Spatial analysis of archaeal community structure in grassland soil

Graeme William Nicol, Lesley Anne Glover, James Ivor Prosser

Research output: Contribution to journalArticle

84 Citations (Scopus)

Abstract

The complex structure of soil and the heterogeneity of resources available to microorganisms have implications for sampling regimens when the structure and diversity of microbial communities are analyzed. To assess the heterogeneity in community structure, archaeal communities, which typically contain sequences belonging to the nonthermophilic Crenarchaeota, were examined at two contrasting spatial scales by using PCR-denaturing gradient gel electrophoresis (DGGE) analysis followed by unweighted pair group method with arithmetic mean analysis of 16S rRNA- and ribosomal DNA-derived profiles. A macroscale analysis was carried out with soil cores taken at 2-m intervals along triplicate 8-m transects from both managed (improved) and natural (unimproved) grassland rhizosphere soils. A microscale analysis was carried out with a single soil core by assessing the effects of both sample size (10, 1, and 0.1 g) and distance between samples. The much reduced complexity of archaeal profiles compared to the complexity typical of the bacterial community facilitated visual comparison of profiles based on band presence and revealed different levels of heterogeneity between sets of samples. At the macroscale level, heterogeneity over the transect could not be related to grassland type. Substantial heterogeneity was observed across both improved and unimproved transects, except for one improved transect that exhibited substantial homogeneity, so that profiles for a single core were largely representative of the entire transect. At the smaller scale, the heterogeneity of the archaeal community structure varied with sample size within a single 8- by 8-cm, core. The archaeal DGGE profiles for replicate 10-g soil samples were similar, while those for 1-g samples and 0.1-g samples showed greater heterogeneity. In addition, there was no relationship between the archaeal profiles and the distance between 1- or 0.1-g samples, although relationships between community structure and distance of separation may occur at a smaller scale. Our findings demonstrate the care required when workers attempt to obtain a representative picture of microbial community structure in the soil environment.

Original languageEnglish
Pages (from-to)7420-7429
Number of pages9
JournalApplied and Environmental Microbiology
Volume69
Issue number12
DOIs
Publication statusPublished - 2003

Keywords

  • GRADIENT GEL-ELECTROPHORESIS
  • 16S RIBOSOMAL-RNA
  • BACTERIAL COMMUNITIES
  • KINGDOM CRENARCHAEOTA
  • PHYLOGENETIC ANALYSIS
  • MANAGEMENT REGIMENS
  • MICROBIAL COMMUNITY
  • TRIFOLIUM-REPENS
  • LOLIUM-PERENNE
  • DIVERSITY

Cite this

Spatial analysis of archaeal community structure in grassland soil. / Nicol, Graeme William; Glover, Lesley Anne; Prosser, James Ivor.

In: Applied and Environmental Microbiology, Vol. 69, No. 12, 2003, p. 7420-7429.

Research output: Contribution to journalArticle

Nicol, Graeme William ; Glover, Lesley Anne ; Prosser, James Ivor. / Spatial analysis of archaeal community structure in grassland soil. In: Applied and Environmental Microbiology. 2003 ; Vol. 69, No. 12. pp. 7420-7429.
@article{b89bf3548a834772965a460bbf18e484,
title = "Spatial analysis of archaeal community structure in grassland soil",
abstract = "The complex structure of soil and the heterogeneity of resources available to microorganisms have implications for sampling regimens when the structure and diversity of microbial communities are analyzed. To assess the heterogeneity in community structure, archaeal communities, which typically contain sequences belonging to the nonthermophilic Crenarchaeota, were examined at two contrasting spatial scales by using PCR-denaturing gradient gel electrophoresis (DGGE) analysis followed by unweighted pair group method with arithmetic mean analysis of 16S rRNA- and ribosomal DNA-derived profiles. A macroscale analysis was carried out with soil cores taken at 2-m intervals along triplicate 8-m transects from both managed (improved) and natural (unimproved) grassland rhizosphere soils. A microscale analysis was carried out with a single soil core by assessing the effects of both sample size (10, 1, and 0.1 g) and distance between samples. The much reduced complexity of archaeal profiles compared to the complexity typical of the bacterial community facilitated visual comparison of profiles based on band presence and revealed different levels of heterogeneity between sets of samples. At the macroscale level, heterogeneity over the transect could not be related to grassland type. Substantial heterogeneity was observed across both improved and unimproved transects, except for one improved transect that exhibited substantial homogeneity, so that profiles for a single core were largely representative of the entire transect. At the smaller scale, the heterogeneity of the archaeal community structure varied with sample size within a single 8- by 8-cm, core. The archaeal DGGE profiles for replicate 10-g soil samples were similar, while those for 1-g samples and 0.1-g samples showed greater heterogeneity. In addition, there was no relationship between the archaeal profiles and the distance between 1- or 0.1-g samples, although relationships between community structure and distance of separation may occur at a smaller scale. Our findings demonstrate the care required when workers attempt to obtain a representative picture of microbial community structure in the soil environment.",
keywords = "GRADIENT GEL-ELECTROPHORESIS, 16S RIBOSOMAL-RNA, BACTERIAL COMMUNITIES, KINGDOM CRENARCHAEOTA, PHYLOGENETIC ANALYSIS, MANAGEMENT REGIMENS, MICROBIAL COMMUNITY, TRIFOLIUM-REPENS, LOLIUM-PERENNE, DIVERSITY",
author = "Nicol, {Graeme William} and Glover, {Lesley Anne} and Prosser, {James Ivor}",
year = "2003",
doi = "10.1128/AEM.69.12.7420-7429.2003",
language = "English",
volume = "69",
pages = "7420--7429",
journal = "Applied and Environmental Microbiology",
issn = "0099-2240",
publisher = "American Society for Microbiology",
number = "12",

}

TY - JOUR

T1 - Spatial analysis of archaeal community structure in grassland soil

AU - Nicol, Graeme William

AU - Glover, Lesley Anne

AU - Prosser, James Ivor

PY - 2003

Y1 - 2003

N2 - The complex structure of soil and the heterogeneity of resources available to microorganisms have implications for sampling regimens when the structure and diversity of microbial communities are analyzed. To assess the heterogeneity in community structure, archaeal communities, which typically contain sequences belonging to the nonthermophilic Crenarchaeota, were examined at two contrasting spatial scales by using PCR-denaturing gradient gel electrophoresis (DGGE) analysis followed by unweighted pair group method with arithmetic mean analysis of 16S rRNA- and ribosomal DNA-derived profiles. A macroscale analysis was carried out with soil cores taken at 2-m intervals along triplicate 8-m transects from both managed (improved) and natural (unimproved) grassland rhizosphere soils. A microscale analysis was carried out with a single soil core by assessing the effects of both sample size (10, 1, and 0.1 g) and distance between samples. The much reduced complexity of archaeal profiles compared to the complexity typical of the bacterial community facilitated visual comparison of profiles based on band presence and revealed different levels of heterogeneity between sets of samples. At the macroscale level, heterogeneity over the transect could not be related to grassland type. Substantial heterogeneity was observed across both improved and unimproved transects, except for one improved transect that exhibited substantial homogeneity, so that profiles for a single core were largely representative of the entire transect. At the smaller scale, the heterogeneity of the archaeal community structure varied with sample size within a single 8- by 8-cm, core. The archaeal DGGE profiles for replicate 10-g soil samples were similar, while those for 1-g samples and 0.1-g samples showed greater heterogeneity. In addition, there was no relationship between the archaeal profiles and the distance between 1- or 0.1-g samples, although relationships between community structure and distance of separation may occur at a smaller scale. Our findings demonstrate the care required when workers attempt to obtain a representative picture of microbial community structure in the soil environment.

AB - The complex structure of soil and the heterogeneity of resources available to microorganisms have implications for sampling regimens when the structure and diversity of microbial communities are analyzed. To assess the heterogeneity in community structure, archaeal communities, which typically contain sequences belonging to the nonthermophilic Crenarchaeota, were examined at two contrasting spatial scales by using PCR-denaturing gradient gel electrophoresis (DGGE) analysis followed by unweighted pair group method with arithmetic mean analysis of 16S rRNA- and ribosomal DNA-derived profiles. A macroscale analysis was carried out with soil cores taken at 2-m intervals along triplicate 8-m transects from both managed (improved) and natural (unimproved) grassland rhizosphere soils. A microscale analysis was carried out with a single soil core by assessing the effects of both sample size (10, 1, and 0.1 g) and distance between samples. The much reduced complexity of archaeal profiles compared to the complexity typical of the bacterial community facilitated visual comparison of profiles based on band presence and revealed different levels of heterogeneity between sets of samples. At the macroscale level, heterogeneity over the transect could not be related to grassland type. Substantial heterogeneity was observed across both improved and unimproved transects, except for one improved transect that exhibited substantial homogeneity, so that profiles for a single core were largely representative of the entire transect. At the smaller scale, the heterogeneity of the archaeal community structure varied with sample size within a single 8- by 8-cm, core. The archaeal DGGE profiles for replicate 10-g soil samples were similar, while those for 1-g samples and 0.1-g samples showed greater heterogeneity. In addition, there was no relationship between the archaeal profiles and the distance between 1- or 0.1-g samples, although relationships between community structure and distance of separation may occur at a smaller scale. Our findings demonstrate the care required when workers attempt to obtain a representative picture of microbial community structure in the soil environment.

KW - GRADIENT GEL-ELECTROPHORESIS

KW - 16S RIBOSOMAL-RNA

KW - BACTERIAL COMMUNITIES

KW - KINGDOM CRENARCHAEOTA

KW - PHYLOGENETIC ANALYSIS

KW - MANAGEMENT REGIMENS

KW - MICROBIAL COMMUNITY

KW - TRIFOLIUM-REPENS

KW - LOLIUM-PERENNE

KW - DIVERSITY

U2 - 10.1128/AEM.69.12.7420-7429.2003

DO - 10.1128/AEM.69.12.7420-7429.2003

M3 - Article

VL - 69

SP - 7420

EP - 7429

JO - Applied and Environmental Microbiology

JF - Applied and Environmental Microbiology

SN - 0099-2240

IS - 12

ER -