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Wang Y, Zhao Q, Sun Z, Li Y, He H, Zhang Y, Yang X, Wang D, Dong B, Zhou H, Zhao M, Zheng H. Whole-genome analysis revealed the growth-promoting mechanism of endophytic bacterial strain Q2H1 in potato plants. Front Microbiol 2022; 13:1035901. [PMID: 36532474 PMCID: PMC9751815 DOI: 10.3389/fmicb.2022.1035901] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/03/2022] [Indexed: 01/09/2024] Open
Abstract
INTRODUCTION Endophytes are non-pathogenic inhabitants of healthy plant tissues and have been found to promote plant growth and health. The endophytic bacterial strain Q2H1 was isolated from the roots of the potato and was identified to exhibit growth-promoting effects in potato plants. METHODS Whole-genome sequencing was performed to reveal the mechanism underlying its growth-promoting effect. The obtained sequencing data of approximately 5.65 MB encompassed 5,533 coding sequences. Of note, nine secondary metabolite gene clusters, including siderophore gene clusters, closely associated with plant growth promotion (PGP) were predicted by antiSMASH software. Comparative genomic analysis revealed that Q2H1 belongs to the genus Peribacillus. By gene function annotation, those genes related to plant growth-promoting activities, including indole-3-acetic acid (IAA) synthesis in tryptophan metabolism, siderophore biosynthetic activity, phosphate solubilization, nitrogen fixation, and related genes, were summarized. IAA (14.4 μg/ml) was presumptively produced by Q2H1 using the Salkowski colorimetric method. A total of five genes, namely, phoU, pstB, pstA1, pstC, and pstS, were annotated for phosphate solubilization, which is associated with the ability of the Q2H1 strain to solubilize phosphate under in vitro conditions. RESULTS It is revealed that genes in the Q2H1 genome associated with nitrogen fixation belonged to three groups, namely, nitrogen fixation (nifU, sufU, salA, and nifS), nitrogen metabolism (nirA, nrtB, and nasA), and glutamate synthesis (glnA, gltB, gltD, and gudB), supported by evidence that Q2H1 grew on medium without nitrogen. We have also identified a siderophore gene cluster located on the chromosome of Q2H1, including seven genes (viz., rbsR, rhbf, rhbE, rhbD, rhbC, rhbA, ddc, and an unknown gene). In the in vitro assay, a prominent brown circle around the colony was produced on the chrome azurol S medium at 48 and 72 h post-inoculation, indicating that the siderophore gene cluster in Q2H1 harbored the ability to produce siderophores. CONCLUSION In summary, these findings implied that identifying strain-specific genes for their metabolic pathways in bacterial endophytes may reveal a variety of significant functions of plant growth-promoting mechanisms.
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Affiliation(s)
- Yuhu Wang
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Qianqian Zhao
- Institute of Agro-Food Technology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Zhenqi Sun
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Yahui Li
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Hongtao He
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Yuanyu Zhang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Xiangdong Yang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Dong Wang
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Baozhu Dong
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Hongyou Zhou
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Mingmin Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Hongli Zheng
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
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Lacava PT, Bogas AC, Cruz FDPN. Plant Growth Promotion and Biocontrol by Endophytic and Rhizospheric Microorganisms From the Tropics: A Review and Perspectives. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.796113] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Currently, the tropics harbor a wide variety of crops to feed the global population. Rapid population expansion and the consequent major demand for food and agriculture-based products generate initiatives for tropical forest deforestation, which contributes to land degradation and the loss of macro and micronative biodiversity of ecosystems. Likewise, the entire dependence on fertilizers and pesticides also contributes to negative impacts on environmental and human health. To guarantee current and future food safety, as well as natural resource preservation, systems for sustainable crops in the tropics have attracted substantial attention worldwide. Therefore, the use of beneficial plant-associated microorganisms is a promising sustainable way to solve issues concerning modern agriculture and the environment. Efficient strains of bacteria and fungi are a rich source of natural products that might improve crop yield in numerous biological ways, such as nitrogen fixation, hormone production, mobilization of insoluble nutrients, and mechanisms related to plant biotic and abiotic stress alleviation. Additionally, these microorganisms also exhibit great potential for the biocontrol of phytopathogens and pest insects. This review addresses research regarding endophytic and rhizospheric microorganisms associated with tropical plants as a sustainable alternative to control diseases and enhance food production to minimize ecological damage in tropical ecosystems.
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Dudeja SS, Suneja-Madan P, Paul M, Maheswari R, Kothe E. Bacterial endophytes: Molecular interactions with their hosts. J Basic Microbiol 2021; 61:475-505. [PMID: 33834549 DOI: 10.1002/jobm.202000657] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 03/07/2021] [Accepted: 03/16/2021] [Indexed: 01/19/2023]
Abstract
Plant growth promotion has been found associated with plants on the surface (epiphytic), inside (endophytic), or close to the plant roots (rhizospheric). Endophytic bacteria mainly have been researched for their beneficial activities in terms of nutrient availability, plant growth hormones, and control of soil-borne and systemic pathogens. Molecular communications leading to these interactions between plants and endophytic bacteria are now being unrevealed using multidisciplinary approaches with advanced techniques such as metagenomics, metaproteomics, metatranscriptomics, metaproteogenomic, microRNAs, microarray, chips as well as the comparison of complete genome sequences. More than 400 genes in both the genomes of host plant and bacterial endophyte are up- or downregulated for the establishment of endophytism and plant growth-promoting activity. The involvement of more than 20 genes for endophytism, about 50 genes for direct plant growth promotion, about 25 genes for biocontrol activity, and about 10 genes for mitigation of different stresses has been identified in various bacterial endophytes. This review summarizes the progress that has been made in recent years by these modern techniques and approaches.
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Affiliation(s)
- Surjit S Dudeja
- Department of Bio & Nanotechnology, Guru Jambeshwar University of Science & Technology, Hisar, India
| | - Pooja Suneja-Madan
- Department of Microbiology, Maharishi Dayanand University, Rohtak, India
| | - Minakshi Paul
- Department of Bio & Nanotechnology, Guru Jambeshwar University of Science & Technology, Hisar, India
| | - Rajat Maheswari
- Department of Microbiology, Maharishi Dayanand University, Rohtak, India
| | - Erika Kothe
- Microbial Communication, Institute of Microbiology, Faculty for Biosciences, Friedrich Schiller University of Jena, Jena, Germany
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Krishnamoorthy A, Gupta A, Sar P, Maiti MK. Metagenomics of two gnotobiotically grown aromatic rice cultivars reveals genotype-dependent and tissue-specific colonization of endophytic bacterial communities attributing multiple plant growth promoting traits. World J Microbiol Biotechnol 2021; 37:59. [PMID: 33660141 DOI: 10.1007/s11274-021-03022-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/19/2021] [Indexed: 01/05/2023]
Abstract
Exploration of community structures, habitations, and potential plant growth promoting (PGP) attributes of endophytic bacteria through next generation sequencing (NGS) is a prerequisite to culturing PGP endophytic bacteria for their application in sustainable agriculture. The present study unravels the taxonomic abundance and diversity of endophytic bacteria inhabiting in vitro grown root, shoot and callus tissues of two aromatic rice cultivars through 16S rRNA gene-based Illumina NGS. Wide variability in the number of bacterial operational taxonomic units (OTUs) and genera was observed between the two samples of the root (55, 14 vs. 310, 76) and shoot (26, 12 vs. 276, 73) but not between the two callus samples (251, 61 vs. 259, 51), indicating tissue-specific and genotype-dependent bacterial community distribution in rice plant, even under similar gnotobiotic growth conditions. Sizes of core bacteriomes of the selected two rice genotypes varied from 1 to 15 genera, with Sphingomonas being the only genus detected in all six samples. Functional annotation, based upon the abundance of bacterial OTUs, revealed the presence of several PGP trait-related genes having variable relative abundance in tissue-specific and genotype-dependent manners. In silico study also documented a higher abundance of certain genes in the same biochemical pathway, such as nitrogen fixation, phosphate solubilization and indole acetic acid production; implying their crucial roles in the biosynthesis of metabolites leading to PGP. New insights on utilizing callus cultures for isolation of PGP endophytes aiming to improve rice crop productivity are presented, owing to constancy in bacterial OTUs and genera in callus tissues of both the rice genotypes.
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Affiliation(s)
- Anagha Krishnamoorthy
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Abhishek Gupta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Mrinal K Maiti
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
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Madhaiyan M, Saravanan VS, Wirth JS, Alex THH, Kim SJ, Weon HY, Kwon SW, Whitman WB, Ji L. Sphingomonas palmae sp. nov. and Sphingomonas gellani sp. nov., endophytically associated phyllosphere bacteria isolated from economically important crop plants. Antonie van Leeuwenhoek 2020; 113:1617-1632. [PMID: 32949307 DOI: 10.1007/s10482-020-01468-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/31/2020] [Indexed: 02/08/2023]
Abstract
In this study, two endophytic bacterial strains designated JS21-1T and S6-262T isolated from leaves of Elaeis guineensis and stem tissues of Jatropha curcas respectively, were subjected for polyphasic taxonomic approach. On R2A medium, colonies of strains JS21-1T and S6-262T are orange and yellow, respectively. Phylogenetic analyses using 16S rRNA gene sequencing and whole-genome sequences placed the strains in distinct clades but within the genus Sphingomonas. The DNA G + C content of JS21-1T and S6-262T were 67.31 and 66.95%, respectively. Furthermore, the average nucleotide identity and digital DNA-DNA hybridization values of strains JS21-1T and S6-262T with phylogenetically related Sphingomonas species were lower than 95% and 70% respectively. The chemotaxonomic studies indicated that the major cellular fatty acids of the strain JS21-1T were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0, and C14:0 2OH; strain S6-262T possessed summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) and summed feature 8 (C18:1 ω6c and/or C18:1 ω7c). The major quinone was Q10, and the unique polyamine observed was homospermidine. The polar lipid profile comprised of mixture of sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and certain uncharacterised phospholipids and lipids. Based on this polyphasic evidence, strains JS21-1T and S6-262T represent two novel species of the genus Sphingomonas, for which the names Sphingomonas palmae sp. nov. and Sphingomonas gellani sp. nov. are proposed, respectively. The type strain of Sphingomonas palmae sp. nov. is JS21-1T (= DSM 27348T = KACC 17591T) and the type strain of Sphingomonas gellani sp. nov. is S6-262T (= DSM 27346T = KACC 17594T).
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Affiliation(s)
- Munusamy Madhaiyan
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
| | | | - Joseph S Wirth
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | - Tan Hian Hwee Alex
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - William B Whitman
- Department of Microbiology, University of Georgia, 527 Biological Sciences Building, Athens, GA, 30602-2605, USA
| | - Lianghui Ji
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
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Madhaiyan M, Saravanan VS, Blom J, Smits THM, Rezzonico F, Kim SJ, Weon HY, Kwon SW, Whitman WB, Ji L. Phytobacter palmae sp. nov., a novel endophytic, N2 fixing, plant growth promoting Gammaproteobacterium isolated from oil palm (Elaeis guineensis Jacq.). Int J Syst Evol Microbiol 2020; 70:841-848. [DOI: 10.1099/ijsem.0.003834] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Munusamy Madhaiyan
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
| | | | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen, Germany
| | - Theo H. M. Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wadenswil, Switzerland
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wadenswil, Switzerland
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - William B. Whitman
- Department of Microbiology, 527 Biological Sciences Building, University of Georgia, Athens, GA 30602-2605, USA
| | - Lianghui Ji
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
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Biodiversity of methylotrophic microbial communities and their potential role in mitigation of abiotic stresses in plants. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00190-6] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Yan X, Wang Z, Mei Y, Wang L, Wang X, Xu Q, Peng S, Zhou Y, Wei C. Isolation, Diversity, and Growth-Promoting Activities of Endophytic Bacteria From Tea Cultivars of Zijuan and Yunkang-10. Front Microbiol 2018; 9:1848. [PMID: 30186243 PMCID: PMC6111150 DOI: 10.3389/fmicb.2018.01848] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/24/2018] [Indexed: 11/13/2022] Open
Abstract
Endophytes are rich in plant tissues and play important roles in plant-microbial interactions and plant-growth regulation. Here, endophytic bacteria from two closely related tea cultivars of Zijuan and Yunkang-10 were isolated, and the diversities were compared. Plant-growth promoting (PGP) activities were determined on the dominant groups or nitrogen-fixing genera from the two cultivars. Endophytic bacteria were isolated by using of different selective media and methods, and the PGP activities were investigated by analytical and molecular technologies. A total of 110 isolates of 18 genera belonging to three phylums (Proteobacteria, Firmicutes, and Bacteroidetes) were obtained from Zijuan, while 164 isolates of 22 genera belonging to two phylums (Proteobacteria and Firmicutes) were obtained from Yunkang-10. PGP screening indicated that Herbaspirillum spp., Methylobacterium spp., and Brevundimonas spp. showed different PGP abilities. The PGP ability decreased in order of Herbaspirillum spp., Brevundimonas spp. and Methylobacterium spp., and the majority of Methylobacterium spp. did not showed PGP activity of nitrogen-fixation, P-solubilization, siderophore, indole-3-acetic acid (IAA) production or 1-aminocyclopropane-1-carboxylate (ACC) deaminase. The study of bacterial community and PGP activities confirmed that endophytes in tea plants are constantly changing in different seasons and tea cultivars, and the PGP bacteria in Zijuan are much abundant than those of Yunkang-10.
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Affiliation(s)
- Xiaomei Yan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Zhi Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Yu Mei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Liqun Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Xu Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Qingshan Xu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Su Peng
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Yu Zhou
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
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Madhaiyan M, Alex THH, Ngoh ST, Prithiviraj B, Ji L. Leaf-residing Methylobacterium species fix nitrogen and promote biomass and seed production in Jatropha curcas. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:222. [PMID: 26697111 PMCID: PMC4687150 DOI: 10.1186/s13068-015-0404-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 11/30/2015] [Indexed: 05/06/2023]
Abstract
BACKGROUND Jatropha curcas L. (Jatropha) is a potential biodiesel crop that can be cultivated on marginal land because of its strong tolerance to drought and low soil nutrient content. However, seed yield remains low. To enhance the commercial viability and green index of Jatropha biofuel, a systemic and coordinated approach must be adopted to improve seed oil and biomass productivity. Here, we present our investigations on the Jatropha-associated nitrogen-fixing bacteria with an aim to understand and exploit the unique biology of this plant from the perspective of plant-microbe interactions. RESULTS An analysis of 1017 endophytic bacterial isolates derived from different parts of Jatropha revealed that diazotrophs were abundant and diversely distributed into five classes belonging to α, β, γ-Proteobacteria, Actinobacteria and Firmicutes. Methylobacterium species accounted for 69.1 % of endophytic bacterial isolates in leaves and surprisingly, 30.2 % which were able to fix nitrogen that inhabit in leaves. Among the Methylobacterium isolates, strain L2-4 was characterized in detail. Phylogenetically, strain L2-4 is closely related to M. radiotolerans and showed strong molybdenum-iron dependent acetylene reduction (AR) activity in vitro and in planta. Foliar spray of L2-4 led to successful colonization on both leaf surface and in internal tissues of systemic leaves and significantly improved plant height, leaf number, chlorophyll content and stem volume. Importantly, seed production was improved by 222.2 and 96.3 % in plants potted in sterilized and non-sterilized soil, respectively. Seed yield increase was associated with an increase in female-male flower ratio. CONCLUSION The ability of Methylobacterium to fix nitrogen and colonize leaf tissues serves as an important trait for Jatropha. This bacteria-plant interaction may significantly contribute to Jatropha's tolerance to low soil nutrient content. Strain L2-4 opens a new possibility to improve plant's nitrogen supply from the leaves and may be exploited to significantly improve the productivity and Green Index of Jatropha biofuel.
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Affiliation(s)
- Munusamy Madhaiyan
- />Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604 Singapore
| | - Tan Hian Hwee Alex
- />Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604 Singapore
| | - Si Te Ngoh
- />Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604 Singapore
| | - Bharath Prithiviraj
- />Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
| | - Lianghui Ji
- />Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604 Singapore
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