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Ecology and evolution of seafloor and subseafloor microbial communities

Nature Reviews Microbiology volume 16, pages 671–683 (2018)Cite this article

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Abstract

Vast regions of the dark ocean have ultra-slow rates of organic matter sedimentation, and their sediments are oxygenated to great depths yet have low levels of organic matter and cells. Primary production in the oxic seabed is supported by ammonia-oxidizing archaea, whereas in anoxic sediments, novel, uncultivated groups have the potential to produce H2 and CH4, which fuel anaerobic carbon fixation. Subseafloor bacteria have very low mutation rates, and their evolution is likely dominated by selection of different pre-adapted subseafloor taxa under oxic and anoxic conditions. In addition, the abundance and activity of viruses indicate that they affect the size, structure and selection of subseafloor communities. This Review highlights how microbial communities survive in the unique, nutrient-poor and energy-starved environment of the seabed, where they have the potential to influence global biochemical cycles.

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Fig. 1: Redox conditions in seafloor and subseafloor ecosystems are linked to sedimentation rate and distance from shore.
Fig. 2: Microbial loops in oxic and anoxic sediments.
Fig. 3: Viruses influence population size and regenerate nutrients for subsisting cells.
Fig. 4: Microbial selection in oxic and anoxic subseafloor sediments.

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Acknowledgements

This work was supported by the Deutsche Forschungsgemeinschaft (DFG) Project OR 417/1-1 granted to W.D.O. The author thanks A. Vuillemin and T. Hohmann for their comments and discussions. The author acknowledges the Center for Dark Energy Biosphere Investigations (C-DEBI), which has supported many of the studies discussed here, as well as the comments and suggestions from the three reviewers, which helped to greatly improve the article.

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Nature Reviews Microbiology thanks Andreas Schramm, Alfred Spormann and Andreas Teske for their contribution to the peer review of this work.

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  1. Department of Earth and Environmental Sciences, Paleontology and Geobiology and GeoBio-Center LMU, Ludwig-Maximilians-Universität München, Munich, Germany

    William D. Orsi

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Glossary

Benthos

The community of organisms living in surface sediments.

Hydrothermal vents

Submarine volcanoes that expel heated fluids that are rich in sulfur, hydrogen and metals.

Cold seeps

Regions in which methane gas bubbles out of the seafloor into the overlying seawater.

Chemosynthetic communities

Ecosystems that are supported by microbial autotrophy in the absence of sunlight.

Terminal electron acceptors

(TEAs). Substrates, such as oxygen, nitrate and sulfate, that are reduced at the end of the electron transport chain during cellular respiration and directly support ATP production.

Abyssal plain

A vast expanse of the ocean floor ranging between 3,000 and 6,000 m water depth.

Oligotrophic

An ecosystem in which primary production is limited by low levels of nutrients.

Horizontal gene transfer

(HGT). The transfer of genetic material between cells by a mechanism other than vertical inheritance, including transformation, transduction and conjugation.

Continental shelf

A broad, flat, sand-covered and mud-covered platform representing a shallow submerged part of a continent.

Remineralization

A process in which microbial metabolism converts organic matter to an inorganic form, for example, CO2.

Dissimilatory reduction

Energy-yielding reduction of terminal electron acceptors during cellular respiration.

Heterotrophs

Organisms that use organic matter as their primary carbon source.

Chemolithoautotrophic

Involving biological carbon fixation that is fuelled by inorganic energy sources other than sunlight.

Pelagic

Belonging to the water column of the ocean.

Mixotrophically

Using both CO2 and organic carbon as major substrates for growth.

Necromass

Non-living cellular material.

Stickland-type reaction

Microbial fermentation of amino acids.

Diagenesis

Chemical alterations of organic matter in sediments during burial.

Dark biomass fermentation

Anaerobic fermentation of dead biomass in the absence of light under anoxic conditions.

Transduction

DNA transfer mediated by a virus.

Transformation

Free DNA from one cell is taken up by another.

Conjugation

DNA transfer that involves contact between cells and a conjugative plasmid in the donor cell.

Flexible genome

The set of genes that are present only in a fraction of a clade or population.

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Orsi, W.D. Ecology and evolution of seafloor and subseafloor microbial communities. Nat Rev Microbiol 16, 671–683 (2018). https://doi.org/10.1038/s41579-018-0046-8

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