1
|
Liebrenz K, Gómez C, Brambilla S, Frare R, Stritzler M, Maguire V, Ruiz O, Soldini D, Pascuan C, Soto G, Ayub N. Whole-Genome Resequencing of Spontaneous Oxidative Stress-Resistant Mutants Reveals an Antioxidant System of Bradyrhizobium japonicum Involved in Soybean Colonization. MICROBIAL ECOLOGY 2022; 84:1133-1140. [PMID: 34782938 DOI: 10.1007/s00248-021-01925-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Soybean is the most inoculant-consuming crop in the world, carrying strains belonging to the extremely related species Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens. Currently, it is well known that B. japonicum has higher efficiency of soybean colonization than B. diazoefficiens, but the molecular mechanism underlying this differential symbiotic performance remains unclear. In the present study, genome resequencing of four spontaneous oxidative stress-resistant mutants derived from the commercial strain B. japonicum E109 combined with molecular and physiological studies allowed identifying an antioxidant cluster (BjAC) containing a transcriptional regulator (glxA) that controls the expression of a catalase (catA) and a phosphohydrolase (yfbR) related to the hydrolysis of hydrogen peroxide and oxidized nucleotides, respectively. Integrated synteny and phylogenetic analyses supported the fact that BjAC emergence in the B. japonicum lineage occurred after its divergence from the B. diazoefficiens lineage. The transformation of the model bacterium B. diazoefficiens USDA110 with BjAC from E109 significantly increased its ability to colonize soybean roots, experimentally recapitulating the beneficial effects of the occurrence of BjAC in B. japonicum. In addition, the glxA mutation significantly increased the nodulation competitiveness and plant growth-promoting efficiency of E109. Finally, the potential applications of these types of non-genetically modified mutant microbes in soybean production worldwide are discussed.
Collapse
Affiliation(s)
- Karen Liebrenz
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Cristina Gómez
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Silvina Brambilla
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Romina Frare
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Margarita Stritzler
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Vanina Maguire
- Instituto Tecnológico Chascomús (INTECH-CONICET), Buenos Aires, Argentina
| | - Oscar Ruiz
- Instituto Tecnológico Chascomús (INTECH-CONICET), Buenos Aires, Argentina
| | - Diego Soldini
- Estación Experimental Agropecuaria Marcos Juárez, INTA, Córdoba, Argentina
| | - Cecilia Pascuan
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Gabriela Soto
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Nicolás Ayub
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina.
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina.
| |
Collapse
|
2
|
Liu B, Zhang D, Pan X. Nodules of wild legumes as unique natural hotspots of antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 839:156036. [PMID: 35597353 DOI: 10.1016/j.scitotenv.2022.156036] [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: 04/15/2022] [Revised: 05/13/2022] [Accepted: 05/14/2022] [Indexed: 06/15/2023]
Abstract
Root nodules (RN) of legumes have distinct microenvironment from their symbiotic roots and surrounding soils. The rhizobia can withstand the host-produced phytoalexins and antimicrobial compounds. We thus hypothesize that the wild legume RN may develop unique natural resistome and be antibiotic resistance gene (ARG) hotspots. In this study, in comparison with rhizosphere soil (RS) and bulk soil (BS), we characterized the feature of antibiotic resistance in the RN of two wild legumes, Medicago polymorpha and Astragalus sinicus, by metagenomics. It was shown that the total relative abundance of ARGs followed the order of RN > RS > BS for both legumes. ARGs encoding antibiotic efflux pump predominated in all samples with increased proportion from BS to RN samples for both legumes. Totally 275 ARG subtypes were detected, and diversity of ARGs in RN was significantly lower than in BS samples for both legumes. 32 and 25 unique ARGs subtypes were detected in RN of both legumes. Bacterial community played a key role in shaping nodule-associated resistome because both ARG profiles and bacterial community differed greatly among BS, RS and RN. Rhizobia potentially hosted 10 and 15 ARGs subtypes for both legumes. The number and proportion of plasmid- and ARG-carrying contigs (ACCs) were higher in RN than in BS. Host tracking analysis of plasmid-ACCs suggests that proportion of rhizobial bacteria identified as their hosts decreased from BS to RN samples. No plasmid-ACCs with multiple ARGs were observed in BS samples, whereas they were detected in RN samples of both legumes. Our study showed that even wild legume nodules are unique natural ARG hotspots and enough attention should be paid to the dissemination risk of ARGs posed by globally produced legume crops.
Collapse
Affiliation(s)
- Bingshen Liu
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Daoyong Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xiangliang Pan
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
| |
Collapse
|
3
|
Liebrenz K, Frare R, Gómez C, Pascuan C, Brambilla S, Soldini D, Maguire V, Carrio A, Ruiz O, McCormick W, Soto G, Ayub N. Multiple ways to evade the bacteriostatic action of glyphosate in rhizobia include the mutation of the conserved serine 90 of the nitrogenase subunit NifH to alanine. Res Microbiol 2022; 173:103952. [PMID: 35436545 DOI: 10.1016/j.resmic.2022.103952] [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: 01/11/2022] [Revised: 04/03/2022] [Accepted: 04/08/2022] [Indexed: 11/30/2022]
Abstract
The genome resequencing of spontaneous glyphosate-resistant mutants derived from the soybean inoculant E109 allowed identifying genes most likely associated with the uptake (gltL and cya) and metabolism (zigA and betA) of glyphosate, as well as with nitrogen fixation (nifH). Mutations in these genes reduce the lag phase and improve nodulation under glyphosate stress. In addition to providing glyphosate resistance, the amino acid exchange Ser90Ala in NifH increased the citrate synthase activity, growth rate and plant growth-promoting efficiency of E109 in the absence of glyphosate stress, suggesting roles for this site during both the free-living and symbiotic growth stages.
Collapse
Affiliation(s)
- Karen Liebrenz
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Buenos Aires, Argentina; Instituto de Genética (IGEAF), Buenos Aires, Argentina
| | - Romina Frare
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Buenos Aires, Argentina; Instituto de Genética (IGEAF), Buenos Aires, Argentina
| | - Cristina Gómez
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Buenos Aires, Argentina; Instituto de Genética (IGEAF), Buenos Aires, Argentina
| | - Cecilia Pascuan
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Buenos Aires, Argentina; Instituto de Genética (IGEAF), Buenos Aires, Argentina
| | - Silvina Brambilla
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Buenos Aires, Argentina; Instituto de Genética (IGEAF), Buenos Aires, Argentina
| | - Diego Soldini
- Estación Experimental Agropecuaria Marcos Juárez, INTA, Córdoba, Argentina
| | - Vanina Maguire
- Instituto Tecnológico Chascomús (INTECH-CONICET), Buenos Aires, Argentina
| | - Alejandro Carrio
- Estación Experimental Agropecuaria Marcos Juárez, INTA, Córdoba, Argentina
| | - Oscar Ruiz
- Instituto Tecnológico Chascomús (INTECH-CONICET), Buenos Aires, Argentina
| | - Wayne McCormick
- Ottawa Research and Development Centre (AAFC), Ottawa, ON, Canada
| | - Gabriela Soto
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Buenos Aires, Argentina; Instituto de Genética (IGEAF), Buenos Aires, Argentina
| | - Nicolás Ayub
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Buenos Aires, Argentina; Instituto de Genética (IGEAF), Buenos Aires, Argentina.
| |
Collapse
|
4
|
Frare R, Pascuan C, Galindo-Sotomonte L, McCormick W, Soto G, Ayub N. Exploring the Role of the NO-Detoxifying Enzyme HmpA in the Evolution of Domesticated Alfalfa Rhizobia. MICROBIAL ECOLOGY 2022; 83:501-505. [PMID: 33966095 DOI: 10.1007/s00248-021-01761-4] [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: 12/29/2020] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
We have previously shown the extensive loss of genes during the domestication of alfalfa rhizobia and the high nitrous oxide emission associated with the extreme genomic instability of commercial inoculants. In the present note, we describe the molecular mechanism involved in the evolution of alfalfa rhizobia. Genomic analysis showed that most of the gene losses in inoculants are due to large genomic deletions rather than to small deletions or point mutations, a fact consistent with recurrent DNA double-strand breaks (DSBs) at numerous locations throughout the microbial genome. Genetic analysis showed that the loss of the NO-detoxifying enzyme HmpA in inoculants results in growth inhibition and high DSB levels under nitrosative stress, and large genomic deletions in planta but not in the soil. Therefore, besides its known function in the effective establishment of the symbiosis, HmpA can play a critical role in the preservation of the genomic integrity of alfalfa rhizobia under host-derived nitrosative stress.
Collapse
Affiliation(s)
- Romina Frare
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (INTA), De Los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Cecilia Pascuan
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (INTA), De Los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Luisa Galindo-Sotomonte
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (INTA), De Los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Wayne McCormick
- Ottawa Research and Development Centre (AAFC), Ottawa, ON, Canada
| | - Gabriela Soto
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (INTA), De Los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Nicolás Ayub
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina.
- Instituto de Genética (INTA), De Los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina.
| |
Collapse
|
5
|
Morgado-Gamero WB, Parody A, Medina J, Rodriguez-Villamizar LA, Agudelo-Castañeda D. Multi-antibiotic resistant bacteria in landfill bioaerosols: Environmental conditions and biological risk assessment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 290:118037. [PMID: 34482243 DOI: 10.1016/j.envpol.2021.118037] [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: 04/24/2021] [Revised: 07/31/2021] [Accepted: 08/22/2021] [Indexed: 06/13/2023]
Abstract
Landfills, as well as other waste management facilities are well-known bioaerosols sources. These places may foment antibiotic-resistance in bacterial bioaerosol (A.R.B.) due to inadequate pharmaceutical waste disposal. This issue may foster the necessity of using last-generation antibiotics with extra costs in the health care system, and deaths. The aim of this study was to reveal the multi-antibiotic resistant bacterial bioaerosol emitted by a sanitary landfill and the surrounding area. We evaluated the influence of environmental conditions in the occurrence of A.R.B. and biological risk assessment. Antibiotic resistance found in the bacteria aerosols was compared with the AWaRE consumption classification. We used the BIOGAVAL method to assess the workers' occupational exposure to antibiotic-resistant bacterial bioaerosols in the landfill. This study confirmed the multi-antibiotic resistant in bacterial bioaerosol in a landfill and in the surrounding area. Obtained mean concentrations of bacterial bioaerosols, as well as antibiotic-resistant in bacterial bioaerosol (A.R.B.), were high, especially for fine particles that may be a threat for human health. Results suggest the possible risk of antibiotic-resistance interchange between pathogenic and non-pathogenic species in the landfill facilities, thus promoting antibiotic multi-resistance genes spreading into the environment.
Collapse
Affiliation(s)
- Wendy B Morgado-Gamero
- Department of Exact and Natural Sciences, Universidad de la Costa, Calle 58#55-66, Barranquilla, Colombia.
| | - Alexander Parody
- Engineering Faculty, Universidad Libre Barranquilla, Cra 46 No. 48-170, Barranquilla, Colombia.
| | - Jhorma Medina
- Department of Exact and Natural Sciences, Universidad de la Costa, Calle 58#55-66, Barranquilla, Colombia.
| | | | - Dayana Agudelo-Castañeda
- Department of Civil and Environmental Engineering, Universidad del Norte, Km 5 via Puerto, Colombia.
| |
Collapse
|
6
|
Frare R, Stritzler M, Pascuan C, Liebrenz K, Galindo-Sotomonte L, Soto G, Nikel PI, Ayub N. Elimination of GlnKAmtB affects serine biosynthesis and improves growth and stress tolerance of Escherichia coli under nutrient-rich conditions. FEMS Microbiol Lett 2021; 367:6006877. [PMID: 33242092 DOI: 10.1093/femsle/fnaa197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022] Open
Abstract
Nitrogen is a most important nutrient resource for Escherichia coli and other bacteria that harbor the glnKamtB operon, a high-affinity ammonium uptake system highly interconnected with cellular metabolism. Although this system confers an advantage to bacteria when growing under nitrogen-limiting conditions, little is known about the impact of these genes on microbial fitness under nutrient-rich conditions. Here, the genetically tractable E. coli BW25113 strain and its glnKamtB-null mutant (JW0441) were used to analyze the impact of GlnK-AmtB on growth rates and oxidative stress tolerance. Strain JW0441 showed a shorter initial lag phase, higher growth rate, higher citrate synthase activity, higher oxidative stress tolerance and lower expression of serA than strain BW25113 under nutrient-rich conditions, suggesting a fitness cost to increase metabolic plasticity associated with serine metabolism. The overexpression of serA in strain JW0441 resulted in a decreased growth rate and stress tolerance in nutrient-rich conditions similar to that of strain BW25113, suggesting that the negative influence on bacterial fitness imposed by GlnK-AmtB can be traced to the control of serine biosynthesis. Finally, we discuss the potential applications of glnKamtB mutants in bioproduction processes.
Collapse
Affiliation(s)
- Romina Frare
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
| | - Margarita Stritzler
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
| | - Cecilia Pascuan
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
| | - Karen Liebrenz
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
| | - Luisa Galindo-Sotomonte
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
| | - Gabriela Soto
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
| | - Pablo Iván Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Nicolás Ayub
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto de Genética (IGEAF), INTA-CONICET, Buenos Aires, Argentina
| |
Collapse
|