Relevance of a crenarchaeotal subcluster related to Candidatus Nitrosopumilus maritimus to ammonia oxidation in the suboxic zone of the central Baltic Sea

ISME J. 2010 Dec;4(12):1496-508. doi: 10.1038/ismej.2010.78. Epub 2010 Jun 10.


Marine pelagic redoxclines are areas of enhanced biogeochemical cycling inhabited by distinct functional groups of prokaryotes. In this study, the diversity and abundance of archaeal and bacterial nitrifying populations throughout a pelagic redoxcline in the central Baltic Sea were examined using a suite of molecular methods. 16S rRNA/rRNA gene as well as bacterial and archaeal amoA mRNA/amoA gene fingerprints and clone libraries revealed that the putative nitrifying assemblages consisted solely of one crenarchaeotal subcluster, named GD2, which was closely related to Candidatus Nitrosopumilus maritimus. Neither distinct differences between transcript- and gene-based fingerprints nor pronounced differences in the crenarchaeotal composition throughout the whole redoxcline were detected. The abundance of this GD2 subgroup, as determined by the oligonucleotide probe Cren537 and the newly developed and more specific probe Cren679 showed that GD2 and total crenarchaeotal cell numbers were nearly identical throughout the redoxcline. The highest GD2 abundance (2.3 × 10⁵ cells ml⁻¹) occurred in the suboxic zone, accounting for around 26% of total prokaryotic cells. Below the chemocline, GD2 abundance was relatively stable (1.5-1.9 × 10⁵ cells ml⁻¹). Archaeal amoA expression was detected only in the putative nitrification zone and formed a narrow band in the suboxic layer, where ammonium, oxygen, nitrate, nitrite and phosphate concentrations were below 5 μmol l⁻¹. To our knowledge this is the first study to show the dominance of only one crenarchaeotal nitrifying key cluster in a natural habitat. The metabolic properties and survival mechanisms present in this cluster inside and outside the nitrification zone remain to be determined.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Ammonia / metabolism*
  • Crenarchaeota / classification*
  • Crenarchaeota / enzymology
  • Crenarchaeota / genetics
  • DNA Fingerprinting
  • DNA, Archaeal / genetics
  • Nitrification*
  • Nucleic Acid Probes
  • Oceans and Seas
  • Oxidation-Reduction
  • Oxidoreductases / genetics
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics
  • Seawater / chemistry
  • Seawater / microbiology*
  • Sequence Analysis, DNA
  • Water Microbiology


  • DNA, Archaeal
  • Nucleic Acid Probes
  • RNA, Ribosomal, 16S
  • Ammonia
  • Oxidoreductases
  • ammonia monooxygenase