Skip to main content
  • Submit
  • About
    • Editorial Board
    • PNAS Staff
    • FAQ
    • Accessibility Statement
    • Rights and Permissions
    • Site Map
  • Contact
  • Journal Club
  • Subscribe
    • Subscription Rates
    • Subscriptions FAQ
    • Open Access
    • Recommend PNAS to Your Librarian
  • Log in
  • My Cart

Main menu

  • Home
  • Articles
    • Current
    • Special Feature Articles - Most Recent
    • Special Features
    • Colloquia
    • Collected Articles
    • PNAS Classics
    • List of Issues
  • Front Matter
  • News
    • For the Press
    • This Week In PNAS
    • PNAS in the News
  • Podcasts
  • Authors
    • Information for Authors
    • Editorial and Journal Policies
    • Submission Procedures
    • Fees and Licenses
  • Submit
  • About
    • Editorial Board
    • PNAS Staff
    • FAQ
    • Accessibility Statement
    • Rights and Permissions
    • Site Map
  • Contact
  • Journal Club
  • Subscribe
    • Subscription Rates
    • Subscriptions FAQ
    • Open Access
    • Recommend PNAS to Your Librarian

User menu

  • Log in
  • My Cart

Search

  • Advanced search
Home
Home

Advanced Search

  • Home
  • Articles
    • Current
    • Special Feature Articles - Most Recent
    • Special Features
    • Colloquia
    • Collected Articles
    • PNAS Classics
    • List of Issues
  • Front Matter
  • News
    • For the Press
    • This Week In PNAS
    • PNAS in the News
  • Podcasts
  • Authors
    • Information for Authors
    • Editorial and Journal Policies
    • Submission Procedures
    • Fees and Licenses

New Research In

Physical Sciences

Featured Portals

  • Physics
  • Chemistry
  • Sustainability Science

Articles by Topic

  • Applied Mathematics
  • Applied Physical Sciences
  • Astronomy
  • Computer Sciences
  • Earth, Atmospheric, and Planetary Sciences
  • Engineering
  • Environmental Sciences
  • Mathematics
  • Statistics

Social Sciences

Featured Portals

  • Anthropology
  • Sustainability Science

Articles by Topic

  • Economic Sciences
  • Environmental Sciences
  • Political Sciences
  • Psychological and Cognitive Sciences
  • Social Sciences

Biological Sciences

Featured Portals

  • Sustainability Science

Articles by Topic

  • Agricultural Sciences
  • Anthropology
  • Applied Biological Sciences
  • Biochemistry
  • Biophysics and Computational Biology
  • Cell Biology
  • Developmental Biology
  • Ecology
  • Environmental Sciences
  • Evolution
  • Genetics
  • Immunology and Inflammation
  • Medical Sciences
  • Microbiology
  • Neuroscience
  • Pharmacology
  • Physiology
  • Plant Biology
  • Population Biology
  • Psychological and Cognitive Sciences
  • Sustainability Science
  • Systems Biology
Research Article

Methanogenic burst in the end-Permian carbon cycle

Daniel H. Rothman, Gregory P. Fournier, Katherine L. French, Eric J. Alm, Edward A. Boyle, Changqun Cao, and Roger E. Summons
PNAS April 15, 2014 111 (15) 5462-5467; first published March 31, 2014; https://doi.org/10.1073/pnas.1318106111
Daniel H. Rothman
aLorenz Center,
bDepartment of Earth, Atmospheric, and Planetary Sciences, and
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: dhr@mit.edu
Gregory P. Fournier
cDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139; and
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Katherine L. French
bDepartment of Earth, Atmospheric, and Planetary Sciences, and
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Eric J. Alm
cDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139; and
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Edward A. Boyle
bDepartment of Earth, Atmospheric, and Planetary Sciences, and
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Changqun Cao
dState Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Roger E. Summons
bDepartment of Earth, Atmospheric, and Planetary Sciences, and
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  1. Edited by John M. Hayes, Woods Hole Oceanographic Institution, Woods Hole, MA, and approved February 4, 2014 (received for review September 27, 2013)

  • Article
  • Figures & SI
  • Info & Metrics
  • PDF
Loading

Significance

The end-Permian extinction is the most severe biotic crisis in the fossil record. Its occurrence has been attributed to increased CO2 levels deriving from massive Siberian volcanism. However, such arguments have been difficult to justify quantitatively. We propose that the disruption of the carbon cycle resulted from the emergence of a new microbial metabolic pathway that enabled efficient conversion of marine organic carbon to methane. The methanogenic expansion was catalyzed by nickel associated with the volcanic event. We support this hypothesis with an analysis of carbon isotopic changes leading up to the extinction, phylogenetic analysis of methanogenic archaea, and measurements of nickel concentrations in South China sediments. Our results highlight the sensitivity of the Earth system to microbial evolution.

Abstract

The end-Permian extinction is associated with a mysterious disruption to Earth’s carbon cycle. Here we identify causal mechanisms via three observations. First, we show that geochemical signals indicate superexponential growth of the marine inorganic carbon reservoir, coincident with the extinction and consistent with the expansion of a new microbial metabolic pathway. Second, we show that the efficient acetoclastic pathway in Methanosarcina emerged at a time statistically indistinguishable from the extinction. Finally, we show that nickel concentrations in South China sediments increased sharply at the extinction, probably as a consequence of massive Siberian volcanism, enabling a methanogenic expansion by removal of nickel limitation. Collectively, these results are consistent with the instigation of Earth’s greatest mass extinction by a specific microbial innovation.

  • methanogenesis
  • horizontal gene transfer
  • microbial evolution
  • biogeochemical dynamics

The greatest rate of taxonomic loss during the end-Permian extinction—the most severe in the fossil record (1)—occurs within 20,000 y, beginning about 252.28 million years ago (Ma) (2) at a time precisely coincident (2) with geochemical signals indicating a severe and equally rapid perturbation to Earth’s carbon cycle (1⇓⇓⇓⇓–6). Although probably related, neither the cause of the extinction nor the origin of the change in the carbon cycle is known. One possible linkage derives from the observation that massive Siberian volcanism occurs at roughly the same time as the extinction (7, 8). However, quantitative estimates of direct volcanic outgassing are much too small to account for the changes in the carbon cycle (9). Secondary effects of Siberian volcanism, such as the combustion of huge deposits of coal (10) or other forms of organic carbon (11), are more attractive quantitatively but still difficult to reconcile with observed geochemical changes (1⇓⇓⇓⇓–6). Reports of marine anoxia in the Late Permian (5, 12, 13) also indicate changes in the carbon cycle. Moreover, the notion that a disturbance of the carbon cycle plays a significant role as a “kill mechanism” derives considerable support from observations of physiological differences between species that survived the extinction and those that did not (14⇓–16).

Here we relate the principal observations of end-Permian environmental change—massive volcanism and changes in marine CO2 and O2 levels—to the transfer of genetic material, from a cellulolytic bacterium to a methanogenic archaeon, that enabled efficient methanogenic degradation of organic carbon (17). Our analysis is constructed from three key observations. First, we show that the form of time-dependent changes in the carbon isotopic record indicates an instability within the carbon cycle that is inconsistent with volcanic combustion of organic sediments but consistent with the expansion of a new microbial metabolic pathway. Second, we identify this pathway with efficient acetoclastic methanogenesis and show that the age of the last common ancestor of Methanosarcina, the genus using this pathway, is consistent with the time of the extinction. Because methanogens are limited by nickel (18, 19), the third component of our study presents an analysis of nickel deposited in South China sediments. We find that nickel concentrations rose just before the extinction, presumably as a consequence of Siberian volcanism, providing a mechanism not only to enhance the methanogenic expansion and its perturbation to the carbon cycle but also to amplify the development of marine anoxia. Taken as a whole, these results reconcile an array of apparently disparate observations about the end-Permian event.

Growth of the Marine Carbon Reservoir

Fig. 1A displays the carbon-isotopic record in Meishan, China (5). Immediately preceding the extinction event, the isotopic composition Graphic of carbonate carbon declines by about 7‰ during a period of about 100 thousand years (Kyr), first slowly, and subsequently rapidly. At the same time, the isotopic composition Graphic of organic carbon also changes. We seek the physical fluxes in the carbon cycle that predict the chemical signals Graphic and Graphic. Of particular interest is whether the apparent downward acceleration of the carbonate signal can provide a quantitative indication of the underlying biogeochemical dynamics.

Fig. 1.
  • Download figure
  • Open in new tab
  • Download powerpoint
Fig. 1.

Carbon isotopic signals immediately preceding the end-Permian extinction in Meishan, China, indicate superexponential growth of the marine inorganic carbon reservoir. (A) Inorganic (Graphic, blue) and organic (Graphic, green) carbon isotopic changes (5). The dates at both ends of the time axis are resolved within Graphic Myr (2); in between, time is interpolated linearly in proportion to stratigraphic height. The peak extinction activity occurs at approximately Graphic Myr (2). (B) Reconstruction (solid blue line) of the dimensionless mass Graphic added to the marine inorganic carbon reservoir, assuming initial condition Graphic and an influx of isotopically light carbon with isotopic composition Graphic. (Inset) The same curve plotted on log-linear axes; the concave upward curvature suggests that Graphic grows superexponentially. The dashed red line compares Graphic to a superexponential growth law proportional to Graphic, where the critical time Graphic is coincident with the extinction peak.

To obtain such understanding, we consider the carbon cycle to be a simple exchange between globally mixed reservoirs of inorganic and organic carbon, via photosynthesis and respiration (20), and assume that the isotopic changes represent a perturbation from a preexisting steady state. We assume that the system is perturbed by an influx of isotopically light inorganic carbon of constant isotopic composition Graphic, forcing Graphic to decline out of its steady state. Because organic carbon is isotopically light, a decrease in its rate of burial is effectively indistinguishable from such light inputs. However, changes in organic burial can account for only a negligible fraction of the peak perturbed flux (SI Text). Changes in the burial flux of carbonate carbon are limited to an even smaller impact because its isotopic composition is identical to that of the inorganic reservoir. We therefore hold both burial rates constant to maintain simplicity. The mass Graphic of the inorganic reservoir then grows with time t in response to the increased inputs, by an amount Graphic, where Graphic is the initial, steady-state, size of the reservoir. The normalized perturbation Graphic is then straightforwardly related to changes in the geochemical signals by (SI Text)Embedded Imagewhere Graphic determines the scale of the perturbation and the “force” F is a weighted sum of two nonsteady-state effects: the nonzero derivative Graphic and the departures of Graphic and Graphic from their unperturbed values. The solution of Eq. 1 for Graphic provides the normalized time-dependent perturbation of the marine reservoir of dissolved inorganic carbon (DIC). The way in which the DIC reservoir grows with time is a function of how it is forced out of its steady state; consequently, knowledge of Graphic can be used to test models of the end-Permian carbon cycle.

The form of Eq. 1 provides an immediate clue. Because Graphic accelerates sharply downward, Graphic is increasingly negative. Consideration of the unforced Graphic equation then suggests that M grows exponentially or faster. Numerical solutions of Eq. 1 confirm this view. Fig. 1B plots Graphic for the case Graphic, representative of the isotopic composition of remineralized organic carbon, assuming a constant sediment accumulation rate between the known dates (2). The curvature of the log-linear plot in Fig. 1B, Inset suggests that the growth of Graphic is faster than exponential. (Although the total quantity of light carbon required for the isotopic excursion depends on Graphic (1, 2, 6, 9), the shape of Graphic is independent of Graphic when, as here, Graphic is much smaller than Graphic.) Superexponential growth of the marine inorganic carbon reservoir implies that the carbon cycle behaves nonlinearly. As we show later, a simple dynamical mechanism containing a leading-order nonlinearity predicts superexponential growth proportional to Graphic. Such a growth law, where Graphic is coincident with the extinction peak, is given by the red-dashed line in Fig. 1B. The burst near Graphic—an incipient singular blow-up—can be traced back to the rapid downward acceleration of the carbonate signal, a feature that is not exhibited by the linearly decreasing isotopic excursions of the Early Triassic (21).

Fig. 2 combines this analysis with the analogous carbon isotopic signal in the Gartnerkofel-I core drilled in the Carnic Alps, Austria (3, 4). Cyclostratigraphic analysis of the Gartnerkofel core indicates that the sediment accumulation rate over the corresponding interval is approximately constant (22). When the accumulation rate is set to 22.5 cm/Kyr, approximately within a factor of 2 of the earlier estimate (22), reconstructions of Graphic for Gartnerkofel are qualitatively similar to that for Meishan. Fig. 2, which superposes both reconstructions in linear, log-linear, and log−log plots, confirms the inferences already drawn from the Meishan data. Moreover, the similarity of the Meishan and Gartnerkofel reconstructions validates our assumption of a constant accumulation rate at Meishan. We conclude that Graphic grows no slower than exponentially, and likely superexponentially.

Fig. 2.
  • Download figure
  • Open in new tab
  • Download powerpoint
Fig. 2.

Rescaled reconstructions of the mass Graphic of the marine inorganic carbon reservoir for both the Meishan (red) and Gartnerkofel (blue) data, as a function of rescaled time Graphic, where Graphic Kyr and time advances to the right. (A) Plots of M vs. Graphic show that both curves behave similarly with respect to a critical time Graphic. (B) Plots of Graphic on log-linear axes suggest that both curves grow superexponentially. (C) Plots of Graphic on log−log axes compare well to a straight line (dashed black) with slope −1, suggesting that both reconstructions grow like Graphic.

These observations impose constraints on interpretations of end-Permian environmental change. For example, CO2 released to the atmosphere from a single, massive Siberian coal−basalt eruption (10) would be mostly transferred to the oceans after about 102–103 y (23). The uptake rate would decrease with time as the oceans acidify, reducing their capacity to take up more CO2 (23). Graphic would then grow sublinearly, qualitatively different from what is shown in Figs. 1 and 2. Alternatively, such an eruption could be more gradual, limited by the rate at which vents form to release overpressured gas arising from contact metamorphism in intruded sills (11). The pressure released by each vent decreases overpressurization. Wherever the pressure is lowered, the rate of vent formation would decrease, and Graphic would again be sublinear. It is possible, however, that vents were sufficiently dispersed in space so that their formation times were essentially independent and randomly distributed over some (possibly small) interval of time; in this case, one expects a roughly constant rate of CO2 emission, and Graphic would grow linearly. Likewise, the release of methane from methane hydrates (1, 9) could be clustered in time, but there is no reason to expect total methane emissions to grow much faster than linearly, in part because any resulting warming—a potential positive feedback—would be only logarithmically sensitive to increased CH4 and CO2 levels (24). Each of these scenarios would produce geochemical signals that qualitatively differ from those predicted by exponential or superexponential growth (SI Text). The constraints provided by this reasoning derive only from the shape of Graphic, not the quantity of isotopically light carbon required for the event.

The Carbon Source and Its Remobilization

We seek a mechanism that can result in growth of Graphic that is exponential or faster. Because such an upheaval of the carbon cycle implies substantial changes within the microbial biosphere, we hypothesize that the perturbation arises from the emergence of a new regime of microbial metabolic activity. We show below how such a mechanism leads to the observed dynamics. Before doing so, we first identify two important ingredients of our hypothesis: a suitably large source of degradable organic carbon and the new metabolic pathway that would be favored for its consumption.

In terms of the modern carbon cycle (25), our reconstructions of Graphic require about 7,000–14,000 Gt of remineralizable organic carbon. In the Late Permian, a low-O2 marine environment (5, 12, 13) would have increased the concentration of organic matter in sediments. The high values of Graphic immediately before the perturbation suggest that organic carbon was sequestered in sediments at a rate at least 50% greater than usual (SI Text), which, in modern terms (25), corresponds to excess sequestration of at least 0.08 Gt C yr−1. Integrated over the first 175 Kyr of Fig. 1A, this corresponds to 14,000 Gt C. We suggest that a substantial fraction remained remineralizable and relatively labile compared with organic carbon in modern sediments, thereby overcoming the apparent limitations (2) posed by the relatively small size of modern pools of isotopically light organic carbon (26) (e.g., methane hydrates, fossil fuels, soil organic carbon, and peat).

The accumulation of sedimentary organic matter would have been especially sensitive to changes in the biosphere’s ability to metabolize the products of fermentation. Among these products, acetate provides a major growth substrate for methanogens. The conversion of acetate to methane by methanogenic archaea—acetoclastic methanogenesis (27)—begins by activating acetate to acetyl coenzyme A (acetyl-CoA). Carbon monoxide dehydrogenase (CODH) then catalyzes the cleavage of acetyl-CoA, after which, in common with the utilization of all methanogenic substrates, methyl-coenzyme M reductase (MCR) catalyzes the reduction of a methyl group to methane (27). The activation to acetyl-CoA within methanogens occurs via two different pathways in two distinct groups of organisms: Members of the family Methanosaetaceae use a single-step acetyl-CoA synthase (ACS) pathway, whereas some members of the genus Methanosarcina use a two-step acetate kinase (AckA)-phosphoacetyl transferase (Pta) pathway (27). The AckA/Pta pathway is more energy efficient, requiring only one ATP molecule per acetate molecule activated, whereas the ACS pathway requires two (28). Growth on acetate using the low-efficiency ACS pathway within Methanosaeta is thermodynamically possible because of unique, poorly understood innovations in their electron transport chain (29); this limitation may be responsible for their observed slow rate of growth (30).

Fournier and Gogarten (17) have recently shown that the high-efficiency pathway in Methanosarcina evolved via a single horizontal gene transfer event, probably from a clade of cellulolytic bacteria belonging to the class Clostridia, after the mid-Ordovician evolution of vascular land plants (450–500 Ma). This is the only methanogenic pathway shown to have evolved via gene transfer. It also appears to be a conspicuously recent event within the evolution of methanogenesis, as all other methanogenic pathways have a broader phylogenetic distribution implying much more ancient origins. Methanosaeta may be more widespread in modern low-acetate marine environments (31). However, the dominance of the high-efficiency AckA-Pta pathway at high acetate concentrations (32) combined with the greater growth potential of Methanosarcina suggests that conditions for the emergence of acetoclastic Methanosarcina—specifically, a low-O2 marine environment (5, 12, 13) and the accumulation of sedimentary organic matter—would have been favorable in the Late Permian. Moreover, reports of significantly reduced marine sulfate concentrations (33⇓⇓–36) suggest that competition from sulfate-reducing bacteria would have been diminished, thereby amplifying the importance of methanogenesis in Late Permian marine sediments.

Phylogenetic Analysis

The relevance of acetoclastic Methanosarcina to the end-Permian event depends crucially on the timing for the ancestor of this group. To obtain an estimate for this date, we reconstructed archaeal phylogenies from 50 representative genomes and constructed relaxed molecular clock chronograms using PhyloBayes 2.3 (SI Text). Fig. 3A illustrates our results. To estimate the time Graphic of the last common ancestor of known acetoclastic representatives of Methanosarcina, we generated chronograms using four independent ribosome-based datasets, separately containing 29 concatenated universally conserved ribosomal proteins, 12 concatenated archaeal-specific ribosomal proteins, 16S ribosomal RNA, and 23S ribosomal RNA. The phylogeny of these ribosomal components reflects the vertical cellular history of the Methanosarcinales, including Methanosarcina and its descendants, the recipient lineage of the ackA/pta transfer. We further assume that ribosomal sequences evolve in a relatively clock-like manner, providing more reliable dates than most other genes in the absence of internal calibration. Our four independent age estimates, shown by the gray bars in Fig. 3A, are consistent with each other. Combining them together yields the joint estimate Graphic depicted by the black bar in Fig. 3A, strikingly close to the end-Permian extinction (SI Text). The discrepancy with a previous estimate (37) derives from the earlier use of an autocorrelated clock model that is less reliable for the estimation of deep-time phylogenies than the approach used here (SI Text).

Fig. 3.
  • Download figure
  • Open in new tab
  • Download powerpoint
Fig. 3.

(A) Subtree of calibrated archaeal chronogram showing Methanosarcinales and related groups. Acetoclastic Methanosarcina (bold) groups with other members of Methanosarcinales, including the distantly related acetoclastic Methanosaetaceae (M. thermophila, M. concilii). Shaded bars indicate the estimated acetoclastic Methanosarcina ancestor age ranges (±1 SD) for each dataset. The combined estimate of Graphic Myr is indicated by the black bar. The tree was generated from the Universal rProtein dataset, with the age of acetoclastic Methanosarcina adjusted to match the combined estimate. (B) Members of the genus Methanosarcina shown to grow on acetate all descend from the ancestor of sequenced clade representatives containing the transferred ackA/pta genes (*), congruent with the age-estimated node in A. The relationships between known taxa are represented by their 16S phylogenetic tree.

Additional phylogenetic character analysis of 16S sequences from 33 species within the genus Methanosarcina lends increased precision to the placement of the gene transfer event within the chronogram of Fig. 3A. As shown in Fig. 3B, all Methanosarcina strains that grow readily on acetate diverge within the M. acetivorans/M. mazei/M. barkeri clade, whereas all strains shown not to grow on acetate diverge more deeply within the tree. This result supports a relatively recent horizontal transfer of ackA/pta within the Methanosarcina genus (SI Text), at a time consistent with the Late Permian. The combined results of Fig. 3 therefore support the hypothesis that the emergence of the acetoclastic pathway in Methanosarcina provided the microbial instigation of the end-Permian burst in the carbon cycle.

Methanogenic Expansion

Wherever sulfate was limiting—because of a widespread drawdown of sulfate levels (33⇓⇓–36), a localized depletion by sulfate reducers, or both—the introduction of the high-efficiency acetoclastic pathway would have diminished a thermodynamic barrier (38) to greater acetate production by fermenters. Not only would acetate be converted more quickly to methane, but also sedimentary organic matter would be fermented more rapidly to acetate. Methanosaeta would have played a supporting role, but a preexisting steady state excludes the possibility that Methanosaeta itself would have excited the perturbation.

The resulting methane burst would have been oxidized to CO2, either by anaerobic methanotrophs at the expense of any remaining sulfate or aerobically. O2 levels, which were likely already low (5, 12, 13), would have been depressed further. Given the assumptions of an effectively unlimited substrate and a preexisting steady state, the size of the acetoclastic methanogenic niche—i.e., the carrying capacity K—would therefore have increased, at a rate proportional to the rate at which nearby sulfate and O2 were depleted. Taking the depletion rate proportional to the methane flux, we then have Graphic, where Graphic is the total methane production and Graphic is a conversion constant. Integrating both rates yieldsEmbedded Imagewhere Graphic is the initial (unperturbed) carrying capacity. At the time scale of the geochemical signals (>103 y), the methanogenic population is always at carrying capacity. The methane production rate is thereforeEmbedded Imagewhere β is the individual metabolic rate. Eqs. 2 and 3 describe unstable growth: Increasing methane production (A) increases the carrying capacity (K), which in turn increases the methane production rate Graphic. Then if β is constant, Graphic grows exponentially.

However, several mechanisms may have acted to increase β. These include the aforementioned interactions with other microbial communities; warming due to higher CO2 and methane levels; adaptive radiation (39) as subtaxa evolved to more efficiently use acetate in particular environments; and greater access to any limiting mineral nutrients as the anoxic, methanogenic niche rose upwards. Each of these mechanisms implies a functional dependence on the total methane production A. We hypothesize a linear response:Embedded Imagewhere Graphic is the initial metabolic rate and Graphic is a constant. Inserting Eqs. 2 and 4 into Eq. 3, we obtainEmbedded Imagewhere Graphic, Graphic, and Graphic. For nonzero Graphic, the solution Graphic blows up at a time Graphic determined by initial conditions. Near Graphic, the dynamics are dominated by the nonlinearity. To leading order,Embedded Imagewhich is drawn as the dashed red curve in Fig. 1B and the dashed straight line in Fig. 2C (as Graphic, using the best-fitting scale factor). The good fit supports the nonlinear model (Eq. 5), but it raises an important question: As t approached Graphic—the time of peak extinction activity—how could the growth of the methanogenic community have been sustained?

Nickel Limitation and the Meishan Nickel Record

Methanogens require nickel (18). The active site of the enzyme MCR, used by all methanogens, is the nickel cofactor Graphic; moreover, the CODH enzyme complex used by acetoclastic methanogens also contains a nickel cofactor (40). Seawater concentrations of nickel have likely been beneath the limiting threshold for methanogens for roughly the last 2 billion years (19). Accordingly, we suggest that methanogenesis in Late Permian sediments was limited by nickel. If so, the methanogenic expansion would have required increased access to nickel.

Kaiho et al. (41) have reported a sharp increase in the concentration of nickel in Meishan sediments coincident with the carbon isotopic spike. Because their analysis extends only through the last Graphic of the Graphic carbon isotopic spike and does not consider the effects of lithologic changes, we have performed new measurements of nickel concentrations at Meishan, not only over the entire interval shown in Fig. 1 but also well above it, and have corrected our measurements for variable concentrations of carbonate (SI Text). Fig. 4 displays our results. Nickel concentrations before the carbon isotopic spike are typically at least twice as high as after, and are up to seven times greater just before the abrupt downturn. With such elevated concentrations, nickel would no longer limit methanogenic activity. All methanogens would have prospered, but the successful evolution and rapid expansion of acetoclastic Methanosarcina would have been especially favored in the substrate-rich end-Permian environment.

Fig. 4.
  • Download figure
  • Open in new tab
  • Download powerpoint
Fig. 4.

Nickel concentrations (red) in the Meishan sediments, compared with the isotopic composition Graphic of carbonate carbon (blue). (A) Approximately 9 m of sedimentary section. (B) Close-up of the changes, over a range of less than 1 m. The largest nickel concentration precedes the smallest value of Graphic. Nickel concentrations are reported in terms of a carbonate-free basis (SI Text).

The nickel likely originated from Siberia. Earth’s largest economic concentration of nickel is in the Noril’sk region, deposited during the emplacement of the Siberian traps (42). The Meishan nickel signal may therefore represent changes in ocean chemistry induced by the Siberian eruptions, thereby linking the growth of acetoclastic Methanosarcina to massive Siberian volcanism. The apparent insensitivity of nickel to redox processes (43⇓–45) supports this interpretation. However, elemental redistribution during diagenetic redox cycling could represent an alternative cause of nickel enrichment in the sediment (46); further analysis of redox-sensitive elements will help evaluate that possibility.

Conclusion

Our principal observations—a superexponential burst in the carbon cycle, the emergence of efficient acetoclastic methanogenesis, and a spike in the availability of nickel—appear straightforwardly related to several features of end-Permian environmental change: Siberian volcanism (7, 8), marine anoxia (5, 12, 13), and ocean acidification (14⇓–16). A single horizontal gene transfer (17) instigated biogeochemical change, massive volcanism acted as a catalyst, and the resulting expansion of acetoclastic Methanosarcina acted to perturb CO2 and O2 levels. The ensuing biogeochemical disruption would likely have been widespread. For example, anaerobic methane oxidation may have increased sulfide levels (47), possibly resulting in a toxic release of hydrogen sulfide to the atmosphere, causing extinctions on land (48). Although such implications remain speculative, our work makes clear the exquisite sensitivity of the Earth system to the evolution of microbial life.

Acknowledgments

We thank Sam Bowring for asking questions that inspired this work, Kevin Peterson for making suggestions that widened its scope, and Shuzhong Shen for leading a field trip to South China. We also thank F. Azam, T. Bosak, S. Burgess, T. Cronin, O. Devauchelle, L. Elkins-Tanton, D. Erwin, D. Fike, C. Follett, Y. Friedman, H. Hartman, K. Noll, J. Payne, A. Petroff, F. Rohwer, and E. Tsiperman for helpful discussions. This work was supported by the National Aeronautics and Space Administration Astrobiology Institute (NNA08CN84A and NNA13AA90A), the National Science Foundation (OCE-0930866, DEB-0936234, and DGE-1122374), the National Natural Science Foundation of China (41290260), and the National Basic Research Program of China (2011CB808905).

Footnotes

  • ↵1To whom correspondence should be addressed. E-mail: dhr{at}mit.edu.
  • Author contributions: D.H.R., G.P.F., K.L.F., E.J.A., E.A.B., and R.E.S. designed research; D.H.R., G.P.F., K.L.F., E.J.A., E.A.B., C.C., and R.E.S. performed research; D.H.R., G.P.F., K.L.F., E.J.A., E.A.B., C.C., and R.E.S. analyzed data; and D.H.R., G.P.F., and K.L.F. wrote the paper.

  • The authors declare no conflict of interest.

  • This article is a PNAS Direct Submission.

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1318106111/-/DCSupplemental.

Freely available online through the PNAS open access option.

References

  1. ↵
    1. Erwin DH
    (2006) Extinction: How Life on Earth Nearly Ended 250 Million Years Ago (Princeton University Press, Princeton).
  2. ↵
    1. Shen SZ,
    2. et al.
    (2011) Calibrating the end-Permian mass extinction. Science 334(6061):1367–1372.
    OpenUrlAbstract/FREE Full Text
  3. ↵
    1. Holser WT,
    2. et al.
    (1989) A unique geochemical record at the Permian/Triassic boundary. Nature 337:39–44.
    OpenUrlCrossRef
  4. ↵
    1. Magaritz M,
    2. Holser WT
    (1991) The Permian−Triassic of the Gartnerkofel-1 core (Carnic Alps, Austria): Carbon and oxygen isotope variation. Abh Geol Bundesanst 45:149–163.
    OpenUrl
  5. ↵
    1. Cao C,
    2. et al.
    (2009) Biogeochemical evidence for euxinic oceans and ecological disturbance presaging the end-Permian mass extinction event. Earth Planet Sci Lett 281(3-4):188–201.
    OpenUrlCrossRef
  6. ↵
    1. Korte C,
    2. Kozur HW
    (2010) Carbon-isotope stratigraphy across the Permian−Triassic boundary: A review. J Asian Earth Sci 39(4):215–235.
    OpenUrlCrossRef
  7. ↵
    1. Renne PR,
    2. Basu AR
    (1991) Rapid eruption of the Siberian Traps flood basalts at the Permo-Triassic boundary. Science 253(5016):176–179.
    OpenUrlAbstract/FREE Full Text
  8. ↵
    1. Reichow MK,
    2. et al.
    (2009) The timing and extent of the eruption of the Siberian Traps large igneous province: Implications for the end-Permian environmental crisis. Earth Planet Sci Lett 277(1-2):9–20.
    OpenUrlCrossRef
  9. ↵
    1. Berner RA
    (2002) Examination of hypotheses for the Permo-Triassic boundary extinction by carbon cycle modeling. Proc Natl Acad Sci USA 99(7):4172–4177.
    OpenUrlAbstract/FREE Full Text
  10. ↵
    1. Ogden DE,
    2. Sleep NH
    (2012) Explosive eruption of coal and basalt and the end-Permian mass extinction. Proc Natl Acad Sci USA 109(1):59–62.
    OpenUrlAbstract/FREE Full Text
  11. ↵
    1. Svensen H,
    2. et al.
    (2009) Siberian gas venting and the end-Permian environmental crisis. Earth Planet Sci Lett 277(3-4):490–500.
    OpenUrlCrossRef
  12. ↵
    1. Wignall PB,
    2. Twitchett RJ
    (1996) Oceanic anoxia and the end Permian mass extinction. Science 272(5265):1155–1158.
    OpenUrlAbstract
  13. ↵
    1. Isozaki Y
    (1997) Permo-Triassic boundary superanoxia and stratified superocean: Records from lost deep sea. Science 276(5310):235–238.
    OpenUrlAbstract/FREE Full Text
  14. ↵
    1. Knoll AH,
    2. Bambach RK,
    3. Canfield DE,
    4. Grotzinger JP
    (1996) Comparative Earth history and Late Permian mass extinction. Science 273(5274):452–457.
    OpenUrlAbstract/FREE Full Text
  15. ↵
    1. Knoll AH,
    2. Bambach RK,
    3. Payne JL,
    4. Pruss S,
    5. Fischer WW
    (2007) Paleophysiology and end-Permian mass extinction. Earth Planet Sci Lett 256(3-4):295–313.
    OpenUrlCrossRef
  16. ↵
    1. Payne JL,
    2. Clapham ME
    (2012) End-Permian mass extinction in the oceans: An ancient analog for the twenty-first century? Annu Rev Earth Planet Sci 40:89–111.
    OpenUrlCrossRef
  17. ↵
    1. Fournier GP,
    2. Gogarten JP
    (2008) Evolution of acetoclastic methanogenesis in Methanosarcina via horizontal gene transfer from cellulolytic Clostridia. J Bacteriol 190(3):1124–1127.
    OpenUrlAbstract/FREE Full Text
  18. ↵
    1. Diekert G,
    2. Konheiser U,
    3. Piechulla K,
    4. Thauer RK
    (1981) Nickel requirement and factor F430 content of methanogenic bacteria. J Bacteriol 148(2):459–464.
    OpenUrlAbstract/FREE Full Text
  19. ↵
    1. Konhauser KO,
    2. et al.
    (2009) Oceanic nickel depletion and a methanogen famine before the Great Oxidation Event. Nature 458(7239):750–753.
    OpenUrlCrossRefPubMed
  20. ↵
    1. Rothman DH,
    2. Hayes JM,
    3. Summons RE
    (2003) Dynamics of the Neoproterozoic carbon cycle. Proc Natl Acad Sci USA 100(14):8124–8129.
    OpenUrlAbstract/FREE Full Text
  21. ↵
    1. Payne JL,
    2. et al.
    (2004) Large perturbations of the carbon cycle during recovery from the end-Permian extinction. Science 305(5683):506–509.
    OpenUrlAbstract/FREE Full Text
  22. ↵
    1. Rampino MR,
    2. Prokoph A,
    3. Adler A
    (2000) Tempo of the end-Permian event: High-resolution cyclostratigraphy at the Permian−Triassic boundary. Geology 28(7):643–646.
    OpenUrlAbstract/FREE Full Text
  23. ↵
    1. Archer D
    (2009) The Long Thaw (Princeton University Press, Princeton).
  24. ↵
    1. Pierrehumbert RT
    (2010) Principles of Planetary Climate (Cambridge University Press, Cambridge).
  25. ↵
    1. Hedges JI,
    2. Keil RG
    (1995) Sedimentary organic matter preservation: An assessment and speculative synthesis. Mar Chem 49(2-3):81–115.
    OpenUrlCrossRef
  26. ↵
    1. Milkov A
    (2004) Global estimates of hydrate-bound gas in marine sediments: How much is really out there? Earth Sci Rev 66(3-4):183–197.
    OpenUrlCrossRef
  27. ↵
    1. Ferry JG
    (1992) Methane from acetate. J Bacteriol 174(17):5489–5495.
    OpenUrlAbstract/FREE Full Text
  28. ↵
    1. Berger S,
    2. Welte C,
    3. Deppenmeier U
    (2012) Acetate activation in Methanosaeta thermophila: Characterization of the key enzymes pyrophosphatase and acetyl-CoA synthetase. Archaea 2012:315153.
    OpenUrlPubMed
  29. ↵
    1. Welte C,
    2. Deppenmeier U
    (2011) Membrane-bound electron transport in Methanosaeta thermophila. J Bacteriol 193(11):2868–2870.
    OpenUrlAbstract/FREE Full Text
  30. ↵
    1. Barber RD,
    2. et al.
    (2011) Complete genome sequence of Methanosaeta concilii, a specialist in aceticlastic methanogenesis. J Bacteriol 193(14):3668–3669.
    OpenUrlAbstract/FREE Full Text
  31. ↵
    1. Mori K,
    2. Iino T,
    3. Suzuki KI,
    4. Yamaguchi K,
    5. Kamagata Y
    (2012) Aceticlastic and NaCl-requiring methanogen “Methanosaeta pelagica” sp. nov., isolated from marine tidal flat sediment. Appl Environ Microbiol 78(9):3416–3423.
    OpenUrlAbstract/FREE Full Text
  32. ↵
    1. Min H,
    2. Zinder SH
    (1989) Kinetics of acetate utilization by two thermophilic acetotrophic methanogens: Methanosarcina sp. strain cals-1 and Methanothrix sp. strain cals-1. Appl Environ Microbiol 55(2):488–491.
    OpenUrlAbstract/FREE Full Text
  33. ↵
    1. Horita J,
    2. Zimmermann H,
    3. Holland HD
    (2002) Chemical evolution of seawater during the Phanerozoic: Implications from the record of marine evaporites. Geochim Cosmochim Acta 66(21):3733–3756.
    OpenUrlCrossRef
  34. ↵
    1. Newton RJ,
    2. Pevitt EL,
    3. Wignall PB,
    4. Bottrell SH
    (2004) Large shifts in the isotopic composition of seawater sulphate across the Permo-Triassic boundary in northern Italy. Earth Planet Sci Lett 218(3-4):331–345.
    OpenUrlCrossRef
  35. ↵
    1. Bottrell SH,
    2. Newton RJ
    (2006) Reconstruction of changes in global sulfur cycling from marine sulfate isotopes. Earth Sci Rev 75(1-4):59–83.
    OpenUrlCrossRef
  36. ↵
    1. Luo G,
    2. et al.
    (2010) Isotopic evidence for an anomalously low oceanic sulfate concentration following end-Permian mass extinction. Earth Planet Sci Lett 300(1-2):101–111.
    OpenUrlCrossRef
  37. ↵
    1. Blank CE
    (2009) Not so old Archaea - the antiquity of biogeochemical processes in the archaeal domain of life. Geobiology 7(5):495–514.
    OpenUrlCrossRefPubMed
  38. ↵
    1. Fenchel T,
    2. Finlay BJ
    (1995) Ecology and Evolution in Anoxic Worlds (Oxford University Press, New York).
  39. ↵
    1. Schluter D
    (2000) The Ecology of Adaptive Radiation (Oxford University Press, New York).
  40. ↵
    1. Ragsdale SW
    (2009) Nickel-based enzyme systems. J Biol Chem 284(28):18571–18575.
    OpenUrlAbstract/FREE Full Text
  41. ↵
    1. Kaiho K,
    2. et al.
    (2001) End-Permian catastrophe by a bolide impact: Evidence of a gigantic release of sulfur from the mantle. Geology 29(9):815–818.
    OpenUrlAbstract/FREE Full Text
  42. ↵
    1. Naldrett AJ
    (2004) Magmatic Sulfide Deposits: Geology, Geochemistry and Exploration (Springer, New York).
  43. ↵
    1. Jacobs L,
    2. Emerson S,
    3. Huested SS
    (1987) Trace metal geochemistry in the Cariaco Trench. Deep-Sea Res Part A 34(5-6):965–981.
    OpenUrlCrossRef
  44. ↵
    1. Haraldsson C,
    2. Westerlund S
    (1988) Trace metals in the water columns of the Black Sea and Framvaren Fjord. Mar Chem 23(3-4):417–424.
    OpenUrlCrossRef
  45. ↵
    1. Lewis BL,
    2. Landing WM
    (1992) The investigation of dissolved and suspended-particulate trace metal fractionation in the Black Sea. Mar Chem 40:105–141.
    OpenUrlCrossRef
  46. ↵
    1. Froelich PN,
    2. et al.
    (1979) Early oxidation of organic-matter in pelagic sediments of the eastern equatorial Atlantic: Suboxic diagenesis. Geochim Cosmochim Acta 43(7):1075–1090.
    OpenUrlCrossRef
  47. ↵
    1. Kaiho K,
    2. et al.
    (2012) Changes in depth-transect redox conditions spanning the end-Permian mass extinction and their impact on the marine extinction: Evidence from biomarkers and sulfur isotopes. Global Planet Change 94-95:20–32.
    OpenUrl
  48. ↵
    1. Kump LR,
    2. Pavlov A,
    3. Arthur MA
    (2005) Massive release of hydrogen sulfide to the surface ocean and atmosphere during intervals of oceanic anoxia. Geology 33(5):397–400.
    OpenUrlAbstract/FREE Full Text
PreviousNext
Back to top
Article Alerts
Email Article

Thank you for your interest in spreading the word on PNAS.

NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. We do not capture any email address.

Enter multiple addresses on separate lines or separate them with commas.
Methanogenic burst in the end-Permian carbon cycle
(Your Name) has sent you a message from PNAS
(Your Name) thought you would like to see the PNAS web site.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Citation Tools
Methanogenic burst in the end-Permian carbon cycle
Daniel H. Rothman, Gregory P. Fournier, Katherine L. French, Eric J. Alm, Edward A. Boyle, Changqun Cao, Roger E. Summons
Proceedings of the National Academy of Sciences Apr 2014, 111 (15) 5462-5467; DOI: 10.1073/pnas.1318106111

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Request Permissions
Share
Methanogenic burst in the end-Permian carbon cycle
Daniel H. Rothman, Gregory P. Fournier, Katherine L. French, Eric J. Alm, Edward A. Boyle, Changqun Cao, Roger E. Summons
Proceedings of the National Academy of Sciences Apr 2014, 111 (15) 5462-5467; DOI: 10.1073/pnas.1318106111
Digg logo Reddit logo Twitter logo Facebook logo Google logo Mendeley logo
  • Tweet Widget
  • Facebook Like
  • Mendeley logo Mendeley
Proceedings of the National Academy of Sciences: 111 (15)
Table of Contents

Submit

Sign up for Article Alerts

Article Classifications

  • Physical Sciences
  • Earth, Atmospheric, and Planetary Sciences
  • Biological Sciences
  • Evolution

Jump to section

  • Article
    • Abstract
    • Growth of the Marine Carbon Reservoir
    • The Carbon Source and Its Remobilization
    • Phylogenetic Analysis
    • Methanogenic Expansion
    • Nickel Limitation and the Meishan Nickel Record
    • Conclusion
    • Acknowledgments
    • Footnotes
    • References
  • Figures & SI
  • Info & Metrics
  • PDF

You May Also be Interested in

Surgeons hands during surgery
Inner Workings: Advances in infectious disease treatment promise to expand the pool of donor organs
Despite myriad challenges, clinicians see room for progress.
Image credit: Shutterstock/David Tadevosian.
Setting sun over a sun-baked dirt landscape
Core Concept: Popular integrated assessment climate policy models have key caveats
Better explicating the strengths and shortcomings of these models will help refine projections and improve transparency in the years ahead.
Image credit: Witsawat.S.
Double helix
Journal Club: Noncoding DNA shown to underlie function, cause limb malformations
Using CRISPR, researchers showed that a region some used to label “junk DNA” has a major role in a rare genetic disorder.
Image credit: Nathan Devery.
Steamboat Geyser eruption.
Eruption of Steamboat Geyser
Mara Reed and Michael Manga explore why Yellowstone's Steamboat Geyser resumed erupting in 2018.
Listen
Past PodcastsSubscribe
Multi-color molecular model
Enzymatic breakdown of PET plastic
A study demonstrates how two enzymes—MHETase and PETase—work synergistically to depolymerize the plastic pollutant PET.
Image credit: Aaron McGeehan (artist).

Similar Articles

Site Logo
Powered by HighWire
  • Submit Manuscript
  • Twitter
  • Facebook
  • RSS Feeds
  • Email Alerts

Articles

  • Current Issue
  • Special Feature Articles – Most Recent
  • List of Issues

PNAS Portals

  • Anthropology
  • Chemistry
  • Classics
  • Front Matter
  • Physics
  • Sustainability Science
  • Teaching Resources

Information

  • Authors
  • Editorial Board
  • Reviewers
  • Librarians
  • Press
  • Site Map
  • PNAS Updates

Feedback    Privacy/Legal

Copyright © 2021 National Academy of Sciences. Online ISSN 1091-6490