Kinetics and modeling of autotrophic thiocyanate biodegradation

Thiocyanate and Organic Carbon Inputs Drive Convergent Selection for Specific Autotrophic Afipia and Thiobacillus Strains Within Complex Microbiomes

Thiocyanate (SCN^–) contamination threatens aquatic ecosystems and pollutes vital freshwater supplies. SCN^–-degrading microbial consortia are commercially adapted for remediation, but the impact of organic amendments on selection within SCN^–-degrading microbial communities has not been investigated. Here, we tested whether specific strains capable of degrading SCN^– could be reproducibly selected for based on SCN^– loading and the presence or absence of added organic carbon. Complex microbial communities derived from those used to treat SCN^–-contaminated water were exposed to systematically increased input SCN concentrations in molasses-amended and -unamended reactors and in reactors switched to unamended conditions after establishing the active SCN^–-degrading consortium. Five experiments were conducted over 790 days, and genome-resolved metagenomics was used to resolve community composition at the strain level. A single Thiobacillus strain proliferated in all reactors at high loadings. Despite the presence of many Rhizobiales strains, a single Afipia variant dominated the molasses-free reactor at moderately high loadings. This strain is predicted to break down SCN^– using a novel thiocyanate desulfurase, oxidize resulting reduced sulfur, degrade product cyanate to ammonia and CO₂ via cyanate hydratase, and fix CO₂ via the Calvin–Benson–Bassham cycle. Removal of molasses from input feed solutions reproducibly led to dominance of this strain. Although sustained by autotrophy, reactors without molasses did not stably degrade SCN^– at high loading rates, perhaps due to loss of biofilm-associated niche diversity. Overall, convergence in environmental conditions led to convergence in the strain composition, although reactor history also impacted the trajectory of community compositional change.

Modelling of simultaneous nitrogen and thiocyanate removal through coupling thiocyanate-based denitrification with anaerobic ammonium oxidation

Thiocyanate (SCN^-)-based autotrophic denitrification (AD) has recently been demonstrated as a promising technology that could be integrated with anaerobic ammonium oxidation (Anammox) to achieve simultaneous removal of nitrogen and SCN^-. However, there is still a lack of a complete SCN^--based AD model, and the potential microbial competition/synergy between AD bacteria and Anammox bacteria under different operating conditions remains unknown, which significantly hinders the possible application of coupling SCN^--based AD with Anammox. To this end, a complete SCN^--based AD model was firstly developed and reliably calibrated/validated using experimental datasets. The obtained SCN^--based AD model was then integrated with the well-established Anammox model and satisfactorily verified with experimental data from a system coupling AD with Anammox. The integrated model was lastly applied to investigate the impacts of influent NH₄⁺-N/NO₂^--N ratio and SCN^- concentration on the steady-state microbial composition as well as the removal of nitrogen and SCN^-. The results showed that the NH₄⁺-N/NO₂^--N ratio in the presence of a certain SCN^- level should be controlled at a proper value so that the maximum synergy between AD bacteria and Anammox bacteria could be achieved while their competition for NO₂^- would be minimized. For the simultaneous maximum removal (>95%) of nitrogen and SCN^-, there existed a negative relationship between the influent SCN^- concentration and the optimal NH₄⁺-N/NO₂^--N ratio needed.

Characterisation of thiocyanate degradation in a mixed culture activated sludge process treating coke wastewater

Microbial degradation of thiocyanate (SCN^-) has been reported to suffer from instability highlighting the need for improved understanding of underlying mechanisms and boundaries. Respirometry, batch tests and DNA sequencing analysis were used to improve understanding of a mixed culture treating coke wastewater rich in SCN^-. An uncultured species of Thiobacillus was the most abundant species (26%) and displayed similar metabolic capabilities to Thiobacillus denitrificans and Thiobacillus thioparus. Thiocyanate was hydrolysed/oxidised to NH₄⁺-N, HCO₃^- and SO₄^2-. Nevertheless, at 360-2100 mg SCN^-/L a breakdown in the degradation pathway was observed. Respirometry tests demonstrated that NH₄⁺-N was inhibitory to SCN^- degradation (IC₅₀: 316 mg/L). Likewise, phenol (180 mg/L) and hydroxylamine (0.25-16 mg/L) reduced SCN^- degradation by 41% and ca. 7%, respectively. The understanding of the SCN^- degradation pathways can enable stable treatment efficiencies and compliance with effluent of <4 mg SCN/L, required by the Industrial Emissions Directive.

Kinetics of Decomposition of Thiocyanate in Natural Aquatic Systems

Rates of thiocyanate degradation were measured in waters and sediments of marine and limnic systems under various redox conditions, oxic, anoxic (nonsulfidic, nonferruginous, nonmanganous), ferruginous, sulfidic, and manganous, for up to 200-day period at micromolar concentrations of thiocyanate. The decomposition rates in natural aquatic systems were found to be controlled by microbial processes under both oxic and anoxic conditions. The Michaelis-Menten model was applied for description of the decomposition kinetics. The decomposition rate in the sediments was found to be higher than in the water samples. Under oxic conditions, thiocyanate degradation was faster than under anaerobic conditions. In the presence of hydrogen sulfide, the decomposition rate increased compared to anoxic nonsulfidic conditions, whereas in the presence of iron(II) or manganese(II), the rate decreased. Depending on environmental conditions, half-lives of thiocyanate in sediments and water columns were in the ranges of hours to few dozens of days, and from days to years, respectively. Application of kinetic parameters presented in this research allows estimation of rates of thiocyanate cycling and its concentrations in the Archean ocean.

Development of a mixed microbial culture for thiocyanate and metal cyanide degradation

The degradation capacity of a mixed culture of Agrobacterium tumefaciens SUTS 1 and Pseudomonas monteilii SUTS 2 for thiocyanate and metal cyanide, in the form of zinc and cadmium, has been determined. The growth of a mixed culture of SUTS 1 and SUTS 2 in cyanide complexes and the cyanide removal efficiency of a fixed-film bio-column system were studied. The results showed that the mixed culture of bacteria can survive and grow in broth media containing thiocyanate and metal cyanide complexes with a maximum cell of 1.03 × 108 CFU/mL on day 3. In addition, the optimal conditions of the fixed-film bio-column system were continuously tested for 24 h, and it was found that this system had the highest removal efficiency at a flow rate of 10 mL/min and 21 min of empty bed retention time, with decreasing thiocyanate, zinc, and cadmium from 85, 0.44, and 0.044 to 65, 0.21, and 0.038 mg/L, respectively; this is in contrast to cyanide, which was not found within 12 h. Next, the conditions were maintained for 30 days, and it was found that the system had removed more than 50% of cyanide complexes, except cadmium. The complex residues were 29.96, 0.16, 0.204, and 0.085 mg/L of thiocyanate, cyanide, zinc, and cadmium, respectively. In addition, the growth of the SUTS 1 and SUTS 2 mixed culture increased. The by-product compounds sulfate and nitrate were found throughout the experiment, whereas bicarbonate and ammonia were found only on certain days.

Effects of temperature and pH on the biokinetic properties of thiocyanate biodegradation under autotrophic conditions

The simultaneous effects of temperature and pH on the biokinetic properties of thiocyanate biodegradation under mixed-culture, autotrophic conditions were investigated using response surface analysis (RSA) combined with biokinetic modeling. A partial cubic model, based on substrate inhibition biokinetics, was constructed for each kinetic coefficient in Andrew model (i.e., maximum specific growth rate (μ(m)), saturation coefficient (K(S)), and substrate inhibition coefficient (K(SI))). Each model proved statistically reliable to approximate the responses of the kinetic coefficients to temperature and pH changes (r(2) > 0.8, p < 0.05). The response surface plots demonstrated that the biokinetic coefficients change with respect to temperature and pH significantly and in different ways. The model response surfaces were substantially different to each other, indicating distinct correlations between the independent (temperature and pH) and dependent (model response) variables in the models. Based on the estimated response surface models, temperature was shown to have significant effects on all biokinetic coefficients tested. A dominant influence of temperature on μ(m) response was observed while the interdependence of temperature and pH was apparent in the K(S) and K(SI) models. Specific growth rate (μ) versus substrate (i.e., thiocyanate) concentration plots simulating using the obtained response surface models confirmed the significant effects of temperature and pH on the microbial growth rate and therefore on the thiocyanate degradation rate. Overall, the response surface models able to describe the biokinetic effects of temperature and pH on thiocyanate biodegradation within the explored region (20-30 °C and pH 6.0-9.0) were successfully constructed and validated, providing fundamental information for better process control in thiocyanate treatment.

Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea

Lithotrophic sulfur oxidation is an ancient metabolic process. Ecologically and taxonomically diverged prokaryotes have differential abilities to utilize different reduced sulfur compounds as lithotrophic substrates. Different phototrophic or chemotrophic species use different enzymes, pathways and mechanisms of electron transport and energy conservation for the oxidation of any given substrate. While the mechanisms of sulfur oxidation in obligately chemolithotrophic bacteria, predominantly belonging to Beta- (e.g. Thiobacillus) and Gammaproteobacteria (e.g. Thiomicrospira), are not well established, the Sox system is the central pathway in the facultative bacteria from Alphaproteobacteria (e.g. Paracoccus). Interestingly, photolithotrophs such as Rhodovulum belonging to Alphaproteobacteria also use the Sox system, whereas those from Chromatiaceae and Chlorobi use a truncated Sox complex alongside reverse-acting sulfate-reducing systems. Certain chemotrophic magnetotactic Alphaproteobacteria allegedly utilize such a combined mechanism. Sulfur-chemolithotrophic metabolism in Archaea, largely restricted to Sulfolobales, is distinct from those in Bacteria. Phylogenetic and biomolecular fossil data suggest that the ubiquity of sox genes could be due to horizontal transfer, and coupled sulfate reduction/sulfide oxidation pathways, originating in planktonic ancestors of Chromatiaceae or Chlorobi, could be ancestral to all sulfur-lithotrophic processes. However, the possibility that chemolithotrophy, originating in deep sea, is the actual ancestral form of sulfur oxidation cannot be ruled out.

Biochemical indication of microbial mass changes using ATP and DNA measurement in biological treatment of thiocyanate

This study was designed to monitor changes in the levels of adenosine 5'-triphosphate (ATP) and deoxyribonucleic acid (DNA) per unit of microbial mass during the autotrophic biodegradation of thiocyanate (SCN(-)). An artificial medium containing trace minerals and 500 mg SCN(-)/L was used as a substrate for bacterial growth. An SCN(-)-degrading bioreactor with a working volume of 6 L, equipped with temperature, pH, and dissolved oxygen controls, was operated in batch mode. During the exponential phase of SCN(-) biodegradation, the ratios of ATP and DNA to microbial dry weight varied from 0.6 to 1.1 microg ATP/mg of volatile suspended solid (VSS), and from 3.5 to 8.8 microg DNA/mg of VSS, respectively. The ATP and DNA concentrations correlated linearly with microbial mass (r (2) > 0.9) within the exponential phase. The linear regression equations were as follows: (1) microbial mass concentration (mg/L) = 0.663 x ATP concentration (microg/L) + 11.1 and (2) microbial concentration (mg/L) = 0.081 x DNA concentration (microg/L) + 10.9. The applicable ranges were 6.8 to 47.4 microg/L for ATP concentration and 41.5 to 395 microg/L for DNA concentration, respectively.

Monitoring thiocyanate-degrading microbial community in relation to changes in process performance in mixed culture systems near washout

Changes in microbial community structure, associated with changes in process performance, were investigated with respect to the sludge retention time (SRT) in bioreactors treating thiocyanate. Among the seven reactors operated at 0.8-3.0 d SRTs, respectively, the reactor at 2.0 d SRT displayed the maximal thiocyanate removal rate of 240.2mg/L/d. However, the thiocyanate removal efficiency suddenly decreased from 96.1% to 43.1% when the SRT was reduced from 2.0 to 1.8d, corresponding to a 50.1% drop in the removal rate. Microbial communities in the reactors operated at short SRTs, near washout, were analyzed by denaturing gradient gel electrophoresis (DGGE) based on bacterial 16S rRNA genes. All band sequences recovered were assigned to two phyla, Proteobacteria and Bacteriodetes. A Thiobacillus-like microorganism was commonly detected in all the reactors and is suggested to be the main organism responsible for thiocyanate decomposition. Several DGGE band sequences were closely related to the environmental clones detected in environments rich in sulfur and/or nitrogen compounds. Statistical analysis of the DGGE profiles demonstrated that the structure of thiocyanate-degrading communities, as well as the process performance, changed with change in SRT. The microbial community profiles were not always more closely related to those at similar SRT than those at less similar SRT on the non-metric multidimensional scaling (NMDS) map. This was also supported by clustering analysis. These results were contrary to the general notion that the community structures in continuous systems will be controlled by the washout of microbial populations. Our experimental results suggest that the structure of a microbial thiocyanate-degrading community at a given SRT would not be determined only by the washout effect.

Microbial thiocyanate utilization under highly alkaline conditions

Three kinds of alkaliphilic bacteria able to utilize thiocyanate (CNS-) at pH 10 were found in highly alkaline soda lake sediments and soda soils. The first group included obligate heterotrophs that utilized thiocyanate as a nitrogen source while growing at pH 10 with acetate as carbon and energy sources. Most of the heterotrophic strains were able to oxidize sulfide and thiosulfate to tetrathionate. The second group included obligately autotrophic sulfur-oxidizing alkaliphiles which utilized thiocyanate nitrogen during growth with thiosulfate as the energy source. Genetic analysis demonstrated that both the heterotrophic and autotrophic alkaliphiles that utilized thiocyanate as a nitrogen source were related to the previously described sulfur-oxidizing alkaliphiles belonging to the gamma subdivision of the division Proteobacteria (the Halomonas group for the heterotrophs and the genus Thioalkalivibrio for autotrophs). The third group included obligately autotrophic sulfur-oxidizing alkaliphilic bacteria able to utilize thiocyanate as a sole source of energy. These bacteria could be enriched on mineral medium with thiocyanate at pH 10. Growth with thiocyanate was usually much slower than growth with thiosulfate, although the biomass yield on thiocyanate was higher. Of the four strains isolated, the three vibrio-shaped strains were genetically closely related to the previously described sulfur-oxidizing alkaliphiles belonging to the genus Thioalkalivibrio. The rod-shaped isolate differed from the other isolates by its ability to accumulate large amounts of elemental sulfur inside its cells and by its ability to oxidize carbon disulfide. Despite its low DNA homology with and substantial phenotypic differences from the vibrio-shaped strains, this isolate also belonged to the genus Thioalkalivibrio according to a phylogenetic analysis. The heterotrophic and autotrophic alkaliphiles that grew with thiocyanate as an N source possessed a relatively high level of cyanase activity which converted cyanate (CNO-) to ammonia and CO2. On the other hand, cyanase activity either was absent or was present at very low levels in the autotrophic strains grown on thiocyanate as the sole energy and N source. As a result, large amounts of cyanate were found to accumulate in the media during utilization of thiocyanate at pH 10 in batch and thiocyanate-limited continuous cultures. This is a first direct proof of a "cyanate pathway" in pure cultures of thiocyanate-degrading bacteria. Since it is relatively stable under alkaline conditions, cyanate is likely to play a role as an N buffer that keeps the alkaliphilic bacteria safe from inhibition by free ammonia, which otherwise would reach toxic levels during dissimilatory degradation of thiocyanate.

Empirical model for the autotrophic biodegradation of thiocyanate in an activated sludge reactor

AIMS

The aim of this investigation was to develop an empirical model for the autotrophic biodegradation of thiocyanate using an activated sludge reactor.

METHODS AND RESULTS

The methods used for this purpose included the use of a laboratory scale activated sludge reactor unit using thiocyante feed concentrations from 200 to 550 mg x l(-1). Reactor effluent concentrations of <1 mg x l(-1) thiocyanate were consistently achieved for the entire duration of the investigation at a hydraulic retention time of 8 h, solids (biomass) retention of 18 h and biomass (dry weight) concentrations ranging from 2 to 4 g x l(-1). A biomass specific degradation rate factor was used to relate thiocyanate degradation in the reactor to the prevailing biomass and thiocyanate feed concentrations. A maximum biomass specific degradation rate of 16 mg(-1) x g(-1) x h(-1) (mg thiocyanate consumed per gram biomass per hour) was achieved at a thiocyanate feed concentration of 550 mg x l(-1). The overall yield coefficient was found to be 0.086 (biomass dry weight produced per mass of thiocyanate consumed).

CONCLUSION

Using the results generated by this investigation, an empirical model was developed, based on thiocyanate feed concentration and reactor biomass concentration, to calculate the required absolute hydraulic retention time at which a single-stage continuously stirred tank activated sludge reactor could be operated in order to achieve an effluent concentration of <1 mg x l(-1). The use of an empirical model rather than a mechanistic-based kinetic model was proposed due to the low prevailing thiocyanate concentrations in the reactor.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results represent the first empirical model, based on a comprehensive data set, that could be used for the design of thiocyanate-degrading activated sludge systems.

Environmental biotechnology informatics

Environmental biotechnology informatics is in its infancy and is growing fast. Computer and information science can assist environmental biotechnology by developing biological databases and building mathematical models of biological systems. Funding and training limitations in this field may, however, hinder its future growth.