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

Deodorizing bacterial consortium: community analysis of biofilms and leachate water collected from an air biofiltration system in a piggery

Intensive livestock production is a source of water, soil, and air contamination. The first aspect that negatively affects the quality of life of residents in the vicinity of piggeries is malodorous aerosols, which are not only responsible for discomfort but can be an etiological factor in the development of various diseases during prolonged exposure. One of the proven and efficient ways to counteract odor emissions is the usage of air biofiltration. The purpose of this study was to qualitatively analyze the bacterial community colonizing the biofilm of a biofilter operating at an industrial piggery in Switzerland. The study material consisted of biofilm and leachate water samples. The microbiological analysis consisted of DNA isolation, amplification of the bacterial 16S rRNA gene fragment (V3-V4), preparation of a library for high-throughput sequencing, high-throughput NGS sequencing, filtering of the obtained sequencing reads, and evaluation of the species composition in the studied samples. The investigation revealed the presence of the following bacterial genera: Pseudochelatococcus, Methyloversatilis, Flexilinea, Deviosia, Chryseobacterium, Kribbia, Leadbetterella, Corynebacterium, Flavobacterium, Xantobacter, Tessaracoccus, Staphylococcus, Thiobacillus, Enhydrobacter, Proteiniclasticum, and Giesbergeria. Analysis of the microbial composition of biofilters provides the opportunity to improve the biofiltration process.

Removal of cyclohexane gaseous emissions using a biotrickling filter system

The removal of cyclohexane from gaseous emissions was studied using a biotrickling filter packed with polyurethane foam. Acivodorax sp. CHX100 was chosen as inoculum due to its ability to use cyclohexane as carbon source. Performance was evaluated by means of different resident times from 18 s to 37 s and concentration levels of 60, 90, 120, 160, 320, 480 and 720 mg C m^-3, respectively. Removal efficiencies of 80%-99% and elimination capacities in the range of 5.4 g C m^-3 h^-1-38 g C m^-3 h^-1 were achieved for concentrations among 60 mg C m^-3-480 mg C m^-3. The removal efficiency decreased to 40% at concentrations of cyclohexane of 720 mg C m^-3. The dynamics of the microbial population showed the strain CHX100 as predominant during the different operational process of biotrickling filter. The results of this study propose a novel approach for cleaning waste air containing cyclohexane by means of a biotrickling filter.

Non-pathogenic Neisseria: members of an abundant, multi-habitat, diverse genus

The genus Neisseria contains the important pathogens Neisseria meningitidis and Neisseria gonorrhoeae. These Gram-negative coccoid bacteria are generally thought to be restricted to humans and inhabit mucosal surfaces in the upper respiratory and genito-urinary tracts. While the meningococcus and gonococcus have been widely studied, far less attention has been paid to other Neisseria species. Here we review current knowledge of the distribution of commensal Neisseria in humans and other hosts. Analysis of the microbiome has revealed that Neisseria is an abundant member of the oropharyngeal flora, and we review its potential impact on health and disease. Neisseria also exhibit remarkable diversity, exhibiting both coccoid and rod-shaped morphologies, as well as environmental strains which are capable of degrading complex organic molecules.

Research into acetone removal from air by biofiltration using a biofilter with straight structure plates

The biological air treatment method is based on the biological destruction of organic compounds using certain cultures of microorganisms. This method is simple and may be applied in many branches of industry. The main element of biological air treatment devices is a filter charge. Tests were carried out using a new-generation laboratory air purifier with a plate structure. This purifier is called biofilter. The biofilter has a special system for packing material humidification which does not require additional energy inputs. In order to extend the packing material's durability, it was composed of thermally treated birch fibre. Pollutant (acetone) biodegradation occurred on thermally treated wood fibre in this research. According to the performed tests and the received results, the process of biodestruction was highly efficient. When acetone was passed through biofilter's packing material at 0.08 m s-1 rate, the efficiency of the biofiltration process was from 70% up to 90%. The species of bacteria capable of removing acetone vapour from the air, i.e. Bacillus (B. cereus, B. subtilis), Pseudomonas (P. aeruginosa, P. putida), Stapylococcus (S. aureus) and Rhodococcus sp., was identified in this study during the process of biofiltration. Their amount in the biological packing material changed from 1.6 × 107 to 3.7 × 1011 CFU g-1.

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.

A comparative study of two composts as filter media for the removal of gaseous reduced sulfur compounds (RSCs) by biofiltration: application at industrial scale

This work presents the use of two composts as filter media for the treatment by biofiltration of odors emitted during the aerobic composting of a mixture containing sewage sludge and yard waste. The chemical analysis of the waste gas showed that the malodorous compounds at trace level were the reduced sulfur compounds (RSCs) which were dimethyl sulfide (Me(2)S), methanethiol (MeSH) and hydrogen sulfide (H(2)S). Laboratory tests for biofiltration treatment of RSCs were performed in order to compare the properties of two filter media, consisted of a mature compost with yard waste (YW) and a mixture of mature compost with sewage sludge and yard waste (SS/YW). The maximum elimination capacity (EC) values obtained with the YW mature compost as packing material were 12.5 mg m(-3)h(-1) for H(2)S, 7.9 mg m(-3)h(-1) for MeSH and 34 mg m(-3)h(-1) for Me(2)S, and the removal efficiency decreased in the order of: H(2)S>MeSH>Me(2)S. Moreover, the YW compost filter medium had a better behavior than the filter medium based on SS/YW in terms of acclimation of the microbial communities and moisture content. According to these results, a YW mature compost as packing material for an industrial biofilter were designed and this industrial biofilter was found effective under specified conditions (without inoculation and addition of water). The results showed that the maximum EC value of RSCs was 935 mg m(-3)h(-1) (100% removal efficiency, RE) for an inlet loads (IL) between 0 and 1000 mg m(-3)h(-1). Thus, YW compost medium was proven efficient for biofiltration of RSCs both at laboratory and industrial scale.

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.

Bacterial dynamics in steady-state biofilters: beyond functional stability

The spatial and temporal dynamics of microbial community structure and function were surveyed in duplicated woodchip-biofilters operated under constant conditions for 231 days. The contaminated gaseous stream for treatment was representative of composting emissions, included ammonia, dimethyl disulfide and a mixture of five oxygenated volatile organic compounds. The community structure and diversity were investigated by denaturing gradient gel electrophoresis on 16S rRNA gene fragments. During the first 42 days, microbial acclimatization revealed the influence of operating conditions and contaminant loading on the biofiltration community structure and diversity, as well as the limited impact of inoculum compared to the greater persistence of the endogenous woodchip community. During long-term operation, a high and stable removal efficiency was maintained despite a highly dynamic microbial community, suggesting the probable functional redundancy of the community. Most of the contaminant removal occurred in the first compartment, near the gas inlet, where the microbial diversity was the highest. The stratification of the microbial structures along the filter bed was statistically correlated to the longitudinal distribution of environmental conditions (selective pressure imposed by contaminant concentrations) and function (contaminant elimination capacity), highlighting the central role of the bacterial community. The reproducibility of microbial succession in replicates suggests that the community changes were presumably driven by a deterministic process.

Ethylene removal evaluation and bacterial community analysis of vermicompost as biofilter material

Biofiltration of ethylene provides an environmentally friendly and economically beneficial option relative to physical/chemical removal, where selection of appropriate bed material is crucial. Here the vermicompost with indigenous microorganisms as bed material was evaluated for ethylene removal through batch test and biofilter experiment. Temporal and spatial dynamics of bacterial community in the vermicompost-biofilter under different ethylene loads were characterized by culture and denaturing gradient gel electrophoresis (DGGE) methods. The results showed that ethylene was effectively degraded by the vermicompost under conditions of 25-50% moisture content and 25-35°C temperature. The vermicompost-biofilter achieved nearly 100% ethylene removal up to an inlet load of 11mg m(-3)h(-1). Local nitrogen lack of the vermicompost in the biofilter was observed over operation time, but the change of pH was slight. DGGE analysis demonstrated that the bacterial abundance and community structure of vermicompost-biofilter varied with the height of biofilter under different ethylene loads. Pseudomonads and Actinobacteria were predominant in the biofilter throughout the whole experiment.

Integrating microbial ecology in bioprocess understanding: the case of gas biofiltration

Biofilters are packed-bed bioreactors where contaminants, once transferred from the gas phase to the biofilm, are oxidized by diverse and complex communities of attached microorganisms. Over the last decade, more and more studies aimed at opening the back box of biofiltration by unraveling the biodiversity-ecosystem function relationship. In this review, we report the insights provided by the microbial ecology approach in biofilters and we emphasize the parallels existing with other engineered ecosystems used for wastewater treatment, as they all constitute relevant model ecosystems to explore ecological issues. We considered three characteristic ecological indicators: the density, the diversity, and the structure of the microbial community. Special attention was paid to the temporal and spatial dynamics of each indicator, insofar as it can disclose the potential relationship, or absence of relation, with any operating or functional parameter. We also focused on the impact of disturbance regime on the microbial community structure, in terms of resistance, resilience, and memory. This literature review led to mitigated conclusions in terms of biodiversity-ecosystem function relationship. Depending on the environmental system itself and the way it is investigated, the spatial and temporal dynamics of the microbial community can be either correlated (e.g., spatial stratification) or uncoupled (e.g., temporal instability) to the ecosystem function. This lack of generality shows the limits of current 16S approach in complex ecosystems, where a functional approach may be more suitable.

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.

Preliminary acclimation strategies for successful startup in conventional biofilters

The question of how to obtain the best inocula for conventional biofilters arises when an acclimation/adaptation procedure is to be applied. Bearing in mind that no standardized procedure for acclimating inocula exists, certain preliminary strategies for obtaining an active inoculum from wastewater treatment sludge are proposed in this work. Toluene was the contaminant to be degraded. Concerning the prior separation of sludge phases, no obvious advantage was found in separating the supernatant phase of the sludge before acclimation. As far as a continuous or discontinuous acclimation mode is concerned, the latter is recommended for rapidly obtaining acclimated sludge samples by operating the system for no longer than 1 month. The continuous mode rendered similar degradation rates, although it required longer operating time. Nevertheless, the great advantage of the continuous system lay in the absence of daily maintenance and the ready availability of the activated sample.

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.

Relationships between biomass, pressure drop, and performance in a polyurethane biofilter

In biofilters for controlling volatile organic compounds (VOCs), clogging in the filter bed due to overgrowth of biomass causes the deterioration of biofilter performance. In this study, the relationships between biofilter performance, biomass concentration (X), and pressure drop (DeltaP) was qualitatively and quantitatively evaluated in a polyurethane (PU) biofilter. Benzene was used as a model VOC. The relationship between DeltaP and X at a moisture content of 80-90% was expressed as log DeltaP (mm H(2)Om(-1))=0.315+3.87 log X (g-dry cell weight (DCW) g-PU(-1)), 0.8<X<2.5. Maximum removal rate (V(m)) for benzene declined with increasing biomass concentration at more than 0.8 g-DCW g-PU(-1), and the following equation was obtained: V(m) (gm(-3)h(-1))=811-261 X (g-DCW g-PU(-1)), 0.8<X<2.5. The quantitative relationships obtained in this study can be applied to assess and optimize PU biofilter performance for long-term operation.

Methanol removal efficiency and bacterial diversity of an activated carbon biofilter

Motivated by the need to establish an economical and environmentally friendly methanol control technology for the pulp and paper industry, a bench-scale activated carbon biofiltration system was developed. This system was evaluated for its performance in removing methanol from an artificially contaminated air stream and characterized for its bacterial diversity over time, under varied methanol loading rates, and in different spatial regions of the filter. The biofilter system, composed of a novel packing mixture, provided an excellent support for growth and activity of methanol-degrading bacteria, resulting in approximately 100% methanol removal efficiency for loading rates of 1-17 g/m(3) packing/h, when operated both with and without inoculum containing enriched methanol-degrading bacteria. Although bacterial diversity and abundance varied over the length of the biofilter, the populations present rapidly formed a stable community that was maintained over the entire 138-day operation of the system and through variable operating conditions, as observed by PCR-DGGE methods that targeted all bacteria as well as specific methanol-oxidizing microorganisms. Phylogenetic analysis of bands excised and sequenced from DGGE gels indicated that the biofilter system supported a diverse community of methanol-degrading bacteria, with high similarity to species in the genera Methylophilus (beta-proteobacteria), Hyphomicrobium and Methylocella (both alpha-proteobacteria).

How to get more out of molecular fingerprints: practical tools for microbial ecology

Community-level molecular techniques are widely used in comparative microbial ecology to assess the diversity of microbial communities and their response to changing environments. These include among others denaturing and temperature gradient gel electrophoresis (DGGE/TGGE), single-strand conformation polymorphism (SSCP), length heterogeneity-PCR (LH-PCR), terminal-restriction fragment length polymorphism (tRFLP) and 16S rRNA gene clone libraries. The amount of data derived from these techniques available in literature is continuously increasing and the lack of a universal way to interpret the raw fingerprint itself makes it difficult to compare between different results. Taking the DGGE technique as an example, we propose a setting-independent theoretical interpretation of the DGGE pattern, based on a straightforward processing on three levels of analysis: (i) the range-weighted richness (Rr) reflecting the carrying capacity of the system, (ii) the dynamics (Dy) reflecting the specific rate of species coming to significance, and (iii) functional organization (Fo), defined through a relation between the structure of a microbial community and its functionality. These Rr, Dy and Fo values, each representing a score to describe a microbial community, can be plotted in a 3D graph. The latter represents a visual ecological interpretation of the initial raw fingerprinting pattern.