The Deep, Dark Energy Biosphere: Intraterrestrial Life on Earth

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Katrina J. Edwards,1 Keir Becker,2 and Frederick Colwell3

1Departments of Biological and Earth Sciences, University of Southern California, Los Angeles, California 90089; email: [email protected] 2Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida 33149 3College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, Oregon 97331

Annu. Rev. Earth Planet. Sci. 2012. 40:551–68 Keywords The Annual Review of Earth and Planetary Sciences is marine microbiology, continental subsurface, geomicrobiology, online at earth.annualreviews.org hydrogeology, geochemistry, extreme environments This article’s doi: 10.1146/annurev-earth-042711-105500 Abstract Copyright c 2012 by Annual Reviews. Most ecosystems on Earth exist in permanent darkness, one or more steps All rights reserved by University of Washington on 11/07/12. For personal use only. removed from the light-driven surface world. This collection of dark habi- 0084-6597/12/0530-0551$20.00 tats is the most poorly understood on Earth, in particular the size, function, and activity of these ecosystems and what influence they have on global biogeochemical processes. The vastest of these ecosystems constitute the Annu. Rev. Earth Planet. Sci. 2012.40:551-568. Downloaded from www.annualreviews.org “deep biosphere”—habitats physically located below the surface of continents and the bottom of the ocean. The deep biosphere has been the subject of considerable—and increasing—study and scrutiny in recent years. New deep biosphere realms are being explored from deep in mines in South Africa, to sediments in the middle of oceanic gyres—and beyond. New technologies are emerging, permitting researchers to do active, manipulable experimentation in situ within the subsurface. This review highlights recent history of the research and the exciting new directions this field of research is going in, and discusses some of the most active and interesting field realms currently under scrutiny by researchers examining this deep, dark, intraterrestrial life.

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INTRODUCTION In the early 1990s, Thomas Gold (1992) famously hypothesized about the deep, dark energy biosphere, which refers to the suite of habitats or ecosystems that are physically located in environments that exist in permanent darkness. The dark biosphere represents the largest collection of habitats for biological ecosystems on Earth—two orders of magnitude by volume larger than the ocean basins and extending kilometers below the ocean floor and below the continental surface. A unifying concept among all these vast and varied chemical and physical regimes, or provinces (Schrenk et al. 2009), is that they are physically and temporally one or more steps removed from the photosynthetic world. Yet nearly all our knowledge of microbiological processes and biogeochemical cycles that are influenced or controlled by the microbial world derives from studies of light ecosystems, such as photosynthetic phytoplankton in aquatic systems and microbial mat ecosystems on land. The “deep” subsurface biosphere can be operationally defined as an ecosystem that persists at least 1 m (if not more, depending on terrain) below the continental surface or seafloor. A unifying feature of these provinces is that they are dominantly microbial habitats—bacteria, archaea, eukaryotes, and viruses can all be found. Given the vast size of these provinces, the collection of deep subsurface biosphere ecosystems is the largest microbiological habitat on Earth. Indeed, hypotheses put forth using the collated data that exist for these realms suggests that, on a global basis, up to 95% of prokaryotes (bacteria and archaea) reside in the deep subsurface of our planet (Whitman et al. 1998) (Figure 1a). Furthermore, if these data are correct, the microbes harbored in the marine subsurface alone may account for up to one-third of Earth’s total biomass carbon! In recent years, study of the deep, dark energy subsurface biosphere has risen appreciably, owing to the recognition of the size of this habitat and speculation on what influences the deep biosphere has on Earth’s system processes. For example, if up to one-third of Earth’s carbon resides in deep marine sediments (Figure 1b), how does this influence the global biogeochemical carbon cycle? Because at least 70% of the igneous ocean crust is composed of hydrologically active (Stein & Stein 1994), circulating fluids and microbes, what influence do the resultant water-rock- microbe interactions have on chemical exchange—carbon, iron, sulfur, etc.—within this reservoir and between the igneous ocean crust and the ocean basins? Herein, we highlight some of the recent results of studies conducted in the dark, deep biosphere. We also provide examples of habitats being studied currently and of technologies emerging to support deep-biosphere investigations.

by University of Washington on 11/07/12. For personal use only. MARINE SUBSURFACE MICROBIOLOGY

Marine Sediments

Annu. Rev. Earth Planet. Sci. 2012.40:551-568. Downloaded from www.annualreviews.org Study of microbial life in marine sediments began approximately a century ago using shallow- sampling techniques. A remarkable finding was that cells were present and detectable to all depths that could be sampled, even in sediments underlying the open ocean (Morita & ZoBell 1955, ZoBell & Anderson 1936). Back then, cultivation-based assays were the only microbiological methods available to scientists, so it was provocative, even in these shallow cores, to find definitive evidence for the presence of life. Technology for deep coring, however, awaited the advent of oceanic drilling for scientific research in the mid-1960s, which has enabled examination of sediments from hundreds of meters to kilometers of depth below the ocean floor. The research field exploring deep-subseafloor sedimentary microbiology grew largely out of the Ocean Drilling Program (ODP): Marking a phase of scientific ocean drilling from 1983 to 2003, microbiologists sailed along with the ODP. These exploratory expeditions presented opportunities for microbiologists to collect mud samples and examine them for basic

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ab Prokaryotic cell numbers Prokaryotic cell numbers in continents and marine provinces in marine provinces only Aquatic 4%

Coastal plains 7%

Continental shelf and slopes 21% Terrestrial subsurface Marine subsurface Deep ocean 39% 55% 72%

Soil 2%

Figure 1 Data plotted from Whitman et al. (1998) for prokaryotic cell numbers represented in major geographical provinces: (a) the continents and marine provinces; (b) marine provinces only.

microbiological information, such as cell abundances (e.g., Tarafa et al. 1987, Whelan et al. 1986; see also summary by Parkes et al. 2000 and references therein). For these studies, cell staining, detection, and enumeration of microbial life were primarily accomplished via ﬂuorescence microscopy. Cell staining and ﬂuorescent microscopy remain the principal means for enumeration of deep, dark life today. The data collected for the sedimentary deep biosphere produced a picture

by University of Washington on 11/07/12. For personal use only. that shocked the scientific community: In this image, prokaryotic life on Earth is dominated by cells that reside in deeply buried sediments (Whitman et al. 1998) (Figure 1a). The findings revealed by Whitman et al. (1998) prompted a new wave of scientific exploration. Although previous studies aimed to present the “global census,” they derived from mainly Annu. Rev. Earth Planet. Sci. 2012.40:551-568. Downloaded from www.annualreviews.org continental margins, which represent only a fraction of the potential global marine sedimentary microbial provinces. As a consequence, an ODP expedition was mounted with the explicit purpose of examining and comparing open ocean versus continental slope and margin environments in the eastern Pacific (Shipboard Sci. Party 2003, D’Hondt et al. 2004). Leg 201 was the first deep- coring expedition motivated by microbiological exploration objectives. It has yielded numerous important scientific findings over the past decade: We now have an understanding of the distinct differences in cell abundances in the open ocean compared with those in the continental margins. We also know of the corresponding differences in activity level—as assayed mainly by isotope incorporation experiments (e.g., 13C bicarbonate)—that are a consequence of the organic matter load in these different regimes. These findings have significant ramifications for our understanding of the global census of deep sedimentary life.

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This initial comparative survey has very recently been followed by new microbiologically motivated Integrated Ocean Drilling Program (IODP) expeditions to the middle of the South Paciﬁc Gyre, the most oligotrophic waters of the world’s ocean (D’Hondt et al. 2010). This work has further underscored the low-abundance biomass in sediments underlying low-productivity oceanic gyres, the largest sedimentary provinces on Earth, which could signiﬁcantly revise our global estimates of biomass abundance—potentially by orders of magnitude (D’Hondt et al. 2009).

The Igneous Ocean Crust Intraterrestrials Study of microbial life in the igneous ocean crust that underlies sediments throughout the oceans, and outcrops prominently at mid-ocean ridges and seamounts, began following the discovery of hydrothermal vents, which became recognized as “windows to the deep biosphere” that is harbored beneath these systems (Deming & Baross 1993). To date, most studies conducted on the deep biosphere in igneous crust have focused on sampling from these windows, because few opportunities have existed to sample crustal environments directly for microbiology. Nevertheless, some initial evidence for the existence of an igneous microbial deep biosphere came from observations of petrographic sections and hand samples that were retrieved using ocean- drilling technology (Banerjee & Muehlenbachs 2003, Fisk et al. 1998). The primary purpose for this sampling was to study the structure, formation, and alteration processes in the igneous crust. However, scientists observed that these samples contained textural features associated with alteration fronts—sites where water-rock reactions have taken place—that were not easily accounted for by known abiotic processes. Hence, they rapidly were dubbed as microbiological features— features that have been observed in crust up to 180 Mya! However, despite these tantalizing lines of evidence, definitive microbiological evidence has been lacking until recently. Sampling of subseafloor crustal fluids has now been done indirectly via diffuse flow vents at the seafloor and directly through the insertion of a sampling probe that created a vent at a seamount and cored rock from the subsurface for analysis (Huber et al. 2006). For these types of studies, collection of fluids from natural or human-made springs, followed by molecular biological approaches to analyze the subseafloor communities, has been the primary method of evaluating community members. The key phylogenetic marker targeted is the 16S rDNA gene—the gene that encodes for ribosomes, which constitute the ribonucleic acid scaffold on which all proteins are synthesized—and is highly conserved among bacteria, archaea, and eukarya. Information about in situ cell abundances in the oceanic crust, however, has not been possible in this habitat. New by University of Washington on 11/07/12. For personal use only. approaches also use sampling and experiments conducted within sealed and instrumented, or “CORKed” (see below), boreholes generated through scientific ocean drilling. Sampling directly from diffuse fluids gives researchers the significant advantage of obtaining

Annu. Rev. Earth Planet. Sci. 2012.40:551-568. Downloaded from www.annualreviews.org relatively uncontaminated fluid material. Studies on diffuse fluid microbiology, using phylogenetic approaches (see above), have revealed the significant presence of sulfur and iron-oxidizing bacterial species in areas ranging from mid-ocean ridge systems to hot-spot volcanoes (Edwards et al. 2011; Huber et al. 2002, 2003; Kennedy et al. 2003a,b). Similarly, insertion of sampling probes directly into the crust permits relatively clean sample collection. Fluids can be studied in parallel for microbiology and geochemistry, and such studies have revealed a covariation of microbiological species including sulfur and hydrogen oxidizers (Huber et al. 2002). A limitation of these methods is that they do not permit in situ deep-biosphere analysis, for example, of indigenous-rock-hosted microbial communities. This problem has, in part, been solved through the collection and analysis of cored-rock materials. This has been successful only in a few cases, because contamination is a major issue for coring of hard rock materials (e.g., Santelli et al. 2010). Nonetheless, molecular biological studies have revealed important findings such as the

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presence of functional genes—genes that encode for the proteins and enzymes that are responsible for key metabolic functions. These studies have revealed, for example, genes that are indicative of hydrocarbon degradation and of methane and toluene oxidation, in addition to genes for other anaerobic metabolisms involving sulfate and nitrate (Mason et al. 2010). The problem of studying uncontaminated indigenous subseafloor microbial communities in rock has been explored further via in situ instrumentation and experiments deployed in boreholes as “CORK” observatories, which are subseafloor experimental laboratories (Becker & Davis 2005, Davis et al. 1992b). Recent CORK observatory designs have permitted fluids to be sampled directly from umbilical lines that tap directly into the subsurface aquifer (Fisher et al. 2005, 2011; Jannasch et al. 2003). Using phylogenetic approaches, these studies revealed the presence of taxa potentially involved in nitrogen and hydrogen cycling in the deep subsurface (Cowen et al. 2003), indicating the existence of a potentially viable in situ microbial community. Additional experiments can also be conducted in situ within boreholes using colonization devices that have been deployed for multiple years. Initial microscopic and phylogenetic studies revealed in situ colonization and ecological succession of iron-oxidizing bacteria followed by colonization by anaerobic thermophilic clades. These were found within boreholes that had been instrumented in conjunction with chemical and biological experiments (Orcutt et al. 2011). These in situ colonization experiments also demonstrate a potentially dynamic subseafloor biosphere in the igneous ocean crust (Orcutt et al. 2011). This strongly contrasts with studies conducted in the deep sedimentary biosphere, which imply a nearly dormant, extremely slowly growing microbial biome (D’Hondt et al. 2010). Importantly, studies to date have not been able to quantify explicitly the fluid-rock-hosted microbiological communities in igneous ocean crust, which are not considered in the current global census of marine subsurface life as presented by Whitman et al. (1998) (Figure 1). Quantification of life in the igneous ocean basement remains a major frontier in deep-subsurface research. New experimental observatory stations have recently been established or are presently being established for multidisciplinary studies that couple microbiological, hydrological, and geochemical experiments. One station is on 3-million-year-old crust on the eastern flank of the Juan de Fuca ( JDF) ridge (Fisher et al. 2011). A series of borehole observatories have been established there and are being actively studied and monitored for microbiological research (e.g., Cowen et al. 2003; Orcutt et al. 2010, 2011; Smith et al. 2011). A similar multiborehole observation network is now being established on the western flank of the mid-Atlantic ridge (North Pond), on 8-million-year-old crust (Edwards et al. 2010). This project builds on a previous single-hole by University of Washington on 11/07/12. For personal use only. CORK observatory system that has been used to study the geophysical and hydrological properties of this mid-Atlantic ridge flank since 1997 (Becker et al. 1998). The new observatory stations will enable deep-biosphere researchers to compare, for the first time, two contrasting thermal,

Annu. Rev. Earth Planet. Sci. 2012.40:551-568. Downloaded from www.annualreviews.org hydrological, and chemical regimes in the igneous ocean crust: JDF is characterized by warm (65◦C), hydrologically sluggish, and anoxic conditions, whereas North Pond is characterized by cool (up to ∼25◦C), hydrologically vigorous, and oxic conditions. Results of these comparative experiments are expected to change fundamentally our understanding of microbial life harbored in igneous ocean crust.

SUBSURFACE MICROBIOLOGY ON THE CONTINENTS

First Principles In contrast to the ﬁrst studies of subseaﬂoor microbiology, the earliest research on microbial communities in continental subsurface environments was usually linked to how we as human

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societies rely on these deep geologic provinces. Water, minerals, hydrocarbons, or repositories— the main reasons for drilling the terrestrial subsurface—and aspects associated with resource degradation or with assurance of waste stability were the practical motivating factors for searching for life below the depths of soil horizons. The quest was to chase additional oil out of the ground (Moses 1987), to understand hydrocarbon stability (Head et al. 2003), or to draw residual metals from low-grade ore (Brierley 1978), which encouraged the study of microbes in engineered or naturally occurring subsurface settings. To resolve the conundrum of how to deal with nuclear waste storage, investigators looked for subsurface repositories that could be stable enough to store this hazardous material for millennia. The associated deep investigations brought microbiologists to examine these materials for microscopic life that may contribute to such stability (cf. Pedersen 1996). Oil and metals are precious enough to explore for economic benefit, but the need to clean tainted underground water supplies yielded the greatest progress in our knowledge of microbial communities beneath continental surfaces. To discover the keys to biological activity, research also explored settings that were shallow but nonetheless nonsurface. That work was critical for the creation of integrated knowledge that would move bioremediation of the subsurface from a curiosity to a proven technology that soci- ety depends on. In the 1980s, many such investigations began with the recognition that digging up contaminated earth materials was a massive undertaking compared with approaches that may encourage specific microbes to degrade or immobilize contaminants. Gasoline leaking from underground tanks, ubiquitous chlorinated organic solvents, radionuclides, and heavy metals are some of the contaminants that were misplaced in aquifers and demanded attention. Among the research enterprises that would reckon with such waste, those sponsored by the U.S. Department of Energy (DOE) and the U.S. Geological Survey (USGS) contributed to pivotal fundamental research in pristine locations to establish principles of deep life before scientists dug into the waste. The DOE Subsurface Science Program (SSP) was notable in several ways. For example, it codified methods to collect samples from the subsurface such that microbiologists could decide whether the captured microbes were representative of the rocks at depth (Griffin et al. 1997, Phelps et al. 1989). These approaches were later adopted and further developed by the IODP (Smith et al. 2000). Also, prior to the SSP, many microbiologists obtained their samples by “piggybacking” on drilling efforts that were conducted for other purposes. However, the SSP dedicated scientific drill sites to teams of researchers from different disciplines, a practice that parallels the one pioneered in deep-sea drilling projects. Drillers and scientists worked together to refine sampling methods. This permitted targeted sample collection and accurate subsurface characterization. SSP research by University of Washington on 11/07/12. For personal use only. determined that microbes were present in many deep continental subsurface sites on coastal plains, in deserts with thick vadose zones, and in ancient rocks that had been exposed to geothermal or direct volcanic heat (cf. Fredrickson & Balkwill 2006; for useful summaries, see also Fredrickson &

Annu. Rev. Earth Planet. Sci. 2012.40:551-568. Downloaded from www.annualreviews.org Fletcher 2001). Through cultivation-based, microscopic activity assays and through molecular approaches, a series of boreholes on the southeastern coastal plain of the United States advanced our knowledge of the excruciatingly slow rates of activity or growth that many microbes sustain when buried (Phelps et al. 1994). Despite its slow rate, however, this biological activity progressively alters the chemistry of porewaters as they travel down the gradient of conﬁned aquifers (Murphy et al. 1992, Murphy & Schramke 1998). Next-generation DOE (and other) programs, some of which continue today, are rooted in the SSP, to which they can trace their cross-disciplinary approach of investigating the principles that guide biogeochemical processes in the deep Earth. Parallel to the DOE South African gold mines efforts, scientists from the USGS explored the subsurface for the properties of deep life. Activity measurements on cores of coastal plains sediments revealed microorganisms at considerable depths that yielded estimates of the rates of metabolism by different communities (Chapelle et al. 1987). In addition, and more directly related

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to remediation of aquifers, a series of studies were conducted by USGS researchers to describe the distribution and movement of microbes in sandy aquifers. For more than a decade, this group and their collaborators advanced our knowledge of how microbes modify waste in the subsurface (Harvey et al. 1984), how microbes move in the subsurface (Harvey 1997), and how protozoa are sustained in these systems (Harvey et al. 1995, Kinner et al. 2002). They conducted one of the earliest studies with a multilevel sampler to tease out relationships between microbial types and the geological or geochemical conditions of the subsurface (Smith et al. 1991). This research was a forerunner of today’s in situ observatories and osmosampler systems that are in constant development and being used in both marine and continental subsurface environments.

Life Without Light? Often, microbes investigated in the subsurface are heterotrophic and depend on photosynthetically derived organic matter that was buried or leached into the subsurface, a process that “contaminated” the continental underground with solar-derived energy sources, similar to the processes that appear to sustain deep-marine sedimentary microbial life. In many locations of the continental (or marine) subsurface, life persists at depth, even though much of this organic matter seems to have derived from surface biology. Also perplexing is the fact that these deep cells need to be weaned off oxidants because metabolism during burial eliminates their access to electron acceptors. That growth is impaired by starvation, however, may serve as an advantage because these cells must eventually be subject to the multiple mechanical stresses of earth loads on their cubic micrometer—or smaller—volumes (Rebata-Landa & Santamarina 2006). Yet, these explanations do not apply to locations where the deposition of organic matter from the surface or the deep circulation beneath the surface through meteoric water transport never allows organic materials to reach signiﬁcant depths. Here, we must ask if there are other processes that could sustain cells. In the mid-1990s, two groups proposed that lithoautotrophic cells—organisms that derive en-

ergy from inorganic chemical reactions and ﬁx CO2 for their cellular carbon needs—are sustained in the deep Earth. Investigations of the Columbia River Basalt Group in the state of Washington determined that microbes appeared to consume small amounts of hydrogen and carbon dioxide at depths where intrusion of organic matter from the surface is limited (Stevens & McKinley 1995). These communities were dubbed subsurface lithoautotrophic microbial ecosystems (SLiMEs). A succession of papers considered the merits of these deep basaltic rocks (Anderson et al. 1998, Stevens & McKinley 2000)—and other subsurface systems (Chapelle et al. 2002)—as the prove- by University of Washington on 11/07/12. For personal use only. nance of life that had no need for energy from light. At about the same time, the granites of Sweden’s Asp¨ o¨ Hard Rock Laboratory in the Fennoscan- dian Shield were understood to be the location for lithoautotrophs able to use hydrogen and carbon

Annu. Rev. Earth Planet. Sci. 2012.40:551-568. Downloaded from www.annualreviews.org dioxide for energy metabolism and growth. This “geogas hypothesis” holds that geological sources of hydrogen (Morita 2000) mixed with ubiquitous inorganic carbon provide the essential energy, oxidant, and carbon sources to sustain life at depth (Pedersen 1997, 2000). The overall premise is that autotrophic life based on fundamental inorganic molecules creates the complex organic compounds (e.g., carbohydrates, simple organic acids) upon which heterotrophic microbial life— and even higher life-forms—can rely, i.e., providing the trophic base for subsurface ecosystems. Subsequent research on the microbiology and biogeochemistry of the Eastern Snake River Plain aquifer (Newby et al. 2004) and on some geothermal systems in Yellowstone National Park (Spear et al. 2005) also suggests that hydrogen-dependent microbes that are not reliant on light energy are active in underground igneous systems beneath the continental surfaces. That lithoautotrophic cells are the basis of life in subsurface environments encouraged the development of several parallel ideas. Researchers concerned with the origins of life on Earth

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considered that the subsurface of the new planet was much quieter than its surface, which was constantly hazed by meteorites and high levels of radiation typical of the early solar system (Stevens 1997). Evidence of SLiMEs stirred the interest of NASA and moved scientists conceptually closer to the notion that planetary bodies other than Earth may sustain life in their relatively sheltered deep underground settings if the appropriate reductants and oxidants are available to cells. And the notion of HyperSLiME communities was advanced to describe geological systems that occur where hydrogen is locally abundant and temperatures are high enough to push the thermal limits of life (Nealson et al. 2005). Today, lithoautotrophy remains a fundamental lifestyle in the subsurface, and its presence is inferred in both subcontinental and subseaﬂoor settings. That this metabolic strategy may be favored or enhanced under conditions where deep geological carbon sequestration is proposed (Onstott 2004) is a provocative hypothesis yet to be explored.

EMERGENT TECHNOLOGY AND THE FUTURE

CORKing the Marine Subsurface Biosphere The ODP/IODP CORK (or Circulation Obviation Retrofit Kit) concept was originally motivated by common observations of the open exchange between ocean-bottom water and formation fluids via ocean crustal boreholes that were left open (e.g., Becker et al. 1983, Hyndman et al. 1976). The original CORK concept (Davis et al. 1992a) was to “plug” selected boreholes near the seafloor, and installments of long-term sensor strings were suspended in the CORKed hole. Signals would then be sent to data loggers that are accessible at the seafloor and hydraulic tubing leading from the sealed section to valves on the seafloor. The original aims were to record borehole temperatures and pressures and sample borehole fluids over long periods as the borehole conditions recovered from drilling disturbances and reequilibrated with formation conditions. Later designs (Fisher et al. 2005, 2011; Jannasch et al. 2003; Mikada et al. 2002) have allowed for novel experiments that involve sealing multiple subsurface hydrological zones in single holes, with formation fluids and pressure signals brought to the wellhead via hydraulic umbilicals. In addition, researchers can suspend in situ recorders and conduct experiments in the sealed boreholes. To date, approximately 25 holes have been instrumented with long-term CORK observatories, primarily in young ocean crust and subduction settings. Since 2004, a novel focus has been to incorporate microbiological capabilities, either through the analysis of formation fluids sampled via umbilical lines from the CORKs or through the addition of in situ microbiological cultivation or perturbation experiments by University of Washington on 11/07/12. For personal use only. to the downhole sensor packages. All these experiments require periodic submersible visits (typi- cally, at 1–3-year intervals) to sample formation fluids at the wellhead and/or recover and replace long-term downhole and wellhead sampling devices. These requirements further demand a long- term “observatory”-style experimental approach to studying microbiology in the intraterrestrial Annu. Rev. Earth Planet. Sci. 2012.40:551-568. Downloaded from www.annualreviews.org marine biosphere.

A Walk into Earth Early on, microbiologists studying the subsurface were constrained by the need to drill from the surface to the depths where their quarry resides. In many cases, this remains a requirement as well as an impediment to research, as drilling practices are inherently dirty and the result is never better than a thin column of sediment or rock that can limit the number of microbes to be investigated. However, in the 1990s, teams of researchers studying microbes in the continental subsurface found new ways to get underground. Rainier Mesa, the erstwhile site for nuclear testing in the Nevada desert, and Asp¨ o¨ were two spots with sample sites that require only a short drive underground. At

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the Mesa, researchers walked to freshly excavated rock faces and then used tunneling machines to chisel multiple cubic meters of blocks from the country rock (Haldeman et al. 1993). These cubes were dissected to determine where microbes situated themselves in the rock mass according to the principal nonbiological parameters that control the cells’ distribution, biomass, and diversity (Russell et al. 1994). Underground at Asp¨ o,¨ where the granite bedrock dictated that only cracks in the rock would have enough fluid movement to sustain cells, the ingenious development of packers to seal fractures while pumping water or colonizing substrates led to an appreciation of these open conduits and their necessity for deep life (Nielsen et al. 2006). This relatively casual access to the subsurface was a seminal tool for studying the continental deep biosphere and matched comparable efforts to explore the geomicrobiology of caves (cf. Engel et al. 2004, Northrup & Lavoie 2001). These early expeditions in underground cavities encouraged similar studies, most notably in South African gold mines. Since the mid-1990s, research in the South African gold mines has been rewarded with interesting new findings related to the microbiology—phylogenetic diversity, physiology, rates of metabolism—of the subsurface. These mines, the deepest in the world, offer a range of environments that can be sampled at centimeter to kilometer scales, where microbes survive and where repeat visits to rock galleries permit progressive science to occur without the cost of drilling from the surface. Contaminating microbes found in “service water” pumped into the mine for excava- tion and drilling activities are distinct from microbes deemed to be native on the basis of microbial type and biomass. Service-water communities are dominated by α-, β-, and γ-Proteobacteria at approximately 104 cells per gram and have mesophilic (grows between 25◦Cand40◦C) and aerobic or anaerobic physiologies (Onstott et al. 2003). This contrasts with the indigenous cells that are sulfate-reducing microbes (including δ-Proteobacteria) that are thermophilic (thrives at 45◦Cto 122◦C) and range from <102 to 103 cells per gram. In mines within stable cratonic features where there is minimal pore space available for microbial penetration, the fractures and fissures are the primary conduits for microbial traffic. These subsurface microbes are different from those previously characterized by 16S rDNA analysis— specifically, the novel representatives of the Euryarchaeota group (Takai et al. 2001) of archaea. A unique star-shaped morphology (when seen in cross section) was found in one of the mines (Wanger et al. 2008). Some of the most intriguing findings come from the fractures in the 2.8- km-deep Mponeng mine: A joint study examining the genomic properties of captured cells and the geochemical features of the rocks where the microbes are found completes a picture of underground survival. At Mponeng, there is evidence of a community dominated by a lone phylotype by University of Washington on 11/07/12. For personal use only. (a phylotype is a microbe known only by genetic evidence but without a cultured representative) that sustains super-low activities over time through its use of geologically produced hydrogen and sulfate (Lin et al. 2006). Known as Desulforudis audaxviator, the as-yet uncultured microbe

Annu. Rev. Earth Planet. Sci. 2012.40:551-568. Downloaded from www.annualreviews.org is a physiological polyglot and apparently self-sufﬁcient given its genomic features that enable sporulation, motility, chemoautotrophy, and thermophily (Chivian et al. 2008). Furthermore, from different mines within the same South African crustal complex, the discovery of a subsurface nematode helps to broaden our view of complex underground life (Borgonie et al. 2011). These worms colonize fractures where they live by grazing on attached microbes.

Future Technologies Future research of the deep subsurface biosphere in both marine and continental realms will demand much from technology. Access to uncontaminated subsurface samples, particularly from igneous hard rock environments, will be critical to advance this ﬁeld (Santelli et al. 2010). More robust and high-throughput sequencing technologies are needed to identify and quantify microbial

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1024C,1025C, 857D+858G 1026B,1027C 794D 1179E U1301A+B U1362A+B 1173B 534A U1309D 482D 418A 1201E 1224F 1256D 395A/396B 801C 843B 1243A 504B+896A 765D 839B 1107A 597C 595B 735B

Figure 2 Locations of existing Deep-Sea Drilling Program/Ocean Drilling Program/Integrated Ocean Drilling Program basement legacy holes. See Table 1 for details on the status of individual holes.

life in the subsurface in situ. Molecular methods need to be adapted for application in this extreme environment: For example, single-cell and genomic approaches, which are being increasingly used in the microbiological sciences (e.g., Walker & Parkhill 2008), are still largely lacking in subsurface research. Cultivation approaches for recovering in situ microbes while avoiding contamination need to be developed. Thus, we need better theory and predictions about what may be found in different subsurface regimes (e.g., Bach & Edwards 2003, Bach et al. 2006), so that the most appropriate methods are devised. Studies should be expanded to encompass the entire microbial

by University of Washington on 11/07/12. For personal use only. world including viruses and eukaryotes, which have been largely neglected. Future infrastructural developments should also support large, multidisciplinary research teams to conduct sophisticated experiments—both long and short term. For example, CORKed observatories should be increasingly networked with cabled observatories, enabling greater access at Annu. Rev. Earth Planet. Sci. 2012.40:551-568. Downloaded from www.annualreviews.org long-term monitoring stations to real-time information concerning physical and thermal fluctu- ations as such conditions ultimately influence the biology and ecology of these systems. Tools need to be developed for in situ rapid detection of microbial life: A current example is the proto- type Dark Energy Biosphere Investigative tool (DEBI-t), which uses deep ultraviolet fluorescence (Bhartia et al. 2010) to detect microbial life on borehole walls as a wire-line tool (K.J. Edwards, E.C. Salas & R. Bhartia, unpublished data). Research teams could also access and use the existing infrastructure more effectively than they currently do. For example, in the marine realm, 28 “legacy” boreholes (Figure 2 and Table 1) exist. Legacy boreholes have been drilled and cased into the upper basement and equipped with a reentry cone for future potential work. These existing holes could be revisited for biological work, such as scanning with DEBI-t and/or establishing new CORKed observatories.

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In the continental realm outside South Africa, research from some mines is yielding important findings regarding the deep, dark biosphere. At the Lupin gold mine in northern Canada, research has also provided a glimpse of microbial communities located beneath the permafrost where they occur in fractures and are composed of bacteria (Onstott et al. 2009). Though it is a human- altered subsurface setting where subsurface life is accelerated by exposure to air, Iron Mountain, California, has enabled research offering insights into the metagenomic, transcriptomic, and pro- teomic themes that enable microbial survival in austere settings (Baker et al. 2006, Denef et al. 2010). This mine is the habitat for microbial biofilms that form a succession of communities in low-pH fluids. The limited diversity and high biomass of the films enable the collection of enough biological material to foster research on the mRNA (messenger RNA) and proteins of the cells. In addition, microbiologists are beginning to explore the microbial communities in soils in the Deep Underground Science and Engineering Laboratory at the former Homestake gold mine in South Dakota (Rastogi et al. 2009, 2010). Initial studies on Homestake microbes focused on samples from surficial debris, so it will be interesting to see future investigations that aim to investigate microbes indigenous to this Precambrian metamorphic structure. Almost certainly, as observed elsewhere, new findings will come from the careful search for life in deep fractures where both the space for cells to colonize and the impetus for fluid movement introduce an essential flow of electron donors, electron acceptors, and trace elements.

CONCLUSIONS While the deep, dark energy biosphere hidden below the surface of our planet remains unex- plored and unknown to science, the tools and technologies that enable deep-biosphere research are becoming increasingly sophisticated, presenting a tantalizing opportunity for in-depth studies in the coming years. To engage in deep-biosphere research, large, highly coordinated multidisciplinary teams are needed to tackle the major outstanding questions. For example, how large, from a quantitative perspective, is the deep biosphere? Current studies are revising prior work in this area, with broad implications for delineating the consequences of such vast ecosystems. What are the limiting factors to survival of microbiota in the deep biosphere? And what are the activities and rates of biogeochemically relevant processes that may be occurring in the deep biosphere? In a practical sense, we have gained signiﬁcant understanding related to the biogeochemistry of contaminated underground sites. Can we transfer this knowledge to new areas that will demand biological expertise? An example is the deep geological sequestration of carbon where microbes by University of Washington on 11/07/12. For personal use only. will need to be considered to assure long-term storage. Coordination of large, interdisciplinary teams can be challenging without coordinating entities and considerable community collaborations. In recent years, several such networked

Annu. Rev. Earth Planet. Sci. 2012.40:551-568. Downloaded from www.annualreviews.org entities have emerged: The Center for Dark Energy Biosphere Investigations (http:// www.darkenergybiosphere.org) and the Dark Energy Biosphere Institute (http:// darkenergybiosphere.org/RCN/) are two organizations supported by the National Science Foundation to focus on marine deep-biosphere research. Other exciting recent developments are the Deep Carbon Observatory (http://dco.gl.ciw.edu/), a program supported by the Sloan Foundation that includes a focus on deep-biosphere work in both marine and continental settings, and the Network of Inner Space Observatories, which is focused on coordinating and integrating research from continental subsurface observatories on an international basis (http://astrobiology.nasa.gov/articles/promoting-international-collaboration-deep- crustal-biosphere-research/). All these organizations are multi-institutional and international in character, which is critically important for addressing deep-biosphere questions in our “inner space” of planet Earth.

www.annualreviews.org • The Deep, Dark Energy Biosphere 561 EA40CH22-Edwards ARI 23 March 2012 15:39 ; reCORK 2011? b Remarks O ION site 2 2004 hole Wire-line CORK 2001; junk below 2,000 mbsf Wire-line CORK, 2001, in place; junk below 2,000 mbsf FARE, 1988; SISMOBS, 1992 CORK, 1997; fill/junk below 600 mbsf CORK, 1991 and 1996 (no longerWire-line working or CORK sealed) 2001; bowspring in hole CORK-II, 2001 LFASE, 1989; DIANAUT, 1989 Wire-line CORK, 2001, in place; bowspring in hole ION seismic observatory Broadband seismometer expedition, 1989 still in hole NERO ION site CORK, 1996 CORK, 1996 CORK, 1996; Biosphere expedition, 1997; CORK-II, CORK, 1996 OSN-1 ION site; pilot expedition, 1998; packer lost in ION seismic observatory Ngendei expedition, 1983; stinger in hole DIANAUT, 1989; junk BHA at 488 mbsf CORK-II, 2004 CORK-II, 2004 CORK-II, 2010 CORK-II, 2010 CORK, 1991 and 1996 (P still working) Advanced CORK, 2001 OSN-2 ION site H /728 /265/277 /265/351 /230/309 /242/272 /59 /212 ∗∗ ∗∗ ∗∗ ∗∗ ∗∗ ∗∗ ∗∗ Casing (m) 90/276 90/276 62/112 25/271 86/191 44/413 43 43 53 53 70/- 120/163 86/533 86/191 25 48 64/388 58/560 49/413 39/166 40/102 38/249 38/578 34/74 30/244 121 39/527 48/573 ∗ (m) a T.D./ B.P. 664/553 2111/1836 936/456 433/175 469/297 176/24 148/47 295/48 632/56 600/170 370/108 583/318 528/292 359/117 529/312 2111/1836 406/254 1647/28 124/56 313/79 469/297 175/147 224/103 756/25 485/100 580/68 734/192 494/123 ∗ (m) Water 4,485 3,474 2,432 2,426 3,459 2,612 2,606 2,658 2,656 4,376 2,656 2,655 2,661 2,661 1,680 3,474 4,465 4,976 5,630 4,418 3,459 4,967 3,882 4,791 5,577 5,710 2,818 1,659 W W W W W W E E E W W W W E W W W W W W W W E W W W W W 43 43 45 39 46 44 01 58 06 46 46 46 46 14 06 59 32 ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ 05 40 31 23 05 ◦ 11 ◦ ◦ ◦ ◦ ◦ 44 43 11 44 43 by University of Washington on 11/07/12. For personal use only. ◦ ◦ ◦ ◦ ◦ ◦ N46 N 128 N 128 N 128 N 128 N 127 N 127 N 135 N 159 N 135 N 127 N 127 N 127 N 127 N33 N43 N75 S 165 N 138 N 159 S88 N 141 N83 N83 N86 N83 N83 N 111 45 27 27 55 53 46 45 15 05 18 45 45 46 45 50 59 21 49 11 21 01 53 ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ 14 13 39 14 13 18 ◦ ◦ ◦ ◦ ◦ ◦ Latitude/longitude 19 28 47 47 47 47 17 47 47 47 47 27 9 32 48 48 22 36 41 22 1 1 1 1 19 23 40 5 Annu. Rev. Earth Planet. Sci. 2012.40:551-568. Downloaded from www.annualreviews.org Location JDF ridge, E flank JDF ridge, E flank JDF ridge, E flank JDF ridge, E flank JDF ridge, E flank JDF ridge, E flank JDF ridge, E flank NW Pacific Mid-Philippine Plate JDF ridge, E flank Shikoku Basin NE Cocos Plate Ninety East Ridge Central E Pacific E Pacific Middle Valley Middle Valley Japan Sea MAR, W flank CRR,Sflank CRR,Sflank MAR, W flank CRR,Sflank MAR, E flank E of Blake Escarpment SW Pacific SW of Oahu CRR,Sflank Table 1 Status of existing DSDP/ODP/IODP basement legacy holes Hole Basement reentry holes presently in use395A or recently used as observatories 504B 857D 858G 896A 1024C 1025C 1026B 1027C 1173B 1179E 1201E 1253A U1301A U1301B U1362A U1362B Basement reentry holes used for past333A wire-line reentry experiments/observatories or intended for504B seismic observatories 396B 534A 595B 794D 843B 896A 1107A 1224F 1243A

562 Edwards · Becker · Colwell EA40CH22-Edwards ARI 23 March 2012 15:39 C ◦ 150 ∼ m; OSN, an ION observatory , a program based on the national Ocean Network; JDF, Juan de casing and subsequent casing strings. Double asterisk ; DSDP, Deep-Sea Drilling Program; EPR, East Pacific Rise; 2-bit cones in hole Bit released at 539 mbsf Jurassic crust HRGB; junk below 600 mbsf Target for deepening Cone plugged with mud Cone plugged with mud; lost BHA in deepest 100 m Good drilling conditions in fast-spread crust Bad hole conditions in basement Bad hole conditions in basement HIG seismic expedition; “man-made hot spring” Lacks second casing; 2-bit cones at bottom Hole plugged by sediments Bad hole conditions Mini-HRGB; slim hole cored with DCS Top of cone at seafloor Target for deepening Needs second casing string; good hole conditions Nautile /269 ∗∗ 95 21 91/933 58/350 50/217 ??/563 25/- 71/0 none 51/481 40/- 57/- 40/- 50/- 66/- 65/- 57/- 90/- 80/- 40/- 51/372 75/- ∗ ∗ 143/91 563/192 1521/1271 1416/1415 762/24 157/59 183/53 1740/- 1605/- 709/366 868/544 187/50 278/14 1229/917 1195/267 594/135 1528/148 79/79 1682/278 551/388 456/165 1208/645 1508/1508 in combination with the manned submersible 4,157 5,302 3,635 1,645 3,957 4,296 4,497 3,900 4,203 5,489 5,519 3,008 3,468 1,289 732 5,724 5,685 2,817 1,803 2,965 1,874 4,654 5,186 Nadia E E E W E E W W E E W W W W W W W E E E W W 22 53 53 31 01 03 00 W 46 34 ◦ ◦ ◦ ◦ ◦ ◦ ◦ 22 16 07 23 43 48 03 03 02 ◦ ◦ 16 ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ 56 56 44 by University of Washington on 11/07/12. For personal use only. ◦ 32 ◦ ◦ ◦ ◦ S 129 N2 S57 S 117 N 156 N 139 N12 N 140 N42 N69 N 101 N10 N10 N68 N68 N 170 N 136 N 108 N 156 N91 S83 N 165 N83 48 13 43 59 39 04 46 06 10 07 01 58 50 07 02 47 59 47 ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ ◦ 36 44 00 15 14 ◦ ◦ ◦ ◦ ◦ 30 6 3 67 40 22 15 18 44 25 25 31 28 18 40 32 15 13 7 1 31 9 32 Annu. Rev. Earth Planet. Sci. 2012.40:551-568. Downloaded from www.annualreviews.org casings. Fracture Zone Central N Atlantic Central Cocos Plate EPR, W flank Norwegian margin SWIR, Atlantis Argo Abyssal Plain W Pacific Jurassic Ontong Java Plateau Iberia Abyssal Plain Izu-Bonin Arc EPR, E flank Peru Basin Galicia Bank Off Morocco S Bermuda Rise S Bermuda Rise Suiko Seamount Shikoku Basin Nauru Basin S Gulf of California CRR, S flank Sumisu Rift Caribbean Sea mbsf, meters below seafloor. T.D., total depth; B.P., basement penetration. denotes sites started with 20 Basement reentry holes potentially suitable for597C wire-line reentry experiments or observatories 642E 735B 765D 801C 807C 809F 899B 793B 1256D U1309D Older reentry holes lacking second casing146 string; unknown prospects for reentry without319A drillship remediation 320B 398D 416A 417D 418A 433C 442B 462A 482D 504A Asterisk indicates “basement,” defined as top of sill/sediment sequence. Ina most cases, casing depths fall belowb the seafloor of shoes of 16 application of seafloor wire-line reentry utilizing the logging shuttle Other abbreviations: BHA, bottom hole assembly; CORK, Circulation Obviation Retrofit Kit; CRR, Costa Rica Rift; DCS, diamond coring system; DIANAUT FARE, Faisabilite Re-Entree; HIG, Hawaii InstituteFuca; of LFASE, Geophysics; HRGB, Navy hard-rock Low guide Frequency base; Acousticstation; IODP, Seismic SISMOBS, Integrated Experiment; sismologie Ocean MAR, Drilling ocean mid-Atlantic Program; bottom ridge; ION, seismometer; NERO, Inter SWIR, an Southwest ION Indian observatory Ridge. station; ODP, Ocean Drilling Progra

www.annualreviews.org • The Deep, Dark Energy Biosphere 563 EA40CH22-Edwards ARI 23 March 2012 15:39

The future offers ripe opportunities for exploration of and experimentation with the deepest habitable portions of our planet to address these major issues, thereby enabling us to take advantage of the current and emerging coordinating infrastructure. All the while, we remain open to the development of new opportunities. The next ten years will bring transformative changes to our understanding of life on our planet and the function of the deeply seated intraterrestrial life.

DISCLOSURE STATEMENT The authors are not aware of any afﬁliations, memberships, funding, or ﬁnancial holding that might be perceived as affecting the objectivity of this review.

ACKNOWLEDGMENTS K.J.E. is supported by the Center for Dark Energy Biosphere Investigations; F.C. and K.J.E. appreciate the support of the Deep Carbon Observatory and the Alfred P. Sloan Foundation. K.B. is grateful to the National Science Foundation for two decades of strong support of CORK observatories, most recently OCE-1030350 and OCE-1060855. This is the Center for Dark Energy Biosphere Investigations contribution number 115.

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Parkes RJ, Cragg BA, Wellsbury P. 2000. Recent studies on bacterial populations and processes in subseafloor sediments: a review. Hydrogeol. J. 8(1):11–28 Pedersen K. 1996. Investigations of subterranean bacteria in deep crystalline bedrock and their importance for the disposal of nuclear waste. Can. J. Microbiol. 42:382–91 Pedersen K. 1997. Microbial life in deep granitic rock. FEMS Microbiol. Rev. 20:399–414 Pedersen K. 2000. Exploration of deep intraterrestrial microbial life: current perspectives. FEMS Microbiol. Lett. 185:9–16 Phelps TJ, Fliermans CB, Garland TR, Pfiffner SM, White DC. 1989. Methods for recovery of deep terrestrial subsurface sediments of microbiological studies. J. Microbiol. Methods 9:267–79 Phelps TJ, Murphy EM, Pfiffner SM, White DC. 1994. Comparison between geochemical and biological estimates of subsurface microbial activities. Microb. Ecol. 28:335–49 Rastogi G, Osman S, Kukkadapu R, Engelhard M, Vaishampayan PA, et al. 2010. Microbial and mineralogical characterizations of soils collected from the deep biosphere of the former Homestake gold mine, South Dakota. Microb. Ecol. 60:539–50 Rastogi G, Stetler LD, Peyton BM, Sani RK. 2009. Molecular analysis of prokaryotic diversity in the deep subsurface of the former Homestake gold mine, South Dakota, USA. J. Microbiol. 47(4):371–84 Rebata-Landa V, Santamarina JC. 2006. Mechanical limits to microbial activity in deep sediments. Geochem. Geophys. Geosyst. 7:Q11006 Russell CE, Jacobson R, Haldeman DL, Amy PS. 1994. Heterogeneity of deep subsurface microorganisms and correlations to hydrogeological and geochemical parameters. Geomicrobiol. J. 12:37–51 Santelli CM, Bach W, Banerjee NR, Edwards KJ. 2010. Tapping the subsurface ocean crust biosphere: Low biomass and drilling-related contamination calls for improved quality controls. Geomicrobiol. J. 27:158–69 Schrenk MO, Huber JA, Edwards KJ. 2009. Microbial provinces in the subseafloor. Oceanography 2:85–110 Shipboard Sci. Party. 2003. Leg 201 summary. Proc. Ocean Drill. Program Initial Rep., ed. S D’Hondt, BB Jørgensen, DJ Miller, et al., 201:1–81. College Station, TX: Ocean Drill. Program. doi: 10.2973/odp.proc.ir.201.2003 Smith A, Popa R, Fisk MR, Nielsen M, Wheat CG, et al. 2011. In situ enrichment of ocean crust microbes on igneous minerals and glasses using an osmotic flow-through device. Geochem. Geophys. Geosyst. 12:Q06007 Smith DC, Spivack AJ, Fisk MR, Haveman SA, Staudigel H. 2000. Tracer-based estimates of drilling-induced microbial contamination of deep sea crust. Geomicrobiol. J. 17:207–17 Smith RL, Harvey RW, LeBlanc DR. 1991. Importance of closely spaced vertical sampling in delineating chemical and microbiological gradients in groundwater studies. J. Contam. Hydrol. 7:285–300 Spear JR, Walker JJ, McCollom TM, Pace NR. 2005. Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem. Proc. Natl. Acad. Sci. USA 102(7):2555–60 by University of Washington on 11/07/12. For personal use only. Stein CA, Stein S. 1994. Constraints on hydrothermal heat flux through the oceanic lithosphere from global heat flow. J. Geophys. Res. 99:3081–95 Stevens TO. 1997. Subsurface microbiology and the evolution of the biosphere. See Amy & Haldeman 1997, pp. 205–23 Annu. Rev. Earth Planet. Sci. 2012.40:551-568. Downloaded from www.annualreviews.org Stevens TO, McKinley JP. 1995. Lithoautotrophic microbial ecosystems in deep basalt aquifers. Science 270:450–54 Stevens TO, McKinley JP. 2000. Abiotic controls on hydrogen production from basalt-water reactions and implications for aquifer biogeochemistry. Environ. Sci. Technol. 34:826–31 Takai K, Komatsu T, Inagaki F, Horikoshi K. 2001. Distribution of archaea in a black smoker chimney structure. Appl. Environ. Microbiol. 67:3618–29 Tarafa ME, Whelan JK, Oremland RS, Smith RL. 1987. Evidence of the microbiological activity in leg 95 (New Jersey transect) sediments. Rep. Deep-Sea Drill. Proj. XCV, Texas A&M Univ. Coll. Geosci., Wash., DC Walker A, Parkhill J. 2008. Single-cell genomics. Nat. Rev. Microbiol. 6:176–77 Wanger G, Onstott TC, Southam G. 2008. Stars of the terrestrial deep subsurface: a novel ‘star-shaped’ bacterial morphotype from a South African platinum mine. Geobiology 6:325–30

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Whelan JJ, Oremland R, Tarafa M, Smith R, Howarth R, Lee C. 1986. Evidence for sulfate-reducing and methane-producing microorganisms in sediments from sites 618, 619, and 622. Rep. Deep-Sea Drill. Proj. XCVI, Texas A&M Univ. Coll. Geosci., Wash., DC Whitman WB, Coleman DC, Wiebe WJ. 1998. Prokaryotes: the unseen majority. Proc. Natl. Acad. Sci. USA 95:6578–83 ZoBell CE, Anderson QA. 1936. Vertical distribution of bacteria in marine sediments. Bull. Am. Assoc. Petrol. Geol. 20(3):258–69 by University of Washington on 11/07/12. For personal use only. Annu. Rev. Earth Planet. Sci. 2012.40:551-568. Downloaded from www.annualreviews.org

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Annual Review of Earth and Planetary Sciences Volume 40, 2012 Contents

Reminiscences From a Career in Geomicrobiology Henry L. Ehrlich ppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp1 Mixing and Transport of Isotopic Heterogeneity in the Early Solar System Alan P. Boss pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp23 Tracing Crustal Fluids: Applications of Natural 129I and 36Cl Udo Fehn pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp45 SETI@home, BOINC, and Volunteer Distributed Computing Eric J. Korpela pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp69 End-Permian Mass Extinction in the Oceans: An Ancient Analog for the Twenty-First Century? Jonathan L. Payne and Matthew E. Clapham pppppppppppppppppppppppppppppppppppppppppppppp89 Magma Oceans in the Inner Solar System Linda T. Elkins-Tanton pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp113

History of Seawater Carbonate Chemistry, Atmospheric CO2, and Ocean Acidiﬁcation Richard E. Zeebe pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp141

by University of Washington on 11/07/12. For personal use only. Biomimetic Properties of Minerals and the Search for Life in the Martian Meteorite ALH84001 Jan Martel, David Young, Hsin-Hsin Peng, Cheng-Yeu Wu, and John D. Young pppp167

Annu. Rev. Earth Planet. Sci. 2012.40:551-568. Downloaded from www.annualreviews.org Archean Subduction: Fact or Fiction? Jeroen van Hunen and Jean-Fran¸cois Moyen ppppppppppppppppppppppppppppppppppppppppppppp195 Molecular Paleohydrology: Interpreting the Hydrogen-Isotopic Composition of Lipid Biomarkers from Photosynthesizing Organisms Dirk Sachse, Isabelle Billault, Gabriel J. Bowen, Yoshito Chikaraishi, Todd E. Dawson, Sarah J. Feakins, Katherine H. Freeman, Clayton R. Magill, Francesca A. McInerney, Marcel T.J. van der Meer, Pratigya Polissar, Richard J. Robins, Julian P. Sachs, Hanns-Ludwig Schmidt, Alex L. Sessions, James W.C. White, Jason B. West, and Ansgar Kahmen ppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp221

viii EA40-FrontMatter ARI 1 April 2012 7:38

Building Terrestrial Planets A. Morbidelli, J.I. Lunine, D.P. O’Brien, S.N. Raymond, and K.J. Walsh pppppppppppp251 Paleontology of Earth’s Mantle Norman H. Sleep, Dennis K. Bird, and Emily Pope pppppppppppppppppppppppppppppppppppppp277 Molecular and Fossil Evidence on the Origin of Angiosperms James A. Doyle pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp301 Infrasound: Connecting the Solid Earth, Oceans, and Atmosphere M.A.H. Hedlin, K. Walker, D.P. Drob, and C.D. de Groot-Hedlin pppppppppppppppppppp327 Titan’s Methane Weather Henry G. Roe ppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp355 Extratropical Cooling, Interhemispheric Thermal Gradients, and Tropical Climate Change John C.H. Chiang and Andrew R. Friedman ppppppppppppppppppppppppppppppppppppppppppppp383

TheRoleofH2O in Subduction Zone Magmatism Timothy L. Grove, Christy B. Till, and Michael J. Krawczynski pppppppppppppppppppppppp413 Satellite Geomagnetism Nils Olsen and Claudia Stolle pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp441 The Compositions of Kuiper Belt Objects Michael E. Brown ppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp467 Tectonics of the New Guinea Region Suzanne L. Baldwin, Paul G. Fitzgerald, and Laura E. Webb ppppppppppppppppppppppppp495 Processes on the Young Earth and the Habitats of Early Life Nicholas T. Arndt and Euan G. Nisbet ppppppppppppppppppppppppppppppppppppppppppppppppppp521 The Deep, Dark Energy Biosphere: Intraterrestrial Life on Earth Katrina J. Edwards, Keir Becker, and Frederick Colwell pppppppppppppppppppppppppppppppp551 by University of Washington on 11/07/12. For personal use only. Geophysics of Chemical Heterogeneity in the Mantle Lars Stixrude and Carolina Lithgow-Bertelloni pppppppppppppppppppppppppppppppppppppppppp569

Annu. Rev. Earth Planet. Sci. 2012.40:551-568. Downloaded from www.annualreviews.org The Habitability of Our Earth and Other Earths: Astrophysical, Geochemical, Geophysical, and Biological Limits on Planet Habitability Charles H. Lineweaver and Aditya Chopra ppppppppppppppppppppppppppppppppppppppppppppppp597 The Future of Arctic Sea Ice Wieslaw Maslowski, Jaclyn Clement Kinney, Matthew Higgins, and Andrew Roberts pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp625 The Mississippi Delta Region: Past, Present, and Future Michael D. Blum and Harry H. Roberts pppppppppppppppppppppppppppppppppppppppppppppppppp655

Contents ix EA40-FrontMatter ARI 1 April 2012 7:38

Climate Change Impacts on the Organic Carbon Cycle at the Land-Ocean Interface Elizabeth A. Canuel, Sarah S. Cammer, Hadley A. McIntosh, and Christina R. Pondell ppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp685

Indexes

Cumulative Index of Contributing Authors, Volumes 31–40 ppppppppppppppppppppppppppp713 Cumulative Index of Chapter Titles, Volumes 31–40 ppppppppppppppppppppppppppppppppppp717

Errata

An online log of corrections to Annual Review of Earth and Planetary Sciences articles may be found at http://earth.annualreviews.org by University of Washington on 11/07/12. For personal use only. Annu. Rev. Earth Planet. Sci. 2012.40:551-568. Downloaded from www.annualreviews.org

xContents