Selective Phylogenetic Analysis Targeted at 16S RRNA Genes of Thermophiles and Hyperthermophiles in Deep-subsurface Geothermal Environments

Overview

Journal Appl Environ Microbiol

Specialties Environmental Health
Microbiology

Date 2006 Jan 5

PMID 16391020

Citations 18

Authors

Hiroyuki Kimura

Maki Sugihara

Kenji Kato

Satoshi Hanada

Affiliations

Soon will be listed here.

Abstract

Deep-subsurface samples obtained by deep drilling are likely to be contaminated with mesophilic microorganisms in the drilling fluid, and this could affect determination of the community structure of the geothermal microflora using 16S rRNA gene clone library analysis. To eliminate possible contamination by PCR-amplified 16S rRNA genes from mesophiles, a combined thermal denaturation and enzyme digestion method, based on a strong correlation between the G+C content of the 16S rRNA gene and the optimum growth temperatures of most known prokaryotic cultures, was used prior to clone library construction. To validate this technique, hot spring fluid (76 degrees C) and river water (14 degrees C) were used to mimic a deep-subsurface sample contaminated with drilling fluid. After DNA extraction and PCR amplification of the 16S rRNA genes from individual samples separately, the amplified products from river water were observed to be denatured at 82 degrees C and completely digested by exonuclease I (Exo I), while the amplified products from hot spring fluid remained intact after denaturation at 84 degrees C and enzyme digestion with Exo I. DNAs extracted from the two samples were mixed and used as a template for amplification of the 16S rRNA genes. The amplified rRNA genes were denatured at 84 degrees C and digested with Exo I before clone library construction. The results indicated that the 16S rRNA gene sequences from the river water were almost completely eliminated, whereas those from the hot spring fluid remained.

Citing Articles

Sediment microbial community structure associated to different ecological types of mangroves in Celestún, a coastal lagoon in the Yucatan Peninsula, Mexico.

Gomez-Acata E, Teutli C, Falcon L, Garcia-Maldonado J, Prieto-Davo A, Yanez-Montalvo A PeerJ. 2023; 11:e14587.

PMID: 36785710 PMC: 9921989. DOI: 10.7717/peerj.14587.

Diversity and Distribution of Anaerobic Ammonium Oxidation Bacteria in Hot Springs of Conghua, China.

Liu L, Lv A, Rao M, Ming Y, Salam N, Li M Front Microbiol. 2022; 12:739234.

PMID: 35145488 PMC: 8822059. DOI: 10.3389/fmicb.2021.739234.

A positive correlation between GC content and growth temperature in prokaryotes.

Hu E, Lan X, Liu Z, Gao J, Niu D BMC Genomics. 2022; 23(1):110.

PMID: 35139824 PMC: 8827189. DOI: 10.1186/s12864-022-08353-7.

Vestiges of Adaptation to the Mesophilic Environment in the Genome of Tepiditoga spiralis gen. nov., sp. nov.

Mori K, Sakurai K, Hosoyama A, Kakegawa T, Hanada S Microbes Environ. 2020; 35(4).

PMID: 32963207 PMC: 7734402. DOI: 10.1264/jsme2.ME20046.

TEMPURA: Database of Growth TEMPeratures of Usual and RAre Prokaryotes.

Sato Y, Okano K, Kimura H, Honda K Microbes Environ. 2020; 35(3).

PMID: 32727974 PMC: 7511790. DOI: 10.1264/jsme2.ME20074.

References

Kimura H, Asada R, Masta A, Naganuma T . Distribution of microorganisms in the subsurface of the manus basin hydrothermal vent field in Papua New Guinea. Appl Environ Microbiol. 2003; 69(1):644-8. PMC: 152445. DOI: 10.1128/AEM.69.1.644-648.2003. View

Hiraishi A . Direct automated sequencing of 16S rDNA amplified by polymerase chain reaction from bacterial cultures without DNA purification. Lett Appl Microbiol. 1992; 15(5):210-3. DOI: 10.1111/j.1472-765x.1992.tb00765.x. View

Yumoto I, Hirota K, Sogabe Y, Nodasaka Y, Yokota Y, Hoshino T . Psychrobacter okhotskensis sp. nov., a lipase-producing facultative psychrophile isolated from the coast of the Okhotsk Sea. Int J Syst Evol Microbiol. 2003; 53(Pt 6):1985-9. DOI: 10.1099/ijs.0.02686-0. View

Williams M, Domingo J, Meckes M, Kelty C, Rochon H . Phylogenetic diversity of drinking water bacteria in a distribution system simulator. J Appl Microbiol. 2004; 96(5):954-64. DOI: 10.1111/j.1365-2672.2004.02229.x. View

Takai K, Gamo T, Tsunogai U, Nakayama N, Hirayama H, Nealson K . Geochemical and microbiological evidence for a hydrogen-based, hyperthermophilic subsurface lithoautotrophic microbial ecosystem (HyperSLiME) beneath an active deep-sea hydrothermal field. Extremophiles. 2004; 8(4):269-82. DOI: 10.1007/s00792-004-0386-3. View

Brenner D, Davis B, Steigerwalt A, Riddle C, McWHORTER A, Allen S . Atypical biogroups of Escherichia coli found in clinical specimens and description of Escherichia hermannii sp. nov. J Clin Microbiol. 1982; 15(4):703-13. PMC: 272169. DOI: 10.1128/jcm.15.4.703-713.1982. View

Lipman D, Pearson W . Rapid and sensitive protein similarity searches. Science. 1985; 227(4693):1435-41. DOI: 10.1126/science.2983426. View

Brody R, Doherty K, Zimmerman P . Processivity and kinetics of the reaction of exonuclease I from Escherichia coli with polydeoxyribonucleotides. J Biol Chem. 1986; 261(16):7136-43. View

Somerville C, Knight I, Straube W, Colwell R . Simple, rapid method for direct isolation of nucleic acids from aquatic environments. Appl Environ Microbiol. 1989; 55(3):548-54. PMC: 184158. DOI: 10.1128/aem.55.3.548-554.1989. View

10.

Stackebrandt E, Charfreitag O . Partial 16S rRNA primary structure of five Actinomyces species: phylogenetic implications and development of an Actinomyces israelii-specific oligonucleotide probe. J Gen Microbiol. 1990; 136(1):37-43. DOI: 10.1099/00221287-136-1-37. View

11.

Gold T . The deep, hot biosphere. Proc Natl Acad Sci U S A. 1992; 89(13):6045-9. PMC: 49434. DOI: 10.1073/pnas.89.13.6045. View

12.

Yamamoto H, Hiraishi A, Kato K, Chiura H, Maki Y, Shimizu A . Phylogenetic evidence for the existence of novel thermophilic bacteria in hot spring sulfur-turf microbial mats in Japan. Appl Environ Microbiol. 1998; 64(5):1680-7. PMC: 106215. DOI: 10.1128/AEM.64.5.1680-1687.1998. View

13.

Galtier N, Tourasse N, Gouy M . A nonhyperthermophilic common ancestor to extant life forms. Science. 1999; 283(5399):220-1. DOI: 10.1126/science.283.5399.220. View

14.

Higashi Y, Sunamura M, Kitamura K, Nakamura K, Kurusu Y, Ishibashi J . Microbial diversity in hydrothermal surface to subsurface environments of Suiyo Seamount, Izu-Bonin Arc, using a catheter-type in situ growth chamber. FEMS Microbiol Ecol. 2009; 47(3):327-36. DOI: 10.1016/S0168-6496(04)00004-2. View

15.

von Wintzingerode F, Landt O, Ehrlich A, Gobel U . Peptide nucleic acid-mediated PCR clamping as a useful supplement in the determination of microbial diversity. Appl Environ Microbiol. 2000; 66(2):549-57. PMC: 91862. DOI: 10.1128/AEM.66.2.549-557.2000. View

16.

Skirnisdottir S, Hreggvidsson G, Hjorleifsdottir S, Marteinsson V, Petursdottir S, Holst O . Influence of sulfide and temperature on species composition and community structure of hot spring microbial mats. Appl Environ Microbiol. 2000; 66(7):2835-41. PMC: 92081. DOI: 10.1128/AEM.66.7.2835-2841.2000. View

17.

Maidak B, Cole J, Lilburn T, Parker Jr C, Saxman P, Farris R . The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 2000; 29(1):173-4. PMC: 29785. DOI: 10.1093/nar/29.1.173. View

18.

Summit M, Baross J . A novel microbial habitat in the mid-ocean ridge subseafloor. Proc Natl Acad Sci U S A. 2001; 98(5):2158-63. PMC: 30109. DOI: 10.1073/pnas.051516098. View

19.

Takai K, Komatsu T, Horikoshi K . Hydrogenobacter subterraneus sp. nov., an extremely thermophilic, heterotrophic bacterium unable to grow on hydrogen gas, from deep subsurface geothermal water. Int J Syst Evol Microbiol. 2001; 51(Pt 4):1425-1435. DOI: 10.1099/00207713-51-4-1425. View

20.

Marteinsson V, Hauksdottir S, Hobel C, Kristmannsdottir H, Hreggvidsson G, Kristjansson J . Phylogenetic diversity analysis of subterranean hot springs in Iceland. Appl Environ Microbiol. 2001; 67(9):4242-8. PMC: 93153. DOI: 10.1128/AEM.67.9.4242-4248.2001. View