Abundance and Diversity of
            <i>Archaea</i>
            in Heavy-Metal-Contaminated Soils

Sandaa, Ruth‐Anne; Enger, Øivind; Torsvik, Vigdis

doi:10.1128/aem.65.8.3293-3297.1999

Cited by 147 publications

(51 citation statements)

References 36 publications

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“…The presence of members of the two major established archaeal kingdoms, Crenarchaeota and Euryarchaeota in nonthermophilic environments has been demonstrated by 16S rRNA gene surveys, with Crenarchaeota often more common in soil environments (Nicol et al, 2003). In particular, nonthermophilic 'Group I' Crenarchaeota have been reported in numerous environments including marine (Delong, 1992;Fuhrman et al, 1992) and freshwater environments (Jurgens et al, 2000), sediments (Hershberger et al, 1996;MacGregor et al, 1997;Schleper et al, 1997), bulk soil (Bintrim et al, 1997;Jurgens et al, 1997;Buckley et al, 1998;Sandaa et al, 1999;Ochsenreiter et al, 2003) and the rhizosphere and mycorrhizosphere (Simon et al, 2000;Bomberg et al, 2003). Estimates based on 16S rRNA gene copy numbers suggest that Crenarchaeota constitute 1-5% of the total prokaryotic community in soils (Buckley et al, 1998;Sandaa et al, 1999;Ochsenreiter et al, 2003), with some estimates as high as 12-38% (Kemnitz et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Soil pH regulates the abundance and diversity of Group 1.1c Crenarchaeota

Lehtovirta

Prosser

Nicol

2009

FEMS Microbiology Ecology

139

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Archaeal communities in many acidic forest soil systems are dominated by a distinct crenarchaeal lineage Group 1.1c. In addition, they are found consistently in other acidic soils including grassland pasture, moorland and alpine soils. To determine whether soil pH is a major factor in determining their presence and abundance, Group 1.1c community size and composition were investigated across a pH gradient from 4.5 to 7.5 that has been maintained for > 40 years. The abundances of Group 1.1c Crenarchaeota, total Crenarchaeota and total bacteria were assessed by quantitative PCR (qPCR) targeting 16S rRNA genes and the diversity of Group 1.1c crenarchaeal community was investigated by denaturing gradient gel electrophoresis (DGGE) and phylogenetic analysis. The abundance of Group 1.1c Crenarchaeota declined as the pH increased, whereas total Crenarchaeota and Bacteria showed no clear trend. Community diversity of Group 1.1c Crenarchaeota was also influenced with different DGGE bands dominating at different pH. Group 1.1c Crenarchaeota were also quantified in 13 other soils representing a range of habitats, soil types and pH. These results exhibited the same trend as that shown across the pH gradient with Group 1.1c Crenarchaeota representing a greater proportion of total Crenarchaeota in the most acidic soils.

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Section: Introductionmentioning

confidence: 99%

Soil pH regulates the abundance and diversity of Group 1.1c Crenarchaeota

Lehtovirta

Prosser

Nicol

2009

FEMS Microbiology Ecology

139

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“…However, the dynamism of soil crenarchaeal communities in response to different environmental factors (e.g. 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).…”

Section: Introductionmentioning

confidence: 99%

“…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.…”

Section: Introductionmentioning

confidence: 99%

Primary succession of soil Crenarchaeota across a receding glacier foreland

Nicol

Tscherko

Embley

et al. 2005

Environmental Microbiology

152

168

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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.

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“…Roling et al (2004a) reported a negative effect on archaea by oil spills in beach sediments in laboratory experiments. Sandaa et al (1999) also observed a decrease in archaeal numbers with increasing heavy-metal contamination in soils. In this study, we found a dramatic decrease in in situ archaea in oil-contaminated soils as indicated by the limited archaeal genes on the array.…”

Section: Discussionmentioning

confidence: 75%

Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oil field

Liang

Nostrand

et al. 2009

FEMS Microbiology Ecology

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To understand better the in situ microbial functional diversity under oil contamination stress, soils were sampled along a contamination gradient at an oil field in north-east China. Microbial community functional structure was examined with a functional gene array, termed GeoChip. Multivariate statistical analysis and meta-analysis were conducted to study the functional gene responses to oil concentrations. The total functional gene abundance and diversity decreased along the gradient of increasing contamination. The overall abundance of soil bacteria, archaea and fungi decreased to 10%, 40% and 80% of those in the pristine soil. Several functional genes in the families pgl, rbcL, nifH and nor and those encoding cellulase, laccase, chitinase, urease and key enzymes in metabolizing organic compounds were significantly decreased with oil contamination, especially under high contamination stress. However, a few genes encoding key enzymes for catechol, protocatechuate, and biphenyl degradation and in the gene families of nir, rbcL and pgl showed a significant increase at a medium level of oil contamination. Oil content and soil available nitrogen were found to be important factors influencing the microbial community structure. The results provide an insight into microbial functional diversity in oil-contaminated soils, providing potential information for on-site management and remediation measures.

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Abundance and Diversity of Archaea in Heavy-Metal-Contaminated Soils

Cited by 147 publications

References 36 publications

Soil pH regulates the abundance and diversity of Group 1.1c Crenarchaeota

Soil pH regulates the abundance and diversity of Group 1.1c Crenarchaeota

Primary succession of soil Crenarchaeota across a receding glacier foreland

Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oil field

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