PMID- 15816932
OWN - NLM
STAT- MEDLINE
DCOM- 20050831
LR  - 20131121
IS  - 1462-2912 (Print)
IS  - 1462-2912 (Linking)
VI  - 7
IP  - 4
DP  - 2005 Apr
TI  - Phenotypic characterization of Rice Cluster III archaea without prior isolation 
      by applying quantitative polymerase chain reaction to an enrichment culture.
PG  - 553-65
AB  - A so far uncultured member of the Euryarchaeota was enriched from an anoxic 
      riparian soil and phenotypically characterized using quantitative polymerase 
      chain reaction (qPCR; "real-time PCR"). The microorganism is related to the 
      Thermoplasmatales and belongs to Rice Cluster III (RC-III). Enrichment cultures 
      utilized yeast extract (YE) by transiently accumulating acetate as major 
      fermentation product, which was subsequently converted to methane. The abundance 
      of RC-III archaea within the enrichment cultures was quantified by analysis of 
      the terminal restriction fragment length polymorphism (T-RFLP) and by qPCR. We 
      developed qPCR assays targeting the 16S rRNA genes (16S rDNA) specific for RC-III 
      as well as for the Archaea in general. The enrichment cultures consisted of a 
      mixed methanogenic community of Bacteria and Archaea, the latter consisting of up 
      to 60% of members of RC-III. The other archaea belonged to Methanosarcinaceae, 
      Methanomicrobiaceae and Methanobacteriaceae. The enriched RC-III archaea were 
      represented by two sequences (LL25A, LL37A) that were highly similar to each 
      other and to those detected in the soil inoculum (>98% similarity). However, the 
      16S rDNA copy numbers of RC-III archaea were about 1000-fold lower than those of 
      Bacteria. Nevertheless, we were able to estimate growth parameters and 
      physiological properties of one of the enriched RC-III archaea (LL25A) by 
      measuring the increase of 16S rDNA copy numbers specific for this group under 
      different growth conditions. The enriched RC-III archaeon grew optimally at 
      temperatures between 20 and 30 degrees C and neutral pH using YE, meat extract, 
      peptone or tryptone under anoxic conditions. Doubling time was approximately 3 
      days. No proliferation was detected on carbohydrates, amino acids, fatty acids, 
      glycerol, alcohols, aromatic compounds, purine and pyrimidine bases or pyruvate. 
      Various exogenous electron acceptors (e.g. ferric iron, S(0)) did not support 
      growth on YE. Proliferation of the enriched RC-III archaeon was hardly affected 
      by the antibiotics ampicillin, kanamycin and streptomycin. These findings suggest 
      that the enriched archaeon is a mesophilic anaerobe, which can grow 
      heterotrophically on peptides. Further enrichment on peptone and kanamycin 
      eventually allowed the microscopic detection of coccoid cells stained by 
      fluorescence in situ hybridization (FISH).
FAU - Kemnitz, Dana
AU  - Kemnitz D
AD  - Max-Planck-Institut fur terrestrische Mikrobiologie, Karl-von-Frisch-Strasse, 
      35043 Marburg, Germany.
FAU - Kolb, Steffen
AU  - Kolb S
FAU - Conrad, Ralf
AU  - Conrad R
LA  - eng
SI  - GENBANK/AJ745133
SI  - GENBANK/AJ745134
SI  - GENBANK/AJ745135
SI  - GENBANK/AJ745136
SI  - GENBANK/AJ745137
SI  - GENBANK/AJ745138
SI  - GENBANK/AJ745139
SI  - GENBANK/AJ745140
SI  - GENBANK/AJ745141
SI  - GENBANK/AJ745142
SI  - GENBANK/AJ745143
SI  - GENBANK/AJ745144
SI  - GENBANK/AJ745145
SI  - GENBANK/AJ745146
SI  - GENBANK/AJ745147
SI  - GENBANK/AJ745148
PT  - Journal Article
PL  - England
TA  - Environ Microbiol
JT  - Environmental microbiology
JID - 100883692
RN  - 0 (Acetates)
RN  - 0 (Anti-Bacterial Agents)
RN  - 0 (DNA, Archaeal)
RN  - 0 (DNA, Bacterial)
RN  - 0 (DNA, Ribosomal)
RN  - 0 (Organic Chemicals)
RN  - 0 (Peptones)
RN  - 0 (RNA, Ribosomal, 16S)
RN  - OP0UW79H66 (Methane)
SB  - IM
MH  - Acetates/metabolism
MH  - Anaerobiosis
MH  - Anti-Bacterial Agents/pharmacology
MH  - Archaea/*classification/cytology/genetics/*physiology
MH  - Bacteria/*classification/genetics
MH  - DNA Fingerprinting
MH  - DNA, Archaeal/analysis/chemistry/genetics/isolation & purification
MH  - DNA, Bacterial/analysis/chemistry/genetics/isolation & purification
MH  - DNA, Ribosomal/analysis/chemistry/genetics/isolation & purification
MH  - Gene Dosage
MH  - Genes, rRNA
MH  - Hydrogen-Ion Concentration
MH  - In Situ Hybridization, Fluorescence
MH  - Methane/metabolism
MH  - Microscopy, Fluorescence
MH  - Molecular Sequence Data
MH  - Organic Chemicals/metabolism
MH  - Peptones/metabolism
MH  - Phylogeny
MH  - Polymerase Chain Reaction
MH  - Polymorphism, Restriction Fragment Length
MH  - RNA, Ribosomal, 16S/genetics
MH  - Sequence Analysis, DNA
MH  - *Soil Microbiology
MH  - Temperature
EDAT- 2005/04/09 09:00
MHDA- 2005/09/01 09:00
CRDT- 2005/04/09 09:00
PHST- 2005/04/09 09:00 [pubmed]
PHST- 2005/09/01 09:00 [medline]
PHST- 2005/04/09 09:00 [entrez]
AID - EMI723 [pii]
AID - 10.1111/j.1462-2920.2005.00723.x [doi]
PST - ppublish
SO  - Environ Microbiol. 2005 Apr;7(4):553-65. doi: 10.1111/j.1462-2920.2005.00723.x.