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Deng RX, Li HL, Sheng CL, Wang W, Hu HB, Zhang XH. Characterization of Lomofungin Gene Cluster Enables the Biosynthesis of Related Phenazine Derivatives. ACS Synth Biol 2024. [PMID: 39250825 DOI: 10.1021/acssynbio.4c00394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Phenazine-based small molecules are nitrogen-containing heterocyclic compounds with diverse bioactivities and electron transfer properties that exhibit promising applications in pharmaceutical and electrochemical industries. However, the biosynthetic mechanism of highly substituted natural phenazines remains poorly understood. In this study, we report the direct cloning and heterologous expression of the lomofungin biosynthetic gene cluster (BGC) from Streptomyces lomondensis S015. Reconstruction and overexpression of the BGCs in Streptomyces coelicolor M1152 resulted in eight phenazine derivatives including two novel hybrid phenazine metabolites, and the biosynthetic pathway of lomofungin was proposed. Furthermore, gene deletion suggested that NAD(P)H-dependent oxidoreductase gene lomo14 is a nonessential gene in the biosynthesis of lomofungin. Cytotoxicity evaluation of the isolated phenazines and lomofungin was performed. Specifically, lomofungin shows substantial inhibition against two human cancer cells, HCT116 and 5637. These results provide insights into the biosynthetic mechanism of lomofungin, which will be useful for the directed biosynthesis of natural phenazine derivatives.
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Affiliation(s)
- Ru-Xiang Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hui-Ling Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chao-Lan Sheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong-Bo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- National Experimental Teaching Center for Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue-Hong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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2
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Lin X, Xu G, Li Y, Yu Y. Chemical fertilizers promote dissemination of ARGs in maize rhizosphere: An overlooked risk revealed after 37-year traditional agriculture practice. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 941:173737. [PMID: 38844214 DOI: 10.1016/j.scitotenv.2024.173737] [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: 03/28/2024] [Revised: 06/01/2024] [Accepted: 06/01/2024] [Indexed: 06/10/2024]
Abstract
Bacterial communities in soil and rhizosphere maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs and antibiotic resistant bacteria (ARB) are well-characterized under traditional farming practices. Here we compared the ARG profiles of maize rhizosphere and their bulk soils using metagenomic analysis to identify the ARG dissemination and explored the potential impact of chemical fertilization on ARB. Results showed a relatively lower abundance but higher diversity of ARGs under fertilization than straw-return. Moreover, the abundance and diversity of MGEs were significantly promoted by chemical fertilizer inputs in the rhizosphere compared to bulk soil. Machine learning and bipartite networks identified three bacterial genera (Pseudomonas, Bacillus and Streptomyces) as biomarkers for ARG accumulation. Thus we cultured 509 isolates belonging to these three genera from the rhizosphere and tested their antimicrobial susceptibility, and found that multi-resistance was frequently observed among Pseudomonas isolates. Assembly-based tracking explained that ARGs and four class I integrons (LR134330, LS998783, CP065848, LT883143) were co-occurred among contigs from Pseudomonas sp. Chemical fertilizers may shape the resistomes of maize rhizosphere, highlighting that rhizosphere carried multidrug-resistant Pseudomonas isolates, which may pose a risk to animal and human health. This study adds knowledge of long-term chemical fertilization on ARG dissemination in farmland systems and provides information for decision-making in agricultural production and monitoring.
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Affiliation(s)
- Xiaolong Lin
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; School of Agriculture, Sun Yat-sen University, Guangzhou 510275, China
| | - Guanghui Xu
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yanjun Li
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yong Yu
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
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3
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Basinski JJ, Bone SE, Klein AR, Thongsomboon W, Mitchell V, Shukle JT, Druschel GK, Thompson A, Aristilde L. Unraveling iron oxides as abiotic catalysts of organic phosphorus recycling in soil and sediment matrices. Nat Commun 2024; 15:5930. [PMID: 39025840 PMCID: PMC11258345 DOI: 10.1038/s41467-024-47931-z] [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: 07/15/2023] [Accepted: 04/16/2024] [Indexed: 07/20/2024] Open
Abstract
In biogeochemical phosphorus cycling, iron oxide minerals are acknowledged as strong adsorbents of inorganic and organic phosphorus. Dephosphorylation of organic phosphorus is attributed only to biological processes, but iron oxides could also catalyze this reaction. Evidence of this abiotic catalysis has relied on monitoring products in solution, thereby ignoring iron oxides as both catalysts and adsorbents. Here we apply high-resolution mass spectrometry and X-ray absorption spectroscopy to characterize dissolved and particulate phosphorus species, respectively. In soil and sediment samples reacted with ribonucleotides, we uncover the abiotic production of particulate inorganic phosphate associated specifically with iron oxides. Reactions of various organic phosphorus compounds with the different minerals identified in the environmental samples reveal up to ten-fold greater catalytic reactivities with iron oxides than with silicate and aluminosilicate minerals. Importantly, accounting for inorganic phosphate both in solution and mineral-bound, the dephosphorylarion rates of iron oxides were within reported enzymatic rates in soils. Our findings thus imply a missing abiotic axiom for organic phosphorus mineralization in phosphorus cycling.
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Affiliation(s)
- Jade J Basinski
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Sharon E Bone
- Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Annaleise R Klein
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, Clayton, VIC, Australia
| | - Wiriya Thongsomboon
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
- Department of Chemistry, Mahasarakham University, Mahasarakham, Thailand
| | - Valerie Mitchell
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, Clayton, VIC, Australia
| | - John T Shukle
- Department of Earth Sciences, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
- ZevRoss Spatial Analysis, Ithaca, NY, USA
| | - Gregory K Druschel
- Department of Earth Sciences, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Aaron Thompson
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA
| | - Ludmilla Aristilde
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA.
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4
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Zhang K, Li H, Wu X, Zhang D, Li Z. Positron Emission Tomography of Nitric Oxide by a Specific Radical-Generating Dihydropyridine Tracer. ACS Sens 2024; 9:2793-2800. [PMID: 38820066 DOI: 10.1021/acssensors.4c00453] [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] [Indexed: 06/02/2024]
Abstract
Nitric oxide (NO) plays a pivotal role as a biological signaling molecule, presenting challenges in its specific detection and differentiation from other reactive nitrogen and oxygen species within living organisms. Herein, a 18F-labeled (fluorine-18, t1/2 = 109.7 min) small-molecule tracer dimethyl 4-(4-(4-[18F]fluorobutoxy)benzyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate ([18F]BDHP) is developed based on the dihydropyridine scaffold for positron emission tomography (PET) imaging of NO in vivo. [18F]BDHP exhibits a highly sensitive and efficient C-C cleavage reaction specifically triggered by NO under physiological conditions, leading to the production of a 18F-labeled radical that is readily retained within the cells. High uptakes of [18F]BDHP are found within and around NO-generating cells, such as macrophages treated with lipopolysaccharide or benzo(a)pyrene. MicroPET/CT imaging of arthritic animal model mice reveals distinct tracer accumulation in the arthritic legs, showcasing a higher distribution of NO compared with the control legs. In summary, a specific radical-generating dihydropyridine tracer with a unique radical retention strategy has been established for the marking of NO in real-time in vivo.
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Affiliation(s)
- Kaiqiang Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Center for Molecular Imaging and Translational Medicine, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen, Fujian 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, Fujian 361102, China
| | - Hua Li
- State Key Laboratory of Vaccines for Infectious Diseases, Center for Molecular Imaging and Translational Medicine, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen, Fujian 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, Fujian 361102, China
| | - Xiaowei Wu
- State Key Laboratory of Vaccines for Infectious Diseases, Center for Molecular Imaging and Translational Medicine, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen, Fujian 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, Fujian 361102, China
| | - Deliang Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Center for Molecular Imaging and Translational Medicine, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen, Fujian 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, Fujian 361102, China
- Department of Nuclear Medicine, Xiang'an Hospital affiliated to Xiamen University, Xiamen, Fujian 361005, China
| | - Zijing Li
- State Key Laboratory of Vaccines for Infectious Diseases, Center for Molecular Imaging and Translational Medicine, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen, Fujian 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, Fujian 361102, China
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5
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Yang X, Liu C, Liang C, Wang T, Tian J. The Phosphorus-Iron Nexus: Decoding the Nutrients Interaction in Soil and Plant. Int J Mol Sci 2024; 25:6992. [PMID: 39000100 PMCID: PMC11241702 DOI: 10.3390/ijms25136992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 06/25/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
Phosphorus (P) and iron (Fe) are two essential mineral nutrients in plant growth. It is widely observed that interactions of P and Fe could influence their availability in soils and affect their homeostasis in plants, which has received significant attention in recent years. This review presents a summary of latest advances in the activation of insoluble Fe-P complexes by soil properties, microorganisms, and plants. Furthermore, we elucidate the physiological and molecular mechanisms underlying how plants adapt to Fe-P interactions. This review also discusses the current limitations and presents potential avenues for promoting sustainable agriculture through the optimization of P and Fe utilization efficiency in crops.
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Affiliation(s)
| | | | | | - Tianqi Wang
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (X.Y.); (C.L.); (C.L.); (J.T.)
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6
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Cao M, Wang F, Ma S, Bashir S, Liu S, Sun K, Xing B. Deciphering the Impact of ZnO Nanoparticles and a Sunscreen Product Containing ZnO on Phosphorus Dynamics and Release in Chlorella pyrenoidosa in Aquatic Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:10262-10274. [PMID: 38809112 DOI: 10.1021/acs.est.4c01126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Zinc oxide nanoparticles (ZnO NPs) expedite the conversion of organic phosphorus (OP) into PO4-P (Pi), facilitating phosphorus (P) absorption by algae. Our study explored the mechanisms of converting OP (2-aminoethylphosphonic acid (AEP) and β-glycerol phosphate (β-GP)) into Pi in Chlorella pyrenoidosa under P deficiency with sunscreen and ZnO NPs. Cell density followed the order of K2HPO4 > β-GP+ZnO > β-GP > AEP+ZnO > AEP > P-free. ZnO NPs promoted the conversion of β-GP, containing C-O-P bonds (0.028-0.041 mg/L), into Pi more efficiently than AEP, which possesses C-P bonds (0.022-0.037 mg/L). Transcriptomics revealed Pi transport/metabolism (phoB (3.99-12.01 fold), phoR (2.20-5.50 fold), ppa (4.49-10.40 fold), and ppk (2.50-5.40 fold)) and phospholipid metabolism (SQD1 (1.85-2.79 fold), SQD2 (2.60-6.53 fold), MGD (2.13-3.21 fold), and DGD (4.08-7.56 fold)) were up-regulated compared to K2HPO4. 31P nuclear magnetic resonance spectroscopy identified intracellular P as polyphosphate, orthophosphate, and pyrophosphate. Synchrotron radiation-based X-ray near-edge structure spectroscopy indicated that K2HPO4 and Zn3(PO4)2 in β-GP+ZnO were increased by 8.09% and 7.28% compared to AEP+ZnO, suggesting superior P storage in β-GP+ZnO. Overall, ZnO NPs improved photoinduced electron-hole pair separation and charge separation efficiency and amplified the ·OH and ·O2- levels, promoting OP photoconversion into Pi and algae growth.
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Affiliation(s)
- Manman Cao
- School of Environment, Beijing Normal University, 19 Xinjiekouwai Street Beijing 100875, China
| | - Fei Wang
- School of Environment, Beijing Normal University, 19 Xinjiekouwai Street Beijing 100875, China
| | - Shuai Ma
- School of Environment, Beijing Normal University, 19 Xinjiekouwai Street Beijing 100875, China
| | - Safdar Bashir
- Department of Soil and Environmental Sciences, Ghazi University, Dera Ghazi Khan 32000, Pakistan
| | - Shuhu Liu
- Laboratory of Synchrotron Radiation, Institute of High Energy Physics, The Chinese Academy of Sciences, Beijing 100039, China
| | - Ke Sun
- School of Environment, Beijing Normal University, 19 Xinjiekouwai Street Beijing 100875, China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst Massachusetts 01003, United States
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7
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Tinoco-Tafolla HA, López-Hernández J, Ortiz-Castro R, López-Bucio J, Reyes de la Cruz H, Campos-García J, López-Bucio JS. Sucrose supplements modulate the Pseudomonas chlororaphis-Arabidopsis thaliana interaction via decreasing the production of phenazines and enhancing the root auxin response. JOURNAL OF PLANT PHYSIOLOGY 2024; 297:154259. [PMID: 38705079 DOI: 10.1016/j.jplph.2024.154259] [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: 10/23/2023] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/07/2024]
Abstract
Management of the plant microbiome may help support food needs for the human population. Bacteria influence plants through enhancing nutrient uptake, metabolism, photosynthesis, biomass production and/or reinforcing immunity. However, information into how these microbes behave under different growth conditions is missing. In this work, we tested how carbon supplements modulate the interaction of Pseudomonas chlororaphis with Arabidopsis thaliana. P. chlororaphis streaks strongly repressed primary root growth, lateral root formation and ultimately, biomass production. Noteworthy, increasing sucrose availability into the media from 0 to 2.4% restored plant growth and promoted lateral root formation in bacterized seedlings. This effect could not be observed by supplementing sucrose to leaves only, indicating that the interaction was strongly modulated by bacterial access to sugar. Total phenazine content decreased in the bacteria grown in high (2.4%) sucrose medium, and conversely, the expression of phzH and pslA genes were diminished by sugar supply. Pyocyanin antagonized the promoting effects of sucrose in lateral root formation and biomass production in inoculated seedlings, indicating that this virulence factor accounts for growth repression during the plant-bacterial interaction. Defence reporter transgenes PR-1::GUS and LOX2::GUS were induced in leaves, while the expression of the auxin-inducible, synthetic reporter gene DR5::GUS was enhanced in the roots of bacterized seedlings at low and high sucrose treatments, which suggests that growth/defence trade-offs in plants are critically modulated by P. chlororaphis. Collectively, our data suggest that bacterial carbon nutrition controls the outcome of the relation with plants.
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Affiliation(s)
- Hugo Alejandro Tinoco-Tafolla
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, C.P. 58030, Morelia, Michoacán, Mexico
| | - José López-Hernández
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, C.P. 58030, Morelia, Michoacán, Mexico
| | - Randy Ortiz-Castro
- Red de Estudios Moleculares Avanzados, Clúster BioMimic®, Instituto de Ecología, Carretera Antigua a Coatepec 351, El Haya, A.C 91073 Veracruz, Mexico
| | - José López-Bucio
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, C.P. 58030, Morelia, Michoacán, Mexico
| | - Homero Reyes de la Cruz
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, C.P. 58030, Morelia, Michoacán, Mexico
| | - Jesús Campos-García
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, C.P. 58030, Morelia, Michoacán, Mexico
| | - Jesús Salvador López-Bucio
- Catedrático (IXM) CONAHCYT-Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, C.P. 58030, Morelia, Michoacán, Mexico.
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8
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Qiu GW, Zheng WC, Yang HM, Wang YY, Qi X, Huang D, Dai GZ, Shi H, Price NM, Qiu BS. Phosphorus deficiency alleviates iron limitation in Synechocystis cyanobacteria through direct PhoB-mediated gene regulation. Nat Commun 2024; 15:4426. [PMID: 38789507 PMCID: PMC11126600 DOI: 10.1038/s41467-024-48847-4] [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: 09/14/2023] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Iron and phosphorus are essential nutrients that exist at low concentrations in surface waters and may be co-limiting resources for phytoplankton growth. Here, we show that phosphorus deficiency increases the growth of iron-limited cyanobacteria (Synechocystis sp. PCC 6803) through a PhoB-mediated regulatory network. We find that PhoB, in addition to its well-recognized role in controlling phosphate homeostasis, also regulates key metabolic processes crucial for iron-limited cyanobacteria, including ROS detoxification and iron uptake. Transcript abundances of PhoB-targeted genes are enriched in samples from phosphorus-depleted seawater, and a conserved PhoB-binding site is widely present in the promoters of the target genes, suggesting that the PhoB-mediated regulation may be highly conserved. Our findings provide molecular insights into the responses of cyanobacteria to simultaneous iron/phosphorus nutrient limitation.
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Affiliation(s)
- Guo-Wei Qiu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Wen-Can Zheng
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Hao-Ming Yang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Yu-Ying Wang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Xing Qi
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Da Huang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Guo-Zheng Dai
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Neil M Price
- Department of Biology, McGill University, 1205 Docteur Penfield, Montreal, Québec, H3A 1B1, Canada
| | - Bao-Sheng Qiu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China.
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9
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Tsypin LMZ, Saunders SH, Chen AW, Newman DK. Genetically dissecting the electron transport chain of a soil bacterium reveals a generalizable mechanism for biological phenazine-1-carboxylic acid oxidation. PLoS Genet 2024; 20:e1011064. [PMID: 38709821 PMCID: PMC11108179 DOI: 10.1371/journal.pgen.1011064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 05/21/2024] [Accepted: 03/25/2024] [Indexed: 05/08/2024] Open
Abstract
The capacity for bacterial extracellular electron transfer via secreted metabolites is widespread in natural, clinical, and industrial environments. Recently, we discovered the biological oxidation of phenazine-1-carboxylic acid (PCA), the first example of biological regeneration of a naturally produced extracellular electron shuttle. However, it remained unclear how PCA oxidation was catalyzed. Here, we report the mechanism, which we uncovered by genetically perturbing the branched electron transport chain (ETC) of the soil isolate Citrobacter portucalensis MBL. Biological PCA oxidation is coupled to anaerobic respiration with nitrate, fumarate, dimethyl sulfoxide, or trimethylamine-N-oxide as terminal electron acceptors. Genetically inactivating the catalytic subunits for all redundant complexes for a given terminal electron acceptor abolishes PCA oxidation. In the absence of quinones, PCA can still donate electrons to certain terminal reductases, albeit much less efficiently. In C. portucalensis MBL, PCA oxidation is largely driven by flux through the ETC, which suggests a generalizable mechanism that may be employed by any anaerobically respiring bacterium with an accessible cytoplasmic membrane. This model is supported by analogous genetic experiments during nitrate respiration by Pseudomonas aeruginosa.
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Affiliation(s)
- Lev M. Z. Tsypin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Scott H. Saunders
- Green Center for Systems Biology—Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Allen W. Chen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
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10
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Conaway A, Todorovic I, Mould DL, Hogan DA. Loss of LasR function leads to decreased repression of Pseudomonas aeruginosa PhoB activity at physiological phosphate concentrations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.586856. [PMID: 38585852 PMCID: PMC10996656 DOI: 10.1101/2024.03.27.586856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
While the Pseudomonas aeruginosa LasR transcription factor plays a role in quorum sensing (QS) across phylogenetically-distinct lineages, isolates with loss-of-function mutations in lasR (LasR- strains) are commonly found in diverse settings including infections where they are associated with worse clinical outcomes. In LasR- strains, the transcription factor RhlR, which is controlled by LasR, can be alternately activated in low inorganic phosphate (Pi) concentrations via the two-component system PhoR-PhoB. Here, we demonstrate a new link between LasR and PhoB in which the absence of LasR increases PhoB activity at physiological Pi concentrations and raises the Pi concentration necessary for PhoB inhibition. PhoB activity was also less repressed by Pi in mutants lacking different QS regulators (RhlR and PqsR) and in mutants lacking genes required for the production of QS-regulated phenazines suggesting that decreased phenazine production was one reason for decreased PhoB repression by Pi in LasR- strains. In addition, the CbrA-CbrB two-component system, which is elevated in LasR- strains, was necessary for reduced PhoB repression by Pi and a Δcrc mutant, which lacks the CbrA-CbrB-controlled translational repressor, activated PhoB at higher Pi concentrations than the wild type. The ΔlasR mutant had a PhoB-dependent growth advantage in a medium with no added Pi and increased virulence-determinant gene expression in a medium with physiological Pi, in part through reactivation of QS. This work suggests PhoB activity may contribute to the virulence of LasR- P. aeruginosa and subsequent clinical outcomes.
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Affiliation(s)
- Amy Conaway
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Igor Todorovic
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Dallas L. Mould
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
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11
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Meyerowitz JT, Larsson EM, Murray RM. Development of Cell-Free Transcription-Translation Systems in Three Soil Pseudomonads. ACS Synth Biol 2024; 13:530-537. [PMID: 38319019 DOI: 10.1021/acssynbio.3c00468] [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] [Indexed: 02/07/2024]
Abstract
In vitro transcription-translation (TX-TL) can enable faster engineering of biological systems. This speed-up can be significant, especially in difficult-to-transform chassis. This work shows the successful development of TX-TL systems using three soil-derived wild-type Pseudomonads known to promote plant growth: Pseudomonas synxantha, Pseudomonas chlororaphis, and Pseudomonas aureofaciens. All three species demonstrated multiple sonication, runoff, and salt conditions producing detectable protein synthesis. One of these new TX-TL systems, P. synxantha, demonstrated a maximum protein yield of 2.5 μM at 125 proteins per DNA template, a maximum protein synthesis rate of 20 nM/min, and a range of DNA concentrations with a linear correspondence with the resulting protein synthesis. A set of different constitutive promoters driving mNeonGreen expression were tested in TX-TL and integrated into the genome, showing similar normalized strengths for in vivo and in vitro fluorescence. This correspondence between the TX-TL-derived promoter strength and the in vivo promoter strength indicates that these lysate-based cell-free systems can be used to characterize and engineer biological parts without genomic integration, enabling a faster design-build-test cycle.
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Affiliation(s)
- Joseph T Meyerowitz
- Division of Biology and Biological Engineering, California Institute of Technology 1200 E. California Blvd, MC 138-78, Pasadena, California 91125, United States
| | - Elin M Larsson
- Division of Biology and Biological Engineering, California Institute of Technology 1200 E. California Blvd, MC 138-78, Pasadena, California 91125, United States
| | - Richard M Murray
- Division of Biology and Biological Engineering, California Institute of Technology 1200 E. California Blvd, MC 138-78, Pasadena, California 91125, United States
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12
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Ragland CJ, Shih KY, Dinneny JR. Choreographing root architecture and rhizosphere interactions through synthetic biology. Nat Commun 2024; 15:1370. [PMID: 38355570 PMCID: PMC10866969 DOI: 10.1038/s41467-024-45272-5] [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: 07/17/2023] [Accepted: 01/18/2024] [Indexed: 02/16/2024] Open
Abstract
Climate change is driving extreme changes to the environment, posing substantial threats to global food security and bioenergy. Given the direct role of plant roots in mediating plant-environment interactions, engineering the form and function of root systems and their associated microbiota may mitigate these effects. Synthetic genetic circuits have enabled sophisticated control of gene expression in microbial systems for years and a surge of advances has heralded the extension of this approach to multicellular plant species. Targeting these tools to affect root structure, exudation, and microbe activity on root surfaces provide multiple strategies for the advancement of climate-ready crops.
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Affiliation(s)
- Carin J Ragland
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Kevin Y Shih
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
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13
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Larsson EM, Murray RM, Newman DK. Engineering the Soil Bacterium Pseudomonas synxantha 2-79 into a Ratiometric Bioreporter for Phosphorus Limitation. ACS Synth Biol 2024; 13:384-393. [PMID: 38165130 DOI: 10.1021/acssynbio.3c00642] [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] [Indexed: 01/03/2024]
Abstract
Microbial bioreporters hold promise for addressing challenges in medical and environmental applications. However, the difficulty in ensuring their stable persistence and function within the target environment remains a challenge. One strategy is to integrate information about the host strain and target environment into the design-build-test cycle of the bioreporter itself. Here, we present a case study for such an environmentally motivated design process by engineering the wheat commensal bacterium Pseudomonas synxantha 2-79 into a ratiometric bioreporter for phosphorus limitation. Comparative analysis showed that an exogenous P-responsive promoter outperformed its native counterparts. This reporter can selectively sense and report phosphorus limitation at plant-relevant concentrations of 25-100 μM without cross-activation from carbon or nitrogen limitation or high cell densities. Its performance is robust over a field-relevant pH range (5.8-8), and it responds only to inorganic phosphorus, even in the presence of common soil organic P. Finally, we used fluorescein-calibrated flow cytometry to assess whether the reporter's performance in shaken liquid culture predicts its performance in soil, finding that although the reporter is still functional at the bulk level, its variability in performance increases when grown in a soil slurry as compared to planktonic culture, with a fraction of the population not expressing the reporter proteins. Together, our environmentally aware design process provides an example of how laboratory bioengineering efforts can generate microbes with a greater promise to function reliably in their applied contexts.
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Affiliation(s)
- Elin M Larsson
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Richard M Murray
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, California 91125, United States
- Control and Dynamical Systems, California Institute of Technology, Pasadena, California 91125, United States
| | - Dianne K Newman
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, California 91125, United States
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California 91125, United States
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14
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Liu MD, Du Y, Koupaei SK, Kim NR, Fischer MS, Zhang W, Traxler MF. Surface-active antibiotic production as a multifunctional adaptation for postfire microorganisms. THE ISME JOURNAL 2024; 18:wrae022. [PMID: 38366029 PMCID: PMC11069360 DOI: 10.1093/ismejo/wrae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/18/2024]
Abstract
Wildfires affect soils in multiple ways, leading to numerous challenges for colonizing microorganisms. Although it is thought that fire-adapted microorganisms lie at the forefront of postfire ecosystem recovery, the specific strategies that these organisms use to thrive in burned soils remain largely unknown. Through bioactivity screening of bacterial isolates from burned soils, we discovered that several Paraburkholderia spp. isolates produced a set of unusual rhamnolipid surfactants with a natural methyl ester modification. These rhamnolipid methyl esters (RLMEs) exhibited enhanced antimicrobial activity against other postfire microbial isolates, including pyrophilous Pyronema fungi and Amycolatopsis bacteria, compared to the typical rhamnolipids made by organisms such as Pseudomonas spp. RLMEs also showed enhanced surfactant properties and facilitated bacterial motility on agar surfaces. In vitro assays further demonstrated that RLMEs improved aqueous solubilization of polycyclic aromatic hydrocarbons, which are potential carbon sources found in char. Identification of the rhamnolipid biosynthesis genes in the postfire isolate, Paraburkholderia kirstenboschensis str. F3, led to the discovery of rhlM, whose gene product is responsible for the unique methylation of rhamnolipid substrates. RhlM is the first characterized bacterial representative of a large class of integral membrane methyltransferases that are widespread in bacteria. These results indicate multiple roles for RLMEs in the postfire lifestyle of Paraburkholderia isolates, including enhanced dispersal, solubilization of potential nutrients, and inhibition of competitors. Our findings shed new light on the chemical adaptations that bacteria employ to navigate, grow, and outcompete other soil community members in postfire environments.
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Affiliation(s)
- Mira D Liu
- Department of Chemistry, University of California, Berkeley, CA 94720, United States
| | - Yongle Du
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, United States
| | - Sara K Koupaei
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, United States
| | - Nicole R Kim
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, United States
| | - Monika S Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, United States
| | - Matthew F Traxler
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, United States
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15
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Ge X, Fan Y, Zhai H, Chi J, Putnis CV, Wang L, Zhang W. Direct observations of nanoscale brushite dissolution by the concentration-dependent adsorption of phosphate or phytate. WATER RESEARCH 2024; 248:120851. [PMID: 37976955 DOI: 10.1016/j.watres.2023.120851] [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: 09/13/2023] [Revised: 11/05/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023]
Abstract
With the development of agricultural intensification, phosphorus (P) accumulation in croplands and sediments has resulted in the increasingly widespread interaction between inorganic and organic P species, which has been, previously, underestimated or even ignored. We quantified the nanoscale dissolution kinetics of sparingly soluble brushite (CaHPO4·2H2O, DCPD) over a broad range of phosphate and/or phytate concentrations by using in situ atomic force microscopy (AFM). Compared to water, we found that low concentrations of phosphate (1-1000 µM) or phytate (1-100 µM) inhibited brushite dissolution by slowing single step retraction. However, with increasing phosphate or phytate concentrations to 10 mM, there was a reverse effect of dissolution promotion at brushite-water interfaces. In situ observations of the coupled dissolution-reprecipitation showed that phosphate precipitated more readily than phytate on brushite surfaces, with the formation of amorphous calcium phosphate (ACP). For a fundamental understanding, zeta potential and in situ Raman spectroscopy (RS) revealed that the concentration-dependent dissolution is attributed to the reverse of outer-sphere to inner-sphere adsorption with increasing phosphate or phytate concentrations. In addition, the mineralization of phytate with outer-sphere adsorption by phytase was higher than that with inner-spere adsorption, and the presence of phytate delayed ACP phase transformation to hydroxylapatite (HAP). These in situ observations and analyses may fill the knowledge gaps of interaction between inorganic and organic P species in P-rich terrestrial and aquatic environments, thereby implicating their biogeochemical cycling and the associated availability.
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Affiliation(s)
- Xinfei Ge
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Yuke Fan
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Hang Zhai
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Jialin Chi
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Christine V Putnis
- Institut für Mineralogie, University of Münster, Münster 48149, Germany; School of Molecular and Life Sciences, Curtin University, Perth 6845, Australia
| | - Lijun Wang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenjun Zhang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
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16
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Burz SD, Causevic S, Dal Co A, Dmitrijeva M, Engel P, Garrido-Sanz D, Greub G, Hapfelmeier S, Hardt WD, Hatzimanikatis V, Heiman CM, Herzog MKM, Hockenberry A, Keel C, Keppler A, Lee SJ, Luneau J, Malfertheiner L, Mitri S, Ngyuen B, Oftadeh O, Pacheco AR, Peaudecerf F, Resch G, Ruscheweyh HJ, Sahin A, Sanders IR, Slack E, Sunagawa S, Tackmann J, Tecon R, Ugolini GS, Vacheron J, van der Meer JR, Vayena E, Vonaesch P, Vorholt JA. From microbiome composition to functional engineering, one step at a time. Microbiol Mol Biol Rev 2023; 87:e0006323. [PMID: 37947420 PMCID: PMC10732080 DOI: 10.1128/mmbr.00063-23] [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: 11/12/2023] Open
Abstract
SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.
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Affiliation(s)
- Sebastian Dan Burz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Senka Causevic
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Alma Dal Co
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Marija Dmitrijeva
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institut de microbiologie, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | | | | | - Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Julien Luneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Bidong Ngyuen
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Omid Oftadeh
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | | | | | - Grégory Resch
- Center for Research and Innovation in Clinical Pharmaceutical Sciences, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | - Asli Sahin
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Janko Tackmann
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Robin Tecon
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Evangelia Vayena
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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17
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Tsypin LM, Saunders SH, Chen AW, Newman DK. Genetically dissecting the electron transport chain of a soil bacterium reveals a generalizable mechanism for biological phenazine-1-carboxylic acid oxidation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.567096. [PMID: 38014283 PMCID: PMC10680695 DOI: 10.1101/2023.11.14.567096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The capacity for bacterial extracellular electron transfer via secreted metabolites is widespread in natural, clinical, and industrial environments. Recently, we discovered biological oxidation of phenazine-1-carboxylic acid (PCA), the first example of biological regeneration of a naturally produced extracellular electron shuttle. However, it remained unclear how PCA oxidation was catalyzed. Here, we report the mechanism, which we uncovered by genetically perturbing the branched electron transport chain (ETC) of the soil isolate Citrobacter portucalensis MBL. Biological PCA oxidation is coupled to anaerobic respiration with nitrate, fumarate, dimethyl sulfoxide, or trimethylamine-N-oxide as terminal electron acceptors. Genetically inactivating the catalytic subunits for all redundant complexes for a given terminal electron acceptor abolishes PCA oxidation. In the absence of quinones, PCA can still donate electrons to certain terminal reductases, albeit much less efficiently. In C. portucalensis MBL, PCA oxidation is largely driven by flux through the ETC, which suggests a generalizable mechanism that may be employed by any anaerobically respiring bacterium with an accessible cytoplasmic membrane. This model is supported by analogous genetic experiments during nitrate respiration by Pseudomonas aeruginosa.
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Affiliation(s)
- Lev M.Z. Tsypin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Scott H. Saunders
- Green Center for Systems Biology - Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Allen W. Chen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
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18
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Zhang Q, Xu N, Lei C, Chen B, Wang T, Ma Y, Lu T, Penuelas J, Gillings M, Zhu Y, Fu Z, Qian H. Metagenomic Insight into The Global Dissemination of The Antibiotic Resistome. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303925. [PMID: 37870180 PMCID: PMC10667823 DOI: 10.1002/advs.202303925] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/09/2023] [Indexed: 10/24/2023]
Abstract
The global crisis in antimicrobial resistance continues to grow. Estimating the risks of antibiotic resistance transmission across habitats is hindered by the lack of data on mobility and habitat-specificity. Metagenomic samples of 6092 are analyzed to delineate the unique core resistomes from human feces and seven other habitats. This is found that most resistance genes (≈85%) are transmitted between external habitats and human feces. This suggests that human feces are broadly representative of the global resistome and are potentially a hub for accumulating and disseminating resistance genes. The analysis found that resistance genes with ancient horizontal gene transfer (HGT) events have a higher efficiency of transfer across habitats, suggesting that HGT may be the main driver for forming unique but partly shared resistomes in all habitats. Importantly, the human fecal resistome is historically different and influenced by HGT and age. The most important routes of cross-transmission of resistance are from the atmosphere, buildings, and animals to humans. These habitats should receive more attention for future prevention of antimicrobial resistance. The study will disentangle transmission routes of resistance genes between humans and other habitats in a One Health framework and can identify strategies for controlling the ongoing dissemination and antibiotic resistance.
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Affiliation(s)
- Qi Zhang
- College of EnvironmentZhejiang University of TechnologyHangzhou310032P. R. China
| | - Nuohan Xu
- College of EnvironmentZhejiang University of TechnologyHangzhou310032P. R. China
| | - Chaotang Lei
- College of EnvironmentZhejiang University of TechnologyHangzhou310032P. R. China
| | - Bingfeng Chen
- College of EnvironmentZhejiang University of TechnologyHangzhou310032P. R. China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang ProvinceHangzhou310012P. R. China
| | - Yunting Ma
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang ProvinceHangzhou310012P. R. China
| | - Tao Lu
- College of EnvironmentZhejiang University of TechnologyHangzhou310032P. R. China
| | - Josep Penuelas
- CSICGlobal Ecology Unit CREAF‐CSIC‐UABBellaterraBarcelonaCatalonia08193Spain
- CREAFCampus Universitat Autònoma de BarcelonaCerdanyola del VallèsBarcelonaCatalonia08193Spain
| | - Michael Gillings
- ARC Centre of Excellence in Synthetic BiologySchool of Natural SciencesMacquarie UniversitySydneyNSW2109Australia
| | - Yong‐Guan Zhu
- Key Laboratory of Urban Environment and HealthInstitute of Urban EnvironmentChinese Academy of SciencesXiamen361021P. R. China
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐environmental SciencesChinese Academy of SciencesBeijing100085P. R. China
| | - Zhengwei Fu
- College of EnvironmentZhejiang University of TechnologyHangzhou310032P. R. China
- College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhou310032P. R. China
| | - Haifeng Qian
- College of EnvironmentZhejiang University of TechnologyHangzhou310032P. R. China
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19
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Holland M, Farinella DN, Cruz-Lorenzo E, Laubscher MI, Doakes DA, Ramos MA, Kubota N, Levin TC. L. pneumophila resists its self-harming metabolite HGA via secreted factors and collective peroxide scavenging. mBio 2023; 14:e0120723. [PMID: 37728338 PMCID: PMC10653783 DOI: 10.1128/mbio.01207-23] [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: 05/10/2023] [Accepted: 07/25/2023] [Indexed: 09/21/2023] Open
Abstract
IMPORTANCE Before environmental opportunistic pathogens can infect humans, they must first successfully grow and compete with other microbes in nature, often via secreted antimicrobials. We previously discovered that the bacterium Legionella pneumophila, the causative agent of Legionnaires' disease, can compete with other microbes via a secreted molecule called HGA. Curiously, L. pneumophila strains that produce HGA is not wholly immune to its toxicity, making it a mystery how these bacteria can withstand the "friendly fire" of potentially self-targeting antimicrobials during inter-bacterial battles. Here, we identify several strategies that allow the high-density bacterial populations that secrete HGA to tolerate its effects. Our study clarifies how HGA works. It also points to some explanations of why it is difficult to disinfect L. pneumophila from the built environment and prevent disease outbreaks.
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Affiliation(s)
- Mische Holland
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Danielle N. Farinella
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Emily Cruz-Lorenzo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Madelyn I. Laubscher
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Darian A. Doakes
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Maria A. Ramos
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Nanami Kubota
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Tera C. Levin
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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20
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Guadarrama-Orozco KD, Perez-Gonzalez C, Kota K, Cocotl-Yañez M, Jiménez-Cortés JG, Díaz-Guerrero M, Hernández-Garnica M, Munson J, Cadet F, López-Jácome LE, Estrada-Velasco ÁY, Fernández-Presas AM, García-Contreras R. To cheat or not to cheat: cheatable and non-cheatable virulence factors in Pseudomonas aeruginosa. FEMS Microbiol Ecol 2023; 99:fiad128. [PMID: 37827541 DOI: 10.1093/femsec/fiad128] [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: 07/23/2023] [Revised: 08/30/2023] [Accepted: 10/11/2023] [Indexed: 10/14/2023] Open
Abstract
Important bacterial pathogens such as Pseudomonas aeruginosa produce several exoproducts such as siderophores, degradative enzymes, biosurfactants, and exopolysaccharides that are used extracellularly, benefiting all members of the population, hence being public goods. Since the production of public goods is a cooperative trait, it is in principle susceptible to cheating by individuals in the population who do not invest in their production, but use their benefits, hence increasing their fitness at the expense of the cooperators' fitness. Among the most studied virulence factors susceptible to cheating are siderophores and exoproteases, with several studies in vitro and some in animal infection models. In addition to these two well-known examples, cheating with other virulence factors such as exopolysaccharides, biosurfactants, eDNA production, secretion systems, and biofilm formation has also been studied. In this review, we discuss the evidence of the susceptibility of each of those virulence factors to cheating, as well as the mechanisms that counteract this behavior and the possible consequences for bacterial virulence.
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Affiliation(s)
- Katya Dafne Guadarrama-Orozco
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Caleb Perez-Gonzalez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Kokila Kota
- Ramapo College of New Jersey, Biology Department, Mahwah, NJ 07430, USA
| | - Miguel Cocotl-Yañez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Jesús Guillermo Jiménez-Cortés
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Miguel Díaz-Guerrero
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Mariel Hernández-Garnica
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Julia Munson
- Ramapo College of New Jersey, Biology Department, Mahwah, NJ 07430, USA
| | - Frederic Cadet
- PEACCEL, Artificial Intelligence Department, AI for Biologics, Paris, 75013, France
| | - Luis Esaú López-Jácome
- Laboratorio de Microbiología Clínica, División de Infectología, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, 14389 Mexico City, Mexico
| | - Ángel Yahir Estrada-Velasco
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Ana María Fernández-Presas
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
| | - Rodolfo García-Contreras
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04360 Mexico City,Mexico
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21
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Li YX, Yue SJ, Zheng YF, Huang P, Nie YF, Hao XR, Zhang HY, Wang W, Hu HB, Zhang XH. Economical Production of Phenazine-1-carboxylic Acid from Glycerol by Pseudomonas chlororaphis Using Cost-Effective Minimal Medium. BIOLOGY 2023; 12:1292. [PMID: 37887002 PMCID: PMC10604798 DOI: 10.3390/biology12101292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/19/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023]
Abstract
Phenazine compounds are widely used in agricultural control and the medicine industry due to their high inhibitory activity against pathogens and antitumor activity. The green and sustainable method of synthesizing phenazine compounds through microbial fermentation often requires a complex culture medium containing tryptone and yeast extract, and its cost is relatively high, which greatly limits the large-scale industrial production of phenazine compounds by fermentation. The aim of this study was to develop a cost-effective minimal medium for the efficient synthesis of phenazine compounds by Pseudomonas chlororaphis. Through testing the minimum medium commonly used by Pseudomonas, an ME medium for P. chlororaphis with a high production of phenazine compounds was obtained. Then, the components of the ME medium and the other medium were compared and replaced to verify the beneficial promoting effect of Fe2+ and NH4+ on phenazine compounds. A cost-effective general defined medium (GDM) using glycerol as the sole carbon source was obtained by optimizing the composition of the ME medium. Using the GDM, the production of phenazine compounds by P. chlororaphis reached 1073.5 mg/L, which was 1.3 times that achieved using a complex medium, while the cost of the GDM was only 10% that of a complex medium (e.g., the KB medium). Finally, by engineering the glycerol metabolic pathway, the titer of phenazine-1-carboxylic acid reached the highest level achieved using a minimum medium so far. This work demonstrates how we systematically analyzed and optimized the composition of the medium and integrated a metabolic engineering method to obtain the most cost-effective fermentation strategy.
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Affiliation(s)
- Yu-Xuan Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.-X.L.); (S.-J.Y.); (P.H.); (Y.-F.N.)
| | - Sheng-Jie Yue
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.-X.L.); (S.-J.Y.); (P.H.); (Y.-F.N.)
| | - Yi-Fan Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.-X.L.); (S.-J.Y.); (P.H.); (Y.-F.N.)
| | - Peng Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.-X.L.); (S.-J.Y.); (P.H.); (Y.-F.N.)
| | - Yan-Fang Nie
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.-X.L.); (S.-J.Y.); (P.H.); (Y.-F.N.)
| | - Xiang-Rui Hao
- Shanghai Nong Le Biological Products Company Limited (NLBP), Shanghai 200240, China
| | - Hong-Yan Zhang
- Shanghai Nong Le Biological Products Company Limited (NLBP), Shanghai 200240, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.-X.L.); (S.-J.Y.); (P.H.); (Y.-F.N.)
| | - Hong-Bo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.-X.L.); (S.-J.Y.); (P.H.); (Y.-F.N.)
- Shanghai Nongle Joint R&D Center on Biopesticides and Biofertilizers, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue-Hong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.-X.L.); (S.-J.Y.); (P.H.); (Y.-F.N.)
- Shanghai Nongle Joint R&D Center on Biopesticides and Biofertilizers, Shanghai Jiao Tong University, Shanghai 200240, China
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22
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Wu T, Liu Y, Zheng T, Dai Y, Li Z, Lin D. Fe-Based Nanomaterials and Plant Growth Promoting Rhizobacteria Synergistically Degrade Polychlorinated Biphenyls by Producing Extracellular Reactive Oxygen Species. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12771-12781. [PMID: 37583057 DOI: 10.1021/acs.est.3c02495] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Plant growth promoting rhizobacteria (PGPR) produce extracellular reactive oxygen species (ROS) to protect plants from external stresses. Fe-based nanomaterials can potentially interact with PGPR and synergistically degrade organic pollutants, yet they have received no study. Here, we studied how the interaction between a typical PGPR (Pseudomonas chlororaphis, JD37) and Fe-based nanomaterials facilitated the degradation of 2,4,4'-trichlorobiphenyl (PCB28), by comparing the zerovalent iron of 20 nm (nZVI20), 100 nm (nZVI100), and 5 μm; iron oxide nanomaterials (α-Fe2O3, γ-Fe2O3, and Fe3O4) of ca. 20 nm; and ferrous and ferric salts. Although all Fe materials (0.1 g L-1) alone could not degrade aqueous PCB28 (0.1 mg L-1) under dark or aerobic conditions, nZVI20, nZVI100, α-Fe2O3, and Fe2+ promoted PCB28 degradation by JD37, with the half-life of PCB28 shortened from 16.5 h by JD37 alone to 8.1 h with nZVI100 cotreatment. Mechanistically, the nanomaterials stimulated JD37 to secrete phenazine-1-carboxylic acid and accelerated the NADH/NAD+ conversion, promoting O2*- generation; JD37 increased Fe(II) dissolution from the nanomaterials, facilitating *OH generation; and the ROS gradually degraded PCB28 into benzoic acid through dihydroxy substitution, oxidation to quinone, and Michael addition. These findings provide a new strategy of nanoenabled biodegradation of organic pollutants by applying Fe-based nanomaterials and PGPR.
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Affiliation(s)
- Ting Wu
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, P. R. China
- Xi'an Center, China Geological Survey, Ministry of Natural Resources, Xi'an 710119, P. R. China
| | - Yangzhi Liu
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, P. R. China
| | - Tianying Zheng
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, P. R. China
| | - Yunbu Dai
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, P. R. China
| | - Zhongyu Li
- Xi'an Center, China Geological Survey, Ministry of Natural Resources, Xi'an 710119, P. R. China
| | - Daohui Lin
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, P. R. China
- Zhejiang Ecological Civilization Academy, Anji 313300, P. R. China
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23
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Liu MD, Du Y, Koupaei SK, Kim NR, Zhang W, Traxler MF. Surface-active antibiotic production is a multifunctional adaptation for postfire microbes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.17.553728. [PMID: 37645719 PMCID: PMC10462131 DOI: 10.1101/2023.08.17.553728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Wildfires affect soils in multiple ways, leading to numerous challenges for colonizing microbes. While it is thought that fire-adapted microbes lie at the forefront of postfire ecosystem recovery, the specific strategies that these microbes use to thrive in burned soils remain largely unknown. Through bioactivity screening of bacterial isolates from burned soils, we discovered that several Paraburkholderia spp. isolates produced a set of unusual rhamnolipid surfactants with a natural methyl ester modification. These rhamnolipid methyl esters (RLMEs) exhibited enhanced antimicrobial activity against other postfire microbial isolates, including pyrophilous Pyronema fungi and Amycolatopsis bacteria, compared to the typical rhamnolipids made by organisms such as Pseudomonas spp . RLMEs also showed enhanced surfactant properties and facilitated bacterial motility on agar surfaces. In vitro assays further demonstrated that RLMEs improved aqueous solubilization of polycyclic aromatic hydrocarbons, which are potential carbon sources found in char. Identification of the rhamnolipid biosynthesis genes in the postfire isolate, Paraburkholderia caledonica str. F3, led to the discovery of rhlM , whose gene product is responsible for the unique methylation of rhamnolipid substrates. RhlM is the first characterized bacterial representative of a large class of integral membrane methyltransferases that are widespread in bacteria. These results indicate multiple roles for RLMEs in the postfire lifestyle of Paraburkholderia isolates, including enhanced dispersal, solubilization of potential nutrients, and inhibition of competitors. Our findings shed new light on the chemical adaptations that bacteria employ in order to navigate, grow, and outcompete other soil community members in postfire environments. Significance Statement Wildfires are increasing in frequency and intensity at a global scale. Microbes are the first colonizers of soil after fire events, but the adaptations that help these organisms survive in postfire environments are poorly understood. In this work, we show that a bacterium isolated from burned soil produces an unusual rhamnolipid biosurfactant that exhibits antimicrobial activity, enhances motility, and solubilizes potential nutrients derived from pyrolyzed organic matter. Collectively, our findings demonstrate that bacteria leverage specialized metabolites with multiple functions to meet the demands of life in postfire environments. Furthermore, this work reveals the potential of probing perturbed environments for the discovery of unique compounds and enzymes.
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24
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Smieska L, Guerinot ML, Olson Hoal K, Reid M, Vatamaniuk O. Synchrotron science for sustainability: life cycle of metals in the environment. Metallomics 2023; 15:mfad041. [PMID: 37370221 DOI: 10.1093/mtomcs/mfad041] [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: 03/25/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023]
Abstract
The movement of metals through the environment links together a wide range of scientific fields: from earth sciences and geology as weathering releases minerals; to environmental sciences as metals are mobilized and transformed, cycling through soil and water; to biology as living things take up metals from their surroundings. Studies of these fundamental processes all require quantitative analysis of metal concentrations, locations, and chemical states. Synchrotron X-ray tools can address these requirements with high sensitivity, high spatial resolution, and minimal sample preparation. This perspective describes the state of fundamental scientific questions in the lifecycle of metals, from rocks to ecosystems, from soils to plants, and from environment to animals. Key X-ray capabilities and facility infrastructure for future synchrotron-based analytical resources serving these areas are summarized, and potential opportunities for future experiments are explored.
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Affiliation(s)
- Louisa Smieska
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
| | - Mary Lou Guerinot
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Karin Olson Hoal
- Department of Earth & Atmospheric Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Matthew Reid
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Olena Vatamaniuk
- School of Integrative Plant Science Plant Biology Section, Cornell University, Ithaca NY 14853, USA
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25
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Thalhammer KO, Newman DK. A phenazine-inspired framework for identifying biological functions of microbial redox-active metabolites. Curr Opin Chem Biol 2023; 75:102320. [PMID: 37201291 PMCID: PMC10524139 DOI: 10.1016/j.cbpa.2023.102320] [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: 01/18/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/20/2023]
Abstract
While the list of small molecules known to be secreted by environmental microbes continues to grow, our understanding of their in situ biological functions remains minimal. The time has come to develop a framework to parse the meaning of these "secondary metabolites," which are ecologically ubiquitous and have direct applications in medicine and biotechnology. Here, we focus on a particular subset of molecules, redox active metabolites (RAMs), and review the well-studied phenazines as archetypes of this class. We argue that efforts to characterize the chemical, physical and biological makeup of the microenvironments, wherein these molecules are produced, coupled with measurements of the molecules' basic chemical properties, will enable significant progress in understanding the precise roles of novel RAMs.
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Affiliation(s)
- Korbinian O Thalhammer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Dianne K Newman
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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26
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Bhattacharyya A, Mavrodi O, Bhowmik N, Weller D, Thomashow L, Mavrodi D. Bacterial biofilms as an essential component of rhizosphere plant-microbe interactions. METHODS IN MICROBIOLOGY 2023; 53:3-48. [PMID: 38415193 PMCID: PMC10898258 DOI: 10.1016/bs.mim.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Affiliation(s)
- Ankita Bhattacharyya
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Olga Mavrodi
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Niladri Bhowmik
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - David Weller
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Linda Thomashow
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Dmitri Mavrodi
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
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27
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Yang G, Hou T, Lin A, Xia X, Quan X, Chen Z, Zhuang L. Sub-inhibitory concentrations of ampicillin affect microbial Fe(III) oxide reduction. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131131. [PMID: 36917911 DOI: 10.1016/j.jhazmat.2023.131131] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/01/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
Antibiotics are ubiquitous in the iron-rich environments but their roles in microbial reduction of Fe(III) oxides are still unclear. Using ampicillin and Geobacter soli, this study investigated the underlying mechanism by which antibiotic regulated microbial reduction of Fe(III) oxides. Results showed that sub-minimal inhibitory concentrations (sub-MIC) of ampicillin significantly affected ferrihydrite reduction by G. soli, with a stimulatory effect at 1/64 and 1/32 MIC and an inhibitory effect at 1/8 MIC. Increasing ampicillin concentration resulted in increasing cell length and decreasing bacterial zeta potential that were beneficial for ferrihydrite reduction, and decreasing outer membrane permeability that was unfavorable for ferrihydrite reduction. The respiratory metabolism ability was enhanced by 1/64 and 1/32 MIC ampicillin and reduced by 1/8 MIC ampicillin, which was also responsible for regulation of ferrihydrite reduction by ampicillin. The ferrihydrite reduction showed a positive correlation with the redox activity of extracellular polymeric substances (EPS) which was tied to the cytochrome/polysaccharide ratio and the content of α-helices and β-sheet in EPS. These results suggested that ampicillin regulated microbial Fe(III) oxide reduction through modulating the bacterial morphology, metabolism activity and extracellular electron transfer ability. Our findings provide new insights into the environmental factors regulating biogeochemical cycling of iron.
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Affiliation(s)
- Guiqin Yang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Tiqun Hou
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Annian Lin
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Xue Xia
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Xiaoyun Quan
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Zhili Chen
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Li Zhuang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China.
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28
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Zhang K, Ho KP, Chatterjee A, Park G, Li Z, Catalano JG, Parker KM. RNA Hydrolysis at Mineral-Water Interfaces. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37216349 DOI: 10.1021/acs.est.3c01407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
As an essential biomolecule for life, RNA is ubiquitous across environmental systems where it plays a central role in biogeochemical processes and emerging technologies. The persistence of RNA in soils and sediments is thought to be limited by enzymatic or microbial degradation, which occurs on timescales that are orders of magnitude faster than known abiotic pathways. Herein, we unveil a previously unreported abiotic pathway by which RNA rapidly hydrolyzes on the timescale of hours upon adsorption to iron (oxyhydr)oxide minerals such as goethite (α-FeOOH). The hydrolysis products were consistent with iron present in the minerals acting as a Lewis acid to accelerate sequence-independent hydrolysis of phosphodiester bonds comprising the RNA backbone. In contrast to acid- or base-catalyzed RNA hydrolysis in solution, mineral-catalyzed hydrolysis was fastest at circumneutral pH, which allowed for both sufficient RNA adsorption and hydroxide concentration. In addition to goethite, we observed that RNA hydrolysis was also catalyzed by hematite (α-Fe2O3) but not by aluminum-containing minerals (e.g., montmorillonite). Given the extensive adsorption of nucleic acids to environmental surfaces, we anticipate previously overlooked mineral-catalyzed hydrolysis of RNA may be prevalent particularly in iron-rich soils and sediments, which must be considered across biogeochemical applications of nucleic acid analysis in environmental systems.
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Affiliation(s)
- Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kun-Pu Ho
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Grace Park
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Zhiyao Li
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jeffrey G Catalano
- Department of Earth & Planetary Sciences, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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29
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Xu N, Shen Y, Jiang L, Jiang B, Li Y, Yuan Q, Zhang Y. Occurrence and risk levels of antibiotic pollution in the coastal waters of eastern China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27500-5. [PMID: 37162672 DOI: 10.1007/s11356-023-27500-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/04/2023] [Indexed: 05/11/2023]
Abstract
In order to preliminarily explore the distribution of antibiotic pollution in the coastal waters of eastern China, the concentrations of 13 antibiotics in 5 representative coastal rivers in Jiangsu and 21 sampling sites in the coastal waters of Jiangsu were analyzed. The total antibiotic concentrations in the 5 rivers ranged from 33.14 to 417.78 ng L-1, and the total antibiotic concentrations in the 21 sampling sites ranged from 0.90 to 86.33 ng L-1. Macrolides exhibited the highest total concentration and the maximum detection frequency in both coastal rivers and the coastal waters. The concentrations of antibiotics in a sampling site decreased as the distance of the sampling site from the coastline increased, indicating that river inputs are important sources of antibiotic pollution in the coastal waters of Jiangsu. The detection frequencies of roxithromycin, lincomycin, azithromycin, and sulfamethoxazole in the rivers and sampling sites were above 70%. Correlation analysis showed that the concentrations of antibiotics were positively correlated with the levels of chemical oxygen demand, total phosphorus, and total nitrogen. Risk assessments revealed that roxithromycin and ofloxacin posed medium ecological and resistance risks, respectively, to the most sensitive aquatic organisms in the coastal waters of Jiangsu. The results of this study highlight the significance of monitoring and controlling the concentrations of antibiotic contaminants in the coastal waters of Jiangsu.
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Affiliation(s)
- Ning Xu
- School of Environmental Science and Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China
| | - Yi Shen
- School of Environmental Science and Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China
| | - Lei Jiang
- School of Environmental Science and Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China
| | - Bin Jiang
- School of Environmental Science and Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China
| | - Ying Li
- School of Environmental Science and Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China
| | - Qingbin Yuan
- School of Environmental Science and Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China
| | - Yunhai Zhang
- School of Environmental Science and Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China.
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30
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Wang Y, Ni K, Zhang Z, Xu N, Lei C, Chen B, Zhang Q, Sun L, Chen Y, Lu T, Qian H. Metatranscriptome deciphers the effects of non-antibiotic antimicrobial agents on antibiotic resistance and virulence factors in freshwater microcosms. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 258:106513. [PMID: 37001199 DOI: 10.1016/j.aquatox.2023.106513] [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: 02/28/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
The emergence and transmission of antibiotic resistance genes (ARGs) and virulence factors (VFs) pose health risks to the ecosystem and humans. Understanding how non-antibiotic antimicrobial agents drive the expression of ARGs and VFs in freshwater ecosystems, however, remains large challenges. Here, we employed freshwater microcosms and performed metatranscriptomic analysis to investigate the expression profiles of ARGs and VFs in response to pollutants of non-antibiotic antimicrobial agents, including silver nanoparticles (AgNPs) and azoxystrobin. Results showed that AgNPs significantly inhibited the total expression of ARGs and VFs and decreased the number of pathogenic microorganisms expressing these genes. Azoxystrobin increased the total expression of ARGs and VFs, as well as the number of pathogens expressing VFs, but concomitantly reduced the number of pathogens expressing ARGs. Two tested pollutants dramatically changed the expression profiles of ARGs and VFs, with distinct patterns: AgNPs displayed a negative effect, while azoxystrobin showed a positive effect on their expression profiles. Our findings provided a systematical insight to demonstrate that non-antibiotic antimicrobial agents with different mechanisms of action showed various effects on ARGs and VFs, and therefore represented different ecological risks.
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Affiliation(s)
- Yan Wang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Kepin Ni
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Chaotang Lei
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Bingfeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yiling Chen
- Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China.
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
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31
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Ciemniecki JA, Newman DK. NADH dehydrogenases are the predominant phenazine reductases in the electron transport chain of Pseudomonas aeruginosa. Mol Microbiol 2023; 119:560-573. [PMID: 36840394 PMCID: PMC11129870 DOI: 10.1111/mmi.15049] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/15/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023]
Abstract
Phenazines are redox-active secondary metabolites produced by diverse bacteria including the opportunistic pathogen Pseudomonas aeruginosa. Extracellular electron transfer via phenazines enhances anaerobic survival by serving as an electron sink for glucose catabolism. However, the specific phenazine reductase(s) used to support this catabolism are unknown. Because electron transport chain components have been previously implicated in phenazine reduction, we sought to determine which of them possess phenazine reductase activity. We show that phenazine-1-carboxamide (PCN) and pyocyanin (PYO) are reduced at the highest rate by cells and are localized to the cell envelope while reduced. Using a coupled genetic and biochemical approach, we show that phenazine reductase activity in membrane fractions is attributable to the three NADH dehydrogenases present in P. aeruginosa and that their order of phenazine reductase activity is Nqr > Nuo > Ndh. In mutants possessing only one functional NADH dehydrogenase, whole cell reduction rates of PCN, but not PYO, recapitulate the pattern of biochemical results, implying that PYO reduction is predominantly occurring in the cytosol. Lastly, we show that ubiquinone rapidly and non-enzymatically oxidizes reduced phenazines, demonstrating that phenazines have the capability to serve in a redox loop between the NADH and ubiquinone pools, a finding that carries bioenergetic implications.
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Affiliation(s)
- John A Ciemniecki
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
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32
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McRose D, Li J, Newman D. The chemical ecology of coumarins and phenazines affects iron acquisition by pseudomonads. Proc Natl Acad Sci U S A 2023; 120:e2217951120. [PMID: 36996105 PMCID: PMC10083548 DOI: 10.1073/pnas.2217951120] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/27/2023] [Indexed: 03/31/2023] Open
Abstract
Secondary metabolites are important facilitators of plant-microbe interactions in the rhizosphere, contributing to communication, competition, and nutrient acquisition. However, at first glance, the rhizosphere seems full of metabolites with overlapping functions, and we have a limited understanding of basic principles governing metabolite use. Increasing access to the essential nutrient iron is one important, but seemingly redundant role performed by both plant and microbial Redox-Active Metabolites (RAMs). We used coumarins, RAMs made by the model plant Arabidopsis thaliana, and phenazines, RAMs made by soil-dwelling pseudomonads, to ask whether plant and microbial RAMs might each have distinct functions under different environmental conditions. We show that variations in oxygen and pH lead to predictable differences in the capacity of coumarins vs phenazines to increase the growth of iron-limited pseudomonads and that these effects depend on whether pseudomonads are grown on glucose, succinate, or pyruvate: carbon sources commonly found in root exudates. Our results are explained by the chemical reactivities of these metabolites and the redox state of phenazines as altered by microbial metabolism. This work shows that variations in the chemical microenvironment can profoundly affect secondary metabolite function and suggests plants may tune the utility of microbial secondary metabolites by altering the carbon released in root exudates. Together, these findings suggest that RAM diversity may be less overwhelming when viewed through a chemical ecological lens: Distinct molecules can be expected to be more or less important to certain ecosystem functions, such as iron acquisition, depending on the local chemical microenvironments in which they reside.
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Affiliation(s)
- Darcy L. McRose
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Jinyang Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
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Effects of Resource Availability and Antibiotic Residues on Intestinal Antibiotic Resistance in Bellamya aeruginosa. Microorganisms 2023; 11:microorganisms11030765. [PMID: 36985338 PMCID: PMC10058807 DOI: 10.3390/microorganisms11030765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Widespread and inappropriate use of antibiotics has been shown to increase the spread of antibiotics and antimicrobial resistance genes (ARGs) in aquatic environments and organisms. Antibiotic use for the treatment of human and animal diseases is increasing continuously globally. However, the effects of legal antibiotic concentrations on benthic consumers in freshwater environments remain unclear. In the present study, we tested the growth response of Bellamya aeruginosa to florfenicol (FF) for 84 days under high and low concentrations of sediment organic matter (carbon [C] and nitrogen [N]). We characterized FF and sediment organic matter impact on the bacterial community, ARGs, and metabolic pathways in the intestine using metagenomic sequencing and analysis. The high concentrations of organic matter in the sediment impacted the growth, intestinal bacterial community, intestinal ARGs, and microbiome metabolic pathways of B. aeruginosa. B. aeruginosa growth increased significantly following exposure to high organic matter content sediment. Proteobacteria, at the phylum level, and Aeromonas at the genus level, were enriched in the intestines. In particular, fragments of four opportunistic pathogens enriched in the intestine of high organic matter content sediment groups, Aeromonas hydrophila, Aeromonas caviae, Aeromonas veronii, and Aeromonas salmonicida, carried 14 ARGs. The metabolic pathways of the B. aeruginosa intestine microbiome were activated and showed a significant positive correlation with sediment organic matter concentrations. In addition, genetic information processing and metabolic functions may be inhibited by the combined exposure to sediment C, N, and FF. The findings of the present study suggest that antibiotic resistance dissemination from benthic animals to the upper trophic levels in freshwater lakes should be studied further.
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Wu JY, Gao JM, Guo JS, Hou XY, Wang DR, Wu JC, Li XJ, Jia CY. Comprehensive analysis of the fates and risks of veterinary antibiotics in a small ecosystem comprising a pig farm and its surroundings in Northeast China. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130570. [PMID: 37055976 DOI: 10.1016/j.jhazmat.2022.130570] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/07/2022] [Accepted: 12/06/2022] [Indexed: 06/19/2023]
Abstract
This study investigated the behavior of veterinary antibiotics (VAs) in a small farm ecosystem. Manure and environmental samples were collected around a large pig farm in northeast China. Thirty-four VAs in six categories were analyzed. Then, a multimedia fugacity model was used to estimate the fates of VAs in the environment. The results showed that VAs were prevalent in manure, soil, water, and sediment, but not in crops. Compared with fresh manure, VA levels were significantly lower in surface manure piles left in the open air for 3-6 months. The main VAs, tetracyclines and quinolones, decreased by 427.12 and 158.45 µg/kg, respectively. VAs from manure piles were transported to the surroundings and migrated vertically into deep soil. The concentrations of ∑VAs detected in agricultural soils were 0.03-4.60 µg/kg; > 94% of the mass inventory of the VAs was retained in soil organic matter (SOM), suggesting that SOM is the main reservoir for antibiotics in soil. Risk assessment and model analysis indicated that the negative impact of mixed antibiotics at low concentrations in farmland on crops may be mediated by indirect effects, rather than direct effects. Our findings highlight the environmental fates and risks of antibiotics from livestock farms.
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Affiliation(s)
- Jian-Yong Wu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Jun-Min Gao
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China.
| | - Jin-Song Guo
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Xian-Yu Hou
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - De-Rui Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Jing-Cheng Wu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Xiao-Jun Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Chun-Yun Jia
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
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Geller-McGrath D, Mara P, Taylor GT, Suter E, Edgcomb V, Pachiadaki M. Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin. Nat Commun 2023; 14:656. [PMID: 36746960 PMCID: PMC9902471 DOI: 10.1038/s41467-023-36026-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/12/2023] [Indexed: 02/08/2023] Open
Abstract
Secondary metabolites play essential roles in ecological interactions and nutrient acquisition, and are of interest for their potential uses in medicine and biotechnology. Genome mining for biosynthetic gene clusters (BGCs) can be used for the discovery of new compounds. Here, we use metagenomics and metatranscriptomics to analyze BGCs in free-living and particle-associated microbial communities through the stratified water column of the Cariaco Basin, Venezuela. We recovered 565 bacterial and archaeal metagenome-assembled genomes (MAGs) and identified 1154 diverse BGCs. We show that differences in water redox potential and microbial lifestyle (particle-associated vs. free-living) are associated with variations in the predicted composition and production of secondary metabolites. Our results indicate that microbes, including understudied clades such as Planctomycetota, potentially produce a wide range of secondary metabolites in these anoxic/euxinic waters.
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Affiliation(s)
| | - Paraskevi Mara
- Geology & Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Elizabeth Suter
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA.,Biology, Chemistry and Environmental Studies Department, Molloy College, Rockville Centre, NY, USA
| | - Virginia Edgcomb
- Geology & Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - Maria Pachiadaki
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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Yu Y, Zhang Q, Zhang Z, Zhou S, Jin M, Zhu D, Yang X, Qian H, Lu T. Plants select antibiotic resistome in rhizosphere in early stage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159847. [PMID: 36461576 DOI: 10.1016/j.scitotenv.2022.159847] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Knowledge of the dissemination and emergence of antibiotic resistance genes (ARGs) in the plant rhizosphere is essential for evaluating the risk of the modern ARGs in soil planetary health. However, little is known about the selection mechanism in the plant rhizosphere. Here, we firstly analyzed the dynamic changes in the rhizosphere antibiotic resistome during the process of three passage enrichment of the rhizosphere microbiome in Arabidopsis thaliana (Col-0) and found evidence that plants directionally enriched levels of beneficial functional bacteria with many ARGs. Using the metagenome, we next evaluated the enrichment potential of the resistome in four common crops (barley, indica rice, japonica rice, and wheat) and found that the wheat rhizosphere harbored more abundant ARGs. Therefore, we finally cultivated the rhizosphere microbiome of wheat for three generations and found that approximately 60 % of ARGs were associated with beneficial bacteria enriched in the wheat rhizosphere, which might enter the soil food web and threaten human health, despite also performing beneficial functions in the plant rhizosphere. Our study provides new insights into the dissemination of ARGs in the plant rhizosphere, and the obtained data may be useful for sustainable and ecologically safe agricultural development.
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Affiliation(s)
- Yitian Yu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Shuyidan Zhou
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Mingkang Jin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
| | - Xiaoru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China.
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Li M, Chen Y, Feng Y, Li X, Ye L, Jiang J. Ecological Responses of Maize Rhizosphere to Antibiotics Entering the Agricultural System in an Area with High Arsenicals Geological Background. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:13559. [PMID: 36294139 PMCID: PMC9603512 DOI: 10.3390/ijerph192013559] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Metal(loid)s can promote the spread and enrichment of antibiotic resistance in the environmental ecosystem through a co-selection effect. Little is known about the ecological effects of entering antibiotics into the environment with long-term metal(loid)s' resistance profiles. Here, cow manure containing oxytetracycline (OTC) or sulfadiazine (SA) at four concentrations (0 (as control), 1, 10, and 100 mg/kg) was loaded to a maize cropping system in an area with high a arsenicals geological background. Results showed that exogenous antibiotics entering significantly changed the nutrient conditions, such as the concentration of nitrate nitrogen, ammonium nitrogen, and available phosphorus in the maize rhizosphere soil, while total arsenic and metals did not display any differences in antibiotic treatments compared with control. Antibiotics exposure significantly influenced nitrate and nitrite reductase activities to reflect the inhibition of denitrification rates but did not affect the soil urease and acid phosphatase activities. OTC treatment also did not change soil dehydrogenase activities, while SA treatment posed promotion effects, showing a tendency to increase with exposure concentration. Both the tested antibiotics (OTC and SA) decreased the concentration of arsenite and arsenate in rhizosphere soil, but the inhibition effects of the former were higher than that of the latter. Moreover, antibiotic treatment impacted arsenite and arsenate levels in maize root tissue, with positive effects on arsenite and negative effects on arsenate. As a result, both OTC and SA treatments significantly increased bioconcentration factors and showed a tendency to first increase and then decrease with increasing concentration. In addition, the treatments decreased translocation capacity of arsenic from roots to shoots and showed a tendency to increase translocation factors with increasing concentration. Microbial communities with arsenic-resistance profiles may also be resistant to antibiotics entering.
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Affiliation(s)
- Mengli Li
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, China
- Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Area, Guilin University of Technology, Guilin 541004, China
| | - Yongshan Chen
- School of Resources and Environmental Science, Quanzhou Normal University, Quanzhou 362000, China
| | - Ying Feng
- School of Resources and Environmental Science, Quanzhou Normal University, Quanzhou 362000, China
| | - Xiaofeng Li
- School of Resources and Environmental Science, Quanzhou Normal University, Quanzhou 362000, China
| | - Lili Ye
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, China
| | - Jinping Jiang
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, China
- Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Area, Guilin University of Technology, Guilin 541004, China
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Wu S, Hua P, Gui D, Zhang J, Ying G, Krebs P. Occurrences, transport drivers, and risk assessments of antibiotics in typical oasis surface and groundwater. WATER RESEARCH 2022; 225:119138. [PMID: 36191526 DOI: 10.1016/j.watres.2022.119138] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/01/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
Intensive use of antibiotics affects biogeochemical cycles and stimulates the evolution of antibiotic resistance, thus threatening global health and social development. The spatiotemporal distributions of antibiotics in single aqueous matrices have been widely documented; however, their occurrence in surface-groundwater systems has received less attention, especially in arid regions that usually have fragile ecosystems. Therefore, we investigated the occurrence of thirty-one antibiotics in the surface water and adjacent groundwater in the Xinjiang Uygur Autonomous Region, China. The results showed that the total concentrations of detected antibiotics varied from 17.37 to 84.09 ng L-1 and from 16.38 to 277.41 ng L-1 in surface and groundwater, respectively. The median concentration of antibiotics showed the pattern of norfloxacin (4.86 ng L-1) > ciprofloxacin (3.93 ng L-1) > pefloxacin (3.39 ng L-1) in surface water; whereas in groundwater, this was in the order of pefloxacin (6.30 ng L-1) > norfloxacin (4.33 ng L-1) > ciprofloxacin (2.68 ng L-1). Heatmap analysis indicated that vertical infiltration had limited effects on antibiotic exchange in surface-ground water systems because of the high potential evaporation and low water storage. Redundancy analysis suggested that the oxidation-reduction potential (p < 0.01) and dissolved oxygen (p < 0.05) jointly affected the distribution of antibiotics in surface water. Ecological risk assessment showed that antibiotics in 98.9% of surface water and 99.1% of groundwater did not pose significant risks to aquatic species. The findings of this study will help develop effective mitigation strategies for antibiotics in aquatic environments.
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Affiliation(s)
- Shixue Wu
- Institute of Urban and Industrial Water Management, Technische Universität Dresden, 01062 Dresden, Germany
| | - Pei Hua
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, 510006 Guangzhou, China; School of Environment, South China Normal University, University Town, 510006 Guangzhou, China.
| | - Dongwei Gui
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 830011 Urumqi, China
| | - Jin Zhang
- Yangtze Institute for Conservation and Development, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, 210098 Nanjing, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 830011 Urumqi, China
| | - Guangguo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, 510006 Guangzhou, China; School of Environment, South China Normal University, University Town, 510006 Guangzhou, China
| | - Peter Krebs
- Institute of Urban and Industrial Water Management, Technische Universität Dresden, 01062 Dresden, Germany
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Yu YY, Zhang Y, Peng L. Investigating the interaction between Shewanella oneidensis and phenazine 1-carboxylic acid in the microbial electrochemical processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156501. [PMID: 35667430 DOI: 10.1016/j.scitotenv.2022.156501] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/28/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Many exoelectrogens utilize small redox mediators for extracellular electron transfer (EET). Notable examples include Shewanella species, which synthesize flavins, and Pseudomonas species, which produce phenazines. In natural and engineered environments, redox-active metabolites from different organisms coexist. The interaction between Shewanella oneidensis and phenazine 1-carboxylic acid (PCA, a representative phenazine compound) was investigated to demonstrate exoelectrogens utilizing metabolites secreted by other organisms as redox mediators. After 24 h in a reactor with and without added PCA (1 μM), the anodic current generated by Shewanella was 235 ± 11 and 51.7 ± 2.8 μA, respectively. Shewanella produced oxidative current approximately three times as high with medium containing PCA as with medium containing the same concentration of riboflavin. PCA also stimulated inward EET in Shewanella. The strong effect of PCA on EET was attributed to its enrichment at the biofilm/electrode interface. The PCA voltammetric peak heights with a Shewanella bioanode were 25-30 times higher than under abiotic conditions. The electrochemical properties of PCA were also altered by the transition from two-electron to single-electron electrochemistry, which suggests PCA was bound between the electrode and cell surface redox proteins. This behavior would benefit electroactive bacteria, which usually dwell in open systems where mediators are present in low concentrations. Like flavins, PCA can be immobilized under both bioanode and biocathode conditions but not under metabolically inactive conditions. Shewanella rapidly transfers electrons to PCA via its Mtr pathway. Compared with wild-type Shewanella, the PCA reduction ability was decreased in gene knockout mutants lacking Mtr pathway cytochromes, especially in the mutants with severely undermined electrode-reduction capacities. These strains also lost the ability to immobilize PCA, even under current-generating conditions.
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Affiliation(s)
- Yi-Yan Yu
- School of Resources & Environment, Southwest University, Chongqing 400716, PR China
| | - Yong Zhang
- School of Resources & Environment, Southwest University, Chongqing 400716, PR China
| | - Luo Peng
- School of Resources & Environment, Southwest University, Chongqing 400716, PR China.
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Dundas CM, Dinneny JR. Genetic Circuit Design in Rhizobacteria. BIODESIGN RESEARCH 2022; 2022:9858049. [PMID: 37850138 PMCID: PMC10521742 DOI: 10.34133/2022/9858049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/31/2022] [Indexed: 10/19/2023] Open
Abstract
Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.
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Affiliation(s)
| | - José R. Dinneny
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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41
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Comparative Metagenomics Highlight a Widespread Pathway Involved in Catabolism of Phosphonates in Marine and Terrestrial Serpentinizing Ecosystems. mSystems 2022; 7:e0032822. [PMID: 35913189 PMCID: PMC9426474 DOI: 10.1128/msystems.00328-22] [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] [Indexed: 11/20/2022] Open
Abstract
Serpentinizing hydrothermal systems result from water circulating into the subsurface and interacting with mantle-derived rocks notably near mid-ocean ridges or continental ophiolites. Serpentinization and associated reactions produce alkaline fluids enriched in molecular hydrogen, methane, and small organic molecules that are assumed to feed microbial inhabitants. In this study, we explored the relationships linking serpentinization to associated microbial communities by comparative metagenomics of serpentinite-hosted systems, basalt-hosted vents, and hot springs. The shallow Prony bay hydrothermal field (PBHF) microbiome appeared to be more related to those of ophiolitic sites than to the Lost City hydrothermal field (LCHF) microbiome, probably because of the meteoric origin of its fluid, like terrestrial alkaline springs. This study emphasized the ubiquitous importance of a set of genes involved in the catabolism of phosphonates and highly enriched in all serpentinizing sites compared to other ecosystems. Because most of the serpentinizing systems are depleted in inorganic phosphate, the abundance of genes involved in the carbon-phosphorus lyase pathway suggests that the phosphonates constitute a source of phosphorus in these ecosystems. Additionally, hydrocarbons such as methane, released upon phosphonate catabolism, may contribute to the overall budget of organic molecules in serpentinizing systems. IMPORTANCE This first comparative metagenomic study of serpentinite-hosted environments provides an objective framework to understand the functioning of these peculiar ecosystems. We showed a taxonomic similarity between the PBHF and other terrestrial serpentinite-hosted ecosystems. At the same time, the LCHF microbial community was closer to deep basalt-hosted hydrothermal fields than continental ophiolites, despite the influence of serpentinization. This study revealed shared functional capabilities among serpentinite-hosted ecosystems in response to environmental stress, the metabolism of abundant dihydrogen, and the metabolism of phosphorus. Our results are consistent with the generalized view of serpentinite environments but provide deeper insight into the array of factors that may control microbial activities in these ecosystems. Moreover, we show that metabolism of phosphonate is widespread among alkaline serpentinizing systems and could play a crucial role in phosphorus and methane biogeochemical cycles. This study opens a new line of investigation of the metabolism of reduced phosphorus compounds in serpentinizing environments.
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Zhang Z, Wang Y, Chen B, Lei C, Yu Y, Xu N, Zhang Q, Wang T, Gao W, Lu T, Gillings M, Qian H. Xenobiotic pollution affects transcription of antibiotic resistance and virulence factors in aquatic microcosms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119396. [PMID: 35525510 DOI: 10.1016/j.envpol.2022.119396] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/08/2022] [Accepted: 04/30/2022] [Indexed: 06/14/2023]
Abstract
Antibiotic resistance genes (ARGs) and virulence factors (VFs) are critical threats to human health. Their abundance in aquatic ecosystems is maintained and enhanced via selection driven by environmental xenobiotics. However, their activity and expression in these environments under xenobiotic stress remains unknown. Here ARG and VF expression profiles were examined in aquatic microcosms under ciprofloxacin, glyphosate and sertraline hydrochloride treatment. Ciprofloxacin increased total expression of ARGs, particularly multidrug resistance genes. Total expression of ARGs and VFs decreased significantly under glyphosate and sertraline treatments. However, in opportunistic human pathogens, these agents increased expression of both ARGs and VFs. Xenobiotic pollutants, such as the compounds we tested here, have the potential to disrupt microbial ecology, promote resistance, and increase risk to human health. This study systematically evaluated the effects of environmental xenobiotics on transcription of ARGs and VFs, both of which have direct relevance to human health. Transcription of such genes has been overlooked in previous studies.
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Affiliation(s)
- Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Yan Wang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Bingfeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Chaotang Lei
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Yitian Yu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310012, PR China
| | - Wenwen Gao
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310012, PR China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Michael Gillings
- ARC Centre of Excellence in Synthetic Biology, Faculty of Science and Engineering, Macquarie University, NSW, 2109, Australia
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China.
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Dai H, Wu B, Chen B, Ma B, Chu C. Diel Fluctuation of Extracellular Reactive Oxygen Species Production in the Rhizosphere of Rice. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:9075-9082. [PMID: 35593708 DOI: 10.1021/acs.est.2c00005] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Reactive oxygen species (ROS) are ubiquitous on earth and drive numerous redox-centered biogeochemical processes. The rhizosphere of wetland plants is a highly dynamic interface for the exchange of oxygen and electrons, presenting the basis of the precedent for ROS production, yet whether extracellular ROS are produced in the rhizosphere remains unknown. Here, we designed a microfluidic chip setup to detect in-situ ROS productions in the rhizosphere of rice with spatial and temporal resolutions. Fluorescence imaging clearly displayed the hot spots of ROS generation in the rhizosphere. The formation concentration of the hydroxyl radical (•OH, a representative ROS, 10-6 M) was comparable to those by the classical photochemical route (10-6-10-7 M) in aquatic systems, therefore highlighting the rhizosphere as an unrecognized hotspot for ROS production. Moreover, the rhizosphere ROS production exhibits diel fluctuation, which simultaneously fluctuated with dissolved oxygen, redox potential, and pH, all driven by radial oxygen loss near the root in the daytime. The production and diel fluctuation of ROS were confirmed in the rhizosphere of rice root incubated in natural soils. We demonstrated that the extracellular ROS production was triggered by the interplay between root-released oxygen and microbial respiration released extracellular electrons, while iron mineral and organic matter might play key roles in storing and shuttling electrons. Our results highlight the rhizosphere as a widespread but previously unappreciated hotspot for ROS production, which may affect pollutant redox dynamics and biogeochemical processes in soils.
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Affiliation(s)
- Hengyi Dai
- Faculty of Agriculture, Life, and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Binbin Wu
- Faculty of Agriculture, Life, and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
| | - Baoliang Chen
- Faculty of Agriculture, Life, and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bin Ma
- Faculty of Agriculture, Life, and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Chiheng Chu
- Faculty of Agriculture, Life, and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
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Naumann C, Heisters M, Brandt W, Janitza P, Alfs C, Tang N, Toto Nienguesso A, Ziegler J, Imre R, Mechtler K, Dagdas Y, Hoehenwarter W, Sawers G, Quint M, Abel S. Bacterial-type ferroxidase tunes iron-dependent phosphate sensing during Arabidopsis root development. Curr Biol 2022; 32:2189-2205.e6. [PMID: 35472311 PMCID: PMC9168544 DOI: 10.1016/j.cub.2022.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 02/21/2022] [Accepted: 04/04/2022] [Indexed: 12/02/2022]
Abstract
Access to inorganic phosphate (Pi), a principal intermediate of energy and nucleotide metabolism, profoundly affects cellular activities and plant performance. In most soils, antagonistic Pi-metal interactions restrict Pi bioavailability, which guides local root development to maximize Pi interception. Growing root tips scout the essential but immobile mineral nutrient; however, the mechanisms monitoring external Pi status are unknown. Here, we show that Arabidopsis LOW PHOSPHATE ROOT 1 (LPR1), one key determinant of Fe-dependent Pi sensing in root meristems, encodes a novel ferroxidase of high substrate specificity and affinity (apparent KM ∼ 2 μM Fe2+). LPR1 typifies an ancient, Fe-oxidizing multicopper protein family that evolved early upon bacterial land colonization. The ancestor of streptophyte algae and embryophytes (land plants) acquired LPR1-type ferroxidase from soil bacteria via horizontal gene transfer, a hypothesis supported by phylogenomics, homology modeling, and biochemistry. Our molecular and kinetic data on LPR1 regulation indicate that Pi-dependent Fe substrate availability determines LPR1 activity and function. Guided by the metabolic lifestyle of extant sister bacterial genera, we propose that Arabidopsis LPR1 monitors subtle concentration differentials of external Fe availability as a Pi-dependent cue to adjust root meristem maintenance via Fe redox signaling and cell wall modification. We further hypothesize that the acquisition of bacterial LPR1-type ferroxidase by embryophyte progenitors facilitated the evolution of local Pi sensing and acquisition during plant terrestrialization.
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Affiliation(s)
- Christin Naumann
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Marcus Heisters
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Wolfgang Brandt
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Philipp Janitza
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Strasse, 06120 Halle (Saale), Germany
| | - Carolin Alfs
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Nancy Tang
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Alicia Toto Nienguesso
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Jörg Ziegler
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Richard Imre
- Gregor Mendel Institute of Molecular Plant Biology, Dr. Bohr Gasse 3, 1030 Vienna, Austria; Research Institute of Molecular Pathology, Vienna BioCenter, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Karl Mechtler
- Gregor Mendel Institute of Molecular Plant Biology, Dr. Bohr Gasse 3, 1030 Vienna, Austria; Research Institute of Molecular Pathology, Vienna BioCenter, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Yasin Dagdas
- Gregor Mendel Institute of Molecular Plant Biology, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Wolfgang Hoehenwarter
- Proteome Analytics, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Gary Sawers
- Institute of Biology/Microbiology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Strasse, 06120 Halle (Saale), Germany; German Center for Integrative Biodiversity Research, Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
| | - Steffen Abel
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany; Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany; Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616 USA.
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Assessment of global health risk of antibiotic resistance genes. Nat Commun 2022; 13:1553. [PMID: 35322038 PMCID: PMC8943045 DOI: 10.1038/s41467-022-29283-8] [Citation(s) in RCA: 222] [Impact Index Per Article: 111.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 03/02/2022] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance genes (ARGs) have accelerated microbial threats to human health in the last decade. Many genes can confer resistance, but evaluating the relative health risks of ARGs is complex. Factors such as the abundance, propensity for lateral transmission and ability of ARGs to be expressed in pathogens are all important. Here, an analysis at the metagenomic level from various habitats (6 types of habitats, 4572 samples) detects 2561 ARGs that collectively conferred resistance to 24 classes of antibiotics. We quantitatively evaluate the health risk to humans, defined as the risk that ARGs will confound the clinical treatment for pathogens, of these 2561 ARGs by integrating human accessibility, mobility, pathogenicity and clinical availability. Our results demonstrate that 23.78% of the ARGs pose a health risk, especially those which confer multidrug resistance. We also calculate the antibiotic resistance risks of all samples in four main habitats, and with machine learning, successfully map the antibiotic resistance threats in global marine habitats with over 75% accuracy. Our novel method for quantitatively surveilling the health risk of ARGs will help to manage one of the most important threats to human and animal health. Antibiotic resistance genes (ARGs) have accelerated microbial threats to human health. Here, Zhang et al. analyze 4572 metagenomic samples to illustrate the global patterns of ARG distribution in diverse habitats. They quantitatively evaluate the health risk to humans of 2561 ARGs by integrating human accessibility, mobility, pathogenicity and clinical availability. With the machine learning, they map the antibiotic resistance threats in global marine habitats.
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Peng W, Li H, Zhao X, Shao B, Zhu K. Pyocyanin Modulates Gastrointestinal Transformation and Microbiota. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:2722-2732. [PMID: 35171599 DOI: 10.1021/acs.jafc.1c07726] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Phenazines are ubiquitously produced by Pseudomonas spp. in the environment and are widely used in agriculture and clinical therapies, making their accumulation through the food chain cause potential risks to human health. Here, we utilized pyocyanin (PYO) as a representative to study the effects of phenazines on digestive tracts. Pharmacokinetic analysis showed that PYO exhibited low systemic exposure, slow elimination, and low accumulation in both rat and pig models. PYO was subsequently found to induce intestinal microbiota dysbiosis, destroy the mucus layer and physical barrier, and even promote gut vascular barrier (GVB) impairment, consequently increasing the gut permeability. Additionally, integral and metabolomic analyses of the liver demonstrated that PYO induced liver inflammation and metabolic disorders. The metabolic analysis further confirmed that all of the metabolites of PYO retain the nitrogen-containing tricyclic structural skeleton of phenazines, which was the core bioactivity of phenazine compounds. These findings elucidated that PYO could be metabolized by animals. Meanwhile, high levels of PYO could induce intestinal barrier impairment and liver damage, suggesting that we should be alert to the accumulation of phenazines.
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Affiliation(s)
- Wenjing Peng
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Hui Li
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing 100013, China
| | - Xiaole Zhao
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Bing Shao
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing 100013, China
| | - Kui Zhu
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
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Perry EK, Meirelles LA, Newman DK. From the soil to the clinic: the impact of microbial secondary metabolites on antibiotic tolerance and resistance. Nat Rev Microbiol 2022; 20:129-142. [PMID: 34531577 PMCID: PMC8857043 DOI: 10.1038/s41579-021-00620-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2021] [Indexed: 02/08/2023]
Abstract
Secondary metabolites profoundly affect microbial physiology, metabolism and stress responses. Increasing evidence suggests that these molecules can modulate microbial susceptibility to commonly used antibiotics; however, secondary metabolites are typically excluded from standard antimicrobial susceptibility assays. This may in part account for why infections by diverse opportunistic bacteria that produce secondary metabolites often exhibit discrepancies between clinical antimicrobial susceptibility testing results and clinical treatment outcomes. In this Review, we explore which types of secondary metabolite alter antimicrobial susceptibility, as well as how and why this phenomenon occurs. We discuss examples of molecules that opportunistic and enteric pathogens either generate themselves or are exposed to from their neighbours, and the nuanced impacts these molecules can have on tolerance and resistance to certain antibiotics.
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Affiliation(s)
- Elena K Perry
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Lucas A Meirelles
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
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Prevalence and correlates of phenazine resistance in culturable bacteria from a dryland wheat field. Appl Environ Microbiol 2022; 88:e0232021. [PMID: 35138927 DOI: 10.1128/aem.02320-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phenazines are a class of bacterially-produced redox-active natural antibiotics that have demonstrated potential as a sustainable alternative to traditional pesticides for the biocontrol of fungal crop diseases. However, the prevalence of bacterial resistance to agriculturally-relevant phenazines is poorly understood, limiting both the understanding of how these molecules might shape rhizosphere bacterial communities and the ability to perform risk assessment for off-target effects. Here, we describe profiles of susceptibility to the antifungal agent phenazine-1-carboxylic acid (PCA) across more than 100 bacterial strains isolated from a wheat field where PCA producers are indigenous and abundant. We find that Gram-positive bacteria are typically more sensitive to PCA than Gram-negative bacteria, but that there is also significant variability in susceptibility both within and across phyla. Phenazine-resistant strains are more likely to be isolated from the wheat rhizosphere, where PCA producers are also more abundant, compared to bulk soil. Furthermore, PCA toxicity is pH-dependent for most susceptible strains and broadly correlates with PCA reduction rates, suggesting that uptake and redox-cycling are important determinants of phenazine toxicity. Our results shed light on which classes of bacteria are most likely to be susceptible to phenazine toxicity in acidic or neutral soils. In addition, the taxonomic and phenotypic diversity of our strain collection represents a valuable resource for future studies on the role of natural antibiotics in shaping wheat rhizosphere communities. Importance Microbial communities contribute to crop health in important ways. For example, phenazine metabolites are a class of redox-active molecules made by diverse soil bacteria that underpin the biocontrol of wheat and other crops. Their physiological functions are nuanced: in some contexts they are toxic, in others, beneficial. While much is known about phenazine production and the effect of phenazines on producing strains, our ability to predict how phenazines might shape the composition of environmental microbial communities is poorly constrained; that phenazine prevalence in the rhizosphere is predicted to increase in arid soils as the climate changes provides an impetus for further study. As a step towards gaining a predictive understanding of phenazine-linked microbial ecology, we document the effects of phenazines on diverse bacteria that were co-isolated from a wheat rhizosphere and identify conditions and phenotypes that correlate with how a strain will respond to phenazines.
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Corbin DA, Miyake GM. Photoinduced Organocatalyzed Atom Transfer Radical Polymerization (O-ATRP): Precision Polymer Synthesis Using Organic Photoredox Catalysis. Chem Rev 2022; 122:1830-1874. [PMID: 34842426 PMCID: PMC9815475 DOI: 10.1021/acs.chemrev.1c00603] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The development of photoinduced organocatalyzed atom transfer radical polymerization (O-ATRP) has received considerable attention since its introduction in 2014. Expanding on many of the advantages of traditional ATRP, O-ATRP allows well-defined polymers to be produced under mild reaction conditions using organic photoredox catalysts. As a result, O-ATRP has opened access to a range of sensitive applications where the use of a metal catalyst could be of concern, such as electronics, certain biological applications, and the polymerization of coordinating monomers. However, key limitations of this method remain and necessitate further investigation to continue the development of this field. As such, this review details the achievements made to-date as well as future research directions that will continue to expand the capabilities and application landscape of O-ATRP.
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50
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Yue H, Miller AL, Khetrapal V, Jayaseker V, Wright S, Du L. Biosynthesis, regulation, and engineering of natural products from Lysobacter. Nat Prod Rep 2022; 39:842-874. [PMID: 35067688 DOI: 10.1039/d1np00063b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Covering: up to August 2021Lysobacter is a genus of Gram-negative bacteria that was classified in 1987. Several Lysobacter species are emerging as new biocontrol agents for crop protection in agriculture. Lysobacter are prolific producers of new bioactive natural products that are largely underexplored. So far, several classes of structurally interesting and biologically active natural products have been isolated from Lysobacter. This article reviews the progress in Lysobacter natural product research over the past ten years, including molecular mechanisms for biosynthesis, regulation and mode of action, genome mining of cryptic biosynthetic gene clusters, and metabolic engineering using synthetic biology tools.
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Affiliation(s)
- Huan Yue
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Amanda Lynn Miller
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Vimmy Khetrapal
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Vishakha Jayaseker
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Stephen Wright
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Liangcheng Du
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
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