Shrinking Majority of the Deep Biosphere

Shrinking majority of the deep biosphere

Bo Barker Jørgensen1 Department of Bioscience, Center for Geomicrobiology, Aarhus University, 8000 Aarhus, Denmark

iving microorganisms were ﬁrst 10 discovered in sediment cores from Black Sea (18) scientiﬁc ocean drilling in the late 9

L -3 1980s when microbiologists observed and counted DNA-stained micro- 8 Peru Shelf, IODP 1227 (17) bial cells under the microscope. During the following decade, new observations 7 Peru Shelf, IODP 1230 (17) were made from drill sites in the Atlantic 6 and Paciﬁc Oceans and the Mediterranean East Paciﬁc, IODP 1225 (17) Sea (1, 2). The combined data on cell 5 numbers from these sites showed a sys-

Log cell numbers cm Peru Basin, IODP 1231 (17) tematic, log-log linear decrease with − 4 depth, from approximately 109 cells·cm 3 6 · −3 South Pacific gyre, SPG-2 (9) near the sediment surface to 10 cells cm 3 at several hundred meters below seafloor, 2345678 where the sediment had been deposited Log age (years) many million years ago (2) (Fig. 1). In their 1998 study, Whitman et al. (3) used Fig. 1. Microbial cells numbers of marine sediments at different subseafloor depths with different sediment ages ranging from 100 y to 100 million years. Data from six sites are plotted as log10 of the cell these data to make a grand estimate of the 3 total number of prokaryotic cells on Earth. numbers per cm vs. log10 of the sediment age in years. The data illustrate the general decrease in cell Their astonishing conclusion was that 55% numbers with age of the buried organic matter that provides the energy for the deep biosphere. The central North and South Pacific have extremely low sediment burial rates and cell numbers (red symbols), of all microbial cells occurred in the deep thereby changing the earlier estimates of the deep biosphere to lower cell numbers. IODP, Integrated seabed whereas most of the rest were Ocean Drilling Program. found in the deep terrestrial subsurface. Even more staggering, the combined deep biospheres appeared to harbor one third early database was skewed toward sedi- “noisy or erratic cell concentration of the total living biomass on Earth. The ments with high cell counts. trends.” By omitting such data, the depth publication of Whitman et al. (3) sparked In stark contrast to the ocean margins, distribution of cell numbers below 0.1 m a rapidly growing interest in the deep the central gyres of the South and North and down to basement could be simulated biosphere, and the data from this study Pacific have the greatest distance from the for each site by a power-law function and were repeatedly cited in the literature in continents, the lowest phytoplankton pro- the total depth-integrated cell numbers the following years. Their biomass esti- ductivity, and the lowest sedimentation could be calculated. Interestingly, the cell mate was later supported by data on intact rate of anywhere in the world ocean. The numbers were inversely correlated to the polar membrane lipids as indicators of red clay covering the basement rock in distance from the continents, which ex- living cells (4). Now, these numbers are these regions has extremely low organic plains why the early estimates based on < being challenged. In PNAS, Kallmeyer carbon content ( 0.5% of dry weight), and ocean margin sites were too high. The et al. (5) conclude that the total cell oxygen penetrates from the seawater and statistical trends observed in the data were fl number for the deep subsea oor bio- deeply into the seabed, even down to the used to calculate areal cell densities in sphere is probably 12-fold lower than the basaltic crust tens of meters below the a1°× 1° gridded map of the world ocean fl earlier estimate whereas the total biomass sea oor (6, 7). Microbial cells are so few and thereby to estimate a new global may be 74-fold lower. Is the deep bio- that they cannot be detected by direct × 29 fi number: 2.9 10 cells in the marine sphere losing signi cance? microscopy in these sediments. A new deep biosphere (5). Given the great scatter The low estimates by Kallmeyer et al. method was therefore developed by which of cell counts and the great diversity in (5) do not result from a correction of the bacteria are first extracted from the sedimentary environments, such a number earlier cell counts. They result from new sediment, concentrated by density centri- still suffers a degree of uncertainty, but it data from the vast desert regions of the fugation to a particle suspension, and is certainly based on stronger data and oceans that have been drilled and sampled then counted (8). With this 100-fold more more advanced statistical methods than by microbiologists for the first time sensitive procedure, cells turned out in- earlier estimates. The effect of rejecting (Fig. 1). These regions were not specifi- deed to be present, yet in numbers that erratic data or of extrapolating to regions cally targeted in the earlier Ocean Drilling were 1,000-fold lower than in most other fi Program (and the later Integrated Ocean sediments (5, 9). By inclusion of such for which no data are available is dif - Drilling Program), as the program pri- desert regions in the global compilation, cult to evaluate for the reader, but the marily aimed to explore plate tectonics, the estimated total cell numbers authors carefully explain their approach. paleoceanography, and other dynamic decreased markedly. A similar statistical analysis is needed processes that were most strongly ex- The entire data set on cell numbers is for the terrestrial deep biosphere, but pressed along the ocean margins. Micro- still limited, and a global extrapolation biologists who joined these geologically remains difficult and highly dependent on motivated drilling expeditions therefore the statistical approach used. Kallmeyer Author contributions: B.B.J. wrote the paper. obtained their samples from ocean margin et al. (5) had data available from five times The author declares no conflict of interest. regions with high organic productivity and as many sites as Whitmann et al. (3), but See companion article on page 16213. high sedimentation rates. As a result, the they rejected 40% of these as a result of 1E-mail: [email protected].

15976–15977 | PNAS | October 2, 2012 | vol. 109 | no. 40 www.pnas.org/cgi/doi/10.1073/pnas.1213639109 Downloaded by guest on September 27, 2021 COMMENTARY

the available data are here still insufficient water reactions (14). The turnover time iologically inactive state (16). Microscopic to detect general correlations to environ- and the size of this microbial community counts of DNA-stained cells include met- mental properties. are not known. If the turnover time were abolically active cells and inactive, dor- It is unexpected that microbial cells of similar to that in deep marine sediments— mant cells as long as the latter are less than 1 μm size may constitute a large say, 100 y—the autotrophic community detectable by fluorescence staining of their fraction of all living biomass on Earth, biomass would, at the maximum, be DNA. However, for cells locked in an ex- 14 including all vascular plants on land and 10 g C, which is a small fraction of the tremely energy-starved and stable envi- × 15 all algae in the sea. The estimate of their 4 10 g C estimated by Kallmeyer et al. ronment that steadily decreases in energy biomass, however, depends on the mean (5) for the deep biosphere in marine flux over millions of years, dormancy cell size and carbon content of the cells. sediments. Another energy source for the would seem to be a dead-end strategy. The Whereas Whitman et al. (3) assumed crustal biosphere is the slow flow of sea- cells would be deprived of whatever energy a mean carbon content of 86 fg C per cell water through the cracked and porous − they could have conserved, had they not (1 fg is equal to 10 15 g), Kallmeyer et al. ocean crust beneath the thick sediment been dormant, and they would need to (5) suggest a sixfold lower value of 14 fg cover, which injects oxygen, inorganic ions, C based on microscopic measurements of and dissolved organic matter into the old spend extra energy on cell repair after cells from Integrated Ocean Drilling Pro- basalt. It is unknown how large microbial awakening. Despite this, some bacteria gram core samples. Their rationale is that communities subsist in the basaltic might still go into the most long-lived microbial cell sizes tend to be smaller un- ocean crust. dormant state known, the endospore for- der strong nutrient limitation because Although correlations are helpful to mation. Bacterial endospores are generally a larger surface-to-volume ratio of small calculate global cell numbers, it would impermeable to the DNA stains applied, cells is of competitive advantage because be interesting to gain a functional un- and spores are therefore not included of more efficient substrate uptake and derstanding of what really controls the cell in the global estimates of microbial cells or thereby faster growth. The deep biosphere numbers in subsurface sediments. Mortal- biomass. The analysis of a specific com- indeed has very low nutrient and energy ity is apparently extremely low, cell turn- ponent of the spore wall, dipicolinic acid, flux, and the microorganisms have ex- over takes hundreds of years, and the in sediment samples has recently shown ceedingly slow turnover with generation environment is stable over millions of that spores may be as abundant as vege- times of 100 to1,000 y (10, 11). However, it years with a decreasing energy flux over tative cells in the deep biosphere (11). It is not obvious that adaptation to extremely time, provided by the buried and slowly may be a matter of definition whether they low metabolic rate in the highly stable decaying organic matter. Under such should be added to the global census of deep biosphere environment should select conditions, the community size may be cell numbers and living biomass. fi for small cell size. controlled by a ne-tuned balance be- The deep biosphere has become widely fl The global data compilation of Kall- tween the available energy ux from or- known, not only for its high cell numbers meyer et al. (5) includes only those mi- ganic matter degradation and the and large biomass but also for the fasci- crobial provinces in the subseafloor (12) minimum energy requirements of the mi- “ ” nating slow life and its important inter- that consist of normal sediments de- crobial cells. Here the critical energy reactions with the geosphere. Kallmeyer posited over geological time. Although quirement is not the biological energy et al. (5) now estimate that there are fewer such sediments indeed cover most of the quantum needed to support ATP synthe- microorganisms all together in the global ocean floor, active plate tectonics also sis, but rather the minimum energy flux create very different environments such as per cell. This minimum energy flux deep biosphere. However, the importance midocean ridges and ridge flanks, sub- appears to be several orders of magnitude of these deeply buried communities for duction zones, and other hotspots of geo- lower than the maintenance energy pre- driving carbon and nutrient cycling and logical and geothermal activity. Chemical dicted from laboratory cultures. The catalyzing a multitude of reactions be- fl alterations are strong in the midocean microorganisms may thus subsist in a tween rocks, sediments, and uids is not ridges and continue for 10 to 15 million physiological state that we currently can- challenged. Neither is the persisting enigma years in the spreading ridge flanks with the not explain from pure culture studies but of slow life beneath the surface of Earth. release of reduced iron, sulfur, and H2 for which indications begin to appear The deep biosphere is still alive. (13). These chemical species serve as en- from laboratory cultures that have been ergy substrates for autotrophic micro- starved for long periods of time (15). ACKNOWLEDGMENTS. The Center for Geomi- organisms that may generate as much An alternative explanation to exceed- crobiology, Aarhus University, is supported by the 12 fl Danish National Research Foundation, the Ger- as 10 g cell C globally per year exclu- ingly low energy ux requirement could be man Max Planck Society, and the European sively from the “dark energy” of rock– dormancy by which the cells are in a phys- Research Council.

1. Parkes RJ, Cragg BA, Fry JC, Herbert RA, Wimpenny JWT 6. Fischer JP, et al. (2009) Oxygen penetration deep into 13. Bach W, Edwards KJ (2003) Iron and sulfide oxidation (1990) Bacterial biomass and activity in deep sediment the sediment of the South Pacific gyre. Biogeosciences within the basaltic ocean crust: Implications for chemo- layers from the Peru margin. Philos Trans R Soc Lond A 6:1467–1478. lithoautotrophic microbial biomass production. Geo- – 331:139–153. 7. Røy H, et al. (2012) Aerobic microbial respiration in 86- chim Cosmochim Acta 67:38712 3887. – 2. Parkes RJ, Cragg BA, Wellsbury P (2000) Recent studies million-year-old deep-sea red clay. Science 336:922 925. 14. Edwards KJ, Becker K, Colwell F (2012) The deep, dark ’ on bacterial populations and processes in subseafloor 8. Kallmeyer J, Smith DC, D Hondt SL, Spivack AJ (2008) energy biosphere: Intraterrestrial life on Earth. Annu New cell extraction procedure applied to deep subsur- Rev Earth Planet Sci 40:551–568. sediments: A review. Hydrogeol J 8:11–28. face sediments. Limnol Oceanogr Methods 6:236–245. 15. Finkel SE (2006) Long-term survival during stationary 3. Whitman WB, Coleman DC, Wiebe WJ (1998) Prokar- 9. D’Hondt S, et al. (2009) Subseafloor sedimentary life in phase: Evolution and the GASP phenotype. Nat Rev yotes: The unseen majority. Proc Natl Acad Sci USA 95: the South Pacific Gyre. Proc Natl Acad Sci USA 106: Microbiol 4:113–120. 6578–6583. 11651–11656. 16. Lennon JT, Jones SE (2011) Microbial seed banks: The 4. Lipp JS, Morono Y, Inagaki F, Hinrichs KU (2008) 10. Jørgensen BB, D’Hondt S (2006) Ecology. A starving ma- ecological and evolutionary implications of dormancy. Significant contribution of Archaea to extant bio- jority deep beneath the seafloor. Science 314:932–934. Nat Rev Microbiol 9:119–130. mass in marine subsurface sediments. Nature 454: 11. Lomstein BA, Langerhuus AT, D’Hondt S, Jørgensen BB, 17. D’Hondt S, et al. (2004) Distributions of microbial activities – 991 994. Spivack AJ (2012) Endospore abundance, microbial in deep subseafloor sediments. Science 306:2216–2221. 5. Kallmeyer J, Pockalny R, Adhikari RR, Smith DC, growth and necromass turnover in deep sub-seafloor 18. Leloup J, et al. (2007) Diversity and abundance of sul- D’Hondt S (2012) Global distribution of microbial sediment. Nature 484:101–104. fate-reducing microorganisms in the sulfate and methane abundance and biomass in subseafloor sediment. Proc 12. Schrenk MO, Huber JA, Edwards KJ (2010) Microbial prov- zones of a marine sediment, Black Sea. Environ Microbiol Natl Acad Sci USA 109:16213–16216. inces in the subseafloor. Annu Rev Mar Sci 2:279–304. 9:131–142.

Jørgensen PNAS | October 2, 2012 | vol. 109 | no. 40 | 15977 Downloaded by guest on September 27, 2021