Archaea

Thomas D. Niederberger; Ian R. McDonald; S. Craig Cary

doi:10.1128/9781555817183.ch2

Chapter 2 : Archaea

Authors: Thomas D. Niederberger¹, Ian R. McDonald², S. Craig Cary³

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Affiliations: 1: College of Earth, Ocean and Environment, University of Delaware, Lewes, DE 19958; 2: Department of Biological Sciences, University of Waikato, Hamilton 3240, New Zealand; 3: Department of Biological Sciences, University of Waikato, Hamilton 3240, New Zealand; 4: College of Earth, Ocean and Environment, University of Delaware, Lewes, DE 19958

Content Type: Monograph

Publication Year: 2012

Category: Environmental Microbiology

Book DOI: 10.1128/9781555817183

Chapter DOI: 10.1128/9781555817183.ch2

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Abstract:

Modern molecular PCR-based methods, typically targeting the 16S rRNA gene, have now revolutionized the field of environmental microbiology and have allowed culture-independent surveys of natural in situ microbial communities. These new approaches have unearthed a wide diversity and ubiquitous presence of Archaea in nonextreme environments such as soils, sediments, and oceans. The archaeal domain is split into two major phyla, the Crenarchaeota and Euryarchaeota. In spite of the extreme environmental conditions in the polar regions, through the application of culture-independent 16S rRNA gene-based surveys, Archaea have been found to inhabit a wide range of polar environments. This chapter reviews the current literature describing archaeal presence and diversity in polar and subpolar habitats. Marine and terrestrial ecosystems are discussed individually for Antarctic and Arctic ecosystems, with final sections discussing comparative studies of archaeal communities between polar regions, the potential response and contribution of Archaea to future climate change models, highlights of recent findings, and future research needs. The first wide-ranging PCR-based survey of archaeal 16S rRNA genes in terrestrial Antarctic sites has recently been reported. 16S rRNA gene clone library-based methods were used to analyze archaeal communities from Kirkpatrickia varialosa, Latrunculia apicalis, Mycale acerata, Homaxinella balfourensis, and Sphaerotylus antarcticus. FISH-based studies have shown that Archaea are typically minor components of pelagic microbial communities in Arctic water bodies. The majority of microbes in any given environment are typically recalcitrant to laboratory cultivation, and as such only a handful of Archaea have been isolated from polar environments.

Citation: Niederberger T, McDonald I, Cary S. 2012. Archaea, p 32-61. In Miller R, Whyte L (ed), Polar Microbiology: Life in a Deep Freeze. ASM Press, Washington, DC. doi: 10.1128/9781555817183.ch2

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Tables

Archaea

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TABLE 1

Archaea isolated from polar environments

a Isolates marked with a star are not validly named and characterized according to the International Code of Nomenclature of Bacteria (1990 Revision). Bacteriological Code. 1992. ASM Press.

10.1128/9781555817183/tab2-1_thmb.gif

10.1128/9781555817183/tab2-1.gif

TABLE 1

Archaea isolated from polar environments

a Isolates marked with a star are not validly named and characterized according to the International Code of Nomenclature of Bacteria (1990 Revision). Bacteriological Code. 1992. ASM Press.

/content/10.1128/9781555817183.chap2.tab2-2

TABLE 2

Concentrations of Archaea in natural polar environments

a Counts are represented as averages and include variations due to various sample types analyzed per study.

b Units: ml–1 for water samples; ml–1/g–1 for sediment and soils samples; 16S rRNA gene copies for qPCR-based studies.

c ND, not determined.

10.1128/9781555817183/tab2-2_thmb.gif

10.1128/9781555817183/tab2-2.gif

TABLE 2

Concentrations of Archaea in natural polar environments

a Counts are represented as averages and include variations due to various sample types analyzed per study.

b Units: ml–1 for water samples; ml–1/g–1 for sediment and soils samples; 16S rRNA gene copies for qPCR-based studies.

c ND, not determined.

/content/10.1128/9781555817183.chap2.tab2-3

TABLE 3a

16S rRNA gene-based community surveys of Archaea in natural polar environments a

a Sequences from these studies are included in the phylogenetic analysis shown in Color Plate 4. Sequences from DGGE-based studies and some recent studies (designated by # in the “Reference” column) are not included in Color Plate 4.