1
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Yang X, Li Y, Pu J, Huang Y, Luan T, Xu M. Effects of cable bacteria on vertical redox profile formation and phenanthrene biodegradation in intertidal sediment responded to tide. WATER RESEARCH 2024; 265:122283. [PMID: 39173361 DOI: 10.1016/j.watres.2024.122283] [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: 01/29/2024] [Revised: 08/09/2024] [Accepted: 08/15/2024] [Indexed: 08/24/2024]
Abstract
Periodic oxygen permeation is critical for pollutant removal within intertidal sediments. However, tidal effects on the vertical redox profile associated with cable bacterial activity is not well understood. In this study, we simulated and quantified the effects of tidal flooding, exposing, and their periodic alternation on vertical redox reactions and phenanthrene removal driven by cable bacteria in the riverbank sediment. Results show that electrogenic sulfur oxidation (e-SOx) mediated by cable bacteria during exposing process drove the vertical permeation of oxidation potential characterized by a decrease in Fe(II) and sulfide concentrations. The sulfate produced was observed in deep sediment (5-10 mm) and served as an electron acceptor for anaerobic oxidation, thereby triggering the functional succession of microbial community. About 78.2 % and 80.8 % of phenanthrene was degraded in deep sediment where cable bacteria grew well under exposing and tidal conditions. Anaerobic processes during tidal flood were also found to be important for the survival of cable bacteria. Higher cable bacteria abundance (up to 1.5 %) was observed under tidal conditions compared to that under continuous exposing conditions and flooding conditions. This might be attributed to lower oxidation stress and sulfide replenishment via sulfate reduction while flooding. Under tidal conditions, the cable bacteria interacted with sulfate reduction bacteria (e.g. Desulfobacca spp. and Desulfatiglans spp.) and maintained the dynamic balance of HS- and SO42- in sediment profiles. This HS--SO42- cycle could serve as a "redox connector" that continuously delivers oxidation potential to deep sediments, resulting in the removal of organic pollutants. The findings provide preliminary evidence of the self-purification mechanisms within intertidal sediments and suggest a potential strategy for sediment remediation.
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Affiliation(s)
- Xunan Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Yu Li
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Jia Pu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Youda Huang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Tiangang Luan
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China; School of Environmental and Chemical Engineering, Wuyi University, Jiangmen 529020, China.
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
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2
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Bonné R, Marshall IPG, Bjerg JJ, Marzocchi U, Manca J, Nielsen LP, Aiyer K. Interaction of living cable bacteria with carbon electrodes in bioelectrochemical systems. Appl Environ Microbiol 2024; 90:e0079524. [PMID: 39082847 PMCID: PMC11337825 DOI: 10.1128/aem.00795-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 07/09/2024] [Indexed: 08/22/2024] Open
Abstract
Cable bacteria are filamentous bacteria that couple the oxidation of sulfide in sediments to the reduction of oxygen via long-distance electron transport over centimeter distances through periplasmic wires. However, the capability of cable bacteria to perform extracellular electron transfer to acceptors, such as electrodes, has remained elusive. In this study, we demonstrate that living cable bacteria actively move toward electrodes in different bioelectrochemical systems. Carbon felt and carbon fiber electrodes poised at +200 mV attracted live cable bacteria from the sediment. When the applied potential was switched off, cable bacteria retracted from the electrode. qPCR and scanning electron microscopy corroborated this finding and revealed cable bacteria in higher abundance present on the electrode surface compared with unpoised controls. These experiments raise new possibilities to study metabolism of cable bacteria and cultivate them in bioelectrochemical devices for bioelectronic applications, such as biosensing and bioremediation. IMPORTANCE Extracellular electron transfer is a metabolic function associated with electroactive bacteria wherein electrons are exchanged with external electron acceptors or donors. This feature has enabled the development of several applications, such as biosensing, carbon capture, and energy recovery. Cable bacteria are a unique class of long, filamentous microbes that perform long-distance electron transport in freshwater and marine sediments. In this study, we demonstrate the attraction of cable bacteria toward carbon electrodes and demonstrate their potential electroactivity. This finding enables electronic control and monitoring of the metabolism of cable bacteria and may, in turn, aid in the development of bioelectronic applications.
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Affiliation(s)
- Robin Bonné
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Ian P. G. Marshall
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Jesper J. Bjerg
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Ugo Marzocchi
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
- Department of Biology, Center for Water Technology (WATEC), Aarhus University, Aarhus, Denmark
| | - Jean Manca
- X-LAB, Hasselt University, Agoralaan, Diepenbeek, Belgium
| | - Lars Peter Nielsen
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Kartik Aiyer
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
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3
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Dong M, Nielsen LP, Yang S, Klausen LH, Xu M. Cable bacteria: widespread filamentous electroactive microorganisms protecting environments. Trends Microbiol 2024; 32:697-706. [PMID: 38151387 DOI: 10.1016/j.tim.2023.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/04/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023]
Abstract
Cable bacteria have been identified and detected worldwide since their discovery in marine sediments in Aarhus Bay, Denmark. Their activity can account for the majority of oxygen consumption and sulfide depletion in sediments, and they induce sulfate accumulation, pH excursions, and the generation of electric fields. In addition, they can affect the fluxes of other elements such as calcium, iron, manganese, nitrogen, and phosphorous. Recent developments in our understanding of the impact of cable bacteria on element cycling have revealed their positive contributions to mitigating environmental problems, such as recovering self-purification capacity, enhancing petroleum hydrocarbon degradation, alleviating phosphorus eutrophication, delaying euxinia, and reducing methane emission. We highlight recent research outcomes on their distribution, state-of-the-art findings on their physiological characteristics, and ecological contributions.
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Affiliation(s)
- Meijun Dong
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou 510070, Guangdong, China
| | - Lars Peter Nielsen
- Center for Electromicrobiology, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Shan Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou 510070, Guangdong, China
| | - Lasse Hyldgaard Klausen
- Center for Electromicrobiology, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark; Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou 510070, Guangdong, China.
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4
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Wang Z, Digel L, Yuan Y, Lu H, Yang Y, Vogt C, Richnow HH, Nielsen LP. Electrogenic sulfur oxidation mediated by cable bacteria and its ecological effects. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 20:100371. [PMID: 38283867 PMCID: PMC10821171 DOI: 10.1016/j.ese.2023.100371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/30/2024]
Abstract
At the sediment-water interfaces, filamentous cable bacteria transport electrons from sulfide oxidation along their filaments towards oxygen or nitrate as electron acceptors. These multicellular bacteria belonging to the family Desulfobulbaceae thus form a biogeobattery that mediates redox processes between multiple elements. Cable bacteria were first reported in 2012. In the past years, cable bacteria have been found to be widely distributed across the globe. Their potential in shaping the surface water environments has been extensively studied but is not fully elucidated. In this review, the biogeochemical characteristics, conduction mechanisms, and geographical distribution of cable bacteria, as well as their ecological effects, are systematically reviewed and discussed. Novel insights for understanding and applying the role of cable bacteria in aquatic ecology are summarized.
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Affiliation(s)
- Zhenyu Wang
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research – UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Leonid Digel
- Center for Electromicrobiology, Department of Biology, Aarhus University, DK-8000, Aarhus, Denmark
| | - Yongqiang Yuan
- Key Laboratory of Karst Georesources and Environment, Ministry of Education, College of Resources and Environmental Engineering, Guizhou University, Guiyang, 550025, China
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Yonggang Yang
- School of Life Science and Engineering, Foshan University, Foshan, 528225, China
- State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510007, China
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research – UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research – UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Lars Peter Nielsen
- Center for Electromicrobiology, Department of Biology, Aarhus University, DK-8000, Aarhus, Denmark
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5
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Xiong X, Li Y, Zhang C. Cable bacteria: Living electrical conduits for biogeochemical cycling and water environment restoration. WATER RESEARCH 2024; 253:121345. [PMID: 38394932 DOI: 10.1016/j.watres.2024.121345] [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: 11/29/2023] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 02/25/2024]
Abstract
Since the discovery of multicellular cable bacteria in marine sediments in 2012, they have attracted widespread attention and interest due to their unprecedented ability to generate and transport electrical currents over centimeter-scale long-range distances. The cosmopolitan distribution of cable bacteria in both marine and freshwater systems, along with their substantial impact on local biogeochemistry, has uncovered their important role in element cycling and ecosystem functioning of aquatic environments. Considerable research efforts have been devoted to the potential utilization of cable bacteria for various water management purposes during the past few years. However, there lacks a critical summary on the advances and contributions of cable bacteria to biogeochemical cycles and water environment restoration. This review aims to provide an up-to-date and comprehensive overview of the current research on cable bacteria, with a particular view on their participation in aquatic biogeochemical cycles and promising applications in water environment restoration. It systematically analyzes (i) the global distribution of cable bacteria in aquatic ecosystems and the major environmental factors affecting their survival, diversity, and composition, (ii) the interactive associations between cable bacteria and other microorganisms as well as aquatic plants and infauna, (iii) the underlying role of cable bacteria in sedimentary biogeochemical cycling of essential elements including but not limited to sulfur, iron, phosphorus, and nitrogen, (iv) the practical explorations of cable bacteria for water pollution control, greenhouse gas emission reduction, aquatic ecological environment restoration, as well as possible combinations with other water remediation technologies. It is believed to give a step-by-step introduction to progress on cable bacteria, highlight key findings, opportunities and challenges of using cable bacteria for water environment restoration, and propose directions for further exploration.
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Affiliation(s)
- Xinyan Xiong
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210024, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210024, PR China.
| | - Chi Zhang
- College of Materials Science and Engineering, Hohai University, Changzhou 213200, PR China.
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6
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Plum-Jensen LE, Schramm A, Marshall IPG. First single-strain enrichments of Electrothrix cable bacteria, description of E. aestuarii sp. nov. and E. rattekaaiensis sp. nov., and proposal of a cable bacteria taxonomy following the rules of the SeqCode. Syst Appl Microbiol 2024; 47:126487. [PMID: 38295603 DOI: 10.1016/j.syapm.2024.126487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 12/23/2023] [Accepted: 01/15/2024] [Indexed: 02/02/2024]
Abstract
Cable bacteria are electrically conductive, filamentous Desulfobulbaceae, which are morphologically, functionally, and phylogenetically distinct from the other members of this family. Cable bacteria have not been obtained in pure culture and were therefore previously described as candidate genera, Candidatus Electrothrix and Ca. Electronema; a representative of the latter is available as single-strain sediment enrichment. Here we present an improved workflow to obtain the first single-strain enrichments of Ca. Electrothrix and report their metagenome-assembled genomes (MAGs) and morphology. Based on these results and on previously published high-quality MAGs and morphological data of cable bacteria from both candidate genera, we propose to adopt the genus names Electrothrix and Electronema following the rules of the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), with Electrothrix communis RBTS and Electronema aureum GSTS, respectively, as the nomenclatural types of the genera. Furthermore, based on average nucleotide identity (ANI) values < 95 % with any described species, we propose two of our three single-strain enrichment cultures as novel species of the genus Electrothrix, with the names E. aestuarii sp. nov. and E. rattekaaiensis sp. nov., according to the SeqCode.
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Affiliation(s)
- Lea E Plum-Jensen
- Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark.
| | - Andreas Schramm
- Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark.
| | - Ian P G Marshall
- Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark.
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7
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Geelhoed JS, Thorup CA, Bjerg JJ, Schreiber L, Nielsen LP, Schramm A, Meysman FJR, Marshall IPG. Indications for a genetic basis for big bacteria and description of the giant cable bacterium Candidatus Electrothrix gigas sp. nov. Microbiol Spectr 2023; 11:e0053823. [PMID: 37732806 PMCID: PMC10580974 DOI: 10.1128/spectrum.00538-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/21/2023] [Indexed: 09/22/2023] Open
Abstract
Bacterial cells can vary greatly in size, from a few hundred nanometers to hundreds of micrometers in diameter. Filamentous cable bacteria also display substantial size differences, with filament diameters ranging from 0.4 to 8 µm. We analyzed the genomes of cable bacterium filaments from 11 coastal environments of which the resulting 23 new genomes represent 10 novel species-level clades of Candidatus Electrothrix and two clades that putatively represent novel genus-level diversity. Fluorescence in situ hybridization with a species-level probe showed that large-sized cable bacteria belong to a novel species with the proposed name Ca. Electrothrix gigas. Comparative genome analysis suggests genes that play a role in the construction or functioning of large cable bacteria cells: the genomes of Ca. Electrothrix gigas encode a novel actin-like protein as well as a species-specific gene cluster encoding four putative pilin proteins and a putative type II secretion platform protein, which are not present in other cable bacteria. The novel actin-like protein was also found in a number of other giant bacteria, suggesting there could be a genetic basis for large cell size. This actin-like protein (denoted big bacteria protein, Bbp) may have a function analogous to other actin proteins in cell structure or intracellular transport. We contend that Bbp may help overcome the challenges of diffusion limitation and/or morphological complexity presented by the large cells of Ca. Electrothrix gigas and other giant bacteria. IMPORTANCE In this study, we substantially expand the known diversity of marine cable bacteria and describe cable bacteria with a large diameter as a novel species with the proposed name Candidatus Electrothrix gigas. In the genomes of this species, we identified a gene that encodes a novel actin-like protein [denoted big bacteria protein (Bbp)]. The bbp gene was also found in a number of other giant bacteria, predominantly affiliated to Desulfobacterota and Gammaproteobacteria, indicating that there may be a genetic basis for large cell size. Thus far, mostly structural adaptations of giant bacteria, vacuoles, and other inclusions or organelles have been observed, which are employed to overcome nutrient diffusion limitation in their environment. In analogy to other actin proteins, Bbp could fulfill a structural role in the cell or potentially facilitate intracellular transport.
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Affiliation(s)
- Jeanine S. Geelhoed
- Department of Biology, Research Group Geobiology, University of Antwerp, Wilrijk, Belgium
| | - Casper A. Thorup
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Jesper J. Bjerg
- Department of Biology, Research Group Geobiology, University of Antwerp, Wilrijk, Belgium
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Lars Schreiber
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Lars Peter Nielsen
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Filip J. R. Meysman
- Department of Biology, Research Group Geobiology, University of Antwerp, Wilrijk, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Ian P. G. Marshall
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
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8
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Bjerg JJ, Lustermans JJM, Marshall IPG, Mueller AJ, Brokjær S, Thorup CA, Tataru P, Schmid M, Wagner M, Nielsen LP, Schramm A. Cable bacteria with electric connection to oxygen attract flocks of diverse bacteria. Nat Commun 2023; 14:1614. [PMID: 36959175 PMCID: PMC10036481 DOI: 10.1038/s41467-023-37272-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 03/08/2023] [Indexed: 03/25/2023] Open
Abstract
Cable bacteria are centimeter-long filamentous bacteria that conduct electrons via internal wires, thus coupling sulfide oxidation in deeper, anoxic sediment with oxygen reduction in surface sediment. This activity induces geochemical changes in the sediment, and other bacterial groups appear to benefit from the electrical connection to oxygen. Here, we report that diverse bacteria swim in a tight flock around the anoxic part of oxygen-respiring cable bacteria and disperse immediately when the connection to oxygen is disrupted (by cutting the cable bacteria with a laser). Raman microscopy shows that flocking bacteria are more oxidized when closer to the cable bacteria, but physical contact seems to be rare and brief, which suggests potential transfer of electrons via unidentified soluble intermediates. Metagenomic analysis indicates that most of the flocking bacteria appear to be aerobes, including organotrophs, sulfide oxidizers, and possibly iron oxidizers, which might transfer electrons to cable bacteria for respiration. The association and close interaction with such diverse partners might explain how oxygen via cable bacteria can affect microbial communities and processes far into anoxic environments.
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Affiliation(s)
- Jesper J Bjerg
- Center for Electromicrobiology (CEM), Section for Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark.
- Microbial Systems Technology Excellence Centre, University of Antwerp, Wilrijk, Belgium.
| | - Jamie J M Lustermans
- Center for Electromicrobiology (CEM), Section for Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Ian P G Marshall
- Center for Electromicrobiology (CEM), Section for Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Anna J Mueller
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology (DOME), University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Signe Brokjær
- Center for Electromicrobiology (CEM), Section for Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Casper A Thorup
- Center for Electromicrobiology (CEM), Section for Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Paula Tataru
- Bioinformatics Research Center (BiRC), Aarhus University, Aarhus C, Denmark
| | - Markus Schmid
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology (DOME), University of Vienna, Vienna, Austria
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology (DOME), University of Vienna, Vienna, Austria
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Lars Peter Nielsen
- Center for Electromicrobiology (CEM), Section for Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Andreas Schramm
- Center for Electromicrobiology (CEM), Section for Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark.
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9
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Vasquez-Cardenas D, Hidalgo-Martinez S, Hulst L, Thorleifsdottir T, Helgason GV, Eiriksson T, Geelhoed JS, Agustsson T, Moodley L, Meysman FJR. Biogeochemical impacts of fish farming on coastal sediments: Insights into the functional role of cable bacteria. Front Microbiol 2022; 13:1034401. [PMID: 36620049 PMCID: PMC9814725 DOI: 10.3389/fmicb.2022.1034401] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Fish farming in sea cages is a growing component of the global food industry. A prominent ecosystem impact of this industry is the increase in the downward flux of organic matter, which stimulates anaerobic mineralization and sulfide production in underlying sediments. When free sulfide is released to the overlying water, this can have a toxic effect on local marine ecosystems. The microbially-mediated process of sulfide oxidation has the potential to be an important natural mitigation and prevention strategy that has not been studied in fish farm sediments. We examined the microbial community composition (DNA-based 16S rRNA gene) underneath two active fish farms on the Southwestern coast of Iceland and performed laboratory incubations of resident sediment. Field observations confirmed the strong geochemical impact of fish farming on the sediment (up to 150 m away from cages). Sulfide accumulation was evidenced under the cages congruent with a higher supply of degradable organic matter from the cages. Phylogenetically diverse microbes capable of sulfide detoxification were present in the field sediment as well as in lab incubations, including cable bacteria (Candidatus Electrothrix), which display a unique metabolism based on long-distance electron transport. Microsensor profiling revealed that the activity of cable bacteria did not exert a dominant impact on the geochemistry of fish farm sediment at the time of sampling. However, laboratory incubations that mimic the recovery process during fallowing, revealed successful enrichment of cable bacteria within weeks, with concomitant high sulfur-oxidizing activity. Overall our results give insight into the role of microbially-mediated sulfide detoxification in aquaculture impacted sediments.
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Affiliation(s)
- Diana Vasquez-Cardenas
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands,Geobiology, Department of Biology, University of Antwerp, Antwerp, Belgium,*Correspondence: Diana Vasquez-Cardenas,
| | | | - Lucas Hulst
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | | | | | | | | | | | - Leon Moodley
- NORCE Norwegian Research Centre, Randaberg, Norway
| | - Filip J. R. Meysman
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands,Geobiology, Department of Biology, University of Antwerp, Antwerp, Belgium
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10
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Liau P, Kim C, Saxton MA, Malkin SY. Microbial succession in a marine sediment: Inferring interspecific microbial interactions with marine cable bacteria. Environ Microbiol 2022; 24:6348-6364. [PMID: 36178156 PMCID: PMC10092204 DOI: 10.1111/1462-2920.16230] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/27/2022] [Indexed: 01/12/2023]
Abstract
Cable bacteria are long, filamentous, multicellular bacteria that grow in marine sediments and couple sulfide oxidation to oxygen reduction over centimetre-scale distances via long-distance electron transport. Cable bacteria can strongly modify biogeochemical cycling and may affect microbial community networks. Here we examine interspecific interactions with marine cable bacteria (Ca. Electrothrix) by monitoring the succession of 16S rRNA amplicons (DNA and RNA) and cell abundance across depth and time, contrasting sediments with and without cable bacteria growth. In the oxic zone, cable bacteria activity was positively associated with abundant predatory bacteria (Bdellovibrionota, Myxococcota, Bradymonadales), indicating putative predation on cathodic cells. At suboxic depths, cable bacteria activity was positively associated with sulfate-reducing and magnetotactic bacteria, consistent with cable bacteria functioning as ecosystem engineers that modify their local biogeochemical environment, benefitting certain microbes. Cable bacteria activity was negatively associated with chemoautotrophic sulfur-oxidizing Gammaproteobacteria (Thiogranum, Sedimenticola) at oxic depths, suggesting competition, and positively correlated with these taxa at suboxic depths, suggesting syntrophy and/or facilitation. These observations are consistent with chemoautotrophic sulfur oxidizers benefitting from an oxidizing potential imparted by cable bacteria at suboxic depths, possibly by using cable bacteria as acceptors for electrons or electron equivalents, but by an as yet enigmatic mechanism.
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Affiliation(s)
- Pinky Liau
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, Maryland, USA
| | - Carol Kim
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, Maryland, USA
| | - Matthew A Saxton
- Department of Biological Sciences, Miami University, Middletown, Ohio, USA
| | - Sairah Y Malkin
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, Maryland, USA
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11
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Geerlings NMJ, Kienhuis MVM, Hidalgo-Martinez S, Hageman R, Vasquez-Cardenas D, Middelburg JJ, Meysman FJR, Polerecky L. Polyphosphate Dynamics in Cable Bacteria. Front Microbiol 2022; 13:883807. [PMID: 35663875 PMCID: PMC9159916 DOI: 10.3389/fmicb.2022.883807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/18/2022] [Indexed: 11/14/2022] Open
Abstract
Cable bacteria are multicellular sulfide oxidizing bacteria that display a unique metabolism based on long-distance electron transport. Cells in deeper sediment layers perform the sulfide oxidizing half-reaction whereas cells in the surface layers of the sediment perform the oxygen-reducing half-reaction. These half-reactions are coupled via electron transport through a conductive fiber network that runs along the shared cell envelope. Remarkably, only the sulfide oxidizing half-reaction is coupled to biosynthesis and growth whereas the oxygen reducing half-reaction serves to rapidly remove electrons from the conductive fiber network and is not coupled to energy generation and growth. Cells residing in the oxic zone are believed to (temporarily) rely on storage compounds of which polyphosphate (poly-P) is prominently present in cable bacteria. Here we investigate the role of poly-P in the metabolism of cable bacteria within the different redox environments. To this end, we combined nanoscale secondary ion mass spectrometry with dual-stable isotope probing (13C-DIC and 18O-H2O) to visualize the relationship between growth in the cytoplasm (13C-enrichment) and poly-P activity (18O-enrichment). We found that poly-P was synthesized in almost all cells, as indicated by 18O enrichment of poly-P granules. Hence, poly-P must have an important function in the metabolism of cable bacteria. Within the oxic zone of the sediment, where little growth is observed, 18O enrichment in poly-P granules was significantly lower than in the suboxic zone. Thus, both growth and poly-P metabolism appear to be correlated to the redox environment. However, the poly-P metabolism is not coupled to growth in cable bacteria, as many filaments from the suboxic zone showed poly-P activity but did not grow. We hypothesize that within the oxic zone, poly-P is used to protect the cells against oxidative stress and/or as a resource to support motility, while within the suboxic zone, poly-P is involved in the metabolic regulation before cells enter a non-growing stage.
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Affiliation(s)
- Nicole M. J. Geerlings
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
- *Correspondence: Nicole M. J. Geerlings,
| | | | - Silvia Hidalgo-Martinez
- Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Renee Hageman
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Diana Vasquez-Cardenas
- Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium
| | | | - Filip J. R. Meysman
- Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Lubos Polerecky
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
- Lubos Polerecky,
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12
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Sachs C, Kanaparthi D, Kublik S, Szalay AR, Schloter M, Damgaard LR, Schramm A, Lueders T. Tracing long-distance electron transfer and cable bacteria in freshwater sediments by agar pillar gradient columns. FEMS Microbiol Ecol 2022; 98:6567839. [PMID: 35416241 DOI: 10.1093/femsec/fiac042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/20/2022] [Accepted: 04/11/2022] [Indexed: 11/14/2022] Open
Abstract
Cable bacteria (CB) perform electrogenic sulphur oxidation (e-SOX) by spatially separating redox-half-reactions over cm-distances. For freshwater systems, the ecology of CB is not yet well understood, partly because they proved difficult to cultivate. This study introduces a new "agar pillar" approach to selectively enrich and investigate CB-populations. Within sediment columns, a central agar pillar is embedded, providing a sediment-free gradient-system in equilibrium with the surrounding sediment. We incubated freshwater sediments from a streambed, a sulfidic lake, and a hydrocarbon polluted aquifer in such agar pillar columns. Microprofiling revealed typical patterns of e-SOx, such as the development of a suboxic zone and the establishment of electric potentials. The bacterial communities in the sediments and agar pillars were analysed over depth by PacBio near-full-length 16S rRNA gene amplicon sequencing, allowing for a precise phylogenetic placement of taxa detected. The selective niche of the agar pillar was preferentially colonized by CB related to Candidatus Electronema for surface-water sediments, including several potentially novel species, but not for putative groundwater CB affiliated with Desulfurivibrio spp. The presence of CB was seemingly linked to co-enriched fermenters, hinting at a possible role of e-SOx-populations as an electron sink for heterotrophic microbes. These findings add to our current understanding of the diversity and ecology of CB in freshwater systems, and to a discrimination of CB from surface and groundwater sediments. The agar pillar approach provides a new strategy that may facilitate the cultivation of redox gradient-dependent microorganisms, including previously unrecognized CB populations.
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Affiliation(s)
- Corinna Sachs
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Germany.,Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health, Germany
| | - Dheeraj Kanaparthi
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Germany.,Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München - German Research Center for Environmental Health, Germany
| | - Anna Roza Szalay
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München - German Research Center for Environmental Health, Germany
| | - Lars Riis Damgaard
- Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Denmark
| | - Andreas Schramm
- Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Denmark
| | - Tillmann Lueders
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Germany
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13
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Huang Y, Wang B, Yang Y, Yang S, Dong M, Xu M. Microbial carriers promote and guide pyrene migration in sediments. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127188. [PMID: 34597936 DOI: 10.1016/j.jhazmat.2021.127188] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Microbial carriers may co-transport polycyclic aromatic hydrocarbons (PAHs), but lack substantial experimental evidence. Cable bacteria use gliding or twitching motility to access sulfide; hence, they could be important microbial carriers in co-transporting PAHs from the sediment-water interface into suboxic zones. In this study, the effect of cable bacteria on pyrene migration was investigated by connecting or blocking the paths of cable bacteria to the suboxic zones. The results showed that downward migration of pyrene in the connecting groups were significantly higher (17.3-49.2%, p < 0.01) than those in the control groups. Meanwhile, significant downward migration of microbial communities in the connecting groups were also observed, including abundant filamentous-motile microorganisms, especially cable bacteria. The adsorption of surrounding particles by cable bacteria were morphologically evidenced. The biomechanical model based on the Peclet number indicated that filamentous-motile microorganisms demonstrated stronger adsorption ability for pyrene than other microorganisms. Supposedly, the downward migration of microbial communities, especially cable bacteria, significantly enhanced pyrene migration, thus influencing the distribution and ecological risk of pyrene in sediments. This study provides new insights into the important roles of motile microorganisms in the migration of PAHs in sediments, shedding lights on guidance for ecological risk assessment of PAHs.
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Affiliation(s)
- Youda Huang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Bin Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Yonggang Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Shan Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Meijun Dong
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
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14
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Marzocchi U, Thorup C, Dam AS, Schramm A, Risgaard-Petersen N. Dissimilatory nitrate reduction by a freshwater cable bacterium. THE ISME JOURNAL 2022; 16:50-57. [PMID: 34215856 PMCID: PMC8692496 DOI: 10.1038/s41396-021-01048-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/10/2021] [Accepted: 06/23/2021] [Indexed: 02/06/2023]
Abstract
Cable bacteria (CB) are filamentous Desulfobulbaceae that split the energy-conserving reaction of sulfide oxidation into two half reactions occurring in distinct cells. CB can use nitrate, but the reduction pathway is unknown, making it difficult to assess their direct impact on the N-cycle. Here we show that the freshwater cable bacterium Ca. Electronema sp. GS performs dissimilatory nitrate reduction to ammonium (DNRA). 15NO3--amended sediment with Ca. Electronema sp. GS showed higher rates of DNRA and nitrite production than sediment without Ca. Electronema sp. GS. Electron flux from sulfide oxidation, inferred from electric potential (EP) measurements, matched the electron flux needed to drive CB-mediated nitrate reduction to nitrite and ammonium. Ca. Electronema sp. GS expressed a complete nap operon for periplasmic nitrate reduction to nitrite, and a putative octaheme cytochrome c (pOCC), whose involvement in nitrite reduction to ammonium remains to be verified. Phylogenetic analysis suggests that the capacity for DNRA was acquired in multiple events through horizontal gene transfer from different organisms, before CB split into different salinity niches. The architecture of the nitrate reduction system suggests absence of energy conservation through oxidative phosphorylation, indicating that CB primarily conserve energy through the half reaction of sulfide oxidation.
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Affiliation(s)
- Ugo Marzocchi
- grid.8767.e0000 0001 2290 8069Department of Chemistry, Vrije Universiteit Brussel, Brussel, Belgium ,grid.7048.b0000 0001 1956 2722Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722Center for Water Technology (WATEC), Department of Biology, Aarhus University, Aarhus, Denmark
| | - Casper Thorup
- grid.7048.b0000 0001 1956 2722Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722Center for Geomicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Ann-Sofie Dam
- grid.7048.b0000 0001 1956 2722Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722Center for Geomicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- grid.7048.b0000 0001 1956 2722Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722Center for Geomicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Nils Risgaard-Petersen
- grid.7048.b0000 0001 1956 2722Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722Center for Geomicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722Section of Aquatic Biology, Department of Biology, Aarhus University, Aarhus, Denmark
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15
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Scholz VV, Martin BC, Meyer R, Schramm A, Fraser MW, Nielsen LP, Kendrick GA, Risgaard‐Petersen N, Burdorf LDW, Marshall IPG. Cable bacteria at oxygen-releasing roots of aquatic plants: a widespread and diverse plant-microbe association. THE NEW PHYTOLOGIST 2021; 232:2138-2151. [PMID: 33891715 PMCID: PMC8596878 DOI: 10.1111/nph.17415] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 04/09/2021] [Indexed: 05/09/2023]
Abstract
Cable bacteria are sulfide-oxidising, filamentous bacteria that reduce toxic sulfide levels, suppress methane emissions and drive nutrient and carbon cycling in sediments. Recently, cable bacteria have been found associated with roots of aquatic plants and rice (Oryza sativa). However, the extent to which cable bacteria are associated with aquatic plants in nature remains unexplored. Using newly generated and public 16S rRNA gene sequence datasets combined with fluorescence in situ hybridisation, we investigated the distribution of cable bacteria around the roots of aquatic plants, encompassing seagrass (including seagrass seedlings), rice, freshwater and saltmarsh plants. Diverse cable bacteria were found associated with roots of 16 out of 28 plant species and at 36 out of 55 investigated sites, across four continents. Plant-associated cable bacteria were confirmed across a variety of ecosystems, including marine coastal environments, estuaries, freshwater streams, isolated pristine lakes and intensive agricultural systems. This pattern indicates that this plant-microbe relationship is globally widespread and neither obligate nor species specific. The occurrence of cable bacteria in plant rhizospheres may be of general importance to vegetation vitality, primary productivity, coastal restoration practices and greenhouse gas balance of rice fields and wetlands.
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Affiliation(s)
- Vincent V. Scholz
- Section for MicrobiologyDepartment of BiologyCenter for ElectromicrobiologyAarhus UniversityNy Munkegade 116Aarhus CDK‐8000Denmark
| | - Belinda C. Martin
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWA6009Australia
- The UWA Oceans InstituteThe University of Western Australia35 Stirling HighwayCrawleyWA6009Australia
- Ooid ScientificWhite Gum ValleyWA6162Australia
| | - Raïssa Meyer
- Section for MicrobiologyDepartment of BiologyCenter for ElectromicrobiologyAarhus UniversityNy Munkegade 116Aarhus CDK‐8000Denmark
- Max Planck Institute for Marine MicrobiologyCelsiusstraße 1BremenD‐28359Germany
| | - Andreas Schramm
- Section for MicrobiologyDepartment of BiologyCenter for ElectromicrobiologyAarhus UniversityNy Munkegade 116Aarhus CDK‐8000Denmark
| | - Matthew W. Fraser
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWA6009Australia
- The UWA Oceans InstituteThe University of Western Australia35 Stirling HighwayCrawleyWA6009Australia
| | - Lars Peter Nielsen
- Section for MicrobiologyDepartment of BiologyCenter for ElectromicrobiologyAarhus UniversityNy Munkegade 116Aarhus CDK‐8000Denmark
| | - Gary A. Kendrick
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWA6009Australia
- The UWA Oceans InstituteThe University of Western Australia35 Stirling HighwayCrawleyWA6009Australia
| | - Nils Risgaard‐Petersen
- Section for MicrobiologyDepartment of BiologyCenter for ElectromicrobiologyAarhus UniversityNy Munkegade 116Aarhus CDK‐8000Denmark
| | - Laurine D. W. Burdorf
- Section for MicrobiologyDepartment of BiologyCenter for ElectromicrobiologyAarhus UniversityNy Munkegade 116Aarhus CDK‐8000Denmark
| | - Ian P. G. Marshall
- Section for MicrobiologyDepartment of BiologyCenter for ElectromicrobiologyAarhus UniversityNy Munkegade 116Aarhus CDK‐8000Denmark
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16
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Using Oxidative Electrodes to Enrich Novel Members in the Desulfobulbaceae Family from Intertidal Sediments. Microorganisms 2021; 9:microorganisms9112329. [PMID: 34835454 PMCID: PMC8618199 DOI: 10.3390/microorganisms9112329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/21/2021] [Accepted: 11/08/2021] [Indexed: 01/04/2023] Open
Abstract
Members in the family of Desulfobulbaceae may be influential in various anaerobic microbial communities, including those in anoxic aquatic sediments and water columns, and within wastewater treatment facilities and bioelectrochemical systems (BESs) such as microbial fuel cells (MFCs). However, the diversity and roles of the Desulfobulbaceae in these communities have received little attention, and large portions of this family remain uncultured. Here we expand on findings from an earlier study (Li, Reimers, and Alleau, 2020) to more fully characterize Desulfobulbaceae that became prevalent in biofilms on oxidative electrodes of bioelectrochemical reactors. After incubations, DNA extraction, microbial community analyses, and microscopic examination, we found that a group of uncultured Desulfobulbaceae were greatly enriched on electrode surfaces. These Desulfobulbaceae appeared to form filaments with morphological features ascribed to cable bacteria, but the majority were taxonomically distinct from recognized cable bacteria genera. Thus, the present study provides new information about a group of Desulfobulbaceae that can exhibit filamentous morphologies and respire on the oxidative electrodes. While the phylogeny of cable bacteria is still being defined and updated, further enriching these members can contribute to the overall understanding of cable bacteria and may also lead to identification of successful isolation strategies.
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17
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Lustermans JJM, Bjerg JJ, Schramm A, Marshall IPG. Phyllobacterium calauticae sp. nov. isolated from a microaerophilic veil transversed by cable bacteria in freshwater sediment. Antonie Van Leeuwenhoek 2021; 114:1877-1887. [PMID: 34491484 DOI: 10.1007/s10482-021-01647-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/23/2021] [Indexed: 11/29/2022]
Abstract
Microaerophilic veils of swimming microorganisms form at oxic-anoxic interfaces, mostly described in sediments where sulfide from below meets oxygen diffusing in from the water phase. However, microaerophilic veils form even when these gradients do not overlap, for example when cable bacteria activity leads to a suboxic zone. This suggests that veil microorganisms can use electron donors other than sulfide. Here we describe the extraction of microorganisms from a microaerophilic veil that formed in cable-bacteria-enriched freshwater sediment using a glass capillary, and the subsequent isolation of a motile, microaerophilic, organoheterotrophic bacterium, strain R2-JLT, unable to oxidize sulfide. Based on phenotypic, phylogenetic, and genomic comparison, we propose strain R2-JLT as a novel Phyllobacterium species, P. calauticae sp. nov.. The type strain is R2-JLT (= LMG 32286T = DSM 112555T). This novel isolate confirms that a wider variety of electron donors, including organic compounds, can fuel the activity of microorganisms in microaerophilic veils.
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Affiliation(s)
- Jamie J M Lustermans
- Section for Microbiology, Center for Electromicrobiology, Department of Biology, Aarhus University, Ny Munkegade 114, Building 1540, 8000, Aarhus C, Denmark
| | - Jesper J Bjerg
- Section for Microbiology, Center for Electromicrobiology, Department of Biology, Aarhus University, Ny Munkegade 114, Building 1540, 8000, Aarhus C, Denmark.,Microbial Systems Technology Excellence Centre, University of Antwerp, Wilrijk, Belgium
| | - Andreas Schramm
- Section for Microbiology, Center for Electromicrobiology, Department of Biology, Aarhus University, Ny Munkegade 114, Building 1540, 8000, Aarhus C, Denmark.
| | - Ian P G Marshall
- Section for Microbiology, Center for Electromicrobiology, Department of Biology, Aarhus University, Ny Munkegade 114, Building 1540, 8000, Aarhus C, Denmark
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18
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Thorup C, Petro C, Bøggild A, Ebsen TS, Brokjær S, Nielsen LP, Schramm A, Bjerg JJ. How to grow your cable bacteria: Establishment of a stable single-strain culture in sediment and proposal of Candidatus Electronema aureum GS. Syst Appl Microbiol 2021; 44:126236. [PMID: 34332367 DOI: 10.1016/j.syapm.2021.126236] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 01/04/2023]
Abstract
Cable bacteria are multicellular filamentous bacteria within the Desulfobulbaceae that couple the oxidation of sulfide to the reduction of oxygen over centimeter distances via long distance electron transport (LDET). So far, none of the freshwater or marine cable bacteria species have been isolated into pure culture. Here we describe a method for establishing a stable single-strain cable bacterium culture in partially sterilized sediment. By repeated transfers of a single cable bacterium filament from freshwater pond sediment into autoclaved sediment, we obtained strain GS, identified by its 16S rRNA gene as a member of Ca. Electronema. This strain was further propagated by transferring sediment clumps, and has now been stable within its semi-natural microbial community for several years. Its metagenome-assembled genome was 93% complete, had a size of 2.76 Mbp, and a DNA G + C content of 52%. Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) suggest the affiliation of strain GS to Ca. Electronema as a novel species. Cell size, number of outer ridges, and detection of LDET in the GS culture are likewise consistent with Ca. Electronema. Based on these combined features, we therefore describe strain GS as a new cable bacterium species of the candidate genus Electronema, for which we propose the name Candidatus Electronema aureum sp.nov. Although not a pure culture, this stable single-strain culture will be useful for physiological and omics-based studies; similar approaches with single-cell or single-filament transfers into natural medium may also aid the characterization of other difficult-to-culture microbes.
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Affiliation(s)
- Casper Thorup
- Section for Microbiology, Department of Biology, Aarhus University, Denmark; Center for Electromicrobiology, Aarhus University, Denmark; Center for Geomicrobiology, Aarhus University, Denmark
| | - Caitlin Petro
- Section for Microbiology, Department of Biology, Aarhus University, Denmark; Center for Electromicrobiology, Aarhus University, Denmark; Center for Geomicrobiology, Aarhus University, Denmark
| | - Andreas Bøggild
- Department for Molecular Biology and Genetics, Aarhus University, Denmark
| | | | - Signe Brokjær
- Section for Microbiology, Department of Biology, Aarhus University, Denmark
| | - Lars Peter Nielsen
- Section for Microbiology, Department of Biology, Aarhus University, Denmark; Center for Electromicrobiology, Aarhus University, Denmark; Center for Geomicrobiology, Aarhus University, Denmark
| | - Andreas Schramm
- Section for Microbiology, Department of Biology, Aarhus University, Denmark; Center for Electromicrobiology, Aarhus University, Denmark; Center for Geomicrobiology, Aarhus University, Denmark.
| | - Jesper Jensen Bjerg
- Section for Microbiology, Department of Biology, Aarhus University, Denmark; Center for Electromicrobiology, Aarhus University, Denmark; Center for Geomicrobiology, Aarhus University, Denmark; ECOBE, Department of Biology, University of Antwerp, Belgium
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19
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Yin H, Aller RC, Zhu Q, Aller JY. The dynamics of cable bacteria colonization in surface sediments: a 2D view. Sci Rep 2021; 11:7167. [PMID: 33785772 PMCID: PMC8010117 DOI: 10.1038/s41598-021-86365-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/02/2021] [Indexed: 11/09/2022] Open
Abstract
Cable bacteria that are capable of transporting electrons on centimeter scales have been found in a variety of sediment types, where their activity can strongly influence diagenetic reactions and elemental cycling. In this study, the patterns of spatial and temporal colonization of surficial sediment by cable bacteria were revealed in two-dimensions by planar pH and H2S optical sensors for the first time. The characteristic sediment surface pH maximum zones begin to develop from isolated micro-regions and spread horizontally within 5 days, with lateral spreading rates from 0.3 to ~ 1.2 cm day-1. Electrogenic anodic zones in the anoxic sediments are characterized by low pH, and the coupled pH minima also expand with time. H2S heterogeneities in accordance with electrogenic colonization are also observed. Cable bacteria cell abundance in oxic surface sediment (0-0.25 cm) kept almost constant during the colonization period; however, subsurface cell abundance apparently increased as electrogenic activity expanded across the entire surface. Changes in cell abundance are consistent with filament coiling and growth in the anodic zone (i.e., cathodic snorkels). The spreading mechanism for the sediment pH-H2S fingerprints and the cable bacteria abundance dynamics suggest that once favorable microenvironments are established, filamentous cable bacteria aggregate or locally activate electrogenic metabolism. Different development dynamics in otherwise similar sediment suggests that the accessibility of reductant (e.g., dissolved phase sulfide) is critical in controlling the growth of cable bacteria.
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Affiliation(s)
- Hang Yin
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794-5000, USA
| | - Robert C Aller
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794-5000, USA.
| | - Qingzhi Zhu
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794-5000, USA.
| | - Josephine Y Aller
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794-5000, USA
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20
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Miran W, Naradasu D, Okamoto A. Pathogens electrogenicity as a tool for in-situ metabolic activity monitoring and drug assessment in biofilms. iScience 2021; 24:102068. [PMID: 33554070 PMCID: PMC7859304 DOI: 10.1016/j.isci.2021.102068] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Concerns regarding increased antibiotic resistance arising from the emergent properties of biofilms have spurred interest in the discovery of novel antibiotic agents and techniques to directly estimate metabolic activity in biofilms. Although a number of methods have been developed to quantify biofilm formation, real-time quantitative assessment of metabolic activity in label-free biofilms remains a challenge. Production of electrical current via extracellular electron transport (EET) has recently been found in pathogens and appears to correlate with their metabolic activity. Accordingly, monitoring the production of electrical currents as an indicator of cellular metabolic activity in biofilms represents a new direction for research aiming to assess and screen the effects of antimicrobials on biofilm activity. In this article, we reviewed EET-capable pathogens and the methods to monitor biofilm activity to discuss advantages of using the capability of pathogens to produce electrical currents and effective combination of these methods. Moreover, we discussed EET mechanisms by pathogenic and environmental bacteria and open questions for the physiological roles of EET in pathogen's biofilm. The present limitations and possible future directions of in situ biofilm metabolic activity assessment for large-scale screening of antimicrobials are also discussed.
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Affiliation(s)
- Waheed Miran
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Divya Naradasu
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
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21
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Scilipoti S, Koren K, Risgaard-Petersen N, Schramm A, Nielsen LP. Oxygen consumption of individual cable bacteria. SCIENCE ADVANCES 2021; 7:7/7/eabe1870. [PMID: 33568484 PMCID: PMC7875522 DOI: 10.1126/sciadv.abe1870] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/23/2020] [Indexed: 05/24/2023]
Abstract
The electric wires of cable bacteria possibly support a unique respiration mode with a few oxygen-reducing cells flaring off electrons, while oxidation of the electron donor and the associated energy conservation and growth is allocated to other cells not exposed to oxygen. Cable bacteria are centimeter-long, multicellular, filamentous Desulfobulbaceae that transport electrons across oxic-anoxic interfaces in aquatic sediments. From observed distortions of the oxic-anoxic interface, we derived oxygen consumption rates of individual cable bacteria and found biomass-specific rates of unheard magnitude in biology. Tightly controlled behavior, possibly involving intercellular electrical signaling, was found to generally keep <10% of individual filaments exposed to oxygen. The results strengthen the hypothesis that cable bacteria indeed have evolved an exceptional way to take the full energetic advantages of aerobic respiration and let >90% of the cells metabolize in the convenient absence of oxidative stress.
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Affiliation(s)
- Stefano Scilipoti
- Center for Electromicrobiology, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark.
| | - Klaus Koren
- Aarhus University Center for Water Technology, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Nils Risgaard-Petersen
- Center for Electromicrobiology, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Andreas Schramm
- Center for Electromicrobiology, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Lars Peter Nielsen
- Center for Electromicrobiology, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark.
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22
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Geerlings NMJ, Geelhoed JS, Vasquez-Cardenas D, Kienhuis MVM, Hidalgo-Martinez S, Boschker HTS, Middelburg JJ, Meysman FJR, Polerecky L. Cell Cycle, Filament Growth and Synchronized Cell Division in Multicellular Cable Bacteria. Front Microbiol 2021; 12:620807. [PMID: 33584623 PMCID: PMC7873302 DOI: 10.3389/fmicb.2021.620807] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/06/2021] [Indexed: 11/13/2022] Open
Abstract
Cable bacteria are multicellular, Gram-negative filamentous bacteria that display a unique division of metabolic labor between cells. Cells in deeper sediment layers are oxidizing sulfide, while cells in the surface layers of the sediment are reducing oxygen. The electrical coupling of these two redox half reactions is ensured via long-distance electron transport through a network of conductive fibers that run in the shared cell envelope of the centimeter-long filament. Here we investigate how this unique electrogenic metabolism is linked to filament growth and cell division. Combining dual-label stable isotope probing (13C and 15N), nanoscale secondary ion mass spectrometry, fluorescence microscopy and genome analysis, we find that the cell cycle of cable bacteria cells is highly comparable to that of other, single-celled Gram-negative bacteria. However, the timing of cell growth and division appears to be tightly and uniquely controlled by long-distance electron transport, as cell division within an individual filament shows a remarkable synchronicity that extends over a millimeter length scale. To explain this, we propose the "oxygen pacemaker" model in which a filament only grows when performing long-distance transport, and the latter is only possible when a filament has access to oxygen so it can discharge electrons from its internal electrical network.
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Affiliation(s)
| | | | | | | | | | | | | | - Filip J. R. Meysman
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Lubos Polerecky
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
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Scholz VV, Müller H, Koren K, Nielsen LP, Meckenstock RU. The rhizosphere of aquatic plants is a habitat for cable bacteria. FEMS Microbiol Ecol 2020; 95:5485638. [PMID: 31054245 PMCID: PMC6510695 DOI: 10.1093/femsec/fiz062] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/03/2019] [Indexed: 11/15/2022] Open
Abstract
Cable bacteria belonging to the family Desulfobulbaceae couple sulfide oxidation and oxygen reduction by long-distance electron transfer over centimeter distances in marine and freshwater sediments. In such habitats, aquatic plants can release oxygen into the rhizosphere. Hence, the rhizosphere constitutes an ideal habitat for cable bacteria, which have been reported on seagrass roots recently. Here, we employ experimental approaches to investigate activity, abundance, and spatial orientation of cable bacteria next to the roots of the freshwater plant Littorella uniflora. Fluorescence in situ hybridization (FISH), in combination with oxygen-sensitive planar optodes, demonstrated that cable bacteria densities are enriched at the oxic–anoxic transition zone next to roots compared to the bulk sediment in the same depth. Scanning electron microscopy showed cable bacteria along root hairs. Electric potential measurements showed a lateral electric field over centimeters from the roots, indicating cable bacteria activity. In addition, FISH revealed that cable bacteria were present in the rhizosphere of Oryza sativa (rice), Lobelia cardinalis and Salicornia europaea. Hence, the interaction of cable bacteria with aquatic plants of different growth forms and habitats indicates that the plant root–cable bacteria interaction might be a common property of aquatic plant rhizospheres.
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Affiliation(s)
- Vincent V Scholz
- Biofilm Centre, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany.,Center for Electromicrobiology, Aarhus University, Ny Munkegade 116, DK-8000 Aarhus C, Denmark
| | - Hubert Müller
- Biofilm Centre, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Klaus Koren
- Aarhus University Centre for Water Technology, Section for Microbiology, Department of Bioscience, Aarhus University, Ny Munkegade 116, DK-8000 Aarhus C, Denmark
| | - Lars Peter Nielsen
- Center for Electromicrobiology, Aarhus University, Ny Munkegade 116, DK-8000 Aarhus C, Denmark
| | - Rainer U Meckenstock
- Biofilm Centre, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
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Karikari-Yeboah O, Skinner W, Addai-Mensah J. Microbial diversity and functional response to the redox dynamics of pyrite-rich sediment and the impact of preload surcharge. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:226. [PMID: 32152784 DOI: 10.1007/s10661-020-8169-6] [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: 08/01/2019] [Accepted: 02/18/2020] [Indexed: 06/10/2023]
Abstract
Microbial diversity and activities play pivotal biogeochemical roles in a redox-sensitive, pyrite-rich sediment's ecosystem. However, very little is known about the microbial community composition and distribution among the redox zones of pyrite-rich sediment and their response to changes caused by the burial of the sediment beneath compacted fill. In the present work, culture-independent, molecular phylogenetic investigations of the prokaryotic population and its diversity in a naturally occurring pyrite-rich sediment were undertaken to determine the microbial community composition, richness, diversity and distributions among the varying redox zones and their functional response to the imposition of surface surcharge, in the form of compacted fill. It was established that the pyrite-rich sediment is a redox-sensitive environment consisting of microhabitats with distinct and discontinuous physico-chemical characteristics, including DO, pH, Eh, temperature, electrical conductivity and salinity. It is a favourable environment for cyclic transformation of inorganic sulphur compounds and a unique environment for the habitation and growth of various microorganisms. Microbes adapted to the microhabitat and lived together in consortia, in response to their physiological and functional requirements. Microbes involved in the sulphur cycle had their populations concentrated in the oxic zone, while those involved in iron and carbon cycles were prevalent in the anoxic zones. As a result, highly diverse microbial populations occurred in isolated peaks within the sediment. The physico-chemical differences within the sediment changed in response to changes in the sediment redox dynamics. Imposition of the surcharge resulted in significant changes in the pH, temperature, Eh, DO, EC and salinity, reflecting marked re-distribution of the microbial population within the ecosystem. The cable bacteria phenomenon was evident in the sediment studied; however, there were doubt regarding their filamentous occurrence.
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Affiliation(s)
| | - W Skinner
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, Adelaide, South Australia
| | - J Addai-Mensah
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, Adelaide, South Australia
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25
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Division of labor and growth during electrical cooperation in multicellular cable bacteria. Proc Natl Acad Sci U S A 2020; 117:5478-5485. [PMID: 32094191 PMCID: PMC7071850 DOI: 10.1073/pnas.1916244117] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Cable bacteria form centimeter-long, multicellular filaments whose energy metabolism involves cooperation among cells that separately perform oxidation of the electron donor and reduction of the electron acceptor. This cooperative division of labor is facilitated via long-range electrical currents that run from cell to cell along a network of conductive fibers. Here we show that biomass synthesis shows a surprising asymmetry along the filament: only the cells oxidizing the electron donor conserve energy for growth, while the other cells reduce electron acceptors without biosynthesis. Our study hence provides insights into the physiology of an unconventional chemolithotroph, which forms a multicellular electrically connected system with unique functional differentiation, integration, and coordination. Multicellularity is a key evolutionary innovation, leading to coordinated activity and resource sharing among cells, which generally occurs via the physical exchange of chemical compounds. However, filamentous cable bacteria display a unique metabolism in which redox transformations in distant cells are coupled via long-distance electron transport rather than an exchange of chemicals. This challenges our understanding of organismal functioning, as the link among electron transfer, metabolism, energy conservation, and filament growth in cable bacteria remains enigmatic. Here, we show that cells within individual filaments of cable bacteria display a remarkable dichotomy in biosynthesis that coincides with redox zonation. Nanoscale secondary ion mass spectrometry combined with 13C (bicarbonate and propionate) and 15N-ammonia isotope labeling reveals that cells performing sulfide oxidation in deeper anoxic horizons have a high assimilation rate, whereas cells performing oxygen reduction in the oxic zone show very little or no label uptake. Accordingly, oxygen reduction appears to merely function as a mechanism to quickly dispense of electrons with little to no energy conservation, while biosynthesis and growth are restricted to sulfide-respiring cells. Still, cells can immediately switch roles when redox conditions change, and show no differentiation, which suggests that the “community service” performed by the cells in the oxic zone is only temporary. Overall, our data reveal a division of labor and electrical cooperation among cells that has not been seen previously in multicellular organisms.
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26
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Cable bacteria, living electrical conduits in the microbial world. Proc Natl Acad Sci U S A 2019; 116:18759-18761. [PMID: 31501332 DOI: 10.1073/pnas.1913413116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Abstract
Cable bacteria of the family Desulfobulbaceae form centimeter-long filaments comprising thousands of cells. They occur worldwide in the surface of aquatic sediments, where they connect sulfide oxidation with oxygen or nitrate reduction via long-distance electron transport. In the absence of pure cultures, we used single-filament genomics and metagenomics to retrieve draft genomes of 3 marine Candidatus Electrothrix and 1 freshwater Ca. Electronema species. These genomes contain >50% unknown genes but still share their core genomic makeup with sulfate-reducing and sulfur-disproportionating Desulfobulbaceae, with few core genes lost and 212 unique genes (from 197 gene families) conserved among cable bacteria. Last common ancestor analysis indicates gene divergence and lateral gene transfer as equally important origins of these unique genes. With support from metaproteomics of a Ca. Electronema enrichment, the genomes suggest that cable bacteria oxidize sulfide by reversing the canonical sulfate reduction pathway and fix CO2 using the Wood-Ljungdahl pathway. Cable bacteria show limited organotrophic potential, may assimilate smaller organic acids and alcohols, fix N2, and synthesize polyphosphates and polyglucose as storage compounds; several of these traits were confirmed by cell-level experimental analyses. We propose a model for electron flow from sulfide to oxygen that involves periplasmic cytochromes, yet-unidentified conductive periplasmic fibers, and periplasmic oxygen reduction. This model proposes that an active cable bacterium gains energy in the anodic, sulfide-oxidizing cells, whereas cells in the oxic zone flare off electrons through intense cathodic oxygen respiration without energy conservation; this peculiar form of multicellularity seems unparalleled in the microbial world.
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28
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Martin BC, Bougoure J, Ryan MH, Bennett WW, Colmer TD, Joyce NK, Olsen YS, Kendrick GA. Oxygen loss from seagrass roots coincides with colonisation of sulphide-oxidising cable bacteria and reduces sulphide stress. THE ISME JOURNAL 2019; 13:707-719. [PMID: 30353038 PMCID: PMC6461758 DOI: 10.1038/s41396-018-0308-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 10/02/2018] [Accepted: 10/09/2018] [Indexed: 02/04/2023]
Abstract
Seagrasses thrive in anoxic sediments where sulphide can accumulate to phytotoxic levels. So how do seagrasses persist in this environment? Here, we propose that radial oxygen loss (ROL) from actively growing root tips protects seagrasses from sulphide intrusion not only by abiotically oxidising sulphides in the rhizosphere of young roots, but also by influencing the abundance and spatial distribution of sulphate-reducing and sulphide-oxidising bacteria. We used a novel multifaceted approach combining imaging techniques (confocal fluorescence in situ hybridisation, oxygen planar optodes, and sulphide diffusive gradients in thin films) with microbial community profiling to build a complete picture of the microenvironment of growing roots of the seagrasses Halophila ovalis and Zostera muelleri. ROL was restricted to young root tips, indicating that seagrasses will have limited ability to influence sulphide oxidation in bulk sediments. On the microscale, however, ROL corresponded with decreased abundance of potential sulphate-reducing bacteria and decreased sulphide concentrations in the rhizosphere surrounding young roots. Furthermore, roots leaking oxygen had a higher abundance of sulphide-oxidising cable bacteria; which is the first direct observation of these bacteria on seagrass roots. Thus, ROL may enhance both abiotic and bacterial sulphide oxidation and restrict bacterial sulphide production around vulnerable roots, thereby helping seagrasses to colonise sulphide-rich anoxic sediments.
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Affiliation(s)
- Belinda C Martin
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- The UWA Oceans Institute, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- Ooid Scientific Graphics and Editing, White Gum Valley, WA, 6163, Australia.
| | - Jeremy Bougoure
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Megan H Ryan
- School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - William W Bennett
- Environmental Futures Research Institute, Griffith University, Parklands Drive, Southport, QLD, 4215, Australia
| | - Timothy D Colmer
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Natalie K Joyce
- Ooid Scientific Graphics and Editing, White Gum Valley, WA, 6163, Australia
| | - Ylva S Olsen
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
- The UWA Oceans Institute, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Gary A Kendrick
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
- The UWA Oceans Institute, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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29
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Stal LJ, Bolhuis H, Cretoiu MS. Phototrophic marine benthic microbiomes: the ecophysiology of these biological entities. Environ Microbiol 2018; 21:1529-1551. [PMID: 30507057 DOI: 10.1111/1462-2920.14494] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 01/02/2023]
Abstract
Phototrophic biofilms are multispecies, self-sustaining and largely closed microbial ecosystems. They form macroscopic structures such as microbial mats and stromatolites. These sunlight-driven consortia consist of a number of functional groups of microorganisms that recycle the elements internally. Particularly, the sulfur cycle is discussed in more detail as this is fundamental to marine benthic microbial communities and because recently exciting new insights have been obtained. The cycling of elements demands a tight tuning of the various metabolic processes and require cooperation between the different groups of microorganisms. This is likely achieved through cell-to-cell communication and a biological clock. Biofilms may be considered as a macroscopic biological entity with its own physiology. We review the various components of some marine phototrophic biofilms and discuss their roles in the system. The importance of extracellular polymeric substances (EPS) as the matrix for biofilm metabolism and as substrate for biofilm microorganisms is discussed. We particularly assess the importance of extracellular DNA, horizontal gene transfer and viruses for the generation of genetic diversity and innovation, and for rendering resilience to external forcing to these biological entities.
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Affiliation(s)
- Lucas J Stal
- IBED Department of Freshwater and Marine Ecology, University of Amsterdam, Amsterdam, The Netherlands.,Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Netherlands Institute for Sea Research, Den Burg, Texel, The Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Netherlands Institute for Sea Research, Den Burg, Texel, The Netherlands
| | - Mariana S Cretoiu
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
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30
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Cornelissen R, Bøggild A, Thiruvallur Eachambadi R, Koning RI, Kremer A, Hidalgo-Martinez S, Zetsche EM, Damgaard LR, Bonné R, Drijkoningen J, Geelhoed JS, Boesen T, Boschker HTS, Valcke R, Nielsen LP, D'Haen J, Manca JV, Meysman FJR. The Cell Envelope Structure of Cable Bacteria. Front Microbiol 2018; 9:3044. [PMID: 30619135 PMCID: PMC6307468 DOI: 10.3389/fmicb.2018.03044] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/26/2018] [Indexed: 11/16/2022] Open
Abstract
Cable bacteria are long, multicellular micro-organisms that are capable of transporting electrons from cell to cell along the longitudinal axis of their centimeter-long filaments. The conductive structures that mediate this long-distance electron transport are thought to be located in the cell envelope. Therefore, this study examines in detail the architecture of the cell envelope of cable bacterium filaments by combining different sample preparation methods (chemical fixation, resin-embedding, and cryo-fixation) with a portfolio of imaging techniques (scanning electron microscopy, transmission electron microscopy and tomography, focused ion beam scanning electron microscopy, and atomic force microscopy). We systematically imaged intact filaments with varying diameters. In addition, we investigated the periplasmic fiber sheath that remains after the cytoplasm and membranes were removed by chemical extraction. Based on these investigations, we present a quantitative structural model of a cable bacterium. Cable bacteria build their cell envelope by a parallel concatenation of ridge compartments that have a standard size. Larger diameter filaments simply incorporate more parallel ridge compartments. Each ridge compartment contains a ~50 nm diameter fiber in the periplasmic space. These fibers are continuous across cell-to-cell junctions, which display a conspicuous cartwheel structure that is likely made by invaginations of the outer cell membrane around the periplasmic fibers. The continuity of the periplasmic fibers across cells makes them a prime candidate for the sought-after electron conducting structure in cable bacteria.
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Affiliation(s)
| | - Andreas Bøggild
- Center for Electromicrobiology, Department of Bioscience Aarhus University, Aarhus, Denmark.,Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Structural Biology Aarhus University, Aarhus, Denmark
| | | | - Roman I Koning
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Anna Kremer
- Bio-imaging Core, Flemish Institute of Biotechnology (VIB), Gent, Belgium
| | | | - Eva-Maria Zetsche
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Lars R Damgaard
- Center for Electromicrobiology, Department of Bioscience Aarhus University, Aarhus, Denmark
| | | | | | | | - Thomas Boesen
- Center for Electromicrobiology, Department of Bioscience Aarhus University, Aarhus, Denmark.,Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Structural Biology Aarhus University, Aarhus, Denmark
| | - Henricus T S Boschker
- Department of Biology, University of Antwerp, Antwerpen, Belgium.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Roland Valcke
- Molecular and Physical Plant Physiology, Hasselt University, Hasselt, Belgium
| | - Lars Peter Nielsen
- Center for Electromicrobiology, Department of Bioscience Aarhus University, Aarhus, Denmark
| | - Jan D'Haen
- Institute for Materials Research (IMO), Hasselt University, Hasselt, Belgium
| | | | - Filip J R Meysman
- Department of Biology, University of Antwerp, Antwerpen, Belgium.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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Abstract
Electron transport within living cells is essential for energy conservation in all respiring and photosynthetic organisms. While a few bacteria transport electrons over micrometer distances to their surroundings, filaments of cable bacteria are hypothesized to conduct electric currents over centimeter distances. We used resonance Raman microscopy to analyze cytochrome redox states in living cable bacteria. Cable-bacteria filaments were placed in microscope chambers with sulfide as electron source and oxygen as electron sink at opposite ends. Along individual filaments a gradient in cytochrome redox potential was detected, which immediately broke down upon removal of oxygen or laser cutting of the filaments. Without access to oxygen, a rapid shift toward more reduced cytochromes was observed, as electrons were no longer drained from the filament but accumulated in the cellular cytochromes. These results provide direct evidence for long-distance electron transport in living multicellular bacteria.
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32
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Cable Bacteria Take a New Breath Using Long-Distance Electricity. Trends Microbiol 2018; 26:411-422. [DOI: 10.1016/j.tim.2017.10.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/29/2017] [Accepted: 10/31/2017] [Indexed: 11/18/2022]
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33
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Martin BC, Gleeson D, Statton J, Siebers AR, Grierson P, Ryan MH, Kendrick GA. Low Light Availability Alters Root Exudation and Reduces Putative Beneficial Microorganisms in Seagrass Roots. Front Microbiol 2018; 8:2667. [PMID: 29375529 PMCID: PMC5768916 DOI: 10.3389/fmicb.2017.02667] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/21/2017] [Indexed: 01/05/2023] Open
Abstract
Seagrass roots host a diverse microbiome that is critical for plant growth and health. Composition of microbial communities can be regulated in part by root exudates, but the specifics of these interactions in seagrass rhizospheres are still largely unknown. As light availability controls primary productivity, reduced light may impact root exudation and consequently the composition of the root microbiome. Hence, we analyzed the influence of light availability on root exudation and community structure of the root microbiome of three co-occurring seagrass species, Halophila ovalis, Halodule uninervis and Cymodocea serrulata. Plants were grown under four light treatments in mesocosms for 2 weeks; control (100% surface irradiance (SI), medium (40% SI), low (20% SI) and fluctuating light (10 days 20% and 4 days 100%). 16S rDNA amplicon sequencing revealed that microbial diversity, composition and predicted function were strongly influenced by the presence of seagrass roots, such that root microbiomes were unique to each seagrass species. Reduced light availability altered seagrass root exudation, as characterized using fluorescence spectroscopy, and altered the composition of seagrass root microbiomes with a reduction in abundance of potentially beneficial microorganisms. Overall, this study highlights the potential for above-ground light reduction to invoke a cascade of changes from alterations in root exudation to a reduction in putative beneficial microorganisms and, ultimately, confirms the importance of the seagrass root environment - a critical, but often overlooked space.
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Affiliation(s)
- Belinda C. Martin
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
- UWA Oceans Institute, The University of Western Australia, Crawley, WA, Australia
| | - Deirdre Gleeson
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - John Statton
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
- UWA Oceans Institute, The University of Western Australia, Crawley, WA, Australia
- Western Australian Marine Science Institution, Perth, WA, Australia
| | - Andre R. Siebers
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Pauline Grierson
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
- West Australian Biogeochemistry Centre, School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Megan H. Ryan
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - Gary A. Kendrick
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
- UWA Oceans Institute, The University of Western Australia, Crawley, WA, Australia
- Western Australian Marine Science Institution, Perth, WA, Australia
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34
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Xie J, Han X, Wang W, Zhou X, Lin J. Effects of humic acid concentration on the microbially-mediated reductive solubilization of Pu(IV) polymers. JOURNAL OF HAZARDOUS MATERIALS 2017; 339:347-353. [PMID: 28668752 DOI: 10.1016/j.jhazmat.2017.06.054] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 04/03/2017] [Accepted: 06/21/2017] [Indexed: 06/07/2023]
Abstract
The role of humic acid concentration in the microbially-mediated reductive solubilization of Pu(IV) polymers remains unclear until now. The effects of humic concentration (0-150.5mg/L) on the rate and extent of reduction of polymeric Pu(IV) were studied under anaerobic and pH 7.2 conditions. The results show that Shewanella putrefaciens, secreting flavins as endogenous electron shuttles, cannot notably stimulate the reduction of polymeric Pu(IV). In the presence of humic acids, the reduction rate of polymeric Pu(IV) increased with increasing humic concentrations (0-15.0mg/L): e.g., a 102-fold increase from 4.1×10-15 (HA=0) to 4.2×10-13mol Pu(III)aq/h (HA=15.0mg/L). The bioreduced humic acids by S. putrefaciens facilitated the extracellular electron transfer to Pu(IV) polymers and thus the reduction of polymeric Pu(IV) to Pu(III)aq became thermodynamically favorable. However, the reduction rate did not increase but decrease with increasing humic concentrations from 15.0 to 150.5mg/L. Humic coatings formed on the polymer surfaces at relatively high humic concentrations limited the electron transfer to the polymers and thus decreased the reduction rate. The finding of the dynamic role of humic acids in the bioreductive solubilization may be helpful in evaluating Pu mobility in the geosphere.
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Affiliation(s)
- Jinchuan Xie
- Northwest Institute of Nuclear Technology, P. O. Box 69-14, Xi'an City, Shanxi Province 710024, PR China.
| | - Xiaoyuan Han
- Northwest Institute of Nuclear Technology, P. O. Box 69-14, Xi'an City, Shanxi Province 710024, PR China
| | - Weixian Wang
- Northwest Institute of Nuclear Technology, P. O. Box 69-14, Xi'an City, Shanxi Province 710024, PR China
| | - Xiaohua Zhou
- Northwest Institute of Nuclear Technology, P. O. Box 69-14, Xi'an City, Shanxi Province 710024, PR China
| | - Jianfeng Lin
- Northwest Institute of Nuclear Technology, P. O. Box 69-14, Xi'an City, Shanxi Province 710024, PR China
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Trojan D, Schreiber L, Bjerg JT, Bøggild A, Yang T, Kjeldsen KU, Schramm A. A taxonomic framework for cable bacteria and proposal of the candidate genera Electrothrix and Electronema. Syst Appl Microbiol 2016; 39:297-306. [PMID: 27324572 PMCID: PMC4958695 DOI: 10.1016/j.syapm.2016.05.006] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/06/2016] [Accepted: 05/09/2016] [Indexed: 11/29/2022]
Abstract
Cable bacteria are long, multicellular filaments that can conduct electric currents over centimeter-scale distances. All cable bacteria identified to date belong to the deltaproteobacterial family Desulfobulbaceae and have not been isolated in pure culture yet. Their taxonomic delineation and exact phylogeny is uncertain, as most studies so far have reported only short partial 16S rRNA sequences or have relied on identification by a combination of filament morphology and 16S rRNA-targeted fluorescence in situ hybridization with a Desulfobulbaceae-specific probe. In this study, nearly full-length 16S rRNA gene sequences of 16 individual cable bacteria filaments from freshwater, salt marsh, and marine sites of four geographic locations are presented. These sequences formed a distinct, monophyletic sister clade to the genus Desulfobulbus and could be divided into six coherent, species-level clusters, arranged as two genus-level groups. The same grouping was retrieved by phylogenetic analysis of full or partial dsrAB genes encoding the dissimilatory sulfite reductase. Based on these results, it is proposed to accommodate cable bacteria within two novel candidate genera: the mostly marine “Candidatus Electrothrix”, with four candidate species, and the mostly freshwater “Candidatus Electronema”, with two candidate species. This taxonomic framework can be used to assign environmental sequences confidently to the cable bacteria clade, even without morphological information. Database searches revealed 185 16S rRNA gene sequences that affiliated within the clade formed by the proposed cable bacteria genera, of which 120 sequences could be assigned to one of the six candidate species, while the remaining 65 sequences indicated the existence of up to five additional species.
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Affiliation(s)
- Daniela Trojan
- Section for Microbiology & Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark.
| | - Lars Schreiber
- Section for Microbiology & Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Jesper T Bjerg
- Section for Microbiology & Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Andreas Bøggild
- Section for Microbiology & Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Tingting Yang
- Section for Microbiology & Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Kasper U Kjeldsen
- Section for Microbiology & Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Andreas Schramm
- Section for Microbiology & Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark.
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