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Karbelkar AA, Font M, Smith TJ, Sondermann H, O’Toole GA. Reconstitution of a biofilm adhesin system from a sulfate-reducing bacterium in Pseudomonas fluorescens. Proc Natl Acad Sci U S A 2024; 121:e2320410121. [PMID: 38498718 PMCID: PMC10990149 DOI: 10.1073/pnas.2320410121] [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: 11/20/2023] [Accepted: 02/21/2024] [Indexed: 03/20/2024] Open
Abstract
Biofilms of sulfate-reducing bacterium (SRB) like Desulfovibrio vulgaris Hildenborough (DvH) can facilitate metal corrosion in various industrial and environmental settings leading to substantial economic losses. Although the mechanisms of biofilm formation by DvH are not yet well understood, recent studies indicate the large adhesin, DvhA, is a key determinant of biofilm formation. The dvhA gene neighborhood resembles the biofilm-regulating Lap system of Pseudomonas fluorescens but is curiously missing the c-di-GMP-binding regulator LapD. Instead, DvH encodes an evolutionarily unrelated c-di-GMP-binding protein (DVU1020) that we hypothesized is functionally analogous to LapD. To study this unusual Lap system and overcome experimental limitations with the slow-growing anaerobe DvH, we reconstituted its predicted SRB Lap system in a P. fluorescens strain lacking its native Lap regulatory components (ΔlapGΔlapD). Our data support the model that DvhA is a cell surface-associated LapA-like adhesin with a N-terminal "retention module" and that DvhA is released from the cell surface upon cleavage by the LapG-like protease DvhG. Further, we demonstrate DVU1020 (named here DvhD) represents a distinct class of c-di-GMP-binding, biofilm-regulating proteins that regulates DvhG activity in response to intracellular levels of this second messenger. This study provides insight into the key players responsible for biofilm formation by DvH, thereby expanding our understanding of Lap-like systems.
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Affiliation(s)
- Amruta A. Karbelkar
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH03755
| | - Maria Font
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, D-22607Hamburg, Germany
| | - T. Jarrod Smith
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH03755
| | - Holger Sondermann
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, D-22607Hamburg, Germany
| | - George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH03755
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2
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Karbelkar AA, Font ME, Smith TJ, Sondermann H, O’Toole GA. Reconstitution of a Biofilm Adhesin System from a Sulfate-Reducing Bacterium in Pseudomonas fluorescens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568322. [PMID: 38045380 PMCID: PMC10690286 DOI: 10.1101/2023.11.22.568322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Biofilms of the sulfate reducing bacterium (SRB) Desulfovibrio vulgaris Hildenborough (DvH) can facilitate metal corrosion in various industrial and environmental settings leading to substantial economic losses; however, the mechanisms of biofilm formation by DvH are not yet well-understood. Evidence suggests that a large adhesin, DvhA, may be contributing to biofilm formation in DvH. The dvhA gene and its neighbors encode proteins that resemble the Lap system, which regulates biofilm formation by Pseudomonas fluorescens, including a LapG-like protease DvhG and effector protein DvhD, which has key differences from the previously described LapD. By expressing the Lap-like adhesion components of DvH in P. fluorescens, our data support the model that the N-terminal fragment of the large adhesin DvhA serves as an adhesin "retention module" and is the target of the DvhG/DvhD regulatory module, thereby controlling cell-surface location of the adhesin. By heterologously expressing the DvhG/DvhD-like proteins in a P. fluorescens background lacking native regulation (ΔlapGΔlapD) we also show that cell surface regulation of the adhesin is dependent upon the intracellular levels of c-di-GMP. This study provides insight into the key players responsible for biofilm formation by DvH, thereby expanding our understanding of Lap-like systems.
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Affiliation(s)
- Amruta A. Karbelkar
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Maria E. Font
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Germany
| | - T. Jarrod Smith
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Holger Sondermann
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Germany
| | - George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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3
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Bacterial, Archaeal, and Eukaryote Diversity in Planktonic and Sessile Communities Inside an Abandoned and Flooded Iron Mine (Quebec, Canada). Appl Microbiol 2023. [DOI: 10.3390/applmicrobiol3010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Abandoned and flooded ore mines are examples of hostile environments (cold, dark, oligotrophic, trace metal) with a potential vast diversity of microbial communities rarely characterized. This study aimed to understand the effects of depth, the source of water (surface or groundwater), and abiotic factors on the communities present in the old Forsyth iron mine in Quebec (Canada). Water and biofilm samples from the mine were sampled by a team of technical divers who followed a depth gradient (0 to 183 m deep) to study the planktonic and sessile communities’ diversity and structure. We used 16S/18S rRNA amplicon to characterize the taxonomic diversity of Bacteria, Archaea, and Eukaryotes. Our results show that depth was not a significant factor explaining the difference in community composition observed, but lifestyle (planktonic/sessile) was. We discovered a vast diversity of microbial taxa, with taxa involved in carbon- and sulfur-cycling. Sessile communities seem to be centered on C1-cycling with fungi and heterotrophs likely adapted to heavy-metal stress. Planktonic communities were dominated by ultra-small archaeal and bacterial taxa, highlighting harsh conditions in the mine waters. Microbial source tracking indicated sources of communities from surface to deeper layers and vice versa, suggesting the dispersion of organisms in the mine, although water connectivity remains unknown.
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Text-Mining to Identify Gene Sets Involved in Biocorrosion by Sulfate-Reducing Bacteria: A Semi-Automated Workflow. Microorganisms 2023; 11:microorganisms11010119. [PMID: 36677411 PMCID: PMC9867429 DOI: 10.3390/microorganisms11010119] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 01/05/2023] Open
Abstract
A significant amount of literature is available on biocorrosion, which makes manual extraction of crucial information such as genes and proteins a laborious task. Despite the fast growth of biology related corrosion studies, there is a limited number of gene collections relating to the corrosion process (biocorrosion). Text mining offers a potential solution by automatically extracting the essential information from unstructured text. We present a text mining workflow that extracts biocorrosion associated genes/proteins in sulfate-reducing bacteria (SRB) from literature databases (e.g., PubMed and PMC). This semi-automatic workflow is built with the Named Entity Recognition (NER) method and Convolutional Neural Network (CNN) model. With PubMed and PMCID as inputs, the workflow identified 227 genes belonging to several Desulfovibrio species. To validate their functions, Gene Ontology (GO) enrichment and biological network analysis was performed using UniprotKB and STRING-DB, respectively. The GO analysis showed that metal ion binding, sulfur binding, and electron transport were among the principal molecular functions. Furthermore, the biological network analysis generated three interlinked clusters containing genes involved in metal ion binding, cellular respiration, and electron transfer, which suggests the involvement of the extracted gene set in biocorrosion. Finally, the dataset was validated through manual curation, yielding a similar set of genes as our workflow; among these, hysB and hydA, and sat and dsrB were identified as the metal ion binding and sulfur metabolism genes, respectively. The identified genes were mapped with the pangenome of 63 SRB genomes that yielded the distribution of these genes across 63 SRB based on the amino acid sequence similarity and were further categorized as core and accessory gene families. SRB's role in biocorrosion involves the transfer of electrons from the metal surface via a hydrogen medium to the sulfate reduction pathway. Therefore, genes encoding hydrogenases and cytochromes might be participating in removing hydrogen from the metals through electron transfer. Moreover, the production of corrosive sulfide from the sulfur metabolism indirectly contributes to the localized pitting of the metals. After the corroboration of text mining results with SRB biocorrosion mechanisms, we suggest that the text mining framework could be utilized for genes/proteins extraction and significantly reduce the manual curation time.
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5
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Ueki T, Lovley DR. Desulfovibrio vulgaris as a model microbe for the study of corrosion under sulfate-reducing conditions. MLIFE 2022; 1:13-20. [PMID: 38818327 PMCID: PMC10989807 DOI: 10.1002/mlf2.12018] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 06/01/2024]
Abstract
Corrosion of iron-containing metals under sulfate-reducing conditions is an economically important problem. Microbial strains now known as Desulfovibrio vulgaris served as the model microbes in many of the foundational studies that developed existing models for the corrosion of iron-containing metals under sulfate-reducing conditions. Proposed mechanisms for corrosion by D. vulgaris include: (1) H2 consumption to accelerate the oxidation of Fe0 coupled to the reduction of protons to H2; (2) production of sulfide that combines with ferrous iron to form iron sulfide coatings that promote H2 production; (3) moribund cells release hydrogenases that catalyze Fe0 oxidation with the production of H2; (4) direct electron transfer from Fe0 to cells; and (5) flavins serving as an electron shuttle for electron transfer between Fe0 and cells. The demonstrated possibility of conducting transcriptomic and proteomic analysis of cells growing on metal surfaces suggests that similar studies on D. vulgaris corrosion biofilms can aid in identifying proteins that play an important role in corrosion. Tools for making targeted gene deletions in D. vulgaris are available for functional genetic studies. These approaches, coupled with instrumentation for the detection of low concentrations of H2, and proven techniques for evaluating putative electron shuttle function, are expected to make it possible to determine which of the proposed mechanisms for D. vulgaris corrosion are most important.
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Affiliation(s)
- Toshiyuki Ueki
- Key Laboratory for Anisotropy and Texture of Materials, Ministry of Education, Electrobiomaterials InstituteNortheastern UniversityShenyangChina
| | - Derek R. Lovley
- Key Laboratory for Anisotropy and Texture of Materials, Ministry of Education, Electrobiomaterials InstituteNortheastern UniversityShenyangChina
- Department of Microbiology University of MassachusettsAmherstMAUSA
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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: 16] [Impact Index Per Article: 5.3] [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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7
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Li E, Wu J, Zhang D. Exogenous autoinducer-2 inhibits biofilm development of Desulfovibrio sp. Huiquan2017. World J Microbiol Biotechnol 2021; 37:124. [PMID: 34170406 DOI: 10.1007/s11274-021-03071-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 05/16/2021] [Indexed: 11/28/2022]
Abstract
Sulfate-reducing bacteria (SRB) are culprits for microbiologically influenced corrosion, and biofilms are believed to play essential roles in the corrosion induced by SRB. However, little is known about the regulation of SRB biofilms. Quorum sensing signal molecules acyl-homoserine lactones (AHLs) and autoinducer-2 (AI-2) regulate biofilm formation of many bacteria. In this study, the production of AHLs and AI-2 by one SRB strain, Desulfovibrio sp. Huiquan2017, was detected, and the effect of exogenous AI-2 on bacterial biofilm formation was discussed. It was found that the cell-free supernatants of Desulfovibrio sp. Huiquan2017 induced luminescence in a ∆luxS mutant strain Vibrio harveyi BB170, indicating the production of functional AI-2 by the bacterium. In the presence of exogenous AI-2, the growth of Desulfovibrio sp. Huiquan2017 and early biofilm formation were not affected, but the later stage of biofilm development was inhibited significantly. The biofilms became looser, smaller, and thinner, and contained less bacteria and extracellular polymeric substances (EPS). The inhibition effect of AI-2 on the biofilm development of Desulfovibrio sp. Huiquan2017 was mainly achieved through reducing the amount of EPS in biofilms. These findings shed light on the biofilm regulation of SRB.
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Affiliation(s)
- Ee Li
- Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
- Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China
| | - Jiajia Wu
- Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
- Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China.
| | - Dun Zhang
- Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
- Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China.
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8
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Lekbach Y, Liu T, Li Y, Moradi M, Dou W, Xu D, Smith JA, Lovley DR. Microbial corrosion of metals: The corrosion microbiome. Adv Microb Physiol 2021; 78:317-390. [PMID: 34147188 DOI: 10.1016/bs.ampbs.2021.01.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Microbially catalyzed corrosion of metals is a substantial economic concern. Aerobic microbes primarily enhance Fe0 oxidation through indirect mechanisms and their impact appears to be limited compared to anaerobic microbes. Several anaerobic mechanisms are known to accelerate Fe0 oxidation. Microbes can consume H2 abiotically generated from the oxidation of Fe0. Microbial H2 removal makes continued Fe0 oxidation more thermodynamically favorable. Extracellular hydrogenases further accelerate Fe0 oxidation. Organic electron shuttles such as flavins, phenazines, and possibly humic substances may replace H2 as the electron carrier between Fe0 and cells. Direct Fe0-to-microbe electron transfer is also possible. Which of these anaerobic mechanisms predominates in model pure culture isolates is typically poorly documented because of a lack of functional genetic studies. Microbial mechanisms for Fe0 oxidation may also apply to some other metals. An ultimate goal of microbial metal corrosion research is to develop molecular tools to diagnose the occurrence, mechanisms, and rates of metal corrosion to guide the implementation of the most effective mitigation strategies. A systems biology approach that includes innovative isolation and characterization methods, as well as functional genomic investigations, will be required in order to identify the diagnostic features to be gleaned from meta-omic analysis of corroding materials. A better understanding of microbial metal corrosion mechanisms is expected to lead to new corrosion mitigation strategies. The understanding of the corrosion microbiome is clearly in its infancy, but interdisciplinary electrochemical, microbiological, and molecular tools are available to make rapid progress in this field.
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Affiliation(s)
- Yassir Lekbach
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, China; Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China
| | - Tao Liu
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai, China
| | - Yingchao Li
- Beijing Key Laboratory of Failure, Corrosion and Protection of Oil/Gas Facility Materials, College of New Energy and Materials, China University of Petroleum-Beijing, Beijing, China
| | - Masoumeh Moradi
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, China; Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China
| | - Wenwen Dou
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Dake Xu
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, China; Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China.
| | - Jessica A Smith
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, CT, United States
| | - Derek R Lovley
- Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China; Department of Microbiology, University of Massachusetts, Amherst, MA, United States.
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9
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Todhanakasem T, Triwattana K, Pom J, Havanapan P, Koombhongse P, Thitisak P. Physiological studies of the Pediococcus pentosaceus biofilm. Lett Appl Microbiol 2021; 72:178-186. [PMID: 33059384 DOI: 10.1111/lam.13351] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/25/2020] [Accepted: 07/05/2020] [Indexed: 12/19/2022]
Abstract
Pediococcus pentosaceus, a bacterium recently used in human and animal probiotics, was used in combination with supports made from polylactic acid composite soybean meal was used to study biofilm formation, and it was found that dense biofilms developed by Day 1. Proteomic comparison between planktonic and biofilm cultures of P. pentosaceus showed distinct expression patterns of intracellular and extracellular proteins. Type I glyceraldehyde-3-phosphate dehydrogenase was upregulated in biofilm cultures and mediated cell adhesion and encouraged biofilm production. GMP synthase, which regulates GMP synthesis and acts as an intracellular signal molecule to control cell mechanisms and has been exploited in the development of new therapeutic agents, was also upregulated in the biofilm mode of growth. The present work serves as a basis for future studies examining the complex network of systems that regulate lactic acid bacterial (LAB) biofilm formation and can serve as a framework for studies of production of therapeutic agents from LAB.
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Affiliation(s)
- T Todhanakasem
- Department of Agro-Industry, Faculty of Biotechnology, Assumption University, Bangkapi, Bangkok, Thailand
| | - K Triwattana
- Department of Agro-Industry, Faculty of Biotechnology, Assumption University, Bangkapi, Bangkok, Thailand
| | - J Pom
- Department of Agro-Industry, Faculty of Biotechnology, Assumption University, Bangkapi, Bangkok, Thailand
| | - P Havanapan
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - P Koombhongse
- National Metal and Materials Technology Center (MTEC), Klong Luang, Thailand
| | - P Thitisak
- K.M.P. Biotech Co. Ltd, Chon Buri, Thailand
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10
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Zhu L, Gong T, Wood TL, Yamasaki R, Wood TK. σ 54 -Dependent regulator DVU2956 switches Desulfovibrio vulgaris from biofilm formation to planktonic growth and regulates hydrogen sulfide production. Environ Microbiol 2019; 21:3564-3576. [PMID: 31087603 DOI: 10.1111/1462-2920.14679] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 05/11/2019] [Indexed: 11/30/2022]
Abstract
Microbiologically influenced corrosion causes $100 billion in damage per year, and biofilms formed by sulfate-reducing bacteria (SRB) are the major culprit. However, little is known about the regulation of SRB biofilm formation. Using Desulfovibrio vulgaris as a model SRB organism, we compared the transcriptomes of biofilm and planktonic cells and identified that the gene for σ54 -dependent regulator DVU2956 is repressed in biofilms. Utilizing a novel promoter that is primarily transcribed in biofilms (Pdvu0304 ), we found production of DVU2956 inhibits biofilm formation by 70%. Corroborating this result, deleting dvu2956 increased biofilm formation, and this biofilm phenotype could be complemented. By producing proteins in biofilms from genes controlled by DVU2956 (dvu2960 and dvu2962), biofilm formation was inhibited almost completely. A second round of RNA-seq for the production of DVU2956 revealed DVU2956 influences electron transport via an Hmc complex (high-molecular-weight cytochrome c encoded by dvu0531-dvu0536) and the Fe-only hydrogenase (encoded by dvu1769, hydA and dvu1770, hydB) to control H2 S production. Corroborating these results, producing DVU2956 in biofilms decreased H2 S production by half, deleting dvu2956 increased H2 S production by 131 ± 5%, and producing DVU2956 in the dvu2956 strain reduced H2 S production. Therefore, DVU2956 maintains SRB in the planktonic state and reduces H2 S formation.
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Affiliation(s)
- Lei Zhu
- Department of Chemical Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Ting Gong
- Department of Chemical Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Thammajun L Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Ryota Yamasaki
- Department of Chemical Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA
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11
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Sivakumar K, Scarascia G, Zaouri N, Wang T, Kaksonen AH, Hong PY. Salinity-Mediated Increment in Sulfate Reduction, Biofilm Formation, and Quorum Sensing: A Potential Connection Between Quorum Sensing and Sulfate Reduction? Front Microbiol 2019; 10:188. [PMID: 30787924 PMCID: PMC6373464 DOI: 10.3389/fmicb.2019.00188] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/23/2019] [Indexed: 11/30/2022] Open
Abstract
Biocorrosion in marine environment is often associated with biofilms of sulfate reducing bacteria (SRB). However, not much information is available on the mechanism underlying exacerbated rates of SRB-mediated biocorrosion under saline conditions. Using Desulfovibrio (D.) vulgaris and Desulfobacterium (Db.) corrodens as model SRBs, the enhancement effects of salinity on sulfate reduction, N-acyl homoserine lactone (AHL) production and biofilm formation by SRBs were demonstrated. Under saline conditions, D. vulgaris and Db. corrodens exhibited significantly higher specific sulfate reduction and specific AHL production rates as well as elevated rates of biofilm formation compared to freshwater medium. Salinity-induced enhancement traits were also confirmed at transcript level through reverse transcription quantitative polymerase chain reaction (RT-qPCR) approach, which showed salinity-influenced increase in the expression of genes associated with carbon metabolism, sulfate reduction, biofilm formation and histidine kinase signal transduction. In addition, by deploying quorum sensing (QS) inhibitors, a potential connection between sulfate reduction and AHL production under saline conditions was demonstrated, which is most significant during early stages of sulfate metabolism. The findings collectively revealed the interconnection between QS, sulfate reduction and biofilm formation among SRBs, and implied the potential of deploying quorum quenching approaches to control SRB-based biocorrosion in saline conditions.
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Affiliation(s)
- Krishnakumar Sivakumar
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Giantommaso Scarascia
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Noor Zaouri
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Tiannyu Wang
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Anna H Kaksonen
- Land and Water, Commonwealth Scientific and Industrial Research Organization, Floreat, WA, Australia
| | - Pei-Ying Hong
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Wood TL, Gong T, Zhu L, Miller J, Miller DS, Yin B, Wood TK. Rhamnolipids from Pseudomonas aeruginosa disperse the biofilms of sulfate-reducing bacteria. NPJ Biofilms Microbiomes 2018; 4:22. [PMID: 30302271 PMCID: PMC6170446 DOI: 10.1038/s41522-018-0066-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 09/11/2018] [Indexed: 01/23/2023] Open
Abstract
Biofilm formation is an important problem for many industries. Desulfovibrio vulgaris is the representative sulfate-reducing bacterium (SRB) which causes metal corrosion in oil wells and drilling equipment, and the corrosion is related to its biofilm formation. Biofilms are extremely difficult to remove since the cells are cemented in a polymer matrix. In an effort to eliminate SRB biofilms, we examined the ability of supernatants from Pseudomonas aeruginosa PA14 to disperse SRB biofilms. We found that the P. aeruginosa supernatants dispersed more than 98% of the biofilm. To determine the biochemical basis of this SRB biofilm dispersal, we examined a series of P. aeruginosa mutants and found that mutants rhlA, rhlB, rhlI, and rhlR, defective in rhamnolipids production, had significantly reduced levels of SRB biofilm dispersal. Corroborating these results, purified rhamnolipids dispersed SRB biofilms, and rhamnolipids were detected in the P. aeruginosa supernatants. Hence, P. aeruginosa supernatants disperse SRB biofilms via rhamnolipids. To determine the genetic basis of how the P. aeruginosa supernatants disperse SRB biofilms, a whole transcriptomic analysis was conducted (RNA-seq); based on this analysis, we identified four proteins (DVUA0018, DVUA0034, DVUA0066, and DVUA0084) of the D. vulgaris megaplasmid that influence biofilm formation, with production of DVUA0066 (a putative phospholipase) reducing biofilm formation 5.6-fold. In addition, the supernatants of P. aeruginosa dispersed the SRB biofilms more readily than protease in M9 glucose minimum medium and were also effective against biofilms of Escherichia coli and Staphylococcus aureus. A subclass of glycolipids produced by the bacterium Pseudomonas aeruginosa breaks down a corrosive bacterial biofilm that afflicts industries such as petroleum extraction. The P. aeruginosa molecules, known as rhamnolipids, have been previously used to break down other bacterial biofilms. Now, a team from the United States, led by Pennsylvania State University’s Thomas Wood, showed that extracts from P. aeruginosa dispersed 98% of Desulfovibrio vulgaris biofilm, which is problematic for many industries, and also dispersed Escherichia coli and Staphylococcus aureus biofilms. Genetic investigations showed rhamnolipids were responsible for the majority of the biofilm inhibition. Further analyses also revealed four D. vulgaris proteins that significantly affect biofilm formation. This research highlights a mechanism that may be used to reduce the impact of industry-affecting biofilms and deepens the understandings of the mechanisms of biofilm formation.
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Affiliation(s)
- Thammajun L Wood
- 1Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802 USA
| | - Ting Gong
- 1Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802 USA
| | - Lei Zhu
- 1Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802 USA
| | - James Miller
- 2Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 USA
| | | | - Bei Yin
- 3Dow Chemical Company, Collegeville, PA 19426 USA
| | - Thomas K Wood
- 1Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802 USA.,2Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 USA.,4Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802 USA
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Charlebois A, Jacques M, Archambault M. Comparative transcriptomic analysis of Clostridium perfringens biofilms and planktonic cells. Avian Pathol 2018; 45:593-601. [PMID: 27207477 DOI: 10.1080/03079457.2016.1189512] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Clostridium perfringens is an opportunistic pathogen that can cause food poisoning in humans and various enterotoxaemias in animal species. Recently, C. perfringens was shown to form biofilms, a structured community of bacterial cells enclosed in a self-produced extracellular matrix. However, very little is known on the subject and no information is available on gene expression in C. perfringens biofilms. To gain insights into the differences between free-living C. perfringens cells and those in biofilms, we used RNA sequencing. In total, 25.7% of genes showed differential expression in the two growth modes; about 12.8% of genes were up-regulated and about 12.9% were down-regulated in biofilms. We show that 772 genes were significantly differentially expressed between biofilms and planktonic cells from the supernatant of biofilms. Genes that were down-regulated in biofilm cells, relative to planktonic cells, included those involved in virulence, energy production, amino acid, nucleotide and carbohydrate metabolism, and in translation and ribosomal structure. Genes up-regulated in biofilm cells were mainly involved in amino acid and carbohydrate metabolism, transcription, inorganic ion metabolism and in defence mechanisms. This study provides new insights into the transcriptomic response of C. perfringens during biofilm formation.
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Affiliation(s)
- Audrey Charlebois
- a Faculté de médecine vétérinaire, Département de pathologie et microbiologie, Centre de Recherche en Infectiologie Porcine et Aviaire (CRIPA) , Université de Montréal , Saint-Hyacinthe , Canada
| | - Mario Jacques
- a Faculté de médecine vétérinaire, Département de pathologie et microbiologie, Centre de Recherche en Infectiologie Porcine et Aviaire (CRIPA) , Université de Montréal , Saint-Hyacinthe , Canada
| | - Marie Archambault
- a Faculté de médecine vétérinaire, Département de pathologie et microbiologie, Centre de Recherche en Infectiologie Porcine et Aviaire (CRIPA) , Université de Montréal , Saint-Hyacinthe , Canada
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14
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De León KB, Zane GM, Trotter VV, Krantz GP, Arkin AP, Butland GP, Walian PJ, Fields MW, Wall JD. Unintended Laboratory-Driven Evolution Reveals Genetic Requirements for Biofilm Formation by Desulfovibrio vulgaris Hildenborough. mBio 2017; 8:e01696-17. [PMID: 29042504 PMCID: PMC5646257 DOI: 10.1128/mbio.01696-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 09/18/2017] [Indexed: 12/28/2022] Open
Abstract
Biofilms of sulfate-reducing bacteria (SRB) are of particular interest as members of this group are culprits in corrosion of industrial metal and concrete pipelines as well as being key players in subsurface metal cycling. Yet the mechanism of biofilm formation by these bacteria has not been determined. Here we show that two supposedly identical wild-type cultures of the SRB Desulfovibrio vulgaris Hildenborough maintained in different laboratories have diverged in biofilm formation. From genome resequencing and subsequent mutant analyses, we discovered that a single nucleotide change within DVU1017, the ABC transporter of a type I secretion system (T1SS), was sufficient to eliminate biofilm formation in D. vulgaris Hildenborough. Two T1SS cargo proteins were identified as likely biofilm structural proteins, and the presence of at least one (with either being sufficient) was shown to be required for biofilm formation. Antibodies specific to these biofilm structural proteins confirmed that DVU1017, and thus the T1SS, is essential for localization of these adhesion proteins on the cell surface. We propose that DVU1017 is a member of the lapB category of microbial surface proteins because of its phenotypic similarity to the adhesin export system described for biofilm formation in the environmental pseudomonads. These findings have led to the identification of two functions required for biofilm formation in D. vulgaris Hildenborough and focus attention on the importance of monitoring laboratory-driven evolution, as phenotypes as fundamental as biofilm formation can be altered.IMPORTANCE The growth of bacteria attached to a surface (i.e., biofilm), specifically biofilms of sulfate-reducing bacteria, has a profound impact on the economy of developed nations due to steel and concrete corrosion in industrial pipelines and processing facilities. Furthermore, the presence of sulfate-reducing bacteria in oil wells causes oil souring from sulfide production, resulting in product loss, a health hazard to workers, and ultimately abandonment of wells. Identification of the required genes is a critical step for determining the mechanism of biofilm formation by sulfate reducers. Here, the transporter by which putative biofilm structural proteins are exported from sulfate-reducing Desulfovibrio vulgaris Hildenborough cells was discovered, and a single nucleotide change within the gene coding for this transporter was found to be sufficient to completely stop formation of biofilm.
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Affiliation(s)
- Kara B De León
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Valentine V Trotter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Gregory P Krantz
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Gareth P Butland
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Peter J Walian
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Matthew W Fields
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
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Quorum Sensing and the Use of Quorum Quenchers as Natural Biocides to Inhibit Sulfate-Reducing Bacteria. Antibiotics (Basel) 2016; 5:antibiotics5040039. [PMID: 27983678 PMCID: PMC5187520 DOI: 10.3390/antibiotics5040039] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/23/2016] [Accepted: 12/06/2016] [Indexed: 11/17/2022] Open
Abstract
Sulfate-reducing bacteria (SRB) are one of the main protagonist groups of biocorrosion in the seawater environment. Given their principal role in biocorrosion, it remains a crucial task to develop strategies to reduce the abundance of SRBs. Conventional approaches include the use of biocides and antibiotics, which can impose health, safety, and environmental concerns. This review examines an alternative approach to this problem. This is achieved by reviewing the role of quorum sensing (QS) in SRB populations and its impact on the biofilm formation process. Genome databases of SRBs are mined to look for putative QS systems and homologous protein sequences representative of autoinducer receptors or synthases. Subsequently, this review puts forward the potential use of quorum quenchers as natural biocides against SRBs and outlines the potential strategies for the implementation of this approach.
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16
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Großkopf T, Zenobi S, Alston M, Folkes L, Swarbreck D, Soyer OS. A stable genetic polymorphism underpinning microbial syntrophy. THE ISME JOURNAL 2016; 10:2844-2853. [PMID: 27258948 PMCID: PMC5042321 DOI: 10.1038/ismej.2016.80] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 03/28/2016] [Accepted: 04/01/2016] [Indexed: 12/22/2022]
Abstract
Syntrophies are metabolic cooperations, whereby two organisms co-metabolize a substrate in an interdependent manner. Many of the observed natural syntrophic interactions are mandatory in the absence of strong electron acceptors, such that one species in the syntrophy has to assume the role of electron sink for the other. While this presents an ecological setting for syntrophy to be beneficial, the potential genetic drivers of syntrophy remain unknown to date. Here, we show that the syntrophic sulfate-reducing species Desulfovibrio vulgaris displays a stable genetic polymorphism, where only a specific genotype is able to engage in syntrophy with the hydrogenotrophic methanogen Methanococcus maripaludis. This 'syntrophic' genotype is characterized by two genetic alterations, one of which is an in-frame deletion in the gene encoding for the ion-translocating subunit cooK of the membrane-bound COO hydrogenase. We show that this genotype presents a specific physiology, in which reshaping of energy conservation in the lactate oxidation pathway enables it to produce sufficient intermediate hydrogen for sustained M. maripaludis growth and thus, syntrophy. To our knowledge, these findings provide for the first time a genetic basis for syntrophy in nature and bring us closer to the rational engineering of syntrophy in synthetic microbial communities.
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Affiliation(s)
- Tobias Großkopf
- School of Life Sciences, The University of Warwick, Coventry, UK
| | - Simone Zenobi
- School of Life Sciences, The University of Warwick, Coventry, UK
| | - Mark Alston
- The Genome Analysis Centre, Norwich Research Park, Norwich, UK
| | - Leighton Folkes
- The Genome Analysis Centre, Norwich Research Park, Norwich, UK
| | - David Swarbreck
- The Genome Analysis Centre, Norwich Research Park, Norwich, UK
| | - Orkun S Soyer
- School of Life Sciences, The University of Warwick, Coventry, UK
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17
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Zhang Y, Pei G, Chen L, Zhang W. Metabolic dynamics of Desulfovibrio vulgaris biofilm grown on a steel surface. BIOFOULING 2016; 32:725-736. [PMID: 27299565 DOI: 10.1080/08927014.2016.1193166] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/18/2016] [Indexed: 06/06/2023]
Abstract
In this study, a comparative metabolomics approach combining gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) was applied first between planktonic cells and biofilms and then between pure cultures and biofilms of Desulfovibrio vulgaris. The results revealed that the overall metabolic level of the biofilm cells was down-regulated, especially for metabolites related to the central carbon metabolism, compared to the planktonic cells and the pure culture of D. vulgaris. In addition, pathway enrichment analysis of the 58 metabolites identified by GC-MS showed that fatty acid biosynthesis in the biofilm cells was up-regulated, suggesting that fatty acids may be important for the formation, maintenance and function of D. vulgaris biofilm. This study offers a valuable perspective on the metabolic dynamics of the D. vulgaris biofilm.
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Affiliation(s)
- Yang Zhang
- a Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology , Tianjin University , Tianjin , PR China
- b Key Laboratory of Systems Bioengineering (Ministry of Education) , Tianjin University , Tianjin , PR China
- c SynBio Research Platform , Collaborative Innovation Center of Chemical Science and Engineering , Tianjin , PR China
| | - Guangsheng Pei
- a Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology , Tianjin University , Tianjin , PR China
- b Key Laboratory of Systems Bioengineering (Ministry of Education) , Tianjin University , Tianjin , PR China
- c SynBio Research Platform , Collaborative Innovation Center of Chemical Science and Engineering , Tianjin , PR China
| | - Lei Chen
- a Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology , Tianjin University , Tianjin , PR China
- b Key Laboratory of Systems Bioengineering (Ministry of Education) , Tianjin University , Tianjin , PR China
- c SynBio Research Platform , Collaborative Innovation Center of Chemical Science and Engineering , Tianjin , PR China
| | - Weiwen Zhang
- a Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology , Tianjin University , Tianjin , PR China
- b Key Laboratory of Systems Bioengineering (Ministry of Education) , Tianjin University , Tianjin , PR China
- c SynBio Research Platform , Collaborative Innovation Center of Chemical Science and Engineering , Tianjin , PR China
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18
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Qi Z, Chen L, Zhang W. Comparison of Transcriptional Heterogeneity of Eight Genes between Batch Desulfovibrio vulgaris Biofilm and Planktonic Culture at a Single-Cell Level. Front Microbiol 2016; 7:597. [PMID: 27199927 PMCID: PMC4847118 DOI: 10.3389/fmicb.2016.00597] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 04/11/2016] [Indexed: 11/13/2022] Open
Abstract
Sulfate-reducing bacteria (SRB) biofilm formed on metal surfaces can change the physicochemical properties of metals and cause metal corrosion. To enhance understanding of differential gene expression in Desulfovibrio vulgaris under planktonic and biofilm growth modes, a single-cell based RT-qPCR approach was applied to determine gene expression levels of 8 selected target genes in four sets of the 31 individual cells isolated from each growth condition (i.e., biofilm formed on a mild steel (SS) and planktonic cultures, exponential and stationary phases). The results showed obvious gene-expression heterogeneity for the target genes among D. vulgaris single cells of both biofilm and planktonic cultures. In addition, an increased gene-expression heterogeneity in the D. vulgaris biofilm when compared with the planktonic culture was also observed for seven out of eight selected genes at exponential phase, and six out of eight selected genes at stationary phase, respectively, which may be contributing to the increased complexity in terms of structures and morphology in the biofilm. Moreover, the results showed up-regulation of DVU0281 gene encoding exopolysaccharide biosynthesis protein, and down-regulation of genes involved in energy metabolism (i.e., DVU0434 and DVU0588), stress responses (i.e., DVU2410) and response regulator (i.e., DVU3062) in the D. vulgaris biofilm cells. Finally, the gene (DVU2571) involved in iron transportation was found down-regulated, and two genes (DVU1340 and DVU1397) involved in ferric uptake repressor and iron storage were up-regulated in D. vulgaris biofilm, suggesting their possible roles in maintaining normal metabolism of the D. vulgaris biofilm under environments of high concentration of iron. This study showed that the single-cell based analysis could be a useful approach in deciphering metabolism of microbial biofilms.
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Affiliation(s)
- Zhenhua Qi
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin UniversityTianjin, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin UniversityTianjin, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin UniversityTianjin, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin UniversityTianjin, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin UniversityTianjin, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin UniversityTianjin, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
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19
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Orange protein from Desulfovibrio alaskensis G20: insights into the Mo–Cu cluster protein-assisted synthesis. J Biol Inorg Chem 2016; 21:53-62. [DOI: 10.1007/s00775-015-1323-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/15/2015] [Indexed: 10/22/2022]
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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Lancaster WA, Menon AL, Scott I, Poole FL, Vaccaro BJ, Thorgersen MP, Geller J, Hazen TC, Hurt RA, Brown SD, Elias DA, Adams MWW. Metallomics of two microorganisms relevant to heavy metal bioremediation reveal fundamental differences in metal assimilation and utilization. Metallomics 2014; 6:1004-13. [PMID: 24706256 DOI: 10.1039/c4mt00050a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although as many as half of all proteins are thought to require a metal cofactor, the metalloproteomes of microorganisms remain relatively unexplored. Microorganisms from different environments are likely to vary greatly in the metals that they assimilate, not just among the metals with well-characterized roles but also those lacking any known function. Herein we investigated the metal utilization of two microorganisms that were isolated from very similar environments and are of interest because of potential roles in the immobilization of heavy metals, such as uranium and chromium. The metals assimilated and their concentrations in the cytoplasm of Desulfovibrio vulgaris strain Hildenborough (DvH) and Enterobacter cloacae strain Hanford (EcH) varied dramatically, with a larger number of metals present in Enterobacter. For example, a total of 9 and 19 metals were assimilated into their cytoplasmic fractions, respectively, and DvH did not assimilate significant amounts of zinc or copper whereas EcH assimilated both. However, bioinformatic analysis of their genome sequences revealed a comparable number of predicted metalloproteins, 813 in DvH and 953 in EcH. These allowed some rationalization of the types of metal assimilated in some cases (Fe, Cu, Mo, W, V) but not in others (Zn, Nd, Ce, Pr, Dy, Hf and Th). It was also shown that U binds an unknown soluble protein in EcH but this incorporation was the result of extracellular U binding to cytoplasmic components after cell lysis.
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Affiliation(s)
- W Andrew Lancaster
- Department of Biochemistry & Molecular Biology, University of Georgia, Life Sciences Bldg., Athens, GA 30602-7229, USA.
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Dall'Agnol LT, Cordas CM, Moura JJ. Influence of respiratory substrate in carbon steel corrosion by a Sulphate Reducing Prokaryote model organism. Bioelectrochemistry 2014; 97:43-51. [DOI: 10.1016/j.bioelechem.2013.10.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 10/07/2013] [Accepted: 10/11/2013] [Indexed: 11/25/2022]
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23
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Clark ME, He Z, Redding AM, Joachimiak MP, Keasling JD, Zhou JZ, Arkin AP, Mukhopadhyay A, Fields MW. Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state. BMC Genomics 2012; 13:138. [PMID: 22507456 PMCID: PMC3431258 DOI: 10.1186/1471-2164-13-138] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 02/27/2012] [Indexed: 11/10/2022] Open
Abstract
Background Desulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations. In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. The biofilms were cultivated with lactate and sulfate in a continuously fed biofilm reactor, and compared to both batch and reactor planktonic populations. Results The functional genomic analysis demonstrated that biofilm cells were different compared to planktonic cells, and the majority of altered abundances for genes and proteins were annotated as hypothetical (unknown function), energy conservation, amino acid metabolism, and signal transduction. Genes and proteins that showed similar trends in detected levels were particularly involved in energy conservation such as increases in an annotated ech hydrogenase, formate dehydrogenase, pyruvate:ferredoxin oxidoreductase, and rnf oxidoreductase, and the biofilm cells had elevated formate dehydrogenase activity. Several other hydrogenases and formate dehydrogenases also showed an increased protein level, while decreased transcript and protein levels were observed for putative coo hydrogenase as well as a lactate permease and hyp hydrogenases for biofilm cells. Genes annotated for amino acid synthesis and nitrogen utilization were also predominant changers within the biofilm state. Ribosomal transcripts and proteins were notably decreased within the biofilm cells compared to exponential-phase cells but were not as low as levels observed in planktonic, stationary-phase cells. Several putative, extracellular proteins (DVU1012, 1545) were also detected in the extracellular fraction from biofilm cells. Conclusions Even though both the planktonic and biofilm cells were oxidizing lactate and reducing sulfate, the biofilm cells were physiologically distinct compared to planktonic growth states due to altered abundances of genes/proteins involved in carbon/energy flow and extracellular structures. In addition, average expression values for multiple rRNA transcripts and respiratory activity measurements indicated that biofilm cells were metabolically more similar to exponential-phase cells although biofilm cells are structured differently. The characterization of physiological advantages and constraints of the biofilm growth state for sulfate-reducing bacteria will provide insight into bioremediation applications as well as microbially-induced metal corrosion.
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Affiliation(s)
- Melinda E Clark
- Center for Biofilm Engineering, Montana State University, Bozeman, USA
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How sulphate-reducing microorganisms cope with stress: lessons from systems biology. Nat Rev Microbiol 2011; 9:452-66. [PMID: 21572460 DOI: 10.1038/nrmicro2575] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Sulphate-reducing microorganisms (SRMs) are a phylogenetically diverse group of anaerobes encompassing distinct physiologies with a broad ecological distribution. As SRMs have important roles in the biogeochemical cycling of carbon, nitrogen, sulphur and various metals, an understanding of how these organisms respond to environmental stresses is of fundamental and practical importance. In this Review, we highlight recent applications of systems biology tools in studying the stress responses of SRMs, particularly Desulfovibrio spp., at the cell, population, community and ecosystem levels. The syntrophic lifestyle of SRMs is also discussed, with a focus on system-level analyses of adaptive mechanisms. Such information is important for understanding the microbiology of the global sulphur cycle and for developing biotechnological applications of SRMs for environmental remediation, energy production, biocorrosion control, wastewater treatment and mineral recovery.
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25
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Abstract
Microorganisms can form tightly knit communities such as biofilms. Many others include marine snow, anaerobic digester granules, the ginger beer plant and bacterial colonies. This chapter is devoted to a survey of the main properties of these communities, with an emphasis on biofilms. We start with attachment to surfaces and the nature of adhesion. The growing community then forms within a matrix, generally of organic macromolecules. Inevitably the environment within such a matrix is different from that outside. Organisms respond by forming crowd-detection and response units; these quorum sensing systems act as switches between planktonic life and the dramatically altered conditions found inside microbial aggregates. The community then matures and changes and may even fail and disappear. Antimicrobial resistance is discussed as an example of multicellular behavior. The multicellular lifestyle has been modeled mathematically and responded to powerful molecular biological techniques. Latterly, microbial systems have been used as models for fundamental evolutionary processes, mostly because of their high rates of reproduction and the ease of genetic manipulation. The life of most microbes is a duality between the yin of the community and the yang of planktonic existence. Sadly far less research has been devoted to adaptation to free-living forms than in the opposite direction.
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Affiliation(s)
- Julian Wimpenny
- Cardiff School of Biosciences, Cardiff University, Cathays Park, Cardiff, Wales
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Gene expression by the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough grown on an iron electrode under cathodic protection conditions. Appl Environ Microbiol 2008; 74:2404-13. [PMID: 18310429 DOI: 10.1128/aem.02469-07] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome sequence of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough was reanalyzed to design unique 70-mer oligonucleotide probes against 2,824 probable protein-coding regions. These included three genes not previously annotated, including one that encodes a c-type cytochrome. Using microarrays printed with these 70-mer probes, we analyzed the gene expression profile of wild-type D. vulgaris grown on cathodic hydrogen, generated at an iron electrode surface with an imposed negative potential of -1.1 V (cathodic protection conditions). The gene expression profile of cells grown on cathodic hydrogen was compared to that of cells grown with gaseous hydrogen bubbling through the culture. Relative to the latter, the electrode-grown cells overexpressed two hydrogenases, the hyn-1 genes for [NiFe] hydrogenase 1 and the hyd genes, encoding [Fe] hydrogenase. The hmc genes for the high-molecular-weight cytochrome complex, which allows electron flow from the hydrogenases across the cytoplasmic membrane, were also overexpressed. In contrast, cells grown on gaseous hydrogen overexpressed the hys genes for [NiFeSe] hydrogenase. Cells growing on the electrode also overexpressed genes encoding proteins which promote biofilm formation. Although the gene expression profiles for these two modes of growth were distinct, they were more closely related to each other than to that for cells grown in a lactate- and sulfate-containing medium. Electrochemically measured corrosion rates were lower for iron electrodes covered with hyn-1, hyd, and hmc mutant biofilms than for wild-type biofilms. This confirms the importance, suggested by the gene expression studies, of the corresponding gene products in D. vulgaris-mediated iron corrosion.
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