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Diversity of thermostable DNA enzymes from Icelandic hot springs

Hjorleifsdottir, Sigridur LU (2002)
Abstract
The diversities of bacteria as well as thermostable DNA enzymes in Icelandic hot springs were studied using different techniques. First of all the bacterial diversity of different microbial mats as well as sediment samples was described by using both molecular methods and cultivation methods. The molecular methods showed a low level of diversity and it was apparently lower as the environment became more extreme, e.g. in terms of higher temperature or higher sulfide concentration. The cultivation methods used gave mainly Thermus isolates. It was suggested that Thermus was the dominant bacterial organotroph in the hot spring studied. There were four different media used in the cultivation approach and they gave a biased selection of isolated... (More)
The diversities of bacteria as well as thermostable DNA enzymes in Icelandic hot springs were studied using different techniques. First of all the bacterial diversity of different microbial mats as well as sediment samples was described by using both molecular methods and cultivation methods. The molecular methods showed a low level of diversity and it was apparently lower as the environment became more extreme, e.g. in terms of higher temperature or higher sulfide concentration. The cultivation methods used gave mainly Thermus isolates. It was suggested that Thermus was the dominant bacterial organotroph in the hot spring studied. There were four different media used in the cultivation approach and they gave a biased selection of isolated species compared to the direct molecular diversity analysis. Some media were also more selective for one Thermus species than another. One new species of Thermus, T. scotoductus was isolated and described. Secondly, activity screenings for three different thermostable DNA enzymes were performed on cultivated strains from a large collection of thermophilic bacteria. The strains tested were from the genera Thermus, Rhodothermus, Bacillus and Hydrogenobacter. The enzymes screened for were thermostable DNA ligases, DNA polymerases and type II restriction endonucleases. Several new enzymes were found. Two of them were purified characterized and commercialized. The third and last approach was a sequence based screening performed both on cultivated strains and on complex environmental DNA samples. A PCR based method using CODEHOP degenerate primers was used for obtaining DNA polymerase gene fragments for sequencing. The phylogenetic relationship of the polymerase gene fragments was analysed. The genetic variability obtained among Thermus species indicated that Thermus is a diverse and still not a fully exhausted resource for searching for potentially valuable DNA polymerases. The polymerase gene fragments obtained from the complex hot spring DNA samples also showed a high number of new thermophilic DNA polymerases. Uncultivated biomass is therefore clearly also a good source for new DNA polymerases. (Less)
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author
supervisor
opponent
  • Professor Birkeland, Nils-Kåre, Bergen, Norge
organization
publishing date
type
Thesis
publication status
published
subject
keywords
thermophiles, microbial diversity, SSU rRNA, Thermus, hot springs, Biotechnology, Bioteknik, Biochemistry, enzymologi, Proteiner, enzymology, metabolism, Proteins, DNA enzymes, Biokemi
pages
130 pages
publisher
Biotechnology, Lund University
defense location
sal K:B, Kemicentrum, Lund
defense date
2002-05-23 10:15:00
external identifiers
  • other:ISRN: LUTKDH/TKBT--02/1059--SE
ISBN
91-89627-07-5
language
English
LU publication?
yes
additional info
Article: I. Hjorleifsdottir S, Skirnisdottir S, Hreggvidsson GO, Holst O, Kristjansson JK. (2001) Species Composition of Cultivated and Non-Cultivated Bacteria from Short Filaments in an Icelandic Hot Spring at 88°C. Microbial Ecol 42: 117-125 Article: II. Skirnisdottir S, Hreggvidsson GO, Hjorleifsdottir S, Marteinsson VT, Petursdottir SK, Holst O, Kristjansson JK. (2000). Influence of sulfide and temperature on species composition and community structure of hot spring microbial mats. Appl Environ Microbiol 66:2835-41 Article: III. Kristjansson JK, Hjorleifsdottir S, Marteinsson VT and Alfredsson GA. (1994). Thermus scotoductus, sp. nov., a pigment-producing thermophilic, bacterium from hot tap water in Iceland and including Thermus sp. X-1. System. Appl Microbiol 17: 44-50 Article: IV. Hjorleifsdottir S, Peturdottir SK, Korpela J, Torsti AM, Mattila P and Kristjansson JK. (1996). Screening for restriction endonucleases in aerobic, thermophilic eubacteria. Biotechnol Tech 10: 13-18 Article: V. Rönkä J, Hjorleifsdottir S, Tenkanen T, Pitkänen K, Mattila P and Kristjansson JK. (1991). RmaI, a type II restriction endonuclease from Rhodothermus marinus which recognizes 5'CTAG 3'. Nucleic Acids Res 19: 2789 Article: VI. Hjorleifsdottir S, Ritterbusch W, Petursdottir SK and Kristjansson JK. (1997). Thermostabilities of DNA ligases and DNA polymerases from four genera of thermophilic eubacteria. Biotechnol Lett 19: 147-150 Article: VII. Hjorleifsdottir S, Hreggvidsson GO, Finnbogadottir E and Kristjansson JK. A comprehensive biodiversity sequence analysis of DNA polymerase genes in the genus Thermus. Manuscript Article: VIII. Hjorleifsdottir S, Hreggvidsson GO, Finnbogadottir E, Thorisdottir A, Marteinsson VT and Kristjansson JK. Isolation of DNA polymerase gene fragments from complex microbial biomass samples using degenerated primers. Manuscript
id
e3d4156b-93e7-4c7f-ab09-8f7a8cd76b91 (old id 464623)
date added to LUP
2016-04-04 11:32:15
date last changed
2018-11-21 21:05:29
@phdthesis{e3d4156b-93e7-4c7f-ab09-8f7a8cd76b91,
  abstract     = {The diversities of bacteria as well as thermostable DNA enzymes in Icelandic hot springs were studied using different techniques. First of all the bacterial diversity of different microbial mats as well as sediment samples was described by using both molecular methods and cultivation methods. The molecular methods showed a low level of diversity and it was apparently lower as the environment became more extreme, e.g. in terms of higher temperature or higher sulfide concentration. The cultivation methods used gave mainly Thermus isolates. It was suggested that Thermus was the dominant bacterial organotroph in the hot spring studied. There were four different media used in the cultivation approach and they gave a biased selection of isolated species compared to the direct molecular diversity analysis. Some media were also more selective for one Thermus species than another. One new species of Thermus, T. scotoductus was isolated and described. Secondly, activity screenings for three different thermostable DNA enzymes were performed on cultivated strains from a large collection of thermophilic bacteria. The strains tested were from the genera Thermus, Rhodothermus, Bacillus and Hydrogenobacter. The enzymes screened for were thermostable DNA ligases, DNA polymerases and type II restriction endonucleases. Several new enzymes were found. Two of them were purified characterized and commercialized. The third and last approach was a sequence based screening performed both on cultivated strains and on complex environmental DNA samples. A PCR based method using CODEHOP degenerate primers was used for obtaining DNA polymerase gene fragments for sequencing. The phylogenetic relationship of the polymerase gene fragments was analysed. The genetic variability obtained among Thermus species indicated that Thermus is a diverse and still not a fully exhausted resource for searching for potentially valuable DNA polymerases. The polymerase gene fragments obtained from the complex hot spring DNA samples also showed a high number of new thermophilic DNA polymerases. Uncultivated biomass is therefore clearly also a good source for new DNA polymerases.},
  author       = {Hjorleifsdottir, Sigridur},
  isbn         = {91-89627-07-5},
  language     = {eng},
  publisher    = {Biotechnology, Lund University},
  school       = {Lund University},
  title        = {Diversity of thermostable DNA enzymes from Icelandic hot springs},
  year         = {2002},
}