Endosymbionts in marine bivalves leave characteristic biosignatures in their host organisms. Two nonseep bivalve species collected in Mediterranean lagoons, thiotrophic symbiotic Loripes lacteus and filter‐feeding nonsymbiotic Venerupis aurea, were studied in detail with respect to generation and presence of such signatures in living animals, and the preservation of these signals in subfossil (late Pleistocene) sedimentary shells. Three key enzymes from sulfur oxidation (APS‐reductase), CO2 fixation (RubisCO) and assimilation of nitrogen [glutamine synthetase (GS)] were detected by immunofluorescence in the bacterial symbionts of Loripes. In Loripes, major activity was derived from GS of the symbionts whereas in Venerupis the host GS is active. In search of geologically stable biosignatures for thiotrophic chemosymbiosis that might be suitable to detect such associations in ancient bivalves, we analyzed the isotopic composition of shell lipids (δ 13C ) and the bulk organic matrix of the shell (δ 13C , δ 15N , δ 34S ). In the thiotrophic Loripes, δ 13C values were depleted compared with the filter‐feeding Venerupis by as much as 8.5‰ for individual fatty acids, and 4.4‰ for bulk organic carbon. Likewise, bulk δ 15N and δ 34S values were more depleted in recent thiotrophic Loripes. Whereas δ 34S values were found to be unstable over time, the combined δ 15N and δ 13C values in organic shell extracts revealed a specific signature for chemosymbiosis in recent and subfossil specimens.

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During the last few years, the analysis of microbial diversity in various habitats greatly increased our knowledge on the kingdom Archaea. At the same time, we became aware of the multiple ways in which Archaea may interact with each other and with organisms of other kingdoms. The large group of euryarchaeal methanogens and their methane oxidizing relatives, in particular, take part in essential steps of the global methane cycle. Both of these processes, which are in reverse to each other, are partially conducted in a symbiotic interaction with different partners, either ciliates and xylophagous animals or sulfate reducing bacteria. Other symbiotic interactions are mostly of unknown ecological significance but depend on highly specific mechanisms. This paper will give an overview on interactions between Archaea and other organisms and will point out the ecological relevance of these symbiotic processes, as long as these have been already recognized.

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