Microbial communities of aerobic granules: granulation mechanisms

Aerobic granulation is an advanced biological wastewater treatment technology. This study for the first time identified the microbial communities of sliced samples of mature granules by polymerase chain reaction (PCR) amplification and denaturing gradient gel electrophoresis (DGGE) technique and those of whole growing granules by high-throughput sequencing technique. The sliced sample study revealed that mature granules have a spherical core with anaerobic Rhodocyclaceae covered by an outer spherical shell with both aerobic and anaerobic strains. The growing granule study showed that the flocculated flocs were first transited to young granules with increased abundances of Flavobacteriaceae, Xanthomonadaceae, Rhodobacteraceae and Microbacteriaceae, then the abundances of anaerobic strains were increased owing to the formation of anaerobic core. Since the present granules were cultivated from flocculated flocs, the microbial community data suggested that granules were formed via a deterministic rather than via a random aggregation-disintegration mechanism.

Changes of bacterial and fungal community compositions during vermicomposting of vegetable wastes by Eisenia foetida

Changes of bacterial and fungal community during vermicomposting of vegetable wastes by hatchling, juvenile and adult Eisenia foetida were investigated through analysis of the extracted bacterial 16S rDNA and fungal 18S rDNA with quantitative polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE) and sequencing. After 60days of composting, significantly lower values of microbial activity and bacterial and fungal densities were revealed in the products of composting with earthworms than in the control (without earthworms). PCR-DGGE images showed vermicomposting significantly enhanced the diversities of bacterial and fungal communities. However, for their structures, sequencing results revealed that, compared to the control where the bacterial Firmicutes were predominant, in the composts with earthworms, the bacterial Bacteroidetes and Actinomycetes, and the fungal Sordariomycetes were found dominant. In addition, some beneficial species of bacteria and fungi against pathogens were also isolated from the vermicomposting products.

Microbial mechanisms of using enhanced ecological floating beds for eutrophic water improvement

Enhanced ecological floating beds were implemented to reduce nutrient quantity and improve the water quality of a eutrophic lake. The results showed that average removal efficiencies of CODCr, total nitrogen, NH3-N and total phosphorus for Canna indica L. set-up were 23.1%, 15.3%, 18.1% and 19.4% higher, respectively, than that of the setup with only substrate, and 14.2%, 12.8%, 7.9% and 11.9% higher than Iris pseudacorus L. ecological floating bed. The microbial community structure had obvious differences between devices and low similarity; bacteria were mainly attached on the fiber filling. The microbial population was abundant at the start and end of the experiment. Shannon index of samples selected ranged from 0.85 to 1.05. The sequencing results showed that fiber filling collected most uncultured bacteria species and the majority of bacteria on the plant roots were β-Proteobacteria and α-Proteobacteria. The co-dominant species attaching to the filling and plant was Nitrosomonadaceae.

The immobilization of heavy metals in soil by bioaugmentation of a UV-mutant Bacillus subtilis 38 assisted by NovoGro biostimulation and changes of soil microbial community

Bacillus subtilis 38 (B38) is a mutant species of Bacillus subtilis acquired by UV irradiation with high cadmium tolerance. This study revealed that B38 was a good biosorbent for the adsorption of multiple heavy metals (cadmium, chromium, mercury, and lead). Simultaneous application of B38 and NovoGro (SNB) exhibited a synergetic effect on the immobilization of heavy metals in soil. The heavy metal concentrations in the edible part of the tested plants (lettuce, radish, and soybean) under SNB treatment decreased by 55.4-97.9% compared to the control. Three single extraction methods, diethylenetriaminepentaacetic acid (DTPA), Mehlich 3 (M3), and the first step of the Community Bureau of Reference method (BCR1), showed good predictive capacities for metal bioavailability to leafy, rhizome, and leguminous plant, respectively. The polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) profiles revealed that NovoGro could enhance the proliferation of both exotic B38 and native microbes. Finally, the technology was checked in the field, the reduction in heavy metal concentrations in the edible part of radish was in the range between 30.8% and 96.0% after bioremediation by SNB treatment. This study provides a practical strategy for the remediation of farmland contaminated by multiple heavy metals.

Removal of bisphenol A (BPA) in a nitrifying system with immobilized biomass

The potential for bisphenol A (BPA) removal by mixed consortia of immobilized microorganisms with high nitrification activity was investigated with BPA concentrations in the influent from 2.5 to 10.0 mg/L. The presence of BPA limited ammonium oxidation; nitrification efficiency decreased from 91.2±1.3% in the control series to 47.4±9.4% when BPA concentration in wastewater was the highest. The efficiency of BPA removal rose from 87.1±5.5% to 92.9±2.9% with increased BPA concentration in the influent. Measurement of oxygen uptake rates by biomass exposed to BPA showed that BPA was mainly removed by heterotrophic bacteria. A strong negative correlation between the BPA removal efficiency and nitrification efficiency indicated the limited contribution of ammonia-oxidizing bacteria (AOB) to BPA biodegradation. Exposure of biomass to BPA changed the quantity and diversity of AOB in the biomass as shown by real-time PCR and denaturing gradient gel electrophoresis.

Effect of organic matter strength on anammox for modified greenhouse turtle breeding wastewater treatment

Anaerobic ammonium-N removal from modified greenhouse turtle breeding wastewater with different chemical oxygen demand (COD) strengths (194.0-577.8 mg L(-1)) at relatively fixed C/N ratios (≈ 2) was investigated using a lab-scale up-flow anaerobic sludge blanket (UASB) anammox reactor. During the entire experiment, the total nitrogen (TN) removal efficiency was about 85% or higher, while the average COD removal efficiency was around 56.5 ± 7.9%. Based on the nitrogen and carbon balance, the nitrogen removal contribution was 79.6 ± 4.2% for anammox, 12.7 ± 3.0% for denitrification+denitritation and 7.7 ± 4.9% for other mechanisms. Denaturing gradient gel electrophoresis (DGGE) analyses revealed that Planctomycete, Proteobacteria and Chloroflexi bacteria were coexisted in the reactor. Anammox was always dominant when the reactor was fed with different COD concentrations, which indicated the stability of the anammox process with the coexistence of the denitrification process in treating greenhouse turtle breeding wastewater.

Transient-state operation of an anoxic biotrickling filter for H2S removal

The application of an anoxic biotrickling filter (BTF) for H₂S removal from contaminated gas streams is a promising technology for simultaneous H₂S and NO₃^- removal. Three transient-state conditions, i.e. different liquid flow rates, wet-dry bed operations and H₂S shock loads, were applied to a laboratory-scale anoxic BTF. In addition, bioaugmentation of the BTF with a H₂S removing-strain, Paracoccus MAL 1HM19, to enhance the biomass stability was investigated. Liquid flow rates (120, 60 and 30 L d^-1) affected the pH and NO₃^- removal efficiency (RE) in the liquid phase. Wet-dry bed operations at 2-2 h and 24-24 h reduced the H₂S elimination capacity (EC) by 60-80%, while the operations at 1-1 h and 12-12 h had a lower effect on the BTF performance. When the BTF was subjected to H₂S shock loads by instantly increasing the gas flow rate (from 60 to 200 L h^-1) and H₂S inlet concentration (from 112 (± 15) to 947 (± 151) ppm_v), the BTF still showed a good H₂S RE (>93%, EC of 37.8 g S m^-3 h^-1). Bioaugmentation with Paracoccus MAL 1HM19 enhanced the oxidation of the accumulated S⁰ to sulfate in the anoxic BTF.

Soil contamination assessment for Pb, Zn and Cd in a slag disposal area using the integration of geochemical and microbiological data

Improper disposal of mining waste is still considered a global problem, and further details on the contamination by potentially toxic metals are required for a proper assessment. In this context, it is important to have a combined view of the chemical and biological changes in the mining dump area. Thus, the objective of this study was to evaluate the Pb, Zn and Cd contamination in a slag disposal area using the integration of geochemical and microbiological data. Analyses of soil organic matter (SOM), pH, Eh, pseudo-total concentration of metals, sequential extraction and microbial community by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) were conducted. Metal availability was evaluated based on the geoaccumulation index (I _geo), ecological risk ([Formula: see text]), Risk Assessment Code (RAC) and experimental data, and different reference values were tested to assist in the interpretation of the indices. The soil pH was slightly acidic to neutral, the Eh values indicated oxidized conditions and the average SOM content varied from 12.10 to 53.60 g kg^-1. The average pseudo-total concentrations of metals were in the order of Zn > Pb > Cd. Pb and Zn were mainly bound to the residual fraction and Fe-Mn oxides, and a significant proportion of Cd was bound to the exchangeable and carbonate fractions. The topsoil (0-20 cm) is highly contaminated (I _geo) with Cd and has a very high potential ecological risk ([Formula: see text]). Higher bacterial diversity was mainly associated with higher metal concentrations. It is concluded that the integration of geochemical and microbiological data can provide an appropriate evaluation of mining waste-contaminated areas.

Heavy metal bioleaching and sludge stabilization in a single-stage reactor using indigenous acidophilic heterotrophs

Simultaneous sludge digestion and metal leaching (SSDML) have been reported at mesophilic temperature. It is generally perceived that while sludge stabilization is effected by heterotrophs at neutral pH, metal bioleaching is done by acidophilic autotrophs. However, little information is available on the microbial communities involved in the process. This study carried out SSDML in a single-stage reactor using sludge indigenous microorganisms and looked at the bacterial communities responsible for the process. Volatile suspended solids were reduced by more than 40%. The concentration of zinc, copper, chromium, cadmium and nickel decreased by more than 45% in the dry sludge. Acidophilic species of Alicyclobacillus genus were the dominant heterotrophs. A few heterotrophic bacteria were detected which can oxidize iron (Alicyclobacillus ferrooxydans, Alicyclobacillus ferripilum and Ferrimicrobium acidiphilum). Acidithiobacillus ferrooxidans (autotroph) was responsible for the oxidation of both iron and sulfur which lead to a change in the pH from neutral to acidic. The presence of acidophilic heterotrophs, which can oxidize either iron or sulfur, enhanced the efficiency of SSDML process with respect to sludge stabilization and metal leaching. This study shows that it is possible to carry out the SSDML in a single-stage reactor with indigenous microorganisms.

Oxalate degradation in a bioelectrochemical system: reactor performance and microbial community characterization

The aim of this work was to investigate the feasibility of using oxalate at the anode in a continuous reactor. Complete oxalate removal was observed, albeit at a maximum coulombic efficiency of 33.9±0.4%. At the cathode side, there was an increase in pH from 8 to 11 showing production of caustic. Analysis of the microbial community demonstrated a clear shift during reactor start-up, resulting in enrichment of microorganisms belonging to Bacteroidetes, Firmicutes, Mollicutes, and β and γ-Proteobacteria. Methane was produced throughout the experiment; Archaea belonging to the Methanosarcinacea, Methanomicrobiaceae and Methanosaetaceae were identified as key representatives.

Enhanced 1,2-dichloroethane degradation in heavy metal co-contaminated wastewater undergoing biostimulation and bioaugmentation

Biostimulation, bioaugmentation and dual-bioaugmentation strategies were investigated in this study for efficient bioremediation of water co-contaminated with 1,2-dichloroethane (1,2-DCA) and heavy metals, in a microcosm set-up. 1,2-DCA concentration was periodically measured in the microcosms by gas chromatographic analysis of the headspace samples, while bacterial population and diversity were determined by standard plate count technique and Polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) analysis, respectively. Dual-bioaugmentation, proved to be most effective exhibiting 22.43%, 26.54%, 19.58% and 30.49% increase in 1,2-DCA degradation in microcosms co-contaminated with As(3+), Cd(2+), Hg(2+) and Pb(2+), respectively, followed by bioaugmentation and biostimulation. Dual-bioaugmented microcosms also exhibited the highest increase in the biodegradation rate constant (k1) resulting in 1.76-, 2-, 1.7- and 2.1-fold increase in As(3+), Cd(2+), Hg(2+) and Pb(2+) co-contaminated microcosms respectively, compared to the untreated microcosms. Dominant bacterial strains obtained from the co-contaminated microcosms were found to belong to the genera Burkholderia, Pseudomonas, Bacillus, Enterobacter and Bradyrhizobium, previously reported for 1,2-DCA and other chlorinated compounds degradation. PCR-DGGE analysis revealed variation in microbial diversity over time in the different co-contaminated microcosms. Results obtained in this study have significant implications for developing innovative bioremediation strategies for treating water co-contaminated with chlorinated organics and heavy metals.

Microbial adaptation to biodegrade toxic organic micro-pollutants in membrane bioreactor using different sludge sources

Biodegradation of toxic organic micro-pollutants in municipal solid waste (MSW) leachate by membrane bioreactor (MBR) was investigated. The MBR systems were seeded with different sludge sources, one was from a pilot-scale MBR system treating MSW leachate and the other was from an activated sludge sewage treatment plant. The biodegradation of BPA, 2,6-DTBP, BHT, DEP, DBP and DEHP, DCP and BBzP, by sludge from both reactors were found improved with time. However, enhanced biodegradation of micro-pollutants was observed in MBR operated under long sludge age condition. Bacterial population analyses determined by PCR-DGGE revealed the development of phenol and phthalate degrading bacteria consortium in MBR sludge during its operation.

Impact of oxygen on the coexistence of nitrification, denitrification, and sulfate reduction in oxygen-based membrane aerated biofilm

Membrane aerated biofilms (MABs) are subject to "counter diffusion" of oxygen and substrates. In a membrane aerated biofilm reactor, gases (e.g., oxygen) diffuse through the membrane into the MAB, and liquid substrates pass from the bulk liquid into the MAB. This behavior can result in a unique biofilm structure in terms of microbial composition, distribution, and community activity in the MAB. Previous studies have shown simultaneous aerobic oxidation, nitrification, and denitrification within a single MAB. Using molecular techniques, we investigated the growth of sulfate-reducing bacteria (SRB) in the oxygen-based MAB attached to a flat sheet membrane. Denaturing gradient gel electrophoresis of the amplified 16S rRNA gene fragments and functional gene fragments specific for ammonia-oxidizing bacteria (amoA), denitrifying bacteria (nirK), and SRB (dsrB) demonstrated the coexistence of nitrifiers, denitrifiers, and SRB communities within a single MAB. The functional diversities of SRB and denitrifiers decreased with an increase in the oxygen concentration in the bulk water of the reactor.

Monitoring the microbial community shift throughout the shock changes of hydraulic retention time in an anaerobic moving bed membrane bioreactor

An anaerobic moving bed membrane bioreactor (AnMBMBR) fed with synthetic domestic wastewater was investigated under hydraulic retention time (HRT) shocks to assess the effects on the microbial (bacteria and archaea) community and reactor performance. 16S rDNA targeted polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach was optimized to relate the metabolic and community composition with biogas generation, methane content and COD removal efficiency. From the drastic decrease of HRT (from 8 h to 4 h), the methane production was significantly reduced due to the HRT shock, while the COD removal efficiency was not affected. The enhanced growth of homoacetogenic bacteria, Thermoanaerobacteraceae competes with methanogens under shock period. When the HRT was recovered to 8 h, the methane generation rate was higher than the initial operation before the shock HRT changes, which would be ascribed to the activity of new emerging hydrogenotrophic archaea, Methanocella sp. and Methanofollis sp.

Changes in bacterial diversity associated with bioremediation of used lubricating oil in tropical soils

Used lubricating oil (ULO) is a widespread contaminant, particularly throughout tropical regions, and may be a candidate for bioremediation. However, little is known about the biodegradation potential or basic microbial ecology of ULO-contaminated soils. This study aims to determine the effects of used ULO on bacterial community structure and diversity. Using a combination of culture-based (agar plate counts) and molecular techniques (16S rRNA gene sequencing and DGGE), we investigated changes in soil bacterial communities from three different ULO-contaminated soils collected from motorcycle mechanical workshops (soil A, B, and C). We further explored the relationship between bacterial community structure, physiochemical soil parameters, and ULO composition in three ULO-contaminated soils. Results indicated that the three investigated soils had different community structures, which may be a result of the different ULO characteristics and physiochemical soil parameters of each site. Soil C had the highest ULO concentration and also the greatest diversity and richness of bacteria, which may be a result of higher nutrient retention, organic matter and cation exchange capacity, as well as freshness of oil compared to the other soils. In soils A and B, Proteobacteria (esp. Gammaproteobacteria) dominated the bacterial community, and in soil C, Actinobacteria and Firmicutes dominated. The genus Enterobacter, a member of the class Gammaproteobacteria, is known to include ULO-degraders, and this genus was the only one found in all three soils, suggesting that it could play a key role in the in situ degradation of ULO-contaminated tropical Thai soils. This study provides insights into our understanding of soil microbial richness, diversity, composition, and structure in tropical ULO-contaminated soils, and may be useful for the development of strategies to improve bioremediation.

Nitrate and COD removal in an upflow biofilter under an aerobic atmosphere

A continuous-upflow submerged biofilter packed with ceramsite was constructed for nitrate removal under an aerobic atmosphere. Pseudomonas stutzeri X31, an aerobic denitrifier isolate, was added to the bioreactor as an inoculum. The influent NO3(-)-N concentrations were 63.0-73.8 mg L(-1). The best results were achieved when dissolved oxygen level was 4.6 mg L(-1) and C/N ratio was 4.5. The maximum removal efficiencies of carbon oxygen demand (COD) and NO3(-)-N were 94.04% and 98.48%, respectively at 30°C, when the hydraulic load was 0.75 m h(-1). The top section of the bioreactor possessed less biofilm but higher COD and NO3(-)-N removal rates than the bottom section. Polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) technique combined with electron microscopic examination indicated P. stutzeri X31 and Paracoccus versutus were the most dominant bacteria. Amoeba sp., Vorticella sp., Philodina sp., and Stephanodiscus sp. were also found in the bioreactor.

Statistical assessment of DNA extraction methodology for culture-independent analysis of microbial community associated with diverse environmental samples

Cost-effectiveness, quality, time-effectiveness and ease of the methodology are the most crucial factors in isolating quality DNA from wide variety of samples. Thus, research efforts focusing on the development of an efficient DNA extraction protocol is the need of the hour. The present study therefore, focuses on development of an efficient, rapid and free of inhibitory substances based methodology for extracting metagenomic DNA from diverse environmental samples viz. anaerobic biogas digesta, ruminant stomach, human feces, soil, and microbial starter cultures used for preparation of fermented food. PCR-DGGE based analysis and quality metagenomic library preparation, using DNA extraction methodology, validates the developed protocol. The developed protocol is cost effective, capable of isolating DNA from small sample size (100-1000 µl), time efficient (1.5-2.0 h protocol) and results in significantly higher DNA yield (4-8 times increased yield) when compared to previously available DNA extraction method and a commercial DNA extraction kit. The DNA extracted from the samples using different protocols was evaluated based on its ability to identify diverse microbial species using PCR-DGGE profiles targeting variable region within the 16S rRNA gene. The results of microbial community analysis revealed comparability of the developed protocol to commercial kits, in effectively identifying dominant representatives of the microbial community in different samples. Using the DNA extracted from the presented methodology, metagenomic libraries were prepared, which were found suitable for sequencing on Illumina platform.

A Glimpse into the Microbiota of Marketed Ready-to-Eat Crickets (Acheta domesticus)

The present study was aimed to get an insight into the bacterial biota of ready-to-eat small crickets (Acheta domesticus) already marketed in the European Union. 16S rRNA gene of the DNAs extracted from thirty-two samples of ready-to-eat crickets commercialized by 4 European Union producers located in Austria, Belgium, France and the Netherlands (2 batches per producer) was analyzed by Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE). The species belonging to the genera Hespellia, Ruminococcus and Clostridium were detected in samples from Austria, while those from genera Lysobacter, Staphylococcus and Clostridium were detected in samples from Belgium. Moreover, samples from France were characterized by Staphylococcus, Pseudomonas, and Hydrogenophilus genera. Finally, the genera Staphylococcus, Hydrogenophilus, Clostridium and Ruminococcus were identified in the samples produced in the Netherlands. When insects are intended for commercialization, rearing, processing and handling could affect the presence of the occurring microbial species. Hence, to assure a safe product, the need for a full standardization of production technologies, including feed supply as well as rearing and processing practices, is recommended.

Nitrifying-denitrifying filters and UV-C disinfection reactor: a combined system for wastewater treatment

Biological treatment systems use the natural processes of ubiquitous organisms to remove pollutants and improve the water quality before discharge to the environment. In this paper, the nitrification/denitrification reactor allowed a reduction in organic load, but offered a weak efficiency in nitrate reduction. However, the additions of the activated sludge in the reactor improve this efficiency. A decrease of [Formula: see text] values from 13.3 to 8 mg/l was noted. Nevertheless, sludge inoculation led to a net increase of the number of pathogenic bacteria. For this reason, a UV-C pilot reactor was installed at the exit of the biological nitrification-denitrification device. Thus, a fluence of 50 mJ.cm^-2 was sufficient to achieve values of 20 MPN/100 ml for fecal coliform and 6 MPN/100 ml for fecal streptococci, conforms to Tunisian Standards of Rejection. On the other hand, the DGGE approach has allowed a direct assessment of the bacterial community changes upon the treated wastewater.

Spatial variations of bacterial community and its relationship with water chemistry in Sanya Bay, South China Sea as determined by DGGE fingerprinting and multivariate analysis

Bacteria play important roles in the structure and function of marine food webs by utilizing nutrients and degrading the pollutants, and their distribution are determined by surrounding water chemistry to a certain extent. It is vital to investigate the bacterial community's structure and identifying the significant factors by controlling the bacterial distribution in the paper. Flow cytometry showed that the total bacterial abundance ranged from 5.27 × 10(5) to 3.77 × 10(6) cells/mL. Molecular fingerprinting technique, denaturing gradient gel electrophoresis (DGGE) followed by DNA sequencing has been employed to investigate the bacterial community composition. The results were then interpreted through multivariate statistical analysis and tended to explain its relationship to the environmental factors. A total of 270 bands at 83 different positions were detected in DGGE profiles and 29 distinct DGGE bands were sequenced. The predominant bacteria were related to Phyla Protebacteria species (31 %, nine sequences), Cyanobacteria (37.9 %, eleven sequences) and Actinobacteria (17.2 %, five sequences). Other phylogenetic groups identified including Firmicutes (6.9 %, two sequences), Bacteroidetes (3.5 %, one sequences) and Verrucomicrobia (3.5 %, one sequences). Conical correspondence analysis was used to elucidate the relationships between the bacterial community compositions and environmental factors. The results showed that the spatial variations in the bacterial community composition was significantly related to phosphate (P = 0.002, P < 0.01), dissolved organic carbon (P = 0.004, P < 0.01), chemical oxygen demand (P = 0.010, P < 0.05) and nitrite (P = 0.016, P < 0.05). This study revealed the spatial variations of bacterial community and significant environmental factors driving the bacterial composition shift. These results may be valuable for further investigation on the functional microbial structure and expression quantitatively under the polluted environments in the world.