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Oliveira MS, Santos KFDN, de Paula RM, Vitorino LC, Bessa LA, Greer A, Di Mascio P, de Souza JCP, Martin-Didonet CCG. Nitric Oxide Detection Using a Chemical Trap Method for Applications in Bacterial Systems. Microorganisms 2023; 11:2210. [PMID: 37764053 PMCID: PMC10536504 DOI: 10.3390/microorganisms11092210] [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: 07/20/2023] [Revised: 08/24/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Plant growth-promoting bacteria (PGPB) can be incorporated in biofertilizer formulations, which promote plant growth in different ways, such as fixing nitrogen and producing phytohormones and nitric oxide (NO). NO is a free radical involved in the growth and defense responses of plants and bacteria. NO detection is vital for further investigation in different agronomically important bacteria. NO production in the presence of KNO3 was evaluated over 1-3 days using eight bacterial strains, quantified by the usual Griess reaction, and monitored by 2,3-diaminonaphthalene (DAN), yielding 2,3-naphthotriazole (NAT), as analyzed by fluorescence spectroscopy, gas chromatography-mass spectrometry, and high-performance liquid chromatography. The Greiss and trapping reaction results showed that Azospirillum brasilense (HM053 and FP2), Rhizobium tropici (Br322), and Gluconacetobacter diazotrophicus (Pal 5) produced the highest NO levels 24 h after inoculation, whereas Nitrospirillum amazonense (Y2) and Herbaspirillum seropedicae (SmR1) showed no NO production. In contrast to the literature, in NFbHP-NH4Cl-lactate culture medium with KNO3, NO trapping led to the recovery of a product with a molecular mass ion of 182 Da, namely, 1,2,3,4-naphthotetrazole (NTT), which contained one more nitrogen atom than the usual NAT product with 169 Da. This strategy allows monitoring and tracking NO production in potential biofertilizing bacteria, providing future opportunities to better understand the mechanisms of bacteria-plant interaction and also to manipulate the amount of NO that will sustain the PGPB.
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Affiliation(s)
- Marilene Silva Oliveira
- Instituto Federal de Educação, Ciência e Tecnologia Goiano, Departamento de Agroquímica, Campus Rio Verde, Rio Verde 75901-970, GO, Brazil; (L.A.B.); (J.C.P.d.S.)
- Câmpus Henrique Santillo de Ciências Exatas e Tecnológicas Henrique Santillo, BR 153 n° 3105—Fazenda Barreiro do Meio, Anápolis 75132-903, GO, Brazil; (K.F.D.N.S.); (R.M.d.P.); (C.C.G.M.-D.)
- Simple Agro Corporation, rua Parque General Borges Forte, 400, Jardim Goiás, Rio Verde 75903-421, GO, Brazil
| | - Karina F. D. N. Santos
- Câmpus Henrique Santillo de Ciências Exatas e Tecnológicas Henrique Santillo, BR 153 n° 3105—Fazenda Barreiro do Meio, Anápolis 75132-903, GO, Brazil; (K.F.D.N.S.); (R.M.d.P.); (C.C.G.M.-D.)
| | - Railane Monteiro de Paula
- Câmpus Henrique Santillo de Ciências Exatas e Tecnológicas Henrique Santillo, BR 153 n° 3105—Fazenda Barreiro do Meio, Anápolis 75132-903, GO, Brazil; (K.F.D.N.S.); (R.M.d.P.); (C.C.G.M.-D.)
| | - Luciana C. Vitorino
- Instituto Federal de Educação, Ciência e Tecnologia Goiano, Departamento de Agroquímica, Campus Rio Verde, Rio Verde 75901-970, GO, Brazil; (L.A.B.); (J.C.P.d.S.)
- Simple Agro Corporation, rua Parque General Borges Forte, 400, Jardim Goiás, Rio Verde 75903-421, GO, Brazil
| | - Layara A. Bessa
- Instituto Federal de Educação, Ciência e Tecnologia Goiano, Departamento de Agroquímica, Campus Rio Verde, Rio Verde 75901-970, GO, Brazil; (L.A.B.); (J.C.P.d.S.)
- Simple Agro Corporation, rua Parque General Borges Forte, 400, Jardim Goiás, Rio Verde 75903-421, GO, Brazil
| | - Alexander Greer
- Department of Chemistry, Brooklyn College, City University of New York, Brooklyn, NY 11210, USA;
- The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Paolo Di Mascio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil;
| | - João C. P. de Souza
- Instituto Federal de Educação, Ciência e Tecnologia Goiano, Departamento de Agroquímica, Campus Rio Verde, Rio Verde 75901-970, GO, Brazil; (L.A.B.); (J.C.P.d.S.)
- Departamento de Química, Faculdade de Ciências, Universidade Estadual Paulista, Av. Eng. Luiz Edmundo Carrijo Coube, 14-01, São Paulo 17033-360, SP, Brazil
| | - Claudia C. G. Martin-Didonet
- Câmpus Henrique Santillo de Ciências Exatas e Tecnológicas Henrique Santillo, BR 153 n° 3105—Fazenda Barreiro do Meio, Anápolis 75132-903, GO, Brazil; (K.F.D.N.S.); (R.M.d.P.); (C.C.G.M.-D.)
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Koul V, Srivastava D, Singh PP, Kochar M. Genome-wide identification of Azospirillum brasilense Sp245 small RNAs responsive to nitrogen starvation and likely involvement in plant-microbe interactions. BMC Genomics 2020; 21:821. [PMID: 33228533 PMCID: PMC7685610 DOI: 10.1186/s12864-020-07212-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 11/05/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Small RNAs (sRNAs) are non-coding RNAs known to regulate various biological functions such as stress adaptation, metabolism, virulence as well as pathogenicity across a wide range of bacteria, mainly by controlling mRNA stabilization or regulating translation. Identification and functional characterization of sRNAs has been carried out in various plant growth-promoting bacteria and they have been shown to help the cells cope up with environmental stress. No study has been carried out to uncover these regulatory molecules in the diazotrophic alpha-proteobacterium Azospirillum brasilense Sp245 to date. RESULTS Expression-based sRNA identification (RNA-seq) revealed the first list of ~ 468 sRNA candidate genes in A. brasilense Sp245 that were differentially expressed in nitrogen starvation versus non-starved conditions. In parallel, in silico tools also identified 2 of the above as candidate sRNAs. Altogether, putative candidates were stringently curated from RNA-seq data based on known sRNA parameters (size, location, secondary structure, and abundance). In total, ~ 59 significantly expressed sRNAs were identified in this study of which 53 are potentially novel sRNAs as they have no Rfam and BSRD homologs. Sixteen sRNAs were randomly selected and validated for differential expression, which largely was found to be in congruence with the RNA-seq data. CONCLUSIONS Differential expression of 468 A. brasilense sRNAs was indicated by RNA-seq data, a subset of which was confirmed by expression analysis. Four of the significantly expressed sRNAs were not observed in nitrogen starvation while 16 sRNAs were found to be exclusively expressed in nitrogen depletion. Putative candidate sRNAs identified have potential mRNA targets primarily involved in stress (abiotic and biotic) adaptability; regulation of bacterial cellular, biological and molecular pathways such as nitrogen fixation, polyhydroxybutyrate synthesis, chemotaxis, biofilm formation and transcriptional regulation. In addition to directly influencing bacteria, some of these sRNAs also have targets influencing plant-microbe interactions through adhesion of bacteria to plant roots directly, suppressing host response, inducing plant defence and signalling.
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Affiliation(s)
- Vatsala Koul
- The Energy and Resources Institute, Darbari Seth Block, India Habitat Centre, Lodhi Road, New Delhi, 110003, India
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, Gurugram-Faridabad Road, Gwal Pahari, Haryana, 122003, India
| | - Divya Srivastava
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, Gurugram-Faridabad Road, Gwal Pahari, Haryana, 122003, India
| | - Pushplata Prasad Singh
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, Gurugram-Faridabad Road, Gwal Pahari, Haryana, 122003, India.
| | - Mandira Kochar
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, Gurugram-Faridabad Road, Gwal Pahari, Haryana, 122003, India.
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Noisette F, Depetris A, Kühl M, Brodersen KE. Flow and epiphyte growth effects on the thermal, optical and chemical microenvironment in the leaf phyllosphere of seagrass ( Zostera marina). J R Soc Interface 2020; 17:20200485. [PMID: 33050780 DOI: 10.1098/rsif.2020.0485] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Intensified coastal eutrophication can result in an overgrowth of seagrass leaves by epiphytes, which is a major threat to seagrass habitats worldwide, but little is known about how epiphytic biofilms affect the seagrass phyllosphere. The physico-chemical microenvironment of Zostera marina L. leaves with and without epiphytes was mapped with electrochemical, thermocouple and scalar irradiance microsensors as a function of four irradiance conditions (dark, low, saturating and high light) and two water flow velocities (approx. 0.5 and 5 cm s-1), which resemble field conditions. The presence of epiphytes led to the build up of a diffusive boundary layer and a thermal boundary layer which impeded O2 and heat transfer between the leaf surface and the surrounding water, resulting in a maximum increase of 0.8°C relative to leaves with no epiphytes. Epiphytes also reduced the quantity and quality of light reaching the leaf, decreasing plant photosynthesis. In darkness, epiphyte respiration exacerbated hypoxic conditions, which can lead to anoxia and the production of potential phytotoxic nitric oxide in the seagrass phyllosphere. Epiphytic biofilm affects the local phyllosphere physico-chemistry both because of its metabolic activity (i.e. photosynthesis/respiration) and its physical properties (i.e. thickness, roughness, density and back-scattering properties). Leaf tissue warming can lead to thermal stress in seagrasses living close to their thermal stress threshold, and thus potentially aggravate negative effects of global warming.
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Affiliation(s)
- Fanny Noisette
- Department of Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research, Hohenbergstraße 2, 24105 Kiel, Germany.,Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Battery Point, 7004 TAS Hobart, Australia
| | - Anna Depetris
- École Polytechnique Fédérale de Lausanne, Route Cantonale, 1015 Lausanne, Switzerland
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark
| | - Kasper Elgetti Brodersen
- Marine Biological Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark
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Doan TH, Doan TA, Kangas MJ, Ernest AE, Tran D, Wilson CL, Holmes AE, Doyle EL, Durham Brooks TL. A Low-Cost Imaging Method for the Temporal and Spatial Colorimetric Detection of Free Amines on Maize Root Surfaces. FRONTIERS IN PLANT SCIENCE 2017; 8:1513. [PMID: 28912796 PMCID: PMC5582365 DOI: 10.3389/fpls.2017.01513] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/16/2017] [Indexed: 05/08/2023]
Abstract
Plant root exudates are important mediators in the interactions that occur between plants and microorganisms in the soil, yet much remains to be learned about spatial and temporal variation in their production. This work outlines a method utilizing a novel colorimetric paper to detect spatial and temporal changes in the production of nitrogen-containing compounds on the root surface. While existing methods have made it possible to conduct detailed analysis of root exudate composition, relatively less is known about where in the root system exudates are produced and how this localization changes as the root grows. Furthermore, there is much to learn about how exudate localization and composition varies in response to stress. Root exudates are chemically diverse secretions composed of organic acids, amino acids, proteins, sugars, and other metabolites. The sensor utilized for the method, ninhydrin, is a colorless substance in solution that reacts with free amino groups to form a purple dye. A detection paper was developed by formulating ninhydrin into a print solution that was uniformly deposited onto paper with a commercial ink jet printer. This "ninhydrin paper" was used to analyze the chemical makeup of root surfaces from maize seedlings grown vertically on germination paper. Through contact between the ninhydrin paper and seedling root surfaces, combined with images of both the seedlings and dried ninhydrin papers captured using a standard flatbed scanner, nitrogen-containing substances on the root surface can be localized and concentration of signal estimated for over 2 weeks of development. The method was found to be non-inhibiting to plant growth over the analysis period although damage to root hairs was observed. The method is sensitive in the detection of free amines at concentrations as little as 140 μM. Furthermore, ninhydrin paper is stable, showing consistent color changes up to 2 weeks after printing. This relatively simple, low-cost method could contribute to a better understanding of root exudates and mechanisms used by plants to interact with the complex soil environment during growth and development.
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Affiliation(s)
- Truc H. Doan
- Department of Biology, Doane University, CreteNE, United States
| | - Tu A. Doan
- Department of Biology, Doane University, CreteNE, United States
| | | | | | - Danny Tran
- Crete High School, CreteNE, United States
| | | | - Andrea E. Holmes
- Department of Chemistry, Doane University, CreteNE, United States
| | - Erin L. Doyle
- Department of Biology, Doane University, CreteNE, United States
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Abstract
Auxin is an essential molecule that controls almost every aspect of plant development. Although the core signaling components that control auxin response are well characterized, the precise mechanisms enabling specific responses are not yet fully understood. Considering the significance of auxin in plant growth and its potential applications, deciphering further aspects of its biology is an important and exciting challenge.
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Affiliation(s)
- Sebastien Paque
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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