Use of PCR-DGGE-Based Molecular Methods to Analyze Nematode Community Diversity

Margherita Festa; Pamela Abbruscato; Barbara Manachini

doi:10.1007/978-1-0716-3638-1_6

Use of PCR-DGGE-Based Molecular Methods to Analyze Nematode Community Diversity

Methods Mol Biol. 2024:2756:247-255. doi: 10.1007/978-1-0716-3638-1_6.

Authors

Margherita Festa¹, Pamela Abbruscato², Barbara Manachini³

Affiliations

¹ CNR - Istituto di Biofisica, Genova, Italy.
² Nuova Genetica Italiana, Villa Guardia, CO, Italy.
³ Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, Italy. barbara.manachini@unipa.it.

PMID: 38427297
DOI: 10.1007/978-1-0716-3638-1_6

Abstract

DGGE (denaturing gradient gel electrophoresis) is a nucleic acid separation technique applied to the evaluation of microbial biodiversity. This technique is quite rapid and cheap compared to other types of analysis. Here we describe the comparison of nematode communities inhabiting different ecosystems. After an ecologically representative sampling collection and the nematode extraction from soil, nematodes are centrifuged in Eppendorf tubes to facilitate DNA extraction. DNA from the whole community of each type of soil is extracted, amplified with primers for 18 S rDNA and used in DGGE analysis. The profiles of DGGE can be analyzed with appropriate software, and biodiversity indices can be estimated.

Keywords: 18S rDNA; Biodiversity indices; Denaturing gradient gel electrophoresis; Ecological indices; Nematofauna.

MeSH terms

Animals
Biodiversity
DNA, Bacterial / genetics
DNA, Ribosomal / genetics
Ecosystem*
Electrophoresis, Polyacrylamide Gel
Nematoda* / genetics
Polymerase Chain Reaction / methods
RNA, Ribosomal, 16S / genetics
Soil
Soil Microbiology

Substances

DNA, Ribosomal
Soil
DNA, Bacterial
RNA, Ribosomal, 16S