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The methano-trophic bacteria deeper in the sediments produce biogenic methane which forms pockets of gas. Protozoans, the thiobios of the microfaunal range, showed adaptations to a completely anaerobic life. Ciliates with symbiotic methanogens in detrital sediments can be major methane producers as well as being hosts for sulphate-reducing bacteria.

Where methane seepages occur together with the release of nutrients such as phosphate and nitrate into the water column, very large craters (pockmarks) are formed in the seafloor, from the explosive releases of microbially formed methane. Microbial methane oxidation leads to carbonate cementation and the formation of spectacular sandstone pillars which provide a favourable colonization substratum for fauna.

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