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Acuña JJ, Rilling JI, Inostroza NG, Zhang Q, Wick LY, Sessitsch A, Jorquera MA. Variovorax sp. strain P1R9 applied individually or as part of bacterial consortia enhances wheat germination under salt stress conditions. Sci Rep 2024; 14:2070. [PMID: 38267517 PMCID: PMC10808091 DOI: 10.1038/s41598-024-52535-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 01/19/2024] [Indexed: 01/26/2024] Open
Abstract
Endophytes isolated from extremophile plants are interesting microbes for improving the stress tolerance of agricultural plants. Here, we isolated and characterized endophytic bacteria showing plant growth-promoting (PGP) traits from plants in two extreme Chilean biomes (Atacama Desert and Chilean Patagonia). Forty-two isolates were characterized as both halotolerant auxin producers (2-51 mg L-1) and 1-aminocyclopropane-1-carboxylate (ACC)-degrading bacteria (15-28 µmol αKB mg protein-1 h-1). The most efficient isolates were tested as single strains, in dual and triple consortia, or in combination with previously reported PGP rhizobacteria (Klebsiella sp. 27IJA and 8LJA) for their impact on the germination of salt-exposed (0.15 M and 0.25 M NaCl) wheat seeds. Interestingly, strain P1R9, identified as Variovorax sp., enhanced wheat germination under salt stress conditions when applied individually or as part of bacterial consortia. Under salt stress, plants inoculated with dual consortia containing the strain Variovorax sp. P1R9 showed higher biomass (41%) and reduced lipid peroxidation (33-56%) than uninoculated plants. Although the underlying mechanisms remain elusive, our data suggest that the application of Variovorax sp. P1R9, alone or as a member of PGP consortia, may improve the salt stress tolerance of wheat plants.
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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
- Network for Extreme Environment Research (NEXER), 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, La Reina, Chile
| | - Joaquin I Rilling
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - 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
| | - Qian Zhang
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, 361102, China
| | - Lukas Y Wick
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318, Leipzig, Germany
| | - Angela Sessitsch
- Bioresources Unit, AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430, Tulln, Austria
| | - 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.
- Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.
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DiLegge MJ, Manter DK, Vivanco JM. Soil microbiome disruption reveals specific and general plant-bacterial relationships in three agroecosystem soils. PLoS One 2022; 17:e0277529. [PMID: 36383522 DOI: 10.1371/journal.pone.0277529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 10/28/2022] [Indexed: 11/17/2022] Open
Abstract
Soil microbiome disruption methods are regularly used to reduce populations of microbial pathogens, often resulting in increased crop growth. However, little is known about the effect of soil microbiome disruption on non-pathogenic members of the soil microbiome. Here, we applied soil microbiome disruption in the form of moist-heat sterilization (autoclaving) to reduce populations of naturally occurring soil microbiota. The disruption was applied to analyze bacterial community rearrangement mediated by four crops (corn, beet, lettuce, and tomato) grown in three historically distinct agroecosystem soils (conventional, organic, and diseased). Applying the soil disruption enhanced plant influence on rhizosphere bacterial colonization, and significantly different bacterial communities were detected between the tested crops. Furthermore, bacterial genera showed significant abundance increases in ways both unique-to and shared-by each tested crop. As an example, corn uniquely promoted abundances of Pseudomonas and Sporocytophaga, regardless of the disrupted soil in which it was grown. Whereas the promotion of Bosea, Dyadobacter and Luteoliobacter was shared by all four crops when grown in disrupted soils. In summary, soil disruption followed by crop introduction amplified the plant colonization of potential beneficial bacterial genera in the rhizosphere.
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He D, Wan W. Distribution of Culturable Phosphate-Solubilizing Bacteria in Soil Aggregates and Their Potential for Phosphorus Acquisition. Microbiol Spectr 2022; 10:e0029022. [PMID: 35536021 PMCID: PMC9241762 DOI: 10.1128/spectrum.00290-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/21/2022] [Indexed: 11/22/2022] Open
Abstract
Deciphering distribution patterns of phosphate-solubilizing bacteria (PSB) and phosphorus-cycling-related genes in soils is important to evaluate phosphorus (P) transformation. However, the linkage between PSB number and P-cycling-related gene abundance in soils, especially soil aggregates, remains largely unknown. Here, we estimated the numbers of PSB and abundances of P-cycling-related genes (i.e., gcd and bpp) in soil aggregates under different fertilization regimes as well as P-solubilizing performance and plant-growth-promoting ability of PSB. We found that tricalcium phosphate-solubilizing bacteria, phytate-degrading bacteria, and gcd and bpp abundances were more abundant in silt plus clay (silt+clay; <53 μm) than in macroaggregate (250 to 2000 μm) and microaggregate (53 to 250 μm). Fertilization treatment and aggregate fractionation showed distinct effects on PSB number and P-cycling-related gene abundance. We found significantly negative correlation between gcd gene abundance and tricalcium phosphate-solubilizing bacterial number (Col-CaP) and dramatically positive correlation between bpp gene abundance and phytate-degrading bacterial number (Col-Phy). P fractions were responsible for PSB number and P-cycling-related gene abundance. The isolated Pseudomonas sp. strain PSB-2 and Arthrobacter sp. strain PSB-5 exhibited good performances for solubilizing tricalcium phosphate. The inoculation of Pseudomonas sp. PSB-2 could significantly enhance plant fresh weight, plant dry weight, and plant height. Our results emphasized distinct distribution characteristics of PSB and P-cycling-related genes in soil aggregates and deciphered a close linkage between PSB number and P-cycling-related gene abundance. Our findings might guide the isolation of PSB from agricultural soils and provide a candidate plant-growth-promoting bacterium for agro-ecosystems. IMPORTANCE Phosphate-solubilizing bacteria are responsible for inorganic P solubilization and organic P mineralization. Elucidating the linkage between phosphate-solubilizing bacterial number and P-cycling-related gene abundance is important to isolate plant-growth-promoting bacteria for agro-ecosystems. Our findings reveal differentiating strategies of phosphate-solubilizing bacteria in soil aggregates, and the deciphered P fractions show strong effects on distribution patterns of phosphate-solubilizing bacteria and P-cycling-related genes. Additionally, we isolated phosphate-solubilizing bacteria with good plant-growth-promoting ability. This study enriches our knowledge of P cycling in soil aggregates and might guide the production and management of farmland.
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Affiliation(s)
- Donglan He
- College of Life Science, South-Central University for Nationalities, Wuhan, People’s Republic of China
| | - Wenjie Wan
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
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Iquebal MA, Jagannadham J, Jaiswal S, Prabha R, Rai A, Kumar D. Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review. Front Microbiol 2022; 13:708335. [PMID: 35655999 PMCID: PMC9152772 DOI: 10.3389/fmicb.2022.708335] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
Agricultural productivity is highly influenced by its associated microbial community. With advancements in omics technology, metagenomics is known to play a vital role in microbial world studies by unlocking the uncultured microbial populations present in the environment. Metagenomics is a diagnostic tool to target unique signature loci of plant and animal pathogens as well as beneficial microorganisms from samples. Here, we reviewed various aspects of metagenomics from experimental methods to techniques used for sequencing, as well as diversified computational resources, including databases and software tools. Exhaustive focus and study are conducted on the application of metagenomics in agriculture, deciphering various areas, including pathogen and plant disease identification, disease resistance breeding, plant pest control, weed management, abiotic stress management, post-harvest management, discoveries in agriculture, source of novel molecules/compounds, biosurfactants and natural product, identification of biosynthetic molecules, use in genetically modified crops, and antibiotic-resistant genes. Metagenomics-wide association studies study in agriculture on crop productivity rates, intercropping analysis, and agronomic field is analyzed. This article is the first of its comprehensive study and prospects from an agriculture perspective, focusing on a wider range of applications of metagenomics and its association studies.
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Affiliation(s)
- Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Jaisri Jagannadham
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ratna Prabha
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
- School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
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Park Y, Solhtalab M, Thongsomboon W, Aristilde L. Strategies of organic phosphorus recycling by soil bacteria: acquisition, metabolism, and regulation. Environ Microbiol Rep 2022; 14:3-24. [PMID: 35001516 PMCID: PMC9306846 DOI: 10.1111/1758-2229.13040] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 05/12/2023]
Abstract
Critical to meeting cellular phosphorus (P) demand, soil bacteria deploy a number of strategies to overcome limitation in inorganic P (Pi ) in soils. As a significant contributor to P recycling, soil bacteria secrete extracellular enzymes to degrade organic P (Po ) in soils into the readily bioavailable Pi . In addition, several Po compounds can be transported directly via specific transporters and subsequently enter intracellular metabolic pathways. In this review, we highlight the strategies that soil bacteria employ to recycle Po from the soil environment. We discuss the diversity of extracellular phosphatases in soils, the selectivity of these enzymes towards various Po biomolecules and the influence of the soil environmental conditions on the enzyme's activities. Moreover, we outline the intracellular metabolic pathways for Po biosynthesis and transporter-assisted Po and Pi uptake at different Pi availabilities. We further highlight the regulatory mechanisms that govern the production of phosphatases, the expression of Po transporters and the key metabolic changes in P metabolism in response to environmental Pi availability. Due to the depletion of natural resources for Pi , we propose future studies needed to leverage bacteria-mediated P recycling from the large pools of Po in soils or organic wastes to benefit agricultural productivity.
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Affiliation(s)
- Yeonsoo Park
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Biological and Environmental EngineeringCornell University, Riley‐Robb HallIthacaNY14853USA
| | - Mina Solhtalab
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Biological and Environmental EngineeringCornell University, Riley‐Robb HallIthacaNY14853USA
| | - Wiriya Thongsomboon
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Chemistry, Faculty of ScienceMahasarakham UniversityMahasarakham44150Thailand
| | - Ludmilla Aristilde
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Biological and Environmental EngineeringCornell University, Riley‐Robb HallIthacaNY14853USA
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Muema EK, Steenkamp ET, Venter SN. Rhizosphere Diazotrophs and Other Bacteria Associated with Native and Encroaching Legumes in the Succulent Karoo Biome in South Africa. Microorganisms 2022; 10:216. [PMID: 35208671 PMCID: PMC8880511 DOI: 10.3390/microorganisms10020216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/04/2021] [Accepted: 12/23/2021] [Indexed: 12/10/2022] Open
Abstract
Total and diazotrophic bacteria were assessed in the rhizosphere soils of native and encroaching legumes growing in the Succulent Karoo Biome (SKB), South Africa. These were Calobota sericea, Lessertia diffusa, Vachellia karroo, and Wiborgia monoptera, of Fabaceae family near Springbok (Northern Cape Province) and neighboring refugia of the Fynbos biome for C. sericea for comparison purposes. Metabarcoding approach using 16S rRNA gene revealed Actinobacteria (26.7%), Proteobacteria (23.6%), Planctomycetes, and Acidobacteria (10%), while the nifH gene revealed Proteobacteria (70.3%) and Cyanobacteria (29.5%) of the total sequences recovered as the dominant phyla. Some of the diazotrophs measured were assigned to families; Phyllobacteriaceae (39%) and Nostocaceae (24.4%) (all legumes), Rhodospirillaceae (7.9%), Bradyrhizobiaceae (4.6%) and Methylobacteriaceae (3%) (C. sericea, V. karroo, W. monoptera), Rhizobiaceae (4.2%; C. sericea, L. diffusa, V. Karroo), Microchaetaceae (4%; W. monoptera, V. karroo), Scytonemataceae (3.1%; L. diffusa, W. monoptera), and Pseudomonadaceae (2.7%; V. karroo) of the total sequences recovered. These families have the potential to fix the atmospheric nitrogen. While some diazotrophs were specific or shared across several legumes, a member of Mesorhizobium species was common in all rhizosphere soils considered. V. karroo had statistically significantly higher Alpha and distinct Beta-diversity values, than other legumes, supporting its influence on soil microbes. Overall, this work showed diverse bacteria that support plant life in harsh environments such as the SKB, and shows how they are influenced by legumes.
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Mohamed AH, Abd El-megeed FH, Hassanein NM, Youseif SH, Farag PF, Saleh SA, Abdel-wahab BA, Alsuhaibani AM, Helmy YA, Abdel-azeem AM. Native Rhizospheric and Endophytic Fungi as Sustainable Sources of Plant Growth Promoting Traits to Improve Wheat Growth under Low Nitrogen Input. J Fungi (Basel) 2022; 8:94. [PMID: 35205849 PMCID: PMC8875171 DOI: 10.3390/jof8020094] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 01/15/2022] [Indexed: 02/06/2023] Open
Abstract
Wheat crops require effective nitrogen fertilization to produce high yields. Only half of chemical N2 fertilizers are absorbed into plants while the rest remains in the soil, causing environmental problems. Fungi could maximize nitrogen absorption, and from an environmental and biodiversity point of view, there is an urgent necessity for bioprospecting native fungi associated with wild plants growing in harsh environments, e.g., St. Katherine Protectorate (SKP) in the arid Sinai. Recovered taxa, either endophytic and/or rhizospheric, were screened for their plant growth-promoting (PGP) traits. Eighteen fungal isolates (15 rhizospheric and 3 endophytic) belonging to anamorphic ascomycetes were recovered from 9 different wild plants, and their PGP traits (indole-3-acetic acid [IAA] production, phosphate solubilization, siderophore production, and hydrolytic enzyme production) were measured. Rhizospheric isolate NGB-WS14 (Chaetosphaeronema achilleae) produced high levels of IAA (119.1 μg mL−1) in the presence of tryptophan, while NGB-WS 8 (Acrophialophora levis) produced high IAA levels (42.4 μg mL−1) in the absence of tryptophan. The highest phosphate-solubilizing activity (181.9 μg mL−1) was recorded by NGB-WFS2 (Penicillium chrysogenum). Endophytic isolate NGB-WFE16 (Fusarium petersiae) exhibited a high percentage level of Siderophore Unit (96.5% SU). All isolates showed variability in the secretion of extracellular hydrolytic enzymes. Remarkably, all isolates had antagonistic activity (55.6% to 87.3% suppression of pathogen growth) against the pathogenic taxon Alternaria alternata (SCUF00001378) in the dual-assay results. Out of the 18 isolates, 4 rhizospheric and 1 endophytic isolate showed significant increases in shoot dry weight and shoot nitrogen and chlorophyll content of wheat plants subjected to low inputs of chemical nitrogen (N) fertilizers (50% reduction) compared with the non-inoculated control in a pot experiment. Potent taxa were subjected to sequencing for molecular confirmation of phenotypic identification. The retrieved ITS sequences in this study have been deposited in GenBank under accession numbers from LC642736 to LC642740. This study considered the first report of endophytic fungi of Cheilanthes vellea, a wild plant with PGPF which improves wheat growth. These results recommend using PGPF as inoculants to alleviate low nitrogen fertilization.
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Astorga-Eló M, Gonzalez S, Acuña JJ, Sadowsky MJ, Jorquera MA. Rhizobacteria from 'flowering desert' events contribute to the mitigation of water scarcity stress during tomato seedling germination and growth. Sci Rep 2021; 11:13745. [PMID: 34215802 DOI: 10.1038/s41598-021-93303-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023] Open
Abstract
Tomato (Solanum lycopersicum L.) is an important vegetable cultivated around the world. Under field conditions, tomato can be negatively affected by water scarcity in arid and semiarid regions. The application of native plant growth-promoting rhizobacteria (PGPR) isolated from arid environments has been proposed as an inoculant to mitigate abiotic stresses in plants. In this study, we evaluated rhizobacteria from Cistanthe longiscapa (syn Calandrinia litoralis and Calandrinia longiscapa), a representative native plant of flowering desert (FD) events (Atacama Desert, Chile), to determine their ability to reduce water scarcity stress on tomato seedlings. The isolated bacterial strains were characterized with respect to their PGPR traits, including P solubilization, 1-aminocyclopropane-1-carboxylate deaminase activity, and tryptophan-induced auxin and exopolysaccharide production. Three PGPR consortia were formulated with isolated Bacillus strains and then applied to tomato seeds, and then, the seedlings were exposed to different levels of water limitations. In general, tomato seeds and seedlings inoculated with the PGPR consortia presented significantly (P ≤ 0.05) greater plant growth (48 to 60 cm of height and 171 to 214 g of weight) and recovery rates (88 to 100%) compared with those without inoculation (37 to 51 cm of height; 146 to 197 g of fresh weight; 54 to 92% of recovery) after exposure to a lack of irrigation over different time intervals (24, 72 and 120 h) before transplantation. Our results revealed the effectiveness of the formulated PGPR consortia from FD to improve the performance of inoculated seeds and seedlings subjected to water scarcity; thus, the use of these consortia can represent an alternative approach for farmers facing drought events and water scarcity associated with climate change in semiarid and arid regions worldwide.
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Priya P, Aneesh B, Harikrishnan K. Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health. J Microbiol Methods 2021; 185:106215. [PMID: 33839214 DOI: 10.1016/j.mimet.2021.106215] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022]
Abstract
Intense agricultural practices to meet rising food demands have caused ecosystem perturbations. For sustainable crop production, biological agents are gaining attention, but exploring their functional potential on a multi-layered complex ecosystem like the rhizosphere is challenging. This review explains the significance of genomics as a culture-independent molecular tool to understand the diversity and functional significance of the rhizosphere microbiome for sustainable agriculture. It discusses the recent significant studies in the rhizosphere environment carried out using evolving techniques like metagenomics, metatranscriptomics, and metaproteomics, their challenges, constraints infield application, and prospective solutions. The recent advances in techniques such as nanotechnology for the development of bioformulations and visualization techniques contemplating environmental safety were also discussed. The need for development of metagenomic data sets of regionally important crops, their plant microbial interactions and agricultural practices for narrowing down significant data from huge databases have been suggested. The role of taxonomical and functional diversity of soil microbiota in understanding soil suppression and part played by the microbial metabolites in the process have been analyzed and discussed in the context of 'omics' approach. 'Omics' studies have revealed important information about microbial diversity, their responses to various biotic and abiotic stimuli, and the physiology of disease suppression. This can be translated to crop sustainability and combinational approaches with advancing visualization and analysis methodologies fix the existing knowledge gap to a huge extend. With improved data processing and standardization of the methods, details of plant-microbe interactions can be successfully decoded to develop sustainable agricultural practices.
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Affiliation(s)
- P Priya
- Environmental Biology Lab, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
| | - B Aneesh
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences Cochin University of Science and Technology, Cochin, Kerala, India.
| | - K Harikrishnan
- Environmental Biology Lab, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
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de Lima DRM, Dos Santos IB, Oliveira JTC, da Costa DP, de Queiroz JVJ, Romagnoli EM, Andreote FD, Freire FJ, Kuklinsky-Sobral J. Genetic diversity of N-fixing and plant growth-promoting bacterial community in different sugarcane genotypes, association habitat and phenological phase of the crop. Arch Microbiol 2020; 203:1089-1105. [PMID: 33161466 DOI: 10.1007/s00203-020-02103-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 10/23/2022]
Abstract
This study aimed to evaluate the genetic diversity of bacterial community associated to different sugarcane genotypes, association habitat and phenological phase of the culture, as well as to isolate, to identify and to characterize your potential for plant growth-promoting. Root and rhizospheric soil samples from RB 92579 and RB 867515 varieties were collected at 120 and 300 days after regrowth (DAR). The diversity of bacterial was evaluated through of the 16S rRNA and nifH genes. We found greater genetic diversity in the root endophytic habitat at 120 DAR. We identify the genera Burkholderia sp., Pantoea sp., Erwinia sp., Stenotrophomonas sp., Enterobacter sp. and Pseudomonas sp. The genera Bacillus sp. and Dyella sp. were only identified in the variety RB 92579. We found indices above 50% for biological nitrogen fixation, production of indole acetic acid and phosphate solubilization, showing that the use of these bacteria in biotechnological products is very promising.
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Affiliation(s)
| | - Isaneli Batista Dos Santos
- Departamento de Microbiologia Agrícola, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, 13418-900, Brasil
| | - João Tiago Correia Oliveira
- Instituto de Estudos do Trópico Úmido, Universidade Federal do Sul e Sudeste do Pará, Marabá, 68507-590, Brasil
| | - Diogo Paes da Costa
- Laboratório de Biotecnologia e Genética Microbiana, Universidade Federal do Agreste de Pernambuco, Garanhuns, 55292-270, Brasil
| | | | - Emiliana Manesco Romagnoli
- Departamento de Microbiologia Agrícola, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, 13418-900, Brasil
| | - Fernando Dini Andreote
- Departamento de Microbiologia Agrícola, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, 13418-900, Brasil
| | - Fernando José Freire
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, 52171-900, Brasil.
| | - Júlia Kuklinsky-Sobral
- Laboratório de Biotecnologia e Genética Microbiana, Universidade Federal do Agreste de Pernambuco, Garanhuns, 55292-270, Brasil
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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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12
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Qessaoui R, Bouharroud R, Furze JN, El Aalaoui M, Akroud H, Amarraque A, Vaerenbergh JV, Tahzima R, Mayad EH, Chebli B. Applications of New Rhizobacteria Pseudomonas Isolates in Agroecology via Fundamental Processes Complementing Plant Growth. Sci Rep 2019; 9:12832. [PMID: 31492898 PMCID: PMC6731270 DOI: 10.1038/s41598-019-49216-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 08/08/2019] [Indexed: 01/17/2023] Open
Abstract
Pseudomonas isolates have frequently been isolated from the rhizosphere of plants, and several of them have been reported as plant growth-promoting rhizobacteria. In the present work, tomato (Solanum lycopersicum) seeds were germinated in greenhouse conditions, and the seedling height, length of plants, collar diameter and number of leaves were measured from plants grown in soil inoculated by bacterial isolates. Pseudomonas isolates were isolated from the rhizosphere. We used the Newman-Keuls test to ascertain pairwise differences. Isolates were identified as a new Pseudomonas species by rpoD gene sequencing. The results showed that isolates of Pseudomonas sp. (Q6B) increased seed germination (P = 0.01); Pseudomonas sp. (Q6B, Q14B, Q7B, Q1B and Q13B) also promoted seedling height (P = 0.01). All five isolates promoted plant length and enlarged the collar diameter (P = 0.01). Pseudomonas sp. (Q1B) also increased leaf number (P = 0.01). The investigation found that Pseudomonas isolates were able to solubilize phosphate, produce siderophores, ammonia, and indole-3-acetic acid and colonize the roots of tomato plants. This study shows that these five novel Pseudomonas sp. isolates can be effective new plant growth-promoting rhizobacteria.
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Affiliation(s)
- R Qessaoui
- Research Unit of Integrated Crop Production, Centre Regional de la Recherche Agronomique d'Agadir, Agadir, Morocco.,Biotechnology and Environmental Engineering Team, Laboratory of Mechanic Process Energy and Environment, National School of Applied Sciences, Ibn Zohr University, Agadir, Morocco
| | - R Bouharroud
- Research Unit of Integrated Crop Production, Centre Regional de la Recherche Agronomique d'Agadir, Agadir, Morocco.
| | - J N Furze
- Laboratory of Biotechnologies and Valorization of Natural Resources Faculty of Sciences - Agadir, Ibn Zohr University, Agadir, Morocco
| | - M El Aalaoui
- Research Unit of Integrated Crop Production, Centre Regional de la Recherche Agronomique d'Agadir, Agadir, Morocco
| | - H Akroud
- Research Unit of Integrated Crop Production, Centre Regional de la Recherche Agronomique d'Agadir, Agadir, Morocco
| | - A Amarraque
- Research Unit of Integrated Crop Production, Centre Regional de la Recherche Agronomique d'Agadir, Agadir, Morocco
| | - J Van Vaerenbergh
- Plant Science Unit - Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - R Tahzima
- Plant Science Unit - Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - E H Mayad
- Biotechnology and Environmental Engineering Team, Laboratory of Mechanic Process Energy and Environment, National School of Applied Sciences, Ibn Zohr University, Agadir, Morocco.,Laboratory of Biotechnologies and Valorization of Natural Resources Faculty of Sciences - Agadir, Ibn Zohr University, Agadir, Morocco
| | - B Chebli
- Biotechnology and Environmental Engineering Team, Laboratory of Mechanic Process Energy and Environment, National School of Applied Sciences, Ibn Zohr University, Agadir, Morocco
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13
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Wang F, Kertesz MA, Feng G. Phosphorus forms affect the hyphosphere bacterial community involved in soil organic phosphorus turnover. Mycorrhiza 2019; 29:351-362. [PMID: 31044298 DOI: 10.1007/s00572-019-00896-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
Interactions between bacteria and arbuscular mycorrhizal (AM) fungi play a significant role in mediating organic phosphorus (P) transformations and turnover in soil. The bacterial community in soil is largely responsible for mobilization of the soil organic P pool, and the released P is taken up by extraradical AM hyphae, which mediate its use for plant growth. However, the functional microbiome involved in organic P mineralization in the hyphosphere remains poorly understood. The aim of this study was to determine how AM hyphae-associated bacterial communities related to P turnover in the hyphosphere of leek (Allium porrum) respond to different forms of soil P. Using a compartmented microcosm, leek was grown with the AM fungus Funneliformis mosseae, and the extraradical mycelium of F. mosseae was allowed to grow into a separate hyphal compartment containing either no added P, or P as KH2PO4 or phytin. High-throughput sequencing showed that the alkaline phosphatase (ALP)-harboring bacterial community associated with the AM hyphae was dominated by Sinorhizobium, Bradyrhizobium, Pseudomonas, and Ralstonia and was significantly changed in response to different P treatments, with Pseudomonas showing higher relative abundance in organic P treatments than in control and inorganic P treatments. Pseudomonas was also the major genus harboring the β-propeller phytase (BPP) gene in the hyphosphere, but the BPP-harboring community structure was not affected by the presence of different P forms. These results demonstrate the profound differences in ALP- and BPP-harboring bacterial communities in the hyphosphere at bacterial genus level, providing new insights to link bacteria and biogeochemical P cycling driven in association with mycorrhizal hyphae.
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Affiliation(s)
- Fei Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, People's Republic of China
- School of Resource and Environmental Sciences, Henan Institute of Science and Technology, Xinxiang, 453003, People's Republic of China
| | - Michael A Kertesz
- Sydney Institute of Agriculture, School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Gu Feng
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, People's Republic of China.
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14
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Houfani AA, Větrovský T, Navarrete OU, Štursová M, Tláskal V, Beiko RG, Boucherba N, Baldrian P, Benallaoua S, Jorquera MA. Cellulase-Hemicellulase Activities and Bacterial Community Composition of Different Soils from Algerian Ecosystems. Microb Ecol 2019; 77:713-725. [PMID: 30209585 DOI: 10.1007/s00248-018-1251-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
Soil microorganisms are important mediators of carbon cycling in nature. Although cellulose- and hemicellulose-degrading bacteria have been isolated from Algerian ecosystems, the information on the composition of soil bacterial communities and thus the potential of their members to decompose plant residues is still limited. The objective of the present study was to describe and compare the bacterial community composition in Algerian soils (crop, forest, garden, and desert) and the activity of cellulose- and hemicellulose-degrading enzymes. Bacterial communities were characterized by high-throughput 16S amplicon sequencing followed by the in silico prediction of their functional potential. The highest lignocellulolytic activity was recorded in forest and garden soils whereas activities in the agricultural and desert soils were typically low. The bacterial phyla Proteobacteria (in particular classes α-proteobacteria, δ-proteobacteria, and γ-proteobacteria), Firmicutes, and Actinobacteria dominated in all soils. Forest and garden soils exhibited higher diversity than agricultural and desert soils. Endocellulase activity was elevated in forest and garden soils. In silico analysis predicted higher share of genes assigned to general metabolism in forest and garden soils compared with agricultural and arid soils, particularly in carbohydrate metabolism. The highest potential of lignocellulose decomposition was predicted for forest soils, which is in agreement with the highest activity of corresponding enzymes.
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Affiliation(s)
- Aicha Asma Houfani
- Laboratoire de Microbiologie Appliquée (LMA), Département de Microbiologie, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000, Bejaia, Algérie
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Oscar U Navarrete
- Laboratorio de Ecología Microbiana Aplicada, Departmento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile
- Scientific and Biotechnological Bioresource Nucleus, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile
| | - Martina Štursová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, 6050 University Avenue, Halifax, NS, B3H 4R2, Canada
| | - Nawel Boucherba
- Laboratoire de Microbiologie Appliquée (LMA), Département de Microbiologie, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000, Bejaia, Algérie
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Said Benallaoua
- Laboratoire de Microbiologie Appliquée (LMA), Département de Microbiologie, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000, Bejaia, Algérie
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada, Departmento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile.
- Scientific and Biotechnological Bioresource Nucleus, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile.
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15
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Granada CE, Vargas LK, Lisboa BB, Giongo A, Martinho CT, Pereira LDM, de Oliveira RR, Bruxel F, de Freitas EM, Passaglia LMP. Bacterial and Archaeal Communities Change With Intensity of Vegetation Coverage in Arenized Soils From the Pampa Biome. Front Microbiol 2019; 10:497. [PMID: 30967845 PMCID: PMC6439421 DOI: 10.3389/fmicb.2019.00497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/26/2019] [Indexed: 02/01/2023] Open
Abstract
Arenization occurs in regions that present sandy soils with normal rainfall levels. Predatory use of environmental sources, the dissolution of arenitic rocks and reworking of non-consolidated surface sands intensify this degradation scenario. Thus, this work aimed to evaluate the impact of the arenization process in the Brazilian Pampa Biome and how this phenomenon affects the soil microbial and plant communities. For this purpose, three arenized areas in Southern Brazil (Pampa Biome) were selected and, in each one, three sampling points were studied: arenized (ARA), arenized to grassland transition (AGT), and grassland (GRA) areas. In the three sampling points, soils presented low levels of nutrients, organic matter, mud and pH acidic in all regions but, the presence of vegetation coverage in AGT and GRA areas preserved the topsoil structure. Our study related ARA with bacterial families Alcaligenaceae, Pseudomonadaceae, and Xanthomonadaceae. AGT with bacterial families Bacillaceae and Burkholderiaceae, and plant species Melinis repens (Willd.) Zizka and Paspalum stellatum Humb. and Bonpl. ex Flüggé, and GRA with bacterial families Koribacteraceae, Hyphomicrobiaceae, and Chthoniobacteraceae, and plant species Croton subpannosus Müll.Arg. ex Griseb., Piptochaetium montevidense (Spreng.) Parodi and Elyonurus sp. The three studied areas (as well as sampling points) present soils extremely poor in nutrients with sandy texture, and the bacterial and plant composition well known to be resistant to environmental stresses were dominant. The vulnerability of these areas causes a degradation scenario, which is worsened by agricultural activities. However, in general, this phenomenon is a natural process that occurs mainly due to soil characteristics (poor soils) and climatic variations.
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Affiliation(s)
- Camille E Granada
- Programa de Pós-graduação em Biotecnologia, Universidade do Vale do Taquari - Univates, Lajeado, Brazil
| | - Luciano Kayser Vargas
- Laboratório de Solos, Fundação Estadual de Pesquisa Agropecuária (FEPAGRO), Porto Alegre, Brazil
| | - Bruno Brito Lisboa
- Laboratório de Solos, Fundação Estadual de Pesquisa Agropecuária (FEPAGRO), Porto Alegre, Brazil
| | - Adriana Giongo
- Instituto do Petróleo e dos Recursos Naturais. Av. Ipiranga, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Caroline Thais Martinho
- Instituto do Petróleo e dos Recursos Naturais. Av. Ipiranga, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Leandro de M Pereira
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Escola de Ciências. Av. Ipiranga, Porto Alegre, Brazil
| | - Rafael R de Oliveira
- Instituto do Petróleo e dos Recursos Naturais. Av. Ipiranga, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Fernanda Bruxel
- Programa de Pós-graduação em Biotecnologia, Universidade do Vale do Taquari - Univates, Lajeado, Brazil
| | - Elisete Maria de Freitas
- Programa de Pós-graduação em Biotecnologia, Universidade do Vale do Taquari - Univates, Lajeado, Brazil.,Universidade do Vale do Taquari - Univates, Programa de Pós-Graduação em Sistemas Ambientais Sustentáveis, Lajeado, Brazil
| | - Luciane M P Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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16
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Rilling JI, Acuña JJ, Sadowsky MJ, Jorquera MA. Putative Nitrogen-Fixing Bacteria Associated With the Rhizosphere and Root Endosphere of Wheat Plants Grown in an Andisol From Southern Chile. Front Microbiol 2018; 9:2710. [PMID: 30524385 PMCID: PMC6256256 DOI: 10.3389/fmicb.2018.02710] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/23/2018] [Indexed: 11/17/2022] Open
Abstract
Acidic ash derived volcanic soils (Andisols) support 50% of cereal production in Chile. Nitrogen (N) is essential for cereal crops and commonly added as urea with consequent environmental concerns due to leaching. Despite the relevance of N to plant growth, few studies have focused on understanding the application, management and ecological role of N2-fixing bacterial populations as tool for improve the N nutrition of cereal crops in Chile. It is known that N2-fixing bacteria commonly inhabits diverse plant compartments (e.g., rhizosphere and root endosphere) where they can supply N for plant growth. Here, we used culture-independent and dependent approaches to characterize and compare the putative N2-fixing bacteria associated with the rhizosphere and root endosphere of wheat plants grown in an Andisol from southern Chile. Our results showed significantly greater bacterial loads in the rhizosphere than the root endosphere. Quantitative PCR results indicated that the copy number of the 16S rRNA gene ranged from 1012~1013 and 107~108 g-1 sample in rhizosphere and root endosphere, respectively. The nifH gene copy number ranged from 105~106 and 105 g-1 sample in rhizosphere and root endosphere, respectively. The total culturable bacteria number ranged from 109~1010 and 107~108 CFU g-1 sample in rhizosphere and 104~105 and 104 CFU g-1 sample in root endosphere using LB and NM-1 media, respectively. Indirect counts of putative N2-fixing bacteria were 103 and 102~103 CFU g-1 sample in rhizosphere and root endosphere using NFb medium, respectively. Sequencing of 16S rRNA genes from randomly selected putative N2-fixing bacteria revealed the presence of members of Proteobacteria (Bosea and Roseomonas), Actinobacteria (Georgenia, Mycobacterium, Microbacterium, Leifsonia, and Arthrobacter), Bacteroidetes (Chitinophaga) and Firmicutes (Bacillus and Psychrobacillus) taxa. Differences in 16S rRNA and putative nifH-containing bacterial communities between rhizosphere and root endosphere were shown by denaturing gradient gel electrophoresis (DGGE). This study shows a compartmentalization between rhizosphere and root endosphere for both the abundance and diversity of total (16S rRNA) and putative N2-fixing bacterial communities on wheat plants grown in Chilean Andisols. This information can be relevant for the design and application of agronomic strategies to enhance sustainable N-utilization in cereal crops in Chile.
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Affiliation(s)
- Joaquin I. Rilling
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco, Chile
| | - Jacquelinne J. Acuña
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Michael J. Sadowsky
- Department of Soil, Water, and Climate, Department of Plant and Microbial Biology, BioTechnology Institute, University of Minnesota, Saint Paul, MN, United States
| | - Milko A. Jorquera
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
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17
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Cid FP, Maruyama F, Murase K, Graether SP, Larama G, Bravo LA, Jorquera MA. Draft genome sequences of bacteria isolated from the Deschampsia antarctica phyllosphere. Extremophiles 2018; 22:537-552. [PMID: 29492666 DOI: 10.1007/s00792-018-1015-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/18/2018] [Indexed: 11/28/2022]
Abstract
Genome analyses are being used to characterize plant growth-promoting (PGP) bacteria living in different plant compartiments. In this context, we have recently isolated bacteria from the phyllosphere of an Antarctic plant (Deschampsia antarctica) showing ice recrystallization inhibition (IRI), an activity related to the presence of antifreeze proteins (AFPs). In this study, the draft genomes of six phyllospheric bacteria showing IRI activity were sequenced and annotated according to their functional gene categories. Genome sizes ranged from 5.6 to 6.3 Mbp, and based on sequence analysis of the 16S rRNA genes, five strains were identified as Pseudomonas and one as Janthinobacterium. Interestingly, most strains showed genes associated with PGP traits, such as nutrient uptake (ammonia assimilation, nitrogen fixing, phosphatases, and organic acid production), bioactive metabolites (indole acetic acid and 1-aminocyclopropane-1-carboxylate deaminase), and antimicrobial compounds (hydrogen cyanide and pyoverdine). In relation with IRI activity, a search of putative AFPs using current bioinformatic tools was also carried out. Despite that genes associated with reported AFPs were not found in these genomes, genes connected to ice-nucleation proteins (InaA) were found in all Pseudomonas strains, but not in the Janthinobacterium strain.
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Affiliation(s)
- Fernanda P Cid
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Avenida Francisco Salazar 01145, Temuco, Chile
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- The Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Tokyo, Japan
| | - Kazunori Murase
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Giovanni Larama
- Department of Mathematical Engineering, Universidad de La Frontera, Temuco, Chile
| | - Leon A Bravo
- Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Forestales, Universidad de la Frontera, Temuco, Chile
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Milko A Jorquera
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile.
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Avenida Francisco Salazar 01145, Temuco, Chile.
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18
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Hussain SS, Mehnaz S, Siddique KHM. Harnessing the Plant Microbiome for Improved Abiotic Stress Tolerance. Plant Microbiome: Stress Response 2018. [DOI: 10.1007/978-981-10-5514-0_2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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19
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Rilling JI, Acuña JJ, Sadowsky MJ, Jorquera MA. Putative Nitrogen-Fixing Bacteria Associated With the Rhizosphere and Root Endosphere of Wheat Plants Grown in an Andisol From Southern Chile. Front Microbiol 2018. [PMID: 30524385 DOI: 10.3389/fmicb.2018.02710/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
Acidic ash derived volcanic soils (Andisols) support 50% of cereal production in Chile. Nitrogen (N) is essential for cereal crops and commonly added as urea with consequent environmental concerns due to leaching. Despite the relevance of N to plant growth, few studies have focused on understanding the application, management and ecological role of N2-fixing bacterial populations as tool for improve the N nutrition of cereal crops in Chile. It is known that N2-fixing bacteria commonly inhabits diverse plant compartments (e.g., rhizosphere and root endosphere) where they can supply N for plant growth. Here, we used culture-independent and dependent approaches to characterize and compare the putative N2-fixing bacteria associated with the rhizosphere and root endosphere of wheat plants grown in an Andisol from southern Chile. Our results showed significantly greater bacterial loads in the rhizosphere than the root endosphere. Quantitative PCR results indicated that the copy number of the 16S rRNA gene ranged from 1012~1013 and 107~108 g-1 sample in rhizosphere and root endosphere, respectively. The nifH gene copy number ranged from 105~106 and 105 g-1 sample in rhizosphere and root endosphere, respectively. The total culturable bacteria number ranged from 109~1010 and 107~108 CFU g-1 sample in rhizosphere and 104~105 and 104 CFU g-1 sample in root endosphere using LB and NM-1 media, respectively. Indirect counts of putative N2-fixing bacteria were 103 and 102~103 CFU g-1 sample in rhizosphere and root endosphere using NFb medium, respectively. Sequencing of 16S rRNA genes from randomly selected putative N2-fixing bacteria revealed the presence of members of Proteobacteria (Bosea and Roseomonas), Actinobacteria (Georgenia, Mycobacterium, Microbacterium, Leifsonia, and Arthrobacter), Bacteroidetes (Chitinophaga) and Firmicutes (Bacillus and Psychrobacillus) taxa. Differences in 16S rRNA and putative nifH-containing bacterial communities between rhizosphere and root endosphere were shown by denaturing gradient gel electrophoresis (DGGE). This study shows a compartmentalization between rhizosphere and root endosphere for both the abundance and diversity of total (16S rRNA) and putative N2-fixing bacterial communities on wheat plants grown in Chilean Andisols. This information can be relevant for the design and application of agronomic strategies to enhance sustainable N-utilization in cereal crops in Chile.
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Affiliation(s)
- Joaquin I Rilling
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco, Chile
| | - Jacquelinne J Acuña
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Michael J Sadowsky
- Department of Soil, Water, and Climate, Department of Plant and Microbial Biology, BioTechnology Institute, University of Minnesota, Saint Paul, MN, United States
| | - Milko A Jorquera
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
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20
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Andrés-Barrao C, Lafi FF, Alam I, de Zélicourt A, Eida AA, Bokhari A, Alzubaidy H, Bajic VB, Hirt H, Saad MM. Complete Genome Sequence Analysis of Enterobacter sp. SA187, a Plant Multi-Stress Tolerance Promoting Endophytic Bacterium. Front Microbiol 2017; 8:2023. [PMID: 29163376 PMCID: PMC5664417 DOI: 10.3389/fmicb.2017.02023] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/04/2017] [Indexed: 11/13/2022] Open
Abstract
Enterobacter sp. SA187 is an endophytic bacterium that has been isolated from root nodules of the indigenous desert plant Indigofera argentea. SA187 could survive in the rhizosphere as well as in association with different plant species, and was able to provide abiotic stress tolerance to Arabidopsis thaliana. The genome sequence of SA187 was obtained by using Pacific BioScience (PacBio) single-molecule sequencing technology, with average coverage of 275X. The genome of SA187 consists of one single 4,429,597 bp chromosome, with an average 56% GC content and 4,347 predicted protein coding DNA sequences (CDS), 153 ncRNA, 7 rRNA, and 84 tRNA. Functional analysis of the SA187 genome revealed a large number of genes involved in uptake and exchange of nutrients, chemotaxis, mobilization and plant colonization. A high number of genes were also found to be involved in survival, defense against oxidative stress and production of antimicrobial compounds and toxins. Moreover, different metabolic pathways were identified that potentially contribute to plant growth promotion. The information encoded in the genome of SA187 reveals the characteristics of a dualistic lifestyle of a bacterium that can adapt to different environments and promote the growth of plants. This information provides a better understanding of the mechanisms involved in plant-microbe interaction and could be further exploited to develop SA187 as a biological agent to improve agricultural practices in marginal and arid lands.
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Affiliation(s)
- Cristina Andrés-Barrao
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Feras F Lafi
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Intikhab Alam
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Axel de Zélicourt
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Abdul A Eida
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ameerah Bokhari
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Hanin Alzubaidy
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Vladimir B Bajic
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Heribert Hirt
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Maged M Saad
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Inostroza NG, Barra PJ, Wick LY, Mora ML, Jorquera MA. Effect of rhizobacterial consortia from undisturbed arid- and agro-ecosystems on wheat growth under different conditions. Lett Appl Microbiol 2017; 64:158-163. [PMID: 27914208 DOI: 10.1111/lam.12697] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 11/07/2016] [Accepted: 11/21/2016] [Indexed: 11/27/2022]
Abstract
Plant growth-promoting rhizobacteria (PGPR) are studied as complements/alternatives to chemical fertilizers used in agriculture. However, poor information exists on the potential of PGPR from undisturbed ecosystems. Here, we have evaluated the plant growth-promoting (PGP) effect of rhizobacterial consortia from undisturbed Chilean arid ecosystems (Consortium C1) and agro-ecosystems (Consortium C2) on plant biomass production. The PGP effects of C1 and C2 were assayed in wheat seedlings (Triticum aestivum L.) grown in pots under growth chamber conditions and in pots placed in an open greenhouse under natural conditions, using two different Chilean Andisols (Piedras Negras and Freire series) kept either at 30 or 60% of their maximum water holding capacity (MWHC). PGP effects depended on the soil type, MWHC and the growth conditions tested. Although both consortia showed PGB effects in artificial soils relative to controls in growth chambers, only C1 provoked a PGP effect at 60% MWHC in phosphorus-poor soil of the 'Piedras Negras' series. At natural conditions, however, only C1 exhibited statistically significant PGP effects at 30% MWHC in 'Piedras Negras', yet and most importantly allowed to maintain similar plant biomass as at 60% MWHC. Our results support possible applications of rhizobacterial consortia from arid ecosystems to improve wheat growth in Chilean Andisols under water shortage conditions. SIGNIFICANCE AND IMPACT OF THE STUDY Wheat seedling inoculated with rhizobacterial consortia obtained from an undisturbed Chilean arid ecosystem showed improved growth in phosphorus-poor and partly dry soil. Arid ecosystems should be considered in further studies as an alternative source of microbial inoculants for agro-ecosystems subjected to stressful conditions by low nutrients and/or adverse climate events.
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Affiliation(s)
- N G Inostroza
- Center of Plant, Soil interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - P J Barra
- Center of Plant, Soil interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - L Y Wick
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - M L Mora
- Center of Plant, Soil interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - M A Jorquera
- Center of Plant, Soil interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
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22
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Jorquera MA, Maruyama F, Ogram AV, Navarrete OU, Lagos LM, Inostroza NG, Acuña JJ, Rilling JI, de La Luz Mora M. Rhizobacterial Community Structures Associated with Native Plants Grown in Chilean Extreme Environments. Microb Ecol 2016; 72:633-646. [PMID: 27406732 DOI: 10.1007/s00248-016-0813-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/29/2016] [Indexed: 06/06/2023]
Abstract
Chile is topographically and climatically diverse, with a wide array of diverse undisturbed ecosystems that include native plants that are highly adapted to local conditions. However, our understanding of the diversity, activity, and role of rhizobacteria associated with natural vegetation in undisturbed Chilean extreme ecosystems is very poor. In the present study, the combination of denaturing gradient gel electrophoresis and 454-pyrosequencing approaches was used to describe the rhizobacterial community structures of native plants grown in three representative Chilean extreme environments: Atacama Desert (ATA), Andes Mountains (AND), and Antarctic (ANT). Both molecular approaches revealed the presence of Proteobacteria, Bacteroidetes, and Actinobacteria as the dominant phyla in the rhizospheres of native plants. Lower numbers of operational taxonomic units (OTUs) were observed in rhizosphere soils from ATA compared with AND and ANT. Both approaches also showed differences in rhizobacterial community structures between extreme environments and between plant species. The differences among plant species grown in the same environment were attributed to the higher relative abundance of classes Gammaproteobacteria and Alphaproteobacteria. However, further studies are needed to determine which environmental factors regulate the structures of rhizobacterial communities, and how (or if) specific bacterial groups may contribute to the growth and survival of native plants in each Chilean extreme environments.
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Affiliation(s)
- Milko A Jorquera
- Center of Plant, Soil Interaction, and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Ave. Francisco Salazar, 01145, Temuco, Chile.
| | - Fumito Maruyama
- Section of Microbiology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Andrew V Ogram
- Soil and Water Science Department, University of Florida, 2181 McCarty Hall, PO Box 110290, Gainesville, FL, 32611, USA
| | - Oscar U Navarrete
- Center of Plant, Soil Interaction, and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Lorena M Lagos
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Nitza G Inostroza
- Center of Plant, Soil Interaction, and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Jacquelinne J Acuña
- Center of Plant, Soil Interaction, and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Joaquín I Rilling
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - María de La Luz Mora
- Center of Plant, Soil Interaction, and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Ave. Francisco Salazar, 01145, Temuco, Chile
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Mendez-trujillo V, Carrillo-beltran M, González-mendoza D, Gutierrez-miceli F, Valdez-salas B. Antifungal Activity and Presence of Lipopeptides Genes in Bacillus subtilis Isolated from the Rhizosphere of Pluchea sericea. Iran J Sci Technol Trans Sci 2018; 42:415-9. [DOI: 10.1007/s40995-016-0110-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Chimwamurombe PM, Grönemeyer JL, Reinhold-Hurek B. Isolation and characterization of culturable seed-associated bacterial endophytes from gnotobiotically grown Marama bean seedlings. FEMS Microbiol Ecol 2016; 92:fiw083. [PMID: 27118727 DOI: 10.1093/femsec/fiw083] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2016] [Indexed: 12/20/2022] Open
Abstract
Marama bean (Tylosema esculentum) is an indigenous non-nodulating legume to the arid agro-ecological parts of Southern Africa. It is a staple food for the Khoisan and Bantu people from these areas. It is intriguing how it is able to synthesize the high-protein content in the seeds since its natural habitat is nitrogen deficient. The aim of the study was to determine the presence of seed transmittable bacterial endophytes that may have growth promoting effects, which may be particularly important for the harsh conditions. Marama bean seeds were surface sterilized and gnotobiotically grown to 2 weeks old seedlings. From surface-sterilized shoots and roots, 123 distinct bacterial isolates were cultured using three media, and identified by BOX-PCR fingerprinting and sequence analyses of the 16S rRNA and nifH genes. Phylogenetic analyses of 73 putative endophytes assigned them to bacterial species from 14 genera including Proteobacteria (Rhizobium, Massilia, Kosakonia, Pseudorhodoferax, Caulobacter, Pantoea, Sphingomonas, Burkholderia, Methylobacterium), Firmicutes (Bacillus), Actinobacteria (Curtobacterium, Microbacterium) and Bacteroidetes (Mucilaginibacter, Chitinophaga). Screening for plant growth-promoting activities revealed that the isolates showed production of IAA, ACC deaminase, siderophores, endoglucanase, protease, AHLs and capacities to solubilize phosphate and fix nitrogen. This is the first report that marama bean seeds may harbor endophytes that can be cultivated from seedlings; in this community of bacteria, physiological characteristics that are potentially plant growth promoting are widespread.
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Affiliation(s)
- Percy Maruwa Chimwamurombe
- Department of Biological Sciences, University of Namibia, Private Bag 13301, Windhoek, Namibia Department of Microbe-Plant Interactions, University of Bremen, PO Box 330440, D-28334 Bremen, Germany
| | - Jann Lasse Grönemeyer
- Department of Microbe-Plant Interactions, University of Bremen, PO Box 330440, D-28334 Bremen, Germany
| | - Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, University of Bremen, PO Box 330440, D-28334 Bremen, Germany
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Valverde A, De Maayer P, Oberholster T, Henschel J, Louw MK, Cowan D. Specific Microbial Communities Associate with the Rhizosphere of Welwitschia mirabilis, a Living Fossil. PLoS One 2016; 11:e0153353. [PMID: 27064484 PMCID: PMC4827806 DOI: 10.1371/journal.pone.0153353] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/29/2016] [Indexed: 11/24/2022] Open
Abstract
Welwitschia mirabilis is an ancient and rare plant distributed along the western coast of Namibia and Angola. Several aspects of Welwitschia biology and ecology have been investigated, but very little is known about the microbial communities associated with this plant. This study reports on the bacterial and fungal communities inhabiting the rhizosphere of W. mirabilis and the surrounding bulk soil. Rhizosphere communities were dominated by sequences of Alphaproteobacteria and Euromycetes, while Actinobacteria, Alphaproteobacteria, and fungi of the class Dothideomycetes jointly dominated bulk soil communities. Although microbial communities within the rhizosphere and soil samples were highly variable, very few “species” (OTUs defined at a 97% identity cut-off) were shared between these two environments. There was a small ‘core’ rhizosphere bacterial community (formed by Nitratireductor, Steroidobacter, Pseudonocardia and three Phylobacteriaceae) that together with Rhizophagus, an arbuscular mycorrhizal fungus, and other putative plant growth-promoting microbes may interact synergistically to promote Welwitschia growth.
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Affiliation(s)
- Angel Valverde
- Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- * E-mail:
| | - Pieter De Maayer
- Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Tanzelle Oberholster
- Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Joh Henschel
- Namib Ecological Restoration and Monitoring Unit, Gobabeb Research and Training Centre, Walvis Bay, Namibia
- SAEON Arid Lands Node, Hadison Park, Kimberly, South Africa
| | | | - Don Cowan
- Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
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26
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Affiliation(s)
- Susana Rodríguez‐Echeverría
- CFE‐Centre for Functional Ecology Department of Life Sciences University of Coimbra Calçada Martim de Freitas 3000‐456 Coimbra Portugal
| | - Yudi M. Lozano
- Estación Experimental de Zonas Áridas Consejo Superior de Investigaciones Científicas Carretera de Sacramento s/n E‐04120 La Cañada de San Urbano Almería Spain
| | - Richard D. Bardgett
- Faculty of Life Sciences The University of Manchester Michael Smith Building Oxford Road Manchester M13 9PT UK
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Suyal DC, Yadav A, Shouche Y, Goel R. Bacterial diversity and community structure of Western Indian Himalayan red kidney bean (Phaseolus vulgaris) rhizosphere as revealed by 16S rRNA gene sequences. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0048] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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28
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Makhalanyane TP, Valverde A, Gunnigle E, Frossard A, Ramond JB, Cowan DA. Microbial ecology of hot desert edaphic systems. FEMS Microbiol Rev 2015; 39:203-21. [DOI: 10.1093/femsre/fuu011] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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29
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El-Sayed WS, Akhkha A, El-Naggar MY, Elbadry M. In vitro antagonistic activity, plant growth promoting traits and phylogenetic affiliation of rhizobacteria associated with wild plants grown in arid soil. Front Microbiol 2014; 5:651. [PMID: 25538687 PMCID: PMC4255609 DOI: 10.3389/fmicb.2014.00651] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/12/2014] [Indexed: 12/02/2022] Open
Abstract
The role of plant growth-promoting rhizobacteria (PGPR) in adaptation of plants in extreme environments is not yet completely understood. For this study native bacteria were isolated from rhizospeheric arid soils and evaluated for both growth-promoting abilities and antagonistic potential against phytopathogenic fungi and nematodes. The phylogentic affiliation of these representative isolates was also characterized. Rhizobacteria associated with 11 wild plant species from the arid soil of Almadinah Almunawarah, Kingdom of Saudi Arabia (KSA) were investigated. From a total of 531 isolates, only 66 bacterial isolates were selected based on their ability to inhibit Fusarium oxysporum, and Sclerotinia sclerotiorum. The selected isolates were screened in vitro for activities related to plant nutrition and plant growth regulation as well as for antifungal and nematicidal traits. Isolated bacteria were found to exhibit capabilities in fix atmospheric nitrogen, produce ammonia, indoleacetic acid (IAA), siderophores, solubilize phosphate and zinc, and showed an antagonistic potential against some phytopathogenic fungi and one nematode species (Meloidogyne incognita) to various extent. Isolates were ranked by their potential ability to function as PGPR. The 66 isolates were genotyped using amplified rDNA restriction analysis (ARDRA) and 16S rRNA gene sequence analysis. The taxonomic composition of the representative genotypes from both rhizosphere and rhizoplane comprised Bacillus, Enterobacter and Pseudomonas. Out of the 10 genotypes, three strains designated as PHP03, CCP05, and TAP02 might be regarded as novel strains based on their low similarity percentages and high bootstrap values. The present study clearly identified specific traits in the isolated rhizobacteria, which make them good candidates as PGPR and might contribute to plant adaption to arid environments. Application of such results in agricultural fields may improve and enhance plant growth in arid soils.
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Affiliation(s)
- Wael S El-Sayed
- Biology Department, Faculty of Science, Taibah University Almadinah Almunawarah, Saudi Arabia ; Microbiology Department, Faculty of Science, Ain Shams University Cairo, Egypt
| | - Abdellah Akhkha
- Biology Department, Faculty of Science, Taibah University Almadinah Almunawarah, Saudi Arabia
| | - Moustafa Y El-Naggar
- Botany and Microbiology Department, Faculty of Science, Alexandria University Alexandria, Egypt
| | - Medhat Elbadry
- Biology Department, Faculty of Science, Taibah University Almadinah Almunawarah, Saudi Arabia ; Agricultural Microbiology Department, Faculty of Agriculture, Fayoum University Fayoum, Egypt
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Suyal DC, Shukla A, Goel R. Growth promotory potential of the cold adapted diazotroph Pseudomonas migulae S10724 against native green gram (Vigna radiata (L.) Wilczek). 3 Biotech 2014; 4:665-668. [PMID: 28324315 PMCID: PMC4235881 DOI: 10.1007/s13205-014-0259-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/01/2014] [Indexed: 12/29/2022] Open
Abstract
It is being confirmed previously the atmospheric nitrogen fixing ability of the cold adapted Pseudomonas migulae S10724 strain at the fluctuating temperatures. Therefore, net house bioinoculation experiment was performed to determine the effectiveness of inoculation of strain S10724 on the growth enhancement of native green gram (Vigna radiata L. Wilczek). The strain significantly (p < 0.05) stimulated the growth of roots (45.3 %) and shoots (45.6 %) of green gram plants. Furthermore, other growth related parameters viz. fresh and dry weight was also found to be increased significantly. Treated plants typically showed more obvious modifications in their biochemical status also. The total chlorophyll and nitrate reductase activity was increased in S10724 inoculated plant as compared to the control one. Moreover, in vitro seed germination assay revealed that the germination was increased in S10724 strain treated seeds by 22 % at 25 °C while 25 % at 12 °C unlikely to respective controls. The results suggest that P.migulae S10724 strain is a potential plant growth promoting bacterium for legume under fluctuating temperature ranges and therefore, could be used effectively as a low cost bioinoculant in Himalayan agricultural belt successfully.
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Affiliation(s)
- Deep Chandra Suyal
- Department of Microbiology, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, 263145, Uttarakhand, India
| | - Anjana Shukla
- Department of Microbiology, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, 263145, Uttarakhand, India
| | - Reeta Goel
- Department of Microbiology, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, 263145, Uttarakhand, India.
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Jin H, Yang XY, Yan ZQ, Liu Q, Li XZ, Chen JX, Zhang DH, Zeng LM, Qin B. Characterization of rhizosphere and endophytic bacterial communities from leaves, stems and roots of medicinal Stellera chamaejasme L. Syst Appl Microbiol 2014; 37:376-85. [PMID: 24958606 DOI: 10.1016/j.syapm.2014.05.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 04/30/2014] [Accepted: 05/02/2014] [Indexed: 11/22/2022]
Abstract
A diverse array of bacteria that inhabit the rhizosphere and different plant organs play a crucial role in plant health and growth. Therefore, a general understanding of these bacterial communities and their diversity is necessary. Using the 16S rRNA gene clone library technique, the bacterial community structure and diversity of the rhizosphere and endophytic bacteria in Stellera chamaejasme compartments were compared and clarified for the first time. Grouping of the sequences obtained showed that members of the Proteobacteria (43.2%), Firmicutes (36.5%) and Actinobacteria (14.1%) were dominant in both samples. Other groups that were consistently found, albeit at lower abundance, were Bacteroidetes (2.1%), Chloroflexi (1.9%), and Cyanobacteria (1.7%). The habitats (rhizosphere vs endophytes) and organs (leaf, stem and root) structured the community, since the Wilcoxon signed rank test indicated that more varied bacteria inhabited the rhizosphere compared to the organs of the plant. In addition, correspondence analysis also showed that differences were apparent in the bacterial communities associated with these distinct habitats. Moreover, principal component analysis revealed that the profiles obtained from the rhizosphere and roots were similar, whereas leaf and stem samples clustered together on the opposite side of the plot from the rhizosphere and roots. Taken together, these results suggested that, although the communities associated with the rhizosphere and organs shared some bacterial species, the associated communities differed in structure and diversity.
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Mendes R, Garbeva P, Raaijmakers JM. The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 2013; 37:634-63. [DOI: 10.1111/1574-6976.12028] [Citation(s) in RCA: 1382] [Impact Index Per Article: 125.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Revised: 05/22/2013] [Accepted: 05/27/2013] [Indexed: 12/18/2022] Open
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33
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Kumar V, Singh P, Jorquera MA, Sangwan P, Kumar P, Verma AK, Agrawal S. Isolation of phytase-producing bacteria from Himalayan soils and their effect on growth and phosphorus uptake of Indian mustard (Brassica juncea). World J Microbiol Biotechnol 2013; 29:1361-9. [PMID: 23546828 DOI: 10.1007/s11274-013-1299-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 02/19/2013] [Indexed: 10/27/2022]
Abstract
Phytase-producing bacteria (PPB) is being investigated as plant growth promoting rhizobacteria (PGPR) to improve the phosphorus (P) nutrition and growth of plants grown in soil with high phytate content. Phytate is dominant organic P forms in many soils and must be hydrolyzed to be available for plants. Indian mustard (Brassica juncea) is a plant with economic importance in agriculture and phytoremediation, therefore biotechnological tools to improve growth and environmental stress tolerance are needed. In this study, we isolated and characterized PPB from Himalayan soils and evaluated their effect on growth and P uptake by B. juncea under greenhouse conditions. Sixty five PPB were isolated and based on phytate hydrolysis, three efficient PPB were chosen and identified as Acromobacter sp. PB-01, Tetrathiobacter sp. PB-03 and Bacillus sp. PB-13. Selected PPB showed ability to grow at wide range of pH, temperature and salt concentrations as well as to harbour diverse PGPR activities, such as: solubilization of insoluble Ca-phosphate (193-642 μg ml(-1)), production of phytohormone indole acetic acid (5-39 μg ml(-1)) and siderophore. Tetrathiobacter sp. PB-03 and Bacillus sp. PB-13 showed 50 and 70 % inhibition of phytopathogen Rhizoctonia solani, respectively. Greenhouse potting assay also showed that the bacterization of B. juncea seeds with Tetrathiobacter sp. PB-03 and Bacillus sp. PB-13 significantly increased the biomass and P content in 30 days old seedlings. This study reveals the potential of PPB as PGPR to improve the growth of B. juncea.
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Jorquera MA, Saavedra N, Maruyama F, Richardson AE, Crowley DE, del C Catrilaf R, Henriquez EJ, de la Luz Mora M. Phytate addition to soil induces changes in the abundance and expression of Bacillus β-propeller phytase genes in the rhizosphere. FEMS Microbiol Ecol 2012; 83:352-60. [PMID: 22928980 DOI: 10.1111/j.1574-6941.2012.01480.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 08/13/2012] [Accepted: 08/14/2012] [Indexed: 11/29/2022] Open
Abstract
Phytate-mineralizing rhizobacteria (PMR) perform an essential function for the mineralization of organic phosphorus but little is known about their ecology in soils and rhizosphere. In this study, PCR-based methods were developed for detection and quantification of the Bacillus β-propeller phytase (BPP) gene. Experiments were conducted to monitor the presence and persistence of a phytate-mineralizing strain, Bacillus sp. MQH19, after inoculation of soil microcosms and within the rhizosphere. The occurrence of the BPP gene in natural pasture soils from Chilean Andisols was also examined. The results showed that the Bacillus BPP gene was readily detected in sterile and nonsterile microcosms, and that the quantitative PCR (qPCR) methods could be used to monitor changes in the abundance of the BPP gene over time. Our results also show that the addition of phytate to nonsterile soils induced the expression of the BPP gene in the rhizosphere of ryegrass and the BPP gene was detected in all pasture soils sampled. This study shows that phytate addition soils induced changes in the abundance and expression of Bacillus BPP to genes in the rhizosphere and demonstrates that Bacillus BPP gene is cosmopolitan in pasture soils from Chilean Andisols.
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Affiliation(s)
- Milko A Jorquera
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile.
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