest. The rhizosphere, rhizosheath, endosphere, and phyllosphere of desert plants display a perfect niche for isolating novel microbes. They are well adapted to extreme environments and offer an unexploited reservoir for bio-fertilizers and bio-control agents against a wide range of abiotic and biotic stresses that endanger diverse agricultural ecosystems. Their properties can be used to improve soil fertility, increase plant tolerance to various environmental stresses and crop productivity as well as benefit human health and provide enough food for a growing human population in an environment-friendly manner. Several initiatives were launched to discover the possibility of using beneficial microbes. In this review, we will be describing the efforts to explore the bacterial diversity associated with desert plants in the arid, semi-arid, and hyper-arid regions, highlighting the latest discoveries and applications of plant growth promoting bacteria from the most studied deserts around the world.
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Affiliation(s)
- Wiam Alsharif
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Maged M. Saad
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Max Perutz Laboratories, University of Vienna, Vienna, Austria
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Raths R, Peta V, Bücking H. Massilia arenosa sp. nov., isolated from the soil of a cultivated maize field. Int J Syst Evol Microbiol 2020; 70:3912-3920. [DOI: 10.1099/ijsem.0.004266] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain MC02T, a Gram-stain-negative, rod-shaped bacterium, was isolated from field soil collected from California, USA. To examine if MC02T represents a novel species, we compared its colony morphology, 16S rRNA gene and whole genome sequence, and its metabolic phenotype using Biolog GenIII and MALDI-TOF analyses compared to reference strains. Based on 16S rRNA gene and whole genome sequencing, MC02T belongs to the genus
Massilia
and
Massilia agri
K-3–1T is the most similar strain with 96.97 % 16S rRNA gene sequence identity. MALDI-TOF analysis revealed that
Massilia aerilata
DSM19289T is the closest match, but the similarity score was much lower than the ≥1.7 threshold for a reliable identification at the genus level. The predominant fatty acids were summed feature 3 (C16 : 1⍵7c and/or C16 : 1⍵6c; 49.07 %) and C16 : 0 (30.01 %). The genome is 5.02 Mbp and the G+C content is 66.2 mol%. Whole genome comparisons to the closest related strains revealed an average amino acid identity value of 67.4 %, an OrthoANI similarity of 77.1 %, and a DNA–DNA-hybridization probability ≥70 %, confirming that MC02T represents a novel species. Strain MC02T can grow at pH 6 but not at pH 5, and a salt concentration of ≥1 % inhibits its growth. In contrast to other
Massilia
strains, MC02T can utilize turanose, inosine and l-serine. The genome of MC02T shows putative endophyte genes such as a nitrate reductase, several phosphatases, and biotin biosynthesis genes, 26 flagellar motility genes and 14 invasion and intracellular resistance genes. Based on its metabolic, physiological and genomic characteristics, we propose that strain MC02T (NRRL B-65554T=ATCC TSD-200T=LMG 31737T) represents a novel species of the genus
Massilia
with the name Massilia arenosa sp. nov.
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Affiliation(s)
- Rachel Raths
- South Dakota State University, Biology and Microbiology Department, Brookings, SD 57007, USA
| | - Vincent Peta
- South Dakota State University, Biology and Microbiology Department, Brookings, SD 57007, USA
| | - Heike Bücking
- South Dakota State University, Biology and Microbiology Department, Brookings, SD 57007, USA
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Du J, Wang T, Zhou Q, Hu X, Wu J, Li G, Li G, Hou F, Wu Y. Graphene oxide enters the rice roots and disturbs the endophytic bacterial communities. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 192:110304. [PMID: 32066006 DOI: 10.1016/j.ecoenv.2020.110304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 02/02/2020] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
The environmental release of graphene oxide (GO) will certainly induce the GO exposure to plants. To date, the influence of GO on the intracellular structures and the endophytic bacterial ecology of plants have been rarely reported. In the present study, the rice seedlings were exposed to GO (5 mg/L) under hydroponic condition for fifteen days with periodic stir. The cellular structures damage, GO deposition and oxidative stress were found in rice root after GO exposure. A Illumina analysis based on the bacterial 16 S rRNA gene showed that the richness, evenness and diversity of endophytic bacterial communities of rice root decreased due to GO exposure. The relative abundance of beneficial endophytic bacterial populations decreased after GO exposure. Out of potential phenotypes predicted by BugBase, the relative abundance of Gram negative, stress-tolerant and biofilm-forming phenotypes, presented an increase trend after GO exposure.
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Affiliation(s)
- Junjie Du
- College of Food Science, Shanxi Normal University, Linfen City, 041004, China; NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100022, China
| | - Ting Wang
- College of Food Science, Shanxi Normal University, Linfen City, 041004, China
| | - Qixing Zhou
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China.
| | - Jianhu Wu
- College of Food Science, Shanxi Normal University, Linfen City, 041004, China
| | - Guifeng Li
- College of Food Science, Shanxi Normal University, Linfen City, 041004, China
| | - Guoqin Li
- College of Food Science, Shanxi Normal University, Linfen City, 041004, China
| | - Fen Hou
- School of Public Administration, Shanxi University of Finance and Economics, Taiyuan, 030000, China
| | - Yongning Wu
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100022, China.
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An Z, Guo F, Chen Y, Bai G, Chen Z. Rhizosphere bacterial and fungal communities during the growth of Angelica sinensis seedlings cultivated in an Alpine uncultivated meadow soil. PeerJ 2020; 8:e8541. [PMID: 32257632 PMCID: PMC7103203 DOI: 10.7717/peerj.8541] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/09/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Angelica sinensis seedlings are grown in alpine uncultivated meadow soil with rainfed agroecosystems to ensure the quality of A. sinensis after seedling transplantation. The aim was to investigate the rhizosphere bacterial and fungal communities during the growth stages of A. sinensis seedlings. METHODS The bacterial and fungal communities were investigated by HiSeq sequencing of 16S and 18S rDNA, respectively. RESULTS Proteobacteria and Bacteroidetes were bacterial dominant phyla throughout growth stages. Fungal dominant phyla varied with growth stages, dominant phyla Ascomycota and Chytridiomycota in AM5, dominant phyla Basidiomycota, Ascomycota and Zygomycota in BM5, and dominant phyla Basidiomycota and Ascomycota in CM5. There was no significant variation in the alpha-diversity of the bacterial and fungal communities, but significant variation was in the beta-diversity. We found that the variation of microbial community composition was accompanied by the changes in community function. The relative abundance of fungal pathogens increased with plant growth. We also identified the core microbes, significant-changing microbes, stage-specific microbes, and host-specific microbes. Plant weight, root length, root diameter, soil pH, rainfall, and climate temperature were the key divers to microbial community composition. CONCLUSIONS Our findings reported the variation and environmental drivers of rhizosphere bacterial and fungal communities during the growth of A. sinensis seedlings, which enhance the understanding of the rhizosphere microbial community in this habitat.
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Affiliation(s)
- Zhigang An
- College of Life Science and Technology, College of Agronomy, Gansu Provincial Key Lab of Good Agricultural Production for Traditional Chinese Medicine, Gansu Provincial Engineering Research Centre for Medical Plant Cultivation and Breeding, Provincial Key Lab of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- Pharmacy Department, Gansu University of Chinese Medicine, Dingxi, China
| | - Fengxia Guo
- College of Life Science and Technology, College of Agronomy, Gansu Provincial Key Lab of Good Agricultural Production for Traditional Chinese Medicine, Gansu Provincial Engineering Research Centre for Medical Plant Cultivation and Breeding, Provincial Key Lab of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Yuan Chen
- College of Life Science and Technology, College of Agronomy, Gansu Provincial Key Lab of Good Agricultural Production for Traditional Chinese Medicine, Gansu Provincial Engineering Research Centre for Medical Plant Cultivation and Breeding, Provincial Key Lab of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- Gansu Engineering Lab of Resource Reservation and Utilization for Characteristic Chinese Medicine, Gansu Tasly Zhongtian Pharmaceutical Co., Ltd., Dingxi, China
| | - Gang Bai
- College of Life Science and Technology, College of Agronomy, Gansu Provincial Key Lab of Good Agricultural Production for Traditional Chinese Medicine, Gansu Provincial Engineering Research Centre for Medical Plant Cultivation and Breeding, Provincial Key Lab of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Zhengjun Chen
- College of Life Science and Technology, College of Agronomy, Gansu Provincial Key Lab of Good Agricultural Production for Traditional Chinese Medicine, Gansu Provincial Engineering Research Centre for Medical Plant Cultivation and Breeding, Provincial Key Lab of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
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Fadiji AE, Babalola OO. Metagenomics methods for the study of plant-associated microbial communities: A review. J Microbiol Methods 2020; 170:105860. [PMID: 32027927 DOI: 10.1016/j.mimet.2020.105860] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/31/2020] [Accepted: 02/02/2020] [Indexed: 12/20/2022]
Abstract
Plant microbiota have different effects on the plant which can be beneficial or pathogenic. In this study, we concentrated on beneficial microbes associated with plants using endophytic microbes as a case study. Detailed knowledge of the microbial diversity, abundance, composition, functional genes patterns, and metabolic pathways at genome level could assist in understanding the contributions of microbial community towards plant growth and health. Recently, the study of microbial community has improved greatly with the discovery of next-generation sequencing and bioinformatics technologies. Analysis of next generation sequencing data and a proper computational method plays a key role in examining microbial metagenome. This review presents the general metagenomics and computational methods used in processing plant associated metagenomes with concentration on endophytes. This includes 1) introduction of plant-associated microbiota and the factors driving their diversity. 2) plant metagenome focusing on DNA extraction, verification and quality control. 3) metagenomics methods used in community analysis of endophytes focusing on maize plant and, 4) computational methods used in the study of endophytic microbiomes. Limitations and future prospects of metagenomics and computational methods for the analysis of plant-associated metagenome (endophytic metagenome) were also discussed with the aim of fostering its development. We conclude that there is need to adopt advanced genomic features such as k-mers of random size, which do not depend on annotation and can represent other sequence alternatives.
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Affiliation(s)
- Ayomide Emmanuel Fadiji
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa.
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35
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Isolation and Identification of Endophytic Bacteria from Mycorrhizal Tissues of Terrestrial Orchids from Southern Chile. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12020055] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Endophytic bacteria are relevant symbionts that contribute to plant growth and development. However, the diversity of bacteria associated with the roots of terrestrial orchids colonizing Andean ecosystems is limited. This study identifies and examines the capabilities of endophytic bacteria associated with peloton-containing roots of six terrestrial orchid species from southern Chile. To achieve our goals, we placed superficially disinfected root fragments harboring pelotons on oatmeal agar (OMA) with no antibiotic addition and cultured them until the bacteria appeared. Subsequently, they were purified and identified using molecular tools and examined for plant growth metabolites production and antifungal activity. In total, 168 bacterial strains were isolated and assigned to 8 OTUs. The orders Pseudomonadales, Burkholderiales, and Xanthomonadales of phylum Proteobacteria were the most frequent. The orders Bacillales and Flavobacteriales of the phylla Firmicutes and Bacteroidetes were also obtained. Phosphate solubilization was detected in majority of isolates; however, it was significantly higher in Collimonas pratensis and Chryseobacterium sp. (PSI = 1.505 ± 0.09 and 1.405 ± 0.24, respectively). Siderophore production was recorded only for C. pratensis (0.657 ± 0.14 mm day−1), Dyella marensis (0.131 ± 0.02 mm day−1), and Luteibacter rhizovicinus (0.343 ± 0.12 mm day−1). Indole acetic acid production was highly influenced by the isolate identity; however, the significantly higher activity was recorded for Pseudomonas spp. (ranging from 5.507 ± 1.57 µg mL−1 to 7.437 ± 0.99 µg mL−1). Additionally, six bacterial isolates were able to inhibit the growth of some potential plant pathogenic fungi. Our findings demonstrate the potential for plant growth promoting capabilities and some antifungal activities of endophytic bacteria inhabiting the mycorrhizal tissue of terrestrial orchids, which may contribute especially at early developmental stages of orchid seedlings.
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36
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Kavamura VN, Robinson RJ, Hughes D, Clark I, Rossmann M, Melo ISD, Hirsch PR, Mendes R, Mauchline TH. Wheat dwarfing influences selection of the rhizosphere microbiome. Sci Rep 2020; 10:1452. [PMID: 31996781 PMCID: PMC6989667 DOI: 10.1038/s41598-020-58402-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/14/2020] [Indexed: 12/23/2022] Open
Abstract
The development of dwarf wheat cultivars combined with high levels of agrochemical inputs during the green revolution resulted in high yielding cropping systems. However, changes in wheat cultivars were made without considering impacts on plant and soil microbe interactions. We studied the effect of these changes on root traits and on the assembly of rhizosphere bacterial communities by comparing eight wheat cultivars ranging from tall to semi-dwarf plants grown under field conditions. Wheat breeding influenced root diameter and specific root length (SRL). Rhizosphere bacterial communities from tall cultivars were distinct from those associated with semi-dwarf cultivars, with higher differential abundance of Actinobacteria, Bacteroidetes and Proteobacteria in tall cultivars, compared with a higher differential abundance of Verrucomicrobia, Planctomycetes and Acidobacteria in semi-dwarf cultivars. Predicted microbial functions were also impacted and network analysis revealed a greater level of connectedness between microbial communities in the tall cultivars relative to semi-dwarf cultivars. Taken together, results suggest that the development of semi-dwarf plants might have affected the ability of plants to recruit and sustain a complex bacterial community network in the rhizosphere.
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Affiliation(s)
- Vanessa N Kavamura
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Rebekah J Robinson
- Plant Pathology Laboratory, Royal Horticultural Society, RHS Garden Wisley, Woking, Surrey, GU23 6QB, United Kingdom
| | - David Hughes
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Ian Clark
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Maike Rossmann
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna-SP, Brazil
| | - Itamar Soares de Melo
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna-SP, Brazil
| | - Penny R Hirsch
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna-SP, Brazil
| | - Tim H Mauchline
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom.
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Cueva-Yesquén LG, Goulart MC, Attili de Angelis D, Nopper Alves M, Fantinatti-Garboggini F. Multiple Plant Growth-Promotion Traits in Endophytic Bacteria Retrieved in the Vegetative Stage From Passionflower. FRONTIERS IN PLANT SCIENCE 2020; 11:621740. [PMID: 33537051 PMCID: PMC7847900 DOI: 10.3389/fpls.2020.621740] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/23/2020] [Indexed: 05/17/2023]
Abstract
Bacteria exhibiting beneficial traits like increasing the bioavailability of essential nutrients and modulating hormone levels in plants are known as plant growth promoting (PGP) bacteria. The occurrence of this specific group of bacteria in the endophytic environment may reflect the decisive role they play in a particular condition. This study aimed to determine the taxonomical diversity of the culturable bacterial endophytes, isolated in the vegetative stage of passionflower (Passiflora incarnata), and assess its potential to promote plant growth by phenotypic and genotypic approaches. The sequencing and phylogenetic analysis of the 16S rRNA gene allowed us to classify 58 bacterial endophytes into nine genera. Bacillus (70.7%) was the most dominant genus, followed by Pseudomonas (8.6%) and Pantoea (6.9%). A few isolates belonged to Rhodococcus and Paenibacillus, whereas the genera Lysinibacillus, Microvirga, Xanthomonas, and Leclercia were represented by only one isolate. The strains were tested for nitrogen fixation, phosphate solubilization, indole-acetic-acid synthesis, and siderophore production. Moreover, PGP related genes (nifH, ipdC, asb, and AcPho) were detected by PCR-based screening. Most of the isolates (94.8%) displayed a potential for at least one of the PGP traits tested by biochemical assays or PCR-based screening. Nine strains were selected based on results from both approaches and were evaluated for boosting the Cape gooseberry (Physalis peruviana) germination and growth. All tested isolates improved germination in vitro, and the majority (78%) increased growth parameters in vivo. The results suggested that most of culturable bacteria inhabiting P. incarnata in the vegetative stage could be used as probiotics for agricultural systems. Besides, their occurrence may be associated with specific physiological needs typical of this development stage.
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Affiliation(s)
- Luis Gabriel Cueva-Yesquén
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Brazil
- Division of Microbial Resources, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, Paulínia, Brazil
- *Correspondence: Luis Gabriel Cueva-Yesquén,
| | - Marcela Cristina Goulart
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Brazil
- Division of Microbial Resources, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, Paulínia, Brazil
| | - Derlene Attili de Angelis
- Division of Microbial Resources, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, Paulínia, Brazil
| | - Marcos Nopper Alves
- Division of Agrotechnology, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, Paulínia, Brazil
| | - Fabiana Fantinatti-Garboggini
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Brazil
- Division of Microbial Resources, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, Paulínia, Brazil
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38
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Draft Genome Sequence of Massilia sp. Strain MC02, Isolated from a Sandy Loam Maize Soil. Microbiol Resour Announc 2019; 8:8/32/e00410-19. [PMID: 31395629 PMCID: PMC6687916 DOI: 10.1128/mra.00410-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
From farmed corn soil in California, we isolated and sequenced a new member of the genus Massilia, Massilia sp. strain MC02. Massilia sp. MC02 has an assembled draft genome of 5,023,356 bp with a total of 4,790 protein-encoding genes and 3,028 predicted proteins, 47 tRNA genes, and 2 rRNA operons. From farmed corn soil in California, we isolated and sequenced a new member of the genus Massilia, Massilia sp. strain MC02. Massilia sp. MC02 has an assembled draft genome of 5,023,356 bp with a total of 4,790 protein-encoding genes and 3,028 predicted proteins, 47 tRNA genes, and 2 rRNA operons.
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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] [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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40
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Borah A, Das R, Mazumdar R, Thakur D. Culturable endophytic bacteria of Camellia species endowed with plant growth promoting characteristics. J Appl Microbiol 2019; 127:825-844. [PMID: 31216598 DOI: 10.1111/jam.14356] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 05/29/2019] [Accepted: 06/14/2019] [Indexed: 12/11/2022]
Abstract
AIM Tea (Camellia sinensis (L.) O. Kuntze) is an economically important caffeine-containing beverage crop with massive plantation in the Northeast corner of the agroclimatic belt of India. The main aim of the work was to isolate, identify and characterize the native plant growth promoting endophytes associated with tea for future microbe based bioformulation. METHODS AND RESULTS A total of 129 endophytic bacteria were isolated and characterized for plant growth promoting traits such as indole-3-acetic acid (IAA), phosphate solubilization, ammonia production, biocontrol traits like siderophore and extracellular enzyme production. BOX-PCR fingerprinting was used to differentiate the various bacterial isolates obtained from six different tea species. 16S rRNA sequencing and blast analysis showed that these isolates belonged to different genera, that is, Bacillus, Brevibacterium, Paenibacillus and Lysinibacillus. Lysinibacillus sp. S24 showed the highest phosphate solubilization and IAA acid production efficiency of 268·4 ± 14·3 and 13·5 ± 0·5 µg ml-1 , respectively. Brevibacterium sp. S91 showed the highest ammonia production of 6·2 ± 0·5 µmol ml-1 . Chitinase, cellulase, protease and pectinase activities were shown by 4·6, 34·1, 27·13 and 13·14% of the total isolates, respectively. Similarly, 41% of the total isolates were positive for 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity. Further, the potent PGP isolates, S24 and S91 were able to enhance the vegetative parameters such as dry/fresh weight of root and shoot of tea plants in nursery conditions. CONCLUSION Our findings corroborate that tea endophytic bacteria possess the potential to demonstrate multiple PGP traits both, in vivo and in vitro and have the potential for further large-scale trials. SIGNIFICANCE AND IMPACT OF THE STUDY The exploration of tea endophytic bacterial community is suitable for the development of bioformulations for an integrated nutrient management and thus sustainable crop production and decreasing the hazardous effects of chemical fertilizers on the environment and human health.
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Affiliation(s)
- A Borah
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, Assam, India
| | - R Das
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, Assam, India
| | - R Mazumdar
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, Assam, India
| | - D Thakur
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, Assam, India
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41
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Luo Y, Wang F, Huang Y, Zhou M, Gao J, Yan T, Sheng H, An L. Sphingomonas sp. Cra20 Increases Plant Growth Rate and Alters Rhizosphere Microbial Community Structure of Arabidopsis thaliana Under Drought Stress. Front Microbiol 2019; 10:1221. [PMID: 31231328 PMCID: PMC6560172 DOI: 10.3389/fmicb.2019.01221] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 05/15/2019] [Indexed: 12/22/2022] Open
Abstract
The rhizosphere is colonized by a mass of microbes, including bacteria capable of promoting plant growth that carry out complex interactions. Here, by using a sterile experimental system, we demonstrate that Sphingomonas sp. Cra20 promotes the growth of Arabidopsis thaliana by driving developmental plasticity in the roots, thus stimulating the growth of lateral roots and root hairs. By investigating the growth dynamics of A. thaliana in soil with different water-content, we demonstrate that Cra20 increases the growth rate of plants, but does not change the time of reproductive transition under well-water condition. The results further show that the application of Cra20 changes the rhizosphere indigenous bacterial community, which may be due to the change in root structure. Our findings provide new insights into the complex mechanisms of plant and bacterial interactions. The ability to promote the growth of plants under water-deficit can contribute to the development of sustainable agriculture.
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Affiliation(s)
- Yang Luo
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Fang Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yaolong Huang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Meng Zhou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jiangli Gao
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Taozhe Yan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Hongmei Sheng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- The College of Forestry, Beijing Forestry University, Beijing, China
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42
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Zhang WH, Sun RB, Xu L, Liang JN, Zhou J. Assessment of bacterial communities in Cu-contaminated soil immobilized by a one-time application of micro-/nano-hydroxyapatite and phytoremediation for 3 years. CHEMOSPHERE 2019; 223:240-249. [PMID: 30784731 DOI: 10.1016/j.chemosphere.2019.02.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 01/30/2019] [Accepted: 02/10/2019] [Indexed: 05/21/2023]
Abstract
Heavy metals contamination of soil has been considered as a global environmental problem, and consequently various soil amendments have been widely used in immobilization. Previous studies have reported that micro-/nano-hydroxyapatite (MHA/NHA) as a novel chemical material could alleviate soil acidity and reduce the bioavailability of heavy metals. However, the mechanism of soil microorganism responding to the application of MHA/NHA is little studied. Presently, an in-situ field experiment was conducted to determine the effects of MHA/NHA and the other three traditional amendments including alkali slag (AS), lime (L) and apatite (AP) on soil copper (Cu) bioavailability and dominate bacterial population. The results showed that the application of MHA/NHA effectively increased soil pH and decreased soil available Cu content, and showed the highest increasing effects on the activities of urease, catalase and acid phosphatase. Compared with the control, MHA/NHA significantly changed the soil bacterial community structure and increased the bacterial abundance and diversity. Besides, analysis of the dominate population showed that the application of MHA/NHA decreased the relative abundance of acidophiles and the indicator of soil degradation. Additionally, the relative abundance of potential plant growth promoting bacteria increased with the addition of MHA/NHA, which was confirmed by the characteristics (the ability of producing indole acetic acid and siderophore) of bacterial strains. These results suggested that these dominate bacterial populations with significant changes may be regarded as the biomarkers for the recovery of soil ecological environment, which provides a theoretical basis for the ecological evaluation of MHA/NHA.
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Affiliation(s)
- Wen-Hui Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing, 210008, China; National Engineering and Technology Research Center for Red Soil Improvement, Red Soil Ecological Experiment Station, Chinese Academy of Sciences, Liujiazhan Plantation, Yingtan, 335211, China
| | - Rui-Bo Sun
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
| | - Lei Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing, 210008, China; National Engineering and Technology Research Center for Red Soil Improvement, Red Soil Ecological Experiment Station, Chinese Academy of Sciences, Liujiazhan Plantation, Yingtan, 335211, China
| | - Jia-Ni Liang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing, 210008, China
| | - Jing Zhou
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing, 210008, China; National Engineering and Technology Research Center for Red Soil Improvement, Red Soil Ecological Experiment Station, Chinese Academy of Sciences, Liujiazhan Plantation, Yingtan, 335211, China; Jiangxi Engineering Research Center of Eco-Remediation of Heavy Metal Pollution, Jiangxi Academy of Science, Nanchang, 330096, China.
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Muresu R, Porceddu A, Sulas L, Squartini A. Nodule-associated microbiome diversity in wild populations of Sulla coronaria reveals clues on the relative importance of culturable rhizobial symbionts and co-infecting endophytes. Microbiol Res 2019; 221:10-14. [PMID: 30825937 DOI: 10.1016/j.micres.2019.01.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 01/30/2023]
Abstract
The culturable bacteria from root nodules of Sulla coronaria growing in spontaneous conditions in Sardinia were characterized. This plant's peculiarity is to represent a legume still found in both wild and cropped statuses. We tested whether culturable bacteria would differ from those commonly isolated from its field-cropped varieties, to date exclusively represented by Rhizobium sullae. 63 isolates from 60 surface-sterilized nodules were analyzed by ARDRA and 16S rDNA sequencing. The official nitrogen-fixing symbiont Rhizobium sullae was found only in 25 nodules out of 60. The remaining nodules did not yield culturable rhizobia but a number of different endophytic genera including Pseudomonas sp. (17 nodules), Microbacterium sp. (15 nodules), Pantoea agglomerans (5 nodules). The situation appears therefore a hybrid between what is commonly observed in other Mediterranean legumes occurring only in wild status (featuring non-culturable rhizobia and arrays of culturable endophytes within nodules), as opposed to cropped legumes (endowed with fully culturable rhizobia and minimal endophytic occurrence). These findings, within a species bridging the ecology between native and cropped conditions, suggest insights on the relative importance of endophytic co-occupancy vs. true N-fixing symbiont culturability within nodules. The latter trait thus appears to accompany the domestication path of plants with a main trade-off of renouncing to interactions with a diversity of endophytic co-invaders; the relationships with those being critical in the non-cropped status. In fact, endophytes are known to promote plant growth in harsh conditions, which can be particularly stressful in the Mediterranean due to drought, highly calcareous soils, and pathogens outbreaks.
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Affiliation(s)
- Rosella Muresu
- Institute for the Animal Production System in Mediterranean Environment-National Research Council (ISPAAM CNR), Traversa La Crucca 3, 07100, Sassari, Italy
| | - Andrea Porceddu
- Dipartimento di Agraria, University of Sassari, Viale Italia 1, 07100, Sassari, Italy
| | - Leonardo Sulas
- Institute for the Animal Production System in Mediterranean Environment-National Research Council (ISPAAM CNR), Traversa La Crucca 3, 07100, Sassari, Italy
| | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, DAFNAE, University of Padova, Viale dell'Università 16, Legnaro, Padova, Italy.
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Escobar Rodríguez C, Mitter B, Antonielli L, Trognitz F, Compant S, Sessitsch A. Roots and Panicles of the C4 Model Grasses Setaria viridis (L). and S. pumila Host Distinct Bacterial Assemblages With Core Taxa Conserved Across Host Genotypes and Sampling Sites. Front Microbiol 2018; 9:2708. [PMID: 30483233 PMCID: PMC6240606 DOI: 10.3389/fmicb.2018.02708] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/23/2018] [Indexed: 01/22/2023] Open
Abstract
Virtually all studied plant tissues are internally inhabited by endophytes. Due to their relevance for plant growth and health, bacterial microbiota of crop plants have been broadly studied. In plant microbiome research the root is the most frequently addressed environment, whereas the ecology of microbiota associated with reproductive organs still demands investigation. In this work, we chose the model grasses Setaria viridis and Setaria pumila to better understand the drivers shaping bacterial communities associated with panicles (representing a reproductive organ) as compared to those associated with roots. We collected wild individuals of both grass species from 20 different locations across Austria and investigated the bacterial assemblages within roots and ripe grain-harboring panicles by 16S rRNA gene-based Illumina sequencing. Furthermore, plant samples were subjected to genotyping by genetic diversity-focused Genotyping by Sequencing. Overall, roots hosted more diverse microbiota than panicles. Both the plant organ and sampling site significantly shaped the root and panicle-associated microbiota, whereas the host genotype only affected root communities. In terms of community structure, root-specific assemblages were highly diverse and consisted of conserved bacterial taxa. In contrast, panicle-specific communities were governed by Gammaproteobacteria, were less diverse and highly origin-dependent. Among OTUs found in both plant tissues, relative abundances of Gammaproteobacteria were higher in panicles, whereas Rhizobiales dominated root communities. We further identified core and non-core taxa within samples of both Setaria species. Non-core taxa included members of the Saccharibacteria and Legionelalles, while core communities encompassed eleven OTUs of seven bacterial orders, together with a set of ten panicle-enriched OTUs. These communities were widespread across root and panicle samples from all locations, hinting toward an evolved form of mutualism through potential vertical transmission of these taxa within Setaria species.
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Affiliation(s)
- Carolina Escobar Rodríguez
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Birgit Mitter
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Livio Antonielli
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Friederike Trognitz
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Stéphane Compant
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Angela Sessitsch
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
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Cullis C, Chimwamurombe P, Barker N, Kunert K, Vorster J. Orphan Legumes Growing in Dry Environments: Marama Bean as a Case Study. FRONTIERS IN PLANT SCIENCE 2018; 9:1199. [PMID: 30158948 PMCID: PMC6104163 DOI: 10.3389/fpls.2018.01199] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 07/26/2018] [Indexed: 05/28/2023]
Abstract
Plants have developed morphological, physiological, biochemical, cellular, and molecular mechanisms to survive in drought-stricken environments with little or no water caused by below-average precipitation. In this mini-review, we highlight the characteristics that allows marama bean [Tylosema esculentum (Burchell) Schreiber], an example of an orphan legume native to arid regions of southwestern Southern Africa, to flourish under an inhospitable climate and dry soil conditions where no other agricultural crop competes in this agro-ecological zone. Orphan legumes are often better suited to withstand such harsh growth environments due to development of survival strategies using a combination of different traits and responses. Recent findings on questions on marama bean speciation, hybridization, population dynamics, and the evolutionary history of the bean and mechanisms by which the bean is able to extract and conserve water and nutrients from its environment as well as aspects of morphological and physiological adaptation will be reviewed. The importance of the soil microbiome and the genetic diversity in this species, and their interplay, as a reservoir for improvement will also be considered. In particular, the application of the newly established marama bean genome sequence will facilitate both the identification of important genes involved in the interaction with the soil microbiome and the identification of the diversity within the wild germplasm for genes involved drought tolerance. Since predicted future changes in climatic conditions, with less water availability for plant growth, will severely affect agricultural productivity, an understanding of the mechanisms of unique adaptations in marama bean to such conditions may also provide insights as to how to improve the performance of the major crops.
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Affiliation(s)
- Christopher Cullis
- Department of Biology, Case Western Reserve University, Cleveland, OH, United States
| | - Percy Chimwamurombe
- Department of Natural and Applied Sciences, Namibia University of Science and Technology, Windhoek, Namibia
| | - Nigel Barker
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Karl Kunert
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Juan Vorster
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
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Rosenblueth M, Ormeño-Orrillo E, López-López A, Rogel MA, Reyes-Hernández BJ, Martínez-Romero JC, Reddy PM, Martínez-Romero E. Nitrogen Fixation in Cereals. Front Microbiol 2018; 9:1794. [PMID: 30140262 PMCID: PMC6095057 DOI: 10.3389/fmicb.2018.01794] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 07/17/2018] [Indexed: 01/30/2023] Open
Abstract
Cereals such as maize, rice, wheat and sorghum are the most important crops for human nutrition. Like other plants, cereals associate with diverse bacteria (including nitrogen-fixing bacteria called diazotrophs) and fungi. As large amounts of chemical fertilizers are used in cereals, it has always been desirable to promote biological nitrogen fixation in such crops. The quest for nitrogen fixation in cereals started long ago with the isolation of nitrogen-fixing bacteria from different plants. The sources of diazotrophs in cereals may be seeds, soils, and even irrigation water and diazotrophs have been found on roots or as endophytes. Recently, culture-independent molecular approaches have revealed that some rhizobia are found in cereal plants and that bacterial nitrogenase genes are expressed in plants. Since the levels of nitrogen-fixation attained with nitrogen-fixing bacteria in cereals are not high enough to support the plant’s needs and never as good as those obtained with chemical fertilizers or with rhizobium in symbiosis with legumes, it has been the aim of different studies to increase nitrogen-fixation in cereals. In many cases, these efforts have not been successful. However, new diazotroph mutants with enhanced capabilities to excrete ammonium are being successfully used to promote plant growth as commensal bacteria. In addition, there are ambitious projects supported by different funding agencies that are trying to genetically modify maize and other cereals to enhance diazotroph colonization or to fix nitrogen or to form nodules with nitrogen-fixing symbiotic rhizobia.
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Affiliation(s)
- Mónica Rosenblueth
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ernesto Ormeño-Orrillo
- Laboratorio de Ecología Microbiana y Biotecnología, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
| | - Aline López-López
- Centro de Investigación en Genética y Ambiente, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Marco A Rogel
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | | | - Pallavolu M Reddy
- The Energy and Resources Institute, India Habitat Centre, New Delhi, India
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Zhang J, Wang P, Tian H, Jiang H, Wang Y, Yan C. Identification of interior salt-tolerant bacteria from ice plant Mesembryanthemum crystallinum and evaluation of their promoting effects. Symbiosis 2018. [DOI: 10.1007/s13199-018-0551-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Core Microbiome of Medicinal Plant Salvia miltiorrhiza Seed: A Rich Reservoir of Beneficial Microbes for Secondary Metabolism? Int J Mol Sci 2018; 19:ijms19030672. [PMID: 29495531 PMCID: PMC5877533 DOI: 10.3390/ijms19030672] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 12/19/2022] Open
Abstract
Seed microbiome includes special endophytic or epiphytic microbial taxa associated with seeds, which affects seed germination, plant growth, and health. Here, we analyzed the core microbiome of 21 Salvia miltiorrhiza seeds from seven different geographic origins using 16S rDNA and ITS amplicon sequencing, followed by bioinformatics analysis. The whole bacterial microbiome was classified into 17 microbial phyla and 39 classes. Gammaproteobacteria (67.6%), Alphaproteobacteria (15.6%), Betaproteobacteria (2.6%), Sphingobacteria (5.0%), Bacilli (4.6%), and Actinobacteria (2.9%) belonged to the core bacterial microbiome. Dothideomycetes comprised 94% of core fungal microbiome in S. miltiorrhiza seeds, and another two dominant classes were Leotiomycetes (3.0%) and Tremellomycetes (2.0%). We found that terpenoid backbone biosynthesis, degradation of limonene, pinene, and geraniol, and prenyltransferases, were overrepresented in the core bacterial microbiome using phylogenetic examination of communities by reconstruction of unobserved states (PICRUSt) software. We also found that the bacterial genera Pantoea, Pseudomonas, and Sphingomonas were enriched core taxa and overlapped among S. miltiorrhiza, maize, bean, and rice, while a fungal genus, Alternaria, was shared within S. miltiorrhiza, bean, and Brassicaceae families. These findings highlight that seed-associated microbiomeis an important component of plant microbiomes, which may be a gene reservoir for secondary metabolism in medicinal plants.
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Shahzad R, Khan AL, Bilal S, Asaf S, Lee IJ. What Is There in Seeds? Vertically Transmitted Endophytic Resources for Sustainable Improvement in Plant Growth. FRONTIERS IN PLANT SCIENCE 2018; 9:24. [PMID: 29410675 PMCID: PMC5787091 DOI: 10.3389/fpls.2018.00024] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 01/08/2018] [Indexed: 05/19/2023]
Abstract
Phytobeneficial microbes, particularly endophytes, such as fungi and bacteria, are concomitant partners of plants throughout its developmental stages, including seed germination, root and stem growth, and fruiting. Endophytic microbes have been identified in plants that grow in a wide array of habitats; however, seed-borne endophytic microbes have not been fully explored yet. Seed-borne endophytes are of great interest because of their vertical transmission; their potential to produce various phytohormones, enzymes, antimicrobial compounds, and other secondary metabolites; and improve plant biomass and yield under biotic and abiotic stresses. This review addresses the current knowledge on endophytes, their ability to produce metabolites, and their influence on plant growth and stress mitigation.
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Affiliation(s)
- Raheem Shahzad
- School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - Abdul L. Khan
- Chair of Oman's Medicinal Plants and Marine Natural Products, University of Nizwa, Nizwa, Oman
| | - Saqib Bilal
- School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - Sajjad Asaf
- Chair of Oman's Medicinal Plants and Marine Natural Products, University of Nizwa, Nizwa, Oman
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
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Terhonen E, Kovalchuk A, Zarsav A, Asiegbu FO. Biocontrol Potential of Forest Tree Endophytes. ENDOPHYTES OF FOREST TREES 2018. [DOI: 10.1007/978-3-319-89833-9_13] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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