The structure of the bacterial and archaeal community in a biogas digester as revealed by denaturing gradient gel electrophoresis and 16S rDNA sequencing analysis.
OBJECTIVE
To identify the bacterial and archaeal composition in a mesophilic biogas digester treating pig manure and to compare the consistency of two 16S rDNA-based methods to investigate the microbial structure.


RESULTS
Sixty-nine bacterial operational taxonomic units (OTU) and 25 archaeal OTU were identified by sequencing two 16S rDNA clone libraries. Most bacterial OTU were identified as phyla of Firmicutes (47.2% of total clones), Bacteroides (35.4%) and Spirochaetes (13.2%). Methanoculleus bourgensis (29.0%), Methanosarcina barkeri (27.4%) and Methanospirillum hungatei (10.8%) were the dominant methanogens. Only 9% of bacterial and 20% of archaeal OTU matched cultured isolates at a similarity index of >or=97%. About 78% of the dominant bacterial (with abundance >3%) and 83% of archaeal OTU were recovered from the denaturing gradient gel electrophoresis (DGGE) bands of V3 regions in 16S rDNAs.


CONCLUSIONS
In the digester, most bacterial and archaeal species were uncultured; bacteria belonging to Firmicutes, Bacteroides and Spirochaetes seem to take charge of cellulolysis, proteolysis, acidogenesis, sulfur-reducing and homoacetogenesis; the most methanogens were typical hydrogenotrophic or hydrogenotrophic/aceticlastic; DGGE profiles reflected the dominant microbiota.


CONCLUSIONS
This study gave a first insight of the overall microbial structure in a rural biogas digester and also indicated DGGE was useful in displaying its dominant microbiota.
Liu
F H
FH
Key Laboratory of Synthetic Biology, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
Wang
S B
SB
Zhang
J S
JS
Zhang
J
J
Yan
X
X
Zhou
H K
HK
Zhao
G P
GP
Zhou
Z H
ZH
D000818:Animals; D001105:Archaea / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D001673:Biodegradation, Environmental; D019149:Bioreactors; D004275:DNA, Ribosomal / Q000235:genetics*; D004586:Electrophoresis / Q000379:methods; D015723:Gene Library; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D008372:Manure / Q000382:microbiology*; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013552:Swine
D004275:DNA, Ribosomal; D008372:Manure; D012336:RNA, Ribosomal, 16S