Ecology

1.
Hugelius, G. et al. Estimated stocks of circumpolar permafrost carbon with quantified uncertainty ranges and identified data gaps. Biogeosciences 11, 6573–6593 (2014).
Google Scholar 
2.
Harden, J. W. et al. Field information links permafrost carbon to physical vulnerabilities of thawing. Geophys. Res. Lett. 39, L15704 (2012).
Google Scholar 

3.
Schädel, C. et al. Circumpolar assessment of permafrost C quality and its vulnerability over time using long-term incubation data. Glob. Change Biol. 20, 641–652 (2014).
Google Scholar 

4.
Schuur, E. A. G. et al. Climate change and the permafrost carbon feedback. Nature 520, 171–179 (2015).
Google Scholar 

5.
Koven, C. D. et al. A simplified, data-constrained approach to estimate the permafrost carbon–climate feedback. Philos. Trans. R. Soc. A 373, 20140423 (2015).
Google Scholar 

6.
Nannipieri, P. et al. Microbial diversity and soil functions. Eur. J. Soil Sci. 68, 12–26 (2003).
Google Scholar 

7.
Harding, T., Jungblut, A. D., Lovejoy, C. & Vincent, W. F. Microbes in High Arctic snow and implications for the cold biosphere. Appl. Environ. Microbiol. 77, 3234–3243 (2011).
Google Scholar 

8.
Thompson, L. R. et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 457–463 (2017).
Google Scholar 

9.
Bier, R. L. et al. Linking microbial community structure and microbial processes: an empirical and conceptual overview. FEMS Microbiol. Ecol. 91, fiv113 (2015).
Google Scholar 

10.
Nunan, N., Leloup, J., Ruamps, L. S., Pouteau, V. & Chenu, C. Effects of habitat constraints on soil microbial community function. Sci. Rep. 7, 4280 (2017).
Google Scholar 

11.
Graham, E. B. et al. Microbes as engines of ecosystem function: when does community structure enhance predictions of ecosystem processes? Front. Microbiol. 7, 214 (2016).
Google Scholar 

12.
Schimel, J. in Arctic and Alpine Biodiversity: Patterns, Causes and Ecosystem Consequences (eds Chapin, F. S. & Körner, C.) 239–254 (Springer, 1995).

13.
Schimel, J. & Schaeffer, S. M. Microbial control over carbon cycling in soil. Front. Microbiol. 3, 348 (2012).
Google Scholar 

14.
Bottos, E. M. et al. Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities. FEMS Microbiol. Ecol. 94, fiy110 (2018).
Google Scholar 

15.
Jansson, J. K. & Tas, N. The microbial ecology of permafrost. Nat. Rev. Microbiol. 12, 414–425 (2014).
Google Scholar 

16.
Mackelprang, R. et al. Microbial survival strategies in ancient permafrost: insights from metagenomics. ISME J. 11, 2305–2318 (2017).
Google Scholar 

17.
Philippot, L. et al. Loss in microbial diversity affects nitrogen cycling in soil. ISME J. 7, 1609–1619 (2013).
Google Scholar 

18.
Monteux, S. et al. Long-term in situ permafrost thaw effects on bacterial communities and potential aerobic respiration. ISME J. 12, 2129–2141 (2018).
Google Scholar 

19.
Johnston, E. R. et al. Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths. Proc. Natl Acad. Sci. USA 116, 15096–15105 (2019).
Google Scholar 

20.
Fierer, N. et al. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc. Natl Acad. Sci. USA 109, 21390–21395 (2012).
Google Scholar 

21.
Sanders, T., Fiencke, C., Hüpeden, J., Pfeiffer, E. M. & Spieck, E. Cold adapted Nitrosospira sp.: a potential crucial contributor of ammonia oxidation in cryosols of permafrost-affected landscapes in Northeast Siberia. Microorganisms 7, 699 (2019).
Google Scholar 

22.
Hill, K. A. et al. Processing of atmospheric nitrogen by clouds above a forest environment. J. Geophys. Res. Atmos. 112, D11301 (2007).
Google Scholar 

23.
Knoblauch, C., Beer, C., Sosnin, A., Wagner, D. & Pfeiffer, E.-M. Predicting long-term carbon mineralization and trace gas production from thawing permafrost of Northeast Siberia. Glob. Change Biol. 19, 1160–1172 (2013).
Google Scholar 

24.
Wild, B. et al. Plant-derived compounds stimulate the decomposition of organic matter in Arctic permafrost soils. Sci. Rep. 6, 25607 (2016).
Google Scholar 

25.
Strauss, J. et al. Deep Yedoma permafrost: a synthesis of depositional characteristics and carbon vulnerability. Earth-Sci. Rev. 172, 75–86 (2017).
Google Scholar 

26.
Wertz, S. et al. Maintenance of soil functioning following erosion of microbial diversity. Environ. Microbiol. 8, 2162–2169 (2006).
Google Scholar 

27.
Fontaine, S. et al. Stability of organic carbon in deep soil layers controlled by fresh carbon supply. Nature 450, 277–280 (2007).
Google Scholar 

28.
Rillig, M. C. et al. Interchange of entire communities: microbial community coalescence. Trends Ecol. Evol. 30, 470–476 (2015).
Google Scholar 

29.
Mackelprang, R. et al. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480, 368–371 (2011).
Google Scholar 

30.
Keuper, F. et al. A frozen feast: thawing permafrost increases plant-available nitrogen in subarctic peatlands. Glob. Change Biol. 18, 1998–2007 (2012).
Google Scholar 

31.
Elberling, B., Christiansen, H. H. & Hansen, B. U. High nitrous oxide production from thawing permafrost. Nat. Geosci. 3, 332–335 (2010).
Google Scholar 

32.
Daims, H. et al. Complete nitrification by Nitrospira bacteria. Nature 528, 504–509 (2015).
Google Scholar 

33.
Gittel, A. et al. Distinct microbial communities associated with buried soils in the Siberian tundra. ISME J. 8, 841–853 (2014).
Google Scholar 

34.
Weiss, N. et al. Thermokarst dynamics and soil organic matter characteristics controlling initial carbon release from permafrost soils in the Siberian Yedoma region. Sediment. Geol. 340, 38–48 (2016).
Google Scholar 

35.
Inglese, C. N. et al. Examination of soil microbial communities after permafrost thaw subsequent to an active layer detachment in the High Arctic. Arct. Antarct. Alp. Res. 49, 455–472 (2017).
Google Scholar 

36.
Wild, B. et al. Microbial nitrogen dynamics in organic and mineral soil horizons along a latitudinal transect in Western Siberia. Glob. Biogeochem. Cycles 29, 567–582 (2015).
Google Scholar 

37.
Voigt, C. et al. Increased nitrous oxide emissions from Arctic peatlands after permafrost thaw. Proc. Natl Acad. Sci. USA 114, 6238–6243 (2017).
Google Scholar 

38.
Wrage-Mönnig, N. et al. The role of nitrifier denitrification in the production of nitrous oxide revisited. Soil Biol. Biochem. 123, A3–A16 (2018).
Google Scholar 

39.
Siljanen, H. M. P. et al. Archaeal nitrification is a key driver of high nitrous oxide emissions from Arctic peatlands. Soil Biol. Biochem. 137, 107539 (2019).
Google Scholar 

40.
Voigt, C. et al. Nitrous oxide emissions from permafrost-affected soils. Nat. Rev. Earth Environ. 1, 420–434 (2020).
Google Scholar 

41.
Keuper, F. et al. Experimentally increased nutrient availability at the permafrost thaw front selectively enhances biomass production of deep-rooting subarctic peatland species. Glob. Change Biol. 23, 4257–4266 (2017).
Google Scholar 

42.
Liu, X.-Y. et al. Nitrate is an important nitrogen source for Arctic tundra plants. Proc. Natl Acad. Sci. USA 115, 3398–3403 (2018).
Google Scholar 

43.
Myrstener, M. et al. Persistent nitrogen limitation of stream biofilm communities along climate gradients in the Arctic. Glob. Change Biol. 24, 3680–3691 (2018).
Google Scholar 

44.
Knoblauch, C., Beer, C., Liebner, S., Grigoriev, M. N. & Pfeiffer, E.-M. Methane production as key to the greenhouse gas budget of thawing permafrost. Nat. Clim. Change 8, 309–312 (2018).
Google Scholar 

45.
Holm, S. et al. Methanogenic response to long-term permafrost thaw is determined by paleoenvironment. FEMS Microbiol. Ecol. 96, fiaa021 (2020).
Google Scholar 

46.
Douglas, T. A. et al. Biogeochemical and geocryological characteristics of wedge and thermokarst-cave ice in the CRREL permafrost tunnel, Alaska. Permafr. Periglac. Process. 22, 120–128 (2011).
Google Scholar 

47.
Long, A. & Péwé, T. L. Radiocarbon dating by high-sensitivity liquid scintillation counting of wood from the Fox permafrost tunnel near Fairbanks, Alaska. Permafr. Periglac. Process. 7, 281–285 (1996).
Google Scholar 

48.
Hamilton, T. D., Craig, J. L. & Sellmann, P. V. The Fox permafrost tunnel: a late Quaternary geologic record in central Alaska. GSA Bull. 100, 948–969 (1988).
Google Scholar 

49.
Shur, Y., French, H. M., Bray, M. T. & Anderson, D. A. Syngenetic permafrost growth: cryostratigraphic observations from the CRREL tunnel near Fairbanks, Alaska. Permafr. Periglac. Process. 15, 339–347 (2004).
Google Scholar 

50.
Howard, M. M., Bell, T. H. & Kao-Kniffin, J. Soil microbiome transfer method affects microbiome composition, including dominant microorganisms, in a novel environment. FEMS Microbiol. Lett. 364, fnx092 (2017).
Google Scholar 

51.
Patra, A. K. et al. Effects of grazing on microbial functional groups involved in soil N dynamics. Ecol. Monogr. 75, 65–80 (2005).
Google Scholar 

52.
Fontaine, S. et al. Fungi mediate long term sequestration of carbon and nitrogen in soil through their priming effect. Soil Biol. Biochem. 43, 86–96 (2011).
Google Scholar 

53.
Elberling, B. et al. Long-term CO2 production following permafrost thaw. Nat. Clim. Change 3, 890–894 (2013).
Google Scholar 

54.
Walz, J., Knoblauch, C., Böhme, L. & Pfeiffer, E.-M. Regulation of soil organic matter decomposition in permafrost-affected Siberian tundra soils—impact of oxygen availability, freezing and thawing, temperature, and labile organic matter. Soil Biol. Biochem. 110, 34–43 (2017).
Google Scholar 

55.
Weedon, J. T. et al. Temperature sensitivity of peatland C and N cycling: does substrate supply play a role? Soil Biol. Biochem. 61, 109–120 (2013).
Google Scholar 

56.
Ping, C. L. Soil temperature profiles of two Alaskan soils. Soil Sci. Soc. Am. J. 51, 1010–1018 (1987).
Google Scholar 

57.
D’Amico, S. et al. Psychrophilic microorganisms: challenges for life. EMBO Rep. 7, 385–389 (2006).
Google Scholar 

58.
Vance, E. D., Brookes, P. C. & Jenkinson, D. S. An extraction method for measuring soil microbial biomass C. Soil Biol. Biochem. 19, 703–707 (1987).
Google Scholar 

59.
Wu, J., Joergensen, R. G., Pommerening, B., Chaussod, R. & Brookes, P. C. Measurement of soil microbial biomass C by fumigation–extraction—an automated procedure. Soil Biol. Biochem. 22, 1167–1169 (1990).
Google Scholar 

60.
Rotthauwe, J. H., Witzel, K. P. & Liesack, W. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ. Microbiol. 63, 4704–4712 (1997).
Google Scholar 

61.
Tourna, M., Freitag, T. E., Nicol, G. W. & Prosser, J. I. Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environ. Microbiol. 10, 1357–1364 (2008).
Google Scholar 

62.
Fowler, S. J., Palomo, A., Dechesne, A., Mines, P. D. & Smets, B. F. Comammox Nitrospira are abundant ammonia oxidizers in diverse groundwater-fed rapid sand filter communities. Environ. Microbiol. 20, 1002–1015 (2018).
Google Scholar 

63.
Pjevac, P. et al. AmoA-targeted polymerase chain reaction primers for the specific detection and quantification of comammox Nitrospira in the environment. Front. Microbiol. 8, 1508 (2017).
Google Scholar 

64.
Muyzer, G., Waal, E. Cde & Uitterlinden, A. G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59, 695–700 (1993).
Google Scholar 

65.
Bartram, A. K., Lynch, M. D. J., Stearns, J. C., Moreno-Hagelsieb, G. & Neufeld, J. D. Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end Illumina reads. Appl. Environ. Microbiol. 77, 3846–3852 (2011).
Google Scholar 

66.
Smith, D. P. & Peay, K. G. Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing. PLoS ONE 9, e90234 (2014).
Google Scholar 

67.
Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahé, F. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).
Google Scholar 

68.
Morgan, M. et al. ShortRead: a Bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics 25, 2607–2608 (2009).
Google Scholar 

69.
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200 (2011).
Google Scholar 

70.
Haas, B. J. et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 21, 494–504 (2011).
Google Scholar 

71.
Kõljalg, U. et al. Towards a unified paradigm for sequence-based identification of fungi. Mol. Ecol. 22, 5271–5277 (2013).
Google Scholar 

72.
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).
Google Scholar 

73.
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
Google Scholar 

74.
Caporaso, J. G. et al. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26, 266–267 (2010).
Google Scholar 

75.
McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 6, 610–618 (2012).
Google Scholar 

76.
Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267 (2007).
Google Scholar 

77.
Lagkouvardos, I., Fischer, S., Kumar, N. & Clavel, T. Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons. PeerJ 5, e2836 (2017).
Google Scholar 

78.
White, D. C., Davis, W. M., Nickels, J. S., King, J. D. & Bobbie, R. J. Determination of the sedimentary microbial biomass by extractible lipid phosphate. Oecologia 40, 51–62 (1979).
Google Scholar 

79.
Olsson, P. A., Bååth, E., Jakobsen, I. & Söderström, B. The use of phospholipid and neutral lipid fatty acids to estimate biomass of arbuscular mycorrhizal fungi in soil. Mycol. Res. 99, 623–629 (1995).
Google Scholar 

80.
Ruess, L. & Chamberlain, P. M. The fat that matters: soil food web analysis using fatty acids and their carbon stable isotope signature. Soil Biol. Biochem. 42, 1898–1910 (2010).
Google Scholar 

81.
Zelles, L. Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review. Biol. Fertil. Soils 29, 111–129 (1999).
Google Scholar 

82.
Frostegård, A. & Bååth, E. The use of phospholipid fatty acid analysis to estimate bacterial and fungal biomass in soil. Biol. Fertil. Soils 22, 59–65 (1996).
Google Scholar 

83.
Lenth, R. Least-squares means: the R package lsmeans. J. Stat. Softw. 69, 1–33 (2016).
Google Scholar 

84.
Wang, Y., Naumann, U., Wright, S. T. & Warton, D. I. mvabund—an R package for model-based analysis of multivariate abundance data. Methods Ecol. Evol. 3, 471–474 (2012).
Google Scholar 

85.
Warton, D. I., Wright, S. T. & Wang, Y. Distance-based multivariate analyses confound location and dispersion effects. Methods Ecol. Evol. 3, 89–101 (2012).
Google Scholar 

86.
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Google Scholar 

87.
McMurdie, P. J. & Holmes, S. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol. 10, e1003531 (2014).
Google Scholar 

88.
Pinto, A. J. et al. Metagenomic evidence for the presence of comammox Nitrospira-like bacteria in a drinking water system. mSphere 1, e00054-15 (2016).
Google Scholar 

89.
Kozlowski, J. A., Kits, K. D. & Stein, L. Y. Comparison of nitrogen oxide metabolism among diverse ammonia-oxidizing bacteria. Front. Microbiol. 7, 1090 (2016).
Google Scholar 

90.
Kits, K. D. et al. Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle. Nature 549, 269–272 (2017).
Google Scholar 

91.
Kuhn, M. caret: Classification and Regression Training v.6.0-86 (2020); https://CRAN.R-project.org/package=caret

92.
Breiman, L. Random forests. Mach. Learn. 45, 5–32 (2001).
Google Scholar 

93.
Hastie, T., Tibshirani, R. & Friedman, J. The Elements of Statistical Learning: Data Mining, Inference, and Prediction 2nd edn (Springer, 2009).

94.
Genuer, R., Poggi, J.-M. & Tuleau-Malot, C. VSURF: an R package for variable selection using random forests. R J. 7, 19–33 (2015).
Google Scholar 

95.
R Core Team. R: a Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2019). More

1.
Boyd ES, Amenabar MJ, Poudel S, Templeton AS. Bioenergetic constraints on the origin of autotrophic metabolism. Philos Trans R Soc A. 2020;378:1471–2962.
Article  CAS  Google Scholar 
2.
Boyd ES, Schut GJ, Adams MWW, Peters JW. Hydrogen metabolism and the evolution of biological respiration. Microbe. 2014;9:361–7.
Google Scholar 

3.
Hoehler TM. Biogeochemistry of dihydrogen (H2). In: Sigel H, and Sigel R (eds.). Metal ions in biological systems. Vol 43. (Taylor & Francis Group, Boca Raton, FL, 2005) pp 9-48.

4.
Weiss MC, Sousa FL, Mrnjavac N, Neukirchen S, Roettger M, Nelson-Sathi S, et al. The physiology and habitat of the last universal common ancestor. Nat Microbiol. 2016;1:1–8.
Google Scholar 

5.
McCollom TM, Klein F, Robbins M, Moskowitz B, Berquó TS, Jöns N, et al. Temperature trends for reaction rates, hydrogen generation, and partitioning of iron during experimental serpentinization of olivine. Geochim Cosmochim Acta. 2016;181:175–200.
CAS  Article  Google Scholar 

6.
Schulte M, Blake D, Hoehler T, McCollom T. Serpentinization and its implications for life on the early Earth and Mars. Astrobiology. 2006;6:364–76.
CAS  PubMed  Article  Google Scholar 

7.
Russell M, Hall A, Martin W. Serpentinization as a source of energy at the origin of life. Geobiology. 2010;8:355–71.
CAS  PubMed  Article  Google Scholar 

8.
Seewald JS, Zolotov MY, McCollom T. Experimental investigation of single carbon compounds under hydrothermal conditions. Geochim Cosmochim Acta. 2006;70:446–60.
CAS  Article  Google Scholar 

9.
McCollom TM, Seewald JS. Abiotic synthesis of organic compounds in deep-sea hydrothermal environments. Chem Rev. 2007;107:382–401.
CAS  PubMed  Article  Google Scholar 

10.
Twing KI, Brazelton WJ, Kubo MDY, Hyer AJ, Cardace D, Hoehler TM, et al. Serpentinization-influenced groundwater harbors extremely low diversity microbial communities adapted to high pH. Front Microbiol. 2017;8:308.
PubMed  PubMed Central  Article  Google Scholar 

11.
Brazelton WJ, Nelson B, Schrenk MO. Metagenomic evidence for H2 oxidation and H2 production by serpentinite-hosted subsurface microbial communities. Front Microbiol. 2012;2:268.
PubMed  PubMed Central  Article  Google Scholar 

12.
Morrill PL, Brazelton WJ, Kohl L, Rietze A, Miles SM, Kavanagh H, et al. Investigations of potential microbial methanogenic and carbon monoxide utilization pathways in ultra-basic reducing springs associated with present-day continental serpentinization: the Tablelands, NL, CAN. Front Microbiol. 2014;5:613.
PubMed  PubMed Central  Article  Google Scholar 

13.
Crespo-Medina M, Twing KI, Sánchez-Murillo R, Brazelton WJ, McCollom TM, Schrenk MO. Methane dynamics in a tropical serpentinizing environment: the Santa Elena Ophiolite, Costa Rica. Front Microbiol. 2017;8:916.
PubMed  PubMed Central  Article  Google Scholar 

14.
Woycheese KM, Meyer-Dombard DR, Cardace D, Argayosa AM, Arcilla CA. Out of the dark: transitional subsurface-to-surface microbial diversity in a terrestrial serpentinizing seep (Manleluag, Pangasinan, the Philippines). Front Microbiol. 2015;6:44.
PubMed  PubMed Central  Article  Google Scholar 

15.
Neubeck A, Sun L, Müller B, Ivarsson M, Hosgörmez H, Özcan D, et al. Microbial community structure in a serpentine-hosted abiotic gas seepage at the Chimaera Ophiolite, Turkey. Appl Environ Microbiol. 2017;83:e03430–16.
PubMed  PubMed Central  Article  Google Scholar 

16.
Lang SQ, Früh-Green G, Bernasconi SM, Brazelton WJ, Schrenk MO, McGonigle JM. Deeply-sourced formate fuels sulfate reducers but not methanogens at Lost City hydrothermal field. Sci Rep. 2018;8:1–10.
Article  CAS  Google Scholar 

17.
Brazelton WJ, Morrill PL, Szponar N, Schrenk MO. Bacterial communities associated with subsurface geochemical processes in continental serpentinite springs. Appl Environ Microbiol. 2013;79:3906–16.
CAS  PubMed  PubMed Central  Article  Google Scholar 

18.
Fones EM, Colman DR, Kraus EA, Nothaft DB, Poudel S, Rempfert KR, et al. Physiological adaptations to serpentinization in the Samail Ophiolite, Oman. ISME J. 2019;13:1750–62.
CAS  PubMed  PubMed Central  Article  Google Scholar 

19.
Rempfert KR, Miller HM, Bompard N, Nothaft D, Matter JM, Kelemen P, et al. Geological and geochemical controls on subsurface microbial life in the Samail Ophiolite, Oman. Front Microbiol. 2017;8:56.
PubMed  PubMed Central  Article  Google Scholar 

20.
Kelemen PB, Matter J, Streit EE, Rudge JF, Curry WB, Blusztajn J. Rates and mechanisms of mineral carbonation in peridotite: natural processes and recipes for enhanced, in situ CO2 capture and storage. Annu Rev Earth Planet Sci. 2011;39:545–76.
CAS  Article  Google Scholar 

21.
Canovas PA, Hoehler T, Shock EL. Geochemical bioenergetics during low-temperature serpentinization: an example from the Samail ophiolite, Sultanate of Oman. J Geophys Res. 2017;122:1821–47.
Article  Google Scholar 

22.
Suzuki S, Ishii S, Wu A, Cheung A, Tenney A, Wanger G, et al. Microbial diversity in The Cedars, an ultrabasic, ultrareducing, and low salinity serpentinizing ecosystem. Proc Natl Acad Sci USA. 2013;110:15336–41.
CAS  PubMed  Article  Google Scholar 

23.
Brazelton WJ, Thornton CN, Hyer A, Twing KI, Longino AA, Lang SQ, et al. Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy. Peer J. 2017;5:e2945.
PubMed  Article  CAS  Google Scholar 

24.
Morrill PL, Kuenen JG, Johnson OJ, Suzuki S, Rietze A, Sessions AL, et al. Geochemistry and geobiology of a present-day serpentinization site in California: The Cedars. Geochim Cosmochim Acta. 2013;109:222–40.
CAS  Article  Google Scholar 

25.
Miller HM, Matter JM, Kelemen P, Ellison ET, Conrad ME, Fierer N, et al. Modern water/rock reactions in Oman hyperalkaline peridotite aquifers and implications for microbial habitability. Geochim Cosmochim Acta. 2016;179:217–41.
CAS  Article  Google Scholar 

26.
Russell MJ, Martin W. The rocky roots of the acetyl-CoA pathway. Trends Biochem Sci. 2004;29:358–63.
CAS  PubMed  Article  Google Scholar 

27.
Martin WF, Weiss MC, Neukirchen S, Nelson-Sathi S, Sousa FL. Physiology, phylogeny, and LUCA. Microbial. Cell. 2016;3:582–7.
Google Scholar 

28.
Ueno Y, Yamada K, Yoshida N, Maruyama S, Isozake Y. Evidence from fluid inclusions for microbial methanogenesis in the early Archaean era. Nature. 2006;440:516–9.
CAS  PubMed  Article  Google Scholar 

29.
Moore EK, Jelen BI, Giovannelli D, Raanan H, Falkowski PG. Metal availability and the expanding network of microbial metabolisms in the Archaean eon. Nat Geosci. 2017;10:629–36.
CAS  Article  Google Scholar 

30.
Etiope G, Vadillo I, Whiticar MJ, Marques JM, Carreira PM, Tiago I, et al. Abiotic methane seepage in the Ronda peridotite massif, southern Spain. Appl Geochem. 2016;66:101–13.
CAS  Google Scholar 

31.
Proskurowski G, Lilley MD, Seewald JS, Früh-Green G, Olson EJ, Lupton JE, et al. Abiogenic hydrocarbon production at Lost City hydrothermal field. Science. 2008;319:604–7.
CAS  PubMed  Article  Google Scholar 

32.
Etiope G. Methane origin in the Samail ophiolite: Comment on “Modern water/rock reactions in Oman hyperalkaline peridotite aquifers and implications for microbial habitability”. Geochim Cosmochim Acta. 2017;197:467–70.
CAS  Article  Google Scholar 

33.
Miller HM, Matter JM, Kelemen P, Ellison ET, Conrad ME, Fierer N, et al. Reply to “Methane origin in the Samail ophiolite: Comment on ‘Modern water/rock reactions in Oman hyperalkaline peridotite aquifers and implications for microbial habitability’”. Geochim Cosmochim Acta. 2017;197:471–3.
CAS  Article  Google Scholar 

34.
Miller HM, Chaudhry N, Conrad ME, Markus B, Kopf SH, Templeton AS. Large carbon isotope variability during methanogenesis under alkaline conditions. Geochim Cosmochim Acta. 2018;237:18–31.
CAS  Article  Google Scholar 

35.
Bradley AS, Hayes JM, Summons RE. Extraordinary 13C enrichment of diether lipids at the Lost City Hydrothermal Field indicates a carbon-limited ecosystem. Geochim Cosmochim Acta. 2009;73:102–18.
CAS  Article  Google Scholar 

36.
Zwicker J, Birgel D, Bach W, Richoz S, Smrzka D, Grasemann B, et al. Evidence for archaeal methanogenesis within veins at the onshore serpentinite-hosted Chimaera seeps, Turkey. Chem Geol. 2018;483:567–80.
CAS  Article  Google Scholar 

37.
Kraus EA, Stamps BW, Rempfert KR, Nothaft DB, Boyd ES, Matter JM, et al. Biological methane cycling in serpentinization-impacted fluids of the Samail ophiolite of Oman. AGU Fall Meeting Abstracts. 2018; (abstract #V13E-0139).

38.
Miller HM, Mayhew LE, Ellison ET, Kelemen P, Kubo M, Templeton AS. Low temperature hydrogen production during experimental hydration of partially-serpentinized dunite. Geochim Cosmochim Acta. 2017;209:161–83.
CAS  Article  Google Scholar 

39.
Neal C, Stanger G. Hydrogen generation from mantle source rocks in Oman. Earth Planet Sci Lett. 1983;66:315–20.
CAS  Article  Google Scholar 

40.
Streit E, Kelemen P, Eiler J. Coexisting serpentine and quartz from carbonate-bearing serpentinized peridotite in the Samail Ophiolite, Oman. Contrib Miner Petr. 2012;164:821–37.
CAS  Article  Google Scholar 

41.
Chavagnac V, Monnin C, Ceuleneer G, Boulart C, Hoareau G. Characterization of hyperalkaline fluids produced by low-temperature serpentinization of mantle peridotites in the Oman and Ligurian ophiolites. Geochem Geophys. 2013;14:2496–522.
CAS  Article  Google Scholar 

42.
Mervine EM, Humphris SE, Sims KWW, Kelemen PB, Jenkins WJ. Carbonation rates of peridotite in the Samail Ophiolite, Sultanate of Oman, constrained through 14C dating and stable isotopes. Geochim Cosmochim Acta. 2014;126:371–97.
CAS  Article  Google Scholar 

43.
Kang DWD, Froula J, Egan R, Wang Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ. 2015;3:e1165.
PubMed  PubMed Central  Article  CAS  Google Scholar 

44.
Stepanauskas R, Fergusson EA, Brown J, Poulton NJ, Tupper B, Labonté JM, et al. Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles. Nat Commun. 2017;8:84.
PubMed  PubMed Central  Article  CAS  Google Scholar 

45.
Colman DR, Lindsay MR, Boyd ES. Mixing of meteoric and geothermal fluids supports hyperdiverse chemosynthetic hydrothermal communities. Nat Commun. 2019;10:1–13.
Article  CAS  Google Scholar 

46.
Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. J Bioinform. 2012;28:1033–4.
CAS  Article  Google Scholar 

47.
Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, et al. Fast, scalable generation of highquality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011;7:539.
PubMed  PubMed Central  Article  Google Scholar 

48.
Nguyen LT, Schmidt HA, von Haesler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268–74.
CAS  PubMed  PubMed Central  Article  Google Scholar 

49.
Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haesler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14:587.
CAS  PubMed  PubMed Central  Article  Google Scholar 

50.
Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 2010;11:119.
Article  CAS  Google Scholar 

51.
Seemann T. Prokka: rapid prokaryotic genome annotation. J Bioinform. 2014;30:2068–9.
CAS  Article  Google Scholar 

52.
Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27–30.
CAS  PubMed  PubMed Central  Article  Google Scholar 

53.
Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 2007;35:W182–5.
PubMed  PubMed Central  Article  Google Scholar 

54.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
CAS  PubMed  PubMed Central  Article  Google Scholar 

55.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.
CAS  PubMed  PubMed Central  Article  Google Scholar 

56.
Greening C, Biswas A, Carere CR, Jackson CJ, Taylor MC, Stott MB, et al. Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival. ISME J. 2016;10:761–77.
CAS  PubMed  Article  Google Scholar 

57.
Peters JW, Schut GJ, Boyd ES, Mulder DW, Shepard EM, Broderick JB, et al. [FeFe]-and [NiFe]-hydrogenase diversity, mechanism, and maturation. BBA-Mol Cell Res. 2015;1853:1350–69.
CAS  Google Scholar 

58.
Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, Lu S, et al. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res. 2016;45:D200–3.
PubMed  PubMed Central  Article  CAS  Google Scholar 

59.
Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: a fast and versatile genome alignment system. PLoS Comput Biol. 2018;14:e1005944.
PubMed  PubMed Central  Article  CAS  Google Scholar 

60.
R Core Team, R: a language and environment for statistical computing. Version 3.0.1. R Foundation for Statistical Computing. 2013.

61.
Leplae R, Lima-Mendez G, Toussaint A. ACLAME: a CLAssification of Mobile genetic Elements, update 2010. Nucleic Acids Res. 2010;38:D57–D61.
CAS  PubMed  Article  Google Scholar 

62.
Lefort V, Longueville J-E, Gascuel O. SMS: smart model selection in PhyML. Mol Biol Evol. 2017;34:2422–4.
CAS  PubMed  PubMed Central  Article  Google Scholar 

63.
Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59:307–21.
CAS  PubMed  Article  Google Scholar 

64.
Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PloS One. 2010;5:e11147.
PubMed  PubMed Central  Article  CAS  Google Scholar 

65.
Harrison KJ, Crécy-Lagard V, Zallot R. Gene Graphics: a genomic neighborhood data visualization web application. J Bioinform. 2018;34:1406–8.
CAS  Article  Google Scholar 

66.
Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, and O’Hara RB vegan: community ecology package. R Foundation for Statistical Computing. 2015.

67.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017;25:725–31.
Article  CAS  Google Scholar 

68.
Suzuki S, Ishii S, Hoshino T, Rietze A, Tenney A, Morrill PL, et al. Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars. ISME J. 2017;11:2584–98.
PubMed  PubMed Central  Article  Google Scholar 

69.
Giovannoni SJ, Thrash JC, Temperton B. Implications of streamlining theory for microbial ecology. ISME J. 2014;8:1553–65.
PubMed  PubMed Central  Article  Google Scholar 

70.
Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R. Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol. 2008;6:579–91.
CAS  PubMed  Article  Google Scholar 

71.
Hendrickson EL, Leigh JA. Roles of coenzyme F420-reducing hydrogenases and hydrogen-and F420-dependent methylenetetrahydromethanopterin dehydrogenases in reduction of F420 and production of hydrogen during methanogenesis. J Bacteriol. 2008;190:4818–21.
CAS  PubMed  PubMed Central  Article  Google Scholar 

72.
Goldman AD, Leigh JA, Samudrala R. Comprehensive computational analysis of Hmd enzymes and paralogs in methanogenic Archaea. BMC Evol Biol. 2009;9:199.
PubMed  PubMed Central  Article  CAS  Google Scholar 

73.
Tersteegen A, Hedderich R. Methanobacterium thermoautotrophicum encodes two multisubunit membrane‐bound [NiFe] hydrogenases: transcription of the operons and sequence analysis of the deduced proteins. Eur J Biochem. 1999;264:930–43.
CAS  PubMed  Article  Google Scholar 

74.
Lie TJ, Costa KC, Lupa B, Korpole S, Whitman WB, Leigh JA. Essential anaplerotic role for the energy-converting hydrogenase Eha in hydrogenotrophic methanogenesis. Proc Natl Acad Sci USA. 2012;109:15473–8.
CAS  PubMed  Article  Google Scholar 

75.
Thauer RK. The Wolfe cycle comes full circle. Proc Natl Acad Sci USA. 2012;109:15084–5.
CAS  PubMed  Article  Google Scholar 

76.
Costa KC, Wong PM, Wang T, Lie TJ, Dodsworth JA, Swanson I, et al. Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase. Proc Natl Acad Sci USA. 2010;107:11050–5.
CAS  PubMed  Article  Google Scholar 

77.
Greening C, Ahmed FA, Mohamed AE, Lee BM, Pandey G, Warden AC, et al. Physiology, biochemistry, and applications of F420-and Fo-dependent redox reactions. Microbiol Mol Biol Rev. 2016;80:451–93.
CAS  PubMed  PubMed Central  Article  Google Scholar 

78.
Yan Z, Ferry JG. Electron bifurcation and confurcation in methanogenesis and reverse methanogenesis. Front Microbiol. 2018;9:1322.
PubMed  PubMed Central  Article  Google Scholar 

79.
Costa KC, Lie TJ, Xia Q, Leigh JA. VhuD facilitates electron flow from H2 or formate to heterodisulfide reductase in Methanococcus maripaludis. J Bacteriol. 2013;195:5160–5.
CAS  PubMed  PubMed Central  Article  Google Scholar 

80.
Schauer NL, Ferry JG. Properties of formate dehydrogenase in Methanobacterium formicicum. J Bacteriol. 1982;150:1–7.
CAS  PubMed  PubMed Central  Article  Google Scholar 

81.
Schauer NL, Ferry JG, Honek JF, Orme-Johnson WH, Walsh C. Mechanistic studies of the coenzyme F420-reducing formate dehydrogenase from Methanobacterium formicicum. Biochemistry. 1986;25:7163–8.
CAS  PubMed  Article  Google Scholar 

82.
Mills DJ, Vitt S, Strauss M, Shima S, Vonck J. De novo modeling of the F420-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy. Elife. 2013;2:e00218.
PubMed  PubMed Central  Article  Google Scholar 

83.
Schut GJ, Boyd ES, Peters JW, Adams MWW. The modular respiratory complexes involved in hydrogen and sulfur metabolism by heterotrophic hyperthermophilic archaea and their evolutionary implications. FEMS Microbiol Rev. 2013;37:182–203.
CAS  PubMed  Article  Google Scholar 

84.
Hamamoto T, Hashimoto M, Hino M, Kitada M, Seto Y, Kudo T, et al. Characterization of a gene responsible for the Na+/H+ antiporter system of alkalophilic Bacillus species strain C125. Mol Microbiol. 1994;14:939–46.
CAS  PubMed  Article  Google Scholar 

85.
Buckel W, Thauer RK. Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation. BBA-Bioenerg. 2013;1827:94–113.
CAS  Article  Google Scholar 

86.
Boone DR, Johnson RL, Liu Y. Diffusion of the interspecies electron carriers H2 and formate in methanogenic ecosystems and its implications in the measurement of Km for H2 or formate uptake. Appl Environ Microbiol. 1989;55:1735–41.
CAS  PubMed  PubMed Central  Article  Google Scholar 

87.
Suzuki S, Nealson KH, Ishii S. Genomic and in-situ transcriptomic characterization of the candidate phylum NPL-UPL2 from highly alkaline highly reducing serpentinized groundwater. Front Micrbiol. 2018;9:3141.
Article  Google Scholar 

88.
Lang SQ, Butterfield DA, Schulte M, Kelley DS, Lilley MD. Elevated concentrations of formate, acetate and dissolved organic carbon found at the Lost City hydrothermal field. Geochim Cosmochim Acta. 2010;74:941–52.
CAS  Article  Google Scholar 

89.
McCollom TM, Seewald JS. Experimental constraints on the hydrothermal reactivity of organic acids and acid anions: I. Formic acid and formate. Geochim Cosmochim Acta. 2003;67:3625–44.  
CAS  Article  Google Scholar 

90.
Zeng Y, Liu J. Short-chain carboxylates in fluid inclusions in minerals. Appl Geochem. 2000;15:13–25.
CAS  Article  Google Scholar 

91.
Brazelton WJ, Baross JA. Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm. ISME J. 2009;3:1420–4.
CAS  PubMed  Article  Google Scholar 

92.
Zhang J, Kasciukovic T, White MF. The CRISPR associated protein Cas4 Is a 5′ to 3′ DNA exonuclease with an iron-sulfur cluster. PloS One. 2012;7:e47232.
CAS  PubMed  PubMed Central  Article  Google Scholar 

93.
Rath D, Amlinger L, Rath A, Lundgren M. The CRISPR-Cas immune system: biology, mechanisms and applications. Biochimie. 2015;117:119–28.
CAS  PubMed  Article  Google Scholar 

94.
Jansen R, van Embden JDA, Gaastra W, Schouls LM. Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol. 2002;43:1565–75.
CAS  PubMed  PubMed Central  Article  Google Scholar 

95.
Reno ML, Held NL, Fields CJ, Burke PV, Whitaker RJ. Biogeography of the Sulfolobus islandicus pan-genome. Proc Natl Acad Sci USA. 2009;106:8605–10.
CAS  PubMed  Article  Google Scholar 

96.
Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome.”. Proc Natl Acad Sci USA. 2005;102:13950–5.
CAS  PubMed  Article  Google Scholar 

97.
Labonté JM, Field EK, Lau M, Chivian D, Van Heerden E, Wommack KE, et al. Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population. Front Microbiol. 2015;6:349.
PubMed  PubMed Central  Google Scholar 

98.
Karnachuk OV, Frank YA, Lukina AP, Kadnikov VV, Beletsky AV, Mardanov AV, et al. Domestication of previously uncultivated Candidatus Desulforudis audaxviator from a deep aquifer in Siberia sheds light on its physiology and evolution. ISME J. 2019;13:1947–59.
CAS  PubMed  PubMed Central  Article  Google Scholar 

99.
Paul BG, Burstein D, Castelle CJ, Handa S, Arambula D, Czornyj E, et al. Retroelement-guided protein diversificiation abounds in vast lineages of bacteria and archaea. Nat Microbiol. 2017;2:17045.
CAS  PubMed  PubMed Central  Article  Google Scholar 

100.
Dirix G, Monsieurs P, Dombrecht B, Daniels R, Marchal K, Vanderleyden J, et al. Peptide signal molecules and bacteriocins in Gram-negative bacteria: a genome-wide in silico screening for peptides containing a double-glycine leader sequence and their cognate transporters. Peptides. 2004;25:1425–40.
CAS  PubMed  Article  Google Scholar  More

1.
Hylander, W. L., Johnson, K. R. & Picq, P. G. Masticatory-stress hypotheses and the supraorbital region of primates. Am. J. Phys. Anthropol. 86, 1–36 (1991).
CAS  PubMed  Article  PubMed Central  Google Scholar 
2.
Taylor, A. B. Diet and mandibular morphology in African apes. Int. J. Primatol. 27, 181–201 (2006).
Article  Google Scholar 

3.
Vogel, E. R. et al. Functional ecology and evolution of hominoid molar enamel thickness: Pan troglodytes schweinfurthii and Pongo pygmaeus wurmbii. J. Hum. Evol. 55, 60–74 (2008).
PubMed  Article  PubMed Central  Google Scholar 

4.
Strait, D. S. et al. The feeding biomechanics and dietary ecology of Australopithecus africanus. Proc. Natl. Acad. Sci. U. S. A. 106, 2124–2129 (2009).
ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

5.
Daegling, D. J. & McGraw, W. S. Functional morphology of the mangabey mandibular corpus: Relationship to dental specializations and feeding behavior. Am. J. Phys. Anthropol. 134, 50–62 (2007).
PubMed  Article  PubMed Central  Google Scholar 

6.
Daegling, D. J. et al. Hard-object feeding in sooty mangabeys (Cercocebus atys) and interpretation of early hominin feeding ecology. PLoS ONE 6, e23095 (2011).
ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

7.
Hylander, W. L. Mandibular function in Galago crassicaudatus and Macaca fascicularis: An in vivo approach to stress analysis of the mandible. J. Morphol. 159, 253–296 (1979).
CAS  PubMed  Article  PubMed Central  Google Scholar 

8.
Hylander, W. L. Stress and strain in the mandibular symphysis of primates: A test of competing hypotheses. Am. J. Phys. Anthropol. 64, 1–46 (1984).
CAS  PubMed  Article  PubMed Central  Google Scholar 

9.
Ungar, P. S. Patterns of ingestive behavior and anterior tooth use differences in sympatric anthropoid primates. Am. J. Phys. Anthropol. 95, 197–219 (1994).
CAS  PubMed  Article  PubMed Central  Google Scholar 

10.
Yamashita, N. Food procurement and tooth use in two sympatric lemur species. Am. J. Phys. Anthropol. 121, 125–133 (2003).
PubMed  Article  Google Scholar 

11.
McGraw, W. S., Vick, A. E. & Daegling, D. J. Sex and age differences in the diet and ingestive behaviors of sooty mangabeys (Cercocebus atys) in the Tai Forest, Ivory Coast. Am. J. Phys. Anthropol. 144, 140–153 (2011).
PubMed  Article  Google Scholar 

12.
McGraw, W. S. et al. Feeding and oral processing behaviors of two colobine monkeys in Tai Forest, Ivory Coast. J. Hum. Evol. 98, 90–102 (2016).
PubMed  Article  Google Scholar 

13.
Ross, C. F., Iriarte-Diaz, J., Reed, D. A., Stewart, T. A. & Taylor, A. B. In vivo bone strain in the mandibular corpus of Sapajus during a range of oral food processing behaviors. J. Hum. Evol. 98, 36–65 (2016).
PubMed  Article  Google Scholar 

14.
Ross, C. F. et al. In vivo bone strain and finite-element modeling of the craniofacial haft in catarrhine primates. J. Anat. 218, 112–141 (2011).
PubMed  Article  Google Scholar 

15.
Smith, R. J. Comparative functional morphology of maximum mandibular opening (gape) in primates. In Food Acquisition and Processing in Primates (eds Chivers, D. J. et al.) 231–255 (Plenum Press, New York, 1984).
Google Scholar 

16.
Daegling, D. J. Mandibular morphology and diet in the genus Cebus. Int. J. Primatol. 13, 545–570 (1992).
Article  Google Scholar 

17.
Daegling, D. J. Relationship of bone utilization and biomechanical competence in hominoid mandibles. Arch. Oral Biol. 52, 51–63 (2007).
PubMed  Article  PubMed Central  Google Scholar 

18.
Daegling, D. J. & Grine, F. E. Mandibular biomechanics and the paleontological evidence for the evolution of human diet. In Evolution of the Human Diet: The Known, the Unknown, and the Unknowable (ed. Ungar, P. S.) 77–105 (Oxford University Press, New York, 2006).
Google Scholar 

19.
Ross, C. F., Iriarte-Diaz, J. & Nunn, C. L. Innovative approaches to the relationship between diet and mandibular morphology in primates. Int. J. Primatol. 33, 632–660 (2012).
Article  Google Scholar 

20.
Chalk, J. et al. Age-related variation in the mechanical properties of foods processed by Sapajus libidinosus. Am. J. Phys. Anthropol. 159, 199–209 (2016).
PubMed  Article  PubMed Central  Google Scholar 

21.
Vinyard, C. J., Thompson, C. L., Doherty, A. & Robl, N. Preference and consequences: A preliminary look at whether preference impacts oral processing in non-human primates. J. Hum. Evol. 98, 27–35 (2016).
PubMed  Article  PubMed Central  Google Scholar 

22.
Strait, D. S. et al. Craniofacial strain patterns during premolar loading: implications for human evolution. In Primate Craniofacial Function and Biology (eds Vinyard, C. J. et al.) 173–198 (Springer, New York, 2008).
Google Scholar 

23.
Ravosa, M. J. Functional assessment of subfamily variation in maxillomandibular morphology among Old World monkeys. Am. J. Phys. Anthropol. 82, 199–212 (1990).
CAS  PubMed  Article  Google Scholar 

24.
Ravosa, M. J. Jaw morphology and function in living and fossil Old World monkeys. Int. J. Primatol. 17, 909–932 (1996).
Article  Google Scholar 

25.
Wright, B. W. et al. Taking a big bite: Working together to better understand the evolution of feeding in primates. Am. J. Primatol. 81, e22981 (2019).
PubMed  Google Scholar 

26.
Greaves, W. S. The jaw lever system in ungulates: A new model. J. Zool. 184, 271–285 (1978).
Article  Google Scholar 

27.
Spencer, M. A. Force production in the primate masticatory system: Electromyographic tests of biomechanical hypotheses. J. Hum. Evol. 34, 25–54 (1998).
CAS  PubMed  Article  PubMed Central  Google Scholar 

28.
Wright, B. W. Craniodental biomechanics and dietary toughness in the genus Cebus. J. Hum. Evol. 48, 473–492 (2005).
PubMed  Article  PubMed Central  Google Scholar 

29.
Wright, B. W. Ecological distinctions in diet, food toughness, and masticatory anatomy in a community of six Neotropical primates in Guyana, South America. Ph.D. Dissertation, University of Illinois at Urbana-Champaign (2004).

30.
Liu, Q. et al. Kinematics and energetics of nut-cracking in wild capuchin monkeys (Cebus libidinosus) in Piauí, Brazil. Am. J. Phys. Anthropol. 138, 210–220 (2009).
CAS  PubMed  Article  PubMed Central  Google Scholar 

31.
Taylor, A. B. & Vinyard, C. J. Jaw-muscle fiber architecture in tufted capuchins favors generating relatively large muscle forces without compromising jaw gape. J. Hum. Evol. 57, 710–720 (2009).
PubMed  PubMed Central  Article  Google Scholar 

32.
Wright, B. W. et al. Fallback foraging as a way of life: Using dietary toughness to compare the fallback signal among capuchins and implications for interpreting morphological variation. Am. J. Phys. Anthropol. 140, 687–699 (2009).
PubMed  Article  Google Scholar 

33.
Kay, R. F. The nut-crackers—A new theory of the adaptations of the Ramapithecinae. Am. J. Phys. Anthropol. 55, 141–151 (1981).
Article  Google Scholar 

34.
Masterson, T. Cranial form in Cebus: An ontogenetic analysis of cranial form and sexual dimorphism. Ph.D. Dissertation, University of Wisconsin (1996).

35.
Thiery, G. & Sha, J. C. M. Low occurrence of molar use in black-tufted capuchin monkeys: Should adaptation to seed ingestion be inferred from molars in primates? Palaeogeogr. Palaeoclimatol. Palaeoecol. 109853 (2020).

36.
Ottoni, E. B. & Izar, P. Capuchin monkey tool use: Overview and implications. Evol. Anthropol. 17, 171–178 (2008).
Article  Google Scholar 

37.
Taylor, A. B., Vogel, E. R. & Dominy, N. J. Food material properties and mandibular load resistance abilities in large-bodied hominoids. J. Hum. Evol. 55, 604–616 (2008).
PubMed  Article  PubMed Central  Google Scholar 

38.
Vogel, E. R. et al. Food mechanical properties, feeding ecology, and the mandibular morphology of wild orangutans. J. Hum. Evol. 75, 110–124 (2014).
PubMed  Article  Google Scholar 

39.
Ashby, M. F. Materials Selection in Mechanical Design (Pergamon Press, Oxford, 2002).
Google Scholar 

40.
Lucas, P. W. Dental Functional Morphology: How Teeth Work (Cambridge University Press, Cambridge, 2004).
Google Scholar 

41.
Marshall, A. J. & Wrangham, R. W. Evolutionary consequences of fallback foods. Int. J. Primatol. 28, 1219 (2007).
Article  Google Scholar 

42.
Foegeding, E. A. et al. A comprehensive approach to understanding textural properties of semi-and soft-solid foods. J. Text. Stud. 42, 103–129 (2011).
Article  Google Scholar 

43.
Herring, S. W. & Herring, S. E. The superficial masseter and gape in mammals. Am. Nat. 108, 561–576 (1974).
Article  Google Scholar 

44.
Perry, J. M. & Hartstone-Rose, A. Maximum ingested food size in captive strepsirrhine primates: Scaling and the effects of diet. Am. J. Phys. Anthropol. 142, 625–635 (2010).
PubMed  Article  Google Scholar 

45.
Hylander, W. L. Functional links between canine height and jaw gape in catarrhines with special reference to early hominins. Am. J. Phys. Anthropol. 150, 247–259 (2013).
PubMed  Article  PubMed Central  Google Scholar 

46.
Izawa, K. Foods and feeding behavior of monkeys in the upper Amazon basin. Primates 16, 295–316 (1975).
Article  Google Scholar 

47.
Izawa, K. Foods and feeding behavior of wild black-capped capuchin (Cebus apella). Primates 20, 57–76 (1979).
Article  Google Scholar 

48.
Izawa, K. & Mizuno, A. Palm-fruit cracking behavior of wild black-capped capuchin (Cebus apella). Primates 18, 773–792 (1977).
Article  Google Scholar 

49.
Fogaça, M. D. Comportamento alimentar e propriedades físicas dos alimentos consumidos por macacos-prego (Sapajus nigritus), no Parque Estadual Carlos Botelho, SP. Ph.D. Dissertation, Universidade de São Paulo (2014).

50.
Bouvier, M. Biomechanical scaling of mandibular dimensions in New World monkeys. Int. J. Primatol. 7, 551–567 (1986).
Article  Google Scholar 

51.
Taylor, A. B., Eng, C. M., Anapol, F. C. & Vinyard, C. J. The functional significance of jaw-muscle fiber architecture in tree-gouging marmosets. In The Smallest Anthropoids (eds Ford, S. M. et al.) 381–394 (Springer, Boston, 2009).
Google Scholar 

52.
McGraw, W. S., Vick, A. E. & Daegling, D. J. Dietary variation and food hardness in sooty mangabeys (Cercocebus atys): Implications for fallback foods and dental adaptation. Am. J. Phys. Anthropol. 154, 413–423 (2014).
PubMed  Article  PubMed Central  Google Scholar 

53.
McGraw, W. S. & Daegling, D. J. Primate feeding and foraging: Integrating studies of behavior and morphology. Annu. Rev. Anthropol. 41, 203–219 (2012).
Article  Google Scholar 

54.
Terborgh, J. W. Five New World Primates (Princeton University Press, Princeton, 1983).
Google Scholar 

55.
Oliveira, P. S. & Marquis, R. J. The Cerrados of Brazil: Ecology and Natural History of a Neotropical Savanna (Columbia University Press, New York, 2002).
Google Scholar 

56.
Howard, A. S., Bernardes, N., Nibbelink, L., Biondi, A., Presotto, D. M., Fragaszy, M. & Madden. A maximum entropy model of the bearded capuchin monkey habitat incorporating topography and spectral unmixing analysis. ISPRS Ann. Photogramm. Remote Sens. Spat. Inf. Sci. 1, 7–11 (2012).

57.
Izar, P. et al. Flexible and conservative features of social systems in tufted capuchin monkeys: Comparing the socioecology of Sapajus libidinosus and Sapajus nigritus. Am. J. Primatol. 74, 315–331 (2012).
PubMed  Article  PubMed Central  Google Scholar 

58.
Chalk-Wilayto, J., Ossi-Lupo, K. & Raguet-Schofield, M. Growing up tough: Comparing the effects of food toughness on juvenile feeding in Sapajus libidinosus and Trachypithecus phayrei crepusculus. J. Hum. Evol. 98, 76–89 (2016).
PubMed  Article  PubMed Central  Google Scholar 

59.
Altmann, J. Observational study of behavior: Sampling methods. Behaviour 49, 227–266 (1974).
CAS  PubMed  Article  PubMed Central  Google Scholar 

60.
Darvell, B. W., Lee, P. K. D., Yuen, T. D. B. & Lucas, P. W. A portable fracture toughness tester for biological materials. Meas. Sci. Technol. 7, 954 (1996).
ADS  CAS  Article  Google Scholar 

61.
Lucas, P. W. et al. Field kit to characterize physical, chemical and spatial aspects of potential primate foods. Folia Primatol. 72, 11–25 (2001).
CAS  Article  Google Scholar 

62.
Lucas, P. W. et al. Indentation as a technique to assess the mechanical properties of fallback foods. Am. J. Phys. Anthropol. 140, 643–652 (2009).
PubMed  Article  Google Scholar 

63.
Lucas, P. W. et al. Measuring the toughness of primate foods and its ecological value. Int. J. Primatol. 33, 598–610 (2011).
Article  Google Scholar 

64.
Berthaume, M. A. Food mechanical properties and dietary ecology. Am. J. Phys. Anthropol. 159, 79–104 (2016).
Article  Google Scholar 

65.
van Casteren, A., Venkataraman, V., Ennos, A. R. & Lucas, P. W. Novel developments in field mechanics. J. Hum. Evol. 98, 5–17 (2016).
PubMed  Article  Google Scholar 

66.
Hothorn, T., Bretz, F. & Westfall, P. Simultaneous inference in general parametric models. Biometr. J. 50, 346–363 (2008).
MathSciNet  MATH  Article  Google Scholar 

67.
R Core Team. R: a language and environment for statistical computing. (R Foundation for Statistical Computing, Vienna, 2017).

68.
Hiiemae, K. M. & Kay, R. F. Evolutionary trends in the dynamics of primate mastication. Craniofac. Biol. Primates 3, 28–64 (1973).
Google Scholar 

69.
Santos, L. P. C. D. Parâmetros nutricionais da dieta de duas populações de macacos-prego: Sapajus libidinosus no ecótono cerrado/caatinga e Sapajus nigritus na Mata Atlântica. Ph.D. dissertation, Universidade de São Paulo, São Paulo, Brazil (2015). More