PMID- 18207592
OWN - NLM
STAT- MEDLINE
DCOM- 20080602
LR  - 20131121
IS  - 0167-7012 (Print)
IS  - 0167-7012 (Linking)
VI  - 72
IP  - 3
DP  - 2008 Mar
TI  - An improved cell recovery method for iron oxidizing bacterial (IOB) enrichments.
PG  - 235-40
LID - 10.1016/j.mimet.2007.12.001 [doi]
AB  - Two cell recovery methods for IOB enrichments were evaluated for DNA extraction 
      and further PCR-based 16S rRNA gene clone library creation. One was a published 
      method consisting of heating plus oxalic acid treatment and the other one was a 
      new method based on enzymatic agarose digestion (using beta-agarase I). The 
      results indicated that the enzymatic method was much gentler on IOB cells and 
      yielded an approximately 5000-fold higher DNA mass than the published method. The 
      16S rRNA gene clone library developed from the beta-agarase I treated IOB 
      enrichments indicated a high IOB community diversity with sequences in alpha-, 
      beta-, gamma-, delta-, epsilon-Proteobacteria, unclassified Proteobacteria, 
      unclassified Bacteroidetes and unclassified Bacteria. In contrast, the published 
      method resulted in mainly gamma-Proteobacterial clone sequences. In addition, 
      only the cells recovered by agarase treatment were amenable to direct 
      fluorescence in situ hybridization (FISH). Therefore, we propose that the agarase 
      method is a better IOB cell recovery method, because it is simpler, faster, and 
      retains more genetic diversity.
FAU - Yu, Ran
AU  - Yu R
AD  - Department of Civil and Environmental Engineering, University of Connecticut, 
      Storrs, CT 06269-2037, USA.
FAU - Graf, Joerg
AU  - Graf J
FAU - Smets, Barth F
AU  - Smets BF
LA  - eng
PT  - Comparative Study
PT  - Journal Article
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20071215
PL  - Netherlands
TA  - J Microbiol Methods
JT  - Journal of microbiological methods
JID - 8306883
RN  - 0 (DNA, Bacterial)
RN  - 0 (RNA, Ribosomal, 16S)
RN  - E1UOL152H7 (Iron)
SB  - IM
MH  - Biodiversity
MH  - Colony Count, Microbial
MH  - DNA, Bacterial/*genetics/*isolation & purification
MH  - Iron/metabolism
MH  - Oxidation-Reduction
MH  - Proteobacteria/*classification/*genetics/isolation & purification
MH  - RNA, Ribosomal, 16S/genetics
MH  - *Water Microbiology
EDAT- 2008/01/22 09:00
MHDA- 2008/06/03 09:00
CRDT- 2008/01/22 09:00
PHST- 2007/10/24 00:00 [received]
PHST- 2007/12/03 00:00 [revised]
PHST- 2007/12/03 00:00 [accepted]
PHST- 2008/01/22 09:00 [pubmed]
PHST- 2008/06/03 09:00 [medline]
PHST- 2008/01/22 09:00 [entrez]
AID - S0167-7012(07)00401-0 [pii]
AID - 10.1016/j.mimet.2007.12.001 [doi]
PST - ppublish
SO  - J Microbiol Methods. 2008 Mar;72(3):235-40. doi: 10.1016/j.mimet.2007.12.001. 
      Epub 2007 Dec 15.