Phylogenetic Analysis of Nonthermophilic Members of the Kingdom Crenarchaeota and Their Diversity and Abundance in Soils

Abstract

Within the last several years, molecular techniques have uncovered numerous 16S rRNA gene (rDNA) sequences which represent a unique and globally distributed lineage of the kingdom Crenarchaeotathat is phylogenetically distinct from currently characterized crenarchaeotal species. rDNA sequences of members of this novel crenarchaeotal group have been recovered from low- to moderate-temperature environments (−1.5 to 32°C), in contrast to the high-temperature environments (temperature, >80°C) required for growth of the currently recognized crenarchaeotal species. We determined the diversity and abundance of the nonthermophilic members of the Crenarchaeota in soil samples taken from cultivated and uncultivated fields located at the Kellogg Biological Station’s Long-Term Ecological Research site (Hickory Corners, Mich.). Clones were generated from 16S rDNA that was amplified by using broad-specificity archaeal PCR primers. Twelve crenarchaeotal sequences were identified, and the phylogenetic relationships between these sequences and previously described crenarchaeotal 16S rDNA sequences were determined. Phylogenetic analyses included nonthermophilic crenarchaeotal sequences found in public databases and revealed that the nonthermophilic Crenarchaeota group is composed of at least four distinct phylogenetic clusters. A 16S rRNA-targeted oligonucleotide probe specific for all known nonthermophilic crenarchaeotal sequences was designed and used to determine their abundance in soil samples. The nonthermophilicCrenarchaeota accounted for as much as 1.42% ± 0.42% of the 16S rRNA in the soils analyzed.

The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria

“…Nevertheless, most soil archaeal sequences fall within the 1.1b lineage (e.g. Buckley et al, 1998;Ochsenreiter et al, 2003), and most of those detected here may fall within this lineage. Therefore, 16S rRNA-based analysis may target largely amoA-possessing organisms if ammonia monooxygenase is possessed by organisms throughout the lineage.…”

Primary succession of soil Crenarchaeota across a receding glacier foreland

“…Organisms belonging to the largely non-thermophilic 'Group 1' Crenarchaeota lineage appear to be ubiquitous in soil systems including grassland, forest, agricultural and rice field soils (e.g. Bintrim et al ., 1997;Jurgens et al ., 1997;Buckley et al ., 1998;Großkopf et al ., 1998;Nicol et al ., 2003a) and may be dominant over euryarchaeal populations in grassland soils (Nicol et al ., 2003b). Despite an increasing understanding of crenarchaeal diversity in the environment, little is known about the drivers of crenarchaeal diversity and their ecological functioning in soil systems (Nicol et al ., 2004).…”

“…Sandaa et al ., 1999;Nicol et al ., 2003a) and their apparent ubiquity but reduced complexity in comparison with bacterial communities make crenarchaea a useful target group when making comparisons between different environmental samples. Crenarchaea have been reported to constitute a significant proportion of soil prokaryotes ranging from 0.16% to 3% of 16S rRNA genes (Ochsenreiter et al ., 2003) and approximately 1% of hybridized whole cells (Sandaa et al ., 1999) or extracted 16S rRNA (Buckley et al ., 1998). Several studies have indicated that soil crenarchaea may have a specific association with plant roots (Großkopf et al ., 1998;Simon et al ., 2000;Chelius and Triplett, 2001) and crenarchaea may therefore play an important role in the rhizosphere.…”

First insight into the genome of an uncultivated crenarchaeote from soil

“…Quantitative estimates have demonstrated the significant occurrence of non-thermophilic crenarchaeota in marine habitats (Massana et al ., 1997;Karner et al ., 2001), in freshwater sediments (McGregor et al ., 1997) and in soil (Buckley et al ., 1998;T. Ochsenreiter and C. Schleper, in preparation).…”