Strain stability in biological systems treating recalcitrant organic compounds

The availability of molecular probing technology in recent years has facilitated investigation of microbial community composition during bio-treatment of organic wastes. Particularly, it has allowed the study of microbial culture stability and correlation between stability and treatment performance. However, most studies to date have only addressed mixed cultures and there is limited information regarding single strain stability. Here we have investigated the microbial community dynamics in two bioreactors, each inoculated with a pure bacterial strain capable of degrading a recalcitrant substrate, namely Xanthobacter aut. GJ10 degrading 1,2-dichloroethane (DCE) and Burkholderia sp. JS150 degrading monochlorobenzene (MCB). Universal and strain specific 16S rRNA oligonucleotide probes were designed and used to follow strain stability. The bioreactor fed with DCE was functionally stable and the percentage of GJ10 cells in the community remained high (around 95% of total cells) throughout, even after introduction of foreign microorganisms. The bioreactor fed with MCB was also functionally stable, but in contrast to the DCE bioreactor, probing results revealed the disappearance of strain JS150 from the bioreactor within a week. The difference in behavior between the two systems is attributed to the specific pathway required to degrade DCE.     

Bioremediation of phenol by a novel partitioning bioreactor using cow dung microbial consortia

A bioreactor has been designed and developed for partitioning of aqueous and organic phases with a provision for aeration and stirring, a cooling system and a sampling port. The potential of a cow dung microbial consortium has been assessed for bioremediation of phenol in a single-phase bioreactor and a two-phase partitioning bioreactor. The advantages of the two-phase partitioning bioreactor are discussed. The Pseudomonas putida IFO 14671 has been isolated, cultured and identified from the cow dung microbial consortium as a high-potential phenol degrader. The methods developed in this study present an advance in bioremediation techniques for the biodegradation of organic compounds such as phenol using a bioreactor. We have also demonstrated the potential of microorganisms from cow dung as a source of biomass.     

Microbial dynamics in an extractive membrane bioreactor exposed to an alternating sequence of organic compounds

Wastewaters containing organic compounds have been treated using extractive membrane bioreactors (EMBs). During treatment, a biofilm normally develops on the surface of the membrane, on the biological side. This study investigates the dynamics of biofilm growth in an EMB exposed to an alternating sequence of organic compounds. Microbial dynamics of both suspended and attached cultures were investigated experimentally in a single-tube extractive membrane bioreactor (STEMB), which comprised a continuous stirred-tank bioreactor (CSTB) coupled to eight single-tube extractive membrane modules (STEMMs) via a recirculating biomedium. A model microbial culture consisting of a Burkholderia sp. strain JS150 (ATCC No. 51283), able to degrade monochlorobenzene, and a Xanthobacter autotrophicus sp. strain GJ10 (ATCC No. 43050), able to degrade 1, 2-dichloroethane, was used. Both microbial strains exhibited exclusive degradative capabilities. The CSTB was monitored by quantification of individual strains and by product and organic compound evolution. To investigate the biofilm growth dynamics, eight STEMMs were run in parallel with the same operating conditions. Every week, STEMMs were stopped for biofilm analysis and the organic compound in the wastewater was changed. Biofilm growth was investigated by quantification of individual strains, by evaluation of the overall biofilm growth, and by microscopic analysis. A biofilm composed of both strains was developed and maintained during the whole experiment in the STEMMs. The biofilm that developed on the membrane improved the response of the system to changes in the wastewater.     

Extraction and biodegradation of a toxic volatile organic compound (1,2-dichloroethane) from waste-water in a membrane bioreactor

An extractive membrane bioreactor has been used to treat a synthetic waste-water containing a toxic volatile organic compound, 1,2-dichloroethane (DCE). Biofilms growing on the surface of the membrane tubes biodegrade DCE while avoiding direct contact between the DCE and the aerating gas. This reduces air stripping by more than an order of magnitude (from 30–35% of the DCE entering the system to less than 1%) relative to conventional aerated bioreactors. Over 99% removal of DCE from a waste-water containing 1600 mg l^–1 of DCE was achieved at waste-water residence times of 0.75 h. Biodegradation was verified as the removal mechanism through measurements of CO₂ and chloride ion evolution in the bioreactor. No DCE was detected in the biomedium over the operating period. The diffusion-reaction phenomena occurring in the biofilm have been described by a mathematical model, which provides calculated solutions that support the experimental results by predicting that all DCE is biodegraded within the biofilm. Experimentally, however, the rate of DCE degradation in the biofilm was found to be independent of O₂ concentration, while the model predictions point to O₂ being limiting.     

Stability and Performance of Xanthobacter autotrophicus GJ10 during 1,2-Dichloroethane Biodegradation

A nucleic acid-based approach was used to investigate the dynamics of a microbial community dominated by Xanthobacter autotrophicus GJ10 in the degradation of synthetic wastewater containing 1,2-dichloroethane (DCE). This study was performed over a 140-day period in a nonsterile continuous stirred-tank bioreactor (CSTB) subjected to different operational regimens: nutrient-limiting conditions, baseline operation, and the introduction of glucose as a cosubstrate. The microbial community was analyzed by a combination of fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE). Under nutrient-limiting conditions, DCE degradation was restricted, but this did not affect the dominance of strain GJ10, determined by FISH to comprise 85% of the active population. During baseline operation, DCE degradation improved significantly to over 99.5% and then remained constant throughout the subsequent experimental period. DGGE profiles revealed a stable, complex community, while FISH indicated that strain GJ10 remained the dominant species. During the addition of glucose as a cosubstrate, DGGE profiles showed a proliferation of other species in the CSTB. The percentage of strain GJ10 dropped to 8% of the active population in just 5 days, although this did not affect the DCE biodegradation performance. The return to baseline conditions was accompanied by the reestablishment of strain GJ10 as the dominant species, suggesting that this system responds robustly to external perturbations, both at the functional biodegradation level and at the individual strain level.     

Stability and performance of Xanthobacter autotrophicus GJ10 during 1,2-dichloroethane biodegradation

A nucleic acid-based approach was used to investigate the dynamics of a microbial community dominated by Xanthobacter autotrophicus GJ10 in the degradation of synthetic wastewater containing 1,2-dichloroethane (DCE). This study was performed over a 140-day period in a nonsterile continuous stirred-tank bioreactor (CSTB) subjected to different operational regimens: nutrient-limiting conditions, baseline operation, and the introduction of glucose as a cosubstrate. The microbial community was analyzed by a combination of fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE). Under nutrient-limiting conditions, DCE degradation was restricted, but this did not affect the dominance of strain GJ10, determined by FISH to comprise 85% of the active population. During baseline operation, DCE degradation improved significantly to over 99.5% and then remained constant throughout the subsequent experimental period. DGGE profiles revealed a stable, complex community, while FISH indicated that strain GJ10 remained the dominant species. During the addition of glucose as a cosubstrate, DGGE profiles showed a proliferation of other species in the CSTB. The percentage of strain GJ10 dropped to 8% of the active population in just 5 days, although this did not affect the DCE biodegradation performance. The return to baseline conditions was accompanied by the reestablishment of strain GJ10 as the dominant species, suggesting that this system responds robustly to external perturbations, both at the functional biodegradation level and at the individual strain level.     

The role of microbial reductive dechlorination of TCE at a phytoremediation site

In April 1996, a phytoremediation field demonstration site at the Naval Air Station, Fort Worth, Texas, was developed to remediate shallow oxic ground water (< 3.7 m deep) contaminated with chlorinated ethenes. Microbial populations were sampled in February and June 1998. The populations under the newly planted cottonwood trees had not yet matured to an anaerobic community that could dechlorinate trichloroethene (TCE) to cis-1,2-dichloroethene (DCE); however, the microbial population under a mature (approximately 22-year-old) cottonwood tree about 30 m southwest of the plantings had a mature anaerobic population capable of dechlorinating TCE to DCE, and DCE to vinyl chloride (VC). Oxygen-free sediment incubations with contaminated groundwater also demonstrated that resident microorganisms were capable of the dechlorination of TCE to DCE. This suggests that a sufficient amount of organic material is present for microbial dechlorination in aquifer microniches where dissolved O2 concentrations are low. Phenol, benzoic acid, acetic acid, and a cyclic hydrocarbon, compounds consistent with the degradation of root exudates and complex aromatic compounds, were identified by gas chromatography/mass spectrometry (GC/MS) in sediment samples under the mature cottonwood tree. Elsewhere at the site, transpiration and degradation by the cottonwood trees appears to be responsible for loss of chlorinated ethenes.     

Comparison of organic matter degradation and microbial community during thermophilic composting of two different types of anaerobic sludge

Changes in organic matter degradation and microbial communities during thermophilic composting were compared using two different types of anaerobic sludge, one from mesophilic methane fermentation, containing a high concentration of proteins (S-sludge), and the other from thermophilic methane fermentation, containing high concentrations of lipids and fibers (K-sludge). The difference in the organic matter degradation rate corresponded to the difference in the organic matter constituents; the CO(2) evolution rate was greater in the composting of S-sludge than of K-sludge; moreover, the NH(3) evolution resulting from the protein degradation was especially higher in the composting of S-sludge. Then the differences in the microbial communities that contributed to each composting were determined by the PCR-DGGE method. Ureibacillus sp., which is known as a degrader with high organic matter degradation activity, was observed during the composting of S-sludge, whereas Thermobifida fusca, which is a well known thermophilic actinomycete that produces enzymes for lignocellulose degradation, were observed during the composting of K-sludge.     

A microbial consortium-based product promotes potato yield by recruiting rhizosphere bacteria involved in nitrogen and carbon metabolisms

The effect of a microbial consortium-based (MCB) biocontrol product, composed of Bacillus subtilis, Trichoderma harzianum strain and diatomaceous earth as a carrier, on potato yield, and potential modes of action for its effect were investigated. The MCB product (300 kg ha⁻¹) was added to furrows in which the potato seed tubers each year for 3 years (2016, 2017 and 2018), while potato planting without the MCB product treatment served as the control. A metagenomic analysis indicated that bacterial phylotypes dominated the microbial community, with a relatively small contribution of archaea and fungal taxa. The relative abundance of beneficial bacterial taxa increased significantly in response to the MCB product treatment. Notably, a higher relative abundance of bacterial taxa with carbon fixation, carbon-degrading and nitrogen metabolism properties were observed in the MCB product-treated potato rhizosphere. This was also reflected in the identification of a greater abundance of genes encoding enzymes involved in nitrogen metabolism, carbon fixation and carbon degradation pathways in the conducted metagenomic analysis. The greater relative abundance of these beneficial bacterial taxa in the rhizosphere of MCB product-treated plots, as well as the higher abundance of genes associated with the indicated cellular processes, were associated with an increase in tuber yield. The observed changes in microbial community structure at an early stage of tuber development appears to have a beneficial impact on tuber yield.     

Determination of pollutant diffusion coefficients in naturally formed biofilms using a single tube extractive membrane bioreactor

A novel technique has been used to determine the effective diffusion coefficients for 1,1,2-trichloroethane (TCE), a nonreacting tracer, in biofilms growing on the external surface of a silicone rubber membrane tube during degradation of 1,2-dichloroethane (DCE) by Xanthobacter autotrophicus GJ10 and monochlorobenzene (MCB) by Pseudomonas JS150. Experiments were carried out in a single tube extractive membrane bioreactor (STEMB), whose configuration makes it possible to measure the transmembrane flux of substrates. A video imaging technique (VIT) was employed for in situ biofilm thickness measurement and recording. Diffusion coefficients of TCE in the biofilms and TCE mass transfer coefficients in the liquid films adjacent to the biofilms were determined simultaneously using a resistances-in-series diffusion model. It was found that the flux and overall mass transfer coefficient of TCE decrease with increasing biofilm thickness, showing the importance of biofilm diffusion on the mass transfer process. Similar fluxes were observed for the nonreacting tracer (TCE) and the reactive substrates (MCB or DCE), suggesting that membrane-attached biofilm systems can be rate controlled primarily by substrate diffusion. The TCE diffusion coefficient in the JS150 biofilm appeared to be dependent on biofilm thickness, decreasing markedly for biofilm thicknesses of >1 mm. The values of the TCE diffusion coefficients in the JS150 biofilms <1-mm thick are approximately twice those in water and fall to around 30% of the water value for biofilms >1-mm thick. The TCE diffusion coefficients in the GJ10 biofilms were apparently constant at about the water value. The change in the diffusion coefficient for the JS150 biofilms is attributed to the influence of eddy diffusion and convective flow on transport in the thinner (<1-mm thick) biofilms.     

Genetic and biochemical analyses of chlorobenzene degradation gene clusters in <Emphasis Type="Italic">Pandoraea</Emphasis> sp. strain MCB032

Pandoraea sp. strain MCB032 was isolated as an emerging chlorobenzene degrader from a functionally stable bioreactor where species succession had occurred. In this study, two gene clusters encoding chlorobenzene metabolic functions have been cloned. Within the cbs gene cluster, CbsA and CbsB are similar to the chlorobenzene dioxygenase and the cis-chlorobenzene dihydrodiol dehydrogenase in Ralstonia sp. JS705 and shown to transform chlorobenzene to 3-chlorocatechol. The clc gene cluster shows strong similarity to the clc genes of Ralstonia sp. JS705 and encodes chlorocatechol 1,2-dioxygenase (ClcA) and other enzymes, which catalyze the conversion of chlorocatechol to 3-oxoadipate. The Michaelis constants (K _m) values of ClcA for catechol, 3-methylcatechol and 3-chlorocatechol were determined as 10.0, 8.9 and 3.4 μM, respectively. CbsX, a putative transport protein present in the cbs cluster of strain MCB032 but not in those of other chlorobenzene degraders, shows 76 and 53% identities to two previously identified transport proteins involved in toluene degradation, TbuX from Ralstonia pickettii PKO1 and TodX from Pseudomonas putida F1. The presence of the transport protein in strain MCB032 likely provides a mechanistic explanation for its higher chlorobenzene affinity and may well be the basis for the competitive advantage of this strain in the bioreactor.     

Design of a large-scale surface-aerated bioreactor for biomass production using a VOC substrate

The design of a large-scale bioreactor for the production of bacterial biomass adapted to the biodegradation of volatile organic compounds was carried out. The bioreactor model used integrated the microbial kinetics and fluid dynamics described by the compartment model approach. The process conditions and kinetic parameters were adopted from the laboratory experimental study of (León, E., Seignez, C., Adler, N., Péringer, P., 1999. Growth inhibition of biomass adapted to the degradation of toluene and xylenes in mixture in a batch reactor with substrates supplied by pulses. Biodegradation 10, 245-250). The performance of the pulsed-batch stirred bioreactor under surface aeration conditions was simulated for different mixing configurations and conditions such as the impeller diameter, number of impellers, stirring speed, and oxygen pressure. The simulations were used for the cost analysis which resulted in the optimal design of the bioreactor.     

Modeling the acclimation of activated sludge to a xenobiotic

This work established a mathematical model that formulated degrader formation by conversion of indigenous microbial cells. Degrader conversion is attributed to genetic induction whose force is dependent on the strength of acclimating xenobiotic and the amount of indigenous cells. After successful conversion, which requires an amount of time proportionate to the lag, degraders grow on the xenobiotic substrate. This model formulated the lag and degrader formation with the sigmoid function and degrader growth with the Haldane kinetics. The model so completed accurately simulates the degradation and biomass courses during acclimation and degradation of a xenobiotic by indigenous activated sludge, wherein the factors relating to the acclimation process are given values. The model serves the need for a rational representation of microbial acclimation to a xenobiotic.     

Sequential bioavailability of sedimentary organic matter to heterotrophic bacteria

Aquatic sediments harbour diverse microbial communities that mediate organic matter degradation and influence biogeochemical cycles. The pool of bioavailable carbon continuously changes as a result of abiotic processes and microbial activity. It remains unclear how microbial communities respond to heterogeneous organic matrices and how this ultimately affects heterotrophic respiration. To explore the relationships between the degradation of mixed carbon substrates and microbial activity, we incubated batches of organic‐rich sediments in a novel bioreactor (IsoCaRB) that permitted continuous observations of CO₂ production rates, as well as sequential sampling of isotopic signatures (δ¹³C, Δ¹⁴C), microbial community structure and diversity, and extracellular enzyme activity. Our results indicated that lower molecular weight (MW), labile, phytoplankton‐derived compounds were degraded first, followed by petroleum‐derived exogenous pollutants, and finally by higher MW polymeric plant material. This shift in utilization coincided with a community succession and increased extracellular enzyme activities. Thus, sequential utilization of different carbon pools induced changes at both the community and cellular level, shifting community composition, enzyme activity, respiration rates, and residual organic matter reactivity. Our results provide novel insight into the accessibility of sedimentary organic matter and demonstrate how bioavailability of natural organic substrates may affect the function and composition of heterotrophic bacterial populations.     

Enhancement of PCB degradation by Burkholderia xenovorans LB400 in biphasic systems by manipulating culture conditions

Two-phase partitioning bioreactors (TPPBs) can be used to biodegrade environmental contaminants after their extraction from soil. TPPBs are typically stirred tank bioreactors containing an aqueous phase hosting the degrading microorganism and an immiscible, non-toxic and non-bioavailable organic phase functioning as a reservoir for hydrophobic compounds. Biodegradation of these compounds in the aqueous phase results in thermodynamic disequilibrium and partitioning of additional compounds from the organic phase into the aqueous phase. This self-regulated process can allow the delivery of large amounts of hydrophobic substances to degrading microorganisms. This paper explores the reactor conditions under which the polychlorinated biphenyl (PCB) degrader Burkholderia xenovorans LB400 can degrade significant amounts of the PCB mixture Aroclor(R) 1242. Aroclor(R) degradation was found to stall after approximately 40 h if no carbon source other than PCBs was available in the reactor. Sodium pyruvate was found to be a suitable carbon source to maintain microbial activity against PCBs and to function as a substrate for additional cell growth. Both biphenyl (while required during the inoculum preparation) and glucose had a negative effect during the Aroclor(R) degradation phase. Initial Aroclor(R) 1242 degradation rates in the presence of pyruvate were high (6.2 mg L(-1) h(-1)) and 85% of an equivalent concentration of 100 mg Aroclor(R) 1242 per L aqueous phase could be degraded in 48 h, which suggest that solvent extraction of PCBs from soil followed by their biodegradation in TPPBs might be a feasible remediation option.     

Investigation of Microbes in the Rhizosphere of Selected Grasses for Rhizoremediation of Hydrocarbon-Contaminated Soils

Hydrocarbon-degrading microorganisms (HDM) associated with the rhizosphere of Paspalum vaginatum and Zoysia tenuifolia grown in bioremediated soil were isolated under controlled laboratory conditions. The isolation process was conducted at 30°C and 45°C to isolate mesophilic and thermotolerant microorganisms, respectively, under aerobic conditions. The isolated HDMs were identified using 16S rRNA gene sequencing and fatty acid methyl ester (FAME) analysis. Although differences in the genera of the isolated HDMs occurred between the two grasses, Arthrobacter spp and Bacillus spp were isolated from the rhizosphere of both plants. The efficiency of the isolated microorganisms in degrading a mixture of hydrocarbon compounds (HC) was also assessed. Among the bacterial isolates, Pseudomonas boreopolis was found to be the most effective HC degrader, while the only fungal isolate, Fusarium solani, demonstrated higher degradation rates than most of the bacterial isolates. A mixture of all the microbial isolates demonstrated a high degradation percent of HC. The isolated microorganisms thus appear to work synergistically to degrade efficiently all the tested organic compounds.     

The use of an oil absorber as a strategy to overcome starvation periods in degrading 1,2-dichloroethane in waste gas

This work investigates the use of an oil absorber as an operational strategy in vapor phase bioreactors exposed to starvation periods, during the treatment of inhibitory pollutants. After being exposed to 1,2-dichloroethane (DCE) starvation periods, the response and stability of a combined oil-absorber-bioscrubber (OAB) system was compared to that of a bioscrubber only (BO) system. In the BO system, after a 5.2 days starvation period, the DCE removal efficiency was reduced to 12%, and 6 days were needed to recover the initial removal efficiency when the DCE feed resumed. The total organic discharged (TOD(DCE)) was 16,500 g(DCE) m(bioscrubber) (-3) after the DCE starvation. Biomass analysis performed using fluorescence in situ hybridisation (FISH) showed that the microbial activity was significantly reduced during the starvation period and that 5 days were needed to recover the initial activity, after the re-introduction of DCE. In contrast, the performance of the OAB system was stable during 5.2 days of DCE starvation. The DCE removal efficiency was not affected when the DCE feed resumed and the TOD(DCE) was significantly reduced to 2,850 g(DCE) m(bioscrubber) (-3). During starvation, the activity of the microbial culture in the OAB system showed a substantially lower decrease than in the BO system and recovered almost immediately the initial activity after the re-introduction of DCE. Additionally, a mathematical model describing the performance of the OAB system was developed. The results of this study show that the OAB system can effectively sustain the biological treatment of waste gas during starvation periods of inhibitory pollutants.     

Response of the microflora in outdoor experimental streams to pentachlorophenol: environmental factors

The 2nd year of a 2-year study of the fate of pentachlorophenol in outdoor artificial streams focused on details of microbial degradation by a combination of in situ and laboratory measurements. Replicate streams were dosed continuously at pentachlorophenol concentrations of 0, 48, and 144 micrograms/L, respectively, for an 88-d period during the summer of 1983. Pentachlorophenol was degraded both aerobically and anaerobically. Aerobic degradation was more rapid than anaerobic degradation. Mineralization of pentachlorophenol was concommitant with pentachlorophenol disappearance under aerobic conditions, but lagged behind loss of the parent molecule under anaerobic conditions. Biodegradation in the streams, or in specific stream compartments such as the sediment or water column, was characterized by an adaptation period (3-5 weeks for the stream as a whole, and reproducible from the previous year), which was inversely dependent on the concentration of pentachlorophenol and microbial biomass. The adaptation in the streams could be attributed to the time necessary for selective enrichment of an initially low population of pentachlorophenol degraders on surface compartments. The extent of biodegradation in the streams (percent loss of initial concentration of pentachlorophenol) increased with increasing pentachlorophenol input, which was explicable by an increase in the pentachlorophenol degrader population with increasing pentachlorophenol concentration. The sediment zone most significant to overall pentachlorophenol biodegradation was the top 0.5- to 1-cm layer as shown by pentachlorophenol migration rates and depth profiles of degrader density within the sediment. Pentachlorophenol profiles in sediment cores taken during and after the adaptation period for degradation showed that diffusion of pentachlorophenol into the sediment was rate limiting to degradation in this compartment.(ABSTRACT TRUNCATED AT 250 WORDS)     

Treatment of odorous volatile fatty acids using a biotrickling filter

In this study, a novel fibrous bioreactor was developed for treating odorous compounds present in contaminated air. The first stage of this work was a preliminary study which aimed at investigating the feasibility of using the fibrous bioreactor for the removal of malodorous volatile fatty acids (VFA) that is a common odorous contaminant generated from anaerobic degradation of organic compounds. The kinetics of microbial growth and VFA degradation in the selected culture, and the performance of the submerged bioreactor at different VFA mass loadings were studied. Above 95% of VFA removal efficiencies were achieved at mass loadings up to 22.4 g/m(3)/h. In the second stage, the odour treatment process was scaled up with system design and operational considerations. A trickling biofilter with synthetic fibrous packing medium was employed. The effects of inlet VFA concentration and empty bed retention time (EBRT) on the process performance were investigated. The bioreactor was effective in removing VFA at mass loadings up to 32 g/m(3)/h, beyond which VFA started to accumulate in the recirculation liquid, indicating the biofilm was unable to degrade all of the VFA introduced. Although VFA accumulated in the liquid phase, the removal efficiency remained above 99%. This suggested that the biochemical reaction rather than gas-liquid mass transfer was the limiting step of the treatment process. In addition, the biotrickling filter was stable for long-term operation with relatively low and steady pressure drop, no clogging and degeneration of the packing material occurred during the four-month study.