Anaerobic methanotrophic community of a 5346-m-deep vesicomyid clam colony in the Japan Trench

Abstract

Vesicomyidae clams harbor sulfide-oxidizing endosymbionts and are typical members of cold seep communities where active venting of fluids and gases takes place. We investigated the central biogeochemical processes that supported a vesicomyid clam colony as part of a locally restricted seep community in the Japan Trench at 5346 m water depth, one of the deepest seep settings studied to date. An integrated approach of biogeochemical and molecular ecological techniques was used combining in situ and ex situ measurements. In sediment of the clam colony, low sulfate reduction rates (maximum 128 nmol mL(-1) day(-1)) were coupled to the anaerobic oxidation of methane. They were observed over a depth range of 15 cm, caused by active transport of sulfate due to bioturbation of the vesicomyid clams. A distinct separation between the seep and the surrounding seafloor was shown by steep horizontal geochemical gradients and pronounced microbial community shifts. The sediment below the clam colony was dominated by anaerobic methanotrophic archaea (ANME-2c) and sulfate-reducing Desulfobulbaceae (SEEP-SRB-3, SEEP-SRB-4). Aerobic methanotrophic bacteria were not detected in the sediment, and the oxidation of sulfide seemed to be carried out chemolithoautotrophically by Sulfurovum species. Thus, major redox processes were mediated by distinct subgroups of seep-related microorganisms that might have been selected by this specific abyssal seep environment. Fluid flow and microbial activity were low but sufficient to support the clam community over decades and to build up high biomasses. Hence, the clams and their microbial communities adapted successfully to a low-energy regime and may represent widespread chemosynthetic communities in the Japan Trench. In this regard, they contributed to the restricted deep-sea trench biodiversity as well as to the organic carbon availability, also for non-seep organisms, in such oligotrophic benthic environment of the dark deep ocean.

Figure 1

Sampling and in situ measurements were performed at a vesicomyid clam colony in the Japan Trench (A) at a water depth of 5346 m (A,B). The map was generated using the esri arcgis software and the General Bathymetric Chart of the Oceans (GEBCO_09 Grid, version 20091120, http://www.gebco.net). (C) Relative positions of in situ measurements and pushcore sampling (white bars) at the investigated clam patch. MP, microprofiler; BC, benthic chamber; DNA, 16S rDNA analyses; SR, sulfate reduction; AOM, anaerobic oxidation of methane; PW, pore water chemistry, methane concentration and isotopy; calcium carbonate, pyrite, and total organic carbon content.

Figure 2

Stratigraphy and mineralogy of the sediment sampled in the center of the JTC colony. Core image and sketch (A) and total organic carbon = TOC (B).

Figure 3

Left panel: Sulfate (black triangles) and DIC (white triangles) concentrations were measured in the pore water from the center (A) and the rim (B) of the JTC colony. Potential SR and AOM horizons according to pore water concentrations are highlighted. Furthermore, methane concentration (black dots) and isotopic composition (white dots) were determined at both locations. Right panel: SR rates (in black) and AOM rates (in white) from the center and the rim of the JTC colony. The different symbols represent replicates of turnover rate measurements.

Figure 4

High resolution microsensor measurements outside of the colony showed an oxygen penetration depth of >1 cm and constant temperature throughout the entire sediment layer.

Figure 5

Microbial lipid profiles in the center of the JTC colony. Concentrations of archaeal and bacterial lipids are shown on the left and the isotopic compositions are on the right panel; abbreviations: PG&PS-OH-archaeol (intact): hydroxyarchaeol (OH-Ar) with phosphatidylglycerol (PG) and phosphati-dylserine (PS) as polar headgroups; OH-Ar (OH-Ar without polar headgroup); DEG (PE, PS): dialkyletherglycerolipid as phosphati-dylethanolamine and PS; MAGE (C₁₆ + C₁₇): sum of C₁₆ and C₁₇ monoalkyl glycerol ethers (MAGE), includes C₁₆ and C₁₇ saturated MAGE and three monounsaturated C₁₆-MAGE.

Figure 6

Relative 16S rRNA clone frequencies. Archaeal and bacterial diversity in the center and at the rim of the JTC colony. The scale bar represents relative clone frequencies in percent. The total number of clones per gene library is indicated below the respective column. DSHVG, Deep Sea Hydrothermal Vent Group, MBGB, Marine Benthic Group B, MG1, Marine Group 1.

Figure 7

Phylogenetic affiliation of Archaea (A), Alpha-, Gamma-, and Epsilonproteobacteria (B) and Deltaproteobacteria (C) of the JTC colony center (red) and colony rim (blue) sediments based on 16S rRNA gene sequences. The scale bars represent 10% estimated sequence divergence.