rRNA and poly-beta-hydroxybutyrate dynamics in bioreactors subjected to feast and famine cycles

Cellular RNA levels define heterotrophic substrate-uptake rate sub-guilds in activated sludge microbial communities

A heterotrophic-specialist model was proposed previously to divide wastewater treatment plant (WWTP) heterotrophs into sub-guilds of consumers of readily or slowly degradable substrates (RDS or SDS, respectively). The substrate degradation rate model coupled to metabolic considerations predicted that RNA and polyhydroxyalkanoate (PHA) levels would be positively correlated in the activated sludge communities with high RNA and PHA occurring in RDS-consumers, and low RNA with no PHA accumulation occurring in SDS-consumers because their external substrates are always present. This prediction was verified in previous studies and in the current one. Thus, RNA and PHA levels were used as biomarkers of the RDS- and SDS-consumer sub-guilds for cell sorting using flow cytometry of samples from three WWTPs. Subsequently, 16S rRNA gene amplicon sequencing revealed that the sorted groups were highly similar over time and among WWTPs, and demonstrated a clear segregation by RNA levels. Predicted ecophysiological traits based on 16S rRNA phylogeny suggested that the high-RNA population showed RDS-consumer traits such as higher rrn copy numbers per genome. Using a mass-flow immigration model, it appeared that the high-RNA populations exhibited high immigration rates more frequently than low-RNA populations, but the differences in frequencies were less with increasing solids residence times.

Microbial life strategy with high rRNA operon copy number facilitates the energy and nutrient flux in anaerobic digestion

Microbial life strategy, reflected by rRNA operon (rrn) copy number, determines microbial ecological roles. However, the relationship between microbial life strategy and the energy and nutrient flux in anaerobic digestion (AD) remains elusive. This study investigated microbial rrn copy number and expression ratio using amplicon sequencing of 16S rRNA gene and 16S rRNA, and monitored CH₄ daily production to approximate the status of energy and nutrient flux in semi-continuous AD. A significantly positive correlation between the mean rrn copy number of microbial communities in digestate and CH₄ daily production was detected in the control treatment fed swine manure. The reduced feedstock complexity, by replacing parts of swine manure with fructose or apple waste, weakened the correlation. When feedstock complexity was increased again, the correlation was strengthened again. Similar results were detected in mean rrn expression ratio of microbial communities. The responses of mean rrn copy number and expression ratio of communities to feedstock addition differed between the reduced feedstock complexity and the control treatment, as well as between in digestate and in straw. Our findings reveal a novel relationship between microbial community life strategy and the energy and nutrient flux, and the roles of feedstock characteristics therein in AD.

Polyhydroxyalkanoate (PHA) production via resource recovery from industrial waste streams: A review of techniques and perspectives

The problem of waste generation in the form of wastewater and solid wastes has caused an urgent, yet persisting, global issue that calls for the development of sustainable treatment and resource recovery technologies. The production of value-added polyhydroxyalkanoates (PHAs) from industrial waste streams has attracted the attention of researchers and process industries because they could replace traditional plastics. PHAs are biopolymers with high degradability, with a variety of applications in the manufacturing sector (e.g. medical equipment, packaging). The aim of this review is to describe the techniques and industrial waste streams that are applied for PHA production. The different enrichment and accumulation techniques that employ mixed microbial communities and carbon recovery from industrial waste streams and various downstream processes were reviewed. PHA yields between 7.6 and 76 wt% were reported for pilot-scale PHA production; while, at the laboratory-scale, yields from PHA accumulation range between 8.6 and 56 wt%. The recent advances in the application of waste streams for PHA production could result in more widely spread PHA production at the industrial scale via its integration into biorefineries for co-generation of PHAs with other added-value products like biohydrogen and biogas.

Biological conversion of methane to polyhydroxyalkanoates: Current advances, challenges, and perspectives

Methane emissions and plastic pollution are critical global challenges. The biological conversion of methane to poly-β-hydroxybutyrate (PHB) not only mitigates methane emissions but also provides biodegradable polymer substitutes for petroleum-based materials used in plastics production. This work provides an early overview of the methane-based PHB advances and discusses challenges and related strategies. Recent advances of PHB, including PHB biosynthetic pathways, methanotrophs, bioreactors, and the performances of PHB materials are introduced. Major challenges of methane-based PHB production are discussed in detail; these include low efficiency of methanotrophs, low gas-liquid mass transfer efficiency, and poor material properties. To overcome these limitations, various approaches are also explored, such as feast-famine regimes, engineered microorganisms, gas-permeable membrane bioreactors, two-phase partitioning bioreactors, poly-β-hydroxybutyrate-co-hydroxyvalerate synthesis, and molecular weight manipulation.

Polyhydroxy butyrate production by Acinetobacter junii BP25, Aeromonas hydrophila ATCC 7966, and their co-culture using a feast and famine strategy

The study aimed to evaluate biopolymer production using two bacterial strains, Acinetobacter junii BP25 and Aeromonas hydrophila ATCC 7966, and their co-culture. Batch experiments were evaluated using acetate and butyrate as carbon sources in feast and famine strategy. Feast phase was studied using carbon, nitrates and phosphate in the ratio of 100:8:1 and famine phase was limited with the phosphate and nitrates. Co-culture resulted in highest specific growth rate (0.30 h^-1) in the feast phase and the famine phase accounted the maximum polyhydroxybutyrate (PHB) accumulation (2.46 g PHB/L), followed by Acinetobacter junii BP25 (0.25 h^-1 and 1.82 g PHB/L) and Aeromonas hydrophila ATCC 7966 (0.17 h^-1 and 1.12 g PHB/L). Fourier-transform infrared spectroscopy (FT-IR) and nuclear magnetic resonance spectroscopy (NMR) structural analysis confirmed as PHB. PHB production using the co-culture could be integrated with biohydrogen process using volatile fatty acids (VFA) as a carbon source in the biorefinery framework.

Composition of heterotrophic specialized sub-guilds defined by a positive RNA and polyhydroxyalkanoate correlation in activated sludge

Microbial heterotrophic guilds in activated sludge wastewater treatment systems have complex population structures and functions. A previously proposed heterotrophic-specialist model states that heterotrophs consist of sub-guilds specialized in consuming specific classes of compounds, either readily degradable substrate (RDS) or slowly degradable substrate (SDS) according to current mathematical modeling practices for wastewater treatment processes. It follows from metabolic considerations that the levels of RNA and polyhydroxyalkanoate (PHA) are correlated for strains of the same species growing in different environments; a conjecture previously tested. The proposed classification of heterotrophs into RDS or SDS consumers predicts that the same correlation would also be found across heterotrophic species in conventional activated sludge systems; this prediction was tested in the current study. The positive correlation between the RNA and PHA levels was observed in 9 conventional activated sludge plants in two independent sampling times and it was also found stable over a 6-month regular sampling period at one of these plants. Together, these results imply that the levels of RNA and PHA can be used to define heterotrophic-specialist sub-guilds. In order to gain insight in the species composition of the defined sub-guilds, flow cytometry cell sorting was used to further analyze one of the activated sludge samples. Four sorted sub-samples were obtained (high-RNA/high-PHA, low-RNA/high-PHA, high-RNA/low-PHA, and low-RNA/low-PHA), and the phylogenetic composition of each was determined using 16S rRNA gene amplicon pyrosequencing. Heterotrophic genera were identified across 12 phyla, and their representation in each sorted sub-sample showed that the high-RNA/high-PHA and low-RNA/low-PHA groups were most dissimilar. The enriched genera in these sorted sub-samples are suggested to represent the composition of heterotrophic-specialized sub-guilds defined by the kinetics of substrate consumption.

Predicting the accumulation of storage compounds by Rhodococcus jostii RHA1 in the feast-famine growth cycles using genome-scale flux balance analysis

Feast-famine cycles in biological wastewater resource recovery systems select for bacterial species that accumulate intracellular storage compounds such as poly-β-hydroxybutyrate (PHB), glycogen, and triacylglycerols (TAG). These species survive better the famine phase and resume rapid substrate uptake at the beginning of the feast phase faster than microorganisms unable to accumulate storage. However, ecophysiological conditions favouring the accumulation of either storage compounds remain to be clarified, and predictive capabilities need to be developed to eventually rationally design reactors producing these compounds. Using a genome-scale metabolic modelling approach, the storage metabolism of Rhodococcus jostii RHA1 was investigated for steady-state feast-famine cycles on glucose and acetate as the sole carbon sources. R. jostii RHA1 is capable of accumulating the three storage compounds (PHB, TAG, and glycogen) simultaneously. According to the experimental observations, when glucose was the substrate, feast phase chemical oxygen demand (COD) accumulation was similar for the three storage compounds; when acetate was the substrate, however, PHB accumulation was 3 times higher than TAG accumulation and essentially no glycogen was accumulated. These results were simulated using the genome-scale metabolic model of R. jostii RHA1 (iMT1174) by means of flux balance analysis (FBA) to determine the objective functions capable of predicting these behaviours. Maximization of the growth rate was set as the main objective function, while minimization of total reaction fluxes and minimization of metabolic adjustment (environmental MOMA) were considered as the sub-objective functions. The environmental MOMA sub-objective performed better than the minimization of total reaction fluxes sub-objective function at predicting the mixture of storage compounds accumulated. Additional experiments with ¹³C-labelled bicarbonate (HCO₃⁻) found that the fluxes through the central metabolism reactions during the feast phases were similar to the ones during the famine phases on acetate due to similarity in the carbon sources in the feast and famine phases (i.e., acetate and poly-β-hydroxybutyrate, respectively); this suggests that the environmental MOMA sub-objective function could be used to analyze successive environmental conditions such as the feast and famine cycles while the metabolically similar carbon sources are taken up by microorganisms.

Recent Advances and Challenges towards Sustainable Polyhydroxyalkanoate (PHA) Production

Sustainable biofuels, biomaterials, and fine chemicals production is a critical matter that research teams around the globe are focusing on nowadays. Polyhydroxyalkanoates represent one of the biomaterials of the future due to their physicochemical properties, biodegradability, and biocompatibility. Designing efficient and economic bioprocesses, combined with the respective social and environmental benefits, has brought together scientists from different backgrounds highlighting the multidisciplinary character of such a venture. In the current review, challenges and opportunities regarding polyhydroxyalkanoate production are presented and discussed, covering key steps of their overall production process by applying pure and mixed culture biotechnology, from raw bioprocess development to downstream processing.

Effect of culture residence time on substrate uptake and storage by a pure culture of Thiothrix (CT3 strain) under continuous or batch feeding

A pure culture of the filamentous bacterium Thiothrix, strain CT3, was aerobically cultured in a chemostat under continuous acetate feeding at three different culture residence times (RT 6, 12 or 22 d) and the same volumetric organic load rate (OLR 0.12gCOD/L/d). Cells cultured at decreasing RT in the chemostat had an increasing transient response to acetate spikes in batch tests. The maximum specific acetate removal rate increased from 25 to 185mgCOD/gCOD/h, corresponding to a 1.8 to 8.1 fold higher respective steady-state rate in the chemostat. The transient response was mainly due to acetate storage in the form of poly(3-hydroxybutyrate) (PHB), whereas no growth response was observed at any RT. Interestingly, even though the storage rate also decreased as the RT increased, the storage yield increased from 0.41 to 0.50 COD/COD. This finding does not support the traditional view that storage plays a more important role as the transient response increases. The transient response of the steady-state cells was much lower than in cells cultured under periodic feeding (at 6 d RT, from 82 to 247mgCOD/gCOD/h), with the latter cells showing both storage and growth responses. On the other hand, even though steady-state cells had no growth response and their storage rate was also less, steady-state cells showed a higher storage yield than cells cultured under dynamic feeding. This suggests that in Thiothrix strain CT3, the growth response is triggered by periodic feeding, whereas the storage response is a constitutive mechanism, independent from previous acclimation to transient conditions.

Bacterial community assembly in activated sludge: mapping beta diversity across environmental variables

Effect of ecological variables on community assembly of heterotrophic bacteria at eight full-scale and two pilot-scale activated sludge wastewater treatment plants (AS-WWTPs) were explored by pyrosequencing of 16S rRNA gene amplicons. In total, 39 samples covering a range of abiotic factors spread over space and time were analyzed. A core bacterial community of 24 families detected in at least six of the eight AS-WWTPs was defined. In addition to the core families, plant-specific families (observed at <50% AS-WWTPs) were found to be also important in the community structure. Observed beta diversity was partitioned with respect to ecological variables. Specifically, the following variables were considered: influent wastewater characteristics, season (winter vs. summer), process operations (conventional, oxidation ditch, and sequence batch reactor), reactor sizes (pilot-scale vs. full-scale reactors), chemical stresses defined by ozonation of return activated sludge, interannual variation, and geographical locations. Among the assessed variables, influent wastewater characteristics and geographical locations contributed more in explaining the differences between AS-WWTP bacterial communities with a maximum of approximately 26% of the observed variations. Partitioning of beta diversity is necessary to interpret the inherent variability in microbial community assembly and identify the driving forces at play in engineered microbial ecosystem.

Extent of intracellular storage in single and dual substrate systems under pulse feeding

The study investigated the effect of acetate/starch mixture on the formation of storage biopolymers as compared with the storage mechanism in systems fed with these compounds as single substrates. Experiments involved two sequencing batch reactor sets operated at steady state, at sludge ages of 8 and 2 days, respectively. Each set included three different runs, one fed with acetate, the other with starch and the last one with the acetate/starch mixture. In single substrate systems with pulse feeding, starch was fully converted to glycogen, whereas 25 % of acetate was utilized for direct microbial growth at sludge age of 8 days, together with polyhydroxybutyric acid (PHB) storage. The lower sludge age slightly increased this fraction to 30 %. Feeding of acetate/starch mixture induced a significant increase in acetate utilization for direct microbial growth; acetate fraction converted to PHB dropped down to 58 and 50 % at sludge ages of 8 and 2 days respectively, while starch remained fully converted to glycogen for both operating conditions. Parallel microbiological analyses based on FISH methodology confirmed that the biomass acclimated to the substrate mixture sustained microbial fractions capable of performing both glycogen and PHB storage.

Short-term and long-term effects on carbon storage of pulse feeding on acclimated or unacclimated activated sludge

This study was aimed to investigate the effect of different feeding patterns on the physiological state of the activated sludge and related microbial composition in an SBR (SRT of 2 days, acetate as the sole carbon source, aerobic conditions). The activated sludge was acclimated to two subsequent feeding patterns, namely to continuous feeding throughout the reaction phase and then to pulse feeding. FISH and microscopy staining procedure (Nile blue) were used to investigate the microbial composition, in combination with quantitative determination of storage. At steady state, storage was significant even under continuous feeding whereas pulse feeding brought a strong increase of both rate and yield of storage. Short-term and long-term effects were clearly distinguishable: the immediate adaptation of biomass coming from continuous feeding to a single spike accounted for a significant portion of the overall increase of both rate and yield of polymer storage that was obtained after long acclimation to pulse feeding. On the contrary, after either type of feeding, both cultures were mainly constituted from the members of Thauera/Azoarcus group. Thus, the same dominant group preferably consumed the acetate via storage or growth depending on acclimation conditions. Our study clearly showed that a progressive increase of storage capacity is not necessarily due to a shift of microbial composition.

Metabolic modelling of polyhydroxyalkanoate copolymers production by mixed microbial cultures

BACKGROUND

This paper presents a metabolic model describing the production of polyhydroxyalkanoate (PHA) copolymers in mixed microbial cultures, using mixtures of acetic and propionic acid as carbon source material. Material and energetic balances were established on the basis of previously elucidated metabolic pathways. Equations were derived for the theoretical yields for cell growth and PHA production on mixtures of acetic and propionic acid as functions of the oxidative phosphorylation efficiency, P/O ratio. The oxidative phosphorylation efficiency was estimated from rate measurements, which in turn allowed the estimation of the theoretical yield coefficients.

RESULTS

The model was validated with experimental data collected in a sequencing batch reactor (SBR) operated under varying feeding conditions: feeding of acetic and propionic acid separately (control experiments), and the feeding of acetic and propionic acid simultaneously. Two different feast and famine culture enrichment strategies were studied: (i) either with acetate or (ii) with propionate as carbon source material. Metabolic flux analysis (MFA) was performed for the different feeding conditions and culture enrichment strategies. Flux balance analysis (FBA) was used to calculate optimal feeding scenarios for high quality PHA polymers production, where it was found that a suitable polymer would be obtained when acetate is fed in excess and the feeding rate of propionate is limited to approximately 0.17 C-mol/(C-mol.h). The results were compared with published pure culture metabolic studies.

CONCLUSION

Acetate was more conducive toward the enrichment of a microbial culture with higher PHA storage fluxes and yields as compared to propionate. The P/O ratio was not only influenced by the selected microbial culture, but also by the carbon substrate fed to each culture, where higher P/O ratio values were consistently observed for acetate than propionate. MFA studies suggest that when mixtures of acetate and propionate are fed to the cultures, the catabolic activity is primarily guaranteed through acetate uptake, and the characteristic P/O ratio of acetate prevails over that of propionate. This study suggests that the PHA production process by mixed microbial cultures has the potential to be comparable or even more favourable than pure cultures.