Community analysis of ammonia and nitrite oxidizers during start-up of nitritation reactors

Total and stable washout of nitrite oxidizing bacteria from a nitrifying continuous activated sludge system using automatic control based on Oxygen Uptake Rate measurements

Partial nitrification (ammonium oxidation to nitrite) has gained a lot of interest among researchers in the last years because of its advantages with respect to complete nitrification (ammonium oxidation to nitrate): decrease of oxygen requirements for nitrification, reduction of COD demand and CO(2) emissions during denitrification and higher denitrification rate and lower biomass production during anoxic growth. In this study, an extremely high-strength ammonium wastewater (3000-4000mg NL(-1)) was treated in a continuous pilot plant with a configuration of three reactors in series plus a settler. The system was operated under the maximum possible volumetric nitrogen loading rate, at mild temperature (around 25 degrees C), with high sludge retention time (around 30d) and significant nitrifying biomass concentration (average of 1800+/-600mg VSSL(-1)). The implemented control loops transformed the system, which was operating with complete nitrification, into a continuous partial nitrification system. Nitrite oxidizing bacteria (NOB) washout was accomplished with local control loops for pH and dissolved oxygen (DO) with proper setpoints for NOB inhibition (pH=8.3 and DO=1.2-1.9mg O(2)L(-1)) and with an inflow control loop based on Oxygen Uptake Rate (OUR) measurements, which allowed working at the maximum ammonium oxidation capacity of the pilot plant in each moment. This operational strategy maximized the difference between ammonia oxidizing bacteria (AOB) and NOB growth rates, which is the key point to achieve a fast and stable NOB washout. The results showed a stable operation of the partial nitrification system during more than 100 days and NOB washout was corroborated with fluorescence in-situ hybridization (FISH) analysis.

High reproducibility of ammonia-oxidizing bacterial communities in parallel sequential batch reactors

AIMS

To investigate whether the ammonia-oxidizing bacterial (AOB) communities of replicate nitrifying bioreactors (i) co-evolve or diverge over time and (ii) are stable or dynamic during periods of complete nitrification.

METHODS AND RESULTS

Three sequential batch reactors (SBR) were inoculated with sludge from a municipal wastewater treatment plant, fed with ammonium-enriched tap water and operated in parallel for 134 days. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) demonstrated co-evolvement of the AOB communities over time. During start-up, temporary decreases in nitrification were noticed, and the AOB community rate of change values (Delta(t(week))) were medium to high (12-22%). During the adjacent period of complete nitrification, low AOB community dynamics were observed (Delta(t(week)) < 5%). Further pragmatic processing of the DGGE profiles revealed a high range-weighted richness and a medium functional organization of the AOB communities.

CONCLUSIONS

After a start-up period, high functional stability and low dynamics of the AOB communities were observed. Deterministic rather than stochastic driving forces led to AOB community co-evolvement in the replicate SBR.

SIGNIFICANCE AND IMPACT OF THE STUDY

Replicates in identical set-ups are reproducible, and pragmatic processing of DGGE patterns is a straightforward tool to score and compare the functionality of the bacterial communities.

Extension of ASM3 for two-step nitrification and denitrification and its calibration and validation with batch tests and pilot scale data

Although traditionally not taken into account by most of activated sludge models the production of nitrite as an intermediate of the nitrification-denitrification processes becomes of interest in some specific plant operational situations or in case of high sensitivity of the receiving ecosystems. The Activated Sludge Model No.3 (ASM3) was therefore extended for two-step nitrification and two-step denitrification in order to better describe nitrite dynamics especially during the treatment of communal wastewater. Nitrite was included as a new model compound and as an intermediate product of biological processes, both for heterotrophic and autotrophic bacteria. Two new model compounds replace X(A), the original autotrophic biomass: Ammonium Oxidizing Bacteria, X(AOB) and Nitrite Oxidizing Bacteria, X(NOB). Growth and decay processes of nitrifiers were split into AOB and NOB processes (3 additional processes) and heterotrophic anoxic processes were also doubled in order to account for two-step denitrification (4 additional processes). Default values from literature as well as laboratory measurements were considered for the choice of kinetic and stoichiometric parameters. The model was calibrated and validated with laboratory scale tests in batch reactors and with data from an Eawag activated sludge pilot plant configured conventionally with nitrification and pre-denitrification for the treatment of communal wastewater.

Performance of a pilot-scale submerged membrane bioreactor (MBR) in treating bathing wastewater

Bathing wastewater was treated by a pilot-scale submerged membrane bioreactor (MBR) for more than 60 days. The results showed that the removal rates of main pollutants of wastewater such as COD(Cr), LAS, NH(4)(+)-N and total nitrogen (TN) were above 93%, 99%, 99%, and 90%, respectively. The results of denaturing gel gradient electrophoresis (DGGE) and fluorescent in situ hybridization (FISH) indicated that the bacteria were stable. The abundant nitrobacteria intercepted by the membrane led to the high removal rate of ammonia and TN. FISH and 16S rDNA gene sequence analysis revealed that some specific phylogenetic group of bacteria, the Pseudomonas sp. Ochrobactrum anthropi sp. and Enterobacter sp. probably played a major role in the development of the mature biofilms, which led to the severe irreversible membrane biofouling.

Seasonal variation in communities of ammonia-oxidizing bacteria based on polymerase chain reaction – denaturing gradient gel electrophoresis in a biofilm reactor for drinking water pretreatment

The diversity and variation of total and active ammonia-oxidizing bacteria in a full-scale aerated submerged biofilm reactor for drinking water pretreatment were characterized by clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA and its gene during a whole year. Sequences obtained from clone libraries affiliated with the Nitrosomonas oligotropha lineage and the Nitrosomonas communis lineage. An uncultured subgroup of Nitrosomonas communis lineage was also detected. Seasonal variations in both total and active ammonia-oxidizing bacteria communities were observed in the DGGE profiles, but an RNA-based analysis reflected more obvious dynamic changes in ammonia-oxidizer community than a DNA-based approach. Statistical study based on canonical correspondence analysis showed that a community shift of active ammonia oxidizers was significantly influenced by temperature and pH, but no significant correlation was found between environmental variables and total ammonia-oxidizer community shift.

Physiological state, growth mode, and oxidative stress play a role in Cd(II)-mediated inhibition of Nitrosomonas europaea 19718

The goal of this study was to determine the impact of physiological growth states (batch exponential and batch stationary growth) and growth modes (substrate-limited chemostat, substrate-sufficient exponential batch, and substrate-depleted stationary batch growth) on several measures of growth and responses to Cd(II)-mediated inhibition of Nitrosomonas europaea strain 19718. The specific oxygen uptake rate (sOUR) was the most sensitive indicator of inhibition among the different responses analyzed, including total cell abundance, membrane integrity, intracellular 16S rRNA/DNA ratio, and amoA expression. This observation remained true irrespective of the physiological state, the growth mode, or the mode of Cd(II) exposure. Based on the sOUR, a strong time-dependent exacerbation of inhibition (in terms of an inhibition coefficient [K(i)]) in exponential batch cultures was observed. Long-term inhibition levels (based on K(i) estimates) in metabolically active chemostat and exponential batch cultures were also especially severe and comparable. In contrast, the inhibition level in stationary-phase cultures was 10-fold lower and invariable with exposure time. Different strategies for surviving substrate limitation (a 10-fold increase in amoA expression) and starvation (the retention of 16S rRNA levels) in N. europaea cultures were observed. amoA expression was most negatively impacted by Cd(II) exposure in the chemostat cultures, was less impacted in exponential batch cultures, and was least impacted in stationary batch cultures. Although the amoA response was consistent with that of the sOUR, the amoA response was not as strong. The intracellular 16S rRNA/DNA ratio, as determined by fluorescence in situ hybridization, also did not uniformly correlate with the sOUR under conditions of inhibition or no inhibition. Finally, Cd(II)-mediated inhibition of N. europaea was attributed partially to oxidative stress.

Redox control bioreactor: A unique biological water processor

The redox control bioreactor (RCB) is a new hollow fiber membrane bioreactor (HFMBR) design in which oxygen and hydrogen gases are provided simultaneously through separate arrays of juxtaposed hollow fiber (HF) membranes. This study applied the RCB for completely autotrophic conversion of ammonia to N(2) through nitrification with O(2) and denitrification using hydrogen as an electron donor (i.e., autohydrogentrophic denitrification). The hypothesis of this research was that efficient biofilm utilization of O(2) and H(2) at respective HFs would limit transport of these gases to bulk fluid, thereby enabling completely autotrophic ammonia conversion to N(2) through the co-occurrence of ammonia oxidation (O(2)-HF biofilms) and autohydrogenotrophic denitrification (H(2)-HF biofilms). A prototype RCB was fabricated and operated for 215 days on a synthetic, organic-free feedstream containing 217 mg L(-1) NH(4)(+)-N. When O(2) and H(2) were simultaneously supplied, the RCB achieved a steady NH(4)(+)-N removal flux of 5.8 g m(-2) day(-1) normalized to O(2)-HF surface area with a concomitant removal flux of 4.4 g m(-2) day(-1) (NO(3)(-))+NO(2)(-))-N based on H(2)-HF surface area. The significance of H(2) supply was confirmed by an increase in effluent NO(3)(-)-N when H(2) supply was discontinued and a decline in NO(3)(-)-N when H(2) supply was restarted. Increases in H(2) pressure caused decreased ammonia utilization, suggesting that excess H(2) interfered with nitrification. Microprobe profiling across radial transects revealed significant gradients in dissolved O(2) on spatial scales of 1 mm or less. Physiological and molecular analysis of biofilms confirmed that structurally and functionally distinct biofilms developed on adjacent, juxtaposed fibers.

Quantification of anammox populations enriched in an immobilized microbial consortium with low levels of ammonium nitrogen and at low temperature

Anaerobic ammonium oxidizing (anammox) bacteria present in microbial communities in two laboratory-scale upflow anoxic reactors supplied with small amounts of ammonium (<3 mg/l) at low temperature were detected and quantified. The reactors, operated at 20 degrees C, were seeded with an immobilized microbial consortium (IMC) and anaerobic granules (AG) from an upflow anaerobic sludge blanket (UASB) treating brewery wastewater. Our results showed that complete ammonium and nitrite removal with greater than 92% total nitrogen removal efficiency was achieved in the reactor inoculated with both the IMC and AG, while that of the reactor inoculated with only the IMC was lower than 40%; enrichment was successful after the addition of AG. Quantitative fluorescence in situ hybridization (FISH) analysis confirmed that anammox bacteria were present only in the reactor inoculated with an IMC and AG. The copy number of the 16S-rRNA gene of the anammox bacteria calculated by most probable number-polymerase chain reaction (MPN-PCR) from the total DNA extracted from both reactors (2.5 x 10(4) copies/mug of DNA) was two orders lower than that of the domain bacteria (2.5 x 10(6) copies/mug of DNA). The results revealed that immobilized multiple seed sludges were optimal for anammox enrichment at low temperature and ammonium concentrations.

Integrating ecology into biotechnology

New high-throughput culture-independent molecular tools are allowing the scientific community to characterize and understand the microbial communities underpinning environmental biotechnology processes in unprecedented ways. By creatively leveraging these new data sources, microbial ecology has the potential to transition from a purely descriptive to a predictive framework, in which ecological principles are integrated and exploited to engineer systems that are biologically optimized for the desired goal. But to achieve this goal, ecology, engineering and microbiology curricula need to be changed from the very root to better promote interdisciplinarity.

Microbial community structure of ethanol type fermentation in bio-hydrogen production

Three continuous stirred-tank reactors (CSTRs) were used for H(2) production from molasses wastewater at influent pH of 6.0-6.5 (reactor A), 5.5-6.0 (reactor B), or 4.0-4.5 (reactor C). After operation for 28 days, the microbial community formed ethanol type (C), propionate type (A) and ethanol-butyrate-mixed type (B) fermentation. The H(2) production rate was the highest for ethanol type fermentation, 0.40 l (g VSS)(-1) day(-1) or 0.45 l H(2) (g COD removed)(-1). Microbial community dynamics and diversity were analysed using double-gradient denaturing gradient gel electrophoresis (DG-DGGE). Denaturing gradient gel electrophoresis profiles indicated that the community structures changed quickly in the first 14 days. Phylogenetic analysis indicated that the dominant bacterial groups were low G+C Gram-positive bacteria, Bacteroides, gamma-Proteobacteria and Actinobacteria; alpha-Proteobacteria, beta-Proteobacteria, delta-Proteobacteria and Spirochaetes were also presented as minor groups in the three reactors. H(2)-producing bacteria were affiliated with Ethanoligenens, Acetanaerobacterium, Clostridium, Megasphaera, Citrobacter and Bacteroides. An ethanol-based H(2)-producing bacterium, Ethanoligenens harbinense CGMCC1152, was isolated from reactor C and visualized using fluorescence in situ hybridization (FISH) to be 19% of the eubacteria in reactor C. In addition, isoenzyme activity staining for alcohol dehydrogenase (ADH) supported that the majority of ethanol-producing bacteria were affiliated with Ethanoligenens in the microbial community.

Quantification of uncultured microorganisms by fluorescence microscopy and digital image analysis

Traditional cultivation-based methods to quantify microbial abundance are not suitable for analyses of microbial communities in environmental or medical samples, which consist mainly of uncultured microorganisms. Recently, different cultivation-independent quantification approaches have been developed to overcome this problem. Some of these techniques use specific fluorescence markers, for example ribosomal ribonucleic acid targeted oligonucleotide probes, to label the respective target organisms. Subsequently, the detected cells are visualized by fluorescence microscopy and are quantified by direct visual cell counting or by digital image analysis. This article provides an overview of these methods and some of their applications with emphasis on (semi-)automated image analysis solutions.

Effect of the concentration of suspended solids on the enzymatic activities and biodiversity of a submerged membrane bioreactor for aerobic treatment of domestic wastewater

A pilot-scale submerged membrane bioreactor was used for the treatment of domestic wastewater in order to study the influence of the variations in the concentration of volatile suspended solids (VSS) on the enzymatic activities (acid and alkaline phosphatases, glucosidase, protease, esterase, and dehydrogenase) and biodiversity of the bacterial community in the sludge. The influence of VSS concentration was evaluated in two separated experiments, which were carried out in two different seasons of the year (experiment 1 through spring-summer and experiment 2 through autumn-winter). Cluster analysis of the temperature gradient gel electrophoresis (TGGE) profiles demonstrated that the community composition was significantly different in both experiments. Within the same experiment, the bacterial community experienced sequential shifts as the biomass accumulated, as shown by the evolution of the population profiles through time as VSS concentration increased. All enzymatic activities studied were significantly lower during experiment 2, except for glucosidase. Concentrations of VSS over 8 g/l induced a strong descent of all enzymatic activities, which overlapped with a significant modification of the community composition. Sequences of the major TGGE bands were identified as representatives of the Alpha-proteobacteria, filamentous bacteria (Thiotrix), and nitrite oxidizers (Nitrospira). Some sequences which were poorly related to any validated bacterial taxon were obtained.

High levels of nitrifying bacteria in intermittently aerated reactors treating high ammonia wastewater

Changes in the fractions of ammonia-oxidizing bacteria and nitrite-oxidizing bacteria in two laboratory-scale reactors were investigated using 16S rRNA probe hybridizations. The reactors were operated in intermittent aeration mode and different aeration cycles to treat anaerobically digested swine wastewater with ammonia concentrations up to 175 mg NH(3)-N/L. High ammonia removals (>98.8%) were achieved even with increased nitrogen loads and lower aeration: non-aeration time ratios of 1h:3h. Nitrosomonas/Nitrosococcus mobilis were the dominant ammonia-oxidizing bacteria in the reactors. Nitrospira-like organisms were the dominant nitrite-oxidizing bacteria during most of the investigation, but were occasionally outcompeted by Nitrobacter. High levels of nitrifiers were measured in the biomass of both reactors, and ammonia-oxidizing bacteria and nitrite-oxidizing bacterial levels adjusted to changing aeration: non-aeration time ratios. Theoretical ammonia-oxidizer fractions, determined by a mathematical model, were comparable to the measured values, although the measured biomass fractions were different at each stage while the theoretical values remained approximately constant. Stable ammonia removals and no nitrite accumulation were observed even when rRNA levels of ammonia oxidizers and nitrite-oxidizers reached a minimum of 7.2% and 8.6% of total rRNA, respectively. Stable nitrogen removal performance at an aeration: non-aeration ratio of 1h:3h suggests the possibility of significant savings in operational costs.

Variation of microbiological parameters within planted soil filter for domestic wastewater treatment

Microbial community structure was assessed in a horizontal subsurface flow planted sand filter treating domestic wastewater with molecular and culture-based methods. The diversity and spatial distribution of the microbial community was investigated using a PCR-DGGE (eubacterial and archaeal primers, ammonia-oxidizing bacteria, and ammonium monooxygenase specific primers), and spread plate and MPN counts. Significant differences were found in the spatial distribution of the microbial community structure. Data analysis revealed that different components of the microbial community possessed different spatial distribution patterns within the filter bed and depending on community type, relationships with soil chemical, and microbiological parameters varied. The most important spatial pattern in microbial community structure within the constructed wetland was related to the depth gradient, followed by differences between inflow and outflow. A comparison of a number of heterotrophic bacteria between inlet and outlet pipes as well as between two sampling depths showed no significant differences. In addition, the variation of the abundance of ammonia-oxidizing bacteria demonstrated no clear spatial pattern.

Phylogeny-function analysis of (meta)genomic libraries: screening for expression of ribosomal RNA genes by large-insert library fluorescent in situ hybridization (LIL-FISH)

We assessed the utility of fluorescent in situ hybridization (FISH) in the screening of clone libraries of (meta)genomic or environmental DNA for the presence and expression of bacterial ribosomal RNA (rRNA) genes. To establish proof-of-principle, we constructed a fosmid-based library in Escherichia coli of large-sized genomic DNA fragments of the mycophagous soil bacterium Collimonas fungivorans, and hybridized 768 library clones with the Collimonas-specific fluorescent probe CTE998-1015. Critical to the success of this approach (which we refer to as large-insert library FISH or LIL-FISH) was the ability to induce fosmid copy number, the exponential growth status of library clones in the FISH assay and the use of a simple pooling strategy to reduce the number of hybridizations. Twelve out of 768 E. coli clones were suspected to harbour and express Collimonas 16S rRNA genes based on their hybridization to CTE998-1015. This was confirmed by the finding that all 12 clones were also identified in an independent polymerase chain reaction-based screening of the same 768 clones using a primer set for the specific detection of Collimonas 16S ribosomal DNA (rDNA). Fosmids isolated from these clones were grouped by restriction analysis into two distinct contigs, confirming that C. fungivorans harbours at least two 16S rRNA genes. For one contig, representing 1-2% of the genome, the nucleotide sequence was determined, providing us with a narrow but informative view of Collimonas genome structure and content.