High bacterial diversity of a waste gas-degrading community in an industrial biofilter as shown by a 16S rDNA clone library

Influence of packing material on the biofiltration of butyric acid: A comparative study from a physico-chemical, olfactometric and microbiological perspective

The influence of bed material on the odor removal performance of a biofilter was studied. A compost-wood biofilter and a wood biofilter were treated with a gaseous stream contaminated with butyric acid and comparatively evaluated at pilot scale using olfactometric, physico-chemical and microbiological approaches. The variables analyzed in both biofilters were correlated with specific families of their microbiota composition. In addition to a higher nutrients content (nitrogen and phosphorus), the compost-wood biofilter registered maximum values in number of aerobic microorganisms (3.6·10⁸ CFU/g) and in aerobic microbiological activity (≈40 mg O₂/g VS of cumulative oxygen demand at 20 h). This may explain the higher performance of this biofilter compared to the wood biofilter, withstanding odor loads of up to 1450 ou_E/m²·s with odor removal efficiencies close to 100%. The analysis of the microbial community showed that Actinobacteria, particularly the mostly aerobic Microbacteriaceae family, might play an important role in butyric acid degradation and hence reduce odor impact. The multidisciplinary analysis carried out in this work could be a very useful strategy for the optimal design of biofiltration operations.

Odor mitigation and bacterial community dynamics in on-site biocovers at a sanitary landfill in South Korea

Unpleasant odors emitted from landfills have been caused environmental and societal problems. For odor abatement, two pilot-scale biocovers were installed at a sanitary landfill site in South Korea. Biocovers PBC1 and PBC2 comprised a soil mixture with different ratios of earthworm casts as an inoculum source and were operated for 240 days. Their odor removal efficiencies were evaluated, and their bacterial community structures were characterized using pyrosequencing. In addition, the correlation between odor removability and bacterial community dynamics was assessed using network analysis. The removal efficiency of complex odor intensity in the two biocovers ranged from 81.1% to 97.8%. Removal efficiencies of sulfur-containing odors (hydrogen sulfide, methanethiol, dimethyl sulfide, and dimethyl disulfide), which contributed most to complex odor intensity, were greater than 91% in both biocovers. Despite the fluctuations in ambient temperature (-8.2 to 31.3 °C) and inlet complex odor intensity (10,000-42,748 of odor dilution ratio), biocovers PBC1 and PBC2 displayed stable deodorizing performance. A high ratio of earthworm casts as an inoculum source led to high odor removability during the first 25 days of operation, but different mixing ratios of earthworm casts did not significantly affect overall odor removability. A bacterial community analysis showed that Methylobacter, Arthrobacter, Acinetobacter, Rhodanobacter, and Pedobacter were the dominant genera in both biocovers. Network analysis results indicated that Steroidobacter, Cystobacter, Methylosarcina, Solirubrobacter, and Pseudoxanthomonas increased in relative abundance with time and were major contributors to odor removal, although these bacteria had a relatively low abundance compared to the overall bacterial community. These data contribute to a more comprehensive understanding of the relationship between bacterial community dynamics and deodorizing performance in biocovers.

Microbial Community in a Biofilter for Removal of Low Load Nitrobenzene Waste Gas

To improve biofilter performance, the microbial community of a biofilter must be clearly defined. In this study, the performance of a lab-scale polyurethane biofilter for treating waste gas with low loads of nitrobenzene (NB) (< 20 g m-3 h-1) was investigated when using different empty bed residence times (EBRT) (64, 55.4 and 34 s, respectively). In addition, the variations of the bacterial community in the biofilm on the longitudinal distribution of the biofilters were analysed by using Illumina MiSeq high-throughput sequencing. The results showed that NB waste gas was successfully degraded in the biofilter. High-throughput sequencing data suggested that the phylum Actinobacteria and genus Rhodococcus played important roles in the degradation of NB. The variations of the microbial community were attributed to the different intermediate degradation products of NB in each layer. The strains identified in this study were potential candidates for purifying waste gas effluents containing NB.

Assessment of bacterial community structure in nitrifying biofilm under inorganic carbon-sufficient and -limited conditions

In this work, nitrification and changes in the composition of the total bacterial community under inorganic carbon (IC)-limited conditions, in a nitrifying moving bed biofilm reactor, was investigated. A culture-independent analysis of cloning and sequencing based on the 16S rRNA gene was applied to quantify the bacterial diversity and to determine bacterial taxonomic assignment. IC concentrations had significant effects on the stability of ammonia-oxidation as indicated by the reduction of the nitrogen conversion rate with high NH4(+)-N loadings. The predominance of Nitrosomonas europaea was maintained in spite of changes in the IC concentration. In contrast, heterotrophic bacterial species contributed to a high bacterial diversity, and to a dynamic shift in the bacterial community structure, under IC-limited conditions. In this study, individual functions of heterotrophic bacteria were estimated based on taxonomic information. Possible key roles of coexisting heterotrophic bacteria are the assimilation of organic compounds of extracellular polymeric substances produced by nitrifiers, and biofilm formation by providing a filamentous structure and aggregation properties.

Investigating bacterial populations in styrene-degrading biofilters by 16S rDNA tag pyrosequencing

Microbial biofilms are essential components in the elimination of pollutants within biofilters, yet still little is known regarding the complex relationships between microbial community structure and biodegradation function within these engineered ecosystems. To further explore this relationship, 16S rDNA tag pyrosequencing was applied to samples taken at four time points from a styrene-degrading biofilter undergoing variable operating conditions. Changes in microbial structure were observed between different stages of biofilter operation, and the level of styrene concentration was revealed to be a critical factor affecting these changes. Bacterial genera Azoarcus and Pseudomonas were among the dominant classified genera in the biofilter. Canonical correspondence analysis (CCA) and correlation analysis revealed that the genera Brevundimonas, Hydrogenophaga, and Achromobacter may play important roles in styrene degradation under increasing styrene concentrations. No significant correlations (P > 0.05) could be detected between biofilter operational/functional parameters and biodiversity measurements, although biological heterogeneity within biofilms and/or technical variability within pyrosequencing may have considerably affected these results. Percentages of selected bacterial taxonomic groups detected by fluorescence in situ hybridization (FISH) were compared to results from pyrosequencing in order to assess the effectiveness and limitations of each method for identifying each microbial taxon. Comparison of results revealed discrepancies between the two methods in the detected percentages of numerous taxonomic groups. Biases and technical limitations of both FISH and pyrosequencing, such as the binding of FISH probes to non-target microbial groups and lack of classification of sequences for defined taxonomic groups from pyrosequencing, may partially explain some differences between the two methods.

Comparative assessment of a biofilter, a biotrickling filter and a hollow fiber membrane bioreactor for odor treatment in wastewater treatment plants

A low abatement efficiency for the hydrophobic fraction of odorous emissions and a high footprint are often pointed out as the major drawbacks of conventional biotechnologies for odor treatment. In this work, two conventional biotechnologies (a compost-based biofilter, BF, and a biotrickling filter, BTF), and a hollow-fiber membrane bioreactor (HF-MBR) were comparatively evaluated in terms of odor abatement potential and pressure drop (ΔP) at empty bed residence times (EBRTs) ranging from 4 to 84 s, during the treatment of methyl-mercaptan, toluene, alpha-pinene and hexane at trace level concentrations (0.75-4.9 mg m(-3)). High removal efficiencies (RE > 90% regardless of the air pollutant) were recorded in the BF at EBRTs ≥ 8 s, although the high ΔP across the packed bed limited its cost-effective operation to EBRTs > 19 s. A complete methyl-mercaptan, toluene and alpha-pinene removal was recorded in the BTF at EBRTs ≥ 4 s and ΔP lower than 33 mmH2O (∼611 Pa mbed(-1)), whereas slightly lower REs were observed for hexane (∼88%). The HF-MBR completely removed methyl-mercaptan and toluene at all EBRTs tested, but exhibited an unstable alpha-pinene removal performance as a result of biomass accumulation and a low hexane abatement efficiency. Thus, a periodical membrane-cleaning procedure was required to ensure a steady abatement performance. Finally, a high bacterial diversity was observed in the three bioreactors in spite of the low carbon source spectrum present in the air emission.

A comparative study of fungal and bacterial biofiltration treating a VOC mixture

Bacterial biofilters usually exhibit a high microbial diversity and robustness, while fungal biofilters have been claimed to better withstand low moisture contents and pH values, and to be more efficient coping with hydrophobic volatile organic compounds (VOCs). However, there are only few systematic evaluations of both biofiltration technologies. The present study compared fungal and bacterial biofiltration for the treatment of a VOC mixture (propanal, methyl isobutyl ketone-MIBK, toluene and hexanol) under the same operating conditions. Overall, fungal biofiltration supported lower elimination capacities than its bacterial counterpart (27.7 ± 8.9 vs 40.2 ± 5.4 gCm(-3) reactor h(-1)), which exhibited a final pressure drop 60% higher than that of the bacterial biofilter due to mycelial growth. The VOC mineralization ratio was also higher in the bacterial bed (≈ 63% vs ≈ 43%). However, the substrate biodegradation preference order was similar for both biofilters (propanal>hexanol>MIBK>toluene) with propanal partially inhibiting the consumption of the rest of the VOCs. Both systems supported an excellent robustness versus 24h VOC starvation episodes. The implementation of a fungal/bacterial coupled system did not significantly improve the VOC removal performance compared to the individual biofilter performances.

Removal of the sesquiterpene β-caryophyllene from air via biofiltration: performance assessment and microbial community structure

Experiments were conducted in a laboratory-scale biofilter to assess the ability of a fixed-film biological process to treat an air stream containing β-caryophyllene, a sesquiterpene emitted by a variety of conifer trees as well as industrial wood processing operations. Treatment performance was evaluated under a variety of pollutant loading conditions and nutrient supply rates over an operational period lasting more than 240 days. At empty bed contact times (EBCTs) as low as 10 s and daily average pollutant loading rate as high as 24.2 g C/(m(3) h) (grams pollutant measured as carbon per cubic meter packed bed volume per hour), removal efficiencies in excess of 95 % were observed when sufficient nutrients were supplied. Results demonstrate that, as with biofilters treating other compounds, biofilters treating β-caryophyllene can experience local nutrient limitations that result in diminished performance. The biofilter successfully recovered high removal efficiency within a few days after resumption of pollutant loading following a 14-day interval of no contaminant loading. Construction of a 16S rRNA gene library via pyrosequencing revealed the presence of a high proportion of bacteria clustering within the genera Gordonia (39.7 % of the library) and Rhodanobacter (37.6 %). Other phylotypes detected at lower relative abundances included Pandoraea (6.2 %), unclassified Acetobacteraceae (5.5 %), Dyella (3.3 %), unclassified Xanthomonadaceae (2.6 %), Mycobacterium (1.8 %), and Nocardia (0.6 %). Collectively, results demonstrate that β-caryophyllene can be effectively removed from contaminated gas streams using biofilters.

Waste gas biofiltration: advances and limitations of current approaches in microbiology

As confidence in gas biofiltration efficacy grows, ever more complex malodorant and toxic molecules are ameliorated. In parallel, for many countries, emission control legislation becomes increasingly stringent to accommodate both public health and climate change imperatives. Effective gas biofiltration in biofilters and biotrickling filters depends on three key bioreactor variables: the support medium; gas molecule solubilization; and the catabolic population. Organic and inorganic support media, singly or in combination, have been employed and their key criteria are considered by critical appraisal of one, char. Catabolic species have included fungal and bacterial monocultures and, to a lesser extent, microbial communities. In the absence of organic support medium (soil, compost, sewage sludge, etc.) inoculum provision, a targeted enrichment and isolation program must be undertaken followed, possibly, by culture efficacy improvement. Microbial community process enhancement can then be gained by comprehensive characterization of the culturable and total populations. For all species, support medium attachment is critical and this is considered prior to filtration optimization by water content, pH, temperature, loadings, and nutrients manipulation. Finally, to negate discharge of fungal spores, and/or archaeal and/or bacterial cells, capture/destruction technologies are required to enable exploitation of the mineralization product CO(2).

Molecular and physiological approaches to understand the ecology of methanol degradation during the biofiltration of air streams

A 13.4 L biofilter treating an off-gas stream supplemented with methanol under two different situations was studied in terms of MeOH removal efficiency, microbial ecology and odor removal. During Period 1 (P1) the reactor was packed with wood bark chips with no pH control, treating an off-gas resulting from the aerobic chamber of a membrane biological reactor treating sewage and located outdoor, whereas during Period 2 (P2) a compressed air stream fed with MeOH was treated using PVC rings and maintaining pH at neutral values. Both systems operated at 96 g MeOH m(-3) h(-1) achieving removal efficiencies of around 90% during P1 and 99.9% during P2. The relative activity of biomass developed in both systems was assessed using respirometric analysis with samples obtained from both biofilms. Higher biomass activity was obtained during P2 (0.25-0.35 kg MeOH kg(-1) VSS d(-1)) whereas 1.1 kg MeOH kg(-1) VSS d(-1) was obtained in the case of P1. The application of molecular and microscopic techniques showed that the eukaryotes were predominant during P1, being the yeast Candida boidinii the most abundant microorganism. A specific Fluorescence in situ hybridization probe was designed for C. boidinii and tested successfully. As a result of the neutral pH, a clear predominance of prokaryotes was detected during P2. Interestingly, some anaerobic bacteria were detected such as Desulfovibrio, Desulfobacteraceae species and also some archaea such as Methanosarcina.

Odor abatement in biotrickling filters: effect of the EBRT on methyl mercaptan and hydrophobic VOCs removal

The performance and microbiology of a biotrickling filter (BTF) treating methyl mercaptan, toluene, alpha-pinene and hexane at the mg m(-3) level was studied at empty bed residence times (EBRT) of 50, 30, 11 and 7 s. Removal efficiencies (REs) higher than 95% were observed for MeSH, toluene and alpha-pinene even at 11 s, while hexane REs exceeded 70%. At 7 s, an irreversible damage of the microbial activity due to the accumulation of toxic metabolites resulted in a decrease of REs. The addition of silicone stabilized process performance but only re-inoculation allowed achieving a complete removal of MeSH, toluene and alpha-pinene, and hexane REs of 80%. The high K(L)a values (ranging from 38 ± 4 to 90 ± 11 h(-1)) explained the good BTF performance at such low EBRTs. A high bacterial diversity, along with a vertical distribution of the bacterial communities was observed, the main phyla being Proteobacteria, Actinobacteria, Nitrospira, Chloroflexi and Gemmatimonadertes.

Efficient bio-deodorization of aniline vapor in a biotrickling filter: metabolic mineralization and bacterial community analysis

A biotrickling filter inoculated with commercial mixed microorganisms B350 was employed to treat N-containing odorous vapor - aniline. Results indicated no aniline could be detected when empty bed residence time (EBRT) was larger than 110s at inlet concentration of 0.30 g m(-3). The variation of inlet concentration did not change removal efficiencies when concentration is less than 0.21 g m(-3) at fixed EBRT 110s. Biodegradation mechanism of aniline was tentatively proposed based on identified intermediates and predicted biodegradation pathway as well as final mineralized products. Aniline was firstly biodegraded to catechol, and then to levulinic acid and subsequently to succinic acid. Finally, about 62% aniline carbon was completely mineralized to CO(2), while about 91% aniline nitrogen was converted into ammonia and nitrate. Bacterial community in biotrickling filter was found that at least seven bands microbes were identified for high efficiencies of bioreactor at stable state. In all, biotrickling filter seeded with B350 would be a better choice for the purification odorous gas containing high concentration aniline.

Butyric acid- and dimethyl disulfide-assimilating microorganisms in a biofilter treating air emissions from a livestock facility

Biofiltration has proven an efficient tool for the elimination of volatile organic compounds (VOCs) and ammonia from livestock facilities, thereby reducing nuisance odors and ammonia emissions to the local environment. The active microbial communities comprising these filter biofilms have not been well characterized. In this study, a trickle biofilter treating air from a pig facility was investigated and proved efficient in removing carboxylic acids (>70% reduction), mainly attributed to the primary filter section within which reduced organic sulfur compounds were also depleted (up to 50%). The secondary filter eliminated several aromatic compounds: phenol (81%), p-cresol (89%), 4-ethylphenol (68%), indole (48%), and skatole (69%). The active butyric acid degrading bacterial community of an air filter sample was identified by DNA stable-isotope probing (DNA-SIP) and microautoradiography, combined with fluorescence in situ hybridization (MAR-FISH). The predominant 16S rRNA gene sequences from a clone library derived from "heavy" DNA from [(13)C(4)]butyric acid incubations were Microbacterium, Gordonia, Dietzia, Rhodococcus, Propionibacterium, and Janibacter, all from the Actinobacteria. Actinobacteria were confirmed and quantified by MAR-FISH as being the major bacterial phylum assimilating butyric acid along with several Burkholderiales-related Betaproteobacteria. The active bacterial community assimilating dimethyl disulfide (DMDS) was characterized by DNA-SIP and MAR-FISH and found to be associated with the Actinobacteria, along with a few representatives of Flavobacteria and Sphingobacteria. Interestingly, ammonia-oxidizing Betaproteobacteria were also implicated in DMDS degradation, as were fungi. Thus, multiple isotope-based methods provided complementary data, enabling high-resolution identification and quantitative assessments of odor-eliminating Actinobacteria-dominated populations of these biofilter environments.

Identification of wastewater bacteria involved in the degradation of triclocarban and its non-chlorinated congener

Triclocarban (TCC) is an antimicrobial additive of personal care products that is only partially degraded during wastewater treatment. Bacteria responsible for its transformation are unknown. We obtained wastewater bacteria capable of using as the sole carbon source TCC or its non-chlorinated analog, carbanilide (NCC). Enrichments established using activated sludge amended with TCC and NCC, respectively, were maintained for 1 year through successive transfers. Enrichments displayed exponential growth after 2 weeks, reaching stationary phase after 1 month. The NCC enrichment was shown to accumulate aniline. Denaturing gradient gel electrophoresis of amplified 16S rRNA genes indicated markedly reduced community richness compared to the inoculum and a single, prominent taxonomic unit emerged in both chlorinated and non-chlorinated carbanilide enrichment cultures. Cloned 16S rRNA genes showed both enrichments were dominated by a single genotype related to uncharacterized organisms within the Alcaligenaceae. Of ∼30 sequences from each enrichment, no other organisms were detected in the TCC enrichment while, a small, flanking community of alpha proteobacteria was detected in the NCC enrichment. Study results demonstrate that growth of wastewater bacteria on TCC and its lower chlorinated analog can be linked to bacteria within the family Alcaligenaceae. These organisms are promising agents for the bioremediation of hazardous phenylurea pollutants.

Effect of nitrogen source on methanol oxidation and genetic diversity of methylotrophic mixed cultures enriched from pulp and paper mill biofilms

Methanol-oxidizing bacteria may play an important role in the development and use of biological treatment systems for the removal of methanol from industrial effluents. Optimization of methanol degradation potential in such systems is contingent on availability of nutrients, such as nitrogen, in the most favorable form and concentration. To that end, this study examined the variation in growth, methanol degradation, and bacterial diversity of two mixed methylotrophic cultures that were provided nitrogen either as ammonium or nitrate and in three different concentrations. Methanol-degrading cultures were enriched from biofilms sampled at a pulp and paper mill and grown in liquid batch culture with methanol as the only carbon source and either ammonium or nitrate as the only added nitrogen source. Results indicate that growth and methanol removal of the mixed cultures increase directly with increased nitrogen, added in either form. However, methanol removal and bacterial diversity, as observed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) methods, were higher when using nitrate as the nitrogen source for enrichment and growth, rather than ammonium. Based on results described here, nitrate may potentially be a better nitrogen source when enriching or working with mixed methylotrophic cultures, and possibly more effective when used as a nutrient addition to biofilters.

Bacterial community analysis of a gas-phase biotrickling filter for biogas mimics desulfurization through the rRNA approach

The bacterial composition of a lab-scale biotrickling filter (BTF) treating high loads of H(2)S was investigated by the rRNA approach. Two 16S rRNA gene clone libraries were established 42 and 189 d after reactor startup, while fluorescent in-situ hybridization (FISH) with DNA probes was performed throughout 260d of reactor operation. Diversity, community structure and metamorphosis were studied from reactor startup to fully-established pseudo-steady state operation at near neutral pH and at an inlet H(2)S concentration of 2000 ppmv (load of 55.6g H(2)S m(-3)h(-1)). In addition, FISH was used for assessing the spatial distribution of sulfur-oxidizing bacteria (SOB) along the length of the reactor under pseudo-steady state operation. A major shift in the diversity of the community was observed with the operating time, from a well-diverse community at startup to pseudo-steady state operation with a majority of retrieved sequences affiliated to SOB of the sulfur cycle including Thiothrix spp., Thiobacillus spp., and Sulfurimonas denitrificans. Although aerobic species were predominant along the BTF, a vertical stratification was encountered, in which facultative anaerobes had a major relative abundance in the inlet part of the BTF, where the sulfide to oxygen ratio was higher. The observed changes were related to the trophic properties of the community, the DO concentration, the accumulation of elemental sulfur and the operation at neutral pH.

Using terminal restriction fragment length polymorphism (T-RFLP) analysis to assess microbial community structure in compost systems

Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified genes is a widely used fingerprinting technique in composting systems. This analysis is based on the restriction endonuclease digestion of fluorescently end-labeled PCR products. The digested product is mixed with a DNA size standard, itself labeled with a distinct fluorescent dye, and the fragments are then separated by capillary or gel electrophoresis using an automated sequencer. Upon analysis, only the terminal end-labeled restriction fragments are detected. An electropherogram is produced, which shows a profile of compost microbial community as a series of peaks of varying height. This technique has also been effectively used in the exploration of complex microbial environments and in the study of bacterial, archaeal, and eukaryal populations in natural habitats.

Characterisation of hexane-degrading microorganisms in a biofilter by stable isotope-based fatty acid analysis, FISH and cultivation

The hexane-degrading bacterial community of a biofilter was characterised by a combination of stable isotope-based phospholipid fatty acid analyses, fluorescence in situ hybridisation and cultivation. About 70 bacterial strains were isolated from a full-scale biofilter used for treatment of hexane containing waste gas of an oil mill. The isolation approach led to 16 bacterial groups, which were identified as members of the Alpha-, Beta- and Gammaproteobacteria, Actinobacteria and Firmicutes. Three groups showed good growth on hexane as the sole source of carbon. These groups were allocated to the genera Gordonia and Sphingomonas and to the Nevskia-branch of the Gammaproteobacteria. Actively degrading populations in the filter material were characterised by incubation of filter material samples with deuterated hexane and subsequent phospholipid fatty acid analysis. Significant labelling of the fatty acids 16:1 cis10, 18:1 cis9 and 18:0 10methyl affiliated the hexane-degrading activity of the biofilter with the isolates of the genus Gordonia. In vitro growth on hexane and in situ labelling of characteristic fatty acids confirmed the central role of these organisms in the hexane degradation within the full-scale biofilter.

Bioaugmentation for electricity generation from corn stover biomass using microbial fuel cells

Corn stover is usually treated by an energy-intensive or expensive process to extract sugars for bioenergy production. However, it is possible to directly generate electricity from corn stover in microbial fuel cells (MFCs) through the addition of microbial consortia specifically acclimated for biomass breakdown. A mixed culture that was developed to have a high saccharification rate with corn stover was added to single-chamber, air-cathode MFCs acclimated for power production using glucose. The MFC produced a maximum power of 331 mW/m2 with the bioaugmented mixed culture and corn stover, compared to 510 mW/m2 using glucose. Denaturing gradient gel electrophoresis (DGGE) showed the communities continued to evolve on both the anode and corn stover biomass over 60 days, with several bacteria identified including Rhodopseudomonas palustris. The use of residual solids from the steam exploded corn stover produced 8% more power (406 mW/m2) than the raw corn stover. These results show that it is possible to directly generate electricity from waste corn stover in MFCs through bioaugmentation using naturally occurring bacteria.

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.

Bacterial diversity in activated sludge from a consecutively aerated submerged membrane bioreactor treating domestic wastewater

The bacterial diversity of activated sludge from submerged membrane bioreactor (SMBR) was investigated. A 16S rDNA clone library was generated, and 150 clones were screened using restriction fragment length polymorphism (RFLP). Of the screened clones, almost full-length 16S rDNA sequences of 64 clones were sequenced. Phylogenetic tree was constructed with a database containing clone sequences from this study and bacterial rDNA sequences from NCBI for identification purposes. The 90.6% of the clones were affiliated with the two phyla Bacteroidetes (50%) and Proteobacteria (40%), and beta-, gamma-, and delta-Proteobacteria accounted for 7.8%, 28.1%, and 4.7%, respectively. Minor portions were affiliated with the Actinobacteria and Firmicutes (both 3.1%). Only 6 out of 64 16S rDNA sequences exhibited similarities of more than 97% to classified bacterial species, which indicated that a substantial fraction of the clone sequences were derived from unknown taxa. Rarefaction analysis of operational taxonomic units (OTUs) clusters demonstrated that 150 clones screened were still insufficient to describe the whole bacterial diversity. Measurement of water quality parameter demonstrated that performance of the SMBR maintained high level, and the SMBR system remained stable during this study.

Olivibacter sitiensis gen. nov., sp. nov., isolated from alkaline olive-oil mill wastes in the region of Sitia, Crete

A novel, Gram-negative, non-motile, non-sporulating, rod-shaped bacterium isolated from a viscous two-phase olive-oil mill waste ('alpeorujo') is described. The strain, designated AW-6T, is an obligate aerobe, forming irregular, pigmented creamy white colonies. The pH and temperature ranges for growth were pH 5-8 and 5-45 degrees C, with optimal pH and temperature for growth of pH 6-7 and 28-32 degrees C, respectively. Strain AW-6T was chemo-organotrophic and utilized mostly D+ -glucose, protocatechuate and D+ -xylose, followed by L-cysteine, D- -fructose, D+ -galactose, L-histidine, lactose, sorbitol and sucrose. Menaquinone-7 was detected in the respiratory chain of strain AW-6T. The major fatty acids of strain AW-6T were C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH, iso-C(15 : 0), iso-C(17 : 0) 3-OH and C(16 : 0). The closest phylogenetic relative of strain AW-6T was clone BIti35 (89.7 % 16S rRNA gene sequence similarity), while Sphingobacterium thalpophilum DSM 11723T was the closest recognized relative within the Sphingobacteriaceae (88.2 % similarity). Strain AW-6T showed a low level of DNA-DNA relatedness to S. thalpophilum DSM 11723T (33.8-37.0 %). The DNA G+C content of strain AW-6T was 45.6 mol%. Physiological and chemotaxonomic data further confirmed the distinctiveness of strain AW-6T from members of the genera Sphingobacterium and Pedobacter. Thus, strain AW-6T is considered to represent a novel species of a new genus within the family Sphingobacteriaceae, for which the name Olivibacter sitiensis gen. nov., sp. nov. is proposed. The type strain is AW-6T =DSM 17696T=CECT 7133T).

Identification and isolation of a Castellaniella species important during biostimulation of an acidic nitrate- and uranium-contaminated aquifer

Immobilization of uranium in groundwater can be achieved through microbial reduction of U(VI) to U(IV) upon electron donor addition. Microbial community structure was analyzed in ethanol-biostimulated and control sediments from a high-nitrate (>130 mM), low-pH, uranium-contaminated site in Oak Ridge, TN. Analysis of small subunit (SSU) rRNA gene clone libraries and polar lipid fatty acids from sediments revealed that biostimulation resulted in a general decrease in bacterial diversity. Specifically, biostimulation resulted in an increase in the proportion of Betaproteobacteria (10% of total clones in the control sediment versus 50 and 79% in biostimulated sediments) and a decrease in the proportion of Gammaproteobacteria and Acidobacteria. Clone libraries derived from dissimilatory nitrite reductase genes (nirK and nirS) were also dominated by clones related to Betaproteobacteria (98% and 85% of total nirK and nirS clones, respectively). Within the nirK libraries, one clone sequence made up 59 and 76% of sequences from biostimulated sediments but only made up 10% of the control nirK library. Phylogenetic analysis of SSU rRNA and nirK gene sequences from denitrifying pure cultures isolated from the site indicate that all belong to a Castellaniella species; nearly identical sequences also constituted the majority of biostimulated SSU rRNA and nirK clone libraries. Thus, by combining culture-independent with culture-dependent techniques, we were able to link SSU rRNA clone library information with nirK sequence data and conclude that a potentially novel Castellaniella species is important for in situ nitrate removal at this site.

Evaluation of gas removal and bacterial community diversity in a biofilter developed to treat composting exhaust gases

The performance of a new, but simply constructed, biofilter system, developed to purify composting exhaust air, was evaluated. The biofilter was packed with mature compost mixed with activated carbon and sludge sourced from a wastewater treatment plant. An alternating air flow system and a bioaerosol reduction device were designed to prevent pressure drop and reduce bioaerosol release. Experimental results demonstrated that satisfactory removal efficiencies of nitrogen-containing compounds, sulfur-containing compounds, fatty acids, total hydrocarbon and odor were achieved at an empty bed retention time (EBRT) of 30s. No significant acidification or alkalinity in the biofilter was observed, and the system was characterized by a small pressure drop and a low level of bioaerosol emission. Denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH) techniques were used to uncover the changes in the bacterial community of the biofilter during the deodorization processes. A minimum of 16 bands were observed in the DGGE profile. Phylogenetic analysis revealed the phylum of Proteobacteria to be predominant, followed by Actinobacteria, Bacteroidetes, and Firmicutes, in descending order. However, the occurrence and predominance of specific bacterial species varied with the environmental conditions of the biofilter. Our results demonstrate - from both an engineering and biological point of view - the feasibility of the biofilter system described herein in purifying the gases derived from composting food waste.

Identification of cellulolytic bacteria in soil by stable isotope probing

Plant residues, mainly made up of cellulose, are the largest fraction of organic carbon material in terrestrial ecosystems. Soil microorganisms are mainly responsible for the transfer of this carbon to the atmosphere, but their contribution is not accurately known. The aim of the present study was to identify bacterial populations that are actively involved in cellulose degradation, using the DNA-stable isotope probing (DNA-SIP) technique. (13)C-cellulose was produced by Acetobacter xylinus and incubated in soil for 7, 14, 30 and 90 days. Total DNA was extracted from the soil, the (13)C-labelled (heavy) and unlabelled (light) DNA fractions were separated by ultracentrifugation, and the structure of active bacterial communities was analysed by bacterial-automated ribosomal intergenic spacer analysis (B-ARISA) and characterized with denaturing gradient gel electrophoresis (DGGE). Cellulose degradation was associated with significant changes in bacterial community structure issued from heavy DNA, leading to the appearance of new bands and increase in relative intensities of other bands until day 30. The majority of bands decreased in relative intensity at day 90. Sequencing and phylogenetic analysis of 10 of these bands in DGGE profiles indicated that most sequences were closely related to sequences from organisms known for their ability to degrade cellulose or to uncultured soil bacteria.

Performance and microbial analysis of defined and non-defined inocula for the removal of dimethyl sulfide in a biotrickling filter

The performance and microbial communities of three differently inoculated biotrickling filters removing dimethyl sulfide (DMS) were compared. The biotrickling filters were inoculated with Thiobacillus thioparus TK-m (THIO), sludge (HANDS) and sludge + T. thioparus TK-m + Hyphomicrobium VS (HANDS++), respectively. The criteria investigated were length of the start-up period, the maximum elimination capacity, and the effects of intermittent loading rates, low pH, peak loading and very low loading rate on the DMS removal efficiency. The HANDS++ reactor exhibited the best performance considering all treatments. HANDS performed almost equally well as HANDS++, except during the determination of the EC(max), while THIO was generally the least efficient. During stable DMS loading at concentrations of 20 ppmv or lower, all reactors exhibited similar and high removal efficiencies (>99%). Denaturing gradient gel electrophoresis (DGGE) analysis showed the establishment of T. thioparus in the biofilm of all reactors, but not of Hyphomicrobium VS. Quantitative monitoring of the introduced bacterial strains was performed with a newly developed real-time PCR protocol. Initially, the inoculated strains were exclusively found in the reactors in which they were added. Afterwards, however, both strains developed in the biofilm of all three reactors, although T. thioparus attained higher cell densities than Hyphomicrobium. The presence of T. thioparus in THIO was related with the DMS loading rates that were applied, in the sense that intermittent DMS loading and very low DMS loading rates (0.5 ppmv) induced a decrease in gene copy numbers. Real-time PCR and DGGE both gave consistent results regarding the presence of Hyphomicrobium VS and Thiobacillus thioparus TK-m in the reactors. Only real-time PCR could be used to detect bacteria comprising of less than 1.4% of the total bacterial community ( approximately 10(5) copies ring(-1)).

Replicability of dominant bacterial populations after long-term surfactant-enrichment in lab-scale activated sludge

Bacterial communities were examined in replicate lab-scale activated sludge reactors after a period of several months of enrichment with non-ionic nonylphenol ethoxylate (NPE) surfactants. Four sequential batch reactors were fed with synthetic sewage, two of which received additionally NPE. Small subunit rDNA-derived denaturing gel gradient electrophoresis (DGGE) profiles and 16S rDNA clone libraries were dominated by clones of Gammaproteobacteria class. Sequences of the other codominant rDNA phylotypes observed only in DGGE from NPE-amended reactors were, respectively, associated with the Group III of the Acidobacteria phylum. Intriguingly, 16S rRNA content from abundant Gammaproteobacteria cells was unexpectedly low. In addition to Acidobacteria, rRNA-derived DGGE profiles were dominated by members of the order Burkholderiales (of the Betaproteobacteria) and of the genus Sphingomonas (a member of the Alphaproteobacteria). Specific oligonucleotide probes for the selected ribotypes were designed and applied for quantitative real time polymerase chain reaction and fluorescence in situ hybridization, confirming their dominance in treated reactors. The parallel abundance of unique phylotypes in replicate reactors implies a distinctive selection of dominant organisms, which are better adapted to specialized niches in the highly selective environment.

H2S degradation is reflected by both the activity and composition of the microbial community in a compost biofilter

In this study, 16S rRNA- and rDNA-based denaturing gradient gel electrophoresis (DGGE) were used to study the temporal and spatial evolution of the microbial communities in a compost biofilter removing H(2)S and in a control biofilter without H(2)S loading. During the first 81 days of the experiment, the H(2)S removal efficiencies always exceeded 93% at loading rates between 4.1 and 30 g m(-3) h(-1). Afterwards, the H(2)S removal efficiency decreased to values between 44 and 71%. RNA-based DGGE analysis showed that H(2)S loading to the biofilter increased the stability of the active microbial community but decreased the activity-based diversity and evenness. The most intense band in both the RNA- and DNA-based DGGE patterns of the H(2)S-degrading biofilter represented the sulfur oxidizing bacterium Thiobacillus thioparus. This suggested that T. thioparus constituted a major part of the bacterial community and was an important primary degrader in the H(2)S-degrading biofilter. The decreasing H(2)S removal efficiencies near the end of the experiment were not accompanied by a substantial change of the DGGE patterns. Therefore, the decreased H(2)S removal was probably not caused by a failing microbiology but rather by a decrease of the mass transfer of substrates after agglutination of the compost particles.

Selective phylogenetic analysis targeted at 16S rRNA genes of thermophiles and hyperthermophiles in deep-subsurface geothermal environments

Deep-subsurface samples obtained by deep drilling are likely to be contaminated with mesophilic microorganisms in the drilling fluid, and this could affect determination of the community structure of the geothermal microflora using 16S rRNA gene clone library analysis. To eliminate possible contamination by PCR-amplified 16S rRNA genes from mesophiles, a combined thermal denaturation and enzyme digestion method, based on a strong correlation between the G+C content of the 16S rRNA gene and the optimum growth temperatures of most known prokaryotic cultures, was used prior to clone library construction. To validate this technique, hot spring fluid (76 degrees C) and river water (14 degrees C) were used to mimic a deep-subsurface sample contaminated with drilling fluid. After DNA extraction and PCR amplification of the 16S rRNA genes from individual samples separately, the amplified products from river water were observed to be denatured at 82 degrees C and completely digested by exonuclease I (Exo I), while the amplified products from hot spring fluid remained intact after denaturation at 84 degrees C and enzyme digestion with Exo I. DNAs extracted from the two samples were mixed and used as a template for amplification of the 16S rRNA genes. The amplified rRNA genes were denatured at 84 degrees C and digested with Exo I before clone library construction. The results indicated that the 16S rRNA gene sequences from the river water were almost completely eliminated, whereas those from the hot spring fluid remained.

Microbial Succession in a Compost-packed Biofilter Treating Benzene-contaminated Air

Air artificially contaminated with increasing concentrations of benzene was treated in a laboratory scale compost-packed biofilter for 240 days with a removal efficiency of 81-100%. The bacterial community in the packing material (PM) at different heights of the biofilter was analysed every 60 days. Bacterial plate counts and ribosomal intergenic spacer analysis (RISA) of the isolated strains showed that the number of cultivable aerobic heterotrophic bacteria and the species diversity increased with benzene availability. Identification of the isolated species and the main bands in denaturing gradient gel electrophoresis (DGGE) profiles from total compost DNA during the treatment revealed that, at a relatively low volumetric benzene load (1.2< or =VBL< or =6.4 g m(-3) (PM) h(-1)), besides low G+C Gram positive bacteria, originally present in the packing compost, bacteroidetes and beta- and gamma-proteobacteria became detectable in the colonising population. At the VBL value (24.8 g m(-3) (PM) h(-1)) ensuring the maximum elimination capacity of the biofilter (20.1 g m(-3) (PM) h(-1)), strains affiliated to the genus Rhodococcus dominated the microflora, followed by beta-proteobacteria comprising the genera Bordetella and Neisseria. Under these conditions, more than 35% of the isolated strains were able to grow on benzene as the sole carbon source. Comparison of DGGE and automated RISA profiles of the total community and isolated strains showed that a complex bacterial succession occurred in the reactor in response to the increasing concentrations of the pollutant and that cultivable bacteria played a major role in benzene degradation under the adopted conditions.

Microbial communities in the garbage composting with rice hull as an amendment revealed by culture-dependent and -independent approaches

The diversity and succession of microbial communities during the garbage composting with rice hull as an amendment were studied by denaturing gradient gel electrophoresis (DGGE) and clone library analysis of PCR-amplified 16S ribosomal DNA (rDNA) with universal primers. Based on temperature changes, the composting process could be divided into thermophilic, cooling-down, and maturing stages. The DGGE profiles and clone library analysis revealed that the microbial community drastically changed during the composting process from the thermophilic to the maturing stages. The dominant bacterial group changed from the phylum Firmicutes in the thermophilic stage to the phylum Bacteroidetes in the maturing stage. This change in microbial communities may be significant for the composting process. The diversity of cultivated bacteria isolated from samples taken at various stages of the composting process was low. A total of 87 isolates were classified as belonging to only four different groups. These groups were also detected in the DGGE profiles and by the clone library analysis. Our study indicated that a combination of culture-dependent and -independent approaches could be very useful for monitoring both bacterial diversity and the succession of communities during the composting process. This study would be beneficial for assessing the ecological consequences of disposal of organic waste.

Community structure and diversity of biofilms from a beer bottling plant as revealed using 16S rRNA gene clone libraries

The microbial composition of biofilms from a beer bottling plant was analyzed by a cultivation independent analysis of the 16S rRNA genes. Clone libraries were differentiated by amplified 16S rRNA gene restriction analysis and representative clones from each group were sequenced. The diversity of the clone libraries was comparable with the diversity found for environmental samples. No evidences for the presence of strictly anaerobic taxa or important beer spoilers were found, indicating that biofilms developed for more than 6 months at the plant formed no appropriate habitat for those microorganisms. The genus Methylobacterium was one of the dominating groups of the clone libraries. The size of this population was assessed by fluorescence in situ hybridization and fatty acid analysis. In addition, considerable numbers of clones were assigned to uncultivated organisms.

Link between spatial structure of microbial communities and degradation of a complex mixture of volatile organic compounds in peat biofilters

AIMS

To investigate the relationships between the operation of the volatile organic compound (VOC) removal biofilter and the structure of microbial communities, and to study the impact on degradation activities and the structuring of microbial communities of biofilter malfunctions related to the qualitative composition of the polluted air.

METHODS AND RESULTS

A microbiological study and a measurement of biodegradation activities were simultaneously carried out on two identical peat-packed columns, seeded with two different inocula, treating polluted air containing 11 VOCs. For both reactors, the spatial structure of the microbial communities was investigated by means of single-strand conformation polymorphism (SSCP) analysis. For both reactors, stratification of degradation activities in function of depth was observed. Oxygenated compounds were removed at the top of the column and aromatics at the bottom. Comparison of SSCP patterns clearly showed a shift in community structure in function of depth inside both biofilters. This distribution of biodegradation activities correlates with the spatialization of microbial density and diversity. Although the operating conditions of both reactors were identical and the biodegradation activities similar, the composition of microflora differed for biofilters A and B. Subdivision of biofilter B into two independent parts supplied with polluted air containing the complex VOC mixture showed that the microflora having colonized the bottom of biofilter B retained their potential for degrading oxygenated compounds.

CONCLUSIONS

This work highlights the spatialization of biodegradation functions in a biofilter treating a complex mixture of VOCs. This distribution of biodegradation activities correlates with the spatialization of microbial density and diversity.

SIGNIFICANCE AND IMPACT OF THE STUDY

This vertical structure of microbial communities must be taken into consideration when dealing with the malfunctioning of bioreactors. These results are also useful information about changes in microbial communities following natural or anthropogenic alterations in different ecosystems (soils and sediments) where structuring of microbial communities according to depth has been observed.

Biofiltration of volatile organic compounds

The removal of volatile organic compounds (VOCs) from contaminated airstreams has become a major air pollution concern. Improvement of the biofiltration process commonly used for the removal of odorous compounds has led to a better control of key parameters, enabling the application of biofiltration to be extended also to the removal of VOCs. Moreover, biofiltration, which is based on the ability of micro-organisms to degrade a large variety of compounds, proves to be economical and environmentally viable. In a biofilter, the waste gas is forced to rise through a layer of packed porous material. Thus, pollutants contained in the gaseous effluent are oxidised or converted into biomass by the action of microorganisms previously fixed on the packing material. The biofiltration process is then based on two principal phenomena: (1) transfer of contaminants from the air to the water phase or support medium, (2) bioconversion of pollutants to biomass, metabolic end-products, or carbon dioxide and water. The diversity of biofiltration mechanisms and their interaction with the microflora mean that the biofilter is defined as a complex and structured ecosystem. As a result, in addition to operating conditions, research into the microbial ecology of biofilters is required in order better to optimise the management of such biological treatment systems.

Similarity of bacterial communities in sawdust- and straw-amended cow manure composts

We analyzed bacterial communities in two cow manure composts derived from the same feed manure and composted in the same location, but composted with different carbon amendments, and in peat-based potting mixes amended with these composts. Bacterial communities were characterized by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of extracted DNAs, and population fingerprints generated for each sample were compared. Sequence analyses of dominant DGGE bands revealed that members of the phylum Bacteroidetes were the most dominant bacteria detected in this study (19 of 31 clones). These analyses demonstrate that bacterial community profiles of individual composts were highly similar, as were profiles of compost-amended potting mixes. However, potting mix profiles differed substantially from the original compost profiles and from that of the peat base. These data indicate that highly similar bacterial populations were active in the two composts, and suggest that the effects of the initial carbon amendment on the mature compost bacterial communities were minor, while factors such as the feed manure and composting location may have been more influential.

N-acyl-l-homoserine lactones (AHLs) affect microbial community composition and function in activated sludge

The role of intercellular signalling in the regulation of genes and phenotypes in a broad range of bacterial species is now firmly established. In contrast, the impact of intercellular signalling on microbial community parameters, such as species diversity and function, is less well understood. In this study the role of N-acyl-l-homoserine lactones (AHLs) in microbial community dynamics in an industrial wastewater treatment system is addressed. Seven proteobacterial strains producing compounds with AHL-like activity were isolated from the treatment plant. Three of these belong to genera with no previously identified AHL producing species. Addition of AHLs at 2 micro M to sludge samples generated changes in both community function (phenol degradation) and composition as determined by length heterogeneity PCR and denaturing gradient gel electrophoresis. Phenol degradation was more stable as a result of the AHL augmentation. A dominant functional member of the Thauera genus was transiently supplanted by a member of the Comomonas genus in response to AHL addition. This suggests that AHLs can play a role in mediating microbial community parameters and has implications for ecosystem function and industrial wastewater treatment.

Microbial community and physicochemical analysis of an industrial waste gas biofilter and design of 16S rRNA-targeting oligonucleotide probes

A study was conducted to investigate the microbial community structure, the physicochemical properties, and the relationships between these parameters of a full-scale industrial biofilter used for waste gas abatement in an animal-rendering plant. Fluorescence in situ hybridization (FISH) was successfully combined with digital image analysis to study the composition of the microbial community. Several new nucleic acid probes were designed and established based on published 16S rDNA sequences and on ones retrieved from the biomass of the biofilter under investigation. Bacterial detection rates varied greatly over time and filterbed depth between 27.2% and 88.1% relative to DAPI counts. Overall, members of the Betaproteobacteria followed by Actinobacteria, Alphaproteobacteria, Cytophaga-Flavobacteria, Firmicutes and Gammaproteobacteria were the most abundant groups. Among the groups below phylum level, members of the Alcaligenes/Bordetella lineage were on average the most abundant group accounting for up to 8.5% of DAPI-stained cells. Whereas the community composition generally showed no vertical gradient, the lower 50 cm of the biofilter proved to be the most active part for the degradation of aldehydes such as 2- and 3-methylbutanal, 2-methylpropanal, and hexanal. This zone of the filterbed being operated in up-flow direction degraded about 80% of these compounds. Dimethyldisulphide was the most common reduced sulphur compound. Statistical analysis of microbial versus waste gas parameters generally revealed only weak or non-significant correlations between the two. Possible explanations for this finding are discussed.