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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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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: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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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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: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Lustermans JJM, Bjerg JJ, Schramm A, Marshall IPG. Phyllobacterium calauticae sp. nov. isolated from a microaerophilic veil transversed by cable bacteria in freshwater sediment. Antonie Van Leeuwenhoek 2021; 114:1877-1887. [PMID: 34491484 DOI: 10.1007/s10482-021-01647-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/23/2021] [Indexed: 11/29/2022]
Abstract
Microaerophilic veils of swimming microorganisms form at oxic-anoxic interfaces, mostly described in sediments where sulfide from below meets oxygen diffusing in from the water phase. However, microaerophilic veils form even when these gradients do not overlap, for example when cable bacteria activity leads to a suboxic zone. This suggests that veil microorganisms can use electron donors other than sulfide. Here we describe the extraction of microorganisms from a microaerophilic veil that formed in cable-bacteria-enriched freshwater sediment using a glass capillary, and the subsequent isolation of a motile, microaerophilic, organoheterotrophic bacterium, strain R2-JLT, unable to oxidize sulfide. Based on phenotypic, phylogenetic, and genomic comparison, we propose strain R2-JLT as a novel Phyllobacterium species, P. calauticae sp. nov.. The type strain is R2-JLT (= LMG 32286T = DSM 112555T). This novel isolate confirms that a wider variety of electron donors, including organic compounds, can fuel the activity of microorganisms in microaerophilic veils.
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Affiliation(s)
- Jamie J M Lustermans
- Section for Microbiology, Center for Electromicrobiology, Department of Biology, Aarhus University, Ny Munkegade 114, Building 1540, 8000, Aarhus C, Denmark
| | - Jesper J Bjerg
- Section for Microbiology, Center for Electromicrobiology, Department of Biology, Aarhus University, Ny Munkegade 114, Building 1540, 8000, Aarhus C, Denmark.,Microbial Systems Technology Excellence Centre, University of Antwerp, Wilrijk, Belgium
| | - Andreas Schramm
- Section for Microbiology, Center for Electromicrobiology, Department of Biology, Aarhus University, Ny Munkegade 114, Building 1540, 8000, Aarhus C, Denmark.
| | - Ian P G Marshall
- Section for Microbiology, Center for Electromicrobiology, Department of Biology, Aarhus University, Ny Munkegade 114, Building 1540, 8000, Aarhus C, Denmark
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