Abstract
The majority of microorganisms in natural environments resist laboratory cultivation. Sometimes referred to as ‘unculturable’, many phylogenetic groups are known only by fragments of recovered DNA. As a result, the ecological significance of whole branches of the ‘tree of life’ remains a mystery; this is particularly true when regarding genetic material retrieved from extreme environments. Geochemically relevant media have been used to improve the success of culturing Archaea and Bacteria, but these efforts have focused primarily on optimizing pH, alkalinity, major ions, carbon sources, and electron acceptor–donor pairs. Here, we cultured thermophilic microorganisms from ‘Sylvan Spring’ (Yellowstone National Park, USA) on media employing different trace element solutions, including one that mimicked the source fluid of the inocula. The growth medium that best simulated trace elements found in ‘Sylvan Spring’ produced a more diverse and faster growing mixed culture than media containing highly elevated trace element concentrations. The elevated trace element medium produced fewer phylotypes and inhibited growth. Trace element concentrations appear to influence growth conditions in extreme environments. Incorporating geochemical data into cultivation attempts may improve culturing success.
Similar content being viewed by others
Notes
For information regarding the naming of this hydrothermal feature, see Meyer-Dombard, et al., 2005.
References
Adams MWW (1995) Thermophilic Archaea: an overview. In: Robb FT, Place AR (eds) Archaea, a laboratory manual: thermophiles. Cold Spring Harbor Press, New York, pp 3–7
Adams MWW (1998) The evolutionary significance of the metabolism of tungsten by microorganisms growing at 100C. In: Weigel J, Adams MWW (eds) Thermophiles: the keys to molecular evolution and the origin of life. Taylor and Francis, Philadelphia, pp 325–338
Allen MB (1959) Studies with Cyanidium caldarium, an anomalously pigmented chlorophyte. Arch Microbiol 32:270–277
Allen ET, Day AL (1935) Hot springs of the Yellowstone National Park. Waverly Press, Baltimore
Alves MP, Rainey FA, Nobre MF, da Costa MS (2003) Thermomonas hydrothermalis sp. nov., a new slightly thermophilic gamma-Proteobacterium isolated from a hot spring in central Portugal. Syst Appl Microbiol 26:70–75
Amend JP, Meyer-Dombard DR, Sheth SN, Zolotova N, Amend AC (2003a) Palaeococcus helgesonii, sp. nov., a facultatively anaerobic, hyperthermophilic Archaeon from a geothermal well on Vulcano Island, Italy. Arch Microbiol 179:394–401
Amend JP, Rogers KL, Shock EL, Inguaggiato S, Gurrieri S (2003b) Energetics of chemolithoautotrophy in the hydrothermal system of Vulcano Island, southern Italy. Geobiology 1:37–58
Atlas RM (2004) Handbook of microbiological media. CRC Press, Boca Raton
Ball JW, Nordstrom DK, Jenne EA, Vivit DV (1998) Chemical analyses of hot springs, pools, geysers, and surface waters from Yellowstone National Park, Wyoming, and vicinity, 1974–1975, US Geological Survey: 45
Ball JW, Nordstrom DK, McCleskey RB, Schoonen MAA, Xu Y (2001) Water chemistry and on-site sulfur-speciation data for selected springs in Yellowstone National Park, Wyoming, 1996–1998, US Geological Survey: 41
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 91:1609–1613
Baross JA (1995) Isolation, growth, and maintenance of hyperthermophiles. In: Robb FT, Place AR (eds) Archaea, a laboratory manual: thermophiles. Cold Spring Harbor Press, New York, pp 15–23
Beeder J, Torsvik T, Lien T (1995) Thermodesulforhadbus norvegicus gen. nov., sp. nov., a novel thermophilic sulfate-reducing bacterium from oil field water. Arch Microbiol 164:331–336
Bodrossy L, Kovaks KL, McDonald IR, Murrell JC (1999) A novel thermophilic methane-oxidising gamma-Proteobacterium. FEMS Microbiol Lett 170:335–341
Bonch-Osmolovskaya EA, Slesarev AI, Miroshnichenko ML, Svetlichnaya TP, Alekseev VA (2001) Characterization of Desulfurococcales amylolyticus n. sp.—a new extremely thermophilic archaebacterium isolated from thermal springs of Kamchatka and Kunashir Island. Mikrobiologiya 57:94–101
Boone DR, Johnson RL, Liu Y (1989) Diffusion of the interspecies electron carriers H2 and formate in methanogenic ecosystems and its implications in the measurement of K m for H2 or formate uptake. Appl Environ Microbiol 55:1735–1741
Boyd ES, Jackson RA, Encarnacion G, Zahn JA, Beard T, Leavitt WD, Pi Y, Zhang CL, Pearson A, Geesey GG (2007) Isolation, characterization, and ecology of sulfur-respiring Crenarchaea inhabiting acid-sulfate-chloride-containing geothermal springs in Yellowstone National Park. Appl Environ Microbiol 73:6669–6677
Boyd ES, Leavitt WD, Geesey GG (2009) CO2 uptake and fixation by a thermoacidophilic microbial community attached to precipitated sulfur in a geothermal spring. Appl Environ Microbiol 75:4289–4296
Brantley SL, Liermann L, Bau M, Wu S (2001) Uptake of trace metals and rare Earth elements from hornblende by a soil Bacterium. Geomicrobiol J 18:37–61
Brierley CL, Brierley JA (1973) A chemoautotrophic and thermophilic microorganism isolated from an acid hotspring. Can J Microbiol 19:183–188
Brock TD (1978) Thermophilic microorganisms and life at high temperatures. Springer, New York
Brock TD, Freeze H (1969) Thermus aquaticus gen. n. and sp. n., a nonsporulating extreme thermophile. J Bacteriol 98:289–297
Burggraf S, Huber R, Mayer T, Rossnagel P, Rachel R (2001) Isolation of hyperthermophilic Archaea previously detected by sequencing rDNA directly from the environment. In: Reysenbach AL, Voytek M, Mancinelli R (eds) Thermophiles: biodiversity ecology and evolution. Kluwer Academic/Plenum Publishers, New York, pp 93–102
Burlage RS, Atlas R, Stahl DA, Geesey G, Sayler G (1998) Techniques in microbial ecology. Oxford University Press, Oxford
Burnett GW, Pelczar MJ Jr, Conn HJ (1957) Preparation of media. In: Conn HJ, Pelczar MJ Jr (eds) Manual of microbiological methods. McGraw-Hill, New York, pp 37–63
Busse H-J, Kampfer P, Moore ERB, Nuutinen J, Tsitko IV, Denner EBM, Vauterin L, Valens M, Rossello-Mora R, Salkinoja-Salonen MS (2002) Thermomonas haemolytica gen nov., sp. nov., a gamma-Proteobacterium from kaolin slurry. Int J Syst Evol Microbiol 52:473–483
Caldwell DE, Wolfaardt GM, Korber DR, Karthikeyan S, Lawrence JR, Brannan DK (2002) Cultivation of microbial consortia and communities. In: Hurst CJ, Crawford RL, Knudsen GR, McInerney MJ, Stetzenbach LD (eds) Manual of environmental microbiology. ASM Press, Washington, DC, pp 92–100
Castenholtz RW (1969) Thermophilic blue-green algae and the thermal environment. Bacteriol Rev 33:476–504
Castenholtz RW (1988a) Culturing methods for cyanobacteria. Methods Enzymol 167:68–93
Castenholtz RW (1988b) Thermophilic cyanobacteria: special problems. Methods Enzymol 167:96–100
Cho J-C, Giovannoni SJ (2004) Cultivation and growth characteristics of a diverse group of oligotrophic marine Gamma Proteobacteria. Appl Environ Microbiol 70:432–440
D’Imperio S, Lehr CR, Oduro H, Druschel GK, Kuhl M, McDermott TR (2008) Relative importance of H2 and H2S as energy sources for primary production in geothermal springs. Appl Environ Microbiol 74:5802–5808
Davis KER, Joseph SJ, Hanssen PH (2005) Effects of growth medium, inoculation size, and incubation time on culturability and isolation of soil Bacteria. Appl Environ Microbiol 71:826–834
de la Torre JR, Goebel BM, Friedmann EI, Pace NR (2003) Microbial diversity of cryptoendolithic communities from the McMurdo Dry Valleys, Antarctica. Appl Environ Microbiol 69:3858–3867
Dhillon A, Teske A, Dillon J, Stahl DA, Sogin ML (2003) Molecular characterization of sulfate-reducing Bacteria in the Guaymas Basin. Appl Environ Microbiol 69:2765–2772
Eder W, Huber R (2002) New isolates and physiological properties of the Aquificales and description of Thermocrinis albus sp. nov. Extremophiles 6:309–318
Edwards KJ, Rogers DR, Wirsen CO, McCollom TM (2003) Isolation and characterization of novel psychrophilic, neutrophilic, Fe-oxidizing, chemolithoautotrophic α- and γ-Proteobacteria from the deep sea. Appl Environ Microbiol 69:2906–2913
Elshahed MS, Senko JM, Najar FZ, Kenton SM, Roe BA, Dewers TA, Spear JR, Krumholz LR (2003) Bacterial diversity and sulfur cycling in a mesophilic sulfide-rich spring. Appl Environ Microbiol 69:5609–5621
Fishbain S, Dillon JG, Gough HL, Stahl DA (2003) Linkage of high rates of sulfate reduction in Yellowstone hot springs to unique types in the dissimilatory sulfate respiration pathway. Appl Environ Microbiol 69:3663–3667
Ghosh D, Bal B, Kashyap VK, Pal S (2003) Molecular phylogenetic exploration of Bacteria diversity in a Bakreshwar (India) hot spring and culture of Shewanella-related thermophiles. Appl Environ Microbiol 69:4332–4336
Giovannoni SJ, Mullins TD, Field KG (1995) Microbial diversity in oceanic systems: rRNA approaches to the study of unculturable microbes. Molecular ecology of aquatic microbes. I. Joint. Springer, Berlin, G 38:217–248
Gotz D, Banta AB, Rushdi AI, Simoneit BRT, Reysenbach A-L (2002) Persephonella marina gen. nov., sp. nov., and Persephonella guaymasensis sp. nov., two novel, thermophilic, hydrogen-oxidizing microaerophiles from deep-sea hydrothermal vents. Int J Syst Evol Microbiol 52:1349–1359
Grant CL, Pramer D (1962) Minor element composition of yeast extract. J Bacteriol 84:869–870
Guirard BM, Snell EE (1981) Biochemical factors in growth. In: Gerhardt P, Murray R, Costilow R, Nester E, Wood W, Krieg N, Phillips GB (eds) Manual of methods for General bacteriology. American Society for Microbiology, Washington, DC, pp 79–111
Hallberg KB, Lindstrom EB (1994) Characterization of Thiobacillus caldus sp. nov., a moderately thermophilic acidophile. Microbiology 140:3451–3456
Handelsman J, Tiedje JM (2007) Revealing the secrets of our microbial planet. NRC Committee on metagenomics: challenges and functional applications. National Academy of Sciences, Washington, DC, 158
Haouari O, Fardeau ML, Cayol JL, Casoit C, Elbaz-Poulichet F, Hamdi M, Joseph M, Ollivier B (2008) Desulfotomaculum hydrothermale sp. nov., a thermophilic sulfate-reducing bacterium isolated from a terrestrial Tunisian hot spring. Int J Syst Evol Microbiol 58:2529–2535
Huber R, Burggraf S, Mayer T, Barns SM, Rossnagel P, Stetter KO (1995) Isolation of a hyperthermophilic Archaeum predicted by in situ RNA analysis. Nature 376:57–58
Huber R, Dyba D, Huber H, Burggraf S, Rachel R (1998a) Sulfur-inhibited Thermosphaera aggregans sp. nov., a new genus of hyperthermophilic Archaea isolated after its prediction from environmentally derived 16S rRNA sequences. Int J Syst Bacteriol 48:31–38
Huber R, Eder W, Heldwein S, Wanner G, Huber H, Rachel R, Stetter KO (1998b) Thermocrinis ruber gen. nov., sp. nov., a pink-filament forming hyperthermophilic Bacterium isolated from Yellowstone National Park. Appl Environ Microbiol 64:3576–3583
Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO (2002) A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417:63–67
Hugenholtz P, Pitulle C, Hershberger KL, Pace NR (1998) Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 180:366–376
Inagaki F, Takai K, Hirayama H, Yamato Y, Nealson KH, Horikoshi K (2003) Distribution and phylogenetic diversity of the subsurface microbial community in a Japanese epithermal gold mine. Extremophiles 7:307–317
Johnson DB (1995) Selective solid media for isolating and enumerating acidophilic bacteria. J Microbiol Meth 23:205–218
Kaeberlein T, Lewis K, Epstein SS (2002) Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 296:1127–1129
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
Köpke B, Wilms R, Engelen B, Cypionka H, Sass H (2005) Microbial diversity in coastal subsurface sediments: a cultivation approach using various electron acceptors and substrate gradients. Appl Environ Microbiol 71:7819–7830
Kreig NR (1981) Enrichment and isolation. In: Gerhardt P, Murray R, Costilow R et al (eds) Manual of methods for general bacteriology. American Society for Microbiology, Washington, DC, pp 112–142
Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–175
LaPaglia C, Hartzell PL (1997) Stress-induced production of biofilm in the hyperthermophilic Archeoglobus fulgidus. Appl Environ Microbiol 63:3158–3163
Lloyd KG, Edgecomb VP, Molyneaux SJ, Boer S, Wirsen CO, Atkins MS, Teske A (2005) Effects of dissolved sulfide, pH, and temperature on growth and survival of marine hyperthermophilic Archaea. Appl Environ Microbiol 71:6383–6387
Meyer-Dombard DR (2004). Geochemical constraints on microbial diversity in Yellowstone National Park. Thesis, Doctor of Philosophy, Washington University in St. Louis
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
Nakagawa S, Shtaih Z, Banta A, Beveridge TJ, Sako Y, Reysenbach A-L (2005) Sulfurihydrogenibium yellowstonense sp. nov., and extremely thermophilic, facultatively heterotrophic, sulfur-oxidizing bacterium from Yellowstone National Park, and emended descriptions of the genus Sulfurihydrogenibium, Sulfurihydrogenibium subterraneum, and Sulfurihydrogenibium azorense. Int J Syst Evol Microbiol 55:2263–2268
Nordstrom DK, Ball JW, McCleskey RB (2005) Ground water to surface water: chemistry of thermal outflows in Yellowstone National Park. In: Inskeep W, McDermott TR, McDermott TR (eds) Geothermal biology and geochemistry in Yellowstone National Park. Thermal Biology Institute, Montana State University, pp 71–94
Nordstrom DK, McCleskey RB, Ball JW (2009) Sulfur geochemistry of hydrothermal waters in Yellowstone National Park: IV Acid-sulfate waters. Appl Geochem 24:191–207
Ochsenreiter T, Selezi D, Quaiser A, Bonch-Osmolovskaya L, Schleper C (2003) Diversity and abundance of Crenarchaeota in terrestrial habitats studies by 16S RNA surveys and real time PCR. Environ Microbiol 5:787–797
Osburn MR, Amend JP (2010) Thermogladius shockii gen. nov., sp. nov., a hyperthermophilic crenarchaeote from Yellowstone National Park, USA. Arch Microbiol 193:45–52
Rappé MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394
Rappé MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630–633
Rathgebar C, Yurkova N, Stackebrandt E, Beatty JT, Yurkov V (2002) Isolation of tellurite- and selenite-resistant Bacteria from hydrothermal vents of the Juan de Fuca Ridge in the Pacific Ocean. Appl Environ Microbiol 68:4613–4622
Reed DW, Fujita Y, Delwiche ME, Blackwelder DB, Sheridan PP, Uchida T, Colwell FS (2002) Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl Environ Microbiol 68:3759–3770
Reysenbach AL, Banta AB, Boone DR, Cary SC, Luther GW (2000a) Microbial essentials at hydrothermal vents. Nature 404:835
Reysenbach AL, Longnecker K, Kirshtein J (2000b) Novel bacterial and archaeal lineages from an in situ growth chamber deployed at a Mid-Atlantic Ridge hydrothermal vent. Appl Environ Microbiol 66(9):3798–3806
Robb FT, Place AR, Sowers KR, Schreier HJ, DasSarma S, Fleischmann EM (1995) Archaea, a laboratory manual: thermophiles. Cold Spring Harbor Press, New York
Schleper C, Jurgens G, Jonuscheit M (2005) Genomic studies of uncultivated Archaea. Nat Rev Microbiol 3:479–488
Segerer A, Neuner A, Kristjansson JK, Stetter KO (1986) Acidianus infernus gen. nov., sp. nov., and Acidianus brierleyi comb. nov.: facultatively aerobic, extremely acidophilic thermophilic sulfur-metabolizing Archaebacteria. Int J Syst Bacteriol 36:559–564
Shock EL, Holland M, Meyer-Dombard DR, Amend JP (2005) Geochemical sources of energy for microbial metabolism in hydrothermal ecosystems: Obsidian Pool, Yellowstone National Park, USA. In: Inskeep W, McDermott TR (eds) Geothermal biology and geochemistry in Yellowstone National Park. Thermal Biology Institute, Montana State University, pp 95–112
Shock EL, Holland ME, Meyer-Dombard DR, Amend JP, Osburn GR, Fisher T (2010) Quantifying inorganic sources of geochemical energy in hydrothermal ecosystems, Yellowstone National Park, USA. Geochim Cosmochim Acta 74:4005–4043
Silver S (1997) The bacterial view of the periodic table: specific functions for all elements. In: Banfield JF, Nealson KH (eds) Geomicrobiology: interactions between microbes and minerals. Mineralogical Society of America, Washington, DC, 35:345–360
Stetter KO, Konig H, Stackebrandt E (1983) Pyrodictium gen, nov., a new genus of submarine disc-shaped sulfur reducing Archaebacteria growing optimally at 105 C. Syst Appl Microbiol 4:535–551
Takai K, Horikoshi K (1999) Genetic diversity of Archaea in deep-sea hydrothermal vent environments. Genetics 152:1285–1297
Takai K, Sako Y (1999) A molecular view of archaeal diversity in marine and terrestrial hot water environments. FEMS Microbiol Ecol 28:177–188
Wackett LP, Dodge AG, Ellis LBM (2004) Microbial genomics and the periodic table. Appl Environ Microbiol 70:647–655
Ward DM, Bateson MM, Ferris MJ, Kuhl M, Wieland A, Koeppel A, Cohan FM (2006) Cyanobacterial ecotypes in the microbial mat community of Mushroom Spring (Yellowstone National Park, Wyoming) as species-like units linking microbial community composition, structure, and function. Philos Trans R Soc Lond B 361:1997–2008
White DE, Hutchinson RA, Keith TEC (1988) The geology and remarkable thermal activity of Norris Geyser Basin, Yellowstone National Park, Wyoming. Washington, US Geological Survey: 84
Wiegel J (1986) Methods for isolation and study of thermophiles. In: Brock TD (ed) Thermophiles: general molecular and applied microbiology. Wiley, New York, pp 17–37
Wolin EA, Wolin MJ, Wolfe RS (1963) Formation of methane by bacterial extracts. J Biol Chem 238:2882–2886
Zengler K, Toledo G, Rappe M, Elkins J, Mathur EJ, Short JM, Keller M (2002) Cultivating the uncultured. Proc Natl Acad Sci 99:15681–15686
Zillig W, Stetter KO (1983) In Validation of the publication of new names and new combinations previously effectively published outside the IJSB. List No. 10. Int J Syst Evol Microbiol 33:438–440
Acknowledgments
This work was funded largely by a NASA Graduate Student Research Program (GSRP) fellowship (NGT5-50348) to D.R.M.D., also NSF-LExEN (OCE-9817730), and NASA Astrobiology Institute (Carnegie Institution) to E.L.S., and a NSF-CAREER grant (0447231) to J.P.A.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by F. Robb.
Rights and permissions
About this article
Cite this article
Meyer-Dombard, D.R., Shock, E.L. & Amend, J.P. Effects of trace element concentrations on culturing thermophiles. Extremophiles 16, 317–331 (2012). https://doi.org/10.1007/s00792-012-0432-5
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00792-012-0432-5