Segregated flux balance analysis constrained by population structure/function data: The case of PHA production by mixed microbial cultures

Abstract

In this study we developed a segregated flux balance analysis (FBA) method to calculate metabolic flux distributions of the individual populations present in a mixed microbial culture (MMC). Population specific flux data constraints were derived from the raw data typically obtained by the fluorescence in situ hybridization (FISH) and microautoradiography (MAR)-FISH techniques. This method was applied to study the metabolic heterogeneity of a MMC that produces polyhydroxyalkanoates (PHA) from fermented sugar cane molasses. Three populations were identified by FISH, namely Paracoccus sp., Thauera sp., and Azoarcus sp. The segregated FBA method predicts a flux distribution for each of the identified populations. The method is shown to predict with high accuracy the average PHA storage flux and the respective monomeric composition for 16 independent experiments. Moreover, flux predictions by segregated FBA were slightly better than those obtained by nonsegregated FBA, and also highly concordant with metabolic flux analysis (MFA) estimated fluxes. The segregated FBA method can be of high value to assess metabolic heterogeneity in MMC systems and to derive more efficient eco-engineering strategies. For the case of PHA-producing MMC considered in this work, it becomes apparent that the PHA average monomeric composition might be controlled not only by the volatile fatty acids (VFA) feeding profile but also by the population composition present in the MMC.

Unveiling PHA-storing populations using molecular methods

“…Despite different uptake rates being obtained when each carbon source was fed individually and mixed with other VFAs, MAR-FISH showed the preference for each VFA by these genera. The selected culture had a highly flexible physiology allowing co-dominance between three main genera that could lead to improved models where the fraction of each PHA-producing population and their corresponding substrate preferences would be incorporated (Pardelha et al 2013). Queirós et al (2014) used hardwood sulfite spent liquor (HSSL), a by-product from the pulp industry, as substrate to acclimatize a MMC and attest its possible valorization.…”

Composition of mixed culture PHA biopolymers and implications for downstream processing

“…The flux predictions given by the segregated model by were slightly better than those obtained by nonsegregated FBA, and coincided with metabolic flux analysis (MFA) estimated fluxes (Pardelha et al 2013). Even though this model does not predict population dynamics it can be a tool to describe the metabolic diversity among the distinct microorganisms in a mixed culture.…”

“…The microbial community composition during the PHA production phase has been considered in the segregated FBA model method proposed by Pardelha et al (2013). The flux predictions given by the segregated model by were slightly better than those obtained by nonsegregated FBA, and coincided with metabolic flux analysis (MFA) estimated fluxes (Pardelha et al 2013).…”

The composition analysis and preliminary cultivation optimization of a PHA-producing microbial consortium with xylose as a sole carbon source

“…Moreover, high temperature may affect the enzyme activity of PHA synthetase. Pardelha et al (2013) found out that the increasing temperature would decrease the dissolved oxygen in the culture, and this phenomenon would lead to a decrease of PHB yield.…”