Cold seep communities establish where tectonic or gravitational forces push free gas, methane-rich pore water, and/or mud upward into sulfate-penetrated surface sediments (Boetius & Wenzhöfer, 2013). High energy availability at and near the sediment surface thereby supports enormous biomasses of chemosynthetic organisms such as siboglinid tubeworms, mytilid and vesicomyid bivalves, and giant sulfide-oxidizing bacteria (Sibuet & Olu, 1998; Levin, 2005; Grünke et al., 2012). These organisms are well adapted to access and use reduced compounds in seep sediments. For instance, most vesicomyid clams have a reduced gut system and thus rely almost entirely on their autotrophic sulfide-oxidizing endosymbionts for nutrient and energy supply (Childress et al., 1993; Goffredi & Barry, 2002, and references therein). To access the sulfide, they dig with their foot several centimeters into the sediment (Dubilier et al., 2008), take the sulfide up, and transport it with their blood to the endosymbionts (Childress et al., 1993). Some vesicomyid species are able to accumulate amounts of sulfide in their body that exceed ambient concentrations more than 60-fold (Childress et al., 1993; Barry & Kochevar, 1998) and are thus found in habitats with a wide range of sulfide concentrations (0.6–20 mm; Barry et al., 1997; Decker et al., 2012; Pop Ristova et al., 2012). Bioturbation by the clams enhances the sulfate transport from the water column into the sediment, resulting in sulfate reduction (SR) at sediment depths that otherwise would be sulfate-limited (Wallmann et al., 1997; Levin et al., 2003; Treude et al., 2003). Hence, vesicomyid clams are able to populate seep sites of low geological activity, where sulfide is not found close to the sediment surface (Fischer et al., 2012).
In methane-enriched seep sediments, sulfide is a product of bacterial SR that is often coupled to the anaerobic oxidation of methane (AOM) mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB; Boetius et al., 2000). High densities of these microbial consortia have been described in seep sediments of all continental margins from shallow waters to the deep sea (Knittel & Boetius, 2009, and references therein). The occurrence, distribution, and activity of the microbes involved in AOM have been intensively studied using different molecular ecological tools and biogeochemical measurements (Boetius et al., 2009; Knittel & Boetius, 2009). So far, there are three main ANME clades ANME-1, ANME-2, and ANME-3 (Hinrichs et al., 1999; Niemann et al., 2006b), which contain several sub-clades, such as thermophilic ANME-1 (Holler et al., 2011), ANME-2a-c (Orphan et al., 2001), and the recently described Methanoperedenaceae (Haroon et al., 2013). The involved SRB are close relatives of either Desulfosarcina/Desulfococcus or Desulfobulbus (Knittel et al., 2003; Schreiber et al., 2010; Kleindienst et al., 2012). The different ANME clades can be distinguished using methods based on nucleic acids (Orphan et al., 2001; Knittel et al., 2005; Pernthaler et al., 2008) and membrane lipids (Hinrichs et al., 1999; Elvert et al., 2003; Rossel et al., 2011).
In the last decade, the improvement in deep-sea technologies such as remotely operated vehicles or submersibles enabled the scientific community to explore seep ecosystems in detail by performing focused sampling and in situ measurements. These in situ investigations have significantly increased our knowledge of the small-scale variability of biodiversity and of biogeochemical activities within and between seep ecosystems (Jørgensen & Boetius, 2007; Boetius & Wenzhöfer, 2013, and references therein). However, only a few studies exist in water depths >4000 m because it is a technological challenge to access these remote abyssal habitats for sampling and in situ measurements (Boetius & Wenzhöfer, 2013). It is known from the Nankai Trough or the Japan Trench that cold seeps occur frequently even down to water depths of at least 7500 m (Kobayashi, 2002; Arakawa et al., 2005, and reference therein). This tectonically active area hosts numerous seeps and the deepest known vesicomyid clam colonies at 6437 m (Sibuet et al., 1988; Ogawa et al., 1996; Fujikura et al., 1999). Japan Trench seeps offer a unique opportunity to study microbial community structure and biogeochemical processes at abyssal seep ecosystems as most seep studies have been conducted at shallower sites (Sibuet et al., 1988; Boetius & Wenzhöfer, 2013).
Although chemosynthetic clam colonies in the Japan Trench are known, detailed insights into the underlying biogeochemical processes and predominant microbial communities fueling these remote and high-biomass seep communities are sparse. Here, we combined analyses of sediment pore water chemistry, sediment–water interface exchange processes, as well as methane and sulfate turnover rate measurements with community analyses based on 16S rRNA genes and intact polar lipids (IPLs) to thoroughly investigate the biogeochemistry and microbial community. To our knowledge, this is the first and most comprehensive study on the functioning of an abyssal seep ecosystem using in situ activity measurements in the Japan Trench to date. Our main hypotheses were (i) the key biogeochemical processes in the sediment that fuel the spatially restricted clam colony are similar to those found at shallow seeps and (ii) the microbial community composition of this ecosystem differs from that of shallow seeps.