Protocol for using autoclaved intertidal sediment as a medium to enrich marine cable bacteria

Li, Cheng; Reimers, Clare E.; Chace, Peter J.

doi:10.1016/j.xpro.2022.101604

Cited by 2 publications

(2 citation statements)

References 29 publications

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“…To jointly tackle these three obstacles, we developed a so-called 'clonal enrichment' of a Ca. Electrothrix strain, which provides a microbial community of strongly reduced complexity that contains a single cable bacterium strain [42,89]. To create this clonal enrichment, we isolated an individual cable bacterium filament from natural sediment through micromanipulation and transferred this filament to the same sediment, but autoclaved.…”

Section: Development Of a Clonal Ca Electrothrix Culturementioning

confidence: 99%

Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads

Hiralal,

Geelhoed,

Hidalgo-Martinez

et al. 2024

Microbial Genomics

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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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Section: Development Of a Clonal Ca Electrothrix Culturementioning

confidence: 99%

Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads

Hiralal,

Geelhoed,

Hidalgo-Martinez

et al. 2024

Microbial Genomics

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“…Cultivations described so far are mostly conducted in natural sediment, collected from the natural habitat of the respective cable bacteria strains (Bjerg et al, 2018 ; Li et al, 2022 ). However, Plum‐Jensen et al were able to cultivate cable bacteria from one habitat on natural sediment from another habitat (Plum‐Jensen et al, 2024 ).…”

Section: Introductionmentioning

confidence: 99%

Towards bioprocess engineering of cable bacteria: Establishment of a synthetic sediment

Stiefelmaier,

Keller,

Neupert

et al. 2024

MicrobiologyOpen

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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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Protocol for using autoclaved intertidal sediment as a medium to enrich marine cable bacteria

Cited by 2 publications

References 29 publications

Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads

Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads

Towards bioprocess engineering of cable bacteria: Establishment of a synthetic sediment

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