1
|
Zhang H, Zhang W, Zong Y, Kong D, Zhao K. Factors Influencing Pseudomonas aeruginosa Initial Adhesion and Evolution at the Dodecane-Water Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:11274-11282. [PMID: 37524061 DOI: 10.1021/acs.langmuir.3c00901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Bacterial adhesion and evolution at the oil-water interface are important for a broad range of applications such as food manufacturing and microbial-enhanced oil recovery, etc. However, our understanding on bacterial interfacial adhesion and evolution, particularly at the single-cell level, is still far from complete. In this work, by employing Pseudomonas aeruginosa PAO1 at the dodecane-water interface as a model system, we have studied the effects of different factors on bacterial interfacial adhesion and the dynamic evolution of bacterial interfacial behavior at the single-cell level. The results show that PAO1 cells displayed a chemotactic behavior toward dodecane. Among the tested factors, bacterial initial interfacial attachment showed a negative correlation with the secreted cell-surface associated lipopolysaccharide and Psl while a positive correlation with type IV pili. Adding nonbiological surfactant Pluronic F-127, as expected, greatly reduced the cell interfacial adhesion. More importantly, the dynamics analysis of cell attachment/detachment at the dodecane-water interface over a long-time scale revealed a reversible to irreversible attachment transition of cells. This transition is accompanied with the interface aging resulting from bacterial activities, which led to an increase of the interfacial viscoelasticity with time and finally the formation of the gel-like interface. Further analysis demonstrated the important role of exopolysaccharides in the latter process. Our findings provide more details of bacterial oil-water interfacial behavior at the single-cell level and may shed light on developing new strategies for controlling bacterial colonization at the oil-water interface.
Collapse
Affiliation(s)
- Hong Zhang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Wenchao Zhang
- School of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Yiwu Zong
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Dongyang Kong
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Kun Zhao
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan 610054, China
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and The Institute of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610054, China
| |
Collapse
|
2
|
Li A, Chen K, Li B, Liang P, Shen C. Biphenyl-degrading Bacteria Isolation with Laser Induced Visualized Ejection Separation Technology and Traditional Colony Sorting. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2022; 109:571-576. [PMID: 35841406 DOI: 10.1007/s00128-022-03574-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
In this work, biphenyl was used as carbon source to enrich microorganisms from polychlorinated biphenyls (PCBs)-contaminated paddy soil samples, and the taxonomic structures in both of the soil samples and the fourth-generation enrichments were examined with high-throughput sequencing. Single cells were isolated from the enrichments via single cell sorting technology named Laser Induced Visualized Ejection Separation Technology (LIVEST) and also traditional single colony sorting, and the genera of the isolates were identified using 16S rRNA sequencing. The results from high-throughput sequencing present that enrichment from generation to generation can considerably change the microbial community. Comparing the two sorting methods, the LIVEST is more time-saving and cell-targeted for microbial resource exploration. Based on the further verification of biphenyl degradation, it was found that some strains belonging to genera Macrococcus, Aerococcus and Metabacillus are capable in degrading biphenyl, which have not been reported yet.
Collapse
Affiliation(s)
- Aili Li
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- China Coal Aerial Photogrammetry and Remote Sensing Group Co., Ltd., 710199, Xi'an, China
| | - Kezhen Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Bei Li
- The State Key Lab of Applied Optics, Fine Mechanics and Physics, Changchun Institute of Optics, CAS, 130033, Changchun, China
| | - Peng Liang
- The State Key Lab of Applied Optics, Fine Mechanics and Physics, Changchun Institute of Optics, CAS, 130033, Changchun, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
| |
Collapse
|
3
|
A tradeoff between physical encounters and consumption determines an optimal droplet size for microbial degradation of dispersed oil. Sci Rep 2022; 12:4734. [PMID: 35304520 PMCID: PMC8933409 DOI: 10.1038/s41598-022-08581-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 03/09/2022] [Indexed: 11/08/2022] Open
Abstract
Immiscible hydrocarbons occur in the ocean water column as droplets of varying diameters. Although microbial oil degradation is a central process in the remediation of hydrocarbon pollution in marine environments, the relationship between droplet size distribution and oil degradation rates by bacteria remains unclear, with a conflicting history of laboratory studies. Despite this knowledge gap, the use of chemical dispersants in oil spill response and mitigation is based on the rationale that increasing the surface-area-to-volume ratio of droplets will enhance net bacterial biodegradation rates. We demonstrate that this intuitive argument does not apply to most natural marine environments, where the abundance of oil droplets is much lower than in laboratory experiments and droplet-bacteria encounters are the limiting factor. We present a mechanistic encounter-consumption model to predict the characteristic time for oil degradation by marine bacteria as a function of the initial oil concentration, the distribution of droplet sizes, and the initial abundance of oil-degrading bacteria. We find that the tradeoff between the encounter time and the consumption time leads to an optimal droplet size larger than the average size generated by the application of dispersants. Reducing droplet size below this optimum can increase the persistence of oil droplets in the environment from weeks to years. The new perspective granted by this biophysical model of biodegradation that explicitly accounts for oil-microbe encounters changes our understanding of biodegradation particularly in the deep ocean, where droplets are often small and oil concentrations low, and explains degradation rate discrepancies between laboratory and field studies.
Collapse
|
4
|
Subbiahdoss G, Osmen S, Reimhult E. Cellulosic biofilm formation of Komagataeibacter in kombucha at oil-water interfaces. Biofilm 2022; 4:100071. [PMID: 35280972 PMCID: PMC8904243 DOI: 10.1016/j.bioflm.2022.100071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/06/2022] [Accepted: 02/09/2022] [Indexed: 11/02/2022] Open
Abstract
Bacteria forming biofilms at oil-water interfaces have diverse metabolism, they use hydrocarbons as a carbon and energy source. Kombucha is a fermented drink obtained from a complex symbiotic culture of bacteria and yeast, where acetic acid bacteria present in kombucha use sugars as a carbon source to produce cellulosic biofilms. We hypothesize that Komagataeibacteraceae in kombucha can adsorb to and use hydrocarbons as the sole energy source to produce cellulosic biofilms. Hence we characterized a kombucha culture, studied bacterial adsorption and cellulosic biofilm formation of kombucha at the n-decane or mineral oil-kombucha suspension interface. The cellulosic biofilms were imaged using fluorescence microscopy and cryo-scanning electron microscopy, and their time-dependent rheology was measured. Komagataeibacter, the dominant bacterial genus in the kombucha culture, produced cellulosic biofilms with reduced cellulose biomass yield at the oil-kombucha suspension interfaces compared to at the air-kombucha suspension interface. The presence of biosurfactants in the supernatant secreted by the kombucha microbes led to a larger and faster decrease in the interfacial tension on both oil types, leading to the formation of stable and elastic biofilm membranes. The difference in interfacial tension reduction was insignificant already after 2 h of biofilm formation at the mineral oil-kombucha suspension interface compared to kombucha microbes resuspended without biosurfactants but persisted for longer than 24 h in contact with n-decane. We also demonstrate that Komagataeibacter in kombucha can produce elastic cellulosic biofilms using hydrocarbons from the oil interface as the sole source of carbon and energy. Thus Komagataeibacter and kombucha shows the potential of this system for producing valued bacterial cellulose through remediation of hydrocarbon waste.
Collapse
|
5
|
Balmuri SR, Phandanouvong-Lozano V, House SD, Yang JC, Niepa TH. Mucoid Coating Provides a Growth Advantage to Pseudomonas aeruginosa at Oil–Water Interfaces. ACS APPLIED BIO MATERIALS 2022; 5:1868-1878. [DOI: 10.1021/acsabm.1c01198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
6
|
Subbiahdoss G, Reimhult E. Biofilm formation at oil-water interfaces is not a simple function of bacterial hydrophobicity. Colloids Surf B Biointerfaces 2020; 194:111163. [DOI: 10.1016/j.colsurfb.2020.111163] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/25/2020] [Accepted: 05/30/2020] [Indexed: 11/25/2022]
|
7
|
Biophysical methods to quantify bacterial behaviors at oil-water interfaces. J Ind Microbiol Biotechnol 2020; 47:725-738. [PMID: 32743734 DOI: 10.1007/s10295-020-02293-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/16/2020] [Indexed: 02/03/2023]
Abstract
Motivated by the need for improved understanding of physical processes involved in bacterial biodegradation of catastrophic oil spills, we review biophysical methods to probe bacterial motility and adhesion at oil-water interfaces. This review summarizes methods that probe bulk, average behaviors as well as local, microscopic behaviors, and highlights opportunities for future work to bridge the gap between biodegradation and biophysics.
Collapse
|
8
|
Meta-analysis, Meta-regression, and GRADE Assessment of Randomized and Nonrandomized Studies of Incisional Negative Pressure Wound Therapy Versus Control Dressings for the Prevention of Postoperative Wound Complications. Ann Surg 2019; 272:81-91. [DOI: 10.1097/sla.0000000000003644] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
9
|
Capozzi SL, Bodenreider C, Prieto A, Payne RB, Sowers KR, Kjellerup BV. Colonization and growth of dehalorespiring biofilms on carbonaceous sorptive amendments. BIOFOULING 2019; 35:50-58. [PMID: 30786761 DOI: 10.1080/08927014.2018.1563892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 12/19/2018] [Indexed: 06/09/2023]
Abstract
Removal of polychlorinated biphenyls (PCBs) from contaminated sediments is a priority due to accumulation in the food chain. Recent success with reduction of PCB bioavailability due to adsorption onto activated carbon led to the recognition of in situ treatment as a remediation approach. In this study, reduced bioavailability and subsequent break-down of PCBs in dehalorespiring biofilms was investigated using Dehalobium chlorocoercia DF1. DF1 formed a patchy biofilm ranging in thickness from 3.9 to 6.7 µm (average 4.6 ± 0.87 µm), while the biofilm coverage varied from 5.5% (sand) to 20.2% (activated carbon), indicating a preference for sorptive materials. Quantification of DF1 biofilm bacteria showed 1.2-15.3 × 109 bacteria per gram of material. After 22 days, coal activated carbon, bone biochar, polyoxymethylene, and sand microcosms had dechlorinated 73%, 93%, 100%, and 83%, respectively. These results show that a biofilm-based inoculum for bioaugmentation of PCBs in sediment can be an efficient approach.
Collapse
Affiliation(s)
- Staci L Capozzi
- a Department of Civil and Environmental Engineering , University of Maryland , College Park , MD , USA
- b Geosyntec Consultants , Columbia , MD , USA
| | - Coline Bodenreider
- a Department of Civil and Environmental Engineering , University of Maryland , College Park , MD , USA
| | - Ana Prieto
- c Department of Civil Engineering , Universidad de Chile , Santiago , Chile
| | - Rayford B Payne
- d Department of Marine Biotechnology, Institute of Marine and Environmental Technology , University of Maryland Baltimore County , Baltimore , MD , USA
| | - Kevin R Sowers
- d Department of Marine Biotechnology, Institute of Marine and Environmental Technology , University of Maryland Baltimore County , Baltimore , MD , USA
| | - Birthe Veno Kjellerup
- a Department of Civil and Environmental Engineering , University of Maryland , College Park , MD , USA
| |
Collapse
|
10
|
Zwanenburg PR, Tol BT, de Vries FE, Boermeester MA. Incisional Negative Pressure Wound Therapy for Surgical Site Infection Prophylaxis in the Post-Antibiotic Era. Surg Infect (Larchmt) 2018; 19:821-830. [DOI: 10.1089/sur.2018.212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Pieter R. Zwanenburg
- Department of Surgery, Amsterdam Gastroenterology and Metabolism, Amsterdam Infection and Immunity, Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Berend T. Tol
- Department of Surgery, Amsterdam Gastroenterology and Metabolism, Amsterdam Infection and Immunity, Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Fleur E.E. de Vries
- Department of Surgery, Amsterdam Gastroenterology and Metabolism, Amsterdam Infection and Immunity, Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Marja A. Boermeester
- Department of Surgery, Amsterdam Gastroenterology and Metabolism, Amsterdam Infection and Immunity, Amsterdam UMC, University of Amsterdam, the Netherlands
| |
Collapse
|
11
|
Lawrence JR, Winkler M, Neu TR. Multi-Parameter Laser Imaging Reveals Complex Microscale Biofilm Matrix in a Thick (4,000 μm) Aerobic Methanol Oxidizing Community. Front Microbiol 2018; 9:2186. [PMID: 30333795 PMCID: PMC6176653 DOI: 10.3389/fmicb.2018.02186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/27/2018] [Indexed: 11/13/2022] Open
Abstract
Although methanol has frequently been used as an inexpensive supplementary carbon source to support treatment processes, knowledge of the resultant microbial biofilms, their 3D architecture, microenvironments, exopolymer chemistry and populations remains limited. We supplied methanol as a supplementary carbon source to biofilms developing in rotating annular reactors. Analysis of circulation waters (1.0 l d-1) indicated that dissolved organic carbon was reduced by 25%, NO3-nitrogen by 95%, and total phosphorus by 70%. Analyses of populations using culture based techniques and fluorescence in situ hybridization indicated enrichment of nitrifiers, denitrifiers, and methylotrophic bacteria relative to reference biofilms not receiving methanol. The biofilms that developed were up to 4,000 μm thick. Staining with fluor conjugated lectins in combination with nucleic acid stains, revealed the presence of discrete bacterial cells inside complex globular polymeric structures. These structures were in turn surrounded by an interstitial polymer containing a variety of bacterial cell types. The globular structures bound FITC-conjugated lectins, from Canavalia ensiformis and Ulex europeaus. The FITC-lectin of Phaseolus vulgaris bound the surface of the globular structures and more generally within the matrix. Chemical analyses of the polymer paralleled the results of lectin analyses indicating that the dominant neutral sugars were glucose, galactose, mannose, rhamnose, with fucose and ribose as minor constituents. Amino sugars were not detected. Dual channel imaging with pH sensitive probes indicated that pH gradients from pH 4 to 7 occurred across the globular microcolonies. Critically for the maintenance of aerobic conditions throughout the thick biofilm it was extensively penetrated by a fine fissure network revealed by the location of fluorescent latex microbeads as detected by confocal laser scanning microscopy. Microelectrode studies confirmed the absence of any detectable Eh gradients within the biofilm. However, mobility of various size-fractionated fluorescent probes indicated that the basal region was only penetrated by the lowest molecular weight probes with a hydrated radius of 2.2 nm or less. These observations indicate the selection of a unique, thick (>4,000 μm) microbial community in which a self-organized architecture promotes the maintenance of optimal conditions and metabolism throughout the biofilm community.
Collapse
Affiliation(s)
- John R Lawrence
- Environment and Climate Change Canada, Saskatoon, SK, Canada
| | | | - Thomas R Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research, Magdeburg, Germany
| |
Collapse
|
12
|
Films of bacteria at interfaces. Adv Colloid Interface Sci 2017; 247:561-572. [PMID: 28778342 DOI: 10.1016/j.cis.2017.07.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/14/2017] [Accepted: 07/14/2017] [Indexed: 11/21/2022]
Abstract
Bacteria are often discussed as active colloids, self-propelled organisms whose collective motion can be studied in the context of non-equilibrium statistical mechanics. In such studies, the behavior of bacteria confined to interfaces or in the proximity of an interface plays an important role. For instance, many studies have probed collective behavior of bacteria in quasi two-dimensional systems such as soap films. Since fluid interfaces can adsorb surfactants and other materials, the stress and velocity boundary conditions at interfaces can alter bacteria motion; hydrodynamic studies of interfaces with differing boundary conditions are reviewed. Also, bacteria in bulk can become trapped at or near fluid interfaces, where they colonize and form structures comprising secretions like exopolysaccharides, surfactants, living and dead bacteria, thereby creating Films of Bacteria at Interfaces (FBI). The formation of FBI is discussed at air-water, oil-water, and water-water interfaces, with an emphasis on film mechanics, and with some allusion to genetic functions guiding bacteria to restructure fluid interfaces. At air-water interfaces, bacteria form pellicles or interfacial biofilms. Studies are reviewed that reveal that pellicle material properties differ for different strains of bacteria, and that pellicle physicochemistry can act as a feedback mechanism to regulate film formation. At oil-water interfaces, a range of FBI form, depending on bacteria strain. Some bacteria-laden interfaces age from an initial active film, with dynamics dominated by motile bacteria, through viscoelastic states, to form an elastic film. Others remain active with no evidence of elastic film formation even at significant interface ages. Finally, bacteria can adhere to and colonize ultra-low surface tension interfaces such as aqueous-aqueous systems common in food industries. Relevant literature is reviewed, and areas of interest for potential application are discussed, ranging from health to bioremediation.
Collapse
|
13
|
Weiland-Bräuer N, Fischer MA, Schramm KW, Schmitz RA. Polychlorinated Biphenyl (PCB)-Degrading Potential of Microbes Present in a Cryoconite of Jamtalferner Glacier. Front Microbiol 2017; 8:1105. [PMID: 28663747 PMCID: PMC5471330 DOI: 10.3389/fmicb.2017.01105] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/31/2017] [Indexed: 12/17/2022] Open
Abstract
Aiming to comprehensively survey the potential pollution of an alpine cryoconite (Jamtalferner glacier, Austria), and its bacterial community structure along with its biodegrading potential, first chemical analyses of persistent organic pollutants, explicitly polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) as well as polycyclic aromatic hydrocarbons (PAHs), revealed a significant contamination. In total, 18 PCB congeners were detected by high resolution gas chromatography/mass spectrometry with a mean concentration of 0.8 ng/g dry weight; 16 PAHs with an average concentration of 1,400 ng/g; and 26 out of 29 OCPs with a mean concentration of 2.4 ng/g. Second, the microbial composition was studied using 16S amplicon sequencing. The analysis revealed high abundances of Proteobacteria (66%), the majority representing α-Proteobacteria (87%); as well as Cyanobacteria (32%), however high diversity was due to 11 low abundant phyla comprising 75 genera. Biodegrading potential of cryoconite bacteria was further analyzed using enrichment cultures (microcosms) with PCB mixture Aroclor 1242. 16S rDNA analysis taxonomically classified 37 different biofilm-forming and PCB-degrading bacteria, represented by Pseudomonas, Shigella, Subtercola, Chitinophaga, and Janthinobacterium species. Overall, the combination of culture-dependent and culture-independent methods identified degrading bacteria that can be potential candidates to develop novel bioremediation strategies.
Collapse
Affiliation(s)
- Nancy Weiland-Bräuer
- Institute for General Microbiology, Christian-Albrechts-Universität zu KielKiel, Germany
| | - Martin A. Fischer
- Institute for General Microbiology, Christian-Albrechts-Universität zu KielKiel, Germany
| | - Karl-Werner Schramm
- Molecular EXposomics, German Research Center for Environmental Health, Helmholtz Zentrum München GmbHNeuherberg, Germany
| | - Ruth A. Schmitz
- Institute for General Microbiology, Christian-Albrechts-Universität zu KielKiel, Germany
| |
Collapse
|
14
|
Miquel Guennoc C, Rose C, Guinnet F, Miquel I, Labbé J, Deveau A. A New Method for Qualitative Multi-scale Analysis of Bacterial Biofilms on Filamentous Fungal Colonies Using Confocal and Electron Microscopy. J Vis Exp 2017. [PMID: 28190036 PMCID: PMC5352296 DOI: 10.3791/54771] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Bacterial biofilms frequently form on fungal surfaces and can be involved in numerous bacterial-fungal interaction processes, such as metabolic cooperation, competition, or predation. The study of biofilms is important in many biological fields, including environmental science, food production, and medicine. However, few studies have focused on such bacterial biofilms, partially due to the difficulty of investigating them. Most of the methods for qualitative and quantitative biofilm analyses described in the literature are only suitable for biofilms forming on abiotic surfaces or on homogeneous and thin biotic surfaces, such as a monolayer of epithelial cells. While laser scanning confocal microscopy (LSCM) is often used to analyze in situ and in vivo biofilms, this technology becomes very challenging when applied to bacterial biofilms on fungal hyphae, due to the thickness and the three dimensions of the hyphal networks. To overcome this shortcoming, we developed a protocol combining microscopy with a method to limit the accumulation of hyphal layers in fungal colonies. Using this method, we were able to investigate the development of bacterial biofilms on fungal hyphae at multiple scales using both LSCM and scanning electron microscopy (SEM). This report describes the protocol, including microorganism cultures, bacterial biofilm formation conditions, biofilm staining, and LSCM and SEM visualizations.
Collapse
Affiliation(s)
| | - Christophe Rose
- Ecologie et Ecophysiologie Forestières - PTEF, UMR 1137, INRA Université de Lorraine
| | - Frédéric Guinnet
- Interactions Arbres - Microorganismes, UMR1136, INRA Université de Lorraine
| | - Igor Miquel
- Interactions Arbres - Microorganismes, UMR1136, INRA Université de Lorraine
| | - Jessy Labbé
- Biosciences Division, Oak Ridge National Laboratory
| | - Aurélie Deveau
- Interactions Arbres - Microorganismes, UMR1136, INRA Université de Lorraine;
| |
Collapse
|
15
|
|
16
|
Zhang Z, Christopher G. Effect of Particulate Contaminants on the Development of Biofilms at Air/Water Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:2724-30. [PMID: 26943272 DOI: 10.1021/acs.langmuir.6b00143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The development of biofilms at air/water or oil/water interfaces has important ramifications on several applications, but it has received less attention than biofilm formation on solid surfaces. A key difference between the growth of biofilms on solid surfaces versus liquid interfaces is the range of complicated boundary conditions the liquid interface can create that may affect bacteria, as they adsorb onto and grow on the interface. This situation is exacerbated by the existence of complex interfaces in which interfacially adsorbed components can even more greatly affect interfacial boundary conditions. In this work, we present evidence as to how particle-laden interfaces impact biofilm growth at an air/water interface. We find that particles can enhance the rate of growth and final strength of biofilms at liquid interfaces by providing sites of increased adhesive strength for bacteria. The increased adhesion stems from creating localized areas of hydrophobicity that protrude in the water phase and provide sites where bacteria preferentially adhere. This mechanism is found to be primarily controlled by particle composition, with particle size providing a secondary effect. This increased adhesion through interfacial conditions creates biofilms with properties similar to those observed when adhesion is increased through biological means. Because of the generally understood ubiquity of increased bacteria attachment to hydrophobic surfaces, this result has general applicability to pellicle formation for many pellicle-forming bacteria.
Collapse
Affiliation(s)
- Zhenhuan Zhang
- Department of Mechanical Engineering, Texas Tech University , Lubbock, Texas 79409-1035, United States
| | - Gordon Christopher
- Department of Mechanical Engineering, Texas Tech University , Lubbock, Texas 79409-1035, United States
| |
Collapse
|
17
|
Amine Ben Mlouka M, Cousseau T, Di Martino P. Application of fluorescently labelled lectins for the study of polysaccharides in biofilms with a focus on biofouling of nanofiltration membranes. AIMS MOLECULAR SCIENCE 2016. [DOI: 10.3934/molsci.2016.3.338] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
18
|
Imaging Bacterial Cells and Biofilms Adhering to Hydrophobic Organic Compound–Water Interfaces. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/8623_2015_80] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
|
19
|
Rühs P, Böcker L, Inglis R, Fischer P. Studying bacterial hydrophobicity and biofilm formation at liquid–liquid interfaces through interfacial rheology and pendant drop tensiometry. Colloids Surf B Biointerfaces 2014; 117:174-84. [DOI: 10.1016/j.colsurfb.2014.02.023] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 02/06/2014] [Accepted: 02/12/2014] [Indexed: 12/17/2022]
|
20
|
Applications of biofilms in bioremediation and biotransformation of persistent organic pollutants, pharmaceuticals/personal care products, and heavy metals. Appl Microbiol Biotechnol 2013; 97:9909-21. [PMID: 24150788 DOI: 10.1007/s00253-013-5216-z] [Citation(s) in RCA: 161] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 08/23/2013] [Accepted: 08/24/2013] [Indexed: 12/25/2022]
Abstract
In this review, the strategies being employed to exploit the inherent durability of biofilms and the diverse nutrient cycling of the microbiome for bioremediation are explored. Focus will be given to halogenated compounds, hydrocarbons, pharmaceuticals, and personal care products as well as some heavy metals and toxic minerals, as these groups represent the majority of priority pollutants. For decades, industrial processes have been creating waste all around the world, resulting in contaminated sediments and subsequent, far-reaching dispersal into aquatic environments. As persistent pollutants have accumulated and are still being created and disposed, the incentive to find suitable and more efficient solutions to effectively detoxify the environment is even greater. Indigenous bacterial communities are capable of metabolizing persistent organic pollutants and oxidizing heavy metal contaminants. However, their low abundance and activity in the environment, difficulties accessing the contaminant or nutrient limitations in the environment all prevent the processes from occurring as quickly as desired and thus reaching the proposed clean-up goals. Biofilm communities provide among other things a beneficial structure, possibility for nutrient, and genetic exchange to participating microorganisms as well as protection from the surrounding environment concerning for instance predation and chemical and shear stresses. Biofilms can also be utilized in other ways as biomarkers for monitoring of stream water quality from for instance mine drainage. The durability and structure of biofilms together with the diverse array of structural and metabolic characteristics make these communities attractive actors in biofilm-mediated remediation solutions and ecosystem monitoring.
Collapse
|
21
|
Sowers KR, May HD. In situ treatment of PCBs by anaerobic microbial dechlorination in aquatic sediment: are we there yet? Curr Opin Biotechnol 2013; 24:482-8. [PMID: 23102490 PMCID: PMC3572274 DOI: 10.1016/j.copbio.2012.10.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Revised: 09/14/2012] [Accepted: 10/03/2012] [Indexed: 11/29/2022]
Abstract
The remediation of polychlorinated biphenyls (PCBs) in soils and sediments remains a particularly difficult problem to solve. The possibility of in situ degradation by microorganisms has been pursued for many years since this approach has the potential to provide a cost-effective and environmentally sustainable alternative to dredging for treatment of PCB impacted sites. Being hydrophobic, PCBs partition into organic material and accumulate in anoxic environments well poised to support anaerobic dechlorination of highly chlorinated congeners; products of which are susceptible to complete aerobic degradation. Laboratory research over the past 25 years is now leading to new microbial technologies that could soon be tested for treatment of PCB impacted sediments in the field.
Collapse
Affiliation(s)
- Kevin R Sowers
- Department of Marine Biotechnology, University of Maryland Baltimore County and Institute of Marine & Environmental Technology, University of Maryland, Baltimore, MD, USA
| | | |
Collapse
|
22
|
Parallel analysis of 7 food-borne pathogens using capillary electrophoresis-based single-strand conformation polymorphism. Food Sci Biotechnol 2010. [DOI: 10.1007/s10068-010-0206-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
|
23
|
Dmitriev VV, Crowley D, Rogachevsky VV, Negri CM, Rusakova TG, Kolesnikova SA, Akhmetov LI. Microorganisms form exocellular structures, trophosomes, to facilitate biodegradation of oil in aqueous media. FEMS Microbiol Lett 2010; 315:134-40. [DOI: 10.1111/j.1574-6968.2010.02184.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
24
|
Correa PA, Lin L, Just CL, Hu D, Hornbuckle KC, Schnoor JL, Van Aken B. The effects of individual PCB congeners on the soil bacterial community structure and the abundance of biphenyl dioxygenase genes. ENVIRONMENT INTERNATIONAL 2010; 36:901-6. [PMID: 19716603 PMCID: PMC2928393 DOI: 10.1016/j.envint.2009.07.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2008] [Revised: 07/19/2009] [Accepted: 07/21/2009] [Indexed: 05/19/2023]
Abstract
Polychlorinated biphenyls (PCBs) are toxic environmental contaminants that represent a class of 209 congeners characterized by different degrees of chlorination and substitution patterns. Most of experimental studies about microbial degradation of PCBs have been conducted on PCB mixtures, even though evidence accumulated in bacteria and other organisms shows that exposure to different congeners may have different biological effects. Microcosm experiments were conducted using aerobic agitated soil slurries individually exposed to PCB congeners with different degrees of chlorination: PCB-3, 15, 28, and 77, and the commercial mixture Aroclor 1242. After four weeks of incubation, PCBs were analyzed by gas chromatography/mass spectrometry (GC/MS) showing different transformation extents: With the exception of PCB-15 that was not significantly transformed (7%), biodegradation rates decreased with the degree of chlorination, from 75% for PCB-3 to 22% for PCB-77 and Aroclor 1242. The bacterial abundance, as measured by colony counting and 16S rDNA quantification by real-time PCR, was lower (of about 40%) in soil microcosms exposed to the higher-chlorinated congeners, PCB-28, PCB-77, and Aroclor 1242, as compared to non-exposed soils and soils exposed to the lower-chlorinated congeners, PCB-3 and PCB-15. The relative abundance of different taxonomic groups, as determined by real-time PCR, revealed an increase of β-Proteobacteria and Actinobacteria in all microcosms exposed to PCBs, as compared with non-exposed soil. In addition, exposure to PCB-77 and Aroclor 1242 resulted in a higher abundance of α-Proteobacteria and Acidobacteria. Globally, these results suggest that exposure to PCBs (and especially to higher-chlorinated congeners and Aroclor 1242) selected bacterial groups involving most known PCB degraders, i.e., β-Proteobacteria and Acidobacteria. The quantification of biphenyl dioxygenase (BPH) genes--involved in the aerobic degradation of PCBs--using real-time PCR showed that exposure to all PCB congeners and Aroclor 1242 resulted in a marked increase of two out of the four BPH genes tested, similarly suggesting the selection of PCB-degrading bacteria. This paper showed that exposure to different PCB congeners leads to different structures of the soil bacterial community and BPH genes expression patterns.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Benoit Van Aken
- Temple University, Philadelphia, PA
- Author for correspondence: Temple University, Civil and Environmental Engineering 1947 North 12th Street, Philadelphia, PA 19122 Tel: 1- 215-204-7800 Fax: 1- 215-204-4696
| |
Collapse
|
25
|
Cell surface properties affect colonisation of raw milk by lactic acid bacteria at the microstructure level. Food Res Int 2010. [DOI: 10.1016/j.foodres.2010.04.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
26
|
Lafortune I, Juteau P, Déziel E, Lépine F, Beaudet R, Villemur R. Bacterial diversity of a consortium degrading high-molecular-weight polycyclic aromatic hydrocarbons in a two-liquid phase biosystem. MICROBIAL ECOLOGY 2009; 57:455-468. [PMID: 18615233 DOI: 10.1007/s00248-008-9417-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Accepted: 06/05/2008] [Indexed: 05/26/2023]
Abstract
High-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs) are pollutants that persist in the environment due to their low solubility in water and their sequestration by soil and sediments. Although several PAH-degrading bacterial species have been isolated, it is not expected that a single isolate would exhibit the ability to degrade completely all PAHs. A consortium composed of different microorganisms can better achieve this. Two-liquid phase (TLP) culture systems have been developed to increase the bioavailability of poorly soluble substrates for uptake and biodegradation by microorganisms. By combining a silicone oil-water TLP system with a microbial consortium capable of degrading HMW PAHs, we previously developed a highly efficient PAH-degrading system. In this report, we characterized the bacterial diversity of the consortium with a combination of culture-dependent and culture-independent methods. Polymerase chain reaction (PCR) of part of the 16S ribosomal RNA gene (rDNA) sequences combined with denaturing gradient gel electrophoresis was used to monitor the bacterial population changes during PAH degradation of the consortium when pyrene, chrysene, and benzo[a]pyrene were provided together or separately in the TLP cultures. No substantial changes in bacterial profiles occurred during biodegradation of pyrene and chrysene in these cultures. However, the addition of the low-molecular-weight PAHs phenanthrene or naphthalene in the system favored one bacterial species related to Sphingobium yanoikuyae. Eleven bacterial strains were isolated from the consortium but, interestingly, only one-IAFILS9 affiliated to Novosphingobium pentaromativorans-was capable of growing on pyrene and chrysene as sole source of carbon. A 16S rDNA library was derived from the consortium to identify noncultured bacteria. Among 86 clones screened, 20 were affiliated to different bacterial species-genera. Only three strains were represented in the screened clones. Eighty-five percent of clones and strains were affiliated to Alphaproteobacteria and Betaproteobacteria; among them, several were affiliated to bacterial species known for their PAH degradation activities such as those belonging to the Sphingomonadaceae. Finally, three genes involved in the degradation of aromatic molecules were detected in the consortium and two in IAFILS9. This study provides information on the bacterial composition of a HWM PAH-degrading consortium and its dynamics in a TLP biosystem during PAH degradation.
Collapse
|
27
|
Polerecky L, Bissett A, Al-Najjar M, Faerber P, Osmers H, Suci PA, Stoodley P, de Beer D. Modular spectral imaging system for discrimination of pigments in cells and microbial communities. Appl Environ Microbiol 2009; 75:758-71. [PMID: 19074609 PMCID: PMC2632136 DOI: 10.1128/aem.00819-08] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2008] [Accepted: 11/24/2008] [Indexed: 11/20/2022] Open
Abstract
Here we describe a spectral imaging system for minimally invasive identification, localization, and relative quantification of pigments in cells and microbial communities. The modularity of the system allows pigment detection on spatial scales ranging from the single-cell level to regions whose areas are several tens of square centimeters. For pigment identification in vivo absorption and/or autofluorescence spectra are used as the analytical signals. Along with the hardware, which is easy to transport and simple to assemble and allows rapid measurement, we describe newly developed software that allows highly sensitive and pigment-specific analyses of the hyperspectral data. We also propose and describe a number of applications of the system for microbial ecology, including identification of pigments in living cells and high-spatial-resolution imaging of pigments and the associated phototrophic groups in complex microbial communities, such as photosynthetic endolithic biofilms, microbial mats, and intertidal sediments. This system provides new possibilities for studying the role of spatial organization of microorganisms in the ecological functioning of complex benthic microbial communities or for noninvasively monitoring changes in the spatial organization and/or composition of a microbial community in response to changing environmental factors.
Collapse
Affiliation(s)
- Lubos Polerecky
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Liu Y, Zhang W, Sileika T, Warta R, Cianciotto NP, Packman A. Role of bacterial adhesion in the microbial ecology of biofilms in cooling tower systems. BIOFOULING 2009; 25:241-53. [PMID: 19177226 PMCID: PMC2723952 DOI: 10.1080/08927010802713414] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The fate of the three heterotrophic biofilm forming bacteria, Pseudomonas aeruginosa, Klebsiella pneumoniae and Flavobacterium sp. in pilot scale cooling towers was evaluated both by observing the persistence of each species in the recirculating water and the formation of biofilms on steel coupons placed in each cooling tower water reservoir. Two different cooling tower experiments were performed: a short-term study (6 days) to observe the initial bacterial colonization of the cooling tower, and a long-term study (3 months) to observe the ecological dynamics with repeated introduction of the test strains. An additional set of batch experiments (6 days) was carried out to evaluate the adhesion of each strain to steel surfaces under similar conditions to those found in the cooling tower experiments. Substantial differences were observed in the microbial communities that developed in the batch systems and cooling towers. P. aeruginosa showed a low degree of adherence to steel surfaces both in batch and in the cooling towers, but grew much faster than K. pneumoniae and Flavobacterium in mixed-species biofilms and ultimately became the dominant organism in the closed batch systems. However, the low degree of adherence caused P. aeruginosa to be rapidly washed out of the open cooling tower systems, and Flavobacterium became the dominant microorganism in the cooling towers in both the short-term and long-term experiments. These results indicate that adhesion, retention and growth on solid surfaces play important roles in the bacterial community that develops in cooling tower systems.
Collapse
Affiliation(s)
- Yang Liu
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Wei Zhang
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Tadas Sileika
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Richard Warta
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Nicholas P. Cianciotto
- Department of Microbiology-Immunology, Northwestern University Medical School, Chicago, IL, USA
| | - Aaron Packman
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| |
Collapse
|
29
|
Towards a nondestructive chemical characterization of biofilm matrix by Raman microscopy. Anal Bioanal Chem 2008; 393:197-206. [DOI: 10.1007/s00216-008-2470-5] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Revised: 10/08/2008] [Accepted: 10/09/2008] [Indexed: 10/21/2022]
|
30
|
Nocker A, Lepo JE, Martin LL, Snyder RA. Genotypic microbial community profiling: a critical technical review. MICROBIAL ECOLOGY 2007; 54:532-42. [PMID: 17351811 DOI: 10.1007/s00248-007-9236-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2006] [Revised: 10/23/2006] [Accepted: 11/23/2006] [Indexed: 05/04/2023]
Abstract
Microbial ecology has undergone a profound change in the last two decades with regard to methods employed for the analysis of natural communities. Emphasis has shifted from culturing to the analysis of signature molecules including molecular DNA-based approaches that rely either on direct cloning and sequencing of DNA fragments (shotgun cloning) or often rely on prior amplification of target sequences by use of the polymerase chain reaction (PCR). The pool of PCR products can again be either cloned and sequenced or can be subjected to an increasing variety of genetic profiling methods, including amplified ribosomal DNA restriction analysis, automated ribosomal intergenic spacer analysis, terminal restriction fragment length polymorphism, denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, single strand conformation polymorphism, and denaturing high-performance liquid chromatography. In this document, we present and critically compare these methods commonly used for the study of microbial diversity.
Collapse
Affiliation(s)
- Andreas Nocker
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, FL 32514, USA
| | | | | | | |
Collapse
|
31
|
Nocker A, Burr M, Camper AK. Genotypic microbial community profiling: a critical technical review. MICROBIAL ECOLOGY 2007; 54:276-89. [PMID: 17345133 DOI: 10.1007/s00248-006-9199-5] [Citation(s) in RCA: 208] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Revised: 11/27/2006] [Accepted: 12/12/2006] [Indexed: 05/14/2023]
Abstract
Microbial ecology has undergone a profound change in the last two decades with regard to methods employed for the analysis of natural communities. Emphasis has shifted from culturing to the analysis of signature molecules including molecular DNA-based approaches that rely either on direct cloning and sequencing of DNA fragments (shotgun cloning) or often rely on prior amplification of target sequences by use of the polymerase chain reaction (PCR). The pool of PCR products can again be either cloned and sequenced or can be subjected to an increasing variety of genetic profiling methods, including amplified ribosomal DNA restriction analysis, automated ribosomal intergenic spacer analysis, terminal restriction fragment length polymorphism, denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, single strand conformation polymorphism, and denaturing high-performance liquid chromatography. In this document, we present and critically compare these methods commonly used for the study of microbial diversity.
Collapse
Affiliation(s)
- Andreas Nocker
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717-3980, USA.
| | | | | |
Collapse
|
32
|
Zinger L, Gury J, Giraud F, Krivobok S, Gielly L, Taberlet P, Geremia RA. Improvements of polymerase chain reaction and capillary electrophoresis single-strand conformation polymorphism methods in microbial ecology: toward a high-throughput method for microbial diversity studies in soil. MICROBIAL ECOLOGY 2007; 54:203-16. [PMID: 17587075 DOI: 10.1007/s00248-006-9151-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Revised: 06/27/2006] [Accepted: 07/24/2006] [Indexed: 05/15/2023]
Abstract
The molecular signature of bacteria from soil ecosystems is an important tool for studying microbial ecology and biogeography. However, a high-throughput technology is needed for such studies. In this article, we tested the suitability of available methods ranging from soil DNA extraction to capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) for high-throughput studies. Our results showed that the extraction method does not dramatically influence CE-SSCP profiles, and that DNA extraction of a 0.25 g soil sample is sufficient to observe overall bacterial diversity in soil matrices. The V3 region of the 16S rRNA gene was amplified by PCR, and the extension time was found to be critical. We have also found that proofreading DNA polymerases generate a better signal in CE-SSCP profiles. Experiments performed with different soil matrices revealed the repeatability, efficiency, and consistency of CE-SSCP. Studies on PCR and CE-SSCP using single-species genomic DNA as a matrix showed that several ribotypes may migrate at the same position, and also that single species can produce double peaks. Thus, the extrapolation between number of peaks and number of species remains difficult. Additionally, peak detection is limited by the analysis software. We conclude that the presented method, including CE-SSCP and the analyzing step, is a simple and effective technique to obtain the molecular signature of a given soil sample.
Collapse
Affiliation(s)
- Lucie Zinger
- Laboratoire d'Ecologie Alpine, Perturbations Environnementales et Xénobiotiques, CNRS UMR 5553, Université Joseph Fourier, Grenoble Cedex 9, France
| | | | | | | | | | | | | |
Collapse
|
33
|
Macedo AJ, Timmis KN, Abraham WR. Widespread capacity to metabolize polychlorinated biphenyls by diverse microbial communities in soils with no significant exposure to PCB contamination. Environ Microbiol 2007; 9:1890-7. [PMID: 17635537 DOI: 10.1111/j.1462-2920.2007.01305.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The purpose of this work was to determine the extent of microbial metabolic potential for polychlorinated biphenyls (PCBs) in soils that have had no previous exposure to this class of xenobiotic pollutants. Soil and sediment samples of distinct characteristics from six sites in Germany were used to inoculate PCB oil (Aroclor 1242) microdroplets. All samples yielded multispecies biofilms, as revealed by single-strand conformation polymorphism (SSCP) analyses of polymerase chain reaction (PCR) analysis of 16S rRNA genes, and sequence analysis of the main amplicons. Microbes representing 20 different operational taxonomic units (OTUs) were identified in the biofilms, but only a few were common to all biofilms, namely those closely related to Aquabacterium sp., Caulobacter sp., Imtechium assamiensis, Nevskia ramosa, Parvibaculum lavamentivorans and Burkholderia sp. The PCB biofilm communities were always distinct from control biofilms developing from the same samples in the absence of PCB. All PCB droplet-grown biofilms degraded multiple PCB congeners but differed in the congener spectra they degraded. These findings reveal that microbial potential to degrade PCBs is widespread in soils that have not been subjected to PCB contamination, and that this potential is characteristic of consortia of very diverse phylogenetic composition.
Collapse
Affiliation(s)
- Alexandre J Macedo
- Helmholtz Center for Infection Research (formerly GBF), Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | | | | |
Collapse
|