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Terminal restriction fragment length polymorphism is an 'old school' reliable technique for swift microbial community screening in anaerobic digestion

Jo De Vrieze (UGent) , Umer Z. Ijaz, Aaron M. Saunders and Susanne Theuerl
(2018) SCIENTIFIC REPORTS. 8.
Author
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Abstract
The microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades. In the last decade, high-throughput 16S rRNA gene amplicon sequencing has replaced these techniques, but the time-consuming and complex nature of high-throughput techniques is a potential bottleneck for full-scale anaerobic digestion application, when monitoring community dynamics. Here, the bacterial and archaeal TRFLP profiles were compared with 16S rRNA gene amplicon profiles (Illumina platform) of 25 full-scale anaerobic digestion plants. The a-diversity analysis revealed a higher richness based on Illumina data, compared with the TRFLP data. This coincided with a clear difference in community organisation, Pareto distribution, and co-occurrence network statistics, i.e., betweenness centrality and normalised degree. The beta-diversity analysis showed a similar clustering profile for the Illumina, bacterial TRFLP and archaeal TRFLP data, based on different distance measures and independent of phylogenetic identification, with pH and temperature as the two key operational parameters determining microbial community composition. The combined knowledge of temporal dynamics and projected clustering in the beta-diversity profile, based on the TRFLP data, distinctly showed that TRFLP is a reliable technique for swift microbial community dynamics screening in full-scale anaerobic digestion plants.
Keywords
GRADIENT GEL-ELECTROPHORESIS, 16S RIBOSOMAL-RNA, SUGAR-BEET SILAGE, BACTERIAL COMMUNITY, PROCESS FAILURE, BIOGAS MICROBIOME, PROCESS STABILITY, SPECIES RICHNESS, RARE BIOSPHERE, CO-DIGESTION

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MLA
De Vrieze, Jo, et al. “Terminal Restriction Fragment Length Polymorphism Is an ‘old School’ Reliable Technique for Swift Microbial Community Screening in Anaerobic Digestion.” SCIENTIFIC REPORTS, vol. 8, 2018, doi:10.1038/s41598-018-34921-7.
APA
De Vrieze, J., Ijaz, U. Z., Saunders, A. M., & Theuerl, S. (2018). Terminal restriction fragment length polymorphism is an “old school” reliable technique for swift microbial community screening in anaerobic digestion. SCIENTIFIC REPORTS, 8. https://doi.org/10.1038/s41598-018-34921-7
Chicago author-date
De Vrieze, Jo, Umer Z. Ijaz, Aaron M. Saunders, and Susanne Theuerl. 2018. “Terminal Restriction Fragment Length Polymorphism Is an ‘old School’ Reliable Technique for Swift Microbial Community Screening in Anaerobic Digestion.” SCIENTIFIC REPORTS 8. https://doi.org/10.1038/s41598-018-34921-7.
Chicago author-date (all authors)
De Vrieze, Jo, Umer Z. Ijaz, Aaron M. Saunders, and Susanne Theuerl. 2018. “Terminal Restriction Fragment Length Polymorphism Is an ‘old School’ Reliable Technique for Swift Microbial Community Screening in Anaerobic Digestion.” SCIENTIFIC REPORTS 8. doi:10.1038/s41598-018-34921-7.
Vancouver
1.
De Vrieze J, Ijaz UZ, Saunders AM, Theuerl S. Terminal restriction fragment length polymorphism is an “old school” reliable technique for swift microbial community screening in anaerobic digestion. SCIENTIFIC REPORTS. 2018;8.
IEEE
[1]
J. De Vrieze, U. Z. Ijaz, A. M. Saunders, and S. Theuerl, “Terminal restriction fragment length polymorphism is an ‘old school’ reliable technique for swift microbial community screening in anaerobic digestion,” SCIENTIFIC REPORTS, vol. 8, 2018.
@article{8583332,
  abstract     = {{The microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades. In the last decade, high-throughput 16S rRNA gene amplicon sequencing has replaced these techniques, but the time-consuming and complex nature of high-throughput techniques is a potential bottleneck for full-scale anaerobic digestion application, when monitoring community dynamics. Here, the bacterial and archaeal TRFLP profiles were compared with 16S rRNA gene amplicon profiles (Illumina platform) of 25 full-scale anaerobic digestion plants. The a-diversity analysis revealed a higher richness based on Illumina data, compared with the TRFLP data. This coincided with a clear difference in community organisation, Pareto distribution, and co-occurrence network statistics, i.e., betweenness centrality and normalised degree. The beta-diversity analysis showed a similar clustering profile for the Illumina, bacterial TRFLP and archaeal TRFLP data, based on different distance measures and independent of phylogenetic identification, with pH and temperature as the two key operational parameters determining microbial community composition. The combined knowledge of temporal dynamics and projected clustering in the beta-diversity profile, based on the TRFLP data, distinctly showed that TRFLP is a reliable technique for swift microbial community dynamics screening in full-scale anaerobic digestion plants.}},
  articleno    = {{16818}},
  author       = {{De Vrieze, Jo and Ijaz, Umer Z. and Saunders, Aaron M. and Theuerl, Susanne}},
  issn         = {{2045-2322}},
  journal      = {{SCIENTIFIC REPORTS}},
  keywords     = {{GRADIENT GEL-ELECTROPHORESIS,16S RIBOSOMAL-RNA,SUGAR-BEET SILAGE,BACTERIAL COMMUNITY,PROCESS FAILURE,BIOGAS MICROBIOME,PROCESS STABILITY,SPECIES RICHNESS,RARE BIOSPHERE,CO-DIGESTION}},
  language     = {{eng}},
  pages        = {{12}},
  title        = {{Terminal restriction fragment length polymorphism is an 'old school' reliable technique for swift microbial community screening in anaerobic digestion}},
  url          = {{http://dx.doi.org/10.1038/s41598-018-34921-7}},
  volume       = {{8}},
  year         = {{2018}},
}
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