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Wu B, Liu F, Liang Z, Wang C, Wang S. Spatial distribution of cable bacteria in nationwide organic-matter-polluted urban rivers in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174118. [PMID: 38925373 DOI: 10.1016/j.scitotenv.2024.174118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/04/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024]
Abstract
An overload of labile organic matter triggers the water blackening and odorization in urban rivers, leading to a unique microbiome driving biogeochemical cycles in these anoxic habitats. Among the key players in these environments, cable bacteria interfere directly with C/N/S/O cycling, and are closely associated with phylogenetically diverse microorganisms in anoxic sediment as an electron conduit to mediate long-distance electron transport from deep-anoxic-layer sulfide to oxic-layer oxygen. Despite their hypothesized importance in black-odorous urban rivers, the spatial distribution patterns and roles of cable bacteria in large-scale polluted urban rivers remain inadequately understood. This study examined the diversity and spatial distribution pattern of cable bacteria in sediment samples from 186 black-odorous urban rivers across China. Results revealed the co-existence of two well-characterized cable bacteria (i.e., Candidatus Electrothrix and Candidatus Electronema), with Candidatus Electrothrix exhibiting a comparatively wider distribution in the polluted urban rivers. Concentrations of DOC, SS, sulfate, nitrate, and heavy metals (e.g., Ni and Cr) were correlated with the cable bacteria diversity, indicating their essential role in biogeochemical cycles. The activation energy of cable bacteria was 0.624 eV, close to the canonical 0.65 eV. Furthermore, cable bacteria were identified as key connectors and module hubs, closely associated with denitrifiers, sulfate-reducing bacteria, methanogens and alkane degraders, highlighting their role as keystone functional lineages in the contaminated urban rivers. Our study provided the first large-scale and comprehensive insight into the cable bacteria diversity, spatial distribution, and their essential function as keystone species in organic-matter-polluted urban rivers.
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Affiliation(s)
- Bo Wu
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, China
| | - Feifei Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; Guangdong Magigene Biotechnology Co. Ltd., 510000 Guangzhou, China
| | - Zhiwei Liang
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, China
| | - Chen Wang
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, China
| | - Shanquan Wang
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, China.
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2
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Hiralal A, Geelhoed JS, Neukirchen S, Meysman FJR. Comparative genomic analysis of nickel homeostasis in cable bacteria. BMC Genomics 2024; 25:692. [PMID: 39009997 PMCID: PMC11247825 DOI: 10.1186/s12864-024-10594-7] [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: 03/27/2024] [Accepted: 07/03/2024] [Indexed: 07/17/2024] Open
Abstract
BACKGROUND Cable bacteria are filamentous members of the Desulfobulbaceae family that are capable of performing centimetre‑scale electron transport in marine and freshwater sediments. This long‑distance electron transport is mediated by a network of parallel conductive fibres embedded in the cell envelope. This fibre network efficiently transports electrical currents along the entire length of the centimetre‑long filament. Recent analyses show that these fibres consist of metalloproteins that harbour a novel nickel‑containing cofactor, which indicates that cable bacteria have evolved a unique form of biological electron transport. This nickel‑dependent conduction mechanism suggests that cable bacteria are strongly dependent on nickel as a biosynthetic resource. Here, we performed a comprehensive comparative genomic analysis of the genes linked to nickel homeostasis. We compared the genome‑encoded adaptation to nickel of cable bacteria to related members of the Desulfobulbaceae family and other members of the Desulfobulbales order. RESULTS Presently, four closed genomes are available for the monophyletic cable bacteria clade that consists of the genera Candidatus Electrothrix and Candidatus Electronema. To increase the phylogenomic coverage, we additionally generated two closed genomes of cable bacteria: Candidatus Electrothrix gigas strain HY10‑6 and Candidatus Electrothrix antwerpensis strain GW3‑4, which are the first closed genomes of their respective species. Nickel homeostasis genes were identified in a database of 38 cable bacteria genomes (including 6 closed genomes). Gene prevalence was compared to 19 genomes of related strains, residing within the Desulfobulbales order but outside of the cable bacteria clade, revealing several genome‑encoded adaptations to nickel homeostasis in cable bacteria. Phylogenetic analysis indicates that nickel importers, nickel‑binding enzymes and nickel chaperones of cable bacteria are affiliated to organisms outside the Desulfobulbaceae family, with several proteins showing affiliation to organisms outside of the Desulfobacterota phylum. Conspicuously, cable bacteria encode a unique periplasmic nickel export protein RcnA, which possesses a putative cytoplasmic histidine‑rich loop that has been largely expanded compared to RcnA homologs in other organisms. CONCLUSION Cable bacteria genomes show a clear genetic adaptation for nickel utilization when compared to closely related genera. This fully aligns with the nickel‑dependent conduction mechanism that is uniquely found in cable bacteria.
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Affiliation(s)
- Anwar Hiralal
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
| | | | - Sinje Neukirchen
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
| | - Filip J R Meysman
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium.
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
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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: 0] [Impact Index Per Article: 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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Stiefelmaier J, Keller J, Neupert W, Ulber R. Towards bioprocess engineering of cable bacteria: Establishment of a synthetic sediment. Microbiologyopen 2024; 13:e1412. [PMID: 38711353 DOI: 10.1002/mbo3.1412] [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: 12/01/2023] [Revised: 04/12/2024] [Accepted: 04/20/2024] [Indexed: 05/08/2024] Open
Abstract
Cable bacteria, characterized by their multicellular filamentous growth, are prevalent in both freshwater and marine sediments. They possess the unique ability to transport electrons over distances of centimeters. Coupled with their capacity to fix CO2 and their record-breaking conductivity for biological materials, these bacteria present promising prospects for bioprocess engineering, including potential electrochemical applications. However, the cultivation of cable bacteria has been limited to their natural sediment, constraining their utility in production processes. To address this, our study designs synthetic sediment, drawing on ion exchange chromatography data from natural sediments and existing literature on the requirements of cable bacteria. We examined the effects of varying bentonite concentrations on water retention and the impacts of different sands. For the first time, we cultivated cable bacteria on synthetic sediment, specifically the freshwater strain Electronema aureum GS. This cultivation was conducted over 10 weeks in a specially developed sediment bioreactor, resulting in an increased density of cable bacteria in the sediment and growth up to a depth of 5 cm. The creation of this synthetic sediment paves the way for the reproducible cultivation of cable bacteria. It also opens up possibilities for future process scale-up using readily available components. This advancement holds significant implications for the broader field of bioprocess engineering.
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Affiliation(s)
- Judith Stiefelmaier
- Chair of Bioprocess Engineering, RPTU Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Joshua Keller
- Chair of Bioprocess Engineering, RPTU Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Wiebke Neupert
- Chair of Bioprocess Engineering, RPTU Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Roland Ulber
- Chair of Bioprocess Engineering, RPTU Kaiserslautern-Landau, Kaiserslautern, Germany
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6
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Pankratov D, Hidalgo Martinez S, Karman C, Gerzhik A, Gomila G, Trashin S, Boschker HTS, Geelhoed JS, Mayer D, De Wael K, J R Meysman F. The organo-metal-like nature of long-range conduction in cable bacteria. Bioelectrochemistry 2024; 157:108675. [PMID: 38422765 DOI: 10.1016/j.bioelechem.2024.108675] [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: 10/31/2023] [Revised: 02/22/2024] [Accepted: 02/24/2024] [Indexed: 03/02/2024]
Abstract
Cable bacteria are filamentous, multicellular microorganisms that display an exceptional form of biological electron transport across centimeter-scale distances. Currents are guided through a network of nickel-containing protein fibers within the cell envelope. Still, the mechanism of long-range conduction remains unresolved. Here, we characterize the conductance of the fiber network under dry and wet, physiologically relevant, conditions. Our data reveal that the fiber conductivity is high (median value: 27 S cm-1; range: 2 to 564 S cm-1), does not show any redox signature, has a low thermal activation energy (Ea = 69 ± 23 meV), and is not affected by humidity or the presence of ions. These features set the nickel-based conduction mechanism in cable bacteria apart from other known forms of biological electron transport. As such, conduction resembles that of an organic semi-metal with a high charge carrier density. Our observation that biochemistry can synthesize an organo-metal-like structure opens the way for novel bio-based electronic technologies.
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Affiliation(s)
- Dmitrii Pankratov
- Geobiology Group, Microbial Systems Technology Excellence Centre, Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium; A-Sense Lab, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerpen, Belgium
| | - Silvia Hidalgo Martinez
- Geobiology Group, Microbial Systems Technology Excellence Centre, Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Cheryl Karman
- Geobiology Group, Microbial Systems Technology Excellence Centre, Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium; A-Sense Lab, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerpen, Belgium
| | - Anastasia Gerzhik
- Institute of Biological Information Processing, Bioelectronics (IBI-3), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Gabriel Gomila
- Nanoscale Bioelectric Characterization Group, Institute for Bioengineering of Catalunya (IBEC), The Barcelona Institute of Science and Technology, Baldiri i Reixac 15-21, 08028 Barcelona, Spain; Department of Electronics and Biomedical Engineering, Universitat de Barcelona, Martí i Franqués 1, 08028 Barcelona, Spain
| | - Stanislav Trashin
- A-Sense Lab, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerpen, Belgium
| | - Henricus T S Boschker
- Geobiology Group, Microbial Systems Technology Excellence Centre, Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, the Netherlands
| | - Jeanine S Geelhoed
- Geobiology Group, Microbial Systems Technology Excellence Centre, Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Dirk Mayer
- Institute of Biological Information Processing, Bioelectronics (IBI-3), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Karolien De Wael
- A-Sense Lab, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerpen, Belgium
| | - Filip J R Meysman
- Geobiology Group, Microbial Systems Technology Excellence Centre, Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, the Netherlands.
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7
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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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8
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Smets B, Boschker HTS, Wetherington MT, Lelong G, Hidalgo-Martinez S, Polerecky L, Nuyts G, De Wael K, Meysman FJR. Multi-wavelength Raman microscopy of nickel-based electron transport in cable bacteria. Front Microbiol 2024; 15:1208033. [PMID: 38525072 PMCID: PMC10959288 DOI: 10.3389/fmicb.2024.1208033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
Cable bacteria embed a network of conductive protein fibers in their cell envelope that efficiently guides electron transport over distances spanning up to several centimeters. This form of long-distance electron transport is unique in biology and is mediated by a metalloprotein with a sulfur-coordinated nickel (Ni) cofactor. However, the molecular structure of this cofactor remains presently unknown. Here, we applied multi-wavelength Raman microscopy to identify cell compounds linked to the unique cable bacterium physiology, combined with stable isotope labeling, and orientation-dependent and ultralow-frequency Raman microscopy to gain insight into the structure and organization of this novel Ni-cofactor. Raman spectra of native cable bacterium filaments reveal vibrational modes originating from cytochromes, polyphosphate granules, proteins, as well as the Ni-cofactor. After selective extraction of the conductive fiber network from the cell envelope, the Raman spectrum becomes simpler, and primarily retains vibrational modes associated with the Ni-cofactor. These Ni-cofactor modes exhibit intense Raman scattering as well as a strong orientation-dependent response. The signal intensity is particularly elevated when the polarization of incident laser light is parallel to the direction of the conductive fibers. This orientation dependence allows to selectively identify the modes that are associated with the Ni-cofactor. We identified 13 such modes, some of which display strong Raman signals across the entire range of applied wavelengths (405-1,064 nm). Assignment of vibrational modes, supported by stable isotope labeling, suggest that the structure of the Ni-cofactor shares a resemblance with that of nickel bis(1,2-dithiolene) complexes. Overall, our results indicate that cable bacteria have evolved a unique cofactor structure that does not resemble any of the known Ni-cofactors in biology.
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Affiliation(s)
- Bent Smets
- Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Henricus T. S. Boschker
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Maxwell T. Wetherington
- Materials Characterization Laboratory, Pennsylvania State University, State College, PA, United States
| | - Gérald Lelong
- Institut de Minéralogie, de Physique des Matériaux et Cosmochimie (IMPMC), Sorbonne Universités, France—Muséum National d’Histoire Naturelle, Paris, France
| | | | - Lubos Polerecky
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Gert Nuyts
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
- Department of Physics, University of Antwerp, Antwerp, Belgium
| | - Karolien De Wael
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Filip J. R. Meysman
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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9
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Hiralal A, Geelhoed JS, Hidalgo-Martinez S, Smets B, van Dijk JR, Meysman FJR. Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads. Microb Genom 2024; 10:001197. [PMID: 38376381 PMCID: PMC10926707 DOI: 10.1099/mgen.0.001197] [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: 11/13/2023] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
Many environmentally relevant micro-organisms cannot be cultured, and even with the latest metagenomic approaches, achieving complete genomes for specific target organisms of interest remains a challenge. Cable bacteria provide a prominent example of a microbial ecosystem engineer that is currently unculturable. They occur in low abundance in natural sediments, but due to their capability for long-distance electron transport, they exert a disproportionately large impact on the biogeochemistry of their environment. Current available genomes of marine cable bacteria are highly fragmented and incomplete, hampering the elucidation of their unique electrogenic physiology. Here, we present a metagenomic pipeline that combines Nanopore long-read and Illumina short-read shotgun sequencing. Starting from a clonal enrichment of a cable bacterium, we recovered a circular metagenome-assembled genome (5.09 Mbp in size), which represents a novel cable bacterium species with the proposed name Candidatus Electrothrix scaldis. The closed genome contains 1109 novel identified genes, including key metabolic enzymes not previously described in incomplete genomes of cable bacteria. We examined in detail the factors leading to genome closure. Foremost, native, non-amplified long reads are crucial to resolve the many repetitive regions within the genome of cable bacteria, and by analysing the whole metagenomic assembly, we found that low strain diversity is key for achieving genome closure. The insights and approaches presented here could help achieve genome closure for other keystone micro-organisms present in complex environmental samples at low abundance.
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Affiliation(s)
- Anwar Hiralal
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
| | | | | | - Bent Smets
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
| | | | - Filip J. R. Meysman
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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10
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van der Veen JR, Valianti S, van der Zant HSJ, Blanter YM, Meysman FJR. A model analysis of centimeter-long electron transport in cable bacteria. Phys Chem Chem Phys 2024; 26:3139-3151. [PMID: 38189548 DOI: 10.1039/d3cp04466a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The recent discovery of cable bacteria has greatly expanded the known length scale of biological electron transport, as these multi-cellular bacteria are capable of mediating electrical currents across centimeter-scale distances. To enable such long-range conduction, cable bacteria embed a network of regularly spaced, parallel protein fibers in their cell envelope. These fibers exhibit extraordinary electrical properties for a biological material, including an electrical conductivity that can exceed 100 S cm-1. Traditionally, long-range electron transport through proteins is described as a multi-step hopping process, in which the individual hopping steps are described by Marcus electron transport theory. Here, we investigate to what extent such a classical hopping model can explain the conductance data recorded for individual cable bacterium filaments. To this end, the conductive fiber network in cable bacteria is modelled as a set of parallel one-dimensional hopping chains. Comparison of model simulated and experimental current(I)/voltage(V) curves, reveals that the charge transport is field-driven rather than concentration-driven, and there is no significant injection barrier between electrodes and filaments. However, the observed high conductivity levels (>100 S cm-1) can only be reproduced, if we include much longer hopping distances (a > 10 nm) and lower reorganisation energies (λ < 0.2 eV) than conventionally used in electron relay models of protein structures. Overall, our model analysis suggests that the conduction mechanism in cable bacteria is markedly distinct from other known forms of long-range biological electron transport, such as in multi-heme cytochromes.
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Affiliation(s)
- Jasper R van der Veen
- Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, Delft, 2628CJ, The Netherlands.
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft, 2629HZ, The Netherlands
| | - Stephanie Valianti
- Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, Delft, 2628CJ, The Netherlands.
| | - Herre S J van der Zant
- Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, Delft, 2628CJ, The Netherlands.
| | - Yaroslav M Blanter
- Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, Delft, 2628CJ, The Netherlands.
| | - Filip J R Meysman
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft, 2629HZ, The Netherlands
- Excellence center for Microbial Systems Technology, University of Antwerp, Universiteitsplein 1, Wilrijk, 2610, Belgium.
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11
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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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12
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Diao M, Dyksma S, Koeksoy E, Ngugi DK, Anantharaman K, Loy A, Pester M. Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction. FEMS Microbiol Rev 2023; 47:fuad058. [PMID: 37796897 PMCID: PMC10591310 DOI: 10.1093/femsre/fuad058] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/01/2023] [Accepted: 10/03/2023] [Indexed: 10/07/2023] Open
Abstract
Sulfate/sulfite-reducing microorganisms (SRM) are ubiquitous in nature, driving the global sulfur cycle. A hallmark of SRM is the dissimilatory sulfite reductase encoded by the genes dsrAB. Based on analysis of 950 mainly metagenome-derived dsrAB-carrying genomes, we redefine the global diversity of microorganisms with the potential for dissimilatory sulfate/sulfite reduction and uncover genetic repertoires that challenge earlier generalizations regarding their mode of energy metabolism. We show: (i) 19 out of 23 bacterial and 2 out of 4 archaeal phyla harbor uncharacterized SRM, (ii) four phyla including the Desulfobacterota harbor microorganisms with the genetic potential to switch between sulfate/sulfite reduction and sulfur oxidation, and (iii) the combination as well as presence/absence of different dsrAB-types, dsrL-types and dsrD provides guidance on the inferred direction of dissimilatory sulfur metabolism. We further provide an updated dsrAB database including > 60% taxonomically resolved, uncultured family-level lineages and recommendations on existing dsrAB-targeted primers for environmental surveys. Our work summarizes insights into the inferred ecophysiology of newly discovered SRM, puts SRM diversity into context of the major recent changes in bacterial and archaeal taxonomy, and provides an up-to-date framework to study SRM in a global context.
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Affiliation(s)
- Muhe Diao
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
| | - Stefan Dyksma
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
| | - Elif Koeksoy
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
| | - David Kamanda Ngugi
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna A-1030, Austria
| | - Michael Pester
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
- Technical University of Braunschweig, Institute of Microbiology, Braunschweig D-38106, Germany
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13
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Xu X, Weng N, Zhang H, van de Velde SJ, Hermans M, Wu F, Huo S. Cable bacteria regulate sedimentary phosphorus release in freshwater sediments. WATER RESEARCH 2023; 242:120218. [PMID: 37390661 DOI: 10.1016/j.watres.2023.120218] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/14/2023] [Accepted: 06/11/2023] [Indexed: 07/02/2023]
Abstract
Previous studies have demonstrated that e-SOx can regulate the sedimentary release of phosphorus (P) in brackish and marine sediments. When e-SOx is active, an iron (Fe) and manganese (Mn) oxide rich layer is formed near the sediment surface, which prevents P release. When e-SOx becomes inactive, the metal oxide layer is reduced via sulfide-mediated dissolution, and P is subsequently released to the water column. Cable bacteria have been shown to also occur in freshwater sediments. In these sediments, sulfide production is limited, and the metal oxide layer would thus dissolve less efficiently, leaving the P trapped at the sediment surface. This lack of an efficient dissolution mechanism implies that e-SOx could play an important role in the regulation of P availability in eutrophied freshwater streams. To test this hypothesis, we incubated sediments from a eutrophic freshwater river to investigate the impact of cable bacteria on sedimentary cycling of Fe, Mn and P. High-resolution depth profiling of pH, O2 and ΣH2S complemented with FISH analysis and high-throughput gene sequencing showed that the development of e-SOx activity was closely linked to the enrichment of cable bacteria in incubated sediments. Cable bacteria activity caused a strong acidification in the suboxic zone, leading to the dissolution of Fe and Mn minerals and consequently a strong release of dissolved Fe2+ and Mn2+ to the porewater. Oxidation of these mobilized ions at the sediment surface led to the formation of a metal oxide layer that trapped dissolved P, as shown by the enrichment of P-bearing metal oxides in the top layer of the sediment and low phosphate in the pore and overlying water. After e-SOx activity declined, the metal oxide layer did not dissolve and P remained trapped at the surface. Overall, our results suggested cable bacteria can play an important role to counteract eutrophication in freshwater systems.
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Affiliation(s)
- Xiaoling Xu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Nanyan Weng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China.
| | - Hanxiao Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Sebastiaan J van de Velde
- Department of Biology, University of Antwerp, Wilrijk, Belgium; Operationale Directorate Natural Environment, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Martijn Hermans
- Baltic Sea Centre, Stockholm University, Stockholm 106 91, Sweden; Environmental Geochemistry Group, Faculty of Science, University of Helsinki, Helsinki 00560, Finland
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Shouliang Huo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China.
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14
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Sereika M, Petriglieri F, Jensen TBN, Sannikov A, Hoppe M, Nielsen PH, Marshall IPG, Schramm A, Albertsen M. Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria. THE ISME JOURNAL 2023; 17:561-569. [PMID: 36697964 PMCID: PMC10030654 DOI: 10.1038/s41396-023-01372-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/26/2023]
Abstract
Cable bacteria of the Desulfobulbaceae family are centimeter-long filamentous bacteria, which are capable of conducting long-distance electron transfer. Currently, all cable bacteria are classified into two candidate genera: Candidatus Electronema, typically found in freshwater environments, and Candidatus Electrothrix, typically found in saltwater environments. This taxonomic framework is based on both 16S rRNA gene sequences and metagenome-assembled genome (MAG) phylogenies. However, most of the currently available MAGs are highly fragmented, incomplete, and thus likely miss key genes essential for deciphering the physiology of cable bacteria. Also, a closed, circular genome of cable bacteria has not been published yet. To address this, we performed Nanopore long-read and Illumina short-read shotgun sequencing of selected environmental samples and a single-strain enrichment of Ca. Electronema aureum. We recovered multiple cable bacteria MAGs, including two circular and one single-contig. Phylogenomic analysis, also confirmed by 16S rRNA gene-based phylogeny, classified one circular MAG and the single-contig MAG as novel species of cable bacteria, which we propose to name Ca. Electronema halotolerans and Ca. Electrothrix laxa, respectively. The Ca. Electronema halotolerans, despite belonging to the previously recognized freshwater genus of cable bacteria, was retrieved from brackish-water sediment. Metabolic predictions showed several adaptations to a high salinity environment, similar to the "saltwater" Ca. Electrothrix species, indicating how Ca. Electronema halotolerans may be the evolutionary link between marine and freshwater cable bacteria lineages.
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Affiliation(s)
- Mantas Sereika
- Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | | | | | - Artur Sannikov
- Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Morten Hoppe
- Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | | | - Ian P G Marshall
- Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Mads Albertsen
- Center for Microbial Communities, Aalborg University, Aalborg, Denmark.
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15
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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: 8] [Impact Index Per Article: 8.0] [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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16
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Huang Y, Hu W, Dong M, Yang Y, Yang X, Huang H, Yang S, Jia W, Wang B, Xu M. Cable bacteria accelerate the anaerobic removal of pyrene in black odorous river sediments. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130305. [PMID: 36356519 DOI: 10.1016/j.jhazmat.2022.130305] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/26/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
Cable bacteria play an essential role in biogeochemical processes in sediments by long-distance electron transport (LDET). A potential relationship has been found between cable bacteria and organic contaminant removal; however, the mechanisms remain unclear. In this study, the response of cable bacteria to pyrene was investigated in sediments with and without pyrene, and the effect of cable bacteria on pyrene removal was explored by connecting and blocking the paths of cable bacteria to the suboxic zones. The results showed that pyrene significantly influenced the microbial community structure and the composition of cable bacteria. The pyrene removal efficiencies significantly increased with the enrichment of cable bacteria, while sulfur-reducing microorganisms and aromatic compound degraders were also significantly enriched and correlated with cable bacteria abundance. Metagenomic analysis showed that cable bacteria have a potential LDET-bound acetate/formate respiratory pathway to gain energy. The presence of pyrene probably selects and enriches cable bacteria with a high tolerance to organic contaminants and changes the related functional microbial community, leading to the acceleration of pyrene removal. This study provides new insights into the interaction mechanisms between contaminants and cable bacteria, shedding light on the applications of cable bacteria in the bioremediation of contaminants in sediments.
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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
| | - Wenzhe Hu
- 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
| | - 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
| | - 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
| | - Haobin 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
| | - 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
| | - Weibin Jia
- 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; Department of Immunology, Binzhou Medical University, Yantai, 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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17
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Kang F, Yang W, Guo M, Pedersen LB, Nielsen LP. Highly Selective Microsensor for Monitoring Trace Phosphine in the Environment. Anal Chem 2023; 95:2460-2468. [PMID: 36656060 DOI: 10.1021/acs.analchem.2c04652] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Monitoring P flux at the Earth's surface-atmosphere interface has many challenges. Therefore, the development of a technology with high selectivity and high sensitivity to in situ trace PH3 in aquatic or sedimentary environments has become a priority. Herein, an amperometric PH3 microsensor meeting the above conditions is developed. The sensor is equipped with a Au-coated Pt working electrode (WE) and a Pt guard electrode (GE) positioned in an outer glass casing. The WE and GE are polarized at a fixed value of +150 mV with respect to a pseudo-reference electrode. The outer casing is filled with an acid electrolyte solution, and the tip is sealed using a thin silicone membrane. Mixed gases from the environment diffuse through the first layer of the silicone membrane, and the major H2S disruptor is eliminated by a ZnCl2-propylene carbonate trap positioned in the front of the microsensor. Later, the gases diffuse into an electrolytic solution through the second layer of the silicone membrane, and PH3 is selectively oxidized into H3PO4 on the Au-coated Pt WE. This electrochemical oxidation thereby creates a current that is proportional to the concentration of PH3 (>2 nmol·L-1). With the aid of the H2S trap casing and selective catalysis, the effects of other gases on the microsensor can be ignored in terms of environmental monitoring. An example from the sedimentary profile shows that high PH3 accumulations are found 13 mm below the sediment surface.
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Affiliation(s)
- Fuxing Kang
- Analysis Center of College of Resources and Environmental Sciences,, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.,Center for Electromicrobiology, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Wei Yang
- Analysis Center of College of Resources and Environmental Sciences,, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Mengwen Guo
- Analysis Center of College of Resources and Environmental Sciences,, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Lars Borregaard Pedersen
- 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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18
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Lustermans JJM, Bjerg JJ, Burdorf LDW, Nielsen LP, Schramm A, Marshall IPG. Persistent flocks of diverse motile bacteria in long-term incubations of electron-conducting cable bacteria, Candidatus Electronema aureum. Front Microbiol 2023; 14:1008293. [PMID: 36910179 PMCID: PMC9998039 DOI: 10.3389/fmicb.2023.1008293] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Abstract
Cable bacteria are centimeters-long filamentous bacteria that oxidize sulfide in anoxic sediment layers and reduce oxygen at the oxic-anoxic interface, connecting these reactions via electron transport. The ubiquitous cable bacteria have a major impact on sediment geochemistry and microbial communities. This includes diverse bacteria swimming around cable bacteria as dense flocks in the anoxic zone, where the cable bacteria act as chemotactic attractant. We hypothesized that flocking only appears when cable bacteria are highly abundant and active. We set out to discern the timing and drivers of flocking over 81 days in an enrichment culture of the freshwater cable bacterium Candidatus Electronema aureum GS by measuring sediment microprofiles of pH, oxygen, and electric potential as a proxy of cable bacteria activity. Cable bacterial relative abundance was quantified by 16S rRNA amplicon sequencing, and microscopy observations to determine presence of flocking. Flocking was always observed at some cable bacteria, irrespective of overall cable bacteria rRNA abundance, activity, or sediment pH. Diverse cell morphologies of flockers were observed, suggesting that flocking is not restricted to a specific, single bacterial associate. This, coupled with their consistent presence supports a common mechanism of interaction, likely interspecies electron transfer via electron shuttles. Flocking appears exclusively linked to the electron conducting activity of the individual cable bacteria.
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Affiliation(s)
- Jamie J M Lustermans
- Section for Microbiology, Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Jesper J Bjerg
- Section for Microbiology, Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark.,Department of Biology, Microbial Systems Technology Excellence Centre, University of Antwerp, Wilrijk, Belgium
| | - Laurine D W Burdorf
- Section for Microbiology, Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark.,Department of Biology, Microbial Systems Technology Excellence Centre, University of Antwerp, Wilrijk, Belgium
| | - Lars Peter Nielsen
- Section for Microbiology, Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Section for Microbiology, Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Ian P G Marshall
- Section for Microbiology, Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
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19
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Dong M, Yang S, Yang X, Xu M, Hu W, Wang B, Huang Y, Xu J, Lu H, Yang Y, Chen X, Huang H, Sun G. Water quality drives the distribution of freshwater cable bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 841:156468. [PMID: 35660596 DOI: 10.1016/j.scitotenv.2022.156468] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Cable bacteria are a group of recently found filamentous sulfide-oxidizing Desulfobulbaceae that significantly impact biogeochemical cycling. However, the limited understanding of cable bacteria distribution patterns and the driving force hindered our abilities to evaluate and maximize their contribution to environmental health. We evaluated cable bacteria assemblages from ten river sediments in the Pearl River Delta, China. The results revealed a clear biogeographic distribution pattern of cable bacteria, and their communities were deterministically assembled through water quality-driven selection. Cable bacteria are diverse in the river sediments with a few generalists and many specialists, and the water quality IV and V environments are the "hot spot." We then provided evidence on their morphology, function, and genome to demonstrate how water quality might shape the cable bacteria assemblages. Reduced cell width, inhibited function, and water quality-related adaptive genomic traits were detected in sulfide-limited water quality III and contaminant-stressed water quality VI environments. Specifically, those genomic traits were contributed to carbon and sulfur metabolism in the water quality III environment and stress resistance in the water quality VI environment. Overall, these findings provided a helpful baseline in evaluating the contribution of cable bacteria in the freshwater ecosystem and suggested that their high diversity and flexibility in phylogeny, morphology, and genome allowed them to adapt and contribute to various environmental conditions.
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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.
| | - 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.
| | - 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.
| | - 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.
| | - Wenzhe Hu
- 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.
| | - 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.
| | - Jiarou 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.
| | - Huibin Lu
- 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.
| | - Xingjuan Chen
- 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.
| | - Haobin 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.
| | - Guoping Sun
- 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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20
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Wang Z, Liu F, Li E, Yuan Y, Yang Y, Xu M, Qiu R. Network analysis reveals microbe-mediated impacts of aeration on deep sediment layer microbial communities. Front Microbiol 2022; 13:931585. [PMID: 36246296 PMCID: PMC9561788 DOI: 10.3389/fmicb.2022.931585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/08/2022] [Indexed: 11/24/2022] Open
Abstract
Over-aeration is a common remediation strategy for black and odorous water bodies, in which oxygen is introduced to impact aquatic microbial communities as an electron acceptor of high redox potential. In this study, black-odorous freshwater sediments were cultured for 9 weeks under aeration to investigate microbial covariations at different depths and time points. Based on community 16S rRNA gene sequencing, the microbial covariations were visualized using phylogenetic microbial ecological networks (pMENs). In the spatial scale, we identified smaller and more compact pMENs across all layers compared with the anaerobic control sediments, in terms of network size, average node connectivity, and modularity. The aerated middle layer had the most connectors, the least module hubs, a network hub, shorter average path length, and predominantly positive covariations. In addition, a significant sulfate accumulation in the aerated middle layer indicated the most intense sulfide oxidation, possibly because aeration prompted sediment surface Desulfobulbaceae, known as cable bacteria, to reach the middle layer. In the time scale, similarly, aeration led to smaller pMEN sizes and higher portions of positive covariations. Therefore, we conclude that elevated dissolved oxygen at the water-sediment interface may impact not only the surface sediment but also the subsurface and/or deep sediment microbial communities mediated by microorganisms, particularly by Desulfobulbaceae.
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Affiliation(s)
- Zhenyu Wang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Feifei Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Enze Li
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Yongqiang Yuan
- Key Laboratory of Karst Georesources and Environment, Ministry of Education, College of Resources and Environmental Engineering, Guizhou University, Guiyang, China
| | - Yonggang Yang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Meiying Xu
| | - Rongliang Qiu
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- *Correspondence: Rongliang Qiu
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21
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Li C, Reimers CE, Chace PJ. Protocol for using autoclaved intertidal sediment as a medium to enrich marine cable bacteria. STAR Protoc 2022; 3:101604. [PMID: 35990745 PMCID: PMC9389416 DOI: 10.1016/j.xpro.2022.101604] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Cable bacteria (CB) are non-isolated filamentous bacteria in the family of Desulfobulbaceae, known for fostering centimeter-long electron transfer in sediments with pronounced redox zonation. This protocol details steps to extract CB filaments from cultured natural sediment, inoculate autoclaved sediment with extracted filaments, and subsequently evaluate the growth and enrichment of CB. We also describe the approaches for collecting suitable sediment, preparing autoclaved sediment, and manufacturing glass needles and hooks for the extraction of CB. Prepare autoclaved sediment as an enrichment medium for cable bacteria Manufacture glass needles and hooks as tools to extract cable bacteria Video demonstration of cable bacteria extraction and autoclaved sediment inoculation Recover prolific cable bacteria biomass grown in autoclaved sediment
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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22
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Zhu P, Yang S, Wu Y, Ru Y, Yu X, Wang L, Guo W. Shifts in Soil Microbial Community Composition, Function, and Co-occurrence Network of Phragmites australis in the Yellow River Delta. Front Microbiol 2022; 13:858125. [PMID: 35928147 PMCID: PMC9344067 DOI: 10.3389/fmicb.2022.858125] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/10/2022] [Indexed: 11/28/2022] Open
Abstract
Soil microorganisms play vital roles in regulating biogeochemical processes. The composition and function of soil microbial community have been well studied, but little is known about the responses of bacterial and fungal communities to different habitats of the same plant, especially the inter-kingdom co-occurrence pattern including bacteria and fungi. Herein, we used high-throughput sequencing to investigate the bacterial and fungal communities of five Phragmites australis habitats in the Yellow River Delta and constructed their inter-kingdom interaction network by network analysis. The results showed that richness did not differ significantly among habitats for either the bacterial or fungal communities. The distribution of soil bacterial community was significantly affected by soil physicochemical properties, whereas that of the fungal community was not. The main functions of the bacterial and fungal communities were to participate in the degradation of organic matter and element cycling, both of which were significantly affected by soil physicochemical properties. Network analysis revealed that bacteria and fungi participated in the formation of networks through positive interactions; the role of intra-kingdom interactions were more important than inter-kingdom interactions. In addition, rare species acted as keystones played a critical role in maintaining the network structure, while NO3−−N likely played an important role in maintaining the network topological properties. Our findings provided insights into the inter-kingdom microbial co-occurrence network and response of the soil microbial community composition and function to different P. australis habitats in coastal wetlands, which will deepen our insights into microbial community assembly in coastal wetlands.
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Affiliation(s)
- Pengcheng Zhu
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
| | - Shuren Yang
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
| | - Yuxin Wu
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
| | - Yuning Ru
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
| | - Xiaona Yu
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Lushan Wang,
| | - Weihua Guo
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
- *Correspondence: Weihua Guo, whguo@
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23
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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: 0] [Impact Index Per Article: 0] [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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24
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Lalinská-Voleková B, Majerová H, Kautmanová I, Brachtýr O, Szabóová D, Arendt D, Brčeková J, Šottník P. Hydrous ferric oxides (HFO's) precipitated from contaminated waters at several abandoned Sb deposits - Interdisciplinary assessment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153248. [PMID: 35051450 DOI: 10.1016/j.scitotenv.2022.153248] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/14/2022] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
The presented paper represents a comprehensive analysis of ochre sediments precipitated from Fe rich drainage waters contaminated by arsenic and antimony. Ochre samples from three abandoned Sb deposits were collected in three different seasons and were characterized from the mineralogical, geochemical, and microbiological point of view. They were formed mainly by poorly crystallized 2-line ferrihydrite, with the content of arsenic in samples ranging from 7 g·kg-1 to 130 g·kg-1 and content of antimony ranging from 0.25 g·kg-1 up to 12 g·kg-1. Next-generation sequencing approach with 16S RNA, 18S RNA and ITS markers was used to characterize bacterial, fungal, algal, metazoal and protozoal communities occurring in the HFOs. In the 16S RNA, the analysis dominated bacteria (96.2%) were mainly Proteobacteria (68.8%) and Bacteroidetes (10.2%) and to less extent also Acidobacteria, Actinobacteria, Cyanobacteria, Firmicutes, Nitrosprae and Chloroflexi. Alpha and beta diversity analysis revealed that the bacterial communities of individual sites do not differ significantly, and only subtle seasonal changes were observed. In this As and Sb rich, circumneutral microenvironment, rich in iron, sulfates and carbonates, methylotrophic bacteria (Methylobacter, Methylotenera), metal/reducing bacteria (Geobacter, Rhodoferax), metal-oxidizing and denitrifying bacteria (Gallionella, Azospira, Sphingopyxis, Leptothrix and Dechloromonas), sulfur-oxidizing bacteria (Sulfuricurvum, Desulphobulbaceae) and nitrifying bacteria (Nitrospira, Nitrosospira) accounted for the most dominant ecological groups and their impact over Fe, As, Sb, sulfur and nitrogen geocycles is discussed. This study provides evidence of diverse microbial communities that exist in drainage waters and are highly important in the process of mobilization or immobilization of the potentially toxic elements.
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Affiliation(s)
| | - Hana Majerová
- Hana Majerová, Cancer Research Institute, Department of Tumor Immunology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 84505 Bratislava, Slovakia
| | - Ivona Kautmanová
- SNM-Natural History Museum, Vajanského náb. 2, P.O. BOX 13, 810 06 Bratislava, Slovakia
| | - Ondrej Brachtýr
- Comenius University in Bratislava, Faculty of Natural Sciences, Department of Mineralogy, Petrology and Economic Geology, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Dana Szabóová
- SNM-Natural History Museum, Vajanského náb. 2, P.O. BOX 13, 810 06 Bratislava, Slovakia
| | - Darina Arendt
- SNM-Natural History Museum, Vajanského náb. 2, P.O. BOX 13, 810 06 Bratislava, Slovakia
| | - Jana Brčeková
- Comenius University in Bratislava, Faculty of Natural Sciences, Department of Mineralogy, Petrology and Economic Geology, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Peter Šottník
- Comenius University in Bratislava, Faculty of Natural Sciences, Department of Mineralogy, Petrology and Economic Geology, Ilkovičova 6, 842 15 Bratislava, Slovakia
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25
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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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26
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Electron transfer in Gram-positive bacteria: enhancement strategies for bioelectrochemical applications. World J Microbiol Biotechnol 2022; 38:83. [DOI: 10.1007/s11274-022-03255-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/21/2022] [Indexed: 12/30/2022]
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27
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Xu X, Huo S, Weng N, Zhang H, Ma C, Zhang J, Wu F. Effects of sulfide availability on the metabolic activity and population dynamics of cable bacteria in freshwater sediment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:151817. [PMID: 34848270 DOI: 10.1016/j.scitotenv.2021.151817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/10/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Cable bacteria occur in many natural environments, and their electrogenic sulfide oxidation (e-SOx) may influence sediment biogeochemistry. The environmental factors determining the growth and diversity of cable bacteria are poorly known, especially in freshwater sediments. We conducted a laboratory incubation experiment, using freshwater sediments with different sulfide supply levels, to study how sulfide availability in sediment affects the metabolic activity and population dynamics of cable bacteria. A moderate increase in the sulfide availability in sediment significantly promoted metabolic activity and the proliferation of the cable bacteria population, as revealed by enhanced e-SOx intensity and increased bacteria abundance. In high-sulfide treatments there was a more significant increase in the population of cable bacteria in the deeper sediment layers, indicating that increased sulfide availability may expand the vertical scale impact of cable bacteria activities on sediment biogeochemistry. The relative proportions of co-existing species in the cable bacteria population also changed with sulfide supply levels, indicating that sulfide availability can be involved in determining the interspecies relationships of cable bacteria. Our findings provide new insight into the relationship between sediment sulfide availability and the growth, depth distribution, and species composition of cable bacteria, implying the consideration of regulating environmental sulfide availability as a potential management practice for the development of cable bacteria-based environmental biotechnologies.
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Affiliation(s)
- Xiaoling Xu
- College of Water Sciences, Beijing Normal University, Beijing 100012, China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Shouliang Huo
- College of Water Sciences, Beijing Normal University, Beijing 100012, China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China.
| | - Nanyan Weng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Hanxiao Zhang
- College of Water Sciences, Beijing Normal University, Beijing 100012, China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Chunzi Ma
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Jingtian Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
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28
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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: 18] [Impact Index Per Article: 9.0] [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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29
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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: 18] [Impact Index Per Article: 6.0] [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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30
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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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Prados MB, Lescano M, Porzionato N, Curutchet G. Wiring Up Along Electrodes for Biofilm Formation. Front Microbiol 2021; 12:726251. [PMID: 34526980 PMCID: PMC8435748 DOI: 10.3389/fmicb.2021.726251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/09/2021] [Indexed: 11/13/2022] Open
Abstract
Millimeter-length cables of bacteria were discovered growing along a graphite-rod electrode serving as an anode of a microbial electrolysis cell (MEC). The MEC had been inoculated with a culture of Fe-reducing microorganisms enriched from a polluted river sediment (Reconquista river, Argentina) and was operated at laboratory controlled conditions for 18 days at an anode poised potential of 240 mV (vs. Ag/AgCl), followed by 23 days at 480 mV (vs. Ag/AgCl). Anode samples were collected for scanning electron microscopy, phylogenetic and electrochemical analyses. The cables were composed of a succession of bacteria covered by a membranous sheath and were distinct from the known "cable-bacteria" (family Desulfobulbaceae). Apparently, the formation of the cables began with the interaction of the cells via nanotubes mostly located at the cell poles. The cables seemed to be further widened by the fusion between them. 16S rRNA gene sequence analysis confirmed the presence of a microbial community composed of six genera, including Shewanella, a well-characterized electrogenic bacteria. The formation of the cables might be a way of colonizing a polarized surface, as determined by the observation of electrodes extracted at different times of MEC operation. Since the cables of bacteria were distinct from any previously described, the results suggest that bacteria capable of forming cables are more diverse in nature than already thought. This diversity might render different electrical properties that could be exploited for various applications.
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Affiliation(s)
- María Belén Prados
- Instituto de Energía y Desarrollo Sustentable, Centro Atómico Bariloche, Comisión Nacional de Energía Atómica, Buenos Aires, Argentina
| | - Mariela Lescano
- Instituto de Energía y Desarrollo Sustentable, Centro Atómico Bariloche, Comisión Nacional de Energía Atómica, Buenos Aires, Argentina
| | - Natalia Porzionato
- Instituto de Investigaciones e Ingeniería Ambiental y Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Gustavo Curutchet
- Instituto de Investigaciones e Ingeniería Ambiental y Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, Buenos Aires, Argentina
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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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33
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Xu X, Huo S, Zhang H, Li X, Wu F. Identification of cable bacteria and its biogeochemical impact on sulfur in freshwater sediments from the Wenyu River. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 769:144541. [PMID: 33482557 DOI: 10.1016/j.scitotenv.2020.144541] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/25/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
Cable bacteria are filamentous sulfur-oxidizing microorganisms that couple the reduction of oxygen or nitrate in surface sediments with the oxidation of free sulfide in deeper sediments by transferring electrons across centimeter scale distances. The distribution and activities of cable bacteria in freshwater sediments are still poorly understood, especially the impact of cable bacteria on sulfur cycling. The goal of this study was to investigate electrogenic sulfide oxidation associated with cable bacteria in laboratory microcosm incubations of freshwater sediments using microsensor technology, 16S full-length rRNA sequencing, and fluorescence in situ hybridization (FISH) microscopy. Their activity was characterized by a pH maximum of 8.56 in the oxic zone and the formation of a 13.7 ± 0.6 mm wide suboxic zone after 25 days of incubation. Full-length 16S rRNA gene sequences related to cable bacteria were recovered from the sediments and exhibited 93.3%-99.4% nucleotide (nt) similarities with those from other reported freshwater cable bacteria, indicating that new species of cable bacteria were present in the sediments. FISH analysis indicated that cable bacteria density increased with time, reaching a maximum of 95.48 m cm-2 on day 50. The cells grew downwards to 40 mm but were mainly concentrated on the top 0-20 mm of sediment. The cable bacteria continuously consumed H2S in deeper layers and oxidized sulfide into sulfate in the 0-20 mm surface layers, thereby affecting the sulfur cycling within sediments. These findings provide new evidence for the existence of higher diversity of cable bacteria in freshwater sediments than previously known.
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Affiliation(s)
- Xiaoling Xu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China; College of Water Sciences, Beijing Normal University, Beijing 100012, China
| | - Shouliang Huo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China.
| | - Hanxiao Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China; College of Water Sciences, Beijing Normal University, Beijing 100012, China
| | - Xiaochuang Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
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Thiruvallur Eachambadi R, Boschker HTS, Franquet A, Spampinato V, Hidalgo-Martinez S, Valcke R, Meysman FJR, Manca JV. Enhanced Laterally Resolved ToF-SIMS and AFM Imaging of the Electrically Conductive Structures in Cable Bacteria. Anal Chem 2021; 93:7226-7234. [PMID: 33939426 DOI: 10.1021/acs.analchem.1c00298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cable bacteria are electroactive bacteria that form a long, linear chain of ridged cylindrical cells. These filamentous bacteria conduct centimeter-scale long-range electron transport through parallel, interconnected conductive pathways of which the detailed chemical and electrical properties are still unclear. Here, we combine time-of-flight secondary-ion mass spectrometry (ToF-SIMS) and atomic force microscopy (AFM) to investigate the structure and composition of this naturally occurring electrical network. The enhanced lateral resolution achieved allows differentiation between the cell body and the cell-cell junctions that contain a conspicuous cartwheel structure. Three ToF-SIMS modes were compared in the study of so-called fiber sheaths (i.e., the cell material that remains after the removal of cytoplasm and membranes, and which embeds the electrical network). Among these, fast imaging delayed extraction (FI-DE) was found to balance lateral and mass resolution, thus yielding the following multiple benefits in the study of structure-composition relations in cable bacteria: (i) it enables the separate study of the cell body and cell-cell junctions; (ii) by combining FI-DE with in situ AFM, the depth of Ni-containing protein-key in the electrical transport-is determined with greater precision; and (iii) this combination prevents contamination, which is possible when using an ex situ AFM. Our results imply that the interconnects in extracted fiber sheaths are either damaged during extraction, or that their composition is different from fibers, or both. From a more general analytical perspective, the proposed methodology of ToF-SIMS in the FI-DE mode combined with in situ AFM holds great promise for studying the chemical structure of other biological systems.
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Affiliation(s)
| | - Henricus T S Boschker
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.,Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Alexis Franquet
- Materials and Components Analysis - Compositional Analysis, Imec vzw, Kapeldreef 75, 3001 Leuven, Belgium
| | - Valentina Spampinato
- Materials and Components Analysis - Compositional Analysis, Imec vzw, Kapeldreef 75, 3001 Leuven, Belgium
| | | | - Roland Valcke
- UHasselt-Molecular and Physical Plant Physiology, Agoralaan, 3590 Diepenbeek, Belgium
| | - Filip J R Meysman
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.,Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Jean V Manca
- UHasselt-X-LAB, Agoralaan, 3590 Diepenbeek, Belgium
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Liu F, Wang Z, Wu B, Bjerg JT, Hu W, Guo X, Guo J, Nielsen LP, Qiu R, Xu M. Cable bacteria extend the impacts of elevated dissolved oxygen into anoxic sediments. THE ISME JOURNAL 2021; 15:1551-1563. [PMID: 33479492 PMCID: PMC8114917 DOI: 10.1038/s41396-020-00869-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 11/26/2020] [Accepted: 12/07/2020] [Indexed: 01/30/2023]
Abstract
Profound biogeochemical responses of anoxic sediments to the fluctuation of dissolved oxygen (DO) concentration in overlaying water are often observed, despite oxygen having a limited permeability in sediments. This contradiction is indicative of previously unrecognized mechanism that bridges the oxic and anoxic sediment layers. Using sediments from an urban river suffering from long-term polycyclic aromatic hydrocarbons (PAHs) contamination, we analyzed the physicochemical and microbial responses to artificially elevated DO (eDO) in the overlying water over 9 weeks of incubation. Significant changes in key environmental parameters and microbial diversity were detected over the 0-6 cm sediment depth, along with accelerated degradation of PAHs, despite that eDO only increased the porewater DO in the millimeter subfacial layer. The dynamics of physicochemical and microbial properties coincided well with significantly increased presence of centimeter-long sulfide-oxidizing cable bacteria filaments under eDO, and were predominantly driven by cable bacteria metabolic activities. Phylogenetic ecological network analyses further revealed that eDO reinforced cable bacteria associated interspecific interactions with functional microorganisms such as sulfate reducers, PAHs degraders, and electroactive microbes, suggesting enhanced microbial syntrophy taking advantage of cable bacteria metabolism for the regeneration of SO42- and long-distance electron transfer. Together, our results suggest cable bacteria may mediate the impacts of eDO in anaerobic sediments by altering sediment physiochemical properties and by reinforcing community interactions. Our findings highlight the ecological importance of cable bacteria in sediments.
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Affiliation(s)
- Feifei Liu
- grid.464309.c0000 0004 6431 5677Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070 China
| | - Zhenyu Wang
- grid.464309.c0000 0004 6431 5677Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070 China ,grid.12981.330000 0001 2360 039XSchool of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Bo Wu
- grid.12981.330000 0001 2360 039XSchool of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Jesper T. Bjerg
- grid.7048.b0000 0001 1956 2722Center for Electromicrobiology, Department of Biology, Aarhus University, DK-8000 Aarhus, Denmark
| | - Wenzhe Hu
- grid.464309.c0000 0004 6431 5677Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070 China
| | - Xue Guo
- grid.216417.70000 0001 0379 7164Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083 China ,grid.12527.330000 0001 0662 3178State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084 China
| | - Jun Guo
- grid.464309.c0000 0004 6431 5677Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070 China
| | - Lars Peter Nielsen
- grid.7048.b0000 0001 1956 2722Center for Electromicrobiology, Department of Biology, Aarhus University, DK-8000 Aarhus, Denmark
| | - Rongliang Qiu
- grid.12981.330000 0001 2360 039XSchool of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006 China ,grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Meiying Xu
- grid.464309.c0000 0004 6431 5677Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070 China
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36
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Dam A, Marshall IPG, Risgaard‐Petersen N, Burdorf LDW, Marzocchi U. Effect of salinity on cable bacteria species composition and diversity. Environ Microbiol 2021; 23:2605-2616. [PMID: 33760391 PMCID: PMC8252435 DOI: 10.1111/1462-2920.15484] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 03/12/2021] [Accepted: 03/23/2021] [Indexed: 01/04/2023]
Abstract
Cable bacteria (CB) are Desulfobulbaceae that couple sulphide oxidation to oxygen reduction over centimetre distances by mediating electric currents. Recently, it was suggested that the CB clade is composed of two genera, Ca. Electronema and Ca. Electrothrix, with distinct freshwater and marine habitats respectively. However, only a few studies have reported CB from freshwater sediment, making this distinction uncertain. Here, we report novel data to show that salinity is a controlling factor for the diversity and the species composition within CB populations. CB sampled from a freshwater site (salinity 0.3) grouped into Ca. Electronema and could not grow under brackish conditions (salinity 21), whereas CB from a brackish site (salinity 21) grouped into Ca. Electrothrix and decreased by 93% in activity under freshwater conditions. On a regional scale (Baltic Sea), salinity significantly influenced species richness and composition. However, other environmental factors, such as temperature and quantity and quality of organic matter were also important to explain the observed variation. A global survey of 16S rRNA gene amplicon sequencing revealed that the two genera did not co-occur likely because of competitive exclusion and identified a possible third genus.
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Affiliation(s)
- Ann‐Sofie Dam
- Center for Electromicrobiology, Section for Microbiology, Department of BiologyAarhus UniversityAarhusDenmark
| | - Ian P. G. Marshall
- Center for Electromicrobiology, Section for Microbiology, Department of BiologyAarhus UniversityAarhusDenmark
| | - Nils Risgaard‐Petersen
- Center for Electromicrobiology, Section for Microbiology, Department of BiologyAarhus UniversityAarhusDenmark
- Section of Aquatic Biology, Department of BiologyAarhus UniversityAarhusDenmark
| | - Laurine D. W. Burdorf
- Center for Electromicrobiology, Section for Microbiology, Department of BiologyAarhus UniversityAarhusDenmark
- Centre of Excellence for Microbial Systems Technology, Department of BiologyUniversity of AntwerpWilrijk2610Belgium
| | - Ugo Marzocchi
- Center for Electromicrobiology, Section for Microbiology, Department of BiologyAarhus UniversityAarhusDenmark
- Center for Water Technology (WATEC), Department of BiologyAarhus UniversityAarhusDenmark
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37
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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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38
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Hu W, Pan J, Wang B, Guo J, Li M, Xu M. Metagenomic insights into the metabolism and evolution of a new Thermoplasmata order (Candidatus Gimiplasmatales). Environ Microbiol 2020; 23:3695-3709. [PMID: 33295091 DOI: 10.1111/1462-2920.15349] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 01/05/2023]
Abstract
Thermoplasmata is a widely distributed and ecologically important archaeal class in the phylum Euryarchaeota. Because few cultures and genomes are available, uncharacterized Thermoplasmata metabolisms remain unexplored. In this study, we obtained four medium- to high-quality archaeal metagenome-assembled genomes (MAGs) from the filamentous fragments of black-odorous aquatic sediments (Foshan, Guangdong, China). Based on their 16S rRNA gene and ribosomal protein phylogenies, the four MAGs belong to the previously unnamed Thermoplasmata UBA10834 clade. We propose that this clade (five reference genomes from the Genome Taxonomy Database (GTDB) and four MAGs from this study) be considered a new order, Candidatus Gimiplasmatales. Metabolic pathway reconstructions indicated that the Ca. Gimiplasmatales MAGs can biosynthesize isoprenoids and nucleotides de novo. Additionally, some taxa have genes for formaldehyde and acetate assimilation, and the Wood-Ljungdahl CO2 -fixation pathway, indicating a mixotrophic lifestyle. Sulfur reduction, hydrogen metabolism, and arsenic detoxification pathways were predicted, indicating sulfur-, hydrogen-, and arsenic-transformation potentials. Comparative genomics indicated that the H4 F Wood-Ljungdahl pathway of both Ca. Gimiplasmatales and Methanomassiliicoccales was likely obtained by the interdomain lateral gene transfer from the Firmicutes. Collectively, this study elucidates the taxonomic and potential metabolic diversity of the new order Ca. Gimiplasmatales and the evolution of this subgroup and its sister lineage Methanomassiliicoccales.
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Affiliation(s)
- Wenzhe Hu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jie Pan
- Shenzhen key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Bin Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jun Guo
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Meng Li
- Shenzhen key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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Löffler M, Wallerang KB, Venceslau SS, Pereira IAC, Dahl C. The Iron-Sulfur Flavoprotein DsrL as NAD(P)H:Acceptor Oxidoreductase in Oxidative and Reductive Dissimilatory Sulfur Metabolism. Front Microbiol 2020; 11:578209. [PMID: 33178160 PMCID: PMC7596348 DOI: 10.3389/fmicb.2020.578209] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/23/2020] [Indexed: 11/13/2022] Open
Abstract
DsrAB-type dissimilatory sulfite reductase is a key enzyme of microbial sulfur-dependent energy metabolism. Sulfur oxidizers also contain DsrL, which is essential for sulfur oxidation in Allochromatium vinosum. This NAD(P)H oxidoreductase acts as physiological partner of oxidative-type rDsrAB. Recent analyses uncovered that DsrL is not confined to sulfur oxidizers but also occurs in (probable) sulfate/sulfur-reducing bacteria. Here, phylogenetic analysis revealed a separation into two major branches, DsrL-1, with two subgroups, and DsrL-2. When present in organisms with reductive-type DsrAB, DsrL is of type 2. In the majority of cases oxidative-type rDsrAB occurs with DsrL-1 but combination with DsrL-2-type enzymes is also observed. Three model DsrL proteins, DsrL-1A and DsrL-1B from the sulfur oxidizers A. vinosum and Chlorobaculum tepidum, respectively, as well as DsrL-2 from thiosulfate- and sulfur-reducing Desulfurella amilsii were kinetically characterized. DaDsrL-2 is active with NADP(H) but not with NAD(H) which we relate to a conserved YRR-motif in the substrate-binding domains of all DsrL-2 enzymes. In contrast, AvDsrL-1A has a strong preference for NAD(H) and the CtDsrL-1B enzyme is completely inactive with NADP(H). Thus, NAD+ as well as NADP+ are suitable in vivo electron acceptors for rDsrABL-1-catalyzed sulfur oxidation, while NADPH is required as electron donor for sulfite reduction. This observation can be related to the lower redox potential of the NADPH/NADP+ than the NADH/NAD+ couple under physiological conditions. Organisms with a rdsrAB and dsrL-1 gene combination can be confidently identified as sulfur oxidizers while predictions for organisms with other combinations require much more caution and additional information sources.
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Affiliation(s)
- Maria Löffler
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Kai B Wallerang
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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40
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Centimeter-Long Microbial Electron Transport for Bioremediation Applications. Trends Biotechnol 2020; 39:181-193. [PMID: 32680591 DOI: 10.1016/j.tibtech.2020.06.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/19/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023]
Abstract
Microbial bioremediation based on nano- to micrometer-scale electron transport has been intensively studied during the past decade, but its application can be hindered by a deficiency of suitable electron acceptors or slow mass transportation at contaminated sites. Microbial long-distance electron transport (LDET), which can couple spatially separated redox reactions across distances in natural environments, has recently emerged at centimeter-length scales. LDET explains a range of globally important biogeochemical phenomena and overcomes the drawbacks of conventional bioremediation by directly linking distant electron donors and acceptors. Here, we highlight recent research outcomes in examining, characterizing, and engineering LDET, and describe how LDET can be exploited to develop advanced technologies for the bioremediation of soils and sediments.
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41
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Geelhoed JS, van de Velde SJ, Meysman FJR. Quantification of Cable Bacteria in Marine Sediments via qPCR. Front Microbiol 2020; 11:1506. [PMID: 32719667 PMCID: PMC7348212 DOI: 10.3389/fmicb.2020.01506] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/10/2020] [Indexed: 11/13/2022] Open
Abstract
Cable bacteria (Deltaproteobacteria, Desulfobulbaceae) are long filamentous sulfur-oxidizing bacteria that generate long-distance electric currents running through the bacterial filaments. This way, they couple the oxidation of sulfide in deeper sediment layers to the reduction of oxygen or nitrate near the sediment-water interface. Cable bacteria are found in a wide range of aquatic sediments, but an accurate procedure to assess their abundance is lacking. We developed a qPCR approach that quantifies cable bacteria in relation to other bacteria within the family Desulfobulbaceae. Primer sets targeting cable bacteria, Desulfobulbaceae and the total bacterial community were applied in qPCR with DNA extracted from marine sediment incubations. Amplicon sequencing of the 16S rRNA gene V4 region confirmed that cable bacteria were accurately enumerated by qPCR, and suggested novel diversity of cable bacteria. The conjoint quantification of current densities and cell densities revealed that individual filaments carry a mean current of ∼110 pA and have a cell specific oxygen consumption rate of 69 fmol O2 cell–1 day–1. Overall, the qPCR method enables a better quantitative assessment of cable bacteria abundance, providing new metabolic insights at filament and cell level, and improving our understanding of the microbial ecology of electrogenic sediments.
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Affiliation(s)
| | - Sebastiaan J van de Velde
- Department of Earth and Planetary Sciences, University of California, Riverside, Riverside, CA, United States
| | - Filip J R Meysman
- Department of Biology, University of Antwerp, Antwerp, Belgium.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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42
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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: 25] [Impact Index Per Article: 6.3] [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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43
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Thiruvallur Eachambadi R, Bonné R, Cornelissen R, Hidalgo‐Martinez S, Vangronsveld J, Meysman FJR, Valcke R, Cleuren B, Manca JV. An Ordered and Fail‐Safe Electrical Network in Cable Bacteria. ACTA ACUST UNITED AC 2020; 4:e2000006. [DOI: 10.1002/adbi.202000006] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/16/2020] [Indexed: 11/10/2022]
Affiliation(s)
| | - Robin Bonné
- UHasselt – X‐LABFaculty of SciencesHasselt University Agoralaan – Building D Diepenbeek B‐3590 Belgium
| | - Rob Cornelissen
- UHasselt – X‐LABFaculty of SciencesHasselt University Agoralaan – Building D Diepenbeek B‐3590 Belgium
| | | | - Jaco Vangronsveld
- Centre for Environmental SciencesHasselt University Agoralaan – Building D Diepenbeek B‐3590 Belgium
- Department of Plant PhysiologyFaculty of Biology and BiotechnologyMaria Curie‐Sklodowska University Lublin 20‐033 Poland
| | - Filip J. R. Meysman
- Department of BiotechnologyDelft University of Technology Van der Maasweg 9 Delft 2629 HZ The Netherlands
| | - Roland Valcke
- UHasselt – Molecular and Physical Plant PhysiologyFaculty of SciencesAgoralaan – Building DHasselt University Diepenbeek B‐3590 Belgium
| | - Bart Cleuren
- UHasselt – Theory LabFaculty of Sciences Agoralaan – Building D Diepenbeek B‐3590 Belgium
| | - Jean V. Manca
- UHasselt – X‐LABFaculty of SciencesHasselt University Agoralaan – Building D Diepenbeek B‐3590 Belgium
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44
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Sandfeld T, Marzocchi U, Petro C, Schramm A, Risgaard-Petersen N. Electrogenic sulfide oxidation mediated by cable bacteria stimulates sulfate reduction in freshwater sediments. THE ISME JOURNAL 2020; 14:1233-1246. [PMID: 32042102 PMCID: PMC7174387 DOI: 10.1038/s41396-020-0607-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 11/08/2022]
Abstract
Cable bacteria are filamentous members of the Desulfobulbaceae family that oxidize sulfide with oxygen or nitrate by transferring electrons over centimeter distances in sediments. Recent studies show that freshwater sediments can support populations of cable bacteria at densities comparable to those found in marine environments. This is surprising since sulfide availability is presumably low in freshwater sediments due to sulfate limitation of sulfate reduction. Here we show that cable bacteria stimulate sulfate reduction in freshwater sediment through promotion of sulfate availability. Comparing experimental freshwater sediments with and without active cable bacteria, we observed a three- to tenfold increase in sulfate concentrations and a 4.5-fold increase in sulfate reduction rates when cable bacteria were present, while abundance and community composition of sulfate-reducing microorganisms (SRM) were unaffected. Correlation and ANCOVA analysis supported the hypothesis that the stimulation of sulfate reduction activity was due to relieve of the kinetic limitations of the SRM community through the elevated sulfate concentrations in sediments with cable bacteria activity. The elevated sulfate concentration was caused by cable bacteria-driven sulfide oxidation, by sulfate production from an indigenous sulfide pool, likely through cable bacteria-mediated dissolution and oxidation of iron sulfides, and by enhanced retention of sulfate, triggered by an electric field generated by the cable bacteria. Cable bacteria in freshwater sediments may thus be an integral component of a cryptic sulfur cycle and provide a mechanism for recycling of the scarce resource sulfate, stimulating sulfate reduction. It is possible that this stimulation has implication for methanogenesis and greenhouse gas emissions.
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Affiliation(s)
- Tobias Sandfeld
- Department of Bioscience, Section for Microbiology, Aarhus University, Aarhus, Denmark
- Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Ugo Marzocchi
- Department of Bioscience, Section for Microbiology, Aarhus University, Aarhus, Denmark
- Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
- Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
- Department of Chemistry, Vrije Universiteit Brussel, Brussel, Belgium
| | - Caitlin Petro
- Department of Bioscience, Section for Microbiology, Aarhus University, Aarhus, Denmark
- Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
- Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Department of Bioscience, Section for Microbiology, Aarhus University, Aarhus, Denmark
- Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
- Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Nils Risgaard-Petersen
- Department of Bioscience, Section for Microbiology, Aarhus University, Aarhus, Denmark.
- Center for Geomicrobiology, Aarhus University, Aarhus, Denmark.
- Center for Electromicrobiology, Aarhus University, Aarhus, Denmark.
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45
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Cable bacteria reduce methane emissions from rice-vegetated soils. Nat Commun 2020; 11:1878. [PMID: 32313021 PMCID: PMC7171082 DOI: 10.1038/s41467-020-15812-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 03/30/2020] [Indexed: 11/25/2022] Open
Abstract
Methane is the second most important greenhouse gas after carbon dioxide and approximately 11% of the global anthropogenic methane emissions originate from rice fields. Sulfate amendment is a mitigation strategy to reduce methane emissions from rice fields because sulfate reducers and methanogens compete for the same substrates. Cable bacteria are filamentous bacteria known to increase sulfate levels via electrogenic sulfide oxidation. Here we show that one-time inoculation of rice-vegetated soil pots with cable bacteria increases the sulfate inventory 5-fold, which leads to the reduction of methane emissions by 93%, compared to control pots lacking cable bacteria. Promoting cable bacteria in rice fields by enrichment or sensible management may thus become a strategy to reduce anthropogenic methane emissions. Rice paddies are a major source of the Earth’s atmospheric methane, making these important food crops potent contributors to greenhouse gas emissions. Here the authors show that inoculation of paddies with a particular bacterium could significantly curb methane production.
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46
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Marzocchi U, Palma E, Rossetti S, Aulenta F, Scoma A. Parallel artificial and biological electric circuits power petroleum decontamination: The case of snorkel and cable bacteria. WATER RESEARCH 2020; 173:115520. [PMID: 32018171 DOI: 10.1016/j.watres.2020.115520] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/13/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
Degradation of petroleum hydrocarbons (HC) in sediments is often limited by the availability of electron acceptors. By allowing long-distance electron transport (LDET) between anoxic sediments and oxic overlying water, bioelectrochemical snorkels may stimulate the regeneration of sulphate in the anoxic sediment thereby accelerating petroleum HC degradation. Cable bacteria can also mediate LDET between anoxic and oxic sediment layers and thus theoretically stimulate petroleum HC degradation. Here, we quantitatively assessed the impact of cable bacteria and snorkels on the degradation of alkanes in marine sediment from Aarhus Bay (Denmark). After seven weeks, cable bacteria and snorkels accelerated alkanes degradation by +24 and +25%, respectively, compared to control sediment with no cable bacteria nor snorkel. The combination of snorkels and cable bacteria further enhanced alkanes degradation (+46%). Higher degradation rates were sustained by LDET-induced sulphide removal rather than, as initially hypothesized, sulphate regeneration. Cable bacteria are thus overlooked players in the self-healing capacity of crude-oil contaminated sediments, and may inspire novel remediation treatments upon hydrocarbon spillage.
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Affiliation(s)
- Ugo Marzocchi
- Center for Electromicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark; Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Napoli, Italy.
| | - Enza Palma
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, Italy
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, Italy
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, Italy
| | - Alberto Scoma
- Section of Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark; Biological and Chemical Engineering (BCE), Department of Engineering, Aarhus University, Aarhus, Denmark
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47
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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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48
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Müller H, Marozava S, Probst AJ, Meckenstock RU. Groundwater cable bacteria conserve energy by sulfur disproportionation. ISME JOURNAL 2019; 14:623-634. [PMID: 31728021 PMCID: PMC6976610 DOI: 10.1038/s41396-019-0554-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 11/25/2022]
Abstract
Cable bacteria of the family Desulfobulbaceae couple spatially separated sulfur oxidation and oxygen or nitrate reduction by long-distance electron transfer, which can constitute the dominant sulfur oxidation process in shallow sediments. However, it remains unknown how cells in the anoxic part of the centimeter-long filaments conserve energy. We found 16S rRNA gene sequences similar to groundwater cable bacteria in a 1-methylnaphthalene-degrading culture (1MN). Cultivation with elemental sulfur and thiosulfate with ferrihydrite or nitrate as electron acceptors resulted in a first cable bacteria enrichment culture dominated >90% by 16S rRNA sequences belonging to the Desulfobulbaceae. Desulfobulbaceae-specific fluorescence in situ hybridization (FISH) unveiled single cells and filaments of up to several hundred micrometers length to belong to the same species. The Desulfobulbaceae filaments also showed the distinctive cable bacteria morphology with their continuous ridge pattern as revealed by atomic force microscopy. The cable bacteria grew with nitrate as electron acceptor and elemental sulfur and thiosulfate as electron donor, but also by sulfur disproportionation when Fe(Cl)2 or Fe(OH)3 were present as sulfide scavengers. Metabolic reconstruction based on the first nearly complete genome of groundwater cable bacteria revealed the potential for sulfur disproportionation and a chemo-litho-autotrophic metabolism. The presence of different types of hydrogenases in the genome suggests that they can utilize hydrogen as alternative electron donor. Our results imply that cable bacteria not only use sulfide oxidation coupled to oxygen or nitrate reduction by LDET for energy conservation, but sulfur disproportionation might constitute the energy metabolism for cells in large parts of the cable bacterial filaments.
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Affiliation(s)
- Hubert Müller
- Biofilm Center, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Sviatlana Marozava
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Alexander J Probst
- Biofilm Center, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Rainer U Meckenstock
- Biofilm Center, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany.
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49
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Meysman FJR, Cornelissen R, Trashin S, Bonné R, Martinez SH, van der Veen J, Blom CJ, Karman C, Hou JL, Eachambadi RT, Geelhoed JS, Wael KD, Beaumont HJE, Cleuren B, Valcke R, van der Zant HSJ, Boschker HTS, Manca JV. A highly conductive fibre network enables centimetre-scale electron transport in multicellular cable bacteria. Nat Commun 2019; 10:4120. [PMID: 31511526 PMCID: PMC6739318 DOI: 10.1038/s41467-019-12115-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 08/19/2019] [Indexed: 11/25/2022] Open
Abstract
Biological electron transport is classically thought to occur over nanometre distances, yet recent studies suggest that electrical currents can run along centimetre-long cable bacteria. The phenomenon remains elusive, however, as currents have not been directly measured, nor have the conductive structures been identified. Here we demonstrate that cable bacteria conduct electrons over centimetre distances via highly conductive fibres embedded in the cell envelope. Direct electrode measurements reveal nanoampere currents in intact filaments up to 10.1 mm long (>2000 adjacent cells). A network of parallel periplasmic fibres displays a high conductivity (up to 79 S cm−1), explaining currents measured through intact filaments. Conductance rapidly declines upon exposure to air, but remains stable under vacuum, demonstrating that charge transfer is electronic rather than ionic. Our finding of a biological structure that efficiently guides electrical currents over long distances greatly expands the paradigm of biological charge transport and could enable new bio-electronic applications. Cable bacteria’ form long multicellular filaments that can transfer electrical currents over centimetre-long distances. Here, Meysman et al. show that the electrical currents run along highly conductive fibres embedded in the cell envelope, and charge transfer is electronic rather than ionic.
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Affiliation(s)
- Filip J R Meysman
- Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610, Wilrijk, Belgium. .,Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands.
| | - Rob Cornelissen
- X-LAB, Hasselt University, Agoralaan D, B-3590, Diepenbeek, Belgium
| | - Stanislav Trashin
- AXES Research group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020, Antwerpen, Belgium
| | - Robin Bonné
- X-LAB, Hasselt University, Agoralaan D, B-3590, Diepenbeek, Belgium
| | - Silvia Hidalgo Martinez
- Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610, Wilrijk, Belgium
| | - Jasper van der Veen
- Department of Quantum Nanoscience, Kavli Institute of Nanoscience, Technical University Delft, Lorentzweg 1, 2628 CJ, Delft, The Netherlands
| | - Carsten J Blom
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Cheryl Karman
- Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610, Wilrijk, Belgium.,AXES Research group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020, Antwerpen, Belgium
| | - Ji-Ling Hou
- X-LAB, Hasselt University, Agoralaan D, B-3590, Diepenbeek, Belgium
| | | | - Jeanine S Geelhoed
- Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610, Wilrijk, Belgium
| | - Karolien De Wael
- AXES Research group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020, Antwerpen, Belgium
| | - Hubertus J E Beaumont
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Bart Cleuren
- Theoretical Physics, Hasselt University, Agoralaan D, B-3590, Diepenbeek, Belgium
| | - Roland Valcke
- Molecular and Physical Plant Physiology, Hasselt University, Agoralaan D, B-3590, Diepenbeek, Belgium
| | - Herre S J van der Zant
- Department of Quantum Nanoscience, Kavli Institute of Nanoscience, Technical University Delft, Lorentzweg 1, 2628 CJ, Delft, The Netherlands
| | - Henricus T S Boschker
- Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610, Wilrijk, Belgium.,Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Jean V Manca
- X-LAB, Hasselt University, Agoralaan D, B-3590, Diepenbeek, Belgium
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50
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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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