Inoculum composition determines microbial community and function in an anaerobic sequential batch reactor

The sustainable recovery of resources from wastewater streams can provide many social and environmental benefits. A common strategy to recover valuable resources from wastewater is to harness the products of fermentation by complex microbial communities. In these fermentation bioreactors high microbial community diversity within the inoculum source is commonly assumed as sufficient for the selection of a functional microbial community. However, variability of the product profile obtained from these bioreactors is a persistent challenge in this field. In an attempt to address this variability, the impact of inoculum on the microbial community structure and function within the bioreactor was evaluated using controlled laboratory experiments. In the course of this work, sequential batch reactors were inoculated with three complex microbial inocula and the chemical and microbial compositions were monitored by HPLC and 16S rRNA amplicon analysis, respectively. Microbial community dynamics and chemical profiles were found to be distinct to initial inoculate and highly reproducible. Additionally we found that the generation of a complex volatile fatty acid profile was not specific to the diversity of the initial microbial inoculum. Our results suggest that the composition of the original inoculum predictably contributes to bioreactor community structure and function.

[1]  M. V. van Loosdrecht,et al.  Anaerobic digestion without biogas? , 2015, Reviews in Environmental Science and Bio/Technology.

[2]  J. Schmidt,et al.  Dark fermentation biorefinery in the present and future (bio)chemical industry , 2015, Reviews in Environmental Science and Bio/Technology.

[3]  P. Hugenholtz,et al.  Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters , 2014, The ISME Journal.

[4]  Otto X. Cordero,et al.  Explaining microbial genomic diversity in light of evolutionary ecology , 2014, Nature Reviews Microbiology.

[5]  M. Cates,et al.  Community history affects the predictability of microbial ecosystem development , 2013, The ISME Journal.

[6]  Eric J. Alm,et al.  Distribution-Based Clustering: Using Ecology To Refine the Operational Taxonomic Unit , 2013, Applied and Environmental Microbiology.

[7]  J. Álvarez-Ramírez,et al.  Monitoring anaerobic sequential batch reactors via fractal analysis of pH time series , 2013, Biotechnology and bioengineering.

[8]  A. Konopka,et al.  Quantifying community assembly processes and identifying features that impose them , 2013, The ISME Journal.

[9]  Kai Xue,et al.  Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community , 2013, mBio.

[10]  E. Trably,et al.  Changes in hydrogenase genetic diversity and proteomic patterns in mixed-culture dark fermentation o , 2011 .

[11]  R. Knight,et al.  Defining seasonal marine microbial community dynamics , 2011, The ISME Journal.

[12]  Peer Bork,et al.  Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy , 2011, Nucleic Acids Res..

[13]  L. T. Angenent,et al.  Waste to bioproduct conversion with undefined mixed cultures: the carboxylate platform. , 2011, Trends in biotechnology.

[14]  Alexander Goesmann,et al.  Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing , 2011, PloS one.

[15]  J. Steyer,et al.  Development of membrane inlet mass spectrometry for examination of fermentation processes. , 2010, Talanta.

[16]  Irina Dana Ofiteru,et al.  Combined niche and neutral effects in a microbial wastewater treatment community , 2010, Proceedings of the National Academy of Sciences.

[17]  William A. Walters,et al.  Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample , 2010, Proceedings of the National Academy of Sciences.

[18]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[19]  Sonia Heaven,et al.  Potential errors in the quantitative evaluation of biogas production in anaerobic digestion processes. , 2009, Bioresource technology.

[20]  Toni Gabaldón,et al.  trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..

[21]  Adam P. Arkin,et al.  FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix , 2009, Molecular biology and evolution.

[22]  W. Verstraete,et al.  Initial community evenness favours functionality under selective stress , 2009, Nature.

[23]  Michel Loreau,et al.  The Princeton Guide to Ecology , 2009 .

[24]  S. Allison,et al.  Resistance, resilience, and redundancy in microbial communities , 2008, Proceedings of the National Academy of Sciences.

[25]  Robbert Kleerebezem,et al.  Energy-based models for environmental biotechnology. , 2008, Trends in biotechnology.

[26]  C. Criddle,et al.  Correlation of patterns of denitrification instability in replicated bioreactor communities with shifts in the relative abundance and the denitrification patterns of specific populations , 2007, The ISME Journal.

[27]  Robbert Kleerebezem,et al.  Influence of the pH on (open) mixed culture fermentation of glucose: A chemostat study , 2007, Biotechnology and bioengineering.

[28]  A. Hector,et al.  Biodiversity and ecosystem multifunctionality , 2007, Nature.

[29]  Jaakko A Puhakka,et al.  The relationship between instability of H2 production and compositions of bacterial communities within a dark fermentation fluidised‐bed bioreactor , 2007, Biotechnology and bioengineering.

[30]  J. Tiedje,et al.  Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.

[31]  M. V. van Loosdrecht,et al.  Mixed culture biotechnology for bioenergy production. , 2007, Current opinion in biotechnology.

[32]  R. De Wit,et al.  'Everything is everywhere, but, the environment selects'; what did Baas Becking and Beijerinck really say? , 2006, Environmental microbiology.

[33]  Eoin L. Brodie,et al.  Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB , 2006, Applied and Environmental Microbiology.

[34]  H. Tettelin,et al.  The microbial pan-genome. , 2005, Current opinion in genetics & development.

[35]  B. Silverman,et al.  The contribution of species richness and composition to bacterial services , 2005, Nature.

[36]  L. T. Angenent,et al.  Production of bioenergy and biochemicals from industrial and agricultural wastewater. , 2004, Trends in biotechnology.

[37]  L. Raskin,et al.  Diversity and dynamics of microbial communities in engineered environments and their implications for process stability. , 2003, Current opinion in biotechnology.

[38]  D. L. Hawkes,et al.  Sustainable fermentative hydrogen production: challenges for process optimisation , 2002 .

[39]  Suiying Huang,et al.  How Stable Is Stable? Function versus Community Composition , 1999, Applied and Environmental Microbiology.

[40]  W. Verstraete,et al.  Inoculum selection is crucial to ensure operational stability in anaerobic digestion , 2014, Applied Microbiology and Biotechnology.

[41]  Jianhua Lin,et al.  Divergence measures based on the Shannon entropy , 1991, IEEE Trans. Inf. Theory.