Bacterial diversity in permanently cold and alkaline ikaite columns from Greenland

Mariane Schmidt Thøgersen, Anders Prieme, Peter Stougaard

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

Bacterial diversity in alkaline (pH 10.4) and permanently cold (4 degrees C) ikaite tufa columns from the Ikka Fjord, SW Greenland, was investigated using growth characterization of cultured bacterial isolates with Terminal-restriction fragment length polymorphism (T-RFLP) and sequence analysis of bacterial 16S rRNA gene fragments. More than 200 bacterial isolates were characterized with respect to pH and temperature tolerance, and it was shown that the majority were cold-active alkaliphiles. T-RFLP analysis revealed distinct bacterial communities in different fractions of three ikaite columns, and, along with sequence analysis, it showed the presence of rich and diverse bacterial communities. Rarefaction analysis showed that the 109 sequenced clones in the 16S rRNA gene library represented between 25 and 65% of the predicted species richness in the three ikaite columns investigated. Phylogenetic analysis of the 16S rRNA gene sequences revealed many sequences with similarity to alkaliphilic or psychrophilic bacteria, and showed that 33% of the cloned sequences and 33% of the cultured bacteria showed less than 97% sequence identity to known sequences in databases, and may therefore represent yet unknown species.
Original languageEnglish
JournalExtremophiles
Volume10
Issue number6
Pages (from-to)551-562
Number of pages12
ISSN1431-0651
DOIs
Publication statusPublished - 2006
Externally publishedYes

Keywords

  • Applied Microbiology and Biotechnology
  • Microbiology
  • Alkaliphiles
  • Diversity estimates
  • Ikaite
  • Phylogeny
  • Psychrophiles
  • Rarefaction analysis
  • Terminal-restriction fragment length polymorphism
  • Alkali
  • Bacterial DNA
  • Fresh Water
  • RNA 16S
  • Bacterium
  • Biodiversity
  • Chemistry
  • Classification
  • Cold climate
  • Comparative study
  • DNA sequence
  • Gene library
  • Genetic database
  • Genetics
  • Greenland
  • Growth, development and aging
  • Isolation and purification
  • Metabolism
  • pH
  • Restriction fragment length polymorphism
  • Ribotyping
  • Sediment
  • Sequence homology
  • Temperature
  • Alkalies
  • Bacteria
  • Cold Climate
  • Databases, Genetic
  • DNA, Bacterial
  • Gene Library
  • Geologic Sediments
  • Hydrogen-Ion Concentration
  • Polymorphism, Restriction Fragment Length
  • RNA, Ribosomal, 16S
  • Sequence Analysis, DNA
  • Sequence Homology, Nucleic Acid
  • Bacteria (microorganisms)
  • Biochemistry
  • Sulfur-oxidizing bacteria
  • Soda lake alkaliphiles
  • Mid-atlantic ridge
  • SP-NOV.
  • GEN. NOV.
  • MICROBIAL DIVERSITY
  • Nonparametric-estimation
  • Southwest Greenland
  • SPECIES RICHNESS
  • East-africa
  • diversity estimates
  • Greenland Denmark, Europe Palearctic region
  • Temperature tolerance
  • Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Endospore-forming Gram-Positives [07810] Bacillus alcalophilus species
  • Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Gram-Negative Aerobic Rods and Cocci [06500] Flavobacterium hydatis species
  • Facultatively Anaerobic Gram-Negative Rods Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Enterobacteriaceae [06702] Serratia fonticola species
  • Facultatively Anaerobic Gram-Negative Rods Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Vibrionaceae [06704] Shewanella arctica species
  • Gram-Negative Aerobic Rods and Cocci Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Neisseriaceae [06507] Psychrobacter glacialis species
  • Gram-Negative Aerobic Rods and Cocci Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Pseudomonadaceae [06508] Pseudomonas alcaligenes species
  • Purple Bacteria Anoxygenic Phototrophic Bacteria Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Purple Nonsulfur Bacteria [08013] Rhodobacter veldkampii species
  • Ikaite tufa
  • rRNA ribosomal RNA
  • 03502, Genetics - General
  • 07502, Ecology: environmental biology - General and methods
  • 10062, Biochemistry studies - Nucleic acids, purines and pyrimidines
  • 30000, Bacteriology, general and systematic
  • 31000, Physiology and biochemistry of bacteria
  • 31500, Genetics of bacteria and viruses
  • Biochemistry and Molecular Biophysics
  • Population Studies
  • Biogeography
  • Molecular Genetics

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