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

Purposely Development of the Adaptive Potential of Activated Sludge from Municipal Wastewater Treatment Plant Focused on the Treatment of Landfill Leachate

Biological treatment is a key technology in landfill leachate treatment However, often its efficiency is not high enough due to the pollutants in concentrations above the critical ones. The present study aimed to investigate the adaptive responses that occur in activated sludge (AS) during landfill leachate purification. A model process with AS from a municipal wastewater treatment plant and landfill leachate in increasing concentrations was constructed. The data showed that when dilutions 25 and 50 times had been applied the structure of the AS was preserved, but the COD cannot be reduced below 209 mg O2/L. The feed of undiluted leachate destroyed the AS structure as SVI was reduced to 1 mL/g, biotic index to 1, floc size was greatly reduced and COD remained high (2526 mg O2/L). The dominant group of protozoa was changed from attached to free-swimming ciliates. An increase of the bacterial groups responsible for the xenobiotics elimination (aerobic heterotrophs, genera Pseudomonas, Acinetobacter, Azoarcus, Thauera, Alcaligenes) was registered. This was accompanied by a significant increase in free bacteria. The obtained data showed that for optimal treatment of this type of water it is necessary to include a combination of biological treatment with another non-biological method (membrane filtration, reverse osmosis, etc.).

Microbial diversity of garden snail mucus

The search for new natural compounds for application in medicine and cosmetics is a trend in biotechnology. One of the sources of such active compounds is the snail mucus. Snail physiology and the biological activity of their fluids (especially the mucus) are still poorly studied. Only a few previous studies explored the relationship between snails and their microbiome. The present study was focused on the biodiversity of the snail mucus used in the creation of cosmetic products, therapeutics, and nutraceuticals. The commonly used cultivation techniques were applied for the determination of the number of major bacterial groups. Fluorescence in situ hybridization for key taxa was performed. The obtained images were subjected to digital image analysis. Sequencing of the 16S rRNA gene was also done. The results showed that the mucus harbors a rich bacterial community (10.78 × 1010  CFU/ml). Among the dominant bacteria, some are known for their ability to metabolize complex polysaccharides or are usually found in soil and plants (Rhizobiaceae, Shewanella, Pedobacter, Acinetobacter, Alcaligenes). The obtained data demonstrated that the snail mucus creates a unique environment for the development of the microbial community that differs from other parts of the animal and which resulted from the combined contribution of the microbiomes derived from the soil, plants, and the snails.

Classical Microbiological Diagnostics of Bacteremia: Are the Negative Results Really Negative? What is the Laboratory Result Telling Us About the "Gold Standard"?

Standard blood cultures require at least 24–120 h to be reported as preliminary positive. The objective of this study was to compare the reliability of Gram staining and fluorescent in-situ hybridization (FISH) for detecting bacteria in otherwise negative blood culture bottles. Ninety-six sets were taken from patients with a diagnosis of sepsis. Six incomplete blood culture sets and eight blood cultures sets demonstrating positive growth were excluded. We performed Gram stain and FISH on 82 sets taken from post-operative septic patients: 82 negative aerobic blood cultures, 82 anaerobic blood cultures, and 82 blood samples, as well as 57 blood samples taken from healthy volunteers. From the eighty-two blood sets analyzed from the septic patients, Gram stain visualized bacteria in 62.2% of blood samples, 35.4% of the negative aerobic bottles, and in 31.7% of the negative anaerobic bottles. Utilizing FISH, we detected bacteria in 75.6%, 56.1%, and 64.6% respectively. Among the blood samples from healthy volunteers, FISH detected bacteria in 64.9%, while Gram stain detected bacteria in only 38.6%. The time needed to obtain the study results using Gram stain was 1 h, for FISH 4 h, and for the culture method, considering the duration of growth, 5 days. Gram stain and FISH allow quick detection of bacteria in the blood taken directly from a patient. Finding phagocytosed bacteria, which were also detected among healthy individuals, confirms the hypothesis that blood microbiome exists.

Comparison of PCR, Fluorescent in Situ Hybridization and Blood Cultures for Detection of Bacteremia in Children and Adolescents During Antibiotic Therapy

The gold standard in microbiological diagnostics of bacteremia is a blood culture in automated systems. This method may take several days and has low sensitivity. New screening methods that could quickly reveal the presence of bacteria would be extremely useful. The objective of this study was to estimate the effectiveness of these methods with respect to blood cultures in the context of antibiotic therapy. Blood samples from 92 children with sepsis were analyzed. Blood cultures were carried out in standard automated systems. Subsequently, FISH (Fluorescent In-Situ Hybridization) and nested multiplex-real-time-PCR (PCR) were performed. Blood cultures, FISH and PCR yielded positive results in 18%, 39.1%, and 71.7% of samples, respectively. Significant differences were found between the results obtained through culture before and after induction of antibiotherapy: 25.5% vs. 9.7%. There was no significant difference in FISH and PCR results in relation to antibiotics. The three methods employed demonstrated significant differences in detecting bacteria effectively. Time to obtain test results for FISH and PCR averaged 4–5 hours. FISH and PCR allow to detect bacteria in blood without prior culture. These methods had high sensitivity for the detection of bacteremia regardless of antibiotherapy. They provide more timely results as compared to automated blood culture, and may be useful as rapid screening tests in sepsis.

Bacterial communities associated with the ectoparasitic mites Varroa destructor and Tropilaelaps mercedesae of the honey bee (Apis mellifera)

Varroa and Tropilaelaps mites have been reported as serious ectoparasites of the honey bee (Apis mellifera). In this study, bacterial communities associated with Varroa destructor and Tropilaelaps mercedesae from northern Thailand were determined, using both culture-dependent and culture-independent approaches. Adult female mites were collected from apiaries in Chiang Mai and Lampang provinces. Culturable bacteria were isolated from individual mites. On average, we observed approximately 1340 and 1140 CFU/mite in Varroa and Tropilaelaps, respectively. All isolates were assigned to the genus Enterococcus. Six samples of genomic DNA from 30-50 mites were extracted and subjected to pyrosequencing of bacterial 16S rRNA amplicons. The resulting 81 717 sequences obtained from Varroa were grouped into 429 operational taxonomic units. The most abundant bacteria in Varroa mites belonged to the family Enterobacteriaceae, especially the genera Arsenophonus, Enterobacter and Proteus. For Tropilaelaps mites, 84 075 sequences were obtained and clustered into 166 operational taxonomic units, within which the family Enterococcaceae (particularly the genus Enterococcus) was predominant. Localization of bacteria in the mites using fluorescence in situ hybridization with two universal bacterial probes revealed that these bacteria were in the cecum of the mites. Taxon-specific Enterobacteriaceae and Arsenophonus probes also confirmed their localization in the cecum of Varroa.

Evaluation of the distribution of fecal indicator bacteria in a river system depending on different types of land use in the southern watershed of the Baltic Sea

The aim of the study was to determine the effects of land use management on changes in the fecal contamination of water in the Łyna River, one of the main lowland watercourses in the southern watershed of the Baltic Sea (northern Poland). A total of 120 water samples were collected in different seasons of 2011 and 2012 at 15 sites where the river intersected forest (FA), agricultural (AA), and urbanized (UA) areas. Fecal indicator bacteria (FIB), the counts of Enterobacteriaceae and Escherichia coli, total bacterial counts (TBCs), and domain Bacteria (EUB338) were determined by culture-dependent and culture-independent methods. Temperature, pH, chemical oxygen demand, dissolved oxygen, total dissolved solids, ammonia nitrogen, nitrite nitrogen, nitrate nitrogen, orthophosphate, and total phosphorus were also determined. The lowest bacterial counts were noted in water samples collected in FA, and the highest in samples collected in UA. Statistically significant differences were determined between bacterial populations across the analyzed land use types and in different sampling seasons. Significant correlations were also observed between the populations of FIB and physicochemical parameters. The results indicate that land use type influenced FIB concentrations in river water. The combined use of conventional and molecular methods improves the accuracy of fecal contamination analyses in river ecosystems.

Analysis of Bacterial Communities during Clostridium difficile Infection in the Mouse

Clostridium difficile infection (CDI) is a major cause of health care-associated disease. CDI initiates with ingestion of C. difficile spores, germination in the gastrointestinal (GI) tract, and then colonization of the large intestine. The interactions between C. difficile cells and other bacteria and with host mucosa during CDI remain poorly understood. Here, we addressed the hypothesis that, in a mouse model of CDI, C. difficile resides in multicellular communities (biofilms) in association with host mucosa. To do this, we paraffin embedded and then sectioned the GI tracts of infected mice at various days postinfection (p.i.). We then used fluorescent in situ hybridization (FISH) with 16S rRNA probes targeting most bacteria as well as C. difficile specifically. The results revealed that C. difficile is present as a minority member of communities in the outer (loose) mucus layer, in the cecum and colon, starting at day 1 p.i. To generate FISH probes that identify bacteria within mucus-associated communities harboring C. difficile, we characterized bacterial populations in the infected mouse GI tract using 16S rRNA gene sequence analysis of bacterial DNA prepared from intestinal content. This analysis revealed the presence of genera of several families belonging to Bacteroidetes and Firmicutes. These data suggest that formation of multispecies communities associated with the mucus of the cecum and colon is an important early step in GI tract colonization. They raise the possibility that other bacterial species in these communities modulate the ability of C. difficile to successfully colonize and, thereby, cause disease.

Functionally redundant but dissimilar microbial communities within biogas reactors treating maize silage in co-fermentation with sugar beet silage

Numerous observations indicate a high flexibility of microbial communities in different biogas reactors during anaerobic digestion. Here, we describe the functional redundancy and structural changes of involved microbial communities in four lab-scale continuously stirred tank reactors (CSTRs, 39°C, 12 L volume) supplied with different mixtures of maize silage (MS) and sugar beet silage (SBS) over 80 days. Continuously stirred tank reactors were fed with mixtures of MS and SBS in volatile solid ratios of 1:0 (Continuous Fermenter (CF) 1), 6:1 (CF2), 3:1 (CF3), 1:3 (CF4) with equal organic loading rates (OLR 1.25 kgVS m(-3)  d(-1) ) and showed similar biogas production rates in all reactors. The compositions of bacterial and archaeal communities were analysed by 454 amplicon sequencing approach based on 16S rRNA genes. Both bacterial and archaeal communities shifted with increasing amounts of SBS. Especially pronounced were changes in the archaeal composition towards Methanosarcina with increasing proportion of SBS, while Methanosaeta declined simultaneously. Compositional shifts within the microbial communities did not influence the respective biogas production rates indicating that these communities adapted to environmental conditions induced by different feedstock mixtures. The diverse microbial communities optimized their metabolism in a way that ensured efficient biogas production.

Seasonal variation of bacterial communities in shellfish harvesting waters: preliminary study before applying phage therapy

The recurrent emergence of infections outbreaks associated with shellfish consumption is an important health problem, which results in substantial economic losses to the seafood industry. Even after depuration, shellfish is still involved in outbreaks caused by pathogenic bacteria, which increases the demand for new efficient strategies to control the shellfish infection transmission. Phage therapy during the shellfish depuration is a promising approach, but its success depends on a detailed understanding of the dynamics of bacterial communities in the harvesting waters. This study intends to evaluate the seasonal dynamics of the overall bacterial communities, disease-causing bacterial populations and bacterial sanitary quality indicators in two authorized harvesting-zones at Ria de Aveiro. During the hot season, the total bacterial community presented high complexity and new prevalent populations of the main shellfish pathogenic bacteria emerged. These results indicate that the spring/summer season is a critical period during which phage therapy should be applied.

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.

Comparison of nested, multiplex, qPCR; FISH; SeptiFast and blood culture methods in detection and identification of bacteria and fungi in blood of patients with sepsis

Background

Microbiological diagnosis of sepsis relies primarily on blood culture data. This study compares four diagnostic methods, i.e. those developed by us: nested, multiplex, qPCR (qPCR) and FISH with commercial methods: SeptiFast (Roche) (SF) and BacT/ALERT® 3D blood culture system (bioMérieux). Blood samples were derived from adult patients with clinical symptoms of sepsis, according to SIRS criteria, hospitalized in the Intensive Care Unit.

Results

Using qPCR, FISH, SF, and culture, microbial presence was found in 71.8%, 29.6%, 25.3%, and 36.6% of samples, respectively. It was demonstrated that qPCR was significantly more likely to detect microorganisms than the remaining methods; qPCR confirmed the results obtained with the SF kit in all cases wherein bacteria were detected with simultaneous confirmation of Gram-typing. All data collected through the FISH method were corroborated by qPCR.

Conclusions

The qPCR and FISH methods described in this study may constitute alternatives to blood culture and to the few existing commercial molecular assays since they enable the detection of the majority of microbial species, and the qPCR method allows their identification in a higher number of samples than the SF test. FISH made it possible to show the presence of microbes in a blood sample even before its culture.

Potentialities of coupling biological processes (biotrickler/biofilter) for the degradation of a mixture of sulphur compounds

This study deals with the potential of biological processes combining a biotrickler and a biofilter to treat a mixture of sulphur-reduced compounds including dimethyl sulphide (DMS), dimethyl disulphide (DMDS) and hydrogen sulphide (H2S). As a reference, duplicated biofilters were implemented, and operating conditions were similar for all bioprocesses. The first step of this work was to determine the efficiency removal level achieved for each compound of the mixture and in a second step, to assess the longitudinal distribution of biodegradation activities and evaluate the total bacteria, Hyphomicrobium sp. and Thiobacillus thioparus densities along the bed height. A complete removal of hydrogen sulphide is reached at the start of the experiment within the first stage (biotrickler) of the coupling. This study highlighted that the coupling of a biotrickling filter and a biofilter is an interesting way to improve both removal efficiency levels (15-20% more) and kinetics of recalcitrant sulphur compounds such as DMS and DMDS. The total cell densities remained similar (around 1 × 10(10) 16S recombinant DNA (rDNA) copies g dry packing material) for duplicated biofilters and the biofilter below the biotrickling filter. The relative abundances of Hyphomicrobium sp. and T. thioparus have been estimated to an average of 10 ± 7.0 and 0.23 ± 0.07%, respectively, for all biofilters. Further investigation should allow achieving complete removal of DMS by starting the organic sulphur compound degradation within the first stage and surveying microbial community structure colonizing this complex system.

Key design factors affecting microbial community composition and pathogenic organism removal in horizontal subsurface flow constructed wetlands

Constructed wetlands constitute an interesting option for wastewater reuse since high concentrations of contaminants and pathogenic microorganisms can be removed with these natural treatment systems. In this work, the role of key design factors which could affect microbial removal and wetland performance, such as granular media, water depth and season effect was evaluated in a pilot system consisting of eight parallel horizontal subsurface flow (HSSF) constructed wetlands treating urban wastewater from Les Franqueses del Vallès (Barcelona, Spain). Gravel biofilm as well as influent and effluent water samples of these systems were taken in order to detect the presence of bacterial indicators such as total coliforms (TC), Escherichia coli, fecal enterococci (FE), Clostridium perfringens, and other microbial groups such as Pseudomonas and Aeromonas. The overall microbial inactivation ratio ranged between 1.4 and 2.9 log-units for heterotrophic plate counts (HPC), from 1.2 to 2.2 log units for total coliforms (TC) and from 1.4 to 2.3 log units for E. coli. The presence of fine granulometry strongly influenced the removal of all the bacterial groups analyzed. This effect was significant for TC (p=0.009), E. coli (p=0.004), and FE (p=0.012). Shallow HSSF constructed wetlands were more effective for removing Clostridium spores (p=0.039), and were also more efficient for removing TC (p=0.011) and E. coli (p=0.013) when fine granulometry was used. On the other hand, changes in the total bacterial community from gravel biofilm were examined by using denaturing gradient gel electrophoresis (DGGE) and sequencing of polymerase chain reaction (PCR)-amplified fragments of the 16S rRNA gene recovered from DGGE bands. Cluster analysis of the DGGE banding pattern from the different wetlands showed that microbial assemblages separated according to water depth, and sequences of different phylogenetic groups, such as Alpha, Beta and Delta-Proteobacteria, Nitrospirae, Bacteroidetes, Acidobacteria, Firmicutes, Synergistetes and Deferribacteres could be retrieved from DGGE bands.

Spatial variation in the bacterial and denitrifying bacterial community in a biofilter treating subsurface agricultural drainage

Denitrifying biofilters can remove agricultural nitrates from subsurface drainage, reducing nitrate pollution that contributes to coastal hypoxic zones. The performance and reliability of natural and engineered systems dependent upon microbially mediated processes, such as the denitrifying biofilters, can be affected by the spatial structure of their microbial communities. Furthermore, our understanding of the relationship between microbial community composition and function is influenced by the spatial distribution of samples.In this study we characterized the spatial structure of bacterial communities in a denitrifying biofilter in central Illinois. Bacterial communities were assessed using automated ribosomal intergenic spacer analysis for bacteria and terminal restriction fragment length polymorphism of nosZ for denitrifying bacteria.Non-metric multidimensional scaling and analysis of similarity (ANOSIM) analyses indicated that bacteria showed statistically significant spatial structure by depth and transect,while denitrifying bacteria did not exhibit significant spatial structure. For determination of spatial patterns, we developed a package of automated functions for the R statistical environment that allows directional analysis of microbial community composition data using either ANOSIM or Mantel statistics.Applying this package to the biofilter data, the flow path correlation range for the bacterial community was 6.4 m at the shallower, periodically in undated depth and 10.7 m at the deeper, continually submerged depth. These spatial structures suggest a strong influence of hydrology on the microbial community composition in these denitrifying biofilters. Understanding such spatial structure can also guide optimal sample collection strategies for microbial community analyses.

The Gut Microbiotassay: a high-throughput qPCR approach combinable with next generation sequencing to study gut microbial diversity

Background

The intestinal microbiota is a complex and diverse ecosystem that plays a significant role in maintaining the health and well-being of the mammalian host. During the last decade focus has increased on the importance of intestinal bacteria. Several molecular methods can be applied to describe the composition of the microbiota. This study used a new approach, the Gut Microbiotassay: an assembly of 24 primer sets targeting the main phyla and taxonomically related subgroups of the intestinal microbiota, to be used with the high-throughput qPCR chip ‘Access Array 48.48′, AA48.48, (Fluidigm®) followed by next generation sequencing. Primers were designed if necessary and all primer sets were screened against DNA extracted from pure cultures of 15 representative bacterial species. Subsequently the setup was tested on DNA extracted from small and large intestinal content from piglets with and without diarrhoea. The PCR amplicons from the 2304 reaction chambers were harvested from the AA48.48, purified, and sequenced using 454-technology.

Results

The Gut Microbiotassay was able to detect significant differences in the quantity and composition of the microbiota according to gut sections and diarrhoeic status. 454-sequencing confirmed the specificity of the primer sets. Diarrhoea was associated with a reduced number of members from the genus Streptococcus, and in particular S. alactolyticus.

Conclusion

The Gut Microbiotassay provides fast and affordable high-throughput quantification of the bacterial composition in many samples and enables further descriptive taxonomic information if combined with 454-sequencing.

Relative effect of bioaugmentation with electrochemically active and non-active bacteria on bioelectrogenesis in microbial fuel cell

Bioelectrogenic activity of microbial fuel cells (MFC) augmented with electrochemically active bacteria (EAB, Pseudomonas aeruginosa) and non-EAB (Escherichia coli) as biocatalysts was investigated. Anodic microflora augmented with P. aeruginosa (AMFCP) yielded higher electrogenic activity (418 mV; 3.87 mA) than E. coli (AMFCE; 254 mV; 1.67 mA) and non-augmented native microflora (MFCC; 235 mV; 1.37 mA). Higher redox currents along with lower Tafel-slopes were observed with AMFCP operation compared to AMFCE and MFCC due to manifestation of bioaugmentation thereby minimizing the losses. A fourfold and twofold increase in capacitance and exchange current was observed with AMFCP and AMFCE operation respectively, when compared to MFCC. Tracking of augmented biocatalyst by fluorescent in situ hybridization (FISH) with defined probes documented the survivability of Pseudomonas sp. in higher numbers than Enterobacteriaceae. Study corroborated enhanced electron transfer capability of mixed consortia owing to the synergistic interaction with EAB due to augmentation.

Microbial community analysis in biotrickling filters treating isopropanol air emissions

The evolution of the microbial community was analysed over one year in two biotrickling filters operating under intermittent feeding conditions and treating isopropanol emissions, a pollutant typically found in the flexography sector. Each reactor was packed with one media: plastic cross-flow-structured material or polypropylene rings. The communities were monitored by fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA region. After inoculation with activated sludge, the biotrickling filters were operated using inlet loads (ILs) from 20 to 65 g C m(-3) h(-1) and empty-bed residence times (EBRTs) from 14 to 160 s. Removal efficiencies higher than 80% were obtained with ILs up to 35 g C m(-3) h(-1) working at EBRTs as low as 24 s. There was an increase in the total percentage of the target domains of up to around 80% at the end of the experiment. Specifically, the Gammaproteobacteria domain group, which includes the well-known volatile organic compound (VOC)-degrading species such as Pseudomonas putida, showed a noticeable rise in the two biotrickling filters of 26% and 27%, respectively. DGGE pattern band analysis revealed a stable band of Pseudomonas putida in all the samples monitored, even in the lower diversity communities. In addition, at similar operational conditions, the biotrickling filter with a greater relative abundance of Pseudomonas sp. (19.2% vs. 8%) showed higher removal efficiency (90% vs. 79%). Results indicate the importance of undertaking a further in-depth study of the involved species in the biofiltration process and their specific function.

Culture-independent investigation of the microbiome associated with the nematode Acrobeloides maximus

Background

Symbioses between metazoans and microbes are widespread and vital to many ecosystems. Recent work with several nematode species has suggested that strong associations with microbial symbionts may also be common among members of this phylu. In this work we explore possible symbiosis between bacteria and the free living soil bacteriovorous nematode Acrobeloides maximus.

Methodology

We used a soil microcosm approach to expose A. maximus populations grown monoxenically on RFP labeled Escherichia coli in a soil slurry. Worms were recovered by density gradient separation and examined using both culture-independent and isolation methods. A 16S rRNA gene survey of the worm-associated bacteria was compared to the soil and to a similar analysis using Caenorhabditis elegans N2. Recovered A. maximus populations were maintained on cholesterol agar and sampled to examine the population dynamics of the microbiome.

Results

A consistent core microbiome was extracted from A. maximus that differed from those in the bulk soil or the C. elegans associated set. Three genera, Ochrobactrum, Pedobacter, and Chitinophaga, were identified at high levels only in the A. maximus populations, which were less diverse than the assemblage associated with C. elegans. Putative symbiont populations were maintained for at least 4 months post inoculation, although the levels decreased as the culture aged. Fluorescence in situ hybridization (FISH) using probes specific for Ochrobactrum and Pedobacter stained bacterial cells in formaldehyde fixed nematode guts.

Conclusions

Three microorganisms were repeatedly observed in association with Acrobeloides maximus when recovered from soil microcosms. We isolated several Ochrobactrum sp. and Pedobacter sp., and demonstrated that they inhabit the nematode gut by FISH. Although their role in A. maximus is not resolved, we propose possible mutualistic roles for these bacteria in protection of the host against pathogens and facilitating enzymatic digestion of other ingested bacteria.

Mass effects meet species sorting: transformations of microbial assemblages in epiphreatic subsurface karst water pools

We investigated the transformations of the microbial communities in epiphreatic karst cave pools with different flooding frequencies. Fingerprinting of 16S rRNA genes was combined with microscopic and sequence analysis to examine if source water would transport comparable microbial inocula into the pools at consecutive flood events, and to assess possible effects of residence time on the microbial assemblages during stagnant periods. Variability in the concentrations of dissolved organic carbon and conductivity indicated differences between floods and changes of pool water over time. High numbers of Betaproteobacteria affiliated with Methylophilaceae and Comamonadaceae were introduced into the pools during floodings. While the former persisted in the pools, the latter exhibited considerable microdiversification. These Betaproteobacteria might thus represent core microbial groups in karst water. A decrease in the estimated total diversity of the remaining bacterial taxa was apparent after a few weeks of residence: Some were favoured by stagnant conditions, whereas the majority was rapidly outcompeted. Thus, the microbial communities consisted of different components governed by complementary assembly mechanisms (dispersal versus environmental filtering) upon introduction into the pools. High overlap of temporary and persistent community members between samplings from two winters, moreover, reflected the seasonal recurrence of the studied microbial assemblages.

Optimization of biohydrogen and methane recovery within a cassava ethanol wastewater/waste integrated management system

Thermophilic co-fermentation of cassava stillage (CS) and cassava excess sludge (CES) were investigated for hydrogen and methane production. The highest hydrogen yield (37.1 ml/g-total-VS added) was obtained at VS(CS)/VS(CES) of 7:1, 17% higher than that with CS digestion alone. The CES recycle enhanced the substrate utilization and improved the buffer capacity. Further increase the CES fraction led to changed VFA distribution and more hydrogen consumption. FISH analysis revealed that both hydrogen producing bacteria and hydrogen consuming bacteria were enriched after CES recycled, and the acetobacteria percentage increased to 12.4% at VS(CS)/VS(CES) of 6:2. Relatively high efficient and stable hydrogen production was observed at VS(CS)/VS(CES) of 5:3 without pH adjusted and any pretreatment. The highest total energy yield, the highest COD and VS degradation were obtained at VS(CS)/VS(CES) of 7:1. GFC analysis indicated that the hydrolysis behavior was significantly improved by CES recycle at both hydrogen and methane production phase.

Culture-Dependent and Culture-Independent Methods in Evaluation of Emission of Enterobacteriaceae from Sewage to the Air and Surface Water

The number of Enterobacteriaceae, with particular attention given to the presence of Escherichia coli and Klebsiella pneumoniae, was determined in hospital effluents and municipal wastewater after various stages of purification. The emission of these microorganisms to the ambient air near wastewater treatment plant (WWTP) facilities and to the river water, which is a receiver of the WWTP effluent, was also studied using fluorescence in situ hybridization (FISH) and cultivation methods. The number of Enterobacteriaceae determined by cultivation and fluorescence methods in different kinds of sewage sample ranged from 0.5 × 10(3) to 2.9 × 10(6) CFU/ml and from 2.2 × 10(5) to 1.3 × 10(8) cells/ml, respectively. Their removal rates during treatment processes were close to 99 %, but the number of these bacteria in the WWTP outflow was quite high and ranged from 5.9 × 10(3) to 3.5 × 10(4) CFU/ml and from 1.1 × 10(5) to 6.1 × 10(5) cells/ml, respectively. In the river water and the air samples, the number of Enterobacteriaceae was also high and ranged from 4.1 × 10(3) to 7.9 × 10(3) CFU/ml and from 3 to 458 CFU/m(3), respectively. The numbers of these microorganisms obtained from fluorescence and cultivation methods were statistically and significantly correlated; however, the analysis of the studied samples indicated that the FISH method gave values up to 10(3)-fold times greater than those obtained by the cultivation method. From a sanitary point of view, this means that the number of viable fecal bacteria is systematically underestimated by traditional culture-based methods. Thus, the FISH proves to be a method that could be used to estimate bacterial load, particularly in air samples and less contaminated river water.

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).

Contrasting trends in distribution of four major planktonic betaproteobacterial groups along a pH gradient of epilimnia of 72 freshwater habitats

The distribution and abundance of Betaproteobacteria and three of its genera - Limnohabitans (R-BT065 lineage), Polynucleobacter (including subclusters Polynucleobacter necessarius and Polynucleobacter acidiphobus/Polynucleobacter difficilis), and Methylophilus - across the epilimnia of 72 limnologically diverse freshwater habitats were investigated using fluorescence in situ hybridization. Moreover, seasonal development of Betaproteobacteria subgroups along the longitudinal axis of a reservoir was followed. Betaproteobacteria comprised on average 29.1%, Polynucleobacter 11.6%, P. necessarius 10.1%, P. acidiphobus/difficilis 0.5%, Limnohabitans 8.9%, and Methylophilus 0.9% of total bacterioplankton cells in the investigated habitats. Polynucleobacter necessarius and Limnohabitans coexisted in the majority of habitats but showed contrasting abundance patterns along the pH gradient of habitats (pH, 3.8-8.5). The observed distribution patterns could theoretically be explained by different preferences for substrate sources, that is, substances of humic origin in acidic waters and algal-derived substances in alkaline waters. However, substrate utilization patterns observed in laboratory experiments indicate no coherent group-specific differences in substrate preferences. Interestingly, similar distribution patterns were revealed for Limnohabitans and P. acidiphobus/difficilis, suggesting similar ecological adaptations of these distantly related taxa. Our findings further emphasize that at least two taxa of freshwater Betaproteobacteria represent ecologically diversified groups. Investigations at higher phylogenetic resolution are required for obtaining further insights into their ecology.

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.

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.

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.

Evaluating seasonal dynamics of bacterial communities in marine fish aquaculture: a preliminary study before applying phage therapy

The increasing problem of antibiotic resistance in common pathogenic bacteria and the concern about the spreading of antibiotics in the environment bring the need to find new methods to control fish pathogens. Phage therapy represents a potential alternative to antibiotics, but its use in aquaculture requires a detailed understanding of bacterial communities, namely of fish pathogenic bacteria. Therefore, in this study the seasonal dynamics of the overall bacterial communities, microbiological water quality and disease-causing bacteria were followed in a marine aquaculture system of Ria de Aveiro (Portugal). Analysis of the bacterial diversity of the water samples by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments indicates that the bacterial community structure varied seasonally, showing a higher complexity during the warm season. The diversity of the main fish pathogenic bacteria, assessed by DGGE targeting the Vibrio genus, showed lower seasonal variation, with new dominating populations appearing mainly in the spring. Bacterial indicators, faecal coliforms and enterococci, enumerated by the filter-membrane method, also varied seasonally. The fluorescent in situ hybridization (FISH) results showed that the specific groups of bacteria varied during the study period and that the non-indigenous Enterobactereaceae family was the most abundant group followed by Vibrio and Aeromonas. The seasonal variation detected in terms of density and structure of total and pathogenic bacterial communities demonstrates the need for a careful monitoring of water through the year in order to select the suitable phages to inactivate fish pathogenic bacteria. The spring season seems to be the critical time period when phage therapy should be applied.

Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis

Disruption of homeostasis between the host immune system and the intestinal microbiota leads to inflammatory bowel disease (IBD). Whether IBD is instigated by individual species or disruptions of entire microbial communities remains controversial. We characterized the fecal microbial communities in the recently described T-bet(-/-) ×Rag2(-/-) ulcerative colitis (TRUC) model driven by T-bet deficiency in the innate immune system. 16S rRNA-based analysis of TRUC and Rag2(-/-) mice revealed distinctive communities that correlate with host genotype. The presence of Klebsiella pneumoniae and Proteus mirabilis correlates with colitis in TRUC animals, and these TRUC-derived strains can elicit colitis in Rag2(-/-) and WT adults but require a maternally transmitted endogenous microbial community for maximal intestinal inflammation. Cross-fostering experiments indicated a role for these organisms in maternal transmission of disease. Our findings illustrate how gut microbial communities work in concert with specific culturable colitogenic agents to cause IBD.

Karst pools in subsurface environments: collectors of microbial diversity or temporary residence between habitat types

We studied bacterial diversity and community composition in three shallow pools of a Swiss karst cave system with contrasting hydrological and hydrochemical properties. The microbial assemblages in the pools were remarkably different, and only one operational taxonomic unit of 16S rRNA genes (OTU, 97% similarity) was shared between the three of them (total OTU number in all pools: 150). Unexpectedly high microbial phylotype richness was found even in the two pools without groundwater contact and with low concentrations of organic carbon and total cell numbers (< 10(4) ml(-1)). One of these seepage water fed systems harboured 15 distinct OTUs from several deeply branching lineages of the candidate phylum OP3, whereas representatives of this group were not detected in the other two pools. A tentative phylogeographic analysis of available OP3-related sequences in the context of our data set revealed that there was generally little agreement between the habitats of origin of closely related sequence types. Two bacterial clades affiliated with the obligate methylamine utilizer Methylotenera mobilis were only found in the pool that was exposed to repeated flooding events. These bacteria formed relatively stable populations of up to 6% of total cell counts over periods of several months irrespective of inundation by groundwater. This suggests that karst water may provide a means of transport for these bacteria from terrestrial to freshwater 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.

A short-oligonucleotide microarray that allows improved detection of gastrointestinal tract microbial communities

Background

The human gastrointestinal (GI) tract contains a diverse collection of bacteria, most of which are unculturable by conventional microbiological methods. Increasingly molecular profiling techniques are being employed to examine this complex microbial community. The purpose of this study was to develop a microarray technique based on 16S ribosomal gene sequences for rapidly monitoring the microbial population of the GI tract.

Results

We have developed a culture-independent, semi-quantitative, rapid method for detection of gut bacterial populations based on 16S rDNA probes using a DNA microarray. We compared the performance of microarrays based on long (40- and 50-mer) and short (16–21-mer) oligonucleotides. Short oligonucleotides consistently gave higher specificity. Optimal DNA amplification and labelling, hybridisation and washing conditions were determined using a probe with an increasing number of nucleotide mismatches, identifying the minimum number of nucleotides needed to distinguish between perfect and mismatch probes. An independent PCR-based control was used to normalise different hybridisation results, and to make comparisons between different samples, greatly improving the detection of changes in the gut bacterial population. The sensitivity of the microarray was determined to be 8.8 × 10⁴ bacterial cells g^-1 faecal sample, which is more sensitive than a number of existing profiling methods. The short oligonucleotide microarray was used to compare the faecal flora from healthy individuals and a patient suffering from Ulcerative Colitis (UC) during the active and remission states. Differences were identified in the bacterial profiles between healthy individuals and a UC patient. These variations were verified by Denaturing Gradient Gel Electrophoresis (DGGE) and DNA sequencing.

Conclusion

In this study we demonstrate the design, testing and application of a highly sensitive, short oligonucleotide community microarray. Our approach allows the rapid discrimination of bacteria inhabiting the human GI tract, at taxonomic levels ranging from species to the superkingdom bacteria. The optimised protocol is available at: . It offers a high throughput method for studying the dynamics of the bacterial population over time and between individuals.

Spatio-temporal niche separation of planktonic Betaproteobacteria in an oligo-mesotrophic lake

We investigated the diversity of planktonic Betaproteobacteria and the seasonal population changes of betaproteobacterial taxa in an oligo-mesotrophic lake (Piburger See, Austria). Focus was put on the vertical distribution of the investigated populations and on differences between their respective cell fractions with apparent amino acid incorporation. On average, 66% of betaproteobacterial cells and 73% of their diversity could be attributed to four clades within three lineages that were further analysed by fluorescence in situ hybridization. The numbers of bacteria from the R-BT subclade of the beta I lineage and from the PnecB subgroup of the beta II lineage were rather constant throughout the water column. In contrast, members of another subgroup of beta II (PnecC) and bacteria related to Methylophilus (beta IV) were particularly numerous in the oxygen-depleted zone. In general, only moderate seasonal changes in abundance were observed in the upper water layers, whereas there was a clear relationship between decreasing oxygen levels and the rise of bacteria from the PnecC and beta IV clades in deeper strata. On average, almost 80% of beta I bacteria, but < 15% of cells from the beta IV clade, showed amino acid incorporation. Our results suggest that the studied populations occupy distinct vertical and ecophysiological niches in Piburger See.

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.

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.

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.

Effect of plants and filter materials on bacteria removal in pilot-scale constructed wetlands

Due to the lack of testing units or appropriate experimental approaches, only little is known about the removal of bacteria in constructed wetlands. However, improved performance in terms of water sanitation requires a detailed understanding of the ongoing processes. Therefore, we analyzed the microbial diversity and the survival of Enterobacteriaceae in six pilot-scale constructed wetland systems treating domestic wastewater: two vertical sand filters, two vertical expanded clay filters and two horizontal sand filters (each planted and unplanted). Samples were taken from the in- and outflow, from the rhizosphere, and from the bulk soil at various depths. Colony-forming units of heterotrophic bacteria and coliforms were analyzed and the removal of bacteria between the in- and outflow was determined to within 1.5-2.5 orders of magnitude. To access the taxon-specific biodiversity of potential pathogens in the filters and to reduce the complexity of the analysis, specific primers for Enterobacteriaceae were developed. While performing PCR-SSCP analyses, a pronounced decrease in diversity from the inflow to the outflow of treated wastewater was observed. No differences were observed between the bulk soil of planted and unplanted vertical filters. Some bands appeared in the rhizosphere that were not present in the bulk soil, indicating the development of specific communities stimulated by the plants. The fingerprinting of the rhizosphere of plants grown on sand or expanded clay exhibited many differences, which show that different microbial communities exist depending on the soil type of the filters. The use of the taxon-specific primers enabled us to evaluate the fate of the Enterobacteriaceae entering the wetlands and to localize harboring in the rhizosphere. The most abundant bands of the profiles were sequenced: Pantoea agglomerans was found in nearly all samples from the soil but not in the effluent, whereas Citrobacter sp. could not be removed by the horizontal unplanted sand and vertical planted expanded clay filters. These results show that the community in wetland system is strongly influenced by the filtration process, the filter material and the plants.

Microbial composition of biofilms in a brewery investigated by fatty acid analysis, fluorescence in situ hybridisation and isolation techniques

Biofilms associated with brewery plants can harbour spoiling microorganisms that potentially damage the final product. Most beer-spoiling microorganisms are thought to depend on numerous interactions with the accompanying microbiota. However, there is no information on the microbial community structure of biofilms from bottling plants. The conveyors that transport the bottles to and from the plant are known as potential sources of microbial contamination of beer. Consequently, the material buildup from two conveyors was analysed using a cultivation/isolation approach, and the culture-independent techniques of whole cell fatty acid analysis and fluorescence in situ hybridisation (FISH). Heterogeneous communities were present at both conveyors. Although characteristic fatty acids for Eukarya were present, FISH-signals for Eukarya were extremely low. The Proteobacteria, in particular the Gammaproteobacteria, were abundant at both sample sites. Bacterial isolates were obtained for every dominating group detected by FISH: the Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria, the Xanthomonadaceae, the Actinobacteria, the Bacteroidetes and the Firmicutes.