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Lo SC, Tsai SY, Chang WH, Wu IC, Sou NL, Hung SHW, Chiang EPI, Huang CC. Characterization of the Pyrroloquinoline Quinone Producing Rhodopseudomonas palustris as a Plant Growth-Promoting Bacterium under Photoautotrophic and Photoheterotrophic Culture Conditions. Int J Mol Sci 2023; 24:14080. [PMID: 37762380 PMCID: PMC10531626 DOI: 10.3390/ijms241814080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Rhodopseudomonas palustris is a purple non-sulfide bacterium (PNSB), and some strains have been proven to promote plant growth. However, the mechanism underlying the effect of these PNSBs remains limited. Based on genetic information, R. palustris possesses the ability to produce pyrroloquinoline quinone (PQQ). PQQ is known to play a crucial role in stimulating plant growth, facilitating phosphorous solubilization, and acting as a reactive oxygen species scavenger. However, it is still uncertain whether growth conditions influence R. palustris's production of PQQ and other characteristics. In the present study, it was found that R. palustris exhibited a higher expression of genes related to PQQ synthesis under autotrophic culture conditions as compared to acetate culture conditions. Moreover, similar patterns were observed for phosphorous solubilization and siderophore activity, both of which are recognized to contribute to plant-growth benefits. However, these PNSB culture conditions did not show differences in Arabidopsis growth experiments, indicating that there may be other factors influencing plant growth in addition to PQQ content. Furthermore, the endophytic bacterial strains isolated from Arabidopsis exhibited differences according to the PNSB culture conditions. These findings imply that, depending on the PNSB's growing conditions, it may interact with various soil bacteria and facilitate their infiltration into plants.
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Affiliation(s)
- Shou-Chen Lo
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; (S.-C.L.); (S.-Y.T.); (W.-H.C.); (I.-C.W.); (S.-H.W.H.)
| | - Shang-Yieng Tsai
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; (S.-C.L.); (S.-Y.T.); (W.-H.C.); (I.-C.W.); (S.-H.W.H.)
| | - Wei-Hsiang Chang
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; (S.-C.L.); (S.-Y.T.); (W.-H.C.); (I.-C.W.); (S.-H.W.H.)
| | - I-Chen Wu
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; (S.-C.L.); (S.-Y.T.); (W.-H.C.); (I.-C.W.); (S.-H.W.H.)
| | - Nga-Lai Sou
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung 402202, Taiwan; (N.-L.S.); (E.-P.I.C.)
| | - Shih-Hsun Walter Hung
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; (S.-C.L.); (S.-Y.T.); (W.-H.C.); (I.-C.W.); (S.-H.W.H.)
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
| | - En-Pei Isabel Chiang
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung 402202, Taiwan; (N.-L.S.); (E.-P.I.C.)
- Program in Microbial Genomics, National Chung Hsing University, Taichung 402202, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung 402202, Taiwan
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; (S.-C.L.); (S.-Y.T.); (W.-H.C.); (I.-C.W.); (S.-H.W.H.)
- Program in Microbial Genomics, National Chung Hsing University, Taichung 402202, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung 402202, Taiwan
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Microbial-Based Products to Control Soil-Borne Pathogens: Methods to Improve Efficacy and to Assess Impacts on Microbiome. Microorganisms 2023; 11:microorganisms11010224. [PMID: 36677516 PMCID: PMC9867489 DOI: 10.3390/microorganisms11010224] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/30/2022] [Accepted: 01/11/2023] [Indexed: 01/17/2023] Open
Abstract
Microbial-based products (either as biopesticide or biofertilizers) have a long history of application, though their use is still limited, mainly due to a perceived low and inconsistent efficacy under field conditions. However, their efficacy has always been compared to chemical products, which have a completely different mechanism of action and production process, following the chemical paradigm of agricultural production. This paradigm has also been applied to regulatory processes, particularly for biopesticides, making the marketing of microbial-based formulations difficult. Increased knowledge about bioinocula behavior after application to the soil and their impact on soil microbiome should foster better exploitation of microbial-based products in a complex environment such as the soil. Moreover, the multifunctional capacity of microbial strains with regard to plant growth promotion and protection should also be considered in this respect. Therefore, the methods utilized for these studies are key to improving the knowledge and understanding of microbial-based product activity and improving their efficacy, which, from farmers' point of view, is the parameter to assess the usefulness of a treatment. In this review, we are thus addressing aspects related to the production and formulation process, highlighting the methods that can be used to evaluate the functioning and impact of microbial-based products on soil microbiome, as tools supporting their use and marketing.
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Lee SK, Chiang MS, Hseu ZY, Kuo CH, Liu CT. A photosynthetic bacterial inoculant exerts beneficial effects on the yield and quality of tomato and affects bacterial community structure in an organic field. Front Microbiol 2022; 13:959080. [PMID: 36118214 PMCID: PMC9479686 DOI: 10.3389/fmicb.2022.959080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/26/2022] [Indexed: 11/25/2022] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) are microorganisms that promote plant health and play a critical role in sustainable agriculture. As a PGPR, Rhodopseudomonas palustris strain PS3, when applied as a microbial inoculant, exhibited beneficial effects on a variety of crops. In this study, we investigated the effects of PS3 on tomato growth, soil properties, and soil microbiota composition in an organic field. The results demonstrated that PS3 inoculation significantly improved the yield of marketable tomato fruit (37%) and the postharvest quality (e.g., sweetness, taste, vitamin C, total phenolic compounds, and lycopene). Additionally, soil nutrient availability (35–56%) and enzymatic activities (13–62%) also increased. We detected that approximately 107 CFU/g soil of R. palustris survived in the PS3-treated soil after harvest. Furthermore, several bacterial genera known to be associated with nutrient cycling (e.g., Dyella, Novosphingobium, Luteimonas, Haliangium, and Thermomonas) had higher relative abundances (log2 fold change >2.0). To validate the results of the field experiment, we further conducted pot experiments with field-collected soil using two different tomato cultivars and obtained consistent results. Notably, the relative abundance of putative PGPRs in the genus Haliangium increased with PS3 inoculation in both cultivars (1.5 and 34.2%, respectively), suggesting that this genus may have synergistic interactions with PS3. Taken together, we further demonstrated the value of PS3 in sustainable agriculture and provided novel knowledge regarding the effects of this PGPR on soil microbiota composition.
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Affiliation(s)
- Sook-Kuan Lee
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Ming-Shu Chiang
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Zeng-Yei Hseu
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- *Correspondence: Chih-Horng Kuo,
| | - Chi-Te Liu
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Chi-Te Liu,
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Physiological changes in Rhodococcus ruber S103 immobilized on biobooms using low-cost media enhance stress tolerance and crude oil-degrading activity. Sci Rep 2022; 12:10474. [PMID: 35729341 PMCID: PMC9213463 DOI: 10.1038/s41598-022-14488-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/07/2022] [Indexed: 11/09/2022] Open
Abstract
For economic feasibility, sugarcane molasses (0.5%, w/v) containing K2HPO4 (0.26%, w/v) and mature coconut water, low value byproducts, were used in cultivation of Rhodococcus ruber S103 for inoculum production and immobilization, respectively. Physiological changes of S103 grown in low-cost media, including cell hydrophobicity, saturated/unsaturated ratio of cellular fatty acids and biofilm formation activity, enhanced stress tolerance and crude oil biodegradation in freshwater and even under high salinity (5%, w/v). Biobooms comprised of S103 immobilized on polyurethane foam (PUF) was achieved with high biomass content (1010 colony-forming units g-1 PUF) via a scale-up process in a 5-L modified fluidized-bed bioreactor within 3 days. In a 500-L mesocosm, natural freshwater was spiked with crude oil (72 g or 667 mg g-1 dry biobooms), and a simulated wave was applied. Biobooms could remove 100% of crude oil within only 3 days and simultaneously biodegraded 60% of the adsorbed oil after 7 days when compared to boom control with indigenous bacteria. In addition, biobooms had a long shelf-life (at least 100 days) with high biodegradation activity (85.2 ± 2.3%) after storage in 10% (w/v) skimmed milk at room temperature. This study demonstrates that the low-cost production of biobooms has potential for future commercial bioremediation.
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Brown B, Wilkins M, Saha R. Rhodopseudomonas palustris: A biotechnology chassis. Biotechnol Adv 2022; 60:108001. [PMID: 35680002 DOI: 10.1016/j.biotechadv.2022.108001] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/18/2022] [Accepted: 06/01/2022] [Indexed: 11/26/2022]
Abstract
Rhodopseudomonas palustris is an attractive option for biotechnical applications and industrial engineering due to its metabolic versatility and its ability to catabolize a wide variety of feedstocks and convert them to several high-value products. Given its adaptable metabolism, R. palustris has been studied and applied in an extensive variety of applications such as examining metabolic tradeoffs for environmental perturbations, biodegradation of aromatic compounds, environmental remediation, biofuel production, agricultural biostimulation, and bioelectricity production. This review provides a holistic summary of the commercial applications for R. palustris as a biotechnology chassis and suggests future perspectives for research and engineering.
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Affiliation(s)
- Brandi Brown
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Mark Wilkins
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Industrial Agricultural Products Center, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Rajib Saha
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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From Lab to Farm: Elucidating the Beneficial Roles of Photosynthetic Bacteria in Sustainable Agriculture. Microorganisms 2021; 9:microorganisms9122453. [PMID: 34946055 PMCID: PMC8707939 DOI: 10.3390/microorganisms9122453] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/16/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022] Open
Abstract
Photosynthetic bacteria (PSB) possess versatile metabolic abilities and are widely applied in environmental bioremediation, bioenergy production and agriculture. In this review, we summarize examples of purple non-sulfur bacteria (PNSB) through biofertilization, biostimulation and biocontrol mechanisms to promote plant growth. They include improvement of nutrient acquisition, production of phytohormones, induction of immune system responses, interaction with resident microbial community. It has also been reported that PNSB can produce an endogenous 5-aminolevulinic acid (5-ALA) to alleviate abiotic stress in plants. Under biotic stress, these bacteria can trigger induced systemic resistance (ISR) of plants against pathogens. The nutrient elements in soil are significantly increased by PNSB inoculation, thus improving fertility. We share experiences of researching and developing an elite PNSB inoculant (Rhodopseudomonas palustris PS3), including strategies for screening and verifying beneficial bacteria as well as the establishment of optimal fermentation and formulation processes for commercialization. The effectiveness of PS3 inoculants for various crops under field conditions, including conventional and organic farming, is presented. We also discuss the underlying plant growth-promoting mechanisms of this bacterium from both microbial and plant viewpoints. This review improves our understanding of the application of PNSB in sustainable crop production and could inspire the development of diverse inoculants to overcome the changes in agricultural environments created by climate change.
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Biswal T, Shadangi KP, Sarangi PK. Application of Nanotechnology in the Production of Biohydrogen: A Review. Chem Eng Technol 2021. [DOI: 10.1002/ceat.202000565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Trinath Biswal
- Veer Surendra Sai University of Technology Department of Chemistry 768018 Burla Odisha India
| | - Krushna Prasad Shadangi
- Veer Surendra Sai University of Technology Department of Chemical Engineering 768018 Burla Odisha India
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Nisrina L, Effendi Y, Pancoro A. Revealing the role of Plant Growth Promoting Rhizobacteria in suppressive soils against Fusarium oxysporum f.sp. cubense based on metagenomic analysis. Heliyon 2021; 7:e07636. [PMID: 34401567 PMCID: PMC8353484 DOI: 10.1016/j.heliyon.2021.e07636] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 09/23/2020] [Accepted: 07/19/2021] [Indexed: 02/04/2023] Open
Abstract
Fusarium oxysporum f.sp. cubense (Foc) is a soil-borne pathogen causing fusarium wilt banana disease. Management of soil-borne disease generally required the application of toxic pesticides or fungicides strongly affect the soil microbiomes ecosystem. Suppressive soil is a promising method for controlling soil-borne pathogens in which soil microbiomes may affect the suppressiveness. The comparative analysis of microbial diversity was conducted from suppressive and conducive soils by analyzing whole shotgun metagenomic DNA data. Two suppressive soil samples and two conducive soil samples were collected from a banana plantation in Sukabumi, West Java, Indonesia. Each soil sample was prepared by mixing the soil samples collected from three points sampling sites with 20 cm depth. Analysis of microbial abundance, diversity, co-occurrence network using Metagenome Analyzer 6 (MEGAN6) and functional analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed. Data showed the abundance of Actinobacteria, Betaproteobacteria, Rhizobiales, Burkholderiales, Bradyrhizobiaceae, Methylobacteriaceae, Rhodopseudomonas palustris, and Methylobacterium nodulans were higher in the suppressive than conducive soils. Interestingly, those bacteria groups are known functionally as members of Plant Growth Promoting Rhizobacteria (PGPR). The co-occurrence analysis showed Pseudomonas, Burkholderia, and Streptomyces were present in the suppressive soils, while Bacillus and more Streptomyces were found in the conducive soils. Furthermore, the relative abundance of Pseudomonas, Burkholderia, Bacillus, and Streptomyces was performed. The analysis showed that the relative abundance of Pseudomonas and Burkholderia was higher in the suppressive than conducive soils. Therefore, it assumed Pseudomonas and Burkholderia play a role in suppressing Foc based on co-occurrence and abundance analysis. Functional analysis of Pseudomonas and Burkholderia showed that the zinc/manganese transport system was higher in the suppressive than conducive soils. In contrast, the phosphate transport system was not found in conducive soils. Both functions are may be responsible for the synthesis of a siderophore and phosphate solubilization. In conclusion, this study provides information that PGPR may be contributing to Foc growth suppressing by releasing secondary metabolites.
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Affiliation(s)
- Lulu' Nisrina
- School of Life Sciences and Technology, Bandung Institute of Technology, Jalan Ganesha 10, 40132, Bandung, Indonesia
| | - Yunus Effendi
- Department of Biology, Al-Azhar Univerisity of Indonesia, Jalan Sisimangaraja 2, 12110, Jakarta, Indonesia
| | - Adi Pancoro
- School of Life Sciences and Technology, Bandung Institute of Technology, Jalan Ganesha 10, 40132, Bandung, Indonesia
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