Strategies to determine diversity, growth, and activity of ammonia-oxidizing archaea in soil

Graeme W Nicol, James I Prosser

Research output: Chapter in Book/Report/Conference proceedingChapter

8 Citations (Scopus)

Abstract

Ecological studies of soil microorganisms require reliable techniques for assessment of microbial community composition, abundance, growth, and activity. Soil structure and physicochemical properties seriously limit the applicability and value of methods involving direct observation, and ecological studies have focused on communities and populations, rather than single cells or microcolonies. Although ammonia-oxidizing archaea were discovered 5 years ago, there are still no cultured representatives from soil and there remains a lack of knowledge regarding their genomic composition, physiology, or functional diversity. Despite these limitations, however, significant insights into their distribution, growth characteristics, and metabolism have been made through the use of a range of molecular methodologies. As well as the analysis of taxonomic markers such as 16S rRNA genes, the development of PCR primers based on a limited number of (mostly marine) sequences has enabled the analysis of homologues encoding proteins involved in energy and carbon metabolism. This chapter will highlight the range of molecular methodologies available for examining the diversity, growth, and activity of ammonia-oxidizing archaea in the soil environment.
Original languageEnglish
Title of host publicationResearch on Nitrification and Related Processes, Part B
EditorsM. G. Klotz, L. Y. Stein
Place of PublicationSan Diego
PublisherElsevier Academic Press
Pages3-34
Number of pages32
Volume496
ISBN (Print)978-0-12-386489-5
DOIs
Publication statusPublished - 2011

Publication series

NameMethods in Enzymology
PublisherELSEVIER ACADEMIC PRESS INC
Volume496
ISSN (Print)0076-6879

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Keywords

  • ammonia
  • archaea
  • biodiversity
  • DNA fingerprinting
  • genes, rRNA
  • oxidoreductases
  • ribotyping
  • sequence analysis, DNA
  • soil microbiology
  • ammonia-oxidizing archaea
  • thaumarchaeota
  • soil
  • ammonia oxidation

Cite this

Nicol, G. W., & Prosser, J. I. (2011). Strategies to determine diversity, growth, and activity of ammonia-oxidizing archaea in soil. In M. G. Klotz, & L. Y. Stein (Eds.), Research on Nitrification and Related Processes, Part B (Vol. 496, pp. 3-34). (Methods in Enzymology; Vol. 496). San Diego: Elsevier Academic Press. https://doi.org/10.1016/B978-0-12-386489-5.00001-4