PMID- 16499709
OWN - NLM
STAT- MEDLINE
DCOM- 20060421
LR  - 20081121
IS  - 0962-1083 (Print)
IS  - 0962-1083 (Linking)
VI  - 15
IP  - 3
DP  - 2006 Mar
TI  - A 'dirty' business: testing the limitations of terminal restriction fragment 
      length polymorphism (TRFLP) analysis of soil fungi.
PG  - 873-82
AB  - Terminal restriction fragment length polymorphism (TRFLP) is an increasingly 
      popular method in molecular ecology. However, several key limitations of this 
      method have not been fully examined especially when used to study fungi. We 
      investigated the impact of spore contamination, intracollection ribosomal DNA 
      internal transcribed spacer (ITS) region variation, and conserved restriction 
      enzyme recognition loci on the results produced by TRFLP to characterize soil 
      fungal communities. We find that (i) the potential for nontarget structures such 
      as spores to contribute DNA to target sample extractions is high; (ii) multiple 
      fragments (i.e. 'extra peaks') per PCR primer-restriction enzyme combination can 
      be detected that are caused by restriction enzyme inefficiency and 
      intracollection ribosomal DNA ITS variation; and (iii) restriction enzyme 
      digestion in conserved vs. variable gene regions leads to different 
      characterizations of community diversity. Based on these results, we suggest that 
      studies employing TRFLP need to include information from known, identified fungi 
      from sites within which studies take place and not to rely only on TRFLP profiles 
      as a short cut to fungal community description.
FAU - Avis, Peter G
AU  - Avis PG
AD  - Department of Botany, The Field Museum, Chicago, IL 60605-2496, USA. 
      pavis@fieldmuseum.org
FAU - Dickie, Ian A
AU  - Dickie IA
FAU - Mueller, Gregory M
AU  - Mueller GM
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
PL  - England
TA  - Mol Ecol
JT  - Molecular ecology
JID - 9214478
RN  - 0 (DNA, Fungal)
RN  - 0 (DNA, Ribosomal Spacer)
RN  - EC 3.1.21.- (DNA Restriction Enzymes)
SB  - IM
MH  - Base Sequence
MH  - DNA Restriction Enzymes
MH  - DNA, Fungal/*analysis/genetics
MH  - DNA, Ribosomal Spacer/genetics
MH  - Fluorescence
MH  - Fungi/*genetics
MH  - *Genetic Variation
MH  - Molecular Sequence Data
MH  - Polymerase Chain Reaction
MH  - *Polymorphism, Restriction Fragment Length
MH  - Soil Microbiology
MH  - Spores
EDAT- 2006/02/28 09:00
MHDA- 2006/04/25 09:00
CRDT- 2006/02/28 09:00
PHST- 2006/02/28 09:00 [pubmed]
PHST- 2006/04/25 09:00 [medline]
PHST- 2006/02/28 09:00 [entrez]
AID - MEC2842 [pii]
AID - 10.1111/j.1365-294X.2005.02842.x [doi]
PST - ppublish
SO  - Mol Ecol. 2006 Mar;15(3):873-82. doi: 10.1111/j.1365-294X.2005.02842.x.