Until a few decades ago, the microbial world was thought to be limited to the upper meters of the seabed, whereas deeper sediments were thought to be sterile in spite of significant amounts of organic material buried at much greater depths. Exploration of the deep subseafloor ecosystem started when the first evidence of microbial activity was provided by studies of methane formation and sulfate reduction in cores obtained from the Deep Sea Drilling Project (DSDP) (Claypool and Kaplan, 1974; Oremland et al., 1982; Whelan et al., 1986; Tarafa et al., 1987). In the late 1980s, John Parkes and Barry Cragg began systematically counting microbial cells in Ocean Drilling Program (ODP) cores (Cragg et al., 1990), an endeavor that over the following two decades led to a large amount of data on the population size of deep biosphere microorganisms (Parkes et al., 2000). For many years, these bacterial counts were considered with some skepticism among microbiologists, mainly because they contradicted the general understanding of minimum requirements for life and because of the difficulty of convincingly proving that the cells were not a result of contamination of the samples from the surface world. Beginning with ODP Leg 185, however, occasional contamination-tracing experiments showed that the vast majority of cells found in deeply buried sediments were indigenous to the sampled sediments (Smith et al., 2000a, 2000b). As the reality of a deep subseafloor ecosystem gradually became widely accepted, Whitman et al. (1998) made a bold global extrapolation based on available data. The authors came to the astonishing conclusion that prokaryotes in subseafloor sediments constitute a "hidden majority" equivalent to 1/2 to 5/6 of Earth's prokaryotic biomass and 1/10 to 1/3 of Earth's total living biomass. This vast population must play a critical role in global carbon cycling by controlling the amount of deposited organic material that becomes buried to great depth in the seabed and stored there for many millions of years. This ecosystem also controls biogenic methanogenesis, which is the main source of modern gas hydrates accumulating in the seabed, a reduced carbon reservoir that vastly exceeds the amount of carbon in all living organisms on Earth (Kvenvolden, 1993).
Leg 201 was the first ocean drilling expedition dedicated to study of life deep beneath the seafloor (D'Hondt, Jørgensen, Miller, et al., 2003). Seven sites were drilled in open-ocean and ocean-margin provinces in the eastern tropical Pacific Ocean (Fig. F1; Table T1). Neogene deep-sea clays and Paleogene nannofossil ooze were cored at Peru Basin Site 1231. Miocene–Holocene carbonate and siliceous oozes and chalk were cored at Sites 1225 and 1226. Miocene–Holocene biogenic oozes and terrigenous sediments of the shallow Peru shelf were cored at Sites 1227, 1228, and 1229. Organic-rich Miocene–Holocene sediments were cored at Site 1230 on the Peru slope, in the accretionary wedge just landward of the Peru Trench. Among the sites drilled, the Peru margin location was particularly pertinent, as Leg 112 working in the same area was one of the earliest ODP expeditions to include study of subseafloor life (Cragg et al., 1990).
Leg 201 counted among its scientific staff a large contingent of microbiologists, biogeochemists, and chemists. An unprecedented range of samples was taken for microbiological and biogeochemical analyses, and many approaches were combined with the aim of identifying and quantifying subsurface populations of microorganisms and their metabolic activities. Onboard analyses of pore water chemistry provided detailed information about the chemical environment and zonation at each site and guided further microbiological sampling. Such data were later used for transport-reaction modeling of those biogeochemical redox processes that involved major pore water species. A novel approach for the JOIDES Resolution and ODP was the extensive use of radioactive isotopes for experimental determination of process rates using tracer methods that were driven to their highest sensitivity in order to detect extremely low rates of metabolism. A radioisotope van was installed on the drillship, and strict procedures were followed to exclude potential contamination. Cultivation of microorganisms was initiated on board the ship using a broad range of incubation techniques that should enable growth of very diverse physiological types of organisms. Because of the exceedingly slow growth of prokaryotes in the deep subsurface, incubations were continued in shore-based laboratories for up to several years until a number of successful isolates were obtained. Growth-independent methods based on deoxyribonucleic acid (DNA) or oxyribonucleic acid (RNA) were used extensively to analyze the size and diversity of in situ microbial populations and their functional key genes. In addition, analyses of physical properties, sedimentology, and geochemistry provided information on the environment of deep subsurface microorganisms and conditions controlling their activity. Important background information on stratigraphy, paleoceanography, and so on, was already available before the cruise because each site had been drilled before during earlier DSDP or ODP legs.
This chapter synthesizes results from Leg 201 with the main emphasis on data obtained through postcruise microbiological and biogeochemical research. Some of the data discussed are included in the following chapters of this volume, whereas other material is published elsewhere in international journals.