Gene sequencing of natural microbial communities in the deep subsurface has provided access to a biosphere of Bacteria, Archaea, and Eukaryotes, characterized by unexpected evolutionary depth and diversity. Despite phylogenetic overlaps with surface environments, the predominant groups of Bacteria and Archaea in the subseafloor differ from those found in surface seafloor environments. The extent and diversity of the deep subsurface biosphere has been mapped to a large extent using gene and genome sequence analysis; these approaches have extended ongoing cultivation efforts on subseafloor microbial communities, including new types of Bacteria, Archaea, and Eukaryotes in pure culture. This chapter starts by introducing the most commonly used, highly conserved, and phylogenetically informative marker gene, the 16S ribosomal RNA gene, then provides an overview on sequence analysis of functional genes that code for proteins and enzymes with distinct biological and process-relevant functions, and concludes with recent metagenome and single-cell sequencing surveys that allow novel insights into microbial diversity and function of the deep subseafloor biosphere.
Scientific ocean drilling has greatly advanced the understanding of subseafloor sedimentary life. Studies of Ocean Drilling Program (ODP) and Integrated ODP samples and data show that mean per-cell rates of catabolic activity, energy flux, and biomass turnover are orders of magnitude slower in subseafloor sediment than in the surface world. They have also shown that potentially competing metabolic pathways co-occur for hundreds of meter depth in subseafloor sediment deposited over millions of years.
Our study of an example site (eastern equatorial Pacific ODP Site 1226) indicates that the energy yields of these competing reactions are pinned to a thermodynamic minimum. The simplest explanation of this long-term coexistence is thermodynamic cooperation, where microorganisms utilize different but coexisting pathways that remove each other's reaction products.
Our Site 1226 results indicate that the energy flux to subseafloor sedimentary microbes is extremely low. Comparison to biomass turnover rates at other sites suggests that most of this flux may be used for building biomolecules from existing components (e.g., amino acids in the surrounding sediment), rather than for de novo biosynthesis from inorganic chemicals.
Given these discoveries, scientific ocean drilling provides a tremendous opportunity to address several mysteries of microbial survival and natural selection under extreme energy limitations. Some of these mysteries are centered on microbial communities: To what extent do counted cells in subseafloor sediment constitute a deep microbial necrosphere? How do different kinds of microbes interact to sustain their mean activity at low average rates for millions of years? Other mysteries relate to individual cells: How slowly can a cell metabolize? How long can a cell survive at such low rates of activity? What properties allow microbes to be sustained by low fluxes of energy? In what ways do subseafloor organisms balance the benefit(s) of maximizing energy recovery with the need to minimize biochemical cost(s) of energy recovery?
A strong scientific ODP will be critical to address these mysteries.
The hydrogeologic properties of igneous ocean crust have been tested directly in only a few locations during IODP, but more common studies of crustal structure and rock alteration (using core samples and wireline logs) provide insight as to how water–rock interactions modify the crust over time. Collectively these studies reveal strong lithologic and hydrogeologic control on the nature of water–rock interactions, with hydrogeology following crustal architectures and histories. Permeability is generally greatest in the upper crust, but is heterogeneously distributed with depth and (at least in one location) may be azimuthally anisotropic. There appears to be a spreading rate dependence of basic patterns of rock alteration in the upper oceanic crust, with more variable and extensive alteration observed in crust created at slow- and medium-rate spreading centers. There may also be a spreading rate dependence of hydrogeologic properties, but we currently lack direct observations to test this hypothesis. The evolution of crustal properties with age is consistent with sustained ridge-flank water–rock interactions, and a continued dependence on fluid flow rates and reaction temperatures.
The origin, evolution, and distribution of life throughout the universe can be better understood by determining the limits to life on Earth. A broad range of many of the physical and chemical constraints that determine the limits to life, such as temperature, pressure, physical space, water content, and the availability of energy and nutrients, are found in subseafloor environments. In fact, several expeditions (Ocean Drilling Program (ODP) and Integrated Ocean Drilling Program (IODP: now International Ocean Discovery Program)) have been at least partially motivated by the desire to explore the boundaries between the habitable and the uninhabitable parts of the subseafloor. In this chapter, the possible subseafloor environments and their physical and chemical characteristics that could signify the limits of the biosphere, particularly the hydrothermally active subseafloor environments, are reviewed. Although the nature and distribution of extreme or fringe biospheres are unknown, previous ODP- and IODP-expedition-based microbiological investigations have shown that the subseafloor hydrothermal systems with relatively abundant energy supplies (sediment-derived organic compounds and serpentinization-derived H2) provide targets for seeking the limits (boundary conditions) in subseafloor environments. Here, we also discuss predicted patterns of the abundance and composition of potential microbial catabolisms in the fringe microbial communities of subseafloor hydrothermal fluids based on the thermodynamic potential of particular catabolic strategies and the computed cost of anabolism in these settings.