PMID- 16309387
OWN - NLM
STAT- MEDLINE
DCOM- 20060210
LR  - 20061115
IS  - 1462-2912 (Print)
IS  - 1462-2912 (Linking)
VI  - 7
IP  - 12
DP  - 2005 Dec
TI  - Bacterial diversity of metagenomic and PCR libraries from the Delaware River.
PG  - 1883-95
AB  - To determine whether metagenomic libraries sample adequately the dominant 
      bacteria in aquatic environments, we examined the phylogenetic make-up of a large 
      insert metagenomic library constructed with bacterial DNA from the Delaware 
      River, a polymerase chain reaction (PCR) library of 16S rRNA genes, and community 
      structure determined by fluorescence in situ hybridization (FISH). The 
      composition of the libraries and community structure determined by FISH differed 
      for the major bacterial groups in the river, which included Actinobacteria, 
      beta-proteobacteria and Cytophaga-like bacteria. Beta-proteobacteria were 
      underrepresented in the metagenomic library compared with the PCR library and 
      FISH, while Cytophaga-like bacteria were more abundant in the metagenomic library 
      than in the PCR library and in the actual community according to FISH. The 
      Delaware River libraries contained bacteria belonging to several widespread 
      freshwater clusters, including clusters of Polynucleobacter necessarius, 
      Rhodoferax sp. Bal47 and LD28 beta-proteobacteria, the ACK-m1 and STA2-30 
      clusters of Actinobacteria, and the PRD01a001B Cytophaga-like bacteria cluster. 
      Coverage of bacteria with > 97% sequence identity was 65% and 50% for the 
      metagenomic and PCR libraries respectively. Rarefaction analysis of replicate PCR 
      libraries and of a library constructed with re-conditioned amplicons indicated 
      that heteroduplex formation did not substantially impact the composition of the 
      PCR library. This study suggests that although it may miss some bacterial groups, 
      the metagenomic approach can sample other groups (e.g. Cytophaga-like bacteria) 
      that are potentially underrepresented by other culture-independent approaches.
FAU - Cottrell, Matthew T
AU  - Cottrell MT
AD  - University of Delaware, College of Marine Studies, 700 Pilottown Road., Lewes, DE 
      19958, USA.
FAU - Waidner, Lisa A
AU  - Waidner LA
FAU - Yu, Liying
AU  - Yu L
FAU - Kirchman, David L
AU  - Kirchman DL
LA  - eng
SI  - GENBANK/AY562245
SI  - GENBANK/AY562246
SI  - GENBANK/AY562247
SI  - GENBANK/AY562248
SI  - GENBANK/AY562249
SI  - GENBANK/AY562250
SI  - GENBANK/AY562251
SI  - GENBANK/AY562252
SI  - GENBANK/AY562253
SI  - GENBANK/AY562254
SI  - GENBANK/AY562255
SI  - GENBANK/AY562256
SI  - GENBANK/AY562257
SI  - GENBANK/AY562258
SI  - GENBANK/AY562259
SI  - GENBANK/AY562260
SI  - GENBANK/AY562261
SI  - GENBANK/AY562262
SI  - GENBANK/AY562263
SI  - GENBANK/AY562264
SI  - GENBANK/AY562265
SI  - GENBANK/AY562266
PT  - Comparative Study
PT  - Journal Article
PT  - Research Support, U.S. Gov't, Non-P.H.S.
PL  - England
TA  - Environ Microbiol
JT  - Environmental microbiology
JID - 100883692
RN  - 0 (RNA, Bacterial)
RN  - 0 (RNA, Ribosomal, 16S)
SB  - IM
MH  - Actinobacteria/genetics/isolation & purification
MH  - Bacteria/genetics/*isolation & purification
MH  - Betaproteobacteria/genetics/isolation & purification
MH  - *Biodiversity
MH  - Burkholderiaceae/genetics/isolation & purification
MH  - Cytophaga/genetics/isolation & purification
MH  - Delaware
MH  - Fresh Water/*microbiology
MH  - *Genomic Library
MH  - In Situ Hybridization, Fluorescence
MH  - Molecular Sequence Data
MH  - *Polymerase Chain Reaction
MH  - RNA, Bacterial/genetics
MH  - RNA, Ribosomal, 16S/genetics
MH  - Species Specificity
MH  - *Water Microbiology
EDAT- 2005/11/29 09:00
MHDA- 2006/02/14 09:00
CRDT- 2005/11/29 09:00
PHST- 2005/11/29 09:00 [pubmed]
PHST- 2006/02/14 09:00 [medline]
PHST- 2005/11/29 09:00 [entrez]
AID - EMI762 [pii]
AID - 10.1111/j.1462-2920.2005.00762.x [doi]
PST - ppublish
SO  - Environ Microbiol. 2005 Dec;7(12):1883-95. doi: 10.1111/j.1462-2920.2005.00762.x.