Methanogens typically occur in reduced anoxic environments. However, in recent studies it has been shown that many aerated upland soils, including desert soils also host active methanogens. Here we show that soil samples from high-altitude cold deserts in the western Himalayas (Ladakh, India) produce CH4 after incubation as slurry under anoxic conditions at rates comparable to those of hot desert soils. Samples of matured soil from three different vegetation belts (arid, steppe, and subnival) were compared with younger soils originating from frontal and lateral moraines of receding glaciers. While methanogenic rates were higher in the samples from matured soils, CH4 was also produced in the samples from the recently deglaciated moraines. In both young and matured soils, those covered by a biological soil crust (biocrust) were more active than their bare counterparts. Isotopic analysis showed that in both cases CH4 was initially produced from H2/CO2 but later mostly from acetate. Analysis of the archaeal community in the in situ soil samples revealed a clear dominance of sequences related to Thaumarchaeota, while the methanogenic community comprised only a minor fraction of the archaeal community. Similar to other aerated soils, the methanogenic community was comprised almost solely of the genera Methanosarcina and Methanocella, and possibly also Methanobacterium in some cases. Nevertheless, ~10(3) gdw(-1) soil methanogens were already present in the young moraine soil together with cyanobacteria. Our results demonstrate that Methanosarcina and Methanocella not only tolerate atmospheric oxygen but are also able to survive in these harsh cold environments. Their occurrence in newly deglaciated soils shows that they are early colonizers of desert soils, similar to cyanobacteria, and may play a role in the development of desert biocrusts.

Institute of Botany Academy of Sciences of the Czech Republic Třeboň Czech Republic

Institute of Botany Academy of Sciences of the Czech Republic Třeboň Czech Republic ; Faculty of Science University of South Bohemia České Budějovice Czech Republic

Max Planck Institute for Terrestrial Microbiology Marburg Germany

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Angel R. (2012). Total nucleic acid extraction from soil. Protoc. Exch. 10.1038/protex.2012.046 DOI

Angel R., Claus P., Conrad R. (2012). Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions. ISME J. 6, 847–862 10.1038/ismej.2011.141 PubMed DOI PMC

Angel R., Conrad R. (2013). Elucidating the microbial resuscitation cascade in biological soil crusts following a simulated rain event. Environ. Microbiol. 15, 2799–2815 10.1111/1462-2920.12140 PubMed DOI

Angel R., Matthies D., Conrad R. (2011). Activation of methanogenesis in arid biological soil crusts despite the presence of oxygen. PLoS ONE 6:e20453 10.1371/journal.pone.0020453 PubMed DOI PMC

Bahl J., Lau M. C. Y., Smith G. J. D., Vijaykrishna D., Cary S. C., Lacap D. C., et al. (2011). Ancient origins determine global biogeography of hot and cold desert cyanobacteria. Nat. Commun. 2, 163 10.1038/ncomms1167 PubMed DOI PMC

Banning N., Brock F., Fry J. C., Parkes R. J., Hornibrook E. R. C., Weightman A. J. (2005). Investigation of the methanogen population structure and activity in a brackish lake sediment. Environ. Microbiol. 7, 947–960 10.1111/j.1462-2920.2004.00766.x PubMed DOI

Bates S. T., Berg-Lyons D., Caporaso J. G., Walters W. A., Knight R., Fierer N. (2011). Examining the global distribution of dominant archaeal populations in soil. ISME J. 5, 908–917 10.1038/ismej.2010.171 PubMed DOI PMC

Belnap J. (2003). Comparative structure of physical and biological soil crusts, in Biological Soil Crusts: Structure, Function and Management Ecological Studies, eds Belnap J., Lange O. L. (Berlin; Heidelberg: Springer; ), 177–191 10.1007/978-3-642-56475-8 DOI

Belnap J., Büdel B., Lange O. L. (2003). Biological soil crusts: characteristics and distribution, in Biological Soil Crusts: Structure, Function and Management Ecological Studies, eds Belnap J., Lange O. L. (Berlin; Heidelberg: Springer; ), 3–30 10.1007/978-3-642-56475-8 DOI

Belnap J., Eldridge D. (2003). Disturbance and recovery of biological soil crusts, in Biological Soil Crusts: Structure, Function, and Management Ecological Studies. eds Belnap J., Lange O. L. (Berlin; Heidelberg: Springer; ), 363–383

Brand W. A. (1996). High precision isotope ratio monitoring techniques in mass spectrometry. J. Mass Spectrom. 31, 225–235 10.1002/(SICI)1096-9888(199603)31:3<225::AID-JMS319>3.0.CO;2-L PubMed DOI

Brankatschk R., Toewe S., Kleineidam K., Schloter M., Zeyer J. (2011). Abundances and potential activities of nitrogen cycling microbial communities along a chronosequence of a glacier forefield. ISME J. 5, 1025–1037 10.1038/ismej.2010.184 PubMed DOI PMC

Brune A. (2011). Methanogens in the digestive tract of termites, in (Endo)symbiotic Methanogenic Archaea Microbiology Monographs, ed Hackstein J. H. P. (Berlin; Heidelberg: Springer; ), 81–100

Bryant J. A., Lamanna C., Morlon H., Kerkhoff A. J., Enquist B. J., Green J. L. (2008). Microbes on mountainsides: contrasting elevational patterns of bacterial and plant diversity. Proc. Natl. Acad. Sci. U.S.A. 105, 11505–11511 10.1073/pnas.0801920105 PubMed DOI PMC

Büdel B. (2003). Synopsis: comparative biogeography of soil-crust biota, in Biological Soil Crusts: Structure, Function, and Management Ecological Studies, eds Belnap J., Lange O. L. (Berlin; Heidelberg: Springer; ), 141–152

Conrad R. (2005). Quantification of methanogenic pathways using stable carbon isotopic signatures: a review and a proposal. Org. Geochem. 36, 739–752 10.1016/j.orggeochem.2004.09.006 DOI

Conrad R., Claus P., Casper P. (2009). Characterization of stable isotope fractionation during methane production in the sediment of a eutrophic lake, Lake Dagow, Germany. Limnol. Oceanogr. 54, 457–471 10.4319/lo.2009.54.2.0457 DOI

Conrad R., Claus P., Casper P. (2010). Stable isotope fractionation during the methanogenic degradation of organic matter in the sediment of an acidic bog lake, Lake Grosse Fuchskuhle. Limnol. Oceanogr. 55, 1932–1942 10.4319/lo.2010.55.5.1932 DOI

Conrad R., Frenzel P. (2002). Flooded soils, in Encyclopedia of Environmental Microbiology, ed Bitton G. (New York, NY: John Wiley and Sons, Inc.), 1316–1333

Deppenmeier U., Mueller V., Gottschalk G. (1996). Pathways of energy conservation in methanogenic archaea. Arch. Microbiol. 165, 149–163 10.1007/BF01692856 DOI

Dridi B., Fardeau M.-L., Ollivier B., Raoult D., Drancourt M. (2012). Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces. Int. J. Syst. Evol. Microbiol. 62, 1902–1907 10.1099/ijs.0.033712-0 PubMed DOI

Dvorský M., Doleܞal J., de Bello F., Klimešová J., Klimeš L. (2011). Vegetation types of East Ladakh: species and growth form composition along main environmental gradients. Appl. Veg. Sci. 14, 132–147 10.1111/j.1654-109X.2010.01103.x DOI

Dvorský M., Doležal J., Kopeckı M., Chlumská Z., Janatková K., Altman J., et al. (2013). Testing the stress-gradient hypothesis at the roof of the world: effects of the cushion plant thylacospermum caespitosum on species assemblages. PLoS ONE 8:e53514 10.1371/journal.pone.0053514 PubMed DOI PMC

Erkel C., Kube M., Reinhardt R., Liesack W. (2006). Genome of rice cluster I archaea - the key methane producers in the rice rhizosphere. Science 313, 370–372 10.1126/science.1127062 PubMed DOI

Evans R. D., Ehleringer J. R. (1993). A break in the nitrogen cycle in aridlands. Evidence from δ 15N of soils. Oecologia 94, 314–317 10.1007/BF00317104 PubMed DOI

Ferry J. G. (1994). Methanogenesis: Ecology, Physiology, Biochemistry and Genetics. New York, NY: Chapman and Hall

Fey A., Claus P., Conrad R. (2004). Temporal change of 13C-isotope signatures and methanogenic pathways in rice field soil incubated anoxically at different temperatures. Geochim. Cosmochim. Acta 68, 293–306 10.1016/S0016-7037(03)00426-5 DOI

Friedrich M. W. (2005). Methyl−coenzyme M reductase genes: unique functional markers for methanogenic and anaerobic methane−oxidizing archaea. Methods Enzymol. 397, 428–442 10.1016/S0076-6879(05)97026-2 PubMed DOI

Gangwar P., Alam S. I., Bansod S., Singh L. (2009). Bacterial diversity of soil samples from the western Himalayas, India. Can. J. Microbiol. 55, 564–577 10.1139/W09-011 PubMed DOI

Glissmann K., Conrad R. (2002). Saccharolytic activity and its role as a limiting step in methane formation during the anaerobic degradation of rice straw in rice paddy soil. Biol. Fertil. Soils 35, 62–67 10.1007/s00374-002-0442-z DOI

Goevert D., Conrad R. (2009). Effect of substrate concentration on carbon isotope fractionation during acetoclastic methanogenesis by Methanosarcina barkeri and M. acetivorans and in rice field soil. .Appl. Environ. Microbiol. 75, 2605–2612 10.1128/AEM.02680-08 PubMed DOI PMC

Großkopf R., Janssen P. H., Liesack W. (1998). Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl. Environ. Microbiol. 64, 960–969 PubMed PMC

Hayes J. M. (1993). Factors controlling 13C contents of sedimentary organic compounds: principles and evidence. Mar. Geol. 113, 111–125 10.1016/0025-3227(93)90153-M DOI

Hoehler T. M., Bebout B. M., Marais D. J. D. (2001). The role of microbial mats in the production of reduced gases on the early Earth. Nature 412, 324–327 10.1038/35085554 PubMed DOI

Janatková K., Řeháková K., Doležal J., Šimek M., Chlumská Z., Dvorskı M., et al. (2013). Community structure of soil phototrophs along environmental gradients in arid Himalaya. Environ. Microbiol. 15, 2505–2516 10.1111/1462-2920.12132 PubMed DOI

Lindström E. S., Langenheder S. (2012). Local and regional factors influencing bacterial community assembly. Environ. Microbiol. Rep. 4, 1–9 10.1111/j.1758-2229.2011.00257.x PubMed DOI

Liu Y., Whitman W. B. (2008). Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann. N.Y. Acad. Sci. 1125, 171–189 10.1196/annals.1419.019 PubMed DOI

Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, et al. (2004). ARB: a software environment for sequence data. Nucleic Acids Res. 32, 1363–1371 10.1093/nar/gkh293 PubMed DOI PMC

Lueders T., Chin K., Conrad R., Friedrich M. (2001). Molecular analyses of methyl−coenzyme M reductase α−subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage. Environ. Microbiol. 3, 194–204 10.1046/j.1462-2920.2001.00179.x PubMed DOI

Middleton N., Thomas D. (1997). World Atlas of Desertification. London: UNEP

Nemergut D. R., Anderson S. P., Cleveland C. C., Martin A. P., Miller A. E., Seimon A., et al. (2007). Microbial community succession in an unvegetated, recently deglaciated soil. Microb. Ecol. 53, 110–122 10.1007/s00248-006-9144-7 PubMed DOI

Nicholson M., Evans P., Joblin K. (2007). Analysis of methanogen diversity in the rumen using temporal temperature gradient gel electrophoresis: identification of uncultured methanogens. Microb. Ecol. 54, 141–150 10.1007/s00248-006-9182-1 PubMed DOI

Nicol G. W., Glover L. A., Prosser J. I. (2003). Molecular analysis of methanogenic archaeal communities in managed and natural upland pasture soils. Global Change Biol. 9, 1451–1457 10.1046/j.1365-2486.2003.00673.x DOI

Nuebel U., Garcia-Pichel F., Muyzer G. (1997). PCR primers to amplify 16S rRNA genes from cyanobacteria. Appl. Environ. Microbiol. 63, 3327–3332 PubMed PMC

Nüsslein B., Eckert W., Conrad R. (2003). Stable isotope biogeochemistry of methane formation in profundal sediments of Lake Kinneret (Israel). Limnol. Oceanogr. 48, 1439–1446 10.4319/lo.2003.48.4.1439 DOI

Offre P., Spang A., Schleper C. (2013). Archaea in biogeochemical cycles. Annu. Rev. Microbiol. 67, 437–457 10.1146/annurev-micro-092412-155614 PubMed DOI

Paul K., Nonoh J. O., Mikulski L., Brune A. (2012). “Methanoplasmatales,” Thermoplasmatales-related archaea in termite guts and other environments, are the seventh order of methanogens. Appl. Environ. Microbiol. 78, 8245–8253 10.1128/AEM.02193-12 PubMed DOI PMC

Peters V., Conrad R. (1995). Methanogenic and other strictly anaerobic bacteria in desert soil and other oxic soils. Appl. Environ. Microbiol. 61, 1673–1676 PubMed PMC

Poplawski A. B., Mårtensson L., Wartiainen I., Rasmussen U. (2007). Archaeal Diversity and community structure in a Swedish barley field: specificity of the Ek510r/(EURY498) 16S rDNA Primer. J. Microbiol. Methods 69, 161–173 10.1016/j.mimet.2006.12.018 PubMed DOI

Quast C., Pruesse E., Yilmaz P., Gerken J., Schweer T., Yarza P., et al. (2013). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 10.1093/nar/gks1219 PubMed DOI PMC

Řeháková K., Chlumská Z., Doležal J. (2011). Soil cyanobacterial and microalgal diversity in dry mountains of Ladakh, NW Himalaya, as related to site, altitude, and vegetation. Microb. Ecol. 62, 337–346 10.1007/s00248-011-9878-8 PubMed DOI

Roy R., Klueber H. D., Conrad R. (1997). Early initiation of methane production in anoxic rice soil despite the presence of oxidants. FEMS Microbiol. Ecol. 24, 311–320 10.1111/j.1574-6941.1997.tb00448.x DOI

Sakai S., Imachi H., Hanada S., Ohashi A., Harada H., Kamagata Y. (2008). Methanocella paludicola gen. nov., sp. nov., a methane-producing archaeon, the first isolate of the lineage “Rice Cluster I,” and proposal of the new archaeal order Methanocellales ord. nov. Int. J. Syst. Evol. Microbiol. 58, 929–936 10.1099/ijs.0.65571-0 PubMed DOI

Scavino A. F., Ji Y., Pump J., Klose M., Claus P., Conrad R. (2013). Structure and function of the methanogenic microbial communities in Uruguayan soils shifted between pasture and irrigated rice fields. Environ. Microbiol. 15, 2588–2602 10.1111/1462-2920.12161 PubMed DOI

Shindell D. T., Faluvegi G., Koch D. M., Schmidt G. A., Unger N., Bauer S. E. (2009). Improved attribution of climate forcing to emissions. Science 326, 716–718 10.1126/science.1174760 PubMed DOI

Sjoeling S., Cowan D. A. (2003). High 16S rDNA bacterial diversity in glacial meltwater lake sediment, Bratina Island, Antarctica. Extremophiles 7, 275–282 10.1007/s00792-003-0321-z PubMed DOI

Soule T., Anderson I. J., Johnson S. L., Bates S. T., Garcia-Pichel F. (2009). Archaeal populations in biological soil crusts from arid lands in North America. Soil Biol. Biochem. 41, 2069–2074 10.1016/j.soilbio.2009.07.023 DOI

Stamatakis A. (2006). RAxML-vi-hpc: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688–2690 10.1093/bioinformatics/btl446 PubMed DOI

Steinberg L. M., Regan J. M. (2008). Phylogenetic comparison of the methanogenic communities from an acidic, oligotrophic fen and an anaerobic digester treating municipal wastewater sludge. Appl. Environ. Microbiol. 74, 6663–6671 10.1128/AEM.00553-08 PubMed DOI PMC

Steven B., Gallegos-Graves L. V., Yeager C. M., Belnap J., Evans R. D., Kuske C. R. (2012). Dryland biological soil crust cyanobacteria show unexpected decreases in abundance under long-term elevated CO2. Environ. Microbiol. 14, 3247–3258 10.1111/1462-2920.12011 PubMed DOI

West A. E., Schmidt S. K. (2002). Endogenous methanogenesis stimulates oxidation of atmospheric methane in alpine tundra soil. Microb. Ecol. 43, 408–415 10.1007/s00248-001-1049-x PubMed DOI

Zinder S. H. (1993). Physiological ecology of methanogens, in Methanogenesis: Ecology, Physiology, Biochemistry and Genetics, ed Ferry J. G. (London: Chapmann and Hall; ), 128–208

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