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Maroniche GA, Puente ML, García JE, Mongiardini E, Coniglio A, Nievas S, Labarthe MM, Wisniewski-Dyé F, Rodriguez Cáceres E, Díaz-Zorita M, Cassán F. Phenogenetic profile and agronomic contribution of Azospirillum argentinense Az39 T, a reference strain for the South American inoculant industry. Microbiol Res 2024; 283:127650. [PMID: 38452553 DOI: 10.1016/j.micres.2024.127650] [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: 12/15/2023] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 03/09/2024]
Abstract
Azospirillum sp. is a plant growth-promoting rhizobacteria largely recognized for its potential to increase the yield of different important crops. In this work, we present a thorough genomic and phenotypic analysis of A. argentinense Az39T to provide new insights into the beneficial mechanisms of this microorganism. Phenotypic analyses revealed the following in vitro abilities: growth at 20-38 °C (optimum, 28 °C), pH 6.0-8.0 (optimum, pH 6.8), and in the presence of 1% (w/v) NaCl; production of variable amounts of PHB as intracellular granules; nitrogen fixation under microaerophilic conditions; IAA synthesis in the presence of L-tryptophan. Through biochemical (API 20NE) and carbon utilization profiling (Biolog) assays, we proved that A. argentinense Az39T is able to use 15 substrates and metabolize 19 different carbon substrates. Lipid composition indicated a predominance of medium and long-chain saturated fatty acids. A total of 6 replicons classified as one main chromosome, three chromids, and two plasmids, according to their tRNA and core essential genes contents, were identified. Az39T genome includes genes associated with multiple plant growth-promoting (PGP) traits such as nitrogen fixation and production of auxins, cytokinin, abscisic acid, ethylene, and polyamines. In addition, Az39T genome harbor genetic elements associated with physiological features that facilitate its survival in the soil and competence for rhizospheric colonization; this includes motility, secretion system, and quorum sensing genetic determinants. A metadata analysis of Az39T agronomic performance in the pampas region, Argentina, demonstrated significant grain yield increases in wheat and maize, proving its potential to provide better growth conditions for dryland cereals. In conclusion, our data provide a detailed insight into the metabolic profile of A. argentinense Az39T, the strain most widely used to formulate non-legume inoculants in Argentina, and allow a better understanding of the mechanisms behind its field performance.
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Affiliation(s)
- G A Maroniche
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata (UNMdP), CONICET, Balcarce, Buenos Aires, Argentina
| | - M L Puente
- Instituto de Microbiología y Zoología Agrícola, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
| | - J E García
- Instituto de Microbiología y Zoología Agrícola, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
| | - E Mongiardini
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), CONICET, La Plata, Buenos Aires, Argentina
| | - A Coniglio
- Laboratorio de Fisiología Vegetal y de la Interacción Planta-Microorganismo, Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Universidad Nacional de Río Cuarto (UNRC), Río Cuarto, Córdoba, Argentina
| | - S Nievas
- Laboratorio de Fisiología Vegetal y de la Interacción Planta-Microorganismo, Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Universidad Nacional de Río Cuarto (UNRC), Río Cuarto, Córdoba, Argentina
| | - M M Labarthe
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata (UNMdP), CONICET, Balcarce, Buenos Aires, Argentina
| | - F Wisniewski-Dyé
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Villeurbanne 69622, France
| | | | - M Díaz-Zorita
- Facultad de Agronomía, Universidad Nacional de La Pampa (UNLPam), CONICET, Santa Rosa, La Pampa, Argentina
| | - F Cassán
- Laboratorio de Fisiología Vegetal y de la Interacción Planta-Microorganismo, Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Universidad Nacional de Río Cuarto (UNRC), Río Cuarto, Córdoba, Argentina.
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2
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Medici IF, Bartrolí L, Guaimas FF, Fulgenzi FR, Molina CL, Sánchez IE, Comerci DJ, Mongiardini E, Soler-Bistué A. The distinct cell physiology of Bradyrhizobium at the population and cellular level. BMC Microbiol 2024; 24:129. [PMID: 38643099 PMCID: PMC11031950 DOI: 10.1186/s12866-024-03272-x] [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] [Received: 08/31/2023] [Accepted: 03/22/2024] [Indexed: 04/22/2024] Open
Abstract
The α-Proteobacteria belonging to Bradyrhizobium genus are microorganisms of extreme slow growth. Despite their extended use as inoculants in soybean production, their physiology remains poorly characterized. In this work, we produced quantitative data on four different isolates: B. diazoefficens USDA110, B. diazoefficiens USDA122, B. japonicum E109 and B. japonicum USDA6 which are representative of specific genomic profiles. Notably, we found conserved physiological traits conserved in all the studied isolates: (i) the lag and initial exponential growth phases display cell aggregation; (ii) the increase in specific nutrient concentration such as yeast extract and gluconate hinders growth; (iii) cell size does not correlate with culture age; and (iv) cell cycle presents polar growth. Meanwhile, fitness, cell size and in vitro growth widely vary across isolates correlating to ribosomal RNA operon number. In summary, this study provides novel empirical data that enriches the comprehension of the Bradyrhizobium (slow) growth dynamics and cell cycle.
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Affiliation(s)
- Ian F Medici
- Instituto de Investigaciones Biotecnológicas, IIB-IIBIO, Universidad Nacional de San Martín- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. 25 de Mayo y Francia CP (1650), San Martín, Prov. de Buenos Aires, Argentina
| | - Leila Bartrolí
- Instituto de Investigaciones Biotecnológicas, IIB-IIBIO, Universidad Nacional de San Martín- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. 25 de Mayo y Francia CP (1650), San Martín, Prov. de Buenos Aires, Argentina
| | - Francisco F Guaimas
- Instituto de Investigaciones Biotecnológicas, IIB-IIBIO, Universidad Nacional de San Martín- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. 25 de Mayo y Francia CP (1650), San Martín, Prov. de Buenos Aires, Argentina
| | - Fabiana R Fulgenzi
- Instituto de Investigaciones Biotecnológicas, IIB-IIBIO, Universidad Nacional de San Martín- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. 25 de Mayo y Francia CP (1650), San Martín, Prov. de Buenos Aires, Argentina
| | - Charo Luciana Molina
- Instituto de Investigaciones Biotecnológicas, IIB-IIBIO, Universidad Nacional de San Martín- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. 25 de Mayo y Francia CP (1650), San Martín, Prov. de Buenos Aires, Argentina
| | - Ignacio Enrique Sánchez
- Laboratorio de Fisiología de Proteínas, Facultad de Ciencias Exactas y Naturales, CONICET Instituto de Química Biológica, Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Diego J Comerci
- Instituto de Investigaciones Biotecnológicas, IIB-IIBIO, Universidad Nacional de San Martín- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. 25 de Mayo y Francia CP (1650), San Martín, Prov. de Buenos Aires, Argentina
| | - Elías Mongiardini
- Instituto de Biotecnología y Biología Molecular (IBBM), Facultad de Ciencias Exactas, UNLP y CCT-La Plata-CONICET, La Plata, Argentina
| | - Alfonso Soler-Bistué
- Instituto de Investigaciones Biotecnológicas, IIB-IIBIO, Universidad Nacional de San Martín- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. 25 de Mayo y Francia CP (1650), San Martín, Prov. de Buenos Aires, Argentina.
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3
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Ye Y, Peng C, Zhu D, Yang R, Deng L, Wang T, Tang Y, Lu L. Identification of sulfamethazine degraders in swine farm-impacted river and farmland: A comparative study of aerobic and anaerobic environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169299. [PMID: 38104834 DOI: 10.1016/j.scitotenv.2023.169299] [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: 09/16/2023] [Revised: 11/20/2023] [Accepted: 12/09/2023] [Indexed: 12/19/2023]
Abstract
Sulfonamides (SAs) are extensively used antibiotics in the prevention and treatment of animal diseases, leading to significant SAs pollution in surrounding environments. Microbial degradation has been proposed as a crucial mechanism for removing SAs, but the taxonomic identification of microbial functional guilds responsible for SAs degradation in nature remain largely unexplored. Here, we employed 13C-sulfamethazine (SMZ)-based DNA-stable isotope probing (SIP) and metagenomic sequencing to investigate SMZ degraders in three distinct swine farm wastewater-receiving environments within an agricultural ecosystem. These environments include the aerobic riparian wetland soil, agricultural soil, and anaerobic river sediment. SMZ mineralization activities exhibited significant variation, with the highest rate observed in aerobic riparian wetland soil. SMZ had a substantial impact on the microbial community compositions across all samples. DNA-SIP analysis demonstrated that Thiobacillus, Auicella, Sphingomonas, and Rhodobacter were dominant active SMZ degraders in the wetland soil, whereas Ellin6067, Ilumatobacter, Dongia, and Steroidobacter predominated in the agricultural soil. The genus MND1 and family Vicinamibacteraceae were identified as SMZ degrader in both soils. In contrast, anaerobic SMZ degradation in the river sediment was mainly performed by genera Microvirga, Flavobacterium, Dechlorobacter, Atopostipes, and families Nocardioidaceae, Micrococcaceae, Anaerolineaceae. Metagenomic analysis of 13C-DNA identified key SAs degradation genes (sadA and sadC), and various of dioxygenases, and aromatic hydrocarbon degradation-related functional genes, indicating their involvement in degradation of SMZ and its intermediate products. These findings highlight the variations of indigenous SAs oxidizers in complex natural habitats and emphasize the consideration of applying these naturally active degraders in future antibiotic bioremediation.
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Affiliation(s)
- Yuqiu Ye
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Chao Peng
- College of Life Sciences, China West Normal University, Nanchong 637002, China; Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong 637009, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Ruiyu Yang
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Linjie Deng
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Tao Wang
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Yun Tang
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China; Key Laboratory of Nanchong City of Ecological Environment Protection and Pollution Prevention in Jialing River Basin, China West Normal University, Nanchong 637009, China.
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4
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Popržen T, Nikolić I, Krstić-Milošević D, Uzelac B, Trifunović-Momčilov M, Marković M, Radulović O. Characterization of the IAA-Producing and -Degrading Pseudomonas Strains Regulating Growth of the Common Duckweed ( Lemna minor L.). Int J Mol Sci 2023; 24:17207. [PMID: 38139036 PMCID: PMC10742903 DOI: 10.3390/ijms242417207] [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] [Received: 09/27/2023] [Revised: 11/16/2023] [Accepted: 12/03/2023] [Indexed: 12/24/2023] Open
Abstract
The rhizosphere represents a center of complex and dynamic interactions between plants and microbes, resulting in various positive effects on plant growth and development. However, less is known about the effects of indole-3-acetic acid (IAA) on aquatic plants. In this study, we report the characterization of four Pseudomonas strains isolated from the rhizosphere of the common duckweed (Lemna minor) with IAA-degradation and -utilization ability. Our results confirm previous reports on the negative effect of IAA on aquatic plants, contrary to the effect on terrestrial plants. P. putida A3-104/5 demonstrated particularly beneficial traits, as it exhibited not only IAA-degrading and -producing activity but also a positive effect on the doubling time of duckweeds in the presence of IAA, positive chemotaxis in the presence of IAA, increased tolerance to oxidative stress in the presence of IAA and increased biofilm formation related to IAA. Similarly, P. gessardii C31-106/3 significantly shortened the doubling time of duckweeds in the presence of IAA, while having a neutral effect in the absence of IAA. These traits are important in the context of plant-bacteria interactions and highlight the role of IAA as a common metabolite in these interactions, especially in aquatic environments where plants are facing unique challenges compared to their terrestrial counterparts. We conclude that IAA-degrading and -producing strains presented in this study might regulate IAA effects on aquatic plants and confer evolutionary benefits under adverse conditions (e.g., under oxidative stress, excess of IAA or nutrient scarcity).
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Affiliation(s)
- Tatjana Popržen
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana Street, 11060 Belgrade, Serbia; (T.P.); (D.K.-M.); (B.U.); (M.T.-M.); (M.M.)
| | - Ivan Nikolić
- Center for Biological Control and Plant Growth Promotion, Faculty of Biology, University of Belgrade, 16 Studentski Trg Street, 11000 Belgrade, Serbia;
| | - Dijana Krstić-Milošević
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana Street, 11060 Belgrade, Serbia; (T.P.); (D.K.-M.); (B.U.); (M.T.-M.); (M.M.)
| | - Branka Uzelac
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana Street, 11060 Belgrade, Serbia; (T.P.); (D.K.-M.); (B.U.); (M.T.-M.); (M.M.)
| | - Milana Trifunović-Momčilov
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana Street, 11060 Belgrade, Serbia; (T.P.); (D.K.-M.); (B.U.); (M.T.-M.); (M.M.)
| | - Marija Marković
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana Street, 11060 Belgrade, Serbia; (T.P.); (D.K.-M.); (B.U.); (M.T.-M.); (M.M.)
| | - Olga Radulović
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana Street, 11060 Belgrade, Serbia; (T.P.); (D.K.-M.); (B.U.); (M.T.-M.); (M.M.)
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5
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Bellés-Sancho P, Liu Y, Heiniger B, von Salis E, Eberl L, Ahrens CH, Zamboni N, Bailly A, Pessi G. A novel function of the key nitrogen-fixation activator NifA in beta-rhizobia: Repression of bacterial auxin synthesis during symbiosis. FRONTIERS IN PLANT SCIENCE 2022; 13:991548. [PMID: 36247538 PMCID: PMC9554594 DOI: 10.3389/fpls.2022.991548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
Rhizobia fix nitrogen within root nodules of host plants where nitrogenase expression is strictly controlled by its key regulator NifA. We recently discovered that in nodules infected by the beta-rhizobial strain Paraburkholderia phymatum STM815, NifA controls expression of two bacterial auxin synthesis genes. Both the iaaM and iaaH transcripts, as well as the metabolites indole-acetamide (IAM) and indole-3-acetic acid (IAA) showed increased abundance in nodules occupied by a nifA mutant compared to wild-type nodules. Here, we document the structural changes that a P. phymatum nifA mutant induces in common bean (Phaseolus vulgaris) nodules, eventually leading to hypernodulation. To investigate the role of the P. phymatum iaaMH genes during symbiosis, we monitored their expression in presence and absence of NifA over different stages of the symbiosis. The iaaMH genes were found to be under negative control of NifA in all symbiotic stages. While a P. phymatum iaaMH mutant produced the same number of nodules and nitrogenase activity as the wild-type strain, the nifA mutant produced more nodules than the wild-type that clustered into regularly-patterned root zones. Mutation of the iaaMH genes in a nifA mutant background reduced the presence of these nodule clusters on the root. We further show that the P. phymatum iaaMH genes are located in a region of the symbiotic plasmid with a significantly lower GC content and exhibit high similarity to two genes of the IAM pathway often used by bacterial phytopathogens to deploy IAA as a virulence factor. Overall, our data suggest that the increased abundance of rhizobial auxin in the non-fixing nifA mutant strain enables greater root infection rates and a role for bacterial auxin production in the control of early stage symbiotic interactions.
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Affiliation(s)
- Paula Bellés-Sancho
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Yilei Liu
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Benjamin Heiniger
- Agroscope, Molecular Ecology and Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Elia von Salis
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Christian H. Ahrens
- Agroscope, Molecular Ecology and Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Nicola Zamboni
- ETH Zürich, Institute of Molecular Systems Biology, Zurich, Switzerland
| | - Aurélien Bailly
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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6
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Qi M, Berry JC, Veley KW, O'Connor L, Finkel OM, Salas-González I, Kuhs M, Jupe J, Holcomb E, Glavina Del Rio T, Creech C, Liu P, Tringe SG, Dangl JL, Schachtman DP, Bart RS. Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons. THE ISME JOURNAL 2022; 16:1957-1969. [PMID: 35523959 PMCID: PMC9296637 DOI: 10.1038/s41396-022-01245-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/12/2022]
Abstract
Drought is a major abiotic stress limiting agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome diversity in the root and rhizosphere. How these changes ultimately affect plant health remains elusive. Toward this end, we combined reductionist, transitional and ecological approaches, applied to the staple cereal crop sorghum to identify key root-associated microbes that robustly affect drought-stressed plant phenotypes. Fifty-three Arabidopsis-associated bacteria were applied to sorghum seeds and their effect on root growth was monitored. Two Arthrobacter strains caused root growth inhibition (RGI) in Arabidopsis and sorghum. In the context of synthetic communities, Variovorax strains were able to protect plants from Arthrobacter-caused RGI. As a transitional system, high-throughput phenotyping was used to test the synthetic communities. During drought stress, plants colonized by Arthrobacter had reduced growth and leaf water content. Plants colonized by both Arthrobacter and Variovorax performed as well or better than control plants. In parallel, we performed a field trial wherein sorghum was evaluated across drought conditions. By incorporating data on soil properties into the microbiome analysis, we accounted for experimental noise with a novel method and were able to observe the negative correlation between the abundance of Arthrobacter and plant growth. Having validated this approach, we cross-referenced datasets from the high-throughput phenotyping and field experiments and report a list of bacteria with high confidence that positively associated with plant growth under drought stress. In conclusion, a three-tiered experimental system successfully spanned the lab-to-field gap and identified beneficial and deleterious bacterial strains for sorghum under drought.
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Affiliation(s)
- Mingsheng Qi
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Kira W Veley
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Lily O'Connor
- Donald Danforth Plant Science Center, St. Louis, MO, USA.,Washington University, St. Louis, MO, USA
| | - Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Plant and Environmental Sciences, Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Molly Kuhs
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Julietta Jupe
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Emily Holcomb
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Cody Creech
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Peng Liu
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Susannah G Tringe
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Daniel P Schachtman
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA.,Center for Plant Science Innovation, University of Nebraska - Lincoln, Lincoln, NE, USA
| | - Rebecca S Bart
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
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7
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Chen J, Yang Y, Ke Y, Chen X, Jiang X, Chen C, Xie S. Sulfonamide-metabolizing microorganisms and mechanisms in antibiotic-contaminated wetland sediments revealed by stable isotope probing and metagenomics. ENVIRONMENT INTERNATIONAL 2022; 165:107332. [PMID: 35687947 DOI: 10.1016/j.envint.2022.107332] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Sulfonamide (SA) antibiotics are ubiquitous pollutants in livestock breeding and aquaculture wastewaters, which increases the propagation of antibiotic resistance genes. Microbes with the ability to degrade SA play important roles in SA dissipation, but their diversity and the degradation mechanism in the field remain unclear. In the present study, we employed DNA-stable isotope probing (SIP) combined with metagenomics to explore the active microorganisms and mechanisms of SA biodegradation in antibiotic-contaminated wetland sediments. DNA-SIP revealed various SA-assimilating bacteria dominated by members of Proteobacteria, such as Bradyrhizobium, Gemmatimonas, and unclassified Burkholderiaceae. Both sulfadiazine and sulfamethoxazole were dissipated mainly through the initial ipso-hydroxylation, and were driven by similar microbes. sadA gene, which encodes an NADH-dependent monooxygenase, was enriched in the 13C heavy DNA, confirming its catalytic capacity for the initial ipso-hydroxylation of SA in sediments. In addition, some genes encoding dioxygenases were also proposed to participate in SA hydroxylation and aromatic ring cleavage based on metagenomics analysis, which might play an important role in SA metabolism in the sediment ecosystem when Proteobacteria was the dominant active bacteria. Our work elucidates the ecological roles of uncultured microorganisms in their natural habitats and gives a deeper understanding of in-situ SA biodegradation mechanisms.
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Affiliation(s)
- Jianfei Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yuyin Yang
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou 510655, China
| | - Yanchu Ke
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xiuli Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xinshu Jiang
- State Key Joint Laboratory of Environment Simulation and Pollution Control (SKJLESPC), Beijing Key Laboratory for Emerging Organic Contaminants Control (BKLEOC), School of Environment, POPs Research Center, Tsinghua University, Beijing 100084, China
| | - Chao Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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8
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Diaconu I, Pârvulescu OC, Topală SL, Dobre T. Effects of process factors on performances of liquid membrane-based transfer of indole-3-acetic acid. Sci Rep 2021; 11:23427. [PMID: 34873229 PMCID: PMC8648829 DOI: 10.1038/s41598-021-02876-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/17/2021] [Indexed: 11/25/2022] Open
Abstract
The paper has aimed at studying the transfer of indole 3-acetic acid (IAA) from a feed aqueous solution to a stripping aqueous solution of NaOH using a chloroform bulk liquid membrane and trioctylamine (TOA) as a ligand (L). Initial molar concentrations of IAA in the feed phase, cIAA,F0 (10–4–10–3 kmol/m3), of TOA in the membrane phase, cL,M0 (10–2 and 10–1 kmol/m3), and of NaOH in the stripping phase, cNaOH,S0 (10–2 and 1 kmol/m3), were selected as process factors. Their effects on the final values of IAA concentration in the feed phase (cIAA,Ff) and stripping solution (cIAA,Sf), extraction efficiency (EF), distribution coefficient (KD), and recovery efficiency (ER) were quantified using multiple regression equations. Regression coefficients were determined from experimental data, i.e., cIAA,Ff,ex = 0.02–1 × 10–4 kmol/m3, cIAA,Sf,ex = 0.22–2.58 × 10–3 kmol/m3, EF,ex = 90.0–97.9%, KD,ex = 9.0–46.6, and ER,ex = 66.5–94.2%. It was found that cIAA,F0 had the most significant positive effect on cIAA,Ff and cIAA,Sf, whereas cNaOH,S0 had a major positive effect on EF, KD, and ER. A deterministic model based on mass transfer of IAA was developed and its parameters, i.e., mass transfer coefficient of IAA-L complex in the liquid membrane (0.82–11.5 × 10–7 m/s) and extraction constant (1033.9–1779.7 m3/kmol), were regressed from experimental data. The effect of cL,M0 on both parameters was significant.
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Affiliation(s)
- Ioana Diaconu
- Department of Analytical Chemistry and Environmental Engineering, University POLITEHNICA of Bucharest, 1-6 Gheorghe Polizu, 011061, Bucharest, Romania
| | - Oana Cristina Pârvulescu
- Department of Chemical and Biochemical Engineering, University POLITEHNICA of Bucharest, 1-6 Gheorghe Polizu, 011061, Bucharest, Romania.
| | - Sorina Laura Topală
- Department of Chemical and Biochemical Engineering, University POLITEHNICA of Bucharest, 1-6 Gheorghe Polizu, 011061, Bucharest, Romania
| | - Tănase Dobre
- Department of Chemical and Biochemical Engineering, University POLITEHNICA of Bucharest, 1-6 Gheorghe Polizu, 011061, Bucharest, Romania
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