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Neu TR, Kuhlicke U, Karwautz C, Lüders T. Unique architecture of microbial snottites from a methane driven biofilm revealed by confocal microscopy. Microsc Res Tech 2024; 87:205-213. [PMID: 37724509 DOI: 10.1002/jemt.24422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/24/2023] [Accepted: 09/06/2023] [Indexed: 09/20/2023]
Abstract
Microbial biofilms occur in many shapes and different dimensions. In natural and semi-artificial caves they are forming pendulous structures of 10 cm and more. In this study a methane driven microbial community of a former medicinal spring was investigated. The habitat was completely covered by massive biofilms and snottites with a wobbly, gelatinous appearance. By using fluorescence techniques in combination with confocal laser scanning microscopy the architecture of these so far unknown snottites was examined. The imaging approaches applied comprised reflection of geogenic and cellular origin, possible autofluorescence, nucleic acid staining for bacterial cells, protein staining for bacteria and extracellular fine structures, calcofluor white for β 1 → 3, β 1 → 4 polysaccharide staining for possible fungi as well as lectin staining for the extracellular biofilm matrix glycoconjugates. The results showed a highly complex, intricate structure with voluminous, globular, and tube-like glycoconjugates of different dimensions and densities. In addition, filamentous bacteria seem to provide additional strength to the snottites. After screening with all commercially available lectins, by means of fluorescence lectin barcoding and subsequent fluorescence lectin binding analysis, the AAL, PNA, LEA, and Ban lectins identified α-Fuc, β-Gal, β-GlcNAc, and α-Man with α-Fuc as a major component. Examination of the outer boundary with fluorescent beads revealed a potential outer layer which could not be stained by any of the fluorescent probes applied. Finally, suggestions are made to further elucidate the characteristics of these unusual microbial biofilms in form of snottites. RESEARCH HIGHLIGHTS: The gelatinous snottites revealed at the microscale a highly complex structure not seen before. The extracellular matrix of the snottite biofilm was identified as clusters of different shape and density. The matrix of snottites was examined by taking advantage of 78 fluorescently-labeled lectins. The extracellular matrix glycoconjugates of snottites identified comprised: α-Fuc, β-Gal, β-GlcNAc, and α-Man. Probing the snottite outer surface indicated an additional unknown stratum.
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Affiliation(s)
- Thomas R Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research - UFZ, Magdeburg, Germany
| | - Ute Kuhlicke
- Department of River Ecology, Helmholtz Centre for Environmental Research - UFZ, Magdeburg, Germany
| | - Clemens Karwautz
- Institute of Groundwater Ecology, Helmholtz Zentrum München-German Research Centre for Environmental Health, Neuherberg, Germany
| | - Tillmann Lüders
- Institute of Groundwater Ecology, Helmholtz Zentrum München-German Research Centre for Environmental Health, Neuherberg, Germany
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Neu TR, Kuhlicke U. Matrix glycoconjugate characterization in multispecies biofilms and bioaggregates from the environment by means of fluorescently-labeled lectins. Front Microbiol 2022; 13:940280. [PMID: 36003926 PMCID: PMC9395170 DOI: 10.3389/fmicb.2022.940280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/29/2022] [Indexed: 12/03/2022] Open
Abstract
Environmental biofilms represent a complex mixture of different microorganisms. Their identity is usually analyzed by means of nucleic acid-based techniques. However, these biofilms are also composed of a highly complex extracellular matrix produced by the microbes within a particular biofilm system. The biochemical identity of this extracellular matrix remains in many cases an intractable part of biofilms and bioaggregates. Consequently, there is a need for an approach that will give access to the fully hydrated structure of the extracellular matrix or at least a major part of it. A crucial compound of the matrix identified as carbohydrate-based polymers represents major structural and functional constituents. These glycoconjugates can be characterized by using fluorescently-labeled lectins in combination with confocal laser scanning microscopy. The lectin approach is defined previously, as fluorescence lectin barcoding (FLBC) and fluorescence lectin-binding analysis (FLBA), where FLBC is equal to the screening of a particular sample with all the commercially available lectins and FLBA is the actual analysis of the matrix throughout an experiment with a selected panel of lectins. As the application of immune-based techniques in environmental biofilm systems is impossible, the lectin approach is currently the only option for probing lectin-specific glycoconjugates in complex biofilms and bioaggregates. From all the commercially available lectins tested, the lectins such as AAL, HAA, WGA, ConA, IAA, HPA, and LEA showed the highest binding efficiency. Furthermore, 20 of the overall lectins tested showed an intermediate signal intensity, nevertheless very useful for the assessment of matrix glycoconjugates. With the data compiled, we shall virtually shed more light on the dark matter of the extracellular matrix and their 3-dimensional distribution in environmental biofilm systems. The results will be helpful in future studies with a focus on the extracellular matrix glycoconjugates present in environmental microbial communities.
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Krause S, Gfrerer S, von Kügelgen A, Reuse C, Dombrowski N, Villanueva L, Bunk B, Spröer C, Neu TR, Kuhlicke U, Schmidt-Hohagen K, Hiller K, Bharat TAM, Rachel R, Spang A, Gescher J. The importance of biofilm formation for cultivation of a Micrarchaeon and its interactions with its Thermoplasmatales host. Nat Commun 2022; 13:1735. [PMID: 35365607 PMCID: PMC8975820 DOI: 10.1038/s41467-022-29263-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 02/28/2022] [Indexed: 01/05/2023] Open
Abstract
Micrarchaeota is a distinctive lineage assigned to the DPANN archaea, which includes poorly characterised microorganisms with reduced genomes that likely depend on interactions with hosts for growth and survival. Here, we report the enrichment of a stable co-culture of a member of the Micrarchaeota (Ca. Micrarchaeum harzensis) together with its Thermoplasmatales host (Ca. Scheffleriplasma hospitalis), as well as the isolation of the latter. We show that symbiont-host interactions depend on biofilm formation as evidenced by growth experiments, comparative transcriptomic analyses and electron microscopy. In addition, genomic, metabolomic, extracellular polymeric substances and lipid content analyses indicate that the Micrarchaeon symbiont relies on the acquisition of metabolites from its host. Our study of the cell biology and physiology of a Micrarchaeon and its host adds to our limited knowledge of archaeal symbioses. The Micrarchaeota lineage includes poorly characterized archaea with reduced genomes that likely depend on host interactions for survival. Here, the authors report a stable co-culture of a member of the Micrarchaeota and its host, and use multi-omic and physiological analyses to shed light on this symbiosis.
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Affiliation(s)
- Susanne Krause
- Department of Applied Biology, Karlsruhe, Institute of Technology (KIT), Karlsruhe, Germany
| | - Sabrina Gfrerer
- Department of Applied Biology, Karlsruhe, Institute of Technology (KIT), Karlsruhe, Germany.,Institute for Biological Interfaces, Karlsruhe, Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Andriko von Kügelgen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom
| | - Carsten Reuse
- Bioinformatics & Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre for Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Boyke Bunk
- Leibniz Institute DSMZ, Braunschweig, Germany
| | | | - Thomas R Neu
- Helmholtz-Centre for Environmental, Research UFZ, Magdeburg, Germany
| | - Ute Kuhlicke
- Helmholtz-Centre for Environmental, Research UFZ, Magdeburg, Germany
| | - Kerstin Schmidt-Hohagen
- Bioinformatics & Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre for Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Karsten Hiller
- Bioinformatics & Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre for Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom.,Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom
| | - Reinhard Rachel
- Center for Electron Microscopy, University of Regensburg, Regensburg, Germany
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands.,Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johannes Gescher
- Department of Applied Biology, Karlsruhe, Institute of Technology (KIT), Karlsruhe, Germany. .,Institute for Biological Interfaces, Karlsruhe, Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany. .,Institute of Technical Microbiology, Technical University of Hamburg, Hamburg, Germany.
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Abstract
Background By altering their habitats, engineering species can improve their own fitness. However, the effect of this strategy on the fitness of coexisting species or on the structure of the respective food web is poorly understood. In this study, bacteria and bacterivorous nematodes with short (Caenorhabditis elegans) and long (Plectus acuminatus) life cycles were exposed to the mucus secreted by the freshwater flatworm Polycelis tenuis. The growth, reproduction, and feeding preferences of the nematodes in the presence/absence of the mucus were then determined. In addition, confocal laser scanning microscopy (CLSM) was used to examine the structural footprint of the mucus and the mucus colonization dynamics of bacteria and protozoans. Results Mucus exposure resulted in a greater reproductive output in P. acuminatus than in C. elegans. In a cafeteria experiment, both nematode species were attracted by bacteria-rich patches and were not deterred by mucus. CLSM showed that the flatworms spread a layer of polysaccharide-rich mucus ca. 15 µm thick from their tails. Subsequent colonization of the mucus by bacteria and protozoans resulted in an architecture that progressively resembled a complex biofilm. The presence of protozoans reduced nematode reproduction, presumably due to competition for their bacterial food supply. Conclusion Animal secretions such as mucus may have broader, community-level consequences and contribute to fueling microbial food webs. Electronic supplementary material The online version of this article (10.1186/s12898-019-0231-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Benjamin Wilden
- Department of Animal Ecology, University of Bielefeld, Konsequenz 45, 33615, Bielefeld, Germany.
| | - Nabil Majdi
- Department of Animal Ecology, University of Bielefeld, Konsequenz 45, 33615, Bielefeld, Germany.,EcoLab, UMR 5245, CNRS, INP, UPS, ENSAT, Université de Toulouse, 118 route de Narbonne, 31062, Toulouse, France
| | - Ute Kuhlicke
- Department River Ecology, Helmholtz Centre of Environmental Research, Brückstr. 3a, 39114, Magdeburg, Germany
| | - Thomas R Neu
- Department River Ecology, Helmholtz Centre of Environmental Research, Brückstr. 3a, 39114, Magdeburg, Germany
| | - Walter Traunspurger
- Department of Animal Ecology, University of Bielefeld, Konsequenz 45, 33615, Bielefeld, Germany
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Gagliano MC, Neu TR, Kuhlicke U, Sudmalis D, Temmink H, Plugge CM. EPS Glycoconjugate Profiles Shift as Adaptive Response in Anaerobic Microbial Granulation at High Salinity. Front Microbiol 2018; 9:1423. [PMID: 30013532 PMCID: PMC6036115 DOI: 10.3389/fmicb.2018.01423] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/11/2018] [Indexed: 11/22/2022] Open
Abstract
Anaerobic granulation at elevated salinities has been discussed in several analytical and engineering based studies. They report either enhanced or decreased efficiencies in relation to different Na+ levels. To evaluate this discrepancy, we focused on the microbial and structural dynamics of granules formed in two upflow anaerobic sludge blanket (UASB) reactors treating synthetic wastewater at low (5 g/L Na+) and high (20 g/L Na+) salinity conditions. Granules were successfully formed in both conditions, but at high salinity, the start-up inoculum quickly formed larger granules having a thicker gel layer in comparison to granules developed at low salinity. Granules retained high concentrations of sodium without any negative effect on biomass activity and structure. 16S rRNA gene analysis and Fluorescence in Situ Hybridization (FISH) identified the acetotrophic Methanosaeta harundinacea as the dominant microorganism at both salinities. Fluorescence lectin bar coding (FLBC) screening highlighted a significant shift in the glycoconjugate pattern between granules grown at 5 and 20 g/L of Na+, and the presence of different extracellular domains. The excretion of a Mannose-rich cloud-like glycoconjugate matrix, which seems to form a protective layer for some methanogenic cells clusters, was found to be the main distinctive feature of the microbial community grown at high salinity conditions.
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Affiliation(s)
- Maria C Gagliano
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Thomas R Neu
- Helmholtz Centre for Environmental Research, Magdeburg, Germany
| | - Ute Kuhlicke
- Helmholtz Centre for Environmental Research, Magdeburg, Germany
| | - Dainis Sudmalis
- Sub-department of Environmental Technology, Wageningen University & Research, Wageningen, Netherlands
| | - Hardy Temmink
- Sub-department of Environmental Technology, Wageningen University & Research, Wageningen, Netherlands
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
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Tawakoli PN, Neu TR, Busck MM, Kuhlicke U, Schramm A, Attin T, Wiedemeier DB, Schlafer S. Visualizing the dental biofilm matrix by means of fluorescence lectin-binding analysis. J Oral Microbiol 2017; 9:1345581. [PMID: 28748044 PMCID: PMC5508396 DOI: 10.1080/20002297.2017.1345581] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 06/20/2017] [Indexed: 11/03/2022] Open
Abstract
The extracellular matrix is a poorly studied, yet important component of dental biofilms. Fluorescence lectin-binding analysis (FLBA) is a powerful tool to characterize glycoconjugates in the biofilm matrix. This study aimed to systematically investigate the ability of 75 fluorescently labeled lectins to visualize and quantify extracellular glycoconjugates in dental biofilms. Lectin binding was screened on pooled supragingival biofilm samples collected from 76 subjects using confocal microscopy. FLBA was then performed with 10 selected lectins on biofilms grown in situ for 48 h in the absence of sucrose. For five lectins that proved particularly suitable, stained biovolumes were quantified and correlated to the bacterial composition of the biofilms. Additionally, combinations of up to three differently labeled lectins were tested. Of the 10 lectins, five bound particularly well in 48-h-biofilms: Aleuria aurantia (AAL), Calystega sepiem (Calsepa), Lycopersicon esculentum (LEA), Morniga-G (MNA-G) and Helix pomatia (HPA). No significant correlation between the binding of specific lectins and bacterial composition was found. Fluorescently labeled lectins enable the visualization of glycoconjugates in the dental biofilm matrix. The characterization and quantification of glycoconjugates in dental biofilms require a combination of several lectins. For 48-h-biofilms grown in absence of sucrose, AAL, Calsepa, HPA, LEA, and MNA-G are recommendable.
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Affiliation(s)
- Pune N Tawakoli
- Clinic of Preventive Dentistry, Periodontology and Cardiology, Centre of Dental Medicine, University of Zurich, Zurich, Switzerland
| | - Thomas R Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research - UFZ, Magdeburg, Germany
| | - Mette M Busck
- Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Ute Kuhlicke
- Department of River Ecology, Helmholtz Centre for Environmental Research - UFZ, Magdeburg, Germany
| | - Andreas Schramm
- Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Thomas Attin
- Clinic of Preventive Dentistry, Periodontology and Cardiology, Centre of Dental Medicine, University of Zurich, Zurich, Switzerland
| | - Daniel B Wiedemeier
- Statistical Services, Centre of Dental Medicine, University of Zurich, Zurich, Switzerland
| | - Sebastian Schlafer
- Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.,Department of Dentistry and Oral Health, Aarhus University, Aarhus, Denmark
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Neu TR, Kuhlicke U. Fluorescence Lectin Bar-Coding of Glycoconjugates in the Extracellular Matrix of Biofilm and Bioaggregate Forming Microorganisms. Microorganisms 2017; 5:microorganisms5010005. [PMID: 28208623 PMCID: PMC5374382 DOI: 10.3390/microorganisms5010005] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/01/2017] [Accepted: 02/06/2017] [Indexed: 12/27/2022] Open
Abstract
Microbial biofilm systems are defined as interface-associated microorganisms embedded into a self-produced matrix. The extracellular matrix represents a continuous challenge in terms of characterization and analysis. The tools applied in more detailed studies comprise extraction/chemical analysis, molecular characterization, and visualisation using various techniques. Imaging by laser microscopy became a standard tool for biofilm analysis, and, in combination with fluorescently labelled lectins, the glycoconjugates of the matrix can be assessed. By employing this approach a wide range of pure culture biofilms from different habitats were examined using the commercially available lectins. From the results, a binary barcode pattern of lectin binding can be generated. Furthermore, the results can be fine-tuned and transferred into a heat map according to signal intensity. The lectin barcode approach is suggested as a useful tool for investigating the biofilm matrix characteristics and dynamics at various levels, e.g. bacterial cell surfaces, adhesive footprints, individual microcolonies, and the gross biofilm or bio-aggregate. Hence fluorescence lectin bar-coding (FLBC) serves as a basis for a subsequent tailor-made fluorescence lectin-binding analysis (FLBA) of a particular biofilm. So far, the lectin approach represents the only tool for in situ characterization of the glycoconjugate makeup in biofilm systems. Furthermore, lectin staining lends itself to other fluorescence techniques in order to correlate it with cellular biofilm constituents in general and glycoconjugate producers in particular.
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Affiliation(s)
- Thomas R Neu
- Helmholtz Centre for Environmental Research - UFZ, 39114 Magdeburg, Germany.
| | - Ute Kuhlicke
- Helmholtz Centre for Environmental Research - UFZ, 39114 Magdeburg, Germany.
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Derlon N, Grütter A, Brandenberger F, Sutter A, Kuhlicke U, Neu TR, Morgenroth E. The composition and compression of biofilms developed on ultrafiltration membranes determine hydraulic biofilm resistance. Water Res 2016; 102:63-72. [PMID: 27318448 DOI: 10.1016/j.watres.2016.06.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/06/2016] [Accepted: 06/08/2016] [Indexed: 06/06/2023]
Abstract
This study aimed at identifying how to improve the level of permeate flux stabilisation during gravity-driven membrane filtration without control of biofilm formation. The focus was therefore on understanding (i) how the different fractions of the biofilms (inorganics particles, bacterial cells, EPS matrix) influence its hydraulic resistance and (ii) how the compression of biofilms impacts its hydraulic resistance, i.e., can water head be increased to increase the level of permeate flux stabilisation. Biofilms were developed on ultrafiltration membranes at 88 and 284 cm water heads with dead-end filtration for around 50 days. A larger water head resulted in a smaller biofilm permeability (150 and 50 L m(-2) h(-1) bar(-1) for biofilms grown at 88 cm and 284 cm water head, respectively). Biofilms were mainly composed of EPS (>90% in volume). The comparison of the hydraulic resistances of biofilms to model fouling layers indicated that most of the hydraulic resistance is due to the EPS matrix. The compressibility of the biofilm was also evaluated by subjecting the biofilms to short-term (few minutes) and long-term variations of transmembrane pressures (TMP). A sudden change of TMP resulted in an instantaneous and reversible change of biofilm hydraulic resistance. A long-term change of TMP induced a slow change in the biofilm hydraulic resistance. Our results demonstrate that the response of biofilms to a TMP change has two components: an immediate variation of resistance (due to compression/relaxation) and a long-term response (linked to biofilm adaptation/growth). Our results provide relevant information about the relationship between the operating conditions in terms of TMP, the biofilm structure and composition and the resulting biofilm hydraulic resistance. These findings have practical implications for a broad range of membrane systems.
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Affiliation(s)
- Nicolas Derlon
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Process Engineering, CH-8600 Dübendorf, Switzerland; ETH Zürich, Institute of Environmental Engineering, CH-8093 Zürich, Switzerland.
| | - Alexander Grütter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Process Engineering, CH-8600 Dübendorf, Switzerland
| | - Fabienne Brandenberger
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Process Engineering, CH-8600 Dübendorf, Switzerland
| | - Anja Sutter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Process Engineering, CH-8600 Dübendorf, Switzerland
| | - Ute Kuhlicke
- Helmholtz Centre for Environmental Research - UFZ, Magdeburg, Germany
| | - Thomas R Neu
- Helmholtz Centre for Environmental Research - UFZ, Magdeburg, Germany
| | - Eberhard Morgenroth
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Process Engineering, CH-8600 Dübendorf, Switzerland; ETH Zürich, Institute of Environmental Engineering, CH-8093 Zürich, Switzerland
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Lawrence JR, Swerhone GDW, Kuhlicke U, Neu TR. In situevidence for metabolic and chemical microdomains in the structured polymer matrix of bacterial microcolonies. FEMS Microbiol Ecol 2016; 92:fiw183. [DOI: 10.1093/femsec/fiw183] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2016] [Indexed: 11/13/2022] Open
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Zhang R, Neu TR, Zhang Y, Bellenberg S, Kuhlicke U, Li Q, Sand W, Vera M. Erratum to: Visualization and analysis of EPS glycoconjugates of the thermoacidophilic archaeon Sulfolobus metallicus. Appl Microbiol Biotechnol 2015; 99:7357. [DOI: 10.1007/s00253-015-6859-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Zhang R, Neu TR, Zhang Y, Bellenberg S, Kuhlicke U, Li Q, Sand W, Vera M. Visualization and analysis of EPS glycoconjugates of the thermoacidophilic archaeon Sulfolobus metallicus. Appl Microbiol Biotechnol 2015; 99:7343-56. [DOI: 10.1007/s00253-015-6775-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 06/14/2015] [Accepted: 06/17/2015] [Indexed: 12/13/2022]
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Zhang RY, Neu TR, Bellenberg S, Kuhlicke U, Sand W, Vera M. Use of lectins to in situ visualize glycoconjugates of extracellular polymeric substances in acidophilic archaeal biofilms. Microb Biotechnol 2014; 8:448-61. [PMID: 25488256 PMCID: PMC4408177 DOI: 10.1111/1751-7915.12188] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 09/23/2014] [Indexed: 01/28/2023] Open
Abstract
Biofilm formation and the production of extracellular polymeric substances (EPS) by meso- and thermoacidophilic metal-oxidizing archaea on relevant substrates have been studied to a limited extent. In order to investigate glycoconjugates, a major part of the EPS, during biofilm formation/bioleaching by archaea on pyrite, a screening with 75 commercially available lectins by fluorescence lectin-binding analysis (FLBA) has been performed. Three representative archaeal species, Ferroplasma acidiphilum DSM 28986, Sulfolobus metallicus DSM 6482T and a novel isolate Acidianus sp. DSM 29099 were used. In addition, Acidianus sp. DSM 29099 biofilms on elemental sulfur were studied. The results of FLBA indicate (i) 22 lectins bound to archaeal biofilms on pyrite and 21 lectins were binding to Acidianus sp. DSM 29099 biofilms on elemental sulfur; (ii) major binding patterns, e.g. tightly bound EPS and loosely bound EPS, were detected on both substrates; (iii) the three archaeal species produced various EPS glycoconjugates on pyrite surfaces. Additionally, the substratum induced different EPS glycoconjugates and biofilm structures of cells of Acidianus sp. DSM 29099. Our data provide new insights into interactions between acidophilic archaea on relevant surfaces and also indicate that FLBA is a valuable tool for in situ investigations on archaeal biofilms.
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Affiliation(s)
- R Y Zhang
- Aquatische Biotechnologie, Biofilm Centre, Universität Duisburg - Essen, Universitätsstraße 5, 45141, Essen, Germany
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Carmona-Martínez AA, Harnisch F, Kuhlicke U, Neu TR, Schröder U. Electron transfer and biofilm formation of Shewanella putrefaciens as function of anode potential. Bioelectrochemistry 2013; 93:23-9. [DOI: 10.1016/j.bioelechem.2012.05.002] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 04/23/2012] [Accepted: 05/03/2012] [Indexed: 12/19/2022]
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Weissbrodt DG, Neu TR, Kuhlicke U, Rappaz Y, Holliger C. Assessment of bacterial and structural dynamics in aerobic granular biofilms. Front Microbiol 2013; 4:175. [PMID: 23847600 PMCID: PMC3707108 DOI: 10.3389/fmicb.2013.00175] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 06/11/2013] [Indexed: 02/01/2023] Open
Abstract
Aerobic granular sludge (AGS) is based on self-granulated flocs forming mobile biofilms with a gel-like consistence. Bacterial and structural dynamics from flocs to granules were followed in anaerobic-aerobic sequencing batch reactors (SBR) fed with synthetic wastewater, namely a bubble column (BC-SBR) operated under wash-out conditions for fast granulation, and two stirred-tank enrichments of Accumulibacter (PAO-SBR) and Competibacter (GAO-SBR) operated at steady-state. In the BC-SBR, granules formed within 2 weeks by swelling of Zoogloea colonies around flocs, developing subsequently smooth zoogloeal biofilms. However, Zoogloea predominance (37-79%) led to deteriorated nutrient removal during the first months of reactor operation. Upon maturation, improved nitrification (80-100%), nitrogen removal (43-83%), and high but unstable dephosphatation (75-100%) were obtained. Proliferation of dense clusters of nitrifiers, Accumulibacter, and Competibacter from granule cores outwards resulted in heterogeneous bioaggregates, inside which only low abundance Zoogloea (<5%) were detected in biofilm interstices. The presence of different extracellular glycoconjugates detected by fluorescence lectin-binding analysis showed the complex nature of the intracellular matrix of these granules. In the PAO-SBR, granulation occurred within two months with abundant and active Accumulibacter populations (56 ± 10%) that were selected under full anaerobic uptake of volatile fatty acids and that aggregated as dense clusters within heterogeneous granules. Flocs self-granulated in the GAO-SBR after 480 days during a period of over-aeration caused by biofilm growth on the oxygen sensor. Granules were dominated by heterogeneous clusters of Competibacter (37 ± 11%). Zoogloea were never abundant in biomass of both PAO- and GAO-SBRs. This study showed that Zoogloea, Accumulibacter, and Competibacter affiliates can form granules, and that the granulation mechanisms rely on the dominant population involved.
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Affiliation(s)
- David G. Weissbrodt
- Laboratory for Environmental Biotechnology, School for Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de LausanneLausanne, Switzerland
- Institute of Environmental Engineering, ETH ZurichZurich, Switzerland
- Department of Process EngineeringEawag, Duebendorf, Switzerland
| | - Thomas R. Neu
- Microbiology of Interfaces, Department of River Ecology, Helmholtz Centre for Environmental Research - UFZMagdeburg, Germany
| | - Ute Kuhlicke
- Microbiology of Interfaces, Department of River Ecology, Helmholtz Centre for Environmental Research - UFZMagdeburg, Germany
| | - Yoan Rappaz
- Laboratory for Environmental Biotechnology, School for Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de LausanneLausanne, Switzerland
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, School for Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de LausanneLausanne, Switzerland
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Buchholz F, Lerchner J, Mariana F, Kuhlicke U, Neu TR, Harms H, Maskow T. Chip-calorimetry provides real time insights into the inactivation of biofilms by predatory bacteria. Biofouling 2012; 28:351-362. [PMID: 22509741 DOI: 10.1080/08927014.2012.673593] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Control or removal of undesired biofilms has frequently been found to be quite difficult. In addition to biocidal or antibiotic chemicals or materials designed to prevent biofouling, biological control agents appear to be promising. Reports of bacterial predators eradicating biofilms or eliminating pathogens motivate a more systematic screening of biofilm-eliminating bacterial predators. Unfortunately, the analysis of the eradication process is demanding. In the present study, chip-calorimetry was applied to monitor the elimination of Pseudomonas sp. biofilms by Bdellovibrio bacteriovorus. The method uses metabolic heat as a real-time parameter for biofilm activity. The method is non-invasive, fast and convenient due to real-time data acquisition. In addition, heat-production data can reveal information about the energetics of the predator-prey interaction. The calorimetric results were validated by confocal laser scanning microscopy. The approach described may be useful for the screening of biofilm susceptibility to different predators.
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Affiliation(s)
- F Buchholz
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
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Abstract
Confocal laser scanning microscopy and fluorescent lectin-binding analyses (FLBA) were used to study the form, arrangement, and composition of exopolymeric substances (EPS) surrounding naturally occurring microcolonies in biofilms. FLBA, using multiple lectin staining and multichannel imaging, indicated that the EPS of many microcolonies exhibit distinct multiple binding regions. A common pattern in the microcolonies is a three zone arrangement with cell-associated, intercellular, and an outer layer of EPS covering the exterior of the colony. Differential binding of lectins suggests that there are differences in the glycoconjugate composition or their arrangement in the EPS of microcolonies. The combination of FLBA with fluorescent in situ hybridization (FISH) indicates that the colonies consist of the major groups, α- and β-Proteobacteria. It is suggested that the EPS arrangement observed provides a physical structuring mechanism that can segregate extracellular activities at the microscale.
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Affiliation(s)
- J R Lawrence
- National Water Research Institute, 11 Innovation Boulevard, Saskatoon, SK S7N3H5, Canada.
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Macedo AJ, Kuhlicke U, Neu TR, Timmis KN, Abraham WR. Three stages of a biofilm community developing at the liquid-liquid interface between polychlorinated biphenyls and water. Appl Environ Microbiol 2005; 71:7301-9. [PMID: 16269772 PMCID: PMC1287684 DOI: 10.1128/aem.71.11.7301-7309.2005] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Soil contaminated with polychlorinated biphenyls (PCB) was used as an inoculum to grow a complex biofilm community on PCB oil (Aroclor 1242) on a substratum (Permanox). The biofilm was monitored for 31 days by confocal laser scanning microscopy, community fingerprinting using single-strand conformational polymorphism (SSCP), amplicons of the 16S rRNA genes, and chemical analyses of the PCB congeners. SSCP analysis of the young biofilm revealed a rather diverse microbial community with species of the genera Herbaspirillum and Bradyrhizobium as dominant members. The biofilm developing on the PCB droplets displayed pronounced stages of PCB degradation and biofilm development not described before from pure-culture experiments. The first step was the colonization of the substratum while the PCB oil was hardly populated. When a certain density of bacteria was reached on the Permanox, the PCB was colonized, but soon the degradation of the congeners was markedly reduced and many cells were damaged, as seen by LIVE/DEAD staining. Finally, the biofilm formed aggregates and invaded the PCB oil, showing lower numbers of damaged cells than before and a dramatic increase in PCB degradation. This sequence of biofilm formation is understood as a maturation process prior to PCB oil colonization. This is followed by a thin biofilm on the PCB droplet, an aggregation process forming pockets in the PCB, and finally an invasion of the biofilm into the PCB oil. Only the mature biofilm showed degradation of pentachlorinated PCB congeners, which may be reductively dechlorinated and the resulting trichlorobiphenyls then aerobically metabolized.
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Affiliation(s)
- Alexandre José Macedo
- GBF-National Research Center for Biotechnology, Environmental Microbiology, Mascheroder Weg 1, 38124 Braunschweig, Germany
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Paje MLF, Kuhlicke U, Winkler M, Neu TR. Inhibition of lotic biofilms by Diclofenac. Appl Microbiol Biotechnol 2002; 59:488-92. [PMID: 12172615 DOI: 10.1007/s00253-002-1042-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2002] [Revised: 05/02/2002] [Accepted: 05/03/2002] [Indexed: 10/27/2022]
Abstract
Diclofenac, a common drug, was subjected to degradation studies using river biofilms grown in rotating annular reactors. Degradation of diclofenac was possible after acclimatisation as confirmed by liquid chromatography-mass spectrometry analyses. Adapted biofilms showed that degradation down to 10-25% of the initial concentration could be achieved within 4 days. In situ observation by confocal laser scanning microscopy, however, revealed slow biofilm development in the presence of diclofenac compared with control experiments grown in river water only. This was substantiated by low cell counts and isolation of fewer kinds of microorganisms from diclofenac-grown biofilms. Fluorescent in situ hybridisation analyses confirmed the presence of various bacterial groups, especially those belonging to the Cytophaga-Flavobacterium and gamma-Proteobacteria groups, in the biofilms. Quantification of image data indicated a negative effect of diclofenac on the growth of bacteria and algae. This is the first report on degradation of diclofenac by lotic biofilms.
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Affiliation(s)
- M L F Paje
- Department of Inland Water Research Magdeburg, UFZ Centre for Environmental Research Leipzig-Halle, Brueckstrasse 3A, 39114 Magdeburg, Germany
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Abstract
A major limitation for the use of two-proton laser scanning microscopy (2P-LSM) in biofilm and other studies is the lack of a thorough understanding of the excitation-emission responses of potential fluorochromes. In order to use 2P-LSM, the utility of various fluorochromes and probes specific for a range of biofilm constituents must be evaluated. The fluorochromes tested in this study included classical nucleic acid-specific stains, such as acridine orange (AO) and 4",6"-diamidino-2-phenylindole (DAPI), as well as recently developed stains. In addition, stains specific for biofilm extracellular polymeric substances (EPS matrix components) were tested. Two-photon excitation with a Ti/Sapphire laser was carried out at wavelengths from 760 to 900 nm in 10-nm steps. It was found that autofluorescence of phototrophic organisms (cyanobacteria and green algae) resulted in strong signals for the entire excitation range. In addition, the coenzyme F(420)-related autofluorescence of methanogenic bacteria could be used to obtain images of dense aggregates (excitation wavelength, 780 nm). The intensities of the emission signals for the nucleic acid-specific fluorochromes varied. For example, the intensities were similar for excitation wavelengths ranging from 780 to 900 nm for AO but were higher for a narrower range, 780 to 810 nm, for DAPI. In selective excitation, fading, multiple staining, and combined single-photon-two-photon studies, the recently developed nucleic acid-specific fluorochromes proved to be more suitable regardless of whether they are intended for living or fixed samples. Probes specific for proteins and glycoconjugates allowed two-photon imaging of polymeric biofilm constituents. Selective excitation-emission was observed for Calcofluor White M2R (780 to 800 nm) and SyproOrange (880 to 900 nm). In addition, fluor-conjugated concanavalin A lectins were examined and provided acceptable two-photon emission signals at wavelengths ranging from 780 to 800 nm. Finally, CellTracker, a fluorochrome suitable for long-term labeling of microbial eucaryote cells, was found to give strong emission at wavelengths ranging from 770 to 810 nm. If fluorochromes have the same two-photon excitation cross section, they are suitable for multiple staining and multichannel recording. Generally, if an appropriate excitation wavelength and fluorochrome were used, it was possible to obtain more highly resolved images for thick biofilm samples with two-photon laser microscopy than with conventional single-photon laser microscopy. Due to its potential for higher resolution in light-scattering tissue-like material, such as biofilms, and extremely localized excitation, 2P-LSM is a valuable addition to conventional confocal laser scanning microscopy with single-photon excitation. However, further development of the method and basic research are necessary to take full advantage of nonlinear excitation in studies of interfacial microbial ecology.
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Affiliation(s)
- Thomas R Neu
- Department of Inland Water Research Magdeburg, UFZ Centre for Environmental Research Leipzig-Halle, Brueckstrasse 3a, 39114 Magdeburg, Germany.
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