Molecular and functional diversity in soil microorganisms.

Research output: Contribution to journalArticle

111 Citations (Scopus)

Abstract

Traditional approaches to the study of microbial diversity have relied on laboratory cultivation of isolates from natural environments and identification by classical techniques, including analysis of morphology, physiological characteristics and biochemical properties. These approaches provide information on fine-scale diversity but suffer from bias, resulting from the media and cultivation conditions employed, and from the inability to grow and isolate significant proportions of natural communities in the laboratory. An alternative approach is the amplification of ribosomal RNA and functional genes from nucleic acids extracted directly from environmental samples, with subsequent analysis by 'fingerprinting' methods or by sequencing and phylogenetic analysis. This approach avoids the need for laboratory cultivation and has provided major insights into species and functional diversity of bacterial and archaeal populations. This article reviews molecular approaches to the characterisation of prokaryote diversity in natural environments, their more recent application to fungal diversity and the advantages and limitations of molecular analyses.

Original languageEnglish
Pages (from-to)9-17
Number of pages8
JournalPlant and Soil
Volume244
DOIs
Publication statusPublished - 2002

Keywords

  • bacteria
  • biodiversity
  • functional diversity
  • fungi
  • molecular ecology
  • ribosomal RNA
  • rRNA
  • soil
  • species diversity
  • 16S RIBOSOMAL-RNA
  • GRADIENT GEL-ELECTROPHORESIS
  • AMMONIA-OXIDIZING BACTERIA
  • COMMUNITY STRUCTURE
  • GENE-SEQUENCES
  • AGRICULTURAL SOIL
  • IN-SITU
  • PCR
  • POPULATIONS
  • DNA

Cite this

Molecular and functional diversity in soil microorganisms. / Prosser, James Ivor.

In: Plant and Soil, Vol. 244, 2002, p. 9-17.

Research output: Contribution to journalArticle

@article{d41ab00a3d10477eabd8b6585b72f1b1,
title = "Molecular and functional diversity in soil microorganisms.",
abstract = "Traditional approaches to the study of microbial diversity have relied on laboratory cultivation of isolates from natural environments and identification by classical techniques, including analysis of morphology, physiological characteristics and biochemical properties. These approaches provide information on fine-scale diversity but suffer from bias, resulting from the media and cultivation conditions employed, and from the inability to grow and isolate significant proportions of natural communities in the laboratory. An alternative approach is the amplification of ribosomal RNA and functional genes from nucleic acids extracted directly from environmental samples, with subsequent analysis by 'fingerprinting' methods or by sequencing and phylogenetic analysis. This approach avoids the need for laboratory cultivation and has provided major insights into species and functional diversity of bacterial and archaeal populations. This article reviews molecular approaches to the characterisation of prokaryote diversity in natural environments, their more recent application to fungal diversity and the advantages and limitations of molecular analyses.",
keywords = "bacteria, biodiversity, functional diversity, fungi, molecular ecology, ribosomal RNA, rRNA, soil, species diversity, 16S RIBOSOMAL-RNA, GRADIENT GEL-ELECTROPHORESIS, AMMONIA-OXIDIZING BACTERIA, COMMUNITY STRUCTURE, GENE-SEQUENCES, AGRICULTURAL SOIL, IN-SITU, PCR, POPULATIONS, DNA",
author = "Prosser, {James Ivor}",
year = "2002",
doi = "10.1023/A:1020208100281",
language = "English",
volume = "244",
pages = "9--17",
journal = "Plant and Soil",
issn = "0032-079X",
publisher = "Springer Netherlands",

}

TY - JOUR

T1 - Molecular and functional diversity in soil microorganisms.

AU - Prosser, James Ivor

PY - 2002

Y1 - 2002

N2 - Traditional approaches to the study of microbial diversity have relied on laboratory cultivation of isolates from natural environments and identification by classical techniques, including analysis of morphology, physiological characteristics and biochemical properties. These approaches provide information on fine-scale diversity but suffer from bias, resulting from the media and cultivation conditions employed, and from the inability to grow and isolate significant proportions of natural communities in the laboratory. An alternative approach is the amplification of ribosomal RNA and functional genes from nucleic acids extracted directly from environmental samples, with subsequent analysis by 'fingerprinting' methods or by sequencing and phylogenetic analysis. This approach avoids the need for laboratory cultivation and has provided major insights into species and functional diversity of bacterial and archaeal populations. This article reviews molecular approaches to the characterisation of prokaryote diversity in natural environments, their more recent application to fungal diversity and the advantages and limitations of molecular analyses.

AB - Traditional approaches to the study of microbial diversity have relied on laboratory cultivation of isolates from natural environments and identification by classical techniques, including analysis of morphology, physiological characteristics and biochemical properties. These approaches provide information on fine-scale diversity but suffer from bias, resulting from the media and cultivation conditions employed, and from the inability to grow and isolate significant proportions of natural communities in the laboratory. An alternative approach is the amplification of ribosomal RNA and functional genes from nucleic acids extracted directly from environmental samples, with subsequent analysis by 'fingerprinting' methods or by sequencing and phylogenetic analysis. This approach avoids the need for laboratory cultivation and has provided major insights into species and functional diversity of bacterial and archaeal populations. This article reviews molecular approaches to the characterisation of prokaryote diversity in natural environments, their more recent application to fungal diversity and the advantages and limitations of molecular analyses.

KW - bacteria

KW - biodiversity

KW - functional diversity

KW - fungi

KW - molecular ecology

KW - ribosomal RNA

KW - rRNA

KW - soil

KW - species diversity

KW - 16S RIBOSOMAL-RNA

KW - GRADIENT GEL-ELECTROPHORESIS

KW - AMMONIA-OXIDIZING BACTERIA

KW - COMMUNITY STRUCTURE

KW - GENE-SEQUENCES

KW - AGRICULTURAL SOIL

KW - IN-SITU

KW - PCR

KW - POPULATIONS

KW - DNA

U2 - 10.1023/A:1020208100281

DO - 10.1023/A:1020208100281

M3 - Article

VL - 244

SP - 9

EP - 17

JO - Plant and Soil

JF - Plant and Soil

SN - 0032-079X

ER -