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Park S, Shin Y, Kim JM, Kim MS, Jung S. Rhizobial oxidized 3-hydroxylbutanoyl glycan-based gelatin hydrogels with enhanced physiochemical properties for pH-responsive drug delivery. Int J Biol Macromol 2024; 264:130538. [PMID: 38432278 DOI: 10.1016/j.ijbiomac.2024.130538] [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: 01/07/2024] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024]
Abstract
Rhizobial exopolysaccharide (EPS) is an acidic polysaccharide involved in nitrogen fixation-related signal transduction in the rhizosphere, serving as a structural support for biofilms, and protecting against various external environmental stresses. Rhizobial EPS as a hydrogel biomaterial was used for a pH-responsive drug delivery system combing with gelatins. Pure gelatin (GA) hydrogels have limited practical applications due to their poor mechanical strength and poor thermal stability. We developed new GA hydrogels using oxidized 3-hydroxylbutanoyl glycan (OHbG) as a polymer cross-linking agent to overcome these limitations. OHbG was synthesized from sodium periodate oxidation of 3-hydroxylbutanoyl glycan directly isolated from Rhizobium leguminosarum bv. viciae VF39. The newly fabricated OHbG/GA hydrogels exhibited 21-fold higher compressive stress and 4.7-fold higher storage modulus (G') than GA at the same strain. This result suggested that OHbG provided mechanical improvement. In addition, these OHbG/GA hydrogels showed effective pH-controlled drug release for 5-fluorouracil, self-healable, and self-antioxidant capacity by uronic acids of OHbG. Cell viability tests using HEK-293 cells in vitro also showed that the OHbG/GA hydrogels were non-toxic. This suggests that the new OHbG/GA hydrogels can be used as a potentially novel biomaterial for drug delivery based on its self-healing ability, antioxidant capacity, and pH-responsive drug delivery.
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Affiliation(s)
- Sohyun Park
- Department of Bioscience and Biotechnology, Microbial Carbohydrate Resource Bank (MCRB), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, South Korea
| | - Younghyun Shin
- Department of Bioscience and Biotechnology, Microbial Carbohydrate Resource Bank (MCRB), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, South Korea
| | - Jin-Mo Kim
- Convergence Technology Laboratory, Kolmar Korea, 61, Heolleung-ro-8-gil, Seocho-gu, Seoul 06792, South Korea
| | - Moo Sung Kim
- Macrocare, 32 Gangni 1-gil, Cheongju 28126, South Korea
| | - Seunho Jung
- Department of Bioscience and Biotechnology, Microbial Carbohydrate Resource Bank (MCRB), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, South Korea; Department of Systems Biotechnology, Microbial Carbohydrate Resource Bank (MCRB), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, South Korea.
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Park S, Shin Y, Jung S. Structural, rheological properties and antioxidant activities analysis of the exopolysaccharide produced by Rhizobium leguminosarum bv. viciae VF39. Int J Biol Macromol 2024; 257:128811. [PMID: 38101683 DOI: 10.1016/j.ijbiomac.2023.128811] [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: 08/01/2023] [Revised: 11/27/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Microbial exopolysaccharide is an eco-friendly and non-toxic biopolymeric materials widely used in various industrial fields such as pharmaceutical, food and cosmetics based on its structural, rheological and physiochemical properties. A microbial exopolysaccharide (VF39-EPS) was directly isolated from Rhizobium leguminosarum bv. viciae VF39. Structural analysis using FTIR and 2D NMR spectroscopy confirmed the complete chemical structures of VF39-EPS as 3-hydroxybutanoylglycan with octasaccharide repeating units containing two pyruvyl, two acetyl, and one 3-hydroxybutanoyl group. VF39-EPS exhibited thermal stability up to 275 °C and showed characteristic rheological behaviors of structural fluid with weak gel-like properties above 4 % the aqueous solution, suggesting VF39-EPS as a potential effective thickener or hydrogel scaffolder. Flow behavior tests validated broad stability at a wide range of both pHs from 2 to 12 and temperatures from 25 to 75 °C, and even in the presence of various salts. Furthermore, VF39-EPS showed excellent antioxidant effects of 78.5 and 62.4 % (n = 3, p < 0.001) in DPPH scavenging activity and hydroxyl radical scavenging activity, respectively. Therefore, those structural, rheological and antioxidant properties suggest that VF39-EPS could be one of the excellent biomaterial candidates for cosmetic, food and pharmaceutical industries based on its characteristic rheological behaviors in various condition and excellent antioxidant activity.
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Affiliation(s)
- Sohyun Park
- Department of Bioscience and Biotechnology, Microbial Carbohydrate Resource Bank (MCRB), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, South Korea
| | - Younghyun Shin
- Department of Bioscience and Biotechnology, Microbial Carbohydrate Resource Bank (MCRB), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, South Korea
| | - Seunho Jung
- Department of Bioscience and Biotechnology, Microbial Carbohydrate Resource Bank (MCRB), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, South Korea; Department of System Biotechnology, Microbial Carbohydrate Resource Bank (MCRB), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, South Korea.
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3
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Chang PE, Wu YH, Tai CY, Lin IH, Wang WD, Tseng TS, Chuang HW. Examining the Transcriptomic and Biochemical Signatures of Bacillus subtilis Strains: Impacts on Plant Growth and Abiotic Stress Tolerance. Int J Mol Sci 2023; 24:13720. [PMID: 37762026 PMCID: PMC10531026 DOI: 10.3390/ijms241813720] [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: 08/10/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Rhizobacteria from various ecological niches display variations in physiological characteristics. This study investigates the transcriptome profiling of two Bacillus subtilis strains, BsCP1 and BsPG1, each isolated from distinct environments. Gene expression linked to the synthesis of seven types of antibiotic compounds was detected in both BsCP1 and BsPG1 cultures. Among these, the genes associated with plipastatin synthesis were predominantly expressed in both bacterial strains. However, genes responsible for the synthesis of polyketide, subtilosin, and surfactin showed distinct transcriptional patterns. Additionally, genes involved in producing exopolysaccharides (EPS) showed higher expression levels in BsPG1 than in BsCP1. Consistently with this, a greater quantity of EPS was found in the BsPG1 culture compared to BsCP1. Both bacterial strains exhibited similar effects on Arabidopsis seedlings, promoting root branching and increasing seedling fresh weight. However, BsPG1 was a more potent enhancer of drought, heat, and copper stress tolerance than BsCP1. Treatment with BsPG1 had a greater impact on improving survival rates, increasing starch accumulation, and stabilizing chlorophyll content during the post-stress stage. qPCR analysis was used to measure transcriptional changes in Arabidopsis seedlings in response to BsCP1 and BsPG1 treatment. The results show that both bacterial strains had a similar impact on the expression of genes involved in the salicylic acid (SA) and jasmonic acid (JA) signaling pathways. Likewise, genes associated with stress response, root development, and disease resistance showed comparable responses to both bacterial strains. However, treatment with BsCP1 and BsPG1 induced distinct activation of genes associated with the ABA signaling pathway. The results of this study demonstrate that bacterial strains from different ecological environments have varying abilities to produce beneficial metabolites for plant growth. Apart from the SA and JA signaling pathways, ABA signaling triggered by PGPR bacterial strains could play a crucial role in building an effective resistance to various abiotic stresses in the plants they colonize.
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Affiliation(s)
| | | | | | | | | | - Tong-Seung Tseng
- Department of Agricultural Biotechnology, National Chiayi University, Chiayi 600355, Taiwan (C.-Y.T.); (I.-H.L.)
| | - Huey-wen Chuang
- Department of Agricultural Biotechnology, National Chiayi University, Chiayi 600355, Taiwan (C.-Y.T.); (I.-H.L.)
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Kim I, Chhetri G, So Y, Park S, Jung Y, Woo H, Seo T. Characterization and Antioxidant Activity of Exopolysaccharides Produced by Lysobacter soyae sp. nov Isolated from the Root of Glycine max L. Microorganisms 2023; 11:1900. [PMID: 37630460 PMCID: PMC10456730 DOI: 10.3390/microorganisms11081900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Microbial exopolysaccharides (EPSs) have attracted attention from several fields due to their high industrial applicability. In the present study, rhizosphere strain CJ11T was isolated from the root of Glycine max L. in Goyang-si, Republic of Korea, and a novel exopolysaccharide was purified from the Lysobacter sp. CJ11T fermentation broth. The exopolysaccharide's average molecular weight was 0.93 × 105 Da. Its monosaccharide composition included 72.2% mannose, 17.2% glucose, 7.8% galactose, and 2.8% arabinose. Fourier-transform infrared spectroscopy identified the exopolysaccharide carbohydrate polymer functional groups, and the structural properties were investigated using nuclear magnetic resonance. In addition, a microstructure of lyophilized EPS was determined by scanning electron microscopy. Using thermogravimetric analysis, the degradation of the exopolysaccharide produced by strain CJ11T was determined to be 210 °C. The exopolysaccharide at a concentration of 4 mg/mL exhibited 2,2-diphenyl-1-picrylhydrazyl free-radical-scavenging activity of 73.47%. Phylogenetic analysis based on the 16S rRNA gene sequencing results revealed that strain CJ11T was a novel isolate for which the name Lysobacter soyae sp. nov is proposed.
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Affiliation(s)
| | | | | | | | | | | | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea; (I.K.); (G.C.); (Y.S.); (S.P.); (Y.J.); (H.W.)
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Sharma S, Roy T, Kashyap Y, Buck M, Schumacher J, Goswami D, Gang S, Saraf M. Characterizing and demonstrating the role of Klebsiella SSN1 exopolysaccharide in osmotic stress tolerance using neutron radiography. Sci Rep 2023; 13:10052. [PMID: 37344631 DOI: 10.1038/s41598-023-37133-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/16/2023] [Indexed: 06/23/2023] Open
Abstract
Exopolysaccharides (EPS) are organic macromolecules naturally secreted by many microorganisms. EPS is increasingly used for agriculture and industrial purposes. This study focuses on isolate Klebsiella pneumonia SSN1, Klebsiella quasipeumonniae SGM81 isolated from rhizosphere to explore its water retention efficiency under drought conditions. Neutron Radiography was used to visualise water distribution in the sand under normal and drought conditions in the presence and absence of EPS producing bacteria. The EPS production was studied by applying Box Behnken design (BBD) under drought stress which was artificially induced by using polyethene glycol 6000 under osmotic stress condition 3.65% w/v of EPS dry weight was obtained. The relative water content (RWC) is used to calculate the amount of water present in the sand and was further studied by Neutron Radiography imaging with appropriate controls. FTIR and HPLC were also carried out for the characterisation of the extracted EPS. The sand experiments revealed that after 24 h of evaporation, the highest RWC was maintained by SSN1 at 29.7% compared to SGM81 (19.06%). SSN1 was found to release L-arabinose as the main sugar of its EPS under drought stress conditions by HPLC method. The FTIR data indicated the presence of β-glucans and polysaccharide α-pyranose between wavenumber 700 cm-1-1500 cm-1 and 1017 cm-1-1200 cm-1 respectively. The HPLC characterization of extracted EPS from osmotic stressed cells (run 3) displayed a peak designated to L-arabinose at 10.3 retention time (RT) for 132.4 mM concentration. While from run 5 with the controlled condition indicated the presence of L-rhamnose at 7.3 RT for 87 mM concentration. Neutron radiography enables the visualisation of water distribution in the sand as well as water transport in root-soil systems in situ. SSN1 has elicited EPS production in drought conditions with a low level of nitrogen and carbon.
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Affiliation(s)
- Sheetal Sharma
- Dept. of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad, 380009, India
| | - Tushar Roy
- Technical Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Yogesh Kashyap
- Technical Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Martin Buck
- Department of Life Science, Faculty of Natural Sciences, Imperial College, London, SW7 2AZ, UK
| | - Jorg Schumacher
- Department of Life Science, Faculty of Natural Sciences, Imperial College, London, SW7 2AZ, UK
| | - Dweipayan Goswami
- Dept. of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad, 380009, India
| | - Shraddha Gang
- Department of Life Science, Faculty of Natural Sciences, Imperial College, London, SW7 2AZ, UK.
| | - Meenu Saraf
- Dept. of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad, 380009, India.
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Albicoro FJ, Vacca C, Cafiero JH, Draghi WO, Martini MC, Goulian M, Lagares A, Del Papa MF. Comparative Proteomic Analysis Revealing ActJ-Regulated Proteins in Sinorhizobium meliloti. J Proteome Res 2023; 22:1682-1694. [PMID: 37017314 PMCID: PMC10834056 DOI: 10.1021/acs.jproteome.2c00731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
To adapt to different environmental conditions, Sinorhizobium meliloti relies on finely tuned regulatory networks, most of which are unexplored to date. We recently demonstrated that deletion of the two-component system ActJK renders an acid-vulnerable phenotype in S. meliloti and negatively impacts bacteroid development and nodule occupancy as well. To fully understand the role of ActJ in acid tolerance, S. meliloti wild-type and S. meliloti ΔactJ proteomes were compared in the presence or absence of acid stress by nanoflow ultrahigh-performance liquid chromatography coupled to mass spectrometry. The analysis demonstrated that proteins involved in the synthesis of exopolysaccharides (EPSs) were notably enriched in ΔactJ cells in acid pH. Total EPS quantification further revealed that although EPS production was augmented at pH 5.6 in both the ΔactJ and the parental strain, the lack of ActJ significantly enhanced this difference. Moreover, several efflux pumps were found to be downregulated in the ΔactJ strain. Promoter fusion assays suggested that ActJ positively modulated its own expression in an acid medium but not at under neutral conditions. The results presented here identify several ActJ-regulated genes in S. meliloti, highlighting key components associated with ActJK regulation that will contribute to a better understanding of rhizobia adaptation to acid stress.
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Affiliation(s)
- Francisco Javier Albicoro
- Instituto de Biotecnología y Biologia Molecular -CONICET CCT La Plata - Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Carolina Vacca
- Instituto de Biotecnología y Biologia Molecular -CONICET CCT La Plata - Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Juan Hilario Cafiero
- Instituto de Biotecnología y Biologia Molecular -CONICET CCT La Plata - Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Walter Omar Draghi
- Instituto de Biotecnología y Biologia Molecular -CONICET CCT La Plata - Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - María Carla Martini
- Instituto de Biotecnología y Biologia Molecular -CONICET CCT La Plata - Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Mark Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, PA. USA
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA. USA
| | - Antonio Lagares
- Instituto de Biotecnología y Biologia Molecular -CONICET CCT La Plata - Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - María Florencia Del Papa
- Instituto de Biotecnología y Biologia Molecular -CONICET CCT La Plata - Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
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Goyal RK, Habtewold JZ. Evaluation of Legume-Rhizobial Symbiotic Interactions Beyond Nitrogen Fixation That Help the Host Survival and Diversification in Hostile Environments. Microorganisms 2023; 11:1454. [PMID: 37374957 DOI: 10.3390/microorganisms11061454] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Plants often experience unfavorable conditions during their life cycle that impact their growth and sometimes their survival. A temporary phase of such stress, which can result from heavy metals, drought, salinity, or extremes of temperature or pH, can cause mild to enormous damage to the plant depending on its duration and intensity. Besides environmental stress, plants are the target of many microbial pathogens, causing diseases of varying severity. In plants that harbor mutualistic bacteria, stress can affect the symbiotic interaction and its outcome. To achieve the full potential of a symbiotic relationship between the host and rhizobia, it is important that the host plant maintains good growth characteristics and stay healthy under challenging environmental conditions. The host plant cannot provide good accommodation for the symbiont if it is infested with diseases and prone to other predators. Because the bacterium relies on metabolites for survival and multiplication, it is in its best interests to keep the host plant as stress-free as possible and to keep the supply stable. Although plants have developed many mitigation strategies to cope with stress, the symbiotic bacterium has developed the capability to augment the plant's defense mechanisms against environmental stress. They also provide the host with protection against certain diseases. The protective features of rhizobial-host interaction along with nitrogen fixation appear to have played a significant role in legume diversification. When considering a legume-rhizobial symbiosis, extra benefits to the host are sometimes overlooked in favor of the symbionts' nitrogen fixation efficiency. This review examines all of those additional considerations of a symbiotic interaction that enable the host to withstand a wide range of stresses, enabling plant survival under hostile regimes. In addition, the review focuses on the rhizosphere microbiome, which has emerged as a strong pillar of evolutionary reserve to equip the symbiotic interaction in the interests of both the rhizobia and host. The evaluation would draw the researchers' attention to the symbiotic relationship as being advantageous to the host plant as a whole and the role it plays in the plant's adaptation to unfavorable environmental conditions.
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Affiliation(s)
- Ravinder K Goyal
- Agriculture and Agri-Food Canada, Lacombe Research and Development Center, Lacombe, AB T4L 1W1, Canada
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Nagaraj A, Rekha PD. Development of a bioink using exopolysaccharide from Rhizobium sp. PRIM17. Int J Biol Macromol 2023; 234:123608. [PMID: 36773865 DOI: 10.1016/j.ijbiomac.2023.123608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/16/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023]
Abstract
Biopolymers play a significant role in tissue engineering, including in the formulation of bioinks that require careful selection of the biopolymers having properties ideal for printability and supporting biological entities such as cells. Alginate is one of the most widely explored natural biopolymers for tissue engineering applications due to its biocompatibility, cross-linking ability, hydrophilic nature, and easy incorporation with other polymers. Here, a succinoglycan-like exopolysaccharide (EPS-R17) produced by a bacterial strain Rhizobium sp. PRIM17 was incorporated with alginate for the development of a bioink. The physicochemical characterization of EPS-R17 was performed before formulating the bioink with alginate. The bioink formulation was prepared by mixing different concentrations of EPS with an alginate solution at room temperature under sterile atmosphere. The prepared bioink was characterized for rheological properties, biocompatibility, and a bioplotting experiment was also conducted to mimick the extrusion bioprinting. The EPS-R17 was composed of glucose, galactose, and rhamnose with a molecular weight of 69.98 kDa. It was thermally stable up to 260 °C and showed characteristic FT-IR peaks (1723.3 cm-1) for succinyl groups. The EPS-R17 showed biocompatibility with keratinocytes (HaCaT), and fibroblasts (HDF) in vitro. The rheological properties of EPS-R17-alginate bioink at different combinations showed shear thinning behavior at 25 and 37 °C. Amplitude sweep measurements showed the gel-like nature of the polymer combinations in the solution system superior to alginate or EPS-R17 alone. The combination of 1 % EPS-R17 and 1.5 % alginate showed good compressive strength and swelling behavior. Extrusion bioprinting mimicked using a bioplotting experiment showed the sustained cell viability in the polymer matrix of EPS-R17-alginate bioink. The results indicate that the EPS-R17 can be used in combination with alginate for bioinks for bioprinting applications for providing physical properties and favorable bioactivities.
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Affiliation(s)
- Athmika Nagaraj
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore 575018, India
| | - Punchappady Devasya Rekha
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore 575018, India.
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Rhizobial migration toward roots mediated by FadL-ExoFQP modulation of extracellular long-chain AHLs. THE ISME JOURNAL 2023; 17:417-431. [PMID: 36627434 PMCID: PMC9938287 DOI: 10.1038/s41396-023-01357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023]
Abstract
Migration from rhizosphere to rhizoplane is a key selecting process in root microbiome assembly, but not fully understood. Rhizobiales members are overrepresented in the core root microbiome of terrestrial plants, and here we report a genome-wide transposon-sequencing of rhizoplane fitness genes of beneficial Sinorhizobium fredii on wild soybean, cultivated soybean, rice, and maize. There were few genes involved in broad-host-range rhizoplane colonization. The fadL mutant lacking a fatty acid transporter exhibited high colonization rates, while mutations in exoFQP (encoding membrane proteins directing exopolysaccharide polymerization and secretion), but not those in exo genes essential for exopolysaccharide biosynthesis, led to severely impaired colonization rates. This variation was not explainable by their rhizosphere and rhizoplane survivability, and associated biofilm and exopolysaccharide production, but consistent with their migration ability toward rhizoplane, and associated surface motility and the mixture of quorum-sensing AHLs (N-acylated-L-homoserine lactones). Genetics and physiology evidences suggested that FadL mediated long-chain AHL uptake while ExoF mediated the secretion of short-chain AHLs which negatively affected long-chain AHL biosynthesis. The fadL and exoF mutants had elevated and depleted extracellular long-chain AHLs, respectively. A synthetic mixture of long-chain AHLs mimicking that of the fadL mutant can improve rhizobial surface motility. When this AHL mixture was spotted into rhizosphere, the migration toward roots and rhizoplane colonization of S. fredii were enhanced in a diffusible way. This work adds novel parts managing extracellular AHLs, which modulate bacterial migration toward rhizoplane. The FadL-ExoFQP system is conserved in Alphaproteobacteria and may shape the "home life" of diverse keystone rhizobacteria.
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Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot. THE ISME JOURNAL 2023; 17:354-370. [PMID: 36536072 PMCID: PMC9938248 DOI: 10.1038/s41396-022-01345-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022]
Abstract
The substrates of the Brazilian campos rupestres, a grassland ecosystem, have extremely low concentrations of phosphorus and nitrogen, imposing restrictions to plant growth. Despite that, this ecosystem harbors almost 15% of the Brazilian plant diversity, raising the question of how plants acquire nutrients in such a harsh environment. Here, we set out to uncover the taxonomic profile, the compositional and functional differences and similarities, and the nutrient turnover potential of microbial communities associated with two plant species of the campos rupestres-dominant family Velloziaceae that grow over distinct substrates (soil and rock). Using amplicon sequencing data, we show that, despite the pronounced composition differentiation, the plant-associated soil and rock communities share a core of highly efficient colonizers that tend to be highly abundant and is enriched in 21 bacterial families. Functional investigation of metagenomes and 522 metagenome-assembled genomes revealed that the microorganisms found associated to plant roots are enriched in genes involved in organic compound intake, and phosphorus and nitrogen turnover. We show that potential for phosphorus transport, mineralization, and solubilization are mostly found within bacterial families of the shared microbiome, such as Xanthobacteraceae and Bryobacteraceae. We also detected the full repertoire of nitrogen cycle-related genes and discovered a lineage of Isosphaeraceae that acquired nitrogen-fixing potential via horizontal gene transfer and might be also involved in nitrification via a metabolic handoff association with Binataceae. We highlight that plant-associated microbial populations in the campos rupestres harbor a genetic repertoire with potential to increase nutrient availability and that the microbiomes of biodiversity hotspots can reveal novel mechanisms of nutrient turnover.
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Tang Y, Wu Z, Zhang Y, Wang C, Ma X, Zhang K, Pan R, Cao Y, Zhou X. Cultivation-dependent and cultivation-independent investigation of O-methylated pollutant-producing bacteria in three drinking water treatment plants. WATER RESEARCH 2023; 231:119618. [PMID: 36706470 DOI: 10.1016/j.watres.2023.119618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/12/2023] [Accepted: 01/15/2023] [Indexed: 06/18/2023]
Abstract
O-methylated pollutants (OMPs) are emerging contaminants in drinking water and mainly produced through bacterial O-methylation. However, the information of OMP-producing bacteria (OMPPB) in drinking water treatment plant (DWTP) is largely unknown so far. In this study, the OMPPB in water samples from three DWTPs (XL, JX and NX) were investigated by using cultivation-dependent and cultivation-independent technologies. Four OMPs were detected and their odor and toxicity risks were assessed. Formation potentials (FPs) of 2,4,6-trichloanisole, 2,3,6-trichloanisole, 2,4,6-tribromoanisole, pentachloroanisole and diclofenac methyl ester were determined in water samples and their values shifted significantly among DWTPs. A most probable number (MPN) method was established to quantify OMPPB numbers and the relationships between total haloanisole FPs (HAFPs) (y) and OMPPB numbers (x) in three DWTPs could be described by the following functions: y = 0.496×0.373 (XL), y = 0.041×0.465 (JX) and y = 0.218×0.237 (NX). Several genera like Bacillus, Ralstonia, Brevundimonas, etc. were newly found OMPPB among the cultivable bacteria, and their OMP products were evaluated in terms of quantity and environment risks (odor, toxicity and bioaccumulation). High-throughput sequencing revealed treatment process was the main driving factor to shape the OMPPB community structures and Mantel test showed HAFP profile was significantly influenced by Mycobacterium and Pelomonas. PICURSt2 analysis discovered four phenolic O-methyltransferases (OMTs) and four carboxylic OMTs which might be responsible for OMP formation. Several strategies were recommended to assess risk and control contamination brought by OMPPB in DWTPs.
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Affiliation(s)
- Yiran Tang
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Zhixuan Wu
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Yanfen Zhang
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Chuanxuan Wang
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Xuelian Ma
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Kejia Zhang
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Renjie Pan
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Yangtze Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Yucheng Cao
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Xinyan Zhou
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China.
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12
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Exopolysaccharide Biosynthesis in Rhizobium leguminosarum bv. trifolii Requires a Complementary Function of Two Homologous Glycosyltransferases PssG and PssI. Int J Mol Sci 2023; 24:ijms24044248. [PMID: 36835659 PMCID: PMC9961541 DOI: 10.3390/ijms24044248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 02/23/2023] Open
Abstract
The Pss-I region of Rhizobium leguminosarum bv. trifolii TA1 comprises more than 20 genes coding for glycosyltransferases, modifying enzymes, and polymerization/export proteins, altogether determining the biosynthesis of symbiotically relevant exopolysaccharides. In this study, the role of homologous PssG and PssI glycosyltransferases in exopolysaccharide subunit synthesis were analyzed. It was shown that the glycosyltransferase-encoding genes of the Pss-I region were part of a single large transcriptional unit with potential downstream promoters activated in specific conditions. The ΔpssG and ΔpssI mutants produced significantly lower amounts of the exopolysaccharide, while the double deletion mutant ΔpssIΔpssG produced no exopolysaccharide. Complementation of double mutation with individual genes restored exopolysaccharide synthesis, but only to the level similar to that observed for the single ΔpssI or ΔpssG mutants, indicating that PssG and PssI serve complementary functions in the process. PssG and PssI interacted with each other in vivo and in vitro. Moreover, PssI displayed an expanded in vivo interaction network comprising other GTs involved in subunit assembly and polymerization/export proteins. PssG and PssI proteins were shown to interact with the inner membrane through amphipathic helices at their C-termini, and PssG also required other proteins involved in exopolysaccharide synthesis to localize in the membrane protein fraction.
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An G, Yan R, Fu Z, Chen Z, Guo Y, Yang J, Zhou Y. Adaptation of anammox consortia in microbial fuel cell to low temperature: Microbial community and predictive functional profiling. BIORESOURCE TECHNOLOGY 2023; 370:128565. [PMID: 36596367 DOI: 10.1016/j.biortech.2022.128565] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
The purpose of this study was to explore the tolerance mechanism of anammox consortia in microbial fuel cell (MFC) system at low temperature. Data showed that nearly 80 % total nitrogen removal was achieved after the temperature decreased from 30 °C to 15 °C. The nitrogenremovalrate (NRR) of the system was decreased by 26.3 %, from 0.441 kgN·m-3·d-1 at 30 °C to 0.325 kgN·m-3·d-1 at 15 °C. Isotope experiment in 15NH4+-containing reactor found that much more 29N2 were produced than 30N2, confirming that anammox was the main 15NH4+ removal pathway and electrochemical oxidation participate in this process. High throughput sequencing analysis indicated the low temperature stimulated the enrichment of heterotrophic bacteria, such as Comamonadaceae and Rhodobacteraceae. While the relative abundance of Candidatus Brocadia, typical anammox bacteria, decreased significantly. Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis showed that the low temperature induced a more efficient expression in synthesis of unsaturated fatty acids (UFAs) and ABC membrane transports. This study indicates that anammox consortia are likely to maintain high nitrogen removal performance of MFC system by changing the proportion of membrane composition and EPS exportation.
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Affiliation(s)
- Geer An
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China
| | - Rong Yan
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China; Inner Mongolia Lvchuang Environmental Protection Technology Co., Ltd., Hohhot 010051, China
| | - Zhimin Fu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China.
| | - Zepeng Chen
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China
| | - Yaru Guo
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China
| | - Jun Yang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China
| | - Yongheng Zhou
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China
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14
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Legumes Regulate Symbiosis with Rhizobia via Their Innate Immune System. Int J Mol Sci 2023; 24:ijms24032800. [PMID: 36769110 PMCID: PMC9917363 DOI: 10.3390/ijms24032800] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
Plant roots are constantly exposed to a diverse microbiota of pathogens and mutualistic partners. The host's immune system is an essential component for its survival, enabling it to monitor nearby microbes for potential threats and respond with a defence response when required. Current research suggests that the plant immune system has also been employed in the legume-rhizobia symbiosis as a means of monitoring different rhizobia strains and that successful rhizobia have evolved to overcome this system to infect the roots and initiate nodulation. With clear implications for host-specificity, the immune system has the potential to be an important target for engineering versatile crops for effective nodulation in the field. However, current knowledge of the interacting components governing this pathway is limited, and further research is required to build on what is currently known to improve our understanding. This review provides a general overview of the plant immune system's role in nodulation. With a focus on the cycles of microbe-associated molecular pattern-triggered immunity (MTI) and effector-triggered immunity (ETI), we highlight key molecular players and recent findings while addressing the current knowledge gaps in this area.
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15
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Functional characterization of a novel GH94 glycoside phosphorylase, 3-O-β-d-glucopyranosyl β-d-glucuronide phosphorylase, and implication of the metabolic pathway of acidic carbohydrates in Paenibacillus borealis. Biochem Biophys Res Commun 2022; 625:60-65. [PMID: 35947916 DOI: 10.1016/j.bbrc.2022.07.098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 07/25/2022] [Indexed: 11/22/2022]
Abstract
Glycoside hydrolase family 94 (GH94) contains enzymes that reversibly catalyze the phosphorolysis of β-glycosides. We conducted this study to investigate a GH94 protein (PBOR_13355) encoded in the genome of Paenibacillus borealis DSM 13188 with low sequence identity to known phosphorylases. Screening of acceptor substrates for reverse phosphorolysis in the presence of α-d-glucose 1-phosphate as a donor substrate showed that PBOR_13355 utilized d-glucuronic acid and p-nitrophenyl β-d-glucuronide as acceptors. In the reaction with d-glucuronic acid, 3-O-β-d-glucopyranosyl-d-glucuronic acid was synthesized. PBOR_13355 showed a higher apparent catalytic efficiency to p-nitrophenyl β-d-glucuronide than to d-glucuronic acid, and thus, PBOR_13355 was concluded to be a novel glycoside phosphorylase, 3-O-β-d-glucopyranosyl β-d-glucuronide phosphorylase. PBOR_13360, encoded by the gene immediately downstream of the PBOR_13355 gene, was shown to be β-glucuronidase. Collectively, PBOR_13355 and PBOR_13360 are predicted to work together in the cytosol to metabolize oligosaccharides containing the 3-O-β-d-glucopyranosyl β-d-glucuronide structure released from bacterial and plant acidic carbohydrates.
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16
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Anand U, Vaishnav A, Sharma SK, Sahu J, Ahmad S, Sunita K, Suresh S, Dey A, Bontempi E, Singh AK, Proćków J, Shukla AK. Current advances and research prospects for agricultural and industrial uses of microbial strains available in world collections. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156641. [PMID: 35700781 DOI: 10.1016/j.scitotenv.2022.156641] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Microorganisms are an important component of the ecosystem and have an enormous impact on human lives. Moreover, microorganisms are considered to have desirable effects on other co-existing species in a variety of habitats, such as agriculture and industries. In this way, they also have enormous environmental applications. Hence, collections of microorganisms with specific traits are a crucial step in developing new technologies to harness the microbial potential. Microbial culture collections (MCCs) are a repository for the preservation of a large variety of microbial species distributed throughout the world. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are vital for the safeguarding and circulation of biological resources, as well as for the progress of the life sciences. Ex situ conservation of microorganisms tagged with specific traits in the collections is the crucial step in developing new technologies to harness their potential. Type strains are mainly used in taxonomic study, whereas reference strains are used for agricultural, biotechnological, pharmaceutical research and commercial work. Despite the tremendous potential in microbiological research, little effort has been made in the true sense to harness the potential of conserved microorganisms. This review highlights (1) the importance of available global microbial collections for man and (2) the use of these resources in different research and applications in agriculture, biotechnology, and industry. In addition, an extensive literature survey was carried out on preserved microorganisms from different collection centres using the Web of Science (WoS) and SCOPUS. This review also emphasizes knowledge gaps and future perspectives. Finally, this study provides a critical analysis of the current and future roles of microorganisms available in culture collections for different sustainable agricultural and industrial applications. This work highlights target-specific potential microbial strains that have multiple important metabolic and genetic traits for future research and use.
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Affiliation(s)
- Uttpal Anand
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Anukool Vaishnav
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh 281406, India; Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland; Plant-Soil Interaction Group, Agroscope (Reckenholz), Reckenholzstrasse 191, 8046 Zürich, Switzerland
| | - Sushil K Sharma
- National Agriculturally Important Microbial Culture Collection (NAIMCC), ICAR-National Bureau of Agriculturally Important Microorganisms (ICAR-NBAIM), Mau 275 103, Uttar Pradesh, India.
| | - Jagajjit Sahu
- GyanArras Academy, Gothapatna, Malipada, Bhubaneswar, Odisha 751029, India
| | - Sarfaraz Ahmad
- Department of Botany, Jai Prakash University, Saran, Chhapra 841301, Bihar, India
| | - Kumari Sunita
- Department of Botany, Faculty of Science, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh 273009, India
| | - S Suresh
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal 462 003, Madhya Pradesh, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, West Bengal, India
| | - Elza Bontempi
- INSTM and Chemistry for Technologies Laboratory, Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze, 38, 25123 Brescia, Italy
| | - Amit Kishore Singh
- Department of Botany, Bhagalpur National College, (A Constituent unit of Tilka Manjhi Bhagalpur University), Bhagalpur 812007, Bihar, India
| | - Jarosław Proćków
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, Kożuchowska 5b, 51-631 Wrocław, Poland.
| | - Awadhesh Kumar Shukla
- Department of Botany, K.S. Saket P.G. College, Ayodhya (affiliated to Dr. Rammanohar Lohia Avadh University, Ayodhya) 224123, Uttar Pradesh, India.
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Zavagna-Witt M, Tahir N, Arus VA, Roy R, Azzouz A. Synthesis of exopolysaccharide-based organo-montmorillonite with improved affinity towards carbon dioxide and hydrophilic character. CR CHIM 2022. [DOI: 10.5802/crchim.175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Kurniawan SB, Imron MF, Sługocki Ł, Nowakowski K, Ahmad A, Najiya D, Abdullah SRS, Othman AR, Purwanti IF, Hasan HA. Assessing the effect of multiple variables on the production of bioflocculant by Serratia marcescens: Flocculating activity, kinetics, toxicity, and flocculation mechanism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 836:155564. [PMID: 35504385 DOI: 10.1016/j.scitotenv.2022.155564] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/19/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Bioflocculants gain attention as alternatives to chemical flocculants because they are more environmentally friendly and highly biodegradable. This study aims to improve the bioflocculant production by Serratia marcescens using one-variable-at-a-time (OVAT) analysis and analyze its flocculating activity performance, toxicity, and the flocculation mechanism. The effect of multiple variables including initial inoculum size, pH, mixing speed, temperature, growth medium, and incubation period was assessed through OVAT. Flocculating activity was then determined via jar test analysis, and toxicity test was performed using Daphnia magna and Daphnia pulex. The flocculation mechanism was determined via particle size distribution and zeta potential analysis. The optimum conditions for the improved bioflocculant production were as follows: 10% v/v initial inoculum size, pH 7, mixing speed of 150 rpm, room temperature, nutrient broth medium, and 72 h of incubation period. Scanning electron microscopy showed flake-like intact structure with coarse surface. The produced bioflocculant showed flocculating activity of 48% in 5227 ± 580 NTU initial kaolin turbidity with 1 mg/L concentration and 5% v/v dosage of bioflocculant, following the second-order kinetics. Toxicity test to D. magna and D. pulex showed the 48 h LC50 values of 8.06 and 6.42 g/L, respectively; these values are greatly higher than the fabricated chemical flocculants. The flocculation process using bioflocculant produced by S. marcescens was suggested to occur via bridging mechanism because it greatly affected the particle size distribution. Results indicated that bioflocculant produced by S. marcescens is much environmentally friendly and has great potential for turbidity removal in water/wastewater.
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Affiliation(s)
- Setyo Budi Kurniawan
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.
| | - Muhammad Fauzul Imron
- Study Program of Environmental Engineering, Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Kampus C UNAIR, Jalan Mulyorejo, Surabaya 60115, Indonesia.
| | - Łukasz Sługocki
- Department of Hydrobiology, Institute of Biology, University of Szczecin, Felczaka 3c, 71-712 Szczecin, Poland; Center of Molecular Biology and Biotechnology, University of Szczecin, Wąska 13, 71-715 Szczecin, Poland
| | - Kacper Nowakowski
- Department of Hydrobiology, Institute of Biology, University of Szczecin, Felczaka 3c, 71-712 Szczecin, Poland
| | - Azmi Ahmad
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia; Department of Polytechnic Education and Community College, Ministry of Higher Education, 62100 Putrajaya, Malaysia
| | - Dhuroton Najiya
- Study Program of Environmental Engineering, Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Kampus C UNAIR, Jalan Mulyorejo, Surabaya 60115, Indonesia
| | - Siti Rozaimah Sheikh Abdullah
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.
| | - Ahmad Razi Othman
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Ipung Fitri Purwanti
- Department of Environmental Engineering, Faculty of Civil, Planning, and Geo Engineering, Institut Teknologi Sepuluh Nopember, Kampus ITS Sukolilo, Surabaya 60111, Indonesia
| | - Hassimi Abu Hasan
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia; Research Centre for Sustainable Process Technology (CESPRO), Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
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Tarsitano J, Ramis LY, Alonso LG, Russo DM, Zorreguieta A. RapD Is a Multimeric Calcium-Binding Protein That Interacts With the Rhizobium leguminosarum Biofilm Exopolysaccharide, Influencing the Polymer Lengths. Front Microbiol 2022; 13:895526. [PMID: 35875570 PMCID: PMC9298526 DOI: 10.3389/fmicb.2022.895526] [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: 03/14/2022] [Accepted: 05/12/2022] [Indexed: 11/15/2022] Open
Abstract
Rhizobium leguminosarum synthesizes an acidic polysaccharide mostly secreted to the extracellular medium, known as exopolysaccharide (EPS) and partially retained on the bacterial surface as a capsular polysaccharide (CPS). Rap proteins, extracellular protein substrates of the PrsDE type I secretion system (TISS), share at least one Ra/CHDL (cadherin-like) domain and are involved in biofilm matrix development either through cleaving the polysaccharide by Ply glycanases or by altering the bacterial adhesive properties. It was shown that the absence or excess of extracellular RapA2 (a monomeric CPS calcium-binding lectin) alters the biofilm matrix’s properties. Here, we show evidence of the role of a new Rap protein, RapD, which comprises an N-terminal Ra/CHDL domain and a C-terminal region of unknown function. RapD was completely released to the extracellular medium and co-secreted with the other Rap proteins in a PrsDE-dependent manner. Furthermore, high levels of RapD secretion were found in biofilms under conditions that favor EPS production. Interestingly, size exclusion chromatography of the EPS produced by the ΔrapA2ΔrapD double mutant showed a profile of EPS molecules of smaller sizes than those of the single mutants and the wild type strain, suggesting that both RapA2 and RapD proteins influence EPS processing on the cell surface. Biophysical studies showed that calcium triggers proper folding and multimerization of recombinant RapD. Besides, further conformational changes were observed in the presence of EPS. Enzyme-Linked ImmunoSorbent Assay (ELISA) and Binding Inhibition Assays (BIA) indicated that RapD specifically binds the EPS and that galactose residues would be involved in this interaction. Taken together, these observations indicate that RapD is a biofilm matrix-associated multimeric protein that influences the properties of the EPS, the main structural component of the rhizobial biofilm.
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Affiliation(s)
- Julián Tarsitano
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Lila Y. Ramis
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Leonardo G. Alonso
- Instituto de Nanobiotecnología (NANOBIOTEC), Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Daniela M. Russo
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- *Correspondence: Daniela M. Russo,
| | - Angeles Zorreguieta
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Angeles Zorreguieta,
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Groppa MD, Zawoznik MS, Benavides MP, Iannone MF. Beneficial effects of magnetite nanoparticles on soybean-Bradyrhizobium japonicum and alfalfa-Sinorhizobium meliloti associations. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 180:42-49. [PMID: 35381465 DOI: 10.1016/j.plaphy.2022.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 03/02/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
Nanoparticles (NPs)-based growth stimulators have promising usage in agriculture. This research analyzed the impact of citric acid-coated magnetite nanoparticles (Fe3O4-NPs; 50 mg Fe L-1) added once at pre-sowing on soybean and alfalfa seedlings growing in association with their corresponding microsymbiont partners, Bradyrhizobium japonicum and Sinorhizobium meliloti; also on the in vitro growth rate of these microorganisms. Fe-EDTA (50 mg Fe L-1) was used as a comparator. Fe3O4-NPs significantly augmented the growth rate constant (7-17%) and extracellular polysaccharides production of both microsymbionts (B. japonicum: 2-fold; S. meliloti: 43%), which probably favored bacterial adhesion to the root hairs. In both legumes, Fe3O4-NPs increased chlorophyll content (up to 56% in soybean) and improved plant growth, evidenced by a greater root biomass system (80-90% higher than the control), and increased shoot biomass (30-40%). Besides, Fe3O4-NPs addition resulted in earlier nodule formation and enhanced nodule biomass (about 2.5-fold in both species). Nodules were mainly located in the crown of the root in the NP50 treatment, while they were evenly distributed along lateral roots in the control and the comparator. Fe3O4-NPs also augmented significantly nodule leghemoglobin content (∼50-70%) and total N in legumes' shoots (ca. 20%). CAT activity increased only under NP50 treatment and no symptoms of oxidative damage were evidenced. In this work, we found that besides not being toxic neither to soybean and alfalfa plants nor to their microsymbiont partners, Fe3O4-NPs do not exert adverse effects on the symbioses establishment; oppositely, a more efficient nodulation pattern was verified in both plant species.
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Affiliation(s)
- María Daniela Groppa
- Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113, Buenos Aires, Argentina; Instituto de Química y Fisicoquímica Biológicas (IQUIFIB-CONICET), Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113, Buenos Aires, Argentina
| | - Myriam Sara Zawoznik
- Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113, Buenos Aires, Argentina
| | - María Patricia Benavides
- Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113, Buenos Aires, Argentina; Instituto de Química y Fisicoquímica Biológicas (IQUIFIB-CONICET), Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113, Buenos Aires, Argentina
| | - María Florencia Iannone
- Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113, Buenos Aires, Argentina; Instituto de Química y Fisicoquímica Biológicas (IQUIFIB-CONICET), Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113, Buenos Aires, Argentina.
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21
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Eardly B, Meor Osman WA, Ardley J, Zandberg J, Gollagher M, van Berkum P, Elia P, Marinova D, Seshadri R, Reddy TBK, Ivanova N, Pati A, Woyke T, Kyrpides N, Loedolff M, Laird DW, Reeve W. The Genome of the Acid Soil-Adapted Strain Rhizobium favelukesii OR191 Encodes Determinants for Effective Symbiotic Interaction With Both an Inverted Repeat Lacking Clade and a Phaseoloid Legume Host. Front Microbiol 2022; 13:735911. [PMID: 35495676 PMCID: PMC9048898 DOI: 10.3389/fmicb.2022.735911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 02/10/2022] [Indexed: 11/15/2022] Open
Abstract
Although Medicago sativa forms highly effective symbioses with the comparatively acid-sensitive genus Ensifer, its introduction into acid soils appears to have selected for symbiotic interactions with acid-tolerant R. favelukesii strains. Rhizobium favelukesii has the unusual ability of being able to nodulate and fix nitrogen, albeit sub-optimally, not only with M. sativa but also with the promiscuous host Phaseolus vulgaris. Here we describe the genome of R. favelukesii OR191 and genomic features important for the symbiotic interaction with both of these hosts. The OR191 draft genome contained acid adaptation loci, including the highly acid-inducible lpiA/acvB operon and olsC, required for production of lysine- and ornithine-containing membrane lipids, respectively. The olsC gene was also present in other acid-tolerant Rhizobium strains but absent from the more acid-sensitive Ensifer microsymbionts. The OR191 symbiotic genes were in general more closely related to those found in Medicago microsymbionts. OR191 contained the nodA, nodEF, nodHPQ, and nodL genes for synthesis of polyunsaturated, sulfated and acetylated Nod factors that are important for symbiosis with Medicago, but contained a truncated nodG, which may decrease nodulation efficiency with M. sativa. OR191 contained an E. meliloti type BacA, which has been shown to specifically protect Ensifer microsymbionts from Medicago nodule-specific cysteine-rich peptides. The nitrogen fixation genes nifQWZS were present in OR191 and P. vulgaris microsymbionts but absent from E. meliloti-Medicago microsymbionts. The ability of OR191 to nodulate and fix nitrogen symbiotically with P. vulgaris indicates that this host has less stringent requirements for nodulation than M. sativa but may need rhizobial strains that possess nifQWZS for N2-fixation to occur. OR191 possessed the exo genes required for the biosynthesis of succinoglycan, which is required for the Ensifer-Medicago symbiosis. However, 1H-NMR spectra revealed that, in the conditions tested, OR191 exopolysaccharide did not contain a succinyl substituent but instead contained a 3-hydroxybutyrate moiety, which may affect its symbiotic performance with Medicago hosts. These findings provide a foundation for the genetic basis of nodulation requirements and symbiotic effectiveness with different hosts.
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Affiliation(s)
- Bertrand Eardly
- Berks College, Penn State University, Reading, PA, United States
| | - Wan Adnawani Meor Osman
- Centre for Crop and Food Innovation, College of Science, Health, Engineering and Education, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Julie Ardley
- Centre for Crop and Food Innovation, College of Science, Health, Engineering and Education, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Jaco Zandberg
- Centre for Crop and Food Innovation, College of Science, Health, Engineering and Education, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Margaret Gollagher
- Murdoch University Associate, Murdoch, WA, Australia.,Sustainability and Biosecurity, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Peter van Berkum
- Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Beltsville, MD, United States
| | - Patrick Elia
- Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Beltsville, MD, United States
| | - Dora Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA, Australia
| | - Rekha Seshadri
- Department of Energy (DOE) Joint Genome Institute, Berkeley, CA, United States
| | - T B K Reddy
- Department of Energy (DOE) Joint Genome Institute, Berkeley, CA, United States
| | - Natalia Ivanova
- Department of Energy (DOE) Joint Genome Institute, Berkeley, CA, United States
| | - Amrita Pati
- Department of Energy (DOE) Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy (DOE) Joint Genome Institute, Berkeley, CA, United States
| | - Nikos Kyrpides
- Department of Energy (DOE) Joint Genome Institute, Berkeley, CA, United States
| | - Matthys Loedolff
- Centre for Crop and Food Innovation, College of Science, Health, Engineering and Education, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Damian W Laird
- Centre for Water Energy and Waste, Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Wayne Reeve
- Centre for Crop and Food Innovation, College of Science, Health, Engineering and Education, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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Wang T, Balla B, Kovács S, Kereszt A. Varietas Delectat: Exploring Natural Variations in Nitrogen-Fixing Symbiosis Research. FRONTIERS IN PLANT SCIENCE 2022; 13:856187. [PMID: 35481136 PMCID: PMC9037385 DOI: 10.3389/fpls.2022.856187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
The nitrogen-fixing symbiosis between leguminous plants and soil bacteria collectively called rhizobia plays an important role in the global nitrogen cycle and is an essential component of sustainable agriculture. Genetic determinants directing the development and functioning of the interaction have been identified with the help of a very limited number of model plants and bacterial strains. Most of the information obtained from the study of model systems could be validated on crop plants and their partners. The investigation of soybean cultivars and different rhizobia, however, has revealed the existence of ineffective interactions between otherwise effective partners that resemble gene-for-gene interactions described for pathogenic systems. Since then, incompatible interactions between natural isolates of model plants, called ecotypes, and different bacterial partner strains have been reported. Moreover, diverse phenotypes of both bacterial mutants on different host plants and plant mutants with different bacterial strains have been described. Identification of the genetic factors behind the phenotypic differences did already and will reveal novel functions of known genes/proteins, the role of certain proteins in some interactions, and the fine regulation of the steps during nodule development.
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Affiliation(s)
- Ting Wang
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
- Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Benedikta Balla
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
- Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Szilárd Kovács
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
| | - Attila Kereszt
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
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23
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Szewczuk-Karpisz K, Bajda T, Tomczyk A, Kuśmierz M, Komaniecka I. Immobilization mechanism of Cd2+/HCrO4-/CrO42- ions and carboxin on montmorillonite modified with Rhizobium leguminosarum bv. trifolii exopolysaccharide. JOURNAL OF HAZARDOUS MATERIALS 2022; 428:128228. [PMID: 35033916 DOI: 10.1016/j.jhazmat.2022.128228] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/27/2021] [Accepted: 01/04/2022] [Indexed: 05/26/2023]
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24
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Franzino T, Boubakri H, Cernava T, Abrouk D, Achouak W, Reverchon S, Nasser W, Haichar FEZ. Implications of carbon catabolite repression for plant-microbe interactions. PLANT COMMUNICATIONS 2022; 3:100272. [PMID: 35529946 PMCID: PMC9073323 DOI: 10.1016/j.xplc.2021.100272] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/17/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Carbon catabolite repression (CCR) plays a key role in many physiological and adaptive responses in a broad range of microorganisms that are commonly associated with eukaryotic hosts. When a mixture of different carbon sources is available, CCR, a global regulatory mechanism, inhibits the expression and activity of cellular processes associated with utilization of secondary carbon sources in the presence of the preferred carbon source. CCR is known to be executed by completely different mechanisms in different bacteria, yeast, and fungi. In addition to regulating catabolic genes, CCR also appears to play a key role in the expression of genes involved in plant-microbe interactions. Here, we present a detailed overview of CCR mechanisms in various bacteria. We highlight the role of CCR in beneficial as well as deleterious plant-microbe interactions based on the available literature. In addition, we explore the global distribution of known regulatory mechanisms within bacterial genomes retrieved from public repositories and within metatranscriptomes obtained from different plant rhizospheres. By integrating the available literature and performing targeted meta-analyses, we argue that CCR-regulated substrate use preferences of microorganisms should be considered an important trait involved in prevailing plant-microbe interactions.
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Affiliation(s)
- Theophile Franzino
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Hasna Boubakri
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Écologie Microbienne, 69622 Villeurbanne, France
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, Graz 8010, Austria
| | - Danis Abrouk
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Écologie Microbienne, 69622 Villeurbanne, France
| | - Wafa Achouak
- Aix Marseille Université, CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), 13108 Saint-Paul-Lez-Durance, France
| | - Sylvie Reverchon
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - William Nasser
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Feth el Zahar Haichar
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
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25
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Plant-Microbe Interaction in Sustainable Agriculture: The Factors That May Influence the Efficacy of PGPM Application. SUSTAINABILITY 2022. [DOI: 10.3390/su14042253] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The indiscriminate use of chemical fertilizers and pesticides has caused considerable environmental damage over the years. However, the growing demand for food in the coming years and decades requires the use of increasingly productive and efficient agriculture. Several studies carried out in recent years have shown how the application of plant growth-promoting microbes (PGPMs) can be a valid substitute for chemical industry products and represent a valid eco-friendly alternative. However, because of the complexity of interactions created with the numerous biotic and abiotic factors (i.e., environment, soil, interactions between microorganisms, etc.), the different formulates often show variable effects. In this review, we analyze the main factors that influence the effectiveness of PGPM applications and some of the applications that make them a useful tool for agroecological transition.
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26
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Biosynthesis and applications of curdlan. Carbohydr Polym 2021; 273:118597. [PMID: 34560997 DOI: 10.1016/j.carbpol.2021.118597] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 01/01/2023]
Abstract
Curdlan is widely applied in the food and pharmaceutical industries. This review focuses on the biosynthetic pathways, regulatory mechanisms and metabolic engineering strategies for curdlan production. Firstly, curdlan biosynthesis is discussed. Furthermore, various strategies to increase curdlan production are summarized from four aspects, including the overexpression of genes for curdlan biosynthesis, weakening/knockdown of genes from competing pathways, increasing the supply of curdlan precursors, and optimization of fermentation conditions. Moreover, the emerging and advanced applications of curdlan are introduced. Finally, the challenges that are frequently encountered during curdlan biosynthesis are noted with a discussion of directions for curdlan production.
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27
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Identification of an Exopolysaccharide Biosynthesis Gene in Bradyrhizobium diazoefficiens USDA110. Microorganisms 2021; 9:microorganisms9122490. [PMID: 34946092 PMCID: PMC8707904 DOI: 10.3390/microorganisms9122490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 01/27/2023] Open
Abstract
Exopolysaccharides (EPS) play critical roles in rhizobium-plant interactions. However, the EPS biosynthesis pathway in Bradyrhizobium diazoefficiens USDA110 remains elusive. Here we used transposon (Tn) mutagenesis with the aim to identify genetic elements required for EPS biosynthesis in B. diazoefficiens USDA110. Phenotypic screening of Tn5 insertion mutants grown on agar plates led to the identification of a mutant with a transposon insertion site in the blr2358 gene. This gene is predicted to encode a phosphor-glycosyltransferase that transfers a phosphosugar onto a polyprenol phosphate substrate. The disruption of the blr2358 gene resulted in defective EPS synthesis. Accordingly, the blr2358 mutant showed a reduced capacity to induce nodules and stimulate the growth of soybean plants. Glycosyltransferase genes related to blr2358 were found to be well conserved and widely distributed among strains of the Bradyrhizobium genus. In conclusion, our study resulted in identification of a gene involved in EPS biosynthesis and highlights the importance of EPS in the symbiotic interaction between USDA110 and soybeans.
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28
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Yurgel SN, Qu Y, Rice JT, Ajeethan N, Zink EM, Brown JM, Purvine S, Lipton MS, Kahn ML. Specialization in a Nitrogen-Fixing Symbiosis: Proteome Differences Between Sinorhizobium medicae Bacteria and Bacteroids. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1409-1422. [PMID: 34402628 DOI: 10.1094/mpmi-07-21-0180-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Using tandem mass spectrometry (MS/MS), we analyzed the proteome of Sinorhizobium medicae WSM419 growing as free-living cells and in symbiosis with Medicago truncatula. In all, 3,215 proteins were identified, over half of the open reading frames predicted from the genomic sequence. The abundance of 1,361 proteins displayed strong lifestyle bias. In total, 1,131 proteins had similar levels in bacteroids and free-living cells, and the low levels of 723 proteins prevented statistically significant assignments. Nitrogenase subunits comprised approximately 12% of quantified bacteroid proteins. Other major bacteroid proteins included symbiosis-specific cytochromes and FixABCX, which transfer electrons to nitrogenase. Bacteroids had normal levels of proteins involved in amino acid biosynthesis, glycolysis or gluconeogenesis, and the pentose phosphate pathway; however, several amino acid degradation pathways were repressed. This suggests that bacteroids maintain a relatively independent anabolic metabolism. Tricarboxylic acid cycle proteins were highly expressed in bacteroids and no other catabolic pathway emerged as an obvious candidate to supply energy and reductant to nitrogen fixation. Bacterial stress response proteins were induced in bacteroids. Many WSM419 proteins that are not encoded in S. meliloti Rm1021 were detected, and understanding the functions of these proteins might clarify why S. medicae WSM419 forms a more effective symbiosis with M. truncatula than S. meliloti Rm1021.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Svetlana N Yurgel
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, P.O. Box 550, Truro, Nova Scotia, B2N 5E3, Canada
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, U.S.A
| | - Yi Qu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, U.S.A
| | - Jennifer T Rice
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, U.S.A
| | - Nivethika Ajeethan
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, P.O. Box 550, Truro, Nova Scotia, B2N 5E3, Canada
- Faculty of Technology, University of Jaffna, Sri Lanka
| | - Erika M Zink
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, U.S.A
| | - Joseph M Brown
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, U.S.A
| | - Sam Purvine
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, U.S.A
| | - Mary S Lipton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, U.S.A
| | - Michael L Kahn
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, U.S.A
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-6340, U.S.A
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29
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Rodríguez-Esperón MC, Eastman G, Sandes L, Garabato F, Eastman I, Iriarte A, Fabiano E, Sotelo-Silveira JR, Platero R. Genomics and transcriptomics insights into luteolin effects on the beta-rhizobial strain Cupriavidus necator UYPR2.512. Environ Microbiol 2021; 24:240-264. [PMID: 34811861 DOI: 10.1111/1462-2920.15845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 11/28/2022]
Abstract
Cupriavidus necator UYPR2.512 is a rhizobial strain that belongs to the Beta-subclass of proteobacteria, able to establish successful symbiosis with Mimosoid legumes. The initial steps of rhizobium-legumes symbioses involve the reciprocal recognition by chemical signals, being luteolin one of the molecules involved. However, there is a lack of information on the effect of luteolin in beta-rhizobia. In this work, we used long-read sequencing to complete the genome of UYPR2.512 providing evidence for the existence of four closed circular replicons. We used an RNA-Seq approach to analyse the response of UYPR2.512 to luteolin. One hundred and forty-five genes were differentially expressed, with similar numbers of downregulated and upregulated genes. Most repressed genes were mapped to the main chromosome, while the upregulated genes were overrepresented among pCne512e, containing the symbiotic genes. Induced genes included the nod operon and genes implicated in exopolysaccharides and flagellar biosynthesis. We identified many genes involved in iron, copper and other heavy metals metabolism. Among repressed genes, we identified genes involved in basal carbon and nitrogen metabolism. Our results suggest that in response to luteolin, C. necator strain UYPR2.512 reshapes its metabolism in order to be prepared for the forthcoming symbiotic interaction.
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Affiliation(s)
- M C Rodríguez-Esperón
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - G Eastman
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - L Sandes
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - F Garabato
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - I Eastman
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - A Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Facultad de Medicina, Instituto de Higiene, Montevideo, Uruguay
| | - E Fabiano
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - J R Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - R Platero
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
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30
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Basile LA, Lepek VC. Legume-rhizobium dance: an agricultural tool that could be improved? Microb Biotechnol 2021; 14:1897-1917. [PMID: 34318611 PMCID: PMC8449669 DOI: 10.1111/1751-7915.13906] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 12/29/2022] Open
Abstract
The specific interaction between rhizobia and legume roots leads to the development of a highly regulated process called nodulation, by which the atmospheric nitrogen is converted into an assimilable plant nutrient. This capacity is the basis for the use of bacterial inoculants for field crop cultivation. Legume plants have acquired tools that allow the entry of compatible bacteria. Likewise, plants can impose sanctions against the maintenance of nodules occupied by rhizobia with low nitrogen-fixing capacity. At the same time, bacteria must overcome different obstacles posed first by the environment and then by the legume. The present review describes the mechanisms involved in the regulation of the entire legume-rhizobium symbiotic process and the strategies and tools of bacteria for reaching the nitrogen-fixing state inside the nodule. Also, we revised different approaches to improve the nodulation process for a better crop yield.
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Affiliation(s)
- Laura A. Basile
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde”Universidad Nacional de San Martín (IIB‐UNSAM‐CONICET)Av. 25 de Mayo y Francia, Gral. San Martín, Provincia de Buenos AiresBuenos AiresB1650HMPArgentina
| | - Viviana C. Lepek
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde”Universidad Nacional de San Martín (IIB‐UNSAM‐CONICET)Av. 25 de Mayo y Francia, Gral. San Martín, Provincia de Buenos AiresBuenos AiresB1650HMPArgentina
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31
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Antunes VDC, Freitag D, Serrato RV. Differential exopolysaccharide production and composition by Herbaspirillum strains from diverse ecological environments. Arch Microbiol 2021; 203:3883-3892. [PMID: 34009446 DOI: 10.1007/s00203-021-02371-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/22/2021] [Accepted: 05/08/2021] [Indexed: 11/26/2022]
Abstract
Bacteria belonging to the genus Herbaspirillum are found in many different ecological niches. Some species are typically endophytic, while others were reported as free-living organisms that occupy various environments. Also, opportunistic herbaspirilli have been found infecting humans affected by several diseases. We have analyzed the production of exopolysaccharides (EPS) by Herbaspirillum strains isolated from different sources and with distinct ecological characteristics. The monosaccharide composition was determined for the EPS obtained for selected strains including free-living, plant-associated and clinical isolates, and the relationship with the ecological niches occupied by Herbaspirillum spp. is proposed.
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Affiliation(s)
- Valquíria D C Antunes
- Department of Biochemistry and Molecular Biology, Setor de Ciências Biológicas-Centro Politécnico, Universidade Federal do Paraná , R. Francisco H. dos Santos, 100 , PO Box 19046, Curitiba, PR, 81531-980, Brazil
| | - Daniela Freitag
- Department of Biochemistry and Molecular Biology, Setor de Ciências Biológicas-Centro Politécnico, Universidade Federal do Paraná , R. Francisco H. dos Santos, 100 , PO Box 19046, Curitiba, PR, 81531-980, Brazil
| | - Rodrigo V Serrato
- Department of Biochemistry and Molecular Biology, Setor de Ciências Biológicas-Centro Politécnico, Universidade Federal do Paraná , R. Francisco H. dos Santos, 100 , PO Box 19046, Curitiba, PR, 81531-980, Brazil.
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Structure and Development of the Legume-Rhizobial Symbiotic Interface in Infection Threads. Cells 2021; 10:cells10051050. [PMID: 33946779 PMCID: PMC8146911 DOI: 10.3390/cells10051050] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/25/2021] [Accepted: 04/27/2021] [Indexed: 02/06/2023] Open
Abstract
The intracellular infection thread initiated in a root hair cell is a unique structure associated with Rhizobium-legume symbiosis. It is characterized by inverted tip growth of the plant cell wall, resulting in a tunnel that allows invasion of host cells by bacteria during the formation of the nitrogen-fixing root nodule. Regulation of the plant-microbial interface is essential for infection thread growth. This involves targeted deposition of the cell wall and extracellular matrix and tight control of cell wall remodeling. This review describes the potential role of different actors such as transcription factors, receptors, and enzymes in the rearrangement of the plant-microbial interface and control of polar infection thread growth. It also focuses on the composition of the main polymers of the infection thread wall and matrix and the participation of reactive oxygen species (ROS) in the development of the infection thread. Mutant analysis has helped to gain insight into the development of host defense reactions. The available data raise many new questions about the structure, function, and development of infection threads.
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33
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Impact of Sinorhizobium meliloti Exopolysaccharide on Adsorption and Aggregation in the Copper(II) Ions/Supporting Electrolyte/Kaolinite System. MATERIALS 2021; 14:ma14081950. [PMID: 33924565 PMCID: PMC8069898 DOI: 10.3390/ma14081950] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/06/2021] [Accepted: 04/10/2021] [Indexed: 12/16/2022]
Abstract
To obtain insight into physicochemical interactions between Cu(II) ions, kaolinite, and exopolysaccharide (EPS) synthesized by Sinorhizobium meliloti Rm 1021 soil bacteria, an adsorption, electrokinetic, and aggregation study was performed in the selected systems. The obtained data showed that supporting electrolyte type affects both EPS and Cu(II) ions adsorption. For initial Cu(II) concentration 100 mg/L, 4.36 ± 0.25 mg/g (21.80 ± 1.00%) of the ions were adsorbed in 0.001 M NaCl and 3.76 ± 0.20 mg/g (18.80 ± 1.00%) in 0.001 M CaCl2. The experimental data were best fitted to the Langmuir model as well as pseudo second-order equation. The EPS adsorbed amount on kaolinite was higher in the CaCl2 electrolyte than in NaCl one. For an initial polymer concentration of 100 mg/L, the EPS adsorbed amount was 4.69 ± 0.08 mg/g (23.45 ± 0.40%) in 0.001 M NaCl and 5.26 ± 0.15 mg/g (26.32 ± 0.75%) in 0.001 M CaCl2. In the mixed system, regardless of electrolyte type, exopolysaccharide contributed to immobilization of higher amount of copper(II) ions on the clay mineral. Also, in the samples containing heavy metal ions and exopolysaccharide simultaneously, the aggregation of kaolinite particles was the strongest. The results presented in the paper may be very helpful in soil bioremediation, especially in the development of technologies reducing the mobility of heavy metals in the environment.
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Computational characterizations of GDP-mannose 4,6-dehydratase (NoeL) Rhizobial proteins. Curr Genet 2021; 67:769-784. [PMID: 33837815 DOI: 10.1007/s00294-021-01184-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/19/2021] [Accepted: 03/29/2021] [Indexed: 10/21/2022]
Abstract
A growing body of evidence suggests that Nod Factors molecules are the critical structural components in nitrogen fixation. These molecules have been implicated in plant-microbe signaling. Many enzymes involved in Nod factors biosynthesis; however, the enzymes that decorate (modify) nod factor main structure play a vital role. Here, the computational analysis of GDP-mannose 4,6-dehydratase (NoeL) proteins with great impact in modification of nod factor structure in four genomes of agriculturally important rhizobia (Bradyrhizobium, Mesorhizobium, Rhizobium, Sinorhizobium) presented. The NoeL number of amino acids was in the range of 147 (M5AMF5) to 372 (A0A023XWX0, Q89TZ1). The molecular weights were around 41 KDa. The results showed that the strain-specific purification strategy should apply as the pI of the sequences varied significantly (in the range of 5.59 to 9.12). The enzyme sequences and eight 3-dimensional structures predicted with homology modeling and machine learning representing the phylogenetic tree revealed the stability of enzymes in different conditions (Instability and Aliphatic index); however, this stability is also strain-specific. Disulphide bonds were observed in some species; however, the pattern was not detected in all members of the same species. Alpha helix was the dominant secondary structure predicted in all cytoplasmic NoeL. All models were homo-tetramer with acceptable sequence identity, GMEAN and coverage (60, - 1.80, 88, respectively). Additionally, Ramachandran maps showed that more than 94% of residues are in favored regions. We also highlight several key characterizations of NoeL from four rhizobia genomes annotation. These findings provide novel insights into the complexity and diversity of NoeL enzymes among important rhizobia and suggest considering a broader framework of biofilm for future research.
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Oleńska E, Małek W, Kotowska U, Wydrych J, Polińska W, Swiecicka I, Thijs S, Vangronsveld J. Exopolysaccharide Carbohydrate Structure and Biofilm Formation by Rhizobium leguminosarum bv. trifolii Strains Inhabiting Nodules of Trifoliumrepens Growing on an Old Zn-Pb-Cd-Polluted Waste Heap Area. Int J Mol Sci 2021; 22:ijms22062808. [PMID: 33802057 PMCID: PMC7998805 DOI: 10.3390/ijms22062808] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 12/03/2022] Open
Abstract
Heavy metals polluting the 100-year-old waste heap in Bolesław (Poland) are acting as a natural selection factor and may contribute to adaptations of organisms living in this area, including Trifolium repens and its root nodule microsymbionts—rhizobia. Exopolysaccharides (EPS), exuded extracellularly and associated with bacterial cell walls, possess variable structures depending on environmental conditions; they can bind metals and are involved in biofilm formation. In order to examine the effects of long-term exposure to metal pollution on EPS structure and biofilm formation of rhizobia, Rhizobium leguminosarum bv. trifolii strains originating from the waste heap area and a non-polluted reference site were investigated for the characteristics of the sugar fraction of their EPS using gas chromatography mass-spectrometry and also for biofilm formation and structural characteristics using confocal laser scanning microscopy under control conditions as well as when exposed to toxic concentrations of zinc, lead, and cadmium. Significant differences in EPS structure, biofilm thickness, and ratio of living/dead bacteria in the biofilm were found between strains originating from the waste heap and from the reference site, both without exposure to metals and under metal exposure. Received results indicate that studied rhizobia can be assumed as potentially useful in remediation processes.
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Affiliation(s)
- Ewa Oleńska
- Department of Microbiology and Biotechnology, Faculty of Biology, University of Białystok, 1J Ciołkowski, 15-245 Białystok, Poland;
- Correspondence: ; Tel.: +48-8-5738-8366
| | - Wanda Małek
- Department of Genetics and Microbiology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, 19 Akademicka, 20-033 Lublin, Poland;
| | - Urszula Kotowska
- Division of Environmental Chemistry, Department of Analytic and Inorganic Chemistry, Faculty of Chemistry, University of Białystok, 1K Ciołkowski, 15-245 Białystok, Poland;
| | - Jerzy Wydrych
- Department of Functional Anatomy and Cytobiology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, 19 Akademicka, 20-033 Lublin, Poland;
| | - Weronika Polińska
- Doctoral School of Exact and Natural Sciences, University of Białystok, 1K Ciołkowski, 15-245 Białystok, Poland;
| | - Izabela Swiecicka
- Department of Microbiology and Biotechnology, Faculty of Biology, University of Białystok, 1J Ciołkowski, 15-245 Białystok, Poland;
- Laboratory of Applied Microbiology, Faculty of Biology, University of Białystok, 1J Ciołkowski, 15-245 Białystok, Poland
| | - Sofie Thijs
- Centre for Environmental Sciences, Faculty of Sciences, Hasselt University, Agoralaan D, B-3590 Diepenbeek, Belgium; (S.T.); (J.V.)
| | - Jaco Vangronsveld
- Centre for Environmental Sciences, Faculty of Sciences, Hasselt University, Agoralaan D, B-3590 Diepenbeek, Belgium; (S.T.); (J.V.)
- Department of Plant Physiology and Biophysics, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, 19 Akademicka, 20-033 Lublin, Poland
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Pirhanov A, Bridges CM, Goodwin RA, Guo YS, Furrer J, Shor LM, Gage DJ, Cho YK. Optogenetics in Sinorhizobium meliloti Enables Spatial Control of Exopolysaccharide Production and Biofilm Structure. ACS Synth Biol 2021; 10:345-356. [PMID: 33465305 DOI: 10.1021/acssynbio.0c00498] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Microorganisms play a vital role in shaping the soil environment and enhancing plant growth by interacting with plant root systems. Because of the vast diversity of cell types involved, combined with dynamic and spatial heterogeneity, identifying the causal contribution of a defined factor, such as a microbial exopolysaccharide (EPS), remains elusive. Synthetic approaches that enable orthogonal control of microbial pathways are a promising means to dissect such complexity. Here we report the implementation of a synthetic, light-activated, transcriptional control platform using the blue-light responsive DNA binding protein EL222 in the nitrogen fixing soil bacterium Sinorhizobium meliloti. By fine-tuning the system, we successfully achieved optical control of an EPS production pathway without significant basal expression under noninducing (dark) conditions. Optical control of EPS recapitulated important behaviors such as a mucoid plate phenotype and formation of structured biofilms, enabling spatial control of biofilm structures in S. meliloti. The successful implementation of optically controlled gene expression in S. meliloti enables systematic investigation of how genotype and microenvironmental factors together shape phenotype in situ.
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Affiliation(s)
- Azady Pirhanov
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Charles M. Bridges
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Reed A. Goodwin
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Yi-Syuan Guo
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Jessica Furrer
- Department of Computer Science, Physics, and Engineering, Benedict College, Columbia, South Carolina 29204, United States
| | - Leslie M. Shor
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
- Center for Environmental Sciences and Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Daniel J. Gage
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Yong Ku Cho
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
- Center for Environmental Sciences and Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, United States
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Castellani LG, Luchetti A, Nilsson JF, Pérez-Giménez J, Wegener C, Schlüter A, Pühler A, Lagares A, Brom S, Pistorio M, Niehaus K, Torres Tejerizo GA. Exopolysaccharide Characterization of Rhizobium favelukesii LPU83 and Its Role in the Symbiosis With Alfalfa. FRONTIERS IN PLANT SCIENCE 2021; 12:642576. [PMID: 33643369 PMCID: PMC7902896 DOI: 10.3389/fpls.2021.642576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/20/2021] [Indexed: 05/03/2023]
Abstract
One of the greatest inputs of available nitrogen into the biosphere occurs through the biological N2-fixation to ammonium as result of the symbiosis between rhizobia and leguminous plants. These interactions allow increased crop yields on nitrogen-poor soils. Exopolysaccharides (EPS) are key components for the establishment of an effective symbiosis between alfalfa and Ensifer meliloti, as bacteria that lack EPS are unable to infect the host plants. Rhizobium favelukesii LPU83 is an acid-tolerant rhizobia strain capable of nodulating alfalfa but inefficient to fix nitrogen. Aiming to identify the molecular determinants that allow R. favelukesii to infect plants, we studied its EPS biosynthesis. LPU83 produces an EPS I identical to the one present in E. meliloti, but the organization of the genes involved in its synthesis is different. The main gene cluster needed for the synthesis of EPS I in E. meliloti, is split into three different sections in R. favelukesii, which probably arose by a recent event of horizontal gene transfer. A R. favelukesii strain devoided of all the genes needed for the synthesis of EPS I is still able to infect and nodulate alfalfa, suggesting that attention should be directed to other molecules involved in the development of the symbiosis.
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Affiliation(s)
- Lucas G. Castellani
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Abril Luchetti
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Juliet F. Nilsson
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Julieta Pérez-Giménez
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | | | | | | | - Antonio Lagares
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Susana Brom
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mariano Pistorio
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | | | - Gonzalo A. Torres Tejerizo
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
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Li R, Feng Y, Chen H, Zhang C, Huang Y, Chen L, Hao Q, Cao D, Yuan S, Zhou X. Whole-Genome Sequencing of Bradyrhizobium diazoefficiens 113-2 and Comparative Genomic Analysis Provide Molecular Insights Into Species Specificity and Host Specificity. Front Microbiol 2020; 11:576800. [PMID: 33329441 PMCID: PMC7709874 DOI: 10.3389/fmicb.2020.576800] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 10/20/2020] [Indexed: 11/24/2022] Open
Abstract
In the present study, we sequenced the complete genome of Bradyrhizobium diazoefficiens 113-2. The genomic characteristics of six selected rhizobial strains (two fast-growing rhizobia, two medium-slow-growing rhizobia and two slow-growing rhizobia) with four different legume hosts were analyzed by comparative genomic analysis. Genomes of B. diazoefficiens 113-2 and B. diazoefficiens USDA110 were found to share a large synteny blocks and a high ANI value, supporting 113-2 as a strain of B. diazoefficiens. 5,455 singletons and 11,656 clusters were identified among the six rhizobia genomes, and most of the pair-wise comparisons clusters were shared by the two genomes of strains in the same genus. Similar genus-specific gene numbers in the assigned COG functional terms were present in the two strains of the same genus, while the numbers were decreased with the increase of growth rate in most of the COG terms. KEGG pathway analysis of B. diazoefficiens 113-2 suggested that the rhizobial genes in ABC transporters and Two-Component system were mainly species-specific. Besides, the candidate genes related to secretion system and surface polysaccharides biosynthesis in the genomes of the six strains were explored and compared. 39 nodulation gene families, 12 nif gene families and 10 fix gene families in the genomes of these six strains were identified, and gene classes in most of gene families and the types and total gene numbers of gene families were substantially different among these six genomes. We also performed synteny analyses for above-mentioned nod, nif, and fix gene groupings, and selected NodW, NolK, NoeJ, NifB, FixK, and FixJ gene families to perform phylogeny analyses. Our results provided valuable molecular insights into species specificity and host specificity. The genetic information responsible for host specificity will play important roles in expanding the host range of rhizobia among legumes, which might provide new clues for the understanding of the genetic determinants of non-legume-rhizobium symbiosis.
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Affiliation(s)
- Rong Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Yong Feng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Haifeng Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Chanjuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Yi Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Limiao Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Qingnan Hao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Dong Cao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Songli Yuan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Xinan Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
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Gao H, Yang L, Tian J, Huang L, Huang D, Zhang W, Xie F, Niu Y, Jin M, Jia C, Zou C, Huang J, Chang Z, Yang X, Jiang D. Characterization and rheological properties analysis of the succinoglycan produced by a high-yield mutant of Rhizobium radiobacter ATCC 19358. Int J Biol Macromol 2020; 166:61-70. [PMID: 33096177 DOI: 10.1016/j.ijbiomac.2020.10.087] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 12/14/2022]
Abstract
Succinoglycan is an industrially important exopolysaccharide biosynthesized by bacteria. In this study, mutant strain 18052 N-11 was obtained from the wild type strain Rhizobium radiobacter ATCC 19358 by NTG mutagenesis. It has a high yield succinoglycan of 32.5 g/L cultured in a 15 L-fementer for 72 h. Succinoglycan SG-A from the wild type strain has two components, and the molecular weights were 1.55 × 107 Da and 1.26 × 106 Da, respectively. While, succinoglycan SG-N from the mutant strain was a homogeneous polysaccharide, and the molecular weight was 1.01 × 107 Da. The molecular weight of both succinoglycan was higher than those reported in literatures. DSC thermogram of SG-A showed a higher endothermic peak than that of SG-N due to the higher crystallinity of SG-A. The dynamic frequency sweep test of SG-A and SG-N showed that the elastic modulus G' and viscosity modulus G" curves intersected at 65 °C, indicating the thermally induced order-disorder conformation. The results of effect of concentrations (2.5-15%) and temperatures (25-75 °C) on apparent viscosity of SG-A and SG-N showed that the succinoglycan solutions exhibited non-Newtonian, shear-thinning behavior. Both SG-A and SG-N showed an excellent emulsification activity. The characterizations and rheological properties make SG-A and SG-N prominent candidates in food, cosmetics, pharmaceutical and petroleum industries.
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Affiliation(s)
- Hongliang Gao
- School of Life Sciences, East China Normal University, Shanghai 200241, People's Republic of China
| | - Li Yang
- School of Life Sciences, East China Normal University, Shanghai 200241, People's Republic of China
| | - Jiangtao Tian
- School of Life Sciences, East China Normal University, Shanghai 200241, People's Republic of China
| | - Lingling Huang
- School of Life Sciences, East China Normal University, Shanghai 200241, People's Republic of China
| | - Dating Huang
- School of Life Sciences, East China Normal University, Shanghai 200241, People's Republic of China
| | - Wei Zhang
- School of Life Sciences, East China Normal University, Shanghai 200241, People's Republic of China
| | - Fangrui Xie
- School of Life Sciences, East China Normal University, Shanghai 200241, People's Republic of China
| | - Yanning Niu
- School of Life Sciences, East China Normal University, Shanghai 200241, People's Republic of China
| | - Mingfei Jin
- School of Life Sciences, East China Normal University, Shanghai 200241, People's Republic of China
| | - Caifeng Jia
- School of Life Sciences, East China Normal University, Shanghai 200241, People's Republic of China
| | - Chunjing Zou
- School of Life Sciences, East China Normal University, Shanghai 200241, People's Republic of China
| | - Jing Huang
- School of Life Sciences, East China Normal University, Shanghai 200241, People's Republic of China
| | - Zhongyi Chang
- School of Life Sciences, East China Normal University, Shanghai 200241, People's Republic of China
| | - Xuexia Yang
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, People's Republic of China.
| | - Deming Jiang
- School of Life Sciences, East China Normal University, Shanghai 200241, People's Republic of China.
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Marczak M, Wójcik M, Żebracki K, Turska-Szewczuk A, Talarek K, Nowak D, Wawiórka L, Sieńczyk M, Łupicka-Słowik A, Bobrek K, Romańczuk M, Koper P, Mazur A. PssJ Is a Terminal Galactosyltransferase Involved in the Assembly of the Exopolysaccharide Subunit in Rhizobium Leguminosarum bv. Trifolii. Int J Mol Sci 2020; 21:ijms21207764. [PMID: 33092221 PMCID: PMC7589315 DOI: 10.3390/ijms21207764] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/16/2020] [Accepted: 10/18/2020] [Indexed: 12/22/2022] Open
Abstract
Rhizobium leguminosarum bv. trifolii produces exopolysaccharide (EPS) composed of glucose, glucuronic acid, and galactose residues at a molar ratio 5:2:1. A majority of genes involved in the synthesis, modification, and export of exopolysaccharide are located in the chromosomal Pss-I region. In the present study, a ΔpssJ deletion mutant was constructed and shown to produce EPS lacking terminal galactose in the side chain of the octasaccharide subunit. The lack of galactose did not block EPS subunit translocation and polymerization. The in trans delivery of the pssJ gene restored the production of galactose-containing exopolysaccharide. The mutant was compromised in several physiological traits, e.g., motility and biofilm production. An impact of the pssJ mutation and changed EPS structure on the symbiotic performance was observed as improper signaling at the stage of molecular recognition, leading to formation of a significant number of non-infected empty nodules. Terminal galactosyltransferase PssJ was shown to display a structure typical for the GT-A class of glycosyltransferases and interact with other GTs and Wzx/Wzy system proteins. The latter, together with PssJ presence in soluble and membrane protein fractions indicated that the protein plays its role at the inner membrane interface and as a component of a larger complex.
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Affiliation(s)
- Małgorzata Marczak
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland; (M.W.); (K.Ż.); (A.T.-S.); (K.T.); (D.N.); (M.R.); (P.K.); (A.M.)
- Correspondence:
| | - Magdalena Wójcik
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland; (M.W.); (K.Ż.); (A.T.-S.); (K.T.); (D.N.); (M.R.); (P.K.); (A.M.)
| | - Kamil Żebracki
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland; (M.W.); (K.Ż.); (A.T.-S.); (K.T.); (D.N.); (M.R.); (P.K.); (A.M.)
| | - Anna Turska-Szewczuk
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland; (M.W.); (K.Ż.); (A.T.-S.); (K.T.); (D.N.); (M.R.); (P.K.); (A.M.)
| | - Kamila Talarek
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland; (M.W.); (K.Ż.); (A.T.-S.); (K.T.); (D.N.); (M.R.); (P.K.); (A.M.)
| | - Dominika Nowak
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland; (M.W.); (K.Ż.); (A.T.-S.); (K.T.); (D.N.); (M.R.); (P.K.); (A.M.)
| | - Leszek Wawiórka
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland;
| | - Marcin Sieńczyk
- Department of Organic and Medical Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Norwida 4/6 St., 50-373 Wrocław, Poland; (M.S.).; (A.Ł.-S.)
| | - Agnieszka Łupicka-Słowik
- Department of Organic and Medical Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Norwida 4/6 St., 50-373 Wrocław, Poland; (M.S.).; (A.Ł.-S.)
| | - Kamila Bobrek
- Department of Epizootiology and Clinic of Bird and Exotic Animals, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Norwida 31 St., 50-375 Wrocław, Poland;
| | - Marceli Romańczuk
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland; (M.W.); (K.Ż.); (A.T.-S.); (K.T.); (D.N.); (M.R.); (P.K.); (A.M.)
| | - Piotr Koper
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland; (M.W.); (K.Ż.); (A.T.-S.); (K.T.); (D.N.); (M.R.); (P.K.); (A.M.)
| | - Andrzej Mazur
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland; (M.W.); (K.Ż.); (A.T.-S.); (K.T.); (D.N.); (M.R.); (P.K.); (A.M.)
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Spribille T, Tagirdzhanova G, Goyette S, Tuovinen V, Case R, Zandberg WF. 3D biofilms: in search of the polysaccharides holding together lichen symbioses. FEMS Microbiol Lett 2020; 367:5731805. [PMID: 32037451 PMCID: PMC7164778 DOI: 10.1093/femsle/fnaa023] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 02/07/2020] [Indexed: 12/14/2022] Open
Abstract
Stable, long-term interactions between fungi and algae or cyanobacteria, collectively known as lichens, have repeatedly evolved complex architectures with little resemblance to their component parts. Lacking any central scaffold, the shapes they assume are casts of secreted polymers that cement cells into place, determine the angle of phototropic exposure and regulate water relations. A growing body of evidence suggests that many lichen extracellular polymer matrices harbor unicellular, non-photosynthesizing organisms (UNPOs) not traditionally recognized as lichen symbionts. Understanding organismal input and uptake in this layer is key to interpreting the role UNPOs play in lichen biology. Here, we review both polysaccharide composition determined from whole, pulverized lichens and UNPOs reported from lichens to date. Most reported polysaccharides are thought to be structural cell wall components. The composition of the extracellular matrix is not definitively known. Several lines of evidence suggest some acidic polysaccharides have evaded detection in routine analysis of neutral sugars and may be involved in the extracellular matrix. UNPOs reported from lichens include diverse bacteria and yeasts for which secreted polysaccharides play important biological roles. We conclude by proposing testable hypotheses on the role that symbiont give-and-take in this layer could play in determining or modifying lichen symbiotic outcomes.
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Affiliation(s)
- Toby Spribille
- Department of Biological Sciences, CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Gulnara Tagirdzhanova
- Department of Biological Sciences, CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Spencer Goyette
- Department of Biological Sciences, CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Veera Tuovinen
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Rebecca Case
- Department of Biological Sciences, CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Wesley F Zandberg
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3427 University Way, Kelowna, BC V1V 1V7, Canada
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Gene expression abundance dictated exopolysaccharide modification in Rhizobium radiobacter SZ4S7S14 as the cell's response to salt stress. Int J Biol Macromol 2020; 164:4339-4347. [PMID: 32931833 DOI: 10.1016/j.ijbiomac.2020.09.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/25/2020] [Accepted: 09/07/2020] [Indexed: 12/24/2022]
Abstract
A molecular and metabolic behaviour of EPS-producing and salt-tolerant bacterium Rhizobium radiobacter SZ4S7S14 along with its practical application in salt-stress was investigated. The research target was identification and expression profiles of a large EPS biosynthesis gene cluster, possible structural modification of EPS under salt-stress effect and analysis of the gene(s) relative expression and structural modification correlation. As expected, transposons insertions were identified within or near the coding regions of exoK and exoM, previously known large gene cluster that is required for EPS I synthesis. Different expression levels of exoK and exoM in different salt-stress models resulted in structural modification of EPS, which was seen basically in monomers molar ratio. As a result of downregulation of the genes the strain produced EPS samples with monomers ratio: (1) Glu:Man:Gal:Xyl:Ara:Rha:Rib = 31.21:3.02:2.77:1:0.91:0.64:0.41 (in 0.25% NaCl); (2) Glu:Man:Gal:Xyl:Ara:Rha:Rib = 7.65:1:0.69:0.22:0.2:0.16:0.1 (in 0.5% NaCl); (3) Glu:Man:Gal:Ara:Xyl:Rha:Rib = 9.39:1.89:1:0.58:0.52:0.46:0.26 (in 1% NaCl); and (4) Glu:Man:Ara:Xyl:Rib:Gal = 7.9:2:2:1.58:1.1:1 (in 2.0% NaCl), whereas in control (without NaCl): Glc:Man:Gal:Xyl:Ara:Rha:Rib = 11.66:1:0.90:0.37:0.37:0.15:0.14. It was found that, salt-stress not only leads to downregulation of a large EPS biosynthesis gene cluster, including exoK and exoM genes, but also impacting on their relative expression degree, re-groups of the monomers within the EPS matrix and dictates molar ratio of the monosaccharides in the final metabolite.
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Exploring the Role of Bacterial Extracellular Polymeric Substances for Sustainable Development in Agriculture. Curr Microbiol 2020; 77:3224-3239. [PMID: 32876713 DOI: 10.1007/s00284-020-02169-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 08/18/2020] [Indexed: 01/02/2023]
Abstract
The incessant need to increase crop yields has led to the development of many chemical fertilizers containing NPK (nitrogen-phosphorous-potassium) which can degrade soil health in the long term. In addition, these fertilizers are often leached into nearby water bodies causing algal bloom and eutrophication. Bacterial secondary metabolites exuded into the extracellular space, termed extracellular polymeric substances (EPS) have gained commercial significance because of their biodegradability, non-toxicity, and renewability. In many habitats, bacterial communities faced with adversity will adhere together by production of EPS which also serves to bond them to surfaces. Typically, hygroscopic, EPS retain moisture in desiccating conditions and modulate nutrient exchange. Many plant growth-promoting bacteria (PGPR) combat harsh environmental conditions like salinity, drought, and attack of pathogens by producing EPS. The adhesive nature of EPS promotes soil aggregation and restores moisture thus combating soil erosion and promoting soil fertility. In addition, these molecules play vital roles in maintaining symbiosis and nitrogen fixation thus enhancing sustainability. Thus, along with other commercial applications, EPS show promising avenues for improving agricultural productivity thus helping to address land scarcity as well as minimizing environmental pollution.
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Papik J, Folkmanova M, Polivkova-Majorova M, Suman J, Uhlik O. The invisible life inside plants: Deciphering the riddles of endophytic bacterial diversity. Biotechnol Adv 2020; 44:107614. [PMID: 32858117 DOI: 10.1016/j.biotechadv.2020.107614] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/14/2020] [Accepted: 08/15/2020] [Indexed: 10/25/2022]
Abstract
Endophytic bacteria often promote plant growth and protect their host plant against pathogens, herbivores, and abiotic stresses including drought, increased salinity or pollution. Current agricultural practices are being challenged in terms of climate change and the ever-increasing demand for food. Therefore, the rational exploitation of bacterial endophytes to increase the productivity and resistance of crops appears to be very promising. However, the efficient and larger-scale use of bacterial endophytes for more effective and sustainable agriculture is hindered by very little knowledge on molecular aspects of plant-endophyte interactions and mechanisms driving bacterial communities in planta. In addition, since most of the information on bacterial endophytes has been obtained through culture-dependent techniques, endophytic bacterial diversity and its full biotechnological potential still remain highly unexplored. In this study, we discuss the diversity and role of endophytic populations as well as complex interactions that the endophytes have with the plant and vice versa, including the interactions leading to plant colonization. A description of biotic and abiotic factors influencing endophytic bacterial communities is provided, along with a summary of different methodologies suitable for determining the diversity of bacterial endophytes, mechanisms governing the assembly and structure of bacterial communities in the endosphere, and potential biotechnological applications of endophytes in the future.
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Affiliation(s)
- Jakub Papik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Magdalena Folkmanova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Marketa Polivkova-Majorova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Jachym Suman
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic.
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Pi S, Qiu J, Li A, Feng L, Wu D, Zhao HP, Ma F. Applied microbiology and biotechnology uncovering the biosynthetic pathway of polysaccharide-based microbial flocculant in Agrobacterium tumefaciens F2. Appl Microbiol Biotechnol 2020; 104:8479-8488. [PMID: 32830292 DOI: 10.1007/s00253-020-10850-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 08/11/2020] [Accepted: 08/17/2020] [Indexed: 11/25/2022]
Abstract
The low yield as bottleneck problem limits the application of microbial flocculant in water treatment. However, genetic information of microbial flocculant-producing strains can guide the regulation of microbial flocculant production, but it remains unknown. Agrobacterium tumefaciens F2 produced polysaccharide-based microbial flocculants in the fermentation medium but none in Luria Bertani medium; hence, the transcriptome was used to analyze the potentially associated genes with the production of microbial flocculants. Glucose, mannose, rhamnose, and galactose are the main sugar monomers, and genes (manA, glmM, manC, rfb genes, exo genes, etc.) with changed expression levels related to sugar monomers metabolism potentially participated in the biosynthesis of polysaccharide-based microbial flocculants. exoC, exoP, and manC were confirmed to participate in the biosynthesis via constructing the mutants F2-dexoC, F2-dexoP, and F2-dmanC. An exoF2 gene cluster was annotated due to the high percentage of matches between the genome sequences of strains F2 and C58, and exo genes in their genome sequences showed the similarity of 86~92%. The hypothetical pathway for the biosynthesis of polysaccharide-based microbial flocculants in strain F2 was proposed, laying the basis for the production yield regulation. KEY POINTS: • An exoF2 gene cluster in the polysaccharide biosynthesis was annotated. • exoC, exoP, and manC genes participated in the polysaccharide biosynthesis. • A hypothetical biosynthesis pathway of polysaccharide in flocculant was proposed. Graphical abstract.
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Affiliation(s)
- Shanshan Pi
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, People's Republic of China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Ang Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, People's Republic of China.
| | - Liang Feng
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, People's Republic of China
| | - Dan Wu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, People's Republic of China
| | - He-Ping Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, People's Republic of China.
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Bhat MA, Kumar V, Bhat MA, Wani IA, Dar FL, Farooq I, Bhatti F, Koser R, Rahman S, Jan AT. Mechanistic Insights of the Interaction of Plant Growth-Promoting Rhizobacteria (PGPR) With Plant Roots Toward Enhancing Plant Productivity by Alleviating Salinity Stress. Front Microbiol 2020; 11:1952. [PMID: 32973708 PMCID: PMC7468593 DOI: 10.3389/fmicb.2020.01952] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/24/2020] [Indexed: 11/20/2022] Open
Abstract
Agriculture plays an important role in a country's economy. The sector is challenged by many stresses, which led to huge loss in plant productivity worldwide. The ever-increasing population, rapid urbanization with shrinking agricultural lands, dramatic change in climatic conditions, and extensive use of agrochemicals in agricultural practices that caused environmental disturbances confront mankind of escalating problems of food security and sustainability in agriculture. Escalating environmental problems and global hunger have led to the development and adoption of genetic engineering and other conventional plant breeding approaches in developing stress-tolerant varieties of crops. However, these approaches have drawn flaws in their adoption as the process of generating tolerant varieties takes months to years in bringing the technology from the lab to the field. Under such scenario, sustainable and climate-smart agricultural practices that avail bacterial usage open the avenues in fulfilling the incessant demand for food for the global population. Ensuring stability on economic fronts, bacteria minimizes plant salt uptake by trapping ions in their exopolysaccharide matrix besides checking the expression of Na+/H+ and high-affinity potassium transporters. Herein we describe information on salinity stress and its effect on plant health as well as strategies adopted by plant growth-promoting rhizobacteria (PGPR) in helping plants to overcome salinity stress and in mitigating loss in overall plant productivity. It is believed that acquisition of advanced knowledge of plant-beneficial PGPR will help in devising strategies for sustainable, environment-friendly, and climate-smart agricultural technologies for adoption in agriculture to overcome the constrained environmental conditions.
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Affiliation(s)
- Mujtaba Aamir Bhat
- Department of Botany, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Vijay Kumar
- Department of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Mudasir Ahmad Bhat
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Ishfaq Ahmad Wani
- Department of Botany, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Farhana Latief Dar
- Department of Botany, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Iqra Farooq
- Department of Botany, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Farha Bhatti
- Department of Botany, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Rubina Koser
- Department of Microbiology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Safikur Rahman
- Department of Botany, Munshi Singh College, Babasaheb Bhimrao Ambedkar Bihar University, Muzaffarpur, India
| | - Arif Tasleem Jan
- Department of Botany, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
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Liu Y, Bellich B, Hug S, Eberl L, Cescutti P, Pessi G. The Exopolysaccharide Cepacian Plays a Role in the Establishment of the Paraburkholderia phymatum - Phaseolus vulgaris Symbiosis. Front Microbiol 2020; 11:1600. [PMID: 32765457 PMCID: PMC7378592 DOI: 10.3389/fmicb.2020.01600] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/18/2020] [Indexed: 12/19/2022] Open
Abstract
Paraburkholderia phymatum is a rhizobial strain that belongs to the beta-proteobacteria, a group known to form efficient nitrogen-fixing symbioses within root nodules of several legumes, including the agriculturally important common bean. The establishment of the symbiosis requires the exchange of rhizobial and plant signals such as lipochitooligosaccharides (Nod factors), polysaccharides, and flavonoids. Inspection of the genome of the competitive rhizobium P. phymatum revealed the presence of several polysaccharide biosynthetic gene clusters. In this study, we demonstrate that bceN, a gene encoding a GDP-D-mannose 4,6-dehydratase, which is involved in the production of the exopolysaccharide cepacian, an important component of biofilms produced by closely related opportunistic pathogens of the Burkholderia cepacia complex (Bcc), is required for efficient plant colonization. Wild-type P. phymatum was shown to produce cepacian while a bceN mutant did not. Additionally, the bceN mutant produced a significantly lower amount of biofilm and formed less root nodules compared to the wild-type strain with Phaseolus vulgaris as host plant. Finally, expression of the operon containing bceN was induced by the presence of germinated P. vulgaris seeds under nitrogen limiting conditions suggesting a role of this polysaccharide in the establishment of this ecologically important symbiosis.
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Affiliation(s)
- Yilei Liu
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Barbara Bellich
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Sebastian Hug
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Paola Cescutti
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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Abstract
Bacteria form diverse interactions with eukaryotic hosts. This is well represented by the Rhizobiales, a clade of Alphaproteobacteria strategically important for their large diversity of lifestyles with implications for agricultural and medical research. To investigate their lifestyle evolution, we compiled a comprehensive data set of genomes and lifestyle information for over 1,000 Rhizobiales genomes. We show that the origins of major host-associated lineages in Rhizobiales broadly coincided with the emergences of their host plants/animals, suggesting bacterium-host interactions as a driving force in the evolution of Rhizobiales. We further found that, in addition to gene gains, preexisting traits and recurrent losses of specific genomic traits may have played underrecognized roles in the origin of host-associated lineages, providing clues to genetic engineering of microbial agricultural inoculants and prevention of the emergence of potential plant/animal pathogens. Members of the order Rhizobiales include those capable of nitrogen fixation in nodules as well as pathogens of animals and plants. This lifestyle diversity has important implications for agricultural and medical research. Leveraging large-scale genomic data, we infer that Rhizobiales originated as a free-living ancestor ∼1,500 million years ago (Mya) and that the later emergence of host-associated lifestyles broadly coincided with the rise of their eukaryotic hosts. In particular, the first nodulating lineage arose from either Azorhizobium or Bradyrhizobium 150 to 80 Mya, a time range in general concurrent with the emergence of legumes. The rates of lifestyle transitions are highly variable; nodule association is more likely to be lost than gained, whereas animal association likely represents an evolutionary dead end. We searched for statistical correlations between gene presence and lifestyle and identified genes likely contributing to the transition and adaptation to the same lifestyle in divergent lineages. Among the genes potentially promoting successful transitions to major nodulation lineages, the nod and nif clusters for nodulation and nitrogen fixation, respectively, were repeatedly acquired during each transition; the fix, dct, and phb clusters involved in energy conservation under micro-oxic conditions were present in the nonnodulating ancestors; and the secretion systems were acquired in lineage-specific patterns. Our study data suggest that increased eukaryote diversity drives lifestyle diversification of bacteria and highlight both acquired and preexisting traits facilitating the origin of host association. IMPORTANCE Bacteria form diverse interactions with eukaryotic hosts. This is well represented by the Rhizobiales, a clade of Alphaproteobacteria strategically important for their large diversity of lifestyles with implications for agricultural and medical research. To investigate their lifestyle evolution, we compiled a comprehensive data set of genomes and lifestyle information for over 1,000 Rhizobiales genomes. We show that the origins of major host-associated lineages in Rhizobiales broadly coincided with the emergences of their host plants/animals, suggesting bacterium-host interactions as a driving force in the evolution of Rhizobiales. We further found that, in addition to gene gains, preexisting traits and recurrent losses of specific genomic traits may have played underrecognized roles in the origin of host-associated lineages, providing clues to genetic engineering of microbial agricultural inoculants and prevention of the emergence of potential plant/animal pathogens.
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49
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Global control of bacterial nitrogen and carbon metabolism by a PTS Ntr-regulated switch. Proc Natl Acad Sci U S A 2020; 117:10234-10245. [PMID: 32341157 DOI: 10.1073/pnas.1917471117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The nitrogen-related phosphotransferase system (PTSNtr) of Rhizobium leguminosarum bv. viciae 3841 transfers phosphate from PEP via PtsP and NPr to two output regulators, ManX and PtsN. ManX controls central carbon metabolism via the tricarboxylic acid (TCA) cycle, while PtsN controls nitrogen uptake, exopolysaccharide production, and potassium homeostasis, each of which is critical for cellular adaptation and survival. Cellular nitrogen status modulates phosphorylation when glutamine, an abundant amino acid when nitrogen is available, binds to the GAF sensory domain of PtsP, preventing PtsP phosphorylation and subsequent modification of ManX and PtsN. Under nitrogen-rich, carbon-limiting conditions, unphosphorylated ManX stimulates the TCA cycle and carbon oxidation, while unphosphorylated PtsN stimulates potassium uptake. The effects are reversed with the phosphorylation of ManX and PtsN, occurring under nitrogen-limiting, carbon-rich conditions; phosphorylated PtsN triggers uptake and nitrogen metabolism, the TCA cycle and carbon oxidation are decreased, while carbon-storage polymers such as surface polysaccharide are increased. Deleting the GAF domain from PtsP makes cells "blind" to the cellular nitrogen status. PTSNtr constitutes a switch through which carbon and nitrogen metabolism are rapidly, and reversibly, regulated by protein:protein interactions. PTSNtr is widely conserved in proteobacteria, highlighting its global importance.
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50
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Velichko NS, Grinev VS, Fedonenko YP. Characterization of biopolymers produced by planktonic and biofilm cells of Herbaspirillum lusitanum P6-12. J Appl Microbiol 2020; 129:1349-1363. [PMID: 32216024 DOI: 10.1111/jam.14647] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/31/2020] [Accepted: 03/20/2020] [Indexed: 11/30/2022]
Abstract
AIMS The goal of this study was to characterize biopolymers from two modes of the Herbaspirillum lusitanum P6-12 growth: planktonic, in which cells are free swimming, and biofilm life style, in which the cells are sessile. METHODS AND RESULTS Differences in biopolymers composition from planktonic and biofilm cells of H. lusitanum strain P6-12 were analysed using Fourier transform infrared spectroscopy (FTIR), sodium dodecyl sulphate-polyacrylamide gel electrophoresis, gas-liquid chromatography and spectrophotometry. A high degree of polymer separation and purification was achieved by ultracentrifugation, and column chromatography allowed us to identify the chemical differences between biopolymers from biofilm and planktonic H. lusitanum. It was shown that planktonic cells of H. lusitanum P6-12 when cultivated in a liquid medium to the end of the exponential phase of growth, produced two high-molecular-weight glycoconjugates (were arbitrarily called CPS-I and CPS-II) of a lipopolysaccharide (LPS) nature and a lipid-polysacharide complex (were arbitrarily called EPS). The EPS, CPS-I, CPS-II had different monosaccharide and lipid compositions. The extracellular polymeric matrix (EPM) produced by the biofilm cells was mostly proteinaceous, with a small amount of carbohydrates (up to 3%). From the biofilm culture medium, a free extracellular polymeric substance (was arbitrarily called fEPS) was obtained that contained proteins and carbohydrates (up to 7%). The cells outside the biofilm had capsules containing high-molecular-weight glycoconjugate (was arbitrarily called CPSFBC ) that consisted of carbohydrates (up to 10%), proteins (up to 16%) and lipids (up to 70%). CONCLUSIONS During biofilm formation, the bacteria secreted surface biopolymers that differed from those of the planktonic cells. The heterogeneity of the polysaccharide containing biopolymers of the H. lusitanum P6-12 surface is probably conditioned by their different functions in plant colonization and formation of an efficient symbiosis, as well as in cell adaptation to existence in plant tissues. SIGNIFICANCE AND IMPACT OF THE STUDY The results of the study permit a better understanding of the physiological properties of the biopolymers, for example, in plant-microbe interactions.
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Affiliation(s)
- N S Velichko
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Saratov, Russia
| | - V S Grinev
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Saratov, Russia
| | - Y P Fedonenko
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Saratov, Russia
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