Sparse microbial populations persist from seafloor to basement in the slowly accumulating oxic sediment of the oligotrophic South Pacific Gyre (SPG). The physiological status of these communities, including their substrate metabolism, is previously unconstrained. Here we show that diverse aerobic members of communities in SPG sediments (4.3‒101.5 Ma) are capable of readily incorporating carbon and nitrogen substrates and dividing. Most of the 6986 individual cells analyzed with nanometer-scale secondary ion mass spectrometry (NanoSIMS) actively incorporated isotope-labeled substrates. Many cells responded rapidly to incubation conditions, increasing total numbers by 4 orders of magnitude and taking up labeled carbon and nitrogen within 68 days after incubation. The response was generally faster (on average, 3.09 times) for nitrogen incorporation than for carbon incorporation. In contrast, anaerobic microbes were only minimally revived from this oxic sediment. Our results suggest that microbial communities widely distributed in organic-poor abyssal sediment consist mainly of aerobes that retain their metabolic potential under extremely low-energy conditions for up to 101.5 Ma.
Marine sediment covers ~70% of Earth’s surface. It harbors a remarkable microbial population that comprises 12–45% of total microbial biomass or ~0.6–2% of total living biomass on Earth1,2,3,4. Since the discovery of the subseafloor sedimentary biosphere5, understanding on the extent, diversity, and physiology of the microbes below the seafloor has greatly expanded6. In 2010, Integrated Ocean Drilling Program (IODP) Expedition 329 retrieved sedimentary sequences from the abyssal plain of the South Pacific Gyre (SPG), to examine subseafloor life and habitability in the lowest productivity region of the world ocean7. Although their abundance is very low, microbial cells are present throughout the entire sedimentary sequence at all the SPG sites. Their abundance (2.2 × 102 to 5.5 × 106 cells cm−3) is one to seven orders of magnitude lower than counts at the same depths in sites of ocean margins and upwelling regions8. The presence of dissolved O2, nitrate (NO3−), phosphate (PO4−), and dissolved inorganic carbon (DIC) throughout the sedimentary sequence from the seafloor to the volcanic basement indicates that cell abundance and activity are not limited by availability of electron acceptors or dissolved major inorganic nutrients. From the Redfield stoichiometry of net dissolved O2 reduction to net nitrate production in the sediment, the microbial cells have been inferred to consume oxygen coupled to oxidation of marine organic matter at extremely slow rates8.
Direct evidence of the physiological nature and survival status of microbial cells in this extremely energy-poor setting is previously lacking. A cell must metabolize a certain amount of carbon relative to its own biomass before it can double its size, divide or even sustain a metabolically active state (basal power requirement9). Bioenergetic calculations indicate that the microbes in SPG abyssal clay have access to very little power10. Very low permeability (1.1–2.0 × 10−17 m2 for IODP Site U1365 4H-3 [26.6 meters below seafloor (mbsf)] and 8.9 × 10−18 m2 for IODP Site U1370 [37.5 mbsf], respectively)11, very low estimated pore size of the abyssal clay (~0.02 microns, calculated using above permeability data according to the equation shown in Tanikawa et al.12), and thick porcellanite layers above the oldest sampled horizons appear to preclude cell migration into the sampled sediment. Consequently, the sampled communities have likely been trapped in the sediment since shortly after its deposition. The physiological status and growth potential of these buried communities and, more generally, the fractions of these energy-starved subseafloor microbes that are alive, dormant, or dead, have been essentially unknown.
To document the ecophysiology of the microbes that persist in these sedimentary habitats, we set up microaerobic incubation experiments with stable isotope-labeled substrates as tracers f