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

Abstract

Propionate accumulation is a common indicator of process imbalances in anaerobic bioreactor systems. The accumulation of propionate can occur due to low retention rates, hydrogen accumulation, or mechanical changes affecting the proximity between propionate oxidizers and partner species, thereby preventing necessary electron transfer. Few studies, however, have observed the changes in microbial community structure during propionate accumulation. We used 454 pyrosequencing of 16S rDNA to evaluate the community membership during propionate accumulations in replicate bioreactors with rumen based cultures. Half of the culture volume from a parent reactor was transferred to a sterile “daughter” reactor, and both systems were run identically. Both reactors experienced a propionate accumulation after roughly 10 days, with the propionate accumulation being less pronounced in the parent reactor as compared to the daughter reactor. Non-metric multidimensional scaling (NMDS) was used to determine clustering patterns of the samples, and correlative methods were used to determine which OTUs were significantly associated with the movements of samples along the NMDS axes. The presence of Saccharofermentans characterized the position of early samples, whereas the presence of Ruminococcus and Succiniclasticum were more indicative of the positions of later samples. Hydrogen accumulation and low sequence counts indicated low methanogen activity. Although bothmore » reactor systems were closed to microbial inputs due to the sterilization of influent media, we recorded significant increases in reactor diversity over time. This suggests that changes in the abundances of dominant community members may affect the sequencing of rare taxa within samples.« less

Authors:
 [1];  [2];  [2];  [2];  [1]
  1. Washington State Univ., Richland, WA (United States). Bioproducts, Sciences and Engineering Lab.
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Biological Sciences Division
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1337728
Report Number(s):
PNNL-SA-106822
Journal ID: ISSN 0168-6496; KP1601030
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: FEMS Microbiology Ecology; Journal Volume: 90; Journal Issue: 3
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Boaro, Amy A., Kim, Young-Mo, Konopka, Allan E., Callister, Stephen J., and Ahring, Birgitte K. Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture. United States: N. p., 2015. Web. doi:10.1111/1574-6941.12435.
Boaro, Amy A., Kim, Young-Mo, Konopka, Allan E., Callister, Stephen J., & Ahring, Birgitte K. Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture. United States. doi:10.1111/1574-6941.12435.
Boaro, Amy A., Kim, Young-Mo, Konopka, Allan E., Callister, Stephen J., and Ahring, Birgitte K. Mon . "Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture". United States. doi:10.1111/1574-6941.12435.
@article{osti_1337728,
title = {Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture},
author = {Boaro, Amy A. and Kim, Young-Mo and Konopka, Allan E. and Callister, Stephen J. and Ahring, Birgitte K.},
abstractNote = {Propionate accumulation is a common indicator of process imbalances in anaerobic bioreactor systems. The accumulation of propionate can occur due to low retention rates, hydrogen accumulation, or mechanical changes affecting the proximity between propionate oxidizers and partner species, thereby preventing necessary electron transfer. Few studies, however, have observed the changes in microbial community structure during propionate accumulation. We used 454 pyrosequencing of 16S rDNA to evaluate the community membership during propionate accumulations in replicate bioreactors with rumen based cultures. Half of the culture volume from a parent reactor was transferred to a sterile “daughter” reactor, and both systems were run identically. Both reactors experienced a propionate accumulation after roughly 10 days, with the propionate accumulation being less pronounced in the parent reactor as compared to the daughter reactor. Non-metric multidimensional scaling (NMDS) was used to determine clustering patterns of the samples, and correlative methods were used to determine which OTUs were significantly associated with the movements of samples along the NMDS axes. The presence of Saccharofermentans characterized the position of early samples, whereas the presence of Ruminococcus and Succiniclasticum were more indicative of the positions of later samples. Hydrogen accumulation and low sequence counts indicated low methanogen activity. Although both reactor systems were closed to microbial inputs due to the sterilization of influent media, we recorded significant increases in reactor diversity over time. This suggests that changes in the abundances of dominant community members may affect the sequencing of rare taxa within samples.},
doi = {10.1111/1574-6941.12435},
journal = {FEMS Microbiology Ecology},
number = 3,
volume = 90,
place = {United States},
year = {Mon Jan 05 00:00:00 EST 2015},
month = {Mon Jan 05 00:00:00 EST 2015}
}