Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture

Journal Article · Mon Dec 01 04:00:00 EST 2014 · FEMS Microbiology Ecology, 90(3):802-15

DOI:https://doi.org/10.1111/1574-6941.12435· OSTI ID:1170062

Boaro, Amy A.; Kim, Young-Mo; Konopka, Allan; Callister, Stephen J.; Ahring, Birgitte K.

Integrated ‘omics have been used on pure cultures and co-cultures, yet they have not been applied to complex microbial communities to examine questions of perturbation response. In this study, we used integrated ‘omics to measure the perturbation response of a cellulose-degrading bioreactor community fed with microcrystalline cellulose (Avicel). We predicted that a pH decrease by addition of a pulse of acid would reduce microbial community diversity and temporarily reduce reactor function such as cellulose degradation. However, 16S rDNA pyrosequencing results revealed increased alpha diversity in the microbial community after the perturbation, and a persistence of the dominant community members over the duration of the experiment. Proteomics results showed a decrease in activity of proteins associated with Fibrobacter succinogenes two days after the perturbation followed by increased protein abundances six days after the perturbation. The decrease in cellulolytic activity suggested by the proteomics was confirmed by the accumulation of Avicel in the reactor. Metabolomics showed a pattern similar to that of the proteome, with amino acid production decreasing two days after the perturbation and increasing after six days. This study demonstrated that community ‘omics data provides valuable information about the interactions and function of anaerobic cellulolytic community members after a perturbation.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 1170062
• Report Number(s): PNNL-SA-105700; 44995; 47418; KP1601010
• Journal Information: FEMS Microbiology Ecology, 90(3):802-15, Journal Name: FEMS Microbiology Ecology, 90(3):802-15
• Country of Publication: United States
• Language: English

Related Subjects

Environmental Molecular Sciences Laboratory
continuous culture
chemostat
community proteomics
community metabolomics
meta’omics
microbial diversity
functional redundancy
454 pyrosequencing
β-glucosidase
Fibrobacter
Prevotella