Biomonitoring of continuous microbial community adaptation towards more efficient phenol-degradation in a fed-batch bioreactor

Identification of metabolite and protein explanatory variables governing microbiome establishment and re-establishment within a cellulose-degrading anaerobic bioreactor

Proteins, metabolites, and 16S rRNA measurements were used to examine the community structure and functional relationships within a cellulose degrading anaerobic bioreactor. The bioreactor was seeded with bovine rumen fluid and operated with a 4 day hydraulic retention time on cellulose (avicel) as sole carbon and energy source. The reactor performance and microbial community structure was monitored during the establishment of the cellulose-degrading community. After stable operation was established in the bioreactor, the mixing intensity was increased in order to investigate the effect of a physical disruption of the microbial community structure. Finally, the original conditions were re-established to understand the stability of the microbial community after a perturbation. All factors measured were found to be inter-correlated during these three distinct phases of operation (establishment, perturbation and re-establishment). In particular, the return of community structure and function to pre-perturbed conditions suggests that propionate fermentation and acetate utilization were the explanatory factors for community establishment and re-establishment.

Community Analysis and Recovery of Phenol-degrading Bacteria from Drinking Water Biofilters

Phenol is a ubiquitous organic contaminant in drinking water. Biodegradation plays an important role in the elimination of phenol pollution in the environment, but the information about phenol removal by drinking water biofilters is still lacking. Herein, we study an acclimated bacterial community that can degrade over 80% of 300 mg/L phenol within 3 days. PCR detection of genotypes involved in bacterial phenol degradation revealed that the degradation pathways contained the initial oxidative attack by phenol hydroxylase, and subsequent ring fission by catechol 1,2-dioxygenase. Based on the PCR denatured gradient gel electrophoresis (PCR-DGGE) profiles of bacteria from biological activated carbon (BAC), the predominant bacteria in drinking water biofilters including Delftia sp., Achromobacter sp., and Agrobacterium sp., which together comprised up to 50% of the total microorganisms. In addition, a shift in bacterial community structure was observed during phenol biodegradation. Furthermore, the most effective phenol-degrading strain DW-1 that correspond to the main band in denaturing gradient gel electrophoresis (DGGE) profile was isolated and identified as Acinetobacter sp., according to phylogenetic analyses of the 16S ribosomal ribonucleic acid (rRNA) gene sequences. The strain DW-1 also produced the most important enzyme, phenol hydroxylase, and it also exhibited a good ability to degrade phenol when immobilized on granular active carbon (GAC). This study indicates that the enrichment culture has great potential application for treatment of phenol-polluted drinking water sources, and the indigenous phenol-degrading microorganism could recover from drinking water biofilters as an efficient resource for phenol removal. Therefore, the aim of this study is to draw attention to recover native phenol-degrading bacteria from drinking water biofilters, and use these native microorganisms as phenolic water remediation in drinking water sources.

Relationship between phenol degradation efficiency and microbial community structure in an anaerobic SBR

Phenol is a common wastewater contaminant from various industrial processes, including petrochemical refineries and chemical compounds production. Due to its toxicity to microbial activity, it can affect the efficiency of biological wastewater treatment processes. In this study, the efficiency of an Anaerobic Sequencing Batch Reactor (ASBR) fed with increasing phenol concentrations (from 120 to 1200 mg L(-1)) was assessed and the relationship between phenol degradation capacity and the microbial community structure was evaluated. Up to a feeding concentration of 800 mg L(-1), the initial degradation rate steadily increased with phenol concentration (up to 180 mg L(-1) d(-1)) and the elimination capacity remained relatively constant around 27 mg phenol removed∙gVSS(-1) d(-1). Operation at higher concentrations (1200 mg L(-1)) resulted in a still efficient but slower process: the elimination capacity and the initial degradation rate decreased to, respectively, 11 mg phenol removed∙gVSS(-1) d(-1) and 154 mg L(-1) d(-1). As revealed by Denaturing Gradient Gel Electrophoresis (DGGE) analysis, the increase of phenol concentration induced level-dependent structural modifications of the community composition which suggest an adaptation process. The increase of phenol concentration from 120 to 800 mg L(-1) had little effect on the community structure, while it involved drastic structural changes when increasing from 800 to 1200 mg L(-1), including a strong community structure shift, suggesting the specialization of the community through the emergence and selection of most adapted phylotypes. The thresholds of structural and functional disturbances were similar, suggesting the correlation of degradation performance and community structure. The Canonical Correspondence Analysis (CCA) confirmed that the ASBR functional performance was essentially driven by specific community traits. Under the highest feeding concentration, the most abundant ribotype probably involved in successful phenol degradation at 1200 mg L(-1) was affiliated to the Anaerolineaceae family.

Cloning of environmental genomic fragments as physical markers for monitoring microbial populations in coking wastewater treatment system

The association between community functional shift and dynamics of genomic DNA composition can be used to identify functionally relevant populations as indicator organisms for systems monitoring. In this work, fingerprinting-based community DNA hybridization was used to monitor community structural dynamics and identify genomic fragments whose abundance shifts were concomitant to changes in COD removal capacity in a reactor. A laboratory-scale anaerobic-anoxic-oxic fixed biofilm system treating coking wastewater was operated with (LR mode) or without effluent recirculation (LNR mode). The contribution to total chemical oxygen demand (COD) removal by the anoxic reactor increased from 4% in LNR mode to 26% in LR mode. Long primer RAPD (randomly amplified polymorphic DNA) community fingerprints of the anoxic reactor also changed most significantly from the one similar to the anaerobic reactor to one similar to the oxic reactor. DNA hybridization revealed one signature band of 2.1 kb shared by the anoxic and oxic reactors in LR, but not LNR mode. Clone library profiling of this band resulted in one predominant 2.1-kb genomic fragment (B3) with no homologous sequences in GenBank. Real-time polymerase chain reaction indicated that copy numbers of B3 in the anoxic reactor under LR mode were 69 times higher than that under LNR mode, concomitant to a significant increase in COD removal capacity in this reactor. The different patterns of distribution of B3 in the laboratory system and a comparable malfunctioning industrial system demonstrated the potential of this genomic fragment as physical markers in systems monitoring. In addition, this genomic fragment may allow sequence-guided isolation of the host microbe.

Anaerobic biological treatment of phenol at 9.5-15 degrees C in an expanded granular sludge bed (EGSB)-based bioreactor

The aims of this study were to demonstrate the (1) feasibility of psychrophilic, or low-temperature, anaerobic digestion (PAD) of phenolic wastewaters at 10-15 degrees C; (2) economic attractiveness of PAD for the treatment of phenol as measured by daily biogas yields and (3) impact on bioreactor performance of phenol loading rates (PLRs) in excess of those previously documented (1.2 kg phenol m(-3)d(-1)). Two expanded granular sludge bed (EGSB)-based bioreactors, R1 and R2, were employed to mineralise a volatile fatty acid-based wastewater. R2 influent wastewater was supplemented with phenol at an initial concentration of 500 mgl(-1) (PLR, 1 kgm(-3)d(-1)). Reactor performance was measured by chemical oxygen demand (COD) removal efficiency, CH(4) composition of biogas and phenol removal (R2 only). Specific methanogenic activity, biodegradability and toxicity assays were employed to monitor the physiological capacity of reactor biomass samples. The applied PLR was increased to 2 kgm(-3)d(-1) on day 147 and phenol removal by day 415 was 99% efficient, with 4 mgl(-1) present in R2 effluent. The operational temperature of R1 (control) and R2 was reduced by stepwise decrements from 15 degrees C through to a final operating temperature of 9.5 degrees C. COD removal efficiencies of c. 90% were recorded in both bioreactors at the conclusion of the trial (day 673), when the phenol concentration in R2 effluent was below 30 mgl(-1). Daily biogas yields were determined during the final (9.5 degrees C) operating period, when typical daily R2 CH4 yields of c. 3.3lCH4g(-1) COD(removed) d(-1) were recorded. The rate of phenol depletion and methanation by R2 biomass by day 673 were 68 mg phenol gVSS(-1)d(-1) and 12-20 ml CH(4) gVSS(-1)d(-1), respectively.

Bacterial community structure of a pesticide-contaminated site and assessment of changes induced in community structure during bioremediation

The introduction of culture-independent molecular screening techniques, especially based on 16S rRNA gene sequences, has allowed microbiologists to examine a facet of microbial diversity not necessarily reflected by the results of culturing studies. The bacterial community structure was studied for a pesticide-contaminated site that was subsequently remediated using an efficient degradative strain Arthrobacter protophormiae RKJ100. The efficiency of the bioremediation process was assessed by monitoring the depletion of the pollutant, and the effect of addition of an exogenous strain on the existing soil community structure was determined using molecular techniques. The 16S rRNA gene pool amplified from the soil metagenome was cloned and restriction fragment length polymorphism studies revealed 46 different phylotypes on the basis of similar banding patterns. Sequencing of representative clones of each phylotype showed that the community structure of the pesticide-contaminated soil was mainly constituted by Proteobacteria and Actinomycetes. Terminal restriction fragment length polymorphism analysis showed only nonsignificant changes in community structure during the process of bioremediation. Immobilized cells of strain RKJ100 enhanced pollutant degradation but seemed to have no detectable effects on the existing bacterial community structure.

Enhanced biodegradation of phenol by a microbial consortium in a solid-liquid two phase partitioning bioreactor

Two phase partitioning bioreactors (TPPBs) operate by partitioning toxic substrates to or from an aqueous, cell-containing phase by means of second immiscible phase. Uptake of toxic substrates by the second phase effectively reduces their concentration within the aqueous phase to sub-inhibitory levels, and transfer of molecules between the phases to maintain equilibrium results in the continual feeding of substrate based on the metabolic demand of the microorganisms. Conventionally, a single pure species of microorganism, and a pure organic solvent, have been used in TPPBs. The present work has demonstrated the benefits of using a mixed microbial population for the degradation of phenol in a TPPB that uses solid polymer beads (comprised of ethylene vinyl acetate, or EVA) as the second phase. Polymer modification via an increase in vinyl acetate concentration was also shown to increase phenol uptake. Microbial consortia were isolated from three biological sources and, based on an evaluation of their kinetic performance, a superior consortium was chosen that offered improved degradation when compared to a pure strain of Pseudomonas putida ATCC 11172. The new microbial consortium used within a TPPB was capable of degrading high concentrations of phenol (approximately 2000 mg l(-1)), with decreased lag time (10 h) and increased specific rate of phenol degradation (0.71 g phenol g(1) cell h). Investigation of the four-member consortium showed that it consisted of two Pseudomonas sp., and two Acinetobacter sp., and tests conducted upon the individual isolates, as well as paired organisms, confirmed the synergistic benefit of their existence within the consortium. The enhanced effects of the use of a microbial consortium now offer improved degradation of phenol, and open the possibility of the degradation of multiple toxic substrates via a polymer-mediated TPPB system.

Anaerobic biological treatment of phenolic wastewater at 15-18 degrees C

Low-temperature, or psychrophilic (<20 degrees C) anaerobic digestion has been proven feasible for the mineralisation of simple wastewaters. In this study, hybrid expanded granular sludge bed-anaerobic filter (EGSB-AF) bioreactors were used to evaluate the feasibility of psychrophilic digestion for the treatment of phenol-containing wastewater. Efficient chemical oxygen demand and phenol removal were observed at organic and phenol loading rates of 5 kg COD m(-3)d(-1) and 0.4-1.2 kg phenol m(-3)d(-1) (400-1200 mg phenol [l wastewater](-1)), respectively. There was no long-term accumulation of volatile fatty acids in the reactor systems. Methanogenic activity was developed under psychrophilic conditions but anaerobic methane-producing populations remained mesophilic throughout the trial of 415 days.

Biodegradation of phenol by acclimatized Pseudomonas putida cells using glucose as an added growth substrate

Biodegradation of phenol, a pollutant derived from many industrial processes, was achieved through acclimatized Pseudomonas putida cells. The strategy to overcome the inhibitory effect of phenol on microbial growth involved the addition of glucose, a conventional carbon source. A factorial experimental design was employed in order to optimize the initial phenol and glucose concentrations. The optimum conditions found were applied in 2-lt bioreactors. The development of acclimatized cells and the use of glucose as an added growth substrate resulted in a significant phenol degradation rate of 60.7 mg L(-1) h(-1) with a complete removal of 1200 mg L(-1) phenol.

Bacterial diversity in cases of lung infection in cystic fibrosis patients: 16S ribosomal DNA (rDNA) length heterogeneity PCR and 16S rDNA terminal restriction fragment length polymorphism profiling

The leading cause of morbidity and mortality in cystic fibrosis (CF) patients stems from repeated bacterial respiratory infections. Many bacterial species have been cultured from CF specimens and so are associated with lung disease. Despite this, much remains to be determined. In the present study, we characterized without prior cultivation the total bacterial community present in specimens taken from adult CF patients, extracting DNA directly from 14 bronchoscopy or sputum samples. Bacterial 16S ribosomal DNA (rRNA) gene PCR products were amplified from extracted nucleic acids, with analyses by terminal restriction fragment length polymorphism (T-RFLP), length heterogeneity PCR (LH-PCR), and sequencing of individual cloned PCR products to characterize these communities. Using the same loading of PCR products, 12 distinct T-RFLP profiles were identified that had between 3 and 32 T-RFLP bands. Nine distinct LH-PCR profiles were identified containing between one and four bands. T-RFLP bands were detected in certain samples at positions that corresponded to pathogens cultured from CF samples, e.g., Burkholderia cepacia and Haemophilus influenzae. In every sample studied, one T-RFLP band was identified that corresponded to that produced by Pseudomonas aeruginosa. A total of 103 16S rRNA gene clones were examined from five patients. P. aeruginosa was the most commonly identified species (59% of clones). Stenotrophomonas species were also common, with eight other (typically anaerobic) bacterial species identified within the remaining 17 clones. In conclusion, T-RFLP analysis coupled with 16S rRNA gene sequencing is a powerful means of analyzing the composition and diversity of the bacterial community in specimens sampled from CF patients.

In-field spatial variability in the degradation of the phenyl-urea herbicide isoproturon is the result of interactions between degradative Sphingomonas spp. and soil pH

Substantial spatial variability in the degradation rate of the phenyl-urea herbicide isoproturon (IPU) [3-(4-isopropylphenyl)-1,1-dimethylurea] has been shown to occur within agricultural fields, with implications for the longevity of the compound in the soil, and its movement to ground- and surface water. The microbial mechanisms underlying such spatial variability in degradation rate were investigated at Deep Slade field in Warwickshire, United Kingdom. Most-probable-number analysis showed that rapid degradation of IPU was associated with proliferation of IPU-degrading organisms. Slow degradation of IPU was linked to either a delay in the proliferation of IPU-degrading organisms or apparent cometabolic degradation. Using enrichment techniques, an IPU-degrading bacterial culture (designated strain F35) was isolated from fast-degrading soil, and partial 16S rRNA sequencing placed it within the Sphingomonas group. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified bacterial community 16S rRNA revealed two bands that increased in intensity in soil during growth-linked metabolism of IPU, and sequencing of the excised bands showed high sequence homology to the Sphingomonas group. However, while F35 was not closely related to either DGGE band, one of the DGGE bands showed 100% partial 16S rRNA sequence homology to an IPU-degrading Sphingomonas sp. (strain SRS2) isolated from Deep Slade field in an earlier study. Experiments with strains SRS2 and F35 in soil and liquid culture showed that the isolates had a narrow pH optimum (7 to 7.5) for metabolism of IPU. The pH requirements of IPU-degrading strains of Sphingomonas spp. could largely account for the spatial variation of IPU degradation rates across the field.

Characterization of bacterial consortia capable of degrading 4-chlorobenzoate and 4-bromobenzoate under denitrifying conditions

4-Chlorobenzoate and 4-bromobenzoate were readily degraded in denitrifying enrichment cultures established with river sediment, estuarine sediment or agricultural soil as inoculum. Stable denitrifying consortia were obtained and maintained by serial dilution and repeated feeding of substrates. Microbial community analyses were performed to characterize the 4-chlorobenzoate and 4-bromobenzoate degrading consortia with terminal restriction fragment length polymorphism (T-RFLP) and cloning of 16S rRNA genes from the cultures. Interestingly, two major terminal restriction fragments (T-RFs) in the 4-chlorobenzoate degrading consortia and one T-RF in the 4-bromobenzoate utilizing consortium were observed from T-RFLP analysis regardless of their geographical and ecological origins. The two T-RFs (clones 4CB1 and 4CB2) in 4-chlorobenzoate degrading consortia were identified as members of the beta-subunit of the Proteobacteria on the basis of 16S rRNA sequencing analysis. Phylogenetic analysis of 16S rRNA genes showed that clone 4CB1 was closely related to Thauera aromatica while clone 4CB2 was distantly related to the genera Limnobacter and Ralstonia. The 4-bromobenzoate utilizing consortium mainly consisted of one T-RF, which was identical to clone 4CB2 in spite of different enrichment substrate. This suggests that degradation of 4-chlorobenzoate and 4-bromobenzoate under denitrifying conditions was mediated by bacteria belonging to the beta-subunit of the Proteobacteria.