Primary succession of soil Crenarchaeota across a receding glacier foreland

Abstract

The development of soil archaeal community structures in relation to primary succession in bulk and rhizosphere soil was examined across the forefield of the receding Rotmoosferner glacier in Austria. Using cloning and denaturing gradient gel electrophoresis (DGGE) analysis of reverse transcription polymerase chain reaction (RT-PCR) products of extracted 16S rRNA, archaeal community structure was compared over a chronosequence representing approximately 150 years of soil development and to reference sites outside the glacier forefield, representing soil exposed for approximately 9500 years. Archaeal community composition was found to be dominated by members of the non-thermophilic or Group 1 Crenarchaeota, where a dramatic yet highly structured successional sequence was observed. Succession over the 150 years sequence could be identified as occurring in three stages, each of which had a phylogenetically distinct 1.1b crenarchaea community with those organisms present in pioneering and intermediate stages belonging to a lineage distinct from those in developed soils. Climax communities also contained organisms belonging to three other major non-thermophilic crenarchaeal lineages. Comparison of archaeal communities in the rhizosphere indicated that plant species composition was not the major driver of specific crenarchaeal populations. These results indicate the potential role of soil crenarchaea in the development of soil substrates, as well as ecological diversity within and between major Group 1 lineages.

Abundance and community structure of ammonia oxidizing bacteria and archaea in a Sweden boreal forest soil under 19-year fertilization and 12-year warming

“…The AOA amoA gene copy numbers decreased along an altitudinal gradient of Mount Everest, whereas that of AOB did not shift significantly with altitude (Zhang et al 2009). More recently, a study in the rhizosphere of a boreal forest tree indicated a decrease of archaeal diversity under soil warming (Bomberg et al 2011) which is consistent with previous findings in a receding glacier foreland of Austria (Nicol et al 2005. In addition, soil moisture has been reported as a major factor affecting soil N mineralization, which influences the N availability, along a temperature gradient in four European shrubland ecosystems (Beier et al 2008).…”

Community history affects the predictability of microbial ecosystem development

“…For DGGE analysis of dsrB amplicons, a denaturant gradient of 40-80% was used. Electrophoresis was carried out on a DCode Universal Mutation Detection System (Bio-Rad, Hemel Hempstead, UK) in 7 L of 1 Â TAE buffer at a constant temperature of 60 1C for 960 min at 75 V. Silver staining of gels was carried out as previously described (Nicol et al, 2005). All DGGE gels included three lanes with a standard set of 11 marker bands (see Supplementary Methods).…”

Microbial biodegradation of aromatic alkanoic naphthenic acids is affected by the degree of alkyl side chain branching

“…Cloning and phylogenetic analysis DNA was extracted from the cell resuspension (950 ml) as described by Griffiths et al (2000) as modified by Nicol et al (2005). Approximately 1357 bp fragments of bacterial 16S rDNA were obtained by a nested PCR using the primers pA/pH 0 and pB/pG 0 for the first and second amplifications, respectively (Edwards et al, 1989).…”

“…Plasmids were extracted using the Qiagen plasmid extraction kit (Qiagen). Clone libraries were screened by PCR amplification using primers for positions 341-534 in Escherichia coli (Muyzer et al 1993) and Denaturing Gradient Gel Electrophoresis performed as described previously (McKew et al, 2007), except gels were silver-stained as described by Nicol et al (2005). Representative clones from each library were selected and sequenced using the primer pG 0 (Edwards et al, 1989) (Source Bioscience Ltd., Cambridge, UK).…”