A diverse bacterial community in an anoxic quinoline-degrading bioreactor determined by using pyrosequencing and clone library analysis

• Published in: Applied microbiology and biotechnology Vol. 91; no. 2; pp. 425 - 434
• Main Authors: Zhang, Xiaojun, Yue, Siqing, Zhong, Huihui, Hua, Weiying, Chen, Ruijia, Cao, Youfang, Zhao, Liping
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer-Verlag 01-07-2011; Springer; Springer Nature B.V
• Subjects: Acidovorax; Actinobacteria - classification; Actinobacteria - genetics; Actinobacteria - isolation & purification; Analysis; Bacteria; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Bacteria - metabolism; Bacteroidetes - classification; Bacteroidetes - genetics; Bacteroidetes - isolation & purification; Biodegradation, Environmental; Biofilms; Biological and medical sciences; Biomedical and Life Sciences; Bioreactors; Bioreactors - microbiology; Biotechnology; Biotechnology - methods; Cloning; Community structure; Ecosystem; Environmental Biotechnology; Fundamental and applied biological sciences. Psychology; Gene Library; Genetics; Libraries; Library technology; Life Sciences; Membrane reactors; Methods. Procedures. Technologies; Microbial Genetics and Genomics; Microbiology; Molecular Sequence Data; Nitrates; Phylogenetics; Proteobacteria - classification; Proteobacteria - genetics; Proteobacteria - isolation & purification; Quinolines - metabolism; RNA, Ribosomal, 16S - genetics; Sequence Analysis, DNA - methods; Studies; Various methods and equipments; Waste Disposal, Fluid - methods; Water treatment; Clone library; Quinoline degradation; Microbial community; Pyrosequencing; 16S rRNA gene; Anoxia; Degradation; Bioreactor; Gene; Ribosomal RNA; Quinoline; 16S-RNA; Bacteria
• ISSN: 0175-7598; 1432-0614
• DOI: 10.1007/s00253-011-3296-1

There is a concern of whether the structure and diversity of a microbial community can be effectively revealed by short-length pyrosequencing reads. In this study, we performed a microbial community analysis on a sample from a high-efficiency denitrifying quinoline-degrading bioreactor and compared the results generated by pyrosequencing with those generated by clone library technology. By both technologies, 16S rRNA gene analysis indicated that the bacteria in the sample were closely related to, for example, Proteobacteria, Actinobacteria, and Bacteroidetes. The sequences belonging to
Rhodococcus
were the most predominant, and
Pseudomonas
,
Sphingomonas
,
Acidovorax
, and
Zoogloea
were also abundant. Both methods revealed a similar overall bacterial community structure. However, the 622 pyrosequencing reads of the hypervariable V3 region of the 16S rRNA gene revealed much higher bacterial diversity than the 130 sequences from the full-length 16S rRNA gene clone library. The 92 operational taxonomic unit (OTUs) detected using pyrosequencing belonged to 45 families, whereas the 37 OTUs found in the clone library belonged to 25 families. Most sequences obtained from the clone library had equivalents in the pyrosequencing reads. However, 64 OTUs detected by pyrosequencing were not represented in the clone library. Our results demonstrate that pyrosequencing of the V3 region of the 16S rRNA gene is not only a powerful tool for discovering low-abundance bacterial populations but is also reliable for dissecting the bacterial community structure in a wastewater environment.