The most detailed understanding of nutrition at seeps has been developed for the large fauna that host endosymbiotic chemoautotrophic bacteria. Much of this information is derived from combined use of stable isotopic signatures, autotrophic enzyme analyses, electron microscopic studies and molecular sequencing of symbionts. Both methane-based and sulphur-based symbioses fuel much of the consumer biomass at seeps via tubeworms, mussels and clams. Vesicomyid clams have exclusively thiotrophic nutrition, with symbionts transmitted through eggs (Peek et al. 1998). Vestimentiferan tubeworms and bathymodiolid mussels may derive their nutrition from thiotrophic, methanotrophic or both types of symbionts (Fisher 1990, Fisher et al. 1997). Among perviate Pogonophora, there is one shallow water methanotroph (Schmaljohann & Flugel 1987) and the rest appear thiotrophic (Tunnicliffe et al. 2003). Cladorhizid sponges have only methanotrophic symbionts (Vacelet et al. 1995). Among the non-vesicomyid taxa, lucinid, solemyid and thyasirid bivalve symbionts all appear to be thiotrophic. The mussels and some clams (e.g., thyasirids) may also be mixotrophic, feeding on particulate organic matter to supplement symbiont-derived nutrition (Page et al. 1990, Dufour & Felbeck 2003).
Very low 815N signatures in invertebrates inhabiting reducing ecosystems have led scientists to investigate inorganic nitrogen assimilation. Symbiont assimilation of ammonium and some nitrate (but not N2) has been documented for vent tubeworms, clams and a methanotrophic seep mussel (Lee & Childress 1994, 1996, Lee et al. 1999b). A shallow water clam, Solemya was shown to assimilate ammonium without the involvement of its symbionts (Lee et al. 1999b), but virtually nothing is known about inorganic nitrogen assimilation for the majority of seep species.
Less information is available about the nutrition of smaller invertebrates that live within seep sediments, although this is changing. Sources of nutrition for these organisms include organic matter derived chemosynthetically from endosymbioses or ectosymbioses, heterotrophic consumption of free-living chemolithotrophic bacteria and archaea, or consumption of photosynthetically
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