ORIGINAL PAPER Comparative analysis of archaeal 16S rRNA and amoA genes to estimate the abundance and diversity of ammonia-oxidizing archaea in marine sediments Soo-Je Park Æ Byoung-Joon Park Æ Sung-Keun Rhee Received: 31 January 2008 / Accepted: 7 April 2008 / Published online: 9 May 2008 Ó Springer 2008 Abstract Considering their abundance and broad distri- bution, non-extremophilic Crenarchaeota are likely to play important roles in global organic and inorganic matter cycles. The diversity and abundance of archaeal 16S rRNA and putative ammonia monooxygenase a-subunit (amoA) genes were comparatively analyzed to study genetic poten- tial for nitrification of ammonia-oxidizing archaea (AOA) in the surface layers (0–1 cm) of four marine sediments of the East Sea, Korea. After analysis of a 16S rRNA gene clone library, we found various archaeal groups that include the crenarchaeotal group (CG) I.1a (54.8%) and CG I.1b (5.8%), both of which are known to harbor ammonia oxidizers. Notably, the 16S rRNA gene of CG I.1b has only previously been observed in terrestrial environments. The 16S rRNA gene sequence data revealed a distinct difference in archaeal community among sites of marine sediments. Most of the obtained amoA sequences were not closely related to those of the clones retrieved from estuarine sediments and marine water columns. Furthermore, clades of unique amoA sequences were likely to cluster according to sampling sites. Using real-time PCR, quantitative analysis of amoA copy numbers showed that the copy numbers of archaeal amoA ranged from 1.1 9 10 7 to 4.9 9 10 7 per gram of sediment and were more numerous than those of bacterial amoA, with ratios ranging from 11 to 28. In conclusion, diverse CG I.1a and CG I.1b AOA inhabit surface layers of marine sediments and AOA, and especially, CG I.1a are more numerous than other ammonia-oxidizing bacteria. Keywords Ammonia-oxidizing archaea Á amoA Á 16S rRNA Á Marine sediment Introduction Cultivation-independent analysis of diversity using the PCR- amplification and sequencing of 16S rRNA gene is a useful method for identifying novel bacterial and archaeal phylo- genetic lineages from different environments. The first detection of crenarchaeotal 16S rRNA genes in ocean envi- ronments was surprising (DeLong 1992; Fuhrman et al. 1992) because they had previously only been cultivated from ther- mal and/or acidic environments. Thereafter, members of the phylum Crenarchaeota have been detected in most moderate and cold environments such as forest and agricultural soils (Bintrim et al. 1997; Buckley et al. 1998; Jurgens et al. 1997; Jurgens and Sanno 1999; Kudo et al. 1997; Reed et al. 2002; Sandaa et al. 1999; Ueda et al. 1995), freshwater sediments (Abreu et al. 2001; Hershberger et al. 1996; Jurgens et al. 2000; MacGregor et al. 1997; Schleper et al. 1997), marine water columns and sediments (Inagaki et al. 2003; Karner et al. 2001; Li et al. 1999; Massana et al. 1997; Vetriani et al. 1999), subsurface environments (Takai et al. 2001), and cold springs (Koch et al. 2006). When the molecular phylogeny of the 16S rRNA gene was analyzed, members of the Cre- narchaeota phylum could be classified into several groups (Schleper et al. 2005): I.1a (marine, freshwater, subsurface), I.1b (soil, freshwater, subsurface), I.1c (forest soil, freshwa- ter), I.2 (marine/freshwater sediment), I.3a (marine, Communicated by L. Huang. Electronic supplementary material The online version of this article (doi:10.1007/s00792-008-0165-7) contains supplementary material, which is available to authorized users. S.-J. Park Á B.-J. Park Á S.-K. Rhee (&) Department of Microbiology, Chungbuk National University, 12 Gaeshin-dong, Heungduk-gu, Cheongju 361-763, Korea e-mail: rhees@chungbuk.ac.kr 123 Extremophiles (2008) 12:605–615 DOI 10.1007/s00792-008-0165-7