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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 and . In spite of the extreme environmental conditions in the polar regions, through the application of culture-independent 16S rRNA gene-based surveys, 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 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 , , , , and . FISH-based studies have shown that 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 have been isolated from polar environments.

Citation: Niederberger T, McDonald I, Cary S. 2012. , 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

Generic image for table
TABLE 1

isolated from polar environments

Isolates marked with a star are not validly named and characterized according to the . 1992. ASM Press.

Citation: Niederberger T, McDonald I, Cary S. 2012. , 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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TABLE 2

Concentrations of in natural polar environments

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

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

ND, not determined.

Citation: Niederberger T, McDonald I, Cary S. 2012. , 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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TABLE 3a

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

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.

Numbers in parentheses refer to locations indicated on map in Color Plate 5. were not detected at sites marked with a star.

ND, not defined in the original study.

Citation: Niederberger T, McDonald I, Cary S. 2012. , 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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TABLE 3b

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

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.

Numbers in parentheses refer to locations indicated on map in Color Plate 5. were not detected at sites marked with a star.

ND, not defined in the original study.

Citation: Niederberger T, McDonald I, Cary S. 2012. , 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
Generic image for table
TABLE 3c

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

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.

Numbers in parentheses refer to locations indicated on map in Color Plate 5. were not detected at sites marked with a star.

ND, not defined in the original study.

Citation: Niederberger T, McDonald I, Cary S. 2012. , 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
Generic image for table
TABLE 3d

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

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.

Numbers in parentheses refer to locations indicated on map in Color Plate 5. were not detected at sites marked with a star.

ND, not defined in the original study.

Citation: Niederberger T, McDonald I, Cary S. 2012. , 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
Generic image for table
TABLE 3e

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

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.

Numbers in parentheses refer to locations indicated on map in Color Plate 5. were not detected at sites marked with a star.

ND, not defined in the original study.

Citation: Niederberger T, McDonald I, Cary S. 2012. , 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
Generic image for table
TABLE 3f

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

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.

Numbers in parentheses refer to locations indicated on map in Color Plate 5. were not detected at sites marked with a star.

ND, not defined in the original study.

Citation: Niederberger T, McDonald I, Cary S. 2012. , 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
Generic image for table
TABLE 3g

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

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.

Numbers in parentheses refer to locations indicated on map in Color Plate 5. were not detected at sites marked with a star.

ND, not defined in the original study.

Citation: Niederberger T, McDonald I, Cary S. 2012. , 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
Generic image for table
TABLE 3h

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

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.

Numbers in parentheses refer to locations indicated on map in Color Plate 5. were not detected at sites marked with a star.

ND, not defined in the original study.

Citation: Niederberger T, McDonald I, Cary S. 2012. , 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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TABLE 4

Oligonucleotides utilized to target in 16S rRNA gene PCR-based culture-independent studies of polar environments

Numbering associated with oligonucleotide names refers to the complementary nucleotide position on the target 16S rRNA gene.

The mismatch, i.e., gap with the oligonucleotide sequence represented by the dash, may represent an error within the original publication ( ).

Citation: Niederberger T, McDonald I, Cary S. 2012. , 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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