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Marbehan X, Roger M, Fournier F, Infossi P, Guedon E, Delecourt L, Lebrun R, Giudici-Orticoni MT, Delaunay S. Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough. Front Microbiol 2024; 15:1336360. [PMID: 38463485 PMCID: PMC10920352 DOI: 10.3389/fmicb.2024.1336360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/24/2024] [Indexed: 03/12/2024] Open
Abstract
Introduction Desulfovibrio vulgaris Hildenborough is a gram-negative anaerobic bacterium belonging to the sulfate-reducing bacteria that exhibits highly versatile metabolism. By switching from one energy mode to another depending on nutrients availability in the environments" it plays a central role in shaping ecosystems. Despite intensive efforts to study D. vulgaris energy metabolism at the genomic, biochemical and ecological level, bioenergetics in this microorganism remain far from being fully understood. Alternatively, metabolic modeling is a powerful tool to understand bioenergetics. However, all the current models for D. vulgaris appeared to be not easily adaptable to various environmental conditions. Methods To lift off these limitations, here we constructed a novel transparent and robust metabolic model to explain D. vulgaris bioenergetics by combining whole-cell proteomic analysis with modeling approaches (Flux Balance Analysis). Results The iDvu71 model showed over 0.95 correlation with experimental data. Further simulations allowed a detailed description of D. vulgaris metabolism in various conditions of growth. Altogether, the simulations run in this study highlighted the sulfate-to-lactate consumption ratio as a pivotal factor in D. vulgaris energy metabolism. Discussion In particular, the impact on the hydrogen/formate balance and biomass synthesis is discussed. Overall, this study provides a novel insight into D. vulgaris metabolic flexibility.
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Affiliation(s)
| | - Magali Roger
- BIP-UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Université, CNRS, Marseille, France
| | | | - Pascale Infossi
- BIP-UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Université, CNRS, Marseille, France
| | | | - Louis Delecourt
- BIP-UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Université, CNRS, Marseille, France
- LISM-UMR 7255, Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Aix-Marseille Université, CNRS, Marseille, France
| | - Régine Lebrun
- IMM-FR3479, Marseille Protéomique, Aix-Marseille Université, CNRS, Marseille, France
| | - Marie-Thérèse Giudici-Orticoni
- BIP-UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Université, CNRS, Marseille, France
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Li H, Kang Z, Zhang K, Gong S, Zhao X, Yan Z, Wang S, Song C. Enhanced inhibition of HEDP on SRB-mediated corrosion with D-phenylalanine. ENVIRONMENTAL RESEARCH 2023; 227:115754. [PMID: 36966998 DOI: 10.1016/j.envres.2023.115754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/04/2023] [Accepted: 03/22/2023] [Indexed: 05/08/2023]
Abstract
Microbiologically influenced corrosion (MIC) caused by biofilm is a serious problem in many industries. D-amino acids could be a potential strategy to enhance traditional corrosion inhibitors due to their roles in biofilm reduction. However, the synergistic mechanism of D-amino acids and inhibitors remains unknown. In this study, D-Phenylalanine (D-Phe) and 1-hydroxyethane-1,1-diphosphonic acid (HEDP) were selected as the typical D-amino acid and corrosion inhibitor to evaluate their effect on the corrosion caused by Desulfovibrio vulgaris. The combination of HEDP and D-Phe obviously slowed down the corrosion process by 32.25%, decreased the corrosion pit depth and retarded cathodic reaction. SEM and CLSM analysis indicated that D-Phe reduced the content of extracellular protein and thus inhibited the biofilm formation. The molecular mechanism of D-Phe and HEDP on corrosion inhibition was further explored via transcriptome. The combination of HEDP and D-Phe down-regulated the gene expression of peptidoglycan, flagellum, electron transfer, ferredoxin and quorum sensing (QS) molecules, leading to less peptidoglycan synthesis, weaker electron transfer and stronger QS factor inhibition. This work provides a new strategy for improving traditional corrosion inhibitors, retarding MIC and mitigating subsequent water eutrophication.
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Affiliation(s)
- Hongyi Li
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China; Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China
| | - Zhengyan Kang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China; Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China
| | - Kaixin Zhang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China; Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China
| | - Shichu Gong
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China; Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China
| | - Xinxin Zhao
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China; Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China
| | - Zhen Yan
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China; Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China
| | - Shuguang Wang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China; Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China; Sino-French Research Institute for Ecology and Environment (ISFREE), School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China.
| | - Chao Song
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China; Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China.
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3
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Yan J, Guo X, Li J, Li Y, Sun H, Li A, Cao B. RpoN is required for the motility and contributes to the killing ability of Plesiomonas shigelloides. BMC Microbiol 2022; 22:299. [PMID: 36510135 PMCID: PMC9743648 DOI: 10.1186/s12866-022-02722-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND RpoN, also known as σ54, first reported in Escherichia coli, is a subunit of RNA polymerase that strictly controls the expression of different genes by identifying specific promoter elements. RpoN has an important regulatory function in carbon and nitrogen metabolism and participates in the regulation of flagellar synthesis, bacterial motility and virulence. However, little is known about the effect of RpoN in Plesiomonas shigelloides. RESULTS To identify pathways controlled by RpoN, RNA sequencing (RNA-Seq) of the WT and the rpoN deletion strain was carried out for comparison. The RNA-seq results showed that RpoN regulates ~ 13.2% of the P. shigelloides transcriptome, involves amino acid transport and metabolism, glycerophospholipid metabolism, pantothenate and CoA biosynthesis, ribosome biosynthesis, flagellar assembly and bacterial secretion system. Furthermore, we verified the results of RNA-seq using quantitative real-time reverse transcription PCR, which indicated that the absence of rpoN caused downregulation of more than half of the polar and lateral flagella genes in P. shigelloides, and the ΔrpoN mutant was also non-motile and lacked flagella. In the present study, the ability of the ΔrpoN mutant to kill E. coli MG1655 was reduced by 54.6% compared with that of the WT, which was consistent with results in RNA-seq, which showed that the type II secretion system (T2SS-2) genes and the type VI secretion system (T6SS) genes were repressed. By contrast, the expression of type III secretion system genes was largely unchanged in the ΔrpoN mutant transcriptome and the ability of the ΔrpoN mutant to infect Caco-2 cells was also not significantly different compared with the WT. CONCLUSIONS We showed that RpoN is required for the motility and contributes to the killing ability of P. shigelloides and positively regulates the T6SS and T2SS-2 genes.
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Affiliation(s)
- Junxiang Yan
- grid.216938.70000 0000 9878 7032TEDA Institute of Biological Sciences and Biotechnology, Nankai University, No. 23, Hongda StreetTianjin Economic and Technological Development Area, Tianjin, 300457 China ,grid.216938.70000 0000 9878 7032Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, No.23, Hongda StreetTianjin Economic and Technological Development Area, Tianjin, 300457 China ,grid.216938.70000 0000 9878 7032Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, No.23, Hongda StreetTianjin Economic and Technological Development Area, Tianjin, 300457 China
| | - Xueqian Guo
- grid.216938.70000 0000 9878 7032TEDA Institute of Biological Sciences and Biotechnology, Nankai University, No. 23, Hongda StreetTianjin Economic and Technological Development Area, Tianjin, 300457 China ,grid.216938.70000 0000 9878 7032Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, No.23, Hongda StreetTianjin Economic and Technological Development Area, Tianjin, 300457 China ,grid.216938.70000 0000 9878 7032Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, No.23, Hongda StreetTianjin Economic and Technological Development Area, Tianjin, 300457 China
| | - Jinghao Li
- grid.216938.70000 0000 9878 7032TEDA Institute of Biological Sciences and Biotechnology, Nankai University, No. 23, Hongda StreetTianjin Economic and Technological Development Area, Tianjin, 300457 China ,grid.216938.70000 0000 9878 7032Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, No.23, Hongda StreetTianjin Economic and Technological Development Area, Tianjin, 300457 China ,grid.216938.70000 0000 9878 7032Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, No.23, Hongda StreetTianjin Economic and Technological Development Area, Tianjin, 300457 China
| | - Yuehua Li
- grid.216938.70000 0000 9878 7032TEDA Institute of Biological Sciences and Biotechnology, Nankai University, No. 23, Hongda StreetTianjin Economic and Technological Development Area, Tianjin, 300457 China ,grid.216938.70000 0000 9878 7032Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, No.23, Hongda StreetTianjin Economic and Technological Development Area, Tianjin, 300457 China ,grid.216938.70000 0000 9878 7032Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, No.23, Hongda StreetTianjin Economic and Technological Development Area, Tianjin, 300457 China
| | - Hongmin Sun
- grid.216938.70000 0000 9878 7032TEDA Institute of Biological Sciences and Biotechnology, Nankai University, No. 23, Hongda StreetTianjin Economic and Technological Development Area, Tianjin, 300457 China ,grid.216938.70000 0000 9878 7032Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, No.23, Hongda StreetTianjin Economic and Technological Development Area, Tianjin, 300457 China ,grid.216938.70000 0000 9878 7032Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, No.23, Hongda StreetTianjin Economic and Technological Development Area, Tianjin, 300457 China
| | - Ang Li
- grid.216938.70000 0000 9878 7032State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin, 300353 China
| | - Boyang Cao
- grid.216938.70000 0000 9878 7032TEDA Institute of Biological Sciences and Biotechnology, Nankai University, No.23, Hongda StreetTianjin Economic and Technological Development Area, Tianjin, 300457 China ,grid.216938.70000 0000 9878 7032Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, No. 23, Hongda StreetTianjin Economic and Technological Development Area, Tianjin, 300457 China ,grid.216938.70000 0000 9878 7032Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, No. 23, Hongda StreetTianjin Economic and Technological Development Area, Tianjin, 300457 China
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Chug MK, Massoumi H, Wu Y, Brisbois EJ. Prevention of medical device infections via multi-action nitric oxide and chlorhexidine diacetate releasing medical grade silicone biointerfaces. J Biomed Mater Res A 2022; 110:1263-1277. [PMID: 35170212 DOI: 10.1002/jbm.a.37372] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/21/2022] [Accepted: 02/01/2022] [Indexed: 12/25/2022]
Abstract
The presence of bacteria and biofilm on medical device surfaces has been linked to serious infections, increased health care costs, and failure of medical devices. Therefore, antimicrobial biointerfaces and medical devices that can thwart microbial attachment and biofilm formation are urgently needed. Both nitric oxide (NO) and chlorhexidine diacetate (CHXD) possess broad-spectrum antibacterial properties. In the past, individual polymer release systems of CHXD and NO donor S-nitroso-N-acetylpenicillamine (SNAP) incorporated polymer platforms have attracted considerable attention for biomedical/therapeutic applications. However, the combination of the two surfaces has not yet been explored. Herein, the synergy of NO and CHXD was evaluated to create an antimicrobial medical-grade silicone rubber. The 10 wt% SNAP films were fabricated using solvent casting with a topcoat of CHXD (1, 3, and 5 wt%) to generate a dual-active antibacterial interface. Chemiluminescence studies confirmed the NO release from SNAP-CHXD films at physiologically relevant levels (0.5-4 × 10-10 mol min-1 cm-2 ) for at least 3 weeks and CHXD release for at least 7 days. Further characterization of the films via SEM-EDS confirmed uniform distribution of SNAP and presence of CHXD within the polymer films without substantial morphological changes, as confirmed by contact angle hysteresis. Moreover, the dual-active SNAP-CHXD films were able to significantly reduce Escherichia coli and Staphylococcus aureus bacteria (>3-log reduction) compared to controls with no explicit toxicity towards mouse fibroblast cells. The synergy between the two potent antimicrobial agents will help combat bacterial contamination on biointerfaces and enhance the longevity of medical devices.
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Affiliation(s)
- Manjyot Kaur Chug
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, Georgia, USA
| | - Hamed Massoumi
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, Georgia, USA
| | - Yi Wu
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, Georgia, USA
| | - Elizabeth J Brisbois
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, Georgia, USA
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Cai Z, Zhou L, Liu L, Wang D, Ren W, Long H, Zhang X, Xie Z. Bacterial epiphyte and endophyte communities of seagrass Thalassia hemprichii: the impact of feed extract solution. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:757-772. [PMID: 34713580 DOI: 10.1111/1758-2229.13019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 09/05/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
The global seagrass bed ecosystem acts as a natural ecological barrier in the littoral coastal zone. In recent years, this ecosystem has suffered from serious eutrophication and destruction caused by the continuous expansion of aquaculture. However, our understanding of the influence of aquaculture on the bacterial community remains limited. In this study, we used 16S amplicon sequencing to evaluate the impact of aquaculture feed extract solution on the composition and function of bacterial epiphytes and endophyte communities of the core seagrass from the seagrass bed ecosystem in Hainan, Thalassia hemprichii. The feed extract solution was the main factor that significantly affected the bacterial epiphyte and endophyte community structure of seagrass leaves but had no marked effect on alpha diversity was observed. Additionally, the bacterial epiphyte and endophyte community of the T. hemprichii leaves alleviated the effects of organic matter, sulfide, and nutrients caused by aquaculture wastewater. The feed extract solution promoted the proliferation of Bacteroidales, Vibrio, Desulfobulbaceae, Desulfobacteraceae, Pseudoalteromonas, Paludibacter, Marinomonas, and Pseudomonas in the leaves and root of T. hemprichii, which can effectively improve the digestibility of eutrophication. In fact, Desulfobacteraceae and Desulfobulbaceae can reduce sulfate to sulfide and oxidize sulfide to sulfur within seagrass, indicating that the increase in Desulfobulbaceae and Desulfobacteraceae facilitated the accumulation of sulfide with the treatment of feed extract solution, which may be the reason for the degradation of seagrass caused by aquaculture wastewater containing high concentrations of organic pollutants. These results suggest that although seagrass beds can withstand low concentrations of aquaculture pollutants, sulfide emissions should be minimized.
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Affiliation(s)
- Zefu Cai
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan Province, 570228, China
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, Hainan Province, 571126, China
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan Province, 570228, China
- College of Marine Sciences, Hainan University, Haikou, Hainan Province, 570228, China
| | - Lei Zhou
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan Province, 570228, China
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan Province, 570228, China
- College of Marine Sciences, Hainan University, Haikou, Hainan Province, 570228, China
| | - Lihua Liu
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan Province, 570228, China
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan Province, 570228, China
- College of Marine Sciences, Hainan University, Haikou, Hainan Province, 570228, China
| | - Daoru Wang
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, Hainan Province, 571126, China
| | - Wei Ren
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan Province, 570228, China
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan Province, 570228, China
- College of Marine Sciences, Hainan University, Haikou, Hainan Province, 570228, China
| | - Hao Long
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan Province, 570228, China
| | - Xiang Zhang
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan Province, 570228, China
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan Province, 570228, China
- College of Marine Sciences, Hainan University, Haikou, Hainan Province, 570228, China
| | - Zhenyu Xie
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan Province, 570228, China
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan Province, 570228, China
- College of Marine Sciences, Hainan University, Haikou, Hainan Province, 570228, China
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Yu C, Yang F, Xue D, Wang X, Chen H. The Regulatory Functions of σ 54 Factor in Phytopathogenic Bacteria. Int J Mol Sci 2021; 22:ijms222312692. [PMID: 34884502 PMCID: PMC8657755 DOI: 10.3390/ijms222312692] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 12/24/2022] Open
Abstract
σ54 factor (RpoN), a type of transcriptional regulatory factor, is widely found in pathogenic bacteria. It binds to core RNA polymerase (RNAP) and regulates the transcription of many functional genes in an enhancer-binding protein (EBP)-dependent manner. σ54 has two conserved functional domains: the activator-interacting domain located at the N-terminal and the DNA-binding domain located at the C-terminal. RpoN directly binds to the highly conserved sequence, GGN10GC, at the −24/−12 position relative to the transcription start site of target genes. In general, bacteria contain one or two RpoNs but multiple EBPs. A single RpoN can bind to different EBPs in order to regulate various biological functions. Thus, the overlapping and unique regulatory pathways of two RpoNs and multiple EBP-dependent regulatory pathways form a complex regulatory network in bacteria. However, the regulatory role of RpoN and EBPs is still poorly understood in phytopathogenic bacteria, which cause economically important crop diseases and pose a serious threat to world food security. In this review, we summarize the current knowledge on the regulatory function of RpoN, including swimming motility, flagella synthesis, bacterial growth, type IV pilus (T4Ps), twitching motility, type III secretion system (T3SS), and virulence-associated phenotypes in phytopathogenic bacteria. These findings and knowledge prove the key regulatory role of RpoN in bacterial growth and pathogenesis, as well as lay the groundwork for further elucidation of the complex regulatory network of RpoN in bacteria.
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Affiliation(s)
- Chao Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (C.Y.); (F.Y.)
| | - Fenghuan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (C.Y.); (F.Y.)
| | - Dingrong Xue
- National Engineering Laboratory of Grain Storage and Logistics, Academy of National Food and Strategic Reserves Administration, No. 11 Baiwanzhuang Street, Xicheng District, Beijing 100037, China;
| | - Xiuna Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Huamin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (C.Y.); (F.Y.)
- Correspondence:
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7
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Tripathi AK, Thakur P, Saxena P, Rauniyar S, Gopalakrishnan V, Singh RN, Gadhamshetty V, Gnimpieba EZ, Jasthi BK, Sani RK. Gene Sets and Mechanisms of Sulfate-Reducing Bacteria Biofilm Formation and Quorum Sensing With Impact on Corrosion. Front Microbiol 2021; 12:754140. [PMID: 34777309 PMCID: PMC8586430 DOI: 10.3389/fmicb.2021.754140] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/24/2021] [Indexed: 01/02/2023] Open
Abstract
Sulfate-reducing bacteria (SRB) have a unique ability to respire under anaerobic conditions using sulfate as a terminal electron acceptor, reducing it to hydrogen sulfide. SRB thrives in many natural environments (freshwater sediments and salty marshes), deep subsurface environments (oil wells and hydrothermal vents), and processing facilities in an industrial setting. Owing to their ability to alter the physicochemical properties of underlying metals, SRB can induce fouling, corrosion, and pipeline clogging challenges. Indigenous SRB causes oil souring and associated product loss and, subsequently, the abandonment of impacted oil wells. The sessile cells in biofilms are 1,000 times more resistant to biocides and induce 100-fold greater corrosion than their planktonic counterparts. To effectively combat the challenges posed by SRB, it is essential to understand their molecular mechanisms of biofilm formation and corrosion. Here, we examine the critical genes involved in biofilm formation and microbiologically influenced corrosion and categorize them into various functional categories. The current effort also discusses chemical and biological methods for controlling the SRB biofilms. Finally, we highlight the importance of surface engineering approaches for controlling biofilm formation on underlying metal surfaces.
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Affiliation(s)
- Abhilash Kumar Tripathi
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Payal Thakur
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Priya Saxena
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Shailabh Rauniyar
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Vinoj Gopalakrishnan
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Ram Nageena Singh
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Venkataramana Gadhamshetty
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States.,BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Department of Civil and Environmental Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Etienne Z Gnimpieba
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Biomedical Engineering Program, University of South Dakota, Sioux Falls, SD, United States
| | - Bharat K Jasthi
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Department of Materials and Metallurgical Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States.,BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Composite and Nanocomposite Advanced Manufacturing Centre-Biomaterials, Rapid City, SD, United States
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Dou W, Xu D, Gu T. Biocorrosion caused by microbial biofilms is ubiquitous around us. Microb Biotechnol 2021; 14:803-805. [PMID: 33320430 PMCID: PMC8085924 DOI: 10.1111/1751-7915.13690] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 11/30/2022] Open
Abstract
Biocorrosion first surfaced in the scientific literature when Richard H. Gaines associated corrosion with bacterial activities in 1910. It is also known as microbiologically influenced corrosion (MIC). In general, it covers two scenarios. One is that microbes cause corrosion directly, which usually means microbes secrete corrosive metabolites or microbes harvest electrons from a metal for respiration to produce energy. In the second scenario, microbes are behind the initiation or acceleration of corrosion caused by a pre-existing corrosive agent such as water and CO2 , by compromising the passive film (often a metal oxide film on a metal). MIC is caused by microbial biofilms. It is everywhere around us. This work dissects some notable examples with perspectives.
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Affiliation(s)
- Wenwen Dou
- Institute of Marine Science and TechnologyShandong UniversityQingdaoChina
| | - Dake Xu
- Shenyang National Lab for Materials ScienceNortheastern UniversityShenyangChina
| | - Tingyue Gu
- Department of Chemical and Biomolecular EngineeringInstitute for Corrosion and Multiphase TechnologyOhio UniversityAthensOH45701USA
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Fiévet A, Merrouch M, Brasseur G, Eve D, Biondi EG, Valette O, Pauleta SR, Dolla A, Dermoun Z, Burlat B, Aubert C. OrpR is a σ 54 -dependent activator using an iron-sulfur cluster for redox sensing in Desulfovibrio vulgaris Hildenborough. Mol Microbiol 2021; 116:231-244. [PMID: 33595838 PMCID: PMC8359166 DOI: 10.1111/mmi.14705] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/15/2021] [Accepted: 02/15/2021] [Indexed: 01/15/2023]
Abstract
Enhancer binding proteins (EBPs) are key players of σ54 -regulation that control transcription in response to environmental signals. In the anaerobic microorganism Desulfovibrio vulgaris Hildenborough (DvH), orp operons have been previously shown to be coregulated by σ54 -RNA polymerase, the integration host factor IHF and a cognate EBP, OrpR. In this study, ChIP-seq experiments indicated that the OrpR regulon consists of only the two divergent orp operons. In vivo data revealed that (i) OrpR is absolutely required for orp operons transcription, (ii) under anaerobic conditions, OrpR binds on the two dedicated DNA binding sites and leads to high expression levels of the orp operons, (iii) increasing the redox potential of the medium leads to a drastic down-regulation of the orp operons expression. Moreover, combining functional and biophysical studies on the anaerobically purified OrpR leads us to propose that OrpR senses redox potential variations via a redox-sensitive [4Fe-4S]2+ cluster in the sensory PAS domain. Overall, the study herein presents the first characterization of a new Fe-S redox regulator belonging to the σ54 -dependent transcriptional regulator family probably advantageously selected by cells adapted to the anaerobic lifestyle to monitor redox stress conditions.
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Affiliation(s)
| | | | | | - Danaé Eve
- Aix Marseille Univ, CNRS, LCB, Marseille, France
| | | | | | - Sofia R Pauleta
- Microbial Stress Lab, UCIBIO, REQUIMTE, Dept. Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Alain Dolla
- Aix Marseille Univ, Toulon Univ, CNRS, IRD, MIO, Marseille, France
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Yamasaki R, Kawano A, Yoshioka Y, Ariyoshi W. Rhamnolipids and surfactin inhibit the growth or formation of oral bacterial biofilm. BMC Microbiol 2020; 20:358. [PMID: 33228524 PMCID: PMC7684882 DOI: 10.1186/s12866-020-02034-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 11/05/2020] [Indexed: 12/16/2022] Open
Abstract
Background Bacteria survive in various environments by forming biofilms. Bacterial biofilms often cause significant problems to medical instruments and industrial processes. Techniques to inhibit biofilm formation are essential and have wide applications. In this study, we evaluated the ability of two types of biosurfactants (rhamnolipids and surfactin) to inhibit growth and biofilm formation ability of oral pathogenic bacteria such as Aggregatibacter actinomycetemcomitans, Streptococcus mutans, and Streptococcus sanguinis. Results Rhamnolipids inhibited the growth and biofilm formation ability of all examined oral bacteria. Surfactin showed effective inhibition against S. sanguinis ATCC10556, but lower effects toward A. actinomycetemcomitans Y4 and S. mutans UA159. To corroborate these results, biofilms were observed by scanning electron microscopy (SEM) and confocal microscopy. The observations were largely in concordance with the biofilm assay results. We also attempted to determine the step in the biofilm formation process that was inhibited by biosurfactants. The results clearly demonstrated that rhamnolipids inhibit biofilm formation after the initiation process, however, they do not affect attachment or maturation. Conclusions Rhamnolipids inhibit oral bacterial growth and biofilm formation by A. actinomycetemcomitans Y4, and may serve as novel oral drug against localized invasive periodontitis. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02034-9.
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Affiliation(s)
- Ryota Yamasaki
- Division of Infections and Molecular Biology, Department of Health Promotion, Kyushu Dental University, Kitakyushu, Fukuoka, 803-8580, Japan.
| | - Aki Kawano
- Division of Infections and Molecular Biology, Department of Health Promotion, Kyushu Dental University, Kitakyushu, Fukuoka, 803-8580, Japan
| | - Yoshie Yoshioka
- Division of Infections and Molecular Biology, Department of Health Promotion, Kyushu Dental University, Kitakyushu, Fukuoka, 803-8580, Japan
| | - Wataru Ariyoshi
- Division of Infections and Molecular Biology, Department of Health Promotion, Kyushu Dental University, Kitakyushu, Fukuoka, 803-8580, Japan
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11
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Kawano A, Yamasaki R, Sakakura T, Takatsuji Y, Haruyama T, Yoshioka Y, Ariyoshi W. Reactive Oxygen Species Penetrate Persister Cell Membranes of Escherichia coli for Effective Cell Killing. Front Cell Infect Microbiol 2020; 10:496. [PMID: 33042869 PMCID: PMC7530241 DOI: 10.3389/fcimb.2020.00496] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 08/10/2020] [Indexed: 02/05/2023] Open
Abstract
Persister cells are difficult to eliminate because they are tolerant to antibiotic stress. In the present study, using artificially induced Escherichia coli persister cells, we found that reactive oxygen species (ROS) have greater effects on persister cells than on exponential cells. Thus, we examined which types of ROS could effectively eliminate persister cells and determined the mechanisms underlying the effects of these ROS. Ultraviolet (UV) light irradiation can kill persister cells, and bacterial viability is markedly increased under UV shielding. UV induces the production of ROS, which kill bacteria by moving toward the shielded area. Electron spin resonance-based analysis confirmed that hydroxyl radicals are produced by UV irradiation, although singlet oxygen is not produced. These results clearly revealed that ROS sterilizes persister cells more effectively compared to the sterilization of exponential cells (**p < 0.01). These ROS do not injure the bacterial cell wall but rather invade the cell, followed by cell killing. Additionally, the sterilization effect on persister cells was increased by exposure to oxygen plasma during UV irradiation. However, vapor conditions decreased persister cell sterilization by reducing the levels of hydroxyl radicals. We also verified the effect of ROS against bacteria in biofilms that are more resistant than planktonic cells. Although UV alone could not completely sterilize the biofilm bacteria, UV with ROS achieved complete sterilization. Our results demonstrate that persister cells strongly resist the effects of antibiotics and starvation stress but are less able to withstand exposure to ROS. It was shown that ROS does not affect the cell membrane but penetrates it and acts internally to kill persister cells. In particular, it was clarified that the hydroxy radical is an effective sterilizer to kill persister cells.
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Affiliation(s)
- Aki Kawano
- Division of Infections and Molecular Biology, Department of Health Promotion, Kyushu Dental University, Kitakyushu, Japan
| | - Ryota Yamasaki
- Division of Infections and Molecular Biology, Department of Health Promotion, Kyushu Dental University, Kitakyushu, Japan
| | - Tatsuya Sakakura
- Division of Functional Interface Engineering, Department of Biological Systems and Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Yoshiyuki Takatsuji
- Division of Functional Interface Engineering, Department of Biological Systems and Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Tetsuya Haruyama
- Division of Functional Interface Engineering, Department of Biological Systems and Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Yoshie Yoshioka
- Division of Infections and Molecular Biology, Department of Health Promotion, Kyushu Dental University, Kitakyushu, Japan
| | - Wataru Ariyoshi
- Division of Infections and Molecular Biology, Department of Health Promotion, Kyushu Dental University, Kitakyushu, Japan
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Wettstadt S. Breaking free from home: biofilm dispersal by a glycosidase from Desulfovibrio vulgaris. Environ Microbiol 2019; 22:557-558. [PMID: 31797512 DOI: 10.1111/1462-2920.14883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 12/01/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Sarah Wettstadt
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, Granada, 18008, Spain
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Anion transport as a target of adaption to perchlorate in sulfate-reducing communities. ISME JOURNAL 2019; 14:450-462. [PMID: 31659234 DOI: 10.1038/s41396-019-0540-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/04/2019] [Accepted: 09/12/2019] [Indexed: 11/09/2022]
Abstract
Inhibitors can be used to control the functionality of microbial communities by targeting specific metabolisms. The targeted inhibition of dissimilatory sulfate reduction limits the generation of toxic and corrosive hydrogen sulfide across several industrial systems. Sulfate-reducing microorganisms (SRM) are specifically inhibited by sulfate analogs, such as perchlorate. Previously, we showed pure culture SRM adaptation to perchlorate stress through mutation of the sulfate adenylyltransferase, a central enzyme in the sulfate reduction pathway. Here, we explored adaptation to perchlorate across unconstrained SRM on a community scale. We followed natural and bio-augmented sulfidogenic communities through serial transfers in increasing concentrations of perchlorate. Our results demonstrated that perchlorate stress altered community structure by initially selecting for innately more resistant strains. Isolation, whole-genome sequencing, and molecular biology techniques allowed us to define subsequent genetic mechanisms of adaptation that arose across the dominant adapting SRM. Changes in the regulation of divalent anion:sodium symporter family transporters led to increased intracellular sulfate to perchlorate ratios, allowing SRM to escape the effects of competitive inhibition. Thus, in contrast to pure-culture results, SRM in communities cope with perchlorate stress via changes in anion transport and its regulation. This highlights the value of probing evolutionary questions in an ecological framework, bridging the gap between ecology, evolution, genomics, and physiology.
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