Crenarchaeal community assembly and microdiversity in developing soils at two sites associated with deglaciation

Graeme William Nicol, D. Tscherko, Lijun Chang, U. Hammesfahr, James Ivor Prosser

Research output: Contribution to journalArticle

42 Citations (Scopus)

Abstract

Non-thermophilic Crenarchaeota are recognized as ubiquitous and abundant components of soil microbial communities. Previous studies of the foreland of the receding Rotmoosferner glacier in the Austrian Central Alps have demonstrated that crenarchaeal communities in soil at different stages of development are distinct from each other, with Group 1.1b crenarchaeal populations dominating throughout the successional gradient, while Group 1.1c crenarchaea are present in mature soils only. To determine whether this highly structured succession was unique to the Rotmoosferner glacier foreland, 1.1b and 1.1c communities were compared with those present along a successional gradient at Odenwinkelkees glacier, 125 km away, by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA reverse transcription polymerase chain reaction products. Similarities in community structure were observed; 1.1b communities were present throughout both successional gradients (though lacking the defined structure at Odenwinkelkees) and 1.1c communities were present only in mature soil. Comigration of bands on DGGE gels indicated that a number of similar crenarchaeal populations were present at both sites. To compare populations, and examine microscale diversity, 16S rRNA genes and complete 16S-23S internal transcribed spacer (ITS) regions representing six major band positions in DGGE analysis were amplified, cloned and sequenced and represented four 1.1b and two 1.1c lineages. The data provide no evidence of endemism, but large differences in the rate of sequence divergence in the ITS region (relative to that in 16S rRNA genes) were observed. Two of the 1.1b lineages (each possessing > 98% 16S rRNA gene similarity) had relatively long and highly divergent ITS sequences. In contrast, two other 1.1b and two 1.1c lineages (each possessing > 99% 16S rRNA gene similarity) exhibited markedly less variation in their respective 16S-23S ITS regions. The results reveal common patterns in the ecology and assembly of crenarchaeal communities in spatially separated soil systems and may indicate different evolutionary rates between soil crenarchaea lineages.

Original languageEnglish
Pages (from-to)1382-1393
Number of pages11
JournalEnvironmental Microbiology
Volume8
Issue number8
DOIs
Publication statusPublished - Aug 2006

Keywords

  • INTERGENIC SPACER ANALYSIS
  • PRIMARY SUCCESSION
  • BOREAL FOREST
  • MICROBIAL DIVERSITY
  • GLACIER FOREFRONT
  • RIBOSOMAL-RNA
  • BULK SOIL
  • ARCHAEA
  • SEQUENCE
  • RHIZOSPHERE

Cite this

Crenarchaeal community assembly and microdiversity in developing soils at two sites associated with deglaciation. / Nicol, Graeme William; Tscherko, D.; Chang, Lijun; Hammesfahr, U.; Prosser, James Ivor.

In: Environmental Microbiology, Vol. 8, No. 8, 08.2006, p. 1382-1393.

Research output: Contribution to journalArticle

Nicol, Graeme William ; Tscherko, D. ; Chang, Lijun ; Hammesfahr, U. ; Prosser, James Ivor. / Crenarchaeal community assembly and microdiversity in developing soils at two sites associated with deglaciation. In: Environmental Microbiology. 2006 ; Vol. 8, No. 8. pp. 1382-1393.
@article{af3ff80df8f24d698c6710920ddf58e7,
title = "Crenarchaeal community assembly and microdiversity in developing soils at two sites associated with deglaciation",
abstract = "Non-thermophilic Crenarchaeota are recognized as ubiquitous and abundant components of soil microbial communities. Previous studies of the foreland of the receding Rotmoosferner glacier in the Austrian Central Alps have demonstrated that crenarchaeal communities in soil at different stages of development are distinct from each other, with Group 1.1b crenarchaeal populations dominating throughout the successional gradient, while Group 1.1c crenarchaea are present in mature soils only. To determine whether this highly structured succession was unique to the Rotmoosferner glacier foreland, 1.1b and 1.1c communities were compared with those present along a successional gradient at Odenwinkelkees glacier, 125 km away, by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA reverse transcription polymerase chain reaction products. Similarities in community structure were observed; 1.1b communities were present throughout both successional gradients (though lacking the defined structure at Odenwinkelkees) and 1.1c communities were present only in mature soil. Comigration of bands on DGGE gels indicated that a number of similar crenarchaeal populations were present at both sites. To compare populations, and examine microscale diversity, 16S rRNA genes and complete 16S-23S internal transcribed spacer (ITS) regions representing six major band positions in DGGE analysis were amplified, cloned and sequenced and represented four 1.1b and two 1.1c lineages. The data provide no evidence of endemism, but large differences in the rate of sequence divergence in the ITS region (relative to that in 16S rRNA genes) were observed. Two of the 1.1b lineages (each possessing > 98{\%} 16S rRNA gene similarity) had relatively long and highly divergent ITS sequences. In contrast, two other 1.1b and two 1.1c lineages (each possessing > 99{\%} 16S rRNA gene similarity) exhibited markedly less variation in their respective 16S-23S ITS regions. The results reveal common patterns in the ecology and assembly of crenarchaeal communities in spatially separated soil systems and may indicate different evolutionary rates between soil crenarchaea lineages.",
keywords = "INTERGENIC SPACER ANALYSIS, PRIMARY SUCCESSION, BOREAL FOREST, MICROBIAL DIVERSITY, GLACIER FOREFRONT, RIBOSOMAL-RNA, BULK SOIL, ARCHAEA, SEQUENCE, RHIZOSPHERE",
author = "Nicol, {Graeme William} and D. Tscherko and Lijun Chang and U. Hammesfahr and Prosser, {James Ivor}",
year = "2006",
month = "8",
doi = "10.1111/j.1462-2920.2006.01031.x",
language = "English",
volume = "8",
pages = "1382--1393",
journal = "Environmental Microbiology",
issn = "1462-2912",
publisher = "BLACKWELL PUBLISHING LTD",
number = "8",

}

TY - JOUR

T1 - Crenarchaeal community assembly and microdiversity in developing soils at two sites associated with deglaciation

AU - Nicol, Graeme William

AU - Tscherko, D.

AU - Chang, Lijun

AU - Hammesfahr, U.

AU - Prosser, James Ivor

PY - 2006/8

Y1 - 2006/8

N2 - Non-thermophilic Crenarchaeota are recognized as ubiquitous and abundant components of soil microbial communities. Previous studies of the foreland of the receding Rotmoosferner glacier in the Austrian Central Alps have demonstrated that crenarchaeal communities in soil at different stages of development are distinct from each other, with Group 1.1b crenarchaeal populations dominating throughout the successional gradient, while Group 1.1c crenarchaea are present in mature soils only. To determine whether this highly structured succession was unique to the Rotmoosferner glacier foreland, 1.1b and 1.1c communities were compared with those present along a successional gradient at Odenwinkelkees glacier, 125 km away, by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA reverse transcription polymerase chain reaction products. Similarities in community structure were observed; 1.1b communities were present throughout both successional gradients (though lacking the defined structure at Odenwinkelkees) and 1.1c communities were present only in mature soil. Comigration of bands on DGGE gels indicated that a number of similar crenarchaeal populations were present at both sites. To compare populations, and examine microscale diversity, 16S rRNA genes and complete 16S-23S internal transcribed spacer (ITS) regions representing six major band positions in DGGE analysis were amplified, cloned and sequenced and represented four 1.1b and two 1.1c lineages. The data provide no evidence of endemism, but large differences in the rate of sequence divergence in the ITS region (relative to that in 16S rRNA genes) were observed. Two of the 1.1b lineages (each possessing > 98% 16S rRNA gene similarity) had relatively long and highly divergent ITS sequences. In contrast, two other 1.1b and two 1.1c lineages (each possessing > 99% 16S rRNA gene similarity) exhibited markedly less variation in their respective 16S-23S ITS regions. The results reveal common patterns in the ecology and assembly of crenarchaeal communities in spatially separated soil systems and may indicate different evolutionary rates between soil crenarchaea lineages.

AB - Non-thermophilic Crenarchaeota are recognized as ubiquitous and abundant components of soil microbial communities. Previous studies of the foreland of the receding Rotmoosferner glacier in the Austrian Central Alps have demonstrated that crenarchaeal communities in soil at different stages of development are distinct from each other, with Group 1.1b crenarchaeal populations dominating throughout the successional gradient, while Group 1.1c crenarchaea are present in mature soils only. To determine whether this highly structured succession was unique to the Rotmoosferner glacier foreland, 1.1b and 1.1c communities were compared with those present along a successional gradient at Odenwinkelkees glacier, 125 km away, by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA reverse transcription polymerase chain reaction products. Similarities in community structure were observed; 1.1b communities were present throughout both successional gradients (though lacking the defined structure at Odenwinkelkees) and 1.1c communities were present only in mature soil. Comigration of bands on DGGE gels indicated that a number of similar crenarchaeal populations were present at both sites. To compare populations, and examine microscale diversity, 16S rRNA genes and complete 16S-23S internal transcribed spacer (ITS) regions representing six major band positions in DGGE analysis were amplified, cloned and sequenced and represented four 1.1b and two 1.1c lineages. The data provide no evidence of endemism, but large differences in the rate of sequence divergence in the ITS region (relative to that in 16S rRNA genes) were observed. Two of the 1.1b lineages (each possessing > 98% 16S rRNA gene similarity) had relatively long and highly divergent ITS sequences. In contrast, two other 1.1b and two 1.1c lineages (each possessing > 99% 16S rRNA gene similarity) exhibited markedly less variation in their respective 16S-23S ITS regions. The results reveal common patterns in the ecology and assembly of crenarchaeal communities in spatially separated soil systems and may indicate different evolutionary rates between soil crenarchaea lineages.

KW - INTERGENIC SPACER ANALYSIS

KW - PRIMARY SUCCESSION

KW - BOREAL FOREST

KW - MICROBIAL DIVERSITY

KW - GLACIER FOREFRONT

KW - RIBOSOMAL-RNA

KW - BULK SOIL

KW - ARCHAEA

KW - SEQUENCE

KW - RHIZOSPHERE

U2 - 10.1111/j.1462-2920.2006.01031.x

DO - 10.1111/j.1462-2920.2006.01031.x

M3 - Article

VL - 8

SP - 1382

EP - 1393

JO - Environmental Microbiology

JF - Environmental Microbiology

SN - 1462-2912

IS - 8

ER -