Microorganisms in Benthic Marine Environments

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Microorganisms in Benthic Marine Environments

Sixty-seven percent of the Earth’s surface lies under the sea, which means that of all the world’s microbial ecosystems. However, the combination of deep-ocean drilling projects and the exploration of geologically active sites, such as submarine volcanoes and hydrothermal vents, has revealed that the study of ocean sediments, or benthos, can be rewarding and surprising.

Marine sediments range from the very shallow to the deepest trenches, from dimly illuminated to completely dark, and from the newest sediment on Earth to material that is millions of years old. The temperature and age of such sediments depend on their proximity to geologically active areas.

Hydrothermal vent communities with large and diverse invertebrates, some of which depend on endosymbiotic chemolithotrophic bacteria, have been intensely investigated since their exciting discovery in the late 1970s. Because the vast majority of Earth’s crust lies at great depth far from geothermally active regions, most benthic marine microbes live under high pressure, without light, and at temperatures between 1°C and 4°C.

Benthic zone of marine ecosystem

Deep-ocean sediments were once thought to be devoid of all life and thus not worth the considerable effort it takes to study them. But sediment samples from water depths up to 8,200 m (at its deepest, the ocean is about 1 1,000 m) reveal the presence of a vast “piezosphere” (Greek, piezein, to squeeze or press).

The piezosphere describes the biome at depths with pressures exceeding 100atm (pressure increases about 1 atm per 10m depth). Here microbes are 10 to 10,000 greater per unit volume than in productive surface waters. Reasons for this difference are complicated but include energy availability and limited grazing pressure. This result is especially surprising because the majority of the ocean floor receives only about 1 gram of organic carbon per square meter per year.

Global extrapolation of measured subsurface microbial cell populations results in the amazing conclusion that the marine deep biosphere (up to 0.6 km below the sediment surface) is the “hidden majority” of all microbial biomass. Estimates range from half to five-sixths of the Earth’s total microbial biomass and up to one-third of Earth’s total living biomass.

As might be predicted, most of these microbes are not amenable to laboratory culture. SSU rRNA sequence analysis of DNA has been surprising in the number of genes that lack homology to known sulfate reducers and methanogens, with the notable exception of the archaeal isolates of the genus Methanocaldococcus.

Furthermore, the sediment surface and subsurface appear to be teeming with viruses; it is estimated that each year viral lysis in the benthos releases up to 630 million tons of carbon that had been sequestered by marine snow and other falling particulates. This exciting finding suggests that a significant fraction of Earth’s biomass is amazingly active yet largely uncharacterized.

Interestingly, recent deep-sea sediment drilling has turned our understanding of bacterial energetics literally upside down, it is generally understood that anaerobic respiration occurs such that there is preferential use of available terminal electron acceptors. Acceptors that yield the most energy (more negative ΔG) from the oxidation of NADH or an inorganic reduced compound (e.g., H2, H2S) will be used before those that produce a less negative ΔG.

Thus, following oxygen depletion, nitrate will be reduced, then manganese, iron, sulfate, and, finally, carbon dioxide. When sediment cores up to 420 m deep were collected off the coast of Peru, this predictable profile of electron acceptors and their microbial-derived reduced products was observed within the upper strata of the sediments. However, when these signature chemical compounds were measured at great depth, the profile was reversed.

Microbial Activity in Deep-Ocean Sediments
This bacterium, usually 100-300 µm in diameter, Occasionally reaches a size of 750 µm (larger than a period on this page), 100 times the size of a common bacterium. T namibiensis uses sulphide from bottom sediments as an energy source and nitrate, which is found in the overlying waters, as an electron acceptor. It appears hollow because it stores high concentrations of nitrate in a central vacuole.

This suggests the presence of unknown sources of these electron acceptors at subsurface depths of more than 420m. In addition, contrary to our long held notion of thermodynamic limits, methane formation (methanogenesis) and iron and manganese reduction co-occur in sediments with high sulfate concentrations. Although the identity of the microbes that make up these communities awaits further study, it is clear that with densities of 108 cells per gram of sediment at the seafloor surface and 104 cells per gram in deep subsurface sediments, these communities are important.

Another outcome of deep-ocean sediment exploration has been the discovery of microbial communities on continental margins fueled by the release of hydrocarbons at depths between 200 and 3,500 m. Depending on the surface topology and the rate at which hydrocarbons are emitted, they are called pockmarks, gas chimneys, mud volcanoes, brine ponds, and oil and asphalt seeps. A variety of microbes can use hydrocarbons as a sole carbon source, oxidizing them with oxygen or sulfate as the electron acceptor.

In addition, methane-oxidizing archaea grow in consortia with sulfate-reducing bacteria of the Desulfococcus and Desulfobulbus groups. Some cold seeps are the sites of microbial mats, which can sometimes cover several hundreds of meters. These mats are dominated by the giant, vacuolated sulfur-oxidizing bacteria in the genera Beggiatoa and Thiomargarita. Thiomargarita spp. are among some of the largest bacteria known; their vacuoles occupy the majority of their intracellular space.

Thiomargarita namibiensis, the World's Largest Known Bacterium
This bacterium, usually 100-300 m in diameter, occasionally reaches a size of 750m (larger than a period on this page), 100 times the size of a common bacterium. T namibiensis uses sulfide from bottom sediments as an energy source and nitrate, which is found in the overlying waters, as an electron acceptor. It appears hollow because it stores high concentrations of nitrate in a central vacuole.

In addition to accumulating elemental sulfur granules, which they use as an electron donor, they also store nitrate for use as the terminal electron acceptor in sulfur oxidation. Perhaps the most industrially important of these hydrocarbon fueled communities are methane hydrates. These pools of trapped methane are produced by archaea that convert acetate to methane.

The lack of associated methane-oxidizing microbes has enabled this pool of natural gas to accumulate in lattice like cages of crystalline water 500m or more below the sediment surface in many regions of the world’s oceans. The formation of methane hydrates requires both cold temperatures and high pressure. This discovery is very significant because there may be up to 1013 metric tons of methane hydrate worldwide. Thus 80,000 times the world’s current known natural gas reserve awaits the development of the technology to access it.

Reference and Sources

  • https://epdf.pub/marine-biology-seventh-edition.html
  • https://www.researchgate.net/publication/226160230_Bacteria_and_Marine_Biogeochemistry
  • https://www.cram.com/flashcards/briefly-discuss-biofilms-microbial-mats-and-microbial-loops-7274060
  • https://www.researchgate.net/publication/222538285_Nitrate_production_beneath_a_High_Arctic_Glacier_Svalbard
  • https://silo.pub/soil-enzymology-soil-biology-volume-22.html
  • https://www.researchgate.net/publication/332311028_A_Mechanistic_Model_for_Relative_Permeability_of_Gas_and_Water_Flow_in_Hydrate-Bearing_Porous_Media_With_Capillarity
  • https://epdf.pub/physical-geology-exploring-the-earth.html
  • https://science.sciencemag.org/content/306/5705/2198.full

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