PMID- 14706747
OWN - NLM
STAT- MEDLINE
DCOM- 20040401
LR  - 20191108
IS  - 0167-7012 (Print)
IS  - 0167-7012 (Linking)
VI  - 56
IP  - 1
DP  - 2004 Jan
TI  - Molecular profiling of microbial communities associated with seeds of Beta 
      vulgaris subsp. Vulgaris (sugar beet).
PG  - 17-26
AB  - The composition of microbial communities on and within seeds may effect their 
      storage and field performance, whether they are indigenous or applied as 
      biocontrol agents. In this study, we have explored the usefulness of profiling 
      small subunit ribosomal (SSR) gene fragments for studying the microflora 
      associated with seeds. DNA was amplified by the polymerase chain reaction (PCR) 
      and the amplicons separated using denaturing gradient gel electrophoresis (DGGE). 
      Primers targeting eukaryotic SSRs were used to investigate fungal communities, 
      and primers targeting bacterial SSRs were employed to study the eubacterial 
      microflora. As a case study, we attempted to profile the fungi and bacteria 
      associated with seeds of Beta vulgaris (sugar beet) to permit an insight into the 
      varying field performance of several well-characterised commercial seed lots. 
      Serious interference with the microbial signals was observed from the plant's own 
      nuclear 18S rRNA genes and chloroplast 16S rRNA genes using standard PCR 
      conditions and DNA extracted from whole seeds as template. Hot-start and 
      touchdown PCR made no appreciable improvement to these signals. Seed imbibition 
      and dissection into operculum and fruit wall and true seed prior to DNA 
      extraction improved signal recovery in the fruit fraction. With primer 
      modification, bacteria and fungi were detected in an excess of plant DNA of 100:1 
      and 10:1, respectively. With this method, microbial communities on seeds could be 
      profiled, however, it is likely that targeted depletion of plant rDNA targets 
      will be a necessary extra step before this approach can be used to screen seeds 
      routinely.
FAU - Dent, Katherine C
AU  - Dent KC
AD  - Plant Establishment and Vegetation Management, Horticulture Research 
      International, Wellesbourne, Warwick, CV35 9EF, UK.
FAU - Stephen, John R
AU  - Stephen JR
FAU - Finch-Savage, William E
AU  - Finch-Savage WE
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - Netherlands
TA  - J Microbiol Methods
JT  - Journal of microbiological methods
JID - 8306883
RN  - 0 (DNA, Bacterial)
RN  - 0 (DNA, Fungal)
RN  - 0 (DNA, Ribosomal)
SB  - IM
MH  - Beta vulgaris/*microbiology
MH  - DNA, Bacterial/chemistry/genetics
MH  - DNA, Fungal/chemistry/genetics
MH  - DNA, Ribosomal/chemistry/genetics
MH  - Electrophoresis, Polyacrylamide Gel
MH  - Gene Expression Profiling
MH  - Polymerase Chain Reaction
MH  - Pseudomonas/*genetics/isolation & purification
MH  - Seeds/microbiology
MH  - Trichoderma/*genetics/isolation & purification
EDAT- 2004/01/07 05:00
MHDA- 2004/04/02 05:00
CRDT- 2004/01/07 05:00
PHST- 2004/01/07 05:00 [pubmed]
PHST- 2004/04/02 05:00 [medline]
PHST- 2004/01/07 05:00 [entrez]
AID - S0167701203002471 [pii]
AID - 10.1016/j.mimet.2003.09.001 [doi]
PST - ppublish
SO  - J Microbiol Methods. 2004 Jan;56(1):17-26. doi: 10.1016/j.mimet.2003.09.001.