Abstract
The conversion of lignocellulosic biomass into biofuels can potentially be improved by employing robust microorganisms and enzymes that efficiently deconstruct plant polysaccharides at elevated temperatures. Many of the geothermal features of Yellowstone National Park (YNP) are surrounded by vegetation providing a source of allochthonic material to support heterotrophic microbial communities adapted to utilize plant biomass as a primary carbon and energy source. In this study, a well-known hot spring environment, Obsidian Pool (OBP), was examined for potential biomass-active microorganisms using cultivation-independent and enrichment techniques. Analysis of 33,684 archaeal and 43,784 bacterial quality-filtered 16S rRNA gene pyrosequences revealed that archaeal diversity in the main pool was higher than bacterial; however, in the vegetated area, overall bacterial diversity was significantly higher. Of notable interest was a flooded depression adjacent to OBP supporting a stand of Juncus tweedyi, a heat-tolerant rush commonly found growing near geothermal features in YNP. The microbial community from heated sediments surrounding the plants was enriched in members of the Firmicutes including potentially (hemi)cellulolytic bacteria from the genera Clostridium, Anaerobacter, Caloramator, Caldicellulosiruptor, and Thermoanaerobacter. Enrichment cultures containing model and real biomass substrates were established at a wide range of temperatures (55–85 °C). Microbial activity was observed up to 80 °C on all substrates including Avicel, xylan, switchgrass, and Populus sp. Independent of substrate, Caloramator was enriched at lower (<65 °C) temperatures while highly active cellulolytic bacteria Caldicellulosiruptor were dominant at high (>65 °C) temperatures.
Similar content being viewed by others
References
Carroll A, Somerville C (2009) Cellulosic biofuels. Annu Rev Plant Biol 60:165–182. doi:10.1146/annurev.arplant.043008.092125
Bayer E, Shoham Y, Lamed R (2006) Cellulose-decomposing bacteria and their enzyme systems. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes. Springer, New York, pp 578–617
Reid NM, Addison SL, Macdonald LJ, Lloyd-Jones G (2011) Biodiversity of active and inactive bacteria in the gut flora of wood-feeding huhu beetle larvae (Prionoplus reticularis). Appl Environ Microbiol 77:7000–7006
Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette M, McHardy AC, Djordjevic G, Aboushadi N, Sorek R, Tringe SG, Podar M, Martin HG, Kunin V, Dalevi D, Madejska J, Kirton E, Platt D, Szeto E, Salamov A, Barry K, Mikhailova N, Kyrpides NC, Matson EG, Ottesen EA, Zhang XN, Hernandez M, Murillo C, Acosta LG, Rigoutsos I, Tamayo G, Green BD, Chang C, Rubin EM, Mathur EJ, Robertson DE, Hugenholtz P, Leadbetter JR (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450:560–565
Fouts DE, Szpakowski S, Purushe J, Torralba M, Waterman RC, MacNeil MD, Alexander LJ, Nelson KE (2012) Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen. PLoS One 7. doi:10.1371/journal.pone.0048289
Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo SJ, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z, Rubin EM (2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331:463–467. doi:10.1126/science.1200387
Brulc JM, Antonopoulos DA, Miller MEB, Wilson MK, Yannarell AC, Dinsdale EA, Edwards RE, Frank ED, Emerson JB, Wacklin P, Coutinho PM, Henrissat B, Nelson KE, White BA (2009) Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci U S A 106:1948–1953. doi:10.1073/pnas.0806191105
Allgaier M, Reddy A, Park JI, Ivanova N, D’Haeseleer P, Lowry S, Sapra R, Hazen TC, Simmons BA, VanderGheynst JS, Hugenholtz P (2010) Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS One 5:e8812. doi:10.1371/journal.pone.0008812
van der Lelie D, Taghavi S, McCorkle SM, Li LL, Malfatti SA, Monteleone D, Donohoe BS, Ding SY, Adney WS, Himmel ME, Tringe SG (2012) The metagenome of an anaerobic microbial community decomposing poplar wood chips. PLoS One 7. doi:10.1371/journal.pone.0036740
Reddy AP, Allgaier M, Singer SW, Hazen TC, Simmons BA, Hugenholtz P, VanderGheynst JS (2011) Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction. Biotechnol Bioeng 108:2088–2098. doi:10.1002/bit.23176
Taylor MP, Eley KL, Martin S, Tuffin MI, Burton SG, Cowan DA (2009) Thermophilic ethanologenesis: future prospects for second-generation bioethanol production. Trends Biotechnol 27:398–405. doi:10.1016/j.tibtech.2009.03.006
Shaw AJ, Podkaminer KK, Desai SG, Bardsley JS, Rogers SR, Thorne PG, Hogsett DA, Lynd LR (2008) Metabolic engineering of a thermophilic bacterium to produce ethanol at high yield. Proc Natl Acad Sci U S A 105:13769–13774. doi:10.1073/pnas.0801266105
Olson DG, McBride JE, Shaw AJ, Lynd LR (2012) Recent progress in consolidated bioprocessing. Curr Opin Biotechnol 23:396–405. doi:10.1016/j.copbio.2011.11.026
Blumer-Schuette SE, Kataeva I, Westpheling J, Adams MW, Kelly RM (2008) Extremely thermophilic microorganisms for biomass conversion: status and prospects. Curr Opin Biotechnol 19:210–217. doi:10.1016/j.copbio.2008.04.007
Yang SJ, Kataeva I, Hamilton-Brehm SD, Engle NL, Tschaplinski TJ, Doeppke C, Davis M, Westpheling J, Adams MWW (2009) Efficient degradation of lignocellulosic plant biomass, without pretreatment, by the thermophilic anaerobe Anaerocellum thermophilum DSM 6725. Appl Environ Microbiol 75:4762–4769
Cha M, Chung D, Elkins JG, Guss AM, Westpheling J (2013) Metabolic engineering of Caldicellulosiruptor bescii yields increased hydrogen production from lignocellulosic biomass. Biotechnol Biofuels 6:85. doi:10.1186/1754-6834-6-85
Svetlitchnyi VA, Kensch O, Falkenhan DA, Korseska SG, Lippert N, Prinz M, Sassi J, Schickor A, Curvers S (2013) Single-step ethanol production from lignocellulose using novel extremely thermophilic bacteria. Biotechnol Biofuels 6:31. doi:10.1186/1754-6834-6-31
Yao S, Mikkelsen MJ (2010) Metabolic engineering to improve ethanol production in Thermoanaerobacter mathranii. Appl Microbiol Biotechnol 88:199–208. doi:10.1007/s00253-010-2703-3
Peacock JP, Cole JK, Murugapiran SK, Dodsworth JA, Fisher JC, Moser DP, Hedlund BP (2013) Pyrosequencing reveals high-temperature cellulolytic microbial consortia in Great Boiling Spring after in situ lignocellulose enrichment. PLoS One 8:e59927. doi:10.1371/journal.pone.0059927
Hugenholtz P, Pitulle C, Hershberger KL, Pace NR (1998) Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 180:366–376
Kashefi K, Holmes DE, Reysenbach AL, Lovley DR (2002) Use of Fe(III) as an electron acceptor to recover previously uncultured hyperthermophiles: isolation and characterization of Geothermobacterium ferrireducens gen. nov., sp. nov. Appl Environ Microbiol 68:1735–1742
Dunfield PF, Tamas I, Lee KC, Morgan XC, McDonald IR, Stott MB (2012) Electing a candidate: a speculative history of the bacterial phylum OP10. Environ Microbiol 14:3069–3080. doi:10.1111/j.1462-2920.2012.02742.x
Hamilton-Brehm SD, Gibson RA, Green SJ, Hopmans EC, Schouten S, van der Meer MT, Shields JP, Damste JS, Elkins JG (2013) Thermodesulfobacterium geofontis sp. nov., a hyperthermophilic, sulfate-reducing bacterium isolated from Obsidian Pool, Yellowstone National Park. Extremophiles 17:251–263. doi:10.1007/s00792-013-0512-1
Hamilton-Brehm SD, Mosher JJ, Vishnivetskaya T, Podar M, Carroll S, Allman S, Phelps TJ, Keller M, Elkins JG (2010) Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Yellowstone National Park. Appl Environ Microbiol 76:1014–1020. doi:10.1128/aem.01903-09
Barns SM, Fundyga RE, Jeffries MW, Pace NR (1994) Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc Natl Acad Sci U S A 91:1609–1613
Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, Hedlund BP, Brochier-Armanet C, Kunin V, Anderson I, Lapidus A, Goltsman E, Barry K, Koonin EV, Hugenholtz P, Kyrpides N, Wanner G, Richardson P, Keller M, Stetter KO (2008) A korarchaeal genome reveals insights into the evolution of the Archaea. Proc Natl Acad Sci U S A 105:8102–8107. doi:10.1073/pnas.0801980105
Podar M, Makarova KS, Graham DE, Wolf YI, Koonin EV, Reysenbach AL (2013) Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park. Biol Direct 8:9. doi:10.1186/1745-6150-8-9
Vishnivetskaya TA, Raman B, Phelps TJ, Podar M, Elkins JG (2012) Cellulolytic microorganisms from thermal environments. In: Anitori RP (ed) Extremophiles: microbiology and biotechnology. Caister Academic Press, Norfolk, pp 131–158
Wang ZW, Hamilton-Brehm SD, Lochner A, Elkins JG, Morrell-Falvey JL (2011) Mathematical modeling of hydrolysate diffusion and utilization in cellulolytic biofilms of the extreme thermophile Caldicellulosiruptor obsidiansis. Bioresour Technol 102:3155–3162. doi:10.1016/j.biortech.2010.10.104
Lochner A, Giannone RJ, Keller M, Antranikian G, Graham DE, Hettich RL (2011) Label-free quantitative proteomics for the extremely thermophilic bacterium Caldicellulosiruptor obsidiansis reveal distinct abundance patterns upon growth on cellobiose, crystalline cellulose, and switchgrass. J Proteome Res 10:5302–5314. doi:10.1021/pr200536j
Lochner A, Giannone RJ, Rodriguez M Jr, Shah MB, Mielenz JR, Keller M, Antranikian G, Graham DE, Hettich RL (2011) Use of label-free quantitative proteomics to distinguish the secreted cellulolytic systems of Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis. Appl Environ Microbiol 77:4042–4054. doi:10.1128/AEM.02811-10
Blumer-Schuette SE, Giannone RJ, Zurawski JV, Ozdemir I, Ma Q, Yin Y, Xu Y, Kataeva I, Poole FL 2nd, Adams MW, Hamilton-Brehm SD, Elkins JG, Larimer FW, Land ML, Hauser LJ, Cottingham RW, Hettich RL, Kelly RM (2012) Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass. J Bacteriol 194:4015–4028. doi:10.1128/JB.00266-12
Spear JR, Walker JJ, McCollom TM, Pace NR (2005) Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem. Proc Natl Acad Sci U S A 102:2555–2560. doi:10.1073/pnas.0409574102
Shock EL, Holland M, Meyer-Dombard DAR, Amend JP (2005) Geochemical sources of energy for microbial metabolism in hydrothermal ecosystems: Obsidian Pool, Yellowstone National Park, USA. In: Inskeep W, McDermott T (eds) Geothermal biology and geochemistry in Yellowstone National Park. Thermal Biology Institute, Montana State University, Bozeman, pp 95–112
Miller TL, Wolin MJ (1974) A serum bottle modification of the Hungate technique for cultivating obligate anaerobes. Appl Microbiol 27:985–987
Raes J, Korbel JO, Lercher MJ, von Mering C, Bork P (2007) Prediction of effective genome size in metagenomic samples. Genome Biol 8:R10. doi:10.1186/gb-2007-8-1-r10
Angly FE, Willner D, Prieto-Davà A, Edwards RA, Schmieder R, Vega-Thurber R, Antonopoulos DA, Barott K, Cottrell MT, Desnues C, Dinsdale EA, Furlan M, Haynes M, Henn MR, Hu Y, Kirchman DL, McDole T, McPherson JD, Meyer F, Miller RM, Mundt E, Naviaux RK, Rodriguez-Mueller B, Stevens R, Wegley L, Zhang L, Zhu B, Rohwer F (2009) The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput Biol 5:e1000593
Ellenbroek FM, Cappenberg TE (1991) DNA-synthesis and tritiated-thymidine incorporation by heterotrophic fresh-water bacteria in continuous culture. Appl Environ Microbiol 57:1675–1682
Mackelprang R, Waldrop MP, DeAngelis KM, David MM, Chavarria KL, Blazewicz SJ, Rubin EM, Jansson JK (2011) Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480:368–371
Porat I, Vishnivetskaya TA, Mosher JJ, Brandt CC, Yang ZK, Brooks SC, Liang L, Drake MM, Podar M, Brown SD, Palumbo AV (2009) Characterization of archaeal community in contaminated and uncontaminated surface stream sediments. Microb Ecol 60:784–795. doi:10.1007/s00248-010-9734-2
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM (2009) The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141–D145. doi:10.1093/nar/gkn879
Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methe B, DeSantis TZ, Petrosino JF, Knight R, Birren BW (2011) Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21:494–504. doi:10.1101/gr.112730.110
Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267
Claesson MJ, O’Sullivan O, Wang Q, Nikkila J, Marchesi JR, Smidt H, de Vos WM, Ross RP, O’Toole PW (2009) Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One 4:e6669. doi:10.1371/journal.pone.0006669
Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9. doi:10.1186/1471-2105-9-386
Parks DH, Beiko RG (2010) Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26:715–721. doi:10.1093/bioinformatics/btq041
Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48:443–453
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541. doi:10.1128/aem.01541-09
Lozupone C, Hamady M, Knight R (2006) UniFrac - an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinforma 7:371–385. doi:10.1186/1471-2105-7-371
Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228–8235. doi:10.1128/aem.71.12.8228-8235.2005
Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163
Fournier RO (1989) Geochemistry and dynamics of the Yellowstone National Park hydrothermal system. Annu Rev Earth Planet Sci 17:13–53. doi:10.1146/annurev.earth.17.1.13
Kennedy BM, Lynch MA, Reynolds JH, Smith SP (1985) Intensive sampling of noble-gases in fluids at Yellowstone. 1. Early overview of the data - regional patterns. Geochim Cosmochim Acta 49:1251–1261. doi:10.1016/0016-7037(85)90014-6
White DE (1981) Active geothermal systems and hydrothermal ore deposits. Economic geology 75th anniversary volume
Meyer-Dombard DR, Shock EL, Amend JP (2005) Archaeal and bacterial communities in geochemically diverse hot springs of Yellowstone National Park, USA. Geobiology 3:211–227. doi:10.1111/j.1472-4669.2005.00052.x
Cole JK, Peacock JP, Dodsworth JA, Williams AJ, Thompson DB, Dong HL, Wu G, Hedlund BP (2013) Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities. ISME J 7:718–729. doi:10.1038/ismej.2012.157
Stout RG, Al-Niemi TS (2002) Heat-tolerant flowering plants of active geothermal areas in Yellowstone National Park. Ann Bot 90:259–267
Ogg CD, Patel BKC (2009) Caloramator australicus sp nov., a thermophilic, anaerobic bacterium from the Great Artesian Basin of Australia. Int J Syst Evol Microbiol 59:95–101. doi:10.1099/ijs.0.000802-0
Orlygsson J, Sigurbjornsdottir MA, Bakken HE (2010) Bioprospecting thermophilic ethanol and hydrogen producing bacteria from hot springs in Iceland. Icel Agric Sci 23:73–85
Vanfossen AL, Verhaart MR, Kengen SM, Kelly RM (2009) Carbohydrate utilization patterns for the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus reveal broad growth substrate preferences. Appl Environ Microbiol 75:7718–7724
Blumer-Schuette SE, Giannone RJ, Zurawski JV, Ozdemir I, Ma Q, Yin YB, Xu Y, Kataeva I, Poole FL, Adams MWW, Hamilton-Brehm SD, Elkins JG, Larimer FW, Land ML, Hauser LJ, Cottingham RW, Hettich RL, Kelly RM (2012) Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass. J Bacteriol 194:4015–4028. doi:10.1128/jb.00266-12
Yang S-J, Kataeva I, Wiegel J, Yin Y, Dam P, Xu Y, Westpheling J, Adams MWW (2009) eclassification of ‘Anaerocellum thermophilum’ as Caldicellulosiruptor bescii strain DSM 6725T sp. nov. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.017731-0, ijs.0.017731-017730
Mathrani IM, Ahring BK (1992) Thermophilic and alkalophilic xylanases from several Dictyoglomus isolates. Appl Microbiol Biotechnol 38:23–27
Mathrani IM, Ahring BK (1991) Isolation and characterization of a strictly xylan-degrading Dictyoglomus from a man-made, thermophilic anaerobic environment. Arch Microbiol 157:13–17
Podosokorskaya OA, Merkel AY, Kolganova TV, Chernyh NA, Miroshnichenko ML, Bonch-Osmolovskaya EA, Kublanov IV (2011) Fervidobacterium reparium sp. nov., a thermophilic anaerobic cellulolytic bacterium isolated from a hot spring. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.026070-0
Acknowledgments
We thank the National Park Service and especially Christie Hendrix for coordinating and allowing sampling under permit #YELL-2008-SCI-5714. Heidi Anderson at the Yellowstone Center for Resources helped with plant species identification. We kindly thank Zamin Koo Yang for the assistance with pyrosequencing and Xiangping Yin for ICP analysis. Christopher W. Schadt provided helpful comments on the manuscript. This work was supported by the BioEnergy Science Center (BESC), which is a U.S. Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science, Oak Ridge National Laboratory. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725.
Author information
Authors and Affiliations
Corresponding author
Additional information
The submitted manuscript has been authored by a contractor of the U.S. Government under contract DE-AC05-00OR22725. Accordingly, the U.S. Government retains a nonexclusive, royalty-free license to publish or reproduce the published form of this contribution, or allow others to do so, for U.S. Government purposes.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Supplementary Table S1
(DOCX 37 kb)
Supplementary Fig. S1
(DOCX 131 kb)
Supplementary Fig. S2
(DOCX 239 kb)
Supplementary Fig. S3
(DOCX 503 kb)
Supplementary Fig. S4
(DOCX 454 kb)
Supplementary Fig. S5
(DOCX 295 kb)
Rights and permissions
About this article
Cite this article
Vishnivetskaya, T.A., Hamilton-Brehm, S.D., Podar, M. et al. Community Analysis of Plant Biomass-Degrading Microorganisms from Obsidian Pool, Yellowstone National Park. Microb Ecol 69, 333–345 (2015). https://doi.org/10.1007/s00248-014-0500-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00248-014-0500-8